AQA biology a-level paper 2

describe and explain the steps in the light dependent reaction of photosynthesis

describe and explain the steps in the light dependent reaction of photosynthesis

1. photoionisation: light reaches chlorophyll in PSII, which is absorbed by an electron, which becomes excited and moves to a higher energy level.
2. the electron passes to a carrier protein in the thylakoid membrane, and is passed down a series of carrier molecules called an electron transfer chain.
3. as the electron moves down, energy is lost from the electron and is released as ATP.
4. the loss of electron from PSII is 'refilled' by an electron produced by photolysis, which also produces hydrogen and oxygen.
5. the lost electron reaches PSI, which absorbs light energy and boosts another electron to a higher energy level (excitation).
6. this electron also goes down an electron transport chain.
7. this reaches the final electron acceptor which is a proton. they combine to form H and reduce NADP to NADPH.

describe and explain the steps in the light independent reaction pf photosynthesis.

1. CO2 diffuses into stroma and combines with ribulose bisphosphate (RuBP) using the enzyme rubisco.
2. this forms an unstable 6 carbon molecule, which splits into 2 3 carbon molecules, glyercate-3-phosphate (G3P) .
3. G3P is reduced by NADPH to triose-phosphate (TP), which is aided by ATP for energy.
4. TP can be converted into useful organic substances.
5. TP can also be reformed into RuBP using ATP.

describe glycolysis in respiration. give net formation.

1. glucose is converted into phosphorylated glucose by 2ATP. this makes it very reactive, so it splits into 2 triose phosphate (TP).
2. 2TP is then oxidised by 2NAD and 4 ATP is formed to form pyruvate.
3. NET: 2ATP, 2Pyruvate, 2NADH, 2H+

describe links reaction in respiration. give net formation.

1. pyruvate diffuses into the matrix of mitochondria.
2. pyruvate is oxidised by NAD. CO2 is lost. this forms acetate.
3. acetate and co-enzyme A combine to form acetyl co-enzyme A.
4. NET: CO2, reduced NAD, acetyl co-enzyme A

describe krebs cycle in respiration. give net formation.

1. acetyl co-enzyme A combines with 4 carbon molecule (oxaloacetate) to form 6 carbon citric acid.
2. CO2 is lost (decarboxylation), molecule is oxidised by NAD and ATP is produce. this forms 5 carbon compound.
3. it is oxidised by 2NADH and FAD, and is decarboxylated.
4. this forms 4 carbon molecule again.

describe oxidative phosphorylation in respiration.

1. reduced coenzyme passes its H to a carrier protein in the ETC. this splits into a proton and electron.
2. the protons pass through the space between inner and outer mitochondrial membrane.
3. electrons pass through proteins on ETC.
4. protons return back via ATP synthase in the membrane, producing ATP.
5. the protons and electrons recombine to form H, which combines with O to form water.
6. oxygen is the last electron acceptor in the ETC.

define biomass

the total mass of organisms in a given area

what is the 'gross primary production'

the chemical energy stored in a plants biomass

what is the 'net primary production'

the chemical energy stores in a plants biomass after respiratory losses have been considered. this energy is available to consumers.

how can you calculate the net primary production?

NPP = GPP - R

why is converting sunlight energy into biomass in producers inefficient?

some light isn't the correct wavelength to be absorbed
some light doesnt hit chloroplast
some light is converted into heat energy
some light energy is reflected

describe the nitrogen cycle.

fixation:
atmospheric nitrogen can be fixed by rhizbium bacteria.
if struck by lightning, it becomes reactive and combines with oxygen to form NO.

ammonification:
saprobionts feed on organic matter and release ammonia, which then forms ammonium ions in the soil.

nitrification:
nitrifying bacteria convert ammonium ions into nitrite ions and then to nirate ions.

denitrification:
anaerobic denitrifying bacteria convert soil nitrates into gaseous nitrogen.

homeostasis

the maintenance of an internal environment within restricted limits in organisms. all cells are in an environment that meets their requirements and allows them to function normally despite external changes.

why is homeostasis important?

1. the enzymes that control biochemical reactions in cells are sensitive to change e.g. in pH or temperature, which can cause them to denature. homeostasis allows enzyme controlled reactions to take place at a suitable rate.

2. homeostasis allows a constant blood glucose concentration to ensure a constant water potential, so cells don't shrink or burst.

3. homeostasis allows organisms to be more independent of external changes.

list the parts of control mechanisms in homeostasis.

1. optimum temperature
2. receptor- detects any deviation from the optimum temperature
3. coordinator- info from receptor to effector
4. effector- often a muscle/gland, brings about change to return the system to optimum level
5. feedback mechanism

what is negative feedback?

this is when the change produced by the system leads to a change in the stimulus detected by the receptor, turning the system off.

what is positive feedback?

this is when a deviation from the optimum causes changes that result in an even greater deviation from the norm

e.g. in neurones, a stimulus leads to an influx of Na+, which increases the membrane permeability to allow further NA+ to enter.

describe the second messenger model.

1. Adrenaline binds to transmembrane protein receptor in the cell surface membrane of a liver cell.
2. the binding of adrenaline causes the protein to change shape on the inside of the membrane.
3. the change in tertiary structure activates adenyl cyclase, which converts ATP to cAMP.
4. cAMP binds to kinase, changes structure and activates it.
5. this catalyses the conversion of glycogen to glucose, which moves out of the liver cell and into the blood by facilitated diffusion.

glycogenesis

conversion of glucose to glycogen. this is when glucose levels are abnormally high.

glycogenolysis

breakdown of glycogen to glucose. this is when glucose levels are abnormally low.

gluconeogenesis

production of glucose from sources other than carbohydrates, such as glycerol or fatty acids. occurs when there's insufficient glycogen.

how does insulin and beta cells in the pancreas affect glucose levels?

1. the beta cells in the pancreas detect a rise in the blood glucose concentration and respond by secreting insulin into blood.
2. insulin binds to glycoprotein receptors on cells.
3. this causes a change in the tertiary structure of the glucose transport proteins, making them more permeable to glucose and so allowing more in by facilitated diffusion.
4. activates the enzymes that convert glucose to glycogen and fat.

how does glucagon and alpha cells in the pancreas affect glucose levels?

1. alpha cells detect a fall in blood glucose levels and so secrete glucagon.
2. glucagon attaches to receptors on cell surface membrane of liver cells.
3. this activates enzymes which convert glycogen to glucose.
4. also activates enzymes that convert amino acids to glucose.

does insulin increase or decrease glucose levels?

decrease

does glucagon increase or decrease glucose levels?

increase

does adrenaline increase or decrease glucose levels?

increase

describe and explain the role of hormones in osmoregulation.

1.osmoreceptors in hypothalamus detect fall in water potential as they begin to shrink, causing hypothalamus to produce ADH.
2. ADH goes to posterior pituitary gland, where it is secreted into capillaries.
3. ADH goes from blood to kidneys, where it binds to receptors on the cells of of distil convoluted tubule and collecting duct.
4. this activates phosphorylase enzyme.
5. this causes vesicles, which contain water channel proteins, to fuse with cell surface membrane. hence, making it more permeable to water.
6. also increases permeability of collecting duct to urea so it passes out and lowers water potential, so more water can pass out by osmosis.

describe what is happening to a neurone at resting potential.

1. neurone is polarised
2. Na+ actively transported out of axon
3. K+ actively transported in to axon
4. 3 sodium move out for every 2 potassium in
hence, the outward movement of Na+ is greater than the inward movement of K+. this creates an electrochemical gradient as the outside is more negative than inside.
5. K+ begins to diffuse back out while Na+ diffuses back in, although most Na+ gates are closed.

describe the processes that occur when an action potential is formed.

1. the energy of a stimulus causes some sodium voltage-gated channels in the axon membrane to open and so Na+ diffuses into axon, down electrochemical gradient.
2. this triggers a reversal in potential difference across the membrane because Na+ is positively charged.
3. as more Na+ goes in, more channels open and so even more Na+ goes in.
4. when action potential is +40mV the Na+ channels close and the K+ channels open.
5. K+ diffuses out of axon.
6. there is overshoot of electrical gradient- hyperpolarisation.
7. K+ gates shut. resting potential is re-established. this is repolarisation.

describe the processes that occur during the passage of an action potential along an unmyelinated axon.

1. at rest- the inside of axon is more negative than outside.
2. a stimulus causes influx of Na+ and so the charge of the axon is reversed- depolarised.
3. this causes localised electrical currents to open up the voltage-gated channels further along the axon, so more Na+ enters here and depolarises this area.
4. in the initial area, Na+ gates close and K+ open, so K+ leave the axon down electrochemical gradient. depolarisation moves along membrane.
5. outward movement of K+ and inward movement of Na+ continues until repolarisation; return to resting state.

why do action potentials travel faster down a myelinated axon?

myelin sheath prevents action potentials forming. action potentials form at the Nodes of Ranvier, and jump from node to node by saltatory conduction.
in an unmyelinated axon, it takes longer as the events of depolarisation take place all the way along an axon.

what are factors that affect the speed of an action potential?

1. myelin sheath
2. diameter of axon: the greater the diameter, the faster the speed, because there's less leakage of ions from a large axon, so membrane potentials are easier to maintain.
3. temperature: the higher the temperature, the greater the rate of diffusion of ions, and hence the faster the impulse.

what is the purpose of the refractory period?

1. Ensures action potentials travel in one direction only, since action potentials cannot move to a refractory region.
2. ensures action potentials are separated from one another.
3. limits the number of action potentials.

spatial summation

a number of different presynaptic neurones collectively release enough neurotransmitters to exceed the threshold value of the postsynaptic neurone, triggering a new action potential.

temporal summation

a single presynaptic neurone releases neurotransmitters many times over a short period. this exceeds the threshold value, triggering a new action potential.

how do drugs affect synaptic transmission and action potentials?

1. stimulate the nervous system by mimicking neurotransmitters, stimulating neurotransmitter release or inhibiting enzymes that break down neurotransmitters, and so create more action potentials.
2. inhibit the nervous system by inhibiting release of neurotransmitter or blocking Na+/K+ channels on postsynaptic neurone, hence creating less action potentials.

describe the processes that occur during synaptic transmission.

1. action potential arrives at end of presynaptic neurone. this stimulates Ca2+ channels to open so Ca2+ enter synaptic knob by facilitated diffusion.
2. this stimulates synaptic vesicles to fuse with presynaptic membrane, releasing acetylcholine into synaptic cleft.
3. acetylcholine binds to receptor sites on Na+ channel proteins on postsynaptic neurone membrane. this causes them to open to Na+ diffuse in.
4. influx of Na+ generates new action potential in postsynaptic neurone.
5. acetylcholinerase hydrolyses acetylcholine into choline and ethanoic acid, which diffuses back across into presynaptic neurone.
6. ATP recombines ethanoic acid and choline, which is stored in synaptic vesicles for later use.

describe slow twitch fibres

contract more slowly and provide less powerful contractions but over a longer period.
adapted for aerobic respiration to avoid lactic acid build up.
adapted for endurance work.
has lots of myoglobin, rich bloody supply and many mitochondria.

describe fast twitch fibres

contract more rapidly and more powerful but over a shorter period of time.
adapted for intense exercise
have thicker and more numerous myosin filament, have more glycogen, have more enzymes to carry out anaerobic respiration, has phosphocreatine.

what is a neuromuscular junction

the point where motor neurone meets a skeletal muscle fibre.

describe the processes that occur during muscle contraction

1. action potential travels down T-tubules, which are in contact with the sarcoplasmic reticulum.
2. calcium ion protein channels on sarcoplasmic reticulum open and calcium ions diffuse out by diffusion, down a concentration gradient.
3. calcium ions cause tropomyosin to change shape and unblock the binding sites on actin.
4. ADP attaches to myosin head, so it changes shape and can now bind to the actin filament, forming a cross bridge.
5. once attached, myosin heads alters angle, pulling the actin along with it. ADP is released.
6. ATP attaches to myosin head, causing it to detach from actin.
7. calcium ions activate ATPase to hydrolyse ATP to ADP, which releases enough energy for the heads to return to initial position.
8. repeat

what type of stimulus does a pacinian corpuscle respond to?

mechanical pressure

when at rest, what occurs at a pacinian corpuscle?

the sodium ion channels on the membrane around the neurone are narrow and so don't allow Na+ to pass along them. it has resting potential.

what happens when pressure is applied to pacinian corpuscle?

1. it deforms, so membrane around neurone stretches.
2. this widens Na+ channels and so Na+ diffuses into neurone.
3. this changes the potential of the membrane, depolarising it. a generator potential is formed.
4. generator potential forms an action potential.

what kind of summation occurs in rod cells?

spatial summation

what kind of summation occurs in cone cells?

temporal summation

where are rod cells absent at?

the fovea

where are cone cells concentrated at?

the fovea

where are rod cells more highly distributed at?

periphery of the retina

do rod cells give good or poor visual acuity?

poor visual acuity

do cone cells give good or poor visual acuity?

good visual acuity

how many types of rod and cone cells are there?

rod- 1
cone- 3, all responding to different wavelengths

why do rod cells give poor visual acuity?

many rod cells link to the same bipolar cells (spatial summation), so when light stimulates rod cells which share the same neurone, only 1 impulse will travel to the brain. so, the brain can't distinguish between separate sources of light that stimulated them. resolution is poor, hence low visual acuity.

why do cone cells give high visual acuity?

each cell is connected to a separate bipolar cell. if 2 separate rod cells are stimulated by light, then 2 separate impulses will be sent to the brain. so, the brain can distinguish between two sources of light that stimulate two different rod cells, hence better resolution, hence better visual acuity.

what is a taxis?

when the direction of a stimulus determines a simple response. motile organisms will move towards it if favourable (positive), or away if unfavourable (negative).

what is a kinesis?

a form of response whereby an organism changes the speed in which it moves and changes direction. this occurs when an organism reaches an area of unfavourable stimuli, so that it may return to a favourable environment.

example of kinesis

woodlice increase rate of movement/turning when they reach a dry area. this will allow them to reach a favourable damp area, where they don't turn as much.

example of taxis

earthworms have negative phototaxis and so stay deeper in soil to aid their chances of survival, so they are more likely to find food, avoid predators, and conserve water.

what is a tropism?

the growth of part of a plant in response to a directional stimulus. there can be positive and negative responses.

describe the control of phototropism by IAA.

1. cells in shoot tip produce IAA which is transported evenly throughout all regions and then down the shoot.
2. light causes IAA to accumulate on the shaded side of the shoot, so much that there is a greater build up of IAA on shaded than unshaded side.
3. IAA causes the shaded side of the shoot to elongate further than the non shaded side. this causes the shoot to eventually grow and bend towards the light.

describe the control of gravitropism by IAA.

1. root tip cells produce IAA, which is distributed evenly and down the root.
2. gravity causes IAA to accumulate on the LOWER side of the shoot than upper side, so there is a higher concentration on lower than upper.
3. IAA inhibits elongation in root cells, so inhibits elongation in lower side than upper side. so, the upper side of the shoot elongates further and bends towards gravity.

what effect does IAA have on roots?

inhibits growth

what effect does IAA have on shoots?

stimulates growth

describe the components of a reflex arc and give an example.

1. stimulus- heat
2. receptor- heat receptors to sensory neurone
3. sensory neurone- impulse to spinal cord
4. relay neurone- to motor neurone
5. motor neurone- spinal cord to muscle
6. effector- muscle in arm contracts
7. response- pulling hand away from heat

which region of the brain controls the changes in heart rate?

medulla oblongata

what are the two centres of the medulla oblongata?

1. a centre that increases heart rate, linked to sinoatrial node by sympathetic NS.

2. a centre that decreases heart rate, linked to the sinoatrial node by parasympathetic NS.

explain how chemoreceptors control heart rate.

1. chemoreceptors in the walls of the carotid arteries are sensitive in changes of pH. when they detect a lower pH (high CO2) then more impulses are sent to the specific heart rate increasing centre in the medulla oblongata.
2. this centre increases frequency of impulses to the sinoatrial node via sympathetic NS. this increases rate of electrical waves being produced.
3. increased heart rate results in increased blood flow, so more CO2 is removed by lungs and CO2 levels return to normal. pH rises to normal.
4. chemoreceptors reduce frequency of impulses, medulla oblongata reduces frequency of impulses. heart rate returns to normal.

describe the control of heart rate by pressure receptors.

1. when blood pressure is higher than normal, pressure receptors in carotid arteries send more impulses to centre in medulla oblongata that decreases heart rate via parasympathetic NS.

2. when blood pressure is lower than normal, pressure receptors send more impulses to the centre of the medulla oblongata that increases heart rate via sympathetic NS.

name the negative effects of using nitrogen containing fertilisers.

1. reduced species diversity
2. leaching
3. eutrophication

why does using nitrogen containing fertilisers result in reduced species diversity?

nitrogen rich soils favour the growth of grasses etc., which can outcompete other species, which die as a result.

what is "leaching"?

the process by which nutrients are removed from the soil. rainwater will dissolve soluble nutrients and carry them deep into the soil, away from plant roots. the leached ions can reach rivers that drain into lakes.

what is "eutrophication"?

the process by which nutrient concentrations increase in bodies of water, often as a result of leaching. may result in algael bloom, which blocks sunlight from reaching plants underneath, causing them to die.

define population.

a group of individuals of one species that occupy the same habitat at the same time and are potentially able to interbreed.

define community.

all the populations of different species living and interacting in a particular place at the same time.

define niche.

the role and position a species has in its environment; how it meets its needs for food and shelter, how it survives, and how it reproduces. A species' niche includes all of its interactions with the biotic and abiotic factors of its environment.

codominance

occurs where heterozygote has a phenotype that is different from both homozygotes.
neither allele is dominant over the other; they both contribute equally to the phenotype.

sex linkage

alleles carried on the X chromosome.

why are sex linked diseases more common in males than females?

because males only have one X chromosome, and so if there is a recessive allele there, then there will be no dominant allele on Y chromosome to "hide" it.

multiple alleles

this is where there are several different alleles of a gene e.g. blood type: IA, IB (codominant), and IO (recessive).

dihybrid inheritance

involves 2 genes at different loci.

epistasis

when one gene locus interacts with another gene at a different locus.

linked genes

genes on the same chromosome

Hardy-Weinberg principle

p2 + 2pq + q2

p2 = homozygous dominant

q2 = homozygous recessive

2pq = heterozygous

In any hardy-weinberg problem, start with homozygous recessive individuals.

what assumptions need to be in place to use the hardy weinberg principle?

1. No mutations
2. Population is isolated
3. No selection
4. Large population
5. Mating is random

how can a population be separated and form different species?

1. Populations become separated. physical barriers may come between two groups.
2. Therefore they stop interbreeding.
3. Populations adapt to new environment. Selection pressures will be different in different areas.
4. Allele frequencies will change in the different populations.
5. Over time they become so different that they can no longer interbreed.

formula to calculate the mean density of individuals from quadrats

total no of individuals counted
------------------------------------
no of quadrats x area of quadrat

allopatric speciation

When populations of a species become geographically isolated. Gene flow between them ceases (reproductive isolation). the new environment will trigger a change in the gene pool due to natural selection imposed on them.
If the populations are relatively small, they may experience a founder effect.
Selection and genetic drift will act differently on these two different genetic backgrounds, creating genetic differences between the two new species.

sympatric speciation

become reproductively isolated from each other even though they occupy the same geographic range. Factors that could lead to them becoming reproductively isolated from each other are things like changes in courtship behavior, changes in feeding behavior, changes in coloration.

The most common way this occurs is polyploidy.
Rapid genetic changes can alter morphology, behavior, and habitat preferences.

totipotent cells

cells that can mature into any kind of specialized body cell. can divide to form a whole organism. they are found in very early mammalian embryos. after this stage, some of the genes become switched off and so are not translated into RNA, hence specialized.

pluripotent cells

can become any kind of specialized body cell, but cannot divide to form a whole organism.

induced pluripotent stem cells

produced from unipotent cells. genetically altered in labs (transcription factors) to make them have the characteristics of embryonic stem cells. they turn on the genes that were otherwise turned off.

multipotent cells

can divide into some, but not all, specialized cells.

unipotent cells

divide to form just one type of cell.

transcription factors

transcription factors bind to the DNA sequence at specific target sequences. RNA polymerase recognizes the complex formed and so transcribes the gene.

methylation of DNA

addition of methyl groups to bases. added throughout life, sometimes in response to environmental factors e.g. diet. causes the DNA to wrap more tightly around histones, so transcriptional factors cannot bind to specific DNA sites and initiate transcription.

acetylation of DNA

acetyl groups added to histones, so DNA is less tightly wound round it, making it easier for RNA polymerase and transcriptional factors to bind, so transcription can occur.

oncogenes

mutated proto-oncogenes form oncogenes. oncogenes are permanently activated (switched off).

explain how to produce DNA fragments with reverse transcriptase.

1. reverse transcriptase forms cDNA from an mRNA strand.
2. single stranded cDNA is isolated when mRNA is hydrolysed with an enzyme.
3. cDNA acts as a template for DNA nucleotides to bind to by complimentary base pairing. DNA polymerase joins them together. a copy of the gene is now formed.

explain how to produce DNA fragments with restriction endonucleases.

1. cuts gene at recognition site. this can result in blunt or sticky ends.
2. promotor gene and terminator gene also inserted. marker genes too.
3. same RE cut out complimentary recognition site in plasmid (vector).
4. DNA ligase is used to bind the nucleotides of the two DNA strands together.
5. plasmids introduced to host organisms. bacteria mixed with plasmids with calcium ions.

what is a DNA probe?

a short single-stranded length of DNA that has some sort of label attached to make it identifiable e.g. radioactively labelled and fluorescently labelled probes.