Module 1 (Biological Molecules) Revision Notes

What are biological molecules? molecules made and used by living organisms e.g. Carbohydrates,
Proteins, Lipids, DNA, ATP, Water, Inorganic Ions

What are the functions of carbohydrates?

 energy source (glucose in respiration)

 energy store (starch in plants, glycogen in animals)
 structure (cellulose in cell wall of plants)

What are the building blocks for carbohydrates called? monosaccharides

Example of monosaccharides? glucose (alpha and beta), galactose, fructose

Formula for monosaccharides? C6H12O6 (isomers = same formula but different arrangement)

Difference between alpha and beta glucose? on Carbon 1, alpha glucose has a OH group on the
bottom and beta glucose has a OH group on the top

How are monosaccharides joined together? condensation reaction (removing water) – between 2
OH groups

Bond in carbohydrate? glycosidic bond (1,4 – between carbon 1 and carbon 4)

Example of disaccharides? glucose + glucose = maltose, glucose + galactose = lactose,

glucose + fructose = sucrose

Formula for disaccharides? C12H22O11

How are polymers separated? hydrolysis (add water)

What is a polysaccharide? many monosacharrides joined by condensation reaction/glycosidic

bonds

Example of polysaccharides?

 Starch (long chain of alpha glucose) which is energy store in plants

 Glycogen (long chain of alpha glucose) which is energy store in animals
 Cellulose (long chain of beta glucose) which makes cell wall in plants

What are Polysaccharides?

 carbohydrates
 made of a long chain of monosaccharides joined by condensation reaction/glycosidic
bonds
 3 examples: Starch, Glycogen, Cellulose
 Starch & Glycogen used as Energy Stores (starch in plants, glycogen in animals), they
are made out of many alpha glucose which are used for respiration
 Cellulose used to form Cell Wall in Plants, made out of many beta glucose
Structure of Starch?

 made from Amylose and Amylopectin

 Amylose = long straight chain of alpha-glucose which is coiled
 Amylopectin = straight chain of alpha-glucose with side branches (1,6-glycosidic bond)

Structure of Glycogen?

straight chain of alpha-glucose (1,4-glycosidic bond) with side branches (1,6-glycosidic bond)

Properties of Starch and Glycogen as energy stores?

 Insoluble = do not affect water potential of the cell, do not diffuse out of the cell
 Coiled/Branched = compact, more can fit into a cell
 Branched/Chained = glucose removed from the end

Structure of Cellulose?

 β-glucose arranged in a straight chain (each alternative β-glucose is rotated 180 degrees)
= cellulose straight chain
 many cellulose chains are cross linked by hydrogen bonds to form microfibrils
 many microfibrils are cross linked to form marcrofibrils
 forms structure of cell wall
 strong material (prevents plant cell from bursting or shrinking)

Test for starch? add iodine, turns blue/black

Test for reducing sugar? heat with benedicts, turns brick red

Test for non-reducing sugar?

 heat with benedicts – no change

 therefore, add dilute hydrochloric acid (hydrolyses glycosidic bond)
 then add sodium hydrogencarbonate (neutralises solution)
 heat with benedict - turns brick red

What are 2 types of proteins? Globular and Fibrous

What are globular proteins? soluble proteins with a specific 3D shape e.g. enzymes, hormones,
antibodies, haemoglobin

What are fibrous proteins? strong/insoluble/inflexible material e.g. collagen and keratin

What are the building blocks for proteins? amino acids

Structure of amino acid? central carbon, carboxyl group to the right (COOH), amine group to
the left (NH2), hydrogen above and R group below

How do amino acids differ? have different R groups e.g. glycine has a hydrogen in its R group –
simplest amino acid
How are amino acids joined together? by condensation reaction between the carboxyl group of
one and amine group of another, leaves a bond between
carbon & nitrogen (called a peptide bond) forming a
dipeptide

Define primary, secondary, tertiary, quaternary structure?

 Primary = sequence of AA, polypeptide chain (held by peptide bonds)

 Secondary = the primary structure (polypeptide chain) coils to form a helix, held by
hydrogen bonds
 Tertiary = secondary structure folds again to form final 3d shape, held together by
hydrogen/ionic/disulfide bonds
 Quaternary = made of more then one polypeptide chain

Examples of quaternary structure proteins? collagen (3 chains), antibodies (3 chains),

haemoglobin (4 chains)

Structure of collagen?

 strong material, used to build tendons/ligaments/connective tissues

 primary structure mainly made up of glycine (simplest amino acid)
 secondary structure forms a tight coil (not much branching due to glycine)
 tertiary structure coils again
 quaternary structure made from 3 tertiary structures wrapped around each other like rope
 = a collagen molecule
 many of these collagen molecules make the tendons/ligaments/connective tissues

Test for protein? add biuret, turns purple

What is an enzyme? a biological catalyst (substance that speeds up the rate of reaction without
being used up – lowers activation energy)

What makes an enzyme specific? has a specific active site shape, only complementary substrates
can bind to the active site to form enzyme-substrate complexes

Lock and Key Model vs Induced Fit Model?

 LK = active site shape is rigid, only exactly complementary substrates can bind to form
ES complexes
 IF = active site changes shape, the substrate binds to the active site – the active site
changes shape so the substrate fits exactly forming an ES complex

Affect of substrate concentration on enzyme activity?

 increase substrate concentration, increases chance of successful collisions, increase

chance of forming an ES complex, increase rate of reaction
 this continues until all the enzyme's active sites are full/saturated = maximum rate of
reaction
Affect of enzyme concentration on enzyme activity?

 increase enzyme concentration, increases chance of successful collisions, increase

chance of forming an ES complex, increase rate of reaction
 this continues until all the substrates are used up = maximum rate of reaction

Affect of temperature on enzyme activity?

 as temperature increases
 the kinetic energy increases
 the molecules move faster
 increase chance of successful collisions
 increase chance of forming ES complex
 increase rate of reaction
 carries on till optimum
 after optimum
 bonds in tertiary structure break (hydrogen and ionic bonds)
 lose active site shape
 substrate no longer complementary
 cant form ES complexes
 enzyme denatured

Affect of pH on enzyme activity? if change pH away from optimum, bonds in tertiary structure
break, lose active site shape, no longer form ES complex,
enzyme denatured

Competitive vs Non-Competitive Inhibitors?

 Competitive = a substance with a similar shape to the substrate and a complementary

shape to the enzyme's active site, binds to the active site, blocking it, preventing ES
complexes from forming
 Non-Competitive = a substance that binds to another site on the enzyme other then the
active site, causes the active site to change shape, so less ES complexes can form

What are the 3 types of Lipids?

 Triglycerides (fat for energy store, insulation, protection of organs)

 Phopholipids (to make membranes)
 Cholesterol (for membrane stability and make hormones)

Structure of triglyceride?

 made of 1 glycerol and 3 fatty acids

 joined by condensation reaction, ester bonds
 bond is COOC
 there are 2 types of triglycerides: saturated fat and unsaturated fat

Saturated vs Unsaturated Fat?

 Saturated = has no carbon double bonds in the R group of the fatty acid
 Unsaturated = has carbon double bonds in the R group of the fatty acid
Structure of phospholipid?

 made of 1 glycerol, 2 fatty acids and 1 phosphate

 phosphate forms a hydrophillic head, fatty acids form hydrophobic tails
 forms a phospholipid bilayer, basic structure of membranes

What are Nucleic Acids? Polymers made from Nucleotides (2 types = DNA and RNA)

What is DNA?

 DeoxyriboNucleic Acid
 found in all organisms (animals, plants, microorganisms)
 carries genes
 genes = section of DNA that codes for a protein
 all organisms are built of proteins

Building block of DNA?

 DNA nucleotide (made of phosphate, deoxyribose sugar, nitrogenous base)

 4 types of nucleotides (each has a different base, either
Adenine/Thymine/Cytosine/Guanine)

DNA structure?

 DNA Double Helix

 join nucleotides by condensation reaction between sugar and phosphate to form a
polynucleotide
 join 2 polynucleotides by hydrogen bond between the bases
 A joins with T, C joins with G (complementary base pairing)
 produces double strand [anti-parallel]
 then coil double strand into Double Helix

Properties of DNA Structure?

 Double Stranded = makes DNA more stable & 2 strands act as templates in semi-
conservative replication
 Coil into Helix = more compact
 Sugar-phosphate backbone = protects bases (bases code for protein)
 Hydrogen bonds between bases = weak, so double strand separates more easily for semi-
conservative replication
 Complementary Base Pairing = ensures identical copies of DNA made by semi-
conservative replication

DNA Replication?

occurs in interphase before mitosis & meiosis

occurs by semi-conservative replication
Describe Semi-Conservative Replication?

DNA double strand separate and act as templates, producing 2 identical copies of the DNA,
each has half the original strand and half the new strand
process:

 DNA Helicase breaks hydrogen bonds between the complementary bases

 double strand separates, leaves 2 template stands
 free complementary nucleotides bind to exposed bases on template strands (A to T, C to G)
 DNA Polymerase joins the sugar-phosphate backbone of the new strand

Evidence for SCR?

 Replicating Bacterial DNA in 2 types of Nitrogen Isotopes, 15N and 14N

 15N = heavy isotope
 14N = light isotope
 Nitrogen found in nitrogenous bases of DNA
 Bacterial DNA made from 15N will have a Heavy Density
 Bacterial DNA made from 14N will have a Light Density
 Experiment = Bacterial DNA made of 15N is replicated in an environment of 14N –
produces DNA molecules with half 15/half 14 (semi-conservative replication, original
strand = 15N & new strand = 14N), therefore, DNA molecule has medium density

What is RNA?

 RiboNucleic Acid
 2 types (mRNA and tRNA)
 mRNA = messenger RNA
 tRNA = transfer RNA
 both single stranded
 both made of RNA Nucleotides (phosphate, ribose sugar, nitrogenous bases - AUCG)

What is ATP? Adenosine Triphosphate (Energy Carrier Molecule – delivers energy for life
processes)
Structure of ATP?

 Adenosine Triphosphate
 made from 1 adenosine and 3 phosphates
 formation: ADP + Pi (+ energy used) = ATP
 condensation reaction using ATP Synthase
 carries energy in its bonds
 breakdown: ATP = ADP + Pi (+ energy released)
 hydrolysis reaction using ATP Hydrolase
 releases energy from its bonds

What makes ATP a good deliverer of energy?

 immediate source = need to only break one bond (plus bond is weak)
 manageable source = releases small amount of energy
Uses of ATP (releases energy) in organisms?

 protein synthesis
 organelle synthesis
 DNA replication
 cell division (mitosis)
 active transport
 metabolic reactions
 movement
 maintaining body temperature

Role of Water in Biology?

 found in living organisms = cytoplasm (all organisms), xylem/phloem (in plants), tissue
fluid and blood (in animals)
 also acts as habitats for living organisms

Properties of Water?

 Water Molecules (H20) are dipolar

 Hydrogen has slightly +ve charge and Oxygen has slightly -ve charge
 therefore H20 molecules can form hydrogen bonds with each other
Role of Water in Living Organisms?

(I) Habitat (e.g. sea): Water has high specific heat capacity meaning that a lot of heat
needs to be applied before it evaporates due to the presence of the hydrogen bonds
between the water molecules. Also when water freezes it becomes Ice, which is less
dense then liquid water – so it floats on the surface insulating the water beneath it,
preventing it from freezing. In both cases the water remains liquid to provide an
habitat for organisms.
(II) Solvent: Because H20 molecules are dipolar they can separate out solutes based on
their charge, +ve Hydrogen side mixes with -ve solute and -ve Oxygen side mixes
with +ve solute, so solute mixes with water and becomes dissolved. This is useful in
cytoplasm of all cells and supports the reaction of these solutes, it is also useful in
the processes of diffusion/active transport, and is also useful in transport such as
blood and phloem.
(III) Hydrostatic Pressure: Water when pressurised can provide a strong physical
pushing force. Used particularly in Mass Flow (where mass of water carries large
amounts of substances e.g. tissue fluid in capillaries and phloem in plants). Also
helps to support turgidity in plants.
(IV) Homeostasis: Mammals and Humans control body temperature by sweating.
Sweat on the skin uses heat from the blood to evaporate, hence, cooling the
individual. Because sweat/water is made up of hydrogen bonds, it has a stable
structure, so requires a large amount of heat for it to evaporate. This is called Latent
Heat of Vaporisation.

What are Inorganic Ions?

 Salts/Minerals
 Inorganic = do not contain carbon, Ion = charged (+ve/-ve)
 e.g. Sodium Ions (Na+), Chloride Ions (Cl-)
Module 2 (Cells) Revision Notes

Kingdoms in Biology?

 Living Organisms can be placed into 5 groups

(Animal, Plant, Bacteria, Fungi, Protoctista)
 Animal and Plant are Multicellular Organisms
(made up of billions of cells working together)
 Bacteria, Fungi, Protoctista are Microorgansism (made up of one or a few cells)
[note: Viruses are not defined as living organisms because they do not have the
standard components of a cell – acellular, and cannot perform MRS GREN without
a host]
 all living organisms are made from cells (multicellular = millions, microorganism =
one/few), all cells have 4 properties = DNA, ribosomes, cytoplasm, cell membrane

Eukaryotic vs Prokaryotic Cells?

 Eukaryotic = animal/plant cell, has membrane bound organelles (nucleus, endoplasmic

reticulum, golgi body, lysosome, mitochondra)
 Prokaryotic = bacteria, has no membrane bound organelles

What are the 2 forms of Reproduction?

 Sexual & Asexual

 Sexual Reproduction in Animals & Some Plants
 Asexual Reproduction in Microorganisms & Some Plants
 Sexual Reproduction uses 2 parents (each provides a gamete which fuse to form a
zygote, zygote develops into organism)
 Asexual Reproduction uses 1 parent to produce genetically identical offspring

How does a Zygote develop into an Organism?

 Zygote is a stem cell

 stem cell = undifferentiated/unspecialised cell, can form any type of cell
 zygote divides by mitosis to make many stem cells
 each stem cell differentiates into specialised cell
 each specialised cell divides by mitosis to make many copies and form a tissue
 different tissues join to form an organ
 different organs join to form an organ system
 this is surrounded by the Body

Define a tissue, organ and organ system?

tissue = a group of specialised cells

organ = made of different tissues
organ system = different organs working together
What is an Animal Cell made of?

 Organelles (nucleus, endoplasmic reticulum, golgi body, lysosomes, mitochondria,

ribosomes) – all have membrane except the ribosomes
 Cytoplasm (site of chemical reaction)
 Cell Membrane (holds cell contents together, controls what enters/leaves cell, cell
signalling)

Structure of Nucleus?

 contains DNA (made of genes, genes code for making proteins)

 DNA wrapped around histones to form Chromatin
 nucleus has a double membrane, called Nuclear Envelope, which contains pores
 at centre of nucleus is Nucleolus – produces mRNA (copy of a gene)
 rest of nucleus made of Nucleoplasm (contains the DNA/chromatin)

Endoplasmic Reticulum?

 2 types = Rough and Smooth

 Rough Endoplasmic Reticulum has ribosomes on it, makes proteins
 Smooth Endoplasmic Reticulum has no ribosomes on it, makes lipids/carbohydrates

Golgi body?

 modifies and packages proteins

 packages them into vesicles for transport
 digestive enzymes are placed into lysosomes (vesicles with membranes around them)

Mitochondria?

 site of respiration, releases energy, produces ATP (energy carrier molecule)

 has a double membrane, inner membrane folded into Cristae (increases surface area for
enzymes of respiration)
 middle portion called Matrix

Ribosomes?

 attached to RER
 site of protein synthesis

What is a Plant Cell made of?

 Organelles (nucleus, endoplasmic reticulum, golgi body, lysosomes, mitochondria,

chloroplast, vacuole, ribosomes) – all have membrane except the ribosomes
 Cytoplasm (site of chemical reaction)
 Cell Membrane (holds cell contents together, controls what enters/leaves cell, cell
signalling)
 Cell Wall (made of cellulose, prevents cell from bursting or shrinking)
Structure of chloroplast?

 organelle for photosynthesis

 has double membrane
 contains discs called thylakoids
 thylakoids contain chlorophyll
 stack of thylakoids called granum
 thylakoids surrounded by a fluid called stroma

Vacuole?

Surrounded by a membrane called a tonoplast, contains Cell Sap (water, sugar, minerals)

What is Bacteria made of?

 No nucleus – loose DNA in the form of a single loop and plasmid

 No membrane bound organelles: smaller ribosomes, mesosomes – infolding of cell
membrane for respiration
 Cytoplasm
 Cell Membrane & Cell Wall (made of peptidoglycan/murein)
 some have a Capsule (reduce water loss, protect from phagocytosis) and Flagella
(movement)

What is Virus made of?

 DNA or RNA (if RNA, also has a enzyme called reverse transcriptase to turn RNA into
DNA)
 Protein Coat called Capsid and Lipid Coat
 Attachment proteins on outside
 (infects host cells by attaching using their attachment protein, send in their DNA which
uses the cell to make the viruses components and uses the cell membrane to make the
viruses lipid coat, hence, producing copies of the virus and destroying the host cell)

What is a Chromosome?

 DNA in coiled form

 formed during interphase of cell division (mitosis/meiosis) in Animals/Plants
 made of 2 identical/sister chromatids joined by a centromere
 carries 2 copies of the same DNA molecule

What is a homologous pair of chromosomes?

a pair of chromosomes: 1 maternal (from mother)/1 paternal (from father)

carries same genes but different alleles – there are 23 pairs in humans
What is Cell Division?

 formation of new cells in multicellular organisms (animals & plants)

 2 methods = mitosis & meiosis
 mitosis = produces genetically identical cells for growth & repair of tissues
 meiosis = produces genetically different haploid cells as gametes for sexual reproduction

What does Mitosis (cell cycle) produce?

2 genetically identical cells, diploid (have full set of chromosomes/DNA)

Benefit of Mitosis? growth and repair of tissues

Stages of Mitosis? Interphase/Mitosis/Cytokinesis

Interphase? G1: protein synthesis

S: DNA replication (doubles set of DNA)
G2: organelle synthesis

Mitosis?

Prophase: DNA coils to form chromosomes, nucleus breaksdown, spindle fibres form
Metaphase: chromosomes line up in middle of cell and attach to spindle fibre via centromere
Anaphase: spindle fibres pull, centromere splits, sister chromatids move to opposite sides
Telophase: chromatids uncoil, nucleus reforms (left with 2 genetically identical nuclei)

Cytokinesis? separating cell into 2 (each receives a nucleus and organelles/cytoplasm)

What happens to DNA mass in mitosis? halves

What happens to Chromosome number in mitosis? stays the same (diploid)

What is Cancer? formation of a tumour due to uncontrolled cell division (uncontrolled mitosis)

How does uncontrolled cell division occur?

 due to mutation of DNA/cells forming cancer cells

 mutation can occur randomly or due to mutagens (chemicals/radiation)
 cancer cells are rapidly dividing cells (like hair cells, skin cells, red blood cells), they
spend less time in interphase and more time in the other stages (mitosis)

Treatment for Cancer?

Surgery = aim is to remove tumour

Chemotherapy = - using drugs that inhibit mitosis in rapidly dividing cancer cells
- problem, also affect normal healthy cells (hair cell, skin cells, rbcs)
causing side effects (hair loss, dry skin, tiredness)
- treatment given as regular doses to allow time for normal healthy
cells to recover in number

Radiotherapy = radiation used to destroy cancer cells

What does Meiosis produce?

4 genetically different cells, haploid (half the amount of chromosome/DNA)

Benefits of Meiosis?

produces gametes which will be used in sexual reproduction in animals & plants
(2 gametes fuse to form a zygote, zygote develops into organisms)

Stages of Meiosis? Interphase/Meiosis I/Meiosis II/Cytokinesis

Interphase? G1: protein synthesis

S: DNA replication (doubles set of DNA)
G2: organelle synthesis

Meiosis I?

Prophase I: DNA coils to form chromosomes, nucleus breaksdown, spindle fibres form,
crossing over occurs
Metaphase I: homologous pair of chromosomes line up in middle of cell and attach to
spindle fibre via centromere by random assortment
Anaphase I: spindle fibres pull, homologous pair of chromosomes separate to opposite sides
by independent segregation
Telophase I: chromosomes uncoil, nucleus reforms (left with 2 nuclei)

Meiosis II?

Prophase II: DNA coils to form chromosomes, nucleus breaksdown, spindle fibres form
Metaphase II: chromosomes line up in middle of cell and attach to spindle fibre via
centromere by random assortment
Anaphase II: spindle fibres pull, centromere splits, sister chromatids move to opposite sides
by independent segregation
Telophase II: chromatids uncoil, nucleus reforms (left with 4 genetically different nuclei)

Cytokinesis? separating cell into 4 (each receives a nucleus and organelles/cytoplasm)

How does Meiosis produce Variation? Crossing Over and Independent Segregation

What is crossing over?

occurs in Prophase I of Meiosis I

homologous pairs of chromosomes wrap around each other and swap equivalent sections of
chromatids – produces new combination of alleles

What is independent segregation?

- in Anaphase I of Meiosis I – the homologous pairs of chromosomes separate

- in Anaphase II of Meiosis II – the chromatids separate
- independent segregation produces a mix of alleles from paternal and maternal
chromosomes in gamete
What happens to DNA mass in meiosis? quarters

What happens to Chromosome number in meiosis? halves (haploid)

How do Bacteria do Cell Division?

 Binary Fission
 Copy their DNA (Single Loop and Plasmids) and then separate into 2 new genetically
identical bacteria [Asexual Reproduction]

2 types of microscopes? Light and Electron (transmission and scanning)

How to judge a microscope? by Magnification and Resolution

Magnification? how much larger the image size is compared to the actual size

Which has higher magnification? TEM > SEM > LM

Formula for magnification? magnification = image size/actual size

Conversion? 1 mm = 1000 micrometre. 1 mm = 1,000,000 nanometre

Why can organelles appear different in images? viewed from different angles and at different
levels/depth

Resolution? minimum distance at which 2 very close objects can be distinguished

Which has higher resolution? TEM > SEM > LM

Why does electron microscopes have a higher resolution? Electron microscope uses electrons
which have a shorter wavelength (light microscope uses light which has a large wavelength)

Difference between TEM and SEM? in Transmission the electrons pass through the specimen,
in Scanning the electrons bounce off the specimen's surface

Advantage and Disadvantage of TEM?

 Advantage = highest magnification and highest resolution

 Disadvantage = works in a vacuum so can only observe dead specimens, specimen needs
to be thin, black and white image, 2D image, artefacts

Advantage and Disadvantage of SEM?

 Advantage = produces 3D image

 Disadvantage = works in a vacuum so can only observe dead specimens, black and white
image, artefacts
Cell Fractionation?

 Breakdown tissue into cells (cut, pestle & mortar)

 add cold/isotonic/buffer solution (cold = reduce enzyme activity, isotonic = same water
potential so organelle does not shrink or burst, buffer = maintains constant pH)
 homogenate – breaks open cells releasing organelles
 filter = removes large debris and intact cells
 centrifuge – spin at low speed, largest organelle builds at bottom (nucleus), leaves
supernatant, spin at higher speed, next heaviest organelle forms at bottom (chloroplast or
mitochondria)
 (organelle by size: nucleus, chloroplast, mitochondria, endoplasmic reticulum/golgi
body/lysosomes, ribosomes)

Simple vs Facilitated Diffusion?

 Simple = molecules move directly through the phospholipid bilayer

 Facilitated = molecules pass through transport proteins (large use carrier, charged use
channel)
Factors that affect rate of diffusion?

 surface area (increase = increase rate of diffusion)

 concentration gradient (increase = increase rate of diffusion)
 thickness (decrease = decrease diffusion distance = increase rate of diffusion)
 temperature (increase = increase kinetic energy = molecules move faster = increase rate
of diffusion)
 size of molecules (smaller molecules = increase rate of diffusion)

What is Ficks Law? (Surface Area x Concentration Gradient)/Thickness

Define Osmosis? movement of water molecules from an area of high water potential to an area of
low water potential through a partially permeable membrane

Which liquid has the highest water potential?

 distilled/pure water
 has a value of 0kPa
 lower water potential by adding solutes (makes water potential negative)
 water moves from less negative water potential (e.g. -35 kPa) to more negative water
potential (e.g. -75 kPa)

Surround animal cell with pure water? swells and burst (water enters by osmosis)

Surround plant cell with pure water?

 swells but does not burst

 cell wall prevents it from bursting
 made of cellulose – strong material
 the cell is Turgid
Surround animal cell with concentrated sugar/salt solution? shrinks (water leaves by osmosis)

Surround plant cell with concentrated sugar/salt solution?

2. water leaves by osmosis

3. cell wall prevents cell from shrinking, keeps it rigid
4. the protoplast (cell membrane plus contents) shrink
5. the cell is Plasmolysed

Define Active Transport? movement of molecules from an area of low concentration to an area of
high concentration using ATP and carrier proteins (against concentration
gradient)
Describe the process of active transport?

 molecules (in area of low concentration) bind to carrier protein

 ATP breaksdown to ADP, Pi and Energy
 the Pi and Energy cause the carrier protein to change shape
 carrier protein releases molecules on opposite side (in area of high concentration)
 the carrier protein releases the attached Pi to return to its original shape

Enzymes of Carbohydrate Digestion?

 Starch/Glycogen (Salivary Amylase in Mouth, Pancreatic Amylase in Small Intestine)

into Maltose
 Maltose (Maltase on lining of Small Intestine) into Glucose
 Lactose (Lactase on lining of Small Intestine) into Glucose and Galactose
 Sucrose (Sucrase on lining of Small Intestine) into Glucose and Fructose

Enzymes of Protein Digestion?

 Endopeptidase (in stomach), hydrolyses peptide bonds in middle of polypeptide chain

into many smaller chains
 Exopeptidase (in small intestine), hydrolyses peptide bonds at end of chains to leave
dipeptides
 Deipeptidase (on lining of small intestine), hydrolyse dipeptides into amino acids

Enzymes of Lipid Digestion?

- Lipase in Small Intestine leaves Monoglyceride and 2 Fatty Acids

Adaptations of SI for Absorption?

folded to form Villus (large surface area)

cells lining SI have Microvilli (large surface area)
wall of SI is thin (short diffusion distance)
rich blood supply (maintains concentration gradient)
cells lining SI have transport proteins, enzymes (maltase, lactase, sucrase, didpeptidase) and
many mitochondria

Absorption of Glucose and Amino Acids in SI?

  sodium ions are actively transported from the cells lining the SI into the blood
 lowers the sodium ion concentration in the cell
 therefore sodium ions move from the lumen of the SI into the cell
 this pulls in glucose and amino acids via a cotransport protein
 therefore glucose and amino acids builds up in the cell and moves into the blood by
diffusion

Absorption of Monoglyceride and Fatty Acids?

 Lipids initially emulsified by Bile into Micelles (smaller droplets)

 Micelles digested by Lipase into Monoglyceride and 2 Fatty Acids
 Monoglyceride and Fatty Acids absorbed by Cells lining SI by simple diffusion
 Form a Chylomicron (lipid + cholesterol + lipoprotein)
 Enters Lymph as Lacteal, then enters Blood

What is Lactose Intolerance

 Person does not make Lactase Enzyme

 Lactose remains Undigested
 Leads to Diarrhoea and Flatulence
 Undigested Lactose in Lumen of Intestine lowers it's water potential, so water enters the
lumen by osmosis leading to water faeces (Diarrhoea)
 Undigested Lactose brokendown by micro-organisms in Large Intestine, giving off gas
(Flatulence)

What is a pathogen?

 a disease causing micro-organism

 e.g. bacteria, virus, fungi
 bacteria cause disease by producing toxins
 virus cause disease by dividing in cells causing them to burst

Body's defence against pathogens?

 I, Barriers (prevents pathogens entering the body)

 II, Phagocytes (perform phagocytosis and stimulate specific response)
 III, Specific Response (uses lymphocytes to produce memory cells and antibodies)

What are the Barriers (I)?

 Skin, an impermeable barrier made of keratin

 Cilia & Mucus in Lungs
 Stomach Acid (denatures/breaksdown pathogens)

Describe the process of Phagocytosis (II)?

  pathogen releases chemicals
 this attracts the phagocyte
 the phagocyte binds to the pathogen
 the phagocyte engulfs the pathogen
 forms a phagosome around the pathogen
 lysosomes inside the phagocyte release digestive enzymes into the phagosome
 breaking down the pathogen by hydrolysis

Describe the Specific Response (III)?

 phagocytes perform phagocytosis (engulf and destroy pathogen) without destroying the
antigen, they place antigens on their surface, they present antigens
 t lymphocytes (t cells) bind to the antigen and become stimulated
 they divide by mitosis to form 3 types of cells: t helper, t killer, t memory
 t helper cells stimulate b lymphocytes (b cells)
 t killer cells kill infected cells (infected by virus)
 t memory cells provide long term immunity
 b lymphocytes (b cells) engulf and present antigens on their surface, the t helper cells
bind to this
 the b cells become stimulated and divide by mitosis to make 2 types of cells: Plasma
Cells & B Memory Cells
 Plasma cells make antibodies
 B memory cells provide long term immunity

What is a antigen? a protein on the surface of a pathogen that stimulates an immune response

How does the immune response lead to production of antibodies? the phagocytes stimulate the t
cells, the t cells form t helper cells, the t helper cells stimulate the b cells, the b cells form plasma
cells, the plasma cells make antibodies

What is an antibody?

 a globular protein
 made by plasma cells
 has 3 regions: variable region, hinge region, constant region
 variable region has a different shape in each antibody, contains the antigen binding sites,
these bind to complementary antigens (on a pathogen) to form an antigen-antibody
complex, destroying the pathogen
 hinge region gives the antibody flexibility
 constant region the same shape in all antibodies, binds to phagocytes to help with
phagocytosis

How do Memory cells (B/T) work?

  made during the specific immune response after a new infection by a pathogen (called a
primary infection)
 B and T memory cells remain in the blood
 if person is reinfected by the same pathogen (called a secondary infection) the memory
cells will recognise the pathogen and produce antibodies RAPIDLY and to a LARGE
amount
 therefore the pathogen is killed before it can cause harm = immunity

How does a vaccine produce immunity? involves giving an injection that contains dead/weakened
pathogens that carry antigens which stimulates the immune response leading to production of
antibodies & memory cells

Active vs Passive immunity?

 Active = individual has memory cells – can make their own antibodies & provides long
term immunity
 Passive = person given antibodies, these work then die, no long term immunity, no
memory cells.

How does activity immunity occur? naturally = by primary infection, artificially = by vaccination

How does passive immunity occur? naturally = from mother to baby (placenta or breast milk),
artificially = by injection

Successful Vaccination Programme?

 produce suitable vaccine (effective – make memory cells, does not cause disease, no
major side effects, low cost, easily produced/transported/stored/administered)
 herd immunity

What is herd immunity? when a large proportion of the population is vaccinated, therefore most
people will be immune, only a few will not be a immune, increases chance of non-immune person
coming into contact with immune person, so the pathogen has no where to go, so it dies out

Problems with Vaccination Programmes?

 vaccine does not work (dead form ineffective, pathogen hides from immune system)
 vaccine not safe (no weak/inactive form, causes major side effects)
 many strains of pathogen
 cannot achieve herd immunity (logistic of vaccinating large proportion)
 antigenic variability

What is antigenic variability? the pathogen mutates, the antigen changes shape, so the memory
cells no longer complementary – do not recognise the pathogen, therefore the pathogen can reharm

What is HIV/AIDs?
 HIV = Human Immunodeficiency Virus
 AIDs = Acquired Immunodeficiency Syndrome
 HIV is the Pathogen, AIDs is the Infectious Disease
 HIV is spread by fluid to fluid contact (unprotected sexual intercourse, sharing needles,
mother to child via placenta or breast feeding)
 HIV damages and destroys T Helper Cells, therefore person no longer produces Immune
Response and has no defence to against pathogens/infections = AIDs
 With AIDs, individual at risk from all sorts of pathogens/infections called Opportunistic
Infections
Module 3 (Exchange and Transport) Revision Notes

How do Microorganisms Obtain Nutrients & Remove Waste?

 by exchange via their surface

 nutrients (e.g. glucose, oxygen) move in by diffusion via their surface
 waste (e.g. carbon dioxide) move out by diffusion via their surface

Why are Microorganisms able to perform exchange via their surface?

 have a large surface area to volume ratio

 have a short diffusion distance
 have low demand

Why can't Animals/Plants perform exchange via their surface?

 have a small surface area to volume ratio

 multicellular (large diffusion distance and high demand)
 impermeable surface (prevent pathogens entering and reduce water loss)
 therefore, require specialised Exchange & Transport systems
 exchange system = increases rate of diffusion of nutrients in and wastes out
 transport system = deliver nutrients and remove waste from all cells

Why do Fish have Specialised Gas Exchange Systems?

 multicellular organism so has a small surface area to volume ratio, large diffusion
distance, high demand & body surface impermeable
 therefore, cannot perform gas exchange (O2 in/CO2 out) via their surface, they
require a specialised gas exchange system called Gills

Structure of Gills in Fish?

 many gill filaments and gill lamellae = large surface area

 gill lamellae have a thin wall (short diffusion distance) and are permeable
 ventilation brings in pure water (high oxygen, low carbon dioxide) and circulation
brings in deoxygenated blood (low oxygen, high carbon dioxide), the water and blood
pass over in opposite directions (countercurrent flow), which maintains concentration
gradient all the way along the gill lamellae

Why do Insects have Specialised Gas Exchange Systems?

 multicellular organism so has a small surface area to volume ratio, large diffusion
distance, high demand & body surface made of exoskeleton (impermeable barrier
to reduce water loss)
 therefore, cannot perform gas exchange (O2 in/CO2 out) via their surface, they
require a specialised gas exchange system called Tracheal System
Structure of Tracheal System in Insects?

 starts with openings on body surface called Spiracles

 spiracles contain valves, open = gas exchange, closed = prevent water loss
 spiracles connect to Trachea
 trachea connect to Tracheoles
 tracheoles connect directly to Respiring Cells (delivering oxygen, removing
carbon dioxide)

How does Gas Exchange occur in Tracheal System of Insects?

 at rest = down a concentration gradient, oxygen moves in & carbon dioxide moves
out by simple diffusion
 when active = by ventilation, air inhaled for mass flow of O2 in & air exhaled for
mass flow of CO2 out

Function of Lungs? site of gas exchange in mammals

(oxygen into blood – used in cells for respiration,
carbon dioxide out of the blood – toxic waste product of respiration)

What is Lungs made up of? Trachea, Bronchi, Bronchioles, Alveoli (+ capillaries)

Function of trachea, bronchi, bronchioles? transport of air and filter air, (bronchioles also
controls amount of air
reaching alveoli)

Structure of trachea/bronchi?

 wall made of c-shaped cartilage

 cartilage is strong so trachea/bronchi do not collapse
 cartilage is c-shaped to give flexibility
 lining made of goblet cells and ciliated epithelial cells
 goblet cells make mucus, which traps pathogens/particles
 ciliated epithelial cells have cilia, which pushes mucus up and out of lungs

Structure of bronchioles?

 wall made of smooth muscle

 smooth muscle contracts, lumen narrows, bronchiole constricts
 (occurs when surrounded by noxious gases – reduces amount reaching alveoli)
 lining made of goblet cells and ciliated epithelial cells

Adaptation of alveoli?

 millions of tiny alveoli that are folded (large surface area)

 thin wall/one cell thick/squamous epithelial cells (short diffusion distance)
 elastic tissue in wall (stretches when breathing in to increase surface area, recoils
when breathing out to push the air out)
 ventilation maintains concentration gradient (high oxygen, low carbon dioxide)
Adaptation of capillaries?

 millions of tiny capillaries (large surface area)

 thin wall/one cell thick/squamous epithelial cells (short diffusion distance)
 narrow lumen (increases diffusion time, decreases diffusion distance)
 circulation maintains concentration gradient (low oxygen, high carbon dioxide)

How O2 moves from the alveoli to the capillaries? by simple diffusion passing thru the
alveolar epithelium and capillary
epithelium

How CO2 moves from capillaries to the alveoli? by simple diffusion passing thru the
capillary epithelium and alveoli
epithelium

Describe the process of Breathing/Ventilation?

 Breathing In/Inhalation = external intercostal muscles contract (rib cage moves up

and out) & diaphragm contracts (flattens), therefore increase in volume in chest
and decrease in pressure, so air moves in
 Breathing Out/Exhalation = external intercostal muscle relax (rib cage moves
down and in) & diaphragm relaxes (back to dome shape), therefore decrease in
volume in chest and increase in pressure, so air pushed out (aided by elastic recoil
in the alveoli)

Formula for Pulmonary Ventilation?

 PV = tidal volume x ventilation rate

 tidal volume = volume of air breathed in/out in one breath
 ventilation rate = number of breaths per minute
 Pulmonary Ventilation = volume of air breathed in/out per minute

Function of Intestines? site of exchange of digested nutrients in mammals

What is Digestion?

 Breakdown of Large Insoluble Molecules into Small Soluble Molecules (so they
can move into the blood and then into the body cells)
 Starch/Glycogen (Carbohydrates) into Glucose by Amylase (Salivary in mouth,
Pancreatic in small intestine) and Maltase/Lactase/Sucrase (on lining of small
intestine)
 Proteins into Amino Acids by Endopeptidase/Exopeptidase/Dipeptidase
(Endopeptidase in stomach, Exopeptidase in small intestine, Dipeptidase on lining
of small intestine)
 Lipids into Monoglyceride and 2 Fatty Acids by Lipase (in small intestine)

What do Intestine Absorb?

 Small Intestine absorbs small soluble nutrients (glucose, amino acids,

 monoglyceride and fatty acid, vitamins and minerals)
 Large Intestine absorbs water

Why do Humans/Mammals require a Specialised Transport System?

 multicellular organisms therefore have large diffusion distances and high demand
 need a transport system to deliver nutrients and remove waste from all cells
 transport system in humans/mammals called Circulatory System
 Circulatory System made of heart, blood vessels, blood
(heart pumps blood, blood vessels carry blood, blood carries nutrients/waste)

Why is the transport system in mammals called a double circulatory system?

the heart pumps twice, the blood goes through the heart twice – generates enough
pressure to supply all
body cells

Why is the transport system in mammals called a closed circulatory system?

blood is transported in blood vessels – helps to maintain pressure and redirect blood
flow

Layout of Circulatory System?

 heart pumps blood which is carried in arteries which flow into arterioles which
flow into capillaries which then are carried in venules then veins back to the heart
 Artery to Arterioles to Capillaries to Venules to Veins
 Artery/Arterioles carry blood away from the heart
(arterioles are small arteries)
 Capillaries are the site of exchange (nutrients out, waste in)
 Veins/Venules return blood back to the heart
(venules are small veins)

Heart?

 job is to pump blood around the body (delivers nutrients to cells and remove
waste)
 made of 4 muscular chambers (2 atria, 2 ventricles)
 atria pumps blood to ventricles, ventricles pump blood out of heart (R to lungs, L
to body)
 ventricles thicker then atria (has to pump blood further)
 left ventricle has a thicker muscular wall then right ventricle, therefore has
stronger contractions, so can generate higher pressure and pump the blood further
around the body
Blood vessels of the heart?

 artery takes blood away from the heart, vein returns blood to the heart
 Vena Cava supplies R atrium (with deoxygenated blood from body)
 Pulmonary Vein supplies L atrium (with oxygenated blood from lungs)
 R ventricle supplies Pulmonary Artery (deoxygenated blood to lungs)
 L ventricle supplies Aorta (oxygenated blood to body)

Job of valves in heart?

 Ensure one way flow of blood, no backflow

 (blood flows from atria to ventricles to arteries)
 2 sets of valves: Atrio-ventricular Valve & Semi-lunar Valve
 AV valve = between atria and ventricles
 SL valve = between ventricles and arteries

When are AV valves open or closed? Open = pressure in atria greater then pressure in
ventricles, Closed = pressure in ventricles greater then
pressure in atria

When are SL valves open or closed? Open = pressure in ventricles greater then pressure in
arteries, Closed = pressure in arteries greater then pressure in ventricles

Describe the processes of the cardiac cycle?

 Filling Stage = atria relaxed, ventricles relaxed, AV valve open, SL valve closed
 Atria Contracts = the SAN located in the R atrium initiates the heart beat and
sends the impulse across both atria making them contract, this pushes all the
remaining blood into the ventricles so it becomes full
 Ventricles Contract = the AVN picks up the impulse, delays it (stops the atria and
ventricles contracting at the same time, so the atria empties and the ventricles
fill), sends the impulse down the septum in the Bundle of His, then at the apex the
impulse goes up both walls of the ventricles in the purkine fibres, so the ventricles
contract from the base upwards, pushing the blood up thru the arteries, when the
ventricles start to contract the AV valve closes then the SL valve opens and blood
leaves the heart
 Ventricles Relax = the SL valve closes then the AV valve opens and filling starts
again

What causes the Heart Sounds?

 when the valves close

 1st = AV closes
 2nd = SL closes
Formula for Cardiac Output?

 CO = Stroke Volume x Heart Rate

 stroke volume = volume of blood pumped out of the heart in one beat
 heart rate = number of beats per minuted
 Cardiac Output = volume of blood pumped out of the heart in one minute

Coronary Heart Disease and Myocardial Infarction?

 high blood pressure damages lining of coronary artery

 fatty deposits/cholesterol builds up beneath the lining, in the wall = Atheroma
 the atheroma breaks thru the lining forming a Atheromatous Plaque on the lining, in
the lumen
 this causes turbulent blood flow
 a blood clot (thrombus) forms
 this block the coronary artery
 therefore less blood flow to the heart muscle
 less glucose and oxygen delivered
 the heart muscle cannot respire
 so it dies (myocardial infarction)

Risk Factors of CHD?

 Age, gender, ethnicity

 Saturated fats (increases LDL, LDL deposits cholesterol in the arteries to form
atheroma)
 Salts (increases blood pressure – lowers water potential of the blood so it holds the
water)
 Smoking (nicotine = increase HR and makes platelets more sticky – blood clot,
carbon monoxide = permanently blocks haemoglobin)
 Obesity and Lack of Exercise

Atheroma & Aneurysm? atheroma weakens wall of artery, blood builds up in the wall, the
wall swells then bursts = aneurysm

Role of Arteries/Arterioles?

 generally carry oxygenated blood away from the heart

 for example, Coronary Artery to heart muscle
Hepatic Artery to liver
Renal Artery to kidneys
 exception = Pulmonary Artery carries deoxygenated blood to lungs

Role of Veins/Venules?

 generally carry deoxygenated blood back to the heart

 for example, Coronary Vein from heart muscle
Hepatic Vein from liver
 Renal Vein from kidneys
 exception 1 = Pulmonary Vein carries oxygenated blood back to the heart
 exception 2 = Hepatic Portal Vein carries deoxygenated blood from digestive
system to liver
(for filtering)

Function of Arteries/Arterioles?

carry blood away from the heart so should be able to withstand high blood pressures
& maintain high blood pressures

Structure of Arteries/Arterioles?

 narrow lumen = maintains pressure

 lining made of squamous epithelial cells = smooth lining to reduce friction
 thick wall = withstand pressure
 elastic tissue in wall,
ventricles contract – elastic tissue stretches to withstand pressure
ventricles relax – elastic tissue recoils to maintain pressure and smooth out
flow
 smooth muscle in wall (particularly in arterioles),
smooth muscle contracts – lumen narrows and arteriole constricts
smooth muscle relaxes – lumen widens and arteriole dilates
 collagen in wall
prevents artery from tearing

Function of Veins/Venules? return blood back to the heart, the blood is under low pressure

Structure of Veins/Venules?

 wide lumen = ease of blood flow

 lining made of squamous epithelial cells = smooth lining to reduce friction
 thin wall = vein can be squashed by skeletal muscle pushing blood back to the heart
 valves in lumen = prevents backflow of blood

Function of Capillaries?

 site of exchange
 3 locations,
With Alveoli, takes in O2 and removes CO2
With Microvilli, takes in glucose/amino acids/monoglyceride and fatty
acids/vitamins/minerals
With All Cells, deliver nutrients and remove waste

Adaptation of Capillaries?

2. many small capillaries = large surface area

3. thin wall, one cell thick, squamous epithelial cells = short diffusion distance
 4. pores between cells = allows fluid to move in and out
5. narrow lumen = increase diffusion time and decrease diffusion distance

Content of Blood?

 main component = Plasma (fluid)

 plasma carries,
 Cells = red blood cells, white blood cells, platelets
 Solutes = nutrients, waste, protein

How does exchange occur between Capillaries & All Cells?

 by mass flow
 fluid moves out of the blood in the capillaries carrying the nutrients
 fluid moves back into blood in the capillaries carrying the waste
 (fluid in the blood called plasma, fluid surrounding cells called tissue fluid, fluid
in lymph system called lymph)

How is tissue fluid formed and returned to circulatory system?

 at the start of the capillary (arterial end) there is a build up hydrostatic pressure
 this pushes fluid out of the capillary via the pores
 the fluid carries the nutrients with it
 the fluid surrounds the cells, this is called tissue fluid
 at the finish of the capillary (venous end) the fluid moves back in by osmosis
 the capillary has low water potential due to the presence of proteins (too large to
move out of capillaries)
 any excess tissue fluid is picked up by the lymph system and deposited in the vena
cava

Why does high blood pressure cause accumulation of tissue fluid?

increases hydrostatic pressure, so more tissue fluid is formed – not as much can be
returned to the circulatory system

Why does diet low in protein cause accumulation of tissue fluid?

the water potential in the capillary is not as low as normal, so not as much fluid can
move back into the capillary by osmosis

Blood Pressure changes along the Circulatory System?

Arteries = - highest pressure (connects directly with heart/ventricles)

- pressure fluctuates (increases when ventricles contract which
causes the elastic tissue to stretch, decreases when
ventricles relax which causes the elastic tissue to recoil)
- overall decrease in pressure due to friction

Arterioles = large decrease in pressure due to increase in total cross-sectional

area (ensures pressure is not to high to damage capillaries)

Capillaries = pressure here is called hydrostatic pressure (decreases due to a

loss in
fluid)

Venules/Veins = blood under low pressure

Job of Red Blood Cells?

 found in humans/mammals (animals)

 carries haemoglobin
 haemoglobin carries oxygen

Structure of Haemoglobin?

 globular protein (soluble & specific 3d shape)

 quaternary structure made of 4 polypeptide chains (2α, 2β)
 each chain carries a haem group
 each haem group carries Fe2+
 each Fe2+ carries an O2
 therefore, each haemoglobin carries 4 lots of O2

Job of Haemoglobin? load oxygen in the lungs and deliver it to the respiring tissues

What is Affinity?

the level of attraction haemoglobin has to oxygen

(high affinity = strong attraction, low affinity = weak attraction)

Role of haemoglobin in oxygen transport?

 haemoglobin has High Affinity in the lungs – due to high partial pressure of
oxygen and low partial pressure of carbon dioxide, so haemoglobin
loads/associates oxygen in the lungs and becomes saturated (full)
 the haemoglobin is transported in the blood in the red blood cell
 at the respiring tissues, haemoglobin has Low Affinity – due to low partial
pressure of oxygen and high partial pressure of carbon dioxide, so oxygen is
unloaded/dissociated/delivered and haemoglobin becomes unsaturated

Relationship between O2 Partial Pressure & Affinity/Saturation of Haemoglobin?

 positive correlation
 as O2 partial pressure increases, affinity/saturation of haemoglobin increases
 the correlation is not linear but is curved (produces a s-shaped, sigmoid curve
called Oxygen Dissociation Curve)
 middle portion of ODC has a steep gradient so when respiring tissues change from
 resting to active and partial pressure of O2 falls, there is a large drop in affinity, so
more O2 would be delivered to the respiring tissues

Relationship between CO2 Partial Pressure & Affinity/Saturation of Haemoglobin?

 negative correlation
 as CO2 partial pressure increases, affinity/saturation of haemoglobin decreases
 this occurs at the site of respiring tissues = the carbon dioxide lowers the pH of
the blood, makes the haemoglobin change shape, so oxygen is released, lowering
affinity. this shifts the ODC to the right, called the bohr shift. benefit = more
oxygen delivered to respiring cells

How does a Fetus receive oxygen? from mother's blood, oxygen dissociates from mother's
haemoglobin and associates with fetal haemoglobin in the placenta – fetal haemoglobin has a
higher affinity compared to mother's haemoglobin

Benefit of fetal haemoglobin having high affinity? fetal haemoglobin's ODC will be to the
left, it has high affinity – so the oxygen will dissociate from the mother's haemoglobin and
associate with the fetal haemoglobin at the low partial pressures of oxygen in the placenta, so
it has enough oxygen for its needs

Why do adults not keep with fetal haemoglobin? the high affinity will mean less oxygen
will be unloaded at the respiring tissues

Affinity of Organisms in a Low Oxygen Environment?

has a high affinity, curve to the left, therefore it can readily associate oxygen at the
low oxygen partial pressures

Affinity of Active Organisms?

has a low affinity, curve to the right, therefore more oxygen can be unloaded to meet
the cell's demand for more respiration

Affinity of Small Organisms?

have a large surface area to volume ratio, lose a lot of heat, needs to respire to
generate heat, therefore has a low affinity, curve to the right, so unloads enough oxygen for
the cells demand of more respiration

What are the Exchange & Transport Systems in Plants?

 exchange systems = leaf and root

 leaf to absorb light and CO2 for photosynthesis
 roots to absorb water and minerals
 transport systems = xylem and phloem
 xylem transports water and minerals
 phloem transports glucose/sugars
 xylem transports in one direction from roots to leaves, phloem transports in both
 directions

Job of the Roots?

absorb water and minerals

absorbs water by osmosis
absorbs minerals by active transport
plants need water for photosynthesis, cytoplasm hydration, turgidity of cells
plants need magnesium, nitrate, phosphate (magnesium to make chlorophyll, nitrate to
make amino acids, phosphate to make phospholipids/ATP/DNA)

Function of the Xylem? transport water and minerals from roots, up the plant, to the leaves

Structure of the xylem?

 long continuous hollow tube (no resistance to water flow)

 narrow lumen
 wall made out of lignin
 lignin: strong, waterproof, adhesive
 wall contains pits/pores (water and minerals can leave)

How does water move up the xylem?

 loss of water at the leaves (transpiration)

 water moves from the top of the xylem into the leaf by osmosis (transpirational pull)
 this applies TENSION to the column of water in the xylem
 the column of water moves up as one as the water particles stick together,
COHESION
 this is is the cohesion-tension theory
 it is supported by capillary action, adhesion and root pressure
 (capillary action = water automatically moves up narrow lumen of xylem)
 (adhesion = water particles stick to lignin in wall of xylem)
 (root pressure = water absorbed at the roots pushes the column of water up slightly by
hydrostatic
pressure)

Why does the diameter of a tree decrease during the day?

 more light and higher temperature

 increase rate of transpiration
 increase transpirational pull
 water pulled up xylem by cohesion-tension
 because the water particles stick to the wall of the xylem (adhesion)
 the walls of the xylem are pulled inwards

Structure of Leaves?
  upper layer called Upper Epidermis
 waxy cuticle on upper epidermis (barrier to reduce water loss)
 beneath the upper epidermis are Palisade Cells
 palisade cells are were photosynthesis takes places
 beneath palisade cells are Spongy Mesophyll Cells
 are loosely packed leaving air spaces to allow ease of gas exchange
 lower layer called Lower Epidermis

Adaptation of palisade cells for photosynthesis?

 located near top of leaf, closer to light

 large size, large surface area for light
 thin cell wall, short diffusion distance for carbon dioxide
 contains many chloroplasts, site of photosynthesis
 large vacuole, pushes chloroplast to the edge of the cell closer to light

Structure of chloroplast?

 organelle for photosynthesis

 has double membrane
 contains discs called thylakoids
 thylakoids contain chlorophyll
 stack of thylakoids called granum
 thylakoids surrounded by a fluid called stroma

How does Exchange occur in Leaves?

 lower epidermis of leaf contains pairs of cells called Guard Cells

 when turgid, guard cells form an opening called Stomata
 gas exchange occurs via the stomata
 In Day, plant photosynthesises and respires, CO2 moves in for photosysnthesis and
O2 moves out (some is used in respiration)
 At Night, plant only respires, O2 moves in for respiration and CO2 moves out

What is Transpiration? loss of water vapour from the leaf via the stomata

How does Transpiration occur?

 moist lining of spongy mesophyll cells evaporate forming water vapour

 water vapour builds up in air spaces
 if water vapour concentration is high enough & stomata is open, water vapour
diffuses out

Factors that increase rate of transpiration?

  light = more light, more stomata open, increase surface area for transpiration
 temperature = more temperature, more evaporation (increase water vapour
concentration) & more kinetic energy
 wind = more wind, maintains concentration gradient
 humidity = less humidity, less water vapour in the surrounding air, increase in water
vapour
concentration gradient

What is a Potometer? apparatus used to measure rate of transpiration

Principle of potometer?

 as transpiration occurs from the leaves, the plant will pull up more water from the
potometer by cohesion-tension causing the bubble to move towards the plant
 the more water lost by transpiration, the more water taken up, the further the
bubble moves

Measuring Rate of Transpiration?

 rate of transpiration = volume of transpiration divided by time

 for volume of transpiration, distance bubble moved x cross-sectional area of tube
(πr2)

How to set up a potometer?

 choose healthy leaf and shoot

 cut shoot underwater and connect to potometer underwater (prevents air bubbles
entering/blocking
xylem)
 ensure potometer is air tight and water tight

What does a potometer actually measure?

measures rate of water uptake as a result of water loss from plant

(water loss can be due to: transpiration, photosynthesis, making cells turgid, loss from

potometer)

What is a Xerophyte? a plant adapted to reduce water loss (reduce transpiration)

Adaptations of Xerophyte?

 spiky, needle like leaves = reduced surface area

 thick waxy cuticle = waterproof, impermeable barrier
 densely packed spongy mesophyll = less air spaces, less water vapour build up
 sunken stomata/hairy leaves/rolled up leaves = traps moist layer of air,
reduces concentration gradient

Function of Phloem? transport organic material (e.g. Sucrose) up and down a plant
Structure of phloem? made of 2 parts (Sieve Tube with Companion Cells alongside)

How does phloem transport organic material like sucrose?

 by principle of Mass Flow (mass flow of water carries the sucrose)

 Sucrose loaded into Phloem at Source
 Hydrogen Ions (H+) actively transported from companion cells into source
 therefore, H+ diffuses back into companion cells from source
 as they do, they pull in sucrose with them by co-transport
 sucrose then diffuses into sieve tube
 this lowers the water potential of sieve tube so water follows by osmosis
 this water will carry the sucrose by hydrostatic pressure (mass flow)
 Sucrose unloaded from Phloem at Sink
 sucrose moves out of phloem/sieve tube into sink by diffusion
 water follows by osmosis

Enzymes of Carbohydrate Digestion?

 Starch/Glycogen (Salivary Amylase in Mouth, Pancreatic Amylase in Small

Intestine) into Maltose
 Maltose (Maltase on lining of Small Intestine) into Glucose
 Lactose (Lactase on lining of Small Intestine) into Glucose and Galactose
 Sucrose (Sucrase on lining of Small Intestine) into Glucose and Fructose

Enzymes of Protein Digestion?

 Endopeptidase (in stomach), hydrolyses peptide bonds in middle of polypeptide

chain into many smaller chains
 Exopeptidase (in small intestine), hydrolyses peptide bonds at end of chains to
leave dipeptides
 Deipeptidase (on lining of small intestine), hydrolyse dipeptides into amino acids

Enzymes of Lipid Digestion?

- Lipase in Small Intestine leaves Monoglyceride and 2 Fatty Acids

Adaptations of SI for Absorption?

folded to form Villus (large surface area)

cells lining SI have Microvilli (large surface area)
wall of SI is thin (short diffusion distance)
rich blood supply (maintains concentration gradient)
cells lining SI have transport proteins, enzymes (maltase, lactase, sucrase,
didpeptidase) and many mitochondria

Absorption of Glucose and Amino Acids in SI?

  sodium ions are actively transported from the cells lining the SI into the blood
 lowers the sodium ion concentration in the cell
 therefore sodium ions move from the lumen of the SI into the cell
 this pulls in glucose and amino acids via a cotransport protein
 therefore glucose and amino acids builds up in the cell and moves into the blood
by diffusion

Absorption of Monoglyceride and Fatty Acids?

 Lipids initially emulsified by Bile into Micelles (smaller droplets)

 Micelles digested by Lipase into Monoglyceride and 2 Fatty Acids
 Monoglyceride and Fatty Acids absorbed by Cells lining SI by simple diffusion
 Form a Chylomicron (lipid + cholesterol + lipoprotein)
 Enters Lymph as Lacteal, then enters Blood

What is Lactose Intolerance

 Person does not make Lactase Enzyme

 Lactose remains Undigested
 Leads to Diarrhoea and Flatulence
 Undigested Lactose in Lumen of Intestine lowers it's water potential, so water
enters the lumen by osmosis leading to water faeces (Diarrhoea)
 Undigested Lactose brokendown by micro-organisms in Large Intestine, giving
off gas (Flatulence)
Module 4 (Diversity) Revision Notes

What is Biodiversity?

 variety in an ecosystem
 variety of habitats and variety of species

What is Species Diversity?

 number of different species

 number of individuals for each species

What is Genetic Diversity?

 variety of alleles in a species population

 the larger number of individuals in a species, the larger the genetic diversity

Benefit of high species diversity?

 Stable ecosystem
 each species is less likely to become extinct (due to high genetic diversity)
 & if a species does become extinct it will not affect the food chain as there are other
species available

How to measure Species Diversity for an area?

 Species Diversity Index

 takes into account the number of different species and how many individuals there are
for each species
 the larger the species diversity index, the larger the species diversity

How does deforestation lower species diversity?

 (deforestation is the removal of trees for wood & space)

 decreases plant species diversity
 less variety of habitats
 less variety of food sources
 decreases animal species diversity

How does agriculture/farming lower species diversity?

 deforestation to make space for farm

 only grow a few plants & keep a few animal species
 selectively breed plants & animals
 use pesticides to kill other species
What is Classification? placing organisms into groups

What is Hierarchical Classification?

 large groups divided into smaller groups with no overlap

 domain, kingdom, phylum, class, order, family, genus, species

What is Binomial Naming System?

 using Genus name and Species name to name organism

 Genus name first in capital, Species name second in lower case
 e.g. tiger = Felix tigris

What is a Species?

a group of individuals with similar characteristics that can interbreed to produce fertile
offspring

Why are the offspring from 2 different species mating infertile?

 offspring will have a odd number of chromosomes

 therefore, cannot perform meiosis, cannot produce gametes
 example: horse + donkey = mule,
mule is infertile,
horse has 64 chromosomes/donkey has 62 chromosomes,
horse gamete has 32 chromosomes/donkey gamete has 31 chromosomes,
therefore, mule has 63 chromosomes

What is Phylogenetic Classification?

based on evolutionary relationships – how closely related different species are and how
recent a common ancestor they have

3 ways of comparing relationship between different species?

DNA Hybridisation: comparing DNA base sequence

- take DNA from 2 species to be compared

- radioactively label one of the DNA
- heat both sets so double strand separates
- cool so single strands join together
- look for Hybrid DNA (one strand from species A, one strand from species B)
- identify Hybrid DNA by 50% radioactivity
- heat Hybrid DNA to measure similarity

results = higher temperature required

more hydrogen bonds present
more complementary base pairing
more similar the base sequence
more similar the species
more closely related
more recent a common ancestor
AA Sequence: comparing AA sequence for the same protein (e.g. haemoglobin in mammals)

results = more similar the AA sequence

more similar the DNA base sequence
more similar the species
more closely related
more recent a common ancestor

(comparing DNA sequence better then comparing AA sequence:

DNA sequence provides information on INTRONS and triplet code is DEGENERATE)

Protein Shape: comparing shape of the same protein (e.g. albumin) using immunological technique

- comparing species A and species B

- take albumin from species A
- place in a blood of rabbit
- rabbit will make antibodies against albumin of species A
- takes these antibodies and place in blood from species B
- if the albumin in species B has a similar shape to species A,
the antibodies will bind to form antigen-antibody complexes,
this will then form a precipitate

results = more precipitate

more complexes
more similar shape
more similar the species
more closely related
more common recent ancestor

What is Variation? difference in characteristics between organisms

Types of Variation?

intraspecific = differences between organisms of the same species

interspecific = differences between organisms of different species

Causes of Intraspecific Variation?

Genetic Factors = same genes but different alleles (allele are different type/forms of genes)

Environmental Factors

Causes of Interspecific Variation?

Genetic Factors = different genes and different alleles

Environmental Factors

Types of Characteristics? Discontinuous and Continuous

Properties of Discontinuous Characteristics?

characteristics fall into certain groups with no overlap (e.g. blood group) – determined by
genetics only (a single gene)

Properties of Continuous Characteristics?

characteristics show a range (e.g. height) – determined by genetics (a few genes, polygenes)
and environment

What is Genetic Diversity? genetic variation, the variety of alleles within a population of a species

Benefit of high genetic diversity? species able to adapt with changes in the environment
e.g. if a new disease arises, some individuals will have characteristics to survive, and will reproduce
passing on their alleles, so the species does not become extinct

What can lower genetic diversity? small population size (e.g. founder effect – where the numbers
start low, or genetic bottleneck – where the numbers decrease)

What is natural selection and adaptation?

 variation in population of species

(genetic diversity/genetic variation/variety in gene pool)
 new alleles arise by random mutation
 environment applies a selection pressure on the population
 those with favourable characteristics/favourable alleles/selection advantage/better
adapted survive, the others die [natural selection]
 the ones that survive will reproduce, passing on their favourable alleles
 if this happens for many generations, then that characteristic will become most common
– the allele will become more frequent [adaptation]

What are the 2 types of selection? stabilising and directional

What is stabilising selection?

 when the environment favours those with the most common characteristic – those on the
extreme dies out
 the common characteristic increases in proportion
 the range (standard deviation) will reduce

What is directional selection?

 when the environment favours those individuals with characteristics on one of the
extremes
 over time this will become the most common characteristic
 normal distribution will shift to that extreme
What is a Gene?

 a section of DNA that codes for a protein

 made out of intron and exon
 intron = non-coding DNA (function e.g. turns gene on or off)
 exon = coding DNA (codes for protein)

How does a Gene/Exon code for a Protein?

 made out of a sequence of bases

 each 3 bases code for 1 amino acid (called triplet code)
 therefore,
 sequence of bases
 determines sequence of triplet codes
 which determine the sequence of AAs
 = polypeptide chain/primary structure (folds to secondary, then to tertiary/quaternary)

Properties of triplet code?

 degenerate = each AA has more than one triplet code

 non-overlapping = each base is read only once
 stop codes = occur at end of sequence – do not code for an AA

How does a mutation lead to a non-functional enzyme?

 change in base sequence

 change in sequence of triplet codes
 change in sequence of AAs
 change in primary structure
 change in hydrogen/ionic/disulfide bonds
 change in tertiary structure (3D shape)
 change in active site shape
 substrate no longer complementary
 can no longer form enzyme-substrate complex

How is a protein assembled?

 by transcription and translation

 transcription = production of a single stranded complementary copy of a gene (called
mRNA)
 translation = use sequence of codons on mRNA to assemble protein (tRNA brings in
AAs)
DNA vs RNA?

 deoxyribose sugar vs ribose sugar

 thymine vs uracil
 double stranded vs single stranded
 one type vs two types (mRNA and tRNA)
What is mRNA?

 messenger RNA
 single stranded complementary copy of a gene
 carries the code for assembling protein (on DNA called triplet code, on mRNA called
codon)

What is tRNA?

 transfer RNA
 single stranded RNA folded over into a 'clover leaf' shape (held by hydrogen bonds
between the bases)
 has an AA attachment site on the top
 has 3 specific bases on the bottom (anticodon)
 anticodon binds to complementary codons on mRNA

What is Transciption?

 occurs in nucleolus of nucleus

 producing a single stranded complementary copy of a gene (called mRNA)
 DNA is double stranded, 1 strand called coding strand & 1 strand called template strand,
the template strand will be used to build mRNA
 process,
 DNA Helicase breaks the hydrogen bonds between complementary bases in the gene
 the double strand of the gene unwinds
 leaves 2 separate strands (1 coding strand and 1 template strand)
 complementary RNA nucleotides bind to exposed bases on the template strand
 RNA Polymerase joins the sugar-phosphate backbone of the RNA strand
 leaves pre-mRNA (contains introns and exons)
 the copies of the introns are removed by splicing
 leaves mRNA

What is Translation?

 takes place on ribosomes of Rough Endoplasmic Reticulum

 uses the sequence of codons on the mRNA to assemble the protein (tRNA brings in AAs)
 process,
 mRNA leaves nucleus via nuclear pore
 mRNA attaches to a ribosome
 complementary tRNA carrying specific AAs bind to the codons on mRNA via their
anticodon
 the AAs on the tRNA are joined by peptide bonds
What does Meiosis produce?

4 genetically different cells, haploid (half the amount of chromosome/DNA)

Benefits of Meiosis?

produces gametes which will be used in sexual reproduction in animals & plants
(2 gametes fuse to form a zygote, zygote develops into organisms)

Stages of Meiosis? Interphase/Meiosis I/Meiosis II/Cytokinesis

Interphase? G1: protein synthesis

S: DNA replication (doubles set of DNA)
G2: organelle synthesis

Meiosis I?

Prophase I: DNA coils to form chromosomes, nucleus breaksdown, spindle fibres form,
crossing over occurs
Metaphase I: homologous pair of chromosomes line up in middle of cell and attach to
spindle fibre via centromere
Anaphase I: spindle fibres pull, homologous pair of chromosomes separate to opposite sides
by independent assortment
Telophase I: chromosomes uncoil, nucleus reforms (left with 2 nuclei)

Meiosis II?

Prophase II: DNA coils to form chromosomes, nucleus breaksdown, spindle fibres form
Metaphase II: chromosomes line up in middle of cell and attach to spindle fibre via
centromere
Anaphase II: spindle fibres pull, centromere splits, sister chromatids move to opposite sides
by independent assortment
Telophase II: chromatids uncoil, nucleus reforms (left with 4 genetically different nuclei)

Cytokinesis? separating cell into 4 (each receives a nucleus and organelles/cytoplasm)

How does Meiosis produce Variation? Crossing Over and Independent Assortment

What is crossing over?

occurs in Prophase I of Meiosis I

homologous pairs of chromosomes wrap around each other and swap equivalent sections of
chromatids – produces new combination of alleles

What is independent assortment?

- in Anaphase I of Meiosis I – the homologous pairs of chromosomes separate

- in Anaphase II of Meiosis II – the chromatids separate
- independent assortment produces a mix of alleles from paternal and maternal
chromosomes in gamete
What happens to DNA mass in meiosis? quarters

What happens to Chromosome number in meiosis? halves (haploid)

What is Mutation?

 Change in DNA
 2 types: Chromosome Mutation and Gene Mutation

What causes mutation? random or due to mutagens (e.g. chemicals, radiation)

What is a Chromosome Mutation?

 In plants, inherit more than one diploid set of chromosomes – called polyploidy
 In animals, homologous pair of chromosome do not separate in meiosis, so either inherit
one extra or one less chromosome – called non-disjunction

What is a Gene Mutation?

 a change in the base sequence of DNA

 2 types = substitution and insertion/deletion
 substitution = replace one base for another, changes one triplet code
can be silent (new triplet code codes for same AA), mis-sense (codes for a different
AA, so protein shape changes slightly), non-sense (codes for a stop codon, so
polypeptide chain not produced)
 insertion = adding a base, deletion = removing a base
both insertion/deletion causes frameshift, all the triplet codes after the mutation
changes, so normal polypeptide chain/protein not produced
Module 5 (Energy) Revision Notes

What is the source of energy for an ecosystem? sunlight

What is the role of producers, consumers, decomposers in an ecosystem?

 producers = plants, perform photosynthesis, use light energy to make biological

molecules
 consumers = animals, cannot make their own biological molecules, need to eat plants
(primary consumers) or other animals
(secondary/tertiary consumers) to obtain biological
molecules
 decomposers = bacteria and fungi, perform saprobiotic decomposition,
release enzyme onto dead plants/dead animals/animal
waste (organic matter) breaking them down to obtain
biological molecules

Why do producers (plants) need biological molecules?

 Glucose = respiration, store as starch, make cellulose

 Amino Acids = make proteins e.g. enzymes
 Fatty Acid & Glycerol = make triglyceride as energy store, make phospholipid for
membranes

Why do consumers (animals) need biological molecules?

 Glucose = respiration, store as glycogen

 Amino Acids = make proteins e.g. enzymes
 Fatty Acid & Glycerol = make triglyceride as energy store and insulation/protection,
make phospholipid for membranes

Why do decomposers (bacteria/fungi) need biological molecules?

 Glucose = respiration
 Amino Acids = make proteins e.g. enzymes
 Fatty Acid & Glycerol = make phospholipid for membranes

How do organisms carry energy?

 Main Source = Glucose

 Stored as Starch in plants and Glycogen in animals
 Alternative Source = Lipids/Fats/Triglycerides and Proteins

How does energy move through an ecosystem? by the food chain, begin with producer and then
moves onto primary consumer, then secondary consumer, then tertiary consumer – with
decomposers occurring at each stage (trophic level)

Why is all the light energy not utilised by plants in photosynthesis? only 2% is used in
photosynthesis – of the rest, a certain part misses the chloroplast, the other parts would be reflected
or the wrong wavelength
Why is energy lost along a food chain?

 not all the glucose made by producers is stored as starch or used to build biomass, as a
certain part is lost in respiration (as heat)
 not all the stored energy in the plant is transferred to primary consumers as certain parts
of the plant are inedible and indigestible (available to decomposers)
 of the energy the primary consumer obtains, a certain amount is used in respiration, the
rest is stored as glycogen and used to build biomass
 not all this stored energy is transferred to secondary consumers due to inedible parts and
indigestible parts (available to decomposers)
 only 10% of energy is transferred from producer to primary consumer
 only 20% of energy is transferred from consumer to consumer
 the losses are due to respiration, inedible parts, indigestible parts
 higher proportion is transferred from consumer to consumer because consumers are
more edible and digestible, producers are made up of cellulose
 the higher consumers have the highest respiratory losses as they have increased
movement (hunt for food)

Effect of energy loss on a food chain? places a limit on the length of a food chain, those at the
higher trophic levels (just quaternary consumers) would not obtain enough energy from the food it
consumes

What is Productivity?

 Productivity = Amount of Glucose/Energy available to organism

 Primary Productivity = Amount of Glucose/Energy available in Plants
 Secondary Productivity = Amount of Glucose/Energy available in Animals
 Net Productivity = Gross Productivity – Respiratory [and Faeces] Losses
 Gross Primary Productivity is amount of glucose made by plant in photosynthesis,
Net Primary Productivity is amount of glucose stored as starch after respiration
 Gross Secondary Productivity is amount of glucose consumed by animal,
Net Secondary Productivity is amount of glucose stored as glycogen after respiration
 in all cases, net productivity is the glucose/energy available to organisms at next stage of
food chain
 respiratory losses are higher in consumers then producers due to movement
 and respiratory losses are higher in secondary/tertiary/quaternary consumers then
primary consumers as they move more to hunt for food
 and respiratory losses are higher in consumers that have to maintain a constant body
temperature (endotherms)

What does a Pyramid of Number represent?

 number of each type of organism at each trophic level – the numbers decrease as we
move up trophic levels due to the loss of energy (not as many individuals can be
supported)
 can look inverted when it does not take into account mass (e.g. 1 oak tree or millions of
fleas)
What does a Pyramid of Biomass represent?

 biomass of each type of organism at each trophic level

 biomass = mass of living tissue (based on dry mass, water excluded)
 biomass includes biological molecules, organelles, cells, tissues, organs
 units for biomass (g per m2 for land based animals, g per m3 for water based animals)
 so as we move along a food chain (up trophic levels) there is a loss of energy due to
respiration/inedible parts/indigestible parts, so there is less energy to build biomass, so
biomass decreases

What does a Pyramid of Energy represent?

 amount of energy found at each trophic level

 as before, loss of energy occurs along a food chain (respiration, inedible parts,
indigestible parts)

What are the units for energy? kJ/m2 /year

What is photosynthesis?

 using light energy to make glucose (and other biological molecules)

 occurs in plants and algae (both have chloroplast)

Adaptation of plant for photosynthesis?

 leaf located near top of plant = closer to light

 leaf is thin and wide = large surface area for light, short diffusion distance for CO2
 has many veins = connect to xylem to bring in water
 has stomata for gas-exchange (CO2/O2)
 has air spaces to support ease of gas-exchange
 palisade cells located near top of leaf close to the light
 palisade cells are large = large surface area for light
 palisade cells have a thin cell wall = short diffusion distance for CO2
 palisade cells contain many chloroplasts (site of photosynthesis)
 palisade cells have a large vacuole = pushes chloroplast to edge of cell closer to light

Structure of chloroplast?

 site of photosynthesis
 has a double membrane (outer and inner)
 contains discs called thylakoids (contain chlorophyll)
 a stack of thylakoids = granum
 thylakoids are surrounded by a fluid material called stroma

How does photosynthesis take place?

 In 2 stages
 light dependent stage = on thylakoids, makes ATP and reduced NADP
 light independent stage = in stroma, uses the ATP and reduced NADP to make glucose
Describe the light dependent stage?

 light hits chlorophyll

 chlorophyll absorbs the light if correct wavelength
 electrons become excited and are lost from the chlorophyll (photoionisation)
 electrons enter an electron carrier system
 electrons move down the system releasing energy
 this pumps protons from stroma into thylakoid space
 protons accumulate in thylakoid space, then diffuse back into stroma
 they pass though ATP Synthase which joins ADP and Pi to make ATP
(mechanism = chmeiosmosis, process = photophosphorylation)
 the electron ends up by joining with NADP to form reduced NADP
 light also hits water
 causes photolysis (breakdown of water due to light)
 forms: H+, e-, O2
 the H+ joins with the reduced NADP (now carries a hydrogen atom: H+ and e-)
 the e- replaces electrons lost from chlorophyll
 O2 given off as waste

Describe the light independent stage?

 involves the calvin cycle

 RuBP (5 carbon) joins with CO2 to make 2 lots of GP (3 carbon)
 the GP is reduced into TP (3 carbon)
 this uses energy from ATP and hydrogen atom from reduced NADP
 the TP can be used to reform RuBP (uses energy from ATP)
 the TP can also be used to form glucose (carbohydrate)
 GP can also be used to form amino acids (proteins) and fatty acids
 TP can also be used to form glycerol
 fatty acids and glycerol will form a lipid
 photosynthesis/calvin cycle = produces all the main biological molecules

What are the limiting factors for photosynthesis? factors that limit the rate of photosynthesis,
when these factors are increased – the rate of photosynthesis increases, these are Light and CO2 and
Temperature

Effect of limiting Light on the calvin cycle?

 RuBP decreases – being converted into GP but not being reformed from TP (no ATP)
 GP increases – not converted into TP (no ATP/reduced NADP) but is being formed from
RuBP

Effect of limiting CO2 on the calvin cycle?

 RuBP increases – not converted into GP (no CO2) but is being reformed from TP
 GP decreases – not being formed from RuBP (no CO2) but being converted into TP
What is the compensation point in plants?

 the point in the day (light intensity) when the CO2 taken in by photosynthesis equals the
amount given out by respiration = no net gas exchange
 at low light intensity: rate of respiration > rate of photosynthesis [CO2 released]
 at high light intensity: rate of photosynthesis > rate of respiration [CO2 absorbed]

How to measure rate of photosynthesis?

 measure amount of CO2 used or measure amount of O2 produced, in a certain time

 one method = photosynthometer

How does a photosynthometer work?

 measures amount of O2 produced

 uses aquatic plants (e.g. elodea), as the O2 produced can be observed and collected
 the plant is surrounded in sodium hydrogencarbonate solution (CO2 source)
 the plant is kept in darkness before experiment runs (uses up all the O2 in the plant)
 as the experiment runs, O2 will be produced, this will be collected in a capillary tube
 the amount collected can be measured, this will be converted into a volume by
multiplying length of oxygen bubble collected by πr2
 volume of O2 collected can then be divided by time to calculate rate of photosynthesis

Structure of ATP?

 Adenosine Triphosphate
 made from 1 adenosine and 3 phosphates
 energy carrier molecule
 formation: ADP + Pi (+ energy used) = ATP
 condensation reaction using enzyme ATP Synthase
 carries energy in its bonds
 breakdown: ATP = ADP + Pi (+ energy released)
 hydrolysis reaction using enzyme ATPase
 delivers energy after breakdown

How can ATP be formed?

 photophosphorylation (light dependent stage of photosynthesis)

 substrate-level phosphorylation (glycolysis and krebs cycle of respiration)
 oxidative phosphorylation (electron transport chain of respiration)

What makes ATP (from respiration) a good source of energy?

 immediate source = need to only break one bond to release energy (plus bond is weak)
 manageable source = releases small amount of energy

Uses of ATP (made by respiration) in organisms?

 protein synthesis
 organelle synthesis
  DNA replication
 cell division (mitosis/meiosis)
 active transport
 metabolic reactions
 movement (e.g. muscle contraction)
 maintaining body temperature

What is respiration?

 releasing energy from glucose to make ATP

 ATP will provide energy for life processes
 occurs in all living organisms
 ATP can be made by substrate-level phosphorylation (glycolysis & krebs cycle) and
oxidative phosphorylation (electron transport chain)

What are the 2 types of respiration? aerobic (with oxygen) and anaerobic (without oxygen)

Describe Aerobic Respiration?

1. occurs in 4 stages: Glycolysis, Link Reaction, Krebs Cycle, Electron Transport Chain
2. glycolysis takes place in cytoplasm of the cell
3. link reaction and krebs cycle take place in matrix of mitochondria
4. electron transport chain takes place on inner membrane of mitochondria (cristae)
5. the main job of the first 3 stages are to provide reduced NAD and reduced FAD for the
last stage, this is where most of the ATP is made by oxidative phosohorylation

 glycolysis
 uses glucose to produce 2x pyruvate, 2x ATP, 2x reduced NAD
 pyruvate enters link reaction
 ATP made by substrate-level phosphorylation
 reduced NAD used in ETC

link reaction
uses pyruvate to produce acetylcoenzyme A, reduced NAD, CO2
pyruvate + coenzyme A + NAD = acetylcoenzyme A + reduced NAD + CO2
acetylcoenzyme A used in krebs cycle
reduced NAD used in ETC
CO2 given off as waste

 krebs cycle
 uses acetylcoenzyme A to produce 3x reduced NAD, 1x reduced FAD, 1x ATP, 2x CO2
 reduced NAD and reduced FAD used in ETC
 ATP made by substrate-level phosphorylation
 CO2 given off as waste

 electron transport chain

 reduced NAD and reduced FAD release the hydrogen atom (H+/e-) they are carrying
 the H+ build up in the matrix of the mitochondria
 the e- enter the ETC
 the electron (e-) moves along the chain releasing energy, this pumps the protons (H+)
from the matrix into the intermembranal space
  the H+ build up in the intermembranal space, then diffuse back into the matrix via a
transport protein carrying ATP Synthase enzyme
 this leads to the production of ATP = oxidative phosphorylation
 oxygen is used as a final electron acceptor and proton acceptor
 it removes the electron from the end of the ETC, so the ETC can continue
 it removes the proton from the matrix, hence maintaining concentration gradient
 it becomes water

Describe anaerobic respiration?

 no oxygen present, so no final electron acceptor and proton acceptor

 ETC stops
 Krebs Cycle and Link Reaction also stop as NAD amd FAD are not reformed in ETC
 Glycolysis can continue as it reforms its own NAD
 so Anaerobic Respiration only relies on Glycolysis (making 2x ATP by substrate-level
phosphorylation
 NAD is reformed from the reduced NAD made in glycolysis
 the reduced NAD donates its hydrogen atom (H+/e-) to pyruvate to reform NAD
 in animals the pyruvate becomes lactate (lactic acid)
 in plants/yeast the pyruvate becomes ethanol and CO2

How to measure rate of respiration?

 measure amount of O2 used or measure amount of CO2 produced, in a certain time

 one method = respirometer

How does a respirometer work?

 measures amount of gas exchange taking place between organism and the air in a test
tube
 the test tube is connected to a manometer (a U-shaped tube that contains a coloured
liquid)
 if the organism takes in more gas then it gives out (more O2 in), the amount of air in the
test tube decreases, therefore there will be less pressure on the coloured liquid in the
manometer, therefore the coloured liquid will move towards the test tube
 if the organism gives out more air than it takes in (more CO2 out), the amount of air in
the test tube increases, therefore there will be more pressure on the coloured liquid in the
manometer, therefore the coloured liquid will move away from the test tube
 the amount/volume by which the coloured liquid moves represents the volume of gas
taken in or given out

What are the Respiratory Substrates?

 Carbohydrates, all forms of carbohydrates (starch/glycogen/lactose/sucrose) are turned

into glucose
 Proteins, excess amino acids are converted into keto acid
[keto acid turned into pyruvate and intermediates of krebs cycle]
 Lipids, provided fatty acids and glycerol
[fatty acids become acetylcoenzyme A, glycerol becomes triose phosphate]

What is the value of Nitrogen to organisms? used to make amino acids & proteins and
 used to make nitrogenous bases in DNA

Describe the nitrogen cycle?

 nitrogen present in the atmosphere as nitrogen gas (N2)

 N2 cannot be absorbed by plants, they can only absorb Nitrate ions (NO3-)
 N2 converted into Ammonium Ions (NH4+) by nitrogen fixation by nitrogen-fixing
bacteria
 there are 2 types of NFB: mutualistic and free-living
 mutualistic NFB are found in the root nodules of leguminous plants, they place the NH4+
ions directly in the roots – these plants can use this to make AA and nucleotides
 free-living NFB are found in the soil – they place NH4+ ions in the soil
 NH4+ ions cannot be absorbed by plants therefore is converted into NO3- by nitrification
by nitrifying bacteria
 Ammonia ions (NH4+) into Nitrite ions (NO2-) into Nitrate ions (NO3-)
 the NO3- ions will be absorbed by plants to make AA/proteins and nucleotides/DNA
 consumers can eat the plant to obtain the AA and nucleotides
 organic material (dead plants, dead animals, animal waste) are broken down by
saprobiotic decomposers, this releases Ammonia ions (NH4+) back into the soil by a
process called ammonification
 Nitrate ions (NO3-) can be converted back into Nitrogen gas (N2) by denitrification by
denitrifying bacteria – they work in anaerobic conditions (when the field is waterlogged
and all the air spaces in the soil are filled with water)

What is the value of Phosphorous to organisms? used to make Phospholipid

used to make DNA
used to make ATP

Describe the phosphorous cycle?

 phosphorous present in sedimentary rock as phosphate ions (PO43-)

 when sedimentary rock erodes, leaves soil containing PO43-)
 plants absorb PO43-) to make phospholipid/DNA/ATP
 consumers eat plants to obtain phospholipid/DNA/ATP
 organic material (dead plants, dead animals, animal waste) are broken down by
saprobiotic decomposers, this releases Phosphate Ions (PO43-) back into the soil
 (if soil sediments and hardens, over time, it returns to a rock state)
 [mycorrhize are fungi in the roots of plants to support uptake of scarce minerals like
phosphate ions]

Agricultural ecosystem?

 description for farming ecosystems

 aim of farms is to grow crops and raise animals
 grow crops to sell & feed farm animals
 raise animals to sell meat & other resources (e.g. wool, eggs, milk, leather)

How are crops intensively farmed for high yield?

  select suitable location (sunlight, water, minerals)
 clear area of plants and animals (deforestation – removes competition/pest)
 selectively breed crop
 use greenhouse to provide high levels of light, CO2, temperature
 provide water by irrigation
 add fertilisers (provides minerals = nitrate, phosphate, magnesium)
 control pests
 polyculture/crop rotation (ensures mineral levels in the soil do not become depleted)
 ploughing (adds air spaces to soil, so bacteria involved in nutrient cycles can aerobically

respire)

What are pests? organisms that harm plants/crops – other plants (weeds) acts as competitors,
insects eat the plant, fungi cause disease

How can pests be controlled? pesticides or biological control

What are pesticides? chemical sprays that kill the pest, for weeds = herbicide,
insects = insecticide, fungi = fungicide

Advantages and Disadvantages of using pesticides?

 advantages
 fast acting
 can control area covered
 disadvantages
 non-specific
 non-biodegradable leading to bioaccumulation and toxicity in the higher trophic levels
 pest may be resistant
 needs to be reapplied

What are biological control? using predators or parasites to the pest

Advantages and Disadvantages of using biological control?

 advantages
 specific
 does not cause bioaccumulation
 pests do not develop resistance
 does not need to be reapplied
 disadvantages
 slow acting
 may become a pest itself
 cannot control area covered

What is Bioaccumulation?
  Pesticides are not biodegradeable
 therefore, they remain stored in organism's tissues
 therefore, they accumulate along a food – up trophic levels
 therefore, they are toxic to consumers at higher trophic levels

What is an integrated pest control system?

 makes use of both pesticides and biological control – the aim is to reduced the amount of
pesticide used, as the pesticide harms food chains and ecosystems
 process:
 keep some native trees (will act as natural habitats to natural biological controls)
 monitor area for pests
 mechanically remove pests if present
 initial dose of pesticide – fast acting
 then apply biological control – will increase in number over time and provide long term
control
 reapply pesticides whenever there is an uncontrollable outbreak

What minerals do fertilisers provide?

 nitrate = make AA, make nitrogenous bases

 phosphate = make ATP, DNA, phospholipids
 magnesium = make chlorophyll

What are the 2 types of fertilisers?

 natural/organic = applying dead plants, dead animals, animal waste (decomposed leading
to ammonification, followed by nitrification to provide source of NO3-)
 artificial/chemical = spraying on concentrated solutions of the minerals

Natural vs Artificial Fertilisers?

 Natural = reduced risk of leaching/eutrophication but slower release of minerals

 Artificial = faster release of minerals and higher concentration but risk of
leaching/eutrophication and lowers water potential of soil
(so plant absorbs less water by osmosis)

What is the benefit of ploughing? increases amount of air spaces in the soil, supports aerobic
respiration of decomposers and bacteria involved in nitrogen cycles (nitrogen fixing bacteria &
nitrifying bacteria preveting denitrifying bacteria)

What is eutrophication?

 if large amounts of chemical fertilisers are sprayed onto fields and heavy rainfall occurs,
the fertiliser may leach into local water sources
 the fertiliser will travel and build up in ponds or lakes
 the mineral (e.g. nitrates to make AA) will be absorbed and used by Algae
 this will lead to an increase growth of algae = algal bloom
 the algae grows on the upper surface of the water, this prevents light reaching the plants
at the bottom of the water
  these plants cannot photosynthesise, so die
 these provide more nutrients to saprobitoic decomposers, so these increase in number
 the decomposers will aerobically respire, using up the oxygen in the water
 therefore fish die as less oxygen is available

Environmental impact of Crop Farming?

 Deforestation = reduces species diversity, reduces plant species diversity, less habitats
and food sources, reduces animal species diversity
 Monoculture = one type of plant/crop grown, depletes certain nutrients in the soil (no
time provided for nutrient levels to recover)
 Selective Breeding = reduces genetic diversity of crop (reduces variation, reduces ability
to adapt to changes in the environment)
 Pollution = bioaccumulation of pesticides, eutrophication from chemical fertilisers

Reducing Environmental impact of Crop Farming?

 keep some native trees (helps to maintain species diversity)

 keep hedgerows (help to maintain species diversity + absorb chemical fertilisers
reducing eutrophication)
 polyculture (grow different crops at different times of the year, allows depleted nutrients
to recover in the soil)
 keep seeds of wild crop (maintain genetic diversity, use if environment changes)
 use biological control for pests & natural fertiliser for minerals

How are animals (domestic livestock) intensively reared in farming?

 selectively bred
 given predigested food (enzymes added), with high protein and high energy levels
 given antibiotics and vaccinations
 given steroid hormones
 restricted movement and kept warm (reduce energy loss)

Natural Ecosystem vs Agricultural Ecosystem (farms)?

 natural = light energy source, agricultural = light + food for farmer + fossil fuel for
machines
 natural = high biodiversity, agricultural = low
 natural = high species diversity, agricultural = low
 natural = high genetic diversity, agricultural = low
 natural = low productivity, agricultural = high
 natural = nutrients recycled, agricultural = nutrients added (fertiliser)
 natural = competition/predators control pests, agricultural = pesticides/biological control
 natural = reaches climax community, agricultural = prevent climax from being reached
Module 6 (Response to Stimuli) Revision Notes

What is a Stimuli? a change in the internal or external environment

Why do Organisms need to Respond to Stimuli? for survival (predator/prey awareness,

homeostasis)

How do Simple Organisms Respond to Stimuli? Taxis and Kinesis

What is Taxis? directional response to a stimuli (towards or away from)

What is Kinesis?

 non-directional movement from an unfavourable area to a favourable area

 organism moves rapidly and randomly in unfavourable area until they reach favourable
area where they move slowly and less randomly
 so spends more time in favourable area, less time in unfavourable area

Example of Response to Stimuli in Plants? Tropism

What is Tropism?

 directional growth in plants in response to a stimuli

 towards = positive, away = negative
 light = photo, water = hydro, gravity = geo
 shoot shows positive phototropism and negative geotropism
 root shows positive geotropism and positive hydrotropism
 controlled by a Plant Growth Factor = Indoleacetic Acid (IAA) - auxin

What is a Plant Growth Factor?

 equivalent to animal hormones

 difference: made by cells throughout the plant, only affects cells locally, affects growth

What are the affects of IAA? promotes growth in the shoot, inhibits growth in the root

How does positive phototropism in the shoot take place?

 normally: shoot tip produces IAA, sending it down both sides causing the shoot to grow
forwards
 if light is present on one side, the IAA redistributes to the opposite side (shaded side)
 this causes the opposite side to grow faster
 so the shoot bends towards the light

How does negative geotropism in the shoot take place?

 if gravity is present on one side, the IAA redistributes to the same side
 this causes the same side to grow faster
 so the shoot bends away from gravity towards the light
How does positive geotropism/hydrotropism in the root take place?

 if gravity/water is present on one side, the IAA redistributes to the same side
 this causes the same side to grow slowly, so the opposite side grows faster
 so the root bends towards the gravity/water

Evidences for Tropism (positive phototropism in shoot)?

 removing or covering shoot tip prevents tropism [tip causes tropism]

 placing micin (prevents movement of chemicals e.g. IAA) across shoot inhibits tropism
[tropism caused by movement of chemicals]
 placing gelatine (prevents movement of electrical signals) across shoot does not affect
tropism [tropism not caused by movement of electrical signals]
 if shoot tip is moved to one side, that side grows faster and the shoot bends the other
way [IAA promotes growth in shoot]
 when in light or darkness the overall levels of IAA remain the same [light does not
inhibit or breakdown IAA but rather redistributes it]

Response to Stimuli in Mammals? uses Nervous System, Hormonal System

(nervous and hormonal systems coordinate response to stimuli)

Job of Nervous System? coordinate response to certain stimuli – response is fast, short acting,
localised
Pathway of Nervous System?

stimuli to receptor to sensory neurone to spinal cord to brain to spinal cord to motor neurone
to effector for response

What does a Receptor do?

 detects stimuli
& converts stimuli energy into nerve impulse
(acts as a transducer – converts one type of energy into another)
 each type of stimuli has a specific receptor
 uses stimuli energy to send Na+ ions into the start of the sensory neurone
 2 examples of receptors: Pacinian Corpuscle, Retina of Eye

What does a Pacinian Corpuscle do?

 touch receptor
 found in skin, fingers and toes
 responds to pressure/touch
 structure = corpuscle (several layers of tissue) wrapped around the start of a sensory
neurone
 process = pressure applied, corpuscle compressed, stretch-mediated Na+ channels
opened, Na+ ions move into the start of the sensory neurone
How does the Retina of the Eye work?

 detects light so the brain can generate an image

 detected by retina (located at back of eye)
 made of Cone and Rod cells
 Cone Cells detect high light intensity only, produces colour image, with high visual
acuity
 Rod Cells can detect low light intensity, produces black and white image, with low
visual acuity
 Cone Cells located in centre of retina (fovea) – site of high light intensity
 Rod Cells located in periphery of retina

Properties of Cone Cells in Retina?

 made of Iodopsin Pirgment which is only broken down at high light intensity
 one cone cell connects to one bipolar neurone which connects to one sensory neurone
(therefore no summation of light can take place so only detects high light intensity)
 but because one cone cell connects to one bipolar neurone which connects to one
sensory neurone, each stimuli can be distinguished = high visual acuity

Properties of Rod Cells in Retina?

 made of Rhodopsin Pigment which can be broken down at low light intensity
 a few rod cells connect to one bipolar neurone which connects to one sensory neurone
(therefore summation of light can take place so can detect low light intensity)
 but because a few rod cells connect to one bipolar neurone which connects to one
sensory neurone, the stimuli will be merged together = low visual acuity

What is the Central Nervous System (CNS)?

 made of brain and spinal cord

 brain = analyses and coordinates response to stimuli
 spinal cord = connects brain to sensory and motor neurones

What is the Peripheral Nervous System (PNS)?

 made of the sensory and motor neurone

 a neurone transmits a nerve impulse
 sensory neurone takes nerve impulse from receptor to CNS
 motor neurone takes nerve impulse from CNS to effector
 sensory neurone has its cell body in the middle and has a dendron and axon
 motor neurone has its cell body at the start and only has a long axon

What are the 2 different types of Motor Neurone?

 Voluntary (Somatic) and Involuntary (Autonomic) Motor Neurones

 Somatic supplies skeletal muscle = under conscious control
 Autonomic supplies cardiac muscle, smooth muscle, glands = under subconscious
control
 Autonomic can be divided into Sympathetic and Parasympathetic (have opposite effects)
What is a Nerve Impulse?

 movement of an action potential along a neurone

 action potential = change in membrane potential (charge' in one section of the neurone
 changes from negative (polarised) to positive (depolarised) back to negative
(repolarised/
hyperpolarised)
What is Resting Potential?

 membrane potential of neurone at rest

 is -65mV
 polarised
 caused by having more positive ions outside neurone compared to inside
 involves Na+/K+ pump, pumping 3 Na+ ions out, 2 K+ ions in
 K+ channel allowing K+ ions to diffuse out
(K+ ions will eventually stop diffusing out due to a positive potential outside)

What happens during an Action Potential?

 stimuli causes Na+ ions to enter the start of the neurone

 makes membrane potential less negative
 if it reaches threshold (-50mV), Na+ channels open
 therefore more Na+ ions diffuse into the neurone, therefore membrane potential becomes
positive (depolarised)
 the membrane potential reaches +40mV
 then the Na+ channels close, the K+ channels open
 therefore K+ ions diffuse out, therefore membrane potential becomes negative
(repolarised)
 too many K+ ions move out, so the membrane potential becomes more negative than
normal (hyperpolarised)
 one action potential = depolarisation, repolarisation, hyperpolarisation

How does an Action Potential move along a Neurone?

 by local currents
 if the stimuli energy is large enough and enough Na+ ions enter the start of the neurone,
threshold will be reached and an AP will occur
(the 1st AP is called a Generator Potential)
 Na+ ions that move in during depolarisation of the generator potential diffuse along the
neurone causing the next section to reach threshold and an AP to occur
 this process continues along the neurone

* an AP will always move along the neurone to the end

* why does AP not move back? because previous section has just finished an AP, therefore it
is in refractory period (Na+ channels cannot be opened) and is hyperpolarised (therefore
threshold cannot be reached)
How does the Size of Stimuli affect a Nerve Impulse?

 does not affect size of AP

(AP is all or nothing – reach threshold = get AP [all]
do not reach threshold = no AP [nothing])
 larger stimuli increases the frequency (number) of APs

What affects Speed of Nerve Impulse?

 temperature = higher temp, higher kinetic energy, faster rate of diffusion of ions
(faster nerve impulse)

 axon diameter = wider diameter, neurone less leaky (faster nerve impulse)

 myelination = schwann cells wrap around axon, insulates axon preventing AP, therefore
AP only occurs in gaps – called node of ranvier, so AP jumps from node
to node = saltatory conduction (faster nerve impulse)

What is a Synapse?

 connection between 2 different neurones

 sends nerve impulse across the gap (synaptic cleft) using neurotransmitters
(e.g. acetylcholine)
 AP arrives in end of presynaptic neurone
 Ca2+ channels open
 Ca2+ ions enter presynaptic neurone
 causes vesicles containing neurotransmitter to move to presynaptic membrane
 vesicle binds to membrane releasing neurotransmitter into cleft
 neurotransmitter diffuses across cleft
 binds to complementary receptors on postsynaptic membrane
 Na+ channels open, Na+ ions enter
 if threshold is reached, AP occurs

(to return to rest: enzyme used to breakdown neurotransmitter, e.g. acetylcholinesterase

breaksdown acetylcholine into ethanoic acid and choline, diffuses back into presynaptic
neurone, ATP used to reform neurotransmitter into vesicle and actively transport Ca2+ ions
out)

What are the Properties of Synapses?

 unidirectionality = AP/nerve impulse travels in one direction, from pre to post, pre has
the neurotransmitter, post has the receptors

 filters out low level stimuli = low level stimuli do not release enough neurotransmitter,
therefore not enough Na+ ion channels open, therefore not enough Na+ ions enter
postsynaptic neurone for threshold to be reached, therefore no AP produced

 summation = low level stimuli add together to release enough neurotransmitter to

produce an AP in postsynaptic neurone, can be temporal or spatial
temporal = low level stimuli present for extended period of time
spatial = a low level stimuli from a few presynaptic neurones add together
  inhibitory = normal synapses are excitatory (cause AP), some can be inhibitory – prevent
action potential from occurring by making postsynaptic neurone hyperpolarised

What is a Reflex?

 a rapid involuntary response to a stimuli

 does not use the brain
 the sensory neurone connects directly to motor neurone
(stimuli to receptor to sensory neurone to relay neurone to motor neurone to effector for response)
 ensures less damage done and does not require learning

How is Heart Rate controlled?

6. the heart is myogenic, its heart beat is initiated by the SAN

7. the Medulla Oblongata in the brain can increase or decrease heart rate
8. receives nerve impulse from chemoreceptors (respond to blood pH) in the carotid
arteries and pressure receptors (respond to blood pressure) in the carotid arteries and
aorta
9. sends impulse in sympathetic nerves to SAN to increase HR and sends impulse in
parasympathetic nerves to SAN to decrease HR

How does Exercise affect Heart Rate?

 exercise = muscle contraction, which requires respiration

 therefore, waste product CO2 is released into blood
 this lower pH of blood (acidic)
 this is detected by chemoreceptors in carotid arteries
 sends impulses to medulla oblongata
 then medulla oblongata sends impulses to SAN via the sympathetic nerves causing the
heart rate to increase
 benefit = increase blood flow to lungs to remove CO2 and take in O2

How does Low Blood Pressure affect Heart Rate?

if a person moves from lying/sitting to standing, blood pressure falls (reducing blood flow to
the brain)
this is detected by pressure receptors in the carotid arteries and aorta
sends impulses to medulla oblongata
then medulla oblongata sends impulses to SAN via the sympathetic nerves causing the heart
rate to increase
benefit = increasing heart rate leads to an increase in blood pressure (so enough blood can
reach the brain)

What are the different types of Muscles?

 Skeletal
 Smooth
 Cardiac
What is the job of the Skeletal Muscle?

 moves the body skeleton

 when the muscle contracts (shortens) the tendon pulls on joints causing movement

Structure of Skeletal Muscle?

 basic structure = sarcomeres

made up of actin and myosin, actin is thin and has tropomysosin wrapped around it,
myosin is thick and has heads, when the sarcomere contracts the whole muscle
contracts, contracts/shortens by the sliding filament mechanism
 many sarcomeres = myofibril
 many myofibrils = muscle fibre
surrounded by a membrane called sarcolemma
contains myofibrils, fluid called sarcoplasm and tubes called sarcoplasmic reticulum
 many muscle fibres = bundle
 many bundles = whole muscle

Locations in a Sarcomere?

 A band = location of myosin [no change in contraction]

 I band = location between the myosin [shortens in contraction]
 H zone = location between the actin [shortens in contraction]
 Z line = end line of sarcomere [moves closer together in contraction]

What occurs in Sliding Filament Mechanism?

 how the sarcomere shortens

 the myosin heads pull the actin inwards
 the somatic motor neurone connects to the skeletal muscle via a neuro-muscular junction
 one motor neurone connects to a few muscle fibres = motor unit
(benefit = simultaneous muscle contraction and can control strength of contraction)
 releases acetylcholine that binds to complementary receptors on the muscle fibre
membrane (sarcomere)
 Na+ channels open, Na+ ions enter the muscle fibre causing depolarisation
 wave of depolarisation travels through sarcoplasmic reticulum
 causes release of Ca2+ ions into the sarcoplasm (fluid surrounding sarcomeres/myofibril)
 this moves the tropomyosin on the actin
 exposes binding sites on the actin
 myosin heads now bind to the actin (form actin-myosin cross bridge)
 a power stroke occurs, the myosin pulling the actin inwards
 ATP attaches to myosin head so it detaches
 ATP brokendown by ATPase to release energy
 causes myosin head to go back to its original position
 so it reattaches, pulling the actin further inwards
Role of Ca2+ ions and ATP in muscle contraction?

 Ca2+ ions causes the tropomyosin to move exposing binding sites on actin
 Ca2+ ions stimulate ATPase
 ATP causes myosin head to detach
 ATP releases energy so myosin head returns to original position
 ATP actively transports Ca2+ ions back into sarcoplasmic reticulum when the muscle is
relaxed

What are the 2 types of Muscle Fibres? Fast Twitch and Slow Twitch

How does Fast Twitch Muscle Fibres work?

 provide powerful but short lasting contractions

 found in biceps and sprinters
 adapted for anaerobic respiration
 has thicker myosin for powerful contractions
 contains more enzymes for anaerobic respiration
 contains phosphocreatine, provides phosphate to ADP to reform ATP

How does Slow Twitch Muscle Fibres work?

 provide less powerful but long lasting contractions

 found in thigh muscles and marathon runners
 adapted for aerobic respiration
 has a rich blood supply
 contains many mitochondria
 contains glycogen
 contains myoglobin (stores oxygen)

Job of the Hormonal System?

 coordinates the response to certain stimuli

 involves chemical messengers released by endocrine glands into the blood (exocrine
glands release substance into open spaces e.g. salivary gland), travels to target cells
causing changes
 protein hormones bind to complementary receptors on target cells, activates enzymes
that convert ATP into Cyclic AMP in the cell, the Cyclic AMP then makes changes in the
cell (=2nd messenger system) e.g. insulin
 lipid hormones enter cells by simple diffusion and cause direct changes e.g. oestrogen

Control of Blood Glucose Levels?

 if high = should be in cells for respiration, also lowers blood water potential
 if low = not enough to supply cells of the brain, also increases blood water potential
 controlled by the Pancreas
 contains the Islets of Langerhans
 made of alpha and beta cells
 alpha cells produce glucagon
 beta cells produce insulin
What happens with High Blood Glucose Levels?

 occurs after a meal

 insulin is released
 most cells in the body have complementary receptors (particularly muscle, liver, brain
cells)
 causes increase in glucose channels and carriers
 glucose taken up and used in respiration
 in muscle and liver cells, glucose also converted into glycogen for storage
(glycogenesis)
 in liver cells, glucose also converted into fat

What happens with Low Blood Glucose Levels?

 occurs after starvation or exercise

 glucagon is released
 only liver cells have complementary receptors
 converts glycogen into glucose (glycogenolysis)
 converts fats and amino acids into glucose (gluconeogenesis)
 glucose is released into blood

Diabetes?

 person loses control of blood glucose levels

 normally high (hyperglycaemia)
 2 types: type 1 and type 2
 type 1 starts at young age, person does not make insulin, beta cells damaged by an
autoimmune disorder (treatment = insulin injections)
 type 2 starts at middle age, person makes insulin but cells are less sensitive, caused by
obesity and diet high in simple sugars (treatment = diet and exercise, drugs, insulin
injection)
 symptoms = tiredness, increase urination, thirst
 diagnosis = high blood glucose levels on random testing & blood glucose levels remain
high following a fasting blood glucose test (person fasts for a number of hours, then
consumes a drink of glucose, should normally rise then decrease due to insulin)

What is Homeostasis?

 maintenance of a constant internal environment (the blood and tissue fluid) in animals
 control body temperature, blood pH, blood glucose levels, blood water levels, blood salt
levels, blood pressure

Homeostasis and Negative Feedback?

the response to the change is to oppose the change to bring levels back to normal
(e.g. body temperature increases – response is to bring it down to normal,
blood glucose levels decrease – response is to increase it back to normal)
What is Positive Feedback? the response to the change is to continue the change (e.g. Na+ ions
entering a neurone stimulating more to enter in depolarisation)

Why do organisms need to Maintain a Constant Body Temperature?

maintain optimum temperature for enzyme activity

What are Endotherms and Ectotherms?

 endotherms = animals that maintain a strict constant internal body temperature

irrespective of external environmental temperature (e.g. mammals)
 ectotherms = animal's internal body temperature maintained more generally and varies
with changes in external environmental temperature (e.g. reptiles)

Benefit of being an Endotherm?

 can maintain activity over a range of settings e.g. early morning or winter

Benefit of being an Ectotherm?

 require less food/energy

How is internal body temperature controlled?

 anatomical, behavioural, physiological changes

 ecotherms mainly rely on behavioural changes
 endotherms mainly rely on physiological changes

Anatomical adaptations in organisms in warm areas?

 small body size = large surface area to volume ratio (lose heat)
 less fur
 less fat
 large extremities e.g. ears/hand/feet (lose heat)

Anatomical adaptations in organisms in cold areas?

 large body size = small surface area to volume ratio

 more fur
 more fat
 small extremities

Behavioural/Physiological changes in Ectotherms?

 warming up = expose to sun, press on warm surface, darker skin colouration to absorb
heat, more respiration in liver, less breathing
 cooling down = shade from sun, press on cold surface, lighter skin colouration,
less respiration in liver, more breathing
Control of Body Temperature in Endotherms?

 controlled by Hypothalamus in the brain

 receives nerve impulse from peripheral thermoreceptors in the skin and
central thermoreceptors in the hypothalamus
 peripheral thermoreceptors monitor changes in external environmental temperature
 central thermoreceptors monitor changes in core body temperature
(blood supplying major organs)

How an Endotherm warms itself up?

 reduce blood flow to the skin surface = vasoconstriction, smooth muscle in arterioles to
the skin contract, lumen narrows, less blood to skin surface, less heat lost from
blood by radiation

 hair on skin stands up = hair erector muscles contract, hairs stand up, traps in air
particles, forms an insulating layer, reduces heat loss

 shivering = involuntary contraction of muscles – friction in sliding filament mechanism

generates heat and respiration generates
heat

 increase respiration in liver = generates heat

How an Endotherm cools itself down?

 increase blood supply to skin surface = vasodilation, smooth muscle in arterioles to the
skin relax, lumen widens, more blood to skin surface, more heat lost from blood
by radiation

 sweating = evaporation of water particles from the skin surface using the heat in the
blood

Structure of Kidneys? Outer region called Cortex, Middle region called Medulla

Role of Kidneys?

filters blood (removes urea, excess salts, excess water – combined known as urine)

Why remove urea? toxic waste product made from excess amino acids

Why remove excess salts and water? maintain correct water potential and pressure in blood

How do Kidneys filter? made up of millions of nephrons

(each nephron filters the blood producing urine)
Structure of Nephron?

1st part = Bowmans Capsules

2nd part = Proximal Convoluted Tubule
3rd part = Loop of Henle
4th part = Distal Convoluted Tubule
5th part = Collecting Duct

Bowmans Capsule?

 start of nephron
 site of ultrafiltration (where blood is filtered)
 occurs between specialised capillaries called Glomerulus and Bowmans Capsule
 glomerulus located in the middle of an arteriole
 afferent arteriole before glomerulus is wide, efferent arteriole after glomerulus is narrow
 so build up of hydrostatic pressure in the glomerulus pushes fluid and small substances
from the glomerulus into the bowmans capsule
 small substances filtered = glucose, amino acids, salts, urea
 only small substances can pass through the 3 layers
(endothelium of glomerulus, basement membrane, podocytes of bowmans capsule)
 results in glomerular filtrate in bowmans capsule
(water + glucose/amino acids/salts/urea)
 the job of the rest of the nephron is to send all the glucose/amino acids and some of the
salts/water back into the blood [reabsorption]

Proximal Convoluted Tubule?

 second part of the nephron

 site of selective reabsorption
 all the glucose/amino acids and some of the salts/water are sent back into blood
(from lumen of PCT, through cells lining PCT, into blood)
how:
 salts (sodium ions) are actively transported from cells lining the PCT into the blood
 this lowers sodium ion concentration in the cells, so sodium ions diffuse from the
lumen of the PCT into the cells
 as sodium ions move, they pull in glucose and amino acids with them via co-
transport
 glucose and amino acids build up in the cell, then diffuse into the blood
 the movement of salt/glucose/amino acids into the blood, lowers it's water potential,
so water follows into blood by osmosis

Loop of Henle?

 third part of the nephron

 site of further water reabsorption
 occurs by hairpin countercurrent multiplier
how:
 sodium and chloride ions are actively transported out of the ascending limb of the
loop of henle into the surrounding medulla of kidney
 this lowers water potential of medulla
 so water moves out of the descending limb of loop of henle (and collecting duct) by
 osmosis into the medulla
 this water then moves into the blood
 the sodium and chloride ions then diffuse into the descending limb of loop of henle
so the above process can be repeated

Distal Convoluted Tubule?

 fourth part of nephron

 site of further salt reabsorption
 corrects required salt balance between blood and urine

Collecting Duct?

 final part of nephron

 site of further water reabsorption and osmoregulation
 end up being left with urine that is sent into the ureter to the bladder
 water reabsorption occurs by the hairpin countercurrent multiplier
 amount of water being reabsorbed is controlled at this stage, this is known as
osmoregulation
 osmoregulation is the process by which the hypothalamus controls water potential of the
blood (an example of homeostasis)
if water levels become low (dehydration):
 osmoreceptors in hypothalamus shrink
 this stimulates the release of ADH from the posterior part of the pituitary gland
 ADH stimulates the cells lining the collecting duct to increase the number of
aqauporins (water channels)
 so more water moves from the collecting duct back into blood
 so less water is lost in the urine
if water levels become high (overhydration):
 less ADH released
 less aquaporins in collecting duct
 less water moves from collecting duct into blood
 more water lost in urine (reduces overhydration)
Module 7 (Population, Evolution, Inheritance) Revision Notes

What is a species? group of organisms with similar characteristics that can interbreed to produce
fertile offspring

What is a population? all the individuals of a particular species in a particular place

What is a community? all the population of different species in a particular place

What is a habitat? the place where an organism lives

What is an ecosystem? a mix of different communities and habitats and how they interact based on
abiotic and biotic factors

What is ecological niche? an organisms role/position in an ecosystem – in terms of its interaction

with abiotic and biotic factors

Why can 2 different species not occupy the same ecological niche? interspecific competition will
take place for the limiting factors/resources (abiotic & biotic factors) – better adapted species will
out compete the other = competitive exclusion principle

How to sample plant species over a large area?

 obtain a map of the area

 divide the map into grids
 select a large number of coordinates using a running mean
 select a random set of coordinates using a random number chart
 in each coordinate place a quadrat
 measure abundance of the plant species in each quadrat = frequency or percentage cover
 calculate average for the whole area

How to sample plants species along a path?

 use a transect
 place a tape along the path, count number of plants touching tape (Line Transect)
 or
 place a tape along the path, at regular intervals along the tape place a quadrat, measure
abundance within the quadrat (Belt Transect)

How to sample animal species in an area?

 mark-release-recapture technique
 set a trap
 capture the animal species [Sample 1]
 mark them (tag or fluorescent marker – ensure its non-toxic and not harmful)
 release them
 after some time (sufficient time for them to mix with the whole population), replace the
trap
 count number in 2nd set [Sample 2] and count the number marked
 estimate population size by: number in sample 1 x number in sample 2
marked in sample 2
Assumptions of Mark-release-recapture technique?

 no births or deaths
 no immigration or emigration
 marked animals mix evenly with population
 mark is not toxic
 mark does not come off
 large population

What are the 3 stages of population growth?

 slow/lag phase: species becomes adapted to new environment

 rapid/log phase: species adapted, abundant resources, doubling with reproduction,
birth rate>death rate
 stationary phase: resources become limited, intraspecific competition occurs,
birth rate = death rate

How are resources/limiting factors grouped?

 abiotic (non-living): light, temperature, water, O2/CO2, minerals, pH, living space
 biotic (living): predator, prey, mates, competition, disease

What is competition? when organisms compete for resources (abiotic and biotic)

What are the 2 types of competition?

 intraspecific: occurs between organisms of the same species, only occurs when resources
become limited, leads to natural selection and adaptation
 interspecific: occurs between organisms of different species, can happen at any time
even if resources are not limited, leads to formation of climax communities

Describe the predator/prey relationship?

 prey increases in number

 more food available for predator
 predator increases in number (more energy available for reproduction & growth)
 predator eats more of the prey
 prey decreases in number
 less food available for predator
 predator decreases in number
 less of the prey are eaten
 prey increases in number [cycle repeats]
What is succession? how an ecosystem changes over time (change in species diversity and habitat
diversity) – relies on environment being made less hostile by present species
via death and decomposition leading to it being outcompeted and replaced by
larger better adapted species

What are the 2 types of succession? primary (occurs on new land) and secondary (occurs on
previously colonised land that has become bare e.g. after a forest fire)

Describe Primary Succession?

 new land appears (glacier retreats exposing rock, lava cools, sand dunes)
 pioneer species settle [adapted to surviving in hostile conditions of bare land]
 pioneer species are:
 producers
 have mutualistic NFB
 asexually reproduce (one parent, genetically identical, faster)
 xerophytes
 handle extreme conditions (extreme wind & extreme temperatures on bare land)
 have wind dispersed seeds (spread wide – reduce competition, find favourable
environments)
 can anchor to land
 over time – the land erodes and soil forms, pioneer species die and decompose adding
humus & nutrients to the soil
 small plants can now grow
 they out compete the pioneer species
 over time – more soil forms, small plants die and decompose adding more humus &
nutrients to the soil
 large plants can now grow, they out compete the small plants
 this process continues until the climax community is reached
 the climax community contains the best adapted species to the environment (they are the
final community, there will be no more succession after them)

Properties of Succession?

 species diversity increases (peaks just before climax – species in climax will out
compete others)
 habitat diversity increases
 environment becomes less hostile
 food chains become more complex & biomass increases

Primary succession vs Secondary succession? secondary succession starts from small plants not
pioneer species (soil and nutrients already present) and secondary succession is faster (soil,
nutrients and seeds already present)

How can conservation be used to prevent succession?

 used to prevent formation of woody forests – either on hill sides (for tourism) and farms
(space for crops)
 involves: deforestation, burning trees, grazing, using pesticides
What is Evolution? change in allele frequency in a population

What are the 2 Types of Evolution? Adaptation and Speciation

What is Adaptation? a species adapting to changes in the environment (e.g. new diseases or
change in climate) – driven by natural selection, where most of the individuals in the species will
have the favourable allele/characteristic for that environment

Process of Adaptation?

 variation in population of species

(genetic diversity/genetic variation/variety in gene pool)
 new alleles arise by random mutation
 environment applies a selection pressure on the population
 those with favourable characteristics/alleles survive, the others die [natural selection]
 the ones that survive will reproduce, passing on their favourable alleles = reproductive
success
 if this happens for many generations, then that characteristic will become most common
– the favourable alleles will become more frequent [adaptation]

What are the 3 types of selection? stabilising and directional and disruptive

What is stabilising selection?

 when the environment favours those with the most common characteristic – those on the
extreme dies out
 the common characteristic increases in proportion
 the range (standard deviation) will reduce

What is directional selection?

 when the environment favours those individuals with characteristics on one of the
extremes
 over time this will become the most common characteristic
 normal distribution will shift to that extreme

What is disruptive selection?

 when the environment changes between both extreme conditions

 hence, individuals on both extremes are favoured at different times and increase in
number
 those in the middle (average) will decrease in number
What is Speciation? process by which new species arise from existing species

What are the 2 Types of Speciation? Allopatric and Sympatric

What is Alloptaric Speciation? speciation driven by geographical isolation

Describe Allopatic Speciation?

 start with a population of species

 variation in the population
 population separated into different groups by geographical isolation
 each group is exposed to different environments/selection pressures
 each group undergoes different directional selections
 therefore each group changes so much in genetic diversity (variety of alleles) that they
can no longer interbreed with each other to produce fertile offspring = different species
 changes include different courtship behaviour or incompatible gametes

What is Sympatric Speciaition? speciation occuring in the same geographical area (driven by
random mutation)

What is inheritance? offspring inheriting a combination of alleles (2 types – paternal/maternal)

for each gene which will help determine characteristics

What is a gene? a section of DNA that codes for a protein

What is an allele? a type/form of a gene

What is a dominant allele? an allele that is always expressed if present

What is a recessive allele? an allele that is only expressed if 2 are present

What is genotype? combination of alleles for a particular gene

What is phenotype? expressed/observed characteristic (if discontinuous – only determined by

genotype, if continuous – determined by genotype and environment)

What is homozygous? having 2 of the same alleles (homozygous dominant – 2 of the same
dominant alleles, homozygous recessive – 2 of the same recessive alleles)

What is heterozygous? having 2 different alleles

What is Monohybrid Inheritance? inheritance dealing with One Characteristic

Examples of Monhybrid Inheritance?

 Dominant/Recessive
 Codominant
 Multiple Allele
 Sex Linkage
What is the Expected Ratio for Monohybrid Dominant/Recessive?

3 Dominant to 1 Recessive

Why are Observed Ratios different from Expected Ratios?

 random fertilisation of gametes

 small sample size
 mutation
 selection

How can 2 parents with a dominant characteristic give birth to a child with a recessive
characteristic? if both parents are Heterozygotes (carriers for recessive allele) they have a 25%
chance of giving birth to a child who is Homozygous Recessive (has the recessive characteristic)

What is co-dominance? when 2 different dominant alleles are inherited, both will be expressed in
the phenotype

What are multiple alleles? when the gene has more than 2 alleles (e.g. blood group)

Alleles for blood group?

 IA, IB, IO
 IA gives A antigen on RBC
 IB gives B antigen on RBC
 IO gives no antigen on RBC
 IA, IB are codominant
 IO is recessive

Genotypes/Phenotype for blood group?

 A = IAIA, IAIO
 B = IB IB, IBIO
 AB = IA IB
 O = IOIO

Can receive blood from whom?

 A = from A & O
 B = from B & O
 AB = from A, B, AB, O
 O = only from O

What is a sex-linked gene? a gene carried on one of the sex chromosomes, normally the X
chromosome

What is an inherited disease? inheriting a mutated allele that leads to production of a faulty
protein, normally a recessive allele (dominant allele will decrease in frequency by natural selection,
recessive allele can be carried by heterozygotes)
What is a sex-linked disease? inheriting a mutated allele carried on one of the sex chromosomes,
normally a recessive allele & normally carried on X chromosome

Why do males have increased chance of inheriting a sex linked disease rather than females?
males only have 1 X chromosome, females have 2 X chromosomes, females can be carriers, males
cannot be carriers

What is Dihybrid Inheritance? inheritance dealing with Two Characteristics

Examples of Dihybrid Inheritance?

 Dominant/Recessive
 Autosomal Linkage
 Epistasis

What is the Expected Ratio for Dihybrid Dominant/Recessive?

9 Dominant/Dominant
3 Dominant/Recessive
3 Recessive/Dominant
1 Recessive/Recessive

What is Autosomal Linkage? 2 Genes (characteristics) carried on the same Chromosome

What is Epistasis? interaction between different genes

What are the 3 Types of Epistasis? Dominant and Recessive and Complementary

What is Dominant Epistasis? dominant genotype on one gene inhibits expression of other gene

What is Expected Ratio for Dominant Epistasis?

12 Epistasis (inhibited)
3 Expressed (dominant)
1 Expressed (recessive)

What is Recessive Epistasis? recessive genotype on one gene inhibits expression of other gene

What is Expected Ratio for Recessive Epistasis?

9 Expressed (dominant)
3 Expressed (recessive)
4 Epistasis (inhibited)

What is Complementary Epistasis? dominant genotype required on both genes to achieve final
product

What is Expected Ratio for Complementary Epistasis?

9 Final Product
7 None
What does Hardy-Weinberg Principle calculate? frequency of an allele in a population

What does the HWP assume? that the frequency will not change over time, based on:

 isolated population
 large population
 random mating
 no mutation
 no selection

What is the HWP?

 p = frequency of dominant allele

 q = frequency of recessive allele
 p + q = 1 (100%, all the population)
 p2 = frequency of homozygous dominant
 2pq = frequency of heterozygous
 p2 + 2pq = frequency of the dominant condition
 q2 = frequency of homozygous recessive (of recessive condition)
 p2 + 2pq + q2 = 1
Module 8 (Genes) Revision Notes

What is a Stem Cell?

 a unspecialised/undifferentiated cell
 potential to form different types of cells

How does a stem cell be come a specialised cell?

 differentiation
 3 changes: cell shape, number of organelles, new content
 occurs by controlling gene expression (some gene are activated, other genes are
inhibited)

Stem Cell in Animals/Mammals/Humans?

 Totipotent = Zygote
 Pluripotent = Embryonic Stem Cells
 Multipotent = Bone Marrow Stem Cell
 Unipotent = Tissues

What are Induced Pluripotent Stem Cells (iPS Cells)?

turning unipotent body cells into pluripotent cells (like embryonic stem cells), involves
activating certain deactivated genes using transcription factors

Stem Cell Therapy in Humans?

 2 uses,
 use stem cells to produce tissues/organs for transplant
 use stem cells to treat irreversible diseases e.g. heart disease, type 1 diabetes, paralysis
(inject stem cells at site of disorder – will differentiate to become local specialised cells
e.g. heart muscle cells, beta cells of pancreas, neurones)

Stem Cell in Plants?

 In embryo = Zygote/Embryonic Stem Cells

 In adult = Meristem Cells in Stem/Shoot/Root

Uses of Stem Cells from Plants?

 traditionally cuttings were taken from plants (stem/shoot/root) and used to grow
genetically identical plants – possible due to presence of meristem cells
 tissue culture (micro propagation) = large scale application of cuttings
 process,
 take cutting from shoot/stem/root (called explant)
 place explant in nutrient rich medium so meristem cells divide by mitosis
 produces a mass of meristem cells (called callus)
 take each meristem cell and grow in plant growth factor medium to promote
differentiation and formation of shoot/root
 transfer plant to soil and greenhouse
  then transfer to field

What is Controlling Gene Expression?

 either Activating or Inhibiting a Gene

 activating gene = protein made
 inhibiting gene = protein not made

Example of activating genes?

 using oestrogen
 oestrogen can enter a cell by simple diffusion and bind to receptors on the transcriptional
factor
 causes transcriptional factor to change shape
 so transcriptional factor can now enter nucleus and bind to promoters on the DNA to
activate transcription
= activated genes (protein to be made)

Example of inhibiting genes?

 using siRNA (small interfering RNA)

 making siRNA = double stranded RNA cut down into small sections, made single
stranded, then attaches to an enzyme
 siRNA will bind to complementary sections on mRNA = the enzyme will cut the mRNA
so translation cannot occur = gene inhibited (protein not made)

What is Epigenetics?

 Heritable changes in gene function without changes to base sequence of DNA

 Changes may due to lifestyle, stress, diet
 Chromatin (DNA-Histone Complex) is surrounded by an Epigenome (chemical layer)
 Epigenome can either cause the Chromatin to become more condensed or more loose
 Chromatin becoming more condensed means transcription factors cannot reach the DNA
and the gene will be inactivated
 Chromatin becoming more loose means transcription factors can reach the DNA and the
gene will be activated
 These changes may be brought about by Acetylation or Methylation

How does Methylation and Acetylation affect the Genome?

 Increased Methylation = adding methyl groups, this attracts proteins which condense the
DNA-Histone Complex so transciption factors cannot gain access (gene inhibited)
 Decreased Acetylation = removing acetyl groups, increases positive charges on the
Histone which increases the attraction to the phosphate groups on DNA which condense
the DNA-Histone Complex so transciption factors cannot gain access (gene inhibited)
What is a Gene Mutation?

 a change in the base sequence of DNA

 2 types = substitution and insertion/deletion
 substitution = replace one base for another, changes one triplet code
can be silent (new triplet code codes for same AA), mis-sense (codes for a different
AA, so protein shape changes slightly), non-sense (codes for a stop codon, so
polypeptide chain not produced)
 insertion = adding a base, deletion = removing a base
both insertion/deletion causes frameshift, all the triplet codes after the mutation
changes, so normal polypeptide chain/protein not produced

What is Cancer?

 formation of a malignant tumour

 due to uncontrolled cell division (mitosis)

Malignant vs Benign Tumour?

Malignant Tumours,

 Rapid Growth (rapidly dividing cells)

 Cells are unspeicialised
 Cells can spread (Metastasis)
 Systemic Effects
 Requires Surgery/Chemotherapy/Radiotherapy

What normally controls Cell Division (mitosis)?

 2 genes: proto-oncogene & tumour-supressor gene

 both produce proteins to control cell division
 proto-oncogene stimulates cell division
 tumour-suppressor gene inhibits cell division
 proto-oncogene produces growth factor and receptor protein, when the growth factor
binds to receptor protein on cells it stimulates DNA replication that leads to cell division
 tumour-suppressor gene produces a protein that inhibits cell division

Cancer?

 caused by mutation of genes that control cell division

 causes of mutation = random or mutagens (chemicals/radiation)
 mutation of proto-oncogene leads to formation of a oncogene = over production of
growth factor or receptor proteins permanently active = over stimulation of cell division
(uncontrolled cell division)
 mutation of tumour-suppressor gene = loss of protein to inhibit cell division
(uncontrolled cell division)
Oestrogen and Cancer?

Oestrogen leads to activation of genes – high levels of oestrogen can lead to over activation
of Proto-Oncogen forming an Oncogene = Cancer (uncontrolled cell division)

Epigenetics and Cancer?

Main Example = increased methylation of tumour suppressor genes leads to inhibition of

tumour suppressor genes leading to cancer (uncontrolled cell division)

What is Genetic Engineering?

 changing the genetic make-up of an organism's DNA by adding or removing a gene

 the DNA becomes Recombinant
 the Organism becomes Genetically Modified (Transgenic)

Why do we Genetically Engineer Animals?

 to give them additional characteristics

 so they can make useful products (proteins)

Examples of genetic engineering in animals?

 additional characteristics,
 add gene for disease resistance
 add gene for growth hormone for growth
 making useful products,
 use to produce anti-thrombin = protein used to make blood clot (people with certain
genetic disease may not produce), use milk producing animal to produce, add gene for
anti-thrombin next to milk producing gene in animal, therefore anti-thrombin protein
will be made in the milk (easily extracted)

Why do we Genetically Engineer Plants?

 to give them additional characteristics

 so they can make useful products (proteins)

Examples of genetic engineering in plants?

 additional characteristics,
 add gene for disease resistance
 add gene for pest resistance
 add gene for pesticide resistance
 add gene to promote growth for high yield
 produce genetically modified tomatoes = prevented from softening therefore remain
hardened (easy for storage and transport), involves preventing formation of softening
enzyme, a gene is added that is complementary to the the softening enzyme gene, so its
mRNA will bind to the mRNA of the softening enzyme preventing translation of the
softening enzyme
 making useful products,
  use to make golden rice (rice that contains beta-carotene, a pre-cursor to vitamin A to
treat malnutrition deficiency)
 use to make protein raw material for polymers

Why do we Genetically Engineer Bacteria? so they can make useful products (proteins)

Genetically engineering bacteria?

 to make useful proteins e,g, Insulin

 normally used animal sources (problems = limited supply, infection risk,
immunorejection)
 involves adding human insulin gene to a plasmid, then inserting this into a bacteria = the
bacteria now has the gene/code to produce the human insulin protein

involves 5 steps =

1. Isolation, 2. Insertion, 3. Transformation, 4. Identification, 5. Growth/Cloning

1. Isolation

 either by Reverse Transcriptase or Restriction Enzyme or Gene Machine

 RT = enzyme found in virus, converts RNA into DNA, obtain mRNA for insulin, the RT
will convert it into cDNA (single stranded complementary DNA), DNA Nucleotides and
DNA Polymerase added to make it double stranded
 RE = enzyme found in bacteria, cuts DNA at certain base sequences (called recognition
sites) by breaking bond between sugar and phosphate, can cut straight or staggered,
staggered used in GE as it leaves exposed bases called 'sticky ends' [cuts staggered at 6
base pair palindromes, were the 6 bases read forward are identical to 6 bases read
backward on both strands]
 GM = build DNA base sequence from know Amino Acid Sequence of the Protein (uses
oligosacchairdes)

end result = Isolated Human Insulin Gene

2. Insertion

 cut plasmid using the same RE from isolation stage

 leaves complementary sticky ends
 join human insulin gene with plasmid via the sticky ends
 use DNA Ligase to join the sugar-phosphate backbone

= Recombinant plasmid (carrying human insulin gene)

3. Transformation

 mix recombinant plasmid with bacteria

 add Ca2+ ions and heat shock
 bacteria will become permeable and take up the recombinant plasmid

= Genetically Modified Bacteria (carrying recombinant plasmid with human insulin

gene)
4. Identification

 identify which of the bacteria have taken up the recombinant plasmid and of these which
ones have accepted the new gene (human insulin gene)

step 1 = choose a plasmid that carries an Ampicillin Resistance Gene, so when Ampicillin is added
only the bacteria that have taken up the recombinant plasmid will survive (as they will have
obtained the ampicillin resistance gene)

step 2 = use gene markers (antibiotic resistant, fluorescent, enzyme) to identify which of the
remaining bacteria have accepted the human insulin gene, the human insulin gene will be placed in
the middle of these gene markers, if the bacteria accepts the human insulin gene they will reject the
gene marker & if the bacteria rejects the human insulin gene they will accept the gene marker
 antibiotic resistant = tetracycline resistance gene lost if human insulin gene accepted,
so bacteria no longer resistant to tetracycline, add tetracycline by replica plating (on
another plate that carries a few of the bacteria from each colony in their same
position), the ones that die are the ones that we want, identify on original plate
 fluorescent = fluorescent gene lost if human insulin gene accepted, so identify
bacteria showing no fluorescence
 enzyme = enzyme gene lost if human insulin gene accepted, therefore add colourless
substrate, where there is no colour change select those bacteria (as enzyme not made
to breakdown colourless substrate for colour change)

end result = Genetically Modified Bacteria

5. Growth/Cloning

 grow genetically modified bacteria (carrying human insulin gene)

 they will produce the protein (human insulin)

What is PCR?

 polymerase chain reaction

 used to replicate DNA artificially
 step 1: heat to 95oC, hydrogen bonds break, double strand separates, left with 2 template
strands
 step 2: cool to 55oC, primers bind (short single stranded sections of DNA) to start of
each template strand, prevents the templates from rejoining and allows DNA Polymerase
to bind to build the new strand
 step 3: heat to 72oC, DNA nucleotides attach to complementary bases, DNA Polymerase
joins sugar-phosphate backbone of the new strands
= 2 copies of DNA (each made of 1 original strand, 1 new strand)

Polymerase Chain Reaction vs Semi-Conservative Replication?

 PCR can only replicate short DNA fragments, SCR can replicate whole DNA
 PCR use 95oC, SCR uses DNA Helicase
 PCR uses primers, SCR does not require primers
In-vitro vs In-vivo method of DNA Replication?

 In-vitro = PCR
 In-vivo = using bacteria to replicate DNA (add DNA fragment to the plasmid, then
replicate the bacteria to make many copies of DNA fragment)
 benefits of in-vitro = more rapid, less complex
 benefits of in-vivo = more accurate (less mutations), less chance of contamination

What is a DNA Probe?

10. short single stranded section of DNA

11. has a specific base sequence, so it binds to complementary genes
12. is radioactively/fluorescently labelled
13. if gene is present in DNA, DNA probe will bind to it and show up be
radioactivity/fluorescence

What is Genetic Screening?

 analyse an individual's DNA for the presence of a particular gene (e.g. mutated allele)
 use DNA Probes (single stranded section of DNA, complementary to a particular gene,
is radioactively labelled)
 obtain individuals DNA, make it single stranded, add the specific DNA Probe for the
gene to be screened for, if the gene is present the DNA Probe will bind, will show up as
radioactivity on an X-ray film

What is Genetic Fingerprinting?

used to produce a unique 'fingerprint' of an individual's DNA (produces a specific banding

pattern)
used in forensics and paternity testing
involves analysing the individual's introns (non-coding DNA)
introns contain repetitive sequences called variable number tandem repeats (VNTR)
the number and length of the VNTR are unique for each individual organism

involves 5 steps:
1. Extraction, 2. Digestion, 3. Separation, 4. Hybridisation, 5. Development

1. Extraction
extracting the individual's DNA
2. Digestion
cutting the DNA down into fragments
use Restriction Enzymes that cut just outside the VNTR (leaves the VNTR of the introns)
3. Separation
separate out the DNA fragments by gel electrophoresis
add alkali to make the separated fragments single stranded
transfer the fragments to a nylon membrane by Southern Blotting
add UV light so the DNA fragments set
4. Hybridisation
add radioactively labelled DNA Probes complementary to the DNA fragments
5. Development
add photographic film and take an x-ray to produce the banding pattern picture
What is Genome Sequencing?

 determining base sequence of a genome (full set of DNA)

 uses Whole-Genome Shotgun (WGS) to cut DNA into smaller sections to be sequenced
 Bioinformatics is the science by which the information is collected and analysed
 uses = supports phylogenetic classification, identify genes related to diseases

What is a Proteome?

 full set of proteins produced by a certain genome