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Biology Study Notes:
1 Cell Biology
1.1 Introduction to cells
The Cell Theory:
All living organisms are composed of one or more cells.
The cell is the basic unit of structure and organisation in organisms.
All cells come from pre-existing cells.
Exceptions to the Cell Theory:
Fungi: consists of narrow thread-like structures called hyphae, which
have both a cell membrane and cell wall. Many are divided by cross wall
like structures called septa. Aseptate hyphae don’t have septa and are
long uninterrupted tubes with many nuclei spread along it.
Algae: Unicellular and some types (giant algae) can grow to be very large
(up to 100mm).
Striated muscle: Much larger than normal animal cells and have an
average length of 30 mm in humans. They are multi-nucleated.
Functions of unicellular organisms:
Metabolism: chemical reactions inside the cell (respiration etc.).
Response: Ability to react to stimuli
Growth: irreversible increase in size.
Reproduction: producing offspring either sexually or asexually.
Excretion: getting rid of the waste products of metabolism
Nutrition: obtaining food to provide energy and the materials needed for
● Homeostasis: keep internal conditions within tolerable limits.
Paramecium as an example of a unicellular organism:
● Nucleus contains genetic material and divides asexually by mitosis..
● Food vacuoles contain smaller organisms, which are slowly digested; the
products are expelled to the cytoplasm where they are assimilated for
energy and growth.
● Contractile vacuoles store water and expel it to the extracellular to
maintain internal water levels.
● Metabolic reactions are enzyme-regulated and occur in the cytoplasm.
● Cilia control movement of the cell and can be controlled by the cell as a
regulated response to environment stimuli.
● Cell membrane controls movements of substances in and out.
● Excretion occurs by diffusion of substances to the extracellular.
Chlamydomonas as an example of a unicellular organism:
● Nuclear can divide via mitosis. Nuclear can also fuse and divide to carry
out sexual reproduction.
● Metabolic reactions occur in the cytoplasm with the enzymes present.
● Cell wall is freely permeable; cell membrane controls what enters/exists
the cell. Oxygen, waste product, diffuses out of the cell.
● Contractile vacuole maintains internal water levels by expelling water
into the extracellular.
● Photosynthesis occurs in the chloroplasts. Carbon Dioxide is absorbed
from carbon compounds of other organisms.
● Light sensitive eyespot enables detection of light and flagellum facilitates
movement towards light.
Limitations to cells size:
● Surface area to volume ratio is important to be maintained because a
small ratio would slow down the rate of exchange between substances in
the extra/intracellular.
● Waste products would be expelled too slowly and products needed for
cellular reactions would be absorbed too slowly.
● This would result in a built up of waste products as they would be
excreted slower than produced.
● Heat production and loss would also be affected as the cell may over heat,
as it would produce heat faster than it loses it over the cell’s surface.
Multicellular organisms:
● Cells in multicellular organisms can be regarded as cooperative groups.
● Individual cells in a group can work together to form distinctive overall
properties called emergent properties. These arise from the interaction of
the component parts of a complex structure.
Cell differentiation in multicellular organisms:
Specialised tissues can develop by cell differentiation in multicellular
● A group of cells to specialise in the same way to perform the same
function are called a tissue. This allows them to be more efficient.
● There are 220 highly specialised cell types in humans (that have been
recognised so far).
Gene expression and cell differentiation:
● Differentiation involves the expression of some genes and not others in a
cell’s genome.
● All tissues have the same genes, however specialisation involves the
‘turning on’, or expression, of particular genes, which define a specific
function. Differentiation occurs because different sequences of genes are
expressed in different cell types.
Stem cells:
● The capacity of stem cells to divide and differentiate along different
pathways is necessary in embryonic development. It also makes them
suitable for therapeutic uses.
● Therapeutic uses of stem cells include replacing damaged skin tissue and
non-therapeutic uses include formation of striated muscle for human
● Stem cells can be found in the bone marrow, skin and liver and can be
used for self-repair.
Use of stem cells to cure Stargardt’s macular dystrophy:
● Stargardt’s macular dystrophy is a genetic disease that develops in
children ages 6-12 years old.
● Recessive mutation of ABCA 4 gene and results in the malfunctioning of a
membrane protein responsible for active transport in retina cells.
● Photoreceptor cell degenerate and vision decays.
● Stem cells are injected into the eye and attach themselves to damaged
cells resulting in improved vision.
Use of stem cells to cure Leukaemia:
● Involves the production of lots of white blood cells at an uncontrollable
● Chemotherapy kills the dividing cells.
● Adult stem cells are extracted from the bone marrow with a large needle
and then frozen.
● Chemotherapy is then executed and kills cells in the bone marrow.
● Stem cells are then returned to the patient’s body.
Sources of stem cells and the ethics of using them:
Embryonic stem cells
Cord blood stem cells
● Can differentiate
into any type of
● Likely
different from the
adult patient.
● Removal of stem
cells kills the
● Easily
and stored.
● Limited
blood cells only.
● Umbilical cord is
Adult stem cells
● Difficult to obtain
because they are
buried deep in
● Less
embryonic stem
● Does not kill the
adult from which
they are taken.
1.2 Ultrastructure of cells:
The resolution of electron microscopes:
● Electron microscopes have a much higher resolution than light
● Resolution is making separate parts of an object distinguishable by the
eye. Light microscopes are inhibited by the wavelength of visible light
(400-700nm). Electrons have shorter wavelengths so electron
microscopes have higher resolution.
● Electron microscopes can see viruses and objects up to 1 nm.
● Light microscopes can see objects up to 200 nm.
Prokaryotic cell structure:
Prokaryotes have no nucleus. They contain a nucleoid with naked DNA.
They have no compartmentalisation and contain only 70s ribosomes.
They have no other cytoplasmic organelles (besides plasmids).
The entire body is filled with cytoplasm, which has several enzymes.
DNA is not associated with proteins (naked).
Peptidoglycan cell wall. - for eubacteria, not for archaeans.
Contains cell membrane.
Contains flagellum and cilia.
Cell division in prokaryotes:
● Occurs through binary fission. Asexual reproduction.
● DNA replicates (as it does in eukaryotes).
● Copies of DNA move to opposite ends of the cell and then cytoplasm
divides each cell get identical DNA.
Eukaryotic cell structure:
Complicated internal structure due to compartmentalisation.
Single/double membrane partitions.
Contains organelles.
Compartmentalisation allows:
o Enzymes and substrates to be concentrated to a specific region.
o Damaging substances can be kept within the membrane of an
organelle (lysosome).
o pH levels can be maintained at an ideal level for particular
o Organelles can be moved around with their contents.
Nucleus: Nuclear membrane is double and has pores (nuclear pores)
through it. Chromosomes within are tightly coiled DNA around histones.
Chromatin is uncoiled chromosome. DNA replication and transcription
occurs in the nucleus.
Rough endoplasmic reticulum (rER): Contains cisternae, which are flat
membranous sacs upon which 80S ribosomes are attached. Protein
synthesis occurs here. Proteins pass into cisternae and are carried by
vesicles to the Golgi.
Golgi Apparatus: Also contains cisternae. Processes and packages proteins
from the rER. Carried in vesicles to the plasma membrane for secretion.
Contents that are being packaged move from CIS to TRANS end.
Lysosomes: Single membrane. Formed by Golgi vesicles. Contain digestive
enzymes that can break down ingested food or dysfunctional organelles.
Mitochondrion: Double membrane. Inner membrane invaginated to form
cristae. Fluid inside called matrix. Produce ATP out of glucose/lipids by
aerobic respiration.
Ribosomes (80S): Synthesise proteins and release them into cytoplasm.
Ribosomes are constructed in the nucleolus, which is present in the
Chloroplasts: Double membrane. Thylakoids are flattened sacs of
membrane. Produce glucose by photosynthesis. Starch grains may be
present. Stroma is the cytoplasm of chloroplasts.
Vacuoles and vesicles: Single membrane. Plant cells have large vacuoles to
store starch Contractile vacuoles expel excess water. Vesicles are small
vacuoles for transport.
Microtubules and centrioles: Cylindrical fibres, which move chromosomes
during cell division. Centrioles are two groups of nine triple microtubules.
Centrioles form an anchor point for microtubules during cell division.
● Cilia and flagella: Contain a ring of nine double microtubules plus two
central ones. One flagellum is usually present. Many cilia are present.
Used for locomotion. Cilia can be used to create a current in extracellular
Exocrine gland cells of the pancreas:
● Exocrine glands secrete hormones into ducts and endocrine glands
secrete them into the bloodstream.
● Exocrine gland cells have organelles for protein synthesis. Contain plasma
membranes, Golgi Apparatuses, Mitochondrion, Vesicles, Nuclei,
Lysosomes and rER’s.
● Since the exocrine gland cells need to synthesise proteins and then
release them into the blood, they need all the organelles required to
synthesise, package and transport proteins.
Palisade mesophyll cells:
● Contain chloroplasts and vacuoles.
● Chloroplasts are important for the absorption of light for photosynthesis
and vacuoles are important for the temporary storage of some produced
glucose (as starch).
1.3 Membrane Structure:
Phospholipid bilayers:
● Phosphate heads, which are hydrophilic; and hydrocarbon tails, which are
● Since they have both hydrophilic/phobic properties, they are
● The arrangement of the bilayer is with the tails facing each other and the
heads facing the water on the intra/extra cellular.
● This is the formation observed in all cell membranes.
● When mixed with water, the phosphate heads are more attracted to each
other than they are to the water and therefore are attracted, whilst the
hydrocarbon tails are less attracted to the water and thus are
● Phospholipids are similar in structure to triglycerides, but instead of
having 3 fatty acids to glycerol, phospholipids have 2 fatty acids bonded
to the glycerol and a phosphate group instead of the 3rd fatty acid.
Membrane proteins:
Hormone binding sites.
Channels for passive transport of hydrophilic/charged molecules.
Immobilised enzymes. (Small intestine)
Matrix for intercellular adhesion.
Pumps for active transport.
Cell-to-cell communication. (Neurotransmitters)
Types of membrane proteins:
o Integral: Trans-membrane and have a hydrophobic part. They
generally project through the phosphate heads on each side. They
are imbedded in the hydrocarbon chains.
o Peripheral: Generally hydrophilic and are embedded on the
surface of the integral proteins. They are not fixedly attached. They
sometimes have a hydrocarbon chain that anchors them onto the
membrane surface.
o More protein content means more active membranes.
Cholesterol in membranes:
● Cholesterol is mostly hydrophobic but has a hydroxyl group on one end
that is partly hydrophilic. Resultantly it is situated in between the bilayer.
It is a type of steroid. Amount of cholesterol in the bilayer varies.
● In the bilayer the phosphate heads usually behave like solids and
hydrocarbon tails usually behave like liquids.
o Cholesterol regulates the extent to which the membrane bilayer is
solid/liquid and also controls the permeability of it.
● Due to its irregular placement within the bilayer it disrupts the
arrangement of the hydrophobic tails and prevents them from
● Also restricts molecular motion to prevent the bilayer from being overly
permeable and provides rigidity to its structure. Permeability reduction
to hydrophilic particles such as hydrogen ions and sodium ions.
● Cholesterol also gives a curved shape, which is usually useful in the
formation of vesicles during endocytosis.
1.4 Membrane Transport
● The fluidity of membranes allows materials to be taken into cells by
endocytosis or released by exocytosis.
● Formation of a vesicle occurs when a small region of a membrane is
pulled from the rest of the membrane and pinched off. Forms on the
inside of the plasma membrane and contains the material that was
outside of the cell.
o Phagocytosis is endocytosis of a solid
o Pinocytosis is endocytosis of a liquid/fluid
o Receptor mediated endocytosis is for specific substances - bind to
receptors then pinching occurs.
● Contains water, solutes and larger molecules that can’t pass through the
Vesicle movement in cells:
● Vesicles can be use to move materials around cells. However sometimes
it is the proteins on the membrane of the vesicles that need to be moved.
● Cell growth occurs with the help of vesicles. Phospholipids are
synthesised near the rER and then embed themselves on the rER
membrane. Ribosomes on the rER synthesise membrane proteins, which
then embed themselves on the rER membrane. Both phospholipids and
membrane proteins are transported via vesicles to the plasma
membrane. They fuse with it and increase its size.
● Vesicle carries substance and binds with the plasma membrane.
● Contents are then expelled to the extracellular.
● Plasma membrane then flattens out.
Simple diffusion:
● Particles, due to random movement, spread out in a volume. This occurs
via a net movement from area of high concentration to low concentration.
● Does not require ATP expenditure.
● Can occur across the bilayer however large/polar molecules are unlikely
to cross in this fashion, because the centre of the bilayer is hydrophobic.
● Oxygen and small polar molecules can diffuse easily.
Facilitated diffusion:
● Large polar particles and other that are unable to diffuse through the
phospholipid bilayer directly, diffuse through channel proteins.
● Channel proteins allow one type of particle to pass through; adds another
dimension of selectiveness to permeability.
● Osmosis is the net movement of water molecules across a partially
permeable membrane. This is caused by the difference in concentration of
solute, not solvent.
● Substances dissolve by forming intermolecular bonds with water, which
restrict water movement. Hence areas with high solute concentration will
see reduced movability of water. As a result water moves from low solute
concentration to high solute concentration - hypotonic to hypertonic.
● This is a passive process. Water molecules are small, but hydrophilic.
However they still pass through the bilayer.
Active Transport:
● Occurs when a particle moves against the concentration gradient and is
an active process (requires ATP).
● Carried out by pump proteins, which are within the plasma membrane.
● Substance enters the pump and goes to the central chamber, which elicits
a conformational change. ATP then joins and causes the substance to be
released on the other side.
Active transport of sodium and potassium pumps in axons:
1. Three sodium ions enter the pump on the inside of the axon and
attach the their binding sites.
2. ATP transfers a phosphate group to the pump, causing a
conformational change and the three ions to be released.
3. Two potassium ions from the extracellular then attach to their binding
4. Binding of potassium causes release of the phosphate group and
causes the pump to open back to the inside, enabling the potassium
ions to enter the ion.
Facilitated diffusion of potassium in axons:
● Potassium ions naturally form bonds with water and have a shell of water
molecules surrounding them.
● In order to pass through a potassium voltage gated channel these bonds
need to be broken and bonds need to be made with amino acids inside the
channel. The voltage-gated channel opens during repolarization, when
there are more positive charges inside the axon than outside.
● Voltage gated channels quickly close with the help of a globular protein
attached to a flexible amino acid chain, which plugs the opening of the
● This voltage-gated channel allows for facilitated diffusion of potassium in
Preventing osmosis in excised tissues and organs
● In a hypertonic solution (high osmolarity), water leaves cells by osmosis
(to enter solution), causing crenellations (indentations) in their plasma
● In a hypotonic solution the opposite occurs and the cells swell up, causing
them to lyse.
● Hence cells need to be bathed in a solution with the same osmolarity
(isotonic) during medical procedures. Saline (Sodium Chloride solution)
is normally used with an osmolarity of 300 milliOsmoles (mOsm).
1.5 The Origin of cells:
Origin of the first cells:
● First cells must have arisen from non-living material.
● Miller and Urey experiment where they passed steam through a mixture
of methane, hydrogen and ammonia. They then passed electrical
discharges to simulate lightning. This formed amino acids and some
carbon compounds.
● These carbon compounds could have been assembled into polymers in
deep-sea vents, which have gushing hot water carrying reduced inorganic
chemicals like iron sulphide, which would’ve provided the energy to
assemble carbon compounds into polymers.
● The formation of membranes would have naturally occurred due to
hydrophobic and hydrophilic properties of certain carbon compounds.
This would’ve allowed internal chemistry to develop.
● Mechanisms for inheritance rely on genes. RNA could have been the
genetic information and is both self-replicating and can act as a catalyst
Endosymbiosis and eukaryotic cells:
● Smaller prokaryotes would’ve developed certain characteristics and then
been absorbed by larger prokaryotes. This would’ve created a mutualistic
relationship between them.
● Smaller cells would’ve supplied larger ones with aerobic respiration and
larger ones would’ve supplied smaller ones with food.
● Chloroplasts and Mitochondria both support this theory:
o They have their own circular DNA molecule.
o Own 70S ribosomes of a size and shape typical of some
o Transcribe their own DNA and use mRNA to synthesize some
o Can only be produced through division of pre-existing
mitochondria and chloroplasts.
o They have double membranes, which suggests they have the
membrane from the cell's vesicle in addition to their own
1.6 Cell division:
The role of mitosis:
● Mitosis is division of the nucleus into two genetically identical daughter
● DNA replicates during interphase. The cytoplasm then splits and both
daughter cells have one set of DNA each.
● G1: Mitochondria grow and divide. Similarly chloroplasts also grow and
● S: DNA replication occurs.
● G2: Further growth occurs in preparation for mitosis.
● G0: entered by cells that do not undergo mitosis, like nerve cells. The G0
phase comes after G1, as cells that do not undergo mitosis do not need to
replicate DNA.
Supercoiling of chromosomes:
● Chromosomes condense by supercoiling during mitosis. Need to package
them into shorter structures. Occurs during the first stage of mitosis.
Histones are associated with DNA in eukaryote chromosomes and help
with supercoiling.
Phases of mitosis:
● Prophase: Chromosomes condense. Nucleolus breaks down. Microtubules
grow and link the poles of the cell. Nuclear envelope disintegrates.
● Metaphase: Microtubules attach to the centromere of each chromosome.
Attach onto opposite ends of the centromere to ensure that each
chromatid is attached to a microtubule from a different pole. The
chromosomes are then aligned along the cell equator. Microtubules pull
slightly with equal force to ensure proper attachment has occurred.
● Anaphase: Microtubules shorten after chromosomes divide at the
centromere, quickly pulling sister chromatids to opposite sides.
● Telophase: At each pole the chromosomes are pulled near the MTOC
(MicroTubule Organising Centre) and a nuclear membrane reforms
around them. Chromosomes uncoil and nucleolus is reformed.
● Mitotic index = Number of cells in mitosis/total number of cells.
● Animal: Cleavage furrow forms at the equator due to contractile proteins
actin and myosin. Cleavage furrow extends along the equator and the cell
is finally pinched off the form two genetically identical daughter cells.
● Plant: Vesicles line up at the equator and merge to form a continuous tube
like structure which acts as the plasma membrane. Vesicles carrying
pectin then move towards the plasma membrane and release the pectin
between the two plasma membranes of the two cells to form the lamella,
which would bind the cellulose for the cell wall. The vesicles then carry
cellulose and release it to the extracellular via exocytosis completing the
formation of the cell wall.
Cyclins and the control of the cell cycle:
● Cyclins are proteins that bind to cyclin dependant kinases.
● Kinases attach phosphate groups to other proteins and activate them at
specific times.
● The proteins carry out tasks specific to the cell cycle.
● Cyclins need to reach a threshold concentration for the cell cycle to
proceed to the next stage.
o Cyclin D triggers cells to move from phase to phase in interphase.
o Cyclin E prepares cell for DNA replication
o Cyclin A activates DNA replication
o Cyclin B prepares cell for mitosis
Tumour formation and cancer:
● Tumours are either benign, and remain as primary tumours, or malignant,
and undergo metastasis to set up secondary tumours in other parts of the
body. Metastasis is the movement of cells from a primary tumour to set
up secondary tumours in other parts of the body.
● Mutations are random changes to the base sequences of genes. Genes that
become cancer causing after being mutated are called oncogenes. These
cells are called proto-oncogenes before being mutated. Proto-oncogenes
are involved with cell cycle and division; hence they lead to rapid division
of cells and tumour formation (if mutated).
● Mutations that occur to proto-oncogenes can result in these genes not
properly regulating cell division and resulting in the uncontrollable
division of cells.
● Carcinogens, including some viruses and high-energy radiation, can cause
2 Molecular Biology
2.1 Molecules to metabolism
Molecular biology:
● Reductionist approach in coming to conclusions. Can’t explain everything
by breaking down complex systems into small parts and studying them
individually. Need to study emergent properties as well, which only occur
when the organisms are studied as a whole.
Synthesis of Urea:
● Ammonia + Carbon Dioxide => Ammonium Carbonate => urea + water
● Synthesised in the liver due to excess amino acids (deamination).
● Excreted in urine.
● Origin of all life comes due to a “vital principle”, which is different to life
being composed purely of chemical + physical forces. Production of Urea
by Fredrich Wohler in 1828, disproved this theory. First organic
compound, which was synthesised artificially; hence without a vital
Carbon Compounds:
● Carbon atoms can form 4 covalent bonds. These can be single or double
● Can form chains/rings of any length.
Classifying Carbon atoms:
● Carbohydrates: Carbon, Hydrogen, Oxygen. H:O => 2:1
● Amino acids: Carbon, Hydrogen, Oxygen, Nitrogen, 2 Amino acids also
contain sulphur.
● Lipids: Insoluble in water. Triglycerides are fats if solid at room
temperature and oils if liquid. Also contain Carbon Hydrogen and Oxygen.
● Nucleic Acids: Chains of nucleotides. Carbon, Hydrogen, Oxygen, Nitrogen
and Phosphate. Form DNA and RNA.
Drawing molecules:
Amine group: NH2
Carboxyl group: COOH
Methyl group: CH3
Hydroxyl group: OH
Ribose: C5H10O5. OH groups on Carbons 1, 2 and 3. Point up, down, down
● Glucose: C6H12O6. OH groups on Carbons 1, 2, 3, 4. Point down, down, up,
down respectively (alpha). On beta glucose, found in cellulose, OH group
on carbon 1 points up.
● Saturated fatty acids: Carbon atoms form an un-branched chain of about
14-20 atoms, no double bonds.
● Amino Acids: Contain Amine group; Carboxyl group; Hydrogen atom; and
R variable group.
● Lipids contain less oxygen than carbohydrates. Proteins usually contain
sulphur. Carbohydrates have a H:O ratio of 2:1.
● Web of all enzyme catalysed reactions in a cell or organism. Most
reactions are enzyme catalysed and generally occur in cell cytoplasm.
● Anabolism: Synthesis of complex molecules from simpler ones. Monomers
=> Macromolecules by condensation reactions. Photosynthesis is an
anabolic process.
● Catabolism: Breakdown of complex molecules into simpler ones including
the hydrolysis of macromolecules into monomers. Digestion, respiration
and decomposition are catabolic processes.
2.2 Water
Hydrogen bonding in water:
● Water molecules are polar and hydrogen bonds form between them.
● Bonds between hydrogen and oxygen involve the unequal sharing of
electrons because oxygen nuclei are more attracted to electrons than
hydrogen nuclei. Hence hydrogen atoms are partially positive and oxygen
atoms are partially negative, forming two poles.
● Adjacent water molecules are therefore attracted to one another
(hydrogen to oxygen) forming hydrogen bonds.
● In general a hydrogen bond forms when a hydrogen atom in one polar
molecule is attracted to a partially negative atom of another polar
covalent molecule.
Water properties:
● Cohesive properties: the binding together of two-like molecules. Water to
water. Hydrogen bonds enable this binding. Used in capillary action.
● Adhesive properties: Hydrogen bonds between water and other polar
molecules. Useful in leaves where water adheres to cellulose molecules in
cell walls. Maintains dampness for diffusion of CO2.
● Thermal properties: High specific heat capacity; restricts temperature of
water in varying environment. This is due to water requiring large
amounts of energy to change by 1˚C. Allows for stability of water, but also
means it is a large store for heat energy, hence serving as a coolant.
● Solvent properties: Polar nature of water means that it forms shells
around other polar molecules. As a result solutes to clump together. Both
positive and negative ions dissolve.
● Hydrophilic and Hydrophobic properties: All chemical substances that
dissolve in water are hydrophilic. Substances that water adheres to are
also hydrophilic. Substances that are insoluble are hydrophobic:
uncharged and non-polar particles, like lipids. When hydrophobic
substances enter water, hydrogen bonds form between water molecules
but not between water and hydrophobic substances. This is because
hydrophobic substances are non-polar and are therefore immune to
hydrogen bonds. Instead hydrophobic interactions occur, as the
substances are more attracted to themselves than they are to water, and
so they end up clumping together.
● Water vs. Methane: Both small molecules linked by single covalent bonds
and have similar masses. However methane is nonpolar and doesn’t form
hydrogen bonds. Water has a higher specific heat capacity, latent heat of
vaporisation and thus a higher boiling point. Methane is liquid over a
range of 22˚C whereas water is liquid over a range of 100˚C.
● Sweat as a coolant: Heat needed for the evaporation of water in sweat is
taken from the tissues of the skin, reducing their temperature. Solutes are
left on the skin. Hypothalamus controls sweat secretion. Adrenaline can
cause the body to sweat even when cold because it anticipates a period of
intense activity.
Transport in blood plasma: Blood transports a variety of substances.
● Sodium Chloride: Dissolves in water to form Na+ and Cl-.
● Amino Acids: Both negative and positive charges. Solubility depends on R
group. All amino acids, however, are soluble enough to dissolve in blood
● Glucose: Freely soluble because it is polar.
● Oxygen: Non-polar molecule. Dissolves due to its small size but saturates
blood at low levels. Higher temperature blood plasma results in lower
bandwidth of absorption. Hence Haemoglobin, an oxygen carrier, is
present in red blood cells.
● Fatty molecules: Entire nonpolar and large. Completely insoluble. Carried
in micelles, which are lipoprotein complexes. Phospholipids act as a
vesicle, with hydrophobic fatty tails on the insides, facing the fatty
molecule. Single layer of phospholipid.
● Cholesterol: Mainly hydrophobic: Insoluble in water. Transported in
lipoprotein complexes. Positioned within the phospholipid monolayers
with the hydrophilic part facing outwards with the phosphate heads.
2.3 Carbohydrates and Lipids:
Carbohydrates: Monosaccharide monomers are linked together by condensation
reactions to form disaccharides and polysaccharide polymers.
● Monosaccharides: Glucose, fructose, galactose and ribose. Single sugar
● Disaccharides: Two monosaccharides linked together. Maltose: glucose +
glucose. Sucrose: glucose + fructose. Lactose: glucose + galactose.
● Polysaccharides: Starch and Glycogen are examples.
● Monosaccharides combine in a condensation reaction. Loss of OH group
from one molecules and hydrogen from another. OH and H form H 2O. This
anabolic process requires energy. Link between two monosaccharides is
called a glycosidic bond.
Polysaccharides: Cellulose and starch in plants. Glycogen in humans.
● OH groups on Carbon 1, 4 and 6 are used to make links. OH on Carbon 6 is
usually for side branches.
● In alpha glucose the OH points downwards and in beta, it points upwards.
● Cellulose: Linking beta glucose in a 1-4 structure makes cellulose. OH
groups point in opposite directions therefore each glucose molecule is
positioned 180˚to the previous one. Hence the beta glucose molecules
alternate ‘up and down’. This results in a straight chain. Un-branched
chains allow them to form bundles, connected by hydrogen bonds and
created cellulose micro-fibrils. These give cellulose its high tensile
strength. Used in cell walls.
● Starch: Made by linking alpha-glucose molecules. Made by 1-4 glycosidic
bonds. All –OH molecules point downwards, hence all molecules have a
similar orientation, which results in a curved structure. This forms two
types: amylose and amylopectin. Due to insolubility of both molecules,
despite them being hydrophilic, they are used as a storage molecule as
they do not cause an influx of water into cells.
● Glycogen: Similar to amylopectin in structure; but has more branching.
The molecule is more compact. Stored in the liver and some muscles.
Stores energy in the form of glucose because large stores of dissolved
glucose would cause osmotic problems. Easy to add/remove glucose
molecules on either branched/unbranched sides of glycogen/starch.
Alpha helix
Hydrophilic but insoluble due to size
Hydrophilic but insoluble due to size
Has only 1-4 linkages
Has some 1-6 linkages in addition to 14 linkages
● Triglycerides are formed by condensation from three fatty acids and a
● All lipids are insoluble.
● Triglycerides are the fat in adipose cells and oils in sunflower seeds.
● Fats are liquid at body temperature (37˚C) but solid at room temperature
● Oils are always liquid.
● 3 fatty acids + glycerol => triglyceride + 3H2O.
● Fatty acids form ester bonds with glycerol, which are generally formed
when an acid reacts with the OH group in alcohol. Energy from
triglyceride can be released from aerobic cell respiration.
Energy storage:
● Lipids are more suitable for long-term energy storage than
● Adipose tissue is located directly beneath the skin and round some organs
including the kidneys.
● Amount of energy released in cell respiration per gram of lipids is double
that of carbohydrates. Therefore it adds half the body mass as
● Fats store as pure droplets whereas glucose stores with two grams of
water (per gram of glucose).
● Effectively lipids are 6 times more efficient in energy storage than
● Lipids are insulators as they are poor conductors of heat. This is why
adipose tissue is subcutaneous.
● They can also act as shock absorbers because they are liquid at body
● However fat cannot be rapidly used and therefore can only be used in
aerobic respiration.
Body Mass Index (BMI):
BMI = Mass (kg)/(Height (m))2.
Units are in kg/m2
Causes of being overweight/underweight vary..
Obesity and anorexia nervosa are both eating disorders, which amount to
unhealthy body composition.
● Can use a nomogram to calculate BMI (its a cross of 2 scales).
Fatty Acids:
Can be mono/polyunsaturated or saturated.
Most fatty acids have 14-20 carbon atoms.
Carbon atoms with a double bond can only link to two hydrogen atoms.
Fatty acids without any double bonds are saturated and those with
double bonds are mono/poly unsaturated, depending on the number of
double bonds present.
● Unsaturated fatty acids:
o Can be ‘cis’ or ‘trans’ isomers.
o Fatty acids are cis if the hydrogen atoms are on the same side of
the double bond. If they are on opposite sides they are trans.
o In cid fatty acids there is a kink at the double bond, which causes
the fatty acid to bend. This contributes to cis’s ability to pack
tightly in regular arrays; far more efficiently stored than saturated
fatty acids. Tight packing also lowers their melting point.
o Trans-fatty acids have no kinks because they have been artificially
hydrogenated in a factory.
Health risks:
● Main concerns is CHD (Coronary Heart Disorder) .
● Coronary arteries getting partially blocked resulting in clotting and
damage. Positive correlation between saturated fats and CHD.
● Cis monosaturated fatty acids are claimed to be good fats.
● Trans fats are the biggest contributors to heart disease.
2.4 Proteins
Amino acids and polypeptides:
● Amino acids are linked together by condensation to form polypeptides.
The linking together occurs on ribosomes during translation.
● Dipeptides: Two amino acids.
● Polypeptide: 20 or more amino acids.
● Oligopeptide: between 2 and 20 amino acids.
Diversity of amino acids:
● 20 different amino acids in polypeptides.
● By changing an amino acid, you essentially get an entirely different
protein. In collagen, the change of one amino acid from proline to
hydroproline, results in a stronger structure.
● 20n , where n is the number of amino acids in the chain.
● Three bases of DNA code for one amino acid. These ‘codons’ are triplet
Proteins and polypeptides:
● Protein may consist of two single polypeptides or more than one
polypeptide linked together.
● Lysozyme: 1 polypeptide.
● Integrin: 2 polypeptides.
● Collagen: 3 polypeptides.
● Haemoglobin: 4 polypeptides.
Protein conformations:
● Amino acid sequence determines the 3D shape of the polypeptide.
repeating Intricate shape with parts that are
helical or sheet-like.
No folding up, amino acid prevents Polypeptide folds up as amino acids
are added on.
Have bonds between the R groups
of the amino acids.
Hydrophobic groups on the inside
and hydrophilic groups on the
Denaturation of protein:
Heat/pH extremes (causes).
Bonds in 3D structure of protein are susceptible to breakage.
This breakage in bonds results in denaturation.
Denatured protein does not normally return back to its former structure.
Soluble proteins become insoluble and form a precipitate because
hydrophobic groups become exposed to water.
● Heat breaks intermolecular bonds or interactions.
● pH changes affect charge on the R groups, breaking ionic bonds with the
protein or causing new ones to form.
Protein functions:
Muscle contractions.
Tensile strengthening.
Blood clotting.
Transport of nutrients and gases.
Cell adhesion.
Membrane transport.
Hormones and receptors.
DNA packing.
Examples of proteins:
● Rubisco: Ribulose phosphate carboxylase. Catalyses the reactions for
carbon fixation.
● Insulin: Signal to cells to absorb glucose. Reduces blood glucose. Shape
and chemical properties correspond to binding site on the receptor.
Secreted by beta cells in pancreas.
● Immunoglobulin: Antibody. Binding sites for bacterial antigens has a
different binding cite – specific immunity.
● Collagen: Rope-like protein made of three polypeptides wound together.
They are located in the skin, blood vessel walls to prevent tearing and
allow for tensile strength.
● Rhodopsin: Pigments of rhodopsin, membrane proteins of rod cells in the
retina are light sensitive molecules surrounded by an opsin polypeptide.
Changes in shape when it absorbs light, triggers opsin and abuses the rod
cell to send an impulse to the brain.
● Spider silk: Polypeptide forms parallel arrays very resistant to breaking.
● All of the proteins produced by a cell, tissue or organism. Genome of an
organised is fixed but a proteome is not because different cells make
different proteins. Proteomes reveal what is happening in a cell at the
time, not what could happen. Proteomes differ due to differences in
amino acid sequences.
2.5 Enzymes:
Active site and enzymes:
● Enzymes have active sites to which specific substrates bind.
● Enzymes are globular proteins that work as catalysts.
● Enzyme substrate specificity: one enzyme can facilitate one particular
substrate only.
● Shape and chemical properties of active site and substrates match each
● Enzyme catalysts require molecular motion and the collision of substrates
with the active site.
o Substrate binds to enzyme.
o Substrate changes in chemical structure.
o Products separate from active site.
● Collision: when enzyme and substrate come together. Collisions occur
because of random movements and are successful when the substrate and
active site are correctly lined up to each other.
Factors affecting enzyme activity
● Temperature: Higher kinetic energy leads to greater rate of collision and
an increased chance of a successful collision as the energy could exceed
the activation energy needed for the reaction to proceed. However, bonds
in enzyme vibrate more and change of breakage increases. Breaking of
bonds changes shape of active site and this is called denaturation. As
temperature increases and more enzymes denature, the rate of collision
● pH: Enzymes have an optimum pH for functionality. Change in pH, or
deviation from the optimum pH, results in reduced rate of reaction. When
the H+ ion concentration is higher/lower than the optimum, enzymes
activity is hindered and the structure of the enzyme is altered – another
example of denaturation. Not all enzymes have the same optimum pH.
● Substrate concentration: Increased substrate concentration would mean
more frequent collisions between enzyme and substrate. After binding
substrate to active site it is unavailable to other substrates until the
products have been created and released. As substrate concentration
rises, active sites are increasingly occupied at a given moment; hence the
rate of reaction will stagnate.
Immobilised enzyme:
● Widely used in industry. Enzymes are immobilised by attaching them to
other substances or into aggregations to restrict movement. Enzymes can
be attached to a glass surface, trapped in alginate gel or bonded together.
● Advantages:
o Easily separated from products of reaction, preventing
contamination of products.
o Recycling of enzymes: more cost efficient.
o Increases durability of enzymes to temperature/pH change
o Higher enzyme concentration can be used for increased reaction
● Lactose free milk: Lactose is broken down into glucose and galactose with
the help of lactase, an enzyme.
o After extracting the lactase from yeast it is used commercially.
o Lactose intolerant individuals benefit off this.
o Galactose + glucose is sweeter so less sugar needs to be used.
o Glucose + galactose are more soluble and hence give a smoother
texture in icecream.
o Bacteria ferment glucose + galactose faster, so it is easily digested.
2.6 Structure of RNA and DNA:
Nucleic acids and nucleotides:
● Nucleic acids, DNA and RNA, are polymers of nucleotides.
● Linking together nucleotides forms nucleic acids.
● They consist of three parts:
o A sugar: Ribose/deoxyribose. Both are five carbon atoms
o Phosphate group: Acidic, negatively charged part of the nucleic
o Nitrogenous base: Made of nitrogen. Either two/one rings of atoms
in its structure (purine (AG)/pyrimidine (CT)).
o Base and phosphate are linked to the sugar by covalent bonds.
o Covalent bonds are also formed between the phosphate of one
nucleotide and the sugar of the next - phosphate with no3 Carbon.
o Creates a backbone of alternating sugar and phosphate groups.
o Base sequence can vary, and this is how information is stored,
through sequencing of 4 bases.
Differences between DNA and RNA:
Deoxyribose - 2nd Carbon has no Ribose
hydroxyl group
Two polymers of nucleotides (double One polymer of nucleotide (single
Structure of DNA:
● Double helix.
● Made of two antiparallel strands of nucleotides linked by hydrogen
bonding between complementary base pairs.
● Each strand consists of a chain of nucleotides linked by covalent bonds.
● Antiparallel strands: One strand runs in the opposite direction to the
● Two strands are wound together to form a double helix and are held
together by hydrogen bonds between the nitrogenous bases. 2 hydrogen
bonds between A and T, 3 hydrogen bonds between C and G.
● Complementary base pairing: Adenine with Thymine (Uracil in RNA) and
Cytosine with Guanine.
2.7 Transcription, Translation and Replication:
Semi-conservative replication of DNA:
New strands of DNA are formed upon the template strand.
The original strand divides.
The free nucleotides are added upon the template strand.
As a result, two new strands are formed, both having 50% pre-existing
● Base sequence of the template strand determines the base sequences on
new strand, due to complementary base pairing.
● A hydrogen bond would not form with a non-complementary nucleotide.
DNA Helicase:
● Unwinds the double helix and separates the two strands by breaking the
hydrogen bonds. Groups of enzymes that use energy from ATP are
required to break the Hydrogen bonds.
● Globular (6) polypeptides arrange around a string of DNA.
● Causes unwinding of the DNA, which separates the strands.
DNA polymerase III:
● Links nucleotides together to form a new strand, using pre-existing strand
as a template.
● Each of the two strands after helicase splits the DNA molecule, are used as
● DNA polymerase moves from the 5’ to 3’ direction, adding a nucleotide at
a time.
● Nucleotides must be complementary to the base position on the template
● Hydrogen bonds are formed between nucleotides.
● After hydrogen bonds, DNA polymerase links the nucleotide to the
existing end of a new strand. This is done by making covalent bonds
between the phosphate groups of the new nucleotide on the new strand
the sugar group of the existing nucleotide on the new strand.
● Very high degree of fidelity is maintained.
Polymerase chain reaction (PCR):
● Use of Taq DNA polymerase to produce multiple copies of a specific DNA
● Very small quantity of DNA is needed at the start.
● Three stages:
o DNA molecule is heated to 95˚C for 15 seconds to break the
hydrogen bonds between the two strands and separate the
o DNA molecule is then cooled to 54˚C for 25 seconds during which
multiple DNA primase enzymes bind RNA primers bind on the
parent strands. This stops them from re-annealing with each other
and also provides a starting point for replication.
o Reaction mixture then heated to 72oC, the temperature at which
Taq DNA polymerase works and adds complementary nucleotides
to template strands.
▪ Taq DNA polymerase is extracted from bacteria,
Thermusaquaticus, and can withstand very high
temperatures. It is used because it will not denature at 95˚C.
Reaction mixture is heated to 72˚C for 80 seconds, during
which 1,000 nucleotides are added per minute.
● Synthesis of mRNA from the DNA base sequence using RNA polymerase.
● Proteins are what determine observable characteristics in an organism.
● Transcription occurs along the antisense strand. RNA polymerase binds
to it at the start of a gene and then moves along to separate the two DNA
strands. Concurrently it pairs RNA nucleotides with complementary
● Uracil replaces thymine and is complementary to Adenine.
● RNA polymerase forms covalent bonds between RNA nucleotides and
then separates from the DNA. Transcription stops at the end of the gene,
the enzyme is then released and the mRNA molecule as well.
● Synthesis of polypeptides on ribosomes: ribosomes consist of a small and
a large subunit. Have binding sites for each molecule that partakes in the
● Large subunit makes peptide bonds between amino acids to link the,
together into a polypeptide.
Messenger RNA and genetic code:
● mRNA determines all sequences of polypeptides according to genetic
● Length of mRNA is usually 2000 nucleotides.
● Only certain genes will be transcribed, depending on which protein is
required to be made.
● Cells that need or secret large amounts of a particular polypeptide will
contain large amounts of the specific mRNA needed to create it.
Genetic code converts base sequence on mRNA into amino acid sequence.
Sequence of three bases is called a codon. 64 possible codons.
Genetic code is degenerate - many codons specify the same amino acid.
Each amino acid is carried by a transfer RNA. Contains a 3 base anticodon complementary to the mRNA codon for that particular amino acid.
Codons and anticodons:
● Translation depends on complementary base pairing between mRNA
codons and tRNA anticodons.
● Ribosomes act as the binding site for both mRNA and tRNA. They catalyse
assembly of polypeptide.
● Translation follows the following process:
o mRNA binds to small subunit.
o tRNA binds to ribosome. Has anti codon complementary to first
mRNA codon.
o 2nd tRNA binds. Maximum of two tRNA can be bound to a ribosome
at one time.
o Amino acids from first tRNA goes to second tRNA and joins by a
peptide bond. 2nd tRNA carries dipeptide.
o Ribosome moves along mRNA and tRNA is removed leaving one
space for new tRNA molecule.
o Similar process continues until a stop codon is reached.
o Polypeptide is released and ribosome complex breaks down.
Human insulin production:
● Occurs in bacteria and is a manifestation of how universal the genetic
code is; allowing gene transfer between species.
● Human insulin is produced synthetically using E. coli bacteria.
● Gene that codes for insulin production is transferred to bacteria.
● Transcription and translation then occur to produce harvestable
quantities of bacteria.
● Earlier bovine insulin was used. Despite slight genetic difference they still
bound to insulin receptors properly.
2.8 Cell Respiration:
Cell respiration:
● Controlled release of energy from organic compounds to produce ATP.
● ATP from cell respiration is immediately available as a source of energy in
the cell.
● The 3 main ATP-requiring activities are:
o Synthesising large molecules: DNA, RNA proteins.
o Pumping molecules/ions across membranes: active transport.
o Moving things around in a cell/ muscle contraction.
● ATP is used by splitting ATP into ADP + P. This is an exothermic reaction
and releases energy. This energy is used by cells and then converted into
heat energy, which is not reusable/recyclable. As a result all energy is
eventually lost to the environment, thus creating a continuous need to
obtain energy through ingestion and then respiration.
Anaerobic respiration:
● Gives a small yield of ATP from glucose, which is broken down without
● Required when a short burst of ATP is needed.
● When oxygen supplies are internally low and in oxygen deficient
● In humans, glucose is converted into lactic acid. However in yeast and
plants it converts to ethanol and carbon dioxide. Both lactate and ethanol
are toxic.
Use of yeast in baking:
● Release of carbon dioxide due to anaerobic respiration causes lighter
texture in bread.
● Carbon dioxide cannot escape and forms bubbles.
● Ethanol evaporates during baking.
● Bioethanol is produced by Yeast converting sugar into ethanol. Only
sugars, mono/di saccharides can be converted. This is an enzymecatalysed reaction. This ethanol is distilled and can be used in vehicles.
Lactate production in humans:
● Used to maximise the power of muscle contractions.
● ATP is created anaerobically when the body requires quick powerful
● Weight lifters, short distance runners are examples of sportsmen who
anaerobically respire during their events.
● Muscles cannot tolerate lactate past a certain extent. It results in oxygen
debt and so must be broken down.
Aerobic respiration:
● Requires oxygen and produces large yield of ATP from glucose. Over 30
ATP produced from a single glucose molecule.
● Molecules of ATP per molecule of glucose.
● Glucose + Oxygen => Carbon Dioxide + Water.
● Most of the reactions happen inside the mitochondria.
2.9 Photosynthesis:
● Production of carbon compounds in cells using light energy.
Photosynthesis is an example of energy conversion. Light energy is
converted to chemical energy in carbon compounds. Produces
carbohydrates, proteins and lipids.
Wavelengths of light:
● Visible light has a range of wavelengths with violet the shortest and red
the longest. This is the spectrum of electromagnetic radiation.
● Visible light ranges between 400-700 nm. Sunlight is a mixture of
different wavelengths.
Light absorption by Chlorophyll:
● Absorbs red/blue light. Reflects green light.
● When drawing an action spectrum for photosynthesis or an absorption
spectrum for chlorophyll, the x-axis should be from 400-700 nm.
● For an action spectrum, the y-axis should be ‘relative rate of
photosynthesis’ from 0-100%.
● On an absorption spectrum the y-axis should be ‘% absorption’ from 0100%.
● Caused by photolysis of water. Light energy splits molecules of water to
release electrons needed in other stages.
● 2H2O => 4e-+4H++O2. Oxygen is therefore a waste product and diffuses
Effects of photosynthesis on Earth:
● Changes to Earth’s atmosphere, oceans and rock deposition due to
● Causes rising oxygen concentration in atmosphere, known as the Great
Oxidation Event.
o Glaciation occurred due to reduction of greenhouse effect – fall in
methane and carbon dioxide concentrations.
o Oxidation of iron deposits in the water result in precipitation on
the sea-bed called banded iron formation – iron ores.
Production of Carbohydrates:
● Energy is needed to produce carbohydrates and other carbon compounds
from carbon dioxide.
● Endothermic reaction to make carbohydrates from carbon dioxide. This
energy is derived from light absorption.
● Light energy is therefore converted to chemical energy.
Limiting factors:
● Temperature, light intensity and carbon dioxide concentrations.
● Can limit photosynthesis if below the optimal level.
● Under any combination of limiting factors only one actually limits the rate
of photosynthesis: the one furthest from its optimum.
● In order to test for effects of limiting factors, two will have to be constant
by controlling them. The third would be the independent variable and
would change by stead increments.
3 Genetics
3.1 Genes
What is a gene?
● A gene is a heritable factor that consists of a length of DNA and influences
a specific characteristic.
● Genes consist of a much shorter length of DNA than a chromosome and
each chromosome carries many genes.
Comparing numbers of genes
E. coli has 3200 genes. Gut bacterium. Prokaryote group.
T. vaginatis has 60,000 genes. Unicellular parasite. Protoctista group.
S cerevisiae has 6,000 genes. Unicellular fungus. Fungi group.
O. sativa has 41,000 genes. Rice. Plant group.
H. sapiens has 23,000 genes. Humans. Animal group.
Where are genes located?
● A gene occupies a specific position on one type of chromosome.
● The number of groups of linked genes = the number of chromosomes. For
example humans have 23 linked genes and 23 chromosomes.
● The specific position of a gene on a chromosome is called the locus.
What are alleles?
● Alleles are the various specific forms of a gene. They are alternate forms
of the same gene.
● There can be two or more alleles per gene and they occupy the same
position on one type of chromosome.
● There can only be one allele of a particular gene at a specific locus.
Differences between alleles:
● Different alleles of a gene have variations in their base sequence.
● A position in a gene that has the option of being filled by more than one
nitrogenous base is known as a single nucleotide polymorphism (SNP).
● These SNPs are ultimately what allow for the formation of alleles as they
allow for variation in the base sequence of the gene.
● New alleles are formed by mutation.
● Most common type: base substitution – one base replaces another, which
gives rise to a new allele.
● Most mutations are either neutral or harmful, because organisms have
already developed over millions of years.
● Mutations in the body cells can’t be inherited, but mutations in gametes
Sickle cell anaemia:
● Sickle cell anaemia is caused by a base substitution in the Hb gene that
codes for alpha-globin polypeptide.
● A base substitution on the sixth codon ‘GAG’ of the Hb gene gives rise to a
new allele ‘GTG’, which translates to the amino acid valine instead of
glutamic acid.
● Valine causes the Haemoglobin groups to stick together in red blood cells
and induce the formation of a rigid sickle cell shape in low oxygen
● Sickle cells block blood capillaries and reduce blood flow, causing damage
to tissues.
● Eventually the plasma membranes and the haemoglobin cells are
damaged and the red blood cells die; their lifespans are shortened to 4
● The body cannot replenish red blood cells at the rate at which they die, so
there is a shortage of red blood cells – anaemia.
● HbS genes code for sickle cells. HbA genes code for the normal red blood
● Whole of the genetic information of an organism.
● Human genome consists of 23 pairs of chromosomes in the nucleus plus
the DNA molecule in the mitochondria.
● Plant species are similar, however the chromosomes of the chloroplasts
must be accounted for too.
● Prokaryote genomes consist of DNA in the circular chromosome plus
plasmid DNA.
● Most of the genome is not transcribed. These sections are called junk
● Some of this junk DNA affects gene expression and some, highly repetitive
sequences, are called satellite DNA.
3.2 Chromosomes:
Bacterial chromosomes:
● DNA in bacteria is not associated with proteins and is therefore naked.
● Prokaryotic DNA consists of one chromosome of circular DNA, which is
double stranded.
● Eukaryotes don’t have plasmids.
● They also consist of circular and naked DNA.
● Do not contain genetic information that is useful for basic life
processes but contain the information for antibiotic resistance, for
● Aren’t replicated at the same time or same rate as chromosomes, and
therefore aren’t always passed down during cell division. Plasmids
can be transferred laterally between cells.
● There may be multiple plasmids in a cell.
Measuring the length of DNA molecules using Cairns’ technique by
● Cell were grown for two generations in a culture medium containing
tritiated thymidine.
o Thymidine consists of the base thymine linked to deoxyribose and
is used by E. coli cells to make nucleotides that it used in DNA
replication. Since tritiated thymidine contains the radioactive
isotope of hydrogen, tritium, the DNA produced by DNA
replication would be radioactively labelled.
● Cells are then placed into a dialysis membrane and their cells walls are
digested by the enzyme lysozyme. This releases their DNA onto the
surface of the dialysis membrane.
● A photographic emulsion film was placed onto the surface of the
membrane and left in the darkness for two months. Atoms of tritium in
the DNA decayed emitting high energy electrons which reacted with the
● Film was then developed and at each point where the tritium atom
decayed was a dark grain, which indicated the position of the DNA.
Eukaryotic DNA:
● Is associated with histone proteins, which are globular proteins.
Differences between chromosomes:
Chromosomes supercoil during mitosis/meiosis and can be seen then.
23 types of chromosome in humans.
Genes are arranged in a standard sequence along a type of chromosome.
Different chromosomes can be of different lengths and can also vary in
the positioning of the centromeres.
● Each chromosome carries a specific sequence of genes arranged along the
linear DNA molecule.
Homologous chromosomes:
● Carry the same sequence of genes but not necessarily the same alleles of
those genes.
● They are therefore differentiated by the fact that different alleles of the
genes occupy a particular locus, even though they have the same genetic
Genome sizes:
● Genome sizes are correlated with the complexity of the organism but
aren’t directly proportional.
● This is because the proportion of DNA that acts as function genes is very
variable and the amount of gene duplication varies.
● Humans have a genome size of 3,000 (million base pairs). Whereas E.coli
have a genome size of 5 (million base pairs).
Haploid nuclei:
● Haploid nuclei have one chromosome of each pair.
● Human haploid nuclei, as found in gametes, have 23 chromosomes, rather
than 23 pairs of chromosomes.
Diploid nuclei:
● Diploid nuclei have pairs of homologous chromosomes.
● They are created when haploid nuclei fuse together as a result of
● Having two copies of each gene means that the harmful effects of
recessive mutations can be avoided if a dominant allele is also present.
Chromosome numbers:
● The number of chromosomes is a characteristic feature of members of a
● Organisms with a different number of chromosomes are unlikely to be
able to interbreed.
● The number of chromosomes can change during the evolution of a
species, however chromosome numbers tend to remain unchanged over
millions of years.
● Humans have 46 chromosomes (23 pairs) whereas Dogs have 78
chromosomes (39 pairs).
Sex determination:
● X and Y-chromosomes determine sex. Small part of the Y chromosome has
the same sequence of genes as a small part of the X chromosome.
● Genes on the remainder of the Y chromosome are not found on the X
chromosome and are not needed for female development.
● X chromosomes don’t contain the TDF (test determining factor) gene;
hence ovaries develop instead of testes, in women.
● All offspring inherit the X chromosome.
● A karyogram shows the chromosomes of an organism in homologous
pairs of decreasing length.
● Stains have to be used to make the chromosomes visible.
● The banding pattern allows chromosomes that are of a different type but
similar size to be distinguished.
● As most cells are diploid, the chromosomes are generally in homologous
● A trisomy on chromosome 21 signifies Down syndrome.
● Karyotypes can also suggest whether an organism is male or female.
3.3 Meiosis
Meiosis in outline:
Meiosis includes two nuclear divisions: Meiosis I and II.
Nucleus undergoing first division of meiosis is diploid.
Daughter cells are haploid.
Halving the chromosome number occurs in the first division, but each cell
still consists of two sister chromatids until after the second division.
● Final gametes are haploid.
Meiosis and sexual life cycles:
● The halving of the chromosome number allows a sexual life cycle with
fusion of gametes.
● In an asexual life cycle, the offspring have the same chromosomes as the
parent, so are genetically identical.
● In a sexual life cycle there is variation between the chromosomes of the
offspring and the parents.
● Fertilization doubles the number of chromosomes each time it occurs,
hence if the gamete number was not halved, there would be a doubling
effect on chromosomal number every generation.
● Meiosis occurs during the process of creating the gametes.
● Body cells are diploid; sex cells are haploid.
Replication of DNA before meiosis:
● DNA is replicated during the interphase before meiosis so that all
chromosomes consist of two sister chromatids.
● Two chromatids that make up each chromosome are genetically identical.
● Replication does not occur again before the second meiotic division,
which results in the halving effect.
● One diploid nucleus divides twice to produce four haploid nuclei, which
each chromosome consisting of one chromatid.
0Formation of bivalents and crossing over:
● Pair of homologous chromosomes: bivalents. This complex is also known
as a tetrad. The pairing of homologous chromosomes occurs through a
process called synapsis.
● Crossing over occurs at the same loci between bivalents. Points at which
crossing over occurs are called chiasmata.
● Crossing over can occur at random positions.
● Chromatids with new combinations of alleles are produced.
Random orientation of bivalents:
● Random orientation is caused by the random positioning of the bivalents
during meiosis I. The poles to which the bivalents are pulled to would
dependent on which way they are facing.
● The orientation of the bivalent is random, but due to the genetic diversity
between bivalents, the different positions would impact the offspring’s
genotype differently.
Halving the chromosome number:
● In meiosis I the centromere does not divide and whole chromosomes
move to opposite poles. Instead disjunction occurs, during which the
bivalents are split at the chiasmata that form between them.
● Disjunction is the splitting of homologous chromosomes.
● This halves the chromosome number of a cell, thus meiosis I is a
reduction division.
Obtaining cells from a foetus:
● Amniocentesis: passes a needle through the mother’s abdomen wall to
withdraw a sample of amniotic fluid containing fetal cells.
● Chorionic villus sampling: sampling tool obtains cells from the chorionic
villi, a membrane from which the placenta develops.
● Risk of miscarriage is 2% using CVS but 1% using amniocentesis.
Divisions of meiosis:
● Prophase I: Cell has 2n chromosomes: n is haploid number of
chromosomes. Double chromatids.
o Homologous chromosomes pair (synapsis).
o Crossing over occurs (at chiasmata).
● Metaphase I: Spindle microtubules move homologous pairs to equator of
the cell.
o Orientation of paternal and maternal chromosomes on either side
of equator is random and independent of other homologous pairs.
● Anaphase I:
o Homologous pairs are separated. One chromosome of each pair
moves to each pole.
● Telophase I:
o Chromosomes uncoil. During the interphase that follows no
replication occurs.
o Reduction of chromosome number from diploid to haploid
o Cytokinesis occurs.
● Prophase II: Chromosomes, which still consist of two chromatids,
condense and become visible.
● Metaphase II: Spindle fibres attach to centromeres.
● Anaphase II: Centromeres separate and chromatids are moved to
opposite poles.
● Telophase II: Chromatids reach opposite poles. Nuclear envelope reforms.
Cytokinesis occurs, forming 4 haploid gametes.
Meiosis and genetic variation:
● Crossing over and random orientation promotes genetic variation.
● Random orientation of bivalents:
o 2n number of random orientations of bivalents, where ‘n’ is the
number of chromosomes possessed by a haploid nucleus of an
organism. Humans have 223~8 million different ways to place
● Crossing over:
o Allows linked genes to be reshuffled to produce new combinations,
called recombinants.
● Fertilization and genetic variation:
o Fusion of gametes is random.
Non-disjunction and Down syndrome:
● Occurs during anaphase I and results in a chromosome excess or
deficiency in a gamete.
● This can lead to trisomy 21 after fertilisation, also known as down
● Maternal age is positively correlated with the occurrence of trisomy 21.
3.4 Inheritance:
Mendel and the principles of inheritance:
● Male and females contribute equally.
● Inheritance is discrete; characteristics that are shown in one generation
don’t necessarily appear in the next.
● Some characteristics show a stronger tendency than others.
Gametes are haploid so contain one allele of each gene.
Male gamete is smaller than the female one.
It is motile, whilst the female is immobile/restricted in its movement.
Male and females make an equal contribution because each gamete is
haploid and come together to form a diploid cell, zygote.
● Zygotes have two alleles of each gene.
● These may be the same alleles or different alleles
● The zygote could contain various combinations of alleles, depending on
the number of available alleles.
● Segregation of alleles into different nuclei.
● Allows new combinations to form in the offspring.
● During meiosis if the parent cell contained two copies of the same allele,
each haploid cell would receive one copy of the allele.
● If PP, all gametes would receive a P. If Pp, 50% of gametes would receive
P and 50% would receive p.
Dominant, recessive and co-dominant alleles:
● Dominant alleles mask the effects of recessive alleles but co-dominant
alleles have joint effects.
● Dominant alleles would be expressed in the phenotype.
● Co-dominant alleles: Cw – White flowers. Ck – Red flowers. CwCk – Pink
● Dominant alleles code for an active protein whereas recessive alleles code
for non-functional proteins.
Punnett grids:
● Parent generation consists of two pure breeds (two of the same allele).
● They then breed to form a hybrid, usually heterozygous. This forms the F1
● These hybrids self-pollinate to form 1 homozygous dominant, two
heterozygous and 1 homozygous recessive. This forms the F2 generation.
ABO blood groups:
● IA is dominant because it codes for an active protein. This active protein
alters the glycoprotein by adding N-acetyl-galactosamine. Those without
IA would not have N-acetyl-galactosamine and would produce anti-A
● IB is dominant because it alters the glycoprotein by the addition of
galactose. Those without this allele would produce anti-A antibodies.
● IAIB causes the glycoprotein to be altered by the addition of both N-acetylgalactosamine and galactose. Anti-A antibodies aren’t produced.
● Allele ‘i’ is recessive because it does not alter the glycoprotein. The
presence of either IA or IB would result in the addition of galactosamine or
galactose respectively.
● IA codes or blood group A, IB codes for blood group B, ii, codes for blood
group O and IAIB codes for blood group AB.
Genetic diseases due to recessive alleles:
Most genetic diseases are caused by a recessive allele.
Will not show symptoms if heterozygous.
Both parents must be carriers of the disease.
Cystic fibrosis is an example of a genetic disease caused by a recessive
● Genetic diseases caused by chromosomes, besides the sex chromosomes,
are called autosomal diseases.
Other causes of genetic diseases:
● Red-green colorblindness and haemophilia are examples of sex-linked
● Huntington’s disease is caused by a dominant allele, and is autosomal.
● Sickle cell anaemia is caused by recessive allele HbS
● Genetic diseases are very rare to inherit and only 75 to 200 alleles among
25,000 genes in the human genome code for any known genetic diseases.
Cystic fibrosis:
● Cystic fibrosis is caused by the recessive allele of the CFTR gene, on
chromosome 7.
● Produces a chloride ion channel involved in sweat secretion, mucus and
digestive juices.
● Recessive allele codes for dysfunctional chloride ion channel, causing
reactions like mucus to be low in NaCl, thus little water moves into the
mucus and they become viscous and sticky.
● The sticky fluid builds up in the lungs and in the pancreatic duct, causing
infections and hindering digestive processes.
● Digestive processes are inhibited because the pancreatic duct is usually
blocked by the mucus so digestive enzymes cannot reach the small
Huntington’s disease:
Caused by the dominant allele of the HTT gene on chromosome 4.
Codes for a protein named huntingtin.
Causes degenerative changes in the brain, onset is around 30-50 years.
Causes changes in behaviour and emotion.
Life expectancy is 20 years after onset.
Sex linkage:
● When inheritance patterns are different in males and females, it is
presumable that the inheritable feature is located on a sex chromosome.
● Males have one copy of chromosome X and females have two copies. Since
X is so much larger than Y, most sex -linked diseases are located on the X
Red-green colorblindness:
Genes are located on the chromosome.
Caused by a recessive allele for a photoreceptor protein-coding gene.
Cone cells in retina are coded for by these.
Detects specific wavelength ranges of visible light.
If males inherit a chromosome carrying this recessive allele, they will be
● Females are less likely to inherit colour blindness unless both their
parents are either carriers or affected.
● Stems from an inability to make clotting Factor VIII.
● The gene that codes for this protein are on the X chromosome, and the
allele that causes haemophilia is recessive.
● Males would be more likely than females to inherit it.
Causes of mutation:
● High-energy radiation can be mutagenic as it can cause chemical changes
to DNA. Gamma rays, short-wave ultraviolet radiation and X rays.
● Some chemical substances like nitrosamines found in tobacco smoke are
also mutagenic. Benzene.
● Nuclear bombs and accidents at nuclear power stations contribute to the
excess amount of radiation of in some areas and massively increase the
number of mutations that occur within organisms in the surrounding
3.5 Genetic modification and biotechnology:
Gel electrophoresis:
● Separates charged molecules in an electric field according to size and
● Gel is immersed in conducting fluid and an electric field is applied.
● Negatively and positively charged molecules will move in opposite
directions. Proteins can be separated according to charge.
● DNA are all negatively charged but are too long to move through the gel
so are broken up into smaller fragments by restriction endonucleases.
● Smaller fragments will move further than larger ones in a set amount of
time, as they move faster.
● Hence electrophoresis can distinguish molecules by size.
DNA profiling:
DNA is obtained from a known individual.
Highly repetitive sequences sequences are selected and copied by PCR.
Copied DNA is then split by restriction endonucleases.
Fragments then undergo gel electrophoresis.
Banding pattern produced is the individual’s profile.
Profiles of different individuals can be compared.
Genetic modification:
● Is carried out by transferring genes between species. It is only possible
because the genetic code is universal.
● This makes it possible to transfer the genes for insulin coding to bacteria
to produce large quantities of insulin for the treatment of diabetics.
Methods of gene transfer:
● Endonucleases cut a section of a plasmid, and cut the desired genes from
a larger DNA molecule.
● The cutting process, leave single stranded sticky ends on both the plasmid
and on the genes from the DNA.
● Hydrogen bonds can form between the bases of the DNA genes and the
● DNA ligase seals the nicks in the sugar phosphate backbone after the
hydrogen bonds between bases have been formed.
Risks of GM crops:
● Environmental benefit of GM crops:
o Use of GM crop varieties reduces the need for ploughing and
spraying crops, so less fuel is needed for farm machinery.
● Health benefits of GM crops:
o Nutritional value of crops can be enhanced by increasing the
vitamin content/ removing allergens that may be present in the
crop naturally.
● Agricultural benefits of GM crops:
o Varieties resistant to drought, cold and salinity can be produced,
expanding the range over which crops can be produced and
increasing yields.
● Environmental risks of GM crops:
o Non-target organisms could be affected by toxins that are intended
to control pests.
● Health risks of GM crops:
o Antibiotic resistance genes used as markers during gene transfer
could spread to pathogenic bacteria.
● Agricultural risks of GM crops:
o Pests may become resistant to toxins used in GM crops,
exacerbating the issue.
Analysing risks to monarch butterflies of Bt corn:
● Gene transferred to corn from Bacillus thuringiensis that codes for Bt
● This kills butterflies, moths, flies, beetles and ants.
● Larvae of the Monarch butterfly feed on milkweed that often grows close
to corn,
● This milkweed could be dusted with the toxic pollen of Bt corn and the
larvae might be poisoned.
● Production of genetically identical organisms is called cloning. A group of
genetically identical organisms is called a clone.
● Identical twins are not clones because they have different fingerprints, for
● A single garlic bulb can clone itself to form several garlic bulbs that are
generally genetically identical.
● Strawberry plants grow long stems with plantlets at the end. These
plantlets grow roots into the soil and become independent of the parent
plant. These are identical to the parent plant.
Cloning animal embryos:
● Process of splitting an embryo is called fragmentation.
● It can be done because embryos are pluripotent.
o Totipotent – Can form any cell type, as well as extra-embryonic
(placental) tissue (e.g. zygote)
o Pluripotent – Can form any cell type (e.g. embryonic stem cells)
o Multipotent – Can differentiate into a number of closely related
cell types (e.g. hematopoietic adult stem cells)
o Unipotent – Can not differentiate, but are capable of self renewal
(e.g. progenitor cells, muscle stem cells)
● This has been observed to occur in coral embryos.
● Each individual embryo would then be placed in a surrogate mother.
● This is most successful at the eight-cell stage of the blastocyst.
Cloning adult animals using differentiated cells:
● Cloning by somatic cell nuclear transfer:
o Adult cells are taken from the udder of a sheep.
o In order to make the genes inactive and lose differentiation
patterns, the cells are grown in a medium of low nutrients.
o Unfertilised eggs are taken from another sheep and the nuclei are
o Cultured cells from the first sheep are placed inside the zona
pellucida around the egg and using an electric pulse they are fused
o With a 10% success rate, the new embryo is then injected into a
surrogate mother using IVF.
4 Ecology
4.1 Species, communities and ecosystems
● Species are groups of organisms that interbreed to produce fertile
● When two members of the same species mate and produce offspring they
are interbreeding.
● Crossbreeding is when members of different species breed together.
● Offspring of crossbreeding tend to be infertile.
● Interbreeding maintains recognizable characteristics of species
● Members of a species may be reproductively isolated in separate
● Population is a group of organisms of the same species that live in the
same area at the same time.
● Two populations may live in different areas but are still have the same
species as long as they could interbreed to produce fertile offspring.
● If they never interbreed it is likely that they may develop differences.
Autotrophs, heterotrophs and mixotrophs:
● Autotrophs make their carbon compounds from carbon dioxide and other
simple substances – self-feeding.
● Photosynthetic plants are an example of autotrophs.
● Parasites are exceptions to autotrophs because they evolved from them
(divergent evolution).
● Heterotrophs obtain carbon compounds from other organisms.
● Mixotrophs can have both auto/heterotrophic tendencies depending on
environmental circumstance. Organisms such as Euglena gracillis can
photosynthesis but also feed on detritus that they ingest by endocytosis.
● Consumers are heterotrophs that feed on living organisms by ingestion.
● They ingest their food; take in undigested material from other organisms,
digest it and absorb the products of digestion.
● Divided into primary, secondary and tertiary
● Many don’t fit into one specific trophic level because their diet includes
material from a variety of trophic groups.
Obtain organic nutrients by internal digestion.
Organic matter – dead leaves, feathers, dead animal parts, feces.
They ingest the dead matter and then absorb the products of digestion.
Unicellular organisms ingest it into food vacuoles whilst multicellular
ingest into gut.
● Saprotrophs are heterotrophs that obtain organic matter by external
● They secrete digestive enzymes into dead organic matter.
● Bacteria and fungi are common examples.
● Known as decomposers because they break down dead matter and
release elements such as nitrogen back into the soil.
● Populations of different species co-existing.
● All species are dependent on relations with other species, which is why no
population of one species can live in isolation ---
except humans, because we're
independent af.
Quadrat sampling:
Base line marked around habitat using measuring tape.
Random numbers are generated using a number generator.
First number is used to determine distance along the measuring tape.
Second is used to determine a distance out across the habitat at right
angles to the tape.
● Quadrat is placed precisely at the distance determined by the two random
● Only suitable for immotile species.
● Results:
o Positive associations: two species occur in the same parts of a
habitat and are therefore associated.
o Negative associations: two species occur in different parts of a
habitat thus tend to not grow around each other and are therefore
o Independent distribution: no association between species (forms
null hypothesis during chi squared test).
● Community forms an ecosystem by its interactions with the abiotic
● Organisms cannot live in isolation as they depend on their non-living
surroundings of air, water, soil or rock ok yea so maybe humans aren't independent.
Inorganic nutrients:
● Autotrophs and heterotrophs obtain inorganic nutrients from the abiotic
● Elements such as Carbon, Hydrogen and Oxygen are needed to make
monomers and polymers of the macronutrients we consume.
● Nitrogen and Phosphates are also needed (for DNA and proteins).
● These are obtained from the abiotic environment.
● Heterotrophs obtain such nutrients from carbon compounds in their food.
They can, however, obtain Calcium, Sodium and Potassium from their
abiotic environment.
Nutrient cycles:
● Supply of inorganic nutrients is maintained by nutrient cycling.
● Carbon cycle and nitrogen cycle are examples.
● Nutrients refer to elements that an organism needs.
Ecosystem sustainability:
● Ecosystems have the potential to be sustainable over long periods of time.
● Three requirements of nutrient sustainability:
o Nutrient availability
o Detoxification of waste products.
o Energy availability.
● Nutrients are often recycled and the waste products of one organism can
be used by another.
● Energy comes in continuous supply from the sun.
4.2 Energy flow
Sunlight and ecosystems:
● Most ecosystems rely on a supply of energy from sunlight.
● Three groups of autotrophs: plants, eukaryotic algae and cyanobacteria.
o not all plants are autotrophs like the dodder, which feeds on the
stems of other plants.
● Autotrophs rely on sunlight directly.
● Heterotrophs rely on sunlight indirectly.
● All energy in the carbon compounds will originally have been harvested
by photosynthesis in producers.
● Amount of sunlight absorbed/available for use, varies around the world.
Energy conversion:
● Light energy is converted to chemical energy in carbon compounds by
● Producers can release energy from their carbon compounds by cell
respiration and then use it for cell activities.
● This energy is eventually lost as waste heat.
● Large parts of carbon compounds remain in the cells and tissues of
producers and are available to heterotrophs.
Energy in food chains:
● Chemical energy in carbon compounds flows through food chains by
means of feeding.
● Consumers obtain energy from the carbon compounds in the organisms
on which they feed.
Respiration and energy release:
● Energy released by respiration is used in living organisms and converted
to heat.
o Need energy for synthesising large molecules (DNA RNA proteins).
o Active transport across membranes also consumes large amounts
of energy.
o Moving things around inside the cell, such as chromosomes or
vesicles or muscle fibres.
● Energy comes from ATP.
o Carbohydrates and lipids are oxidised during cell respiration.
o Oxidation is exothermic and therefore energy releasing – the
energy released is stored in ATP.
● Second law of thermodynamics states that energy transformations are
never 100% efficient.
o Energy that isn’t transferred from glucose to ATP is converted to
o Heat is also produced during cellular activities. (ATP => heat)
Heat energy in ecosystems:
● Heat energy cannot be converted to any other form of energy; hence
when it is produced it is generally lost to the environment.
● Heat makes living organisms warmer. It is therefore used as a mechanism
of homeostasis.
● Heat passes from hotter bodies to cooler bodies which is why it is
eventually lost to the abiotic environment.
Energy losses from ecosystems:
● Only about 10% of the energy at each tropic level becomes part of the
biomass of the organism in the next trophic level.
o As a result there is less and less bioavailable energy in each trophic
o This limits the number of trophic levels in food chains.
o Energy in faeces does not pass along the food chain and instead
passes to ‘decomposers’ like saprotrophs and detritivores.
o There is a lot of uneaten material, bones or hair, which passes to
decomposers and gets excluded from the energy chain.
o A large part of energy is lost to heat, due to respiration and other
cellular activities. The only energy available to organisms is the
chemical energy in carbon compounds.
● Biomass, measured in grams, also diminishes along food chains due to
loss of carbon dioxide and water from respiration and
uneaten/undigested parts of food.
o Biomass therefore decreases in higher trophic levels.
4.3 Carbon cycling:
Carbon fixation:
● Autotrophs convert carbon dioxide into carbohydrates and other carbon
compounds via carbon fixation.
● This reduces carbon dioxide concentrations in the air.
Carbon dioxide in solution:
● Carbon dioxide is present as a dissolved gas or hydrogen carbonate ions
in aquatic habitats.
● Disassociation of carbon dioxide to form H+ and HCO3- causes acidity.
● Aquatic plants to make carbohydrates and other carbon compounds
absorb carbon dioxide and HCO3- ions.
Absorption of carbon dioxide:
● Carbon dioxide taken in by autotrophs.
● Since carbon dioxide is used to produce carbon compounds within
autotrophs, there is a continuous debt of carbon dioxide causing a
concentration gradient with the atmosphere.
● This may happen through stomata on leaves or pores on stems.
Release of carbon dioxide from cell respiration:
● Release of carbon dioxide from cell respiration through diffusion.
● Non-photosynthetic cells in producers for example root cells in plants;
animal cells; saprotrophs and other decomposers of dead organic matter.
● Diffuses into water or atmosphere.
● Methane is produced from organic matter in anaerobic conditions by
methanogenic archaeans and some diffuses into the atmosphere.
● Methane is a waste product of anaerobic respiration.
o Bacteria convert organic matter into a mixture of organic acids,
alcohol, hydrogen and carbon dioxide.
o Bacteria use the organic acids and alcohol to produce acetate,
carbon dioxide and hydrogen.
o Archaeans produce methane from carbon dioxide, hydrogen and
▪ CO2 + 4H2 = CH4 + 2H2O
▪ CH3COOH = CH4 + CO2
● Archaeans are methanogenic. They carry out this process in mud along
shores, swamps, mires, mangroves, guts of animals, peat deposits and
landfill sites. Essentially anywhere that is predominantly considered as an
anaerobic environment.
Oxidation of methane:
● Methane is oxidised to carbon dioxide and water in the atmosphere.
● Monatomic oxygen and highly reactive hydroxyl radicals are involved in
methane oxidation.
● Results in low atmospheric concentrations despite large production on
Peat formation:
● Forms when organic matter is not fully decomposed because of anaerobic
conditions in waterlogged soils.
● Saprotrophs obtain oxygen that they need for respiration from air spaces
in the soil.
● Waterlogged soil is anaerobic so saprotrophs can’t respire as completely,,
so dead organic matter is left partially decomposed.
● Acidic conditions develop which further inhibit saprotrophs and
methanogens from breaking down the organic matter.
● This results in peat.
Fossilised organic matter:
● Partially decomposed organic matter was converted into oil and gas in
porous rocks/coal.
● Large deposits are a result of incomplete decomposition of organic matter
and its burial in sediments that became rock.
● Coal is formed when peat is buried under other sediments. Peat is
compressed and heated, turning into coal.
● Oil and natural gas is formed in the mud at the bottom of seas and lakes.
o Caused by incomplete decomposition in aerobic environments
o Compression and heating due to sedimentation causes chemical
changes to occur.
o Porous rocks hold methane and the sedimentation is formed by
impervious rocks placed above and below that prevent the
deposit’s escape.
● Carbon dioxide is produced by the combustion of biomass and fossilised
organic matter.
● Heating to ignition in the presence of oxygen causes combustion.
● Products are carbon dioxide and water.
● Combustion of forest/grassland is natural but can also be artificially
induced for agricultural purposes.
● Coal, oil and natural gas are burned as fuels.
● Animals such as reef-building corals and molluscs have hard parts that
are composed of calcium carbonate.
o These can be fossilized in limestone.
● Post mortem, in neutral/alkaline conditions, these exoskeletons form
deposits on the seabed or can precipitate to form limestone rock.
● 12% of calcium carbonate is carbon; it is therefore a large carbon sink.
Pool versus flux:
● Pool is a reserve of an element whilst flux is the transfer of an element
from one pool to another.
● Carbon cycle features the flux of carbon from one pool to another.
4.4 Climate Change:
Greenhouse gases:
● Gases in the atmosphere retain heat, similar to how glass retains heat in
● Water vapour and carbon dioxide are the two most potent greenhouse
● Water in clouds continues to retain heat and radiate it back to the earth’s
● Also reflects heat energy back from the Earth’s surface.
Other greenhouse gases:
● Methane:
o Released during extraction of fossil fuels and from melting ice.
o Also released from methanogens.
● Nitrous oxide:
o Released by bacteria and by agricultural processes/vehicle
● Greenhouse gases absorb longer wave radiation.
Assessing the impact of greenhouse gases:
● Two factors that determine the warming impact of a gas are:
o Their ability to absorb longer-wave radiation.
o The concentration of the gas in the atmosphere.
Long-wavelength emissions from Earth:
● Earth absorbs short-wave energy and re-emits longer wavelengths in the
form of infrared radiation.
● Solar radiation is short length.
Greenhouse gases:
● 30% of solar radiation is absorbed by ozone (UV rays).
● 80% of light reaching earth is radiated back towards atmosphere.
● Greenhouse gases capture 85% of remitted light; some of this energy is
radiated back to earth as it is scattered in all directions when re-emitted.
Global temperatures and carbon dioxide concentrations:
● Carbon dioxide concentrations from ice cores are consistent with the
positive correlation between carbon dioxide concentration and global
● There seems to have a large fluctuation in global temperatures over the
span of Earth’s lifetime. These fluctuations, when analysed, reveal that
higher global temperatures are usually preceded by higher
concentrations of carbon dioxide in the atmosphere.
● This shows that an increase in greenhouse gases could result in
increasing global temperatures.
● The consequences in any rise in global average temperature, however,
would not be evenly spread, and some areas would experience different
changes (like getting colder or experience more rain etc.).
Industrialisation and climate change:
● Industrialisation has caused the combustion of fossil fuels and biomass on
a wider and more profound level.
● This increases atmospheric concentration of carbon dioxide rapidly,
which as affected and will continue to affect rising average global
● Releasing sinks of carbon stored as fossil fuels into the atmosphere.
Coral reefs and carbon dioxide:
Ocean acidification will increase as carbon dioxide concentrations in the
atmosphere increase.
● Marine animals, such as reef-building corals, that deposit calcium
carbonate in their skeletons, need to absorb carbonate ions from
● Carbon dioxide, when dissolved in water, makes carbonate ion
concentrations lower due to the reduction of carbonate to form HCO3.
● This reduces carbonate levels, which are crucial to the survival of corals.
o Carbonates are used by corals to make their skeletons.
o Also if the seawater ceases to be saturated with carbonate ions,
existing calcium carbonate tends to dissolve, putting existing
skeletons of corals at threat.
5 Evolution and biodiversity
5.1 Evidence for evolution:
Evolution in summary:
● Evolution only concerns heritable characteristics.
● Occurs when heritable characteristics of a species change.
Evidence from fossils:
● Fossil records show the sequence in which organisms evolved and can
link together existing organisms with their likely ancestors.
● Sequence in which fossils appear matches the sequence in which they
would be expected to evolve.
● The sequence also fits in with the ecology of the groups (plant fossils
before animal fossils) etc.
● Many sequences of fossils are known, which link together existing
organisms with their likely ancestors.
Evidence from selective breeding:
● Selective breeding through artificial selection provides evidence for
● Considerable changes have occurred.
● However this only proves that selection has caused evolution, not that
evolution occurs naturally.
Evidence from homologous structures:
● Evolution of homologous structures by adaptive radiation explains
similarities in structures when there are differences in function.
● Analogous structures: different origins but have diverged due to the
performance of a similar function. Convergent evolution.
● Homologous structures: Look superficially different and perform different
functions but are similar in structure. E.g. pentadactyl limb. Same origin
but have diverged due to use/function. Adaptive radiation.
● Vestigial structures: structures that have no function and have slowly
diminished over time. Appendix; pelvic bone in whales.
Pentadactyl limbs:
Humerus/femur: single bone in the proximal part.
Radius+ulna/tibia+fibia: two bones in the distal part.
Carpals/Tarsals: group of wrist/ankle bones.
Metacarpals+Phalanges/metatarsals+phalanges: series of bones in each
of five digits.
● Populations of a species can gradually diverge into separate species by
● The characteristics of the two populations will gradually diverge to the
extent where they will no longer be able to interbreed to produce fertile
● Endemic species: one found only in a certain geographical area. Occurs by
migration and subsequent divergence.
Evidence from patterns of variation:
● Continuous variation across the geographical range of related populations
matches the concept of gradual divergence.
● Decision to lump populations together or split them into separate species
remains arbitrary.
Industrial melanism:
● Dark varieties of light insects are called melanistic.
● Biston Betularia, peppered moth.
● Melanic moths are better camouflaged in polluted areas as sulphur
dioxide blackens bark of trees and kills light coloured lichens.
● Example of evolution by natural selection as melanism affects survival
5.2 Natural selection:
● Natural selection occurs when variation amongst members of the same
species occurs.
● This way specific characteristics can be favoured over others, resulting in
higher chances of those characteristics becoming predominant in a gene
Sources of variation:
● Mutation: base-shift or base substitution. Produces new alleles, due to
base substitution at SNPs, enlarging the gene pool.
● Meiosis: New combination of alleles by breaking up existing
combinations. Every new cell created by meiosis is likely to carry a
different combination of alleles. Crossing over (recombination),
independent orientation.
● Sexual reproduction. Gametes come from different parents – combination
of alleles from two individuals. Allows mutations in different individuals
to be brought together.
● Characteristics that make an individual suited to its environment.
● These occur over time by natural selection.
● Acquired characteristics develop during the lifetime of an individual but
these are considered to be non-inheritable.
Overproduction of offspring:
● Overproduction of offspring means more offspring produced than
supportable by the environment. This is a selection pressure.
● This leads to a struggle for existence in which only the fittest and most
well adapted would survive.
Differential survival and reproduction:
● Well-adapted individuals survive and reproduce whereas less welladapted die or fail to reproduce.
● Favourable characteristics are therefore inherited by offspring as they
allow their ancestors to survive and reproduce successfully.
● This is therefore the process of natural selection.
● Individuals that reproduce pass on characteristics to their offspring.
● These are significant to evolution.
● Acquired characteristics are not.
Progressive change:
● Natural selection increases the frequency of characteristics that make
individuals better adapted and decreases the frequency of other
● This causes change within species towards adapting to the demands of
their environment.
Antibiotic resistance:
● Causes:
o Widespread use of antibiotics.
o Bacteria reproduce rapidly.
o Large populations of bacteria mean higher chance of gene
mutation forming resistance.
o Bacteria can pass genes between each other laterally using
● Process:
o Resistance gene either formed by mutation or received by another
o Use of antibiotic provides environment for natural selection to
occur (it is a selection pressure).
o Bacteria with resistance survive and reproduce rapidly forming
more resistant organisms in the population.
● This is why high risk patients are given a cocktail of antibiotics - to kill off
the bacteria that become resistant to one type of antibiotic with another
5.3 Classification of biodiversity:
The binomial system:
● Genus species:
o Genus name, upper case.
o Species name, lower case.
● Can be abbreviated to G. species after first use.
Hierarchy of taxa:
● Domain, Kingdom, phylum, class, order, family, genus, species.
o Delicious Katy Perry Came Over For Great Sex.
● Each taxon includes more species with fewer commonalities.
The three domains:
● Eukaryota:
o Histones in DNA.
o Lots of introns.
o Cellulose cell walls/ not present.
o Glycerol-ester lipids, d-form glycerol.
● Eubacteria:
o No histones.
o No introns (rare).
o Peptidoglycan cell wall.
o Glycerol-ester lipids; d-form glycerol.
● Archaea:
o Histone like proteins in DNA.
o Occasional presence of introns.
o Cell wall not made of peptidoglycan.
o Glycerol-ester lipids; I-form glycerol.
● Archaeans are found in extreme habitats of salinity/temperature/acidity.
Methanogens are an example.
● Viruses aren’t considered living and are therefore not classified in any of
the three domains.
Examples of classification:
● Grey wolf:
o Eukaryota, Animalia, Chordata, Mammalia, Carnivora, Canidae,
Canis, lupus.
● Date palm:
o Eukaryota, Plantae, Angiospermophyta, Monocotyledoneae,
Palmales, Araceae, Phoenix, dactylifera.
Natural classification:
● All members of a genus or higher taxon should have a common ancestor.
● This is called natural classification.
● Natural groups share many characteristics.
Reviewing classification:
● Evidence sometimes shows that members of a group do not actually have
a common ancestor.
● This results in splitting the group into two/more taxa.
● The opposite can also occur, uniting taxa.
Advantages of natural classification:
● Identification of species is easier. Dichotomous keys can be used to help
with this process. They can be assigned to a specific kingdom, phylum
class, etc. and therefore be identified relative to other known species.
● Because all of the members of a group in a natural classification have
evolved from a common ancestral species, they inherit common
characteristics. This allows prediction of characteristic within a group.
Bryophyta: mosses.
Filicinophyta: ferns.
Coniferophyta: conifers.
Angiospermophyta: flowering plants.
e organs –
Rhizoids but Root’s stems and leaves are present.
no true roots.
No cambium.
Present in confers and most
angiosperms. Allows secondary
thickening of stems
No pollen produced
Produced in Produced
male cones
No ovaries/ovules
Produced in Enclosed
female cones ovaries.
No seeds
Seeds are produced and dispersed
No fruits
Xylem and phloem are both present.
Fruits produced for
dispersal of seeds.
Porifera: Sponges.
Cnidaria: Jelly fish, sea anemone.
Platyhelminthes: Tapeworms.
Mollusca: Squid.
Annelids: Leeches.
Arthropoda: Insects, crabs.
Surface pores
hard Tentacles
have Mantle
shell made of secretes
cavity with segments,
fluid under with bristles
no No
system/ gas
bodies and
of legs/other
of appendages.
Bony ray-finned fish.
Bony ray-fish
Impermeable Skin
permeable to skin, in scales feathers made
and of keratin.
of keratin
Gills covered Simple lungs Lungs
an with
small extensive
and folding
moist ksin
surface area
No limbs
follicles with
hair made of
using ribs and
hollow wings
adapted for
Four legs or
two legs/two
are or two
Pentadactyl limbs
legs Four legs
supported by when adult
Eggs and sperm released for Sperm passed into the female for internal
external fertilization
in Larval
in Female lays Female lays
water, adult eggs with soft eggs
through their on land.
hard shells
life cycle
Swim bladder
Eggs coated in Teeth
No constant body temperature
5.4 Cladistics:
No teeth
have beak)
birth to live
young. Have
( Teeth
Constant body temperature
● A group of organisms that have evolved from a common ancestor.
Identifying members of a clade:
● Members of a particular clade can be identified by their base or amino
acid sequence.
● Species that diverged from a common ancestor long ago are likely to have
many differences.
Molecular clocks:
● Differences in base/amino acid sequences accumulate gradually.
● Positive correlation between number of differences between two species
and the time since they diverged from a common ancestor.
● Number of differences can be used to deduce when species split.
● Molecular clocks basically show how often a mutation occurs.
Analogous and homologous traits:
● Homologous is due to similar ancestry. E.g. pentadactyl limb.
● Analogous structures are similar due to convergent evolution. Evolve
independently and have similar uses/functions for the limb in question.
● Show probable sequence of divergence in clades.
● Principle of parsimony: computer programmes show how clades could
have evolved based on differences in their base sequences. Indicates
sequence of evolution.
● Branching point on a cladogram is called a node.
Cladograms and reclassification:
● Cladistics highlights that classifications made by structure are not always
accurate depictions of how the organism actually evolved.
Classification by morphology:
● Classification
characteristics rather than base sequence/amino acid sequence.
● Inaccurate.
6 Human Physiology
6.1 Digestion and absorption:
Structure of the digestive system:
● Mouth: chewing (mechanical digestion). Saliva contains amylase
(enzyme) and lubricants.
● Oesophagus: Peristalsis from mouth to stomach.
● Stomach: Churning into chime. Water and acid kills bacteria and
pathogens. Protein digestion.
● Small intestine: Digestion of lipids, carbohydrates, proteins, and nucleic
acids. Neutralisation of stomach acid and absorption of nutrients through
● Pancreas: Secretes lipase, amylase and protease.
● Liver: Secretion of surfactants in bile break up lipid droplets.
● Gall bladder: Stores/releases bile.
● Large intestine: reabsorbs water; carbohydrates are digested further by
symbiotic bacteria; formation/storage of faeces.
Structure of the wall of the small intestine:
● Serosa – Outer coat.
● Muscle layers – Longitudinal/circular muscle.
● Sub-mucosa – Tissue containing blood/lymph vessels.
● Mucosa – Lining of small intestine, epithelium absorbs nutrients on its
inner surface.
● Contraction of circular and longitudinal muscle layers of the small
intestine translocates food and mixes it with enzymes.
● Circular and longitudinal muscle in the wall of the gut is smooth muscle.
● Consists of short cells.
● Exerts continuous moderate force and short periods of forceful
● These contractions are called peristalsis.
● Circular muscles contract to prevent backflow of food - narrowing the
lumen behind the food.
● Contraction of longitudinal muscle assists movement forward - dilating
the lumen at and slightly ahead of the food.
● Controlled by the enteric nervous system.
● Unidirectional movement of food, away from the mouth.
● Main function of peristalsis in the intestine is churning of semi-digested
food to mix with enzymes.
Pancreatic juice:
● Secretes enzymes into the lumen of the small intestine.
● Two types of gland tissue:
o Cells responsible for sugar control (cells in the islets of Langerhans
- your alpha and beta cells) and;
o Cells responsible for digestive enzymes.
Controlled by enteric nervous system and hormones secreted by
Enzymes are secreted into ducts.
Enzymes synthesised on the rough endoplasmic reticulum (rER) of
Processed by the Golgi apparatus (GA) and secreted by exocytosis.
Amylase, lipases and proteases.
Digestion in the small intestine:
● Enzymes digest most macromolecules in food into monomers in the small
● Enzymes secreted by pancreas carry out hydrolysis reactions.
o Starch => Maltose (amylase).
o Triglycerides => fatty acids and glycerol (lipase).
o Phospholipids => fatty acids, glycerol and phosphate
o Proteins/polypeptides => shorter peptides (protease).
● Walls of small intestine produce other enzymes.
o Gland cells secrete enzymes into the intestinal juice, however most
enzymes are immobilised in the plasma membrane of the
o Types of enzymes are: nucleases, maltase, lactase, sucrase,
exopeptidases (break peptide chains into dipeptides) and
dipeptidases (break dipeptides into amino acids).
o These break all the nutrients down until they are reduced to the
● Some substances (like cellulose) remain undigested because humans are
unable to synthesise the necessary enzymes.
Villi and the surface area for digestion:
● Villi increase the surface area of the epithelium (mucosa) over which
absorption is carried out.
They are finger-like projections of the mucosa.
● Increase surface area by a factor of 10.
They have microvilli, which increases the surface area even more.
Absorption by villi:
● Absorb monomers formed by digestion as well as mineral ions and
o Any monosaccharides, amino acids, fatty acids, monoglycerides,
glycerol and nitrogenous bases are absorbed.
● The liver detoxifies harmful substances that pass through the villi; un-
harmful but unwanted substances are also absorbed by the liver but are
later excreted through urination.
● Bacteria passes through are eliminated through phagocytosis.
Methods of absorption:
● Methods of membrane transport are required to absorb different
● Nutrients move from the lumen of the small intestine, through the plasma
membrane, through the epithelium and into the lacteal/blood capillaries
of the villus.
● Fats:
o Triglycerides:
▪ Glycerol diffuse into villus epithelium. They can pass
through phospholipids.
▪ Fatty acids require facilitated diffusion (fatty acid
transporters) in the microvilli membrane).
▪ Fatty acids and Glycerol combine to form triglycerides once
inside the epithelium.
o Triglycerides coalesce with cholesterol to form larger droplets.
o Lipoproteins are released by exocytosis through the plasma
membrane on the inner side of the villus and either enter the
lacteal, or enter the blood capillaries.
● Glucose:
o Glucose cannot pass through simple diffusion because it is polar
and hydrophilic.
o Sodium-Potassium pumps in the inner part of the plasma
membrane pump sodium ions out from the cytoplasm into the
interstitial spaces of the villus and potassium ions in the opposite
o Creates low sodium concentration in the villus epithelium.
o Sodium-glucose co-transporter proteins in microvilli transport one
molecule of sodium and glucose together into the epithelium.
o Due to the low concentration of sodium into the villus epithelium,
and the relatively high concentration of sodium in the lumen of the
small intestine, the movement into the villus epithelium is passive,
through facilitated diffusion. Even though glucose is moving
against its concentration gradient, it moves into the epithelium
because sodium is moving down its own conc gradient.
o Glucose channels allow movement by facilitated diffusion into the
blood capillaries in the villus.
Starch digestion in the small intestine:
● Starch is a macromolecule composed of alpha glucose monomers linked
It is too large to be absorbed.
The breakdown of starch is exothermic but is too slow without enzymes.
Consists of two molecules:
o Amylose (1,4) unbranched
o Amylopectin (1,6) branched.
Amylase breaks down any 1,4 bonds in starch.
o Amylose is therefore broken down into maltose and maltotriose.
o Amylase cannot break down 1,6 bonds due to its active site
o Fragments containing 1,6 bonds are called dextrins.
Enzymes in microvilli on villi epithelium cells (maltase, glucosidase and
dextrinase) digest the three products of amylase digestion (maltose,
maltotriose and dextrin) into glucose.
The glucose is then co-transported with sodium ions into the villus
epithelium and into the blood capillaries, where it is sent to the liver via
the hepatic portal vein and any excess is turned into glycogen.
6.2 The blood system:
● Arteries convey blood at high pressure from the ventricles to the tissues
of the body.
● Elastic tissue contains elastin fibres.
o These fibres store energy to stretch them.
o The subsequent recoil of the fibres releases the energy and forces
the blood down the artery.
● Smooth muscle controls the diameter of the lumen and overall blood flow.
● Both elastic and smooth tissues prevent aneurysm (swelling of artery).
● Blood’s movement through arteries is pulsatile, reflecting each heartbeat.
Artery walls:
Have muscle and elastic fibres in their walls.
Tunica externa – tough outer layer.
Tunica media – thick layer with smooth/elastic fibres
Tunica intima – smooth endothelium.
Arterial blood pressure:
● Smooth and elastic fibres maintain blood pressure between pump cycles.
o Systolic pressure (peak pressure reached in an artery).
▪ Stores potential energy in elastin due to high pressure.
o Diastolic pressure (lowest pressure in arteries).
Elastin fibres squeeze blood in the lumen when pressure in
the lumen falls at the end of a heartbeat.
● Blood flow remains continuous, although pulsating, due to maintenance
of relative high pressure.
● Vasoconstriction: contraction of circular muscles.
o Form a ring so during vasoconstriction, the circumference reduces
and lumen is narrowed.
o Blood pressure is increased as a result.
o Arterioles have more circular muscles that control blood flow that
is usually hormone/neutrally regulated.
o Vasoconstriction restricts blood flow and vasodilation increases it.
● Allow the exchange of materials between cells in tissue and blood in the
● Supply blood to every tissue except cornea and lens.
● Capillary wall consists of a layer of endothelial cells.
o Single cell structure makes it very permeable.
o Permeability does however vary, and depends on the needs of the
tissues they perfuse.
● Blood cells are suspended in plasma.
o Some plasma leaks out of capillaries to become tissue fluid that
contains oxygen, glucose, etc. but not large protein molecules,
which can’t pass out of capillaries.
o Tissue fluid flows between cells so they can absorb nutrients and
oxygen and excrete metabolic waste into it.
o Tissue fluid then re-enters the capillaries.
● Collect blood at low pressure from body tissue and return it to the atria
from capillary networks.
● Much lower pressure (than arteries). Have thinner walls than arteries.
● Have fewer smooth/elastic fibres.
● Much larger lumen, hold more blood.
● Blood flow in veins is increased by contraction of muscles (muscles that
are not part of the blood vessel) in any activity.
● Most body parts are linked to more than one vein.
● Non pulsatile flow of blood.
Valves in veins:
● Ensure circulation by preventing backflow.
● Due to low blood pressure in veins, backflow is possible. Hence pocket
valves prevent this.
Flaps of pocket valves catch blood, fill with it, and block the vein’s lumen.
This increases pressure and past a certain pressure threshold the blood
pushes through the flaps and continues flowing towards the heart.
This allows for unidirectional blood flow.
Maximises the use of intermittent pressures by muscular and postural
10 Around 10 um
Relative thickness Relatively
thick Extremely thin
and wall and narrow
diameter of lumen lumen
Much larger than
10 um
Thin wall
wide lumen
Number of layers Three
layers, One layer, tunica Three
in wall
which are sub- intima.
(same as artery)
divided into more
Muscle and elastic Abundant
fibres in the wall
Small amounts
Present in most
Double circulation:
● Lungs are supplied with blood by a separate circulation.
● Blood is pumped to lungs at a lower pressure (which is why the right
ventricle is smaller than the left).
● Pulmonary circulation: to and from the lungs.
● Systemic circulation: to and from all other organs.
● Pulmonary artery carries deoxygenated blood and pulmonary vein carries
oxygenated blood.
● Caused by fatty tissue (atheroma) developing adjacent to the endothelium
in artery walls.
o Low-density lipoproteins (LDL) accumulate, and phagocytes are
attracted due to signals from endothelial cells. The combination of
LDL and phagocytes forms the atheroma.
● Smooth muscle cells form a tough cap on the atheroma, causing artery
wall to bulge and impeding blood flow.
● Coronary occlusion:
o Narrowing of blood arteries that supply the heart with oxygen.
● Causes angina, which impairs ability to contract – faster heart beat.
● Fibrous cap covering atheromas sometimes rupture, causing blood clots.
● Caused by:
o High LDL intake, diabetes, high blood pressure, production of
trimethylamine N-oxide by microbes in intestine.
Sinoatrial node:
● Initiates heartbeat and located in the right atrium.
● Myogenic; does not require stimulation from motor neurons.
● Contraction of cell depolarises the membrane causing surrounding cells
to depolarise too (due to local currents and impulse propagation).
● Have proteins that offset contraction also have most extensive
membranes to affect surrounding cells (depolarise).
● First to depolarise in a cardiac cycle.
Initiating the heartbeat:
● SA node acts as a pacemaker.
● Initiates each heartbeat, therefore setting the pace for the heart beat.
● Can be replaced by an artificial pacemaker (placed under the skin with
electrodes attached to wall of the heart).
Atrial and ventricular contraction:
● SA node’s electrical signals stimulate contraction in walls of atria and
● Electrical signal spreads through adjacent fibres in the heart and reach
atria in less than 1/10 of a second.
● Left and right walls of atria contract first.
● 0.1 seconds later the ventricles contract, once the electric impulse reaches
Changing the heart rate (HR):
● HR can be increased/decreased. This is caused by impulses brought the
heart through two nerves from the medulla of the brain (parasympathetic
to increase heart rate, sympathetic to decrease heart rate)
● SA node responds to signals from outside the heart, including two nerves
from medulla. Specific part of the brain – cardiovascular centre in the
● One nerve increases frequency of heartbeats (parasympathetic) and the
other nerve decreases frequency (sympathetic).
● Cardiovascular centre in brain responds to blood pressure, pH and
oxygen concentrations in the body.
Increases HR to prepare for vigorous physical activity.
SA node also responds to epinephrine (adrenaline). Increases HR.
Produced by adrenal glands, which sit on top of kidneys.
“Fight or flight” hormone.
NOTE: Notes are a bit weak with the cardiovascular system, specifically the
cardiac cycle. Look through study guide for this.
6.3 Defence against infectious diseases:
Skin as a barrier to infection:
● Skin and mucous membranes form a primary defence against pathogens
that cause infectious disease.
o Tough outer layer provides physical barrier.
o Sebaceous glands, associated with hair follicles, secrete sebum,
moisture and lowers pH.
▪ Inhibits growth of bacteria.
● Mucous membranes are found in nasal passages, penis, and vagina.
o Secrete sticky solution of glycoproteins, which acts as a physical
barrier by trapping pathogens. Goblet cells in the esophagus do
o Enzyme lysozyme gives anti-bacterial properties.
Cuts and clots:
● Cuts in the skin are sealed by blood clots.
● Blood changes from being liquid to a semi-solid gel.
● Clots prevent entry of pathogens.
Platelets and blood clotting:
● Clotting factors are released from platelets.
● Platelets aggregate at the cut, forming a plug and then release clotting
Fibrin production:
● Conversion of fibrinogen to fibrin by thrombin, which is activated by
prothrombin activator from prothrombin to thrombin.
● Release of clotting factors from platelets results in thrombin being
● Converts soluble protein fibrinogen into insoluble fibrin.
● Mesh of fibrin traps platelets and blood cells, increasing the clot.
Coronary thrombosis:
● Coronary arteries supply blood to the walls of the heart – oxygen and
glucose for cell respiration.
● Blood clot is called a thrombus in medical terms.
● Blood clot in the coronary arteries can result in heart being deprived of
molecules required for respiration.
o Cardiac muscles are unable to contract properly with the shortage
of ATP and become irregular and uncoordinated.
o Results in fibrillation.
● Occlusion in the coronary arteries occurs when an atheroma develops,
hardening the artery and damaging them.
● Lesions occur when the atheroma ruptures.
● These ruptures trigger the clotting process and results in fibrillation.
● Caused by smoking, high blood cholesterol concentration, and high blood
● White blood cells that give non-specific immunity.
● After skin and mucous membranes, the WBC gives a secondary line of
● They engulf pathogens by endocytosis and digest them with enzymes
from lysosomes.
● Infection of wounds results in pus – large amount of phagocytes
aggregating at the infected site.
Antibody production:
● Lymphocytes produce antibodies providing specific immunity.
● Proteins on the surface of the pathogen (antigens) are recognised as
foreign bodies and trigger a specific immune response.
● Antibodies bind to the antigen.
● Each lymphocyte produces one type of antibody.
● Few of these, but the antigens on the pathogens stimulate cell divisions
that produce the appropriate type of antibody.
● Plasma cells, clones of the antibody producing lymphocytes, then secrete
antibodies to control the pathogen.
● Have a hyper-variable region that binds to an antigen.
● Have another region that prevents viruses from docking to host cells and
makes pathogens more recognisable to phagocytes.
● Antibodies and plasma cells don’t remain after the infection.
o Some of the lymphocytes, instead of becoming plasma cells,
become memory cells, which remain inactive until the body is
invaded by the pathogen again.
Human immunodeficiency virus (HIV):
● HIV invades and destroys helper T cells and as a result antibodies cannot
be produced.
● HIV positive if body begins making antibodies against HIV
● Retrovirus uses reverse transcriptase to make DNA copies of its genes.
o Antiretroviral drugs can slow destruction of T helper cells.
o Results in weak immune system due to acquired immune
deficiency syndrome (AIDS).
o Occurs due to sex or sharing of hypodermic needles.
● Antibiotics block metabolic processes in prokaryotic cells, resulting in
their death
o These metabolic processes are not present in viruses (they don't
have metabolic processes as they rely on the host cells to carry out
their metabolic processes for them. This is why antibiotics don't
affect viruses.
● Does not affect human cells.
● Block DNA replication, transcription, translation, ribosomal function and
cell wall formation.
Viruses and antibiotics:
● Viral diseases cannot be treated using antibiotics because they lack a
● Live off the chemical processes of a host cell.
● Do not synthesise proteins and depend on a host for ATP synthesis.
● Using antibiotics to treat viral infections are redundant, and contribute to
the overuse of antibiotics, which contributes to antibiotic resistance.
● Antivirals can target viral enzymes (neuraminidase and hemagglutinin)
without affecting host cells.
Resistance to antibiotics:
● Bacteria have evolved with genes that confer resistance to antibiotics.
● Natural selection results in resistance. Some strains have developed such
as MRSA - methicillin resistant staphylococcus aureus.
● Doctors must prescribe antibiotics for serious bacterial infections only.
● Antibiotics courses must be completed.
● High standards of hygiene in hospitals.
● Animal feeds should not contain antibiotics.
6.4 Gas exchange:
● Maintains concentration gradients of oxygen and carbon dioxide between
air in alveoli and blood flowing in adjacent capillaries.
● Gas exchange happens by diffusion between air in alveoli and blood in
● Air in alveoli has higher oxygen concentration than in blood capillaries.
● Ventilation is the maintenance of this concentration gradient by supplying
the alveoli with fresh air.
Ventilation rate:
● Number of times air is drawn in/expelled in a minute.
● Tidal volume: volume of air drawn in and expelled with each inhalation or
Type I pneumocytes:
● Type I pneumocytes are extremely thin alveolar cells that are adapted to
carrying out gas exchange.
● Make up a large part of the epithelium.
● Thinness of the cells means shorter diffusion pathways.
Type II pneumocytes:
● Type II pneumocytes secrete a solution containing surfactant.
● Creates moist surface inside the alveoli to prevent the sides from sticking
together; this reduces surface tension.
● The fluid also dissolves oxygen, which can then diffuse to the blood in the
alveolar capillaries.
● Pulmonary surfactant: contained within fluid released by Type II
o Monolayer on the surface of the moisture lining the alveoli;
hydrophilic heads face the moisture and hydrophobic tails face the
o Reduces surface tension and prevents water from adhering to the
sides of the alveoli during exhalation.
Airways for ventilation:
● Air is carried to the lungs in the trachea and bronchi and then to the
bronchioles, which have alveoli.
● Rings of cartilage in trachea keep it open even when pressure is low or
surrounding tissue pressure is high.
Pressure changes during ventilation:
● Muscle contractions cause the pressure changes inside the thorax that
force air in and out of the lungs to ventilate them.
● Muscle contractions cause the pressure inside the thorax to drop below
atmospheric pressure, which results in inspiration (movement of
atmospheric air into thoracic cavity).
● The opposite leads to expiration (movement of air into the atmosphere
from the thoracic cavity).
Antagonistic muscles:
● Muscles are required for inspiration and expiration.
● Muscles are pulled into an elongated state by the contraction of another
● Contraction and relaxation of muscles to cause movement are known as
antagonistic pairs.
Antagonistic muscle action in ventilation during inspiration (opposite occurs
during expiration):
● Diaphragm: downwards and flattens (contracts).
● Ribcage: Moves upwards and outwards.
o External intercostal muscles contract.
o Internal intercostal muscles relax.
● Abdominal muscles relax.
● This allows volume inside the thorax to increase; internal pressure
decreases as a result.
Causes of lung cancer:
Smoking: Tobacco smoke contains mutagenic chemicals.
Passive smoking: non-smokers inhale tobacco smoke exhaled by smokers.
Air pollution: diesel exhaust fumes, nitrogen oxides.
Radon gas: radioactive gas that leaks out of certain rocks.
Asbestos: contained in dust and other particles that can be inhaled.
Results in larger air sacs with thicker walls.
Longer diffusion pathways lead to more inefficient gas exchange.
Less surface area for gas exchange.
Ventilation is therefore more difficult because lungs are less elastic.
Cilia that line the airways and get rid of mucus are damaged and stop
functioning. Mucus builds up as a result and causes infections. White
blood cells that combat these infections are damaged (inflamed and
damaged) by toxins in cigarette smoke, causing these WBCs and
surrounding cells to release trypsin, which breaks down the elastic fibres
in the lungs.
● Results in low oxygen saturation in the blood.
6.5 Neurons and synapses
● Neurons transmit electrical impulses. A nerve impulse is an electrical
● Cell body (cytoplasm + nucleus) and nerve fibres, along which impulses
● Dendrite: short branched nerve fibres.
● Axons: Elongated nerve fibres.
Myelinated nerve fibres:
● Myelinated nerve fibres: myelinations allows for saltatory conduction.
● Basic structure of a nerve fibre:
o Fibre is cylindrical in shape.
o Plasma membrane surrounds cytoplasm.
o One micrometre diameter.
o Conducts nerve impulses at a speed of 1 meter per second.
● Myelination is the formation of many layers of phospholipid bilayers,
created by Schwann cells.
o Each time a Schwann cell goes around the nerve fibre, a double
layer of phospholipid bilayer is deposited.
● Node of Ranvier is the gap between two myelinations.
o Nerve impulses jump from one node to the next – saltatory
o Much quicker than continuous conduction.
o Rate of 100 meters per second.
Resting potential:
● Maintenance of a resting potential by pumping of sodium ions out of the
axoplasm and potassium ions into the axoplasm.
● Sodium-potassium pumps transfer ions across the membrane in ratio of
● Potassium is pumped into axoplasm and sodium is pumped out of
● Membrane is more permeable to potassium than sodium, so more
potassium ions leak back than sodium.
● Negatively charged proteins/chlorine ions inside nerve fibre increases
charge imbalance.
● All factors contribute to creating a -70mV resting potential.
Action potential:
● Consists of depolarization and repolarization of the neuron.
● Depolarization is the change from negative to positive charge and
repolarisation is the change from positive to negative charge.
● Depolarization: Opening of sodium channels allowing sodium ions to
diffuse into the neuron. This raises membrane potential to +30mV.
● Repolarization: closing of the Sodium voltage gated channels and the
subsequent opening of the potassium voltage gated channels.
o Potassium ions then diffuse out down their concentration
o Membrane potential falls below resting potential -90mV.
● Refractory period: restoration of resting potential. This is
hyperpolarization, where the potential changes from -90mV to -70mV by
the action of the sodium potassium pump.
Propagation of action potentials:
● Occurs because the ion movements that depolarise one part of the neuron
trigger depolarization in the neighbouring part of the neuron (local
currents of Na+ ions moving diffusing to other areas of the axoplasm).
● Impulse propagation is unidirectional and moves along the axon.
● Refractory period prevents backwards propagation.
Local currents:
● Cause each successful part of the axon to reach the threshold potential.
● Depolarisation results in the influx of sodium ions.
o This results in there being a different sodium concentration at the
part of the axon where influx occurred, than a neighbouring part of
the axon.
o So, sodium ions diffuse between these regions both inside and
outside the axon.
● Movement of sodium ions between polarised parts to depolarised parts
(and vice versa) are known as local currents.
● By decreasing the concentration gradient (of sodium ions) in the part that
is still polarised, the membrane potential rises from -70mV to -50mV,
which is the threshold potential required to open the sodium voltage
gated channels and cause depolarisation.
o Thus local currents increase the membrane potential to the
threshold potential.
● Junctions between neurons and other neurons/receptor/effector cells.
● Neurotransmitters are used to send the electrical impulse across the
synapse in chemical form.
● Presynaptic and postsynaptic cells make this occur.
● Gap is called the synaptic cleft – 20 nanometres wide.
Synaptic transmission:
● Nerve impulse reaches the end of a neuron and depolarises the
presynaptic membrane.
● This results in the release of calcium ions to diffuse in, through channels,
into the membrane.
● This triggers vesicles with neurotransmitters to fuse with the presynaptic
membrane and the neurotransmitters to be released by exocytosis.
● Neurotransmitters then diffuse across the synaptic cleft and bind to
receptors on postsynaptic membrane.
● Triggers sodium ion channels to open and sodium ions to diffuse into the
postsynaptic neuron.
o Causes it to reach threshold potential and an action potential to be
● Neurotransmitters are then broken down and removed from the synaptic
● Used as a neurotransmitter.
● Produced by combining choline with an acetyl group.
● Loaded into vesicles and released into the synaptic cleft during synaptic
● Bind the specific receptors on postsynaptic membrane.
● Acetylcholinesterase rapidly breaks acetylcholine into acetyl and choline.
● Choline is then reabsorbed into the presynaptic neuron.
● Block synaptic transmission at cholinergic synapses in insects by binding
of neonicotinoid pesticides to acetylcholine receptors.
● Acetylcholinesterase does not break down neonicotinoids, so the binding
is irreversible.
● Synaptic transmission is therefore prevented.
● Not very effective on humans, however concerns regarding honeybees
have been raised.
Threshold potentials:
● Nerve impulses follow an all-or-nothing principle.
● If the threshold potential is reached then an action potential is triggered,
if not then it isn’t.
● If threshold potential is reached there will always be full depolarization.
● If the threshold potential is not reached in postsynaptic membrane,
sodium potassium pumps pump out the sodium ions that have entered
the postsynaptic neuron.
o The postsynaptic membrane returns to the resting potential.
● Most postsynaptic neurons in the brain have synapses with many
presynaptic neurons.
● Many of these release neurotransmitters at the same time so the
threshold potential will be reached.
6.6 Hormones, homeostasis and reproduction:
Control of blood glucose concentration:
● Insulin and glucagon are secreted by beta and alpha cells in the pancreas
to control blood glucose concentration.
● The maintenance levels of glucose in the body are 5 mmol/L. Variation
from this triggers a homeostatic response.
● Pancreas: exocrine (into ducts)and endocrine (release straight into
blood). Insulin and glucagon are released directly into the blood
● Islets of Langerhans contain alpha and beta cells.
● Glucagon increases blood glucose concentration by turning glycogen into
o Stimulates the liver cells to break glycogen down into glucose and
release the glucose. This increases blood glucose level.
● Insulin reduces blood glucose concentration.
o Stimulates uptake of glucose by various tissues (eg liver and
muscle cells) and for these cells to convert glucose to glycogen.
o Broken down by the cells it acts upon, so requires continuous
o Insulin stimulates other cells to use glucose in cell respiration
instead of fat.
● Consistently elevated blood glucose levels. Damages tissues; decreases
reabsorption of water from urine, resulting in dehydration.
● Type I: early onset.
o Inability to produce insulin. Autoimmune disease arising from the
destruction of beta cells.
● Type II: late onset.
o Inability to process/respond to insulin due to deficiency of insulin
receptors or glucose transporters.
o Caused by sugary or fatty diets, lack of exercise and genetic factors.
● Treatments:
o Type I: Constant blood sugar tests and insulin injections. Done
before a meal to prevent spikes in blood sugar. Implanted devices
that release insulin into blood as necessary. Stem cells can become
fully functional beta cells.
o Type II: Adjusting diet to reduce peaks and troughs of blood
glucose. Small frequent amounts of food. No sugary foods; only low
glycaemic carbs (slow digesting). Exercise and weight loss.
● Secreted by thyroid gland to regulate metabolic rate and control body
● Contains four atoms of iodine. Iodine is therefore important to the diet.
● Targets all body cells.
● Most metabolically active cells (liver, brain and muscle) are main targets.
● High metabolic rates = more protein synthesis and growth. Increases
body heat generation.
● Cooling triggers increased thyroxin secretion.
● Thyroxin deficiency:
o Lack of energy, forgetfulness and depression, weight gain,
● Tries to maintain normal body temperature by regulating metabolic
processes of the body → negative feedback.
o Less thyroxin secreted when body temp is too high= reduced
metabolic rate, reduced respiration and vasodilation of skin
o More thyroxin secreted when body temp is too low = increased
metabolic rate, increased respiration and vasoconstriction of skin
● Secreted by cells in adipose tissue and acts on the hypothalamus of the
brain to inhibit appetite.
● Blood leptin concentrations are controlled by: food intake and adipose
tissue amount in the body.
Targets group of cells in the hypothalamus that control appetite. Binds
onto them.
As adipose tissue increases, leptin concentrations rise, inhibiting appetite.
Obese mice had two copies of a recessive allele, ob. Those with
homozygous recessive could not produce leptin.
In obese humans, however, cells seem to have developed resistance to
leptin. Increased leptin levels, therefore, have no/reduced effect on
appetite restriction.
● Is secreted by the pineal gland to control circadian rhythms.
● Circadian rhythms are controlled by suprachiasmatic nuclei cells (SCN) in
the hypothalamus.
● Control secretion of melatonin from the pineal gland.
● Secretion increases in the evening and decreases at dawn.
● Melatonin release results in falling core body temperature.
● Melatonin receptors in the kidney lead to decreased urine production at
● Ganglion cells that detect whether it is light or dark and pass impulses to
the SCN, which allows it to adjust to the 24hr day and night cycle.
● Jet lag:
o SCN and pineal gland continue to set a circadian rhythm for the
point of departure rather than destination.
o Impulses sent by ganglion help regulate body to point of
o Melatonin tablets prevents onset of jetlag by promoting deeper
sleep etc.
Sex determination in males:
● Gene on Y chromosome causes embryonic gonads to develop as testes and
secrete testosterone.
● In the presence of the SRY gene, which codes for the TDF, testes develop.
● This gene is only found on the Y chromosome.
● TDF is not produced in girls, as they don’t have Y-chromosomes.
● TDF stimulates expression of genes for testis development.
● Causes prenatal development of male genitals and both sperm
production and development of male secondary sexual characteristics
during puberty.
o Testes develop in the 8th week.
o Until the 15th week, testosterone-secreting cells produce
testosterone, during which genitalia develop.
o At puberty, primary sexual characteristics (sperm) develop.
o Testosterone causes onset of secondary sexual characteristics
during puberty: enlargement of penis, pubic hair, deepening of
Sex determination in females:
● Oestrogen and progesterone cause prenatal development of female
reproductive organs and female secondary sexual characteristics during
● SRY gene is not present so embryonic gonads develop as ovaries.
● Oestrogen and progesterone are secreted by the mother’s ovaries and
then placenta.
● In the absence of fetal testosterone, the maternal oestrogen and
progesterone will contribute to the development of ovaries.
● Oestrogen causes the prenatal development of female reproductive
organs such as the fallopian tubes, uterus and vagina.
● Puberty causes the development of breasts and growth of pubic and
underarm hair.
o Also results in increased oestrogen and progesterone production.
o Positive feedback, as raised levels of oestrogen during puberty
cause development of female secondary sexual characteristics.
Reproductive systems of males and females:
Produce sperm and testosterone
Hold testes at lower than core body
Store sperm until ejaculation
Seminal vesicle
Secrete fluid containing alkali, proteins
and fructose that is added to sperm to
make semen and make it sticky.
Prostate Gland
Secretes alkaline fluid that is added to
sperm at the start of ejaculation and
helps sperm to swim.
Sperm duct/Vas eferens
Transfer sperm during ejaculation.
Transfer semen during ejaculation and
urine during urination.
Penetrate the vagina for ejaculation of
semen near the cervix.
Oviduct/Fallopian Tubes
Collect eggs at ovulation, provide a site
for fertilization then move the embryo
to the uterus.
Provide for the needs (protection, food,
oxygen and removal of waste
products) of the embryo and then fetus
during pregnancy.
Protect the fetus during pregnancy and
then dilate to provide a birth canal.
Stimulate penis to cause ejaculation
and provides a birth canal.
Protect internal parts of the female
reproductive system.
Menstrual cycle:
● Is controlled by negative and positive feedback mechanisms involving
ovarian and pituitary hormones.
● Follicular phase: follicles develop in ovary.
o An egg is stimulated to grow in each follicle. Endometrium is
repaired and thickens.
o Most developed follicle breaks open, egg is released into oviduct,
and other follicles degenerate.
Luteal phase: Corpus luteum formed from wall of follicle that released
o Endometrium continues to develop for implantation. If fertilisation
doesn’t occur, corpus luteum breaks down. Endometrium also
Towards the end of the menstrual cycle, FSH rises to a peak and follicle
development is stimulated.
o Secretion of oestrogen from follicle wall is also stimulated.
Oestrogen peaks at the end of a follicular phase and stimulates the repair
and thickening of the endometrium.
o Also increases FSH receptors, making follicles more receptive to
FSH and further stimulating the secretion of oestrogen (positive
feedback). At high levels, oestrogen then inhibits FSH.
LH rises suddenly at the end of follicular phase and stimulates:
o Completion of meiosis I in the oocyte and;
o Partial digestion of follicle wall so it can burst open at ovulation.
o Assists development of follicular wall into corpus luteum postovulation.
o This (Corpus Luteum) secretes more oestrogen and progesterone.
Progesterone levels rise at the beginning of the luteal phase and drop
back down by the end of the phase.
o Promotes thickening and maintenance of the endometrium and
inhibits FSH and LH secretion by the pituitary gland.
In vitro fertilisation IVF:
● Drugs are taken to stop FSH and LH secretion.
o Allows external control of menstrual cycle.
o Intramuscular injections of FSH and LH are administered for 10
days to stimulate follicle development.
o High concentration of FSH results in around 12 developed follicles
● HCG is then administered to stimulate maturation of follicles.
o Each egg is then mixed with 100000 sperm cells and incubated for
● After fertilization, eggs are placed in the uterus.
o Progesterone tablet placed in the vagina to ensure uterus lining is
7 Nucleic Acids
7.1 DNA structure and replication:
The Watson and Crick model suggested semi-conservative replication:
● DNA structure suggested a mechanism for DNA replication.
● Pyrimidine paired with purine.
● Bases are upside down in relation to one another as strands are
● Adenine has a surplus positive charge and Thymine has a surplus
negative charge.
o They are therefore electrically compatible.
● Cytosine paired with Guanine forms three hydrogen bonds, enhancing
The role of nucleosomes in DNA packing:
● Nucleosomes help to supercoil DNA.
● 2 copies of 4 types of histones linked together by linker DNA.
o Connects one nucleosome to the next.
o H1 (histone number 9) serves to bind DNA to the core particle of 8
● Process is supercoiling.
o Tails of histone proteins interact with tails from histone proteins
in other nucleosomes to tighten and supercoil the chromosome.
● H1 histone bins to form structure called the 30nm fibre that facilitates
further packing.
● Packed together in the nucleosome.
The leading strand and the lagging strand:
● Replication is continuous on the leading strand along the replication fork
as it opens; and discontinuous on the lagging strand moving away from
the replication fork.
● Replication occurs anti-parallel.
● Fragments on the lagging strand are called Okazaki fragments.
Proteins involved in replication:
● Proteins are involved as enzymes at each stage but also serve several
other functions.
DNA is unwound by DNA Helicase at the replication fork.
The strain developing ahead of helicase is released for unwinding by DNA
Gyrase (this is a specific class of DNA Topoisomerases).
The two strands are kept apart by single stranded binding proteins to
allow the template strand to be copied.
Multiple RNA primers on lagging strand but only one on leading strand.
o Necessary to start replication.
o These are created by DNA primase.
o Initiates activity of DNA polymerase III.
o DNA polymerase I replaces the primer with complementary
DNA Polymerase III covalently links deoxyribonucleotide-triphosphates
to the 3’ end of the growing strand.
DNA ligase links Okazaki fragments - specifically, creates sugar phosphate
bonds between the fragments.
Direction of replication:
● Replication begins at the origin of replication, where the RNA primer is
placed by DNA primase.
● Replication occurs in the 5’ to 3’ direction (nucleotides are added to the 3’
end of the primer)
Non-coding regions of DNA have important functions:
● Non-coding DNA has some function.
o Regulate gene expression.
o Produce tRNA and rRNA.
o Called introns.
● Repetitive sequences:
o 60% of human genome.
● Telomeres:
o Occur at the ends of eukaryotic chromosomes.
o Serve to protect DNA.
o Genes at the end of chromosomes would be lost if replication
continued to the end of a chromosome without a telomere.
o Telomere’s highly repetitive sequences are sacrificed.
DNA profiling:
● Variable number tandem repeats (VNTR) distinguishes individuals based
on the number of times this short sequence of DNA repeats.
● Inherited as an allele and is analysed in DNA profiling.
● Sections of VNTR allele combinations are cut from DNA using restriction
enzymes and analysed using gel electrophoresis.
● Two individuals can be compared in this way.
● Paternal lineage can be deduced by analysing alleles of VNTR from the Y
● Maternal lineage can be deduced by analysing variations in mitochondrial
DNA at specific hyper-variable region.
DNA sequencing:
● Copies of DNA are placed into test tubes with deoxyribonucleotides and
enzymes for replication.
● Small quantities of fluorescent dideoxyribonucleotides are added which
will stop replication upon being added.
o Dideoxyribonucleotides have H instead of OH on the 3rd carbon,
which prevents the binding of a phosphate group to it, hence
stopping the DNA replication process.
● Fragments created will be analysed through gel electrophoresis and
sequences will be determined through colour pattern of fluorescent
o New technology allows for the fluorescent dideoxyribonucleotides
to be detected by computers and quick interpretation of results.
7.2 Transcription and gene expression:
Regulation of gene expression by proteins:
● Promoter: non-coding DNA to which RNA polymerase binds. Not
● There are unregulated proteins that are necessary for survival and
regulated proteins that are only produced in certain amounts.
● Prokaryotic cells:
o Environmental factors influence regulation of gene expression.
o Specific genes are expressed to breakdown lactose but an absence
of lactose activates repressor proteins that repress the expression
of lactose metabolism genes.
● Eukaryotic gene expression is regulated in response to environmental
o Regulation of gene expression is crucial during embryonic
development and cellular differentiation.
● Three types of regulatory sequences on DNA:
o Enhancers: speed up transcription rates.
o Silencers: slow down transcription rates.
o Promoter-proximal elements: near to the promoter region.
Binding of proteins to them is essential for the start of
The impact of the environment on gene expression:
● Human behaviour or phenotype should be attributed to environment or
to heredity.
● Production of skin pigmentation in sunlight.
● Morphogens: impact gene expression in the embryo depending on where
the embryo cells are placed (endo/meso/ectoderm).
● Selective breeding and temperature can also impact gene expression.
Nucleosomes regulate transcription:
● Tails of histones are chemically modified to impact transcription.
● Acetylation, methylation or phosphorylation impact transcription.
● Acetylation neutralises positive charges that stops binding of lysine (on
DNA) to other negatively charged DNA therefore stopping tight packaging
and allowing for higher transcription levels.
● Chemical modification increases the accessibility of genes to transcription
● Direct methylation of DNA reduces transcription as it aids in supercoiling.
● These chemical modifications are called epigenetic tags and impact
● Epigenome: sum of all epigenetic tags. Can be inherited. Environment
affects inheritance.
o Most of the epigenome, however, is erased during reprogramming
during fertilisation.
o 1% survives – this is called imprinting.
The direction of transcription:
● Transcription occurs in a 5’ to 3’ direction.
● RNA polymerase binds to promoter region and unwinds RNA.
● Slides across it synthesising a single strand of RNA.
Post-transcriptional modification:
● Does not occur in prokaryotes.
o Impacts gene expression.
o Prokaryotic expression occurs during transcription, not after.
o No nuclear membrane around genetic material in prokaryotes
hence translation and transcription occur concurrently.
● Compartmentalisation in eukaryotes enables post-transcriptional
o Removal of introns.
o Pre-mRNA is spliced leaving the mature mRNA with exons only,
o 5’ cap and poly A tail to 3’ end are added.
mRNA splicing:
● Impacts number of proteins an organism can produce,
● Alternatively spliced mRNAs will differ in their AA sequence and
biological functions because particular exons may not be included in the
mature mRNA.
● Tropomyosin is spliced differently in different tissues resulting in five
forms of the protein.
o Exon 2 is missing from mRNA of skeletal muscle whilst exons 3
and 10 are absent from mRNA in smooth muscle.
7.3 Translation:
The structure of the ribosome:
● Two subunits:
o Large and small.
● Three binding sites:
o Aminoacyl.
o Peptidyl
o Exit
● tRNA:
o loops of seven unpaired bases.
▪ Three form an anticodon.
o Two other loops.
o CCA at 3’ end is site for AA attachment.
o Have hydrogen bonds.
tRNA-activating enzymes:
● Activation of the tRNA occurs when tRNA activating enzyme adds an
amino acid to the 3’ terminal.
● 20 different tRNA activating enzymes
o Active site of each is specific to an amino acid and a tRNA.
● Energy from ATP is needed to attach the amino acid onto the active site of
the enzyme.
o Once ATP and amino acid are attached, the amino acid is activated
by the formation of a bond between the enzyme and AMP
(adenosine monophosphate). Release of two phosphate groups
causes this.
o Activated amino acid is then covalently attached to tRNA.
● Energy from covalent bond later links amino acid to growing polypeptide
Initiation of translation:
● Initiation of translation involves assembly of the components that carry
out the process.
o mRNA binds to small ribosomal subunit at the binding site.
o tRNA molecule carrying methionine binds to start codon (AUG).
● Large ribosomal subunit binds to the small one.
● Initiator tRNA is in the P site, another tRNA binds to the A site.
o Peptide bond forms between the amino acids in the P and A sites.
● Synthesis of the polypeptide involves a repeated cycle of events
o Ribosome translocates three bases along the mRNA.
o tRNA moves to E site and is released; subsequent tRNA binds to P
site, with growing polypeptide chain and a new tRNA binds to A
o This cycle repeats.
● Disassembly of the components follows termination of translation.
o Stop codon is reached.
o Free polypeptide is released.
● Occurs in 5’ to 3’ direction.
Free ribosomes:
● Proteins for use primarily within the cell.
● Proteins destined for use in the cytoplasm, mitochondria and chloroplasts
are synthesised by ribosomes free in the cytosol.
Bound ribosomes:
● Synthesise proteins primarily for secretion or use in lysosomes.
● Destined for use in the endoplasmic reticulum, Golgi apparatus,
lysosomes, plasma membrane, extracellular.
● Signal sequence present of polypeptide determines whether a ribosome is
bound or free.
o This is translated first.
o Once the section is translated it is bound to a signal recognition
protein that stops the translation until it can bind to a receptor on
the surface of the endoplasmic reticulum.
o In the absence of the signal sequence, the polypeptide will
continue to be translated in a free ribosome.
Transcription and translation:
● Occurs concurrently in prokaryotes due to absence of nuclear
membranes. As soon as transcription ends translation begins.
● Polysomes represent multiple ribosomes attached to a single mRNA
● Polysomes are present in eukaryotes as well.
Primary structure:
● Number and sequence of amino acids in a polypeptide is the primary
● Huge diversity of proteins.
● 20^n, where n is the number of amino acids in a polypeptide.
Secondary structure:
● Secondary structure is the formation of alpha helices and beta-pleated
sheets stabilised by hydrogen bonds.
● Amino acids in a polypeptide have polar covalent bonds in their
backbones; they fold in a way that allows for hydrogen bonds between
carboxyl groups and amino acids.
Tertiary structure:
● 3D shape of a protein.
● Interaction of R groups with each other and with the surrounding water
● Positively charged R groups interact with negatively charged R groups.
● Hydrophobic amino acids orient themselves towards the centre whilst
hydrophilic orient themselves outwards.
● Polar R groups form hydrogen bonds amongst each other.
● Disulphide bridge formed by covalent bonds between R groups of
Quaternary structure:
● Exists in proteins with more than one polypeptide chain.
● Insulin is made of two chains and haemoglobin of four.
● Addition of non-polypeptide components is present; haemoglobin
consists of four chains and four haem groups.
● pH and temperature can distort the structure.
8 Metabolism,
8.1 Metabolism:
Metabolic pathways:
● Metabolic pathways consist of chains and cycles of enzyme-catalysed
● Small sequence of steps.
● Some metabolic pathways are chain reactions whilst some are cycles.
Enzymes and activation energy:
● Enzymes lower the activation energy of the chemical reactions that they
● Energy is required for substrates to reach a transition state, this is called
the activation energy (breaks or weakens bonds).
● Enzymes bind to the active site and are altered by this.
● This binding reduces activation energy and therefore elicits higher
efficiency and speed.
● Net amount of energy released by the reaction is unchanged by the
enzyme; only the activation energy is reduced, therefore increasing rate
of reaction.
Types of enzyme inhibitors:
● Competitive inhibition:
o Inhibitor binds to active site so substrates cannot bind.
o Increasing substrate concentration can overpower inhibitor and
restore full capacity.
o Sulfadiazine binds to dihydropteroate synthetase and in doing so
blocks para-aminobenzoate.
● Non competitive inhibition:
o Inhibitor binds to the allosteric site distorting the active site.
o Increasing substrate concentration will have a slight positive
effect; however since some enzymes are rendered dysfunctional by
the inhibitor, rate of reaction will still be lowered overall.
o Xylital-5-phosphate binds to allosteric site; disallows fructose-6phosphate from binding to active site of phosphofructokinase.
● End-product inhibition:
o Substance that binds to the allosteric site is the end product of the
pathway (in some cases); this acts as an inhibitor so the pathway
can be switched off to stop excess product generation.
o Reactions are therefore monitored by equilibrium, measured by a
ratio between product and substrate.
o Concentration of product increasing means reaction will slow
down and stop to maintain a balance.
o End product inhibition therefore stops excess final product and
also excess build up of intermediate products.
o Threonine dihydretase => Isoleucine.
▪ Isoleucine acts as a non-competitive inhibitor by binding to
the active site of the first enzyme in the chain – threonine
8.2 Cell respiration:
Oxidation and reduction:
Oxidation is the loss of electrons.
Reduction is the gain of electrons.
NAD + 2H => NADH + H+
Gaining oxygen is oxidation because oxygen has a high affinity for
electrons so draws electrons away from other parts of the molecule or
● Nitrifying bacteria oxidise nitrite ions to nitrate.
o NO2+0.5O2 => NO3
● Phosphorylation makes the phosphorylated molecule unstable.
● Adds phosphate group (PO4)3 – ‘activates’ the molecule.
● Addition of phosphate group is endergonic (energy absorbing) and
requires energy from hydrolysis of ATP, which is exergonic (energy
● Glucose => (ATP to ADP) => Glucose-6-phosphate.
Glycolysis and ATP:
● Glycolysis gives a small net gain of ATP without the use of oxygen.
● Metabolic pathway:
o Glucose.
o Glucose-6-phosphate (requires ATP=>ADP).
o Fructose-6-phosphate.
o Fructose-6-bisphosphate (requires ATP=>ADP).
o 2 x triose phosphate.
▪ Oxidised by removal of hydrogen atoms.
▪ Hydrogen atom accepted by NAD+ which because NAD++H+.
o Glycerate-3-phosphate.
▪ Created by oxidation of triose phosphate.
▪ The oxidation of triose phosphates provides the energy to
dephosphorylate them.
▪ Dephosphorylated to change ADP to ATP.
The link reaction:
● Pyruvate is converted into acetyl coenzyme A.
● Decarboxylation occurs first, ridding the three-carbon pyruvate of one
carbon, which is released along with oxygen as carbon dioxide.
● Then the pyruvate is oxidised, resulting in the reduction of NAD+
● The energy from these oxidations is used to associate the pyruvate with a
carrier molecule, resulting in the formation of acetyl CoA.
The Krebs cycle:
● Final breakdown of glucose molecule. Oxidation of acetyl groups is
coupled to the reduction of hydrogen carriers.
● Most of the energy is released in oxidations and the link reaction and the
Krebs cycle are used to reduce hydrogen carriers. This allows energy,
instead of being lost as heat, to remain in chemical form and be used in
oxidative phosphorylation.
● For 2 turns of every cycle, 6 NADH are produced, 4 decarboxylations
occur, 2 FADH are produced and 2 ATP are produced.
● Outline of the Krebs cycle:
o Acetyl CoA carboxylates oxaloacetate to form a 6 carbon
compound (citric acid/citrate)
o Citrate is decarboxylated, forming carbon dioxide, and oxidised to
create a molecule of reduced NAD.
o The five-carbon compound is decarboxylated, forming carbon
dioxide, and oxidised to reduce a molecule of NAD.
o On molecule of ADP is phosphorylated to form ATP and one
molecule of FAD is reduced to form FADH2. Reduction of FAD
provides energy for the phosphorylation of ADP.
o The four-carbon compound undergoes further oxidation and one
molecule of NAD+ is reduced to NAD.
● All the reduced NAD and FAD provide energy for oxidative
phosphorylation during the electron transport chain.
Electron transport chain:
● ETC – transfer of electrons between carriers of differing electron
● As electrons are transferred hydrogen ions are pumped into the intermembrane space from the matrix and across the inner membrane,
● They then diffuse through ATP synthase to provide the energy for ADP
phosphorylation to ATP.
● NADH+H+ supplies pairs of hydrogen atoms to the first carrier in the
o These hydrogen atoms donate their electrons to the electron
transport chain and move into the inner membrane space as
hydrogen ions. (Oxidation of hydrogen atoms).
o Concentration gradient of protons forms as a result and is a store
of potential energy.
● To maintain to the energy gradient between each electron carrier, the
electrons are transferred to a terminal electron acceptor, oxygen, which
then combines with two H+ ions from the matrix to become water.
o This is one of the waste products of respiration, and contributes to
the proton gradient and H+ ions are being removed from the
matrix. Thus there is also a need to refresh H+ ion supply.
● Energy released by protons moving through ATP synthase is used to
phosphorylate ATP. This is oxidative phosphorylation.
The role of oxygen:
● Oxygen is needed to bind with the free protons to form water to maintain
the hydrogen gradient.
● H+ ions in the matrix need to be used up to maintain concentration for the
diffusion of H+ ions through ATP synthase.
Structure and function of mitochondria:
● Semi-autonomous organelle. Grows and reproduces independently.
● 70S ribosomes and naked loop of DNA.
● Outer mitochondrial membrane compartmentalises the cell especially for
biochemical reactions of aerobic respiration.
● Oxidative phosphorylation occurs in the inner mitochondrial membrane.
ATP synthase and electron transport chain are contained here.
● Cristae increase surface area of inner membrane.
● Proteins build up in the inner membrane space.
o Volume of space is small so concentration gradient builds up
o Matrix site of Krebs cycle and link reaction.
▪ Contains enzymes for these reactions.
8.3 Photosynthesis:
Location of light-dependent reactions:
● Chloroplast has inner and outer membrane.
● Inner membrane encloses thylakoid membranes.
o Within this exists the thylakoid space.
● Light dependent reactions take place in the thylakoid space and across
the thylakoid membranes.
Products of the light-dependent reaction:
● NADP and ATP are produced in the LDR.
● Light energy => chemical energy (ATP) and NADPH+H+
Location of the light-independent reactions:
Light independent reactions take place in the stroma.
Inner membrane of the chloroplast encloses the stroma
Like cytoplasm it contains enzymes for the LIR.
LIR therefore occurs in the stroma.
Calvin cycle (LIR) is endergonic (creation of larger molecule fuelled by the
hydrolysis of ATP and oxidation of reduced NADP).
● Absorption of light by photosystems generates excited electrons.
● Photosystems: chlorophyll and accessory pigments groups together.
Called light harvesting arrays.
● Located in thylakoids; two photosystems – PSI and PSII.
● Besides the light harvesting arrays they contain reaction centres.
● When chlorophyll molecules absorb light, an electron within them gets
excited (photoactivation).
● These chlorophylls donate excited electrons to a central special
chlorophyll molecule, which donates the excited electrons to an electron
● LDR begins at PSII.
o First electron acceptor: plastoquinone.
▪ Collects two excited electrons from PSII and then moves to
another position for the ETC.
▪ Hydrophobic – stays within the membrane.
▪ Is reduced by the electrons.
o This processes occurs twice so PSII loses 4 electrons and two
reduced plastoquinones are created
● Photolysis of water provides electrons for use in the LDR.
o Chlorophyll in the reaction centres, after reducing plastoquinone,
are oxidised by inducing photolysis.
o Nearby water molecules split and give up electrons.
o 2H2O => O2+4H+4e-.
o Photolysis leads to the production of oxygen.
▪ Waste product diffuses away.
Electron transport chain:
● Transfer of excited electrons occurs between carriers in thylakoid
● Production of ATP from energy derived from light photophosphorylation.
● Carried out by thylakoids (stacks of membranes).
Photon gradient:
● Excited electrons from PSII are used to generate a proton gradient.
● Protons are pumped into thylakoid space as electrons pass from carrier to
● Concentration of protons develops in thylakoids spaces, store of potential
● 4H+ from photolysis also contributes to the proton gradient.
● ATP synthase in thylakoids generates ATP using the proton gradient.
● Protons pass through ATP synthase, providing energy for the
photophosphorylation of ADP.
● Plastocyanin is the final electron acceptor (water soluble) needed for next
Reduction of NADP:
● Excited electrons from PSI reduce NADP.
● Reduced NADP carries pairs of electrons that can carry out reduction
● Chlorophyll molecules in PSI undergo photoactivation and the same
process with the ETC occurs.
● However the final electron acceptor is called ferredoxin.
● Two molecules of reduced ferredoxin reduce NADP to form reduced
● Electrons carried by plastocyanine from PSII replace lost electrons in PSI.
● Sometimes, when NADP runs out, electrons carried by plastocyanin to PSI
go back to the start of the ETC and are used to phosphorylate ADP again
● This is known as cyclic photophosphorylation.
Carbon fixation:
● In the LIR, a carboxylase catalyses the carboxylation of ribulosebiphosphate.
● Occurs in the stroma.
● Produces Glycerate-3-phosphate.
● Rubisco (Rubp carboxylase) catalyses carboxylation of Rubp (5C) to form
a 6C compound that breaks down into 2 x 3C compound (G3P).
● G3P is converted into triose phosphate by:
o 2 x ATP => 2 x ADP + P
o 2 x reduced NADP => 2 x NADP
The fate of triose phosphate:
Triose phosphate regenerates RuBP and produces carbohydrates.
1 RuBp molecule is carboxylated in one turn of the Calvin cycle.
2 triose phosphates produced.
5 carbons out of six used to regenerate RuBP, so only one contributes to
formation of hexose (starch).
● Therefore 6 turns of the Calvin cycle create one carbohydrate hexose.
RuBP regeneration:
● RuBP is reformed using ATP.
● 5 triose phosphates ((3ATP=>3(ADP+P))=3RuBp.
Chloroplast structure and function:
Structure of the chloroplast is adapted to its function in photosynthesis
Double membrane forming outer chloroplast envelope.
Internal membranes (thylakoids).
Fluid filled thylakoids space.
Stroma, surrounding thylakoids, containing enzymes.
Stacks of thylakoids called grana
Starch grains/lipid droplets if photosynthesis happens at a fast rate.
Chloroplast’s structure-function relationship:
● Contain light absorbing arrays/ photosystems/ chloroplasts. Deep grana
increase light absorption.
● ATP by photophosphorylation.
● Proton gradient develops in small volume inside thylakoids.
● Chemical reactions of the Calvin cycle. Stroma contain all the enzymes
9 Plant Biology
9.1 Transport in the xylem of plants:
● Inevitable consequence of gas exchange in the leaf.
● Exchange of oxygen and carbon dioxide must occur to sustain
● Carbon dioxide is absorbed and Oxygen is released through stomata on
epidermis (underside) of the leaf.
● However the opening of the stomata to absorb CO2 and release O2 results
in the loss of water vapour (transpiration).
● Guard cells minimise water loss, which controls the aperture of the stoma.
Xylem structure helps withstand low pressure:
● Cohesive property of water and the structure of xylem vessels allow
transport under tension.
● Xylem: long continuous tubes, walls thickened with lignin, which
strengthens the wall to withstand very low internal pressures.
● Xylem vessels are arranged end-to-end.
● Mature xylem vessels are non-living so water flow is passive (cohesion
and adhesion).
● Internal pressures are much lower than atmospheric pressure.
● Cohesion:
o Formed due to hydrogen bonding in water, due to its polar
● Adhesion:
o Water is attracted to hydrophilic parts of the xylem.
● Cohesion and adhesion allow for passive movement of water up the xylem
(capillary action).
Tension in leaf cell walls maintains the transpiration stream:
● Adhesive property of water and evaporation generate tension forces in
leaf cell walls. The cohesion of water molecules to other water molecules
propagates this tension.
● The evaporation of water in the leaf causes water to be drawn into the
leaf from the xylem vessels in the veins of the leaf.
● This is caused by adhesion.
● The pressure in the xylem is already low, so for water to move out from a
low pressure environment would mean the force of adhesion between
water and the cell walls in the leaf is very strong.
● Movement of water out of the xylem reduces its pressure further and
causes a pulling force (movement from high pressure to low pressure)
that facilitates water movement.
o This is called the transpiration pull.
o IT depends on cohesion between water molecules to work.
Active transport of minerals in the roots:
● Active uptake of mineral ions in the roots causes absorption of water by
● Osmosis between root cell and soil occurs because solute concentration in
root cells is greater (100 times).
● Active transport establishes these concentration gradients.
o Mineral pumps in the plasma membrane of root cell.
o Each mineral ion has a specific protein pump.
o Mineral ions come in contact with protein pumps due to
diffusion/mass flow alongside water movement.
● Fungi facilitate the movement of mineral ions into the root hair cell.
o Create a symbiotic relationship with the plant.
o Fungi grow on the surface of the roots and into the cells of roots.
o Mineral ions are absorbed into the thread-like hyphae of the fungi
and are supplied to the plant.
o In exchange the plant proved the fungi with sugars.
o Example of a mutualistic relationship.
● Water movement from roots into xylem
o Apoplast pathway: through the cell walls.
o Symplast pathway: through the cytoplasm.
▪ Easy way to remember this - SYMPlast, ie simple - through
Replacing losses from transpiration:
● Plants transport water from roots to leaves to replace losses from
● Soil => roots (osmosis) =>Xylem (apoplast/symplast way is from roots or
other cells to xylem) => leaves.
Adaptations for water conservation:
● Xerophytes (desert plants):
o Increase rate of water uptake from the soil and reduced rate of
water loss by transpiration.
o Ephemeral: short life cycle, only alive during rainfall.
o Perennial: Store water in specialised leaves, stems/ roots.
o Cacti: Leaves are reduced in size. They have a thick waxy cuticle.
▪ Stoma are sparsely placed. Open at night to prevent water
▪ Carbon dioxide is absorbed at night and stored as malic
acid, which then released carbon dioxide slowly during the
day to be used for photosynthesis whilst stoma are kept
▪ Called crassulacean acid metabolism (CAM).
o Small hairs near stoma stop air from increasing transpiration rate.
o Stoma sit buried deep into epidermis.
o Film of water surrounding stoma reduces transpiration by
decreasing the concentration gradient of water.
● Halophytes (saline soil plants):
o Has salt concentration higher than in the saline soils surrounding
▪ This cannot be done just by increasing Na+ conc as this
would have adverse effects on cell activities such as protein
▪ Other solutes such as K+ and sugars are maintained at high
concs in the cytoplasm.
▪ Na+ can be maintained at high conc in vacuoles.
o Saline soils contain high salt concentrations.
o Leaves are small.
o Leaves shed during water scarcity.
o Stem becomes green and photosynthesises.
o Water storage structures in leaves.
o Thick waxy cuticle, multiple layer epidermis (longer diffusion
pathway for water).
o Sunken stoma.
o Long roots search for water.
o Structures to remove salt build-up.
9.2 Transport in the phloem of plants:
Translocation occurs from source to sink:
● Phloem is composed of sieve tubes, which are made up of specialised
sieve tube cells.
● Sieve tube cells are separated by perforated walls called sieve tube plates.
● Plants transport organic compounds from source to sink in a process
called translocation.
● Sugars and solutes are translocating.
● Phloem can transport biochemical in both directions.
● Pressure gradients caused movement of fluid.
● Energy is required to generate pressures (active process).
Photosynthetic tissues:
● Mature green leaves.
● Green stems.
Storage organs that are unloading their
● Storage tissues in germinating
● Tap roots or tubers at the start
of growth season
Roots that are growing or absorbing
mineral ions using energy from cell
Parts of the plant that are growing or
develop food stores:
Tap roots.
Phloem loading:
● Active transport is used to load organic compounds into phloem sieve
tubes at the source.
● Sucrose is the most prevalent solute in phloem sap.
● Makes a good transport form of carbohydrate because it is not readily
available to be metabolised.
● Phloem loading is the process by which sugars are brought into the
● Apoplast route:
o Sucrose travels from cell walls of mesophyll cells to cell walls of
companion cells.
o Transport proteins then actively transport sugar into the phloem.
Hydrogen ions are pumped out of the companion cells into the
interstitial spaces of the cell wall of the companion cell.
o They then flow back into the cell through a co-transport protein,
which provides the energy to carry sucrose into the companion
cell-sieve tube complex.
● Symplast route:
o Sucrose travels through plasmodesmata, which run between cells.
o This is down a concentration gradient.
o Sucrose converted to oligosaccharide in the companion cell to
maintain the sucrose concentration gradient.
Pressure and water potential differences play a role in translocation:
● Incompressibility of water allows transport by hydrostatic pressure
● Build up of sucrose in phloem draws water into the companion cell
through osmosis from the xylem.
● Rigidity of cell walls plus incompressibility of water results in hydrostatic
pressure build up.
● Water flows down pressure gradient.
● Sucrose is withdrawn from phloem at the sink end of the phloem and
used as an energy source or converted to starch.
● Loss of solute results in reduction in osmotic pressure and water is drawn
back into the transpiration stream (xylem).
Phloem sieve tubes:
● Sieve tubes consist of sieve tube cells.
● They have a nucleus and cytoplasm.
● They are living and depend on living cells to establish sucrose/organic
molecule concentrations through active transport.
● Sieve tube cells and companion cells share the same parent cell.
● Companion cells perform the genetic and metabolic functions of the sieve
tube cells.
● Companion cells contain large amounts of mitochondria for active
transport of H+ ions for sucrose co-transport.
● Infolds of plasma membrane in companion cells increases the loading
capacity of phloem using the apoplastic route.
● Plasmodesmata link cytoplasm of companion cells with sieve tube cells.
● Rigidity of cell walls of the sieve tube cell allow for establishment of a
pressure gradient.
● Perforated walls (sieve plates) plus reduced cytoplasm means that
phloem sap will move easier.
9.3 Growth in plants
Growth in plants:
● Undifferentiated cells in the meristems of plants allow indeterminate
● Plant growth is indeterminate, cells continue to divide indefinitely.
● Some plant’s cells, unlike animal cells, are totipotent.
● Meristems are composed of undifferentiated cells.
● Primary meristems are at the tips of stems/roots (apical meristems).
● Dicotyledonous plants also have lateral meristems.
Role of mitosis in stem extension and leaf development.
● Mitosis and cells division in the shoot apex provide cells needed for
extension of the stem and development of leaves.
● Cells in the meristem are small but increase in volume by absorbing
nutrients and water.
● With each division one cell remains as a meristem whilst the other
increases in size and differentiates.
● Apical meristem can give rise to specialised cells: procambium (vascular
tissue), protoderm (epidermis) and ground tissue (pith).
● Young leaves are produced at the sides of the shoot apical meristems,
known as leaf primordia.
Plant hormones affect shoot growth:
● Plant hormones control growth in the shoot apex.
● Auxins have a broad range of functions: initiating growth of roots,
development of fruits and regulating leaf development.
● IAA (indole-3-acetic acid).
● Controls growth in the shoot apex through elongation of cells in stems.
● Synthesised in the apical meristem and transported down the stem to
stimulate growth, but can inhibit growth in very high concentrations.
● Axillary buds grow at the node between stem and base of leaf.
● Meristems are left behind at the node as shoot apical meristems grow and
form leaves.
● Auxin produced by shoot apical meristem inhibits growth at these nodes
(apical dominance).
o The further the distance between the node and the shoot apical
meristem, the lower the concentration of auxin at the node and the
less likely growth at the node will be inhibited.
o Cytokinins, produced in the root, promote axillary bud growth.
o Ratio between cytokinins and auxin determine whether
development in the axillary bud will occur.
o Gibberellins will contribute to stem elongation.
Plant tropisms:
● Plants respond to the environment by tropisms.
● Light and gravity influence growth directionality.
● Phototropism and gravitropism (geotropism).
Auxin influences gene expression:
● Auxin influences cell growth rates by changing the pattern of gene
● Phototropins absorb light in the first stage of phototropism.
● Light of a specific wavelength (blue light) alters their structure to trigger
off movements of auxin by active transport. This is carried out by auxin
pumps in the plasma membrane.
● Once the auxin is pumped out of the membrane into the cell wall of the
next cell it binds to a proton and diffuses into a cell through the plasma
● It is then pumped out by an efflux pump again after it loses its proton.
● The auxin efflux pumps are moved around in accordance to light intensity
differences, so they set up a conc gradient of auxin from lower conc on the
lighter side to higher conc on the darker side.
● Auxin binds to auxin receptor, promoting the transcription of specific
genes. The expression of these genes causes the secretion of hydrogen
ions into the cell wall, which interacts with the cellulose fibres and
loosens them, allowing cell expansion.
Intracellular pumps:
● Auxin efflux pumps set up concentration gradients of auxin in plant tissue.
● Auxin is transported to the shaded area during phototropism.
● Higher concentrations of auxin in the shaded area cause growth here, so
the stem curves towards the brighter light.
● Gravitropism:
o Gravity causes cellular organelles caused statoliths to accumulate
at the tip of roots.
o PIN3 transporter proteins direct auxin transport to the cells.
o Therefore downward growth occurs here.
Micropropagation of plants:
In vitro procedure that produces large numbers of identical plants.
Depends on the totipotency of plant tissue.
Tissues are cut into pieces called explants.
Least differentiated tissue serves as the source tissue (meristem).
Placed into growth media that includes plant hormones, cytokinins and
● This creates an undifferentiated mass called a callus.
● If growth media contains a 10:1 ratio of auxins to cytokinins then roots
develop (rooting media). If less than 10:1 then shoots develop (shoot
media). Cloned parts can be transferred to soil.
Micropropagation is used for rapid bulking up:
● Viruses are transported within a plant from cell-to-cell through vascular
tissue and via plasmodesmata.
● Micropropagation can be used to produce virus free strains of plants.
● Can also be used to produce plants with specific characteristics.
● Also being used to preserve species of orchids.
● Micropropagated plants can be stored in liquid nitrogen
Differences between monocots and dicots:
9.4 Reproduction in plants:
Flowering and gene expression:
● Flowering involves change of gene expression in the shoot apex.
● Vegetative structures: roots, stems and leaves.
o These form during seed germination during the vegetative phase.
● The productive phase causes flower growth.
o Meristems produce flowers instead of leaves.
● Flowers allow for sexual reproduction; are produced by the shoot apical
meristem and are a reproductive shoot.
● Temperature plays a role in transforming leaf-producing shoot into
flower-producing shoot.
● Light plays a role in producing inhibitors/ activators of genes that control
● Long day:
o Activation of pigment phytochrome results in transcription of FT
gene (flowering time).
o FT mRNA then transported to shoot apical meristem and
translated into FT protein that binds to a transcription factor and
causes the consequential activation of many flowering genes.
o This transforms leaf-producing apical meristems into reproductive
Photoperiods and flowers:
● Switch to flowering is a response to the length of light and dark periods in
many plants.
● Long day plants (LDP) flower when nights are shorter.
● Shorter day plants (SDP) flower when nights are long.
● Length of darkness is the trigger for flowering, not length of daylight.
● Pr is converted to Pfr with 660nm sunlight, this happens in abundance
because sunlight mostly comprises of this wavelength (red).
● Pfr is converted to Pr in 730 nm. Less important because sunlight contains
little of this wavelength (far red).
● In darkness, however, Pfr gradually changes into Pr because Pr is a more
stable form.
● Pfr is the active form of phytochrome and binds to receptor proteins
present in the cytoplasm which control for the transcription of genes (FT
gene) needed for flowering.
● In long-day plants large amounts of Pfr remain to bind to the receptor and
therefore transcription is promoted.
● In short-day plants the binding of Pfr to a receptor inhibits flowering.
However because there is such little Pfr remaining at the end of a long
night, the inhibition fails and flowering proceeds.
Inducing plants to flower out of season:
● Plants can be induced to flower out of season.
● This can be done by manipulating the length of days and nights.
Animal pollinated flowers:
● Carpel:
o Stigma
o Style.
● Stamen:
o Anther
o Filament
● Sepal
● Ovary
Mutualism between flowers and pollinators:
● Most flowering plants use mutualistic relationships with pollinators in
sexual reproduction.
● Sexual reproduction requires the transfer of pollen from one plant’s
stamen to another plant’s style.
● Wind pollination and water pollination exist, however animals are most
common pollinators.
● Birds, bats, insects and bees.
● Pollinators gain food from nectar and plants gain a means to reproduce –
hence mutualism.
Pollination, fertilization and seed dispersal:
Each pollen grain on the stigma grows a tube down the style to the ovary.
Carries the male gametes to fertilise the ovary.
Located inside the ovule.
Ovule develops into seed and ovary into fruit.
Seed dispersal reduces competition between offspring and parent, and
spreads species geographically.
● Means of seed dispersal varies depending on the type of seed.
Structure of seeds:
● Seed consists of:
o Embryo plant:
▪ Embryo root.
▪ Embryo shoot (plumute).
▪ One/two cotyledons.
o Food reserves
o Protective seed coat.
● Cotyledons are the embryo leaves and contain the food reserves of the
● In some plants endosperm store food.
● Seed coat is known as testa.
● Micropyle is a small hole through the testa.
Germination experiment design:
● Dormancy:
o Non-germination even when provided with favourable conditions.
o Water is required for germination, either for rehydration or to
wash out a hormone that inhibits germination.
o Growth of embryo root/shoot also requires water.
● Germination:
o After absorption of water, metabolic rate of seed increases, and
energy is released by aerobic respiration.
o Oxygen is also required.
o Warmth is required for enzyme functionality during germination.
● Synthesis of gibberellin occurs at the start of germination.
o This hormone stimulates mitosis and cell division in the embryo
and stimulates amylase production, which breaks down starch in
the food reserves into maltose, which is then converted into
● Sucrose/glucose can be transferred via the phloem to where they are
needed (translocation).
● Embryo root/shoot require sugars for growth and glucose for aerobic
10 Genetics and Evolution
10.1 Meiosis:
Chromosome replication:
● Protein based structure forms between the homologous chromosomes
called the synaptonemal complex.
● Crossing over occurs between non-sister homologous chromatids.
Exchange of genetic materials:
● Crossing over is the exchange of DNA material between non-sister
homologous chromatids.
● Non-sister chromatids “invade” a homologous sequence on a non-sister
chromatids and bind to the region.
● They continue to adhere to the point, and these points of connection are
called chiasmata.
Chiasmata formation:
● Breaks occur in chromosomes and non-sister chromosomes invade a
homologous sequence and bind to its region.
● Connected points are called chiasmata.
● Serves to stabilise bivalents.
● Increases genetic variability.
● Exchange of DNA between maternal and paternal chromosomes.
● Independent assortment arises because linked alleles can be decoupled.
● Crossing over can occur multiple times between different chromatids
within the same homologous pair.
New combinations of alleles:
● Crossing over produces new combinations of alleles on the chromosomes
of the haploid cells.
● Occurs because genes are linked.
Meiosis I:
● Sister chromatids remain associated with each other.
● Homologous chromosomes behave in a coordinated fashion in prophase.
● Homologous chromosomes exchange DNA leading to genetic
● Meiosis I is a reduction division in that it reduces the chromosome
number by half.
Independent assortment:
● Occur due to random orientation of pairs of homologous chromosomes in
meiosis I.
● Random movement to poles during anaphase I is caused by independent
orientation: direction in which chromosomes face does not affect the
direction in which any other chromosomes are facing.
● There is an equal probability of a particular combination being produced.
Meiosis II:
● Interphase does not reoccur between meiosis I and II.
● Mitosis and Meiosis II both separate a replicated chromosome into
● However these sister chromatids are likely to be non-identical sister
chromatids due to crossing over.
Segregation and independent assortment:
● Unlinked genes segregate independently as a result of meiosis.
● Segregation is the separation of two alleles of a particular gene.
● Genes that are unlinked – exist on different chromosomes – will segregate
independently because the chromosomes will be pulled to opposite poles.
● Genes on the same chromosome are linked.
● These will not segregate independently. Genes that are on the same
chromosome but are placed far apart have a higher change to form an
● They may be separated during crossing over and therefore will function
as unlinked genes.
Punnett squares for dihybrid traits:
● Used to predict the occurrence of a particular geno/phenotype.
● The Mendelian ratio for independently assorted traits is 9:3:3:1.
o This is for the F2 generation.
● The chance of a particular gamete of the F1 generation containing an
allele is ½, if there are two alleles and inheritance is independent.
● Hence, a particular combination of alleles would be (1/2*1/2)=1/4.
● This corresponds to the law of independent assortment, where unlinked
genes segregate independently from each other.
Linked genes:
Group of genes were all located on the X chromosome of Drosophila.
These genes were arranged in a linear sequence.
Locus of a gene: specific position of a gene on one chromosome type.
Homologous: two chromosomes with the same sequence of genes.
o They vary in the alleles of genes present at a particular point.
● 8 chromosomes in a diploid Drosophila.
o Males have an XY and females have an XX.
o The other 6 are autosomes and are common to both.
o 3 autosomal pairs.
● Two types of gene linkage:
o Autosomal and sex.
● Sex linkage means the genes are located on the X chromosomes.
Polygenic characteristics:
● Polygenic characteristics tend to show continuous variation.
● Two or more genes have an additive effect hence affecting the same
phenotypic characteristic.
● This additive effect is caused by co-dominant alleles that are unlinked.
● The F2 generation would show ratios based on alternating levels of
Pascal's triangle.
● Number and frequency of variants would be affected by the number of codominant alleles for a particular gene – an increasing number of which
would bring the distribution close to the normal distribution.
● Height/intelligence in humans are all examples of polygenic inheritance.
Environmental influence:
● Environmental factors blur the differences in phenotype to make them
● Sunlight stimulates the production of black pigment melanin in the skin.
● Skin colour is also influence by several genes and is therefore polygenic.
Identifying recombinants:
● Linked genes are part of the same chromosomes and therefore do not
follow the laws of independent assortment (9:3:3:1).
o Alleles of such genes would pass together into a gamete.
o Results in a higher frequency of the parental combinations than
predicted from Mendelian ratios.
● Linkages between pairs of genes are not complete and therefore new
combinations are formed as a result of crossing over.
o Formation of new combinations is called recombination.
o An individual with a recombinant chromosome is called a
10.3 Gene pools and speciation:
Gene pools:
● Gene pools consist of all possible genes and alleles of an interbreeding
● Some populations of the same species are geographically isolated so it is
possible for multiple gene pools to exist for the same species.
● Gene equilibrium: all members of a population have an equal chance of
contributing to the future gene pool.
Allele frequency and evolution:
● Evolution requires that allele frequencies change with time in
● Occurs due to:
o Mutations.
o Selection pressures favouring certain traits.
o Barriers to gene flow between different populations.
Patterns of natural selection:
● Fitness of geno/phenotype: Likelihood that it will be found in the next
● Three patterns of natural selection:
o Stabilizing: Extremities are removed e.g. preference of the average
over the extreme.
o Disruptive: Favour extremes over intermediate varieties. Longer
necks in giraffes are preferred.
o Directional: Population changes, as one extreme of a range is
better adapted.
There are different categories of reproductive isolation:
● Reproductive isolation can be temporal behavioural or geographic.
● Allopatric speciation: speciation that occurs due to geographic separation.
● Sympatric speciation: isolation within the same geographic area;
isolation is behavioural. Different mating practises/ courtship
● Temporal speciation: Occurs as species are only active during specific
seasons etc. therefore don’t reproduce.
Gradualism versus punctuated equilibrium in speciation:
● Speciation due to divergence of isolated populations can be gradual.
● Gradualism states that species change through many intermediate forms.
● Countered by punctuated equilibrium which states that speciation can
occur abruptly.
o Stability is punctuated by periods of rapid evolution.
o This explains that gaps in the fossil record are simply evidence for
this punctuation.
o Allopatric speciation can lead to rapid speciation.
o Rapid change is more common in organisms with short generation
Polyploidy can lead to speciation:
● Can lead to sympatric speciation.
● Polyploidy can only mate with each other.
● Caused by hybridization events between different species/nondisjunction
in meiosis.
Polyploidy has occurred frequently in Allium:
● Around 50 to 70% of angiosperms have experienced a polyploidy.
● Allium genus includes onions.
● Allium reproduces asexually and polyploidy may confer an advantage
over diploidy under certain selection pressures.
11 Animal physiology
11.1 Antibody production and vaccination:
Antigens in blood transfusion:
● Every organism has unique molecules on the surface of their cells.
● Molecules that trigger a foreign response are called antigens and are
found on the surface of cells.
● Immune systems function based on recognising foreign antigens from
● Antigens on the surface of RBC stimulate antibody production in a person
with a different blood group.
● Antigen B: galactose. Antigen A: n-acetyl-galactosamine. Antigen AB: both.
● Wrong blood type results in agglutination followed by haemolysis
o Antibodies clump incompatible RBC (agglutination) and then
destroy them (haemolysis).
The specific immune response:
● B-lymphocytes are activated by T lymphocytes.
● Pathogens ingested by macrophages and antigens (from the pathogens)
are displayed on the plasma membrane of the macrophages on the
antigen presenting cells.
● T helper cells bind to antigens displayed by macrophages and are
● T helper cells then bind to B-lymphocyte cells.
o Specific B-lymphocytes are selected depending on whether they
have the receptor protein for the antigen that the T helper cell
● B cells are activated accordingly and become mature B cells
The role of plasma cells:
● Plasma cells secrete antibodies.
● They are mature B-lymphocyte cells and secrete antibodies during
immune response.
● Cell’s cytoplasm contains lots of rER to produce antibodies (specific to
● Range of genes expressed is much lower, since only a specific antibody is
Clonal selection and memory cell formation:
● Activated B cells multiply to form a clone of plasma cells but also some
memory cells.
● Division by mitosis occurs to form plasma cells with a specific antibody
type; this is called clonal selection.
● Antibodies last in the body for a few weeks and are quite short term.
● Hence memory cells are produced and this forms immunity.
The role of antibodies:
● Opsonization: makes pathogens more recognisable.
● Neutralisation of viruses and bacteria: prevents viruses from docking to
host cells.
● Neutralisation of toxins: binds to toxins to prevent them from affecting
● Activation of complement: Complement creates a perforation in the
membranes of pathogens. Antibodies activate a complement cascade
which forms a membrane attack complex. Water and ions then enter the
pathogen and cause it to burst.
● Agglutination: causes sticking together of pathogens so they are
prevented from entering cells/ easier for phagocytes to ingest.
Immunity depends on the persistence of memory cells.
Antibodies present + memory cells present = immunity.
These need to be specific to the antigen.
Immunity develops once the immune system is challenged.
Reaction is much quicker during the secondary response, due to
Vaccines lead to immunity:
● Contain antigens that trigger immunity but do not cause the disease.
● Attenuated version of the disease therefore does not cause problems.
● Stimulates a primary immune response and results in the creation of
memory B cells.
● Injecting attenuated strain of pathogen is a form of artificial active
● Tetanus shots are artificial, but a passive form of immunity because the
antibodies are being injected.
Zoonosis is a growing global health concern:
● Pathogens can be species-specific although others can cross species
● Pathogens are generally highly specialised, however there are some
which can affect a large number of hosts.
● Zoonosis is a pathogen which can cross a species barrier.
● Such diseases have increased due to growing contact between animals
and humans.
The immune system produces histamines:
● White cells release histamine in response to allergens.
● Mast cells are immune cells found in connective tissue.
o They release histamine, which causes the dilation of small blood
o This allows more blood flow to infected area, carrying antibodies
and WBCs, resulting in specific and nonspecific responses.
Effects of histamines:
● Cause allergic symptoms:
o Cells in many tissues have membrane bound histamine receptors.
o Brings symptoms of allergens in the nose.
o Itching, inflammation of tissues, mucus secretion and sneezing.
● Plays a role in formation of rashes and dangerous swelling (anaphylaxis).
● Antihistamines can be taken to avoid these effects.
The process for creating hybridoma cells:
● Tumour cell fused with an antibody-producing plasma cell creates a
hybridoma cell.
● Monoclonal antibodies are highly specific and are derived from a single
cell and recognise only one antigen.
● Myeloma cells (cancer cells) are fused with B-plasma cells from the spleen
of a rat, forming hybridoma.
Production of monoclonal antibodies:
● Hybridomas are tested to find the one that contains the specific antibody.
● The selected hybridomas are then allowed to divide.
o Multiplication occurs in a fermenter.
● The super-specific hybridomas are called monoclonal antibodies.
Monoclonal antibodies are used to test for human chorionic gonadotropin (HCG)
in pregnancy tests:
● Antibodies to HCG are immobilised in the strip and dye bearing
antibodies that cause colour change in the presence of HCG.
● HCG is present in high amounts during pregnancy.
11.2 Movement:
Bones and exoskeletons anchor muscles and act as levers:
● Exoskeletons surround and protect the body surface of animals.
● Bones and exoskeletons facilitate movement.
● Levers can change the size and direction of forces.
o Effort force
o Pivot force.
o Resultant force.
● First class lever: fulcrum between effort and load.
● Second class lever: fulcrum before effort and load, at edge
o Load closer to fulcrum than effort is.
● Third class lever: fulcrum before effort and resultant forces.
o Effort closer to fulcrum than load is.
Skeletal muscles are antagonistic:
● Antagonistic muscles occur in pairs.
● When one contracts, the other relaxes.
● This is true for skeletal muscles.
● Opposite movements are produced at a joint.
Example of a synovial joint:
● Articulation:
o Movement of bones in relation to one another.
● Joint:
o Point where bones meet.
● Cartilage prevents contact between bones, preventing friction.
o Also absorbs shock.
● Synovial fluid fills cavity between cartilages on the ends of bones.
o Lubricates the joint, to prevent friction.
● Joint capsule seals the joint and holds synovial fluid.
o Prevents dislocation.
● Ligaments are tough cords of tissue that connect bones on opposite sides
of a joint. THey restrict movement and help to prevent dislocation.
Different joints allow for different ranges of movement:
● Synovial joints allow for certain movements.
● Knees act as hinge joints, for flexion and extension.
● Hip joints are ball and socket joints.
o They can flex, extend, rotate and abduct (sideways)/adduct
Structure of muscle fibres:
● Skeletal muscle fibres are multinucleated and contain specialised
endoplasmic reticulum (sarcoplasmic reticulum).
● Striated muscle is composed of bundles of cells called muscle fibres.
● Single plasma membrane called the sarcolemma surrounds each muscle
● Many nuclei present and are much longer than normal cells.
● Embryonic muscle cells fuse together to form muscle fibres.
● Endoplasmic reticulum wraps around myofibrils, conveying contraction
signals to all part of the muscle fibres at once.
● Sarcoplasmic reticulum stores calcium.
● Mitochondria provide the ATP needed for contractions and are found
between the myofibrils.
● Muscles fibres contain many myofibrils.
● Parallel elongated structures.
● Alternating light and dark bands, which give striated muscle its stripes.
● In the centre of each light band is the ‘Z’ line.
Structure of myofibrils:
● Made up of contractile sarcomeres.
● Part of a myofibril between one ‘Z’ line and the next is called a sarcomere,
which is the functional unit of a myofibril.
● Actin filaments at the end of the sarcomeres (light bands) and myosin +
actin filaments in the middle (dark bands).
Mechanism of skeletal contraction:
● Sliding of actin and myosin filaments causes contraction of skeletal
● Myosin filaments pull actin filaments towards the centre of the
sarcomere, shortening the sarcomere and overall length of muscle fibres.
● Myosin heads bind to special binding sites on actin filaments, creating
cross bridges.
● Regular spacing of heads and binding sites allows many to bind at once.
● ATP gives energy for sliding.
The control of skeletal muscle contractions:
● Calcium ions and the proteins tropomyosin and troponin control muscle
● Tropomyosins block binding sites on actin.
● When motor neurons send impulses to muscle fibres, sarcoplasmic
reticulum releases calcium ions which bind to troponin and cause
tropomyosin to move
● Myosin heads then bind.
The role of ATP in the sliding of filaments:
● ATP hydrolysis and cross-bridge formation are necessary for the
filaments to slide.
● ATP attach to myosin heads, resulting in cross bridges to break.
● ATP is hydrolysed into ADP+P, which releases energy for myosin heads to
swivel into a ‘cocked’ position, storing potential energy.
● New cross bridges form to binding sites, each head binding to one
position further from the centre of the sarcomere.
● ADP is released, which allows for energy stored as potential energy to
then used to swivel the myosin heads inwards towards the centre of the
sarcomere and move the actin filament accordingly.
● This continues until a motor neuron stops sending signals to muscle
● Calcium ions are pumped back into the sarcoplasmic reticulum and
tropomyosin re-covers the myosin-binding site.
11.3 The kidney and osmoregulation:
Different responses to changes in osmolarity in the environment:
● Animals are either osmoregulators or osmoconformers.
o Osmoregulators maintain a constant internal solute concentration.
o Osmoconformers’ internal solute concentration tends to be the
same as the concentration of solutes in the environment.
The Malphighian tubule system: THIS IS BASICALLY JUST USING WATER AS A
● Arthropods have a circulating fluid known as hemolymph, which
combines characteristics of tissue fluid and blood.
● Osmoregulation is a form of homeostasis that maintains the concentration
of hemolymph within a specific range.
● Nitrogenous waste in animals is produced from the breakdown of amino
acid (uric acid/urea).
● Malpighian tubules branch off from intestinal tract.
● Cells lining the tubules are responsible for actively transporting ions and
uric acid into the lumen of the tubules.
● Water the moves into the lumen by osmosis. All contents in the tubules
are emptied into the gut.
● Contents then move to the hindgut where most of the water and salts are
reabsorbed while the nitrogenous waste is excreted with the faeces.
Drawing the human kidney:
Comparing the composition of blood in the renal artery and the renal vein:
● Kidneys remove substance from the blood that are unnecessary or
harmful. Hence blood that enters the kidney is different from that which
leaves the kidney.
● 1/5th of blood plasma is filtered in the kidney (all substance in plasma
besides large protein molecules). Specific substances are then actively
reabsorbed. Unwanted substances pass out through urine.
Renal Artery
Renal Vein
Enters the kidney
Leaves the kidney
Higher concentration of toxins that
have noT been completely
metabolised (drugs/pigments).
Nitrogenous waste.
Carbon Dioxide is a waste product
of respiration and will be present
in higher amounts in the renal
Blood in the renal artery will
Blood in the renal vein will have a
contain a variable amount of
fixed amount of water and salt.
Oxygenated blood.
Deoxygenated blood because
metabolic activity in the kidneys
will require blood oxygen.
High concentrations of glucose
Low concentrations of glucose,
since it would have been broken
down by metabolism in the
Plasma proteins are present in equal amounts in both renal vein and
The ultrastructure of glomerulus and Bowman’s capsule facilitate ultrafiltration:
● Glomerular filtrate is formed because:
o Blood pressure in capillaries is exceptionally high in the
o Capillary walls are particularly permeable, resulting in
large amounts of tissue fluid forming.
▪ Tissue fluid forms when blood plasma is pushed out
of capillaries due to high internal pressure.
o Most solutes are filtered out freely alongside blood plasma,
except large protein molecules.
o Ultrafiltration is the separation of molecules based on size.
● Fenestration:
o Allow fluid to escape but not blood cells.
● Basement membrane:
o Prevents plasma proteins from being filtered out. Made of
negatively charged glycoproteins and therefore repels
negatively charged protein molecules.
● Podocytes: Inner wall of Bowman’s capsule – wrap around
capillaries of glomerulus with foot processes. Gaps between foot
processes prevent certain small molecules being filtered out of
blood in the glomerulus. The foot processes make a fibrous mesh.
The role of the proximal convoluted tubule:
● Selectively reabsorbs useful substances by active transport.
● Glomerular fluid contains 1.5kg of salt and 5.5 kg of glucose and is around
180 dm^-3 in volume. Volume of urine is only 1.5 dm^3, hence a very
large part of glomerular filtrate is selectively reabsorbed in the PCT.
● PCT reabsorbs all glucose, amino acids and 80% of water, sodium and
mineral ions
Sodium ions
Actively transported from filtrate to
space outside tubule by pump proteins
located on the outer membrane of the
tubule. Ions are then passed on to
peritubular capillaries.
Chloride ions
Active transport of sodium ions sets up
a charge gradient that causes chloride
ions to simply move down this charge
gradient from filtrate to space outside
the tubule.
Glucose ions
Glucose is co-transported using
specific proteins. Movement of Sodium
ions down concentration gradient from
outside tubule to inside provides
energy to proteins for glucose to move
to space outside tubule.
Pumping of solutes to space outside
the solute sets up a solute
concentration gradient. Therefore
reabsorption of water occurs through
The nephron and the Bowman’s capsule:
● Bowman’s capsule: Collects the fluid filtered from the blood.
● PCT: Has many mitochondria to provide ATP for active transport of ions.
● Loop of Henlé: Descending limb carries filtrate into medulla and
ascending limb brings it back out to cortex.
● Distal convoluted tubule (DCT): Fewer microvilli and fewer mitochondria
(than PCT). Collecting duct: Carries filtrate back through cortex and
medulla to renal pelvis.
● Blood flows through vessels in this order:
o Afferent arteriole (blood from renal artery into kidney);
o Glomerulus (high pressure capillary bed during which
ultrafiltration occurs);
o Efferent arteriole (Narrow vessel which generates high pressure in
o Peritubular capillaries (low pressure capillary bed which absorbs
fluid from convoluted tubules;
o Vasa recta (unbranched capillaries with a descending limb and
ascending limb); Venules (carry blood to the renal vein)
The role of the loop of Henlé:
● The loop of Henlé maintains hypertonic conditions in the medulla.
o Loop of Henlé creates a gradient of solute concentration in the
medulla. In the ascending limb, sodium ions are pumped out of the
filtrate to the fluid in the medulla (interstitial fluid).
● Wall of ascending limb is impermeable to water, so water is retained in
the filtrate.
● Interstitial concentration of 500 mOsm is achieved.
● Cells in the wall of the descending limb are permeable to water, the highly
hypertonic interstitial fluid in the medulla causes water to be drawn out
of filtrate in the descending limb until the volume of water = volume of
interstitial fluid.
● This results in the ascending limb being able to pump out more sodium
ions into interstitial fluid raising concentration to 700 mOsm. This
process can continue until the interstitial fluid reaches a concentration of
around 1200 mOsm (in humans). This is an example of a countercurrent
multiplier system. Counter current because the fluid flows in opposite
direction and a multiplier because it allows a steeper concentration
gradient to develop than would develop with a concurrent system.
Some animals have relatively long loops of Henlé:
● Length of loop of Henlé is positively correlated with the need for water
conservation in animals.
● The longer the loop, the more water will be acquired. Thicker medullas
will accommodate longer loops of Henelé.
Function for ADH:
● ADH controls reabsorption of water in the collecting duct. Solute
concentration is hypotonic in DCT, because proportionately more solutes
than water passed out of filtrate in the loop of Henlé. Low solute
concentration means little water can be reabsorbed into filtrate. Hence
large volume of urine is produced with low solute concentration and
blood solute concentration is increased (as interstitial fluid contains high
solute concentration). This is not favourable.
1) If solute concentration of the blood is too high, ADH is released
from the pituitary gland, which causes the walls of the DCT and collecting
duct to become more permeable to water.
2) As a result, most of the water in the filtrate is reabsorbed into the
3) Filtrate passing down collecting duct deep into medulla where
solute concentration of interstitial fluid is high creates concentration
gradient for water to be continually to reabsorbed into the blood.
4) The filtrate, as a result, becomes a small volume of concentrated
Animals vary in the types of nitrogenous waste they produce:
● The type of nitrogenous waste in animals is correlated with evolutionary
● Ammonia is produced due to the breakdown of amino acids and nucleic
acids. Highly basic and alters pH balance.
o Highly reactive chemical (hence toxic).
● In freshwater habitats, organisms can release waste as ammonia as it can
be diluted in the environment. Amphibians release waste as ammonia
during larval form and then switch to urea. This is to save energy
● Terrestrial organisms expend energy to convert ammonia to less toxic
forms (urea/uric acid).
o Birds and insects release waste as uric acid (requires the most
energy to create) but does not require water to be released.
o For birds not carrying water for excretion means saving energy
during flight.
o Uric acid is released as it is not soluble and crystallises rather than
building up to toxic concentrations within the egg.
Dehydration and overhydration:
● Dehydration: high solute concentration in filtrate results in darker urine.
o Water is necessary to remove metabolic waste so lethargy and
tiredness are symptoms due to decreased muscle functionality at
being exposed to metabolic waste.
o Blood pressure falls resulting in increased heart rate.
o Body temperature regulation is affected due to inability to sweat.
● Overhydration is less common: results in body fluids becoming hypotonic
and swelling of cells. Headache and nerve function disruption.
Treatment options for kidney failure:
● Blood in tubing flows through dialysis fluid.
o Tubing is partially permeable and allows small molecules to pass
through into dialysis fluid but not blood cells and protein
o Purified blood is returned to patient via a vein.
● Kidney transplant is also a viable option.
o Donors can be deceased or alive.
o Only one kidney needed to survive.
11.4 Sexual reproduction:
Similarities between oogenesis and spermatogenesis:
● Both involve mitosis, cell growth, two divisions of meiosis and
● Oogenesis:
o Production of egg cells in the ovaries.
o Germinal epithelium cells in the fetal ovary divide by mitosis and
distribute themselves through the cortex of the ovary.
o At 4/5 months (foetus), the cells grow and start to divide by
o By 7 months they are in the first division of meiosis and follicle
cells form around them.
o This is called the primary follicle of which there are 400,000 at
o No more primary follicles are produced, but at the start of each
menstrual cycle a small batch are stimulated to develop and one
becomes a mature follicle containing a secondary oocyte.
● Spermatogenesis:
o Production of sperm and occurs in the testes.
o Testes are composed of narrow tubes (seminiferous tubules) with
groups of cells filling the gaps between the tubules.
o The cells are called interstitial cells.
o Outer layer of cells in the seminiferous tubules are called he
germinal epithelium, where sperm production begins.
o Cells in the germinal epithelium that are closer to lumen (fluid
filled centre) of seminiferous tubules are more mature.
o Spermatogonium are at the outermost part of the germinal
o Spermatozoa are cells that have developed tails (flagella).
o Sertoli cells are nurse cells and exist in the walls of the
seminiferous tubule.
o Spermatogenesis follows the following sequence of events:
▪ Germinal epithelium cells (2n) divide by mitosis.
▪ Diploid cells grow larger to become primary spermatocytes
▪ Each primary spermatocyte carries out first division of
meiosis to produce two secondary spermatocytes (n).
▪ Each secondary spermatocyte carries out the second
division of meiosis to produce two spermatids (n).
▪ Spermatids associate with Sertoli cells to develop flagellum
and become spermatozoa.
▪ Sperm detach from Sertoli cells and are carried out by the
fluid in the seminiferous tubule.
Diagrams of sperm and egg:
Haploid nucleus.
Two centrioles.
First polar cell.
Plasma membrane.
Layer of follicle cells.
Zona pellucida.
Cortical granules.
Sperm cells consist of:
● Head:
o Haploid nucleus.
o Centriole.
o Plasma membrane.
● Mid-piece:
o Helical
● Flagella:
o Protein fibres to strengthen tail.
o Microtubules.
Differences in the outcome of spermatogenesis:
● Processes in spermatogenesis and oogenesis result in different numbers
of gametes with different amounts of cytoplasm.
● Each mature sperm consists of different parts to a mature egg.
● Each meiotic division results in four spermatids.
● Sperm differentiation eliminates most of the cytoplasm, whereas the egg
increases its cytoplasm.
● First meiotic division in eggs produces one large egg cell and one polar
body and the second meiotic division produces a similar result, therefore
only one egg is produced per meiotic division.
● Egg is much larger than sperm.
● Sperm are produced continuously whilst only a few hundred mature eggs
are produced during the lifetime of a female.
Preventing polyspermy:
● Acrosome reaction: Sperm binds to egg and enzymes from acrosome
digest the zona pellucida.
● Penetration of egg membrane: Sperm and egg fuse together and sperm
nucleus enters the egg cell (fertilisation).
● Cortical reaction: Acrosome reaction exposes area on tip of the sperm that
has proteins that bind to egg membrane. Sperm activates egg. Contents of
cortical granules are released from the egg by exocytosis.
o Cortical vesicle enzymes digest binding proteins so that no further
sperm can bind. Enzymes also harden zona pellucida and make it
impermeable to other sperm.
Internal and external fertilization:
● Fertilization in animals can be internal or external.
● Aquatic animals release gametes directly into water and have behaviours
that bring eggs into proximity with sperm. This is dangerous as it is prone
to predation and environmental fluctuation.
● Terrestrial animals generally display internal fertilization as gametes may
dry out. Sperm and ova are placed in close proximity to each other.
Marine mammals still use internal fertilization. Developing embryos can
be protected inside the female.
Implantation of the blastocyst:
Blastocyst forms after pregnancy.
Upon fertilization, mitotic division occurs to form a 2-cell embryo.
Occurs again to form a four cell embryo by 48 hrs.
This continues slowly, alongside the migration of other cells, which gives
the embryo the shape of a hollow ball (blastocyst).
By 7 days the blastocyst is 125 cells and has reached the uterus after
being brushed down the oviduct by the cilia of cells in the oviduct wall.
Zona pellucida then breaks down and blastocyst sinks into the
endometrium (implantation).
Finger like projections on blastocyst allows it to penetrate uterus lining.
Exchanges materials with mother’s blood (food and oxygen).
By 8 weeks, begins to develop bone tissue and is considered a foetus.
Role of HCG in early pregnancy:
● HCG (Human chorionic gonadotropin) stimulates the ovary to secrete
progesterone during early pregnancy.
● This helps maintain the uterus lining during pregnancy.
● HCG stimulates the corpus luteum to continue to secrete progesterone
and oestrogen.
Materials exchange by the placenta:
● Placenta facilitates the exchange of materials between the mother and
● Humans are placental mammals.
● Two other groups of mammals include:
o Monotremes (egg laying) and;
o Marsupials (offspring develop inside a pouch).
● Placenta is needed because the body surface area to volume ratio
becomes smaller as the foetus grows.
● Foetal tissues with contact to maternal tissues in the uterus wall. Foetus
develops membranes that form the amniotic sac, which encompasses the
amniotic fluid for the support and protection of the foetus.
● Placental villus increase in number during pregnancy and assist in the
exchange of materials with the mother.
o Maternal blood flows in the inter-villous spaces around the villi
(not confined to blood vessels/capillaries).
o Foetal blood circulates in capillaries close to the surface of each
o Distance between foetal and maternal blood is small, and cells that
separate them form the placental barrier.
o This barrier is selectively permeable.
Release of hormones by the placenta:
● The placenta secretes oestrogen and progesterone.
● This means that the corpus luteum is no longer needed for this role.
● Switch over from corpus luteum to placenta occurs.
The role of hormones in parturition:
● Birth is mediated by positive feedback involving oestrogen and oxytocin.
● Progesterone inhibits secretion of oxytocin by the pituitary gland and
inhibits contraction of the myometrium.
● The foetus (at the end of pregnancy) produces hormones to that cause the
placenta to stop secreting progesterone and oxytocin is therefore
secreted which stimulates contraction of the myometrium.
● Stretch receptors detect contractions, which signal for greater oxytocin
secretion, and more vigorous contractions as a consequence.
● This is an example of positive feedback, which gradually increases
myometrium contractions.
● Relaxation of muscle fibres cause cervix to dilate and uterine contractions
then burst the amniotic sac.
● Further uterine contractions then push the baby out.
Gestation times, mass and growth, and development strategies:
● Altricial species (born weak and defenceless and immobile). Short
gestation period.
● Precocial: born with open eyes, hair, mobile, and are often able to defend
themselves. Long gestation period.
Option A: Neurobiology and Behaviour
A.1 Neural development:
Development of the neural tube:
● Infolding of ectoderm followed by elongation of the tube forms neural
tube of embryonic chordates.
● Process is called neurulation.
● An area of the ectoderm cells on the dorsal surface develops into the
neural plate.
● Cells in the neural plate change shape causing the plate to fold inwards.
● This forms a groove on the ectoderm.
● The neural plate eventually separates from the rest of the ectoderm and
forms the neural tube.
● The neural tube elongates as the embryo develops.
Development of neurons:
● Neurons are initially produced by differentiation in the neural tube.
● Part of the ectoderm develops into neuro-ectodermal cells in the neural
● The nervous system is formed from these.
● Continuing proliferation of cells and differentiation in the neural plate
forms the neural tube.
● Neural tube is therefore comprised of functioning neurons.
● To form the mature CNS proliferation of neurons continues in the
developing spinal cord and brain.
Neurulation in Xenopus:
Ectoderm, mesoderm and endoderm: Day 13.
Formation of neural tube: Day 18.5.
Wall of developing gut and cavity: Day 20.
Notocord: Day 22.
Developing dorsal fin: Day 36.
Spina bifida:
● Centrum provides support to the vertebrae.
● These develop on the ventral side of the neural tube
● Tissue migrates from both sides of the centrum to form the vertebral arch
but in some cases the arch never fuses together properly.
● This is called spina bifida.
● Symptoms can vary from mild to severe.
Migration of neurons:
● Immature neurons migrate to a final location.
● This occurs by moving the cytoplasm and organelles from the trailing end
to the leading edge by contractile actin filaments.
● It is an important occurrence in brain development as neurons may grow
in one part but are needed in another part.
● Mature, functional neurons don’t usually move but their axons and
dendrites can regrow if damaged.
Growth and development of axons:
● An axon grows from each immature neuron in response to chemical
● Immature neurons consist of a cell body with cytoplasm and a nucleus.
● One axon develops on each neuron.
● Smaller dendrites that bring impulses from other neurons also develop.
● Chemical stimuli determine neuron differentiation and the growth
● Some axons extend beyond the neural tube to reach other parts of the
● Axons can be more than a meter long in humans.
● They carry impulses to other neurons or effector cells.
● If the cell body remains intact the axon can grow if damaged.
● Recovery depends on correct connections being re-established between
the axon and the cell with which it should be communicating.
● Developing neurons forms multiple synapses.
● Growth of axons or dendrites are directed so that they reach the cell with
which they interact.
● A synapse forms between the neuron and the other cell.
● Synapse development involves special structures being assembled in the
membranes on either side of the synapse and in the synaptic cleft.
● In practise neurons develop many synapses but the smallest number is 2.
Elimination of synapses:
● Synapses that are not used do not persist.
● New synapses can be formed at any stage of life.
● Transmission occurs at a synapse chemical markers are left that
strengthen the synapse.
● When the synapse isn’t used these chemical markers aren’t made and so
the synapse becomes weaker and weaker until it is eventually eliminated.
Neural pruning:
Involves the loss of unused neurons.
More neurons in new-born babies’ brains than in adults.
Apoptosis is the process by which neurons destroy themselves.
Elimination of part of a neuron or the whole cell is known as neural
Plasticity of the nervous system:
● Plasticity of the nervous system allows it to change with experience.
● Connections between neurons can be changed by growth of
axons/dendrites, establishment of new synapses and pruning,
● Stimulus for change comes with how the person’s nervous system is used.
● It is important in repairing damage to the brain and spine.
● Ischemic stroke is a disruption of the supply of blood to a part of the
brain. Bleeding from a blood vessel is another cause.
● Brain is deprived of oxygen and glucose and therefore neurons become
irreparably damaged and die.
● 1/3 of sufferers make full recovery and another 1/3 survive but with
A.2 The human brain:
Development of the brain:
Anterior part of the neural tube expands to form the brain.
This process is called cephalisation.
Human brain contains around 86 billion neurons.
Brain is the central control centre for the body.
Directly from cranial nerves and indirectly via the spinal cord and
Roles of the parts of the brain:
● Medulla oblongata: autonomic control of gut muscles, breathing, blood
vessels and heart muscle.
Cerebellum: coordinates unconscious functions – posture, non-voluntary
movement and balance.
Hypothalamus: Interface between brain and pituitary gland. Synthesises
the hormones secreted by the posterior pituitary. Regulates secretion of
hormones by anterior pituitary.
Pituitary gland: posterior lobe stores and releases hormones and anterior
lobe produces and releases hormones.
Cerebral hemispheres: carry out high complex functions such as learning,
memory and emotions.
Methods of brain research:
● Lesions have been analysed via autopsy and relating the position of the
lesion to observed changes in behaviour
● MRI is used to investigate the internal structure of the body.
● FMRI allows the identification of activated parts of the brain as these
parts receive increased blood flow.
o The scans can show which part of the brain responds to a specific
Examples of brain functions:
● Both cerebral hemispheres have a visual cortex.
● Visual signals from light sensitive rod and cone cells in the retina are
processed here.
o Information is first projected in region called V1, the information is
then analysed by V2 to V5.
● Broca’s are is a part of the left cerebral hemisphere.
o Damage to this area inhibits the production of meaningful words
and sentences; even if the individual knows what they want to say,
they can’t. say it.
● Nucleus Accumbens is in each of the cerebral hemispheres which is the
pleasure or reward centre of th brian.
o Variety of stimuli including food and sex cause the release of
dopamine that cuses feelings of satisfaction.
The autonomic nervous system:
● Autonomic nervous system controls involuntary processes in the body
using centers located in the medulla oblongata.
● The peripheral nervous system comprises all of the nerves outside the
central nervous system.
● Divided into voluntary and autonomic.
● Autonomic has two parts: sympathetic and parasympathetic.
o Parasympathetic nerves cause an increase of blood flow to the gut
wall during digestion and absorption.
o Sympathetic nerves cause a decrease in blood flow during fasting.
● Therefore parasympathetic and sympathetic nerves have contrary effects
to each other.
Activities coordinated by the medulla:
● Activities coordinated by the medulla are swallowing, breathing and heart
rate. Passing down of food from the pharynx to stomach via the
oesophagus is involuntary and controlled by the medulla oblongata.
● Two centres in the medulla control breathing. One controls the timing of
inspiration and the other controls the force of inspiration and active
voluntary expiration.
o This is controlled by chemoreceptors in the medulla that monitor
blood pH. Co2 concentration increases acidity of blood and
therefore a fall in pH results in deeper/more frequent breathing.
● Cardiovascular centre of the medulla regulates the rate of heartbeat.
o Receptor cells monitor Blood pH and pressure.
o Heart rate will be adjusted according to these factors, to maintain a
constant state of blood pH and pressure. Signals are sent to the SA
node (pacemaker).
o Signals carried by the sympathetic system speed up heart rate and
those carried by the parasympathetic system slowdown the heart
The cerebral cortex:
● Use of pupil reflex to evaluate brain damage.
o Impulses carried to radial muscle fibres cause them to
contract/dilate the pupil; impulses carried by parasympathetic
system cause contraction.
o When bright light is shone into the eyes photoreceptive ganglion
cells send impulses to the mid brain, which trigger the
parasympathetic system to contract the radial cells and the pupil
to be constricted.
o If the pupils do not constrict at once the medulla oblongata is
probably damaged.
● The cerebral cortex forms a larger proportion of the brain and is more
highly developed in humans that other animals.
o It is the outer layer of the cerebral hemisphere with up to 6
different layers of neurons.
o Processes the most complex tasks of the brain. In birds and
reptiles the cells are organised in clusters instead of layers.
The evolution of the cerebral cortex:
● Human cerebral cortex has become enlarged by an increase in total area
with extensive folding to accommodate it.
● Most of the surface area of the cerebral cortex is in the folds rather than
on the outer surface.
Functions of the cerebral hemispheres:
● Cerebral hemispheres are responsible for high order functions.
o Learning memory speech and emotion.
● Most sophisticated processes occur in the frontal and prefrontal lobes.
● They use stimuli from different sources, eyes ears and also memory.
o Rely on complex network of neurons.
Sensory inputs to the cerebral hemispheres:
● The left cerebral hemisphere receives sensory input from sensory
receptors in the right side of the body and the right side of the visual field
in both eyes and vice versa for the right hemisphere.
● Inputs from the eyes pass to the visual area of the occipital lobe (visual
Motor control by the cerebral hemispheres:
● Motor control by the cerebral hemispheres: Left cerebral hemisphere
controls muscle activity in the right side of the body and vice versa for the
right hemisphere.
● Posterior part of the frontal lobe called the primary motor cortex controls
muscles throughout the body.
● Homunculi basically represent how much of the brain is used to control a
certain part of the body – motor homunculus.
● It also shows how much of each part is devoted to sensory inputs from the
brain – sensory homunculus.
Energy of the brain:
● Brain metabolism requires large energy inputs.
● Energy is required to maintain resting potential in neurons.
● Also needed for synthesis of neurotransmitters and other signal
● Brain contains lots of neurons therefore requires large amounts of
glucose and oxygen to generate this energy.
● 10% of the energy consumed by basal metabolism is in the brain.
A.3 perception of stimuli:
Sensory receptors:
● Receptors detect changes in the environment. Nerve endings of sensory
neurons act as receptors.
● Body also has specialised receptor cells that pass impulses to sensory
neurons (light sensitive rod and cones).
o Mechanoreceptors.
o Chemoreceptors.
o Thermoreceptors.
o Photoreceptors.
Olfactory receptors:
● Detection of chemicals in the air by the many different olfactory
● Located inside the epithelium of the nose.
● Membrane contains odorant receptor molecules, which detect chemicals
in the air.
● Volatile chemicals can be smelled.
● Odorants from food can pass through mouth and nasal cavities to reach
the nasal epithelium.
● A different gene encodes each odorant receptor protein. Each receptor
cell has one type of odorant receptor in its membrane. But there are
several of each receptor cell type.
● Photoreceptors: rods and cones are photoreceptors located in the retina.
Light is focussed on the retina by the cornea and the lens.
● Many nocturnal mammals have only rods and cant distinguish colours.
Rods and cones convert the light into neural signals.
Differences between rods and cones:
● Rods and cones differ in their sensitivities to light intensities and
● Rods are:
o Sensitive to light (work well in dim light).
o Are bleached by bright light.
o Absorb a wide range of visible wavelengths.
o Can’t respond selectively to different colours.
● Cones are:
o Red Blue and Green.
o Each absorbs a different range of light.
o Relative stimulation of each cone type produces signal carrying
specific colour.
o Stimulated by bright light and colour vision fades in dim light.
Red-green colour-blindness:
● Red green colour blindness as a variant of normal trichromatic vision.
● Absence of gene for photoreceptor pigments essential in either red or
green cone cells.
● Sex linked condition.
● Normal alleles are dominant so it’s a recessive disorder.
● Much commoner among males.
Structure of a retina:
Bipolar cells:
● Bipolar cells send the impulses from rods and cones to ganglion cells.
● If rods and cones don’t receive light they send a inhibitory
neurotransmitter to the bipolar cell (with which they synapse), which
hyperpolarises it to stop it from transmitting impulses.
● When rods or cones absorb light, they become hyperpolarised.
● As a result they stop sending inhibitory neurotransmitters to the bipolar
cells and allow the bipolar cells to depolarise and activate ganglion cells.
Ganglion cells:
● Ganglion cells have cell bodies with dendrites that form synapses with
bipolar cells.
● Long axons along which impulses pass to brain at a low frequency when
ganglion cells aren’t being activated and at an increased rate when
ganglion cells are stimulated.
● Pass across the front of the retina to form a bundle at the blind spot. This
area has no rods and cones. Axons of ganglion cells pass via the optic
nerve to the optic chiasma in the brain.
Vision in the right and left fields:
● The information from the right field of vision from both eyes is sent to the
left part of the visual cortex and vice versa.
● Stimuli from both sides of one eye are integrated by the axons of ganglion
● Crossover of axons between left and right sides happens at the optic
Structure of the ear:
● Outear:
o Pinna.
● Middle ear:
o Incus
o Malleus
o Stapes
● Inner ear:
o Round window.
o Oval window.
o Semi-circular canals.
o Auditory nerve.
o Cochlea.
The middle ear:
● Middle ear transmits and amplifies sound.
● It’s an air-filled chamber between the outer ear and the inner ear,
separated by the eardrum.
● Tiny bones (malleus, incus and stapes) form connections between the
eardrum and oval window.
● Ossicles (three bones) transmit vibrations from eardrum to oval window,
which amplifies them 20 times.
● This occurs because oval window is so much smaller than the eardrum.
● Contraction of muscles in the ossicles during loud sounds weakens
connections between the ossicles and dampens the vibrations.
The cochlea:
Sensory hairs of the cochlea detect sounds of specific wavelengths.
Cochlea is where vibrations are transduced into neural signals.
Layers of tissue (membranes) to which sensory cells are attached.
Bundle of hairs stretch from one membrane to another.
Vibrations from the oval window resonate with the hair bundles,
stimulating the sensory cells and activating them.
Selective activation results into distinguishing between different pitches.
Fluid in cochlea is incompressible.
The round window is therefore a thin sheet that allows movement of the
oval window.
When oval window pushes fluid in the cochlea inwards, the round
window moves outwards.
The auditory nerve:
● Impulses caused by sound perception are transmitted to the brain via the
auditory nerve.
● Hair cells in the cochlea depolarise by vibrations and release
neurotransmitters across a synapse, which triggers a sensory neuron.
● An action potential is triggered and an impulse is propagated to the brain
along the auditory nerve.
Cochlear implants:
● Cochlear implants in deaf patients.
● If hair cells in the cochlea are defective then a cochlear implant is
● External parts are a microphone to detect sounds, speech processor
which selects specific frequencies of speech and filters out others.
● Internal parts include a receiver that picks up sound signals, a stimulator
that converts the signals to electrical impulses and electrodes that carry
impulses to the cochlea that stimulate auditory nerve directly.
Directing head movements:
● Hair cells in the semi-circular canals detect movement of the heads.
● Fluid-filled semi-circular canals have a swelling at one end in which there
are sensory hair cells.
The hair cells are embedded in gel, forming the cupula.
Every time the head moves in a specific direction, the fluid flows past the
cupula, which is detected by hair cells and sends impulses to the brain.
Three semi-circular canals are at right angels to each other so each is in a
different plane.
Brain can deduce the direction of movement by the relative amount of
stimulation of the hair cells in each of the semi-circular canals.
A.4 Innate and Learned Behaviour:
Innate behaviour:
● Innate behaviour is inherited from parents and so develops
independently of the environment.
● It is unaffected by external influences (like experience) and develops
independently of environmental factors.
● Palmar grasp reflex (babies grabbing onto objects).
● It is genetically programmed and inherited.
● Can change through evolution if natural selection favours one behaviour
pattern over others.
Invertebrate behaviour experiments:
● ‘Taxis’ is movement towards or away from a directional stimulus.
● Kinesis is movement as a response but is non-directional in nature.
o Speed of movement is measure/ number of turns.
● Autonomic and involuntary responses are referred to as reflexes.
● Stimulus is a change in the environment that is detected by a receptor and
elicits a response.
● Response can be a change carried out by muscle or gland (usually).
● Involuntary responses are carried out by the autonomic nervous system,
known as reflexes – a rapid response to a stimulus (involuntary).
● Pupil reflex, in response varying light conditions, controlled by the radial
Reflex arcs:
● Reflex arcs comprise the neurons that mediate reflexes.
● Receptor perceives the stimulus and eventually relays the impulse to the
effector, which is a muscle or gland and carried a response.
● The sequence of neurons that links the two is known as the reflex arc.
Sensory neuron and motor neuron.
● Most reflex arcs contain more than two neurons (more than one relay
neuron connects the sensory neuron to the motor neuron.
Withdrawal reflex:
● Withdrawal reflex of the hand from a painful stimulus.
● Innate response to pain.
o Activate sensory neurons (thermoreceptors to heat) and carry
impulses from the finger to the spinal cord via the dorsal root of
the spinal nerve.
o Impulses ravel to the grey matter of the spinal cord in which there
are synapses with relay neurons.
o Relay neurons have synapses with motor neurons that then carry
impulses out of the spinal cord via the ventral root to the muscles
in the arm.
o Muscle fibres contract and pull the arm away.
Learned behaviour:
Learned behaviour develops as a result of experience.
Acquisition of new patterns of behaviour.
Language is a learned behaviour.
Ability to make sense of vocal patterns and make them oneself is innate
but the specific language spoken is learned.
Development of birdsong:
● Partly innate and partly learned.
● All members of a bird species share innate aspects of song; that means
each individual recognises other members of the species. Many species
learn mating calls from their father. Learned aspects causes slight
differences to the song and some species mates are chosen based on the
quality of singing.
Reflex conditioning:
● Reflex conditioning involves forming new associations.
● Establishes new neural pathways in the brain.
● Conditioned reflexes are used extensively in animal behaviour and can
greatly increase survival chances.
● Innate reflex to dislike bitter foods, but learned behaviour to know which
foods have that taste.
● Insect with yellow and black stripes having a bitter taste would mean that
all insects of that type would have a bitter taste and would therefore be
● The colour is associated with a taste, in this case.
Pavlov’s experiments:
● Rang a bell every time it was dinnertime.
● Unconditioned stimuli were that the dog salivated at the smell of food.
● The bell ringing every time food was served posed as the conditioned
● After a while, the dog would salivate even with the ringing of the bell,
even if no food were present.
● Imprinting is learning occurring at a particular life stage and is
independent of the consequences of behaviour.
● It is the establishment of preference of stimulus that elicits behaviour
patterns of trust and recognition.
● For example, the mother is the first big large moving object that the
hatchlings see, so they follow her around for a few weeks of their life and
are protected and fed.
● If they do not see their mother, they follow another large object that they
● This occurs regardless of whether they may be put in danger by following
that object.
● Hence imprinting is independent of the consequences of behaviour.
Operant conditioning:
● Operant conditioning is a form of learning that consists of trial and error
● The environment imposing a stimulus on an animal initiates reflex
conditioning, whereas an animal testing out a behaviour pattern to
become aware of the consequences initiates operant conditioning.
● If the behaviour pattern is positive in consequence then it is reinforced,
otherwise it is inhibited.
● For example, lambs don’t touch electric fencing due to operant
conditioning; the pain from carrying out an action inhibits them from
displaying that behaviour.
● Learning is the acquisition of skill or knowledge.
● Could be the acquisition of behavioural patterns or the loss of them.
● These are often the result of growth and maturation, however growth and
maturation is generally supplemented, or instigated, by learning.
● Motor skills such as walking, talking, or playing the violin are learned.
● Knowledge has to be learned.
● Useful things for survival etc. need to be learned.
● Higher order function, so humans have a greater capacity of doing it
because of their larger frontal and prefrontal cortex.
● Social animals are likely to learn from each other.
● Process of encoding, storing and accessing information.
● Higher order function.
● Encoding is the process of converting information into a storable form (by
the brain).
● Accessing is the recall of information so that it can be used actively in
thought processes.
● Hippocampus is related to memory.
o Removal of the hippocampus can result in the inability to make
new memories, besides from procedural ones.
o Synapses in the hippocampus can be pruned.
A.5 Neuropharmacology:
Excitatory and inhibitory neurotransmitters:
● Some neurotransmitters are excitatory (they excite nerve impulses in
post-synaptic neurons) and others are inhibitory (they inhibit nerve
impulses in the post-synaptic neuron).
● Excitatory neurotransmitters excite the post-synaptic neuron by
depolarising it.
● Ones that inhibit the formation of action potentials make the membrane
potential more negative (rather than positive, which is required to
depolarise) and therefore hyperpolarise it.
● As a result post-synaptic neurons cannot reach the threshold potential.
● Inhibitory neurotransmitters are small molecules that are inactivated by
specific enzymes in the membrane of the post-synaptic neuron.
● Nerve impulses are initiated or inhibited in post-synaptic neurons as a
result of summation of all excitatory and inhibitory neurotransmitters
received from pre-synaptic neurons.
● Single release of an excitatory neurotransmitter from one pre-synpatic
neuron is insufficient to trigger an action potential.
● As a result excitatory neurotransmitters need to be released repeatedly
from one pre-synaptic neuron or from several adjacent pre-synaptic
neurons (since many can synapse with one post-synaptic neuron).
● This additive effect is called summation.
● Summation involves combining the effect of excitatory and inhibitory
● Formation of an action potential depends on the balance between the two.
● Integration of different sources is the basis of decision making in the CNS.
Slow and fast neurotransmitters:
● Many different slow-acting neurotransmitters modulate fast synaptic
transmission in the brain.
● Fast-acting neurotransmitters are the ones which cause the opening or
closing of voltage gated ion channels.
● Slow acting ones take several hundreds of milliseconds and generally
diffuse through liquid in synaptic cleft to affect a group of neurons.
● Dopamine, non-adrenaline and serotonin are examples.
● They do not affect ion movement but release secondary messengers
inside post-synaptic neurons, which essentially regulate fast synaptic
transmission (opening/closing of voltage gated channels).
Memory and learning:
● Memory and learning involve changes in neurons caused by slow-acting
● Slow acting neurotransmitters cause the release of secondary messengers
within the post-synaptic neurons and increase the number of receptors in
the post-synaptic membrane which result in an increased rate of ion
movement when a neurotransmitter binds (fast acting).
o These secondary messengers cause long-term potentiation, which
is central to synaptic plasticity that is necessary for memory and
● Learning of new skills results in formation of new synapses in the
hippocampus and elsewhere in the brain.
● Pain receptors in the skin and other parts of the body detect stimuli.
● These receptors are the endings of sensory neurons that convey impulses
to the CNS.
● When the impulse reaches a sensory area of the cerebral cortex, we
experience pain.
● Endorphins are oligopeptides that are secreted by the pituitary gland and
act as painkillers.
● Bind to the receptors in synapses in the pathways used in the perception
of pain, inhibiting synaptic transmission and preventing pain from being
Psychoactive drugs:
● Affect the brain by either increasing or decreasing post-synaptic
● Over a hundred different neurotransmitters are known.
● Psychoactive drugs alter the functioning of some synapses.
● Some drugs are excitatory and some are inhibitory.
o Nicotine, cocaine and amphetamines are excitatory.
o Benzodiazepines, alcohol and tetrahydrocannabinol (THC) are
● Anaesthetics act by interfering with neural transmission between areas of
sensory perception and the CNS.
● Cause a reversible loss of sensation in part or all of the body.
● Local anaesthetics cause an area to be numbed and general anaesthetics
result in unconsciousness.
Anaesthetics and awareness:
● Patients under general anaesthesia are completely unaware.
● Sometimes it is undesirable or unnecessary for this level of
o For example, a spinal block is used during a caesarean section so
that the mother stays alive and breathing normally but pain cannot
be felt below the spinal cord.
Stimulant drugs:
● Stimulant drugs mimic the stimulation provided by the sympathetic
nervous system.
o Make a person more alert.
o Increased heart rate, blood pressure and body temperature.
● This is basically what the sympathetic nervous system does, so stimulants
mimic it.
● Caffeine and cocaine are examples of stimulants.
Examples of stimulants and sedatives:
● Pramipexole mimics dopamine and binds to dopamine receptors in postsynaptic membranes at dopaminergic synapses.
o Has the same effect as dopamine when it binds. Used in early
stages of Parkinson’s and can be used as an anti-depressant.
● Cocaine acts at synapses that use dopamine.
o Binds to dopamine reuptake transporters which pump dopamine
back into the pre-synaptic neuron.
o Cocaine blocks these transporters so dopamine builds up in the
synaptic cleft and the post-synaptic neuron is continuously
● Diazepam (valium) binds to an allosteric site on GABA receptors in postsynaptic membranes.
o GABA is an inhibitory neurotransmitter and causes the
hyperpolarization of the post-synaptic neuron by opening chloride
ion channels.
o Diazepam causes chloride ions to enter at a greater rate therefore
causes greater hyperpolarisation. It is therefore a sedative
● THC binds to cannabinoid receptors in pre-synaptic membranes.
o This inhibits the release of neurotransmitters that cause excitation
of post-synaptic neurons.
o It is therefore inhibitory.
o Cannabinoid receptors are found in the cerebellum, hippocampus
and cerebral hemispheres.
o Hence they result in stimulation of appetite, psychomotor
behaviour and short-term memory impairment.
Drug addiction:
● Addiction can be affected by genetic predisposition, social environment
and dopamine secretion.
● Some people are far more susceptible to addiction than others (genetic
o DRD2 codes for dopamine receptor protein. People with A1 allele
consumed less alcohol than those homozygous for the A2 allele.
● Social environment can greatly affects the likelihood of taking drugs.
o Peer pressure, poverty and social deprivation, traumatic life
experiences and mental health.
● Addictive drugs affect dopamine-secreting synapses.
o This is attractive to the drug user and they find it difficult to
A.6 Ethology:
● Ethology is the study of animal behaviour in natural conditions.
● Animals won’t display the same behaviour in zoos as they would in their
natural habitat because the stimuli would be different.
Natural selection and animal behaviour:
Natural selection can change the frequency of observed animal behaviour.
House finches are generally sedentary (native population in California).
Small number were released and spread throughout eastern US.
Within 20 years migratory behaviour was observed.
This change in behaviour was likely due to natural selection.
The mechanism of natural selection:
● Behaviour that increases the chances of survival and reproduction will
become more prevalent in a population.
● However only genetically determined behaviour can be inherited.
● Parus major is an example of how behaviour evolves by natural selection,
especially in response to environmental changes.
o Availability of food rises to a peak in spring.
o Due to global warming peak availability has become earlier and so
a birds that lay their eggs a few days earlier than the mean date
had a greater chance of survival when they were young.
o As a result, mean date of egg-laying evolved to become earlier.
Breeding strategies in salmon:
● Coho salmon die after breeding and the young live in the river for a year
before migrating to the ocean.
● They return to spawn.
● Breeding strategies:
o Hooknoses fight each other for access to females laying eggs
(winer sheds sperm over the eggs to fertilise them).
o Jacks sneak up on females and attempt to shed sperm over their
eggs before being noticed.
o Whether a male becomes a jack or hooknose depends on his
growth rate.
o Larger fish are hooknoses whilst Jacks are smaller and can
therefore go unnoticed.
Synchronised oestrus:
● Oestrus is a period of increased sexual receptivity.
● Synchronised oestrus in female lions in a pride is an example of innate
behaviour that increases the chances of survival and reproduction of
o Males can only breed if they overcome the dominant male in
another pride by fighting.
o When a new male takes over a pride, he kills all the suckling cubs
causing the females to come into oestrus more quickly so that he
can mate with them.
o Two or more closely related males may fight together for
o Females can only breed when they come into oestrus, which
enables them to have their cubs at the same time so they are all
lactating together.
o This means they can suckle each other’s cubs when they are
hunting, increasing the cubs’ chances of survival.
o Also, a group of male cubs can seek dominance more effectively if
they all leave the pack at the same time.
Blackcap migration:
● Migratory behaviour in blackcaps is an example of the genetic basis of
behaviour and its change by natural selection.
● Until recently almost all blackcaps migrated to Spain and Portugal for the
● However recently some were found to be migrating to Britain and Ireland
● Winters in Britain are now warmer due to global warming and it is much
closer than Spain.
● Also people in Britain feed wild birds, which increases survival of
● Britain, minimum day length is shorter so birds are prompted to go back
to Germany (breeding grounds) quicker and can dominate the best
Vampire bats:
● Blood sharing in vampire bats is an example of the evolution of altruistic
behaviour by natural selection.
● Vampire bats regurgitate blood for those who have not fed.
● This blood sharing is altruistic because:
o The blood sharing is not a kin-selection;
o And giving blood to an individual who has not fed incurs a cost to
the giver because their daily diet is lost.
o Blood sharing is an example of reciprocal altruism because if
Individual A feed B then on a later night when A can’t feed, B may
be able to feed A. If B died, then B would not be able to feed A
when A needs it. Hence it aids the chances of survival.
Foraging in shore crabs:
● Foraging behaviour in shore crabs is an example of increased chances of
survival by optimal prey choice.
● Foraging is searching for food.
● Prey chosen by animals is that which gives the highest rate of energy
● Hence crabs choose to eat mussels of intermediate size because they are
the most profitable in terms of the energy yield per second of time spent
breaking open the shells.
Courtship in birds of paradise:
● Courtship in birds of paradise is an example of mate selection.
● Plumage and courtship displays of male birds are reasons for exaggerated
● The traits are of no benefit in terms of flight but are there only to attract
female attention.
● Males gather at a site called a lek and females select mates depending on
who has the best display.
o The plumage and courtship dances help the female identify
whether the male belongs to her species.
o Exaggerated traits could also suggest overall fitness – if the male
had enough energy to grow and maintain the elaborate plumage, it
must have fed very efficiently.
o The male would therefore be better adapted to living and
Changing learned and innate behaviour:
● Learned behaviour can spread through a population or be lost from it
more rapidly than innate behaviour.
● Innate behaviour can be modified by natural selection slowly because
there needs to be variation in the alleles that affect such behavioural
o Changes in allele frequencies in populations need to occur.
● Learned patterns take longer to develop in an individual.
o However since they don’t require genetic modification and
changes in allele frequencies, they can spread relatively rapidly.
o However they can also be forgotten quickly.
Blue tits and cream:
● Feeding on cream from milk bottles in blue tits is an example of the
development and loss of learned behaviour.
● Blue tits peck through the aluminium foil to drink the cream from milk
● This behaviour caused their migration far further than usual.
● German occupation of the Netherlands stopped deliveries of milk for eight
years; however soon after the resumption of deliveries blue tits
throughout the Netherlands were pecking through bottle tops.
● This shows that this behavioural pattern is learned. Since milk has been
delivered to doorsteps less, and a lot of it is skimmed (without cream),
blue tits have stopped displaying such behaviour.