A2 Biology Notes 2016

A2 BIOLOGY
9700
CORE
2014-2015
ARRANGED BY: MARWA FAWZI
MOBILE NUMBER: 0598908698
EMAIL ADDRESS: maraweeka@yahoo.com
A2 BIOLOGY MARWA FAWZI

Syllabus
And
Paper 5 skills
INDEX

CORE:
L- ENERGY AND RESPIRATION
M-PHOTOSYNTHESIS
N-REGULATION AND CONTROL
O-INHERITED CHANGES
P-SELECTION AND EVOLUTION
APPLICATIONS:
Q-BIODIVERSITY AND CONSERVATION
R-GENE TECHNOLOGY
S-BIOTECHNOLOGY
T-CROP PLANTS
U- ASPECTS OF HUMAN REPRODUCTION
PAPER 5 SKILLS AND STATISTICS
Energy and Respiration
The need for energy in living organism:

Energy is used in living organisms to do work.
WORK:
Work in a living organism includes:
1- The synthesis of complex substances from simpler ones (anabolic reactions) such as the synthesis
of polypeptides from amino acids;
2- The active transport of substances against a concentration gradient such as the activity of
sodium-potassium pump;
3- Mechanical work such as muscle contraction and other cellular movements, for example the
movement of cilia and flagella, amoeboid movement and the movement of vesicles through
cytoplasm;
4- In a few organisms, bioluminescence and electrical discharge.
5- Mammals and birds use thermal energy from metabolic reactions to maintain a constant body
temperature.
The Structure ofATP as a phosphorylated nucleotide:

-adenosine triphosphate is made of a nucleotide with two more phosphate groups attached:
1-adenosine (a nucleoside): made of ribose sugar (pentose 5C) ,with a nitrogen base (adenine)
attached to its carbon number one
2-three phosphate groups attached to carbon number five
Similarities and differences between ATP and nucleotides:
Similarities Differences
-Both contain pentose sugar. -The pentose sugar in ATP is always ribose
-Both contain nitrogen containing base. while in nucleotides it may be ribose and
-Both contain phosphate. deoxyribose.
-in both the nitrogen containing base is -The nitrogen containing base in ATP is always
joined to carbon number one, and the Adenine while in nucleotide it may be
phosphate group is joined to carbon number Adenine, Thymine, Cytosine, Guanine or
five. Uracil.
-In ATP there are three phosphate groups
while in nucleotide there is only one.

The Universal Role of ATP as the Energy Currency In all living
organisms:
1- Loss of phosphate leads to energy release / hydrolysis releases 30.5 kJ.
2- ADP + Pi ATP (reversible reaction);
3- Small packets of energy;
4- Small / water soluble, so can move around cell
5- Used by cells as immediate energy donor
6- Turnover or interconversion rate of ATP & ADP is high to provide energy.
7- Two examples of use; protein synthesis; active transport, muscle contraction.
Outline the need for energy in living organisms using named

examples:
1- ATP as universal energy / currency
2- Light energy needed for photosynthesis
3- ATP used conversion of GP to TP during photosynthesis
4- ATP used to regenerate RuBP during photosynthesis
5-(energy needed for) anabolic reactions
6- Protein synthesis / starch formation / triglyceride formation
7- Activation energy of enzymes
8- (Activate) glucose in glycolysis
9- Active transport.
10- Example; e.g. sodium / potassium pump, Movement / locomotion, muscle contraction / cilia
beating, Endocytosis / exocytosis / pinocytosis / bulk transport, Temperature regulation.
Fate of excess energy that was used to make ATP:
-Energy transfers are inefficient. Some is converted to thermal energy whenever energy is
transferred. At the different stages in a multi-step reaction, such as respiration, the energy made
available may not be enough to perfectly correspond with the energy needed to synthesize ATP.
-Any "excess" energy is converted to thermal energy. Also, many energy- requiring reactions in cells
use less energy than that released by hydrolysis of ATP to ADP. Again, any extra energy will be
released as thermal energy.
Difference between an energy currency and energy storage molecule:

1- An Energy currency molecule acts as the immediate donor of energy to the cell's energy-requiring
reactions.
2-An energy storage molecule is a short-term (glucose or sucrose) or long-term (glycogen, starch,
or triglyceride) store of chemical potential energy.

RESPIRATION
Define:
-Respiration is the sequence of enzyme-controlled steps by which an organic molecule, usually
glucose, is broken down so that its chemical potential energy can be used to make the energy
currency, ATP.
-The main fuel for most cells is carbohydrate, usually glucose. Many cells can only use glucose as
their respiratory substrate, but others break down fatty acids, glycerol and amino acids in
respiration.
The main Sources of Energy Produced by Cells:

1-Direct synthesis by ATP
2-Adding hydrogen to co-enzymes such as NAD& FAD
Hydrogenation
Oxidized Reduced
NAD & FAD NAD & FAD
-Reduced NAD & FAD are used to drive the synthesis of ATP in certain reactions where each
reduced NAD molecule is used to produce 2.5 or 3 ATP, while each reduced FAD molecule is used to
produce 1.5 or 2 ATP
3-Re-organization of bonds in molecules during glycolysis and Krebs's cycle.
4-from Cells that did not use all energy released from hydrolysis of ATP, so extra energy is released
as thermal energy.
Types of Respiration:
aerobic anaerobic
nition -It is the release of a relatively -It is the release of a relatively

large amount of energy in cells small amount of energy by the
by the breakdown of food breakdown of food substances
substances in the presence of in the absence of oxygen
oxygen
es 1-Glycolysis 1-Glycolysis
2-Link Reaction
3 - Krebs cycle
4 - ETC & Oxidative
phosphorylation
(A) Aerobic Respiration

-In the complete oxidation of glucose (C6H12O6) in aerobic conditions a large quantity of energy is
made available.
C6H12O6+ 6O2 6CO2 + 6H2O + 2870 kj
-Glucose breakdown can be divided into four stages:
1-Glycolysis
2-The link reaction
3-The Krebs cycle
4- Oxidative phosphorylation
-Although the complete oxidation of glucose to carbon dioxide and water has a very high energy
yield, the reaction does not happen easily.
-Glucose is actually quite stable, because of the activation energy that has to be overcome
before any reaction takes place.
-In living organisms this is overcome by lowering the activation energy using enzymes and also by
raising the energy level of the glucose by phosphorylation.
Structure and Function of Mitochondria:

Function:
In eukaryotic organisms, the mitochondrion is the site of the Krebs Cycle and the electron transport
chain, of aerobic respiration to release energy in the form of ATP
Structure:
1-Mitochondria are rod-shaped, or filamentous organelles about 0.5 1.0 m in diameter.
2-The number of mitochondria in a cell depends on its activity. Mammalian liver cells contain
between 1000 and 2000 mitochondria, occupying 20% of the cell volume.
3-Each mitochondrion is surrounded by an envelope of two phospholipids membranes. The outer

membrane is smooth, but the inner is much folded inwards to form cristae (singular crista). These
give the inner membrane a large total surface area for enzymes and cytochromes (protein carriers)
needed for the electrons transfer and ATP production
4-Cristae in mitochondria from different type of cells show considerable variation, but, in general,
mitochondria from active cells have longer, more densely packed cristae than those from less active
cells.
5-the two membranes have different compositions and properties. The outer membrane is relatively
permeable to small molecules, whilst the inner membrane is less permeable.
6-The inner membrane is studded with tiny spheres, about 9nm in diameter, which are attached to
the inner membrane by stalks. The spheres are the enzyme ATP synthase, it is used to make ATP
from ADP and Pi .
7-The inner membrane is the site of the electron transport chain and contains the proteins
(cytochromes) necessary for this.
8-The space between the two membranes of the envelope usually has a lower pH than the matrix of
the mitochondrion as a result of the hydrogen ions that are released into the intermembrane space
by the activity of the electron transport chain, than the matrix of the mitochondrion to build up a
hydrogen ion gradient in chemiosmosis
9-The matrix of the mitochondrion is the site of the link reaction and the Krebs cycle where
substrates and enzymes can freely interact, and contains the enzymes needed for these reactions. It
also contains small (70 S) ribosome for protein synthesis (enzymes), and several identical copies of
looped mitochondrial DNA for self replication
Note: When water leave mitochondria by osmosis, the hydrogen bonds between glycoprotein of the
membranes and water molecules decrease, and so membrane is less stable and loses its structure.

(A) Stages of aerobic respiration
1-Glycolysis:
- It is the splitting or lysis of glucose. It takes place in cytoplasm.
During glycolysis phosphorylated glucose cannot diffuse out of

muscle because:
1- Addition of phosphate made it too large to pass through channels.
2- used up as soon as it is made.
3- Cannot pass through phospholipid bilayer.
4- Has no specific transport protein.

Yield of Glycolysis: 4 ATP + 2 reduced NAD + 2 Pyruvate
Net Yield : 2 ATP + 2 reduced NAD + 2 Pyruvate
2- The Link Reaction

-It takes place in matrix.
1-Pyruvate passes by active transport (using energy from ATP) from the cytoplasm, through the
outer and inner membranes of a mitochondrion and into the mitochondrial matrix.
2- It is the decarboxylated (that is carbon dioxide is removed)
3-then it is dehydrogenated
4- Then Combined with coenzyme A (CoA) to give acetyl coenzyme A.
- Coenzyme A is a complex molecule of a nucleoside (adenine + ribose) with a vitamin (pantothenic

acid) and acts as a carrier of acetyl groups (2C) to the Krebs cycle. The hydrogen removed from
pyruvate is transferred to NAD.
Pyruvate + CoA + NAD = acetyl CoA + CO 2 + reduced NAD
-Fatty acids from fat metabolism may also be used to produce acetyl coenzyme A. Fatty acids are
broken down in the mitochondrion in a cycle of reactions in which each turn of the cycle shortens the
fatty acid chain by a two carbon acetyl unit. Each of these can react with coenzyme A to produce
acetyl coenzyme A, which, cycle like that produced from pyruvate, now enters the Krebs cycle.
Net Yield: 2 ATP + 4 reduced NAD + 2 Acetyl CoA
3- The Krebs cycle Or The Citric Acid Cycle Or Tricarboxylic Acid Cycle
-It takes place in matrix. It is controlled by enzymes
-Its aim is the release of hydrogens in the form of reduced NAD & reduced FAD which can be used in
oxidative phosphorylation (step 4) to provide energy to make ATP.
Steps of Krebs Cycle:

-Acetyl coenzyme A combines with a four carbon compound (oxaloacetate) to form a six-carbon
compound (citrate)
-the citrate is decarboxylated and dehydrogenated in a series of steps, to yield carbon dioxide, which
is given off as a waste gas, and hydrogens which are accepted by the carriers NAD and FAD (flavin
adenine dinucleotide)
-oxaloacetate is regenerated to combine with another acetyl coenzyme A.
Yield in each turn of Kerbs cycle

2 CO2 (waste gas), 1 reduced FAD, 3 reduced NAD, 1 ATP
Yield of two turns of Kerbs cycle
4 CO2 , 2 reduced FAD , 6 reduced NAD , 2 ATP
Net yield
10 reduced NAD , 2 reduced FAD , 4 ATP
Role of dehydrogenase enzyme in Krebs cycle:

-to Provide H+ & electrons for NAD to form reduced NAD that will be used in ETC during oxidative
phosphorylation to release ATP and form water.
How formation of ATP in Krebs Cycle or glycolysis differ from oxidative

phosphorylation?
- Substrate level phosphorylation (an enzyme is used to transfer phosphate group from organic
molecule to ADP,
Forming ATP)
- No ETC.
- No ATP synthase.
- No proton pump.
4-Oxidative Phosphorylation (addition of Pi to ADP in presence of O2 to make ATP)

and the Electron Transport Chain ETC:
-It takes place in Cristae of the inner mitochondrial membrane.
Net Yield:
10 NAD (red) * 3 = 30 10 * 2.5 = 25
2 FAD *2 = 4 or 2 * 1.5 = 3
4 ATP Glycolysis +Krebs cycle = 4 4 = 4
Total = 38 total = 32
Oxidative phosphorylation:
-The hydrogens picked up by NAD and FAD are now split into electrons and protons or hydrogen ion
(H+). The electrons are passed along the electron transport chain on the inner membrane of the
mitochondrion.
-most of the carriers are associated with membrane proteins of 4 types. A functional unit, called
respiratory complex, consists of one of each of these proteins, arranged in such a way that
electrons can be passed from one to another down an energy gradient
-As the electrons move along the chain of electron carriers, they lose energy. This energy is used to
actively transport hydrogen ions. The transfer of electrons along the series of electron carriers
makes energy available which is used to convert ADP + P i to ATP. As an electron passes from a
carrier at a higher energy level to one that is lower, energy is released.
-The energy released is usually lost as heat, but at particular points in the chain the energy released
is sufficient to produce ATP. Potentially, three molecules of ATP can be produced from each reduced
NAD molecule and two ATP from each reduced FAD molecule. However, this yield cannot be realized
unless ADP and Pi are available inside the mitochondrion.
-About 25% of the total energy yield of electron transfer is used to transport ADP into the
mitochondrion and ATP into the cytoplasm. Hence, each reduced NAD molecule entering the chain
produces on average two and a half molecules of ATP and each reduced FAD produces one and a half
molecule of ATP. Also some energy are used to move pyruvate and reduce NAD into the matrix of
mitochondria (NAD 2.5 ATP, FAD 1.5 ATP)
-The movement of the hydrogen ions from the matrix of the mitochondrion, across the inner
membrane and into the space between the inner and outer membranes. This builds up a high
concentration of hydrogen ions in this space.

-The hydrogen ions are allowed to diffuse back into the matrix through special channel proteins that
work as ATPases (ATP synthases enzymes). The movement of the hydrogen ions through the
ATPases provides enough energy to cause ADP and inorganic phosphate to combine to make ATP.
-At the end of the chain, the electrons reunite with the protons from which they were originally split.
They combine with oxygen to produce water. This is why oxygen is required in aerobic respiration
it acts as the final acceptor for hydrogens removed from the respiratory substrate during glycolysis,
the link reaction and the Krebs cycle.
-The most widely accepted explanation for the synthesis of ATP intoxicative phosphorylation is that
of chemiosmosis.
-Lack of oxygen in mitochondria will not make electron flow in ETC, as there will be no final acceptor
for electrons, so reduced NAD will not be oxidized, and both oxidative phosphorylation and Krebs
cycle will stop.
-Note: Oxidative phosphorylation yields more ATP than substrate level phosphorylation (32 / 34 vs.
4 /6 ATPs)
Chemiosmosis:
-The energy released by the electron transport chain is used to pump hydrogen ions from the
mitochondrial matrix into the space between the two membranes of the mitochondrial envelope. The
concentration of hydrogen ions in the intermembrane space therefore becomes higher than that in
the matrix, so a concentration gradient is set up.
-Hydrogen ions pass back into the mitochondrial matrix through protein channels in the inner
membrane, associated with each channel in the enzyme ATP synthase. The transfer of three
hydrogen ions allows the production of one ATP molecule inside the organelle. This process occurs in
both mitochondria and chloroplasts.
- As the ions pass through the channel, their electrical potential energy is used to synthesize ATP
from ADP + Pi
stage Products
Glycolysis ATP , reduced NAD, Pyruvate
Link reaction Reduced NAD , Acetyl co A, CO2
Krebs Cycle CO2 , reduced NAD , reduced FAD , ATP
ETC Oxidized NAD , oxidized FAD ,ATP , H2O
ATP Synthase:

-ATP synthase has three binding sites and a part of the molecule () that rotates as hydrogen ions
pass. This produces structural changes in the binding sites, and allows them to pass sequentially
through three phases:
1 - binding ADP and Pi 2 - forming tightly bound ATP 3 - releasing ATP
Explain the role of NAD in aerobic respiration:

1-coenzymes
2-for dehydrogenase
3-reduced
4-carries electrons
5-and protons / H+/ H / hydrogen
6-from Krebs cycle
7-and from glycolysis
8-to cytochromes/electron transfer chain
9-reoxidised/regenerated
10-ATP produced
11- 3/2.5(molecules of ATP) per reduced NAD
(B) Anaerobic Respiration

-It is one step reaction (Glycolysis), takes place in cytoplasm, It yields 2 ATP / glucose molecule, in
absence of oxygen.
Comparison between aerobic and anaerobic respiration
Feature Aerobic Anaerobic

Oxygen Used No Used
Carbon dioxide Produced In Alcohol fermentation
only
Energy Large Small
Site Mitochondria or cytoplasm and Cytoplasm
cell membrane of bacteria
Why anaerobic respiration produces ATP less than aerobic?

1-Only glycolysis occur / Krebs cycle stops
2-pyruvate does not enter mitochondria
3-ETC stop
4- No oxidative phosphorylation
5- No chemiosmosis
-When free oxygen is not present, hydrogen cannot be disposed of by combination with oxygen. The
electron transfer chain therefore stops working and no further ATP is formed by oxidative
phosphorylation.
- However, since the products of anaerobic reaction, ethanol or lactate, are toxic, the reactions
cannot continue indefinitely.
-The pathway leading to ethanol cannot be reversed and the remaining chemical potential energy of
ethanol is wasted.

-The lactate pathway can be reversed in mammals. Lactate is carried by the blood plasma to the
liver and converted back to pyruvate. The liver oxidizes some (20%) of the incoming lactate to
carbon dioxide and water via aerobic respiration when oxygen is available again. The remainder of
the lactate is converted by the liver to glycogen. The oxygen needed to allow this removal of lactate
is called the oxygen debt.
(1) Alcoholic Fermentation:

The overall equation
Glucose ethanol + carbon dioxide
C6 H12 O6 2 C2 H5 OH + 2 CO2
Why the rate of glycolysis increases significantly when yeast shifts

from aerobic to anaerobic respiration?
- Aerobic respiration produces more ATP
- So to produce same ATP molecules, more glucose needed to be broken down by glycolysis.
- Glycolysis is the only part of respiration used / no ETC.
:Lactic Acid Fermentation (2)

:The effect of lactic acid in muscles during exercise
- During vigorous activity, oxygen supply to the cells become insufficient, despite faster breathing.
Breathing requires energy due to chest movement / anaerobic respiration occurs at the same time
as aerobic respiration to supply extra energy in the form of ATP for muscle contraction. Lactic acid
accumulates on muscles and may cause cramps and fatigue, also an oxygen debt is built up.
- The lactic acid enters the bloodstream and passes to liver where it is converted to glucose as the
oxygen debt is repaid. The glucose is returned to muscles and stored as glycogen.
The overall equation

Glucose Lactate (lactic acid)
C6 H12 O6 2 C3H6 O3 Study: J 2013 P41 Q4
(b i)

Oxygen Debt
1- Standing still, the person absorbs oxygen at the resting rate of 0.2 dm 3 min- 1 . (This is a measure
of the person's metabolic rate.)
2- When exercise begins, more oxygen is needed to support aerobic respiration in the person 's
muscles, increasing the overall demand 2.5 dm 3 min- 1 . However, it takes four minutes for the heart
and lungs to meet this demand, and during this time lactic fermentation occurs in the muscles. Thus
the person builds up an oxygen deficit. For the next three minutes, enough oxygen is supplied.
3- When exercise stops, the person continues to breathe deeply and absorb oxygen at a higher rate
than when at rest. This post-exercise uptake of extra oxygen, which is "paying back" the oxygen
deficit, is called the oxygen debt. The oxygen is needed for:
Conversion of lactate to glycogen in the liver.
Re-oxygenation of haemoglobin in the blood. Study: J 2013 P41 Q4 (b
A high metabolic rate, as many organs are operating at above resting levels.
i)
Respiratory Substrates:
-Although glucose is the essential respiratory substrate for some cells, such as neurons in the brain,
red blood cells and lymphocytes, other cells can oxidize lipids and amino acids.
-When lipids are respired, carbon atoms are removed in pairs, as acetyl CoA, from the fatty acid
chains and fed into the Krebs cycle.
-The carbon-hydrogen skeletons of amino acids are converted into pyruvate or into acetyl CoA.
Comparison between alcoholic / lactic acid fermentation:

In mammals: lactic acid fermentation
1- Lactate produced / no ethanol produced;
2- No decarboxylation / carbon dioxide released;
3- Single step;
4- Lactate dehydrogenase enzyme is used;
5- Reversible pathway;
Oxygen present in the liver
Pyruvate lactic acid
Oxygen absent in muscles
Comparison between aerobic and anaerobic respiration:

In anaerobic respiration:
1- Only glycolysis occurs / Krebs cycle stops / link reaction stops;
2- Glucose, not fully broken down /still contains energy;
3- Pyruvate does not enter mitochondrion;
4- no oxygen, so no final electron acceptor (in ETC);
5- ETC stops;
6- No oxidative phosphorylation;

Energy Values of Respiratory Substrates:
-Most of the energy liberated in aerobic respiration comes from the oxidation of hydrogen to water.
-When reduced NAD and reduced FAD are passed to the electron transport chain, hence, the greater
the number of hydrogens in the structure of the substrate molecule, the greater the energy value.
-Fatty acids have more hydrogen per molecule than carbohydrates and so lipids have a greater
energy value per unit mass, or energy density, than carbohydrates or proteins.
-The energy value of a substrate is determined by burning a known mass of the substance in oxygen
in a calorimeter. The energy liberated by oxidizing the substrate can be determined from the rise in
temperature of a known mass of water in the calorimeter.
Explain the different energy values of carbohydrate, lipid and

protein as respiratory substrates
1- Lipid > protein > carbohydrate / ;A lipid has more energy than either protein or carbohydrate.
2- Comparative figures; e.g. 39.4, 17.0 and 15.8
3- Kj g-1/ per unit mass
4-More hydrogen atoms in molecule, more energy
5-lipids have more, hydrogen atoms / C-H bonds
6-(most) energy comes from oxidation of hydrogen to water
7-using reduced, NAD / FAD
8-in ETC (explain)
9-ATP production

RESPIRATORY QUOTIENT (RQ):
Define:
-It is the volume of carbon dioxide produced divided by the volume of oxygen used during respiration
-It can also be determined theoretically by calculation RQ =CO 2 produced/ O2 used
-e.g. for carbohydrates C6 H12O6 + 6 O2 6 CO2 + 6 H2O RQ = 6/6 = 1
-e.g. for a lipid: 2 C57 H110O6 + 163 O2 114 CO2 + 110 H2O RQ = 114/163 = 0.
C18 H36 O2 + 26 O2 18 CO2+ 18 H2O RQ = CO 2 / O2= 18/26

= 0.69 (almost 0.7)
Importance of using RQ:

1-To find out what is the substrate used in respiration
2-To find out whether aerobic or anaerobic respiration is taking place
Significance of values of RQ:
RQ VALUE SIGNIFICANCE
1.0 Carbohydrates OR after having a meal
0.9 Protein
0.7 Lipid or If you are fasting (no sugar) or in Diabetics (as sugar is not used)
2.0 In reality, some respiration in the yeast cell will be aerobic and so a small
volume of oxygen will be taken up and the RQ will be <2. High values of RQ
indicate that alcoholic fermentation is occurring.
1.0 Anaerobic respiration, or, conversion of carbohydrates to fats in hibernating

animals
0.0 Lactic acid fermentation in muscles (no CO 2 produced or O2 used)
Alcohol Fermentation in Yeast, no oxygen used , only carbon dioxide produced


Using Respirometer to measure the effect of temperature on the
rate of respiration and to measure RQ value :
-Oxygen uptake during respiration can be measured using a Respirometer. A Respirometer is
suitable for measuring the rate of oxygen consumption of small terrestrial invertebrates at different
temperature
-Oxygen consumption in unit time can be measured by reading the level of the manometer fluid
against the scale. Changes in temperature and pressure alter the volume of air in the apparatus and
so the temperature of the surroundings must be kept constant whilst readings are taken, for
example by using a thermostatically controlled water bath.
-The presence of a control tube containing an equal volume of inert material to the volume of the
organisms used helps to compensate for changes in atmospheric pressure. Once measurement has
been taken at a series of temperatures, a graph can be plotted of oxygen consumption against
temperature.
-The same apparatus can be used to measure the RQ of an organism. First, oxygen consumption at a
particular temperature is found (x cm3 min-1). Then the respirometer is set up with the same
organism at the same temperature, but with no chemical to absorb carbon dioxide. The manometer
scale will show whether the volumes of oxygen absorbed and carbon dioxide produced are the same.
- When the volumes are the same, the level of the manometer fluid wills not change and the RQ = 1.
When more carbon dioxide is produced than oxygen absorbed, the scale will show an increase in the
volume of air in the respirometer (by y cm3 min-1). The RQ can then be calculated:
RQ = CO2 / O2 = x + y /x
- when less carbon dioxide is produced than oxygen absorbed, the volume of air in the respirometer
will decrease by (z cm3 min-1) and the calculation will be:
RQ = CO2 / O2 = x - z /x
Take readings of oxygen consumption at one temperature, say 15 oC, including replicate readings to
give a mean value. Increase the temperature to, say, 25 oC. Leave the organisms at that temperature
for about 10 minutes for the rate of respiration to equilibrate. Take readings as before. Repeat at
other temperatures.

ALCOHOL or ETHANAL
ETHANAL ETHANOL
Dehydrogenase
What is the importance of coronary arteries:

- Coronary arteries supply blood to heart cells with oxygen, and nutrients (e.g. glucose and amino
acid), to provide energy by respiration, so that heart muscle can contract and can work properly.
Explain the role of ATP in active transport and in anabolic

reaction:
1- ATP provides energy;
2- In active transport: - movement against concentration gradient through carrier proteins
3- In anabolic reactions: - synthesis of complex substance from simpler ones. E.g
Starch from glucose by glycosidic bond, fat from fatty acid and glycerol by ester bond, proteins
from amino acids by peptide bond

M Photosynthesis
Define Photosynthesis:
The process of photosynthesis transfers light energy into chemical potential energy of organic
molecules. This energy can then be released for work in respiration.
OR Photosynthesis is the trapping (fixation) of carbon dioxide and its subsequent reduction of
carbohydrate, using hydrogen from water.
Living Organisms are divided according to their nutrition into two groups:
Autotrophs Heterotrophs
Organisms which can use an inorganic carbon source in the form of carbon organisms
dioxide called autotrophs needing a
ready- made
Photoautotroph Chemoautotroph organic supply
of carbon are
Almost all the energy transferred to A few autotrophs do not depend on light heterotrophs
all The ATP molecules in all living energy, but use chemical energy sources.
organisms Is derived from light These chemoautotrophs include the
energy used in Photosynthesis by nitrifying bacteria which are so important
autotrophs. Such Photoautotrophs in the nitrogen cycle. These bacteria
are green plants, the obtain their energy from oxidizing
Photosynthetic prokaryotes and bot ammonia to nitrite, or nitrite to nitrate
h single-celled and many-celled
protoctists(Including the green, red
and brown algae)
Equation of photosynthesis:

Structure of a chloroplast:
- Biconvex disc, 3-10m diameter, double, membrane / envelope, internal membrane system
-flattened or fluid-filled sacs / thylakoids, arranged in sacks / grana
-hold pigments /chlorophyll pigments/clusters of pigments
-(membrane of grana) hold ATP synthase, intergranal lamellae, stroma / ground substance, lipids /
starch grains stored
-contains enzymes of Calvin cycle, stroma contains ribosomes / DNA, They show variation in shape
between species

Photosynthetic Pigments:
-Light energy is trapped by photosynthetic pigments. Different pigments absorb different
wavelengths of light.
-The photosynthetic pigments of higher plants form two groups; the chlorophylls and carotenoids.
Pigment color
Chlorophylls Chlorophyll a Yellow-green
Chlorophyll b Blue-green
Carotenoids carotene Orange
Xanthophylls Yellow
Types of photosynthetic pigments:

-The photosynthetic pigments fall into two categories: Primary pigments and Accessory
pigments
1-The primary pigments are two forms of chlorophyll a with slightly different absorption peak.
2-The accessory pigments include other forms of chlorophyll a, chlorophyll b and the carotenoids.
The pigments are arranged in light-harvesting clusters called photosystems.
A-Chlorophylls absorbs mainly in the red and blue-violet regions of the light spectrum. They reflect
green light, which is why plants look green. The chlorophyll molecule (see figure) has a flat, light-
absorbing head end which contains a magnesium atom at its center. This explains the need for
magnesium by plants and the fact that magnesium deficiency reduces chlorophyll production and
causes yellowing. The chlorophyll molecule also has a long hydrocarbon tail which is hydrophobic
(water-hating).
1- Chlorophyll a is the most abundant pigment in most plants. Its absorption peaks are 430 nm
(blue) and 662nm (red). It emits an electron when it absorbs light
2- Chlorophyll b is similar to chlorophyll a, but its absorption peaks are 453nm and 642nm. It
has similar role to chlorophyll a, but is not as abundant
B- Carotenoids absorb mainly in the blue-violet region of the spectrum.
1- carotenes are accessory pigments. They are orange pigments that protect chlorophyll from
damage by the formation of single oxygen atoms (free radicals). they can also absorb
wavelengths of light that chlorophyll cannot absorb, and pass on some of the energy from
light to chlorophyll

2- Xanthophylls are also accessory pigments, capturing energy from wavelengths of light that
are not absorbed by chlorophyll
Note:
-In the process of photosynthesis, the light energy absorbed by the photosynthetic pigments is
converted to chemical energy. The absorbed light energy excites electrons in the pigment molecules.
- If you illuminate a solution of chlorophyll a or b with ultraviolet light, you will see a red
fluorescence. (In the absence of a safe ultraviolet light, you can illuminate the pigment with a
standard fluorescent tube).
-The ultraviolet light is absorbed and electrons are excited but, in a solution which only contains
extracted pigment, the absorbed energy cannot usefully be passed on to do work. (not used to make
ATP)
-The electrons return to their unexcited state and the absorbed energy is transferred to the
surroundings as thermal energy and as light at a longer (less energetic) wavelength than that which
was absorbed, and is seen as the red fluorescence. In the functioning photosynthetic system it is this
energy that drives the process of photosynthesis.
Separation of chlorophyll pigments by chromatography:

-grind leaf with solvent, e.g. prop none
-leaf extract contains mixture of pigments, concentrate extract; by heating

-further detail; e.g. pencil line drawn / extract placed on chromatography paper repetitive spotting /
drying between spots.
-paper placed (vertically) in jar of (different) solvent, solvent rises up paper, each pigment travels at
different speed
-pigments separated as they ascend, distance moved by each pigment is unique, calculate RF value
- use two dimensional chromatography for better separation of pigments
Photosystems
-In a photosystem, several hundred accessory pigment molecules surround a primary pigment
molecule and the energy of the light absorbed by the different pigments is passed to the primary
pigment (see figure). The primary pigments are said to act as reaction centers.
Types of Photosystems:
PSI (P700) PSII (P680)
Photosystem I is arranged around Photosystem II is based on a molecule

molecule of chlorophyll a with a peak of chlorophyll a With a peak absorption of
absorption at 700nm. The reaction 680nm.
center of photosystem I is therefore The reaction center of photosystem II is
known as P700 therefore known as P680
Describe the structure of photosystems:

-they arranged in light harvesting, clusters / system;
-primary pigments / chlorophyll a, at reaction center
- P700 / PI, absorbs at 700 (nm), while P680 / PII, absorbs at 680 (nm)
- Accessory pigments / chlorophyll b / carotenoids, surround, primary pigment / reaction center /
chlorophyll a;
- Accessory pigments Pass energy to. Primary pigment / reaction center / chlorophyll a;

Absorption and action spectra:
-An absorption spectrum is a graph of the absorbance of different wave lengths of light by a
pigment (see figure)
-An action spectrum is a graph of the rate of photosynthesis (or volume of oxygen gas given off at
certain period of time) at different wave lengths of light (see figure).
- Significance of absorption and action spectra: to shows the effectiveness of the different
wavelengths, which is, of course, related to their absorption and to their energy content. The shorter
the wavelength, the greater the energy contents.
Explain the action spectrum graph:
1-high rate of photosynthesis at 430 & 655 nm, as shorter wavelength has high (more) energy
2-lowest rate of photosynthesis at 500 nm , as low light absorption here
5-absorbed light used for photosynthesis in light-dependent stage
stages of photosynthesis
(1)Light- dependent reaction in thylakoids (2) light-independent
reaction (Calvin
In grana cycle
CO2 fixation) in stroma
(a)Photolysis of water (b) Photophosphorylation
(I)Cyclic (II) Non-Cyclic
Summary of photosynthesis process:

-Two sets of reactions are involved. These are the light-dependent reactions, for which light
energy is necessary, and the light-independent reactions, for which light energy is not needed.
The light-dependent reactions only take place in the presence of suitable pigments which absorb
certain wavelengths of light.
-Light energy is necessary for the splitting of water into hydrogen and oxygen; oxygen is a waste
product. Light energy is also needed to provide chemical energy (ATP) for the reduction of carbon
dioxide to carbohydrates in the light-independent reactions.

1- Light Dependent Reaction:
-it takes place in the thylakoids, in grana, inside chloroplasts
(a)Photolysis of water
Photoactivation of chlorophyll:
1- Chlorophyll absorbs mainly red and blue light by antenna complex.
2- Energy is transferred to reaction centers P 700 / P680.
3- Light energy excites electrons that pass to higher energy levels.
4- Electrons are lost from chlorophyll.
-Light absorbed by PSI & PSII by accessory pigments focus energy to reaction centers to excite and
emit electrons from chlorophyll. This energy is used in photolysis
-Photosystem II includes a water-splitting enzyme which catalyses the breakdown of water:
H2O 2H+ + 2e- + 1/2 O2
-Oxygen is a waste product of this process. The hydrogen ions combine with electrons from
photosystem I and the carrier molecule NADP to give reduced NADP.
This passes to the light-independent reactions and is used in the synthesis of carbohydrate. The
photolysis of water can be demonstrated by the Hill reaction.
The Hill Reaction:

-In 1939, Robert Hill showed that isolated chloroplasts had "reducing power", and liberated oxygen
from water in the presence of an oxidizing agent. The reducing power was demonstrated by using a
redox agent which changed color on reduction. Hill used Fe 3+ ions as his acceptor, but various redox
agents, such as the blue dye DCPIP (dichloro-phenol-indophenols)
(b)Photophosphorylation
- It is the synthesis of ATP from ADP and Pi using light energy in photosynthesis.
- Photophosphorylation of ADP to ATP can be cyclic or non-cyclic depending on the pattern of
electron flow in one or both photosystems.
1-Cyclic Photophosphorylation
-Cyclic Photophosphrylation involves only photosystem I.
- Light is absorbed by photosystem I and is passed to chlorophyll a (P700).
- An electron in the chlorophyll a molecule is excited to a higher energy level and is emitted from the
chlorophyll molecule.
- Instead of falling back into the photosystem and losing its energy as fluorescence, it is captured by
an electron acceptor and passed back to a chlorophyll a (P700) molecule via a chain of electron
carriers.
- During this process enough energy is released to synthesize ATP from ADP and an inorganic
phosphate group (Pi ). The ATP then passes to the light-independent reactions.

2-Non-Cyclic Photophosphorylation
-Noncyclic Photophosphorylation involves both photosystems in the so- called "Z scheme" of
electron flow (see figure).
- Light is absorbed by both photosystems and excited electrons are emitted from the primary
pigments of both reaction centers (P680 and P700).
-These electrons are absorbed by electron acceptors and pass along chains of electron carriers
leaving the photosystems positively charged.
- The P700 of photosystem I absorbs electrons from photosystem II. P680 receives replacement
electrons from the splitting (photolysis) of water. Oxidized NADP accepts electrons from P700 and
protons from photolysis of water to form reduced NADP
- As in cyclic Photophosphorylation, ATP is synthesized as the electrons lose energy whilst passing
along the carrier chain.
-ATP is synthesized by ATPsynthase enzyme during chemiosmosis by joining ADP +Pi
-The advantage of having both photosystems, ETC and ATP synthase in thylakoids is to be close
together, so short diffusion distance.
Comparisons:
feature Photophosphorylation Oxidative Phosphorylation
site chloroplast mitochondria
products Produce ATP Produce water and ATP
oxygen Produce oxygen Needs oxygen
Proton Produce reduced NADP Produce oxidized NAD

carrier
light Needs light Do not need light
process In light-dependent reaction of In aerobic respiration

photosynthesis

Feature Cyclic Non- cyclic
Pathway of electrons Cyclic, Electrons Non- cyclic, Electrons

return to their original do not return to their
position original position
First electron donor (source of Photosystem I (P700) water

electrons)
Last electron acceptor(destination Photosystem I (P700) NADP

of electrons)
Products Useful: ATP only Useful: ATP, reduced

NADP
Waste: O2
Photosystems involved I only I and II
Reduced NADP Not formed formed
Photolysis of water Does not take place Takes place
Feature Photosystem I Photosystem II
Peak of absorption P700 P680
Replacement of electron comes PSII Photolysis of water

from
Emitted electron goes to NADP PSI
Share in photophosphorylation Cyclic, non-cyclic Only non-cyclic
Water splitting enzyme absent present
2-Light Independent Reactions or (Calvin cycle / CO 2 Fixation):

-It takes place in stroma of a chloroplast. It is controlled by enzymes.
1-The fixation of carbon dioxide is a light-independent process in which carbon dioxide combines
with a five carbon sugar, ribulose Biphosphate (RuBP), to give two molecules of a three-carbon
compound, glycerate 3-phosphate (GP). (This compound is also sometimes known as PGA). The
enzyme ribulose Biphosphate carboxylase (RUBISCO), which catalyzes the combination of carbon
dioxide and RuBP, is the most common enzyme in the world.
2- GP, in the presence of ATP releases energy (ATP ADP + Pi) and reduced NADP from the light-
dependent stages provides hydrogen, is reduced to triose phosphate (TP), a three carbon sugar. This
is the point at which carbohydrate is produced in photosynthesis.
3-Some of these triose phosphates condense to form hexose phosphates, sucrose, starch and
cellulose or are converted to acetyl coenzyme A to make amino acids, proteins, fatty acids and lipids
to make cell membranes. Others regenerate RuBP.
What happens when light is off:

RuBP GP
-decrease as there is No reduced NADP -increase for a while, as still there are some
and no ATP are available to RuBP available to bind with CO2, and form
regenerate RuBP from TP it.
-when RuBP is consumed, it stops
increasing, and start to decrease because it
may be used to make other compounds
(e.g. hexose)
If the thylakoids membranes get closer (shrink)and grana is reduced, then:

- Less surface area, Less absorption of light., Less light-dependent reaction, Less ATP produced,
Less reduced NADP produced, Less rate of Calvin cycle, So less CO 2 uptake, less sugar produced

Leaf Structure an d Function
The leaf is the main photosynthetic organ in dicotyledons. It has a broad, thin lamina, a midrib and
a network of veins. It may also have a leaf stalk (petiole).
Describe how the structure of a dicotyledonous leaf is related to

its function in photosynthesis.
- Thin / flat to give large surface area to volume ratio;
- Held at right angles to sun to allow maximum light absorption.
- Arrangement of cells in palisade mesophyll, closely packed to absorb (maximum) light
- Spongy mesophyll provides large surface area for CO 2 uptake / gaseous exchange
-spongy mesophyll cells with irregular packing to provide large air spaces for gas exchange
- Many stomata / guard cells and entry of CO 2 or exit of O2
- Moist cell surfaces to ease dissolving of gases
- Xylem and supply of water / mineral ions , and support;
- Phloem for translocation of products of photosynthesis;
- waxy, transparent cuticle on upper surface to reflect light , reduce water loss by transpiration , to
allow light penetration
-thin, flat cells of the upper epidermis to allow light penetration to mesophyll cells
Explain the adaptations of palisade cells for photosynthesis.

1-Closely packed to absorb (maximum) light;
2- Vertical or long cylinders/ at right angles to surface of leaf to reduce number of cross walls;
3- Large vacuole pushes chloroplasts to edge of cell;
4- Chloroplasts at edge of short diffusion path for carbon dioxide;
5- Chloroplasts at edge to absorb (maximum) light;
6- Large number of chloroplast to absorb (maximum) light;
7- Cylindrical cells or air spaces to circulate gases / provide a reservoir of CO 2;
8- Moist cell surfaces for diffusion of gases;
9- Cell walls are thin for maximum light penetration / diffusion of gases;
10- Chloroplast can move towards light to absorb maximum light;
11- Chloroplast can move away from high light intensity to avoid damage;


How Stomata Open :
1-in the absence of the hormone abscisic acid ABA absence
2- H+ transported out of guard cells, actively / using ATP;
3- Low H+ concentration / causes negative charge, inside cell;
4- K+ channels open / K+ diffuses into cell;
5-Water potential of cell falls;
6- Water moves into cell by osmosis;
7- Volume of guard cells increase / turgor increases;
Adaptations of Guard cells:

1- Have hoops of cellulose microfibrils which ensure increase in length rather than diameter;
2- Have ends that are joined together;
3- Have, thicker inner walls / thinner outer walls;
4- Curve apart / bend, (to open stoma)
How O 2 enter phosphsynthetic cells of leaf?
- through stomata, by diffusion, to air spaces, many spaces between palisade and spongy mesophyll
cells, dissolve in moist cell wall, and enters through cell wall

Describe how the structure of a chloroplast is related to its
function (adaptations):
1-ground substance /stroma
2-for, light independent stage/Calvin cycle
3-contains enzymes / named enzymes e.g. rubisco;
4-also sugars / lipids/ starch/ ribosomes/ DNA
5-internal membrane system
6-for light dependent stage;
7-fluid-filled sacs / thylakoids;
8-grana are stacks thylakoids;
9-(grana) hold (photosynthetic) pigments
10-(grana) have large surface area for (maximum) light absorption
11-(pigments are arranged in), light harvesting clusters / photosystems;
12-primary pigment / reaction center / chlorophyll a, surrounded by accessory pigments;
13-(accessory pigments) pass energy to, primary pigment/reaction center/chlorophyll a
14-different photosystems absorbs light at different wavelengths;
15-membranes hold, ATP synthase/electron carriers;
16-for, Photophosphorylation / chemiosmosis;

Limiting Factor:
-Is any factor that is when in short supply, it restricts process or a rate of reaction.
Lining Factors of Photosynthesis:
internal external
Leaf surface area Carbon dioxide
Number of stomata Light intensity
Number of Water and minerals
chloroplasts
chlorophyll temperature
1-light intensity: Light energy is necessary to increase the rate of the light-dependent
reactions because they are driven by energy transferred in light rays to generate ATP &
reduced NADP
2-temperature: It affects the rate of light-independent reactions. At higher temperatures,
molecules have more kinetic energy so collide more often and more likely to react when they
do collide. The rate of the light-dependent reactions is not affected by temperature, as the
energy that drives this process is light energy and not heat energy
3-carbon dioxide concentration in the atmosphere (0.04%): It is a reactant in
photosynthesis that is fixed by a reaction with ribulose Biphosphate in the initial reaction of
the Calvin cycle
4-water availability: It is a reactant in photosynthesis, short supply of water usually affects
photosynthesis indirectly, because plant would close its stomata preventing carbon dioxide
from diffusing into the leaf
Blackman investigation on the effect of light intensity and temperature on

the rate of photosynthesis:
-At Constant temperature, the rate of photosynthesis varies with the light intensity, initially
increasing as the light intensity increase since light intensity is a limiting factor (see figure).
However, at higher light intensities this relationship no longer holds and the rate of photosynthesis
reaches a plateau since light intensity is not a limiting factor anymore , and there is another limiting
factor e.g. carbon dioxide concentration.
-The effect on the rate of photosynthesis of varying the temperature at constant light intensities can
be seen in figure. At high light intensities the rate of photosynthesis increases as the temperature is
increased over a limited range.
-At low light intensities, increasing the temperature has little effect on the rate of photosynthesis.
- the same concept of limiting factor applies to changing the concentration of carbon dioxide .At low
concentrations of carbon dioxide, the supply of carbon dioxide is the rate-limiting factor.
- At higher concentrations of carbon dioxide, other factors are rate-limiting, such as light intensity or
temperature.
Explain why at temperature above 25C the rate of

photosynthesis decreases:
-enzymes, denatured / active site changes shape; rubisco / enzymes in cyclic Photophosphorylation;
-Calvin cycle affected since less CO2 fixation, less photolysis; less ATP produced;
-Increased rate of respiration;-respiration rated faster than photosynthesis rate /
- Compensation point (the point at which the rate of respiration = rate of photosynthesis)
-increased rate of transpiration; (to cool plant), stomatal closure; (less transpiration), less CO 2
uptake;
Discuss the effects that variations in carbon dioxide

concentration and light intensity have on the rate of
photosynthesis
Carbon dioxide 0.03 %

-the major limiting factor if found low in atmosphere;
-increase in carbon dioxide concentration and increase in rate; during day when light and warm;
-ref. to variations in conc. e.g., within canopy / at soil surface;
Light intensity
-ref. to wavelengths of light;
-light saturated below full sun;
-idea of limiting and saturation, with other key factor limiting;
-light and stomatal aperture; temperature of leaf and enzymes;
-day length and season / morning and evening; high light and damage to pigments;
Homeostasis, Control and Coordination
(1) Homeostasis
Homeostasis:
Maintaining a constant environment for the cells within the body despite change in external
environment.
-For a cell, its immediate environment is the tissue fluid that surrounds it. Homeostatic mechanisms
work by controlling the composition of blood, which therefore controls the composition of tissue fluid.
Many features of the environment affect the functioning of the cell. Three such features are:
1-temperature-low temperatures slow metabolic reactions, while high temperature causes
denaturation of proteins including enzymes.
2-amount of water- lack of water in the tissue fluid causes water to be drawn out of cells by
osmosis, causing metabolic reactions in the cell to slow or stop, while too much water entering the
cell may cause it to swell and burst.
3-amount of glucose- glucose is the fuel for respiration, so lack of it causes respiration to slow or
stop, depriving the cell of an energy source, while too much glucose may draw water out of the cell
by osmosis.
4- metabolic wastes, particularly carbon dioxide and urea.
5- blood pH.
6- the concentrations in the blood of the respiratory gases, oxygen and carbon dioxide.
Feedback: A change initiates a response that brings things back to normal

Types of feedback:
1-Positive 2- Negative Feedback
Feedback
- If A increases, B - If A increases, B decreases
increases - Define: a mechanism to keep changes in the factor within narrow
- It cannot play any limits.
role in keeping
things constant
- e.g. if CO2
The role of negative feedback in homeostasis in
concentration mammals:
increases in blood, 1- maintains, constant / stable, internal environment; R normal
rate of breathing 2- a change in, some parameters / example of parameter; (like
increases blood glucose or temperature), stimulus (either external or
-e.g.. transmission internal)
3- detected by a , sensor / receptor
of nerve impulses
4- receptors send information about stimulus to a central control in
brain or spinal cord
5- central control brings about response via an effector (muscle or
gland) / ref. corrective mechanism;
6- ref. return to, normal / set point
7- named, receptor / effector ; (control of blood glucose level by
insulin and glucagon hormones)
8- Continuous monitoring of the parameter by the receptor
produces continuous adjustments of the output, which keeps the
parameter oscillating around a particular "ideal level", or set point.

(2) Excretion
Excretion:
The elimination from the body of waste compounds produced during the metabolism of cells,
including, for a human, carbon dioxide (excreted through the lungs) and urea (excreted through the
kidneys in urine).
Importance of Excretion:
-to control / maintain, water / solute, concentration / potential; of, body fluids / internal
environment / cells ;
Excretory substances:
-In mammals the two major excretory products are:
1- Carbon dioxide:
- produced by aerobic respiration. Carbon dioxide dissolves in water to produce a weak acid, so if too
much builds up in body fluids the pH drops, which can damage cells and disrupt metabolism. Carbon
dioxide is transported to the lungs dissolved in blood plasma and excreted in expired air.
2-nitrogenous excretory products:
a) Urea.
- Excess amino acids are deaminated since they cannot be stored in the body. In the liver amino
acids are converted to ammonia which is highly soluble and toxic to terrestrial animals, then
converted to urea which is less soluble and less toxic CO (NH2)2, and a keto acid. The keto acid can
be respired to provide energy, or converted to fat for storage. The urea dissolves in the blood plasma
and is removed and excreted by the kidneys dissolved in water as urine.
b) Creatine (small amounts)
- Creatine is made in the liver, from certain amino acids. Much of this creatine is used in the muscle,
in the form of creatine phosphate, where it acts as an energy store. However, some is converted to
creatinine and excreted.
c) Uric Acid (small amounts)
Uric acid is made from the breakdown of nucleic acids, not from amino acids.
The source and importance of removing nitrogenous waste

products from the body:
Sources of nitrogenous wastes:
-deamination of excess amino acids in liver to form ammonia then urea
- Ornithine cycle :The urea cycle (also known as the ornithine cycle) is a cycle of biochemical
reactions occurring in many animals that produces urea ((NH2)2CO) from ammonia (NH3).
- Not same quantity of urea / produced each day / always some present;
- Creatinine and uric acid are also formed; and ammonium ions (ammonia + hydrogen ion)
Importance:

-toxic; if allowed to accumulate; potential damage to tissues
The Structure of the Kidney:

-A longitudinal section through a kidney shows that it has three main areas:
1- The whole kidney is covered by a fairly tough capsule
2- Beneath the capsule lies the cortex
3- The central area is made up of the medulla
4- Where the ureter joins, there is an area called the pelvis
5- Nephrons: kidney is made up of thousands of tiny tubes that are called Nephrons
The structure of a nephron:

(1) Renal (Bowmans Capsule)
A cup-shaped structure found at one end of the tube located in cortex of kidney
(2) Proximal convoluted tubules

The first twisted region in the renal cortex
(3) Loop of Henle

A hairpin loop or (u shaped) in the medulla
(4) Distal convoluted tubule

The second twisted region in the renal cortex
(5) Collecting duct(s)

Found in renal medulla and leading down into pelvis where they join the ureter
(6) Afferent arteriole

Each renal capsule is supplied with blood by a branch of renal artery called afferent arteriole
(7) Glomerulus
Afferent-arterioles split into a knot or a tangle of capillaries in the "cup" of the capsule, called a
glomerulus
(8) Efferent arteriole

The capillaries of the glomerulus region join to form an efferent arteriole. This leads off to form a
network of capillaries running closely alongside the rest of the nephron, before linking up with other
capillaries to feed into a branch of the renal vein.

How urine is produced in a nephron:
1-Ultra filtration:
- involves filtering small molecules, including urea, out of the blood through the glomerulus and into
the renal capsule. From here they flow along the nephron towards the ureter.
-The blood in a glomerulus is separated from the space inside the renal capsule by:
1-The capillary wall of glomerulus (endothelium)
Which is one cell thick and has many tiny holes in it, and has more gaps between the cells than
normal capillaries to allow small substances to pass out of blood, e.g. glucose, amino acids, urea,
water, salts, .etc
2-The basement membrane of the wall of the renal capsule
Is made of collagen and glycoprotein, which acts as a filter or a barrier of large proteins and large
blood Cells (white and red)
3-The layer of the epithelial cells (Podocytes) making up the wall of the renal capsule:
They many tiny finger-like projections (foot or minor process), with gaps (slits) between them to
allow glomerular filtrate to pass through.
The process of ultrafiltration:

-The blood in a glomerulus is at a relatively high pressure, because the efferent arteriole is narrower
than the afferent arteriole.
-This forces molecules from the blood through these three structures, into the renal capsule. The
pores in the capillary endothelium and the slits between the Podocytes will let all molecules through,
but the basement membrane acts as a filter and will only let small molecules pass through.
-Substances that can pass through include water, glucose, inorganic ions such as Na +, K+ and Cl- and
urea.
-Substances that cannot pass through include red and white blood cells and plasma proteins (such
as albumen and fibrinogen) with molecular mass > 69000.
-The liquid that seeps through into the renal capsule is called glomerular filtrate.
What is required for ultrafiltration to occur or what are the

Factors affecting glomerular filtrate rate:
-The rate at which fluid seeps from the blood in the glomerular capillaries, into the renal capsule, is
called the glomerular filtration rate. In a human, for all the glomeruli in both kidneys, this is
about 125 cm3 min-1.
1-Blood pressure (hydrostatic) in glomerular capillaries is high

-because the diameter of the afferent-arteriole (enter) is wider than that of the efferent (exit)
arteriole to force fluid to flow and to maintain high blood pressure.
2- High solute concentration in blood plasma in the capillaries

-although the basement membrane acts as filter or selective barriers for large proteins and blood
cells (red and white), Overall, the water potential of the blood plasma in the glomerulus is higher
than the water potential of the liquid in the renal capsule. So water continues to move down this
water potential gradient, from the blood into the capsule.
Comparison of the composition of blood and glomerular filtrate

Component Blood Glomerular filtrate
Cells Contains red cells, white No cells
cells and platelets
Water / gdm-3 900 900
Inorganic ions (including 7 7
Na+, K+ and Cl-)/ gdm-3
Plasma proteins / gdm-3 45 0.0 (too large to pass
through basement
membrane)
Glucose / gdm-3 1 1
Urea / gdm-3 0.3 0.3
Relative concentrations of substances in the blood and in the glomerular filtrate

Substance Concentration in blood Concentration in glomerular
plasma (gdm-3) filtrate (gdm-3)
Water 900 900
Proteins 80.0 0.05
Amino acid 0.5 0.5
Glucose 1.0 1.0
Urea 0.3 0.3
Uric acid 0.04 0.04
Creatinine 0.01 0.01
Inorganic ions 7.2 7.2
(Mainly Na+, K+ and Cl-

2-Selective Reabsorption:
-The second stage, reabsorption, involves taking back any useful molecules from the fluid in the
nephron as it flows along back to the blood. Many of the substances in the filtrate need to be kept in
the body, so they are reabsorbed into the blood as the fluid passes along the nephron. Since only
certain substances are reabsorbed, the process is called selective reabsorption.
a) In PCT b)In Loop of Henl c) In DCT
a) Selective reabsorption in PCT

-Most selective reabsorption takes place in PCT
- pct cells have villi / microvilli / large surface areas of the inner surface facing the lumen ;
-(pct cells have) many mitochondria to provide energy for (Na+ - K+ ) pump proteins in the outer
membranes of the cells ;
-Na+ leave pct cells; by active transport;
-Na+ concentration falls in (pct) cells / Na + concentration gradient;
-Na+ (diffuse) from lumen into (pct) cells; through, transporter / carrier, proteins in the membrane
facing the lumen. This provides energy to move glucose even against the gradient
-co- transport of, glucose / amino acids / vitamins / chloride ions;(From pct cells) into intercellular
fluid; then diffusion into blood. This is an example of indirect or secondary active uptake
-normally all glucose is reabsorbed,
- Renal threshold: it is the concentration of glucose above which some glucose will appear in the
urine and will not be reabsorbed
-some water is reabsorbed by osmosis from glomerular filtrate back to the blood
-some urea is reabsorbed by diffusion due to its high concentration in glomerular filtrate
-creatinine is secreted into lumen by the cells of PCT

b) Selective reabsorption in the loop of Henl:
The function of the loop of Henl

-The loop of Henl allows water to be conserved in the body, rather than lost in urine.
Structure of the loop of Henl.

-The hairpin loop runs deep down into the medulla of the kidney, before turning back towards the
cortex again. The first part of the loop is therefore called the descending limb, and the second part
the ascending limb.
Adaptation of the loop of Henl

- having the two limbs of the loop running side by side like this, with the fluid flowing down in one
and up in the other, enables the maximum concentration to be built up both inside and outside the
tube at the bottom of the loop. This mechanism is called a counter-current multiplier.
-The longer the loop of Henl , the greater the concentration that can be built up in the medulla, and
the greater the concentration of the urine which can be produced. Desert animals such as kangaroo
rats, which need to conserve as much water as they possibly can, have especially long loops of
Henl and thicker medulla. Humans, however, only have long loops of Henle in about one third of
their nephrons, the other two thirds hardly dipping into the medulla at all.

c) Selective reabsorption in DCT and collecting duct:
-The first part of the distal convoluted tubule behaves in the same way as the ascending limb
of the loop of Henl , while the second part behaves in the same way as the collecting duct
- In the distal convoluted tubule and collecting duct, sodium ions are actively pumped from the
fluid in the tubule into the tissue fluid, from where they pass into the blood. Potassium ions are
actively transported into the tubule. The rate at which these two ions are moved into and out of the
fluid in the nephron can be varied, and helps to regulate the amount of these ions in the blood.
-The fluid inside the tubule as it leaves the loop of Henl and moves into the collecting duct has lost
a little more water and more Na+ than it had when it entered the loop. Because more water has been
lost, the concentration of urea has increased.
-Now, in the distal convoluted tubule, Na+ is actively transported out of the fluid.
-The fluid then flows through the collecting duct. This passes through the medulla, where you have
seen that a low water potential has been produced by the loop of Henl.
-As the fluid continues to flow through the collecting duct, water moves down the water potential
gradient from the collecting duct and into the tissues of the medulla.
-This further increases the concentration of urea in the tubule. The fluid that finally leaves the
collecting duct and flows into the ureter is urine.
-DCT is also responsible for the removal of excess hydrogen ions to maintain pH of the blood
Why urine has no proteins, no glucose, and too much urea?

1-proteins found in glomerulus but not in filtrate, because they are too large to pass through
basement membrane.

2-no glucose in urine as it was all selectively reabsorbed in PCT.
3-urea is more concentrated in urine, as water is reabsorbed in distal convoluted tubule and
collecting duct.
How the kidney removes metabolic wastes from the body:

- Ultrafiltration; of blood in glomerulus; Forming filtrate in Bowman 's capsule;
-Soluble molecules; including urea; and ammonium ions pass into filtrate;
-filtrate is concentrated by removal of water (in collecting ducts);
- Formation of ammonium ions in distal convoluted tubule; from ammonia and protons;
-removal of metabolic water (formed as a waste product from break down of fats); osmoregulation;
by collecting ducts, formation of urine;
-distal convoluted tubule excrete excess acid and hydrogen ions ;
Selective reabsorption
Proximal convoluted Loop of Henl Distal convoluted Collecting duct
tubule tubule
Glucos Glucose concentration drops
e rapidly to 0.02 as the fluid
passes through the pct ------------- ---------- ------------
because all of it is
reabsorbed into the blood.
Urea Urea concentration The concentration of urea The first part behaves When ADH is secreted,
increases as the water is is higher than in pct as as the ascending limb, it binds to receptor on
reabsorbed from the tubule. water is lost from the and second part membrane that makes
descending limb. behaves as the the wall of the
collecting duct. So the collecting duct more
concentration of urea permeable to water
is much higher than in than normal, so the
PCT and loop of Henl urea concentration
as more water is increases greatly as
reabsorbed. water flows out of the
collecting duct
Na+ The concentration of Na+ The counter-current Sodium ions are actively pumped out of the
and K+ remains constant in multiplier builds up Na+ tubule, but this is counter- balanced by the
the pct, although some are and K+ concentration in continued removal of water from the tubule,
reabsorbed here, but this is the lower parts of the which increases its concentration in dct and
balanced by the loop, the concentration collecting duct.
K+ reabsorption of water. drops as it passes up the Potassium ions are actively transported into the
ascending limb towards tubule, so increasing their concentration more
the distal convoluted than that of sodium ions.
tubule.
Osmoregulation
Define:
- It is to maintain the water potential and dissolved solutes concentration of the body fluids at a
constant level.
- Water content is regulated by a negative feedback mechanism through ADH hormone to bring
things back to normal level, where receptor is cells in the hypothalamus, and the effectors are
the pituitary gland and the walls of the collecting ducts
The release of ADH:

-The amount of water in the blood is constantly monitored by cells, called osmoreceptor, within the
hypothalamus.
- It is not known exactly how this work, but it is probable that differences in water content of the
blood cause water to move either into them 9swell) or out of them (shrink) by osmosis.
- When water content of the blood is low, the loss of water from the osmoreceptor cells reduces their
volume, which triggers simulation of nerve cells in the hypothalamus.
-These nerve cells are rather different from other nerve cells because they produce a chemical called
antidiuretic hormone, or ADH.
-ADH is a polypeptide made up of just nine amino acids. It is made in the cell bodies of the nerve
cells, and passes along them to their endings in the posterior lobe of the pituitary gland. When
the nerve cells are stimulated by the osmoreceptor cells, electrical impulses called action
potentials travel down them. This causes ADH to be released from their endings into the blood in
capillaries in the posterior pituitary gland, then carried all over the body.

The role of collecting ducts in osmoregulation in the kidneys to
reduce water loss from the body by ADH:
- The word "diuresis" means the production of dilute urine. Antidiuretic hormone gets its name
because it stops dilute urine being produced by:
1- ADH affects collecting duct;

2- Binds to receptor on membrane of cells in the wall of collecting ducts;
3- Increase membrane permeability (to water) / more water channels;
4- This triggers enzyme controlled reactions;
5- Produces (active enzyme) phosphrylase;
6- (Which causes) vesicles with, water channels / aquaporins;
7- to, move to / fuse with, (plasma) membrane;
8- More water flows out of collecting duct;
9- Down / along, water potential gradient;
10- Then into blood;
11- Urine becomes more concentrated / small volume of urine;
12- This mechanism is controlled by negative feedback
Negative feedback in the control of water content :

-When the blood water content rises and is back to normal level, the osmoreceptors are no longer
stimulated, and stop stimulating their neighboring nerve cells.
-So ADH secretion slows down. This affects the cells in the walls of the collecting ducts.
-The water permeable channels are moved out of the plasma membrane of the collecting duct cells,
back into the cytoplasm.
-Thus, the collecting duct becomes less permeable to water. The liquid flowing down it retains more
of its water, flowing into the ureter as dilute urine.
-The collecting duct cells do not respond immediately to the reduction in ADH secretion by the
posterior pituitary gland.
-This is because it takes some time for the ADH already in the blood to be broken down;
approximately half of it is destroyed every 15 20 minutes. However, once ADH stops arriving at the

collecting duct cells, it takes only 10 15 minutes for the water-permeable channels to be removed
from the plasma membrane and taken back into the cytoplasm for storage.
Kidney failure:
It is when a person's kidney stops working due to an infection that damaged the kidney cells. if this
happens, then the kidneys can no longer remove urea or excess water from the blood. The person
feels very ill, and will die if no treatment is available
Treatments of kidney failure:
1-controlled diet:
-reduced intake of protein (less urea produced); less salt and water (less urine volume); and in
particular less potassium rich foods, e.g. oranges, chocolate, mushrooms (high potassium ions can
stop the heart)
-if this fails to help and blood urea level rises to five times than normal, the kidneys must be either
assisted by dialysis or replace by a healthy transplanted one
2-kidney transplant:
- A healthy kidney from a person only just dead or a living relative is surgically inserted near the
bladder. Certain precautions must be taken to avoid death of the transplanted kidney:
1-the blood group and tissue type of the donor and recipient of the kidney must be the same to
avoid rejection
2-the recipient's antibody system must be suppressed by immuno-suppressive drugs for the rest
of his or her life to avoid rejection, but also risks serious illness from other ordinary, infections. So
antibiotics are often given
3-Dialysis by 'kidney machine':

Dialysis:
It is the process of diffusion of different molecules according to their concentration gradients through
a partially or selectively permeable membrane
How kidney machine works?

1-blood from a vein in the patient's arm is pumped out to flow into the kidney machine
2-here, it passes through a dialyser that contains fluid containing water and other substances, such
as salt
3-as the patient's blood passes through the dialyser, it is separated from the fluid by a partially
permeable membrane (blood cells and proteins can't pass out)
4-as there is no urea in the fluid, most of the urea in the blood diffuses through the membrane into
the fluid
5-the amount of other substances remaining in the blood can be regulated by controlling their
concentrations in the fluid
6-blood is passed through a filter and a bubble trap then is pumped back to the patient's arm via a
vein
Disadvantages of using kidney machine:

1-expensive
2-timeand energy consuming
3-risk of getting infected
4-machine is not available all the time in all places
5-has to be repeated many times per week
6-uncomfortable to some people or painful
Precaution:
1-dialysis fluid must be sterile to prevent the entry of pathogens
2-dialysis fluid must be as warm as the body temperature to be suitable for enzyme activity
3-dialysis fluid must be changed frequently otherwise, diffusion of urea and salts stops
4- A bubble trap must be used to prevent the entry of air bubbles in the blood

Advantages of transplants
1- Long term solution / person no longer needs (regular) dialysis
2-increased freedom / better quality of life
3-more efficient control of composition of blood
4- Can have wider diet.
the control of body temperature (thermoregulation)

- This involves both coordination systems nervous and endocrine.
- All mammals can maintain a constant body temperature. As a result, they are not dependent on
absorbing heat from their surroundings and can be active at any time of day or night, whatever the
external temperature.
- Most other animals, with the exception of birds, rely on external sources of heat and are often
relatively inactive when it is cold.
- The hypothalamus in the brain is the central control for body temperature; it is the body 's
thermostat.
-it receives a constant input of sensory information about the temperature of the blood and about
the temperature of the surroundings.
- The hypothalamus has thermoreceptor cells that continually monitor the temperature of the
blood flowing through it.
- The temperature it monitors is the core temperature the temperature inside the body that
remains very close to the set point, which is 37C in humans. This temperature fluctuates a little, but
is kept within very narrow limits by the hypothalamus.
- The hypothalamus receives information about temperature from the skin receptors that monitor
changes in skin temperature, or change in the temperature of the surroundings.
- The hypothalamus sends impulses that activate the following physiological responses:

In Winter (Cold) In Summer (Hot)
Physiolo 1- Vasoconstriction muscles in the walls of 1- Vasodilation the muscles in the

gical arterioles that supply blood to capillaries near arterioles in the skin relax, allowing
Respons the skin surface contact. This narrows the more blood to flow through the
e lumens of the arterioles and reduces the capillaries so that heat is lost to the
supply of blood to the capillaries so that less surroundings.
heat is lost from the blood.
2- Lowering body hairs muscles
2- Shivering the involuntary contraction of attached to the hairs relax so they lie
skeletal muscles generates heat which is flat, reducing the depth of fur and the
absorbed by the blood and carried around the layer of insulation.
rest of the body.
3- Increasing sweat production
3- Raising body hairs muscles at the base sweat glands increase the production
of hairs in the skin contract to increase the of sweat which evaporates on the
depth for fur so trapping air close to the skin. surface of the skin so removing heat
Air is a poor conductor of heat and therefore a from the body.
good insulator. This is not of much use in
humans, but is highly effective for most
mammals.
4- Decreasing the production of sweat

this reduces the loss of heat by evaporation
from the skin surface.
5- Increasing the secretion of adrenaline

this hormone from the adrenal gland
increases the rate of heat production in the
liver.
Metaboli 1- The hypothalamus releases a hormone -When an increase in environmental

c which activates the anterior pituitary gland to temperature is detected by skin
Respons release thyroid stimulating hormone (TSH). receptors or the central
e TSH stimulates the thyroid gland to secrete thermoreceptor, the hypothalamus
the hormone thyroxin into the blood. increases the loss of heat from the
body and reduces heat production by
-Thyroxin increases metabolic rate, which radiation or by conduction.
increases heat production especially in the
liver.
When temperature start to increase again, the
hypothalamus responds by reducing the
release of TSH by the anterior pituitary gland
so less thyroxin is released from the thyroid
gland.
2- The heat that mammals generate is

released during respiration. Much of the
heat is produced by the liver cells that have a
huge requirement for energy. The heat they
produce is absorbed by the blood flowing
through the liver and distributed around the
rest of the body.
Behavior 1- The hypothalamus also stimulates higher 1-The behavioral responses of animals
al centers in the brain about some behavioral to heat include resting or lying down
Respons responses. with the limbs spread out to increase
e the body surface exposed to the air.
2- Some animals respond by curling up to
reduce the surface area exposed to the air 2- We respond by wearing loose fitting
and by grouping together. clothing, turning on fans or air
3- We respond by finding a source of warmth conditioning and taking cold drinks.
and putting on warm clothing.
(4) Nervous System
The need for a communication system in mammals:

1- To allow information to pass between different parts of their bodies, so their activities are
coordinated.
2- To help them to respond to changes in their internal and external environment (stimuli).
3- Mammals responses must be either fast or slow to control cycles, or short or long and term
processes (nervous and hormonal control or electrochemical or chemical). This is achieved by the
nervous system and the endocrine system.
Comparison between nervous and hormonal control:

Similarities:
1- Both are responsible for coordination
2- Both responses are triggered by stimuli
Differences:
endocrine Nervous
Transmission of chemicals or hormones Transmission of electrochemical impulses

Transmission via blood Transmission in nerves
Slow transmission Rapid transmission
Hormones dispersed throughout body Impulses sent directly to target organ
Long-term effects Short-lived effect
Nervous System (NS)

S (central) PNS (peripheral)
d Spinal Cord Spinal Nerves and Cranial

Nerves

Neurons:
-Nervous system is composed of specialized nerve cells called "neurons", which carry signals or
impulses.
Types and functions of neurons:

Sensory Relay or intermediate Motor
-Transmits impulses -Found in CNS -Transmits impulses from

from body receptor -Receives impulses from sensory CNS to body effector
to CNS neurons to be processed and pass (muscle or gland)
it to motor neuron
Describe the structure of a motor neuron.

- The cell body of a motor neuron lies within the spinal cord or brain, Nucleus in cell body
- (Short), dendrites
- Axon; (Axon) much longer than, many dendrites (not dendrons) ,highly branching to give large
surface area for the ending with other neurons.
- Cell body contains, mitochondria / RER /Golgi / groups of ribosomes;
- Many mitochondria at, synaptic knob / terminal branch;
- Synaptic vesicles; Neurotransmitter / named neurotransmitter; Ach
- Schwann cells / myelin sheath; Nucleus in Schwann cell;
- Node of Ranvier:
- Motor end plate / (dendrites) have receptors (for neurotransmitters)
Describe the structure and use of myelin sheath.

- Schwann cells; Wrap around axon; Sheath mainly lipid; (Sheath) insulates axon (membrane) ;
- Na+ / K+, cannot pass through sheath / can only pass through membrane nodes;
- Depolarization (of axon membrane) cannot occur where there is sheath / only at nodes of Ranvier;
- Action potentials "jump" between nodes; Saltatory conduction;
- Increase speed / reduces time, of impulse transmission; up t 100 ms -1, Speed in non myelinated
neurons about 0.5 ms-1 ;
Reflex arc and reflex actions:

Reflex arc:
-is the pass way along which impulses are carried from receptor to effector without the conscious
regions of the brain (during reflex action).
Reflex actions:
-is a fast, automatic response to a stimulus without the conscious of brain.
Describe a reflex arc and explain why a reflex action is needed:

- If there is a Strong stimulus in receptor,
- Action potential / impulses, along sensory neuron; to Dorsal root of spinal nerve; Into spinal cord;
- Synapse with intermediate neuron
- (Then) motor neuron; role of motor neuron: carry impulses from relay neuron in CNS through
synaptic Clift, and transfer it to effector via neuromuscular junction to produce response; Action
potential / impulses, to effector;
- Action potential / impulses, to brain;
- Response is produced; e .g. knee jerk;

Importance:
- Fast / immediate; Stops / limits, damage / danger; Automatic / no conscious thought; Innate /
instinctive;
Transmission of nerve impulses:

-Nerve impulses are transmitted in the form of electrochemical impulses or signals
-Neurons transmit impulses as electrical signals. These signals travel very rapidly along the plasma
membrane from one end of the cell to the other and are not a flow of electrons like an electric
current. Rather, the signals are very brief changes in the distribution of electrical charge across the
plasma membrane, caused by the very rapid movement of d potassium ions into and out of the
axon.
Stages of nerve impulse transmission:

a) Resting potential when a neuron is not transmitting impulses
b) Action potential when a neuron is stimulated and transmitting impulses through it.
c) Restoring resting potential when neuron is recovering from an action potential
A- Resting Potential:
Describe how resting potential is maintained in an axon:
- Axon phospholipid bilayer impermeable to K+ / Na+;
- Sodium potassium pump; transmembrane / globular protein / has ATP binding site;
- Active process / ATP used / energy needed;
- 3 Na+ (pumped) out / 2 K+ (pumped) in; K+ (diffuse) out / Na+ (diffuse) in; Through, protein channels
transport proteins;
- More K+ channels open than Na+ channels; therefore, membrane more permeable to K + or more K+
leave than Na+ enter (axon);
-Inside relatively more negative than outside; polarized
- Potential difference is -65 mV; or 70mV. Some axon in some organisms, such as squids and earth
worms, are very wide, and it is possible to insert tiny electrodes into their cytoplasm to measure
these changes in electrical charge.
- leaking K+ responsible for resting potential /
-an electrochemical gradient or "a double gradient" is produced
- Voltage-gated channels closed;
B- Action Potential:
-The rapid, fleeting change in potential difference across the membrane is called an action
potential. It is caused by changes in the permeability of the plasma membrane to Na + and K+.
- Na+ and K+ pass across membranes of nerve cells by: Sodium - potassium pump and voltage
gated channels that only open triggered by stimuli.
- An action potential is transmitted as a successive series of:
1) Depolarization: inside membrane more positive (+ 40mV), as Na + channels open and Na+ ions
flow in.
2) Hyperpolarization: inside much more negative than at resting potential, as more K + flow out
than expected.

3) ) Repolarization: inside membrane more negative (below -70mV), as K + channels open and K+
ions move out
4) This sequence of events is called an action potential. The time taken for the axon to restore
its resting potential after an action potential is called the refractory period.
- There are several consequences of their being refractory periods.

Action potentials are discrete events, they do not merge into one another.
there is a minimum time between action potentials occurring at any one place on a neurone.
the length of the refractory period determines the maximum frequency at which impulses are
transmitted along neurons.
-The axon is unable to generate another action potential until the refractory period is over. If an
action potential has been travelling in one direction from a point of stimulation, a "new" action
potential is only generated "ahead" of, and not behind it. This is because the region behind it will still
be recovering from the action potential it has just had and its distribution of sodium and potassium
ions will not yet be back to normal since most of sodium channels are closed. It is therefore
incapable of producing a new action potential for a short time.
Describe how action potential is transmitted along a motor

neutron:
- When a neuron is stimulated;
- Na+ channels open; Na+ enter cell; Inside becomes less negative / positive / +40mV / depolarized;
-depolarization triggers more channels to open so more sodium can enter , so more depolarization is
occurring . This is an example of positive feedback
- Na+ channels close;
- K+ channels open; K+ move out (of cell); Inside becomes negative, hyperpolarized /sodium-
potassium pump restores resting potential ; repolarized;
-Local Circuits cause an action potential to move along an axon:
-Sodium ions flow sideways inside the axon, away from the positively charged region (action)
towards the negatively charged regions (resting)on either side. This depolarizes these
adjoining regions and so generates an action potential in them.
- (myelin sheath / Schwann cells) insulate axon / do not allow movement of ions;
- Action potential / depolarization, only at nodes (of Ranvier) / gaps; causing Saltatory conduction
- Saltatory conduction: When action potential is transmitted along a myelinated axon (100
m/s ) ,action potentials "jump" from one node to the next, a distance of 1-3 mm. This is called
Saltatory conduction. It can increase the speed of transmission by up to 50 times that in a non-
myelinated axon
Speed of Conduction:
Describe how the structure of neurons speed up the transmission
of action potentials:
- Myelin sheath / Schwann cell; Insulates, axon / Dendron;
- It is Impermeable to Na+ and K+ ; so Depolarization only at nodes of Ranvier; local circuits;
- Action potentials "jump" from node to node; by Saltatory conduction;
- Speed increased by 50 times /o.5 ms -1 (in non-myelinated neurons) to 100 ms-1 (in myelinated
neurons);
- Axons with large diameter / giant axon; speeds up transmission of an action potential; reduce
resistance;
- Elongated axon / Dendron / neuron; for transmission of action potential for long distance
Receptors and Generator(Receptor) Potential :
Describe, using named examples, how sensory receptor in mammals
generates an action potential:
- To Respond to stimuli; (Some) receptors are the ends of sensory neurons; (Some) receptors are
cells; found in sense organs; these receptors are energy transducers;
-Transduction is the name given to the process by which a receptor converts a stimulus into a
nerve impulse.
-stimulus causes sodium ion channels to open, sodium ions enter the cell, depolarization, causes
local generator potential to be produced in the receptor
-if the receptor potential is greater than the threshold then action potential is generated in the
sensory neurone. This is an example of the all-or-nothing law: neurons either transmit impulses
from one end to the other or they do not.
-increased stimulus strength leads to increased frequency of action potentials
Example: Chemoreceptor cells found in human tongue:

The tongue is covered in many papillae. Each papilla has many taste buds over its surface.
Within each taste bud are between 50 and 100 receptor cells that are sensitive to chemicals in the
liquids that we drink or chemicals from our food that dissolve in saliva.
Each chemoreceptor is covered with receptor proteins that detect these different chemicals.
There are several types of receptor proteins, each detecting a different type of chemical and giving
us a different sensation.
There are five tastes: sweet, sour, salt, bitter and umami (savoury).
How receptor potential & action potential are generated & transmitted in
chemoreceptor?
a-salt Chemoreceptors:
1- Chemoreceptors in the taste buds that detect salt are directly influenced by sodium ions.
2- sodium ions diffuse through highly selective channel proteins in the cell surface membrane of the
microvilli and this leads to depolarization of the membrane.
3- The increase in positive charge inside the cell is the receptor potential.
4- If there is sufficient stimulation by sodium ions in the mouth then, then the receptor potential
becomes large enough to stimulate the opening of voltage-gated calcium ion channels.
5- Calcium ions enter the cytoplasm and lead to exocytosis of vesicle containing neurotransmitter
from the basal membrane.
6- The neurotransmitter stimulates an action potential in the sensory neurone that transmits
impulses to the taste centre in the cerebral cortex of the brain.
Sweet chemoreceptor
1- The cells that are sensitive to sweet have protein receptors that stimulate a G protein, which
activates an enzyme to produce many molecules of cyclic AMP.
2- Cyclic AMP acts as a second messenger activating a cascade to amplify the signal leading to
the closure of potassium ion channels.
3- This also depolarizes the membrane.

How Action Potentials carry information:
1- Action potentials do not change in size or the speed at which it travels. However long an axon is,
the action potential will continue to reach a value of +40mV inside all the way along.
2- The intensity of the stimulus which originally generated the action potential has absolutely no
effect on the size of the action potential.
Effect of the strength of a stimulus
A- Strong stimulus B- Weak stimulus
More frequency of action potentials, i.e. rapid Fewer action potentials per second
successes of action potentials per second
Stimulates more neurons Stimulates less neurons
How brain detects type (strong/weak) and nature (light, sound

etc) of a stimulus:
-The brain can interpret the frequency of action potentials along the axon of a sensory neuron, and
the number of neurons carrying action potentials, to get information about the strength of the
stimulus, whether it is light, heat, touch or so on, is deduced from the position of the sensory
neutron bringing the information.
-If the neuron is from the retina of the eye, then the brain will interpret the information as meaning
"light". If for some reason a different stimulus, such as pressure, stimulates a receptor cell in the
retina, the brain will still interpret the action potentials from this receptor as meaning "light". This is
why rubbing your eyes when they are shut can cause you to "see" patterns of light.
S y n a p s e s:
What is meant by synapses:
Where two neurons meet, they do not actually touch. There is a small gap between them called a
synaptic cleft. The membrane of the neurons just before the synapse is called a presynaptic
membrane, and the one on the other side is the postsynaptic membrane. The whole structure is
called a synapse.
Neuromuscular Junction:
Here, the nerve forms motor end plates and the synapse is called a neuromuscular Junction.
Such synapses function in the same way as typical synapses. An action potential is produced in the
muscle, which may cause it to contract.

Explain the role of synapse in transmitting Ach during an action
potential:
- Action potential / depolarization, reaches presynaptic membrane;
- (Ca2+) channels open in presynaptic membrane / presynaptic membrane becomes more

permeable to (Ca2+);
- Ca2+ (flood) into presynaptic, neuron / knob;
- (This causes) vesicles of, acetylcholine / ACh;(To) move towards presynaptic membrane / (to) fuse
with presynaptic membrane;
- ACh released into synaptic cleft / by exocytosis of ACh;
- ACh diffuses across (cleft) in less than 0.5 ms; ACh binds to receptor (proteins); on postsynaptic
membrane;
- Proteins change shape / channels open;
- Sodium ions (rush) into postsynaptic neuron; Postsynaptic membrane depolarized;
- Action potential / nerve impulse is passed to the next neuron;
- Action of acetyl cholinesterase:
- If the ACh remained bound to the postsynaptic receptors, the sodium channels would remain open,
and action potentials would fire continuously.
-To prevent this from happening, and also to avoid wasting the ACh, it is recycled. The synaptic cleft
contains an enzyme, acetyl cholinesterase, which splits each ACh molecule into acetate and
choline.
-The choline is taken back into the presynaptic neuron, where it is combined with acetyl co-enzyme A
to form ACh once more. The ACh is then transported into the presynaptic vesicles, ready for the next
action potential. The entire sequence of events, from initial arrivals of the action potentials to the re-
formation of ACh, takes about 5-10 ms
Explain why synaptic transmission is slower than impulse

transmission along the axon:
1- Myelinated axons acts as insulators speeding up transmission 100 m/s
2- Synaptic delay time due to:
a) Time to fuse vesicle with presynaptic membrane.
b) Time to release ACh by exocytosis and its diffusion across the cleft.
c) Time to reach receptor in postsynaptic membrane to initiate an action potential.
Types of synapses:
-more than 40 different transmitter substances are known; noradrenaline and Ach are found
throughout the nervous system, while dopamine , glutamic acid and gamma-aminobutyric
acid (GABA) are found in the brain only

The effect of other chemicals at synapses:
Many drugs and other chemicals act by affecting the events at synapses.
1- Nicotine is one of the main chemicals found in cigarette smoke. Part of the nicotine molecule
is similar in shape to ACh molecules, and will fit into the ACh receptors on postsynaptic
membranes. This produces similar effects to ACh, however, nicotine is not rapidly broken down by
enzymes, and so remains in the receptors longer than Ach. This is why nicotine is a stimulant. A
large dose of nicotine can be fatal.
2- The botulinum toxin is produced by an anaerobic bacterium which occasionally breeds in

contaminated canned food. It acts at the presynaptic membrane where it prevents the
release of ACh. Eating food that contains this bacterium is frequently fatal.
3- Organophosphorous insecticides inhibit the action of acetyl cholinesterase, thus

allowing ACh to cause continuous production of action potentials in the postsynaptic membrane.
Several nerve gases also act in this way. People involved in the production of these chemicals have
regular checks of their free acetyl cholinesterase levels to monitor their safety.

The roles of synapses
Describe the role of synapse in the nervous system:
1- Ensure one-way transmission; Receptor (proteins) only in postsynaptic, membrane /neuron;
Vesicles only in presynaptic neuron;
2- Adaptation;
A-Excitatory Synapses: An excitatory synapse leads to depolarization in the postsynaptic
membrane, leading to an action potential travelling along neuron.
B- Inhibitory Synapses: An inhibitory synapse leads to Hyperpolarization in post synaptic
membrane, making the neuron less likely to trigger an action potential.
3- The amount of a filter out low level stimuli of no significance; by discrimination / integration
4- Increased range of actions in response to a stimulus; Due to interconnection of many
nerve pathways (see, hear, and move at the same time); Synapses allow for a wide variety of
responses by effectors
5- Involved in memory / learning; Due to new synapses being formed;
6-Summation: Is the addition of excitatory postsynaptic potentials to overcome threshold level
needed to transmit an action potential.
Advantages of synapses (read only):
1- Uni- The releases of transmitted substance at the presynaptic membrane, and
direcionality. the location of receptor sites on the postsynaptic membrane, ensure that
nerve impulses can pass only in one direction along a given pathway. This
gives precision to the nervous system, allowing nerve impulses to reach
particular destinations
2- Amplification Sufficient acetylcholine is released, a neuromuscular junction by each nerve
impulse excite the postsynaptic membrane to produce response in the
muscle fiber. Thus nerve impulses arriving at the neuromuscular junction,
however weak are adequate to produce a response from the effector thereby
increasing the sensitivity of the system.
3- Fatigue The amount of transmit substance released by a synapse steadily falls off
response to constant stimulation until the supply transmitter substance is
exhausted and the synaptic transmitter substance is exhausted and the
synapse described as fatigued. Further passage of informat along this
pathway is not possible until after a period recovery. The significance of
fatigue is that it prevents damage to an effector through overstimulation.
4-Adaptation: Most receptors initially respond to a strong constant stimulus by producing a
high frequency of impulses in the sensory neuron. The frequency of these
impulses gradually declines and this reduction in response, with time, is
called adaptation.
A-Rapidly adapting receptors: respond to changes in stimulus level by
producing a high frequency of impulses at the moments when the stimulus is
switched "on" or "off". For example, the Pacinian corpuscle and other
receptors concerned with touch and the direction of sudden changes act in
this way. They register change in the stimulus.

B-Slowly adapting receptors: Register a constant stimulus with a slowly
decreasing frequency of impulses.
5-Integration, A postsynaptic neuron may receive impulses from a large number of

convergence, and excitatory and inhibitory presynaptic neurons. This is known as
spatial summation convergence, and the postsynaptic neuron is able to summate the stimuli
from all the presynaptic neurons. This spatial summation enables the
synapse to act as a center for the integration of stimuli from a variety of
sources and the production of a coordinated response
6-Facilitation. Where each stimulus leaving the synapse more responsive to the next
stimulus. The sensitivity of the synapse has therefore been increased, and
subsequent weaker stimuli may cause a response.
Muscle Contraction:
-It is very important that the activities of the different muscles in our bodies are coordinated.
-When a muscle contracts, it exerts a force on a particular part of the body, such as a bone. This
results in a particular response.
- The nervous system ensures that the behavior of each muscle is coordinated with all the other
muscles, so that together they can bring about the desired movement without causing damage to
any parts of the skeletal or muscular system.
The structure of striated muscle:

- A muscle such as a biceps is made up of thousands of muscle fibres. Each muscle fibre is a very
specialised "cell"
- Some biologists prefer not to call it a cell, because it contains many nuclei. Instead they prefer the
term syncytium to describe multinucleate muscle fibre.
- The cell surface membrane is the sarcolemma, the cytoplasm is sarcoplasm and the
endoplasmic reticulum is sarcoplasmic reticulum (SR).
- The cell surface membrane has many deep infoldings into the interior of the muscle fibre, called
transverse system tubules or T-tubules for short. These run close to the sarcoplasmic reticulum.
- The membranes of the sarcoplasmic reticulum have huge numbers of protein pumps that
transport calcium ions into the cisternae of the SR.
- The sarcoplasm contains a large number of mitochondria, often packed tightly between the
myofibrils. These carry out aerobic respiration, generating the ATP that is required for muscle
contraction.
-Striations are produced by a very regular arrangement of many myofibrils in the sarcoplasm
- Each myofibril is striped in exactly the same way, and is lined up precisely against the next one, so
producing a pattern.
-Striations are made up of protein. The thick filaments are made mostly of myosin, whilst the thin
ones are made mostly actin.
- The darker parts of the strips, the A bands, correspond to the thick (myosin) filaments.
- The very dark parts of the A band are produced by the overlap of thick and thin filaments, while the
lighter area within the A band, known as the H band, represents the parts where only the thick
filaments are present.
- A line known as the Z line provides an attachment for the actin filaments, while the M line does
the same for the myosin filaments.
- The part of a myofibril between two Z lines is called a sarcomere.
- Myofibrils are cylindrical in shape, so the Z line is in fact a disc separating one sarcomere from
another and is also called the Z disc
Structure of thick and thin filaments

A) Thick filaments are composed of many molecules of myosin, which is a fibrous protein with a
globular head. The fibrous portion helps to anchor the molecule into the thick filament. Within the
thick filament, many myosin molecules all lie together in a bundle with their globular heads all
pointing away from the M line.
B) Thin filaments are composed of actin which is a globular protein. Many actin molecules are
linked together to form a chain. Two of these chains are twisted together to form a thin filament.
Also twisted around the actin chains is a fibrous protein called tropomyosin. Another protein,
troponin, is attached to the actin chain at regular intervals.

How muscles contract (study figure):
-Muscles cause movement by contracting.
- The sarcomeres in each myofibril get shorter as the Z discs are pulled closer together. It is known
as the sliding filament model of muscle contraction.
-The energy for the movement comes from ATP molecules that are attached to the myosin heads.
Each myosin head is an ATPase

Stimulating muscle to contract (see figure):
- When there is no longer any stimulation from the motor neurone, there are no impulses conducted
along the T-tubules.
- Released from stimulation, the calcium ion channels in the SR close and the calcium pumps move
calcium ions back into stores in the sarcoplasmic reticulum.
- As calcium ions leave their binding sites on troponin, tropomyosin moves back to cover the myosin-
binding sites on the thin filaments.
- When there are no cross-bridges between thick and thin filaments, the muscle is in a relaxed state.
- There is nothing to hold the filaments together so any pulling force applied to the muscle will
lengthen the sarcomeres so that they are ready to contract (and shorten) again.

- Each skeletal muscle in the body has an antagonist- a muscle that restores sarcomeres to their
original lengths when it contracts. For example, the triceps is the antagonist of the biceps.
Providing ATP for muscle contraction:
- A contracting muscle uses a lot of ATP.The very small quantity of ATP in the muscle fibres in a
resting muscle is used up rapidly once the muscle starts to contract. More ATP is produced by
respiration both aerobic respiration inside the mitochondria and, when that cannot supply
ATP fast enough, also by lactic fermentation in the sarcoplasm.
- Muscles also have another source of ATP, produced from a substance called creatine phosphate
stored in their sarcoplasm. It is their immediate source of energy once they have used the small
quantity of ATP in the sarcoplasm.
- A phosphate group can quickly and easily be removed from each creatine phosphate molecule and
combined with ADP to produce more ATP.
creatine phosphate + ADP creatine + ATP
- Later, when the demand for energy has slowed down or stopped, ATP molecules produced by
respiration can be used to "recharge" the creatine:
creatine + ATP creatine phosphate + ADP
- In the meantime, if energy is still being demanded by the muscles and there is no ATP spare to
generate the creatine phosphate, the creatine is converted to creatinine and excreted in urine.

(3) Hormonal Control
A Endocrine System:
- Hormone: A substance or a chemical secreted by an endocrine gland that is carried in blood
plasma to another part of the body (target cell or organ) where it has an effect.
- A gland is a group of cells which produces and releases one or more substances, by a process
known as "secretion".
- Endocrine gland: a gland containing specialized secretory cells that release a hormone into the
blood stream at a distance from the hormone's target organ (ductless).
- Exocrine glands: "exocrine" means secreting to the outside. The secretory cells of exocrine
glands secrete their substances, which are not hormones, into a tube or duct, along which the
secretion the secretion flows, e.g. salivary glands secrete saliva into salivary ducts, which carry
the saliva into the mouth.
Common features of mammalian hormones:
- Small molecules
- Made of proteins (e.g. insulin) or steroids (e.g. testosterone)
- Transported in blood plasma
- Formed in very small concentrations (mg or g), since they are secreted at low rate by exocytosis
(active process)
- They are short-lived in the body (they are broken by enzymes and excreted in urine by kidney)
- They are secreted in response to a stimulus, e.g. Adrenaline is fight or flight or fright hormone
- They affect target cells that contain specific receptors to the hormones.
Receptors of hormones and Target cells:

Protein hormone Steroids hormone
-The receptors for protein hormones (too -steroids hormones are lipid-soluble,
large to enter the cell), such as insulin, are and so can pass easily through the
on the plasma membrane. These hormones plasma membrane into the cytoplasm.
bind with the receptors on the outer surface The receptors for steroid hormones are
of the membrane, causing a response by the inside the cell, in the cytoplasm
cell without actually entering it.
Compare between nervous and hormonal control:
Endocrine
- Hormones; Chemical messengers; secreted by Ductless glands / (released) into blood; to Target,
organs / cells that have receptors on cell membranes; or inside the cell.

- Example of named hormone and effect; insulin secreted by islets of Langer Hans that is scattered
on pancreas, lowers high blood glucose level to normal level
Nervous
- Impulses /action potentials; along, neurons / nerve fibers (not nerves); Synapse (with target)
neuromuscular junction;
- Receptors receive stimulus and send action potentials by sensory neuron to CNS/ effector produces
response when it receives information from CNS transmitted as action potentials through motor
neuron;
Differences endocrine
- Slow effect / long lasting effect /widespread effect / (see table in nervous system chapter)
Describe the role of negative feedback in homeostasis in
mammals:
1- Maintains, constant / stable, internal environment;
2- A change in, some parameters / example of parameter; (like blood glucose or temperature)
3- Detected by a sensor / receptor;
4- Brings about response via an effector /describe the corrective mechanism;
5- To return conditions back to normal / set point;
6- Named, receptor / effector;
Pancreas:
-The pancreas is a very unusual gland, because parts of it functions as an exocrine gland, while other
parts function as an endocrine gland.
-The exocrine function is the secretion of pancreatic juice, which flows along the pancreatic duct into
the duodenum, where it helps indigestion.
-The endocrine function is carried out by group of cells called the islets of Langerhans, which are
scattered throughout the pancreas.
-The islets contain two types of cells; cells secrete glucagon, while cells secrete insulin. These
two hormones (both small proteins), are involved in the control of blood glucose levels.
Describe parts of pancreas involved in its endocrine function:

- Islets of Langerhans containing and cells, surrounded by blood supply to take away hormones.
The control of blood glucose concentration:

- Carbohydrate is transported through the human bloodstream in the form of glucose, dissolved in
the blood plasma.
- For storage, glucose can be converted into the polysaccharide glycogen, a large and insoluble
molecule made up of many glucose units linked together, which can be stored inside cells, especially
liver and muscle cells.
- In a healthy human, each 100 cm3 of blood normally contains 80 120 mg of glucose. If
blood glucose level drops, then cells may run short of glucose for respiration, and be unable to carry
out their normal activities. This is especially important for cells that can only respire glucose, such as
brain cells.
- Very high blood glucose levels can also cause major problems, upsetting the normal behavior of
cells.
- Hormones are involved in the control of blood glucose concentration by negative feedback
include insulin and glucagon.

If blood glucose concentration rises above normal level:
- Homeostasis, Maintenance of constant / stable, internal environment; Despite changes in external
environment;
- Negative feedback;
- Receptor and effector; are Beta cells; in islets of Langerhans / pancreas;
- Release insulin (into blood), (globular protein);
- Alpha cells stop releasing glucagon;
-insulin Affects liver / muscle cells;
- When insulin molecules bind to receptors on muscle cells, the vesicles with GLUT4 proteins are
moved to the cell surface membrane and fuse with it. GLUT4 proteins facilitate the movement of
glucose into the cell.
Insuline also stimulates the activation of the enzyme glucokinase, which phosphorylates glucose.
This traps glucose inside cells, because phosphorylated glucose cannot pass through the
transporters in the cell surface membrane. Insulin also stimulates the activation of two other
enzymes, phosphofructokinase and glycogen synthase, which together add glucose molecules to
glycogen. This increases the size of the glycogen granules inside the cell (short term storage).
- Increased permeability of cells to glucose / absorption from blood;
- Increased uptake of glucose (by cells) especially skeletal muscle;
- Increased use of glucose in respiration;
-glucose converted to fat;
- Increase in the use of glucose rather than other substances, such as fat, as a source of energy for
cell respiration;
- Increase in the rate of uptake of amino acids into cells and the rate of protein synthesis (active
process);
- Decrease in gluconeogenesis (production of glucose from other compounds like fats);
- Increase in conversion of glucose to glycogen by glycogenesis;
- Stored in liver and muscles;
- When there is a fall in blood glucose concentration / return to normal;

- Normal concentration of blood glucose is 80 120 mg / 100 cm 3; insulin production is switched off,
insulin is broken down and excreted.
-describe how insulin secretion is controlled ( K + channels close / role of Ca2+); (see next page)
If blood glucose concentration falls below normal level:

- Homeostasis, Maintenance of constant / stable, internal environment; Despite changes in external
environment;
- Negative feedback;
- Receptor and effector; are Alfa cells; in islets of Langerhans / pancreas;
-. The Alfa cells respond by secreting glucagon,
- cells respond by stopping the secretion of insulin thus stopping the increased uptake and usage
of glucose by liver and muscle cells, although uptake still continues at amore "normal" rate.
- The presence of glucagon affects the activities of the liver cells. (Muscle cells are not responsive to
glucagon because they do not have receptors for glucagon).
- These effects include:
a) The breakdown of glycogen to glucose by glycogenolysis.
b) The use of fatty acids instead of glucose as the main fuel in respiration.
c) The production of glucose from other compounds such as fats by gluconeogenesis.
- The liver releases glucose into the blood. This blood flows around the body, passing through the
pancreas. Here, the cells sense the raised glucose levels, switching off glucagon secretion.
- When there is a rise in blood glucose concentration / return to normal;
- Normal concentration of blood glucose is 80 120 mg / 100 cm 3; glucagon production is switched
off, glucagon is broken down and excreted
-Note:
-Blood glucose concentrations never remain constant, even in the healthiest person. One reason for
this is the inevitable time delay between changes in the blood glucose concentration and the onset
of actions to correct it.
-Time delays in control systems result in oscillation, where things do not stay absolutely constant but
sometimes rise slightly above and sometimes drop slightly below the 'required concentration'.
- Like insulin, Glucagon cannot cross membranes to have their effects inside their target cells.
Instead they both work by activating messenger molecules within the cell, the case of glucagon;
this second messenger is cyclic AMP, which activates enzymes within the cell to increase blood
glucose level to normal.
*The hormone adrenaline:
-also increases the concentration of blood glucose.
- Hormone-receptor interaction at the cell surface (binding)
- Formation of cyclic AMP which binds to kinase proteins
- An enzyme cascade involving activation of enzymes by phosphorylation to amplify the signal,
Leading to the same end result the breakdown of glycogen by glycogen phosphorylase.
Adrenalin also stimulates the breakdown of glycogen stored in muscle during exercise. The glucose
produced remains in the muscle cell where it is needed for respiration
ne analysis and diagnosis:

Advantages:
a- It is much easier to collect a urine sample from someone than a blood sample.
b- Simple tests on urine can give early indications of health problems.
How urine analysis helps in diagnosis:

1- The presence of glucose and ketones in urine in urine indicates that a person may have
diabetes. If blood glucose concentration increases above a certain value, known as the renal
threshold, not all of the glucose is reabsorbed from the filtrate in the proximal convoluted tubule of
the kidney and some will be present in the urine.
2- The presence of protein in the urine indicates that there is something wrong with the kidneys.
Most protein molecules are too large to be filtered. However, some protein molecules are filtered,
but these are reabsorbed by endocytosis in the proximal convoluted tubule, broken down and the
amino acids absorbed into the blood. It is not unusual for some protein to be present in the urine for
short periods of time, such as during a high fever, after vigorous exercise and during pregnancy.
However, a large quantity or the long-term presence of protein the urine indicates there may be a
disease
affecting the glomeruli or there is a kidney infection. Protein in the urine is also associated with
high blood pressure, which is a risk factor in heart disease.
Diabetes Mellitus:
Types of diabetes
Type I - Juvenile-onset diabetes Type II- Non-Insulin dependent

(Insulin dependent diabetes) diabetes
1- The pancreas is incapable of secreting 1- The pancreas does secrete insulin,

sufficient insulin. but the liver and muscle cells do not
2- It is thought that this might be due to a respond properly to it.
deficiency in the gene which codes for the 2- It frequently begins relatively late in
production of insulin, or because of an attack on life and is often associated with obesity.
the cells by the person's own immune system.
3- This form of diabetes, as suggested by its
name, usually begins very early in life.
Symptoms of both types of diabetes:

1- Rise in blood glucose level after a meal of carbohydrates, and staying high;
2- Glucose passes out in the urine, since the kidneys cannot reabsorb all the glucose;
3- Frequent urination, since extra water and salts are lost in urine;
4- Extreme hunger and thirst;
5- Glucose uptake by cells is slow, so metabolism of fats and proteins as an alternative source of
energy and weight loss;
6- This can lead to accumulation of keto acids in blood, lowering blood pH causing dehydration or
coma;
Why people with diabetes have no glycogen to be mobilized?

- Since no insulin, or no response to insulin, cells cannot take up glucose in excess or do not convert
it into glycogen.
- if glucose is not taken by cells, then the Lack of glucose in cells may cause coma due to lack of
respiration.
Treatment of diabetes:
1-In insulin - dependent diabetes, regular injections of insulin, together with a carefully controlled
diet, are used to keep blood glucose levels near normal.
2- The person must monitor their own blood glucose level, taking a blood sample several times a
day.
3- In non-insulin- dependent diabetes, insulin injections are not normally needed, control is by diet
only.
Some disadvantages of using insulin Some advantages of using genetically

obtained from animals such as pigs & engineered human insulin
cattle
1- Expensive 1- More rapid response

2- Many animals are killed 2- Shorter duration of response
3- May cause allergy (different from human 3-Less chance of an immune response to the
insulin) insulin developing
4- Small quantities are produced 4- Effective in people who have developed a
5- More risk in transmitting disease tolerance for animal-derived insulin
5- More acceptable to people who feel it is
unethical to use pig or cattle insulin
6- Cheaper
Using immobilised enzymes in Dipsticks and Biosensors In the

quantitative measurement of glucose:
(1) Dipsticks:
-Glucose is not usually detectable in the urine of healthy mammals although it is filtered out of the
blood in the kidney. It is reabsorbed in the proximal tubules. Humans with diabetes are unable to
control the levels of glucose in their blood their urine will usually contain variable amounts.
-One way to determine the quantity of insulin needed is to test a sample of urine with glucose
dipstick.
- A small pad at one end of the dipstick contains immobilised glucose oxidase and peroxidase. It
also contains potassium iodide chromogen.
-When the pad is in contact with glucose, the glucose oxidase converts the glucose to gluconic acid
and hydrogen peroxide.

-The peroxidase then catalyses a reaction of the hydrogen peroxide with the potassium iodide
chromogen. Different colours are produced according to the quantity of hydrogen peroxide formed,
which in turn depends on the original concentration of glucose in the liquid.
-The colour can be compared with a colour chart to give a reading for the glucose concentration.
(2) Biosensor:
-It is a device which makes use of a biological molecule (such as an enzyme or an antibody or
sometimes a cell) to detect and measure by a meter, a chemical compound.
The glucose biosensor works as follows:

1- It contains a layer of immobilised glucose oxidase enzyme.
2- This enzyme binds with any glucose in the blood, which is oxidised with dissolved oxygen from the
solution to form hydrogen peroxide and gluconic acid.
3- Gluconic acid releases H+ that forms positive charges causing a current flow.
4- An electrode (usually platinum) measures the drop in oxygen concentration (from step 2) as it is
used to make hydrogen peroxide. The electrode generates an electrical signal.
5- The size of the electrical signal (current flow) is proportional to the concentration of glucose in the
blood.
6- A digital readout gives the user a figure for the glucose concentration.
Advantage of using biosensor rather than a dipstick:

1- Exact glucose value is measured or more precise reading is obtained (in biosensor).
2- Hard to judge and match the colour with the colour on chart (in dipstick).
3- Hard to decide if the Colour obtained is between two colours on the chart (in dipstick).
4- Biosensor is used many times while dipstick is used once and disposed.
The menstrual cycle:

-The menstrual cycle is a repeating process of change in the ovaries, oviducts and uterus, which
takes place approximately every 28 days from puberty to menopause. It is controlled by four
hormones. It usually begins between the ages of 10 and 14, and continues until the woman reaches
the menopause at around 50 years old.
The role of hormones in the human menstrual cycle and changes in

the ovary and uterus during the cycle
-There are a number of hormones involved in the control of the human menstrual cycle.
Two steroid hormones produced by the ovaries:
1- Oestrogen (produced by follicle cells) or granulosa cells.
2- Progesterone (produced by corpus luteum) or granulosa cells.

-Two Gonadotropic glycoprotein hormones are secreted by the anterior pituitary gland:
1- Luteinizing Hormone (LH).
2- Follicle Stimulating Hormone (FSH).
- Oestrogen begins to be secreted at the onset of puberty; it brings an increase in the size of the
reproductive organs and the development of secondary sexual characteristics.
- The duration of a normal menstrual cycle is 28 days day 1 is the first day of menstruation.
-Hormones receptors:
- Cells that carry FSH receptors : follicle / granulosa cells.
- Cells that carry LH receptors : corpus luteum / granulosa cells.
The main hormonal changes during the cycle are as follows:

1- Secretion of FSH and LH increases slightly during the first few days. This causes a number of
primary follicles to develop, though only one in one ovary continues to develop.
2- The granulosa cells of the developing follicle secrete oestrogen, the levels of which start to rise
sharply during the first half of the cycle.
3- The increase in the level of oestrogen inhibits any further secretion of FSH and LH and their
levels start to fall.
4- The oestrogen causes the endometrium to thicken by day 12 it is 3 4 mm thick. The
endometrium (lining of the uterus), causing the cells to divide to form a thicker layer, ready to
receive an embryo if the egg is fertilized
5- Oestrogen also affects the oviduct, causing the development of larger and more active cilia on the
cells lining its walls. It also increases the secretion of more glycoprotein; these changes prepare the
oviduct for the arrival of an oocyte, which will be moved along the oviduct by the cilia.
6-Around day 12 the secretion of LH suddenly rises very sharply. This causes the granulosa cells to
reduce their secretion of oestrogen and start to secrete progesterone.

7- LH also causes ovulation, which normally occurs on day 14 (i.e. half way through the cycle).
8- At day 13 or 14, a surge in LH causes the primary oocyte in a single ovarian follicle to complete
meiosis I and continue to metaphase of meiosis II. It also causes the follicle to shed the secondary
oocyte into the oviduct. This is ovulation.
9- When the egg has been released, the remaining granulosa cells of secondary follicle enlarge and
fill up with a yellow substance. It is now called a corpus luteum or yellow body, which continues to
secrete large amounts of progesterone and smaller amounts of oestrogen.
10- Progesterone becomes the dominant steroid hormone from 5 days after ovulation (which is when
an embryo would enter the uterus). Progesterone causes the cells in the endometrium to
differentiate to form a thick vascularised layer (full of blood capillaries and blood vessels) increasing
is supply of blood, and increasing the amount of glycogen and lipids in its cells. The thickness of the
endometrium reaches 5 6 mm and it is prepared for implantation, if the egg has been fertilized.
11- If fertilization has not occurred, the oestrogen and progesterone inhibit the secretion of FSH and
LH from the anterior pituitary gland. As a result, the corpus luteum degenerates from day 23, so the
secretion of progesterone also decreases. This causes the breakdown of the endometrium, leading to
the start of menstruation on day 0 of the start of the next cycle.
12- All four hormones now fall to a low level and, once the oestrogen and progesterone have
dropped far enough, the anterior pituitary again begins to secrete FSH and LH and the cycle begins
again (negative feedback mechanism).
13- The fall in oestrogen and progesterone causes the endometrium to breakdown and menstruation
occurs during the next four to seven days of the cycle.
Negative feedback in the menstrual cycle:

1- High concentrations of oestrogen inhibit the secretion of FSH and LH by the anterior pituitary
gland. This happens during the first half of the menstrual cycle, causing the levels of FSH and LH to
fall.
2- However, when oestrogen levels are very high, a surge of LH secretion occurs, which brings about
ovulation.
3- Towards the end of the cycle, as oestrogen and progesterone levels fall, the inhabitation of FSH
and LH secretion is lifted, so the concentration of these two hormones begins to increase, leading to
the start of a new cycle.
SUMMARY:

a) Role of FSH in menstrual cycle:
1- Bind to receptor of follicle.
2- Stimulate the development / maturation of follicle.
3- Thus follicle releases oestrogen.
4- To thicken lining of uterus.
5- To inhibit further FSH production.
b) Role of oestrogen in menstrual cycle:

1- Thickness of uterus lining.
2- Repair of uterus lining.
3- Inhibits FSH, thus preventing development of more oocytes.
4- Stimulates the secretion of LH for ovulation.
c) Role of progesterone in menstrual cycle:

1- Secreted by corpus luteum after day 14.
2- Stop secretion of FSH and LH, thus preventing developing of new follicle, no further ovulation or
fertilization.
3- Maintain thickness of uterus lining, to be ready for implantation.
4- Prevent menstruation during pregnancy, and maintain blood vessels in endometrium
d) Role of LH in menstrual cycle:

1- Causes ovulation.
2- Stimulates production of progesterone by corpus luteum to maintain the lining of the uterus
(endometrium), making it ready to receive the embryo(implantation) if fertilization occurs.
Factors that may affect the menstrual cycle other than hormones:
-Irregularity of cycle might be caused by . illness / travel / stress/seasons / synchronicity
CONTRACEPTION:
control methods
ntraceptive Pills 2-Anti-implantation Methods:

mones): -Prevent Implantation of uterus
nt Fertilization Example, IUD, and morning after pills
(hormones)

[1] -The biological basis of the oestrogen / progesterone contraceptive
pill:
1- The oestrogen / progesterone contraceptive pill is also known as the 'combined oral contraceptive
pill' or, more commonly as 'the pill'.
2- Usually synthetic hormones rather than natural ones are used, because they are not broken so
rapidly in the body and therefore act for longer.
3- There are many different types, with slightly different ratios of these two hormones, because
women are not all alike in the way their bodies respond to the pill.
4- With most types of oral contraceptive, the woman takes one pill daily for 21 days and then stops
for 7 days, during which menstruation occurs.
5- In some types, she continues to take a different coloured, inactive pill for these seven days just to
keep the habit.
6- As well as being taken orally, the hormones can be administered by injections or by slow release
skin patches; it is a very effective method of contraception.
Effect of contraceptive pills:

1- Reduce production of FSH and LH by negative feedback; From anterior pituitary gland;
2- Lack of FSH prevents maturation of follicle;
3- Lack of LH prevents ovulation;
4- Prevent fertilization;
5- Prevent Implantation;
6- Increase mucus in cervix forming a 'mucus plug this makes it more difficult for the sperm to get
through to the uterus. 7-It also makes the lining of the uterus thinner, making it extremely unlikely
that a fertilized egg could implant.
[2] The morning after pill:

-This form of birth control is intended to be taken after a woman has had unprotected sexual
intercourse and thinks that she might get pregnant.
-It might be taken by a woman who forgot to take her oral contraceptive pill, or if a condom broke, or
by someone who was raped, as well as by a woman who simply did not take any precautions to
prevent pregnancy.
- It works up to 72 hours afterwards, not just the 'morning after'.
-The pill contains a synthetic progesterone-like hormone. If taken early enough, it reduces the
chances of a sperm reaching and fertilizing an egg by forming a mucus plug. However, in most
cases, it probably prevents a pregnancy by stopping the embryo implanting into the uterus by
thinning the uterus lining.
The Biological, Social, and Ethical Implications of the use of

Contraception:
Advantages and Disadvantages of using Contraception:

Advantages and Benefits Disadvantages, Side Effects
and Possible Risks
Biologic -methods of contraception which do not 1- Subjected to human error when taking pills.
al involve hormones (e.g. barrier methods) 2- Some women may develop nausea and
do not really have any biological headaches.
implicati 3- Tiredness and mood changes.
implications.
ons 4- Rise in blood pressure.
-However, there are many biological
5- Increased risk of thrombosis. In some women
implications when using the oestrogen / this can very serious may cause a stroke or a
progesterone pill. blood clot in the lungs
1- Reduces the risks of developing certain 6- Small increased risk of breast cancer.
ovarian cysts. 7- Sexual intercourse with more partners
2- Reduces the risk of developing cancer of increases the risk of the spread of diseases
the ovary or uterus. such as HIV / AIDS, and can also increase the
3- Menstruation is more regular and it may risk of marriage breakdown or stress.
help to relieve pre-menstrual tension.
4- Reduces the risk of pelvic infection the
mucus plug may prevent bacteria getting into
the uterus.
Social -in many parts of the world, the use of 1- The sexual freedom conferred by easy and
implicatio contraception is referred to as 'Family reliable contraception may have contributed to
ns Planning'. As this suggests the availability of the breakdown of a higher percentage of
contraception means that: marriages than was happening up to the
1950s.
1- It is easier to choose when to have children. 2- More children are now being brought up by
It also easier to choose not to have children. one parent, and this may sometimes cause
2- In those parts of the world where difficulties for the parent and the child.
contraception is not freely available, there 3- Parents are concerned that their children
continue to be problems of overpopulation may be sexually active without their
and the implications that this has for supply of knowledge, because young people can get
food, water and other resources. contraceptive easily and in privacy.
3- Family size can be kept to the level desired 4- The result is that it is possible to plan
by the parents, which could potentially reduce families around careers and other
poverty and make it more possible for each considerations, such as financial
child to have a better standard of living circumstances. It has also meant that, in some
including better nutrition, health care and countries, the population size has not increased
education. to the extent that it would have done in the
4- Partners who do not wish to have children absence of contraception. Indeed in some
for reasons such as the risk of inheriting a areas, there is concern that there are too few
genetic disorder can still have an active sex children being born to be able to sustain the
life population in the future (promotes extinction).
5- Use of the contraceptive pill can enable 5- A man may feel that he can have intercourse
women to determine their own fertility, so with his female partner whenever he wishes,
they can avoid having unwanted child even if even if she does not want this pregnancy.
their partner does not take this responsibility.
Ethical -For many people the benefits of using 1- Families from many religious groups see
implicatio contraception in terms of control of fertility birth control as a God-given way of spacing out
ns and birth-control far outweigh any ethical their pregnancies and maximizing the life-
objections. The benefits may be seen in terms chances of their children.
of the opportunities for: - For others, ethical objections are seen as
1- A woman to decide when and if she will outweighing any potential benefits and so
conceive. some Christians (e.g. Catholics) believe that
2- Countries to control their population sexual activity within marriage is God-given for
growth. the purpose of reproduction, and so artificial
3- Those at medical or psychological risk if contraception such as the pill is morally wrong.
pregnant, to avoid such pregnancy. 2- With no fear of becoming pregnant, a
4- Reduced chance of unplanned pregnancy in woman may be more prepared to have sexual
sexually active teenagers. intercourse with more partners, there is that
5- Use of contraception avoids unwanted the widespread availability of contraception
pregnancies and therefore reduces the has increased promiscuity among young
number of abortions; abortion is stressful for a people.
woman (and her partner) and is held to be 3- Some people see the use of anti-
morally undesirable by many people. implantation pills as being equivalent to
'unsupervised abortion on demand'.

The need of communication system in flowering plants:
1- To respond to changes in the internal and external environment (sensitivity = producing response
to stimulus)
2- Irritability is an adaptive response in plants to a stimulus
3- Plants need to coordinate flowering, seed germination, and growth
4- Plants have only slow responses controlled by growth hormones (auxins and other hormones)
5- In some species electrical signals or action potential can be detected, that travel only very slowly
and are very weak. Plant cells have sodium-potassium pumps that produce electrochemical gradient
across their membranes in just the same way as in animals. Some chemicals if coming in contact
with plants surface induce an action potential e.g. Acid rain on soya beans
Examples
a - In the sensitive plant Mimosa which responds to touch by folding up its leaves, an electrical
signal similar to that of action potential can be detected.
b - In the Venus fly-trap which is an insectivorous plant, when an insect touches the sensitive
hair in the plant, an action potential is set up and passes to the leaves to close trapping the insect.

(B) Homeostasis in plants
- A stoma is the hole between the guard cells, but the term is usually used to refer to the two
guard cells and the hole between them.
- Stomata may look very simple, but guard cells are highly specialized cells that respond to a wide
range of environmental stimuli and thus control the internal atmosphere of the leaf.
- Stomata show daily rhythms of opening and closing. Even when kept in constant light or constant
dark, these rhythms persist.
a- Opening during the day as light intensity increases to allow diffusion of carbon dioxide into the
air spaces within the leaf for photosynthesis and the allow diffusion of oxygen out of the leaf.
However, it also allows diffusion of water vapour out of the leaf during transpiration.
b- Closure of stomata at night when photosynthesis cannot occur reduces rates of transpiration and
conserves water.
- Stomata close in response to:
Darkness.
High carbon dioxide concentrations in the air spaces in the leaf.
Low humidity.
High temperature.
Water stress, when the supply of water from the roots is limited and / or there are high rates of
transpiration.
- The disadvantage of closing is that during daylight, the supply of carbon dioxide decreases so
the rate of photosynthesis decreases.
- The advantage of closing is that water is retained inside the leaf which is important in times of
water stress.

Plant Growth Regulators
Properties of plant hormones:

1-most communication within plants depends on chemicals. These are known as plant hormones
or plant growth regulators.
2- Unlike animal hormones, plant growth regulators are not produced in endocrine glands, but in
a variety of tissues.
3- They are usually produced in such small quantities that it has proved very difficult to discover
exactly where some of them are made.
4- They move in the plant either directly from cell to cell (by diffusion or active transport) or
carried in the phloem sap or xylem vessels. Some may not move at all from their site of
synthesis.
5- Because they are usually found in only very, very low concentrations, it is difficult to determine
precisely what some of them do. Moreover, some seem to have very different effects when they are
present in a relatively low concentration than when they are in a relatively high concentration.
6- They can have different effects in different tissues, in different species, or at different stages of a
plant's development.
7- Two or more plant growth regulators acting together can have very different effects from either of
them acting alone.
(A)- Auxins (IAA = Indole 3 acetic acid) and elongation growth:

1- Auxin produced in apical bud /root or shoot tip or so called meristems;
2- Diffuses down stem, or up in root;
3- Active transport (cell to cell);
4- through plasmodesmata;
5- Also in phloem;
6- Growth occurs in three stages: cell division by mitosis, cell elongation by absorption of water, and
cell differentiation. Auxin is involved in controlling growth by elongation.
Mechanism of elongation:
1- Molecules of Auxin bind to a receptor protein on the cell surface membrane.
2- The binding of Auxin stimulates ATPase proton pumps to move hydrogen ions across the cell
surface membrane from the cytoplasm into the cell wall.
3- In the cell walls are proteins known as expansins that are activated by the decrease in pH.
4- The expansins loosen the linkages between cellulose microfibrils. It is not known exactly how they
do this, but it is thought that expansins disrupt the non-covalent interactions between the cellulose
microfibrils and surrounding substances, such as hemicelluloses, in the cell wall.
5- This disruption occurs briefly so that microfibrils can move past each other allowing the cell to
expand without losing much of the overall strength of the wall.
6-Potassium channels open, potassium enters the cell, water potential decreases
7- The cell absorbs water by osmosis through aquaporins and the pressure potential causes the wall
to stretch so that these cells become longer, or elongate.

(B)- Gibberellins; seed germination and stem elongation:
-Gibberellins are plant growth regulators that are synthesized in most parts of plants. They are
present in especially high concentrations in young leaves and in seeds, and are also found in stems,
where they have an important role in their growth.
1- Stem Elongation:
1- The height of some plants is partly controlled by their genes.
2- For example, tallness in peas is affected by a gene with two alleles; if the dominant allele (Le) is
present, the plants can grow tall, but plants homozygous for the recessive (le) allele always remain
short or dwarf.
3- The dominant allele of this gene regulates the synthesis of an enzyme that catalyses the
synthesis of an active form of gibberellins, GA 1.
4- If only the recessive allele is present, then the plant contains only inactive forms of gibberellin.
5- Active gibberellin stimulates cell division and cell elongation in the stem, so causing the plant to
grow tall.
6- Applying active gibberellin to plants which would normally remain short, such as cabbages,
stimulate them to grow tall.
7- Yet, little is known about how gibberellins cause these effects.
2-Germination of barley seeds:

Structure of barley seed:
1- When the seed is shed from the parent plant, it is in a state of dormancy; that it contains very
little water and is metabolically inactive. This is useful, as it allows the seed to survive in adverse
conditions such as through a cold winter, only germinating when the temperature rises in spring.
2- The seed contains an embryo (plumule and radical), which will grow to form the new plant
when the seed germinates.
3- The embryo is surrounded by endosperm tissue which is a food store, containing the
polysaccharide starch to provide glucose for ATP production by aerobic respiration during
germination.
4-On the outer edge of the endosperm is a protein-rich aleurone layer.
5- The whole seed is covered by a tough, waterproof, protective layer; seed coat.
Seed Germination:
1- Seed absorbs water; By osmosis;
2- Gibberellin produced by embryo plant; Passes to aleurone layer;
3- Switches on / activation, transcription of mRNA coding for amylase enzyme genes;
4- Storage proteins broken down to amino acids to synthesis amylase;
5- Stimulates synthesis / release of amylase; Gibberellins cause these effects by regulating genes
that are involved in the synthesis of amylase. In barely seeds, it has been shown that application of
gibberellins causes an increase in the transcription of mRNA coding for amylase. It has this action by
promoting the destruction of DELLA proteins that inhibit factors that promote transcription .DELLA
stands for the first 5 amino acids in the primary sequence of the DELLA protein
6- Amylase diffuses / moves into endosperm;
7- Breaks down / hydrolyses starch to maltose; Maltose is broken down to glucose;
8- Glucose diffuses / moves into embryo plant; Provides source of energy for growth of embryo plant;

(C)- Abscisic Acid (ABA) & Stomatal Closure:
- It is found in a very wide variety of plants, including ferns and mosses as well as flowering plants;
- It can be found in every part of the plant, and is synthesized in almost all cells that possess
chloroplast or amyloplasts (organelles like chloroplast, but that contain large starch grains and no
chlorophyll).
Describe the role of ABA in stomata closure :

1- Stress hormone;
2- Secreted in high temperature / drought;
3- Binds to receptors;
4- On plasma membrane of guard cells;
5- Inhibits proton pumps;
6- So H+ concentration will increase in guard cells;
7- ABA also stimulates the movement of calcium ions into the cytoplasm through the cell surface
membrane and the tonoplast (membrane around the vacuole);
8- Calcium acts as a second messenger to activate channel proteins to open that allows negatively
charged ions to leave the guard cells;
9- This, in turn: A) stimulates the opening of channel proteins which allows the movement of
potassium ions out of the cell. B) At the same time, calcium ions also stimulate the closure of the
channel proteins that allow potassium ions to enter;
10- So water potential of guard cells increase;
11- Water move outside by osmosis;
12- Volume of guard cells decrease;
13- Guard cells become flaccid;
14- Stomata close quickly.
Control and coordination in plants

Plant responses involve:
1- Changing some aspects of their growth to respond to factors such as gravity, light and water
availability.
2- Plant can also respond fairly quickly to changes in carbon dioxide concentration, lack of water,
grazing by animals and infection by fungi and bacteria. Some of these responses are brought about
by quick changes in turgidity, as happens when stomata respond to changes in humidity, carbon
dioxide concentration and water availability.
Electrical communication in plants

Example (1)- Plant cells have electrochemical gradients across their cell surface membrane in the
same way as in animal cells. They also have resting potentials. As in animals, plant action potentials
are triggered when the membrane is depolarized. In at least some species, some responses to
stimuli are coordinated by action potentials. The "sensitive plant", Mimosa, responds to touch by
folding up its leaves.

Example (2)- The Venus fly trap is a carnivorous plant that obtains a supply of nitrogen
compounds by trapping and digesting small animals, mostly insects.
Structure of the leaf of the Venus fly trap

1- The specialized leaf is divided into two lobes either side of a midrib.
2- The inside of each lobe is often red and has nectar-secreting glands around the edge to attract
insects.
3-Each lobe has three stiff sensory hairs that respond to being deflected.
4- The outer edges of the lobes have stiff hairs that interlock to trap the insect inside.
5- The surface of the lobes has many glands that secrete enzymes for the digestion of trapped
insects.
6- The touch of a fly or other insect on the sensory hairs on the inside of the folded leaves of the
Venus fly trap stimulates action potentials that travel very fast across the leaf causing it to fold and
trap the insect.
Adaptation of Venus fly trap to avoid unnecessarily closing and washing energy:
1- The stimulation of a single hair does not trigger closure. This prevents the traps closing when it
rains or when a piece of debris falls into the trap.
2- The gaps between the stiff hairs that form the "bars" of the trap allow very small insects to crawl
out. The plant would waste energy digesting a very small "meal".
Explain how the closure of the trap is achieved?

1-sensory hairs are stimulated by the touch of an insect.
- If two of these hairs are stimulated within a period of 20 35 seconds, or one hair is touched twice
within the same time interval, action potentials travel across the trap.
-if the second touch takes too long to occur after the first, the trap will not close.
-The time between stimulus and response is about 0.5 second. It takes the trap less than 0.3 second
to close and trap the insect.
2- The deflection of a sensory hair activates calcium ion channels in cells at the base of the hair.
Calcium channels open so that calcium ions flow in to generate a receptor potential.
3- when the trap is open:
-The lobes of the leaf bulge upward and they are convex in shape
-when the trap is shut:
-The lobes rapidly change into a concave shape, bending downwards .This happens too fast as a
result of decrease in the elastic tension in the cell walls.
4- However, the trap is not completely closed at this moment. To seal the trap, it requires ongoing
activation of the hairs by the trapped prey. Unless the prey is able to escape, it will further stimulate
the inner surface of the lobes, thereby triggering further action potentials. This forces the edges of
the lobes together, sealing the trap to form an external "stomach" in which prey digestion occurs.
5- Further deflections of the sensory hairs by the trapped insect stimulate the entry of calcium ions
into gland cells. Calcium ions stimulate the exocytosis of vesicles containing digestive enzymes in a
similar way to their role in synapses.
6- The traps stay shut for up to a week for digestion to take place. Once the insect is digested, the
cells on the upper surface of the midrib grow slowly so the leaf reopens and tension builds in the
cell walls of the midrib so the trap is set again
.
Note: Please watch a video about how the
trap is closed

Leaf abscission:
1-Abscisic acid takes its name from the fact that it was thought to be closely involved in leaf or fruit
fall, which is known as abscission.
2- Some trees regularly drop their leaves at certain times in the year. In Britain, for example, as in
many other temperate countries, deciduous trees such as oak and ash drop their leaves in autumn,
as the days grow shorter and cooler.
3- The leaves fall because the leaf stalk, or petiole, breaks off from the stem. First, useful
substances are withdrawn from the leaves and taken back into the stem; this involves the
breakdown of some of the pigments in the leaves, changing their green color to yellow, gold and red.
4- An abscission zone forms where the petiole meet the stem, made up of two layers of cells.
5- Nearest to the leaf is the separation layer, which is made of small cells with quite thin cell walls.
6- Nearest to the stem is the protective layer, made up of cells whose walls contain suberin.
(Suberin is a waxy waterproof substance).
7- Enzymes then break down the cell walls in the separation layer, and the petiole breaks at this
point.
8- The protective layer remains, forming a "scar" on the stem where the leaf used to be. These leaf
scars can sometimes be very visible.

Inherited Change
1- Meiosis
Reproduction
Asexual Sexual
-In asexual reproduction, a single -In sexual reproduction, the offspring that are
organism produces offspring that are produced are genetically different from each
genetically identical to itself. other and from their parent or parents.
-The cells of the new organisms are -Each parent produces four specialized
formed as a result of mitosis in reproductive cells, known as gametes as a
eukaryotes or binary fission in result of meiosis that fuse together in
prokaryotes. fertilization to produce the first cell of the
new organism- a zygote.
Significance of meiosis:
1- To reduce chromosome number to half in the produced cells (gametes)
Diploid haploid
(2n) (n)
(In ovary, tests or anther) (Gametes; ovule, sperm, pollen))
2- To prevent duplication of chromosome number after fertilization in the zygote
2n + 2n 4n
Ovule sperm zygote
3- Genetic Variation:
Different combination of alleles in each daughter cell and different from the parent cell
Comparison between meiosis and mitosis

feature mitosis meiosis(reduction division)
definition A type of nuclear division where A type of nuclear division where

the resulted 2 daughter cells the results in halving the number
have the same number and of chromosomes. The cells
type of chromosomes as the produced are called gametes.
parent cells. When egg and sperm fuse
together during fertilization, a
diploid zygote is produced
number of 2 4
daughter cells
produced
offspring Genetically Identical to parent Genetically Different from
(clone) parents (variation)
number of 46 23
chromosomes in
each human cell
type of cells Diploid (2n) haploid (n)
produced
significance 1-Growth and development of 1- production of haploid gametes
muscles and bones for sexual reproduction
2-to avoid duplication of
2-tissue repair e.g. skin
chromosomes number after
3-asexual reproduction e.g. fertilization in zygote
budding in yeast 3-variation
4-regeneration of a body part e.g
arms of star fish
5-immune response: cloning of
B&T lymphocytes
Homologous chromosomes:
-A pair of chromosomes in a diploid cell have the same structure as each other, with the same genes
(not necessarily the same alleles of those genes) at the same loci (location), and that pair together
to form a bivalent during the first division of meiosis
-The pairs of chromosomes can be distinguished because each pair has a distinctive banding pattern
when stained
-each member of a homologous pair of chromosomes comes from one of the parents. In humans 23
chromosomes are maternal (from mother) and 23 are paternal (from father). There are therefore
23 homologous pairs in humans
-a human cell has 46 chromosomes; 44 autosomes (control all traits except sex), and 2 sex
chromosomes (XX female, XY male). Y chromosome is smaller than the X chromosome
-each chromosome contains two DNA molecules. DNA is the molecule of inheritance and is made up
of series of genes. Each gene controls the inheritance of one characteristic of the organism. The
gene for a particular characteristic is always found at the same position, or locus (pleural loci), on a
chromosome.
.
The cell cycle:

-it includes, interphase, nuclear division, and cytokinesis.
-interphase is not a resting phase but it is a stage of preparation for cell division, it takes almost 90%
of the cell cycle time.
Interphase = G1 + S
+G2
Phase Events within cell
G1 Intensive cellular synthesis, including new cell organelles. Cell metabolic rate
high.
Cell growth occurs. Substances produced to inhibit or stimulate onset of next
phase as appropriate.
S DNA replication occurs. Protein molecules called histones are synthesized

and cover each DNA strand. Each chromosome becomes two chromatids. At
this stage the cell is 4n (4 copies of each DNA molecule, 2 in each
homologous chromosome)
Note: there is no chromosome duplication prior to meiosis II
G2 Intensive cellular synthesis. Mitochondria and chloroplasts divide. Energy

stores increase. Microtubule of spindle begins to form, centrioles
replicate, energy storage increases.
M Nuclear division occurs in four phases.
C Equal distribution of organelles and cytoplasm into each daughter cell.
Stages of meiosis:

Meiosis and variation:
Explain how meiosis and fertilization can result in genetic
variation amongst offspring:
- Chiasma formation/ crossing over; between non-sister chromatids; of, homologous chromosomes /
bivalent;
In prophase1;
- Exchange of genetic material, linkage groups broken; new / different combination of alleles are
formed;
- Independent assortment; metaphase 1;
- Independent assortment: during the first division of meiosis, the pairs of homologous chromosomes
line up on the equator before being pulled to opposite ends of the cell. Each pair behaves

independently (randomly) from every other pair, so there are many different combinations that can
end up together.
- Possible mutation ;diseases, or expression of rare recessive alleles
- Random mating;
-random fusions of gametes
Gametogenesis:
- It is the production of haploid gametes from diploid somatic (body) cells.
[1] Spermatogenesis:
- The production of sperm takes place in the testes.
Stages of Spermatogenesis:
1- The process begins at the outer edge in the germinal epithelium and the new cells that are
produced form towards the inner edge.
2- in the testes, there are cells called spermatogonia. These cells are diploid and divide by mitosis
to form more spermatogonia
3- Some spermatogonia increase in size (growth) to form primary spermatocytes.
4- The primary spermatocytes divide by meiosis. After the first meiosis division, two haploid cells
are formed the secondary spermatocytes.
5- The secondary spermatocytes undergo a second meiotic division, giving a total of four haploid
spermatids.
6- Each spermatid will mature (adapted or specialized) into a spermatozoan.
Summary
Spermatogonia mitosis many Spermatogonia Growth primary
spermatocytes meiosis 1
Secondary spermatocytes meiosis 2 spermatid maturation sperm
(spermatozoa)
[2] Oogenesis:
-the production of eggs (or ova) takes place in the ovaries. However, unlike the production of sperm,
the process begins very early in the life of the female, when she is still only an embryo.
Stages of Oogenesis:
1- About five weeks after the formation of a female embryo, cells in ovaries start to divide by
mitosis, forming diploid oogonia.
2- Up until about 6 months after birth, the oogonia will begin the first division of meiosis. The
resulting cells are called primary oocytes. However, they do not complete the division and remain
at prophase 1 for many years. Not all the primary oocytes survive and, at puberty, there will be
around 400,000 in the ovaries.
3- At puberty, the primary oocyte completes the first meiotic division, producing one large cell
and one tiny cell, called the polar body. The large, haploid cell is called the secondary oocyte,
which continues straight into the second meiotic division to form an ovum or the female gamete
and one polar body ( polar body has no role)
4-every month, one secondary oocyte is released into the oviduct, if it is fertilized, it continues its
division by meiosis

Comparison between Spermatogenesis and Oogenesis
Features Male Female
A-Similarities 1-In both, spermatogonia and oogonia start from germinal

epithelium
2-In both, spermatogonia and oogonia grow to produce primary
oocyte and primary spermatocytes
3- In both, primary oocyte and primary spermatocytes divide by
meiosis to form secondary oocyte and secondary
spermatocytes
B- Differences Male Female
1 Starting time At puberty When female is an embryo or

fetus in the uterus
2 Place Seminiferous tubule/ testis Ovary
3 Produced cell spermatozoa Secondary oocyte
4 Polar body Not present Present
5 Cytoplasm Equally divided Not equally divided

6 Number of gametes 4 1
required
7 Resting phase Does not rest [complete Take some resting phase in
meiosis on release] meiosis (complete meiosis
after ovulation)
8 Age period 12 65 9 40
9 Total number of million One per cycle

gametes
1 Differentiation Yes, into spermatide No
0
1 Hormone needed testosterone Estrogen
1
1 Size of produced cell smaller larger
2

Gametogenesis in flowering plants:
-The figure shows the structure of a typical flower. Male gametes are produced in the anthers, and
female gametes in the ovules.
(A) Production of pollen grains:
1- Inside the anthers, diploid pollen mother cells divide by meiosis to form four haploid cells.
2- The nuclei of each of these haploid cells then divide by mitosis, but the cell itself does not
divide by (cytokinesis does not take place) resulting in cells that each contain two haploid nuclei.
3- These cells mature into pollen grains, each surrounded by a protective wall made up of a tough
exine and thinner intine.
4- One of the haploid nuclei is called the tube nucleus, and the other is the generative nucleus
.these are the male gametes.
(B) Production of embryo sacs:
1- In the ovary, inside each ovule, a large, diploid, spore mother cell develops.
2- This cell divides by meiosis to produce four haploid cells.
3- Three cells degenerate, and the one surviving haploid cell develops into an embryo sac.
4- The embryo sac grows larger, and its haploid nucleus divides by mitosis three times, forming
eight haploid nuclei.
5- One of these becomes the female gamete.
Note:
- In plants, unlike animals, the gametes are not formed directly by meiosis. Instead, meiosis is used
in the production of pollen grains and the embryo sac and the gametes are then formed inside these
structures by mitotic divisions.
2- Genetics

Some important definitions:
Genetics: The study of heredity and the variation of inherited characteristics
Gene: a length on DNA that codes for a particular protein or polypeptide.
Locus: The position of a gene or other specific piece of DNA (such as a marker) on a chromosome.
The same gene is always found at the same locus of the same chromosome (unless there, has been
a mutation). The locus is designated by the chromosome number, its arm, and its place. For
example, the gene associated with ABO blood groups is at locus 9q34, meaning the gene is found on
chromosome 9, on the long arm (q) at region 34. The gene associated with sickle cell anaemia is at
locus 11p15.5, meaning chromosome 11, short arm (p), and region 15.5.
Allele: one of two or more alternative nucleotide sequences at a single gene locus, so alleles are
variant forms of a gene. For example, the alleles of the ABO blood group gene are found at a locus
on chromosome 9, with the alleles including I A, IB and IO. Diploid body cells contain two copies of
each homologous chromosome, so have two copies of chromosome 9, and so have two copies of the
gene. These may be the same allele (homozygous), for example, I A, IA or ,IB, IB or IO, IO ,or they may
be different alleles (heterozygous), for example, I A, IB or IA, IO or IB, IO . The gene for producing the
haemoglobin
- polypeptide has a number of alleles. Two of these are the normal allele Hb A and the sickle cell
allele, HbS , giving HbA HbA and HbS as a homozygous genotype.
Dominant: An allele with a phenotype that is expressed even when present with an allele that is
recessive to it. For example, in the ABO blood group gene, I A is dominant to IO. Therefore a person
with the genotype IA IO has blood group A because only the dominant allele is expressed.
Recessive: An allele with a phenotype that is not expressed when an allele that is dominant to it is
present. For example, IO is recessive to IA, so a person with the genotype I A IO has blood group A , and
a person can only be blood group O if they are homozygous recessive I O IO .
Codominant: Alleles that are both expressed if they are present together in a heterozygous person.
For example, alleles IA and IB of the ABO blood group gene are codominant. Therefore, in a
heterozygous person, IA IB , both alleles are expressed and the blood group is AB. In the case of the
haemoglobin - polypeptide gene, codominance means that the phenotype of a person who has Hb A
HbA is unaffected by sickle cell disorder, the phenotype of a person who has Hb A HbS is the less
severe sickle cell trait and the phenotype of a person who has Hb S HbS is the more severe sickle
anaemia.

Homozygous: A term describing a diploid organism that has the same allele of a gene at the gene's
locus on both copies of the homologous chromosomes in its cells (e.g. Hb A HbA ) and therefore
produces gametes with identical genotypes (all Hb A ). A homozygote is an organism that is
homozygous.
Heterozygous: A term describing a diploid organism that has the different allele of a gene at the
gene's locus on both copies of the homologous chromosomes in its cells (e.g. Hb A HbS) and therefore
produces gametes with two different genotypes
(0.5 HbA and 0.5 HbS). A heterozygote is an organism that is heterozygous.
Phenotype: The physical, detectable expression of the particular alleles of a gene or genes present
in an individual. It may be possible to see the phenotype (e.g. human eye colour) or tests may be
required (e.g. ABO blood group). When the phenotype is controlled by a small number of alleles of
particular gene, it may be genetically determined (e.g. human eye colour), giving rise to
discontinuous variation. When the phenotype is controlled by the additive effects of many genes
(polygenic), it may be affected by the environment as well as genes (e.g. human height), giving rise
to continuous variation.
Genotype: The particular alleles of a gene at the appropriate locus on both copies of the
homologous chromosomes of its cells (for example IA IB). It is sometimes described as the genetic
constitution of an organism with respect to a gene or genes.
Diploid: A eukaryotic cell or organism containing two complete sets of chromosomes (two copies of
each homologous chromosome), shown as 2n, such as a human body (somatic cell).
Haploid: A eukaryotic cell or organism containing only one complete set of chromosomes (only one
of each homologous chromosome), shown as n, such as a human sperm or secondary oocyte.
Triplet Code: Sequence of three successive bases in DNA that codes for a certain amino acid, and is
complementary to mRNA codes.

Sex Inheritance:
-In a diploid human cell; there are 46 chromosomes; 44 out of them are autosomes and 2 sex
chromosomes that are either X or Y. Females have two X chromosomes, while males have one X
and one Y chromosomes.
Monohybrid crosses:
-It considers the inheritance of only one pair of contrasting characteristic or trait.
Homozygous dominant X homozygous recessive: (offspring ratio

1:0)

Heterozygous X homozygous recessive ((offspring ratio 1:1):
Heterozygous X heterozygous (offspring ratio 3:1):
Test Crosses:
- It is an experimental technique used to determine the genotype of a dominant trait in an organism
by crossing it with its contrasting recessive one.
- If all offspring expresses dominant traits, then parent is homozygous, some are dominant and some
are recessive, then parent is heterozygous.
e.g. wing type in drosophila fly; long is dominant, vestigial is recessive.

Co-dominance:
-where both alleles are expresses in the same organism, or a blend or intermediate of both is
produced.
e.g.1. blood groups ABO inheritance. A and B alleles are equally dominant, O is
recessive.
e.g.2. in some special plant species having red or white flowers
- Both alleles of red and white colors are equally dominant, 3 phenotypes can be
produced, red, pink and white

e.g. 3 the production of Andalusian fowl

Dihybrid inheritance (crosses):
-It is a genetic cross in which 2 different genes are considered
homozygous dominant x homozygous recessive (offspring ratio 1:0 dominant ,

heterozygous)
heterozygous x heterozygous (offspring ratio 9:3:3:1)
e.g.
9 in 16 or 9/16
Proportion 3 in 16 or 3/16
3 in 16 or 3/16
1 in 16 or 1/16
Ratio 9:3:3:1
% 56.25 18.75 18.75 6.25
Approximated % 56 19 19 6

Multiple alleles:
-The existence of three or more alleles of a gene, as for example, in the determination of A, B, O
blood groups.
-There is one gene (blood group gene), But three Phenotyp Genotype alleles:
e
1- allele A
A AA
AO
2- allele B
AB AB
3- allele O B BB
BO
-A and B alleles are Codominant, while O is O OO recessive to both
A, B. The diploid (somatic) cell carries only two alleles.
Blood Groups:
Group Antigen in RBC Antibody in Donor to Recipient from

plasma
A A anti B A, AB A, O
B B anti A B, AB B, O
AB A &B none AB all (UNIVERSAL)
O none anti A & B all (UNIVERSAL) O
-When a patient needs a blood transfusion, his blood is carefully matched against the blood of the
donor to check that it is compatible, i.e. that mixing the two bloods will not cause clumping of red
cells (agglutination) which may result in blockage of blood vessels, and possible death.
Sex Linkage:
Define sex linkage:
-Allele is on X chromosome; Because Y is shorter; So female has two copies of allele; Male has only
one copy of allele
E.g haemophilia as a sex linked disease:
The X chromosome contains many different genes. one of them is a gene that codes for the
production of a protein needed for blood clotting, called factor VIII. There are two alleles of this
gene, the dominant one H producing normal factor VIII, and the recessive one h resulting in lack of
it. People who are homozygous for the recessive allele X hXh suffer from the disease haemophilia, in
which blood fails to clot properly.

Explain how the allele for haemophilia may be passed from a man
to his grandchildren
-haemophilia allele on X chromosome; sex-linked; haemophilia allele recessive;
- man, heterogametic / has one X chromosome; Y chromosome does not have blood clotting gene;
- Only daughter(s) get his X chromosome; daughter(s) carrier(s) of (haemophilia) allele;
- grandson(s) 50% chance of having, (haemophilia) allele / haemophilia;
- granddaughter(s) 50% chance of carrying, (haemophilia) allele;
-if you will show on a , diagram you must include the following:
- Correct symbols; e.g. XH and Xh explained
- Mans genotype; e.g. XhY
- F1 (daughter's) genotype; e.g. XHXh
- F2 (grandson's) genotypes; e.g. XhY , XHY
- F2 (granddaughter's) genotype; e.g. XHXH XHXh or . XhXh XHXh
Environment and genes:
Explain using examples, how the environment may affect the

phenotype of an organism
- Phenotype variation results from interaction of genotype and environment /VP = VG + VE

- Environment may limit expression of gene(s) ;

- Because, food / nutrients / ion, missing / malnutrition;
- named, nutrient / ion / mineral, missing; protein, Ca ++ , vitamin D;
- Environment may, trigger / switch on, gene;
-e.g.1 low temperature and change in animal color;
-the development of the dark tips to ears, nose, paws and tail in the Himalayan coloring of rabbits.
This coloring is caused by an allele which allows the formation of the dark pigment only at low
temperature. The parts of the rabbit which grow dark fur are the coldest parts. If an area somewhere
else on its body is plucked of fur and kept cold, the new fur growing in this region will be dark.
-e.g.2 high temperature and, curled wing in Drosophila (high temperature then vestigial curly
wing, low temperature then normal wing) /gender in crocodiles; (cool then females, warm then
males)
-e.g.3 UV light and melanin production;
-e.g.4 wavelength of light and, flowering / germination / fruit color;
-e.g.5 Lactase Production in Escherichia coli
-The bacterium Escherichia coli has a gene that codes for the production of the enzyme lactase,
which hydrolyses the disaccharide lactose to glucose and galactose. This gene is only expressed
when the bacterium encounters lactose in its environment.
- Environment effect is usually greater on polygenes;
- Environment may induce mutation affecting phenotype;
Interactions between Ioci

-You have already seen interactions between alleles at the same locus, namely:
Codominant alleles in flower colour in snapdragons
Dominant and recessive alleles in tomato plant stem colour
Multiple alleles in the inheritance of the ABO blood groups
- There are also cases where different loci interact to affect one phenotypic character.
- Example (1):
- In the inheritance of feather colour in chickens, there is an interaction between two gene loci,
I/i and C/c.
- Individuals carrying the dominant allele, I, have white feathers even if they also carry the dominant
allele, C, for coloured feathers
- Birds that are homozygous recessive are also white.
- White Leghorn chickens have the genotype IICC, while white Wyandotte chickens have the
genotype iicc.
These genotypes will also result in coloured feathers in chicken iiCC and iiCc
- A white Leghorn is X with a white Wyandotte.

-The usual 9 : 3 : 3 : 1 ratio expected in this generation has been modified to (9 + 3 + 1 )
: 3 giving 13 white : 3 coloured.
Example (2):
- A different interaction is shown by the inheritance of flower colour in Salvia. A pure-breeding,
pink flowered variety of Salvia was crossed with a pure-breeding, white flowered variety.
- The offspring had purple flowers. Interbreeding these offspring to give another generation resulted
in purple, pink and white-flowered plants in a ratio of 9 : 3 : 4.
-Two loci, A/a and B/b, on different chromosomes is involved:
-The homozyote recessive aa affects the B/b locus.

-Neither the dominant allele, B, for purple flower colours, nor the recessive allele, b, for pink flower
colour can be expressed in the absence of a dominant A allele.

9 : 3 : 4 ratio in the second generation.
Autosomal linkage:
- When two or more gene loci are on the same chromosome, they do not assort independently in the
meiosis as they would if they were on different chromosomes. The genes are said to be linked.
-Genes on a chromosome other than the sex chromosomes are said to be autosomally linked.
- Linkage: is the presence of two genes on the same chromosome, so that they tend to be inherited
together and do not assort independently.
- The genes of any organism fall into a number of linkage groups equal to the number of pairs of
homologous chromosomes.
- Total linkage is very rare. Almost always, the linkage groups are broken by crossing over
during meiosis.
- Example:
-The fruit fly, Drosophila, normally has striped body and antennae with a feathery arista.
- The gene for body colour and the gene for antennal shape are close together on the same
chromosome and so are linked.
- A black body with no strips results from a recessive allele called "ebony". A recessive allele for
antennal shape, called "aristopedia", gives an antenna looking rather like a Drosophila leg, with two
claws on the end.
- To help keep track of linked alleles in a genetic diagram, you can bracket each linkage group.
- In this case the genotype of the stripped body fly with normal antenna is written (EA) (EA) and
not EEAA, which would indicate that the genes were not on the same chromosomes.

[1] Homozygous striped body and normal antenna X homozygous ebony body &
aristopedia antenna
100 % all the offspring had striped bodies and normal antennae.
[2] Heterozygous striped body & normal antenna X homozygous ebony & aristopedia antenna
- The test cross gives a 1 : 1 ratio of the two original parental types and not the 1 : 1 : 1 : 1
ratio expected from a dihybrid cross. (If you are uncertain about these ratios, repeat the cross above
but assume that the genes are not linked. This should result in 1 Ee Aa : 1 Eeaa: 1 eeAa : 1 eeaa).
- The dihybrid cross has behaved as a monohybrid cross. The allele s that went into the cross
together remained together.
Crossing over
- During prophase I of meiosis, a pair of homologous chromosomes (a bivalent) can be seen to be
joined by chiasmata.
- The chromatids of a bivalent may break and reconnect to another, non-sister chromatid.
- This results in an exchange of gene loci between a maternal and parental chromatid.
- Return to the Drosophila cross described before, and test cross the female offspring.
- Large numbers of the parental types of flies are produced. They are in a 1: 1 ratio.
- Smaller numbers of recombinant flies are produced.
- These result from crossing over and "recombine" the characteristics of the original parents into
some flies that have a striped body and aristopedia antennae and others that have an ebony body
with normal antennae.
- The two recombinant classes themselves are in a 1: 1 ratio.
- In this particular cross, we would typically find:
The cross over value:

-it is the percentage of offspring that belong to recombinant classes.
- In this case it is 6% + 6% = 12%. This is a measure of the distance apart of the two gene loci on
their chromosomes.
- The smaller the cross over value, the closer the loci are together.
- The chance of a cross over taking place between two loci is directly proportional to their
distance apart.
MUTATIONS
-it is a random unpredictable change in the DNA in cells.
-A change in the sequence of bases in DNA may result in a change in the sequence of amino acids in
protein.
- Mutations are most likely to occur during DNA replication, for example when a "wrong" base may
slot into position in the new strand being built. Almost all of these mistakes are immediately repaired
by enzymes, but some may persist.
Causes of mutations (Mutagen): is a substance that increases the chances of mutation
occurrence.
- All types of ionizing radiation (alpha, beta and gamma radiation) can damage DNA molecules,
altering the structure of the bases within them.
- Ultraviolet radiation has a similar effect, as do many chemicals, for example mustard gas or
smoking
Types of Mutations:
Chromosome Mutation Gene Mutation
- An addition of extra DNA to a - A change in the sequence of bases in

chromosome, or a loss of DNA from it one part of a DNA molecule.
- A change in the total number of e.g. Cystic Fibrosis, albinism, Sickle
chromosomes in a cell. e.g. Down's cell anaemia, Huntington's disease
Syndrome
(1) Chromosome Mutation

(2) Gene Mutation:
Describe the ways by which gene mutations can occur:

- mutation is a change in, base / nucleotides, sequence (in DNA); during DNA replication;
-e.g. base, substitution / addition / deletion
a) Base substitution, where one base simply takes the place of another. For example:
CCT GAG, GAG may change to CCT GTG GAG
-Base substitution; often have no effect at all. A mutation that has no apparent on an organism is
said to be a silent mutation. Base substitutions are often silent mutations because many amino
acids have more than one triplet code, so even if one base is changed the same amino acid is still
coded for and the correct protein is formed.
c) Base addition, where one or more extra bases are added to the sequence. For example:
CCT GAG, GAG may change to CCA TGA GGA G.
d) Base deletion, where one or more bases are lost from the sequence. For example:

CCT GAG, GAG may change to CCG AGG AG.
- frame shifts:
Base additions or deletions always have large effects, because they alter every set of three bases
that "follows" them in the DNA molecule. They are said to cause frame shifts in the code. Often,
the effects are so large that the protein that is made is totally useless or non-functional. Or they may
introduce a "stop" triplet partway through a gene, so that a complete protein is never made at all.
- Mutations produce different / new, allele;
- Mutations happen randomly / spontaneous;
- Mutagens; ionizing radiation; UV radiation / mustard gas;
e.g.(1), Sickle Cell Anaemia

-sickle cell anaemia is widely spread in regions where malaria is widely spread such as tropical
regions, because the people with normal blood cells usually die there by the effect of malaria. Also
condition in tropics, such as rainfall and high temperature favors the development of mosquitoes
larvae.
enotype Phenotype
HN Normal
HS Normal, but with sickle cell
trait
HS Sickle cell anaemia
Genotypes and phenotypes for sickle cell anaemia
Relationship between sickle cell anaemia and malaria:
-sickle cell widely spread in malarial areas.

- HbA HbA (dominant) dies by malaria
- HbS HbS (recessive) dies by anaemia
- HbA HbS are resistant to malaria and have 50% normal blood, and are selected to survive,
reproduce, and pass the recessive allele to their offspring.
Example [2] Albinism

Phenotype of an Albino
- Albinism provides an example of the relationship between a gene, an enzyme and a human
phenotype.
- In albinism, the dark pigment melanin is totally or partially missing from the eyes, skin and hair.
- In humans this results in pale blue or pink irises in the eyes and very pale skin and hair.
- The pupils of the eyes appear red. The condition is often accompanied by poor vision by rapid,
jerky movements of the eyes and by a tendency to avoid bright light.
Genotype of an Albino
- An autosomal recessive and individuals that are homozygous for the recessive allele show
albinism.
- It is not sex-linked.
Causes of albinism
- A mutation in the gene for the enzyme tyrosinase results in either the absence of tyrosinase or
the presence of inactive tyrosinase in the cells responsible for melanin production cannot take
place.
- Tyrosine cannot be converted into DOPA and dopaquinone.
- Tyrosinase is an oxidase and has two copper atoms in its active site which bind an oxygen
molecule.
- It is a transmembrane protein and is found in the membrane of large organelles called
melanosomes in the melanocytes.
- Most of the tyrosinase is inside the melanosomes.
- Tyrosinases occur in plant as well as in animal tissues.
- The action of the enzyme can be seen in the blackening of a slice of potato left exposed to the air.
Example [3] Huntington's disease

Phenotype:
- HD is a neurological disorder resulting in involuntary movements (chorea) and progressive mental
deterioration.Brain cells are lost and the ventricles of the brain become larger.
- The age of onset is variable, but occurs most commonly in middle age, so that individuals may
have children before they know that they themselves have the condition
Genotype
- Huntington's disease (HD) provides an example of a mutation that is inherited as a dominant
allele.
- This means that most people with the condition are heterozygous and have a 1 in 2 chance of
passing on the condition to a child.
Causes of the disease
- The mutation is an unstable segment in a gene on chromosome 4 coding for a protein, huntingtin.
- In people who do not have HD, the segment is made up of a small number of repeats of the triplet
of bases CAG.
- People with HD have a larger number of repeats of the CAG triplet. This is called a "stutter".
- There is enough inverse correlation between the number of times the triplet of bases is repeated
and the age of onset of the condition; the more stutters, the earlier the condition appears.
Explain how changes in nucleotides sequence in DNA affect the

amino acid sequence in a protein
- (amino acid) code is three, bases / nucleotides; triplet code
- (gene) mutation; base / nucleotide, substitution / addition / deletion

- Addition / deletion, has large effect (on amino acid sequence);
- frame shift; results in completely new code after mutation / alters every 3 base sequence which
follows;
- Substitution may have little or no effect / silent mutation; different triplet but same amino acid /
new amino acid in non-functional part protein;
- base addition may have big effect (on amino acid sequence); could produce "stop" codon;
- e.g. sickle cell anaemia / cystic fibrosis;
- Reference to transcription or translation in correct context;
- Protein produced, is non-functional / not produced / incomplete
Gene Control
A) Gene control in prokaryotes
- In both prokaryotes and eukaryotes, transcription of a gene is controlled by transcription factors.
Transcription factor
- are proteins that bind to a specific DNA sequence and control the flow of information from DNA to
RNA by controlling the formation of mRNA.
Comparison
Structural genes Regulatory genes
Genes that code for proteins required by a cell Genes that code for proteins that regulate the
are called structural genes. Such proteins may expression of other genes are called regulatory
literally form part of a cellular structure, but they genes.
may also have some other role, such as acting as
an enzyme.
Repressible enzymes Inducible enzymes
1- The synthesis of a repressible enzyme can be 1- The synthesis of an inducible enzyme occurs
prevented by binding a repressor protein to a when its substrate is present. Transcription of the
specific site, called an operator, on a gene occur as a result of the inducer (the
bacterium's DNA enzyme's substrate) interacting with the protein
2- It is an enzyme that is produced produced by the regulatory gene
continuously unless production is 2- It is an enzyme that is only produced or
repressed by excess of an inhibitor formed in response to an inducing agent,
often its substrate.
Example: The lac operon (see figure):

- The enzyme - glactosidase hydrolyses the disaccharide lactose to the monosaccharides
glucose and galactose.

- In the bacterium, Escherichia coli, the number of molecules of this enzyme present in a
bacterial cell varies according to the concentration of lactose in the medium in which the
bacterium is growing.
- The bacterium has one copy of the gene coding for - glactosidase and so, to alter the
concentration of the enzyme in its cell, it must regulate the transcription of the gene.
An operon:
-it is a length DNA making up a unit of gene expression in a bacterium.
-operon = operator gene + structural genes with their promoter
- It consists of one or more structural genes and also contains regions of DNA (operator) that
are recognized by the products of regulatory genes (repressor).
Promoter:
-It is a length of DNA (usually about 40 bases long) situated next to genes and which identify
the point at which transcription should begin (RNA polymerase must bind to the promoter
before it can begin transcription of DNA into mRNA).
The lac operon:

-it consists of a cluster of three structural genes and a length of DNA including operator
and promoter regions. The Three structural genes are:
lac Z, coding for - glactosidase
lac Y, coding for permease (which allows lactose to enter the cell)
lac A, coding for transacetylase
- Close to the promoter, but not actually part of the operon is its regulatory gene.
- The sequence of events when there is no lactose in the medium in which the
bacterium is growing is as follows:
the regulatory gene codes for a protein called a repressor
the repressor binds to the operator region, close to the gene for - glactosidase (lac Z)
in the presence of bound repressor at the operator, RNA polymerase cannot bind to DNA at
the promoter region
No transcription of the three structural genes can take place. No protein synthesis, no
enzyme formed.
- The repressor protein is allosteric. This means that it has two binding sites.

- When the protein binds to a molecule at one site, this affects its ability to bind to a
different molecule at the other binding site.
- The site that binds to DNA is separate from the site that binds to lactose.
- When lactose binds to its site, the shape of the protein changes to that the DNA-binding
site is closed.
- When lactose is present in the medium in which the bacterium is growing:

Lactose is taken up by the bacterium
Lactose binds to the repressor protein, distorting its shape and preventing it from binding
to DNA at the operator site.
Transcription is no longer inhibited and messenger RNA is produced from the three
structural genes. The genes have been switched on and are transcribed together.
Advantages of the lac operon:

1- It allows the bacterium to produce - glactosidase, permease and transacetylase only
when lactose is available in the surrounding medium and to produce them in equal
amounts.
2- It avoids the waste of energy and materials in producing enzymes for taking up and
hydrolyzing a sugar that the bacterium may never meet so the sugar can be hydrolysed
when it is available since the enzyme - glactosidase is an inducible enzyme.
3- The bacterium uses glucose in preference to other sugars. When a bacterium finds both
glucose and lactose in the medium in which it is growing; it represses the use of lactose by
suppressing the lac operon by means of a different transcription control factor.
B) Gene control in eukaryotes

- In general, the number of different proteins that act as transcription factors increases with
increasing size of the genome.
- This means that eukaryotes have many more ways of regulating gene expression
than have prokaryotes.
- In humans, for example, about 10% of the genes code for proteins which act as
transcription factors.
- The factors may bind to the promoter region of gene. This may increase or decrease the
transcription of the gene to make sure that genes are expressed in the correct cell at the
correct time and to the correct extent.
- Effects of transcription factors include the following:

Transcription factors are necessary for transcription to occur. They form part of the
protein complex that binds to the promoter region of the gene concerned.
Other factors activate appropriate genes in sequence, allowing the correct pattern of
development of body regions.
A transcription factor is responsible for the determination of sex in mammals.
Transcription factors allow responses to environmental stimuli, such as switching on
the correct genes to respond to high environmental temperatures.
The products of proto-oncogenes and tumour suppressor genes 9proteins), regulate the
cell cycle, growth and apoptosis (programmed cell death).

Hormones have their effect through transcription factors
Example: the plant hormone, gibberellins
-it controls seed germination in plants such as wheat and barley by stimulating the
synthesis of amylase by affecting transcription.
- in barley seeds, application of gibberellins causes an increase in the transcription of mRNA
coding for amylase.
- Gibberellin has this effect by causing the breakdown of DELLA proteins.
- A DELLA protein inhibits the binding of a transcription factor, such as
phytochrome interacting protein (PIF), to a gene promoter.
- By causing the breakdown of DELLA protein, gibberellin allows PIF to bind to its target
promoter.
- Transcription of the gene can then take place, resulting in an increase in amylase
production

Note: How the shape of a protein is maintained:
- Peptide bonds between amino acids maintain primary structure.
- Hydrogen bonds maintain secondary structure.
- Tertiary / globular shape [structure] maintained by disulphide bonds / ionic bonds / hydrophobic
bonds.
Chi-squared test (x2 -test):

Selection and Evolution
1- Variation:
- It means the difference in phenotype or character between members of a population of same
species. It is either continuous or discontinuous.
Causes of genetic variation:
-Sexual reproduction produces genetic variation amongst the individuals in a population. Genetic
variation is caused by:
1- Independent assortment of chromosomes, and therefore alleles, during meiosis; metaphase I
2- Crossing over between chromatids of homologous chromosomes during meiosis; prophase I
3- Random mating between organisms within a species;
4-random fusion of gametes between organisms within a species
5- Mutation:
Types of Mutations:
Gene Chromosome In somatic Cells In gametes or gonads (ovary ,
tests)
e.g. e.g. - In body cells - In sex cells
Sickle Down's Syndrome - Cannot be passed - Effect of mutation is seen in offspring
cell to offspring, - Can be passed to offspring during
anaemia e.g. cancer sexual reproduction
-Mutation can produce completely new alleles. This may happen, for example, if a mistake occurs in
DNA replication, so that a new base sequence occurs in a gene.
-Most mutated cells are recognized as foreign by the body's immune systems and are destroyed.
-These first 4 processes re-shuffle alleles in the population. Offspring have combinations
of alleles which differ from their parents resulting in phenotypic variation.
-mutations dont re-shuffle alleles that are already present , but they produce completely
new allels
TYPES OF VARIATION:
(1) Continuous variation:
- is influenced by gene and environment resulting in a range of phenotypes between two extremes,
e.g. height in humans, hair color, or number of seeds.
In graphs of continuous variation:
1- Mean: is the average number of such group
2- Mode: is the most common of the groups.
3- Median: is the central value of a set of values.

Examples:
1- Hair color in cats
-Many different genes determine hair color in cats. At least 8 different genes, at different loci, are
known to influence hair color. These are known as polygenes. Depending on the particular
combination of alleles that a cat has for each of these genes. It can have any of a very wide range of
colors.
-Hair color in cats is an example of continuous variation. This is a variation in which there are no
clear-cut categories. There is a continuous range of variation in color between the very lightest and
very darkest extremes.
-The cat hair color genes exert their effect by coding for the production of enzymes. One such gene
is found at the C locus. Siamese cats have two copies of a recessive allele of this gene called C8. This
gene codes for an enzyme which is sensitive to temperature. It produces dark hair at the extremities
of paws, ears and tail where the temperature is lower, and light hair in warmer parts of the body. The
colouring of a Siamese cat is therefore the result of interaction between genes and environment.
2- Human height:
-Human height is also affected by many different genes at different loci. It is also affected by
environment. Even if a person inherits alleles of these genes that give the potential to grow tall, he
or she will not grow tall unless the diet supplies plenty of nutrients such as proteins, calcium, and
vitamin D to allow this to happen. Poor nutrition, especially in childhood, reduces the maximum
height that is attained.
3- Cancer
- It is a disease that results from a breakdown in the usual control mechanisms that regulate cell
division; certain cells divide uncontrollably by mitosis and form tumors, from which cells may break
away and for secondary tumors in other areas of the body (metastasis).
-The risk of developing cancer is influenced by both genes and environment. For example, a woman
with particular alleles of the genes BRCA1 or BRCA2 has a 50% to 80% of chance of developing
breast cancer at some stage in her life. This is a much higher risk than for people who do not have
these alleles. The normal alleles of these genes protect cells from changes that could lead to them
becoming cancerous.
-environment also affects this risk. Smoking, for example, increases the risk even further. Taking the
drug tamoxifen can reduce the risk.
4- Monoamine oxidase A
-Monoamine oxidase A (MAO-A) is an enzyme that is found in mitochondria in the nervous system,
and also in the liver and digestive system. In the nervous system, it is involved in the inactivation of
neurotransmitters including noradrenalin and serotonin.
-Some alleles of the monoamine oxidase gene produce low activity MAO-A, while others produce
high activity MAO-A. It has been found that children with the high activity form, if maltreated are
more likely to show antisocial behavior than similarly treated children with the low activity form.
-Other behaviors, such as novelty seeking, also appear to be associated with particular alleles of this
gene. However, in all cases the environment also has large effects on behavior; behavior is produced
by interaction between this gene (and probably others as yet unidentified) and the environment.

(2) Discontinuous variation:
- is caused by genes alone and results in a limited number of distinct phenotypes with no
intermediates, e.g. A, B, AB and O blood groups in humans or tongue rolling.
The genetic basis of continuous and discontinuous variation

- Both qualitative and quantitative differences in phenotype may be inherited and may
involve several different genes.
Differences between both types of variation:
1- In discontinuous (qualitative) 2- In continuous (quantitative)

variation variation
Qualitative difference fall into clearly - Quantitative differences between

distinguishable categories with no individual heights or masses may be small
intimidates. and difficult to be measured.
- There are no distinguishable height
classes.
- There is range between two extremes.
1- Different alleles at a single gene locus 1- Different alleles at a single gene locus
have large effects on the phenotype. have small effects on the phenotype
2- Different genes have quite different 2- Different genes have the same, often
effects on the phenotype. additive, effect on the phenotype.
3- A large number of genes may have a
- The inheritance of sickle cell anaemia combined effect on a particular phenotypic
and haemophilia are examples of trait; these genes are known as
discontinuous variation in humans. polygenes
- Flower colour in snapdragon, stem colour of
tomato plants and feather colour of chickens
are examples from other organisms. From
these examples, you can see that
dominance and gene interaction tend to
reduce phenotypic variation.
The additive effect of a gene can be seen in a hypothetical example of the
inheritance of an organism's height.
- Suppose that the height of an organism is controlled by two unlinked (that is, on different
chromosomes) genes: A/a and B/b. The recessive alleles of both genes (a and b) each
contribute x cm to the height of the organism.
- The dominant alleles (A and B) each add 2xm. Since the effect of such genes is additive,
the homozygote recessive (aabb) is therefore potentially 4xm tall and the homozygote
dominant (AABB) is potentially 8xm tall. The other genotypes will fall between these
extremes.
- Interbreeding these potentially 6xm tall offspring, gives all possible genotypes and
phenotypes among the 16 possibility.
- The number of offspring and their potential heights according to their genotypes are
summerised in the histogram in the figure. These results fall on a normal distribution
curve.
- These hypothetical results come from assuming that two unlinked genes, each with two
alleles, contribute to the height of the organism.

- if more genes are controlling the quantitative character, each with an additive effect
(polygenes), then a greater range of intermediates will be produced (the number of discrete
height classes increases and the differences between these classes get less )
2-Over production:
The sigmoid (s- shaped) growth curve for a population:
1- Lag phase: birth rate is higher than death rate, slow increase in population growth as organisms
are still adjusting to the environment.
2- Log or exponential phase: rapid increase in population growth, organisms are well adjusted to
the environment, high reproductive rate, enough food and space are available.
3- Stationary phase: birth rate = death rate, limiting factors are found, e.g. food shortage,
competitionetc
4- Death or decline phase: death rate is higher than birth rate, accumulation of wastes, and
severe shortage of food.
a) All species of organisms have the reproductive potential to increase the sizes of their
populations, but in the long term, this rarely happens. This is because environmental factors come
into play to limit population growth. Such factors decrease the rate of reproduction, or increase the
rate of mortality so that many individuals die before reaching reproductive age.
b) The number of young produced is far greater than the number which will survive to adulthood.
Many young die before reaching reproductive age.
Environmental factors affecting reproductive potential, and thus affecting population
size
Biotic (living) Factors A biotic (non-living) Factor

ation 1-Water supply
petition for food 2-Nutrient levels in soil
ction by Pathogen 3-pH of soil
rowding) 4- Temperature / wind speed/climate
e.g.
1) In the 19th century in Australia (in 1859), twelve pairs of rabbits from Britain were released on a
ranch in Victoria, as a source of food. The rabbits found conditions to their liking. Rabbits feed on low
growing vegetation, especially grasses, of which there was abundance. There were very few
predators to feed on them, so the number of rabbits increased greatly. Their numbers became so
great that they seriously affected the availability of grazing for sheep.
2) Rabbits were eaten by foxes, so their numbers decreased again.
3) Over a period of time, the population will oscillate (go up & down) about a mean level.

3-Selection:
I- Artificial Selection
Describe and explain using an example, the process of artificial

selection:
1-selection pressure is applied by humans;
2-parents with desirable feature;
3-e.g. organism and feature ;( see examples below)
4-bred / crossed;
5-select offspring with desirable feature;
6-repeat over many generations;
7-increase in frequency of desired allele(s) / decrease in frequency of undesired allele(s);
8-background genes; within each organism's genotype are all the alleles of genes that
adapt it to its particular environment.
9-loss of hybrid vigour / increase in homozygosity / inbreeding depression;
10-detail of breeding techniques,(see examples below)
Examples:
(1) Selective breeding of Cattle
- Desired features include docility (making the animal easier to control), fast growth rates and high
milk yields.
- Increase in these characteristics has been achieved by selective breeding.
-e.g.Cows with high milk production are crossed with Bulls whose mothers/sisters/female relatives
have high milk production
-then, the same procedures are used as described above
- In many cases, 'disadvantageous' alleles are lost entirely.
- Such selective breeding of dairy cattle presents the breeder with problems. The animals are large
and take time to reach maturity. The gestation period is long and the number of offspring produced
is small. A bull cannot be assessed for milk production since this a sex-limited trait (note that this is
not the same as sex-linked). Instead, the performance of the bull's female offspring is looked at to
see whether or not to use the bull in further crosses. This is called progeny testing and is a
measure of the bull's value to the breeder.
(2) Selective breeding of wheat

-Aims to obtain desirable characteristics such as high yield, resistance to pests, grain quality such as
the level of protein content and short stem length (to reduce wastage as straw of stem has little
value).
Procedure
-It takes place by crossing two different varieties which have different alleles such as choosing one of
high yield of high protein grains and another with excellent resistance to yellow dust disease.
- The crossing is done by removing the anthers from the flowers of one plant and dusting pollen from
the other plant onto its stigma, and then bagged to stop any other pollen to reach the stigma.
- The resulting seeds are collected, sown and grown.
- The breeders then select the individual plants from this first generation which most nearly have the
characteristics they want. Then the produced plants are self pollinated and seeds are used, this

takes place for several generations, eventually the individual plants become homozygous of true
breeding.
Advantages of this process
- Being of identical characteristics, it is easier to harvest as plants grow to the same height, and are
ready to harvest at the same time, and produce grains of the same quality, making it easier to sell.
Problems of interbreeding (breeding closely related organisms together)
- Reduces variety and makes no evolution, even breeders cannot improve the plant's characteristics
as there are no different alleles.
- If a new disease arrives to which the plant has no natural resistance, the plant will die, and
therefore breeders try to maintain sources of genetic diversity in crop plants.
II-Natural Selection
-The organisms with the most useful features are more likely to survive, to reach adulthood
and reproduce in their environment. Their alleles will be passed on to their offspring. Over
many generations, the alleles that confer useful characteristics on an individual are
therefore likely to become more common. Alleles that do not produce such useful
characteristics are less likely to be passed on to successive generations and will become
less common.
Describe and explain how natural selection leads to evolution:
1-Individuals in population have great reproduction potential;

2- Numbers in population tends to remain roughly constant;
3- There will be genetic variation in members of population;
4- Environmental factors / named factor (biotic or abiotic);selection pressure
5- (Cause) many, fail to survive / die / do not reproduce;
6- Those best adapted survive / survival of the fittest;
7- (Reproduce to) pass on alleles; (not genes)
8- Genetic variation leads to change in phenotype;
9- Changes in, gene pool / allele frequency in a population;
10- Overtime produces evolutionary change;
11- New species arise from existing ones / speciation;
12- Stabilizing, directional selection;
Types of Natural Selection (see figure)

1-stabilizing 2-directional 3-disruptive
How stabilizing force is maintained?

- Conditions remain the same
- Extreme phenotypes are selected against (excluded)
- Only those who are best adapted [at intermediate] will survive
How disruptive selection is maintained in a species.

-Selection pressure that acted against allele frequency of the intermediate,
- e.g. predation increased, thus leading to death of most of them,
-while both of the extremes were chosen to survive, (polymorphism)
-reproduce and pass their alleles to offspring.
How directional selection is produced?.

1- a new environmental factor is applied
2- a new allele appears, then allele frequencies may also change.
3-only one of the extremes is favoured
differences between artificial selection and natural selection
Artificial Selection Natural Selection
Selection (pressure by) humans Environmental selection pressure
Genetic diversity lowered Genetic diversity remains high
Inbreeding common Out breeding common
Loss of vigour / inbreeding depression increased vigour / less chance of inbreeding

depression
Increased homozygosity /decreased decreased homozygosity /increased

heterozygosity heterozygosity
No isolation mechanisms operating Isolation mechanisms do operate
Usually faster Usually slower
Selected feature for human benefit Selected feature for organism's benefit
Not for, survival / evolution Promotes, survival / evolution
individuals without these characteristics will there is still a chance that they might breed
not breed at all

Evolution:
-it is a long term change in the characteristics of a species, or in the frequency of particular alleles
within the species.
The Darwin- Wallace theory of evolution by natural selection:

Observati Organisms produce more offspring than are needed to replace the parents
on 1
Observati Natural populations tend to remain stable in size over long periods.
on 2
Deduction There is competition for survival (a 'struggle for existence').
1
Observati There is variation among the individuals of a given species.
on 3
Deduction The best adapted variants will be selected for by the natural conditions
2 operating at the time. In other words, natural selection will occur. The 'best'
variants have a selective advantage; 'survival of the fittest' occurs.
Examples of natural selection leading to evolution:

1-Sickle cell anaemia and malaria:
-There are three possible genotype due to the presence of this mutant allele
1- Normal red blood cells with normal heamoglobin HH = HB N HBN , no aneamia, die from
malaria
2- Heterozygous = sickle cell anemia trait or carrier Hh = HB N HBS , no or mild aneamia
,resists malaria
3- Homozygous recessive = sickle cell anemia hh = HB S HBS , die from anemia
describe the link between the frequency of sickle cell anaemia and
the number of cases of malaria
1- Frequency of sickle cell anaemia is highest in areas where malaria is common;
2- Sickle cell anaemia red blood cells cannot carry oxygen very well / sickling blocks capillaries;
3- Homozygous Hs / Hs Hs have sickle cell anaemia / may die;
4- Homozygous HN / HN HN have normal, Hb / red blood cells;
5- Heterozygotes have sickle cell trait; red blood cells not (severely) affected;
6- Malaria parasite / Plasmodium, affects red blood cells;
7- Malaria is lethal;
8- Sickle cell trait people / heterozygotes, less likely to suffer from (severe effect of) malaria;
9- Have selective advantage; but in parts of the world where malaria is not common, there is no
selective advantage for carriers of this allele
10- Pass on both HN and Hs ;
11- Malaria selects against, homozygous HN / HN HN ;
12- Sickle cell anaemia selects against, homozygous HS / HS HS ;
13- Sickle cell allele is maintained within population because of sickle cell trait individuals;
2-Development of antibiotic-resistant bacteria:

- Antibiotics are chemicals produced by living organisms, which inhibit or kill bacteria, but do not
normally harm human tissue. Some bacteria cause infections that are treated with antibiotics
prevent the formation of cell wall in bacteria which make them die faster.
-,Some bacteria mutate their DNA changes ,and become resistant to antibiotics by producing thick
cell walls for protection or enzyme to breakdown antibiotic, as bacteria have only a single loop of
DNA, they have only one copy of each gene, so the mutant allele will have an immediate effect on
the phenotype of any bacterium possessing it. These individuals have a tremendous selective
advantage.
-Resistant bacteria is naturally selected to survive, reproduce rapidly by binary fission and increase
in number and pass their allele to offspring , while non-resistant bacteria die.
-Gradually, resistant bacteria dominate over non-resistant ones, and the whole population becomes
resistant to antibiotics. Therefore, nature selected the resistant bacteria to survive.
-the more we use antibiotics, the greater the selection pressure we exert on bacteria to evolve
resistance to them.
3-Peppered moth in Britain:

- There are two forms of moth, a pale speckled form (recessive) and a dark form (dominant). Moth
feeds and rest on tree's trunks. Their main predator is birds.
- It was noticed that the number of pale and dark forms differs from one to another according to the
degree of pollution in the area. This is due to:
Non polluted areas Polluted areas
Pale form predominate Dark form predominate

Tree trunks covered with white lichens Tree trunks covered with black soot
Birds eat dark moth because they are easily seen Birds eat pale moth because they are easily
against the white lichens seen against the black trunks of trees
Birds eat less pale moth because they are better Birds eat less dark moth because they are
camouflaged better camouflaged
In this area, pale form is selected to survive, so In this area dark form is selected to survive,
they reproduce and their number increase so they reproduce and their number increase
The process that affects allele frequency in a population:

A- Mutation being random process, it may lead to the formation of new allele which occasionally
may lead to useful feature with a selective advantage that enable the organism having this allele to
be more likely to survive and reproduce and so the new allele will be more common in the
population.
B- The changes in allele frequency are the basis of evolution, as evolution occurs because natural
selection gives some alleles a better chance of survival than others, over many generations;
populations may gradually change becoming better adapted to their environments.
C- Genetic drift:
- The examples of natural selection given before show the effect of a non-random process on the
allele frequencies of a population of organisms.
- These allele frequencies may also change due to a random process called genetic drift
- Genetic drift is a change in allele frequency that occurs by chance, because only some of the
organisms of each generation reproduce OR It is the change in allele frequency due to the small size
of a population
- It is most noticeable when a small number of individuals are separated from the rest of a large
population.
- They form only a small sample of the original population and so are unlikely to have the same allele
frequencies as the large population.

-Further genetic drift in the small population will alter the allele frequencies still more and evolution
of this population may take a different direction from that of the larger parent population.
- This process, occurring in a recently isolated small population, is called the founder effect.
Why VARIAION is important in natural selection?

-Continuous / discontinuous variation;
-Inherited / genetic variation;
-Variation in phenotype;
-Caused by genotype & environmental variation;
-Competition & struggle for existence;
-Best adapted will survive;
-Bad adapted will die;
-Best ones will reproduce & pass the good alleles to offspring
- The variation of two populations can be compared using the t-test
The Hardy-Weinberg principle:

- When a particular phenotypic trait is controlled by two alleles of a single gene, A/a, the
population will be made up of three genotypes: AA, Aa, and aa.
- Calculations based on the Hardy-Weinberg principle allow the proportions of each of
these genotypes in a large, randomly mating populations to be calculated.
- The frequency of a genotype is its proportion of the total population.
- The total is the whole (that is 1) and the frequencies are given as decimals (e.g. 0.25) of
the total.
- We use the letter p to represent the frequency of the dominant allele, A, in the
population and the letter q to represent the frequency of the recessive allele, a. Then,
since there are only two alleles of this gene:
P + q = 1
(Equation 1)
The chance of an offspring inheriting a dominant allele from
both parents = p x p = p2
The chance of an offspring inheriting a recessive allele from

both parents = q x q = q2

the father and a recessive allele from the mother = p x p = pq

the mother and a recessive allele from the father = p x p = pq
So, p2 + 2pq + q2 = 1
- These Hardy-Weinberg calculations do not apply when the population is small or when
there is:
significant selective pressure against one of the genotypes
migration of individuals carrying one of the two alleles into, or out of, the population
non-random mating
- What is the use of these calculations?

-When the ratios of the different genotypes in a population have been determined, their
predicted ratios in the next generation can be compared with the observed values.
- Any differences can be tested for significance using the x2 test.
- If the differences are significant and migration and non-random mating can be discounted,
then there is evidence that directional selection is occurring in the population.
Crop Improvement:
-New varieties of crops are produced by both conventional breeding techniques (selective
breeding) and genetic modification.
-Selective breeding is more common, easier, faster, and cheaper and can be done by farmers
themselves ,compared to genetic engineering.
(A) CROP IMPROVEMENT BY SELECTIVE BREEDING

Example (1): Hybridisation leading to polyploidy in wheat: (see
figure)
Hybrid:
-it is a plant which is the result of interbreeding between two different species.
Polyploid:
-It is a plant which has more two sets of chromosomes.
1- The formation of polyploids has been important in the evolution of plant species though less
important in animals, as animal polyploids are often not viable.
2- It is now possible to include the formation of polyploids by preventing spindle formation, using
chemicals such as colchicines.
3- Among plant species, polyploids are generally hardy and higher yielding than their parent species
making them important food crops.
4-The ancestors of wheat are small, not very robust, and produce small ears of small seeds, in
contrast to modern hexaploid (6n) wheat.
Advantages of (6n) wheat:
1- Put all energy in making seed rather than being tall.
2- Easy to harvest as they are short.
3- Produces less straw, so less money is needed to get rid of it, Less pollution (usually straw is
burnt).
4- Hybrid vigour: it grows larger ears (more grains) than diploid plant (2n).
5- Today, selective breeding has produced many different varieties of wheat. Much of it is grown to
produce grains rich in gluten, which makes them good for making bread flour. For making other food
products, such as pastry, varieties that contain less gluten are best.
6- Breeding for resistance to various fungal diseases, such as head blight, caused by Fusarium, is
important, because of the loss of yield resulting from such infections.
7- Successful introduction of an allele giving resistance takes many generations, especially when it
comes from a wheat grown in a different part of the world. Commercial plant breeders' aim is to

support the development of new varieties by screening seed collections for plants with traits such as
disease resistance, climate resilience, or efficient use of nitrogen fertilisers. Any plant with suitable
trait is grown in large numbers and passed to the commercial breeders.
When farmer do pure breeding of crop to increase yield, but it does

not increase steadily then this is because:
1- Genetic variation.
2- Environmental variations.
3- Experimental error or mutation
Example (2): The incorporation of mutant allele for gibberellin

synthesis into dwarf varieties to increase yield by having a greater
proportion of energy put into grains:
- Wheat plants now have much shorter stems than they did about 50 years ago.
- This makes them easier to harvest and means they have higher yields (because they put more
energy into making seeds rather than growing tall).
- The shorter stem also make the plants less susceptible to being knocked flat by heavy rains, and
means they produce less straw, which has little value and costs money to dispose of.
- Most of the dwarf varieties of wheat carry mutant alleles of two reduced height (Rht) genes.
- These genes code for DELLA proteins which reduce the effect of gibberelln on growth.
- The mutant alleles cause dwarfism by producing more of, or more active forms of, these
transcription inhibitors.
- A mutant allele of a different gene called "Tom Thumb" has its dwarfing effect because the plant
cells do not have receptors for gibberellins and cannot respond to the hormone.
Example (3): Introducing a disease resistance allele to rice:

- Rice, Oryza sativa, is also used a lot in selective breeding
- The International Rice Research Institute holds the rice gene bank and together with the Global
Rice Science Partnership coordinates research aimed at improving the ability of rice farmers to
feed growing populations.
- The yield of rice can be reduced by bacterial diseases such as bacterial blight, and by a range of
fungal diseases including various "spots" and "smuts".The most significant fungal disease is rice
blast, caused by the fungus Magnaporthe.
- Researchers are hoping to use selective breeding to produce varieties of rice that show some
resistance to all these diseases.
Example (4): Producing vigorous, uniform maize through

selective inbreeding and hybridisation:
-Maize is one of the most widely grown crop plants. Growing conditions will vary considerably in
different parts of the world (soil, type, prevailing temperature, and rainfall.etc) hence, through
selection, inbreeding and hybridisation, growers have been able to produce varieties that grow
vigorously (and are therefore high yielding) and uniformly under the prevailing conditions.
- Assuming that conditions remain similar year after year, farmers can continue to grow the same
variety and expect to obtain a similar crop.
The characteristics which are desirable in a crop plant such as maize
are:
1- High yielding.
2- Disease resistant.
3- Good quality in terms of desirability to market.
4- Vigorous growth under the prevailing conditions.
5- Plants all grow to a similar height (making harvesting easier),(i.e. genetically identical)
6- Crops are all ready to harvest at the same time.( i.e. genetically identical)
7- Plants can grow in soil that is low in nutrition or water supply.
- Genetic uniformity is usually achieved through inbreeding (breeding a plant with itself, or with
other plants with the same genotype) for many generations. However, in maize, inbreeding results
in weak plants with low yields. This is called inbreeding depression.
- Maize breeding therefore involves producing hybrids between two inbred lines. Like most selective
breeding of cereal crops, it is done by commercial organisations not by farmers themselves.
-Outbreeding-crossing with other, less closely related plants produces heterozygous plants that
are healthier, grow taller and produce high yields
Method:
1-Inbred lines (genetically uniform populations) of maize with desirable characteristics are identified,
and crossed with other inbred lines with different sets of desirable characteristics to produce a
hybrid more vigour than parents.
- Seeds which result from such breeding are grown and plants showing the desirable characteristics
are bred again the process can be repeated for many generations.
2- In order to carry out the inbreeding, or to carry out a cross to form a hybrid, pollen from a specific
male parent must be used to fertilise a specific female parent to:
a)-Ensure that the cross intended is the only one that occurs, anthers are removed from some
flowers which will form the female parent. Pollen is transferred from the anthers of the male parent
flowers to the stigmas of the flowers without anthers. Muslin bags are then around the fertilised
flowers to prevent pollination by any other pollen.
b)-Selection for measurable characteristics such as yield is done by measuring the characteristic and
choosing from breeding those plants that express it most strongly, e.g. having the highest yield,
Selection for disease or pest resistance is done by exposing the plants to disease or pest, which kills
any that are not resistant. The best of these hybrids are then chosen for commercial production.
3- Large quantities of the two inbred lines from which the hybrid was bred are grown, as it is from
these that all the seed to be sold will be produced.
4-Each year the two inbred lines are bred together, and the seed collected from them to sell as
hybrid seed.

Advantages of producing seeds by hybridization:
1- This method of breeding avoids problems of inbreeding depression.
2- The hybrid plants are genetically uniform (Although they will be heterozygous for several genes),
because they all have the same two inbred parents.
Disadvantages of producing seeds by hybridization:
1- Expensive.
2- Farmers have to buy seeds every year rather than saving their own seeds to ensure uniformity
and heterozygosity since homozygous seeds show no hybrid vigour.
Hybrid vigour in produced maize:
- If two inbred lines are crossed, it will produce a hybrid that has a greater yield and is more vigorous
than either of the parental lines. This is known as hybrid vigour.
-This hybrid is heterozygous for most genes, so deleterious recessive alleles are hidden, but at the
same time it inherits the lack of variability from its parents. Such single cross hybridisation has been
used for selective breeding since the early 1960's to double the yield (from 4 8 tonnes per
hectare) and to breed uniform, high yielding maize.

4-Species and Speciation:
Species:
A group of organisms that are reproductively isolated, interbreeding to produce fertile
offspring. Organisms belonging to a species have morphological (structural), physiological,
Biochemical similarities, which are often used to identify to which species they belong.
-'Morphological' features are structural features, while 'physiological' features are the way
that the body works. 'Biochemical' features include the sequence of bases in DNA molecules
and the sequence of amino acids in proteins.
- Example: all donkeys can breed with other donkeys to produce more donkeys which
themselves can interbreed. All donkeys belong to the same species. Donkeys can
interbreed with organisms of another similar species, horse, to produce offspring called
mules. However, mules are infertile, that is they cannot breed and are effectively a 'dead-
end'. Thus donkeys and horses belong to different species (Reproductively isolated)
-When two species are unable to reproduce to produce fertile offspring, and are
reproductively isolated, then they are considered as two different species.
How to know if two organisms belong to the same species or not:

1- They are allowed to interbreed, if they produce fertile offspring, they are of the same
species.
2- Test DNA.
Difficulties facing this process:

1- If organisms are dead, for example, museum specimen of fossils.
2- Organisms are of the same sex.
3- Organisms reproduce asexually.
4- Organisms are immature and are unable to reproduce yet.
5- Many years may be needed for producing offspring.
6- It can be extremely difficult to decide when these features are sufficiently similar or
different to define two organisms as belonging to the same or different species. This leads to
great uncertainties and disagreements about whether to group many slightly different
variations of organisms together into one species, or whether to split them up into many
different species.
To overcome such difficulties:

1- Morphological features are usually used.
2- Sometimes biochemical and structural features, but they are time-consuming and
expensive.
Explain the role of isolating mechanisms in the evolution of new

species/ or Explain how a new species can evolve from one original
species:
A-allopatric speciation;
- Geographical isolation / spatial separation;
- e.g. of barrier; mountain, river, or any physical barrier
- e.g. of organism
- A population of a species of bird, somehow arrived on one of the Hawaiian Islands from mainland
America, they might have been blown off course by a storm. Here, separated by hundreds of miles of
ocean from the rest of their species on mainland America..
- No breeding / gene flow, between populations;
- Mutations occur; can result in different chromosome numbers;
- Different selection pressures / different (environmental) conditions;
- Genetic change; e.g. different alleles selected for / change in allele frequency / change in gene pool
/ advantageous alleles passed on;
- Genetic drift;
- Become, reproductively isolated from the original species/ cannot interbreed together with original
species
- Reproductive isolation can take very different forms:
a-Prezygotic (before a zygote is formed) isolating mechanisms include:
1- Individuals not recognizing one another as potential mates or not responding to mating behavior
2- Animals being physically unable to mate
3- Incompatibility of pollen and stigma in plants
4- Inability of a male gamete to fuse with a female gamete
b-Postzygotic isolating mechanisms include:
1- Failure of cell division in the zygote
2-non-viable offspring (offspring that soon die)
3- Viable, but sterile offspring.
- Only inbreeding between individuals of same species
Note:

-If the two species that were separated by geographical barrier are united again, they will not
interbreed successfully, and will compete for resources.
B-sympatric speciation;
-Example, the development of Spartina anglica grass;
-Meiosis problems;
-Polyploidy;
-behavioral / temporal (time / season) / ecological / structural, isolation;
- (isolated) populations, prevented from interbreeding / can only breed amongst themselves
-no, gene flow / gene mixing, (between populations);
-different selection pressures operate;
-natural selection;
-change in allele frequencies;
-different gene pool;
-over time (differences prevent interbreeding);
-reproductively isolated;
C-Adaptive radiation:
-It is the production of many new species from one ancestral species, e.g. Darwin's Finches.
Note:
-IF QUESTION says what is type of speciation then: allopatric / sympatric
-IF QUESTION says what is type of isolation mechanism then: geographical barrier / behavioral,
temporal,etc
Polyploidy:
What is a polyploidy organism?
-it is an organism with more than two sets of chromosomes in its somatic cell
What causes a polyploidy organism to be produced?

-If meiosis goes wrong leading to formation of gametes each with two sets of chromosomes
instead of one. If two such gametes fuse together the zygote gets four sets of chromosomes
and is known as Tetraploid.
Tetraploid:
-Tetraploid organisms are often sterile as they fail to produce gametes by meiosis because
there are four pairs of each kind of chromosomes which cannot pair up during meiosis 1.
-Tetraploid may grow perfectly and reproduce asexually because in mitosis chromosomes do
not need to pair together.
Triploid:
-If Tetraploid plant goes through a faulty meiosis and produce gametes, they will be diploid
gametes. If one of the diploid gametes fuses with a normal gamete from other normal plant,
the produced zygote is triploid.
-The triploid individual can grow normally but it is sterile because the three sets of
chromosomes cannot be shared evenly in gametes
- The normal diploid plant and the Tetraploid plants cannot interbreed to produce fertile
offspring, so they are considered different species (Reproductive isolation).
Autopolyploid and allopolyploid:
1- Autopolyploid: When the four sets of chromosomes of the tetraploid organism all from
the same species.
2- Allopolyploid: When the tetraploid organism has two sets of chromosomes from one
species and two sets from another species.
-Allopolyploid can produce gametes by meiosis as where the chromosomes from each
species can pair together but in
Autopolyploid meiosis is less likely to occur as chromosomes cannot get together in fours,
therefore allopolyploid is fertile but autopolyploid is not.
-Allopolyploid is a new species as it cannot interbreed with the parent species.

E.g. one well-documented instance of speciation through allopolyploid is the cord
grass Spartina anglica. This is a vigorous grass that grows in salt marshes.
METHOD
Spartina alterniflor
Spartina maritima
(Diploid fertile)
(Diploid fertile)
(AA)
(BB)
Meiosis
Meiosis
(Gametes)
(Gametes)
(Haploid)
(Haploid)
(A) (B)
Fertilization / Hybridization
Spartina towsandi (AB)

(Diploid, sterile)
Wrong meiosis produced Diploid

gametes
(AB)
(AB)
(Diploid gamete)
(diploid gamete)
Fertilization (fusion of gametes)
Spartina anglica (AABB)

(Tetraploid)
(Allopolyploid)
(Fertile)
Molecular comparisons between species

- Molecular evidence from comparisons of the amino acid sequences and of the nucleotide
sequences of mitochondrial DNA can be used to reveal similarities between closely related
species.
A) - Comparing amino acid sequences of proteins:

- The primary structure of a protein may cause a dramatic change in its structure and
function.
- For many proteins, small changes in the amino acid sequence leave the overall structure
and the function of the protein unaltered. Typically, the part of the molecule essential for its
function (such as the active site of an enzyme) remains the same, but other parts of the
molecule may show changes.
- When the amino acid sequence of a particular protein is compared in different species, the
number of differences gives a measure of how closely related the species are.
- E.g. cytochrome c . Cytochrome c is a component of the electron transfer chain in
oxidative phosphorylation in mitochondria.
- A protein with such an important function is expected to have a similar sequence of amino
acids in different species since a poorly adapted cytochrome c molecule would result in the
death of the organism.
- When the sequence of cytochrome c from humans, mice and rats were compared, it was
found that:
1- All three molecules consist of 104 amino acids;
2- The sequences of mouse and rat cytochromes c are identical;
3- Nine amino acids in human cytochrome c are different from the mouse or rat sequence;
4- Most of these substitutions in human cytochrome c are of amino acids with the same type
of R group.
- This means that mice and rats are closely related species, sharing a recent common
ancestor, and that humans are more distantly related, sharing a common ancestor with
mice and rats less recently.
- When the sequences of cytochrome c from other species, such as a fruit fly or nematode
worm, are also examined, the numbers of differences from the human sequence increase.
These organisms are less closely related to humans.
B) - Comparing nucleotide sequences of mitochondrial DNA

- Differences in the nucleotide sequences of mitochondrial DNA (mtDNA) can be used to
study the origin and spread of our own species Homo sapiens
- Human mitochondrial DNA is inherited through the female line. A zygote contains the
mitochondria of the ovum, but not of the sperm.
- Since the mitochondrial DNA is circular and cannot undergo any form of crossing over,
changes in the nucleotide sequence can only arise by mutation.
- Mitochondrial DNA mutates faster than nuclear DNA, acquiring one mutation every 25000
years.
- Unlike nuclear DNA, mitochondrial DNA is not protected by histone proteins, and oxidative
phosphorylation in the mitochondria can produce forms of oxygen that act as mutagens.
- Different human populations show differences in mitochondrial DNA sequence.

-These provide evidence for the origin of Homo sapiens in Africa and for the subsequent
migrations of the species around the world.

- These studies have led to the suggestion that all modern humans, of whatever race, are
descendants from one woman, called, Mitochondrial Eve, who lived in Africa between
150000 and 200000 years ago.
- This date is derived from the "molecular clock" hypothesis, which assumes a constant rate
of mutation over time and that the greater the number of differences in the sequence of
nucleotides, the longer ago those individuals shared a common ancestor.
- The "clock" can be calibrated by comparing nucleotide sequences of species whose date of
speciation can be estimated from fossil evidence.
- Analysis of mitochondrial DNA of the different species of anole lizards that are found
throughout the Caribbean and the adjacent mainland provides evidence of their
relationships.
- Each island species of lizard is found only on one island or a small group of islands.
- These results show that the three species Anolis brunneus, A. smaragdinus and A.
carolinensis are more closely related to A. porcatus than they are to each other.
- This suggests that these species have each originated from separate events in which a few
individuals of A. porcatus spread from Cuba to three different places.
- The mitochondrial DNA analysis shows that allopatric speciation has occurred.
Extinctions:
- Species may become extinct, perhaps as a result of a change in climate or increased
competition from a better adapted species.
The Red List of threatened species:
*Four categories of risks are identified:
1-Rare: not in immediate danger of extinction, but their number is small and they are either
scattered widely or restricted to localized habitats.
2-Vulnerable: species declining in numbers and may suffer from extinction in the future.
3-Endangered: species with low population numbers at danger of extinction.
4-Extinct: species cannot be found again in any habitat.
These species are all low in numbers and under threat of extinction and disappearing
forever from the Earth. Of course millions of species have become extinct in the past,
sometimes huge numbers at one time in so-called mass extinctions. However, these
events were all natural, thought to have been caused by sudden and huge changes in the
environment, such as a large asteroid colliding with the Earth. We are currently facing
likelihood of another mass extinction, this time caused by humans.
*Why the red list has more vertebrates than invertebrate / green plants as
opposed to protoctists. There are no prokaryotes on the list

1- People are more interested in vertebrates.
2- Vertebrates are larger than others.
3- People are much more aware of vertebrates (know more about them).
*Why some species are less endangered than others? Because:
1- Of no use to humans.
2- Hide in small places.
3- Camouflaged.
4- Produce large number of offspring.
5- Variety of food.
6-small quantity of food required.
- In 2011, the western black rhino of Africa was declared extinct. These rhino extinctions,
despite years of conservation efforts, are the result of:
1- A lack of political support for conservation;
2- An increasing demand for rhino horn;
3- Internationally organized criminal groups targeting rhinos.
- Generally, the main reasons for the extinction of a species are:

1- Climate change: change in temperature / lack of rain ....etc
2- Competition for food / water / mate ...etc
3- Habitat loss: e.g. deforestation / desertification
4- Killing by humans, for food / sport / fun / raw materials / or because they raid crops /
rampage through villages
5- Poaching.
- Some conservationists now think that it is time to stop concentrating on some of the
world's high-profile species and to turn to others where conservation efforts are likely to
have greater degrees of success.
- This would involve focusing efforts on certain animals and plants that can be saved, at the
expense of those that are too difficult or too costly to preserve in the wild.
- Conservation programmes now often try to conserve whole ecosystems, rather than
concentrating on a single species.
BIODIVERSITY, CLASSIFICATION & CONSERVATION

Classification:
-Biologists classify organisms (sort them into groups) according to how closely they believe they are
related to one another. Each species has evolved from a previously existing species.
-We do not usually have any information about these ancestral species, so we judge the degree of
relatedness between two organisms by looking carefully at their physiology, anatomy and
biochemistry. The greater the similarities, the more closely they are thought to be related. (Study
2007 sp q3)
- Scientific names: when a new species is discovered, it is given a scientific name using the
binomial system that was developed by the Swedish scientist Linnaeus in the 18 th century. Each
species is given two names: the first is its genus and the second is the species name
-The system used for classification is a taxonomic system. This involves placing organisms in a
series of taxonomic units which form a hierarchy. The largest unit is the kingdom. Kingdoms are
subdivided into phyla, classes, orders, families, genera and species.
An example of classification

Classification Systems
(1) A six-kingdom system
Eubacteri Archaebacte Protoctist Planta Fungi Animalia

a or ria a e
(2) A three-domain system
Bacteria Archaea EUKARYA

) )
Eubacteri Archaebacter
Note:
-The three-domain system highlights the importance of archaebacteria as a life-form.

-Notice that the domain Eukarya includes members of the kingdom Protista, Plantae, Fungi, and
Animalia, which are all made up of eukaryotic organisms.
(3) The five-kingdom classification system
One method of classification is to place all living organisms into five kingdoms. These are:
1- Prokaryota 2- Protoctists 3- Fungi 4- Plantae 5- Animalia
Three domains:
- Biologists used to divide organisms into two large groupings based on their cell structure;
Prokaryotes and eukaryotes
- In the 1970s, prokaryotes were discovered living in extreme environments, such as hot springs
where temperatures often exceed 100C. These extremophiles, as they are known, were not like
typical bacteria.
- Studies revealed that the genes coding for the RNA that makes up their ribosomes were like those
of eukaryotes.
- They were found to share features with both typical bacteria and eukaryotes.
- At this time, studies of molecular biology assumed a much greater significance in taxonomy.
- This meant that a new taxon, the domain, had to be introduced to reflect the differences between
these extremophiles and typical bacteria.
- The domain in the taxon at the top of the hierarchy.
- The prokaryotes are divided between the domains Bacteria and Archaea and all the eukaryotes
are placed into the domain Eukarya.
- Many Archaea live in extreme environments, such as hot springs, around deep volcanic vents
(black smokers) in the ocean and in lakes where there is a very high concentration of salt.
- Some of them produce methane, cannot survive where there is oxygen and have many unusual
enzymes.
- Since they were discovered in extreme environments they have been found in many less extreme
environments; for example, they form an important part of the plankton in the oceans.
- In several ways, the Archaea appear to have more in common with the Eukarya than with Bacteria.
- It is thought that Bacteria and Archaea separated from other very early in the evolution of life. The
Archaea and Eukarya probably diverged later.
[1] Domain Bacteria

- Bacteria are prokaryotic as their cells have no nucleus. They are small organisms that vary in size
between that of the largest virus and the smallest single-celled eukaryote. The characteristic
features of the bacteria are:
1- Cells with no nucleus;
2- DNA exists as a circular "chromosome" and does not have histone proteins associated with it;
3- Smaller circular molecules of DNA called plasmids are often present;
4- No membrane-bound organelles (such as mitochondria, endoplasmic reticulum, Golgi body,
chloroplasts) are present;
5- Ribosomes (70S) are smaller than in eukaryotic cells;
6- Cell wall is always present and contains peptidoglycans (not cellulose);
7- Cells divide by binary fission, not by mitosis;
8- Usually exist as single cells or small groups of cells.
[2] Domain Archaea
- Archaeans are also prokaryotic as their cells have no nucleus. Their range of size is similar to that
of bacteria.
- Many inhabit extreme environments.
- The characteristic features of archaeans are:
1- Cells with no membrane-bound organelles;
2- DNA exists as a circular "chromosome" and does have histone proteins associated with it;
3- Smaller circular molecules of DNA called plasmids are often present;
4- Ribosomes (70S) are smaller than in eukaryotic cells, but they have features that are similar to
those in eukaryotic ribosomes;
5- Cell wall is always present but does not contain peptidoglycans;
6- Cells divide by binary fission, not by mitosis;
7- Usually exist as single cells or small groups of cells.
- The metabolism of archaeans is similar to that of bacteria, but the way in which transcription
occurs has much in common with eukaryotes.
[3] Domain Eukarya
- All the organisms classified into this domain have cells with nuclei and membrane-bound
organelles.
- Their characteristic features are:
1- Cells with a nucleus and membrane-bound organelles;
2- DNA in the nucleus arranged as linear chromosomes with histone proteins;
3- Ribosomes (80S) in the cytosol are larger than in prokaryotes, chloroplasts and mitochondria have
70S ribosomes, like those in prokaryotes;
4- Chloroplast and mitochondrial DNA is circular as in prokaryote;
5- A great diversity of forms, there are unicellular, colonial and multicellular organisms;
6- Cell division is by mitosis;
7- Many different ways of reproducing-asexually and sexually.
*Kingdom Prokaryota
-Many biologists now split this kingdom into two: the Achaea and the Bacteria. They look similar, but
their biochemistry is very different.
Characteristic features:
1- Cells with no nucleus;
2-DNA exists as a circular 'chromosome';
3-Smaller circular molecules of DNA called plasmids are often present;
4-No membrane-bound organelles (e.g. mitochondria, endoplasmic reticulum);
5-Ribosomes smaller than in eukaryotic cells;
6-Cell wall containing peptigoglycans;
7-Usually exist as single cells or small groups of cells;
*Kingdom Protoctista
-This group is made up of a very diverse range of organisms, which may actually be more closely
related to organisms in other kingdoms than they are to each other. For example, there are strong

arguments for classifying algae as plants. Any eukaryote that is not a fungus, plant or animal is
classified as protoctists.
1- Eukaryotic;
2- Mostly single-celled, or exist as groups of similar cells;
3- Some have animal-like cells (no cell wall) and are sometimes known as protozoa; e.g.
plasmodium causing malaria.
4-Others have Plant-like cells (with cellulose cell walls and chloroplasts) and are sometimes known
as algae;
*Kingdom Fungi
1- Eukaryotic;
2- Do not have chlorophyll and do not photosynthesize they feed heterotrophically;
3- Simple body form, which may be unicellular or made up of long threads called hyphae ( with or
without cross walls); large fungi such as mushrooms also have a compacted mass of cells as part of
their life cycle;
4- Reproduce by means of spores;
5- Cells have cell walls made of chitin or other substances, not cellulose;
6- Never have cilia or flagella.
*Kingdom Plantae
1-Multicellular eukaryotes with cells that are differentiated to form tissues and organs;
2- Few types of specialised cells;
3-Some cells have chloroplasts and photosynthesis;
4- Cells have large, often permanent vacuoles for support
5- Autotrophic nutrition
6-Cells walls are always present and are made of cellulose;
7-Cells may occasionally have flagella for example, male gametes in ferns.
*Kingdom Animalia
1-Multicellular eukaryotes with many different types of specialised cells;
2-Cells that are differentiated to form tissues and organs;
3-Cells do not have chloroplasts and cannot photosynthesise (although some, such as coral polyps
have photosynthetic protoctists living within their tissues);
4- Cell vacuoles are small and temporary (for example, lysosomes and food vacuoles) ;
5- Heterotrophic nutrition;
6- Cells do not have cell walls;
7- Communication is by the nervous system;
8- Cells sometimes have cilia or flagella.
Prokaryotes and Eukaryotes Cells
*Differences between prokaryotic and eukaryotic cells

Prokaryotes (before Eukaryotes (true nucleus)
nucleus)
Average diameter of cell 0.5-5.0 Cells commonly up to 40 m diameter and commonly
m (smaller) 1000-10000 times the volume of prokaryotic cells (larger)
DNA is circular and lies free in DNA is not circular and is contained in a nucleus. The
the cytoplasm nucleus is surrounded by an envelope of two membranes.
DNA is naked DNA is associated with protein, forming structures called

chromosomes

Slightly smaller ribosomes Slightly larger ribosomes (about 22nm diameter) or 80s.
(about 18nm diameter) or 70s
No ER present ER present, to which ribosomes may be attended.
Very few cell organelles; none -Some organelles are bounded by a single membrane, e.g.
are surrounded by an envelope lysosomes, Golgi apparatus, vacuoles, ER
of two membranes -Some are bounded by two membranes (an envelope) of a
nucleus, mitochondrion, and chloroplast.
-Some have no membrane, e.g. ribosomes, nucleolus and
centrioles.
Cell wall always present, made Cell wall sometimes present, e.g. in plants made of
of peptidoglycan cellulose, in fungi made of chitin
Note:
-Mitochondria and chloroplast are thought to be prokaryotes that lived with mutual
(symbiotic or exchange of benefits) relationship with eukaryotic cells but they have lost their
cell walls during this relationship, this is due to:
1-Presence of DNA, ribosomes
2-Being self- replicating and synthesizing their own proteins
3-Their membrane structure resembles cell membrane of cells
List the structural features that prokaryotic and eukaryotic cells

have in common
1- Plasma membrane
2- Cytoplasm
3- Ribosomes
4- DNA
5-cell wall (except in animal cells)
Viruses:
Nature of viruses:
- Viruses are only visible with electron microscope.
- Viruses are non-cellular they do not have a cellular structure like bacteria and fungi.
- Viruses are not in the classification system we have discussed. This is because viruses
have none of the features that we traditionally use for classification.
- There is an argument that they should not be considered to be living organisms at all.
Structure of viruses:
- They do have particles made of proteins and nucleic acids that are found in all cellular
organisms.
- When they are free in the environment, they are infectious, but they have no metabolism.
- When they infect cells, they make use of the biochemical machinery of the host cell to
copy their nucleic acids and to make their proteins, often leading to destruction of the host
cell.
- The energy for these processes is provided by respiration in the host cell.
The taxonomic system for classifying viruses:

- It is based on the diseases which they cause, the type of nucleic acid they contain (DNA or
RNA) and whether the nucleic acid is single-stranded or double-stranded.
- In cellular organisms, DNA is double-stranded and RNA is single- stranded but in viruses
both can be either single-stranded or double-stranded.
Some important definitions:
Ecology: The study of the inter-relationships between organisms and all living (biotic) and non-living
(abiotic) components of their environment.
Ecosystem: A unit made up of biotic and abiotic components interacting and functioning together,
including all the living organisms of all types in a given area and all the abiotic physical and
chemical factors in their environment, linked together by energy flow and cycling of nutrients.
- An ecosystem is a relatively self-contained, interacting community of organisms, and the
environment in which they live and with which they interact.
-Ecosystem may vary in size but always form a functional entity; for example a decomposing log, a
pond, a meadow, a reef, a forest, or the entire biosphere.
Species: A group of organisms that share similar morphology and physiology, and that can
interbreed to produce fertile offspring. They are reproductively from other species.
Population: All of the organisms of one particular species within a specified area at a particular
time, sharing the same gene pool and more or less isolated from other populations of the same
species.
Community: All of the populations of all of the different species within a specified area at a
particular time.
Producers: Autotrophic organisms at the first trophic level in food chains, which can use simple
inorganic compounds (such as carbon dioxide and inorganic nitrogen) plus energy from light

(photosynthesis) or oxidation of inorganic chemicals (chemosynthesis) to manufacture energy-rich
organic compounds.
Consumers: Heterotrophic organisms that get energy- rich organic compounds by eating or
decomposing other organisms. They exist at the second (e.g. herbivore) or higher (e.g. carnivore)
trophic levels in food chains.
Decomposers: Saprotrophic organisms that feed on dead organisms and organic waste (such as
dead leaves or faeces), releasing nutrients for re-use and so playing an important role in the carbon
and nitrogen cycle.
Habitat: The particular location and type of local environment occupied by a population or
organism, characterized by its physical features or by its dominant producers (such as rocky shore or
sugar cane field).
- A habitat describes the place where a species lives within an ecosystem.
Niche: The functional role or place of a species of organism within an ecosystem, including
interactions with other organisms (such as feeding interactions), habitat life-cycle and location,
adding up to a description of the specific environmental features to which the species is well
adapted.
- A niche is the role of an organism in an ecosystem
Magnification:
-It is the size of an image of an object compared to the actual size. It is calculated using the formula:
M=I/A
-M is magnification, I is the size of the image, and A is the actual size of the object, using the same
units for both sizes.
- This formula can be rearranged to give the actual size of an object where the size of the image and
magnification are known:
A=I/M
Biodiversity and Conservation:

* Biodiversity: includes the range of habitats (environments) and species in an area, and the
genetic diversity within a species.
* Endangered species: any species whose numbers have become so low that they are unlikely to
be maintained by normal rates of reproduction and are in danger of becoming extinct.
* Conservation: involves attempting to slow down, stop or even reverse the loss of biodiversity.
Species diversity
- The number of species in a community is known as species richness.
- Species diversity takes species richness into account, but also includes a measure of
the evenness of the abundance of the different species.
- The more species there are, and the more evenly the number of organisms is distributed among
the different species, the greater the species diversity. E.g. Coral reefs have a very high
biodiversity; such an ecosystem offers many different ecological niches, which are used by different
species.

- Species diversity is considered important because ecosystems with high species diversity tend to
be more stable than ones with limited diversity; they are able to resist changes.
- Some ecosystems are dominated by one or two species and other species may be rare..
- The tropics are important centres for biodiversity possibly because living conditions are not too
extreme (no frost, snow or ice), there is light of high intensity all year round and birds and mammals
do not need to expend energy keeping warm
Genetic diversity
- Genetic diversity is the diversity of alleles within the genes in the genome of a single species.
- All the individuals of a species have the same genes, but they do not all have the same alleles of
those genes.
- Genetic diversity within a species can be assessed by finding out what proportion of genes has
different alleles and how many alleles there are per gene.
- Similar genetic diversity, although not always so obvious, exists in natural populations.
- The genetic differences between populations of the same species exist because populations may
be adapted slightly in different parts of their range.
- There is also genetic diversity within each population. This diversity is important in providing
populations with the ability to adapt to changes in biotic and abiotic factors, such as competition
with other species, evading new predators, resisting new strains of disease and changes in
temperature, salinity, humidity and rainfall.
Threats to biodiversity:
-Biodiversity is under threat in many aquatic and terrestrial ecosystems as:
- There are five threats to biodiversity:
1-Habitat loss and the degradation of the environment
2- Climate change
3- Excessive use of fertilizers and industrial and domestic forms of population
4- The overexploitation and unsustainable use of resources since the human population continues to
increase
5- The effects of invasive alien species on native species, especially endemics.
( A ) Threats to biodiversity of terrestrial ecosystems

[1] Habitat-loss / Fragmentation & Deforestation
- The destruction of the natural environment leads to habitat loss.

- The clearing of land for agriculture, housing, transport, leisure facilities and industry removes
vegetation.
- Consequently, many species of plant and animal either lose their habitats completely, or their
habitats become divided into small areas, this is known as habitat fragmentation.
- Most at risk of extinction are endemic species on small islands.
- Much of the forest has been cleared by humans, or replaced with cattle ranches and plantations of
oil palm, which have much lower biodiversity or the removal by logging companies of valuable trees,
such as teak and mahogany, at a rate faster than they can regenerate.
- Deforestation can lead to sever land degradation as a result of soil erosion once the vegetation is
removed.
[2] Hunting and Poaching

- The African bush elephant is a keystone species of the savanna grassland.
- Bush elephants are very destructive of vegetation as they push over and eat many tree species.
- This extreme form of grazing helps to maintain this ecosystem, which is renowned for its diversity
of large mammals as well as many other species.
- Elephant dung provides a very rich habitat in fact almost an ecosystem in itself for many
organisms including fungi and dung beetles.
- Elephants were once hunted widely for their ivory and their populations decreased considerably.
- Now protected by international agreements, they are still at risk of poaching to supply illegal trade
in ivory.
[3] Pollution
- Pollution is a major threat to many ecosystems.
- In many countries, industrial and domestic waste is processed to reduce its impact on the
environment.
- For example, sewage is treated before it reaches aquatic ecosystems, such as rivers and the sea.
- Much toxic industrial waste is collected and disposed of so that it cannot leak into the environment.
- However, this does not happen everywhere with the result that many ecosystems are polluted,
often with substances that animals' bodies are unable to metabolise or excrete.
Example (1): Polychlorinated Biphenyls (PCBs)

- Polychlorinated Biphenyls (PCBs) were used in many manufacturing processes.
- Waste from factories used o flow directly into rivers without any form of treatment.
- Even though PCBs are no longer used, the substance persists in the environment and has entered
food chains.
- Among its effects are the weakening of immune systems and reduction in fertility in birds and
mammals.
- PCBs were one of the factors contributing to the death of seals in the North Sea from a viral
infection.
- Non-biodegradable plastic is a major marine pollutant.
- Animals, such as dolphins and turtles, get caught in discarded fishing nets and die.
- Turtles eat plastic bags mistaking them for jelly fish.
Example (2): Over-used Fertilizers

- Much of the world's farmland is in low-lying land near coasts.
- Fertilizers that have not been absorbed by crop plants drain into the sea.
- The extra nutrients that become available to river and marine ecosystems cause growth of
producers, such as algae.
- This often occurs faster than herbivorous organisms, such as fish, can feed on them to keep their
growth under control.
- Many of these algae produce toxic substances and their growth often unbalances food webs.
- Excess growth of algae has catastrophic effects on coral reefs and hugely reduces biodiversity.
Example (3): Combustion of fuel with high sulfur content

- Pollution of the air leads to problems for aquatic and terrestrial ecosystem.
- The combustion of fuel with high sulfur content, such as coal, leads to high concentrations of sulfur
dioxide in the atmosphere.
- This reacts with water vapour to fall as acid rain.
- Acid rain has destroyed vegetation and led to the acidification of aquatic ecosystems in parts of the
world downwind of highly industrialized areas.
- Few animals can survive and / or breed in waters of low pH, so the biodiversity has decreased
markedly.
- Many ecosystems are still at risk from acid rain.
Example (4): Greenhouse gases & global warming (climatic change)

- Industrialisation and the extraction and combustion of fossil fuels have also led to an increase in
the concentration of carbon dioxide and methane in the atmosphere. These are both greenhouse
gases.
- High emissions of methane are associated with cattle and rice farming and the breakdown, under
anaerobic conditions, of organic waste in landfill sites.
- The build-up of greenhouse gases is leading to climate change such as Global warming which
can produce changes in the distribution of terrestrial ecosystem.
- Organisms are expected to migrate north or south to cooler latitudes and also to higher latitudes.
There will be competition between migrating organisms and species in existing communities.
- The acidification of the oceans may cause catastrophe for coral reefs and those species, such as
many molluscs, that make their skeletons and shells from calcium carbonate. Also corals are very
sensitive to temperatures increases.
- The algae that live inside the polyps tend to leave the animals if the temperature remains high for
a period of time. This leads to coral turning white or Coral bleaching, can lead to the death of the
coral.
- Coral reefs are one of the most diverse ecosystems on Earth. We rely on them to provide protection
for many coastlines.
- A large proportion of coral reefs have already been destroyed or degraded by overfishing, mining
and fertilizer run-off.
- The rise in sea levels associated with global warming will bring many problems for coastal
ecosystems which are some of the most productive on Earth.
- The frequency of natural catastrophes, such as hurricanes, typhoons, severe storms and flooding is
thought to be on the increase. Following typhoons in the Pacific, flooding increases the concentration
of nutrients in coastal waters.
- This encourages growth of phytoplankton which provides food for the larvae of the crown-of thorns
starfish, Acanthaster planci. Huge numbers of the adults then eat the coral. Eventually the numbers
of the starfish decrease and the coral regrows.
(B) Threats to biodiversity of Aquatic ecosystems

[1] Overexploitation of resources

- Although agriculture provides most of our food, we still rely on taking wild fish from the
environment.
- It is very difficult to know whether fish stocks are sustainable, but the history of the fishing industry
suggests that many species have been driven to near extinction by overfishing.
- The response to the steep decrease in large, predatory species is to fish further down the food
chain taking smaller fish that other animals, such as marine mammals and sea birds, depend upon.
- Fishing is just one example of the overexploitation of resources.
[2] Hunting
- The loss of the species can have devastating efforts on the rest of its community.
- The Pacific sea otter is a predator of sea urchins in kelp forests.
- Otters were hunted for their fur and there was a striking change to the whole of the food web as
urchins exploded in numbers.
- The kelp forests organisms like the sea otter that play a central role in an ecosystem, are known as
keystone species.
- Sea otters are now protected and their numbers increased in the latter half of the 20 th century but
now they are being predated by killer whales that may have less prey to hunt because of
overfishing.
[3] Pollution
See threats of terrestrial ecosystem
The reasons for the need to maintain biodiversity:

(A) Moral and ethical reasons
1- For many people, the loss of biodiversity is a simple moral or ethical issue: we share our planet
with a huge range of other organisms and we have no right to drive them to extinction.
2- Some people believe that humans have custody of the Earth and should therefore value and
protect the organisms that share the planet with us.
(B) Ecological reasons

1- In general, the higher the diversity of an ecosystem, the less likely it is to be unbalanced by
changes in conditions or threats such as pollution.
- All the organisms in an ecosystem interact in many different ways, and, as we have seen, if one
key species disappears, this can affect the whole community, e.g. maintains the balance of the
ecosystem and prevent disturbance of food chains / webs.
2- Ecosystems are of direct value to humans. Many of the drugs that we use originate from living
organisms.
- Antibiotics are isolated form fungi and bacteria; anti-cancer drugs have been isolated from plants.
3- To prevent loss of habitat of many species:
- by flash-and burn agriculture
- by over-harvesting for medical use and collection for fuel.
4- Suggest why tropical rain forests have high biodiversity of animal species:
-Rapid growth of plants (providing food and shelter)
-Large number of different species and types of plants (species richness)
-Wide variety of food for animals
-Provide habitats
(C) Aesthetic reasons

- There is an aesthetic argument for maintaining biodiversity:
1- Many people gain pleasure from studying or just appreciating the natural world, which continues
to provide much inspiration for artists, photographers, poets, writers and other creative people.
2- Wildlife is a source of income for many countries as ecotourism has increased I popularity. This
form of tourism provides employment and contributes to the economies of these nations.
(D) Social and commercial reasons

(1)- Our crop plants do not have as much genetic diversity as their wild relatives, because
it has been lost by selective breeding for uniform, high-yielding crops.
- The wild relatives of maize, they can provide the genetic resources we might need to widen the
genetic diversity of cultivated maize if it is affected by disease or by other catastrophes.
- Many of these wild relatives are threatened by:

climate change habitat destruction perhaps the spread of genetically modified crops
a) - A species of rice which grows wild is not suitable for cultivation as a crop plant because of its
low yield and poor taste, but it is resistant to a large number of different strains of the disease of rice
known as bacterial blight.
- It has been successfully interbred with cultivated other species of rice, to give varieties of rice with
resistance to the disease
b) Another plant example is the potato . There are about 150 species of potato growing in the
Andes, but outside that region the world's crop come from a single species.
- This means that the crop is vulnerable to diseases, such as potato blight.
- The Andean species was used as a source of alleles for resistance.
- These alleles have been introduced into the crop species both by interbreeding and by gene
technology.
- Obviously it is important to conserve all the Andean potato species.
(2)- The contribution of microorganisms which are the source of many useful products,
not just antibiotics.
- E.g. the heat-stable enzyme Taq polymerase was discovered in a thermophilic bacterium, from a
hot spring.
- This enzyme is mass produced by genetically modified bacteria for use in the polymerase chain
reaction which is used by forensic and other scientists to increase quantities of DNA for analysis
(E) Other services

1- Forests and peat bogs absorb carbon dioxide and may help to reduce the effect of increases in
carbon dioxide in the atmosphere.
2- Organic waste material added to waters is broken down by microorganisms.
3- The transpiration of plants contributes to the water cycle providing us with drinking and irrigation
water.
4- Termites and ants along with many species of fungi and bacteria recycle elements, such as
carbon, nitrogen, sulfur and phosphorus.
5- Without this recycling, the supply of nitrates sulfates and phosphates for plants would become
limiting. Plant growth would slow and there would be less food available for organisms in other
trophic levels.

Methods of protecting endangered species
(A) National Parks (habitat conservation)
- They are areas where wildlife and the environment have protection, and where the activities of
humans are limited.
- For example, conservation areas may be set up where there are strict limits on building,
grazing farm animals, hunting or other activities that might adversely affect animals and
plants that live there.
- Even though species and habitats are protected, the threats remain so great that some species
have to be removed from their natural environment and placed somewhere safer.
- The standard of management of parks and reserves varies throughout the world. Some
countries have the resources and the national will to provide excellent protection and careful
management, others do not.
e.g. [1] the Galapagos Islands as a national park.

- Since its establishment over 50 years ago, the park authorities have done much active
conservation.
- They have restricted access to the uninhabited islands and limited access to other areas which are
sensitive to human interference.
- National parks are set up to conserve rare / endangered species and maintain important habitats.
Often, legislation is passed to ensure that such areas are protected under the law.
- The ways in which National Parks protect their resident species include:
1- Wardens, rangers and volunteers from the local people can be used to patrol the parks.
2- Access by humans can be restricted often footpaths are created and maintained to avoid
interference with wild life.
3- Agriculture activities can be strictly controlled traditional farming methods can be encouraged.
4- Industrial activities and mining can be limited and controlled.
5- The building of roads, dwellings and other developments can be strictly controlled.
6- Maintaining the parks via tourism money.
7- Employing some of the local people as wardens or rangers, besides allowing them to use some
areas of the park for herding their animals or growing crops to make them feel that the park is
"theirs".
8- Visitor centres can be established to educate the general public in the importance conservation
within the park.
9- Wild life can be protected directly, e.g. 24 hours surveillance of nets and breeding sites.
10- Alien animal species, such as rats and goats, are being removed and invasive plants, such as
elephant grass, dug up and destroyed.
11-There are captive breeding and reintroduction programmes.
e.g. [2] Marine Parks

- They have been set up in many places to conserve fragile ecosystems and areas at risk of
overfishing, dredging and pollution.
- The establishment of marine parks and reserves has increased biodiversity and also led to an
increase in fish catches.
- Some conservation areas are designated by international bodies.
- Wetland habitats, such as estuaries, salt marshes, blanket bogs, ponds and mangrove forests, are
ecosystems with high biodiversity.
-Ramsar sites are wetlands considered to be important for the conservation of wildlife. Under the
terms of the conservation, a designated site must be "used wisely". This gives protection against
such threats as building development and extraction of minerals.

(B) Zoos
- One way of protecting endangered species of animals is to capture some from the wild and place
them in captivity.
- In this way, it is possible to make sure that they are well fed, protected from predators and disease
and isolated from other potential problems which might be encountered in their habitat.
- Zoos also have an important role in researches, especially in trying to gain a better understanding
of breeding habits, habitat requirements and ways to increase genetic diversity.
-If such animals are simply placed in zoos, the zoo is really acting as an "ark" and little is actually
being achieved in terms of maintaining or increasing populations in the wild.
- If the animals will breed in captivity, then it is possible to maintain or even increase numbers.
- If such captive-bred individuals can be returned to their natural habitat, then it might be possible to
increase numbers in the wild, thereby preventing the endangered from becoming extinct.
-Arguments against using the zoo to protect endangered species: freedom, inbreeding depression,
difficulty in re-introduction program
Problems which reduce the success rate of releasing captive individuals into the
wild
(Re-introducing programmes) include:
1- Habitat destruction (usually as a result of man's activities) might mean that there is very little
suitable habitat available
in which to release the animals.
2- Having been in captivity, animals might not find it easy to move around in their natural habitat.
3- It may not be easy for them to find food especially if they have been used to being fed in
captivity.
4- They may not be able to communicate with other members of their species in the wild and may
not integrate into social groups or to avoid predators
5- This may be susceptible to diseases in the wild.
6- A problem with breeding animals from small populations is inbreeding. Genetic diversity among
some species is very low because they nearly became extinct and only a few survived.
Captive breeding has a number of advantages:

1- It is possible to monitor the health of the mother and the development of foetus during the
pregnancy;.
2- Sperm and eggs can be obtained from the captive individuals;
3- These can be stored in a frozen form;
4- It allows the possibility of artificial insemination;
5- Also in vitro fertilization;
6- Fertilized embryo may be implanted in surrogate mothers (which might even be a different
species). It is sometimes possible to split early embryos, thereby cloning them and increasing their
numbers.
7- There is the possibility of international co-operation and the transfer of breeding individuals
between different zoos;
8- It allows the keeping of breeding records and the genetic relatedness of captive individuals.
9- Fewer animals are caught for zoos;
10- Anti-natal or post-natal care;
11- Reintroduction in wild;
12- Increase in number;

13- Researches are easier with them.
Reasons why animals do not always breed successfully when in captivity:

1- They are no longer living in their natural habitat;
2- The conditions experienced in captivity can cause stress and behavioral changes;
3- The stress can disrupt normal reproductive cycles and breeding behavior;
4- They often have little choice of mate and may reject the chosen mate;
5- Only one sex;
6- No interest in mates;
7- Stress leads to hormonal disturbance;
8- Need some seasonal or environmental change to start mating;
9- Cannot get food and cannot interact with others, and easy to get pathogens;
10- Inbreeding may occur.
(C) Assisted Reproduction

1- Sperm Banks
- Assisted reproduction is a solution to the problem of inbreeding.
- Zoos used to transport large mammals between them as part of their captive breeding
programmes.
- Movement of large mammals is difficult and expensive and breeding did not always happen.
- A much cheaper option is to collect semen and keep it frozen in a sperm bank.
- Samples are collected from males, checked for sperm activity and then diluted with a medium
containing a buffer solution and albumen.
- Small volumes of semen are put into thin tubes known as straws, which are stored in liquid
nitrogen at - 196C.
2- Artificial Insemination (AI)

- Different methods of assisted reproduction solve the problem of males and females who do not
show any courtship behavior and will not mate.
- In artificial insemination (AI), a straw is placed into warm water so that sperm become active
and then put into a catheter, which is inserted into the vagina, through the cervix and into the
uterus.
- This may happen when the female is naturally "on heat", but also may follow hormone treatment
so she ovulates at the time of AI.
3- Hormone Treatment and Embryo Transfer

- The hormone treatment can stimulate the female to "super-ovulate" to produce a large number of
follicles.
- Following AI, the resulting embryos may be "flushed out" of the uterus and transferred to other
females that have had hormonal treatment to prepare them for pregnancy.
- These females need not be of the same species they could be a related, but not endangered
species.
- This process of embryo transfer protects the endangered animal from the risks of pregnancy and
means that she can be a source of many offspring.
4- Surrogacy
- Females that receive embryos like this are surrogate mothers.

5- In Vitro Fertilisation (IVF)
- In order to carry out in vitro fertilisation (IVF), oocytes are collected by inserting a needle into the
ovaries and withdrawing some mature follicles.
- The oocytes are kept in a culture medium for a short time and then mixed with semen.
- The resulting zygotes divide to form embryos, which are cultured for several days and then placed
into the mother or into several females of the same or different species.
6- Frozen Zoo
- Eggs (oocytes) and embryos can also be stored in much the same way as sperm.
- Eggs are more difficult to freeze as they are more likely to be damaged by the freezing or thawing
processes.
- Eggs are large cells with lots of water which tends to form ice crystals that damage internal
membranes.
- Eggs are fertilized in vitro and then frozen until such time as a surrogate mother becomes
available.
- A "frozen zoo", holds genetic resources in the form of sperm, eggs and embryos from
many endangered and vulnerable species.
- Frozen zoos can hold much more genetic diversity than a normal zoo and the material can be kept
for very long periods of time.
(D) Botanic Gardens

- Botanic gardens are similar to zoos, but for plants rather than animals.
- Like zoos, they can be safe areas for threatened plant species, and are involved in breeding
programmes, reintroduction programmes, education and research.
- Endangered species of plants can be grown in botanic gardens.
- Clearly, it is possible to create ideal growing conditions either outdoors or in glasshouses, when it
is possible to control very carefully the growing conditions. This applies to the availability of light
nutrients, water and the atmospheric conditions.
- Within such botanic gardens, it is also possible to propagate endangered species either by growing
from a seed or by some means of vegetative propagation, such as cuttings where you take small
samples of the cell and grow them on agar in sterile conditions. The cells divide by mitosis to give a
mass of cells that can be cloned by subdividing them.
- When the cells are transferred to a medium containing an appropriate mixture of plant hormones,
they grow stems and roots and can then be transferred to grow in soil.
- These techniques of tissue culture and cloning are used to produce large numbers of plants from
a few original specimens.
- The roles of botanic gardens are to:

1- Protect endangered plant species; the world's botanic gardens already cultivate around one-third
of the world's known plant species, many of which are increasingly threatened in the wild by
environmental degradation and climate change.
2- Research methods of reproduction and growth so that species cultivated in botanic gardens can
be grown in appropriate conditions and be propagated.
3- Research conversation methods so plant can be introduced to new habitats if their original habitat
has been destroyed.

4- Reintroduce species to habitats where they have become very rare or extinct. It often takes a long
time to reintroduce a plant species and ensure its survival. This is especially true with slow-growing
plants.
5- Educate the public in the many roles of plants in ecosystems and their economic value.
(E) Seed Banks

- Many seeds will live for a very long time in dry conditions, but others need more specialised
storage environments. A few of the seeds are germinated every so often so that fresh seeds can be
collected and stored.
- Many plants produce seeds which are long-lived and large numbers can be stored in a relatively
small space.
- Such a collection of seeds is referred to as a seed bank.
- The life span of such seeds can be extended if they are kept in carefully controlled conditions
especially in an atmosphere of low oxygen levels, moisture and temperature.
- A seed bank built into the permafrost (permanently frozen ground) in Norway, aims to
preserve seed from the entire world's food crops.
- It also contains seeds of endangered plants from the entire world, and from all sites to maintain
total gene pool for species.
- Given that the seeds will contain all the genetic material of any given species, it also means the
gene the gene pool of that species is being maintained.
- Clearly, if the seeds of the endangered species are stored in this way, such seeds can be
germinated at any time and plants can be grown in botanic gardens or restored to the wild.
- Plants in natural habitat must survive grazing, rainfall, competition for food supply (sunlight).
However, in seed banks they only need to survive low temperature and low humidity and stay
dormant for long time.
Why seed bank is important

1- Prevent extinction;
2- Maintain genetic diversity;
3- Storage of alleles;
4- For use in future;
5- For surviving any change in environment, or in genetic engineering or artificial selection.
Problems with seed bank:
(1)- Some species produce seeds which have a limited longevitykeeping their seeds in seed banks
is not possible. Such plants would need to be maintained in botanic gardens, or every 4-5
years,grow seeds into plant and collect new seeds.
- Most seeds are easy to store, but some plants have seeds that cannot be dried of frozen.
- These "recalcitrant seeds" as they are called, include seeds of economically important tropical
species, such as rubber, coconut palm, coffee and cocoa.
- The only ways to keep the genetic diversity of these species are to collect seeds and grow
successive generations of plants or to keep them as tissue culture.
- Coconut palms are particularly difficult to bank. The seed (the coconut) is very large, and the
embryo is too large to freeze successfully. Collectors remove the embryo from the seeds, culture
them in sterile tubes and eventually plant them.
(2)- Many plants produce seeds, known as orthodox seeds, that remain viable for at least 15 years
if they are carefully dehydrated until they contain only about 5% water, and then stored at around
-15 to -20C.

- With this small water content, there is little danger that cells in the seed will be damaged by ice
crystals during freezing and thawing.
(F) Controlling alien species

- Alien or invasive species are those that have moved from one ecosystem to another where they
were previously unknown.
Causes:
1- People have been responsible for the movement of species about the globe by trading animals
and plants or unwittingly carrying them on ships
2-some species have been introduced as biological control agents to control pests
3-other alien species are escapees or animals introduced for sport
4-pet owners found that they could not look after them anymore and just let them go into the wild
5-some species escaped from aquaria and spread through seas or oceans eating so many local
species and coral reefs
Harmful Effects:
1- it became a predator of other animals;
2- It has become a pest as it breeds rapidly and has spread across the country. Since it had few
predators, mainly because it produces a powerful toxin that kills most animals that eat it;
3- It probably competes with some other species for food;
4- More loss of biodiversity than any other factor;
5- This makes it difficult to conserve endangered species in the national park;
6- May introduce diseases;
7- Some invasive plants grow so successfully that they cover huge areas of land or water. The water
hyacinth is a floating aquatic plant that spreads rapidly when introduced to new habitats. It blocks
sunlight from reaching native aquatic plants and reduces the oxygen concentration of the water, so
killing fish.
8- Water hyacinth also provides a habitat for mosquito larvae so its control is important for the sake
of human health too.
9- Japanese knotweed, Fallopia japonica, has a very vigorous root system and its growth is so strong
that it can force its way through concrete and damage buildings, roads and walls.
10- Also outcompetes native species simply by reducing the space where they can grow.
Roles of International Conservation Organisations

[1]- CITES
- In 1973, 145 countries signed an agreement to control the trade in endangered species
and any products from them, such as furs, skins and ivory.
- This agreement is called the Convention on International Trade in Endangered
Species of Wild Flora and Fauna, CITES for short.
- CITES considers the evidence presented to it about endangered and vulnerable species
and assigns them to one of three Appendices as shown in the table below.
- The species listed in the CITES appendices are reviewed by expert committees and the list
is growing.
- However, there is concern that a CITES listing does not always benefit a species.
- If trade in a species or its products becomes illegal, then the price that can be obtained for
those products rises, and this is likely to make it worthwhile for people to break the law.

- Particular problems arise when it is announced in advance that a species will go on the list;
in the months between the announcements of the new law, trade in that species tends to
increase.
[2]- World Wide Fund for Nature

- The World Wide Fund for Nature (WWF) is one of the best known campaigning groups for
wildlife.
- Established on 1961, WWF is the largest international non-government organization (NGO)
specializing in conservation.
- Its mission statement is "to stop the degradation of the planet's natural environment and
to build a future in which humans live in harmony with nature",
- To this end, it funds conservation projects, puplicises environmental issues and campaigns
to save ecosystems from degradation and species from extinction.
- One of its recent campaigns is to stop prospecting for oil in Africa's oldest national park.
Problems of successful conservation

- Sometimes, conservation practices have been too successful and the organism saved from
extinction has increased in numbers beyond the capacity of the ecosystem to sustain such
numbers.
How to overcome this problem?
1- Culling is often used to reduce numbers although it is a practice that arouses much emotion,
especially when it is used to control the numbers of elephants, to limit the growth of the population.
- Transferring animals to places where there are small populations is one option, but that is not easy
over large distances and is expensive.
2-birth control
a) Sedating male wild mammals and cutting their sperm ducts (vasectomy).

b) Chemical contraceptives are available, but unlike the contraceptives that women may use
these are not steroid hormones. Instead a vaccine is used which targets the region surrounding the
layer of glycoproteins around the egg
- When the vaccine is injected into a female animal, it stimulates an immune response that produces
antibodies against these glycoproteins.
- These antibodies attach to the glycoproteins around the female's own eggs, so blocking sperm from
fertilizing the egg.
Restoring degraded habitats

- Conservation involves restoring areas that have been degraded by human activity or by natural
catastrophes, such as flood, fire, hurricane, typhoon and earthquake.
Methods:
1- This can be done on a small scale when a farmer decide to plant trees on land that is no longer
needed for food production or has become degraded by overuse.
2- After centuries of deforestation, soil erosion and severe land degradation in Haiti, efforts are now
being made to restore some of the forest that used to cover the country.
- About 70% of the country's land is not suitable for agriculture anymore and there is a severe
shortage of firewood.
- Many NGOs are working with community groups in reforestation project.
e.g. Mangrove forests are found throughout the tropics.

- This is an extremely rich ecosystem that that provides valuable protection to coastlines from
storms.
- Many mangrove forests have been cut down to make way for coastal developments.
- This area with high diversity is at risk of rising sea levels and replanting mangrove is thought
likely to offer some protection against the effects of this.
Importance of mangrove ecosystem:

a- Mangrove forests provide important "ecosystem services".
b- They reduce coastal erosion by reducing the effects of strong waves during storms and act as a
barrier to rising sea level by trapping sediment.
c- They are also important nurseries for young fish.
3- Set areas to educating people in plant biodiversity and the need for conservation.
- Visitors learn about the major roles that plants play in our economy and the extent to which we
depend on them.
Assessing species diversity
Collecting organisms and making lists:
- Imagine you are in an ecosystem like that in figure below.

- The most obvious species are the large plants and maybe some of the larger animals, particularly
bird species.
- The first task when assessing species diversity is to identify and catalogue the types of organisms
and build a species list.
- Biologists use identification keys to name the organisms that they find. The most common of this is
a dichotomous key. This requires good skills of observation.
- At first do a timed search throughout the area you are studying to see how many species you can
collect and then identify.
- If you cannot identify particular species, take photographs of them and name them as a species A,
species B, and so on.
- Some animals will be hard to find and collect especially small ones such as tiny beetles.
- A pooter is a simple piece of apparatus that is used to collect these animals. Breathing air into the
mouth suck up small anima into a plastic container. They can then be removed and studied and
identified using a hand lenses and then return to their habitat.
- In an area of grassland or woodland, you might choose to concentrate on just one or two groups,
such as flowering plants and insects.
- On a rocky shore, a study may involve the most obvious organisms such as seaweeds and
molluscs.
There are now two questions to ask about:

-How are the different species spread throughout the ecosystem?
-How many individuals of each species are there?
The answers to these two questions are to find out:
1- Distribution 2- Abundance
Sampling
- To find out which species are present in an ecosystem, and the size of the population of each of
them; you must:
1- Identify and count every single organism that lives there.
- We can sometimes do this if the area is very small or the species are very large.

2- Or we take samples from the area interested in, and use these to make an estimate of the total
numbers in the area.
Types of sampling:
1- Random 2- Systematic
(A) Random sampling

- If areas looks reasonably uniform, or if there is no clear pattern to the way species are distributed,
then it is best to use random sampling.
Methods:
(1) Random sampling using quadrats

- Quadrat is a square frame that marks off an area of ground, or water, where you can identify the
different species present and / or take a measurement of their abundance.
- decide on a suitable size for the quadrat and how many samples you will take.
- Samples must be taken randomly to avoid any bias. For example, you might choose to take all of
your samples from the place with fewest species simply because it is the easiest to do. This would
not be representative of the whole area you are surveying.
- The usual way to ensure that a sample is random is to mark out an area with measuring tapes and
use a random number generator, such as an app on a mobile phone.
- The random numbers give you the coordinates of the sampling points in relation to the two tapes
you have used to mark out the area.
(2) Estimating numbers of mobile animals
- Quadrats are obviously of no use for finding or counting mobile animals, so different methods have
to be used for these.
- Small mammals, such as mice and voles, can be caught in traps that are filled with hay for bedding
and suitable food as bait.

- Insects and other invertebrates, such as spiders, can be captured by sweep netting.
- Pond nets are used for sampling aquatic organisms.
- The techniques for this vary according to the size of the body of water, and whether it is still or
moving.
- Single birds can be counted quite easily, although his does become more difficult in dense forest.
- Flocks of birds are much more difficult to count, although it can be done by counting a group of ten
birds and estimating how many such groups there are.
- A good method of estimating the population size of mobile organisms, if used with care, is the
mark release capture technique.
- First, as many individuals as possible are caught.
- Each individual is marked, in a way that will not affect its future chance of survival.
- The marked individuals are counted, returned to their habitat and left to mix randomly with the rest
of the population.
- When enough time has elapsed for the mixing to take place, another large sample is captured.
- The number of marked and unmarked individuals is counted.
- The proportion of marked to unmarked individuals is then used to calculate an estimate of the total
number in the population.
Formula:
Estimated number of animals in a population= No. of caught & marked 1st time X No.
caught 2nd sample
No. in the 2nd sample that had
been marked
(B) Systematic Sampling

When to use systematic sampling?

- You might want to investigate how species are distributed in an area where the physical conditions,
such as altitude, soil moisture content, soil type, soil pH, exposure or light intensity change.
- For example, suppose you want to investigate the change at the edge of a field where it becomes
very marshy.
- In this case, you should randomly select a starting point in the field and lay out a measuring tape in
a straight line to the marshy area.
- Then you sample the organisms that are present along the line, which is called a transect.
The simplest way to do this is to record the identity of the organisms that touch the line at set
distance for example, every two meters.
- This line transect will give qualitative data that can be presented as in figure next page.
- You can also use the belt transect technique by placing quadrat at regular intervals along the line
and recording the abundance of each species within the quadrat.
What is the use of the results obtained from using systematic sampling?
- Data from a line transect can be shown as a drawing.
- Data from a belt transect can be plotted as a set of bar charts or a kite diagram.
What is the use of the results obtained from using quadrats?

1- Calculate specie frequency 2- Species density 3- Percentage cover
Species frequency:
-it is a measure of the chance of a particular species being found within any one quadrat.
- You simply record whether the species was present in each quadrat that you analyse.
- For example, if you placed your quadrat 50 times, and found daisy plants in 22 of your samples,
then the species frequency for daisies is:
22 x 100 =44%
50
Species density:
-it is a measure of how many individuals there are per unit area for example, per square meter.
- The number of individuals that you have counted is divided by the total area of all your quadrats.
- It is not always possible to count individual plants and animals because of the way that they grow.
- For example, many animals and plants grow over surfaces forming a covering and it is almost
impossible to count individuals.
Percentage cover:
- How do you decide how many grass plants there are in a quadrat that you have placed on a lawn?
you can estimate the percentage cover of the species within your quadrat.
- To help with this, you can use a 100cm x 100cm quadrat with wires running across it at 10cm
intervals in each direction, dividing the quadrat into 100 smaller squares.
- You then decide approximately what percentage of the area inside the quadrat is occupied by each
species.
- These percentages may not add up to 100%.
- For example, there might be bare ground in the quadrat, so the numbers will come to less than
100%.
- Or there may be plants overlying one another, in which case the numbers may add up to more than
100%.
- An alternative to estimating percentage cover of each species is to use an abundance scale, such
as the Braun-Blanquet scale for number and plant cover.

Correlation
- While doing random sampling or carrying out a belt transect (systematic sampling), you may
observe that two plant species always seem to occur together. Is there in fact an association
between them?
- Or you might want to know if there is any relationship between the distribution and abundance of a
species and an abiotic factor, such as exposure to light, temperature, soil water content or salinity
(saltiness).
- To decide if there is an association:

1- You can plot scatter graphs and make a judgment by eye.
2-or you can calculate a correlation coefficient (r) to assess the strength of any correlation that
you suspect to exist.
- The strongest correlation you can have is when all the points lie on a straight line: there is a linear
correlation. This is a correlation coefficient of 1.
- If as variable A increases so does variable B, the relationship is a positive correlation.
- If as variable A increases, variable B decreases then the relationship is a negative correlation.
- A correlation coefficient of 0 means there is no correlation at all.
- You can calculate a correlation coefficient to determine whether there is indeed a linear relationship
and also to find out the strength of that relationship. The strength means how close the points are to
the straight line.
a- Pearson's correlation coefficient can only be used where you can see that there might be a
linear correlation and when you have collected quantitative data as measurements (for
example, length, height, depth, light intensity, mass) or counts (for example, number of plant
species in quadrants).The data must be distributed normally
b- Sometimes you may not have collected quantitative data, but used an abundance scale, or you
may not be sure if your quantitative data is normally distributed. It might also be possible
that a graph of your results shows that the data is correlated, but not in a linear fashion.
- If so, then you can calculate Spearman's rank correlation coefficient, which involves ranking
the data recorded for each variable and assessing the difference between the ranks.
- You should read pages in chapter P2 which show you how to calculate these correlation
coefficients.

[1] Simpson's Index of Diversity
- When you have collected information about the abundance of the species in the area you are
studying, you can use your results to calculate a value for the species diversity in the area.
- We can do this using Simpson's Index of Diversity, D. One formula for this is:
-Where n is the total number of organisms of a particular species, and N is the total number of
organisms of all species.
- Values of D range from 0 to 1, a value near 0 represents low species diversity. A value near 1
represents very high species diversity.
- One advantage of this method is you do not need to identify all, or even any, of the organisms
present to the level of specie.
- So long as you can recognize that they are different species, you do not need to find their scientific
names.
- But beware: some species have many phenotypic forms e.g a species of snails could be banded or
not banded
- The higher the number we get for D, the greater the diversity.
- You can probably see that the diversity depends on the number of different species there
are(richness), and also the abundance of each of those species.
- A community with 10 species, but where only one species is present in large numbers and the
other 9 are very rare, is less diverse than one with the same number of species but where several
different species have a similar abundance.
- Comparison using this diversity index is done if the communities are similar. For example, it should
not be used to compare the diversity fish in a lake with the diversity of moths in the forest.

[2] Pearson's linear correlation
- In many investigations, the data collected are for two continuous variables and the data within
each variable show normal distribution.
- When this is the case, Pearson's correlation coefficient can be used.
-This also calculates numbers between +1 and -1 and the result is interpreted in the same way.
- The first step is to check whether the relationship between the two continuous variables appears to
be linear by drawing a scatter graph.
- The correlation coefficient should not be calculated if the relationship is not linear.
- For correlation only purpose, it does not really matter on which axis the variables are plotted.
- The nearer the scatter of points is to a straight line, the higher the strength of association between
the variables.
e.g.- As trees grow older, they tend to get cracks in their bark.
- A student measured the width of cracks on many pine trees in a plantation and found that they
varied considerably.
- The data she collected showed a normal distribution.
- She noticed that the larger, and presumably older, trees tended to have wider cracks in their bark
than the smaller trees.
- She wanted to see if there was a correlation between the size of the trees and the size of these
cracks.
- She chose to measure the circumference of each tree as a measure of their overall size.
- She measured the width of the cracks in the bark.
- This means that she collected continuous data for each of the two variables tree circumferences
and crack width.
- She investigated this by selecting twelve trees at a random and measuring the circumference of
each trunk and the width of three cracks on the bark at head height.
- Her results are in the Table.
- The student plotted these results on a scatter graph and found that they look as if there might be a
linear correlation between them.
- She then used the following formula to calculate Pearson's correlation coefficient, r .
- The student calculated the correlation coefficient as r = 0.79

[3] Spearman's rank correlation
- As ecologist was studying the composition of vegetation on moorland following a reclamation
scheme.
- Two species common heather, Calluna vulgaris, and bilberry, Vaccinium myrtillus appeared to be
growing together.
- He assessed the abundance of these two species by recording the percentage cover in 11 quadrats
as shown in Table.
- To find out if there is a relationship between the percentage cover of these two species, the first
task is to make a null hypothesis that there is no correlation between the percentage cover of
the two species.
- The equation to calculate the Spearman rank correlation, rs is:
-Where n is the number of pairs of items in the sample and D is the difference between each pair of
ranked measurements and is the "sum of"
- The next step is to draw a scatter graph to see if it looks as if here is a correlation between the
abundance of the two species.
- You can now follow the steps shown in chapter P2 to calculate the value for rs.
- The ecologist calculated the value of rs to be 0.930.
- A correlation coefficient of +0.930 is very close to +1, so we can conclude that there is a positive
correlation between the two species and that the strength of the association is very high.
- The ecologist was also able to reject the null hypothesis that there is a correlation between the
abundance of C. vulgaris and V. myrtillus on this reclaimed moorland.

GENE TECHNOLOGY
Gene technology:
- A technology in which we can use knowledge and understanding of genes to change the
way in which cells behave.
- We can change the DNA in a cell, and so change the proteins which that cell synthesises.
Genetically modified organism (GM):

- An organism whose DNA is altered by gene technology.
Genetic Engineering:
-The transfer of a gene from one organism (the donor) to another (the recipient) so that he
gene is expressed in its new host. The DNA that has been altered by this process and which
now contains lengths of nucleotides from two different organisms is called recombinant
DNA (rDNA). The organism which now expresses the new gene or genes is known as a
transgenic organism or genetically modified organism (GMO).
Recombinant DNA:
- is DNA made by joining pieces from two or more different sources.
Uses of genetic engineering:

- The structure of DNA, and the way in which it codes for protein synthesis, this knowledge
has developed so much that we can:
1- Change the DNA in a cell, and thereby change the proteins which that cell synthesises.
2- We can sequence the nucleotides in DNA and compare nucleotide sequences in different
organism.
3- It is possible to carry out genetic tests to see if people are carriers of genetic diseases
4- Use gene therapy to treat those who have these diseases.
An overview of gene transfer:

- There are many different ways in which a GMO may be produced, but these steps are
essential.
1- The gene that is required is identified. It may be cut from a chromosome, made from
mRNA by reverse transcription or synthesised from nucleotides.
2- Multiple copies of the gene are made using the technique known as the polymerase chain
reaction (PCR).
3- The gene is inserted into a vector which delivers the gene to the cells of the organism.
Examples of vectors are plasmids, viruses and liposomes.
4- The vector takes the gene into the cells.
5- The cells that have the new the new gene are identified and cloned.

Tools for the gene technologist
[1] Restriction enzymes

- Restriction endonucleases are a class of enzymes from bacteria which recognise and break
down the DNA of invading viruses known as bacteriophages (phages for short).
- Bacteria make enzymes that cut phage DNA into smaller pieces.
- These enzymes cut the sugar-phosphate backbone of DNA at specific place within the molecule.
- This is why they are known as endonucleases ("endo" means within).
- Their role in bacteria is to restrict a viral infection, hence the name restriction endonucleases or
restriction enzyme.
- Each restriction enzyme binds to a specific target site on DNA and cuts at that site.
- Bacterial DNA is protected from such an attack either by chemical markers or by not having the
target sites.
- These target sites, or restriction sites, are specific sequences of bases.
- You will notice that this sequence reads the same in both directions: it is a palindrome. Most
restriction sites are palindromic.
- Restriction enzymes either cut straight across the sugar-phosphate backbone to give blunt ends
or they cut in a staggered fashion to give sticky ends. Sticky ends are short lengths of unpaired
bases. They are known as sticky ends because they can easily form hydrogen bonds with
complementary sequences.
- Restriction enzymes are named by an abbreviation which indicates their origin (see Table).Roman
numbers are added to distinguish different enzymes from the same source. Example, EcoRI comes
from Escherichia coli (strain RY13), and was the first to be identified from this source.
Uses Restriction enzymes

1- Gel electrophoresis
2- PCR

[2] Synthesis of artificial DNA or cDNA:
- Now that many proteins have been sequenced, it is possible to use the genetic code to synthesise
DNA artificially from nucleotides rather than cutting it out of chromosomal DNA or making it by
reverse transcription.
- Genes, and even complete genomes, can be made directly from DNA nucleotides without the need
for template DNA.
Steps:
1- Choosing codons on mRNA for the amino acid sequence that they need.
2- The sequence of nucleotides is held in a computer that directs the synthesis of short fragments of
DNA.
3- These fragments are then joined together to make a longer sequence of nucleotide.
4- Nucleotides can be inserted into plasmids for use in genetic engineering. This method is used to
generate novel genes that are used, for example, in the synthesis of vaccines and they have even
been used to produce the genomes of bacteria consisting of a million base pairs.
Identifying the human insulin gene by isolating mRNA using reverse

transcriptase
- Insulin-producing cells from human pancreas tissue synthesise large amounts of the protein,
insulin, for which they make large amounts of mRNA.
- This mRNA has a genetic code complementary to the key portions (exons) of the human insulin
gene.
- Some of this mRNA was isolated from such cells.
- The mRNA was incubated with a mixture of free DNA nucleotides and reverse transcriptase (an
enzyme from Retroviruses that use RNA as their genetic material).
- This produced a single strand of DNA known as complementary DNA or cDNA, which is a copy of
the informational strand of the human insulin gene.
- Isolating mRNA from B cell is easier than isolating DNA of insulin because it has many genes, but
mRNA in B cell is only for insulin, and in large numbers.
[3] Vectors
Inserting a gene into a plasmid vector
- In order to get a new gene into a recipient cell, a vector often has to be used.
- One type of vector is a plasmid. These are small, circular pieces of double-stranded DNA.
- Plasmids occur naturally in bacteria and often contain genes for antibiotic resistance. They can be
exchanged between bacteria even between different species of bacteria.
- If a genetic engineer inserts a piece of DNA into a plasmid, then the plasmid can be used to take
the DNA into a bacterial cell.
- To get the plasmids, the bacteria containing them are treated with enzymes to break down their
cell walls.
- The "naked" bacteria are then spun at high speed in a centrifuge, so that the relatively large
bacterial chromosomes are separated from the much smaller plasmids.
- The circular DNA of the plasmid is cut open using a restriction enzyme. The same enzyme as the
one used to cut out the gene should be used, so that the sticky ends are complementary.
- The opened plasmids and the lengths of DNA are mixed together.
- Some of the plasmid sticky ends pair up with the sticky ends of the new gene.
- The enzyme DNA ligase is used to link together the sugar-phosphate backbones of the DNA
molecule and the plasmid, producing a closed circle of double-stranded DNA containing the new
gene. This is now recombinant DNA.
- Plasmids can also be made artificially. For example, the pUC group of plasmids have:
1- A low molecular mass, so they are readily taken up by bacteria;
2- An origin of replication so they can be copied;
3- Several single target sites for different restriction enzymes in a short length of DNA
called a polykiller;

4- One or more marker genes, allowing identification of cells that have taken up the
plasmid.
Other types of vectors:

- Viruses can also be used as vectors.
- Liposomes, which are tiny spheres of lipid containing the DNA.
[4] Getting the plasmids into bacteria

a- calcium ions treatment:
The bacteria are treated by putting them into a solution with a high concentration of calcium ions,
then cooled and given a heat shock to increase the chances of plasmids passing through the cell
surface membrane.
b-Electroporation:
-Subjecting bacteria to electric current causing short-lived holes in thin cell walls and cell
membranes through which the modified plasmid enters.
- A small proportion of the bacteria, perhaps 1% takes up plasmids with gene, and are said to be
transformed.

- The rest either take up plasmids that have closed without incorporating a gene or do not take up
any plasmids at all.
*Why bacteria are preferred in making recombinant DNA?
1- They have plasmids that can be extracted out and returned easily into the bacterial cells;
2- The gene introduced to the plasmid can be expressed in the properties or products of the
bacterial cell;
3- The rapid asexual reproduction in bacteria makes them ideal for quick production of large
quantities of genes or their products.
*Difficulties facing this process

1- Only some of the plasmids pick up and anneal with recombinant DNA.
2- Only few of the bacterial cells take the altered plasmids.
[5] Identifying bacteria with recombinant DNA

- It is important to identify which bacteria have been successfully transformed so that they can be
used to make the gene product. This is achieved by using markers
Marker:
-it is a gene which is deliberately transferred along with the required gene during the process of
genetic engineering.
-It is easily recognised and used to identify those cells to which the gene has been successfully
transferred.
METHOD (1)
*To sort out the bacteria which have taken up a plasmid that carries recombinant gene:
- This is used to be done by spreading the bacteria on agar plates each containing an antibiotic.
- So if, for example, the insulin gene had been inserted into the plasmid at a point in the gene for
tetracycline resistance in pBR322, then any bacteria which had taken up plasmids with the
recombinant DNA would not be able to grow on agar containing tetracycline.
* Concerns about using antibiotic resistance genes as markers:
1- One potential problem with using antibiotic markers in this way is that they are present on
plasmids, which are commonly transferred between bacteria of the same species and also of
different species. This means that if the genetically engineered bacteria come into contact with
pathogenic bacteria (e.g. pathogenic strains of E. coli or even pathogens that cause TB or cholera)
the plasmid with its antibiotic resistance genes could be transferred into the pathogen, giving it
instant resistance to the antibiotics involved.
2- If this did happen, it would then become much more difficult to control the spread of such bacteria
or treating some diseases by using these antibiotics.
METHOD (2)
- DNA polymerase in bacteria copies the plasmids; the bacteria then divide by binary fission so
that each daughter cell has several copies of the plasmid.
- The bacteria transcribe the new gene and may translate it to give the required gene product, such
as insulin.
METHOD (3)
1- One other way is the use of enzymes that produce fluorescent substances. These enzymes are
obtained from jellyfish, and they make a protein that fluoresces bright green in ultraviolet
light. The gene for the enzyme is inserted into the plasmids. So all that needs to be done is to
identify the bacteria that have taken up the plasmid is to shine ultraviolet light onto them. The ones
that glow green are the genetically modified ones.
2- Another Method, used for example in genetic manipulation of papaya, was to incorporate a
marker gene for a protein that fluoresces green under ultra-violet light, along with the

desired genes. The genes were added, as in now common in plants, using a micro-projectile to shoot
them into the plant cell nuclei.
3- Another approach in genetic manipulation of fungi is to insert alongside the desired gene, another
marker gene that produces a harmless product that is easily stained and is not normally produced by
the cells. An example of this is the gene for -glucuronidase (GUS) which produces a harmless
product that is easily stained blue.
* Examples of marker genes:
1-antibiotic resistance
2- Gene for - galactosidase; Blue colour from X-gal medium;
3- Gene for - glucuronidase (GUS);originated from bacteria E.coli , Produces product that easily
stains any colourless or non-fluorescent substances into fluorescent or coloured blue, used in plants
mainly
4- Gene for, from jellyfish GFP / green fluorescent protein; (not fluorescent / fluorescence, gene);
Fluorescence detected when present;
*Advantage of using fluorescent substances as markers:
-We use fluorescence to know which cells produce light, and these cells are the ones which fused
with plasmids, Can identify transformed cell.
-Avoid antibiotics.
-Easy to detect.
-Do not show side effects on GM organism.
-quicker to insert into cells and detect results
- produces a higher proportion of transformed organism
*Disadvantage of fluorescent marker gene (GFP)
1- May not fluoresce very brightly / may be difficult to detect;
Explanation
1- Only a few molecules of GFP produced;
2- Each enzyme molecule produces more fluorescent substance / idea of enzymes can be re-used.
PROMOTER:
-It is a length of DNA (usually about 40 bases long) situated next to genes and which identify the
point at which transcription should begin (RNA polymerase must bind to the promoter before it can
begin transcription of DNA into mRNA).
*Why to insert a promoter alongside with the desired gene:

1- Promoter required ensuring expression of the introduced genes;
2- To cause manufacture of the protein coded by this gene;
3- Suitable promoter might not be present in the selected cells;
4- Suitable promoter might not be in the correct position relative to the introduced genes;
5- Suitable promoter to make only the protein required by the cell to be produced;
6- The promoter not only allows RNA polymerase to bind to DNA but also ensures that it recognises
which of the two DNA strands is the template strand. Within the sequence of nucleotides in the
promoter region is the transcription start point the first nucleotide of the gene to be transcribed. In
this way, the promoter can be said to control the expression of a gene
(A) - In Prokaryotes:
1- In the case of insulin, the first successful recombinant DNA involved using the promoter of an
existing non-essential gene for an enzyme involved in lactose metabolism ( galactosidase).
2- The human insulin gene was inserted into the existing gene. The promoter for this gene remained
intact.

3- There is also a lactose-sensitive regulatory sequence that is designed to turn on the natural
galactosidase in the presence of lactose
4- The promoter, regulator and the insulin gene, are together called an operon, in this case the lac-
operon.
5- The effect of all this is that when the genetically engineered E coli, containing the human insulin
gene in its lac-operon, was exposed to lactose, it transcribed a polypeptide that contained the first
part of the B galactosidase, followed by human insulin.
(B) - In Eukaryotes:
- In eukaryotes various proteins known as transcription factors are also required to bind to the
promoter region or to RNA polymerase before transcription can begin.
Gene Technology for Insulin Production:

- One form of diabetes mellitus is caused by the inability of the pancreas to produce insulin.
- People with disease need regular injections of insulin which, until recently was extracted from the
pancreas of pigs or cattle
- This extraction had many disadvantages compared to mass production of human insulin using
bacteria.
What are the advantages of using E-coli insulin than animal's insulin?
1-It is chemically identical to human insulin;
2- Works better than non-human insulin / more rapid response;
3- No / fewer, rejection problems / side effects / allergic reactions;
4- Ethical / moral / religious issues; it avoids any ethical issues that might arise from the use of pig
orb cattle insulin from, for example, religious objections to the use of pig insulin or objections from
vegetarians to the use of animal product;
5- Cheaper to produce in large volume / unlimited availability; (not cheap to produce)
6- Less risk of transmitting disease / infection;
7- Good for people who have developed intolerance / allergic reactions / immune responses to
animal insulin;
8- Because it is an exact fit in the human insulin receptors in human cell surface membranes, it
brings about a much more rapid response than pig or cow insulin;
9- Like natural human insulin, the duration of the response is much shorter than pig or cattle insulin.
Insulin Analogues
- Genetic engineers changed the nucleotide sequence of the insulin gene to give molecules with
different amino acid sequences
- These insulin analogues have different properties; for example, they can either act faster than
animal insulin (useful for taking immediately after meal) or more slowly over a period of between 8
and 24 hours to give a background blood concentration of insulin.
Many diabetics take both these forms of recombinant insulin at the same time.
Gene Technology for human factor VIII production to treat Haemophilia

1- A similar method, like that of producing insulin is used to produce human factor VIII (protein
used to stop bleeding and causes blood clotting, which is not produced in people suffering from
haemophilia, absence of this protein leads to excessive bleeding and may cause death especially in
females during menstruation).
2- The recombinant DNA is inserted into eukaryotic cell, e.g. transfer kidney or ovary cell of a
hamster, because such cells have Golgi body that is used to modify proteins since factor VIII is a
glycoprotein.
3- Using factor VIII from genetic engineering is better than by blood transfusion, because it reduces
rate of infection by diseases like HIV and reduces tissue rejection.
ELECTROPHORESIS:
- It is a technique that is used to separate different molecules.
- It is used in the analysis of proteins and DNA.
-This technique involves placing a mixture of molecules into wells cut into agarose gel and applying
an electric field.
Factors affecting the electrophoresis:
1- Net (overall) charge negatively charged molecules move towards the anode (+) and positively
charged molecules move towards the cathode (-); highly charged molecules move faster than those
with less overall charge;
2- Size of molecules and impedance of the gel smaller molecules move through the gel faster
than larger molecules;
3- Composition of the gel common gel are: polyacrylamide for proteins and agarose for DNA, the
size of the "pores" within the gel determines the speed with which proteins and fragments of DNA
move.
- It is used for genetic profiling (genetic fingerprinting) and for analysing proteins and nucleic
acids.
*Procedures:
[1] Electrophoresis of DNA (study MS)
1- A region of DNA that is known to vary between different people is chosen. These regions often
contain variable numbers of repeated DNA sequences and are known as variable number tandem
repeats, or VNTRs.
-DNA can be extracted from almost anything that has come from a person's body the root of a hair,
a tiny spot of blood or semen at a crime scene, or saliva where someone has drunk from a cup.
2- Usually, the quantity of DNA is increased by using the polymerase chain reaction, PCR for short,
which makes many copies of the DNA that has been found.
3- The DNA is then chopped into pieces using restriction enzymes that are known to cleave it close
to the VNTR regions. These enzymes cut the DNA at specific restriction sites, but these sites are
randomly distributed along the length of the DNA so the fragments are of varied lengths.
4- Now the DNA is ready for electrophoresis. This uses a tank containing a very pure form of agar
called agarose gel.
5- A direct current is passed continuously through the gel.
6- The DNA fragments are attracted to the anode (the positively charged electrode) and are slowly
pulled through the gel by this attractive force. DNA fragments are negatively charged due to
presence of phosphate groups in nucleotides. The smaller the fragments, the faster they move and
travel further in a given time. The distance moved in a given time will depend on the mass of the
molecule of fragment
7- When the current is turned off, the gel contains DNA fragments that have ended up in different
places.

8-The DNA is transparent and invisible, so the fragments must be treated to make them visible.
There are two key ways of doing this:
A-One is based on staining all of the DNA fragments, for example using ethidium bromide (toxic,
fluoresces in short wave UV radiation), methylene blue (fades quickly and stains gel as well as DNA)
and Nile blue A (does not stain gel and visible in ordinary light).
B-The other is based on using probe .The gene probe is a single stranded piece of DNA with a
base sequence complementary to the DNA that you wish to identify
-this is achieved by creating a gene probe that is able to do complementary binding:
- Either to a commonly repeated bit of DNA that will therefore be present on many of the fragments.
- Or to a base sequence that is specific to a particular gene or allele of a gene which will therefore be
present on no more than one of the fragments.
-. In order to make it possible to locate which fragment or fragments the gene probe has attached
itself to, the gene probe must be labelled. The most common forms of labelling are:
1- To make the probe radioactive and to detect it by its ability to expose the photographic film used
to make X-ray photographs.
2- To stain the probe with a fluorescent stain such as vital red, which will fluoresce with bright
visible light when placed in ultraviolet light, making the location of the probe and therefore of the
fragment or fragments visible.
Role of electrophoresis in Genetic Fingerprinting:

1- Genetic fingerprinting: is the analysis of DNA in order to identify the individual from which the
DNA was taken to establish the genetic relatedness of individuals.
2- This can be used to:

-Determine if a sample of semen, blood or other tissue found at a crime scene could have come
from the victim or
-Determine whether a particular person could be the child, mother, father of someone.
-It is now commonly used in forensic science (for example to identify someone from a blood sample)
and to determine whether individuals of endangered species in captivity have been bred or captured
from the wild.
3- Once the DNA fragments have been separated by gel electrophoresis they can be compared with
other samples of DNA, thereby allowing determination of the source of the DNA (as in forensic
investigations) or whether the samples are derived from related individuals (paternity testing).
The use of DNA fingerprinting to convict a suspect of a crime has proved not to be quite
straightforward as was originally thought because:
1-It depends on an assumption that there is virtually no possibility of two people producing identical
DNA for fingerprinting, but in small communities where there is a lot of intermarrying genetic
variation is much less than general population, and this must be taken into consideration.
2-The tiny amount of DNA taken from body fluid samples may be contaminated with tiny amounts
taken from somewhere else perhaps from the scientists performing the investigation.

[2] Electrophoresis of PROTEINS
- The charge on proteins is dependent on the ionisation of the R groups on the amino acid residues.
-amino acids have R groups that can be positively charged (- NH 3+) and some have R groups that can
be negatively charged
(-COO-). Whether these R groups are charged or not depends on the pH.
- When proteins are separated by electrophoresis, the procedure is carried out at a constant pH
using buffer solution.
- Usually proteins have a net negative charge.
- Gel electrophoresis has been used to separate the polypeptides produced by different alleles of
many genes.
- For example, allozymes are variant forms of enzymes produced by different alleles of the same
gene.
- There are also many variants of haemoglobin. Adult haemoglobin is composed of four
polypeptides: 2-globins and 2-globins.
- In sickle cell anaemia, a variant of -globin has an amino acid with a non-polar R group instead of
one with an R group that is charged.
- These two variants of the -globin can be separated by electrophoresis because they have different
net charges.
- This means that haemoglobin molecules in people who have sickle cell anaemia have slightly lower
negative charge than normal haemoglobin and so the molecules do not move as far through the gel
as molecules of normal haemoglobin.
- The test to find out whether someone carries the sickle cell allele makes use of this difference.

Polymerase chain reaction (PCR)
- It is a method for rapid production of a very large number of copies of a particular fragment of
DNA.
- First the DNA is denatured, usually by heating it. This separates the DNA molecule into two strands,
leaving bases exposed.
- The enzyme DNA polymerase is then used to build new strand of DNA against the exposed one.
- DNA polymerase cannot just begin doing this with no "guidance", so a primer is used to begin
the process.
- This is a short length of DNA, often about 20 base pairs long, that has a base sequence
complementary to the start of the part of the DNA strand that is to be copied.
- The primer attaches to the start of the DNA strand, and then the DNA polymerase continues to add
nucleotides all along the rest of the DNA strand.
- Once the DNA has been copied, the mixture is heated again, to separates the two strands in each
DNA molecule, leaving them available for copying again, the primers fix themselves to the start of
each strand of unpaired nucleotide, and DNA polymerase makes complementary copies of them.
- The three stages in each round of copying need different temperatures:

denaturing the double-stranded DNA molecules to make single-stranded ones requires a high
temperature around 95C.
attaching the primers to the ends of the single-stranded DNA molecules (known as annealing)
requires a temperature of about 65C.
Building up complete new DNA strands using DNA polymerase (known as elongation)
requires a temperature of around 72C. The DNA polymerases used for the process come from
microorganisms that have evolved to live in hot environments.
PCR machine:
- Most laboratories that work with DNA have a machine that automatically changes the temperature
of the mixture.
- The DNA sample is placed into a tube together with the primers, free nucleotides, a buffer solution
and the DNA polymerase.
- The PCR machine is switched on and left to work.

- The tubes are very small (they hold about 0.05 cm 3) and have very thin walls, so when the
temperature in the machine changes, the temperature inside the tubes changes very quickly.
- PCR is now routinely used in forensic science to amplify DNA from the smallest tissue samples left
at the scene of a crime.
- Many crimes have been solved with the help of PCR together with analysis of DNA using gel
electrophoresis.
Taq Polymerase
- Taq polymerase was the first heat-stable DNA polymerase to be used in PCR.
- It was isolated from the thermophilic bacterium, Thermus aquaticus, which is found in hot
springs
- It was valuable for PCR for two reasons:
1- It is not destroyed by the denaturation step, so it does not have to be replaced during each cycle.
2- Its high optimum temperature means that the temperature for the elongation step does not have
to be dropped below that of the annealing process, so efficiency is maximised.
Microarrays
What is a microarray?
- A microarray is made of a small piece of glass or plastic (solid surface) usually 2cm 2 where Short
lengths of single stranded DNA (spots) are attached to this glass support in a regular two-
dimensional pattern, with 10000 or more different positions per cm 2. Each individual position has
multiple copies of the same DNA probe placed by an automated on the microarray.
Uses of a microarray
[1] To identify the genes present in an organism's genome;
[2] To study very large numbers of genes in a short period of time, increasing the information
available.
[3] To compare the genes present in two different species:

Method:
1- DNA is collected from each species and cut up into fragments and denatured by heating to give
lengths of single-stranded DNA.
2- The DNA is labelled with fluorescent tags so that for example DNA from one species may be
labelled with green tags and DNA from the other species with red tags.
3- The labelled DNA samples are mixed together and allowed to hybridise (pair) with the probes on
the microarray.
4- Any DNA that does bind to probes on the microarray is washed off (because they are not required
or needed)
5- The microarray is then inspected using ultraviolet light, which causes the tags to fluoresce.
- This means that hybridisation has taken place because the DNA fragments are complementary to
the probes.

a- Green and red fluorescent spots indicate where DNA from one species only has hybridised
with the probes.
b- Yellow spots indicate Where DNA from both species hybridise with a probe. This means that the
two species have DNA with exactly the same base sequence. This suggests that they have the same
genes
c- no colour (or a blue colour) for a particular position on the microarray ,it means that no DNA
has hybridised with the probe and that a particular gene is not present in either species.
6- The microarray is then scanned so that the data can be read by a computer.
7- Data stored by the computer indicate which genes are present in both species, which genes are
only found in one of the species and which genes are not present in either species.
[4] Detect which genes are being expressed at any specific time in each cell in the body:
Example:
- The genes that are expressed in a cancer cell are different from those active in non-cancerous cells.
- Microarrays are used to compare the genes that are active by identifying the genes that are being
transcribed into mRNA.
Method:
1- The mRNA from the two types of cell is collected and reverse transcriptase is used to covert
mRNA to cDNA.
2- AS the quantity of mRNA in a cell at one time is quite small, the quantity of cDNA may need to be
increased by PCR.
3- The cDNA is labelled with fluorescent tags, denatured by heating to give single-stranded DNA and
allowed to hybridise (pair) with probes on the microarray.
4- Spots on the microarray that fluoresce indicate the genes that were being transcribed in the cell.
5- The intensity of light emitted by each spot indicates the level of the activity of each gene.
6- A high intensity indicates that many mRNA molecules were present in the sample, while a low
intensity indicates that there were very few.
- The results therefore not only show which genes are active, but also their level of activity.
- This information can help the way in which cancers are treated.
Bioinformatics
Define
- Bioinformatics is the collection, processing and analysis of biological information and data using
computer software.
Uses of bioinformatics
1- Bioinformatics combines biological data with computer technology and statistics.
2- It builds up databases and allows links to be made between them.
- The databases hold gene sequences, sequences of complete genomes, amino acid sequences of
protein and protein structures e.g primary structure, the coordinates required to show 3D models
hold details of over 100 000 different proteins and nucleic acids, and UniProt (universal protein
resource) holds information on the primary sequences of proteins and the functions of many
proteins, such as enzymes.
3- Computer technology facilitates the collection analysis of this mass information and allows access
to it via the internet.
- The database holds data on the genomes of eukaryotic organisms e.g. the human genomes, zebra
fish and mice that are used a lot in research.

4- The information needs to be in a form that can be searched, so software developers play an
important role in developing systems that allow this.
5- The search tool BLAST (basic local alignment search tool) is an algorithm for comparing primary
biological sequence information, such as the primary sequences of different proteins or the
nucleotide sequences of genes. Researchers use BLAST to find similarities between sequences that
they are studying and those already saved in databases.
6-The role of bioinformatics following the sequencing of genome (nucleotides squances):
- When a genome has been sequenced, comparisons can be made with other known genomes.
- For example, the human genome can be compared to the genomes of the fruit fly, Drosophila, the
nematode worm, Caenorhabditis, or the malaria parasite, Plasmodium. Sequences of nucleotides
can be matched and degrees of similarity calculated.
7- Comparisons can be made between amino acid sequences of proteins or structures of

proteins. Close similarities indicate recent common ancestry (evolutionary relationships)
- e.g.1Caenorhabditis elegans was the first multicellular organism to have its genome fully
sequenced.
- It has fewer than 1000 cells in its body, of which about 300 are nerve cells.
- It is conveniently transparent, allowing the developmental fate of each of its cells to be mapped.
- Because of its simplicity, it is used as a model organism for studying the genetics of organ
development, the development of neurones into a nervous system and many other areas of biology
such as cell death, ageing and behaviour.
- e.g.2 All the information we have about the genome of Plasmodium is now available in
databases.
- This information is being used to find new methods to control the parasite. For example, being able
to read gene sequences is providing valuable information in the development of vaccines for
malaria.
relationship between microarrays and bioinformatics:
1- Human genes, such as those that are concerned with development, may be found in other
organisms such as Drosophila.
- This makes Drosophila a useful model for investigating the way in which such genes have their
effect.
2- Microarrays can be used to find out when and where genes are expressed during the development
of a fruit fly.
3- Researchers can then use bioinformatics to access information about these genes and the
proteins that they code for.
- For example, they can search databases for identical or similar base sequences in other
organisms, compare primary structures of proteins and visualise the 3D structure of the
proteins.

Genetic technology and medicine
- Genetic technology allows products specific to humans to be made.
- you have already looked at the advantages of producing human insulin by recombinant DNA
techniques.
- Other human proteins are produced by similar techniques for example:
human growth hormone
thyroid stimulating hormone
factor VIII a blood clotting protein.
Advantages in using bacteria, yeast and cultures of mammalian cells to produce these
proteins:
1- These cells have simple nutritional requirements;
2- large volume of product are produced;
3- the production facilities do not Require much space and the processes can be carried out almost
anywhere in the world.
4- There are few practical and ethical problems, because proteins do not have to be extracted from
animal sources or by collecting blood from any donors.
Disadvantage of using bacteria to produce human proteins :
1- bacteria do not modify their proteins in the same way that eukaryotes do.
- It is much better, therefore, to use eukaryotic cells to produce human proteins.
Example (1)
- Genetically modified hamster cells are used by several companies to produce factor VIII.
- This protein is essential for blood clotting, and people who cannot make it are said to have
haemophilia.
- The human gene for making factor VIII has been inserted into hamster kidney and ovary cells which
are then cultured in fermenters.
- The cells constantly produce factor VIII which is extracted and purified before being used to treat
people with haemophilia.
- These people need regular injections of factor VIII which, before the availability of recombinant
factor VIII, came from donated blood.
- Using donated blood carried risks of infection for example, from HIV.
- Recombinant factor VIII avoids such problems.
Example (2)
- High yields of the enzyme adenosine deaminase (ADA) which is used to treat severe combined
immunodeficiency disease (SCID), are made by a genetically modified insect larva, the cabbage
looper moth caterpillar.
- This enzyme is administered to patients while they are waiting for gene therapy or when gene
therapy is not possible.
Example (3)
- Some proteins are even produced by transgenic animals.
- Sheep and goats have been genetically modified to produce human proteins in their milk:
human antithrombin is produced by goats this protein is used to stop blood clotting
human alpha-antitrypsin is produced by sheep this is used to treat people with emphysema.

Genetic screening
- it is the testing of samples of DNA from a group of people to identify the presence or absence of
particular alleles and thus the risk of having or passing on particular genetic conditions.
- This can be done in adults, in a fetus or embryo in the uterus, or in a newly formed embryo
produced by in vitro fertilisation
*Types of screening:
1- Carrier screening:
a)- All the individuals in a family may be screened if one family member develops a particular
condition that may be genetic.
b)- Potential parents may be screened where there is the possibility that one or both of them might
carry a recessive allele for some particular condition, e.g. cystic fibrosis, or a dominant allele, e.g.
Huntington disease.
2- Prenatal Screening:
- This used to determine aspects of the genetic makeup of an unborn child. Such testing can detect:
a) - Chromosomal abnormalities such as Down's syndrome (of particular importance if the
mother is over 34), trisomy 13 and trisomy 18.
b) - Single gene disorders, such as haemophilia, sickle cell anaemia and cystic fibrosis.
c) - Neural tube defects, such as spina bifida and anencephaly.
Methods of Pre-natal screening: (embryo biopsy)

- may be carried out in different ways and at different stages of the pregnancy:
[A] - Chorionic villus sampling CVS:

- Where the early placental tissue is sampled, usually done at 10- 12 weeks of the pregnancy. (More
risks for miscarriage but earlier diagnosis). A small sample of part of the placenta called the chorion
is removed by a needle. The needle is narrow (less than 0.8 mm in diameter). The procedure is
monitored by ultrasound scanning.
[B] - Amniocentesis:
-Where foetal cells in amniotic fluid are sampled, usually done at 13- 18 weeks of the pregnancy.
(less risky for miscarriage)
An ultrasound probe is placed so that the needle, when inserted, will show up on the scan as a bright
spot. At the insertion point, the skin surface is swabbed with a disinfectant. Then about 20 cm 3 of
amniotic fluid is withdrawn using a sterile hypodermic syringe with a narrow needle. The insertion
site is protected from infection with a dressing.
[C] - Intra-uterine blood test:

-Where foetal blood is sampled, usually done at 16 18 weeks of the pregnancy.
3- Newborn screening:
-In some countries, all newborn babies are screened for genetic conditions such as phenylketonuria
(PKU) by a simple blood test. This test enables the affected individual to be put onto a protective diet
low in the amino acid phenylalanine, for the rest of their life, to protect them from the damaging
symptoms of the condition.

Examples for using genetic screening
Example (1)
- An adult woman with a family history of breast cancer may choose to be screened for the faulty
alleles of the genes Brca-1 and Brca-2, which considerably increase an individual's chance of
developing breast cancer.
- If the results are positive, the woman may choose to have her breasts tissues removed (elective
mastectomy) before such cancer appears.
Example (2)
- Thalassaemia is a blood disease similar to sickle cell anaemia.
- It used to be a common genetic disease in countries around the Mediterranean: Cyprus, Greece
and southern Italy.
- The incidence of the disease has decreased significantly over recent years as a result of genetic
screening and giving advice to couples who are identified as carriers of the mutant allele.
- Testing during pregnancy was also carried out.
- When a fetus was identified as having inherited the disorder, couples received advice about the
possibility of terminating the pregnancy.
- Terminating pregnancies for a medical reason, rather than for any other, is known as therapeutic
abortion.
Example (3)
- Huntington's disease is a late-onset disease symptoms do not usually appear until middle age, by
which time people have usually already had children.
- There is no cure for this disease and the treatments available can only alleviate the symptoms.
- People in families with Huntington's face a dilemma: should they have the genetic test to find out
whether or not they have the dominant allele for the disease?
- This also poses ethical dilemmas: would you rather be told that you are at high risk of developing
this disease, even though nothing can be done about it, or live with the uncertainty of not knowing?
- Is it a good idea to have this information before you start a family?
- Decisions are made even more difficult by the possibility that a person with the dominant allele for
Huntington's may live their whole life completely free of the disorder as it sometimes does not
develop.
When to do genetic screening

1- Might be advised by genetic councillor to a (couple marriage between relatives);
2- So that they can identify a carrier (heterozygous) before marriage;
3- To know whether the child is a carrier for disease or not;
4- So that they can make decisions; mother decides to have her pregnancy terminated or not
5- Start treating the diseased child immediately after birth;
6- If they have a family history of a disease;
7- If the person belongs to an ethnic group which has a high % of individuals with a particular allele;

8- In pre-implantation genetic diagnosis (PGD): To check the gene of an embryo produced in vitro
(that is by fertilisation outside the body IVF) before it is placed in the mother's uterus; this can
ensure that only embryos that do not have the genes for a genetic disease are implanted;
9-To identify people who will develop a genetic condition later in life, for example, Huntington's
disease is caused by a dominant allele, but does not manifest itself until middle age; a person with
this disease in the family could check if they have the gene before they decide to have children
themselves;
10- To identify people with alleles that put them at risk of developing other diseases; for example, a
woman who has relatives with breast cancer could find out if she has the BRAC alleles that are
known to be associated with an increased risk of breast cancer, and could decide to have a
mastectomy to stop the possibility of her developing the illness.
Ethical and moral considerations regarding genetic screening

- Ethics are sets of standards by which a particular group of people agree to regulate their
behaviour, distinguishing an acceptable from an unacceptable activity. Ethics change with time,
because people alter their views according to their knowledge and experience.
1- Who decides who should be screened or tested?
2- Which specific disorders should be screened?
3- Who should be providing the screening?
4- Should we screen or test for disorders for which there is no known treatment or cure?
5- What psychological impact might the results have on the individuals involved?
6- Should the results be confidential?
7- If not, who should be able to have access to the information?
8- Should the results be made available to potential employers, insurers etc?
9- Should the law allow more or less rules with such issues?
10- Should we allow pregnancy termination because of an embryo having a genetic disease or not?
11- Some parents have decided to terminate pregnancies simply because the child is not the sex
that they want. They have also used PGD to select the sex of the embryo that they choose to
implant. Many think that this sex preselection as it is called is totally unethical.
Gene Therapy:
- It involves the insertion of correct / normal allele of a gene into the affected cells by a vector [e.g.
viruses] to prevent the cause of disease for genetic disorders such as sickle anaemia and cystic
fibrosis.
*The diseases that are caused by one recessive allele are easily cured
by gene therapy as they:
1-Are caused by one gene;
2-Are caused by recessive alleles;
3-Only one dominant allele needed to be delivered to few cells by vector to be cured;
4-Serious disease for which treatment is limited and no other cure is possible;
Advantages of using Gene therapy:
1- Treats the cause, so eliminate symptoms;
2- No need for antibiotics (avoid resistance to antibiotics);
Disadvantage of using Gene therapy:
1- Lasts only for few days;
2- Does not target all affected cells;
3- Known methods have some side effects;
4- Only a few cells took up the normal gene, so only these cells produced normal mucus;

5- It was only possible for cells in the respiratory passages to take up the normal gene, not cells in
the pancreas or reproductive organ;
6- Cells in the surface of the respiratory passages do not live for very long, so treatment would need
to be repeated every few weeks; since the effect of the therapy on chloride ion transport has so far,
lasted only a few days.
- This virus does not insert its genes into the host genome and so they are not passed on to
daughter cells when a cell divides.
- This is a problem when the host cells are short-lived (such as lymphocytes), but the virus has been
used successfully with long-lived cells such as liver cells and neurones.
7- When using the virus as a vector, some people developed serious lung infections; or allergic or
other immune responses.
8- Current liposome vectors have proved inefficient at delivering genes into cells.
9- Gene therapy brought out significant ethical issues when germ-line gene therapy is introduced;
where changes are made to human gamete cells that are inherited by the next generation.
10- Retroviruses insert their genes into the host's genome, but they do so randomly.
- This means that they may insert their genes within another gene or, more dangerously, into the
regulatory sequence of the gene, which may then activate a nearby gene causing cancer.
Treatment using Gene Therapy:
- A vector must be used to deliver the DNA containing the functional CFTR allele into the lung cells.
A) Viral delivery systems:
Example (1):
- Some viruses such as Retroviruses or lentiviruses can be used as the vector.
- Normally, viruses which infect lung cells are used, their virulence (ability to cause disease) is
removed and they are genetically engineered to carry the functional human CFTR allele a gene along
with its promoter.
-Early trials have involved either injection with the genetically engineered viruses or inhale them
from an aerosol directly into the lungs.
-The intention is that the lung surface cells are infected with the virus, which releases the genetic
material into the cells where it is expressed.
Example (2):
-The rare genetic disorder known as severe combined immunodeficiency (SCID).
- In this disorder, the immune system is crippled and sufferers die in infancy from common
infections.
- Children showing the condition are often isolated inside plastic "bubbles" to protect them from
infections.
- The defect in SCID involves the inability to make an enzyme, adenosine deaminase (ADA) which is
vital for the functioning of the immune system.
- Some of the child's T-lymphocytes were removed and normal alleles of the ADA gene were
introduced into them, using a virus as a vector.
- The cells were then replaced.
- This way not a permanent cure.
- Regular transfusions (every three to five months) were necessary to keep the immune system
functioning.
B) Non- Viral delivery systems

- Other systems are also being developed and have been trialled for safety but not been used
therapeutically e.g.:

1- Creation of a lipid sphere of liposome, containing the DNA. An aerosol is sprayed into the
lungs where the liposome will be able to pass through the target cell membrane and carry the DNA
into the cell.
-Whether the DNA is introduced into the cells by viruses or some other system, the intention is that
the gene will be incorporated into the cell's genome and will start to be expressed, to produce CFTR
protein to carry chloride ions through its membrane.
2-Naked DNA can be used

- Occasionally, DNA has been inserted directly into tissues without the use of any vector.
- This so-called naked DNA has been used in trials of gene therapy for skin, muscular and heart
disorders.
- The advantage of using this method is that it removes the problems associated with using vectors.
[B] Genetic Counselling:

1-A genetic counsellor will help people to interpret the result of the screening and help them to
make decisions.
2-also can explain the results, implications, dangers, diagnosis, and treatment
3- For the individual- Helps to find the recessive allele that can be hidden in a family for many
years. This is because most people who are who are also carriers. And even if they do, there is only a
1 4 chance that any one of their children will have the disease. Depending on the nature of any
detected allele (dominant or recessive),he/she will explain the possible future consequences in terms
of the health of the individual, education, or employment. In some cases, it might affect their
prospects of obtaining insurance.
4- For couples who want to have children again, depending on the nature of the inheritance, it will
need to be explained what the probabilities are of any children inheriting the defective allele and
the chances of any child actually having the disease i.e. it showing in their phenotype. All of this will
depend on whether the allele is dominant, recessive or sex-linked.
5- The counsellor will apply knowledge of inheritance to the information she/he is given about
relatives and the results of genetic screening of the parents. It may improve a pedigree analysis in
which information going back for several generations is used.
When A couple are likely to be referred the genetic counsellor:

1- Either of them has genetic disease in their family;
2- They belong to a group that is known to have a high risk of genetic disease (for example, a group
in which marriage between close relatives is common);
3-There is a history of recurrent miscarriages;
4- The woman is over 38 (because the risk of the child having Down's syndrome is relatively high);
5- As part of the management of a high risk pregnancy.

Why do couples need to discuss results of genetic screening with a
genetic counsellor?
1- To explain the outcomes of the test.
2- Give advice.
3- Help them to decide whether to terminate pregnancy or not.
4- Make them revise, or think about costs of curing a diseased child.
5- To know whether there is a successful gene therapy for that disease or not.
CYSTIC FIBROSIS (CF):

* What is CF:
-CF is hereditary disease affecting the exocrine (mucus) glands of the lungs, liver, pancreas, and
intestine.
*what Causes of CF:

-There are several different mutations that result in changes in the CFTR protein.
-Some mutations involve a change in just one base in the gene coding for the CFTR protein.
-The commonest mutation, however, involves the loss of three bases from the gene, meaning that
one amino acid is missed out when the CFTR protein is being made. In all cases, the protein that is
made does not work properly.
- Normally, chloride ions are transported out of the cells through the CFTR protein by active uptake,
then water follows by osmosis.
- When the CFTR protein is not working, this does not happen. There is therefore less water on the
outer surface of the cells than there should be. The mucus that is produced in these areas therefore
does not mix water in the usual way. The mucus is thick and sticky.
- Although most people without CF have two working copies (alleles) of the CFTR gene, only one is
needed to prevent cystic fibrosis, so individuals who are heterozygous for this allele do not
have CF.
- CF develops when neither allele can produce functional CFTR protein. Therefore, CF is considered
an autosomal recessive not sex-linked disease, on chromosome number 7.
*Side effects of mucus in lungs:

1- Mucus cannot be removed by cilia
2- Narrowing air ways;
3- Inflammation;
4- Sever coughing;

5- Change of epithelial cells and their replacement by scar tissue;
6- Bacterial infection;
7- Lungs are scarred;
*Treatments for CF:

1- Physiotherapy to remove mucus from lungs;
2- Antibiotics to stop lung infections;
3- Enzyme supplements to enhance digestion;
4- Adding functional copies of the CFTR gene to the cells of people with CF (gene therapy).
Using Drugs in treating CF:

-PTC 124 is the drug used to treat the CF caused by substitution of bases.
-More recently, a different approach has been taken. In some people with cystic fibrosis, the
mutation in the gene has simply replaced one base with another. This has created a 'stop' codon in
the middle of the gene. The gene is transcribed (that is mRNA is made from DNA) in the normal way,
but translation on the ribosomes stops when this codon is reached.
-This means that:
1- Only a short length of the CFTR protein is made;
2- Translation will not occur normally;
3- No amino acid added to chain when stop codon reached; Protein chain not completed / protein
only partially made;
-the drug PTC 124 has been found to allow translation to just keep going across this stop codon, so
the entire protein is
made, albeit with a wrong or missing amino acid in the middle of it.
-Clinical trials have shown hopeful signs that this may allow enough CFTR to be made to significantly
relieve the symptoms of some people with cystic fibrosis.
-It is much easier to do than 'classic' gene therapy, because it only involves the patient taking a pill
every day.
Comparison between drug and gene therapy of CF:

Drug PTC124 Gene Therapy
Can be taken orally Delivered (by vector) into respiratory tract

Self- administered Requires medical treatment
Is readily taken up by cells Poor take up by cells
No vectors needed / fewer or no side effects Possibly of side effects (from vectors) named
side effects
Only needs to enter cytoplasm Difficulty in inserting gene into host DNA
No need to switch on gene Difficulty in switching on gene
- This work on vectors has led to increasingly successful gene therapies in the last few years,
including the following:
The eyesight of young men with a form of hereditary blindness, Leber congenital amaurosis, in
which retinal cells die off gradually from an early age, has been improved.
The normal allele of the -globin gene has been successfully inserted into blood stem cells to
correct the disorder, -Thalassaemia.
people with haemophilia B (in which factor IX is missing) have at least seen their symptoms
reduced.
children were successfully treated for SCID in 2013.
Gene therapy by Somatic and germ cell gene therapy

1- So far, all attempts to do this in humans have involved placing the allele in body cells, otherwise
known as somatic cells.
2- However, another possibility would be to insert the allele into germ cells that are involved in
sexual reproduction, such as gametes or an early embryo.
3- For example, in theory, a woman with cystic fibrosis could opt to try to conceive a baby using IVF.
4- Eggs (secondary oocytes) would be harvested from her in the normal way.
5- Then the 'correct' allele of the CFTR gene could be injected into an egg and this egg fertilised by a
sperm to produce a zygote.
6- When the child grows up and produces eggs or sperms, these gametes will also contain the allele
and therefore it will be passed on to their children. We say that the allele is in the germ line, being
passed on from generation to generation.
Genetic technology and agriculture

genetically modified plants:
- Proteins for use in medicine can be produced from genetically modified plants, so avoiding any
problem of contamination by animal proteins.
- Examples include vaccines, albumin and the proteins found in breast milk that are used to treat
diarrhoea in infants.
- However, the vast bulk of genetically modified plants grown around the world are crop plants
modified to be resistant to herbicides, such as glufosinate and glyphosphate, or crops that are
resistant to insect pests.
- These modifications increase crop yield.
- A few crops, such as vitamin A-enhanced rice, provide improved nutrition.

Example (1) Herbicide resistant oil seed rape:
(A) - Oil seed rape (Brassica napus) is grown in many parts of the world as a source of vegetable oil
which is used as biodiesel fuel, as a lubricant and in human and animal foods. Natural rape seed oil
contains substances (erucic acid and glucosinolates) that are undesirable in oil that is to be used in
human or animal food. A hybrid, bred in Canada to produce low concentrations of these undesirable
substances, was called canola (Canadian Oilseed Low Acid), and this name is now often used to
mean any variety of oil seed rape.
(B) - Genes that confer resistance to herbicides (weed killer) containing glyphosate and glufosinate
have been inserted into oil seed rape cells. Oil seed rape plants containing this gene do not die when
this herbicide is sprayed on them. This allows farmers to control weeds in their crops by spraying the
field with glufosinate, which kills all the plants except the oil seed rape. Killing any weeds that
compete with the crop for space, light, water or ions allows the increase in the yield of the crop.
(C) - METHODS:
(1) Using Agrobacterium tumifaciens:
1- Agrobacterium tumifaciens is a soil-inhabiting bacterium that may invade growing plants at the
junction of root and stem, where it can cause a cancerous growth known as a crown gall.

2- The bacterium, which infects dicotyledonous plants only, contains a plasmid (known as a Ti
plasmid) that carries the genes for tumour formation.
3- When the bacterium invades the host cells, the Ti plasmid enters the host nuclei.
4- Part of the Ti plasmid becomes inserted into a chromosome, introducing genes for the synthesis of
a plant hormone (causing proliferation of host cells) and secretion of special amino acids called
opines, on which the bacteria in the host and in the surrounding soil feed.
5- In effect, the bacterium carries out genetic engineering on its own behalf.
6- Molecular geneticists have exploited the Ti plasmid by inserting a short length of DNA (a gene) in
place of an existing gene in the plasmid.
7- This recombinant DNA becomes integrated with the DNA of a chromosome of the host plant, and
the engineered gene is subsequently expressed.
8- This method has been used to engineer a gene for herbicide resistance into crop
plants. Then, when the field was sprayed with herbicide the weeds were killed but the
crop survived.
(2) Using 'biolistics' (using gene guns):

1- A biolistics machine literally fires genes into tissues.
2- The genes are coated on to tiny gold or tungsten 'bullets' and fired into a tissue sample.
3- Plant or animal tissues are routinely successfully engineered to carry additional genes by this
method.
(D) Mechanisms of action of the herbicide:

1- Oil seed rape that is resistant to the herbicide glyphosate, or to the related glufosinate, is grown
in a number of countries.
2- Glyphosate inhibits an enzyme involved in the synthesis of three amino acids: phenylalanine,
tyrosine and tryptophan.
3- Glyphosate is absorbed by a plant's leaves and is transported to the growing tips.
4- The amino acids are needed for producing essential proteins, so the plant dies.
5- Various microorganisms have versions of the enzyme involved in the synthesis of phenylalanine,
tyrosine and tryptophan that are not affected by glyphosate.
6- The gene that was transferred into crop plants came from a strain of the bacterium
Agrobacterium
Advantages and disadvantages of producing Herbicide-resistant oils

seed rape (GM):
Advantages Disadvantages
High rate of growth of GM. More use of herbicides, more pollution.
Herbicide resistant. There was no evidence that genetic engineering increased the
invasiveness of oil seed rape plants, where differences between
normal and genetically modified plants existed, the genetically
engineered plants were slightly less invasive than the unmodified
plants.
No need for sexual GM crops may be genetically unstable, causing mutation.

reproduction.
Other useful genes are not Genes from the GM (genetically modified) oil seed rape plants
harmed. might be able to spread into wild Brassica plants growing nearby,
and make them resistant to the herbicides.

Desirable genes can be Reduces hybridisation. Oil seed rape is able to hybridise with wild
identified and cloned. relatives, which are often, found growing close to rape fields.
However, after several years in which the GM oil seed rape has
been grown on a very large scale in Canada, and in trials in
Europe, only a very low such hybrids have been found.
Easy to control weeds. Some of the GM seeds produced could not germinate (infertile),
so less chances of producing a population of resistant plants.
Only weeds are killed, not -The risk of pollen transfer, by wind or by insects, is real. Oil seed
crops. rape interbreeds easily with two related species, wild radish and
wild turnip. Its flowers are adapted for insect pollination, but are
also pollinated by wind.
-Safe planting distances should be increased to allow the organic
farming industry to maintain its 'GM-free' certification.
Transgenic (GM crops) The genetically modified plant may become an agricultural weed.
production is much faster than
conventional breeding Pollen will transfer the gene to wild relatives, producing hybrid
offspring that are invasive weeds.
Herbicide-resistant weeds will evolve because so much of the

same herbicide is used.
Example (2): Insect resistant maize and cotton:

-Yields of maize can be greatly reduced by an insect larva called the corn borer. Cotton yields are
reduced by the cotton boll worm, which is also an insect larva.
-Pesticides sprayed onto the crops can kill these insects. However, the pesticides can also harm
other beneficial pollinating insects. The insects also evolve resistance to the pesticides.
-Genes that code for the production of a protein derived from the bacterium Bacillus thuringiensis,
called Bt toxin, have been inserted into maize and cotton plants. The plants therefore produce the
protein, which is converted into the toxin once inside the gut of the insects that have eaten the
leaves. This means that the toxin kills insects that feed on the plants, but not other insects.
METHOD: by protoplast fusion:

1- The plant cell wall is a rigid structure and potentially a barrier to the introduction of new genes.
2- Plant cell walls can be removed by the gentle action of enzymes including cellulase,
hemicellulase and pictinase.
3- Plant cells from which the wall has been removed are called protoplast.

4- They can be cultured in liquid medium provided the water potential of the medium is
appropriately regulated.
5- Under these conditions the protoplasts quickly regenerates a new cell wall, but before it can do so
there is an opportunity for the molecular geneticist to adjust the genome of the cell.
6- For example, plasmids of bacterial origin can be induced to enter by using the 'zapping'
(Electroporation) technique to open pores in the plasma membrane.
7- The bacterium Bacillus thuringiensis has a plasmid-based gene for the production of a protein that
is toxic to many insect larvae (a naturally occurring insecticide).
8- Copies of these plasmids have been introduced into protoplasts of potato, cotton and tobacco
species.
9- From these genetically engineered protoplasts, plants have been produced with natural defences
against a range of insect pests.
Advantages and Disadvantages of producing maize & cotton insect-resistant

rather than using pesticides
advantages Disadvantages
Cheaper The evolution of resistance by the insect pests.
Less time consuming (no spraying) A damaging effect on other species of insects.
Specific to a certain type of pest The transfer of the added gene to other species
of plant.
Less pollution, since less need to use The seed of Bt corn and cotton costs more for
pesticides farmers to buy than non-GM seed, making it
difficult for farmers in developing countries to
afford it, and therefore making it difficult for them
to compete with farmers in richer countries
(expensive).
It is possible that some non-pest insects might be

harmed by the Bt toxin. However, overall it is
found that there are more non-pest insects
present in the fields where Bt corn or Bt cotton
are grown than in fields where non-Bt crops are
grown and sprayed with pesticides
.
Will reduce side effects of pesticides on GM crops may be genetically unstable, causing
organisms in higher levels (humans) mutations, e.g. cancer.
Crops are pest resistant More use of pesticides
Pesticides are expensive and time consuming to
apply
Less harm to useful insects / pests .

The toxin harms only insects that eat the
plant, not other insects as happens when
insecticides are sprayed on crops. Danger of losing biodiversity
Less loss of the crop to insect pests, so Pesticides are rarely selective and kill harmless
greater yields are obtained which can and useful organisms as well, such as pollinators.
keep costs down.
Some pesticides accumulate in the environment
and cause long-term changes in animals or
humans.
It is less likely that insect pests will evolve The large numbers of crop plants containing the
resistance to the Bt toxin than to genes for toxins may simply accelerate the
pesticides. However, there are signs that evolution of resistance to the toxins in the larvae
resistance can develop in some pest
species. This can be counteracted by
using slightly different forms of the Bt
toxin, or a combination of two different Bt
toxins, in GM crops
Experimental evidence: There is some evidence of reduced population of

Maize is attacked by the European corn micro-organisms in soil in which Bt maize has
borer, an insect larva that tunnels into the been growing.
plant from eggs laid on the undersides of
leaves. In field trials normal and
genetically engineered maize plants were Various aquatic insect larvae live in the streams
deliberately infested with larvae and the in the maize-growing areas of the U.S.A. leaves
results monitored over 6 weeks. The from genetically modified Bt plants end up in the
average length of the tunnels in the streams and may be eaten by, for example,
engineer plants was 6.3cm and in the caddis larvae. Experiments showed a small
normal plant was 40.7cm. The engineered reduction in growth of larvae fed on Bt leaves.
plans also suffered less leaf damage.
Example (3): Vitamin A enhanced rice

-The green parts of rice plants contain beta-carotene, which is a vital component of vitamin A.
However, there is no beta-carotene in the grains and those parts of the world where rice is the
principal staple food; small children are very prone to vitamin A deficiency.
What is vitamin A?
-Vitamin A is a fat soluble vitamin found in oily fish, eggs, liver and dairy products. It is also made in
our bodies from carotene, the orange pigment found in carrots.

Where is vitamin A found in the rice grain?
1- Vitamin A is present in the aleurone layer of rice grains but not in the endosperm.
2- The aleurone layer is removed from rice when it is polished to produce white rice.
3- Brown rice still contains the aleurone layer.
4- In tropical countries, the aleurone layer goes rancid if the rice is stored for any length of time,
which is why white rice is produced and eaten instead.
5- Brown rice has more protein than white rice as protein is in aleurone layer, which is only in brown
rice (not polished).
6- Brown rice has less carbohydrate than white rice, as may be its endosperm is less in size than
white rice, or as it has more protein, so less carbohydrates per gram.
What is the importance of vitamin A?

-Vitamin A is essential for the operation of the body's immune system and a deficiency causes
increased risk of infection, night blindness and, in some cases, total blindness.
How the crop was improved by GM to solve this problem?

-The genetically modified rice is called golden rice, because it contains a lot of the orange pigment
carotene, which can be converted by human cells into vitamin A.
-Then the genetically modified rice was bred with other varieties of rice, to produce varieties that
would grow well in the conditions in different parts of the world.
Method of producing GM rice (golden rice):

- The first version of this rice used genes taken from daffodils and a bacterium Erwinia uredovora,
but the quantity of
carotene produced was not very large. Since then, new varieties containing genes from maize and
rice itself have been produced, which contain up to 31 g of carotene per 100g of rice.
- However, in the case of rice (and other crop plants, such as maize) a method has been developed
where the genes are delivered directly into the cells using small m-sized tungsten or gold bullets
coated with DNA. The bullets are fired from a device that works similar to a shotgun. This delivery
device is known as 'gene gun' and is now a common method used in the genetic transformation of
rice.
Steps:
1- Gene of vitamin A is extracted from a kind of bacteria ( Pantoea ananatis), maize and daffodil
flowers.
2- Gene with its promoter is added to the plasmids.
3- Plasmids are taken by Agrobacterium tumifaciens.
4- Bacteria infect rice embryo.
5- Rice embryo with vitamin A gene will grow to adult plant that has vitamin A in its endosperm.
Advantages and Disadvantages of producing GM rice (golden rice):
Reduce blindness among The rice has to undergo further tests, for example, to check its
children. Children whose effects on human health, before it will become widely available.
diet consists largely of rice
would be able to get more
than half of their daily
requirement for vitamin A
by eating 200g of this rice
per day.
The researchers who It will also be necessary to incorporate the genes into different
developed this GM rice will varieties of rice that are suitable for growing in different parts of the
donate it free of charge for world.
use in developing
countries.
Cheap seeds The existence of this GM rice would possibly lessen efforts to tackle
the root causes of poverty and poor diet in some parts of the world.
Better quality food Some people argue that the changes made to the genes in the rice
could have harmful effects on people who eat it; however, there is no
evidence for this.
Improve health and GM crops still have not been grown in field trials in Asia as long as
immunity of individuals. many agricultural experts and environmental groups believe the
solution is not to go down the route of GM crops, but rather to aim for
a more balance diet, which would include more fresh vegetables,
which have a naturally high content of beta-carotene.
GM seed could be difficult for farmers in developing countries to

obtain
High cost of buying (new) GM seed / cannot use own seed
May not grow well in all conditions (as other traits not selected for)
Too expensive for people to buy / or for farmers to sell
Might reduce efforts to relieve poverty
May be genetically unstable, causes mutation, cancer
Reduces hybridisation
Reduces biodiversity
Genetically modified animals

- Genetically modified animals for food production are much rarer than crop plants.
- An example is the GM Atlantic salmon, developed in the USA and Canada.
- A growth-hormone regulating gene from a Pacific Chinook salmon and a promoter from another
species of fish, an ocean pout, were injected into a fertilised egg of an Atlantic salmon.

- By producing growth hormone throughout the year, the salmon are able to grow all year, instead of
just in spring and summer.
- As a result, fish reach market size in about eighteen months, compared with the three years
needed by an unmodified fish
- It is proposed to rear only sterile females and to farm them in land-based tanks.
- The characteristics of the GM salmon reduce their ability to compete with wild salmon in a natural
environment.
- This has led the US Food and Drug Administration (FDA) to declare that they are "highly unlikely to
have any significant effects on the environment" and "as safe as food as conventional Atlantic
salmon".
- In 2013, Canada approved the production of GM salmon eggs on a commercial scale, but neither
Canada nor the USA had yet given permission for GM salmon to enter the human food chain.
GENETIC ENGINEERING ISSUES OF CONCERN
(A) Economic issues to consider:

1- Genetic engineering is a costly technology.

2- Genetic engineering is of most benefit to people of developed nations.
3- The funds available for genetic engineering could be diverted to solve more basic problems such
as housing, health, employment and nutrition of the poor worldwide.
4- Like some transgenic animals, certain transgenic plants can be potentially "pharmed" to produce
large quantities of medically important proteins, such as antibodies against the herpes virus (used in
treating diseases).
5- The results of some experiments also showed that the genetically engineered virus is being
marketed as a biopesticide, since although it kills caterpillars faster than the unmodified virus, the
caterpillars still have time to eat holes in the cabbage leave. (Crop loss continued)
6- 'Safe' planting distances should be increased to allow the organic farming industry to maintain its
'GM-free' certification.
(B) Ethical issues to consider:

1- Humans should not tamper with nature
2- GM crops may produce or behave in an unpredicted ways
3- Some people are concerned about the safety of dealing with genetically engineered organisms. To
address these concerns, scientists carry out recombinant DNA technology under specific safety
guidelines. Scientists are trying to find ways to remove the marker genes after transformation.
4- Some people are concerned about the health effects of consuming foods derived from GM crops
and think that such foods should be restricted. For example, critics say that some consumers may
develop food allergies.
5- Genetic engineering is a relatively new development, experience of it is limited and a large
number of people know virtually nothing about it. Also, development of the techniques has been
rapid.
(C) Environmental issues to consider:

1- There are far more potential dangers once unrestricted release of GM organisms is granted.
2- Might a gene, added to a genome, function in an unforeseen manner, and perhaps even triggering
cancer in the recipient.
3- Might an introduced gene for resistance to adverse conditions get transferred from a crop plant or
farm animal into a weed species or to some predator, or even to pathogenic bacteria, so marker
genes must be removed from the GM organism after transformation.
4- May encourage the use of greater amounts of herbicides.
5- Could a harmless organism, such as the human gut bacterium E.coli, with recombinant DNA
technology, be transformed into a harmful pathogen that escapes into the outer population.
6- The maize has a bacterial gene which increases its resistance to pests and diseases, but also has
a gene for resistance to the antibiotic ampicillin. Some organisations are threatening that a legal
action must be taken.
7- They might also affect food chains in an unpredictable ways, disturbing the balance of the
ecosystem.
8- 'Safe' GM plants distances should be increased, since pollen can be transferred by insects or wind
to unmodified plants.
9- GM plants are slightly less invasive than the unmodified plants, so there was no need to modify
them genetically in the first place.
10- Loss of biodiversity.

The social and ethical implications of gene technology:
A) The social impact of gene technology:

- it is to do with its potential and actual impact of human society and individuals. In terms of social
impact, gene technology could:
1- Enhance crop yields and permit crops to grow outside their usual location or season so that
people have more food;
2- Enhance the nutritional content of crops so that people are better fed;
3- Permit better targeted clean-up of wastes and pollutants;
4- Lead to production of more effective and cheaper medicines and treatments through genetic
manipulation of microorganisms and agricultural organisms to make medicines and genetic
manipulation of human cells and individuals (gene therapy);
5- Produce super-weeds or otherwise interfere with ecosystems in unexpected ways, reduction crop
yields so that people have less food;
6- Increase costs of seed and prevent seed from being retained for sowing next year (by inclusion of
genes to kill any seed produced this way) reducing food production;
7- Reduce crop biodiversity by out- competing natural crops so that people are less well fed;
8- Damage useful materials such as oil or plastic in unexpected ways;
9- Cause antibiotics to become less useful and cause allergic reactions disease in other unexpected
ways.
10-For (GM crops):
-such results of testing likely to have a negative effect on public perception (of GM crops);
-might reduce work for researchers in this area;
-might reduce income of companies (producing GM crops);
-increased use of pesticides.
B) The ethical impact of gene technology:

-it is about the application of moral frameworks concerning the principles of conduct governing
individuals and groups, including what might be thought to be right or wrong, good or bad. So in the
context of gene technology, it is to do with issues of whether is right or wrong to conduct research
and develop technologies, whether it is good or bad. Judgement may that:
1- It is good to conduct such research to develop technologies that might improve nutrition, the
environment of health.
2- It is good to use the results of such research to produce food, to enhance the environment or
improve health.
3-It is wrong to continue such research when the potential impact of the technology is unknown and
many aspects of it remain to be understood.
4- It is wrong to use the results of such research even when the organisms are kept in carefully
regulated environments such as sterile fermenters, as the risks of the organisms or the genes they
contain escaping are too great and unknown.
5- It is wrong to use the results of such research when this involves release of gene technology into
the environment as once it is released it cannot be taken back the genes are self perpetuating, and
the risks that they might cause in future are unknown.
6-genetic engineering is in principle acceptable, and I f so, in what circumstances;
7-it is acceptable to patent a genetically engineered organism or to patent a gene sequence;
8-it is acceptable to engineer any organism to produce a product useful to humans;
9-it is acceptable to engineer animals to show human diseases for research into those diseases;
10-genetically modified food is acceptable;
11-products on sale are adequately labelled to indicate that genetic engineering was involved in
their production;

The benefits and hazards of gene technology
(A) Benefits of gene technology:
-Through gene technology, it is now possible to produce:
1- Genetically modified organisms for a specific purpose. Previously, such genetic change would
have to be brought about by selective breeding which requires organisms to be of the same species
(able to breed successfully together), takes many generations and involves transfer of whole
genomes, complete with undesirable background genes. Gene technology is much faster and
involves transferring one or few genes, which may come from completely unrelated organisms, even
from different kingdoms.
2- Specific products, such as human insulin and human growth hormone, thereby reducing the
dependence on products from other, less reliable sources, such as pig or cow insulin.
3- Reduce use of agrochemicals such as herbicides and pesticides since crops can be made resistant
to particular herbicides, or can be made to contain toxins that kill insects.
4- Clean up specific pollutants and waste materials bioremediation.
5- Potential for use of gene technology to treat genetic diseases such as cystic fibrosis and SCID
(Severe Combined Immune Deficiency) as well as in cancer treatment.

(B) Hazards:
1- Genes inserted into bacteria could be transferred into other bacteria species, potentially
including antibiotic resistance genes and those for other materials, which could result I antibiotic
resistance pathogens, or in bacteria that can produce toxic materials or break down useful materials.
- Regulation is designed to minimise the risks of escape of such genes. There is little evidence that
such genes have escaped into wild bacterial populations.
2- Food that is delivered from genetically engineered organisms may prove to be unexpectedly toxic
or to trigger allergic reactions when consumed. There is little reliable evidence that this has been
so, but the risk remains.
- Food containing the expressed products of antibiotic resistance marker genes could be consumed
at the same time as treatment with the antibiotic was occurring, which would potentially reduce
the effectiveness of the treatment.
3- Crop plants have, by their nature, to be released into the environment to grow, and many millions
of hectares of genetically engineered crops, both experimental and commercial, are planted across
the globe.
-So far, fears that they might turn out to be 'super-weeds' resistant to herbicides and
spreading uncontrollably, or that their genes might transfer into other closely related wild
species, forming a different kind of 'super weeds' or they might reduce biodiversity by genetic
contamination of wild relatives seem to have proved unfounded.
- A paper was published in Nature in 2001 showing that Mexican wild maize populations were
contaminated with genes from genetically manipulated maize, but the methods used were flawed
(not good)and subsequent studies have not confirmed this contamination, suggesting that the wild
maize is not genetically contaminated.
-There is some evidence that Bt toxin, genetically engineered into plants such as cotton and maize,
whilst very effective in killing the target species may kill other, desirable, insects such as bees and
butterflies, and may also cause natural selection of Bt toxin resistant insects. Future events may
show that such environmental risks are greater than they look at present.
-the herbicide that can now be used on the crop will itself leave toxic residues in the crop.
Potentially, it could breed new animal and plant diseases, new sources of cancer, novel epidemics;
-summary of the concerns about such genetically engineered crops also include:
-the modified crop plants will become agricultural weeds or invade natural habitats;
-the introduced gene(s) will be transferred by pollen to wild relatives whose hybrid offspring will
become more invasive;
-the introduced gene(s) will be transferred by pollen to unmodified plants growing on a farm with
'organic' certification;
-the modified plants will be a direct hazard to humans, domestic animals or other beneficial animals,
by being toxic or producing allergies or diseases like cancer;
-may reduce biodiversity, disturbing balance in food chains, or webs, or ecosystem
-we can only say potential hazards because:

a- experiments are done in laboratory and not out in the ecosystem.
b- Scientists only predict what could happen.

SUMMARY
SOCIAL ISSUES OF GENE THERAPY AND GENE MANIPULATION
OOD BAD
crease crop yield Reduce crop biodiversity
crease nutritional content Increase cost of seeds
M crop can grow in different regions Cause antibiotics to be useless/less

the world effective
ore effective, and cheaper Genetic modified bacteria may damage

edicines oils and plastics if escaped
prove health, or environment, or Super weeds may interfere with

crease food supply ecosystem
Harmful bacteria may be resistant
Expensive prices
May have unknown side effects
Risk of organism may escape
Release of altered gene to environment,

so it cannot be restored
It is not good and safe to play with the

nature
Genetically modified organisms may be

subjected to danger due to unexpected
mutations
The organisms may affect food chains,

when they are modified/disturb ecological
balance
Genetically engineered food may be

dangerous to humans, and cause allergy,
cancer
S-BIOTECHNOLOGY
Define:
Biotechnology is the use of living organisms- usually microorganisms- to provide us with a
substance or a process.
e.g. (1) Escherichia coli can be genetically modified and then used to manufacture human insulin.
(2) The manufacture of antibiotics.
(3) Mining of low-grade ores (ore = metal compounds that make rocks).
(4) Production of biosensors that can help to diagnose pregnancy.
(5) Bacteria are used to make yoghurt and cheese.
(6) Yeast is used make wine and beer.
[1] Mining with microorganisms (Bioleaching) or the use of

microorganisms to extract heavy metals from low-grade ores:
-Some bacteria are described as chemoautotrophic i.e. they drive their energy for growth, cell
division and synthesis of molecules such as proteins via the breakdown of inorganic chemicals. In
some cases, this involves the breakdown of ores of heavy metals, as a result of which the metal
itself is released.
-Metals which can be extracted in this way include copper, uranium, cobalt, lead, zinc, iron, nickel
and gold.
-Bacteria of the genus Thiobacillus are commonly used in this process e.g. Thiobacillus
ferrooxidans is used in extraction of copper and uranium.
-Some species of bacteria actually accumulate metals. This property can be made of use, both in the
extraction of metals, and the detoxifying of waste. For example, some species of
Pseudomonas are known to accumulate mercury and uranium, while some species of Thiobacillus
accumulate silver.
BIOLEACHING:
Bacteria
Metal sulphide (water insoluble) + oxygen metal sulphate
Metal sulphate (water soluble) + water metal + H2SO4
Properties of bacteria used in bioleaching:

1- Bacteria can survive in highly acidic conditions, because sulphuric acid is produced as a result of
the reaction.
2- They also need to be able to work in a fairly wide range of temperatures, so that they can be used
in different parts of the world and at different depths underground (it gets hotter the deeper down
you go).
Example (1):
-A bacterium called Acidithiobacillus ferrooxidans can change iron sulphide into iron sulphate in
this reaction:
26 FeS2 + 13 O2 13 Fe2 (SO4 )2 + 13 H2SO4
Acidithiobacillus ferrooxidans is an aerobic, rod-shaped bacterium. It obtains its energy from the
oxidation of iron sulphide. The oxygen required is obtained from the air.
Example (2):
- Similar reactions can be catalyzed by other bacteria on other sulphide ores. Acidithiobacillus
thiooxidans and Leptospirillum ferrooxidans are two examples. About 20 % of all the copper that is
being mined is extracted by bacterial leaching using these bacteria.
Advantages of Bioleaching Disadvantages of

Bioleaching

1- Cheaper, as less workers are needed; 1- Unsightly;
2- Bacteria is self replicating; 2- Takes large surface area;
3- Used for extraction of low-grade ores; 3- Continuous water supply is
4- No high tech-equipment needed; needed;
5- More friendly to environment; 4- Produce H2 SO4 ;
6- No need for mining (work in situ); 5- copper and iron are toxic to
7- No need for filters, as SO2 is not plants
produced;
8- No experts or workers are needed;
9- Use in situ (bacteria can work
underground);
10- Less fossil fuel is used;
11- Few safety hazards;
12- Easy to obtain organism;
13- Easy to dispose wastes.
BATCH AND CONTINUOUS CULTURES

Definition Exam Advantages Disadvantages
ple
Batch 1- A method of culturing Penicillin 1-The culture is easy to set up. 1- High labour cost, skilled
Culture organisms in which all the enzymes 2- Environmental conditions labour is required.
components are added at are relatively easy to control. 2- Much idle time: sterilization,,
the beginning. A batch 3- The types of vessels used growth of inoculums, cleaning
culture uses a container can be used for different after fermentation.
with growing population of processes at different times 3- Safety problems: when
organisms (for example, of after being cleaned. filling, emptying, cleaning.
4- If the culture becomes 4- Greater running costs for
microorganisms suspended
in a fermenter or fish in a contaminated, it is only one preparing and maintaining
pond) where there is a batch that is lost. stock cultures.
limited supply of raw 5- The level of nutrients drops, 5- Since there is no flow stream
materials. Population which can create the to take effluent out (as it is a
growth follows a sigmoid conditions necessary for the closed system) toxins can form.
pattern and there is a total microorganisms to 6- Limitation and depletion of
harvest of the contents of manufacture secondary the substance.
metabolite such as penicillin. 7-Might be less cost effective
the container.
2- When fermentation is 6- Little risk of infection or since there is no need of
carried out in a closed or strain mutation. cleaning between batches.
7- Allow fermentation to 8- More down time.
batch fermenter.
Microorganisms and continue with minimal
nutrient medium are attention.
8- Normally, no blockages can
added to the fermenter
occur.
and left for a period of
8- Initial capital expendeniture
time. During the process,
is lower.
nothing is added to or
removed from the
fermenter (except for the
venting of waste gases).
The product is separated
from the mixture at the
end. Temperature is
controlled and nutrients
are usually depleted at the
end.
Continu 1- A method of culturing Mycopro 1- It can be carried out in small 1-Microbial growth, clumping of
organisms using a tein, the vessels, given that the micro- cells and foaming can tend to
ous
container with a growing choice of organisms are maintained in block up inlet pipes.
Culture 2- It can be difficult to control
population of organisms which the exponential phase and
( for example, of culture productivity is thereof high. all the environmental factors- if
microorganisms suspended to use 2- The high productivity for they are not controlled
in a fermenter or fish in a depends biomass and intra-and extra- adequately, there can be a
pond) that is continuously on the cellular enzymes is more cost considerable amount of waste.
supplied with new raw conditio effective. 3- It is not possible to create
materials and ns that 3- The process is continuous, the low- nutrient, high stress
continuously harvested in the so there is no 'Down Time' conditions under which
order to keep the culture in microorg while the vessels are cleaned secondary metabolites such as
exponential population anism out and set up again. penicillin are produced.
4- Less labours needed. 4- If there is a contamination or
growth. requires
5- Automation may be very error, the entire product might
2- When fermentation is in order
appealing. be contaminated.
carried out in an open to 6- Constant product quality. 5- Difficult to set up (more
fermenter. Nutrients are synthesi 7- Good utilization of reactor. equipments) and requires
added and product se the 8-Steady growth can be
continuous monitoring to
removed at a steady rate desired achieved even if mixed
ensure conditions are
throughout the process. product. cultures are implemented.
maintained.
This will maintain the 9- Productivity can be high
6- Cells can Clump together
microorganisms at the
and block inlet or outlet pipes.
exponential phase of 7- Mutation of microorganisms
growth. It is very important to non-producing strain can
to monitor pH, occur.
temperature and oxygen 8- Inflexible: can rarely be used
concentration as well as for other productions.
level of nutrients and 9- Often disappointing:
product. All of these should promised continuous
be kept constant. production for months fails due
to: a) infection, b) spont-
aneous mutation of
microorganisms to non-
producing strain.
Inflexible: can rarely be used
for other productions without
substantial retrofitting.
Culturing microorganisms industrially:

-We use many different organisms to make products that can be used in medicine and as food. This
normally involves culturing microorganisms in containers called fermenters. The way in which this
is done depends on the nature of the product that we want to be made, and the kind of
microorganism that is being used.
e.g. (1) Manufacturing enzymes (In batch culture):

Uses of Enzymes:
-In medicine or food technology, for example, proteases and lipases are added to washing powders
to help in the removal of stains; digestive enzymes are added to cattle feeds to increase the quantity
of nutrients that cattle can absorb; enzymes are used in the leather industry to prepare skins, meat
tenderizers, cheese production by rennin to digest casein protein in milk
Stages of protease enzyme production:
1-the microorganism is grown.
2-the enzyme is extracted
3-the enzyme is purified and concentrated.
Stage (1): Growing microorganism in fermenter:
1-Microorganism used:
-Many different kinds of bacteria and fungi can be used to produce enzymes. Often a thermophilic
(heat-loving) organism such as Bacillus Stearothermophilus is used. These bacteria live in hot
springs and they have evolved enzymes that are not denatured until temperatures as high as 70 o C
or more are reached. These heat resistant enzymes are very useful in industrial processes in which
higher temperatures are encountered, and also in products such as biological washing powders.
2- A culture of the microorganism is placed in the fermenter, together with the nutrients it requires
for reproduction. These will normally include:
*a carbohydrate (as an energy source) such as Soya beans which provide a cheap source of carbon
and nitrogen or remains of sugar cane, or glucose for carbon (less pollution and cheap);
*Ammonia for nitrogen to build up cell membranes, nucleotides, and proteins.
*If the organism is aerobic, air will be bubbled through the culture to provide oxygen.
*Temperature is usually controlled by passing cold water through a jacket surrounding the
fermenter; this is because the metabolic reactions of the microorganism are often exothermic and
would cause temperature to increase.
*pH is controlled by using buffers.
Stage (2): Extraction of enzymes:
(A)Intracellular enzymes: where enzymes remain inside the cells of microorganism.
How to extract the enzymes from inside cells: (see figure)
1- Heating and cooling to kill organisms;
2- Centrifugation to separate cells from fluid;
3- Disintegration to break the cells to allow escape of enzymes from cells to dissolve in culture
medium.
4- Extraction of enzymes by;
5- Centrifugation to separate cells from remains;
6- Ultra filtration to get pure enzymes, leaving cell fragments behind;
7- Concentrate enzyme.
(B) Extracellular enzymes: where enzymes are secreted intothe medium around the cells so only
filtration is needed
Stage (3): Purification of enzymes:
-Finally, the enzymes can be purified (if required-this is not always necessary) and packaged in a
form that can be easily used.
- Enzymes to be used in washing powders are formed into tiny capsules covered with a non-reactive
substance. This is to prevent them coming into contact with the skin of the person using the washing
powder, as they can cause irritation or allergies in some people.

e.g.(2) Manufacturing Mycoprotein (biomass) ,(by continuous
culture):
- Sometimes, the entire organism that is grown in a fermenter is required, not just a substance that
it secretes. One example is Mycoprotein.
- Mycoprotein means 'fungus protein'
(a) Microorganism used:

-The fungus that is cultured is called Fusarium. It is made up of long, thin threads called hyphae.
-The fermenter does not contain moving paddles, as these would break up the fungal hyphae or
become entangled in them.
(b) Stages of production of Mycoprotein:

1- Use sterile large steel vessel called fermenter to grow the micro-organism
2- This fermenter must be supplied with:
*glucose, which is usually obtained from starch that has been hydrolysed by enzymes. This provides
the growing fungus with a respiratory substrate for the release of energy, and also carbon that can
be used to make new carbohydrate, protein and fat molecules for growth and cell division.
*air, for oxygen to be used in aerobic respiration
*ammonia; as a source of nitrogen to make proteins and nucleotides
*water and salts; are needed for protein synthesis
*small amount of trace elements such as Zn, Cu, iron are added in manufacturing of Mycoprotein
to act as co-enzyme
*The temperature, pH and oxygen content of the fermenter are kept constant, providing optimum
growing conditions
3- Then cells produced by asexual reproduction are collected and dried, this product is called SCP.
(c) Extraction and Purification:

- The liquid culture containing the fungi is run off from the base of the fermenter and then
centrifuged to separate the hyphae from the liquid.
- Then filtration and steam treatment to purify the product.
Advantages of SCP Disadvantages of SCP
1-Cheap 1-Not accepted by people

2-Source of proteins and fibres for 2-Has unpleasant taste.
vegetarians -The fungal hyphae contain high
3-Rapid source of proteins concentrations of RNA, which would give
4-Free of hazards as pesticides it an unpleasant taste. Enzymes are
5-Source of minerals and vitamins used to break this down
6-Low in fat, no cholesterol 3-Has no smell; not attractive
7-Easily stored as a powder
8-Makes use of some wastes as
molasses
9-Less energy wasted
10-Less pollution
e.g.(3) Manufacturing Penicillin Antibiotic: (In batch culture):

Antibiotic: is a chemical substance, produced by a micro-organism (bacterium or fungus) which
will inhibit the growth or replication of other micro-organisms without harming cells of the injected
organism.
-Penicillin is produced by a variant of batch culture process called fed batch culture. During the
fermentation, a carbohydrate source (often corn steep liquor) is added about every 30 minutes. This
can keep the fermentation going for a longer time, and therefore produces more penicillin, than
standard batch culture would do.
(a) Microorganism used:
-A fungus called Penicillium.
(b) Stages of penicillin production:
1- A fermenter is set up as described before.(see figure)
2- Penicillium does not make penicillin all the time.
3- Penicillin production only begins after the fungus has been growing in the medium for a while.
4- It is said to be a secondary metabolite produced during stationary phase with limited nutrient
supply.
5- This means that we have to keep on setting up new fermentations.
6- The fungus is grown in the fermenter until the maximum amount of penicillin has been produced.
7- Then the fermentation is stopped and the antibiotic harvested.
8- The fermenter is cleaned out, and then a new culture of Penicillium is put in and the process
started all over again.
The sigmoid (s-shaped) growth curve for a population:

1-lag phase:
-birth rate is higher than death rate, slow increase in population growth as organisms are still
adapting to the environment.
2-log or exponential phase:
-rapid increase in population growth, organisms are well adapted to the environment, high
reproductive rate; enough nutrients and space are available.
3-stationary phase:
-birth rate = death rate, limiting factors are found, e.g. nutrients shortage, competition..etc
4-death or decline phase:
-death rate is higher than birth rate, accumulation of wastes, and severe shortage of nutrients,
spread of disease.
How antibiotics help to kill micro-organisms in general:

1-inhibiting protein synthesis interfering with transcription or translation
2-interfering with the synthesis of bacterial cell walls such antibiotics are only effective when the
bacteria are growing.
3-interfering with the functioning of the cell membrane the bacteria will lose its ability to control
the uptake or removal of water and other molecules.
4-inhibiting enzyme activity this will disrupt metabolism.

The mode of action of Penicillin on bacteria:
-Penicillin is described as a broad spectrum antibiotic i.e. it is effective against a wide range of
bacteria.
- It is one of the antibiotics which work by interfering with the synthesis of new cell walls.
Specifically, it inhibits the enzymes involved in the synthesis of cross links between the
peptidoglycan polymers in bacterial cell walls.
1- Bacterial cells have walls made of substances called peptidoglycans. These are long molecules
containing peptides (chains of amino acids) and sugars.
2- In the bacterial cell wall, they are held together by cross-links that form between them.
3- Penicillin inhibits the enzymes that build these cross-links, the glycoprotein peptidases.
4- When a newly formed bacterial cell is growing, it secretes enzymes called autolysins, which
make little holes in its cell wall.
5- These little holes allow the wall to stretch, and new peptidoglycan chains link up across it.
6- Penicillin prevents the peptidoglycan chains from linking up, but the autolysins keep making new
holes.
7- The cell wall therefore becomes progressively weaker.
8- Because the bacteria are always in a watery environment, they constantly take up water by
osmosis, and eventually the weakened wall cannot withstand the pressure exerted on it by the cell
contents and the cell bursts.
Why penicillin does not affect viruses:

1- Viruses do not have any form of cell structure such as cell wall, peptidoglycan , or glycoprotein
peptidase or metabolism hence antibiotics are ineffective against viruses.
2- Viruses replicate only within the living host cells, and make use of the living host cell's
transcription and translation mechanisms. These are eukaryotic mechanisms and thus are not
affected by any antibiotics, which affect only prokaryotic mechanisms.
3- The absence of any sort of cell wall means that penicillin has no effect on viruses.
explain why the widespread use of antibiotics increases the

likelihood that resistant strains of bacteria will evolve:
1-mutation in bacterial plasmid; changing their DNA
2-whithin natural population of bacteria, some individuals have alleles of genes on their plasmids
which give them resistance to a particular antibiotic
-resistant bacteria possess enzymes that break down penicillin such as penicillinase or B-
lactamase e.g. all strains of Mycobacterium tuberculosis are resistant to penicillin
3-bacteria cause an infection, leading to treatment of the infected person with antibiotic
4-the antibiotic will kill susceptible bacteria, but resistant bacteria will survive
5-only resistant bacteria will reproduce, resulting in an increase in the frequency of the bacteria
that are resistant to that particular antibiotic
6-there will be an increase in the allele frequency for the allele of the gene that gives resistance
in the population of bacteria
7-in the future, people will be infected by bacteria more likely to carry the alleles for resistance
8-to make matter worse, plasmids can be even transferred between different species of pathogenic
bacteria easily by vertical transmission, or horizontal transmission, or transduction. This
increases the chance that resistance strains of harmful bacteria may develop and make it extremely
difficult to treat diseases
vertical and horizontal transmission of resistance in bacteria:

-resistance genes are usually carried on the small, circular pieces of DNA called plasmids.
-A plasmid with one or more antibiotic resistance genes on it is called an R plasmid.
- When the bacteria are exposed to an antibiotic, most of them are killed, but the one or two
resistant ones may survive.
- They can now breed freely, producing a whole population of bacteria that have inherited the
resistance gene.
-Plasmids carry genes that control their own replication, so that they can multiply independently of
the bacterial
- R plasmids pass into new bacterial cells in two ways:
1) When a bacterial cell divides, each daughter cell receives a copy of the bacterial chromosome
and about half of the parent cell's plasmids. This is called vertical transmission.
2) A bacterium a copy of a plasmid to another bacterial cell in the process of conjugation. This is
called horizontal transmission. The recipient bacterium may be of the same or of a different
species, increasing the chance that resistant strains of harmful bacteria may develop.
-Sometimes, plasmid DNA is incorporated into the bacteria chromosome, and then it can be
transferred between by bacteriophage viruses in a process called transduction.
-Where there is widespread use of antibiotics, such as in hospitals or on farms, resistance quickly
spreads among different species of bacteria. Resistance may first appear in a non-pathogenic
bacterium, but then be passed by conjugation to a pathogen. Bacteria where there is widespread
use of antibiotics may have R plasmids carrying resistance genes for several different antibiotics,
giving multiple resistances.
problem caused by development of antibiotic resistant strains of

bacteria:
-This presents major problems for doctors:
1- A patient suffering from an infection by a resistant strain of a bacterium, givin the usual antibiotic,
may become seriously ill before the resistance is recognized and another antibiotic used.
2- Some antibiotics need to be kept as 'last resort' to be given to patients suffering infection from a
strain of bacteria with multiple resistances. But when such an antibiotic is used, there is the risk of
the bacterium developing resistance to it. Alternatively, a different bacterium may develop
resistance, and this could spread to the species with multiple resistances by conjugation.
Example (1):
-At one time the antibiotic vancomycin was the antibiotic of last resort. Methicillin-resistant
Staphylococcus aureus (MRSA) had become resistant to several antibiotics and caused dangerous
infections after surgery, which were mostly controlled by vancomycin. Then, another bacterium,
Enterococcus, developed resistance to vancomycin, and now vancomycin resistance is common.
Example (2):
-Recently, antibiotics called carbapens have been the antibiotics of last resort for use on bacteria
with multiple resistances. In 2009, carbapens-resistant Klebsiella pneumoniae was found in Greece.
By 2010 it was also found in Cyprus, Hungary and Italy, and in Greece the proportion of infections of
Klebsiella pneumoniae that were carbapens resistant had risen to over 25 %. In 2010, Greece used
more antibiotics than any other European country.
How to reduce chances of developing more antibiotic-resistant

bacteria:
-Fortunately, a bacterium resistant to a particular antibiotic may not be resistant to that antibiotic
with a slightly altered chemical structure. Chemists can make such semi-synthetic antibiotics to
extend the range available.
1- Using antibiotics only when appropriate and necessary. Also we can use two combined antibiotic
to kill resistant bacteria
2- Reducing the number of countries in which antibiotics are sold without a doctor's prescription.
3- Avoiding the use of so-called 'wide spectrum' antibiotics and using instead an antibiotic specific to
the infection.
4- Making sure that patients complete their course of medication.
5- Avoiding using antibiotics in farming to prevent, rather than cure, infections.
6-change the selection pressure used in killing resistant bacteria e.g water, nutrients, salt
concentration instead of antibiotics

e.g.(4) monoclonal antibodies:
ANTIBODIES
Definitions that you must know from AS:
Self: the products of the body's own genotype, which contain proteins (normally, but see antigen)
that do not trigger an immune response in the body's own immune system. Inside the body that
produced them, self proteins do not act as antigens (and so do not stimulate an immune response)
but, if introduced into another body, they become non-self.
Non-self: proteins (normally, but see antigen) that contain sequences of amino acids that are not
the same as any self proteins and that can be recognised by immune system cells and can trigger an
immune response in the body. Sometimes these are termed non-self antigens. When cells are
infected by an antigen, or become cancerous, some of their antigens may be changed from self to
non-self.
Antibody: A globular glycoprotein secreted by a plasma cell. An antibody binds to the specific
antigen that triggered the immune response, leading to destruction of the antigen (and any
pathogen or other cell to which the antigen is attached). Antibodies have regions that vary in shape
(variable regions) that are complementary to the shape of the antigen. Some antibodies are called
antitoxins and prevent the activity of toxins (prevent the activity of sometimes called neutralise,
which does not mean that this is anything to do with pH).
Antigen: a protein (normally some carbohydrates and other macromolecules can act as antigens)
that is recognised by the body as foreign (so as non-self) and that stimulates an immune response.
The specificity of antigens (which is a result of the variety of amino acid sequences that are possible)
allows for responses that are customised to specific pathogens.
How antibody works?

1-has many binding site to cause agglutination of bacteria.
2-attach to bacteria making them less active and easier for phagocyte to engulf.
3-neutralise viral and bacterial toxins and prevent them entering cell.
4-they can make holes in bacterial cell walls, with the help of other molecules so that they will die
from excessive water uptake.
During a Primary Immune Response:

1- T-helper lymphocytes detect the presence of an antigen or a non-self protein, then secrets
cytokine to stimulate the specific B-lymphocyte
2- B-lymphocytes respond by dividing by mitosis.
3- It forms memory and plasma cells.
4-Plasma cells secrete antibodies.
5-Having early infection of a disease will cause the production of antibodies against this disease in
your body, so even after you have recovered, and you do not have the infection any more, the
antibodies will still appear in your blood and this helps during the secondary immune response if you
are re-infected by the same antigen again.
Features of active and passive immunity

Features
Immuni antigen immune Time before antibodies product of protectio
ty encountere response appear in blood memory n
d cells
Active yes yes Several weeks during yes permanen
primary response (slow) t
Passiv no no Immediate(fast) no temporary
e
MONOCLONAL ANTIBODIES:
Monoclonal antibodies:
-they are large quantities of identical antibodies produced by a clone of genetically identical plasma
cells.
-They have many uses in medicine, and they are produced to be effective against a single, specific
antigen.
The general idea of producing monoclonal antibodies using the hybridoma method:
-Monoclonal antibodies are obtained from clones of single B cells. Unfortunately, B cells will not grow
in culture and this problem has to be overcome by fusing them with malignant B myeloma cells
(cancerous cells).
-Myeloma cells will continue to grow and divide indefinitely, though they do not produce antibodies.
The fused cells produced from myeloma cells with B cells are known as hypridomas.
-The hybridoma cells will also continue to grow and divide (given suitable and adequate nutrients)
and they do secrete antibodies.
-The antibodies that they secrete are the specific antibodies that were produced by the original clone
of B cells.
Stages of the production of monoclonal antibodies:

1- A mouse is injected with antigen for which the antibodies are required.
2- An immune response takes place and the mouse plasma cells start to make the antibody.
3- Plasma cells are extracted from the mouse spleen.
4- The plasma cells are fused with B cell myeloma cells using Fusogen (a chemical that makes
surface cell membranes join).
5- The resulting hybridoma cells are separated individually and allowed to grow, divide and produce
antibodies.
6- Some antibodies are removed and tested with the relevant antigen, to make sure they are the
correct monoclonals.
7- Those hybridoma cells which are producing the required antibodies are cultured in a large
fermenter.
8- The monoclonal antibodies are harvested and purified.
The use of monoclonal antibodies in the diagnosis and treatment of
disease and pregnancy testing:
(a)DIAGNOSIS:
-because the monoclonal antibodies produced from a clone of B cells are all identical, they can be
used to identify macromolecules with a very high degree of specificity. For example, they are now
routinely used for the following:
1- Blood typing before transfusion.
2- Tissue typing before transplant.
3- Identification of pathogens: using monoclonals, it is now possible to distinguish between different
strains of certain pathogens, which would otherwise be very difficult. This can speed up the choice of
patient treatment.
4- Identification and location of tumours.
5- Detection of HIV, e.g. ELISA test.
6- Distinguishing between different types of leukaemia (blood cancer).
Example (1): ELISA test:

-Monoclonal antibodies can be used in an ELISA test to diagnose an infectious disease, by detecting
the presence of particular antigens in the blood. ELISA stands for enzyme-linked
immunosorbent assay.
1- The monoclonal antibody is immobilised on the surface of a small container, such as a small glass
well. The liquid to be tested (for example, blood plasma) is added to the well. If the antigens are
present, they will bind to the antibodies.
2- The contents of the well are then rinsed out. The antigens stay tightly bound to the antibodies.
3- Now another solution containing the same monoclonal antibodies is added to the well. These
antibodies also have a reporter enzyme combined with them. They bind with the antigens already
attached to the antibodies in the well. The well is again rinsed out, so the enzymes will all be washed
away unless they have bound with the antigen.
4- The substrate of the enzyme is then added. If the enzyme is present - this is only the case if the
antigen investigated was present, then the substrate is changed to a coloured product by the
enzyme. The colour change therefore indicates the presence of the antigen in the fluid being tested.
Example (2): identifying Location of blood clots in the body of a person thought to have
thrombosis:
1- The antibodies are produced by injecting a mouse with human fibrin (the main protein found in
blood clots).
2- The mouse makes many B lymphocytes that secrete the antibody against fibrin, and these plasma
cells are collected from its spleen.
3- The plasma cells are fused with cancer cells to form hybridomas that secrete the antifebrin
antibody, which is labelled using a radioactive chemical that produces gamma radiation.
4- The labelled antibodies are then introduced into the patient's blood. As they are carried around
the body in the bloodstream, they bind to any fibrin molecules with which they come into contact.
5- A gamma- ray camera is then used to detect the position of the antibodies, and therefore blood
clots, in the person's body.
Example (3): Identifying location of a tumour:

-a monoclonal antibody can be used to track down cancer cells, which have different proteins in their
cell surface membranes than normal body cells and can therefore be picked out by antibodies.
Advantages of using monoclonal antibodies than conventional

(normal) methods to diagnose disease:
1- Quicker diagnosis than having to culture organism.
2- So quicker treatment.
3- Not all viruses can be identified by conventional methods.
4- Difficult to identify pathogen by microscope.
5- Non-pathogenic diseases like cancer are only found by antibody (specifically).
7- Will not harm other cells.
8- Reduce dose of drug, thus reducing the side effects.
(b) TREATMENT:
-there are two ways in which monoclonal antibodies are used in the treatment of disease:
1- Production of passive vaccines monoclonal antibodies can be injected directly in the blood to
attack a particular pathogen.

2- 'Magic bullets' monoclonal antibodies can be produced which will combine specifically with
cancer cells. It is now possible to bond cancer drugs to such antibodies. In this way, the
drugs can be delivered directly to the tumour, thereby reducing the risk of damaging
healthy cells.
Example: The monoclonal antibody rituximab binds with a protein called CD20, which is found only
on B lymphocytes. This can be useful in the treatment of a type of cancer called non-Hodgkin
lymphoma, in which B cells divide uncontrollably, when rituximab binds to the B cells, it makes them
'visible to the immune system which destroys them. New B cells are made in the bone marrow, and
these replacement cells may not be cancerous.
Difficulties in using monoclonal antibodies in treatment of disease:

1- It can be difficult to produce antibodies that bind only to cancer cells and not to other body cells.
2- Another problem is that, because the monoclonals have been produced by mice, they are
recognised as foreign by the human patient's body and may be destroyed before they reach their
target.
(c) PREGNANCY TESTING:
-soon after becoming pregnant, women produce a hormone called human chorionic
gonadotrophin (HCG). This hormone is produced by the placenta, so can only be present during
pregnancy.
-Monoclonal antibodies are now used to detect the presence of this hormone in the urine such a
pregnancy test can be done very quickly and easily.
-This type of pregnancy testing kits work as follows:

1- The kit consists of a 'sampler' which is a type of dipstick with an absorbent pad.
2- On the surface of the pad are monoclonal antibodies, specific to HCG and to which coloured latex
dye particles are attached when the pad is moistened, the molecules of the antibody begin to
move.
3- The sampler is dipped into urine if HCG is present, it will bind to the monoclonal antibodies and
will be drawn up the pad.
4- Further up the pad is an area at which there is a line of immobilised HCG antibodies.
5- Any HCG molecules drawn up the pad will bind with these antibodies and the latex dye particles
will create a coloured line. This is a positive result.

6- Further along the pad is a second line of immobilised, to which will bind any HCG antibodies
without HCG. A coloured line in this second area (but no coloured line in the first area) will confirm
that the HCG antibodies have moved up the pad, but that the result is negative.
OR:
1. (stick / kit) dipped in (early morning) urine sample ;
2. hCG / urine, moves up strip ;
3. idea that hCG acts as antigen ;
4. (mobile) antibody also bound to, indicator / gold ;
5. (mobile) antibody in stick binds to hCG ;
6. ref. to variable region (of antibody) ;
7. ref. to specificity (of antibody) ;
8. ref. to monoclonal (antibody) ;
first window or region
9. second antibody is, immobilised / fixed ;
10. first antibody and hCG complex binds to second antibody ;
11. coloured band indicates pregnancy ;
second window or region
12. immobile antibody binds to mobile antibody-gold complex ;
13. second coloured band shows strip is working
Advantages of using monoclonal antibodies in pregnancy testing:

1- Can be done at home as it is easy to use.
2- Cheap.
3- Result produced quickly.
4- Result produced accurately.
5- Done in early pregnancy.
6- Safe to use.

T Crop Plants
-In most parts of the world, there has traditionally been one food that forms the bulk and basis of
most people's diets. This is called the staple food. It is usually a starchy, cheap food, providing
plenty of carbohydrates to supply the bodies daily energy needs.
Cereal Crops:
-Some of these foods rice, wheat, barley, sorghum and millet are cereal crops. A cereal is a
grass, which we grow to harvest and eat the grain (seeds) that it produces.
-Taro, by contrast, is not a cereal; it is a kind of yam that is grown for its starchy underground stem.
In South America, potatoes may form the staple food. They form starchy, swollen underground
stem tubers.
-Dates are the fruit of palm trees, and of course banana are also fruit and contain a lot of sugar as
well as starch.
Note: To increase the yield of a growing crop especially staple foods:

1- Add Fertilizers 2- Pest control 3- Irrigation 4- Optimum CO 2 5- Optimum light 6-
Optimum temperature
The significance of the inclusion of cereal grains in the human diet:
(a)-The final nutritional value of a cereal crop depends greatly on the amount of processing
involved. The nutritional value of cereal grains include:
1- Carbohydrates (mainly starch stored in the endosperm) are a major component of cereals
usually 70 to 80 %. Hence, they are a very important source of energy.
2- Source of protein (stored in the aleurone layer). Most cereals have a protein content of
between 6 and 14 %. In general, millets, rice and maize are at the low end of the protein range, rye
and barley are intermediate and wheat and oats are high. Cereals do not always provide a balance
of amino acids. They are especially low in lysine, an essential amino acid, which means that other
sources of this need to be included in a balanced diet.
3- All cereal grains are low in fat. This is usually 2 4 %, though oats are an exception with 7.5 %.
However, they are high in essential fatty acids, such as linoleic acid. Most of the fat is found in the
germ of the grain.
4- Vitamins all cereals provide a good source of the B group vitamins (thiamin, riboflavin, niacin,
B6, folic acid, biotin and pantothenic acid) and the fat soluble vitamin E. However, they are deficient
in vitamins A, D and C.

5- Minerals a range of minerals are found in most cereals. These include potassium, magnesium,
phosphorus, iron and zinc. Also cereals contain plenty of calcium (present in the 'glue' that holds
their cell walls together).
6- Fibre of cellulose and lignin cereals are an excellent source of dietary fibre. Wholegrain meal
or flour will contain much more fibre than grains which have been processed and refined. Fibre helps
peristalsis to take place in the alimentary canal.
(b)- Cereal grains are dry since they have very little water content in their seeds , and can therefore
be stored for long periods of time.
(c)- They can be cultivated in different environmental conditions all over the world.
C4 Plants:
-In the light-independent stage of photosynthesis, carbon dioxide combines with RuBP to form a six-
carbon compound, which immediately splits to form two three-carbon molecules. Plants that do this
are called C3 plants.
-Sugarcane, rice, maize and sorghum are C4 plants. This means that instead of first making a 3-
carbon compound during the Calvin cycle, they produce a 4-carbon compound.
- At high temperatures and high light intensities, the enzyme rubisco tends to catalyze the
combination of RuBP with oxygen rather than with carbon dioxide. This is wasteful and reduces the
rate of photosynthesis since less RuBP is available for CO 2 fixation. This reaction is called
'photorespiration', because it uses oxygen.
Photorespiration:
-it is a reaction in which RuBP combines with oxygen rather than carbon dioxide, it occurs at high
temperatures and high light intensities
*Why the rate of photosynthesis in C4 plants is high at higher

temperature:
1- C4 enzymes are very tolerant / have higher optimum temperature (45 C ) than C3 (30 C).
2- Has structural features to reduce photorespiration (see below).
3- Adapted to survive in hot climate.
Stages of photosynthesis in C4 plants:

1- Carbon dioxide is absorbed by the mesophyll cells, which are in contact with air.
2- These cells contain an enzyme called PEP carboxylase, which catalyses the combination of
carbon dioxide from the air with a three-carbon substance called phosphoenolpyruvate, or PEP to
form oxaloacetate.
3- Still inside the mesophyll cells, the oxaloacetate is converted to malate.
4- Malate is passed on to the bundle sheath cells.
5- Now the carbon dioxide is removed from the malate molecules and delivered to RuBP by rubisco
in the normal way. The light-independent reaction or the Calvin cycle then proceeds as normal,
inside the bundle sheath cells.
The structural adaptations of the leaves in C4 plants to avoid photorespiration:
1- Around the vascular bundles are arranged a group cells known as bundle sheath cells. These
cells contain RuBP and Rubisco, but have no direct contact with the air and, therefore are not
exposed to high concentrations of oxygen. Bundle sheath cells contain starch-rich plastids that
store starch.
2- Around the bundle sheath cells is another ring of mesophyll cells. These are tightly packed cells
and are in contact with air spaces, but have no air spaces between them, ensuring that no oxygen
reaches the bundle sheath cells. Mesophyll cells contain green chloroplast, where the light-
dependent reactions of photosynthesis take place.
3- The mesophyll cells contain an enzyme called PEP carboxylase, which catalyses the
combination of carbon dioxide with a compound called phosphoenolpyruvate or PEP to form
oxaloacetate. PEP carboxylase, has high optimum temperature (does not denature easily), has
higher affinity for CO2, and does not accept O2 unlike RUBISCO enzyme.
4- This oxaloacetate is then converted to malate (malate shunt), which is passed on to the bundle
sheath cells, where carbon dioxide is removed from the malate. This Maintains high CO 2
concentration in bundle sheath cells. Then carbon dioxide is combined with RuBP in the usual way.
The Calvin cycle then proceeds as normal.
5- Photorespiration is avoided.
6- Hinge (motor) cells are big cells in upper epidermis, used to roll leaf to reduce its surface area .
7- Thick waxy cuticle to reduce water loss or transpiration, so wax does not melt, and provides
shiny surface that reflects radiation
FLOWER AND FRUIT STRUCTURE

I-FLOWERS:
-Flowers are the organ in plants in which sexual reproduction takes place. The male gametes are
contained in pollen grains, which are made in anthers attached to long filaments. The female
gametes are contained in ovules, inside ovaries. At the top of the ovary is a long style, with a sigma
at the top. During pollination, pollen grains are deposited on the sigma.
Stages of sexual reproduction in a flowering plant:

(A) - POLLINATION:
-It is the transfer of pollen grains from the male part of the plant (anther of stamen) to the female
part of the plant (stigma) by wind or insects.
-There are two types of pollination:
Self Pollination Cross Pollination
- It is the transfer of pollen from any stamen to - It is the transfer of pollen from one plant to
any stigma on the same plant (not necessary on the sigma of another plant of the same
the same flower), e.g. in cereal crops, grasses. species
The genetic outcomes of self and cross pollination:

-Assuming that pollination results in successful fertilization, the genetic outcomes will be as follows:
Self Pollination Cross Pollination
Decreased genetic variation / increased Increased genetic variation / Decreased genetic

genetic uniformity uniformity
Increased homozygosity / decreased Increased heterozygosity / decreased homozygosity

heterozygosity
Harmful recessive characteristics more Harmful recessive characteristics less likely to be

likely to be expressed in offspring expressed
Reduction in gene pool Maintenance of gene pool
Inbreeding depression reduces fitness Gives hybrid vigour ( heterosis = outbreeding

(plant becoming weak and the strain is enhancement), so fitness maintained (reduces
dying out) inbreeding depression)
Increase desirable characteristics, e.g.(resistance

to disease and high nutrients content)
Some organisms may mutate to survive changing
environment (well adapted)
-All of these outcomes mean that populations which result largely from cross pollination are
phenotypically more variable, which gives them more evolutionary potential, and means that they
are better able to adapt to changes in the habitat or environment.
NOTE:
Inbreeding sexual reproduction between closely related organisms (as a result of self
pollination)
Interbreeding two different families crossed to increase hybridisation
Outbreeding sexual reproduction between two unrelated organisms (as a result of cross
pollination)
*Flowers can be pollinated either by insects or wind:
(1) Adaptations of insect pollinated flowers:

feature Description
Flower Larger
Petals Attractive, coloured, scented, often with nectar and guide lines to attract insects,
large to protect stamens and carpels inside.
Stamen Stiff filament and anther to obstruct visiting insects to make sure pollen is stuck
s on their backs.
Pollen Small quantities, rough or sticky to catch insect hairs.
Stigmas Small, unexposed, with stiff style to obstruct insects.
(2)Adaptations of wind pollinated flowers:

-All cereal crops have flowers that are pollinated by the wind. The structure of a maize plant and its
flowers shows characteristic of wind-pollinated plants. Maize plants have separate male flowers and
female flowers, both on the same plant.
feature description
Flower -Flowers are borne at the end of long stalks, held well high above the foliage so that the
wind can catch them. In some cases the flowers appear before the leaves.
-The male flowers are above the female flowers, enabling pollen to fall onto the stigmas
below.
Petals There are no petals, as there is no need to attract insects, and petals would shield the
anthers and stigmas from the wind.
Stigma Stigmas are large, branched and feathery to provide large surface area and held
outside the flower to catch the wind-blown pollen.
Stame Stamens are pendulous and also hang outside the flower.
n
anther -Anthers are versatile i.e. they are attached at the midpoint, so they will swing freely in
the wind.
-The anthers dangle out of the flower on long, flexible filament, so it is easy for the pollen
to be blown away
pollen -Pollen grains are relatively light, small and smooth, so easily can be carried by the wind.
-Pollen grains are produced in large quantities.
nectar Absence of nectarines.
scent Absence of scent.
An insect-pollinated flower A wind-

pollinated flower
(B) FERTILISATION:
-it is the fusion of haploid male gamete nucleus with female haploid gamete nucleus to form a
diploid zygote.
1- Pollen grain has three haploid nuclei (2 male gametes + 1 haploid tube nucleus).
2- Pollen tube grows through the style grows in response to chemicals on the stigma and penetrates
the ovule through micropyle, and pass through synergid cells [used to support egg cell].
3- One male gamete fuses with egg cell nucleus forming diploid (2n) zygote.
4- Second male gametes fuse with the diploid primary endosperm nucleus (2n) forming triploid
endosperm (3n) nucleus.
-This is why plants are known to have double-fertilisation.
5- Antipodal cells are used for nutrition.
Example: Maize as a wind pollinated plant:

-Maize, Zea mays, is also known as corn in some parts of the world. It is a sturdy, tall grass with
broad, strap-shaped leaves. -Maize grows best in climates with long hot summers, which provide
plenty of time for its cobs (seed heads) to ripen.

(C) SEED AND FRUIT FERMATION:

II-The structure of the fruit in maize and the function of the
endosperm:
-The individual fruit of maize is a dry fruit (known, botanically, as a caryopsis) and contains a single
seed.
1- After pollinations and fertilisation, the fertilised ovule develops into a seed. The zygote develops
into an embryo plant, inside the seed the embryo or the germ consists of a miniature plant axis
to which are attached around five embryonic leaves (plumule) and a radical, from which the root will
develop. The germ is the source of maize 'vegetable oil'.
2- Endosperm nucleus (3n) in the ovary develops into the endosperm tissue. This contains food
stores, mostly starch, which will be used by the embryo when the seed germinates. Endosperm store
nutrients for energy release by respiration needed for growth of embryo until the leaves are formed
and are able to photosynthesise. -The
endosperm takes up about two thirds of the volume of the seed and accounts for around 86 % of its
dry weight. The principal component of the endosperm is starch, together with about 10 % protein
(gluten).
3- Around the end of the endosperm is aleurone layer. This contains enzymes that are activated
when the seed germinates. The enzymes break down the starch in the endosperm.
4- The ovary develops into a fruit (the maize grain), with the seeds inside it. In maize, each ovary
contained a single ovule, so each fruit contains a single seed.
5-The outer layer of a seed is the fruit coat which is formed by the fusion of testa and fruit wall.
Testa developed from the integuments of the ovule, and the fruit wall or the pericarp developed
from the ovary wall

How sorghum is adapted to survive in arid environments:
- Xerophyte:
-it is a plant which has a number of structural and physiological features which allow it to live
successfully in areas of low water supply, i.e. arid environments.
-Sorghum is the fifth most important cereal crop in the world. It is of a particular importance in
areas of low rainfall
Sorghum can be grown even where it is too dry to grow maize..
Adaptations of sorghum for growth in dry conditions:
Features How it helps the plant to survive in dry conditions
Sorghum plants have a relatively This reduces the area from which water can evaporate in
small leaf area. transpiration, therefore reducing the rate of water loss.
Sorghum leaves (especially lower -This is impermeable to water and therefore decreases
surface) and internodes are covered water loss.
with a layer of wax. -also to reflect radiations
Sorghum leaves have a row of -This decreases the surface area of the leaves in contact
motor cells (bulliform cells) along with air, and therefore reduces the rate of loss of water
the mid rib that allow the leave and vapour from the leaves to the air.
strengthening tissue -Moist air is trapped inside the rolled leaf.
(sclerenchyma) below the vascular -less wilting of the plant
bundles to roll up when the cells Note:
are short of water, hiding away half -when roots of plants are exposed to dry air, its water
of the stomata potential decreases, as water is lost by evaporation, and no
water uptake by root cells to compensate the loss.
-Sorghum leaves have relatively -Moist air, with a high water potential, is trapped around the
few stomata and few air spaces, stomata. This reduces the water potential gradient between
and these are sunken below the leaf the air spaces in the leaf and the outside, reducing the rate
surface. of loss of water vapour from the leaf.
-They are only found well away from - to increase the distance that the water has to diffuse
the vascular tissues, before it is lost from the leaf
The root system is extensive and The roots are able to absorb water even when there is very
finely branched, also wide and deep little water in the soil.
spread in soil
The plant can close its stomata and The plant is able to survive during a prolonged drought,
become dormant for long periods or resuming growth when conditions improve.
Dormancy during drought In which their metabolism slows right down. When it rains,
they begin growing again.
it is a C4 plant As long as there is sufficient water, sorghum can continue

to photosynthesise even when it is very hot and sunny.
Their enzymes have a higher optimum temperature and can
avoid photorespiration
How rice is adapted to grow with its roots submerged in water:

- Rice may be described as 'swamp plants'. As crop plant, it is often grown partly submerged in
paddy fields. Fields are flooded, then ploughed and the young rice plants are planted in the resulting
mud. Oxygen levels in the mud fall very rapidly as the oxygen is used up by respiration of bacteria in
the mud and levels remain very low in the flooded paddy fields since oxygen can only diffuse very
slowly through the water.
Adaptations of rice for growth with roots submerged in water:
Features How it helps the plant to survive when roots are

submerged
Cells are tolerant to high -When roots are submerged in water, less oxygen is available
concentrations of ethanol. than when the soil contains air spaces. Cells therefore respire
anaerobically.
-This results in the production of alcohol, which would normally
be toxic. Rice root cells show an unusually high tolerance to
alcohol they are able to produce high levels of the enzyme
alcohol dehydrogenase which breaks down ethanol. This
allows the plants to grow actively even when oxygen is scarce,
using energy from anaerobic respiration.
Stems have tissues called -Aerenchyma allows oxygen from the air to diffuse down to the
aerenchyma, containing large roots. Gases are able to diffuse through the aerenchyma to
air spaces. other parts of the plant including those under the water. This is
supplemented by air that is trapped in between the ridges of
the underwater leaves.
-These leaves have a hydrophobic, corrugated surface that
holds a thin layer of air in contact with the leaf surface.

Some types of rice are able to The leaves remain exposed to the air, which facilitates gas
grow elongated stems to keep exchange (CO2, O2, also light) for photosynthesis and
their leaves above the water as respiration. The extra growth is controlled by ethylene (ethane),
its level rises. a gaseous plant growth substance produced more rapidly in the
submerged parts of the plant. It collects in these parts because
it diffuses only very slowly through water. The ethylene
stimulates the production of gibberellin, which stimulates cell
division and cell elongation.
The roots are very shallow This allows them some access to the higher levels of oxygen in
the surface water.
Rice is a C4 plant Can continue to photosynthesise even when it is very hot and
sunny. rice enzymes have a higher optimum temperature and
can avoid photorespiration
Crop Improvement:
-New varieties of crops are produced by both conventional breeding techniques (selective
breeding) and genetic modification.
-Selective breeding is more common, easier, faster, and cheaper and can be done by farmers
themselves ,compared to genetic engineering.
(A) CROP IMPROVEMENT BY SELECTIVE BREEDING
Example (1): Hybridisation leading to polyploidy in wheat:

(see figure)
Hybrid:
-it is a plant which is the result of interbreeding between two different species.
Polyploid:
-It is a plant which has more two sets of chromosomes.
1- The formation of polyploids has been important in the evolution of plant species though less
important in animals, as animal polyploids are often not viable.
2- It is now possible to include the formation of polyploids by preventing spindle formation, using
chemicals such as colchicines.
3- Among plant species, polyploids are generally hardy and higher yielding than their parent species
making them important food crops.
4-The ancestors of wheat are small, not very robust, and produce small ears of small seeds, in
contrast to modern hexaploid (6n) wheat.

Advantages of (6n) wheat:
1- Put all energy in making seed rather than being tall.
2- Easy to harvest as they are short.
3- Produces less straw, so less money is needed to get rid of it, Less pollution (usually straw is
burnt).
4- Hybrid vigour: it grows larger ears (more grains) than diploid plant (2n).
5- Today, selective breeding has produced many different varieties of wheat. Much of it is grown to
produce grains rich in gluten, which makes them good for making bread flour. For making other food
products, such as pastry, varieties that contain less gluten are best.
When farmer do pure breeding of crop to increase yield, but it does

not increase steadily then this is because:
1- Genetic variation.
2- Environmental variations.
3- Experimental error or mutation.
Example (2): Producing vigorous, uniform maize through

inbreeding and hybridisation:
-Maize is one of the most widely grown crop plants. Growing conditions will vary considerably in
different parts of the world (soil, type, prevailing temperature, and rainfall.etc) hence, through
selection, inbreeding and hybridisation, growers have been able to produce varieties that grow
vigorously (and are therefore high yielding) and uniformly under the prevailing conditions.
- Assuming that conditions remain similar year after year, farmers can continue to grow the same
variety and expect to obtain a similar crop.
The characteristics which are desirable in a crop plant such as maize
are:
1- High yielding.
2- Disease resistant.
3- Good quality in terms of desirability to market.
4- Vigorous growth under the prevailing conditions.
5- Plants all grow to a similar height (making harvesting easier),(i.e. genetically identical)
6- Crops are all ready to harvest at the same time.( i.e. genetically identical)
7- Plants can grow in soil that is low in nutrition or water supply.
-Genetic uniformity is usually achieved through inbreeding (breeding a plant with itself, or with
other plants with the same genotype) for many generations. However, in maize, inbreeding results
in weak plants with low yields. This is called inbreeding depression.
-Maize breeding therefore involves producing hybrids between two inbred lines. Like most selective
breeding of cereal crops, it is done by commercial organisations not by farmers themselves.

Method:
1-Inbred lines (genetically uniform populations) of maize with desirable characteristics are identified,
and crossed with other inbred lines with different sets of desirable characteristics to produce a
hybrid more vigour than parents.
2- In order to carry out the inbreeding, or to carry out a cross to form a hybrid, pollen from a specific
male parent must be used to fertilise a specific female parent to:
a-Ensure that the cross intended is the only one that occurs, anthers are removed from some flowers
which will form the female parent. Pollen is transferred from the anthers of the male parent flowers
to the stigmas of the flowers without anthers. Muslin bags are then around the fertilised flowers to
prevent pollination by any other pollen.
b-Selection for measurable characteristics such as yield is done by measuring the characteristic and
choosing from breeding those plants that express it most strongly, e.g. having the highest yield,
Selection for disease or pest resistance is done by exposing the plants to disease or pest, which kills
any that are not resistant. The best of these hybrids are then chosen for commercial production
3-Seeds which result from such breeding are grown and plants showing the desirable characteristics
are bred again the process can be repeated for many generations.
4- Large quantities of the two inbred lines from which the hybrid was bred are grown, as it is from
these that all the seed to be sold will be produced.
5- 5-Each year the two inbred lines are bred together, and the seed collected from them to sell as
hybrid seed.
Advantages of producing seeds by hybridization:

1- This method of breeding avoids problems of inbreeding depression.
2- The hybrid plants are genetically uniform (Although they will be heterozygous for several genes),
because they all have the same two inbred parents.
Disadvantages of producing seeds by hybridization:
1- Expensive.
2- Farmers have to buy seeds every year rather than saving their own seeds to ensure uniformity
and heterozygosity since homozygous seeds show no hybrid vigour.
Hybrid vigour in produced maize:
- If two inbred lines are crossed, it will produce a hybrid that has a greater yield and is more vigorous
than either of the parental lines. This is known as hybrid vigour.
-This hybrid is heterozygous for most genes, so deleterious recessive alleles are hidden, but at the
same time it inherits the lack of variability from its parents. Such single cross hybridisation has been
used for selective breeding since the early 1960's to double the yield (from 4 8 tonnes per
hectare) and to breed uniform, high yielding maize.

(B) CROP IMPROVEMENT BY GENETIC MODIFICATION (ENGINEERING)
Example (1): Vitamin A enhanced rice

-The green parts of rice plants contain beta-carotene, which is a vital component of vitamin A.
However, there is no beta-carotene in the grains and those parts of the world where rice is the
principal staple food; small children are very prone to vitamin A deficiency.
What is vitamin A?
-Vitamin A is a fat soluble vitamin found in oily fish and dairy products. It is also made in our bodies
from carotene, the orange pigment found in carrots.
Where is vitamin A found in the rice grain?

1- Vitamin A is present in the aleurone layer of rice grains but not in the endosperm.
2- The aleurone layer is removed from rice when it is polished to produce white rice.
3- Brown rice still contains the aleurone layer.
4- In tropical countries, the aleurone layer goes rancid if the rice is stored for any length of time,
which is why white rice is produced and eaten instead.
5- Brown rice has more protein than white rice as protein is in aleurone layer, which is only in brown
rice (not polished).
6- Brown rice has less carbohydrate than white rice, as may be its endosperm is less in size than
white rice, or as it has more protein, so less carbohydrates per gram.
What is the importance of vitamin A?

-Vitamin A is essential for the operation of the body's immune system and a deficiency causes
increased risk of infection, night blindness and, in some cases, total blindness.
How the crop was improved by GM to solve this problem?

-The genetically modified rice is called golden rice, because it contains a lot of the orange pigment
carotene, which can be converted by human cells into vitamin A.
-Then the genetically modified rice was bred with other varieties of rice, to produce varieties that
would grow well in the conditions in different parts of the world.
Method of producing GM rice (golden rice):

- The first version of this rice used genes taken from daffodils and a bacterium Erwinia uredovora,
but the quantity of
carotene produced was not very large. Since then, new varieties containing genes from maize and
rice itself have been produced, which contain up to 31 g of carotene per 100g of rice.
- However, in the case of rice (and other crop plants, such as maize) a method has been developed
where the genes are delivered directly into the cells using small m-sized tungsten or gold bullets
coated with DNA. The bullets are fired from a device that works similar to a shotgun. This delivery
device is known as 'gene gun' and is now a common method used in the genetic transformation of
rice.
Steps:
1- Gene of vitamin A is extracted from a kind of bacteria and daffodil flowers.
2- Gene with its promoter is added to the plasmids.
3- Plasmids are taken by Agrobacterium tumefaciens.
4- Bacteria infect rice embryo.
5- Rice embryo with vitamin A gene will grow to adult plant that has vitamin A in its endosperm.
Advantages and Disadvantages of producing GM rice (golden rice):
Reduce blindness among The rice has to undergo further tests, for example, to check its
children. Children whose effects on human health, before it will become widely available.
diet consists largely of rice
would be able to get more
than half of their daily
requirement for vitamin A
by eating 200g of this rice
per day.
The researchers who It will also be necessary to incorporate the genes into different
developed this GM rice will varieties of rice that are suitable for growing in different parts of the
donate it free of charge for world.
use in developing
countries.
Cheap seeds The existence of this GM rice would possibly lessen efforts to tackle
the root causes of poverty and poor diet in some parts of the world.
Better quality food Some people argue that the changes made to the genes in the rice
could have harmful effects on people who eat it; however, there is no
evidence for this.

Improve health and GM crops still have not been grown in field trials in Asia as long as
immunity of individuals. many agricultural experts and environmental groups believe the
solution is not to go down the route of GM crops, but rather to aim for
a more balance diet, which would include more fresh vegetables,
which have a naturally high content of beta-carotene.
GM seed could be difficult for farmers in developing countries to

obtain
High cost of buying (new) GM seed / cannot use own seed
May not grow well in all conditions (as other traits not selected for)
Too expensive for people to buy / or for farmers to sell
Might reduce efforts to relieve poverty
May be genetically unstable, causes mutation, cancer
Reduces hybridisation
Reduces biodiversity
Advantages and disadvantages of producing Herbicide-resistant oils

seed rape (GM):
High rate of growth of GM. More use of herbicides, more pollution.
Herbicide resistant. There was no evidence that genetic engineering increased the
invasiveness of oil seed rape plants, where differences between
normal and genetically modified plants existed, the genetically
engineered plants were slightly less invasive than the unmodified
plants.
No need for sexual GM crops may be genetically unstable, causing mutation.

reproduction.
Other useful genes are not Genes from the GM (genetically modified) oil seed rape plants
harmed. might be able to spread into wild Brassica plants growing nearby,
and make them resistant to the herbicides.
Desirable genes can be Reduces hybridisation. Oil seed rape is able to hybridise with wild
identified and cloned. relatives, which are often, found growing close to rape fields.
However, after several years in which the GM oil seed rape has
been grown on a very large scale in Canada, and in trials in
Europe, only a very low such hybrids have been found.
Easy to control weeds. Some of the GM seeds produced could not germinate (infertile),
so less chances of producing a population of resistant plants.
Only weeds are killed, not -The risk of pollen transfer, by wind or by insects, is real. Oil seed
crops. rape interbreeds easily with two related species, wild radish and
wild turnip. Its flowers are adapted for insect pollination, but are
also pollinated by wind.
-Safe planting distances should be increased to allow the organic
farming industry to maintain its 'GM-free' certification.
Transgenic (GM crops) The genetically modified plant may become an agricultural weed.
production is much faster
than conventional breeding Pollen will transfer the gene to wild relatives, producing hybrid
offspring that are invasive weeds.
Herbicide-resistant weeds will evolve because so much of the

same herbicide is used.
Example (3): Insect resistant maize and cotton:

-Yields of maize can be greatly reduced by an insect larva called the corn borer. Cotton yields are
reduced by the cotton boll worm, which is also an insect larva.
-Pesticides sprayed onto the crops can kill these insects. However, the pesticides can also harm
other beneficial pollinating insects. The insects also evolve resistance to the pesticides.
-Genes that code for the production of a protein derived from the bacterium Bacillus thuringiensis,
called Bt toxin, have been inserted into maize and cotton plants. The plants therefore produce the
protein, which is converted into the toxin once inside the gut of the insects that have eaten the
leaves. This means that the toxin kills insects that feed on the plants, but not other insects.
METHOD: by protoplast fusion:

1- The plant cell wall is a rigid structure and potentially a barrier to the introduction of new genes.
2- Plant cell walls can be removed by the gentle action of enzymes including cellulase,
hemicellulase and pictinase.
3- Plant cells from which the wall has been removed are called protoplast.
4- They can be cultured in liquid medium provided the water potential of the medium is
appropriately regulated.
5- Under these conditions the protoplasts quickly regenerates a new cell wall, but before it can do so
there is an opportunity for the molecular geneticist to adjust the genome of the cell.
6- For example, plasmids of bacterial origin can be induced to enter by using the 'zapping'
(Electroporation) technique to open pores in the plasma membrane.
7- The bacterium Bacillus thuringiensis has a plasmid-based gene for the production of a protein that
is toxic to many insect larvae (a naturally occurring insecticide).
8- Copies of these plasmids have been introduced into protoplasts of potato, cotton and tobacco
species.
9- From these genetically engineered protoplasts, plants have been produced with natural defences
against a range of insect pests.

Advantages and Disadvantages of producing maize & cotton insect-resistant rather than
using pesticides:
advantages Disadvantages
Cheaper The evolution of resistance by the insect pests.
Less time consuming (no spraying) A damaging effect on other species of insects.
Specific to a certain type of pest The transfer of the added gene to other species
of plant.
Less pollution, since less need to use The seed of Bt corn and cotton costs more for
pesticides farmers to buy than non-GM seed, making it
difficult for farmers in developing countries to
afford it, and therefore making it difficult for them
to compete with farmers in richer countries
(expensive).
It is possible that some non-pest insects might be

harmed by the Bt toxin. However, overall it is
found that there are more non-pest insects
present in the fields where Bt corn or Bt cotton
are grown than in fields where non-Bt crops are
grown and sprayed with pesticides
.
Will reduce side effects of pesticides on GM crops may be genetically unstable, causing
organisms in higher levels (humans) mutations, e.g. cancer.
Crops are pest resistant More use of pesticides
Less harm to useful insects / pests Pesticides are expensive and time consuming to
The toxin harms only insects that eat the apply.
plant, not other insects as happens when
insecticides are sprayed on crops.
Less loss of the crop to insect pests, so Pesticides are rarely selective and kill harmless
greater yields are obtained which can and useful organisms as well, such as pollinators.
keep costs down.
Some pesticides accumulate in the environment
and cause long-term changes in animals or
humans.
It is less likely that insect pests will evolve The large numbers of crop plants containing the
resistance to the Bt toxin than to genes for toxins may simply accelerate the
pesticides. However, there are signs that evolution of resistance to the toxins in the larvae
resistance can develop in some pest
species. This can be counteracted by
using slightly different forms of the Bt
toxin, or a combination of two different Bt
toxins, in GM crops
Experimental evidence: In parts of the world where a great deal of a

Maize is attacked by the European corn genetically modified crop is grown, there is the
borer, an insect larva that tunnels into the danger of losing
plant from eggs laid on the undersides of Biodiversity.
leaves. In field trials normal and
genetically engineered maize plants were There is some evidence of reduced population of
deliberately infested with larvae and the micro-organisms in soil in which Bt maize has
results monitored over 6 weeks. The been growing.
average length of the tunnels in the
engineer plants was 6.3cm and in the Various aquatic insect larvae live in the streams
normal plant was 40.7cm. The engineered in the maize-growing areas of the U.S.A. leaves
plans also suffered less leaf damage. from genetically modified Bt plants end up in the
streams and may be eaten by, for example,
caddis larvae. Experiments showed a small
reduction in growth of larvae fed on Bt leaves.
Note:
(A) - Many populations of corn borers in the U.S.A. are now resistant to Bt toxin in the concentrations
expressed in the plants. For some time, it has been necessary for growers to plant up to 50 % of
their maize as non-genetically modified maize in so called 'refuges'. Bt resistance in corn borers
happens to be a recessive allele. Adult corn borers in the refuges are mostly homozygous dominant
or heterozygous. These insects supply the dominant alleles to counteract resistance when adult corn
borers from fields and refuges mate.
(B) The pollen of Bt maize expresses the gene and has been found to disperse at least 60 m by
wind. In the U.S.A, milkweed frequently grows around the edge of maize fields and is fed upon by the
caterpillars of the monarch butterfly. Half of the summer population of monarch butterflies is found
in the maize-growing areas of the U.S.A.
-An experiment was set up in which caterpillars were fed milkweed leaves dusted with pollen from Bt
maize, pollen from unmodified maize or no pollen at all. Caterpillar survival after four days of feeding
on leaves dusted with pollen from Bt maize was 56 %, whereas no caterpillars died after eating
leaves dusted with pollen from unmodified maize or leaves with no pollen.

GENETIC ENGINEERING ISSUES OF CONCERN
(A) Economic issues to consider:

1- Genetic engineering is a costly technology.
2- Genetic engineering is of most benefit to people of developed nations.
3- The funds available for genetic engineering could be diverted to solve more basic problems such
as housing, health, employment and nutrition of the poor worldwide.
4- Like some transgenic animals, certain transgenic plants can be potentially "pharmed" to produce
large quantities of medically important proteins, such as antibodies against the herpes virus (used in
treating diseases).
5- The results of some experiments also showed that the genetically engineered virus is being
marketed as a biopesticide, since although it kills caterpillars faster than the unmodified virus, the
caterpillars still have time to eat holes in the cabbage leave. (Crop loss continued)
6- 'Safe' planting distances should be increased to allow the organic farming industry to maintain its
'GM-free' certification.
(B) Ethical issues to consider:

1- Humans should not tamper with nature
2- GM crops may produce or behave in an unpredicted ways
3- Some people are concerned about the safety of dealing with genetically engineered organisms. To
address these concerns, scientists carry out recombinant DNA technology under specific safety
guidelines. Scientists are trying to find ways to remove the marker genes after transformation.
4- Some people are concerned about the health effects of consuming foods derived from GM crops
and think that such foods should be restricted. For example, critics say that some consumers may
develop food allergies.

5- Genetic engineering is a relatively new development, experience of it is limited and a large
number of people know virtually nothing about it. Also, development of the techniques has been
rapid.
(C) Environmental issues to consider:

1- There are far more potential dangers once unrestricted release of GM organisms is granted.
2- Might a gene, added to a genome, function in an unforeseen manner, and perhaps even triggering
cancer in the recipient.
3- Might an introduced gene for resistance to adverse conditions get transferred from a crop plant or
farm animal into a weed species or to some predator, or even to pathogenic bacteria, so marker
genes must be removed from the GM organism after transformation.
4- May encourage the use of greater amounts of herbicides.
5- Could a harmless organism, such as the human gut bacterium E.coli, with recombinant DNA
technology, be transformed into a harmful pathogen that escapes into the outer population.
6- The maize has a bacterial gene which increases its resistance to pests and diseases, but also has
a gene for resistance to the antibiotic ampicillin. Some organisations are threatening that a legal
action must be taken.
7- They might also affect food chains in an unpredictable ways, disturbing the balance of the
ecosystem.
8- 'Safe' GM plants distances should be increased, since pollen can be transferred by insects or wind
to unmodified plants.
9- GM plants are slightly less invasive than the unmodified plants, so there was no need to modify
them genetically in the first place.
10- Loss of biodiversity.
U Aspects of human Reproduction

-Humans reproduce sexually, producing male and female haploid gametes whose nuclei fuse at
fertilisation to form a diploid zygote. The zygote develops into an embryo and then a foetus in its
mother's uterus, attached to the uterus wall by a placenta, through which it obtains nutrients and
oxygen and gets rid of urea and carbon dioxide.
Male and female reproductive systems:
-Figures show the arrangement of the various organs that make up the reproductive system in males
and females. Because the organs of the urinary system (kidneys and bladder) are closely associated
with the reproductive organs, this is sometimes known as the urinogenital system.

Histology of the mammalian ovary and testis: See figures

Gametogenesis:
- it is the production of haploid gametes from diploid somatic (body) cells. Spermatogenesis takes
place in the tests, and oogenesis in the ovaries.In men, spermatozoa (sperm for short) are made in
the testes. In women, eggs (sometimes called ova) are made in the ovaries.
- It involves mitosis, growth, meiosis and maturation (becoming adapted or specialized)
Mitosis:
- A type of nuclear division. During the process, a single cell divides to form two cells, which have
the same number of chromosomes and are genetically identical, both to each other and the parent
cell. This type of division used in growth, repair and asexual respiration.
Meiosis:
-it is the type of nuclear division involved in gametogenesis. A single cell divides twice, to form four
cells, which are all genetically different and contain only half the number of chromosomes of the
parent cell. For this reason, it is referred reduction division.
Growth:
-it is the increase in size and dry mass by cell division and cell enlargement.
[1] Spermatogenesis:
- The production of sperm takes place in the testes. The process begins between the ages of 11 and
15 and will continue for life. Between 100 and 200 million sperm will normally be made every day.
-The tests are made up of many seminiferous tubules, and it is in the walls of these tubules that
spermatogenesis takes place.
Stages of Spermatogenesis:

1- The process begins at the outer edge in the germinal epithelium and the new cells that are
produced form towards the inner edge.
2- Attached to the epithelial layer of the seminiferous tubules are cells called spermatogonia.
These cells are diploid and divide by mitosis to form more spermatogonia (germinal epithelia).
3- Some spermatogonia move towards the lumen of the seminiferous tubule and increase in size
(growth) at this stage, they are called primary spermatocytes.
4- The primary spermatocytes divide by meiosis. After the first meiosis division, two haploid cells
are formed the secondary spermatocytes.
5- The secondary spermatocytes undergo a second meiotic division, giving a total of four haploid
spermatids.
6- Each spermatid will mature (adapted or specialized) into a spermatozoan. They are all lined up
with their heads attached to the wall of the tubule and their tails hanging free in the lumen.
7- The developing sperm are nourished and protected by Sertoli cells (nurse cells).
8- The whole process takes approximately 64 days.
9- The whole process is controlled by hormones secreted by the pituitary gland and leydig cells
(produce testosterone) to regulate the sperm production
Summary
Spermatogonia mitosis many Spermatogonia Growth primary
spermatocytes meiosis 1
Secondary spermatocytes meiosis 2 spermatid maturation sperm
(spermatozoa)
Adaptation of sperms:
1- Long tail to swim. Flagellum has many microtubules made of proteins that slide over each other to
make the tail bend and move forward from side to side.
2- Mitochondria to provide energy (ATP) by aerobic respiration (for swimming).
3- Acrosome that releases enzymes to digest way into the egg.
4- Small in size, thus reducing energy needed to swim.
[2] Oogenesis:
-the production of eggs (or ova) takes place in the ovaries. However, unlike the production of sperm,
the process begins very early in the life of the female, when she is still only an embryo.
Stages of Oogenesis:
-The stages of this process take place in the ovary, but the ovum is not actually formed until
fertilisation.
1- About five weeks after the formation of a female embryo, some germinal epithelial cells in the
tiny developing ovaries start to divide by mitosis, forming diploid oogonia.
2- When the embryo is 24 weeks old, there will be millions of oogonia in the ovaries.
3- Up until about 6 months after birth, the oogonia will begin the first division of meiosis. The
resulting cells are called primary oocytes. However, they do not complete the division and remain
at prophase 1 for many years. Not all the primary oocytes survive and, at puberty, there will be
around 400,000 in the ovaries. They are each approximately 20 m in diameter.
4- When the primary oocyte enters prophase 1, some surrounding cells form a layer around it,
forming a primordial follicle. The primordial follicle remains in this state for many years. Some of
these then develop into primary follicles, with several layers of surrounding cells, called
granulosa cells. Other cells from yet more surrounding cells, called the theca (follicle wall) and

the granulosa cells secrete a protective layer of glycoproteins called the zona pellucid. Also
granulosa cells surround and protect the oocyte and secrete hormones. The primary follicle will then
remain like this until the girl reaches puberty.
5- A the onset of puberty, hormones will stimulate the primary follicles to develop into secondary
follicles. The oocyte enlarges and a fluid-filled cavity develops that is called the antrum.
6- One primary oocyte begins to grow rapidly, forming a Graafian or ovarian follicle, which is
between 1 and 1.5 cm in diameter.
7- The primary oocyte now completes the first meiotic division, producing one large cell and one
tiny cell, called the polar body. The large, haploid cell is called the secondary oocyte, which
continues straight into the second meiotic division. However, it stops again before the division is
complete, remaining at the stage of metaphase 2.
8- The follicle now ruptures and releases the secondary oocyte, surrounded by granulosa cells
(ovulation).
9- The oocyte is drawn into the oviduct (fallopian tube), mainly by peristalsis, although there are cilia
present in addition. In the oviduct, if fertilisation takes place, it will complete the second division of
meiosis. If not fertilised, the secondary oocyte survives only two days then it disintegrates.
10-the follicle transforms into a corpus luteum
Adaptations of egg (primary oocyte):

1- Large in size to store nutrients for early embryo, these are present in lipid droplets.
2- Surrounded by protective layer of zona pellucida.
3- Zona pellucida also acts as receptors for sperms while fertilisation.

INFERTILITY:
-A couple is described as being infertile if they have failed to conceive a child after 12 months of
trying.
- While the incident of infertility has remained roughly the same the past 20 years, the number of
couples seeking help with conceiving a child has tripled.
-this is due to an increasing reluctance by couples to accept their infertility; there is a greater
assumption now that they have a 'right' to have children and expect to be given help if it is required.
Many infertile couples see their problem as a major life crisis, and feel devastated and powerless.
-Another factor is that many couples are delaying having their first child until much later than was
the norm in the past. As a woman ages beyond 25, her fecundity the probability of conceiving
during one monthly cycle falls considerably.
Causes of infertility:
Why a man can be infertile:
1- Low number or absence of sperm.
2- Abnormal sperms: no nucleus, or two heads, short tail that it cannot swim.
3- Blocked sperm ducts due to bacterial infection, or genetic condition like CF.
4- Reduced testosterone.
5- Incomplete development of testes.
6- Autoimmune disease killing sperms.
Why women become infertile as they grow up:
1- As the chances of miscarriage increase.
2- Due to hormonal disturbance.
3- Due to increase in mutation causing diseases like Down syndrome.
4- Ovulation and implantation are less likely to occur.
5- Oocytes are less likely to be fertilized.
6- Fecundity of female decreases after age 25.

Some treatments of infertility:
1) In-vitro fertilization (IVF):
1- 'In- vitro' means 'In glass' and refers to the fact that fertilization occurs in glassware (for example,
a Petri dish) in the laboratory, rather than in woman's oviduct.
2- In-vitro fertilization (IVF) is a technique whereby eggs are fertilized outside the woman's body. The
process involves controlling ovulation through the administration of hormones, removing eggs from
the ovaries and allowing sperm to fertilize them in a fluid medium.
Stages of IVF treatment:
1- Ovarian Stimulation:
-treatment would normally start on the third day of menstruation. This involved the administration
of hormones which will have a similar action to FSH and will stimulate the development of multiple
secondary follicles in the ovaries (super-ovulation). Usually, about 10 days of injections will be
necessary.
2- Oocyte Retrieval:
-when the development of follicles is judged to be adequate (usually by monitoring oestrogen
levels), the hormone human chorionic gonadotrophin (HCG) is given. This has a similar effect to LH
and would be expected to cause ovulation about 42 hours after injection. (HCG) will stimulate the
formation of a corpus luteum, which will secrete progesterone.
-This is necessary to prepare the woman's oviduct and endometrium to receive an embryo.
-in practice a needle is used to remove eggs directly from the ovaries prior to ovulation taking place
under general anesthetic
-On the same day, semen is collected from the woman's partner. The sperms are washed and placed
in a fluid that contains nutrients that will enable the sperms to become ready to fertilize an egg
(capacitation).
3- Fertilization:
- The eggs are stripped of any surrounding cells and are incubated with sperm (in a ratio of
approximately 75,000: 1) for about 18 hours. By that time fertilization should have taken place.
- Where the sperm count is very low, it is now possible to inject a single sperm directly into the egg
using a micro-needle.
-The fertilized egg will now be placed in a special growth medium and left for 48-72 hours, by which
time it should have reached the 6 8 cell stage.

4- Embryo Transfer:
- Embryos which are growing successfully are transferred to the patient's uterus through a thin,
plastic catheter. Often, several embryos are transferred to improve the chances of implantation and
pregnancy. Two embryos will be chosen and inserted into the uterus using a tube passing through
the vagina and cervix. Two are normally used to give a greater likelihood that at least one will
implant, while avoiding the risk of having triplets or even more babies.
-during the next two weeks the woman will be administrated progesterone, which will help to keep
the uterus lining thickened and suitable for implantation.
In-vitro fertilization and its ethical and social implications:

Advantages and Disadvantages of using IVF:
Advantages
Give chance for infertile couple to have a baby.
Woman with blocked oviduct is able to have a baby and make family.
Sperms of husband can be stored in sperm banks, and used by wife when husband is
away or dead.
Embryo can be frozen, and used if first implantation did not go well.
Embryos that are produced by IVF, and are not needed for implantation could be used by
scientists to produce organs, as they can divide repeatedly. (Pleuripotent stem cells
producing organs to be transplanted to treat different diseases).
For many people, IVF is acceptable, for example, to permit selection of embryos that do
not contain lethal alleles of key genes, for example, the allele that causes Huntington's
disease.
IVF has allowed women to become pregnant often the menopause.
The fate of the 'unused' embryos raises ethical issues. Some people believe them to be
human beings, who should be treated as such. Others see things differently; it is certain
that many early embryos conceived naturally are lost from the mother's body well before
they implant in the uterus, so it can be argued that the loss of embryos after IVF is only
mirroring natural processes.

Disadvantages
Making pregnancy look more as technological or medical method rather than natural.
Expensive and time consuming, so unavailable for many people and may reduce life-chances
of children who cost more to create than through natural conception.
Fertilizing more embryos than will be needed, and then discarding the unwanted ones.
Freezing and long-term storage of embryos with unknown potential effects.
The potential to create embryos for research or to grow tissues and organs for transplant is not
always accepted.
The potential to select and modify embryos may not be good. People have more difficulty with
the potential to select embryos for intelligence, gender or absence of minor defects.
Another partner may be needed for sperm donation.
If deformed child is formed, it may be rejected by parents.
May break family, if child needed to know real father.
May lead to multiple pregnancies that affect health of both mother and babies.
The possibility of birth defects is a controversial subject in IVF treatment though most studies
do not show a significant increase compared with normal fertilization
The chances of a successful pregnancy using IVF is approximately 20 30 %. There are many
factors which can influence the success rate for example, age of the patient, quality of the
eggs and sperm and health of the uterus.
IVF also allows babies to be created away from the traditional mother-father model. The
process requires sperm, eggs and a uterus potentially, any of these can be provided by a
third party, creating additional ethical and legal considerations. It also provides more
possibilities for single people and same sex couples to have children.
Some religious groups, (e.g. Catholic Christians) are totally opposed to IVF sometimes seeing
infertility as a call from God to adopt children and may see IVF as usurping the role of God in
bringing into the world the children that he wants.
IVF has allowed women to become pregnant after the menopause. Even after the menopause,
the uterus is able to carry out its function though the egg would have to come from an egg
donor. This would mean that there would be no genetic link between the woman and the child
to which she gives birth. People vary in how acceptable they find some of these issues.
Generally, from two to five-day old embryos are transferred. However, some doctors prefer to
transfer more embryos. This can lead to multiple embryos developing in the uterus, which are
less likely to be healthy than a single one.

It is possible for a woman to have children using sperm from a man who is not her partner.
Some people believe this is not ethically acceptable. There are also difficulties if the man who
donated the sperm does not want any resulting children to know that he is the father.
It is possible for a woman who is past child-bearing age and who has reached the menopause
to have children in this way. This could mean that a child to a mother who will not have a
sufficiently long active life to care for him or her.
While many people think it is important that a woman should have the right to bear a child,
others feel that there are enough children in the world already and that a person who is
biologically unable to have one should not be treated, especially if the cost is borne by tax-
payers or if her treatment prevents the treatment of someone else with a life- threatening
condition.
Some of the embryos resulting from IVF will not be implanted. They could be allowed to die, or
they could be used for research. Some people are concerned that we do not have the right to
dispose embryos in this way.
It is possible for semen from a partner to be collected and frozen. A woman could then have
his child by IVF after the partnership has broken up, or after he has died, without his
permission.
The embryos produced by IVF are usually tested to ensure they are viable (able to survive)
before implanting them. This may include checking for the presence of undesirable alleles
such as those that can cause genetic conditions like cystic fibrosis. It is also possible to choose
an embryo of a particular sex. There are some ethical issues concerning the ability to do these
choices.
2) Frozen Embryo replacement:

-One possible use of any 'spare' embryos following IVF is to freeze them using liquid nitrogen, in
which they can be stored for many years. About 70 % of the frozen embryos survive. The embryos
remain in suspended animation and can be thawed and transferred to the mother's uterus when
needed.
Advantages and Disadvantages of frozen embryo replacement:
This process may be used when a woman The ethical issues associated with this process are
has to undergo treatment that may the same as those described for IVF.
damage her ovaries, usually when she is
being given radiotherapy or chemotherapy
as part of her treatment for cancer.
It is also helpful when she has to undergo Normally, the permission of both members of the
many cycles of fertility treatment before partnership
conceiving, as it avoids having to stimulate Will be required before implantation of the stored
her ovaries repeatedly and having to embryos can be carried out. This can cause
undergo the collection of oocytes from her difficulties if the male partner no longer wants the
oviducts (saves time and enegy). woman to have his child.
The risk that the frozen embryos will get mixed up.
This causes great distress to the mother and her
partner, who know that their biological child is
growing up with another family, while the child that
they are bringing up is not biologically theirs.

3) Gamete Intrafallopian Transfer:
-A similar process to IVF is called gamete intrafallopian transfer, or GIFT. In this procedure, oocytes
and sperm are collected and examined as in IVF. Then one or two oocytes and a sample of sperm are
inserted by means of a fine tube into a woman's oviduct. (Oviducts are also called 'fallopian tubes).
This raises fewer ethical concerns than IVF, because fertilization takes place within the body.
4) Intracytoplasmic Sperm Injection:

-Intracytoplasmic sperm injection is known as ICSI. It is a modification of the normal IVF procedure in
which a sperm is actually injected into an egg, rather than just allowing the sperm to fertilize the
eggs by themselves.
-It may be used when the man's sperm are not able to do this, perhaps because they do not swim
normally or because they do not become fully active.
-It is better to remove the acrosome from sperm before injecting it in the oocyte in IVF, as it may
damage oocyte or stop the development of fertilized oocyte.
Advantage of injecting sperm to oocyte:
1-ensure sperm enters oocyte (fertilization).
Disadvantage of injecting sperm to oocyte :
1- Cannot tell if it was genetically suitable, because in this procedure there is a slightly increased risk
of abnormalities in a child that is born as a result. Normally, only 'fit' sperm will manage to fertilize
an oocyte, and it is possible that a less than perfect sperm could carry genes that can cause a
congenital abnormality.
5) Sperm Banks:
- Consisting of samples of sperm that can be used in many infertility treatments. The technique of
storing frozen cells is called 'cryopreservation'.
-Sperms used in IVF or artificial insemination are provided either by the woman's partner or a donor.
How to build up and use a donor profile:
1- Potential donors may be asked to give information about their family history, their interests and
their educational background.
2- They undergo a thorough health check, looking for infectious diseases as hepatitis and HIV / AIDS,
and genetic testing to check for hereditary diseases such as sickle cell anaemia.
3- All of this information is used to build up a donor profile.
4- If the profile suggests that the semen may be safe to use then a sample will be taken and frozen.
It will be kept for at least six months before use, during which time the donor will be repeatedly
tested for infectious diseases, to reduce the likelihood that something was in an early and
undetectable stage of development when the sample was collected.
5- A woman who is going to be given donated sperm is provided with the profiles of the donors, but
not their names and she can use this to help her to choose the donor she would like to use.
Advantages and Disadvantages of using sperm banks:
Sperm from a donor may be used if the Risk of transferring HIV to the woman along
parent's sperm is incapable of fertilizing an with the sperm or any other disease.
egg
-Most artificial insemination or IVF procedures Each sperm sample is labeled carefully and
use the sperm of the woman's partner. kept frozen in liquid nitrogen. The samples are
-Sperm cryopreservation allows long-term kept in a secure area so that tampering is not
sperm storage for a man who is perhaps possible, and the levels of liquid nitrogen are
facing medical treatment or a progressive regularly checked, but still it is subjected to
illness that is likely to make him infertile. human error if mixed.
The child may grow wanting to know his / her

biological father causing stress for both sides.
PAPER (5)
PLANNING
ANALYSIS

CONCLUSION
EVALUATION SKILLS
SUMMARY
(A)Planning an investigation:
1- Independent Variable
What is it? How to change it?
2- Dependent Variable
What is it? How to measure it?
3- Procedures or Method
-include working e.g. r 2 x distance = volume in tube
Rate = volume of oxygen / time or 1/time
-Allow to equilibrate, i.e. to give time to adjust (acclimatize) to new conditions.
4- Standardized (controlled) Factors

What are they? How to control them?
E,g, temperature, using thermostatically controlled water bath or an incubator
5- Safety Precaution
-Goggles gloves care when handling toxic material
-Wear mask for allergy with pollen and plants
-low risk investigation
6- Reliability
1- Repeat procedure three times, Remove anomalous results (the ones that dont fit with trend),
then calculate mean
2- Use greater range of intermediates
3-Use statistical test
4- Use larger sample size or number
5- Use fresh solutions, e.g. H2 SO4 or Na H CO3 or hydrogen peroxide to avoid decreasing
concentration due to their breakdown, or use fresh absorbent of CO 2 e.g. soda lime
7- Data presentation
-Use tables, graphs, units, charts .etc
(B) Question of To what extent

2 Marks Support + evidence or Reject + evidence
4Marks Support + evidence and Reject + evidence
*keywords used in rejecting or not supporting hypothesis:

-no enough replica
-no enough range of intermediates
-no statistical test
-no enough data collected
-some data are anomalous
-small sample size
(C)Statistical Test
-name of test
-what is it used for
-components of the formula of the test
-what does the value of the calculated test mean
(D) State the null hypothesis

-There is no significant difference in ..
-then we either accept or reject the null hypothesis depending on the results
(E) Resources of Paper (5)

-past papers + MS
-statistics
-experiment:
*Respirometer A2
*Chromatography A2
*Photosynthesis OL
*Auxins OL
*Potometer AS
*Stage micrometer and Eye piece graticule AS
(F) In calculations, why to calculate % change in mass instead of change of mass?

-To make it easier to compare when initial data (starting numbers) are not equal
(G) General remarks and Notes while solving paper 5 questions
1- When calculating surface area of leaf: use grid to measure both sides of leaf to get total surface
area
-calculating surface area of an object:
1-using grid:
-calculate the area of one square in cm 2
-count the number of whole squares covered by the object, and sum the areas of partially covered
squares
-calculate the area of the object by multiplying the area of one square by the number of squares
covered by the object in cm2
-it is more reliable to use a grid with smaller squares
2-using geometrical shapes:
-either by completing the shape of the object into the nearest geometrical shape e.g. rectangle, and
calculating its area = height x width
-or cutting the object into known geometrical shapes, calculate their areas, then sum them up all
together
-when measuring rate of water loss: use Potometer and measure distance moved by water in
capillary tube
2- Temperature from microscope lamp may affect the results, so it may be better to use microscope
with mirror
3- When writing range of independent concentrations, then use as minimum "6"
4- To transfer pollen, use: paint brush or pollen brush or Cotton bud

Shake anther on stigma [then cover]
5- When examining a plant embryo:

a- allow seeds to germinate by placing on a piece of cotton soaked with water
b- Use knife to take section from plumule
c- Put on slide and add drops of DNA dye to stain chromosomes
d- Use high power objective lens of a microscope and look during metaphase at 3 different samples
and take the mean
6- How to make results more accurate?

-using a better tool such as using graduated pipette instead of a graduated cylinder
7- When providing oxygen to an apparatus say: bubble oxygen [by syringe], and stir by stirrer to
spread it, or use H2 O2 and delivery tube for O2 (no direct contact)
8- When you talk about using colorimeter, do not forget to say that you use it to find light
absorbance reading in the coloured solution
9-to change light intensity (units= lux or candela) use:

a- lambs with different wattages
b- Different distance and some lamps of the same voltage unit
c- Different lamps with different wattages, and same distance
d-light filter
10 -to change wavelength (unit= nm) use: different colours and coloured filter (to allow only one
colour to pass)
11-when you cannot find any variables to control, say: all environmental conditions must be the
same
12-always mention buffer solution in electrophoresis, to break hydrogen bonds between DNA
strands and make them single [and say "smaller / bigger"]
13-two way chromatography gives a better solution because:

a- Some pigments are less soluble or insoluble in solvent 1 but soluble in solvent 2.
b- Some pigments have the same solubility in solvent 1.
c- Solvent 2 separates pigments that are not separated by solvent 1.
14-In the dependent variable of chromatography say: position / location of pigments (not number),
or you can say RF value.
RF value = Distance moved by spot / Distance moved by solvent
15-What does "t" value tell us?

-The "t" test is a measure of the overlap between 2 sets of data
(1) t = Large / Small = Large t
Large values of t mean there is no or little overlap, significant difference, reject null hypothesis,
not due to chance but due to other environmental factors or errors
(2) t = Small / Large = Small t
Small values of t means great overlap, no significant difference, accept null hypothesis, any
difference is due chance
16-What is x2 ?
-to find if there is a significant difference between expected and observed data
- If your value is greater than the critical value for p=0.05 you can reject the null hypothesis and
accept that there is a significant difference between the observed and expected values
Note:
1-you repeat the experiment and calculate average to:
a-increase reliability b-reduce error c-detect the anomalies results
2-you keep all conditions the same during an investigation e.g temperature, volume , pH..ets to
have a fair test

Important definitions for paper 5
t -test - a statistical procedure used to determine whether the means of two samples differ
significantly.
Chi-squared (x2) test a statistical test that can be used to determine if any difference between
observed results and expected results is significant, or is due to chance
Standardized (controlled) variables: the variables in an experiment or investigation that are

kept the same so they do not influence the measurement of the dependent variable
Standard deviation: the spread of a set of data from the mean of the sample is a measure of the
variability of a population from a sample. A small standard deviation indicates that the data is more
reliable.
Standard error: an estimate of the reliability of the mean of a population sample. A small standard
error indicates that the mean value is close to the actual mean of the population.
Confidence limit: the range in which a population value is likely to fall. This is usually taken as 95
% of the time a measurement will fall in this range. In a normally distributed population, the
observed value falls in the middle of the confidence limit.
Dependent variable: the variable in an experiment or investigation that is measured.
Independent variable: the variable in an experiment or investigation that is manipulated or

changed.
Reliability: reliable results are repeatable by the same student and reproducible by others. (S, S M
are used).
Validity: valid results are reliable and successful at measuring the intended dependent variables. (t-
test used)
Magnification: the size of an image of an object compared to the actual size. It is calculated using
the formula M = I / A (M is magnification, I is the size of the image and A is the actual
size of the object, using the same units for both sizes). This formula can be rearranged to give the
actual size of the object where the size of the image and magnification are known: A = I / M.
Resolution: ability of a microscope to distinguish two objects as separate from one another. The
smaller and closer objects that can be distinguished are the higher the resolution. Resolution is
determined by the wavelength of the radiation used to view the specimen. If the parts of the
specimen are smaller than the wavelength of the radiation, then the waves are not stopped by them
and they are not seen. Light microscopes have limited resolution (200 nm) compared to electron
microscopes (0,5 nm)because light has a much longer wavelength than the beam of electrons in an
electron microscope.
Accuracy: (using a better tool to make correct measurement). An accurate reading is a true reading.
For your readings of volume to be accurate, then the gas syringe must have been calibrated
correctly, so that when it says the volume of gas is 8.8 cm 3, then there really is exactly 8.8 cm3 of
gas in there.
Mean: add or sum all values together, then divide them by the number of measurements
Median: arrange values in order, and then take the middle value of the range
Mode: take the most frequent measurement

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A2 BIOLOGY

A2 BIOLOGY MARWA FAWZI

A2 BIOLOGY MARWA FAWZI

PAPER 5 SKILLS AND STATISTICS

Energy and Respiration

The need for energy in living organism:

The Structure ofATP as a phosphorylated nucleotide:

Similarities and differences between ATP and nucleotides:

A2 BIOLOGY MARWA FAWZI

Outline the need for energy in living organisms using named

Fate of excess energy that was used to make ATP:

Difference between an energy currency and energy storage molecule:

A2 BIOLOGY MARWA FAWZI

The main Sources of Energy Produced by Cells:

nition -It is the release of a relatively -It is the release of a relatively

(A) Aerobic Respiration

Structure and Function of Mitochondria:

1-Mitochondria are rod-shaped, or filamentous organelles about 0.5 1.0 m in diameter.

3-Each mitochondrion is surrounded by an envelope of two phospholipids membranes. The outer

A2 BIOLOGY MARWA FAWZI

- It is the splitting or lysis of glucose. It takes place in cytoplasm.

During glycolysis phosphorylated glucose cannot diffuse out of

A2 BIOLOGY MARWA FAWZI

Net Yield : 2 ATP + 2 reduced NAD + 2 Pyruvate

2- The Link Reaction

2- It is the decarboxylated (that is carbon dioxide is removed)

4- Then Combined with coenzyme A (CoA) to give acetyl coenzyme A.

- Coenzyme A is a complex molecule of a nucleoside (adenine + ribose) with a vitamin (pantothenic

Pyruvate + CoA + NAD = acetyl CoA + CO 2 + reduced NAD

Net Yield: 2 ATP + 4 reduced NAD + 2 Acetyl CoA

Steps of Krebs Cycle:

Yield in each turn of Kerbs cycle

Role of dehydrogenase enzyme in Krebs cycle:

How formation of ATP in Krebs Cycle or glycolysis differ from oxidative

4-Oxidative Phosphorylation (addition of Pi to ADP in presence of O2 to make ATP)

A2 BIOLOGY MARWA FAWZI

Glycolysis ATP , reduced NAD, Pyruvate

Link reaction Reduced NAD , Acetyl co A, CO2

Krebs Cycle CO2 , reduced NAD , reduced FAD , ATP

ETC Oxidized NAD , oxidized FAD ,ATP , H2O

A2 BIOLOGY MARWA FAWZI

Explain the role of NAD in aerobic respiration:

(B) Anaerobic Respiration

Comparison between aerobic and anaerobic respiration

Feature Aerobic Anaerobic

Why anaerobic respiration produces ATP less than aerobic?

A2 BIOLOGY MARWA FAWZI

(1) Alcoholic Fermentation:

Why the rate of glycolysis increases significantly when yeast shifts

:Lactic Acid Fermentation (2)

The overall equation

A2 BIOLOGY MARWA FAWZI

Comparison between alcoholic / lactic acid fermentation:

Oxygen present in the liver

Pyruvate lactic acid

Oxygen absent in muscles

Comparison between aerobic and anaerobic respiration:

A2 BIOLOGY MARWA FAWZI