AQA(B) A2 Module 4

Energy, Control And Continuity










Human Nervous system

Nerve Cells


The Reflex Arc


The Nerve Impulse






The eye


The Brain






The Kidney



Temperature Homeostasis

Blood Sugar Homeostasis

Blood water Homeostasis

Classical Genetics



Monohybrid cross

Sex Determination


Multiple Alleles

Dihybrid Crosses

Population Genetics


Natural Selection




Module 4 Specification


The relationship between photosynthesis and respiration. The synthesis of ATP from ADP and inorganic phosphate, and its role as the immediate source of energy for biological processes.

Cellular Respiration

Respiration as the process by which energy in organic molecules is made available for other processes within an organism. The structure and role of mitochondria in respiration. The biochemistry of aerobic respiration only in sufficient detail to show that:


Photosynthesis as a process in which light energy is used in the synthesis of organic molecules. The structure and role of chloroplasts in relation to photosynthesis.

Control and Coordination

Organisms increase their chances of survival by responding to changes in their environment.

The Human Nervous System

Information is transferred in the nervous system through detection of stimuli by receptors and the initiation of a nerve impulse, leading to an associated response by effectors by means of a coordinator. A simple reflex arc involving three neurones.

The general role of the sympathetic and parasympathetic components of the autonomic nervous system. The specific effects of the autonomic nervous system on controlling:

Neurones and the Action Potential

Synapses and Drugs

The Eye

The Brain

The principal functions of the cerebral hemispheres:


Muscles are effectors that enable movement to be carried out


Waste products of metabolism are frequently toxic and must be removed from the body. Deamination of excess amino acids and the production of urea. (Details of the ornithine cycle not required.)

The Kidney

The processes involved in the formation of urine in the kidney, including ultrafiltration in the renal capsule and selective reabsorption in the proximal convoluted tubule. The role of the loop of Henle in maintaining a gradient of ions across the medulla.

Human Endocrine System

Information is transferred by hormones released by endocrine glands and affecting the physiological activities of target cells.


Physiological control systems operate in mammals to maintain a constant internal environment – this is homeostasis. The principle of negative feedback and its role in restoring systems to their original levels.


Meiosis and Fertilisation

The principal events associated with meiosis, to include: pairing by homologous chromosomes; formation of bivalents; chiasma formation and exchange between chromatids; separation of chromatids; production of haploid cells. (Details and names of individual stages of meiosis are not required.)

Candidates should be able to explain the behaviour of alleles and homologous chromosomes during meiosis and fertilisation, i.e.

Classical Genetics

The genotype is the genetic constitution of an organism. The expression of this genetic constitution and its interaction with the environment is the phenotype.

A gene can exist in different forms called alleles which are positioned in the same relative position (locus) on homologous chromosomes. The alleles at a specific locus may be either homozygous or heterozygous. Alleles may be dominant, recessive or codominant.

Candidates should be able to apply the above principles to interpret and use fully annotated genetic diagrams to predict the results of:

Population Genetics

Individuals within a species may show a wide range of variation. Similarities and differences between individuals within a species may be the result of genetic factors, differences in environmental factors, or a combination of both. Variation between individuals may be either continuous or discontinuous.

Candidates should be able to interpret data to determine the relative effects of genetic and environmental factors involved in continuous and discontinuous variation. Candidates should be able to explain how crossing over, independent assortment of chromosomes, random fusion of gametes and mutation contribute to genetic variation.

Natural Selection and Evolution

Predation, disease and competition result in differential survival and reproduction. Those organisms with a selective advantage are more likely to survive, reproduce and pass on their genes to the next generation.

Use specific examples to explain how natural selection produces changes within a species. Interpret data and use unfamiliar information to explain how natural selection produces change within a population. Evolutionary change over a long period of time has resulted in a great diversity of forms among living organisms.

The concept of the species in terms of production of fertile offspring. Natural selection and isolation may result in changes in the allele and phenotype frequency and lead to the formation of a new species.


A classification system comprises a hierarchy in which groups are contained within larger composite groups with no overlap. The phylogenetic groupings are based on patterns of evolutionary history. The principles and importance of taxonomy.

One hierarchy comprises Kingdom, Phylum, Class, Order, Family, Genus, Species. The distinguishing features of the five kingdoms – prokaryotes, protoctists, fungi, plants and animals.



Metabolism refers to all the chemical reactions taking place in a cell. There are thousands of these in a typical cell, and to make them easier to understand, biochemists arrange them into metabolic pathways. The intermediates in these metabolic pathways are called metabolites.

Photosynthesis and respiration are the reverse of each other, and you couldn’t have one without the other. The net result of all the photosynthesis and respiration by living organisms is the conversion of light energy to heat energy.


Cellular Respiration

The equation for cellular respiration is usually simplified to:

glucose + oxygen Õ carbon dioxide + water (+ energy)

But in fact respiration is a complex metabolic pathway, comprising at least 30 separate steps. To understand respiration in detail we can break it up into 3 stages:

Before we look at these stages in detail, there are a few points from this summary.


Much of respiration takes place in the mitochondria. Mitochondria have a double membrane: the outer membrane contains many protein channels called porins, which let almost any small molecule through; while the inner membrane is more normal and is impermeable to most materials. The inner membrane is highly folded into folds called christae, giving a larger surface area. The electron microscope reveals blobs on the inner membrane, which were originally called stalked particles. These have now been identified as the enzyme complex that synthesises ATP, are is more correctly called ATP synthase (more later). the space inside the inner membrane is called the matrix, and is where the Krebs cycle takes place. The matrix also contains DNA, tRNA and ribosomes, and some genes are replicated and expressed here.

Details of Respiration

1. Glucose enters cells from the tissue fluid by passive transport using a specific glucose carrier. This carrier can be controlled (gated) by hormones such as insulin, so that uptake of glucose can be regulated.

2. The first step is the phosphorylation of glucose to form glucose phosphate, using phosphate from ATP. Glucose phosphate no longer fits the membrane carrier, so it can’t leave the cell. This ensures that pure glucose is kept at a very low concentration inside the cell, so it will always diffuse down its concentration gradient from the tissue fluid into the cell. Glucose phosphate is also the starting material for the synthesis of pentose sugars (and therefore nucleotides) and for glycogen.

3. Glucose is phosphorylated again (using another ATP) and split into two triose phosphate (3 carbon) sugars. From now on everything happens twice per original glucose molecule.

4. The triose sugar is changed over several steps to form pyruvate, a 3-carbon compound. In these steps some energy is released to form ATP (the only ATP formed in glycolysis), and a hydrogen atom is also released. This hydrogen atom is very important as it stores energy, which is later used by the respiratory chain to make more ATP. The hydrogen atom is taken up and carried to the respiratory chain by the coenzyme NAD, which becomes reduced in the process.

(oxidised form Õ) NAD + H Õ NADH (← reduced form)

Pyruvate marks the end of glycolysis, the first stage of respiration. In the presence of oxygen pyruvate enters the mitochondrial matrix to proceed with aerobic respiration, but in the absence of oxygen it is converted into lactate (in animals and bacteria) or ethanol (in plants and fungi). These are both examples of anaerobic respiration. Pyruvate can also be turned back into glucose by reversing glycolysis, and this is called gluconeogenesis.

5. Once pyruvate has entered the inside of the mitochondria (the matrix), it is converted to a compound called acetyl coA. Since this step is between glycolysis and the Krebs Cycle, it is referred to as the link reaction. In this reaction pyruvate loses a CO2 and a hydrogen to form a 2-carbon acetyl compound, which is temporarily attached to another coenzyme called coenzyme A (or just coA), so the product is called acetyl coA. The CO2 diffuses through the mitochondrial and cell membranes by lipid diffusion, out into the tissue fluid and into the blood, where it is carried to the lungs for removal. The hydrogen is taken up by NAD again.

6. The acetyl CoA then enters the Krebs Cycle, named after Sir Hans Krebs, who discovered it in the 1940s at Leeds University. It is one of several cyclic metabolic pathways, and is also known as the citric acid cycle or the tricarboxylic acid cycle. The 2-carbon acetyl is transferred from acetyl coA to the 4-carbon oxaloacetate to form the 6-carbon citrate. Citrate is then gradually broken down in several steps to re-form oxaloacetate, producing carbon dioxide and hydrogen in the process. As before, the CO2 diffuses out the cell and the hydrogen is taken up by NAD, or by an alternative hydrogen carrier called FAD. These hydrogens are carried to the inner mitochondrial membrane for the final part of respiration.

The Respiratory Chain

The respiratory chain (or electron transport chain) is an unusual metabolic pathway in that it takes place within the inner mitochondrial membrane, using integral membrane proteins. These proteins form four huge trans-membrane complexes called complexes I, II, II and IV. The complexes each contain up to 40 individual polypeptide chains, which perform many different functions including enzymes and trans-membrane pumps. In the respiratory chain the hydrogen atoms from NADH gradually release all their energy to form ATP, and are finally combined with oxygen to form water.

1. NADH molecules bind to Complex I and release their hydrogen atoms as protons (H+) and electrons (e-). The NAD molecules then returns to the Krebs Cycle to collect more hydrogen. FADH binds to complex II rather than complex I to release its hydrogen.

2. The electrons are passed down the chain of proteins complexes from I to IV, each complex binding electrons more tightly than the previous one. In complexes I, II and IV the electrons give up some of their energy, which is then used to pump protons across the inner mitochondrial membrane by active transport through the complexes. Altogether 10 protons are pumped across the membrane for every hydrogen from NADH (or 6 protons for FADH).

3. In complex IV the electrons are combined with protons and molecular oxygen to form water, the final end-product of respiration. The oxygen diffused in from the tissue fluid, crossing the cell and mitochondrial membranes by lipid diffusion. Oxygen is only involved at the very last stage of respiration as the final electron acceptor, but without the whole respiratory chain stops.

4. The energy of the electrons is now stored in the form of a proton gradient across the inner mitochondrial membrane. It’s a bit like using energy to pump water uphill into a high reservoir, where it is stored as potential energy. And just as the potential energy in the water can be used to generate electricity in a hydroelectric power station, so the energy in the proton gradient can be used to generate ATP in the ATP synthase enzyme. The ATP synthase enzyme has a proton channel through it, and as the protons "fall down" this channel their energy is used to make ATP, spinning the globular head as they go. It takes 4 protons to synthesise 1 ATP molecule.

This method of storing energy by creating a protons gradient across a membrane is called chemiosmosis, and was discovered by Peter Mitchell in the 1960s, for which work he got a Nobel prize in 1978. Some poisons act by making proton channels in mitochondrial membranes, so giving an alternative route for protons and stopping the synthesis of ATP. This also happens naturally in the brown fat tissue of new-born babies and hibernating mammals: respiration takes place, but no ATP is made, with the energy being turned into heat instead.


How Much ATP is Made in Respiration?

We can now summarise respiration and see how much ATP is made from each glucose molecule. ATP is made in two different ways:

The table below is an "ATP account" for aerobic respiration, and shows that 32 molecules of ATP are made for each molecule of glucose used in aerobic respiration. This is the maximum possible yield; often less ATP is made, depending on the circumstances. Note that anaerobic respiration (glycolysis) only produces 2 molecules of ATP.


molecules produced per glucose

Final ATP yield

(old method)

Final ATP yield

(new method)


2 ATP used



4 ATP produced (2 per triose phosphate)



2 NADH produced (1 per triose phosphate)



Link Reaction

2 NADH produced (1 per pyruvate)



Krebs Cycle

2 ATP produced (1 per acetyl coA)



6 NADH produced (3 per acetyl coA)



2 FADH produced (1 per acetyl coA)






Other substances can also be used to make ATP. Triglycerides are broken down to fatty acids and glycerol, both of which enter the Krebs Cycle. A typical triglyceride might make 50 acetyl CoA molecules, yielding 500 ATP molecules. Fats are a very good energy store, yielding 2.5 times as much ATP per g dry mass as carbohydrates. Proteins are not normally used to make ATP, but in times of starvation they can be broken down and used in respiration. They are first broken down to amino acids, which are converted into pyruvate and Krebs Cycle metabolites and then used to make ATP.


Photosynthesis is essentially the reverse of respiration. It is usually simplified to:

carbon dioxide + water (+ light energy) Õ glucose + oxygen

But again this simplification hides numerous separate steps. To understand photosynthesis in detail we can break it up into 2 stages:

We shall see that there are many similarities between photosynthesis and respiration, and even the same enzymes are used in some steps.


Photosynthesis takes place entirely within chloroplasts. Like mitochondria, chloroplasts have a double membrane, but in addition chloroplasts have a third membrane called the thylakoid membrane. This is folded into thin vesicles (the thylakoids), enclosing small spaces called the thylakoid lumen. The thylakoid vesicles are often layered in stacks called grana. The thylakoid membrane contains the same ATP synthase particles found in mitochondria. Chloroplasts also contain DNA, tRNA and ribososomes, and they often store the products of photosynthesis as starch grains and lipid droplets.



Chloroplasts contain two different kinds of chlorophyll, called chlorophyll a and b, together with a number of other light-absorbing accessory pigments, such as the carotenoids and luteins (or xanthophylls). These different pigments absorb light at different wavelengths, so having several different pigments allows more of the visible spectrum to be used. The absorption spectra of pure samples of some of these pigments are shown in the graph on the left. A low absorption means that those wavelengths are not absorbed and used, but instead are reflected or transmitted. Different species of plant have different combinations of photosynthetic pigments, giving rise to different coloured leaves. In addition, plants adapted to shady conditions tend to have a higher concentration of chlorophyll and so have dark green leaves, while those adapted to bright conditions need less chlorophyll and have pale green leaves.

By measuring the rate of photosynthesis using different wavelengths of light, an action spectrum is obtained. The action spectrum can be well explained by the absorption spectra above, showing that these pigments are responsible for photosynthesis.



Chlorophyll is a fairly small molecule (not a protein) with a structure similar to haem, but with a magnesium atom instead of iron. Chlorophyll and the other pigments are arranged in complexes with proteins, called photosystems. Each photosystem contains some 200 chlorophyll molecules and 50 molecules of accessory pigments, together with several protein molecules (including enzymes) and lipids. These photosystems are located in the thylakoid membranes and they hold the light-absorbing pigments in the best position to maximise the absorbance of photons of light. The chloroplasts of green plants have two kinds of photosystem called photosystem I (PSI) and photosystem II (PSII). These absorb light at different wavelengths and have slightly different jobs in the light dependent reactions of photosynthesis.

The Light-Dependent Reactions

The light-dependent reactions take place on the thylakoid membranes using four membrane-bound protein complexes called photosystem I (PSI), photosystem II (PSII), cytochrome complex (C) and ferredoxin complex (FD). In these reactions light energy is used to split water, oxygen is given off, and ATP and hydrogen are produced.

1. Chlorophyll molecules in PSII absorb photons of light, exciting chlorophyll electrons to a higher energy level and causing a charge separation within PSII. This charge separation drives the splitting (or photolysis) of water molecules to make oxygen (O2), protons (H+) and electrons (e-):

2H2O O2 + 4H+ + 4e-

Water is a very stable molecule and it requires the energy from 4 photons of light to split 1 water molecule. The oxygen produced diffuses out of the chloroplast and eventually into the air; the protons build up in the thylakoid lumen causing a proton gradient; and the electrons from water replace the excited electrons that have been ejected from chlorophyll.

2. The excited, high-energy electrons are passed along a chain of protein complexes in the membrane, similar to the respiratory chain. They are passed from PSII to C, where the energy is used to pump 4 protons from stroma to lumen; then to PSI, where more light energy is absorbed by the chlorophyll molecules and the electrons are given more energy; and finally to FD.

3. In the ferredoxin complex each electron is recombined with a proton to form a hydrogen atom, which is taken up by the hydrogen carrier NADP. Note that while respiration uses NAD to carry hydrogen, photosynthesis always uses its close relative, NADP.

4. The combination of the water splitting and the proton pumping by the cytochrome complex cause protons to build up inside the thylakoid lumen. This generates a proton gradient across the thylakoid membrane. This gradient is used to make ATP using the ATP synthase enzyme in exactly the same way as respiration. This synthesis of ATP is called photophosphorylation because it uses light energy to phosphorylate ADP.

The Light-Independent Reactions

The light-independent, or carbon-fixing reactions, of photosynthesis take place in the stroma of the chloroplasts and comprise another cyclic pathway, called the Calvin Cycle, after the American scientist who discovered it.

1. Carbon dioxide binds to the 5-carbon sugar ribulose bisphosphate (RuBP) to form 2 molecules of the 3-carbon compound glycerate phosphate. This carbon-fixing reaction is catalysed by the enzyme ribulose bisphosphate carboxylase, always known as rubisco. It is a very slow and inefficient enzyme, so large amounts of it are needed (recall that increasing enzyme concentration increases reaction rate), and it comprises about 50% of the mass of chloroplasts, making the most abundant protein in nature. Rubisco is synthesised in chloroplasts, using chloroplast (not nuclear) DNA.

2. Glycerate phosphate is an acid, not a carbohydrate, so it is reduced and activated to form triose phosphate, the same 3-carbon sugar as that found in glycolysis. The ATP and NADPH from the light-dependent reactions provide the energy for this step. The ADP and NADP return to the thylakoid membrane for recycling.

3. Triose phosphate is a branching point. Most of the triose phosphate continues through a complex series of reactions to regenerate the RuBP and complete the cycle. 5 triose phosphate molecules (15 carbons) combine to form 3 RuBP molecules (15 carbons).

4. Every 3 turns of the Calvin Cycle 3 CO2 molecules are fixed to make 1 new triose phosphate molecule. This leaves the cycle, and two of these triose phosphate molecules combine to form one glucose molecule using the glycolysis enzymes in reverse. The glucose can then be used to make other material that the plant needs.


The Human Nervous System

Humans, like all living organisms, can respond to their environment. Humans have two complimentary control systems to do this: the nervous system and the endocrine (hormonal) system. We’ll look at the endocrine system later, but first we’ll look at the nervous system. The human nervous system controls everything from breathing and producing digestive enzymes, to memory and intelligence.

Nerve Cells

The nervous system composed of nerve cells, or neurones:

A neurone has a cell body with extensions leading off it. Numerous dendrons and dendrites provide a large surface area for connecting with other neurones, and carry nerve impulses towards the cell body. A single long axon carries the nerve impulse away from the cell body. The axon is only 10µm in diameter but can be up to 4m in length in a large animal (a piece of spaghetti the same shape would be 400m long)! Most neurones have many companion cells called Schwann cells, which wrap their cell membrane around the axon many times in a spiral to form a thick insulating lipid layer called the myelin sheath. Nerve impulse can be passed from the axon of one neurone to the dendron of another at a synapse. A nerve is a discrete bundle of several thousand neurone axons.

Humans have three types of neurone:

The Reflex Arc

The three types of neurones are arranged in circuits and networks, the simplest of which is the reflex arc.

In a simple reflex arc, such as the knee jerk, a stimulus is detected by a receptor cell, which synapses with a sensory neurone. The sensory neurone carries the impulse from site of the stimulus to the central nervous system (the brain or spinal cord), where it synapses with an interneurone. The interneurone synapses with a motor neurone, which carries the nerve impulse out to an effector, such as a muscle, which responds by contracting.

Reflex arc can also be represented by a simple flow diagram:



The Organisation Of The Human Nervous System

The human nervous system is far more complex than a simple reflex arc, although the same stages still apply. The organisation of the human nervous system is shown in this diagram:

It is easy to forget that much of the human nervous system is concerned with routine, involuntary jobs, such as homeostasis, digestion, posture, breathing, etc. This is the job of the autonomic nervous system, and its motor functions are split into two divisions, with anatomically distinct neurones. Most body organs are innervated by two separate sets of motor neurones; one from the sympathetic system and one from the parasympathetic system. These neurones have opposite (or antagonistic) effects. In general the sympathetic system stimulates the "fight or flight" responses to threatening situations, while the parasympathetic system relaxes the body. The details are listed in this table:



Sympathetic System

Parasympathetic System



Tear glands

Salivary glands






Dilates pupil

No effect

Inhibits saliva production

Dilates bronchi

Speeds up heart rate

Inhibits peristalsis

Stimulates glucose production

Inhibits urination

Constricts pupil

Stimulates tear secretion

Stimulates saliva production

Constricts bronchi

Slows down heart rate

Stimulates peristalsis

Stimulates bile production

Stimulates urination


The Nerve Impulse

Neurones and muscle cells are electrically excitable cells, which means that they can transmit electrical nerve impulses. These impulses are due to events in the cell membrane, so to understand the nerve impulse we need to revise some properties of cell membranes.

The Membrane Potential

All animal cell membranes contain a protein pump called the Na+K+ATPase. This uses the energy from ATP splitting to simultaneously pump 3 sodium ions out of the cell and 2 potassium ions in. If this was to continue unchecked there would be no sodium or potassium ions left to pump, but there are also sodium and potassium ion channels in the membrane. These channels are normally closed, but even when closed, they "leak", allowing sodium ions to leak in and potassium ions to leak out, down their respective concentration gradients.

The combination of the Na+K+ATPase pump and the leak channels cause a stable imbalance of Na+ and K+ ions across the membrane. This imbalance causes a potential difference across all animal cell membranes, called the membrane potential. The membrane potential is always negative inside the cell, and varies in size from –20 to –200 mV in different cells and species. The Na+K+ATPase is thought to have evolved as an osmoregulator to keep the internal water potential high and so stop water entering animal cells and bursting them. Plant cells don’t need this as they have strong cells walls to prevent bursting.

The Action Potential

In nerve and muscle cells the membranes are electrically excitable, which means that they can change their membrane potential, and this is the basis of the nerve impulse. The sodium and potassium channels in these cells are voltage-gated, which means that they can open and close depending on the voltage across the membrane.

The nature of the nerve impulse was discovered by Hodgkin, Huxley and Katz in Plymouth in the 1940s, for which work they received a Nobel prize in 1963. They used squid giant neurones, whose axons are almost 1mm in diameter, big enough to insert wire electrodes so that they could measure the potential difference across the cell membrane. In a typical experiment they would apply an electrical pulse at one end of an axon and measure the voltage changes at the other end, using an oscilloscope:

The normal membrane potential of these nerve cells is –70mV (inside the axon), and since this potential can change in nerve cells it is called the resting potential. When a stimulating pulse was applied a brief reversal of the membrane potential, lasting about a millisecond, was recorded. This brief reversal is called the action potential:

The action potential has 2 phases called depolarisation and repolarisation.

1. Depolarisation. The stimulating electrodes cause the membrane potential to change a little. The voltage-gated ion channels can detect this change, and when the potential reaches –30mV the sodium channels open for 0.5ms. The causes sodium ions to rush in, making the inside of the cell more positive. This phase is referred to as a depolarisation since the normal voltage polarity (negative inside) is reversed (becomes positive inside).

2. Repolarisation. When the membrane potential reaches 0V, the potassium channels open for 0.5ms, causing potassium ions to rush out, making the inside more negative again. Since this restores the original polarity, it is called repolarisation.

The Na+K+ATPase pump runs continuously, restoring the resting concentrations of sodium and potassium ions.

How do Nerve Impulses Start?

In the squid expe