Chapter One

Introduction
 The meaning and scope of biology
• Biological Sciences is the study of life and living
organisms.
• The Greek word ‘bio‘ means life and ‘logos‘
means study of.
• In the late 1700s Pierre-Antoine de Monet and
Jean-Baptiste de Lamarck coined the term
biology.
• Earlier study of living things was restricted to the
pure Science like Botany and Zoology that
together comprise the Biology, but as the time
passed new branches evolved.
• New technologies developed in pure subjects
as well as in applied fields, which gave rise to
a very broad concept of science called
Biological Sciences.
• Biological Sciences is an extensive study
covering the minute workings of chemical
substances inside living cells to the broad
scale concepts of ecosystems and global
environmental changes.
• It is also concerned with the physical
characteristics and behaviors of organisms
living today and long ago.
– How they came into existence and what relation
they possess with each other and their
environments?
• Intimate study of details of the human brain,
the composition of our genes, and even the
functioning of our reproductive system are
dealt in Biological sciences.
• Therefore, Biology is the science of Living
Things. That is why Biology is sometimes
known as Life Science. The life sciences can be
defined as “a systematic study of living beings
or study of nature.”
 The origin and nature of life
• One of the biggest and most important of emergent
phenomena is that of the origin or emergence of life.
• The mystery of life's origin is still a big debating issue in
science.
• The question “what is life?” is so hard to answer; we
really want to know much more than what it is, we
want to know why it is, “we are really asking, in
physical terms, why a specific material system is an
organism and not something else”.
• To answer this why question we need to understand
how life might have originated. There are a number of
theories about the origin of life.
• The evolution of life on earth has involved the
following sequence of events.
• The first living things to appear were the simplest
creatures, single-celled organisms.
• From these came more complex, multi-cellular
organisms.
• Becoming more complex meant more than just an
increase in cell number but more cells showed cellular
specialization, where certain cells within the multi-
cellular organism carried out specific tasks.
• Millions, even billions of years of changes of organisms
led to the living things we now call plants and animals.
• Since this basic sequence of events is in accord with that agreed upon by
most geologists, paleontologists, biologists, and even theologians, one
might conclude that Moses, Aristotle, and Darwin were all keen observers
and naturalists who were able to logically assess the most probable
creation story.
• Scientists generally concur (agree) that the time from the formation of our
solar system until now has been on the order of some 4.5 billion years.
• Those who believe the world as we know it was created in six days are
often called creationists.
– Their method of inquiry is based on the belief that the Bible is to be
accepted as a completely accurate accounting of all about which it
speaks.
• Scientists, on the other hand, utilize what they call the scientific method,
which allows them to test hypotheses and theories and to develop
concepts and ideas.
 Theories on Origin of life
Theory of Special Creation: according to this theory, all the different
forms of life that occur today on planet earth have been created by
God, the almighty.
Theory of Spontaneous Generation: this theory assumed that living
organisms could arise suddenly and spontaneously from any kind of
non-living matter. One of the firm believers in spontaneous generation
was Aristotle, the Greek philosopher (384-322 BC).
Theory of Catastrophism: It is simply a modification of the theory of
Special Creation. It states that there have been several creations of life
by God, each preceded by a catastrophe resulting from some kind of
geological disturbance. According to this theory, since each
catastrophe completely destroyed the existing life, each new creation
consisted of life form different from that of previous ones.
Cosmozoic Theory (Theory of Panspermia): according to this
theory, life has reached this planet Earth from other heavenly
bodies such as meteorites, in the form of highly resistance
spores of some organisms. This idea was proposed by Richter in
1865 and supported by Arrhenius (1908) and other
contemporary scientists. The theory did not gain any support.
This theory lacks evidence, hence it was discarded.
Theory of Chemical Evolution: this theory is also known as
Materialistic Theory or Physico-chemical Theory. According this
theory, Origin of life on earth is the result of a slow and gradual
process of chemical evolution that probably occurred about 3.8
billion years ago. This theory was proposed independently by
two scientists - A.I.Oparin, a Russian scientist in 1923 and J.B.S
Haldane, an English scientist, in 1928.
 Nature and characteristics of life
• Life is defined as a "condition" that distinguishes animals
and plants from inorganic materials and dead organisms.
– Life is comprised of processes and is a maintained state.
– The most sophisticated form of life is man as a result of this we
focuses upon the nature of the life and death of man.
• Man demonstrates three lives or aspects of life:
– Physical life is basic existence
– Mind contributes effectiveness and scope
– Spiritual entity contributes maximum living
• Physiology: The existence of life physical is demonstrated
by the presence of functions.
• Living tissues and organisms exhibit:
– Irritability: the ability to be excited or detect stimuli
and to respond thereto
– Growth and reproduction: this consists of the power
of multiplication and duplication, regeneration and
differentiation
– Adaptability: permitting both change and
maintenance of balances (homeostasis) Finally and
most characteristic of all is
• Metabolism: the transformation of energy and the use of
materials.
• These properties, however, can be retained for a
while by tissues after death of the organism so
there is another mystery of life which we
understand only in part.
• Excretion: excretion and osmoregulation
regulation are two important homeostatic
processes occurring in living cells, helping them
to maintain a constant internal environment, or
steady state.
– Excretion is the removal from the cell of waste
products of metabolism
 Scientific methods
• The scientific method is a process for experimentation that
is used to explore observations and answer questions.
• It is an empirical method of acquiring knowledge. It is also
the technique used in the construction and testing of a
scientific hypothesis.
• The scientific method has five basic steps, plus one
feedback step:
– Make an observation.
– Ask a question.
– Form a hypothesis, or testable explanation.
– Make a prediction based on the hypothesis.
– Test the prediction.
– Iterate: use the results to make new hypotheses or predictions.
• Observation - Quantitative and qualitative measurements of the
world.
• Inference - Deriving new knowledge based upon old knowledge.
• Hypotheses –A suggested explanation.
• Rejected Hypothesis - An explanation that has been ruled out
through experimentation.
• Accepted Hypothesis - An explanation that has not been ruled out
through excessive experimentation and makes verifiable predictions
that are true.
• Experiment - A test that is used to rule out a hypothesis or validate
something already known.
• Scientific Method - The process of scientific investigation.
• Theory - A widely accepted hypothesis that stands the test of time.
– Often tested, and usually never rejected.
• The scientific method is based primarily on the
testing of hypotheses by experimentation.
– This involves a control, or subject that does not
undergo the process in question. A scientist will also
seek to limit variables to one or another very small
number, single or minimum number of variables. The
procedure is to form a hypothesis or prediction about
what you believe or expect to see and then do
everything you can to violate that, or falsify the
hypotheses. Although this may seem unintuitive, the
process serves to establish more firmly what is and
what is not true
Thank you!
 Chapter Two

Biological Molecules
 Carbohydrates
• A carbohydrate molecule is made of atoms of carbon, hydrogen and
oxygen.
• They are an important source of energy and they also provide structural
support for cells and help with communication between cells (cell-cell
recognition).
• They are found in the form of either a sugar or many sugars linked
together, called saccharides.
• Based on the number of sugar units they contain, they are categorized into
three, as follows.
– A single sugar molecule containing carbohydrate is known as a
monosaccharides,
– two sugar molecule containing carbohydrate is known as disaccharides and
– More than two sugar molecule containing carbohydrate is known as
polysaccharides
• Each of the sugar molecules are bonded together through the glycosidic linkage/s.
• The three different types of carbohydrates are all important for different
reasons
• Carbohydrates are polyhydroxy aldehydes or ketones,
or substances that yield these compounds on
hydrolysis. Example: Glucose is an aldehyde while
fructose is a ketone.
• Monosaccharides - simple sugars with multiple OH
groups. Based on number of carbons (3, 4, 5, 6), a
monosaccharide is a triose, tetrose, pentose or hexose.
• Disaccharides - 2 monosaccharides covalently linked
• Oligosaccharides - a few monosaccharides covalently
linked.
• Polysaccharides - polymers consisting of chains of
monosaccharide or disaccharide
 .

Fischer projection of D-glucose Fischer projection of D-fructose

Fig: Structures of monosaccharides (glucose and fructose)

Fig: 2.2. A structure of maltose (disaccharide)
 Monosaccharides
• Monosaccharides containing the aldehyde group
are classified as aldoses, and those with a ketone
group are classified as ketoses.
• Aldoses are reducing sugars; ketoses are non-
reducing sugars.
– This is important in understanding the reaction of
sugars with Benedict's reagent. However, in water
pentoses and hexoses exist mainly in the cyclic form,
and it is in this form that they combine to form larger
saccharide molecules.
Glucose
• Glucose is the most important carbohydrate fuel in human
cells.
• Its concentration in the blood is about 1 gdm-3 .
• The small size and solubility in water of glucose molecules
allows them to pass through the cell membrane into the
cell.
• Energy is released when the molecules are metabolized.
• Two glucose molecules react to form the dissacharide
maltose.
• Starch and cellulose are polysaccharides made of glucose
units.
Galactose
• Galactose molecules look very similar to glucose molecules.
• They can also exist in α and β forms.
• Galactose reacts with glucose to make the dissacharide
lactose.
• However, glucose and galactose cannot be easily converted
into one another.
• Galactose cannot play the same part in respiration as
glucose.
• This comparison of glucose and galactose shows why the
precise arrangement of atoms in a molecule (shown by the
displayed formula) is so important.
Fructose
• Fructose, glucose and galactose are all hexoses.
• However, whereas glucose and galactose are aldoses
(reducing sugars), fructose is a ketose (a non-reducing
sugar).
• It also has a five-atom ring rather than a six-atom ring.
• Fructose reacts with glucose to make the dissacharide
sucrose.
Ribose and deoxyribose
• Ribose and deoxyribose are pentoses.
• The ribose unit forms part of a nucleotide of RNA.
• The deoxyribose unit forms part of the nucleotide of DNA.
 Disaccharides
• Monosaccharides are rare in nature.
• Most sugars found in nature are disaccharides.
• These form when two monosaccharides react.
• Disaccharides are soluble in water, but they are
too big to pass through the cell membrane by
diffusion.
• They are broken down in the small intestine
during digestion to give the smaller
monosaccharides that pass into the blood and
through cell membranes into cells.
– C12H22O11 + H2O  C6H12O6 + C6H12O6
• This is a hydrolysis reaction and is the reverse of a
condensation reaction and it releases energy.
• A condensation reaction takes place by releasing water.
– This process requires energy.
• A glycosidic bond forms and holds the two monosaccharide
units together.
• The three most important disaccharides are sucrose,
lactose and maltose.
• They are formed from the a forms of the appropriate
monosaccharides.
• Sucrose is a non-reducing sugar.
• Lactose and maltose are reducing sugars.
• Monosaccharides are used very quickly by cells.
• However, a cell may not need all the energy
immediately and it may need to store it.
• Monosaccharides are converted into disaccharides in
the cell by condensation reactions.
• Further condensation reactions result in the formation
of polysaccharides.
– These are giant molecules which, importantly, are too big
to escape from the cell.
– These are broken down by hydrolysis into
monosaccharides when energy is needed by the cell.
 Polysaccharides
• Monosaccharides can undergo a series of condensation
reactions, adding one unit after another to the chain
until very large molecules (polysaccharides) are
formed.
• This is called condensation polymerisation, and the
building blocks are called monomers. The properties of
a polysaccharide molecule depend on:
– Its length (though they are usually very long)
– The extent of any branching (addition of units to the side
of the chain rather than one of its ends)
– Any folding which results in a more compact molecule
– Whether the chain is 'straight' or 'coiled'
Starch
• Starch is often produced in plants as a way of storing energy.
• It exists in two forms: amylose and amylopectin. Both are made
from α-glucose. Amylose is an unbranched polymer of α glucose.
The molecules coil into a helical structure. It forms a colloidal
suspension in hot water. Amylopectin is a branched polymer of α-
glucose. It is completely insoluble in water.
Glycogen
• Glycogen is amylopectin with very short distances between the
branching side-chains.
• Starch from plants is hydrolysed in the body to produce glucose.
• Glucose passes into the cell and is used in metabolism.
• Inside the cell, glucose can be polymerised to make glycogen which
acts as a carbohydrate energy store.
Cellulose
• Cellulose is a third polymer made from glucose.
• But this time it's made from β-glucose molecules and the
polymer molecules are 'straight'.
• Cellulose serves a very different purpose in nature to starch
and glycogen.
• It makes up the cell walls in plant cells.
• These are much tougher than cell membranes.
• This toughness is due to the arrangement of glucose units in
the polymer chain and the hydrogen-bonding between
neighboring chains.
• Cellulose is not hydrolysed easily and, therefore, cannot be
digested so it is not a source of energy for humans.
• The stomachs of Herbivores contain a specific enzyme called
cellulase which enables them to digest cellulose.
 Lipids
• Lipids are a highly variable group of molecules
that include fats, oils, waxes and some steroids.
• They are esters of fatty acids and alcohol (glycerol
or chains of alcohols).
• Fatty acids are made mostly from chains of
carbon and hydrogen and they bond to a range of
other types of atoms to form many different
lipids.
• The primary function of lipids is to store energy.
• A lipid called a triglyceride is a fat if it is solid at room
temperature and oil if it is liquid at room temperature.
• In addition, triglycerides are stored in the fat cells, also
called adipocytes or lipocytes, and are responsible in
storing fats and lipids which will facilitate energy store in
animals‘ body.
• Fat cells are categorized in white fat cells and brown fat
cells.
• The difference is made from their ways of storing lipids.
• White fat cells store one large lipid drop while brown fat
cells store smaller and multiple droplets of lipids spreading
in the whole body of the cell.
• Various types of lipids occur in the human
body, namely
– triacylglycerol,
– cholesterol, and
– polar lipids, which include phospholipids,
glycolipids and sphingolipids.
• Plant leaves are coated with lipids called
waxes to prevent water loss, and the
honeycomb in a beehive is made of beeswax.
• The basic structure of a lipid includes fatty acid tails as shown
in Figure in the next slide.
• Each tail is a chain of carbon atoms bonded to hydrogen and
other carbon atoms by single or double bonds.
• Lipids that have tail chains with only single bonds between
the carbon atoms are called saturated fats because no more
hydrogens can bond to the tail.
• Lipids that have at least one double bond between carbon
atoms in the tail chain can accommodate at least one more
hydrogen and are called unsaturated fats.
• Fats with more than one double bond in the tail are called
polyunsaturated fats.
Properties of lipids
• Insoluble in water
• Longer chains
– More hydrophobic, less soluble
• Double bonds increase solubility
• Melting points:
– Depend on chain length and saturation
– Double bonds lead acyl chain disorder and low melting
temperatures
– Unsaturated fatty acids are solid at room temperature.
Importance of lipids
– As the main component of cell membranes (phospholipids)
– Insulation of heat and water,
– Storing energy, protection and cellular communication.
 Proteins
• A protein is a compound made of small carbon
compounds called amino acids.
• Amino acids are small compounds that are
made of carbon, nitrogen, oxygen, hydrogen,
and sometimes sulfur.
• All amino acids share the same general
structure.
• Amino acids have a central carbon atom like the one shown in Fig.
below.
• Recall that carbon can form four covalent bonds. One of those
bonds is with hydrogen. The other three bonds are with an amino
group (–NH2), a carboxyl group (–COOH), and a variable group (–R).
• The variable group makes each amino acid different.
• There are 20 different variable groups, and proteins are made of
different combinations of all 20 different amino acids.
• Several covalent bonds called peptide bonds join amino acids
together to form proteins, which are also shown in Fig. below.
• A peptide forms between the amino group of one amino acid and
the carboxyl group of another.
 Variable group

Fig: peptide bond b/n amino acids

Fig: Basic structure of amino acid
• Based on the variable groups contained in the different amino
acids, proteins can have up to four levels of structure.
• The number of amino acids in a chain and the order in which
the amino acids are joined define the protein‘s primary
structure.
• After an amino acid chain is formed, it folds into a unique
three-dimensional shape, which is the protein‘s secondary
structure.
• A protein might contain many helices, pleats, and folds. The
tertiary structure of many proteins is globular, such as the
hemoglobin protein, but some proteins form long fibers.
• Some proteins form a fourth level of structure by combining
with other proteins.
• Proteins make up about 15% of your total body
mass and are involved in nearly every function of
your body.
• For example, your muscles, skin, and hair all are
made of proteins. Your cells contain about 10,000
different proteins that provide structural support,
transport substances inside the cell and between
cells, communicate signals within the cell and
between cells, speed up chemical reactions, and
control cell growth.
 Nucleic acids
• Nucleic acids are complex macromolecules that
store and transmit genetic information.
• Nucleic acids are made of smaller repeating
subunits called nucleotides.
• Nucleotides are composed of carbon, nitrogen,
oxygen, phosphorus, and hydrogen atoms.
• There are six major nucleotides, all of which have
three units a phosphate, a nitrogenous base, and
a ribose sugar, as shown in Fig. below
Fig. Basic structure of nucleotide
• There are two types of nucleic acids in living organisms:
deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA).
• In nucleic acids such as DNA and RNA, the sugar of one
nucleotide bonds to the phosphate of another
nucleotide.
• There are five different bases found in nucleotide
subunits that make up DNA and RNA, Adenine,
Cytosine, Guanine, Thymine and Uracil.
• Each of these nitrogenous base that sticks out from the
chain is available for hydrogen bonding with other
bases in other nucleic acids.
Fig: Nitrogenous bases
• A nucleotide with three phosphate groups is
adenosine triphosphate (ATP).
• ATP is a storehouse of chemical energy that
can be used by cells in a variety of reactions.
• It releases energy when the bond between the
second and third phosphate group is broken.
 Vitamins
• Vitamins are organic compounds that are needed in small amounts
for metabolic activities.
• Many vitamins help enzymes function well.
• Vitamin D is made by cells in your skin.
• Some B vitamins and vitamin K are produced by bacteria living in
the large intestine.
• Sufficient quantities of most vitamins cannot be made by the body,
but a well-balanced diet can provide the vitamins that are needed.
• Some vitamins that are fat-soluble can be stored in small quantities
in the liver and fatty tissues of the body.
• Other vitamins are water-soluble and cannot be stored in the body.
• Foods providing an adequate level of these vitamins should be
included in a person‘s diet on a regular basis.
 Water
• Water molecules are formed by covalent bonds that link
two hydrogen (H) atoms to one oxygen (O) atom, and each
water molecule has the same structure.
• It is one of the most plentiful and essential of compounds,
which is a tasteless and odorless, existing in gaseous, liquid,
and solid states.
• It has the important ability to dissolve and as a media for
transportation of many other substances.
• In reality, the versatility of water as a solvent is essential to
living organisms, as well.
• Water molecules have an unequal distribution of charges
and are called polar molecules, meaning that they have
oppositely charged regions.
 Minerals
• Minerals are inorganic compounds used by the body as
building material, and they are involved with metabolic
functions.
• For example, the mineral iron is needed to make
hemoglobin and it binds to hemoglobin in red blood cells
and is delivered to body cells as blood circulates in the
body.
• Calcium, and other minerals, is an important component of
bones and is involved with muscle and nerve functions and
they serve as cofactors for enzymes.
• Magnesium is an important component of the green
pigment, chlorophyll, involved in photosynthesis.
Thank you!
 Chapter Three

The cellular basis of life

 The Cell Theory
1. All organisms are made of cells.
2. The cell is the basic unit of life in all
living things. Schleiden

3. All cells come from existing cells.

This is important because it shows that all living things share a

similar structure

Schwann
• The activity of an organism depends on both the
individual and the collective activities of its cells.
• According to the principle of complementarity of
structure and function, the biochemical activities
of cells are dictated by their shapes or forms, and
by the relative number of their specific sub-
cellular structures.
• All cells arise from pre-existing cells (continuity of
life from one generation to another has a cellular
basis).
Animal cell
 Cell organelles
• An organelle is a specialized subunit within a cell that has a specific
function.
• In eukaryotes an organelle is a membrane bound structure found
within a cell.
• Just like cells have membranes to hold everything in, these mini-
organs are also bound in a double layer of phospholipids to insulate
their little compartments within the larger cells.
• Prokaryotes are cells that do not have membrane bound organelles.
• You can think of organelles as smaller rooms within the factory,
with specialized conditions to help these rooms carry out their
specific task (like a break room stocked with goodies or a research
room with cool gadgets and a special air filter).
• These organelles are found in the cytoplasm, a viscous liquid found
within the cell membrane that houses the organelles and is the
location of most of the action happening in a cell.
• There are two kinds of cell organelles on the basis
membrane covering, membranous and non
membranous organelles.
• Endoplasmic reticulum (Rough and Smooth),
Golgi bodies, mitochondria, chloroplasts, nucleus,
lysosomes, peroxisomes and vacuoles are
membranous whereas, non-membrane bound
cell organelles are ribosomes (70S and 80S),
centrosomes, cilia and flagella, microtubules,
basal bodies and microfilaments.
The nucleus
• This is distinctly oval or spherically shaped largest central structure
surrounded by a double-layered membrane.
• In the nucleus, DNA directs protein synthesis and serves as a
genetic blueprint during cell replication.
• DNA gives codes, or “instruction” for directing synthesis of specific
structure and enzymes proteins within the cell.
• By monitoring these protein synthesis activity, the nucleus
indirectly governs most cellular activities and serves as the cell’s
master.
• Three types of RNA are involved in protein synthesis.
• At first, DNA’s genetic code for a particular protein is transcribed
into a messenger-RNA, which leaves nucleus through the nuclear
pores of the nuclear membrane.
• And, within the cytoplasm, mRNA delivers the coded
message to the ribosomal RNA, which "reads"
message/code and translates it into the appropriate
amino acids sequence for the designated protein being
synthesized.
• Finally, transfer-RNA transfers the appropriate amino
acids within the cytoplasm to their designated site in
the protein under production. During cell replication,
DNA ensures the continuing of the identical types of
cell line within the body. Furthermore, in the gametes,
the DNA blueprint serves to pass the genetic
characteristics to future generation.
Generally, the nucleus may be:

• Rounded  e.g. in hepatocytes.

• indented (segmented)  e.g. in neutrophils.
• Binucleated  e.g. in parietal cells, cardiac muscle cells.
• Multinucleated  e.g. in osteoclasts, skeletal muscle cells.
• very large (many DNA)  e.g. in megakaryocytes.
• absent  e.g. in mature erythrocytes, blood platelets.

• The nucleus is surrounded by a nuclear envelope and

contains chromatin and one or more nucleoli.
• The Nuclear envelope
 surrounds nuclear material
consists of outer and inner membrane
perforated at intervals by nuclear pores
 through this pores most ions and water
soluble molecules to transfer b/n nucleus and
cytoplasm.
Chromatin
• The term chromatin means "colored material"
and refers to the fact that this material is
easily stained for viewing with microscope,
and it is composed mainly of coils DNA bound
to basic protein called histones. The DNA is so
long that it has to be packed in an
organization manner or it would get entangled
like unraveled ball of string.
Nucleoli
• The nuclei of most cells contain one or more lightly stained
structures called nucleoli that actively engage in
synthesizing of ribosomes.
• The nucleolus, unlike most of the organelles, does not have
a limiting membrane.
• Instead, it is simply a structure that contains large amounts
of RNA and protein of the type found in ribosomes.
• The nucleolus becomes considerably enlarged when a cell
is actively synthesizing proteins.
• The genes of five separate chromosome pairs synthesize
the ribosomal RNA and then store it in the nucleolus.
The Cytoplasm
• The cytosol is the material of cell interior not occupied by the
nucleus, containing a number of distinct, highly organized
membrane-enclosed structures- the organelles- dispersed within a
complex jelly – like marrow called the “cytosol”.
• All cells contain six main types of organelles- the endoplasmic
reticulum, Golgi complex, lysosomes, peroxisomes, mitochondria,
and vacules.
• They are similar in all cells, but with some variations depending on
the cell specialization.
• Each organelle is a separate compartment, containing different
chemically setting for fulfilling a partial or cellular function.
• These organelles occupy about half of the total cell volume.
• The remaining part of the cytoplasm is cytosol.
• A typical eukaryotic cell has 3 major parts:
– The plasma membrane: the outer boundary of the
cell.
– The cytoplasm: the intracellular fluid packed with
organelles, small structures that perform specific
cell functions.
– The nucleus: an organelle that controls cellular
activities.
• Typically the nucleus resides near the cell’s center.
Endoplasmic reticulum (ER)
• The endoplasmic reticulum is a fluid-filled membrane
system extensively present throughout the cytosol.
• The ER is one continuous organelle with many
communicating channels.
• The two different types are smooth endoplasmic
reticulum and the rough ER.
• The smooth ER is a meshwork of interconnected
tubules, whereas the rough ER projects outwards from
the reticulum as stacks of flattened sacs.
• Though different in structure and function, they are
continuous with each other.
The rough Endoplasmic Reticulum:
• The outer surface of the rough ER contains dark particles called
ribosomes, which are ribosomal RNA protein complexes that
produce protein under the direction of nuclear DNA.
• Messenger-RNA carries the genetic message from the nucleus to
the ribosomes “workshop” where proteins are synthesized.
• Some ribosomes are “free” dispersed throughout the cytosol.
• The rough ER in association with ribosomes produces and releases a
variety of proteins, into the fluid-filled space enclosed by the
membrane.
• Some proteins for export as secretory products (hormones or
enzymes).
• Other proteins are transported to sites within the cell for use in the
construction of new plasma membrane or new organelle
membrane.
• Cellular membrane contains predominantly fats and proteins.
• ER membrane also contains enzymes required for the synthesis of
almost all the lipids needed for the production of new membranes.
• These lipids enter the ER lumen along with the proteins.
• This structure is well developed in cells producing digestive
enzymes or in rapidly growing cells.
• Each ribosome is involved in producing only one type of protein.
• The free ribosomes synthesize enzyme protein that are used intra-
cellularly within the cytosol.
Smooth Endoplasmic Reticulum
• Since it does not have ribosomes, it looks “smooth” and
does not produce proteins.
• It serves a variety of other functions that differ in cell types.
• In most cells, the smooth ER is sparse and serves in
packaging and discharging site for protein molecules that
are to be transported from the ER.
• All new proteins and fats pass from ER gathered in the
smooth ER.
• Portions of the smooth ER then “bud off/pinch off”, giving
rise to “transport vesicles”, they contain the new molecule
wrapped in a membrane derived from the smooth ER
membrane.
• Transport vesicles move to the Golgi complex for
further processing of their cargo.
• Some specialized cells have an extensive smooth
ER, which has additional functions as follows:
 The smooth ER is well developed in cells
specialized in lipid metabolism- cells that
synthesize steroid hormones. The membrane wall
of the smooth ER contains enzymes for synthesis
of lipids. This is an additional site for synthesis in
addition for ER to keep pace with demands for
hormone secretion.
 In liver cells, the smooth ER contains enzymes involved in
detoxifying harmful endogenous substances produced
within the body by metabolism or exogenous substances
entering the body from outside as drugs or other foreign
compounds. The detoxifying enzymes alter toxic substances
so that they could be easily eliminated in the urine. But
unfortunately, in some instances the same enzyme
transforms otherwise harmless substance into carcinogens
that play a role in cancer development.
 The smooth ER has a special role in skeletal muscle cells.
They have an elaborate network of smooth ER, which
stores ionic calcium and plays a crucial role in the process
of muscle contraction.
Endoplasmic Reticulum
Golgi Bodies
• The Golgi complex is elaborately associated with
the ER and contains sets of flattened, curved,
membrane- enclosed sacs, or cisternae, stacked
in layers.
• Number of stacks vary in cells; cells specialized
for protein secretion have hundreds of stacks,
whereas some have only one.
• The majority of newly formed molecules budding
off from the smooth ER enter a Golgi complex
stacks.
• It performs the following important functions.
1. Processing the raw material into finished products. In the
Golgi complex, the “raw” protein from the ER are modified
into their final state mainly by adjustment made in the sugar
attached to the protein.
This is a very elaborate, precisely programmed activity,
specific for each final product.
2. Sorting and directing finished product to their final
destination. According to their function and destination,
different types of products are segregated by the Golgi
complex, i.e., molecules that are destined for secretion to the
exterior, molecules that will eventually become part of the
plasma membrane, and the molecules that will become
incorporated into other organelles.
3. The smooth ER of the liver and kidney cells
are responsible for the detoxification and
inactivation of drugs. Enzymes within the
smooth ER can inactivate or destroy a variety of
chemicals including alcohol, pesticides, and
carcinogens.
4. In skeletal muscle cells, a modified form of
smooth ER stores Ca2+ to be released for muscle
contraction.
Golgi Bodies
Lysosomes
• Lysosomes serve as the intracellular “digestive system”.
• Lysosomes are membrane-enclosed sacs containing powerful
hydrolytic enzymes capable of digesting and removing unwanted
cellular debris and foreign materials such as bacteria that have been
internalized within the cell.
• Lysosomes vary in size and shape, and about 300μm in a cell.
• Surrounding membrane confines these enzymes, preventing from
destroying the cell that houses them.
• Extrinsic material to be attacked by lysosomal enzymes is brought
into the interior of the cell through the process of endocytosis.
• If the fluid is internalized by endocytosis, the process is called
pinocytosis. Endocytosis is also accomplished by phagocytosis.
• In pinocytosis, ECF and a large molecule such as protein is engulfed.
• A specific molecule may bind to surface receptor, triggering
pinocytosis- receptor-mediated endocytosis.
• Dynamin, a molecule forms rings wrapping around, severing the
vesicle from the surface membrane in pinocytosis.
• In phagocytosis, large multimolecular particles are internalized by
endocytosis; this is achieved by only a few specialized cells- white
blood cells that play an important role in the body’s defense
mechanism.
• When a leukocyte encounters large multimolecular particle, such as
bacteria or tissue debris, it extends projection (pseudopodia) that
completely surround or engulf the particle, forming an internalized
vesicle that traps the large multimolecular particle within it.
• A lysosome fuses with the membrane of the
internalized vesicle and releases its contents
of hydrolytic enzymes into the vesicle.
• These enzymes safely attack the microbes or
other trapped material within the enclosed
confines of the vesicle without damaging the
remainder of the cell.
• Lysosomes can take up old organelles such as mitochondria
and break down into their component molecules.
• Those molecules that can be released are reabsorbed into
the cytosol, and the rest are dumped out of the cell.
• The process by which worn-out organelles are digested is
called autophagy a human liver cell recycles about half its
content every week.
• In the inherited condition known as lysosomal storage
disease (Tay-Sachs disease) lysosomes are not effective
because they lack specific enzymes.
• As a result, harmful waste products accumulate disrupting
the normal function of cells, often with fatal results.
Lysosome
Peroxisome
• Peroxisome is membrane-enclosed sacs containing
oxidative enzymes and catalase that detoxify various
wastes.
• Oxidative enzymes need oxygen to remove hydrogen
from specific substance/molecule; such reactions are
important in detoxifying various waste products within
the cell or foreign compounds that have entered in,
such as ethanol consumed in alcoholic drinks (in liver
and kidneys).
• The major product generated is hydrogen peroxide;
hydrogen peroxide itself is a powerful oxidant.
• It also contains catalase, and antioxidant enzyme
decomposing hydrogen peroxide into harmless water and
oxygen.
• This reaction is an important safety reaction that destroys
deadly hydrogen peroxide, at the site of production,
thereby preventing possible devastating escape into the
cytosol.
• It is shorter and smoother than lysosome and several
hundreds may present in one cell.
• Peroximal disorders disrupt the normal processing of lipids
and can severely disrupt the normal function of the
nervous system by altering the structure of the nerve cell
membrane
Mitochondria
• Mitochondria are the “power houses” of a cell; they extract energy
from nutrients in food and transform it into usable form to energize
cell activity.
• Their number varies depending on the energy needs of each
particular cell types.
• A single cell may have few hundreds or thousands.
• Mitochondria are rod or oval shaped about the size of a bacterium.
• Each is enclosed by a double membrane - a smooth outer that
surrounds the mitochondria, and an inner membrane that forms a
series of enfolding or shelves called cristae, which project into an
inner cavity filled with a jelly-like matrix (See figure).
• These cristae contain proteins that convert much
of the energy in food into a usable form (the
electron transport protein).
• The enfolding increase the surface area available
for keeping these important proteins.
• The matrix contains a mixture of hundreds of
different dissolved enzymes (Citric acid cycle
enzymes) that are important in preparing
nutrient molecules for the final extraction of
usable energy by the cristae proteins.
• Carbon-hydrogen bonds in ingested food are the source of energy
stored in the chemical forms.
• Body cell can extract energy from food nutrients and convert it into
energy form that they can use.
• The high energy phosphate bonds of ATP contain adenosine with 3
phosphate groups. When high energy phosphate bond is split, a
substantial amount of energy is released. ATP is the universal
energy carrier, the common energy “currency” of the body.
• Cells can “cash in” ATP to pay the energy “price” for running the
cellular machine.
• To get immediate usable energy, cells can split terminal phosphate
bond of ATP, which yields ADP with phosphate group attached - plus
inorganic phosphate (Pi) plus energy. (See figure below).
Mitochondrial structure
• Mitochondria are unusual organelles in two
ways:
– In the matrix they have their own unique DNA
called mitochondrial DNA.
– Mitochondria have the ability to replicate
themselves even when the cell to which they
belong is not undergoing cell division.
Chloroplasts
• Chloroplasts are useful organelles among plastids as they
highly participate in the process of photosynthesis which is
a process by which plants synthesize their own food.
• They are located in outer surface of the cell to receive
enough light.
• Chloroplasts are green colored due to the chlorophyll
pigments found in its internal parts.
• Some of important characteristics of plant is its ability to
carry out photosynthesis as the way they use in making
their own food and pass through converting light energy in
chemical energy.
• Vesicles are membrane bound sacs that are used
to store or transport substances around the cell.
Lysosomes are actually Vesicles.
• Vacuoles are essentially larger Vesicles, and they
are formed by the joining together of many
Vesicles. They are membrane bound organelles
that have no specific shape and contain water
with a number of different compounds within it.
Their function varies greatly depending on the
type of cell they are part of. In plant cells they are
important in maintaining Turgor Pressure.
Cytoskeleton
• The cytoskeleton is a complex protein network
that act as the “bone and muscle” of the cell. This
necessary intracellular scaffoldings supports and
organizes cellular components arrangements and
to control their movements; this provides distinct
shape, size to the cell.
• This network has at least four distinct elements:
Microtubules, Microfilaments, Intermediate
filaments and Microtubular lattice
• The different parts of the cytoskeleton are structures linked
and functionally coordinated to provide integration of the
cell.
• The microtubule is the largest of the group; slender, long,
hollow tubes composed of a globular protein molecule (6
nm diameter) tubulin.
– They provide asymmetrical shape to the cell, such as a neuron
with cell body and long axon. They coordinate numerous
complex cell movements in transport of secretory vesicles from
region to region of the cell, movements of cilia and flagella,
distribution of chromosomes during cell division
• microfilaments are important to cellular contractile system
and as mechanical stiffeners.
• The microfilaments are the smallest of the
cytoskeleton composed of protein molecule actin
having a globular shape similar to tubulin.
Generally, cytoskeletons determine/ provide the:
– shape of a cell
– structural support
– organizing its contents
– substances movement through cell (cilia, flagella and
intracytoplasmic vesicles), and
– contribute to movements of the cell as a whole.
Cytoskeleton
Plasma/cell membrane
• The plasma membrane is extremely thin layer of lipids and
proteins forming outermost boundary of living cell and
enclosing the intracellular fluid (ICF).
• It serves as a mechanical barrier that traps needed
molecules within the cell; plasma membrane plays an
active role in determining the composition of cell by
selective permeability of substances to pass between the
cell and its ECF environment.
• There are some differences in the composition of plasma
membrane between cell types, which permits the cell to
interact in different ways with essentially the same
extracellular fluid (ECF) environment.
• The plasma membrane is a fluid lipid bilayer
embedded with proteins. It appears as
‘trilaminar’ layer structure having two dark
layers separated by a light middle layer as a
result of specific arrangement of the
constituent molecules.
• All plasma membrane are made up of lipids and proteins
plus small amount of carbohydrates.
• Phospholipids are most abundant with a lesser amount of
cholesterol.
• Phospholipids have a polar charged head having a
negatively charged phosphate group and two non-polar
(electrically neutral) fatty acid tails.
• The polar end is hydrophilic (water loving) because it can
interact with water molecule, which is also polar; the non-
polar end is hydrophobic (water fearing) and will not mix
with water.
• Such two-sided molecule self assemble into a lipid bilayer, a
double layer of lipid molecules when in contact with water.
• The hydrophobic tails bury themselves in the center away from the
water, while the hydrophilic heads line up on both sides in contact
with water.
• The water surface of the layer is exposed to ECF, whereas the inner
layer is in contact with the intracellular fluid (ICF).
• The lipid is fluid in nature, with consistency like liquid cooking oil.
• Cholesterol provides to the fluidity as well as the stability;
cholesterol lies in between the phosphate molecules, preventing
the fatty acid chain from packing together and crystallizing that
could decrease fluidity of the membrane.
• Cholesterol also exerts a regulatory role on some of the membrane
proteins.
• For fluidity of the membrane, it gives flexibility to the cell to change
its shape; transport process are also dependent on the fluidity of
the lipid bilayer.
• The membrane proteins are either attached to or inserted
within the lipid bilayer; some extending through the entire
membrane thickness; they have polar region at both ends
joined by a non-polar central portion.
• Other proteins are on either the outside or inner surface,
anchored by interactions with proteins that spans the
membrane or by attachment to the lipid bilayer.
• On account of membrane fluidity, many proteins float
freely, although the mobility of protein that have special
function in a particular area of the membrane is restricted -
this gives ever changing mosaic pattern of the protein
embedded in the lipid layer.
• Only the outer surface of the plasma
membrane contains a small amount of
carbohydrate.
• Short-chain carbohydrates are bound
primarily to membrane proteins and to a
lesser extent to lipids, forming glycoproteins
and glycolipids.
• The plasma membrane is actually asymmetrical;
the two surfaces are not the same; carbohydrate
is only on the outer surface; different amount of
different proteins are on the outer and inner
surfaces and even the lipid structures of the outer
and inner half is not the same.
• The plasma membrane is highly complex,
dynamic, regional differentiated structure.
• The lipid layer forms the primary barrier to
diffusion, whereas proteins perform most of the
specific membrane functions.
• Lipid bilayer forms the basic structure of the
membrane, is a barrier to passage of water
soluble substances between the ICF and ECF;
and is responsible for the fluidity of the
membrane.
• Membrane proteins are variety of different proteins within the
plasma membrane; have the following special functions:
1. Some form water-filled passage ways or channels, across the lipid
bilayer; such channels allow ions to pass through without coming in
direct contact with lipid interior. The channels are highly selective; they
can selectively attract or repel particular ions. This selectively attracts
or repels particular ions. This selectivity is to specific charged amino
acids group. Number and kind of channels vary in cells. Channels open
and close in response to a controlling mechanism.
2. Other proteins serve as carrier molecule that transport specific
molecule that cannot cross on their own. They differ in cells, e.g.,
thyroid epithelial cell possesses carriers for iodine.
3. Many proteins on the outer surface serve as “receptor sites” that
recognize and bind with specific molecules in the cell environment.
• This binding triggers a series of membrane and intracellular
events that alter the activity of the target cell. In this way
hormones influence specific cell, even though every cell is
exposed to the same chemical messenger via its
widespread distribution by the blood
4. Another group of proteins act as membrane-bound
enzymes that control specific chemical reactions on either
side of the plasma membrane e.g., outer layer of the plasma
membrane of skeletal muscle contains enzyme
Acetylcholinesterase (AChE) that destroys the chemical
messenger that triggers contraction.
5. Some proteins are arranged as filaments
network/meshwork on the inner side and are secured to
certain internal protein elements of the cytoskeleton.
• They maintain cell shape.
6. Other proteins function as cell adhesion
molecules (CAMs). These molecules protrude from
the membrane surface that grip each other and grip
the connective tissue fibers that interlace between
cells.
7. Some proteins, especially in conjunction with
carbohydrate are important in the cell’s ability to
recognize “self” and in cell-to-cell interactions.
Plasma/cell membrane
Membrane protein
• Membrane Carbohydrate: Short-chain carbohydrate on the outer
membrane surface serves as self-identity marker enabling cells to
identify and interact with each other in the following ways:
• Recognition of “self” and cell-to-cell interactions. Cells recognize
each other and form tissues; complex carbohydrates act as a
“trademark” of a particular cell type, for recognition.
• Carbohydrate-containing surface markers are important in growth.
Cells do not overgrow their own territory. Abnormal surface
markers present in tumor cells, and abnormality may underline
uncontrolled growth.
• Some CAMS have carbohydrate, on the outermost tip where they
participate in cell adhesion activity.
• Functions of biological membranes
• The phospholipid bilayers provides the basic structure
of the membrane and they also restrict entry and exit
of polar molecules and ion. The other molecules in the
membrane have a variety of function:
– Channel protein and carrier protein: these proteins are
involved in the selective transport of polar molecule and
ion across the membrane
– Enzymes: membrane proteins sometimes act as enzymes,
For example, the microvilli on epithelial cells lining some
part of the gut contain digestive enzymes in their cell
surface membrane.
– Receptor molecules: proteins have very specific shapes
and this makes them ideal as receptor molecules for
chemical signaling between cells.
• For example, hormones are chemical messengers, which circulate
in the blood but, only bind to specific target cells, which have the
correct receptors sites. Neurotransmitters, the chemicals that
enable nerve impules from one nerve cell to the next, also fit into
specific receptor proteins in nerve cells.
– Antigens: these act as cell identity markers or ''name tag''.
They are glycoproteins that is proteins with branching
carbohydrates side chains like antennae. There is an
enormous number of possible shapes to these side chains,
so each type of cell can have its own specific markers.
• This enables cells to recognize other cells, and
to behave in an organized way, for example,
during development of tissues and organs in
multicellular organisms . It also means that
foreign antigens can be recognized and
attacked by the immune system.
– Glycolipids- also have branching carbohydrate side
chain and are involved in cell-cell recognition. They
may act as a receptor sites for chemical signals. With
glycoproteins they also involved in sticking the correct
cell together in tissues. Eg. sperm recognition of ova
– Energy Transfer in photosynthesis and respiration
proteins take part in the energy transfer systems that
exist in the membranes of chloroplast and
mitochondria respectively.
– Cholosterole: acts like a plug, reducing even further
the escape or entry of polar molecules through the
membrane.
Cellular Anatomy
Cellular diversity
• Cells are found in different organisms, and are very diverse in their
size, shape and their internal structure and this also applies to cells
found in the same organism. This diversity is influenced by their
roles and function within organism’s body.
• Cell Shape
• Cells have different shapes due to appropriate function. It is
possible to find other cells which are flat, most of these cells are
body cells and their function is protecting and covering body
surface. Nerve cells have long extensions. Skin cells have a shape
which is flat. Egg cells have shape which is like sphere, and some
bacteria are rod in shape. Some plant cells are rectangular.
Various types of animal cells (shape)
• Cell Size
• Some cell can be seen without using
magnification instruments as they are enough
to be seen by the naked eye. Example, egg of
birds/reptiles and a neuron cell of giraffe,
which is 2 meters in length.
• Transport across the cell membranes
• The plasma membrane is selectively permeable. Lipid-
soluble substances and small ions can passively diffuse
through the plasma membrane down their electro-
chemical gradients.
• Highly lipid-soluble particles are able to dissolve in the lipid
bilayer and pass through the membrane. Uncharged/non-
polar molecules oxygen, carbon dioxide and fatty acids are
highly lipid-soluble and readily permeate the membrane.
• Charged particle sodium/potassium ions and polar
molecules such as glucose and proteins have low lipid
solubility, but are very soluble in water.
• For water-soluble ions of less than 0.8 nm diameter, protein
channels serve as an alternate route for passage. Ions for which
specific channels are available can permeate the plasma
membrane. Particles with low lipid-permeability and too large for
channels, cannot permeate the membrane on their own. The
phospholipid bilayer is a good barrier around cells, especially to
water soluble molecules. However, for the cell to survive some
materials need to be able to enter and leave the cell. There are 4
basic mechanisms:
1. Diffusion and facilitated diffusion
2. osmosis
3. active transport
4. bulk transport
• Two forces are involved in facilitating
movement across the plasma membrane:
1. Forces that do not require the cell to expend
energy for movement – passive force
2. Forces requiring energy (as ATP) to be
expended to transport across the membrane -
active force.
• Diffusion
• Diffusion is the net movement of molecules (or ions) from a
region of their high concentration to a region of their lower
concentration.
• The molecules move down a concentration gradient.
• Molecules have kinetic energy, which makes them move
about randomly.
• All molecules in liquid and gases are in continuous random
motion in any direction as they have more room to move
before colliding with another.
• As a result of this haphazard movement, the molecules
frequently collide bouncing off each other in different
directions.
• The greater the concentration, the greater the
likelihood of collision. Such a difference in
concentration in molecules between two
adjacent areas is chemical /concentration
gradient. The net movement of the molecule
by diffusion will be from the higher area of
concentration to the area of lower
concentration.
• Certain additional factors that influence the
rate of net diffusion across a membrane are:
1. permeability of the membrane
2. surface area of the membrane
3. molecular weight of the substance (lighter
one diffuses rapidly)
4. distance through which diffusion must take
place
• N.B:- Increasing all the factors increases rate
of net diffusion, except distance - thickness,
that if increased, decreases the rate of
diffusion; and molecular weight if increased,
decreases rate of diffusion.
• As a result of diffusion, molecules reach an
equilibrium where they are evenly spread out.
This is when there is no net movement of
molecules from either side.
• Movement along electrical gradient
• Movement of charged particles is also affected by
their electrical gradient. If a relative difference in
charges exist between two adjacent areas, the
cations tend to move towards more negatively
charged area, whereas the anions tend to move
toward the more positively charged areas.
• The simultaneous existence of an electrical and
concentration (chemical) gradient for a particular
ion is referred to as an electro-chemical gradient.
Concentration difference (A) and difussion (B)
Diffusion of lipid molecules
• Carrier- Mediated Transport
• All carrier proteins span the thickness of the plasma
membrane and are able to undergo reversible changes
in shape so that specific binding site can alternately be
exposed at either side of the membrane.
• As the molecule to be transported attaches to a
binding site on the carrier on one side of the
membrane, it triggers a change in the carrier shape
that causes the same site to be exposed to the other
side of the membrane. Their having movement in this
way, the bound molecule detaches from the carrier.
• This transport displays three characteristics:
1. Specificity: each cell possesses protein specified to transport a
specific substance or few closely-related chemical compounds. Amino
acid cannot bind to glucose carrier, but similar amino acids may use
the same carrier. Type of carriers vary in cells. A number of inherited
disorders involve defects in transport system for a particular
substance.
2. Saturation: in a given time, only a limited amount of a substance can
be transported via a carrier; limited number of carrier site are available
within a particular plasma membrane for a specific molecule. This limit
is known as transport maximum (Tm).
The substance’s rate of transport across the membrane are directly
related to its concentration. When the Tm is reached, the carrier is
saturated, and the rate of transport is maximum.
• Further increase in the substance concentration is
not accompanied by corresponding increase in
the rate of transport. Saturation of carrier is a
critical rate-limiting factor to the transport of
selected substances across the plasma membrane
in kidney and the intestine. There is a mechanism
to increase the number of carriers in the plasma
membrane.
3. Competition: Several closely related compounds
may compete for ride across the plasma membrane
on the same carrier.
• Facilitated Diffusion
• Facilitated diffusion uses a carrier protein to facilitate the transfer of a
particular substance across the membrane ''downhill'' from higher to
lower concentration.
• This process is passive and does not require energy because movement
occurs naturally down a concentration gradient.
• Active transport, on the other hand, requires the carrier to expend energy
to transfer its passenger ''uphill'' against a concentration gradient from an
area of lower concentration to an area of higher concentration.
• Active transport requires protein carrier to transfer a specific substance
across the membrane, transporting against concentration gradient.
• Carrier phophorylation increases the affinity for its passenger.
• The carrier has ATPase activity splitting high-energy phosphate from an
ATP to yield ADP plus a free Pi. This phosphate group gets bound to the
carrier.
• Phosphorylation and binding of particle on the low
concentration side induces a conformational change in the
carrier protein so that passenger is now exposed to the
high concentration side of the membrane.
• This change in carrier shape is accompanied by
dephosphorylation. Removal of phosphate reduces the
affinity of the binding site for the passenger, so the
passenger is released on the high concentration side.
• The carrier then returns to the original conformation. This
active transport mechanisms are often called “pumps”,
analogous to lift water by pump that need energy to lift
water against the downward pull of gravity; Hydrogen-
pump, Na-KATPase pump (Na-K-Pump).
• Osmosis
• Osmosis is the net diffusion of water down its own
concentration gradient.
• Water can readily permeate the plasma membrane.
The driving force for diffusion of water is its
concentration gradient from area of higher water
concentration (low solute) to the area of lower water
(high solute) concentration. This net diffusion of water
is known as osmosis. Special mechanisms are used to
transport selected molecules unable to cross the
plasma membrane on their own.
Movement across membranes
• Similarly, positively charged ions (cations) tend to be
attracted in to cell. Thus both concentration and charge are
important in deciding the direction in which ions cross the
membrane. The pump is essential in controlling the
osmotic balance in animal cells (osmoregulation) . If the
pump is inhibited, the cell swells and brusts because of the
building up of Na+, which results in excess water entering
in to the cell by osmosis . The pump is also important in
maintaining electrical activity in nerve and muscle cells and
in driving active transport of some other substances such as
sugar and amino acids. In addition, high concentration of
potassium are needed inside cells for protein synthesis,
glycolysis, photosynthesis and other vital processes.
• Na+-K+-pump plays three important roles
1. It establishes sodium and potassium concentration
gradients across the plasma membrane of all cells; these
gradients are important in the nerve and muscle to generate
electrical signals.
2. It helps regulate cell volume by controlling the
concentration of solutes inside the cell and thus minimizing
osmotic effects that would induce swelling or shrinking of the
cell.
3. The energy used to run the pump also indirectly serves as
the energy source for the cotransport of glucose and amino
acids across the membrane (intestine and kidney cell).
Sodium-potasium pump
Exocytocis and Endocytisis
• Vesicular Transport:
• The special cell membrane transport system selectively
transports ions and small polar molecules. But large
polar molecules and even multimolecular material may
leave or enter the cell, such as hormone secretion or
ingestion of invading microbe by leukocytes. These
materials cannot cross the plasma membrane but are
to be transferred between the ICF and ECF not by usual
crossing but by wrapped in membrane. This process of
transport into or out of the cell in a membrane-
enclosed vesicle is - vesicular transport.
• Transport into the cell is termed endocytosis,
whereas transport out of the cell is called
exocytosis. In endocytosis, the transported
material is wrapped in a piece of the plasma
membrane, thus gaining entrance to the
interior of the cell. Endocytosis of fluid is
called pinocytosis (cell drinking), whereas
endocytosis of large multimolecular particle is
known as phagocytosis (cell eating).
• Endocytosis and exocytosis are active processes involving the bulk
transport of materials through membranes, either in to cells
(endocytosis) or out of cells (exocytosis).
• Endocytosis occurs by an in folding or extension of cell surface
membrane to form a vesicle or vacuole.
• It is of two types.
– Phagocytosis (cell eating) material taken up is in solid form. Cells
specializing in the processes are called phagocytes and are said to be
phagocytic. The sac formed during the uptake is called a phagocytic
vacuole.
– Pinocytosis( cell drink) material taken up is in liquid form. Vesicles
formed are extremely small , in which case the process is known as
micropinocytosis and the vesicles as micropinocytic vesicles.
Pinocytosis is used by the human egg cell to take up nutrients from the
surrounding follicle cells.
Exocytosis
• Exocytosis. is the reverse process of
endocytosis. Waste materials such as solid and
undigested remains from phagocytic vacuoles
may be removed from cells or useful materials
may be secreted. Secretion of enzymes from
the pancreas is achieved in this way. Plant
cells use exocytosis to export the materials
needed to form cell wall.
• Active transport
• Active transport is energy consuming transport of
molecules or ions across a membrane against its natural
tendency to diffuse in the opposite direction. The
movement of molecules in active transport is in one
direction only; unlike diffusion that is reversible the energy
is supplied by the broke down of ATP, which energy carrier
is made in respiration
– The major ions within the cells and their surrounding are
sodium (Na+ ), potassium (K+ ) and chloride (Cl- ). In recent
years it has been shown that the cell surface membrane of most
cell have sodium pump is coupled with a potassium pump that
actively moves potassium ion from outside to inside the cell.
The combined pump is called the sodium pump (Na+ -K - pump).
• The pump is a carrier protein that spans across the
membrane from one side to the other. The transfer of
sodium and potassium across the membrane is brought
about by the changes in the shape of the protein. Note
that for every 2K+ions taken into the cell, 3Na+ ions are
removed.
– Thus a potential difference is built up across the
membrane, with the inner side of the cell being negative.
This tends to restrict the entry of negatively charged ions
(anions) such as chloride and favoring diffusion of cations
into the cell. This explains why chloride concentration
inside red cell is less than the outside despite the fact that
chloride ions can diffuse in and out by facilitated diffusion.
Thank You!
 Chapter Four

Cellular Metabolism and Metabolic

Disorders
Cellular metabolism
• Living cells are in a constant activity.
Macromolecules are assembled and broken
down, substances are transported across cell
membranes, and genetic instructions are
transmitted. All of these cellular activities
require energy.
• Living organisms are unique in that they can extract energy
from their environments and use it to carry out activities
such as movement, growth and development, and
reproduction.
• But the basic question is how living organisms or, their cells
extract energy from their environments, and how cells use
this energy to synthesize and assemble the components
from which the cells are made.
• The answers to these questions lie in the enzyme-mediated
chemical reactions that take place in living matter
(metabolism). Hundreds of coordinated, multistep
reactions, fueled by energy obtained from nutrients and/or
solar energy, ultimately convert readily available materials
into the molecules required for growth and maintenance.
• Metabolism is thus the sum of chemical
reactions that takes place within each cell of a
living organism and that provides energy for
vital processes and synthesizing of new
organic materials. Broadly, these reactions can
be divided into catabolic reactions that
convert nutrients to energy and anabolic
reactions that lead to the synthesis of larger
biomolecules.
• In metabolism, a series of chemical reactions in which
the product of one reaction is the substrate for the
next reaction is called a metabolic pathway.
• Catabolic pathways release energy by breaking down
larger molecules into smaller molecules.
• Anabolic pathways use the energy released by
catabolic pathways to build larger molecules from
smaller molecules, insuring the continual flow of
energy within an organism.
• The reactants and products of these chemical reactions
are metabolites.
• The major classes of metabolites include proteins,
carbohydrates, nucleotides, lipids, coenzymes, and
cofactors.
• These classes of compounds encompass an enormous
diversity of molecular structures, physicochemical
properties, functions, and abundances.
• Due to the analytical challenges posed by this diversity,
most studies require division into subsets of
metabolites.
• The most common criteria for this distinction rely on
the hydrophilic (polar) and hydrophobic (nonpolar)
nature of metabolites.
• Polar metabolites are soluble in aqueous solutions and
include most sugars, purines and pyrimidines, nucleotides
and nucleosides, acyl carnitines, organic acids, hydrophilic
acids, amino acids, and phosphorylated compounds.
• These metabolites include most of the reactants and
products involved in cellular respiration (e.g., glycolysis, the
TCA cycle, or in other pathways) and in the production of
building blocks for synthesis of large biopolymers such as
DNA, RNA, proteins, and oligosaccharides.
• The nonpolar or hydrophobic metabolites are commonly
lipids. These metabolites function in energy storage,
membrane structure, and signal transduction.
• At the cellular level of organization, the main chemical
processes of all living matter are similar, if not identical.
• This is true for animals, plants, fungi, or bacteria; where
variations occur (such as, the secretion of antibodies by
some molds), the variant processes are but variations on
common themes.
• Thus, all living matter is made up of large molecules called
proteins, which provide support and coordinated
movement, as well as storage and transport of small
molecules, and, as catalysts, enable chemical reactions to
take place rapidly and specifically under mild temperature,
relatively low concentration, and neutral conditions (i.e.,
neither acidic nor basic).
• The chemical reactions that take place in living cells are
similar as well. Green plants use the energy of sunlight
to convert water (H2O) and carbon dioxide (CO2) to
carbohydrates (sugars and starches), other organic
(carbon-containing) compounds, and molecular oxygen
(O2).
• The process of photosynthesis requires energy, in the
form of sunlight, to split one water molecule into one-
half of an oxygen molecule (O2; the oxidizing agent)
and two hydrogen atoms (H; the reducing agent), each
of which dissociates to one hydrogen ion (H+) and one
electron.
• Through a series of oxidation-reduction reactions,
electrons (denoted e−) are transferred from a
donating molecule (oxidation), in this case water,
to an accepting molecule (reduction) by a series
of chemical reactions; this “reducing power” may
be coupled ultimately to the reduction of carbon
dioxide to the level of carbohydrate.
• In effect, carbon dioxide accepts and bonds with
hydrogen, forming carbohydrates (Cn[H2O]n).
• Living organisms that require oxygen reverse this
process: they consume carbohydrates and other
organic materials, using oxygen synthesized by plants
to form water, carbon dioxide, and energy.
• The process that removes hydrogen atoms (containing
electrons) from the carbohydrates and passes them to
the oxygen is an energy-yielding series of reactions.
• In plants, all but two of the steps in the process that
converts carbon dioxide to carbohydrates are the same
as those steps that synthesize sugars from simpler
starting materials in animals, fungi, and bacteria.
• Similarly, the series of reactions that take a
given starting material and synthesize certain
molecules will be used in other synthetic
pathways are similar, or identical, among all
cell types.
• For instance, from a metabolic point of view,
the cellular processes that take place in a lion
are only marginally different from those that
take place in a dandelion.
Enzymes and their role in metabolism
• Most chemical reactions within cells do not
occur spontaneously. Instead, they need a
catalyst to get them started.
• In many cases, heat may be a catalyst, but this
is inefficient because heat cannot be applied
to molecules in a controlled fashion. Thus,
most chemical reactions require biological
catalyst called enzymes.
• Enzymes are protein catalysts that speed
biochemical reactions by facilitating the
molecular rearrangements that support cell
function.
• Enzymes speed up (catalyze) chemical reactions;
in some cases, enzymes can make a chemical
reaction millions of times faster than it would
have been without it. Almost all metabolic
processes in the cell need enzyme catalysis in
order to occur at rates fast enough to sustain life
• Enzymes bind with particular reactants until the
chemical reaction occurs, then free themselves. Thus,
at any given time, the numerous pathways involved in
building up and breaking down cellular components
must be monitored and balanced in a coordinated
fashion. To achieve this goal, cells organize reactions
into various enzyme-powered pathways.
• Enzymes speed up reactions by lowering activation
energy. Many enzymes change shape when substrates
bind. This is termed "induced fit", meaning that the
precise orientation of the enzyme required for catalytic
activity can be induced by the binding of the substrate.
Chemical nature and classification of enzymes
• All known enzymes are proteins with the
exception of recently discovered RNA
enzymes.
• Some enzymes may additionally contain a
non-protein group. Enzymes are high
molecular weight compounds made up
principally of chains of amino acids linked
together by peptide bonds.
• Many enzymes require the presence of other
compounds (cofactors) before their catalytic
activity can be exerted. This entire active
complex is referred to as the holoenzyme; i.e.,
apoenzyme (protein portion) plus the cofactor
(coenzyme, prosthetic group or metal-ion
activator).
• on the basis of differences in chemical nature, the enzymes
may be described as follows:
– Simple enzymes: Simple enzymes are made up of only
protein (polypeptide). They contain no chemical groups
other than amino acid residues. Digestive enzymes such as
pepsin, and trypsin are of this nature.
– Conjugate Enzymes: It is an enzyme which is formed of two
parts – a protein part called apoenzyme (e.g., flavoprotein)
and a non-protein part named cofactor. The complete
conjugate enzyme, consisting of an apoenzyme and a
cofactor, is called holoenzyme. There can be an enzymatic
activity only when both components (apoenzyme and
cofactor) are present together. The cofactor is sometimes a
simple divalent metallic ion (e.g. Ca, Mg, Zn, Co, etc), and
sometimes a nonprotein organic compound.
• However, some enzymes require both kinds of
cofactors. If the cofactor is firmly bound to the
apoenzyme, it is called prosthetic group. For
example, cytochromes are the enzymes that
possess porphyrins as their prosthetic groups.
• If, instead of being more or less permanently
bound to the apoenzyme the cofactor
attaches itself to the apoenzyme only at the
time of reaction, it is called a coenzyme.
– Metallo-enzymes: The metal cofactors involved in
enzymic reactions are monovalent (K+ ) and divalent
cations (Mg++, Mn++ and Cu++). These may be loosely
held by the enzyme, or as in some cases, go into the
composition of the molecule itself. If the metal forms
part of the molecule, as iron of haemoglobin or
cytochrome, the enzymes are called metallo-enzymes.
– Isoenzymes (Isozymes): At one time it was believed
that an organism has only a single enzyme for a given
step of a metabolic reaction. It was later discovered
that a substrate may be acted upon by a number of
variants of an enzyme producing the same product.
• Classes of enzymes based on the substrate
they act up on
Mechanisms of enzyme action
• Mechanisms of enzyme catalysis vary, but are all similar in
principle to other types of chemical catalysis in that the
crucial factor is a reduction of energy barrier(s) separating
the reactants from the products.
• The reduction of activation energy increases the fraction of
reactant molecules that can overcome this barrier and form
the product.
• An important principle is that since they only reduce energy
barriers between products and reactants, enzymes always
catalyze reactions in both directions, and cannot drive a
reaction forward or affect the equilibrium position.
• An enzyme attracts substrates to its active site,
catalyzes the chemical reaction by which products are
formed, and then allows the products to dissociate
(separate from the enzyme surface).
• The combination formed by an enzyme and its
substrates is called the enzyme– substrate complex.
• The substrates are attracted to the active site by
electrostatic and hydrophobic forces, which are called
noncovalent bonds because they are physical
attractions and not chemical bonds.
Factors affecting enzymatic activities
• The activity of an enzyme is affected by its environmental
conditions such as temperature and pH. Changing these alter the
rate of reaction caused by the enzyme. In nature, organisms adjust
the conditions of their enzymes to produce an optimum rate of
reaction, where necessary, or they may have enzymes which are
adapted to function well in extreme conditions where they live.
Temperature
• Increasing temperature increases the kinetic energy that molecules
possess. In a fluid, this means that there are more random collisions
between molecules per unit time. Since enzymes catalyse reactions
by randomly colliding with substrate molecules, increasing
temperature increases the rate of reaction, forming more product.
• However, increasing temperature also increases the vibrational
energy that molecules have, specifically (in this case enzyme
molecules), which puts strain (damage) on the bonds that hold
them together.
• As temperature increases, more bonds, especially the weaker
hydrogen and ionic bonds, will break as a result of this strain.
breaking bonds within the enzyme will cause the active site to
change shape.
• This change in shape means that the Active Site is less
complementary to the shape of the Substrate, so that it is less likely
to catalyse the reaction. Eventually, the enzyme will become
denatured and will no longer function.
• The temperature at which the maximum rate of reaction occurs is
called the enzyme’s Optimum Temperature. This is different for
different enzymes.
pH - Acidity and Basicity
• pH is a measure of the hydrogen ion (H+)
concentration, and therefore a good indicator of the
hydroxide ion (OH-) concentration.
• Lower pH values mean higher H+ concentrations and
lower OH concentrations. H+ and OH ions are charged
and therefore interfere with hydrogen and ionic bonds
that hold together an enzyme, since they will be
attracted or repelled by the charges created by the
bonds. This interference causes a change in shape of
the enzyme, and importantly, its active site.
• Different enzymes have different optimum pH values.
This is the pH value at which the bonds within them
are influenced by H+ and OH- ions in such a way that
the shape of their active site is the most
complementary to the shape of their substrate.
• At the optimum pH, the rate of reaction is at an
optimum. Any change in pH above or below the
optimum will quickly cause a decrease in the rate of
reaction, since more of the enzyme molecules will have
active sites whose shapes are not (or at least are less)
complementary to the shape of their substrate.
• Small changes in pH above or below the optimum do not
cause a permanent change to the enzyme, since the bonds
can be reformed.
• However, extreme changes in pH can cause enzymes to
denature and permanently lose their function. Enzymes in
different locations of our body have different optimum pH
values since their environmental conditions may be
different. For example, the enzyme pepsin functions best at
around pH-2 and is found in the stomach, which contains
hydrochloric acid.
• Because enzymes are sensitive to changes in acidity, most
living systems are highly buffered; i.e., they have
mechanisms that enable them to maintain a constant
acidity
Substrate and enzyme concentration
• Changing the enzyme and substrate concentrations affect the rate
of reaction of an enzyme catalysed reaction.
• Controlling these factors in a cell is one way that an organism
regulates its enzyme activity and so its metabolism.
• Changing the concentration of a substance only affects the rate of
reaction if it is the limiting factor.
• If it is the limiting factor, increasing concentration will increase the
rate of reaction up to a point, after which any increase will not
affect the rate of reaction.
• This is because it will no longer be the limiting factor and another
factor will be limiting the maximum rate of reaction.
Substrate concentration
• Increasing substrate concentration increases the
rate of reaction. This is because more substrate
molecules will be colliding with enzyme
molecules, so more product will be formed.
• However, after a certain concentration, any
increase will have no effect on the rate of
reaction, since substrate concentration will no
longer be the limiting factor. The enzymes will
effectively become saturated, and will be working
at their maximum possible rate.
Enzyme concentration
• Increasing enzyme concentration will increase
the rate of reaction, as more enzymes will be
colliding with substrate molecules.
• However, this too will only have an effect up
to a certain concentration, where the enzyme
concentration is no longer the limiting factor.
Enzyme inhibitors
• Enzyme activity can be inhibited in various ways.
Inhibition could be reversible or irreversible.
Reversible inhibition
• Competitive inhibition: occurs when molecules
very similar to the substrate molecules bind to
the active site and prevent binding of the actual
substrate. Penicillin, for example, is a competitive
inhibitor that blocks the active site of an enzyme
that many bacteria use to construct their cell
walls.
Competitive inhibition
• Noncompetitive inhibition: occurs when an
inhibitor binds to the enzyme at a location other
than the active site.
• In some cases of noncompetitive inhibition, the
inhibitor is thought to bind to the enzyme in such
a way as to physically block the normal active
site.
• In other instances, the binding of the inhibitor is
believed to change the shape of the enzyme
molecule, thereby deforming its active site and
preventing it from reacting with its substrate.
• This latter type of noncompetitive inhibition is
called allosteric inhibition; the place where
the inhibitor binds to the enzyme is called the
allosteric site.
• Frequently, an end-product of a metabolic
pathway serves as an allosteric inhibitor on an
earlier enzyme of the pathway. This inhibition
of an enzyme by a product of its pathway is a
form of negative feedback.
• Activators: Allosteric control can involve stimulation of
enzyme action as well as inhibition.
– An activator molecule can be bound to an allosteric site
and induce a reaction at the active site by changing its
shape to fit a substrate that could not induce the change
by itself.
• Common activators include hormones and the
products of earlier enzymatic reactions.
• Allosteric stimulation and inhibition allow production
of energy and materials by the cell when they are
needed and inhibit production when the supply is
adequate.
Noncompetitive inhibition
Irreversible inhibition
• Irreversible inhibitors usually covalently modify an
enzyme, and inhibition can therefore not be reversed.
• Irreversible inhibitors often contain reactive functional
groups. Irreversible inhibition is different from
reversible enzyme inactivation. Irreversible inhibitors
are generally specific for one class of enzyme and do
not inactivate all proteins; they do not function by
destroying protein structure but by specifically altering
the active site of their target.
Thank You!
Chapter 4 - II
 Bioenergetics and biosyntheses
Cellular respiration
• Most living organisms obtain energy by
breaking down organic molecules (catabolism)
during cellular respiration.
• The function of cellular respiration is to
harvest electrons from carbon compounds,
such as glucose, and use that energy to make
Adenosine Tri Phosphate (ATP).
• This catabolic process can be divided into 3 phases.

• Phase I - Breakdown of large complex biomolecules like

polysaccharides, proteins and lipids into their respective
building blocks (hydrolysis).
– The chemical reactions occurring during this stage do not
release much energy. E.g gycolysis
• Phase II - These building blocks are usually oxidized to a
common intermediate, acetyl - CoA.
• Phase III – This consists of the citric acid cycle (i.e. oxidation of
acetyl - CoA to CO2, formation of NADH and FADH2) followed
by electron transport and oxidative phosphorylation.
– Energy released by electron transport to O2 is coupled to ATP
synthesis.
– This cycle is responsible for the release of much energy ( TCA cycle and
ETC).
• Cellular respiration occurs in two main parts:
glycolysis and aerobic respiration.
– The first stage, glycolysis, is an anaerobic process.
– Anaerobic metabolic processes do not require
oxygen.
– Aerobic respiration includes the Krebs cycle and
electron transport chain and is an aerobic process.
• Aerobic metabolic processes require oxygen.
 Glycolysis
Glucose structures
 Glycolysis: anaerobic respiration
• Glucose is a key metabolite in metabolism.
– Glucose is the body’s most readily available source of energy
• Various pathways that are concerned with the utilization, storage, and
regeneration of glucose exist.
– Glycogen is a polymeric storage form of glucose in human and it is
most abundant in the liver and in striated muscle, although some is
found in other tissues also.
• Glycogen is synthesized when glucose supply is high, and its
degradation helps to maintain the blood glucose level when we
are fasting.
• When glycogen is depleted, more glucose is synthesized from
scratch in gluconeogenesis. This pathway’s most important
substrates are amino acids, which are obtained either from a
protein-rich diet-for example, during fasting on meat exclusively-
or, during starvation, from breakdown of cellular protein, mainly in
skeletal muscle.
• Gluconeogenesis occurs in the liver and in the kidneys.
 Glycolysis …
 Greek word- glycos meaning sweet/sugar and
lysis meaning dissolution
 Also known as Embden-Meyerhof ( its
discoverers) Pathway
 Glycolysis, the major pathway for glucose
oxidation, occurs in the cytosol of all cells.
 It is unique, in that it can function either
aerobically or anaerobically, depending on the
availability of oxygen and intact mitochondria.
 It allows tissues to survive in presence or absence of
oxygen, e.g., skeletal muscle.
• The first step in the degradation of glucose is glycolysis, which
breaks down glucose to pyruvate.
• The main purpose of glycolysis is the generation of energy
(ATP). A modest amount of ATP is produced in glycolysis
directly, but much more ATP is formed downstream of
glycolysis through the complete oxidation of pyruvate.
• Glycolysis is the most common pathway for glucose
degradation to pyruvate and is found in animals, plants and
microorganism.
• This pathway is used by anaerobic as well as aerobic
organisms.
• The process takes place in the cytoplasm of prokaryotes and
eukaryotes and does not require oxygen.
• Under aerobic conditions, most of the pyruvate formed in
glycolysis undergoes complete oxidative degradation to CO2
and H2O.
• Pyruvate intended for complete degradation is
transported to the mitochondria, where it is
decarboxylated to acetyl-CoA by pyruvate
dehydrogenase.
• Acetyl-CoA is completely degraded in the citric
acid cycle (or tricarboxylic acid cycle; TCA cycle
for short).
– The “H2” that is produced here is not gaseous but
bound to co-substrates, as NADH and FADH2, which is
subsequently oxidized in the respiratory chain.
 coenzyme A (CoA)

Acetyl-CoA (acetyl coenzyme A)

• If glucose is available in excess of immediate
needs and glycogen is already stocked up to
capacity, it will still be broken down by glycolysis
and pyruvate dehydrogenase to acetyl-CoA.
• However, acetyl-CoA will then not be oxidized,
but it will instead be used for fatty acid synthesis;
the fatty acids are converted to triacylglycerol.
• Fatty acid synthesis occurs in the cytosol of cells
in the liver and fat tissue .
Triglyceride structure
Stages of Glycolysis

Two Stages
A. Preparatory Stage (ATP consuming)
B. ATP producing
• Glycolysis involves ten enzymatic reactions as
described below.
• The first five are preparatory phases or
investment phase.
– Here, glucose is phosphorylated, rearranged and
phosphorylated again, with the two phosphate
groups coming from ATP.
1. The phosphorylation of glucose at carbon-6 by hexokinase
forming glucose 6- phosphate (G6P).
• This reaction consumes ATP, but it acts to keep the glucose
concentration low, promoting continuous transport of glucose
into the cell through the plasma membrane transporters. In
addition, it blocks the glucose from leaking out – the cell lacks
transporters for G6P, and free diffusion out of the cell is
prevented due to the charged nature of G6P. Glucose may
alternatively be formed from the phosphorolysis or hydrolysis
of intracellular starch or glycogen
• In animals, an isozyme of hexokinase called glucokinase is also
used in the liver, has a much lower affinity for glucose, and
differs in regulatory properties. The different substrate affinity
and alternate regulation of this enzyme are a reflection of the
role of the liver in maintaining blood sugar levels.
2. The conversion of glucose-6-phosphate(G6P) to fructose-6-
phosphate(F6P) by phosphohexose isomerase
• The change in structure is an isomerization, in which the
G6P has been converted to F6P. This reaction is freely
reversible under normal cell conditions. However, it is often
driven forward because of a low concentration of F6P,
which is constantly consumed during the next step of
glycolysis. Under conditions of high F6P concentration, this
reaction readily runs in reverse. This phenomenon can be
explained through Le Chatelier's Principle, ''Isomerization
to a keto sugar is necessary for carbanion (negative charge
of carbon that is stable) stabilization in the fourth reaction
step (below)''.
3. The phosphorylation of fructose-6-phosphate to the
1,6-bisphosphate by phosphofructokinase
• The energy expenditure of another ATP in this step is
justified in 2 ways: The glycolytic process (up to this
step) becomes irreversible, and the energy supplied
destabilizes the molecule. Because the reaction
catalyzed by Phosphofructokinase 1 (PFK-1) is coupled
to the hydrolysis of ATP (an energetically favorable
step) it is, in essence, irreversible, and a different
pathway must be used to do the reverse conversion
during gluconeogenesis. This makes the reaction a key
regulatory point. This is also the rate-limiting step.
• The second phosphorylation event is necessary to
allow the formation of two charged groups (rather than
only one) in the subsequent step of glycolysis, ensuring
the prevention of free diffusion of substrates out of the
cell.
• The same reaction can also be catalyzed by
pyrophosphate-dependent phosphofructokinase (PFP
or PPi-PFK), which is found in most plants, some
bacteria, archea, and protists, but not in animals. This
enzyme uses pyrophosphate (PPi) as a phosphate
donor instead of ATP. It is a reversible reaction,
increasing the flexibility of glycolytic metabolism.
4. The cleavage of fructose-1,6-bisphosphate by aldolase.
– This yields two different products, dihydroxyacetone phosphate and
glyceraldehyde-3-phosphate,
• Destabilizing the molecule in the previous reaction allows the
hexose ring to be split by aldolase into two triose sugars:
dihydroxyacetone phosphate (a ketose), and glyceraldehyde 3-
phosphate (an aldose). There are two classes of aldolases: class I
aldolases, present in animals and plants, and class II aldolases,
present in fungi and bacteria; the two classes use different
mechanisms in cleaving the ketose ring.
• Electrons delocalized in the carbon-carbon bond cleavage associate
with the alcohol group. The resulting carbanion is stabilized by the
structure of the carbanion itself via resonance charge distribution
and by the presence of a charged ion prosthetic group.
5. The isomerization of dihydroxyacetone
phosphate to a second molecule of glyceraldehyde-
3-phosphate by triose phosphate isomerase
• Triosephosphate isomerase rapidly interconvert
dihydroxyacetone phosphate with glyceraldehyde
3-phosphate (GADP) that proceeds further into
glycolysis. This is advantageous, as it directs
dihydroxyacetone phosphate down the same
pathway as glyceraldehyde 3-phosphate,
simplifying regulation
6. The dehydrogenation and concomitant phosphorylation of
glyceraldehyde-3-phosphate to 1,3-bis-phosphoglycerate by
glyceraldehyde-3-phosphate dehydrogenase
• The aldehyde groups of the triose sugars are oxidised, and
inorganic phosphate is added to them, forming 1, 3-
bisphosphoglycerate.
• The hydrogen is used to reduce two molecules of NADH, a
hydrogen carrier, to give NADH + H+ for each triose.
• Hydrogen atom balance and charge balance are both
maintained because the phosphate (Pi) group actually
exists in the form of a hydrogen phosphate anion (HPO42- ),
which dissociates to contribute the extra H ion and gives a
net charge of -3 on both sides.
7. The transfer of the 1-phosphate group from 1,3-bis-
phosphoglycerate to ADP by phosphoglycerate kinase, which
yields ATP and 3-phosphoglycerate.
• At this step, glycolysis has reached the break-even point: 2
molecules of ATP were consumed, and 2 new molecules
have now been synthesized. This step, one of the two
substrate-level phosphorylation steps, requires ADP; thus,
when the cell has plenty of ATP (and little ADP), this
reaction does not occur. Because ATP decays relatively
quickly when it is not metabolized, this is an important
regulatory point in the glycolytic pathway.
• ADP actually exists as ADPMg− , and ATP as ATPMg2−,
balancing the charges at -5 both sides.
8. The isomerization of 3-phosphoglycerate to 2-phosphoglycerate by
phosphoglycerate mutase (PGAM)

9. The dehydration of 2-phosphoglycerate to phosphoenolpyruvate by

enolase.

10. The transfer of the phosphate group from phosphoenolpyruvate to

ADP by pyruvate kinase, to yield a second molecule of ATP.
• A final substrate-level phosphorylation now forms a molecule of
pyruvate and a molecule of ATP by means of the enzyme pyruvate
kinase. This serves as an additional regulatory step, similar to the
phosphoglycerate kinase step.
Glycolysis steps
Glycolysis
Regulation (glycolysis)
• Three reactions physiologically irreversible
• These are the major sites of regulation.
i. Hexokinase / Glucokinase
ii. Phosphofructokinase Key regulatory enzymes
iii. Pyruvate Kinase
Biochemical logic for the presence of regulatory steps
• The existence of more than one point of regulation
indicates that intermediates between those points enter
and leave the glycolysis pathway by other processes. For
example, in the first regulated step, hexokinase converts
glucose into glucose-6-phosphate. Instead of continuing
through the glycolysis pathway, this intermediate can be
converted into glucose storage molecules, such as glycogen
or starch. The reverse reaction, breaking down, e.g.,
glycogen, produces mainly glucose-6-phosphate; very little
free glucose is formed in the reaction. The glucose-6-
phosphate so produced can enter glycolysis after the first
control point.
• In the second regulated step (the third step of
glycolysis), phosphofructokinase converts fructose-6-
phosphate into fructose-1, 6-bisphosphate, which then
is converted into glyceraldehyde-3-phosphate and
dihydroxyacetone phosphate. The dihydroxyacetone
phosphate can be removed from glycolysis by
conversion into glycerol-3-phosphate, which can be
used to form triglycerides. Conversely, triglycerides can
be broken down into fatty acids and glycerol; the latter,
in turn, can be converted into dihydroxyacetone
phosphate, which can enter glycolysis after the second
control point.
Overall Reaction (of glycolysis)

Aerobic
Glc + 2NAD+ + 2ADP + 2Pi

2 pyruvate + 2NADH + 2H+ + 2ATP + 2H2O

Glc + 2ADP + 2Pi 2 Lactate + 2ATP + 2H2O

Anaerobic
Glycolysis - Summary

Glucose Glucose
2 ATP
4 ADP
2 ADP 2 ATP
4 ADP
4 ATP
2 ADP
2 NAD 4 ATP

2 NADH + H

2 Pyruvate 2 Lactate
Bioenergetics
• AEROBIC GLYCOLYSIS

2NADH + H+ = 2 x 2.5ATP = 5 ATP

Substrate Level = 2 x 2 ATP = 4 ATP

_____________________________________

TOTAL = 9 ATP

Consumed = -2 ATP
_____________________________________

Net Balance = 7 ATP

Bioenergetics
• ANAEROBIC GLYCOLYSIS (e.g. RBC)
Substrate Level = 4 ATP
Consumed = -2 ATP
____________________________
Net Balance = 2 ATP
Entry of other hexoses into glycolysis
Galactose
Galactokinase
Galactose Gal-1-Phosphate
Mg+2
ATP ADP
UDP-Glc
Gal-1-P-uridyl UDP-Gal-4-epimerase
transferase
UDP-Gal

Glc-1-Phosphate

Mutase

Glc-6-Phosphate Glycolysis
Fructose (Major pathway) (Liver)
ATP ADP Fr-1-P
Mg++ Aldolase
Fructose Fr-1-Phosphate DHAP + Glyceraldehyde
Fructokinase
ATP
Triose
PTI ADP Kinase

Glycolysis Glyceraldehyde -3-Phosphate

Fructose (Minor pathway) (Liver)

ATP ADP
Mg++
Fructose Fr-6-Phosphate  Glycolysis
Hexokinase
Thank You!
Chapter 4 - III
 TCA Cycle
• Discovered by Hans Krebs in 1937

• He received the Nobel Prize in

physiology or medicine in 1953 for
his discovery
 Three Phases
[1] Acetyl-CoA production—Organic fuels (glucose,
amino acids, fats) ➔ Acetyl-CoA
[2] Acetyl-CoA oxidation—Acetyl-CoA enters TCA
and is enzymatically oxidized; energy is conserved
in electron carriers: NADH, FADH2
[3] Electron transfer—energy rich e- from NADH,
FADH2 reduce O2 to H2O
TCA cycle and ETC: Aerobic respiration
• One fate of pyruvate is that it enters to TCA cycle
for complete oxidation. But there are
intermediate processes that convert pyruvate to a
acetyl coA. The enzyme complex converts
pyruvate into Acetyl-CoA by the following
chemical changes:
– Decarboxylation of pyruvate (loss of CO2)
– Formation of acetyl group
– Linkage of acetyl group to coenzyme A forming acetyl
- CoA.
The Tricarboxylic Acid (TCA) Cycle (Phase III)
• The TCA cycle also called Krebs or Citric acid cycle, is
considered as central pathway of aerobic metabolism,
as it serves two purposes-bioenergetics and
biosynthesis:
1. Bioenergetic - The cycle carries out complex
degradation of acetyl group in acetyl - CoA to CO2,
resulting in release of energy (ATP or GTP) and reducing
power (NADH and FADH2).
• TCA oxidizes two-carbon units, producing two
molecules of CO2, one molecule of GTP, and high-
energy electrons in the form of NADH and FADH2.
Steps of the Krebs cycle
• Prior to the Krebs cycle, pyruvate first reacts with coenzymeA (CoA)
to form a 2-carbon intermediate called acetyl CoA. At the same
time, carbon dioxide is released and NAD is converted to NADH.
Acetyl CoA then moves to the mitochondrial matrix. The reaction
results in the production of two carbon dioxide molecules and two
NADH.
– The Krebs cycle begins with acetyl CoA combining with a 4-carbon
compound to form a 6-carbon compound known as citric acid.
– Citric acid is then broken down in the next series of steps, releasing
two molecules of carbon dioxide and generating one ATP, three NADH,
and one FADH. FAD is another electron carrier similar to NADH and
NADPH.
– Finally, acetyl CoA and citric acid are generated and the cycle
continues.
The TCA cycle
• Recall that two molecules of pyruvate are
formed during glycolysis, resulting in two
“turns” of the Krebs cycle for each glucose
molecule. The net yield from the Krebs cycle is
six carbon dioxide molecules, two ATP, eight
NADH, and two FADH2. NADH and FADH2
move on to play a significant role in the next
stage of aerobic respiration.
2. Biosynthesis - It supplies precursors for several biosynthetic
pathways of amino acids, pyrimidines, purines etc.
– As already mentioned, the TCA cycle is also an important source
of biosynthetic precursors e.g. α-ketoglutarate and oxaloacetate
are used for synthesis of a number of amino acids like glutamic
acid, asparatic acid etc.
• Succinyl - CoA is used to form porphyrin ring of
cytochromes, chlorophyll etc.
• Oxaloacetate can also be converted to
phosphoenolpyruvate, which is a precursor of glucose.
• Acetyl - CoA is the starting material for fatty acid
biosynthesis.
• Net Result of the Citric Acid Cycle
– Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O →

2CO2 + 3NADH + FADH2 + GTP + CoA + 3H+

Regulation of Citric Acid Cycle
Where do all the NADH’s and FADH2’s Go?
Electron Transport Chain
Electron Transport Chain
• In aerobic respiration, electron transport is the
final step in the break-down of glucose. It also
is the point at which most of the ATP is
produced. High-energy electrons and
hydrogen ions from NADH and FADH2
produced in the Krebs cycle are used to
convert ADP to ATP.
Electron Transport Chain
• As shown in Fig above, electrons move along the
mitochondrial membrane from one protein to another. As
NADH and FADH2 electrons, the energy carriers are
converted to NADH release and FAD, and H ions are
released into the mitochondrial matrix. The H ions are
pumped into the mitochondrial matrix across the inner
mitochondrial membrane. H ions then diffuse down their
concentration gradient back across the membrane and into
the matrix through ATP synthase molecules in
chemiosmosis. Electron transport and chemiosmosis in
cellular respiration are similar to these processes in
photosynthesis. Oxygen is the final electron acceptor in the
electron transport system in cellular respiration. Protons
and electrons are transferred to oxygen to form water.
ETC:
Biosynthesis …
• Biosynthesis is a multi-step, enzyme-catalyzed process
where substrates are converted into more complex
products in living organisms. In biosynthesis, simple
compounds are modified, converted into other compounds,
or joined together to form macromolecules. This process
often consists of metabolic pathways. Some of these
biosynthetic pathways are located within a single cellular
organelle, while others involve enzymes that are located
within multiple cellular organelles. Examples of these
biosynthetic pathways include the production of lipid
membrane components and nucleotides. Biosynthesis is
usually synonymous with anabolism.
• The prerequisite elements for biosynthesis
include: precursor compounds, chemical energy
(e.g. ATP), and catalytic enzymes which may
require coenzymes (e.g.NADH, NADPH).
• These elements create monomers, the building
blocks for macromolecules. Some important
biological macromolecules include: proteins,
which are composed of amino acid monomers
joined via peptide bonds, and DNA molecules,
which are composed of nucleotides joined via
phosphodiester bonds.
Requirements of Biosynthesis
• Sometimes all that is required for biosynthesis is
for two substances to physically join together to
make a new physical substance, which is called a
macromolecule. A very simplified equation for
biosynthesis of one form of macromolecule: two
substances join together to form a new, more
complex substance.
• Photosynthesis (reading assignment)
• Oxygenic photosynthesis is written as follows:
6CO2 + 12H2O + Light Energy → C6H12O6 + 6O2 + 6H2O
• Similarly, the various anoxygenic photosynthesis
reactions can be represented as a single
generalized formula:
CO2 + 2H2A + Light Energy → [CH2O] + 2A + H2O
• The letter A in the equation is a variable and H2A
represents the potential electron donor. For
example, A may represent sulfur in the electron
donor hydrogen sulfide (H2S).
Structure of chloroplast
Basic structures of major photosynthetic pigments
 Metabolic disorders, diagnosis and
treatments
• Metabolism is the breaking down of food to
its simpler components: proteins,
carbohydrates (or sugars), and fats.
• Metabolic disorders occur when these normal
processes become disrupted.
• Disorders in metabolism can be inherited, in
which case they are also known as inborn
errors of metabolism, or they may be acquired
during your lifetime.
Inherited metabolic disorders
• Inherited metabolic disorders are one cause of
metabolic disorders, and occur when a
defective gene causes an enzyme deficiency.
These diseases, of which there are many
subtypes, are known as inborn errors of
metabolism. Metabolic diseases can also
occur when the liver or pancreas do not
function properly.
• There are numerous examples of inherited metabolic
disorders, which can be classified based on the type of
food-related building block that they affect, including
amino acids (the building block for proteins),
carbohydrates, and fatty acids (the building block for fats).
Inherited causes of metabolic disorders include:
– Carbohydrate disorders; examples include Diabetes insipidus,
hereditary fructose intolerance, galactosemia, pyruvate
metabolism disorders, von Gierke‘s disease, McArdle disease,
Pompe‘s disease, and Forbes‘ disease
– Fatty acid oxidation defects; examples include Gaucher‘s
disease, Niemann-Pick disease, Fabry‘s disease, and medium-
chain acyl-coenzyme A dehydrogenase (MCAD) deficiency
 von Gierke‘s disease

McArdle disease

Forbes‘ disease
Gaucher‘s disease

Niemann-Pick disease

Fabry‘s disease
Tay-Sachs disease
– Amino acid disorders; examples include Tay-Sachs
disease, phenylketonuria, tyrosinemia, maple
syrup urine disease, and homocystinuria
– Acid-base imbalance, Disorders of calcium
metabolism, DNA repair-deficiency disorders, Iron
metabolism disorders, Mitochondrial diseases,
Phosphorus metabolism disorders, Malabsorption
syndromes, Water-electrolyte imbalance are some
of the disorders associated with metabolism.
Other causes of metabolic disorders
• Metabolic disorders can be due to other factors, such as a
combination of inherited and environmental factors. Some
of the conditions that can cause metabolic disorders
include:
– Alcohol abuse, Diabetes (chronic disease that affects your
body‘s ability to use sugar for energy)
– Diuretic abuse, Gout (type of arthritis caused by a buildup of
uric acid in the joints)
– Ingestion of poison or toxins, including excessive aspirin,
bicarbonate, alkali, ethylene glycol, or methanol
– Kidney failure, Pneumonia, respiratory failure, or collapsed lung
– Sepsis (life-threatening bacterial blood infection)
Risk factors of metabolic disorders
• A number of factors increase the risk of developing metabolic
disorders. Not all people with risk factors will get metabolic
disorders. Risk factors for metabolic disorders include:
– Certain chronic medical conditions, such as lung or kidney disease
(includes any type of kidney problem, such as kidney stones, kidney
failure and kidney anomalies) and Diabetes (it is more likely to have
metabolic syndrome if a person had diabetes during pregnancy
(gestational diabetes) or if he/she have a family history of type 2
diabetes.
– Family history of genetic metabolic disorder.
– Race and ethnicity: people with African, Hispanic, First Nations, Asian,
and Pacific Islander backgrounds are at higher risk than whites for type
2 diabetes.
– HIV/AIDS and other diseases; the risk of metabolic
syndrome is higher if a person ever had nonalcoholic fatty
liver disease, polycystic ovary syndrome or sleep apnea
– Age- the risk of metabolic syndrome increases with age.
– Obesity and lack of exercise: carrying too much weight,
especially in your abdomen, increases your risk of
metabolic syndrome
– Hormone imbalance: a hormone disorder such as
polycystic ovary syndrome (PCOS), a condition in which the
female body produces too much of certain hormones, is
linked with metabolic syndrome.
– Insulin resistance: a situation in which a body cannot use
insulin properly.
Diagnosis of metabolic disorders
• Metabolic syndrome is more effectively diagnosed by testing
different blood markers (specific markers of insulin resistance),
obesity (especially abdominal obesity), high blood pressure, and
lipid abnormalities. Specifically, metabolic syndrome is diagnosed if
any three of the following five markers are present:
– Elevated waist circumference: 40 inches or more for men; 35 inches or
more for women
– Elevated triglycerides: 150 mg/dL or higher
– Reduced high-density lipoprotein (HDL) levels (AKA ''good''
cholesterol): less than 40 mg/dL in men; less than 50 mg/dL in women
– Elevated blood pressure: 130/85 mm Hg or higher or are already
taking blood pressure medications
– Elevated fasting glucose: 100 mg/dL or higher or are already taking
glucose-lowering medications
Treatments of metabolic disorders
• The treatment approach for metabolic disorders depends on the
specific disorder. Inborn errors of metabolism (inherited metabolic
disorders) are often treated with nutritional counseling and
support, periodic assessment, physical therapy, and other
supportive care options. Multiple treatment options are available
for inherited metabolic disorders and examples include: bone
marrow transplantation, enzyme replacement therapy in selected
patients, gene therapy in selected patients, medications to reduce
symptoms, such as pain or low blood sugar, mineral
supplementation, nutritional counseling, surgery to relieve pain or
symptoms, vitamin supplementation and etc.
• Acquired metabolic disorder treatment will include normalizing the
metabolic balance by both reversing the cause and administering
medications.
Potential complications of metabolic disorders
• Complications of untreated metabolic disorders
can be serious, even life threatening in some
cases. The risk of serious complications can be
minimized following the treatment plan designed
by health care professional. Complications of
metabolic disorders include: organ
failure/dysfunction, seizures and tremors, and
unconsciousness and coma.
Thank You!
 Unit Five

Genetics and Evolution

• Genetics is a field of biology that studies how traits are passed from
parents to their offspring.
• The passing of traits from parents to offspring is known as heredity;
therefore, genetics is the study of heredity.
• The basic components of genetics are DNA, RNA, genes,
chromosomes and genetic inheritance.
• DNA molecules hold all the genetic information for almost all
organisms. It provides cells with the information they need to
perform tasks that allow an organism to grow, survive and
reproduce.
• A gene is one particular section of a DNA molecule that tells a cell
to perform one specific task.
• Heredity is what makes offspring look like their parents. During
reproduction, DNA is replicated and passed from a parent to their
offspring. This inheritance of genetic material by offspring
influences the appearance and behavior of the offspring. The
environment that an organism lives in can also influence how genes
are expressed.
• Genes (and, thus, the traits they code for) are
passed from parent to offspring. From
generation to generation, well-understood
molecular mechanisms reshuffle, duplicate,
and alter genes in a way that produces genetic
variation. This variation is the raw material for
evolution.
Basic Principles of Mendelian genetics
and patterns of inheritance
• By experimenting with pea plant breeding, Gregor Mendel
developed three principles of inheritance that described the
transmission of genetic traits
• Traits are passed down in families in different patterns. Pedigrees
can illustrate these patterns by following the history of specific
characteristics, or phenotypes, as they appear in a family.
• The inheritance pattern in which traits of generation passed down
through the family tree is considered dominant, because it is
observable in every generation. Thus, every individual who carries
the genetic code for this characteristic will show evidence of the
characteristic.
• A characteristic may disappear in one generation, only to reappear
in a subsequent one. This pattern of inheritance, in which the
parents do not show the phenotype but some of the children do, is
considered recessive.
Pedigree
• Gregor Johann Mendel formulated his idea
after conducting simple hybridisation
experiments with pea plants (Pisum sativum)
he had planted in the garden of his monastery.
From these experiments, he induced two
generalizations which later became known as
Mendel's Principles of Heredity or Mendelian
inheritance.
 Law of Segregation
• During the formation of gametes (eggs or sperm), the
two alleles responsible for a trait separate from each
other.
• Alleles for a trait are then "recombined" at fertilization,
producing the genotype for the traits of the offspring.
Applying the Law of Segregation
 Law of Independent Assortment
• Alleles for different traits are distributed to sex cells
(& offspring) independently of one another.
• This law can be illustrated using dihybrid crosses.
 Dihybrid Cross
Traits: Seed shape & Seed color
Alleles: R round
r wrinkled
Y yellow
y green

RrYy x RrYy

RY Ry rY ry RY Ry rY ry

All possible gamete combinations

 RY Ry rY ry

RY Round/Yellow: 9
RRYY RRYy RrYY RrYy

Ry Round/green: 3
RRYy RRyy RrYy Rryy

wrinkled/Yellow: 3
rY RrYY RrYy rrYY rrYy
wrinkled/green: 1
ry RrYy Rryy rrYy rryy 9:3:3:1 phenotypic
ratio
Round/Yellow: 9
Round/green: 3
wrinkled/Yellow: 3
wrinkled/green: 1
9:3:3:1
• An important aspect of Mendel's success can
be traced to his decision to start his crosses
only with plants he demonstrated were true-
breeding. He only measured discrete (binary)
characteristics, such as color, shape, and
position of the seeds, rather than
quantitatively variable characteristics. He
expressed his results numerically and
subjected them to statistical analysis.
How Mendel Began?

Mendel
produced pure
strains by
allowing the
plants to self-
pollinate for
several
generations
Pea plant characters studied by Mendel
 Mendel’s Experimental Results
• Ratios of dominant to recessive in Mendel’s
plants
 Mendel's conclusions
1. Characters are unitary.
– That is, they are discrete (purple vs. white, tall vs. dwarf).
2. Genetic characteristics have alternate forms, each
inherited from one of two parents.
– Today, we call these alleles.
3. One allele is dominant over the other.
– The phenotype reflects the dominant allele.
4. Gametes are created by random segregation.
– Heterozygotic individuals produce gametes with an equal
frequency of the two alleles.
5. Different traits have independent assortment.
– In modern terms, genes are unlinke
 Thanks!
Have a nice Time!
Any Q?
 Unit Five

Genetics and Evolution

Part II
Molecular genetics and inheritance
DNA, Gene, Chromosomes and Cell division
• DNA stands for deoxyribonucleic acid and it is the
molecule that holds the genetic information for a cell
and an organism. DNA molecule contains a code that
can be used by a cell to express certain genes. Specific
sections of a DNA molecule provide the information to
build specific proteins which can then be used by a cell
to express the desired gene. DNA comes in the form of
a long, linear molecule referred to as a strand. Each
strand of DNA is bonded to a second strand of DNA to
form a DNA double helix. In eukaryotic cells, DNA is
found in the nucleus as a tightly coiled double helix.
• DNA molecules are replicated during cell
division. When a cell divides, the two new
cells contain all the same DNA that the
original cell had. In sexual reproduction with
two parents, half of the DNA of the offspring is
provided by each of the parents. The genetic
material of a child is made from 50% of their
mother‘s DNA and 50% their father‘s DNA.
Example

4
Structure of DNA and chromosome
• Chromosome is a thread- like structure that is
made up of DNA (deoxyribonucleic acid) and
histone (a set of globular (30) proteins).
• DNA is the molecule that stores genetic
information whereas histone is the core of a
chromosome around which chromosome‘s DNA
wrapped.
• The loosely organized form of chromosome
throughout the nucleus in loops when the cell is
not dividing is called Chromatin.
• Individual chromosomes are not easily
distinguished unless condensed. On the
condensed organization of chromosome,
genes are inactive while uncondensed or loose
organization allows the genes to be active. As
a cell prepares for cell division, the chromatin
loops will have duplicated themselves and
become compacted or ―condensed to form a
chromosome that is visible under light
microscope.
 Chromosome Structure
Metaphase chromosome as seen in the electron microscope

7
Chromosome Structure …

8
• DNA-is made up two strands of polynucleotides joined
together and twisted into a double helix and the strands
are anti-parallel to each other. The basic unit of DNA strand
is a nucleotide (monomers of DNA). There are four types of
nucleotides:-
– Adenine (A) – containing nucleotide
– Guanine (G) – containing nucleotide
– Cytosine (C) - containing nucleotide
– Thymine (T) – containing nucleotide (in DNA, or Uracil (U)
nucleotide in RNA)
• All nucleotides have: a phosphate group, a pentose sugar
(deoxyribose in DNA and ribose sugar in RNA) and one of
four nitrogen bases- adenine, cytosine guanine and either
thymine (DNA) or uracil (RNA).
Structures of deoxyribose and ribose in DNA and RNA:

• The only difference is at the 2C position, where RNA

has a hydroxyl (OH) group, while DNA has only a
hydrogen.
10
 DNA Nucleotide

Phosphate
Group

O=P-O 5'

O
O
N
1' Nitrogenous base
4' (A, G, C, or T)

Sugar
(deoxyribose)
3'
2' 11
Notice that the 1’, 2’, … refer to a numbering system for
the carbon atoms that make up the sugar.

12
 Nitrogenous Bases

• Purines have double carbon-nitrogen rings

Adenine (A)
Guanine (G)
A or G
• Pyrimidines have single rings of carbon-nitrogen
Thymine (T)
Cytosine (C)
T or C

13
• Bonds between the sugar in one nucleotide and the
phosphate group in the next hold the nucleotides together.
• The base does not take in this linking of the nucleotides in a
strand. That is the reason why we say sugar- phosphate‘
backbone. The nucleotides in one strand are paired with the
nucleotides in the other strand according to the base pairing-
rule.
– Adenine – Thymine(uracil in RNA)
– Cytosine – Guanine
• DNA is a very stable molecule at normal temperature. The
hydrogen bonds hold the two strands together in position
through the bases.
• The stability of the DNA molecule is important in ensuring the
genetic code in the DNA molecule – does not become
corrupted.
 Base Pairing Rule
• Purines only pair with Pyrimidines-This is called
complementary base pairing
• A (adenine) pairs with T (thymine)
• C (cytosine) pairs with G (guanine)
 Charfaff’s rule:
C = G and T = A
• Three hydrogen bonds required to bond Guanine & Cytosine
3 H-bonds

G C

15
• Two hydrogen bonds are required to bond Adenine
& Thymine

T A

16
 DNA
5 O 3

3 O
P 5 P
5 O
1 G C 3
2
4 4
2 1
3 5
O
P P
5
T A 3
O

O
5
P 3 P
17
Structure of DNA
DNA replication and cell division (stop
radA)
• The ability of DNA to make copy of itself (DNA-
replication) is the basis for reproduction and
inheritance. DNA molecule exists within
chromosome (in the nucleus) and is surrounded
by a 'soup' of free DNA nucleotides (which is to
build new DNA molecules). DNA structure is
double helix and must replicate semi-
conservatively.
• Replication is called semiconservative because
each new double helix is composed of an old
(parental) strand and a new (daughter) strand
 Mechanism of DNA Replication:
semiconservative

Proposed DNA Replication Models:

• Conservative replication model
• Dispersive replication model
• Semiconservative replication

20
21
• Several Enzymes are involved in this process and the
main are:
1. DNA helicase enzyme - break H-bonds to reveal two
single strands and unwind (open) the helix DNA
2. DNA polymerase follows the helicase enzyme along
each single-stranded region, which acts as a template for
the synthesis of a new strand. DNA polymerase
assembles free DNA nucleotides into new strands
alongside each of the template strands. The base
sequence in each of these new strands is complementary
to its template strand because of base-pairing rule, A-T, C-
G.
DNA replication
DNA replication …

24
 Cell division
• Cell division is the process by which a parent cell
divides into two or more daughter cells. Cell
division usually occurs as part of a larger cell
cycle. In eukaryotes, there are two distinct types
of cell division: a vegetative division, whereby
each daughter cell is genetically identical to the
parent cell (mitosis), and a reproductive cell
division, whereby the number of chromosomes in
the daughter cells is reduced by half to produce
haploid gametes (meiosis).
• Meiosis results in four haploid daughter cells
by undergoing one round of DNA replication
followed by two divisions. Homologous
chromosomes are separated in the first
division, and sister chromatids are separated
in the second division. Both of these cell
division cycles are used in the process of
sexual reproduction at some point in their life
cycle. Both are believed to be present in the
last eukaryotic common ancestor.
• Prokaryotes (bacteria) undergo a vegetative
cell division known as binary fission, where
their genetic material is segregated equally
into two daughter cells. While binary fission
may be the means of division by most
prokaryotes, there are alternative manners of
division, such as budding, that have been
observed. All cell divisions, regardless of
organism, are preceded by a single round of
DNA replication.
• For simple unicellular microorganisms such as amoeba, one
cell division is equivalent to reproduction; an entire new
organism is created.
• On a larger scale, mitotic cell division can create progeny
from multicellular organisms, such as plants that grow from
cuttings.
• Mitotic cell division enables sexually reproducing organisms
to develop from the one-celled zygote, which itself was
produced by meiotic cell division from gametes.
• After growth, cell division by mitosis allows for continual
construction and repair of the organism.
• The human body experiences about 10 quadrillion cell
divisions in a lifetime.
• The primary concern of cell division is the
maintenance of the original cell's genome.
• Before division can occur, the genomic
information that is stored in chromosomes must
be replicated, and the duplicated genome must
be separated cleanly between cells.
• A great deal of cellular infrastructure is involved
in keeping genomic information consistent
between generations.
Major types of cell division
 Protein synthesis
• Code for protein synthesis is specified by DNA and has to be sent to
ribosome. DNA is a huge molecule and remains in nucleus to
assemble amino acids in the correct sequence to form protein.
• Events during protein synthesis
i. Transcription – DNA code for protein is rewritten in a molecule of
messenger RNA (mRNA)
ii. mRNA travels from nucleus to ribosome
iii. Free amino acids are transported from cytoplasm to ribosome by
transfer RNA (tRNA) molecules
iv. Ribosome read mRNA code and assembles amino acids presented
by tRNA into a protein by a process = translation. Translation – is
process in which mRNA code is converted into a sequence of amino
acids
DNA code  mRNA codon  protein/ polypeptide
 Thanks!
Have a nice week!
 Unit Five

Genetics and Evolution

Part III
 Protein synthesis
• Code for protein synthesis is specified by DNA and has to be sent to
ribosome. DNA is a huge molecule and remains in nucleus to
assemble amino acids in the correct sequence to form protein.
• Events during protein synthesis
i. Transcription – DNA code for protein is rewritten in a molecule of
messenger RNA (mRNA)
ii. mRNA travels from nucleus to ribosome
iii. Free amino acids are transported from cytoplasm to ribosome by
transfer RNA (tRNA) molecules
iv. Ribosome read mRNA code and assembles amino acids presented
by tRNA into a protein by a process = translation. Translation – is
process in which mRNA code is converted into a sequence of amino
acids
DNA code → mRNA codon → protein/ polypeptide
 Genetic code
• The genetic code is held in the DNA molecule.
It is because of the nucleotides sequence in
the DNA molecule made a gene that codes for
protein to that each amino acid in the protein
is coded for by a triplet /sequence of three
bases. Hence, a gene is a sequence of base
triplets in the DNA molecule that carries a
code for a protein.
1. Since there are 4 bases, there is 43 = 64 possible
triplet codes /amino acids/ but only 20 amino acids
are used to make all different proteins. None of
them is spare or redundant.
2. Only one strand of a DNA molecule carries the
code for proteins (It is called sense strand or coding
stand) and the other strand is non-coding or
antisense strand.
3. Most amino acids have more than one code, only
methionine and tryptophan have one code.
– Arginine has six codes
4. Three triplets (TAA, TAG, and TGA) do not code
for amino acids and they are called stop codons.
stop codes signify the end of the coding sequence
5. Degenerate code – the DNA code is non-
overlapping codes i.e., each triplet is distinct from
all other triplets.
6. The genetic code is also a universal code i.e. the
triplet code TAT in the DNA code for amino acid
tyrosine in human, redwood tree, bacterium or in
any organism E.g. ACC – threonine, GGG-glycine
Genetic code
N.B. It is not just the base that matter but the sequence,
e.g. ATT codes of different amino acid from TTA
• The enzyme DNA-dependent RNA polymerase binds
with a section of DNA next to the gene to be
transcribed. Transcription factors activate the enzyme.
The enzymes ― unwind and separate the strands of a
DNA molecule. The polymerase assembles free RNA
nucleotides on the complementary strand (antisense
strand). mRNA (transcribed RNA) leaves the DNA; the
strands of DNA rejoin & re-coil.
• N.B. The mRNA molecule now contains the code for
the protein that was held in the DNA of the genes
• Translation of mRNA code into a protein depends on
the interaction within a ribosome between mRNA and
tRNA. All tRNA molecules have same basic structure.
The ''cloverleaf'' configuration of the molecules has at
one end a triplet of bases called anticodon. The
anticodon is a triplet on tRNA. The other end of tRNA
molecule has an attachment site for the aminoacid that
is specified by the mRNA codon.
• Ribosomes are made from ribosomal RNA and proteins
organized into large & small subunits. Within ribosome,
there are three sites called A, P and E sites.
 Transfer RNA (tRNA)
amino acid
attachment site
Methionine amino acid

U A C
anticodon 9
10
 Events during translation of proteins
• The first two codons of the mRNA enter the
ribosome and tRNA molecules (with amino
acid attached) that have complementary
anticodons to the 1st two codons of the
mRNA bind to those codons. A peptide bond
forms between amino acid carried by two
tRNA molecules and dipeptide is transferred
to the tRNA in the A-site. The Ribosome
moves along the mRNA by one codon bringing
the 3rd codon into the ribosome.
• At the same time the free tRNA exits the ribosome
from the E-site and tRNA with the dipeptide moves
into the P-site. A tRNA with complementary anticodon
binds with the third codon and brings its amino acid
into position next to the 2nd. A peptide bond is formed
between 2nd and 3rd amino acid. The whole process is
repeated until a ''stop'' codon is in position and
translation is stopped.
Note: - TGA, TAA and TAG – are stop codons.
N.B. The translation of the mRNA code into a protein
molecule requires energy that comes from hydrolysis of
GTP /guanoisne triphosphate/ not ATP
 mRNA Codons Join the Ribosome

Large
subunit P A
Site Site

mRNA
A U G C U A C U U C G
Small subunit 15
 Initiation
aa2
aa1

2-tRNA
1-tRNA

anticodon
G A U
U A C
hydrogen A U G C U A C U U C G A
bonds codon mRNA
16
 Elongation
peptide bond
aa3
aa1 aa2

3-tRNA

1-tRNA 2-tRNA G A A
anticodon
U A C G A U
hydrogen A U G C U A C U U C G A
bonds codon mRNA
17
 aa1 peptide bond
aa3
aa2

1-tRNA

3-tRNA
U A C
(leaves)
2-tRNA G A A

G A U
A U G C U A C U U C G A
mRNA

Ribosomes move over one codon 18

 peptide bonds
aa1 aa4

aa2 aa3

4-tRNA

2-tRNA 3-tRNA G C U

G A U G A A
A U G C U A C U U C G A A C U
mRNA

19
 peptide bonds
aa1 aa4
aa2

aa3

2-tRNA
4-tRNA
G A U
(leaves)
3-tRNA G C U

G A A
A U G C U A C U U C G A A C U
mRNA

Ribosomes move over one codon 20

 peptide bonds aa5
aa1
aa2
aa4
aa3

5-tRNA

U G A
3-tRNA 4-tRNA

G A A G C U
G C U A C U U C G A A C U
mRNA

21
 aa1 peptide bonds aa5
aa2
aa3
aa4

5-tRNA

3-tRNA U G A
G A A 4-tRNA

G C U
G C U A C U U C G A A C U
mRNA

Ribosomes move over one codon 22

 aa5
aa4 aa199
Termination
aa200
aa3 primary
structure
aa2 of a protein

aa1
terminator
200-tRNA
or stop
codon

A C U C A U G U U U A G
mRNA

23
 End Product –The Protein!
• The end products of protein synthesis is a
primary structure of a protein
✓A sequence of amino acid bonded
together by peptide bonds

aa5
aa3 aa4
aa2 aa199

aa1 aa200
24
• Though it is similar to eukaryotes, there are
some differences like: Prokaryotic cell have no
nucleus. Prokaryotic mRNA does not need
post-transcriptional process because it only
contains exons (coding genes) not introns
(non-coding genes). Transcription and
translation are coupled - mRNA translated at
one end of ribosome while it starts
transcribing from DNA at other end.
• Transamination: - is a process of amino group
of an amino acid is removed and transferred
to a keto acid, then it becomes a different
amino acid/keto acid E.g. pyruvic acid (keto
acid) → alanine (amino acid) - by
transamination.
• Note. Not all amino acids are produced by
transamination only those we obtain from our
food. They are called essential amino acid.
 Control of Gene expression
• Genes are switched on by "transcription factors"-
are proteins that bind to a regulatory sequence of
DNA near to the gene they influence. They
operate in the following way: The transcription
factors bind to a promoter sequence of DNA near
the gene to be activated. RNA polymerase binds
to the DNA/ transcription factor complex. The
RNA polymerase activated and moves away from
the DNA along the gene. The RNA polymerase
transcribes the antisense strand of the DNA and
the gene is now being expressed.
• Like transcription factors that promote gene
expression, there are factors to repress (switched off)
gene action. Short interfering RNA (siRNA)
– are unusual-very short
– only 21-23 nucleotides
– double stranded
– They don‘t act on the gene itself, but interfere/silence the
mRNA once it has been transcribed from DNA.
– Is post transcriptional interference
• If mRNA is prevented from translating its Codons into
amino acid then the protein for which the gene codes
for cannot be built (silenced).
 Mutations
• Mutation is the alteration of the nucleotide sequence of the
genome of an organism, virus, or extrachromosomal DNA.
– Mutation could occur spontaneously (accidentally) during
duplication.
– They are rare events.
1
– Each cell contains 6x109 /billion/ base parts 50𝑥106 occurrence
– Each new cell has an average 120 mutations. But
• Most mutations detected & repaired
• 95% of our DNA is non-coding, most mutation unlikely to
affect coding gens.
– Rate of mutations can be increased by:-
• Carcinogenic - chemical in tobacco smoke
• High energy radiation- ultraviolet radiation, x- ray
• There are many different ways that DNA can be changed,
resulting in different types of mutiation as described below:
1. Point mutations- changes that involves a single base. There are
several types of point mutations, some of these are:
– Substitution- one base is replaced by other base
– Addition – an extra base is added
– Deletions – a base is missed out during DNA replication.
2. Chromosomal Mutations- situation where part /segment/ of a
chromosome sequence of DNA is disturbed/ a chromosome is
missed/added. Types of chromosomal mutations:
• Euploidy: having a chromosome number that is an exact
multiple of the haploid number
– Polyploidy: the condition in which a normally diploid cell or
organism acquires one or more additional sets of
chromosomes. E.g – Triploid, Tetraploid
• Aneuploidy – is a condition where an organism/a cell lost from
or added to one or more chromosomes to/the normal set of
chromosome
– 2 n+1 = trisomy/47 chromosomes, e.g. Down‘s syndrome
– 2n-1 = monosomics – turner syndrome/45chr.
– 2n+1+1 = double trisomy
– 2n-2 – nullisomic, organisms that loss one homologous
chromosome.
• Gidu syndrome = mental retardation – caused by part of
deletion of chromosome number 5 of man.
 Consequence of gene-mutations
• Mutations on body cell (non- sex cell) cannot be
inherited but may result in one of the following:
– harmless
– damage the cell
– kill the cell
– Make cell cancerous- which might kill the person.
• Mutations in different genes will obviously
produce different effects but two types of gene
are important in regulating cell division and
preventing the formation of a tumor.
a. Proto-oncogenes: when proto-oncogenes
mutate, they often become active oncogenes which
stimulate cell to divide in an uncontrolled manner.
b. Tumor-suppressor genes: recognize this
uncontrolled cell division and act to suppress cell
division.
– If these genes mutate and become inactive, a tumor
will form as uncontrolled cell division continues.
– Tumor-is a mass of cells created when cell replication
gets out of control and cause cancer.
Thanks!
 Unit Five

Genetics and Evolution

Part IV
 Protein synthesis
• Code for protein synthesis is specified by DNA and has to be sent to
ribosome. DNA is a huge molecule and remains in nucleus to
assemble amino acids in the correct sequence to form protein.
• Events during protein synthesis
i. Transcription – DNA code for protein is rewritten in a molecule of
messenger RNA (mRNA)
ii. mRNA travels from nucleus to ribosome
iii. Free amino acids are transported from cytoplasm to ribosome by
transfer RNA (tRNA) molecules
iv. Ribosome read mRNA code and assembles amino acids presented
by tRNA into a protein by a process = translation. Translation – is
process in which mRNA code is converted into a sequence of amino
acids
DNA code  mRNA codon  protein/ polypeptide
 Genetic code
• The genetic code is held in the DNA molecule.
It is because of the nucleotides sequence in
the DNA molecule made a gene that codes for
protein to that each amino acid in the protein
is coded for by a triplet /sequence of three
bases. Hence, a gene is a sequence of base
triplets in the DNA molecule that carries a
code for a protein.
1. Since there are 4 bases, there is 43 = 64 possible
triplet codes /amino acids/ but only 20 amino acids
are used to make all different proteins. None of
them is spare or redundant.
2. Only one strand of a DNA molecule carries the
code for proteins (It is called sense strand or coding
stand) and the other strand is non-coding or
antisense strand.
3. Most amino acids have more than one code, only
methionine and tryptophan have one code.
– Arginine has six codes
4. Three triplets (TAA, TAG, and TGA) do not code
for amino acids and they are called stop codons.
stop codes signify the end of the coding sequence
5. Degenerate code – the DNA code is non-
overlapping codes i.e., each triplet is distinct from
all other triplets.
6. The genetic code is also a universal code i.e. the
triplet code TAT in the DNA code for amino acid
tyrosine in human, redwood tree, bacterium or in
any organism E.g. ACC – threonine, GGG-glycine
Genetic code
N.B. It is not just the base that matter but the sequence,
e.g. ATT codes of different amino acid from TTA
• The enzyme DNA-dependent RNA polymerase binds
with a section of DNA next to the gene to be
transcribed. Transcription factors activate the enzyme.
The enzymes ― unwind and separate the strands of a
DNA molecule. The polymerase assembles free RNA
nucleotides on the complementary strand (antisense
strand). mRNA (transcribed RNA) leaves the DNA; the
strands of DNA rejoin & re-coil.
• N.B. The mRNA molecule now contains the code for
the protein that was held in the DNA of the genes
• Translation of mRNA code into a protein depends on
the interaction within a ribosome between mRNA and
tRNA. All tRNA molecules have same basic structure.
The ''cloverleaf'' configuration of the molecules has at
one end a triplet of bases called anticodon. The
anticodon is a triplet on tRNA. The other end of tRNA
molecule has an attachment site for the aminoacid that
is specified by the mRNA codon.
• Ribosomes are made from ribosomal RNA and proteins
organized into large & small subunits. Within ribosome,
there are three sites called A, P and E sites.
 Transfer RNA (tRNA)
amino acid
attachment site
Methionine amino acid

U A C
anticodon 9
10
 Events during translation of proteins
• The first two codons of the mRNA enter the
ribosome and tRNA molecules (with amino
acid attached) that have complementary
anticodons to the 1st two codons of the
mRNA bind to those codons. A peptide bond
forms between amino acid carried by two
tRNA molecules and dipeptide is transferred
to the tRNA in the A-site. The Ribosome
moves along the mRNA by one codon bringing
the 3rd codon into the ribosome.
• At the same time the free tRNA exits the ribosome
from the E-site and tRNA with the dipeptide moves
into the P-site. A tRNA with complementary anticodon
binds with the third codon and brings its amino acid
into position next to the 2nd. A peptide bond is formed
between 2nd and 3rd amino acid. The whole process is
repeated until a ''stop'' codon is in position and
translation is stopped.
Note: - TGA, TAA and TAG – are stop codons.
N.B. The translation of the mRNA code into a protein
molecule requires energy that comes from hydrolysis of
GTP /guanoisne triphosphate/ not ATP
 mRNA Codons Join the Ribosome

Large
subunit P A
Site Site

mRNA
A U G C U A C U U C G
Small subunit 15
 Initiation
aa2
aa1

2-tRNA
1-tRNA

anticodon
G A U
U A C
hydrogen A U G C U A C U U C G A
bonds codon mRNA
16
 Elongation
peptide bond
aa3
aa1 aa2

3-tRNA

1-tRNA 2-tRNA G A A
anticodon
U A C G A U
hydrogen A U G C U A C U U C G A
bonds codon mRNA
17
 aa1 peptide bond
aa3
aa2

1-tRNA

3-tRNA
U A C
(leaves)
2-tRNA G A A

G A U
A U G C U A C U U C G A
mRNA

Ribosomes move over one codon 18

 peptide bonds
aa1 aa4

aa2 aa3

4-tRNA

2-tRNA 3-tRNA G C U

G A U G A A
A U G C U A C U U C G A A C U
mRNA

19
 peptide bonds
aa1 aa4
aa2

aa3

2-tRNA
4-tRNA
G A U
(leaves) 3-tRNA G C U

G A A
A U G C U A C U U C G A A C U
mRNA

Ribosomes move over one codon 20

 peptide bonds aa5
aa1
aa2
aa4
aa3

5-tRNA

U G A
3-tRNA 4-tRNA

G A A G C U
G C U A C U U C G A A C U
mRNA

21
 aa1 peptide bonds aa5
aa2
aa3
aa4

5-tRNA

3-tRNA U G A
G A A 4-tRNA

G C U
G C U A C U U C G A A C U
mRNA

Ribosomes move over one codon 22

 aa5
aa4 aa199
Termination
aa200
aa3 primary
structure
aa2 of a protein

aa1
terminator
200-tRNA
or stop
codon

A C U C A U G U U U A G
mRNA

23
 End Product –The Protein!
• The end products of protein synthesis is a
primary structure of a protein
A sequence of amino acid bonded
together by peptide bonds

aa5
aa3 aa4
aa2 aa199

aa1 aa200
24
• Though it is similar to eukaryotes, there are
some differences like: Prokaryotic cell have no
nucleus. Prokaryotic mRNA does not need
post-transcriptional process because it only
contains exons (coding genes) not introns
(non-coding genes). Transcription and
translation are coupled - mRNA translated at
one end of ribosome while it starts
transcribing from DNA at other end.
• Transamination: - is a process of amino group
of an amino acid is removed and transferred
to a keto acid, then it becomes a different
amino acid/keto acid E.g. pyruvic acid (keto
acid) → alanine (amino acid) - by
transamination.
• Note. Not all amino acids are produced by
transamination only those we obtain from our
food. They are called essential amino acid.
 Control of Gene expression
• Genes are switched on by "transcription factors"-
are proteins that bind to a regulatory sequence of
DNA near to the gene they influence. They
operate in the following way: The transcription
factors bind to a promoter sequence of DNA near
the gene to be activated. RNA polymerase binds
to the DNA/ transcription factor complex. The
RNA polymerase activated and moves away from
the DNA along the gene. The RNA polymerase
transcribes the antisense strand of the DNA and
the gene is now being expressed.
• Like transcription factors that promote gene
expression, there are factors to repress (switched off)
gene action. Short interfering RNA (siRNA)
– are unusual-very short
– only 21-23 nucleotides
– double stranded
– They don‘t act on the gene itself, but interfere/silence the
mRNA once it has been transcribed from DNA.
– Is post transcriptional interference
• If mRNA is prevented from translating its Codons into
amino acid then the protein for which the gene codes
for cannot be built (silenced).
 Mutations
• Mutation is the alteration of the nucleotide sequence of the
genome of an organism, virus, or extrachromosomal DNA.
– Mutation could occur spontaneously (accidentally) during
duplication.
– They are rare events.
1
– Each cell contains 6x109 /billion/ base pairs. occurrence
50𝑥106
– Each new cell has an average 120 mutations. But
• Most mutations detected & repaired
• 95% of our DNA is non-coding, most mutation unlikely to
affect coding gens.
– Rate of mutations can be increased by:-
• Carcinogenic - chemical in tobacco smoke
• High energy radiation- ultraviolet radiation, x- ray
• There are many different ways that DNA can be changed,
resulting in different types of mutiation as described below:
1. Point mutations- changes that involves a single base. There are
several types of point mutations, some of these are:
– Substitution- one base is replaced by other base
– Addition– an extra base is added
– Deletions – a base is missed out during DNA replication.
2. Chromosomal Mutations- situation where part /segment/ of a
chromosome sequence of DNA is disturbed/ a chromosome is
missed/added. Types of chromosomal mutations:
• Euploidy: having a chromosome number that is an exact
multiple of the haploid number
– Polyploidy: the condition in which a normally diploid cell or
organism acquires one or more additional sets of
chromosomes. E.g – Triploid, Tetraploid
• Aneuploidy – is a condition where an organism/a cell lost from
or added to one or more chromosomes to/the normal set of
chromosome
– 2 n+1 = trisomy/47 chromosomes, e.g. Down‘s syndrome
– 2n-1 = monosomics – turner syndrome/45chr.
– 2n+1+1 = double trisomy
– 2n-2 – nullisomic, organisms that loss one homologous
chromosome.
• Gidu syndrome = mental retardation – caused by part of
deletion of chromosome number 5 of man.
 Consequence of gene-mutations
• Mutations on body cell (non- sex cell) cannot be
inherited but may result in one of the following:
– harmless
– damage the cell
– kill the cell
– Make cell cancerous- which might kill the person.
• Mutations in different genes will obviously
produce different effects but two types of gene
are important in regulating cell division and
preventing the formation of a tumor.
a. Proto-oncogenes: when proto-oncogenes
mutate, they often become active oncogenes which
stimulate cell to divide in an uncontrolled manner.
b. Tumor-suppressor genes: recognize this
uncontrolled cell division and act to suppress cell
division.
– If these genes mutate and become inactive, a tumor
will form as uncontrolled cell division continues.
– Tumor-is a mass of cells created when cell replication
gets out of control and cause cancer.
 Manipulation of DNA
Genetic engineering
• Genetic engineering is a process by which the
genome of an organism is altered, usually by
having extra (foreign) gene from different
organisms, and the organism is termed
genetically modified organism (GMO),
transgenic organism or genetically engineered
organism.
• Genetic engineering is early done on Bactria,
to produce useful products like:
– Insulin, antibiotics, washing enzyme
– Enzyme for food processing industry
– Human growth hormone
– Vaccines-Hepatitis B
– Bovine somatotrophin, high yield milk and muscle
development in cattle.
• Plants are also genetically modified:
– To absorb more CO2 – global warming
– Disease (drought) resistant
– Improved yield
– To produce specific product E.g. golden rice
produce beta-carotene (in vitamin 'A') prevent
night blindness.
• Moreover, animals are genetically modified for
the following purposes
– high yield of protein, high growth rate
– Specific products eg. insulin,
– Detection of water pollution = glofish glow in the
dark b/c they have had bioluminescent gene from
jelly fish.
– Genetically modified salmon and Tilapia fish grow
bigger and faster.
• Some other potential application of genetic
engineering are:
– Disease could be prevented by detecting defected
genes.
– To treat infectious diseases by implanting antiviral
proteins (antibodies).
– To produce plants and animals that have high growth
rate and reduced susceptibility to disease – reduce
use of fertilizers and pesticides.
– Animals and plants can be 'tailor made' to show
desirable characteristics
 ABO blood groups and Rh Factors
• Early experiments with human blood
transfusion often resulted in the death of the
patient for unknown reasons. In 1901, it was
discovered that there were three blood types,
A, B, and O, and that mixing blood from
different types caused an immune response
that resulted in clumping. Type AB is rare and
was discovered later.
• ABO Blood Type: An individual's red blood
cells will contain proteins of type A, or B, or
both, or neither.
• The body produces antibodies that will attack
any foreign type. Alleles of types IA and IB are
dominant over type i.
 Types of blood
Genotype Blood Type Antigens Antibodies Donate To Receive
From

ii Type O None Anti-A and A, B, AB, O O

Anti-B

I AI A Type A A Anti-B A, AB A, O

I Ai Type A A Anti-B A, AB A, O

IBIB Type B B Anti-A B, AB B, O

IBi Type B B Anti-A B, AB B, O

I AI B Type AB A and B None AB A, B, AB, O

• Rh Factor (D antigen): The Rh factor, the second
most important blood group system after the
ABO blood group system, was first discovered in
Rhesus monkeys.
• The Rh factor is inherited independently from the
ABO blood type. Genotypes for the Rh factor are
+/+, +/-, and -/-. People who are +/+ or +/-
possess the Rh(D) antigen and test as Rh positive.
People who are -/- do not possess the Rh(D)
antigen and test as Rh negative.
Genotype Phenotype Blood Blood Donate To Receive
Proteins Antibodies From
+/+ Rh+ Rh(D) None Rh+ Rh+ or Rh-
proteins
+/- Rh+ Rh(D) None Rh+ Rh+ or Rh-
proteins
-/- Rh- None Anti-Rh(D) Rh+ or Rh- Rh-
• Rh Sensitization: One interesting medical scenario
involves an Rh negative mother who carries an Rh
positive baby.
• The baby of an Rh positive father and an Rh
negative mother can be +/- or -/-.
• If the baby is +/-, the first pregnancy causes Rh
sensitization in the mother, because she is
exposed to foreign proteins and builds up
antibodies against them.
• Future pregnancies can be increasingly difficult,
as the mother's antibodies attack the baby.
46
 Introduction to Evolution
• Evolution is the gradual change of organisms
on the earth over long periods, with new
forms replacing old ones.
• As evolution has progressed new species are
arising, the biodiversity of the planet
increasing, larger and more complex
organisms replaced the smaller and some
species has get extinct.
• Evolution can also be the change in genetic
composition of a population over successive
generations which may be caused by meiosis,
hybridization, natural selection or mutation.
• This leads to a sequence of events by which the
population diverges from other populations of the
same species and may lead to the origin of a new
species.
Theories about the origin of life on Earth
• The theory of evolution describes how the various
forms of life on earth (including humans) emerged and
developed.
• There are five main theories of the origin of
life on Earth:
– special creationism
– spontaneous generation
– eternity of life
– cosmozoan theory
– biochemical origin
a) Special creationism
• Special creation theory states that the different
forms of life on earth were created by a Supreme
Being/ God/ at once with six days.
• Special creation is always linked to religion and
mainly focused on spiritual matters that cannot
be seen, touched or measured effectively.
• There are two views on the origin of life:
Types of creationism theory
• Gap creation – discusses a large gap between the formation of
the earth and the creation of all the animals and plants. The
gap could be billions or millions of year.
• Progressive creation – accepts the Big Bangs as the origin of
the universe. It accepts the fossil record of a series of creation
for all of the organisms but it does not accept these as part of
a continuing process (each is seen as unique creation).
• Evolutionary creationism (Theistic evolution) – This view of
evolution maintains that God “invented” evolution and takes
some form of an active part in the ongoing process of
evolution.
• Intelligent design – a theory states that life developed
(formed) due to a combination of natural forces and the
intervention of a supernatural being.
b) Spontaneous generation theory
• Suggests that life can evolve 'spontaneously' from
non-living objects. E.g. people believed that
rotting meat turned into flies.
c) Eternity of life
• The theory of eternity of life states that the
universe has always existed and that there has
always been life in the universe.
• There is no beginning and no end to life on earth
and so life is neither created nor generated from
non-living matters
d) Cosmozoan Theory
• States that life on the earth originally came
from elsewhere in the universe (possibly from
another planet). E.g. Meteorites brought
bacterial spores, germs to the earth.
• This theory did not gain any significant
support because it lacks evidence and it is
strongly linked to the “eternity of life” theory
of the origin of life.
e) Biochemical theory
• It suggests that life on earth originated as a result of a
number of biochemical reactions producing organic
molecules, which combined (associated) to form cells.
• This theory is also called abiogenesis; states life
originates from chemical inanimate (abiotic
substances).
• The two scientists (biologists) who developed the
theory of abiogenesis (origin of life from chemicals)
were:- Aleksander Oparin (1924) and John Haldane
(1929). They both suggested:
• The primitive atmosphere of the earth was a
reducing atmosphere – no free oxygen (no
oxygen gas).
– primitive atmosphere: NH3, H2, water vapour (H2O
(g)) and CH4
• There was an appropriate supply of energy, such
as lightening or ultraviolet light (Uv – rays).
• This would provide the energy for reactions that
would synthesize a wide range of organic
compounds (amino acids, sugars and fatty acids).
• Oparin suggested that the atmosphere of the primitive
earth contained NH3, H2, water vapour (H2O (g)) and
CH4. He suggested that at high temperature (above
boiling point), these gases could have undergone a
series of chemical reactions and might have formed
colloidal aggregates or coacervates (collections of
droplets that composed of molecules of different
types).
• Oparin considered that these coacervates were able to
absorb and assimilate organic compounds (amino
acids, DNA and others) and leading to the first true
cells.
• J. Haldane – proposed that the chemical
reactions of these gases were occurred in the
primitive sea by solar energy and the sea
became a “hot dilute soup” of organic
monomers and small polymers.
• In 1953, Stanley Miller tested the biochemical
theory. He applied electrical sparks repeatedly
through a mixture of gases (NH3, water, H2 and
CH4) that were represent the primitive
atmosphere of the earth (no oxygen) connected a
flask of heated water.
• Miller leaving the equipment for longer periods
of time, a larger variety and more complex
organic molecules were formed including:
• amino acids - to form proteins
• pentose sugar - to form nucleic acids
• hexose sugar - need for respiration and to
form starch and cellulose.
• Hydrogen cyanide (HCN)- starting point for
synthesizes of nitrogen containing bases in
nucleotides. This experiment gave strong
evidence to support the Oparin-Haldane
hypothesis.
• Origin of Autotrophy: The first life (cell) appeared
on earth – about 4 billion years ago and they
were:- anaerobes, heterotrophs and prokaryotes.
• They would have fed on organic chemicals (soup)
which formed spontaneously in the waters of the
earth. The three consecutive lines of evolution of
organisms on earth leading to:
– Archaebacteria - are first appeared organisms. They
are prokaryotes including thermophilic (high temp.
loving), sulphobacteria, methanobacteria and
halophilic (salt loving) bacteria.
• They can survive under harsh (extreme)
environment.
• Eubacteria – are true (ordinary) bacteria,
ordinary bacteria and cyanobacteria (blue –
green algae)
• Prokaryotes – evolved into protista, fungi,
plants, animals (nearly all are aerobes).
• Later (3.5 billion years ago) – the first autotrophs
(photosynthetic organisms) like cyanobacteria (blue-
green algae) came in existence. With the evolution of
chlorophyll molecules, oxygen (O2) was released as a
by-product of photosynthesis and this changes the
earth’s atmosphere from the reducing to an
atmosphere containing oxygen.
• The fossil record shows that cyanobacteria had been
producing oxygen by photosynthesis from about 305
million years ago but the levels of oxygen in
atmosphere did not rise for almost 1 billion years ago.
Because oxygen was absorbed by the vast amount iron
in the earth it rusted.
Theories of Evolution
• There have been many theories of evolution
that have explained:- how does evolution
happen? And what drives the population to
become a new species?
A. Lamarck Theory of evolution
• In the 19th century (1809), Lamarck published a
paper entitled Philosophic “Zoologique” in which
he described the two-part mechanism by which
change was gradually introduced into the species
and passed down through the generations. This
theory is also called “theory of transformation”
or Lamarckism. The two parts of Lamarck theory
are:
– Use and disuse
– Inheritance acquired traits
• Use and disuse – Lamarck suggested that a
structure or process in organism that can be used
continuously will become enlarged or more
developed but any structure that is not. Example,
• According to Lamarck, giraffe had short neck but
they stretched their neck to reach high branches,
developed an elongated neck - use theory.
• The wings of penguins would have become
smaller than those of other birds because
penguins do not use their wings to fly - disuse
theory.
• Inheritance of Acquired traits – Lamarck believed
that traits changed (acquired during an
organism’s lifetime could be passed on to its
offsprings. Example: - Giraffes that had acquired
long necks would have offspring with long necks.
• Note: - Nowadays, Lamarck’s theories are not
accepted because the environmental changes
that were believed by Lamarck have brought
about the changes in the phenotypes (Physical
appearance) of the organisms have no effect on
their gametes and hence their heredity.
B. Charles Darwin and Natural Selection
• In 1858, both Charles Darwin and Alfred Wallace
jointly published a scientific paper that proposed
species were modified by natural selection.
• Darwin visited five of the Galapagos Islands,
made drawings, and collected species. In
particular, Darwin studied the finches found on
the different islands and noted there were many
similarities between them but have some obvious
differences.
• Darwin concluded that an “ancestral finch” had
colonized the Islands from mainland and been able to
adapt to the different conditions on the islands and
evolve into different species. E.g. He suggested that
some finches had evolved into insect eaters (pointed
peak), other in to seedeaters (crushing peak).
• Darwin summarized his observations in two main
ideas:
– all species tend to produce more offsprings than can
possibly survive (Fecundity)
– there is a variation among the offsprings.
• From these observation Darwin deduced
(concluded) that:
– There will be a “struggle for existence” between
members of a species because they are over –
reproduced and resources are limited.
– Some members of a species will be better adapted
than others to the environment because there is a
variation in the offspring.
• Darwin proposed: - Those members of a species,
which are best adapted to their environment, will
survive and reproduce in greater number than
other less adapted (died out).
C. Neo – Darwinism Theory
• Charles Darwin knew very little about genetics and did
not propose how variations in the population was
passed to the next generation.
• Nowadays, genes and gene action are the driving force
of evolution in the theory of Natural selection.
• A Gene pool is all the alleles in the population. It might
be evolve a population into a new species. Suppose an
allele determines a feature that gives an organism an
advantage in its environment. The following will
happen
• Those individuals with the advantageous allele
of a gene will survive to reproduce in greater
number than other types
• Advantageous allele pass to their offsprings in
greater numbers than other genes (alleles).
• The frequency of the advantageous allele will
be higher in the next generation of a
population.
• Mutations are important in introducing variation into
population. Any mutation could produce an allele
which:
– increase in frequency if they are beneficial in their effect,
may increase slowly, stable or decrease if they are neutral
and decrease and could disappear if they are harmful
(disadvantages) in their effects.
• Neo-Darwinism is a modification of Darwin’s original
theory that takes into account:- genetics and ethology
(behavioural pattens can also be advantageous or not).
E.g. Young geese “imprint” upon the first moving
object after they are hatched.
Thanks!