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1 Cell Biology
1.1 Introduction to cells
The Cell Theory:
I. All living organisms are composed of one or more cells.
II. The cell is the basic unit of structure and organisation in organisms.
III. All cells come from pre-existing cells.
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.
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
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consumption.
● Stem cells can be found in the bone marrow, skin and liver and can be used
for self-repair.
Phospholipid bilayers:
● Phosphate heads, which are hydrophilic; and hydrocarbon tails, which are
hydrophobic.
● Since they have both hydrophilic/phobic properties, they are amphipathic.
● 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 hydrophobic.
● 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.
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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
crystallizing.
● 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.
Endocytosis:
● 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
bilayer.
Exocytosis:
● 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:
● 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.
Interphase:
● G1: Mitochondria grow and divide. Similarly chloroplasts also grow and
divide.
● 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.
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Cytokinesis:
● 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.
2 Molecular Biology
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.
Vitalism:
● 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
principle.
Carbon Compounds:
● Carbon atoms can form 4 covalent bonds. These can be single or double
bonds.
● Can form chains/rings of any length.
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
respectively.
● 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.
● Amino Acids: Contain Amine group; Carboxyl group; Hydrogen atom; and
R variable group.
Metabolism:
● 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
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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
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
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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.
Amylose Amylopectin
Branched Unbranched
Alpha helix Globular
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 1-
4 linkages
Lipids:
● Triglycerides are formed by condensation from three fatty acids and a
glycerol.
● 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
(20˚C).
● Oils are always liquid.
Triglycerides:
● 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 carbohydrates.
● Adipose tissue is located directly beneath the skin and round some organs
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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
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Protein conformations:
● Amino acid sequence determines the 3D shape of the polypeptide.
Fibrous Globular
Elongated, with a repeating Intricate shape with parts that are
structure helical or sheet-like.
No folding up, amino acid prevents Polypeptide folds up as amino acids
it. are added on.
Have bonds between the R groups of
the amino acids.
Hydrophobic groups on the inside
and hydrophilic groups on the
outside.
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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:
● Catalysis.
● Muscle contractions.
● Cytoskeletons.
● Tensile strengthening.
● Blood clotting.
● Transport of nutrients and gases.
● Cell adhesion.
● Membrane transport.
● Hormones and receptors.
● DNA packing.
● Immunity.
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.
Proteomes:
● 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.
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2.5 Enzymes:
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
rate.
● Lactose free milk: Lactose is broken down into glucose and galactose with
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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 other.
● 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.
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.
Transcription:
● 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 bases.
● 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.
Ribosomes:
● Synthesis of polypeptides on ribosomes: ribosomes consist of a small and
a large subunit. Have binding sites for each molecule that partakes in the
process.
● Large subunit makes peptide bonds between amino acids to link the,
together into a polypeptide.
Codons:
● 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 anti-codon
complementary to the mRNA codon for that particular amino acid.
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.
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
oxygen.
● Required when a short burst of ATP is needed.
● When oxygen supplies are internally low and in oxygen deficient
environments.
● 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.
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:
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.
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
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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.
● 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.
Mutation:
● 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
can.
Genome:
● 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.
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● Most of the genome is not transcribed. These sections are called junk
DNA.
● 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.
Plasmids:
● 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
example.
● 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
autoradiography:
● 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.
● 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.
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
sequence.
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
fertilization.
● 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
species.
● 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;
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Karyograms:
● 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
pairs.
● 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.
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
completed.
o Cytokinesis occurs.
● Prophase II: Chromosomes, which still consist of two chromatids, condense
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3.4 Inheritance:
Gametes:
● 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:
● 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.
Separation:
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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
generation.
● These hybrids self-pollinate to form 1 homozygous dominant, two
heterozygous and 1 homozygous recessive. This forms the F2 generation.
diseases.
● 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
intestine.
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
chromosome.
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
colour-blind.
● Females are less likely to inherit colour blindness unless both their parents
are either carriers or affected.
Haemophilia:
● 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.
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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
areas.
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.
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.
Cloning:
● 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
example.
● 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.
4 Ecology
Species:
● Species are groups of organisms that interbreed to produce fertile
offspring.
● 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
Populations:
● Members of a species may be reproductively isolated in separate
populations.
● 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.
(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:
● 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.
Detritivores:
● 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:
● Saprotrophs are heterotrophs that obtain organic matter by external
digestion.
● 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.
Community:
● 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
numbers.
● 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
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associated.
o Independent distribution: no association between species (forms
null hypothesis during chi squared test).
Ecosystems:
● Community forms an ecosystem by its interactions with the abiotic
environment
● 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
environment.
● 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.
Energy conversion:
● Light energy is converted to chemical energy in carbon compounds by
photosynthesis.
● 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.
level.
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.
Carbon fixation:
● Autotrophs convert carbon dioxide into carbohydrates and other carbon
compounds via carbon fixation.
● This reduces carbon dioxide concentrations in the air.
Methanogenesis:
● Methane is produced from organic matter in anaerobic conditions by
methanogenic archaeans and some diffuses into the atmosphere.
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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
earth.
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.
Combustion:
● Carbon dioxide is produced by the combustion of biomass and fossilised
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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.
Limestone:
● 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.
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.
Evolution in summary:
● Evolution only concerns heritable characteristics.
● Occurs when heritable characteristics of a species change.
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.
Speciation:
● Populations of a species can gradually diverge into separate species by
evolution.
● The characteristics of the two populations will gradually diverge to the
extent where they will no longer be able to interbreed to produce fertile
offspring.
● Endemic species: one found only in a certain geographical area. Occurs by
migration and subsequent divergence.
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
rates.
Variation:
● 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
pool.
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
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Adaptations:
● 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.
Inheritance:
● 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
characteristics.
● 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
plasmids.
● Process:
o Resistance gene either formed by mutation or received by another
bacterium.
o Use of antibiotic provides environment for natural selection to
occur (it is a selection pressure).
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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:
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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.
Plants:
● Bryophyta: mosses.
● Filicinophyta: ferns.
● Coniferophyta: conifers.
● Angiospermophyta: flowering plants.
Animals:
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Porifera: Sponges.
Cnidaria: Jelly fish, sea anemone.
Platyhelminthes: Tapeworms.
Mollusca: Squid.
Annelids: Leeches.
Arthropoda: Insects, crabs.
Vertebrates:
● Bony ray-finned fish.
● Amphibians/
● Repitles
● Birds.
● Mammals.
5.4 Cladistics:
Clades:
● A group of organisms that have evolved from a common ancestor.
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.
Cladograms:
● 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.
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Classification by morphology:
● Classification based on physical characteristics/anatomical characteristics
rather than base sequence/amino acid sequence.
● Inaccurate.
6 Human Physiology
Peristalsis:
● 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
contraction.
● 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;
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Absorption by villi:
● Absorb monomers formed by digestion as well as mineral ions and
vitamins.
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.
● Nutrients move from the lumen of the small intestine, through the plasma
membrane, through the epithelium and into the lacteal/blood capillaries of
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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
direction.
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.
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.
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.
Capillaries:
● Allow the exchange of materials between cells in tissue and blood in the
capillary.
● 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
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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.
Veins:
● 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
changes.
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
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oxygenated blood.
Atherosclerosis:
● 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.
Epinephrine:
● 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.
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
produced.
● 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
pressure.
Phagocytes:
● White blood cells that give non-specific immunity.
● After skin and mucous membranes, the WBC gives a secondary line of
defence.
● 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
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Antibodies:
● 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.
Antibiotics:
● 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.
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.
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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
exhalation.
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.
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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
pneumocytes.
o Monolayer on the surface of the moisture lining the alveoli;
hydrophilic heads face the moisture and hydrophobic tails face the
air.
o Reduces surface tension and prevents water from adhering to the
sides of the alveoli during exhalation.
Antagonistic muscles:
● Muscles are required for inspiration and expiration.
● Muscles are pulled into an elongated state by the contraction of another
muscle.
● Contraction and relaxation of muscles to cause movement are known as
antagonistic pairs.
Emphysema:
● 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.
Resting potential:
● Maintenance of a resting potential by pumping of sodium ions out of the
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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 gradient.
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.
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.
Synapses:
● 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
triggered.
● Neurotransmitters are then broken down and removed from the synaptic
cleft.
Acetylcholine:
● Used as a neurotransmitter.
● Produced by combining choline with an acetyl group.
● Loaded into vesicles and released into the synaptic cleft during synaptic
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transmission.
● Bind the specific receptors on postsynaptic membrane.
● Acetylcholinesterase rapidly breaks acetylcholine into acetyl and choline.
● Choline is then reabsorbed into the presynaptic neuron.
Neonicotinoids:
● 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.
instead of fat.
Diabetes:
● 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.
Thyroxin:
● Secreted by thyroid gland to regulate metabolic rate and control body
temperature.
● 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,
constipation.
● 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
arterioles.
o More thyroxin secreted when body temp is too low = increased
metabolic rate, increased respiration and vasoconstriction of skin
arterioles.
Leptin:
● 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
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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.
Melatonin:
● 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
night.
● 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
destination.
o Melatonin tablets prevents onset of jetlag by promoting deeper
sleep etc.
Testosterone:
● 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
voice.
puberty.
● 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.
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
ovum.
o Endometrium continues to develop for implantation. If fertilisation
doesn’t occur, corpus luteum breaks down. Endometrium also
sheds.
● 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 post-
ovulation.
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.
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7 Nucleic Acids
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.
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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
markers.
o New technology allows for the fluorescent dideoxyribonucleotides
to be detected by computers and quick interpretation of results.
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
modification.
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:
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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
chain.
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.
Elongation:
● 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 site.
o This cycle repeats.
Termination:
● Disassembly of the components follows termination of translation.
o Stop codon is reached.
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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.
Primary structure:
● Number and sequence of amino acids in a polypeptide is the primary
structure.
● 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
medium.
● Positively charged R groups interact with negatively charged R groups.
● Hydrophobic amino acids orient themselves towards the centre whilst
hydrophilic orient themselves outwards.
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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.
8.1 Metabolism:
Metabolic pathways:
● Metabolic pathways consist of chains and cycles of enzyme-catalysed
reactions.
● Small sequence of steps.
● Some metabolic pathways are chain reactions whilst some are cycles.
● 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
dehydratase.
Phosphorylation:
● 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
releasing).
● Glucose => (ATP to ADP) => Glucose-6-phosphate.
● 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.
Chemiosmosis:
● NADH+H+ supplies pairs of hydrogen atoms to the first carrier in the chain.
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.
8.3 Photosynthesis:
Photoactivation:
● 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 acceptor.
● 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:
● 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.
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
carrier.
● Concentration of protons develops in thylakoids spaces, store of potential
energy.
● 4H+ from photolysis also contributes to the proton gradient.
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Chemiosmosis:
● 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
stage.
Reduction of NADP:
● Excited electrons from PSI reduce NADP.
● Reduced NADP carries pairs of electrons that can carry out reduction
reactions
● 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 NADP.
● 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 ribulose-
biphosphate.
● 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
RuBP regeneration:
● RuBP is reformed using ATP.
● 5 triose phosphates ((3ATP=>3(ADP+P))=3RuBp.
9 Plant Biology
Transpiration:
● Inevitable consequence of gas exchange in the leaf.
● Exchange of oxygen and carbon dioxide must occur to sustain
photosynthesis.
● 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.
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.
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● Phloem loading is the process by which sugars are brought into the phloem.
● 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.
Growth in plants:
● Undifferentiated cells in the meristems of plants allow indeterminate
growth.
● 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.
Plant tropisms:
● Plants respond to the environment by tropisms.
● Light and gravity influence growth directionality.
● Phototropism and gravitropism (geotropism).
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
auxins.
● 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.
Structure of seeds:
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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.
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
recombination.
● 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
chromatids.
● However these sister chromatids are likely to be non-identical sister
chromatids due to crossing over.
10.2 Inheritance:
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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 co-
dominant 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:
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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
recombinant.
Gene pools:
● Gene pools consist of all possible genes and alleles of an interbreeding
population.
● 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.
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11 Animal physiology
11.1 Antibody production and vaccination:
● Antibodies last in the body for a few weeks and are quite short term.
● Hence memory cells are produced and this forms immunity.
Immunity:
● 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
immunity.
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.
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.
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).
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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 Carbon Dioxide is a waste product
have noT been completely of respiration and will be present
metabolised (drugs/pigments). in higher amounts in the renal
Nitrogenous waste. vein.
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.
water/salt.
through into dialysis fluid but not blood cells and protein
molecules.
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.
▪ Sperm detach from Sertoli cells and are carried out by the
fluid in the seminiferous tubule.
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
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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
plate.
● 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.
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
pruning.
Strokes:
● 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
disability.
hormones.
Homunculi:
● 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.
Olfactory receptors:
● Detection of chemicals in the air by the many different olfactory
receptors.
● Located inside the epithelium of the nose.
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Photoreceptors:
● 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.
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:
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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.
● 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 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.
Cochlear implants:
● Cochlear implants in deaf patients.
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Reflexes:
● 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
muscles.
Reflex arcs:
● Reflex arcs comprise the neurons that mediate reflexes.
● Receptor perceives the stimulus and eventually relays the impulse to the
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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.
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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
avoided.
● 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
stimuli.
● After a while, the dog would salivate even with the ringing of the bell,
even if no food were present.
Imprinting:
● 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
see.
● 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
experiences.
● The environment imposing a stimulus on an animal initiates reflex
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Learning:
● 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.
Memory:
● 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.
Summation:
● Nerve impulses are initiated or inhibited in post-synaptic neurons as a
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Endorphins:
● 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
felt.
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Psychoactive drugs:
● Affect the brain by either increasing or decreasing post-synaptic
transmission.
● 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
inhibitory.
Anaesthetics:
● 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.
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.
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
predisposition).
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
abstain.
A.6 Ethology:
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.
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
offspring.
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
dominance.
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
winter.
● However recently some were found to be migrating to Britain and Ireland
(10%).
● Winters in Britain are now warmer due to global warming and it is much
closer than Spain.
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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.