AQA(B) A2 Module 4

Energy, Control And Continuity

Contents

Human Nervous system

Hormones

Excretion

Excretion

The Kidney

Homeostasis

Homeostasis

Temperature Homeostasis

Blood Sugar Homeostasis

Blood water Homeostasis

Classical Genetics

Gregor Mendel

Monohybrid cross

Sex Determination and Sex-Linkage

Codominance

Multiple Alleles

Dihybrid Cross

Polygenes

Epistasis

Meiosis

Population Genetics

Variation

Natural Selection

Speciation

Classification

 

The Hormone System

Humans have two complementary control systems that they can use to respond to their environment: the nervous system and the endocrine (hormonal) system. We’ll now look briefly at the hormone system.

Hormones are secreted by glands into the blood stream. There are two kinds of glands:

This table shows some of the main endocrine glands and their hormones. The hormones marked with a * are ones that we shall look at in detail later.

Once a hormone has diffused into the blood stream it is carried all round the body to all organs. However, it only affects certain target organs, which can respond to it. These target organs have specific receptor molecules in their cells to which the hormone binds. These receptors are protein molecules, and they form specific hormone-receptor complexes, very much like enzyme-substrate complexes. Cells without the specific receptor will just ignore a hormone. The hormone-receptor complex can affect almost any aspect of a cell’s function, including metabolism, transport, protein synthesis, cell division or cell death.

There are three different ways in which a hormone can affect cell function:

Some hormones affect the permeability of the cell membrane. They bind to a receptor on the membrane, which then activates a transporter, so substances can enter or leave the cell. (E.g. insulin stimulates glucose uptake.)

 

 

Some hormones release a "second messenger" inside the cell. They bind to a receptor on the membrane, which then activates an enzyme in the membrane, which catalyses the production of a chemical in the cytoplasm, which affects various aspects of the cell. (E.g. adrenaline stimulates glycogen breakdown.)

The steroid hormones are lipid-soluble so can easily pass through membranes by lipid diffusion. They diffuse to the nucleus, where the bind to a receptor, which activates protein synthesis.

(E.g. testosterone stimulates spermatogenesis.)

So in most cases, the hormone does not enter the cell. The effect of a hormone is determined not by the hormone itself, but by the receptor in the target cell. So the same hormone can have different effects in different target cells.

Comparison of Nervous and Hormone Systems

Nervous System

Hormone System

Transmitted by specific neurone cells

Effect localised by neurone anatomy

Fast-acting (ms–s)

Short-lived response

Transmitted by the circulatory system

Effect localised by target cell receptors

Slow-acting (mins–days)

Long-lived response

The two systems work closely together: endocrine glands are usually controlled by the nervous system, and a response to a stimulus often involves both systems.

Excretion and Homeostasis

Excretion means the removal of waste products from cells. There are five important excretory organs in humans:

  • Skin

excretes sweat, containing water, ions and urea

  • Lungs

excrete carbon dioxide and water

  • Liver

excretes bile, containing bile pigments, cholesterol and mineral ions

  • Gut

excretes mucosa cells, water and bile in faeces. (The bulk of faeces comprises plant fibre and bacterial cells, which have never been absorbed into the body, so are not excreted but egested.)

  • Kidneys

excrete urine, containing urea, mineral ions, water and other "foreign" chemicals from the blood.

This section is mainly concerned with the excretion of nitrogenous waste as urea. The body cannot store protein in the way it can store carbohydrate and fat, so it cannot keep excess amino acids. The "carbon skeleton" of the amino acids can be used in respiration, but the nitrogenous amino group must be excreted.

Amino Acid Metabolism

Amino acid metabolism takes place in the liver, this module focuses on two main stages:

1. Deamination

In this reaction an amino group is removed from an amino acid to form ammonia and an organic acid. The most common example is glutamate deamination:

This reaction is catalysed by the enzyme glutamate dehydrogenase. The NADH produced is used in the respiratory chain; the a-ketoglutarate enters the Krebs cycle; and the ammonia is converted to urea in the urea cycle.

2. Urea Synthesis

In this reaction ammonia is converted to urea, ready for excretion by the kidney.

Ammonia is highly toxic. Urea is less toxic than ammonia, so it is safer to have in the bloodstream. The disadvantage is that it "costs" 3 ATP molecules to make one urea molecule. This process of converting ammonia into urea shown above is not a single reaction, but is a summary of another cyclic pathway, called the ornithine cycle.

The Kidney

The kidneys remove urea and other toxic wastes from the blood, forming a dilute solution called urine in the process. The two kidneys have a very extensive blood supply and the whole blood supply passes through the kidneys every 5 minutes, ensuring that waste materials do not build up. The renal artery carries blood to the kidney, while the renal vein carries blood, now with far lower concentrations of urea and mineral ions, away from the kidney. The urine formed passes down the ureter to the bladder.

The important part of the kidney is a folded tube called a nephron. There are a million nephrons in each kidney. There are five steps in producing urine in a nephron:

1. Renal capsule – Ultrafiltration

The renal artery splits into numerous arterioles, each feeding a nephron. The arteriole splits into numerous capillaries, which form a knot called a glomerulus. The glomerulus is enclosed by the renal capsule (or Bowman’s capsule)- the first part of the nephron. The blood pressure in the capillaries of the glomerulus forces plasma out of the blood by ultrafiltration. Both the capillary walls and the capsule walls are formed from a single layer of flattened cells with gaps between them, so that all molecules with a molecular mass of <70k are squeezed out of the blood to form a filtrate in the renal capsule. Only blood cells and large plasma proteins remain in the blood.

2. Proximal Convoluted Tubule – Reabsorption.

The proximal convoluted tubule is the longest (14mm) and widest (60µm) part of the nephron. It is lined with epithelial cells containing microvilli and numerous mitochondria. In this part of the nephron over 80% of the filtrate is reabsorbed into the tissue fluid and then to the blood. This ensures that all the "useful" materials that were filtered out of the blood (such as glucose and amino acids) are now returned to the blood.

3. Loop of Henle – Formation of a Salt Bath.

The job of the loop of Henle is to make the tissue fluid in the medulla hypertonic compared to the filtrate in the nephron. The purpose of this "salt bath" is to reabsorb water as explained in step 5. The loop of Henle does this by pumping sodium and chloride ions out of the filtrate into the tissue fluid. The first part of the loop (the descending limb) is impermeable to ions, but some water leaves by osmosis. This makes the filtrate more concentrated as it descends. The second part of the loop (the ascending limb) contains an Na+ and a pump, so these ions are actively transported out of the filtrate into the surrounding tissue fluid. Water would follow by osmosis, but it can’t, because the ascending limb is impermeable to water. So the tissue fluid becomes more salty (hypertonic) and the filtrate becomes less salty (hypotonic). Since the filtrate is most concentrated at the base of the loop, the tissue fluid is also more concentrated at the base of the medulla, where it is three times more concentrated than seawater.

4. Distal Convoluted tubule – Homeostasis and Secretion

The distal convoluted tubule is relatively short and has a brush border (i.e. microvilli) with numerous membrane pumps for active transport. Final Na+ reabsorption occurs and the process of water reabsorption explained next in step 5 also takes place to a degree in the distal convoluted tubule

5. Collecting Duct – Concentration

As the collecting duct passes through the hypertonic salt bath in the medulla, water leaves the filtrate by osmosis, so concentrating the urine and conserving water. The water leaves through special water channels in the cell membrane called aquaporins. These aquaporin channels can be controlled by the hormone ADH, so allowing the amount of water in the urine to be controlled. More ADH opens the channels, so more water is conserved in the body, and more concentrated urine is produced. This is described in more detail in water homeostasis later.

The Bladder

The collecting ducts all join together in the pelvis of the kidney to form the ureter, which leads to the bladder. The filtrate, now called urine, is produced continually by each kidney and drips into the bladder for storage. The bladder is an expandable bag, and when it is full, stretch receptors in the elastic walls send impulses to the medulla, which causes the sphincter muscles to relax, causing urination. This is an involuntary reflex response that we can learn to control to a certain extent when we are young.

Homeostasis

Homeostasis literally means "same state" and it refers to the process of keeping the internal body environment in a steady state. The importance of this cannot be over-stressed, and a great deal of the hormone system and autonomic nervous system is dedicated to homeostasis. In module 3 we saw how the breathing and heart rates were maintained. Here we shall look at three more examples of homeostasis in detail: temperature, blood glucose and blood water.

All homeostatic mechanisms use negative feedback to maintain a constant value (called the set point). Negative feedback means that whenever a change occurs in a system, the change automatically causes a corrective mechanism to start, which reverses the original change and brings the system back to normal. It also means that the bigger then change the bigger the corrective mechanism. Negative feedback applies to electronic circuits and central heating systems as well as to biological systems.

So in a system controlled by negative feedback the level is never maintained perfectly, but constantly oscillates about the set point. An efficient homeostatic system minimises the size of the oscillations.

 

Temperature Homeostasis (thermoregulation)

One of the most important examples of homeostasis is the regulation of body temperature. Not all animals can do this. Animals that maintain a fairly constant body temperature are called homeotherms, while those that have a variable body temperature are called poikilotherms. The homeotherms maintain their body temperatures at around 37°C, so are sometimes called warm-blooded animals, but in fact piokilothermic animals can also have very warm blood during the day by basking in the sun.

In humans temperature homeostasis is controlled by the thermoregulatory centre in the hypothalamus. It receives input from two sets of thermoreceptors: receptors in the hypothalamus itself monitor the temperature of the blood as it passes through the brain (the core temperature), and receptors in the skin monitor the external temperature. Both pieces of information are needed so that the body can make appropriate adjustments. The thermoregulatory centre sends impulses to several different effectors to adjust body temperature:

The thermoregulatory centre is part of the autonomic nervous system, so the various responses are all involuntary. The exact responses to high and low temperatures are described in the table below. Note that some of the responses to low temperature actually generate heat (thermogenesis), while others just conserve heat. Similarly some of the responses to heat actively cool the body down, while others just reduce heat production or transfer heat to the surface. The body thus has a range of responses available, depending on the internal and external temperatures.

Effector

Response to low temperature

Response to high temperature

Smooth muscles in peripheral arterioles in the skin.

Muscles contract causing vasoconstriction. Less heat is carried from the core to the surface of the body, maintaining core temperature. Extremities can turn blue and feel cold and can even be damaged (frostbite).

Muscles relax causing vasodilation. More heat is carried from the core to the surface, where it is lost by radiation. Skin turns red.

Sweat glands

No sweat produced.

Glands secrete sweat onto surface of skin, where it evaporates. Water has a high latent heat of evaporation, so it takes heat from the body.

Erector pili muscles in skin (attached to skin hairs)

Muscles contract, raising skin hairs and trapping an insulating layer of still, warm air next to the skin. Not very effective in humans, just causing "goosebumps".

Muscles relax, lowering the skin hairs and allowing air to circulate over the skin, encouraging convection and evaporation.

Skeletal muscles

Muscles contract and relax repeatedly, generating heat by friction and from metabolic reactions.

No shivering.

Adrenal and thyroid glands

Glands secrete adrenaline and thyroxine respectively, which increase the metabolic rate in different tissues, especially the liver, so generating heat.

Glands stop releasing adrenaline and thyroxine.

Behaviour

Curling up, huddling, finding shelter, putting on more clothes.

Stretching out, finding shade, swimming, removing clothes.

The thermoregulatory centre normally maintains a set point of 37.5 ± 0.5 °C in most mammals. However the set point can be altered is special circumstances:

Blood Glucose Homeostasis

Glucose is the transport carbohydrate in animals, and its concentration in the blood affects every cell in the body. Its concentration is therefore strictly controlled within the range 80-100 mg 100cm-3, and very low level (hypoglycaemia) or very high levels (hyperglycaemia) are both serious and can lead to death.

Blood glucose concentration is controlled by the pancreas. The pancreas has glucose receptor cells, which monitor the concentration of glucose in the blood, and it also has endocrine cells (called the islets of Langerhans), which secrete the hormones glucagon, and insulin. These two hormones are antagonistic, and have opposite effects on blood glucose:

After a meal, glucose is absorbed from the gut into the hepatic portal vein, increasing the blood glucose concentration. This is detected by the pancreas, which secretes insulin in response. Insulin causes glucose to be taken up by the liver and converted to glycogen. This reduces blood glucose, which causes the pancreas to stop secreting insulin. If the glucose level falls too far, the pancreas detects this and releases glucagon. Glucagon causes the liver to break down some of its glycogen store to glucose, which diffuses into the blood. This increases blood glucose, which causes the pancreas to stop producing glucagon.

These negative feedback loops continue all day, as shown in this graph:

Diabetes Mellitus

Diabetes is a disease caused by a failure of glucose homeostasis. There are two forms of the disease. In insulin-dependent diabetes (also known as type 1 or early-onset diabetes) there is a severe insulin deficiency due to autoimmune killing of b cells. In non insulin-dependent diabetes (also known as type 2 or late-onset diabetes) insulin is produced, but the insulin receptors in the target cells don’t work, so insulin has no effect. In both cases there is a very high blood glucose concentration after a meal, so the active transport pumps in the proximal convoluted tubule of the kidney can’t reabsorb it all from the kidney filtrate, so much of the glucose is excreted in urine (diabetes mellitus means "sweet fountain"). This leads to the symptoms of diabetes:

Diabetes can be treated by injections with insulin or by careful diet.

 

 

Blood Water Homeostasis (Osmoregulation)

The water potential of the blood must be regulated to prevent loss or gain of water from cells. Blood water homeostasis is controlled by the hypothalamus. It contains osmosreceptor cells, which can detect changes in the water potential of the blood passing through the brain. In response, the hypothalamus controls the sensation of thirst, and it also secretes the hormone ADH (antidiuretic hormone). ADH is stored in the pituitary gland, and its target cells are the endothelial cells of the collecting ducts of the kidney nephrons. These cells are unusual in that water molecules can only cross their membranes via water channels called aquaporins, rather than through the lipid bilayer. ADH causes these water channels to open. The effects of ADH are shown in this diagram:

Classical Genetics

In module 2 we studied molecular genetics. Here we are concerned with classical genetics, which is the study of inheritance of characteristics at the whole organism level. It is also known as transmission genetics or Mendelian genetics, since it was pioneered by Gregor Mendel.

Gregor Mendel

Mendel (1822-1884) was an Austrian monk at Brno monastery. He was a keen gardener and scientist, and studied at Vienna university, where he learnt statistics. He investigated inheritance in pea plants and published his results in 1866. They were ignored at the time, but were rediscovered in 1900, and Mendel is now recognised as the "Father of Genetics". His experiments succeeded where other had failed because:

A typical experiment looked like this:

Mendel made several conclusions from these experiments:

  1. There are no mixed colours (e.g. pink), so this disproved the widely-held blending theories of inheritance that characteristics gradually mixed over time.
  2. A characteristic can disappear for a generation, but then reappear the following generation, looking exactly the same. So a characteristic can be present but hidden.
  3. The outward appearance (the phenotype) is not necessarily the same as the inherited factors (the genotype) For example the P1 red plants are not the same as the F1 red plants.
  4. One form of a characteristic can mask the other. The two forms are called dominant and recessive respectively.
  5. The F2 ratio is always close to 3:1. Mendel was able to explain this by supposing that each individual has two versions of each inherited factor, one received from each parent. We’ll look at his logic in a minute.

Mendel’s factors are now called genes and the two alternative forms are called alleles. So in the example above we would say that there is a gene for flower colour and its two alleles are "red" and "white". One allele comes from each parent, and the two alleles are found on the same position (or locus) on the homologous chromosomes. With two alleles there are three possible combinations of alleles (or genotypes) and two possible appearances (or phenotypes):

Genotype

Name

Phenotype

RR

homozygous dominant

red

rr

homozygous recessive

white

Rr, rR

heterozygous

red

 

The Monohybrid Cross

A simple breeding experiment involving just a single characteristic, like Mendel’s experiment, is called a monohybrid cross. We can now explain Mendel’s monohybrid cross in detail.

At fertilisation any male gamete can fertilise any female gamete at random. The possible results of a fertilisation can most easily be worked out using a Punnett Square as shown in the diagram. Each of the possible outcomes has an equal chance of happening, so this explains the 3:1 ratio observed by Mendel.

 

This is summarised in Mendel’s First Law, which states that individuals carry two discrete hereditary factors (alleles) controlling each characteristic. The two alleles segregate (or separate) during meiosis, so each gamete carries only one of the two alleles.

The Test Cross

You can see an individual’s phenotype, but you can’t see its genotype. If an individual shows the recessive trait (white flowers in the above example) then they must be homozygous recessive as it’s the only genotype that will give that phenotype. If they show the dominant trait then they could be homozygous dominant or heterozygous. You can find out which by performing a test cross with a pure-breeding homozygous recessive. This give two possible results:

How does Genotype control Phenotype?

Mendel never knew this, but we can explain in detail the relation between an individual’s genes and its appearance. A gene was originally defined as an inherited factor that controls a characteristic, but we now know that a gene is also a length of DNA that codes for a protein. It is the proteins that actually control phenotype in their many roles as enzymes, pumps, transporters, motors, hormones, or structural elements. For example the flower colour gene actually codes for an enzyme that converts a white pigment into a red pigment:

Sometimes the gene actually codes for a protein apparently unrelated to the phenotype. For example the gene for seed shape in peas (round or wrinkled) actually codes for an enzyme that synthesises starch! The functional enzyme makes lots of starch and the seeds are full and rounded, while the non-functional enzyme makes less starch so the seeds wrinkle up.

This table shows why the allele that codes for a functional protein is usually dominant over an allele that codes for a non-function protein. In a heterozygous cell, some functional protein will be made, and this is usually enough to have the desired effect. In particular, enzyme reactions are not usually limited by the amount of enzyme, so a smaller amount will have little effect.

Genotype

Gene product

Phenotype

homozygous dominant (RR)

all functional enzyme

red

homozygous recessive (rr)

no functional enzyme

white

heterozygous (Rr)

some functional enzyme

red

 

Sex Determination

In module 2 we saw that sex is determined by the sex chromosomes (X and Y). Since these are non-homologous they are called heterosomes, while the other 22 pairs are called autosomes. In humans the sex chromosomes are homologous in females (XX) and non-homologous in males (XY), though in other species it is the other way round. The inheritance of the X and Y chromosomes can be demonstrated using a monohybrid cross:

This shows that there will always be a 1:1 ratio of males to females. Note that female gametes (eggs) always contain a single X chromosome, while the male gametes (sperm) can contain a single X or a single Y chromosome. Sex is therefore determined solely by the sperm. There are techniques for separating X and Y sperm, and this is used for planned sex determination in farm animals using IVF.

Sex Linkage

The X and Y chromosomes don’t just determine sex, but also contain many other genes that have nothing to do with sex determination. The Y chromosome is very small and seems to contain very few genes, but the X chromosome is large and contains thousands of genes for important products such as rhodopsin, blood clotting proteins and muscle proteins. Females have two copies of each gene on the X chromosome (i.e. they’re diploid), but males only have one copy of each gene on the X chromosome (i.e. they’re haploid). This means that the inheritance of these genes is different for males and females, so they are called sex linked characteristics.

The first example of sex linked genes discovered was eye colour in Drosophila fruit flies. Red eyes (R) are dominant to white eyes (r) and when a red-eyed female is crossed with a white-eyed male, the offspring all have red eyes, as expected for a dominant characteristic (left cross below). However, when the opposite cross was done (a white-eye male with a red-eyed female) all the male offspring had white eyes (right cross below). This surprising result was not expected for a simple dominant characteristic, but it could be explained if the gene for eye colour was located on the X chromosome. Note that in these crosses the alleles are written in the form XR (red eyes) and Xr (white eyes) to show that they are on the X chromosome.

Males always inherit their X chromosome from their mothers, and always pass on their X chromosome to their daughters.

Another well-known example of a sex linked characteristic is colour blindness in humans. 8% of males are colour blind, but only 0.7% of females. As explained on p31, the genes for green-sensitive and red-sensitive rhodopsin are on the X chromosome, and mutations in either of these lead to colour blindness. The diagram below shows two crosses involving colour blindness, using the symbols XR for the dominant allele (normal rhodopsin, normal vision) and Xr for the recessive allele (non-functional rhodopsin, colour blind vision).

Other examples of sex linkage include haemophilia, premature balding and muscular dystrophy.

Codominance

In most situations (and all of Mendel’s experiments) one allele is completely dominant over the other, so there are just two phenotypes. But in some cases there are three phenotypes, because neither allele is dominant over the other, so the heterozygous genotype has its own phenotype. This situation is called codominance or incomplete dominance. Since there is no dominance we can no longer use capital and small letters to indicate the alleles, so a more formal system is used. The gene is represented by a letter, and the different alleles by superscripts to the gene letter.

A good example of codominance is flower colour in snapdragon (Antirrhinum) plants. The flower colour gene C has two alleles: CR (red) and CW (white). The three genotypes and their phenotypes are:

Genotype

Gene product

Phenotype

homozygous RR

all functional enzyme

red

homozygous WW

no functional enzyme

white

heterozygous (RW)

some functional enzyme

pink

In this case the enzyme is probably less active, so a smaller amount of enzyme will make significantly less product, and this leads to the third phenotype. The monohybrid cross looks like this:

Note that codominance is not an example of "blending inheritance" since the original phenotypes reappear in the second generation. The genotypes are not blended and they still obey Mendel’s law of segregation. It is only the phenotype that appears to blend in the heterozygotes.

Another example of codominance is sickle cell haemoglobin in humans. The gene for haemoglobin Hb has two codominant alleles: HbA (the normal gene) and HbS (the mutated gene). There are three phenotypes:

HbAHbA

Normal. All haemoglobin is normal, with normal red blood cells.

HbAHbS

Sickle cell trait. 50% of the haemoglobin in every red blood cell is normal, and 50% is abnormal. The red blood cells are slightly distorted, but can carry oxygen, so this condition is viable. However these red blood cells cannot support the malaria parasite, so this phenotype confers immunity to malaria.

HbSHbS

Sickle cell anaemia. All haemoglobin is abnormal, and molecules stick together to form chains, distorting the red blood cells into sickle shapes. These sickle red blood cells are destroyed by the spleen, so this phenotype is fatal.

Other examples of codominance include coat colour in cattle (red/white/roan), and coat colour in cats (black/orange/tortoiseshell).

 

Lethal Alleles

An unusual effect of codominance is found in Manx cats, which have no tails. If two Manx cats are crossed the litter has ratio of 2 Manx kittens to 1 normal (long-tailed) kitten. The explanation for this unexpected ratio is explained in this genetic diagram:

The gene S actually controls the development of the embryo cat’s spine. It has two codominant alleles: SN (normal spine) and SA (abnormal, short spine). The three phenotypes are:

SNSN

Normal. Normal spine, long tail

SNSA

Manx Cat. Last few vertebrae absent, so no tail.

SASA

Lethal. Spine doesn’t develop, so this genotype is fatal early in development. The embryo doesn’t develop and is absorbed by the mother, so there is no evidence for its existence.

Many human genes also have lethal alleles, because many genes are so essential for life that a mutation in these genes is fatal. If the lethal allele is expressed early in embryo development then the fertilised egg may not develop enough to start a pregnancy, or the embryo may miscarry. If the lethal allele is expressed later in life, then we call it a genetic disease, such as muscular dystrophy or cystic fibrosis.

 

Multiple Alleles

An individual has two copies of each gene, so can only have two alleles of any gene, but there can be more than two alleles of a gene in a population. An example of this is blood group in humans. The red blood cell antigen is coded for by the gene I (for isohaemaglutinogen), which has three alleles IA, IB and IO. (They are written this way to show that they are alleles of the same gene.) IA and IB are codominant, while IO is recessive. The possible genotypes and phenotypes are:

Phenotype (blood group)

Genotypes

antigens on red blood cells

plasma antibodies

A

IAIA, IAIO

A

anti-B

B

IBIB, IBIO

B

anti-A

AB

IAIB

A and B

none

O

IOIO

none

anti-A and anti-B

The cross below shows how all four blood groups can arise from a cross between a group A and a group B parent.

Other examples of multiple alleles are: eye colour in fruit flies, with over 100 alleles; human leukocyte antigen (HLA) genes, with 47 known alleles.

Multiple Genes

So far we have looked at the inheritance of a single gene controlling a single characteristic. This simplification allows us to understand the basic rules of heredity, but inheritance is normally much more complicated than that. We’ll now turn to the inheritance of characteristics involving two genes. This gets more complicated, partly because there are now two genes to consider, but also because the two genes can interact with each other. We’ll look at three situations:

The Dihybrid Cross

Mendel also studied the inheritance of two different characteristics at a time in pea plants, so we’ll look at one of his dihybrid crosses. The two traits are seed shape and seed colour. Round seeds (R) are dominant to wrinkled seeds (r), and yellow seeds (Y) are dominant to green seeds (y). With these two genes there are 4 possible phenotypes:

Genotypes

Phenotype

RRYY, RRYy, RrYY, RrYy

round yellow

RRyy, Rryy

round green

rrYY, rrYy

wrinkled yellow

rryy

wrinkled green

Mendel’s dihybrid cross looked like this:

All 4 possible phenotypes are produced, but always in the ratio 9:3:3:1. Mendel was able to explain this ratio if the factors (genes) that control the two characteristics are inherited independently; in other words one gene does not affect the other. This is summarised in Mendel’s second law (or the law of independent assortment), what states that alleles of different genes are inherited independently.

We can now explain the dihybrid cross in detail:

The gametes have one allele of each gene, and that allele can end up with either allele of the other gene. This gives 4 different gametes for the second generation, and 16 possible genotype outcomes.

Dihybrid Test Cross

There are 4 genotypes that all give the same round yellow phenotype. Just like we saw with the monohybrid cross, these four genotypes can be distinguished by crossing with a double recessive phenotype. This gives 4 different results:

Original genotype

result of test cross

RRYY

all round yellow

RRYy

1 round yellow : 1 round green

RrYY

1 round yellow : 1 wrinkled yellow

RrYy

1 round yellow : 1 round green: 1 wrinkled yellow: 1 wrinkled green

 

Polygenes

Sometimes two genes at different loci (i.e. separate genes) can combine to affect one single characteristic. An example of this is coat colour in Siamese cats. One gene controls the colour of the pigment, and black hair (B) is dominant to brown hair (b). The other gene controls the dilution of the pigment in the hairs, with dense pigment (D) being dominant to dilute pigment (d). This gives 4 possible phenotypes:

Genotypes

Phenotype

F2 ratio

BBDD, BBDd, BbDD, BbDd

"seal" (black dense)

9

BBdd, Bbdd

"blue" (black dilute)

3

bbDD, bbDd

"chocolate" (brown dense)

3

bbdd

"lilac" (brown dilute)

1

The alleles are inherited in exactly the same way as in the dihybrid cross above, so the same 9:3:3:1 ratio in the F2 generation is produced. The only difference is that here, we are looking at a single characteristic, but with a more complicated phenotype ratio than that found in a monohybrid cross.

A more complex example of a polygenic character is skin colour in humans. There are 5 main categories of skin colour (phenotypes) controlled by two genes at different loci. The amount of skin pigment (melanin) is proportional to the number of dominant alleles of either gene:

Phenotype

(skin colour)

Genotypes

No. of dominant alleles

F2 ratio

Black

AABB

4

1

Dark

AaBB, AABb

3

4

Medium

AAbb, AaBb, aaBB

2

6

Light

Aabb, aaBb

1

4

White (albino)

aabb

0

1

Some other examples of polygenic characteristics are: eye colour, hair colour, and height. The important point about a polygenic character is that it can have a number of different phenotypes, and almost any phenotypic ratio.

Epistasis

In epistasis, two genes control a single character, but one of the genes can mask the effect of the other gene. A gene that can mask the effect of another gene is called an epistatic gene (from the Greek meaning "to stand on"). This is a little bit like dominant and recessive alleles, but epistasis applies to two genes at different loci. Epistasis reduces the number of different phenotypes for the character, so instead of having 4 phenotypes for 2 genes, there will be 3 or 2. We’ll look at three examples of epistasis.

1. Dependent genes. In mice one gene controls the production of coat pigment, and black pigment (B) is dominant to no pigment (b). Another gene controls the dilution of the pigment in the hairs, with dense pigment (D) being dominant to dilute pigment (d). This is very much like the Siamese cat example above, but with one important difference: the pigment gene (B) is epistatic over the dilution gene (D) because the recessive allele of the pigment gene is a mutation that produces no pigment at all, so there is nothing for the dilution gene to affect. This gives 3 possible phenotypes:

Genotypes

Phenotype

F2 ratio

BBDD, BBDd, BbDD, BbDd

Black (black dense)

9

BBdd, Bbdd

Brown (black dilute)

3

bbDD, bbDd, bbdd

White (no pigment)

4

2. Enzymes in a pathway. In a certain variety of sweet pea there are two flower colours (white and purple), but the F2 ratio is 9:7. This is explained if the production of the purple pigment is controlled by two enzymes in a pathway, coded by genes at different loci.

Gene P is epistatic over gene Q because the recessive allele of gene P is a mutation that produces inactive enzyme, so there is no compound B for enzyme Q to react with. This gives just two possible phenotypes:

Genotypes

Phenotype

F2 ratio

PPQQ, PPQq, PpQQ, PpQq

Purple

9

PPqq, Ppqq, ppQQ, ppQq, ppqq

White

7

3. Duplicate Genes. This occurs when genes at two different loci make enzyme that can catalyse the same reaction (this can happen by gene duplication). In this case the coloured pigment is always made unless both genes are present as homozygous recessive (ppqq), so the F2 ratio is 15:1.

Genotypes

Phenotype

F2 ratio

PPQQ, PPQq, PpQQ, PpQq, PPqq, Ppqq, ppQQ, ppQq

Purple

15

ppqq

White

1

So epistasis leads to a variety of different phenotype ratios.

Meiosis

Meiosis is the special form of cell division used to produce gametes. It has two important functions:

Meiosis comprises two successive divisions, without DNA replication in between. The second division is a bit like mitosis, but the first division is different in many important respects. The details are shown in this diagram for a hypothetical cell with 2 pairs of homologous chromosomes (n=2):

First Division

Second Division

Interphase I

  • chromatin not visible
  • DNA & proteins replicated

Interphase II

  • Short
  • no DNA replication
  • chromosomes remain visible.

Prophase I

  • chromosomes visible
  • homologous chromosomes join together to form a bivalent

Prophase II

  • centrioles replicate and move to new poles.

Metaphase I

  • bivalents line up on equator

Metaphase II

  • chromosomes line up on equator.

Anaphase I

  • chromosomes separate (not chromatids- centromere doesn’t split)

Anaphase II

  • centromeres split
  • chromatids separate.

Telophase I

  • nuclei form
  • cell divides
  • cells have 2 chromosomes, not 4 chromatids.

Telophase II

  • 4 haploid cells, each with 2 chromatids
  • cells often stay together to form a tetrad.

 

Genetic Variation in Sexual Reproduction

As mentioned in module 2, the whole point of meiosis and sex is to introduce genetic variation, which allows species to adapt to their environment and so to evolve. There are three sources of genetic variation in sexual reproduction:

We’ll look at each of these in turn.

1. Independent Assortment

This happens at metaphase I in meiosis, when the bivalents line up on the equator. Each bivalent is made up of two homologous chromosomes, which originally came from two different parents (they’re often called maternal and paternal chromosomes). Since they can line up in any orientation on the equator, the maternal and paternal versions of the different chromosomes can be mixed up in the final gametes.

In this simple example with 2 homologous chromosomes (n=2) there are 4 possible different gametes (22). In humans with n=23 there are over 8 million possible different gametes (223). Although this is an impressively large number, there is a limit to the mixing in that genes on the same chromosome must always stay together. This limitation is solved by crossing over.

2. Crossing Over

This happens at prophase I in meiosis, when the bivalents first form. While the two homologous chromosomes are joined in a bivalent, bits of one chromosome are swapped (crossed over) with the corresponding bits of the other chromosome.

The points at which the chromosomes actually cross over are called chiasmata (singular chiasma), and they involve large, multi-enzyme complexes that cut and join the DNA. There is always at least one chiasma in a bivalent, but there are usually many, and it is the chiasmata that actually hold the bivalent together. The chiasmata can be seen under the microscope and they can give the bivalents some strange shapes at prophase I. There are always equal amounts crossed over, so the chromosomes stay the same length.

Crossing over means that maternal and paternal alleles can be mixed, even though they are on the same chromosome.

3. Random Fertilisation

This takes place when two gametes fuse to form a zygote. Each gamete has a unique combination of genes, and any of the numerous male gametes can fertilise any of the numerous female gametes. So every zygote is unique.

These three kinds of genetic recombination explain Mendel’s laws of genetics.

 

 

Variation

Variation means the differences in characteristics (phenotype) within a species. There are many causes of variation as this chart shows:

Variation in a population can be studied by measuring the characteristic (height, eye colour, seed shape, or whatever) in a large number of different individuals and then plotting a frequency histogram. This graph has the values of the characteristic on the X axis (grouped into bins if necessary) and the number of individuals showing that characteristic on the Y axis. These histograms show that there are two major types of variation: discontinuous and continuous.

Discontinuous Variation

Sometimes the characteristic has just a few discrete categories (like blood group). The frequency histogram has separate bars (or sometimes peaks).

This is discontinuous variation. The characteristics:

Discontinuous characteristics are rare in humans and other animals, but are more common in plants. Some examples are human blood group, detached ear lobes, flower colour, seed colour, etc. these characteristics are very useful for geneticists because they give clear-cut results.

Continuous Variation

Sometimes the character has a continuous range of values (like height). The frequency histogram is a smooth curve (usually the bell-shaped normal distribution curve).

This is continuous variation. The characteristics:

Continuous characteristics are very common in humans and other animals. Some examples are height, hair colour, heart rate, muscle efficiency, intelligence, growth rate, rate of photosynthesis, etc.

Sometimes you can see the effect of both variations. For example the histogram of height of humans can be bimodal (i.e. it’s got two peaks). This is because the two sexes (a discontinuous characteristic) each have their own normal distribution of height (a continuous characteristic).

 

 

 

Evolution and Natural Selection

History of ideas of Life on Earth

17th Century

Most people believed in Creationism, which considered that all life was created just as it is now. This was not based on any evidence, but was instead a belief.

18th Century

Naturalists began systematic classification systems (especially Linnaeus 1707-1778) and noticed that groups of living things had similar characteristics and appeared to be related. So their classifications looked a bit like a family tree.

 

European naturalists travelled more widely and discovered more fossils, which clearly showed that living things had changed over time, so were not always the same. Extinctions were also observed (e.g. dodo), so species were not fixed.

19th Century

Lamark (1809) proposed a theory that living things changed by inheriting acquired characteristics. e.g. giraffes stretched their necks to reach food, and their offspring inherited stretched necks. This is now known to be wrong, since many experiments (and experience) have shown that acquired characteristics are not inherited, but nevertheless Lamark's theory was the first to admit that species changed, and to try to explain it.

 

Charles Darwin (1859) published "On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life", which has been recognised as one of the most important books ever written. A very similar theory was also proposed by Alfred Wallace, and Darwin and Wallace agreed to publish at the same time.

 

Darwin's Theory of Evolution by Natural Selection

Darwin's theory was based on four observations:

Darwin's concluded that individuals that were better adapted to their environment compete better than the others, survive longer and reproduce more, so passing on more of their successful characteristics to the next generation. Darwin used the memorable phrases survival of the fittest, struggle for existence and natural selection.

Darwin explained the giraffe's long neck as follows. In a population of horse-like animals there would be random genetic variation in neck length. In an environment where there were trees and bushes, the longer-necked animals were better adapted and so competed well compared to their shorter-necked relatives. These animals lived longer, through more breeding seasons, and so had more offspring. So in the next generation there were more long-neck genes than short-neck genes in the population. If this continued over very many generations, then in time the average neck length would increase. [Today it is thought more likely that the selection was for long legs to run away from predators faster, and if you have long legs you need a long neck to be able to drink. But the process of selection is just the same.]

Darwin wasn't the first to suggest evolution of species, but he was the first to suggest a plausible mechanism for the evolution - natural selection, and to provide a wealth of evidence for it.

Darwin used the analogy of selective breeding (or artificial selection) to explain natural selection. In selective breeding, desirable characteristics are chosen by humans, and only those individuals with the best characteristics are used for breeding. In this way species can be changed over a long period of time. All domesticated species of animal and plant have been selectively bred like this, often for thousands of years, so that most of the animals and plants we are most familiar with are not really natural and are nothing like their wild relatives (if any exist). The analogy between artificial and natural selection is a very good one, but there is one important different - Humans have a goal in mind, nature does not.

Types of Natural Selection

There are three kinds of Natural Selection.

1. Directional Selection

This occurs whenever the environment changes in a particular way. There is therefore selective pressure for species to change in response to the environmental change.

"Environment" includes biotic as well as abiotic, so organisms evolve in response to each other. e.g. if predators run faster there is selective pressure for prey to run faster, or if one tree species grows taller, there is selective pressure for other to grow tall. Most environments do change (e.g. due to migration of new species, or natural catastrophes, or climate change, or to sea level change, or continental drift, etc.), so directional selection is common.

2. Stabilising (or Normalising) Selection.

This occurs when the environment doesn't change. Natural selection doesn't have to cause change, and if an environment doesn't change there is no pressure for a well-adapted species to change. Fossils suggest that many species remain unchanged for long periods of geological time. One of the most stable environments on Earth is the deep ocean.

3. Disruptive (or Diverging) Selection.

This occurs where an environment changes to become two close but distinct environments.

Speciation

A species is defined as a group of interbreeding populations that are reproductively isolated from other groups. Reproductively isolated can mean that sexual reproduction between different species is impossible for physical, ecological, behavioural, temporal or developmental reasons. For example horses and donkeys can apparently interbreed, but the offspring (mule) doesn't develop properly and is infertile. This definition does not apply to asexually reproducing species, and in some cases it is difficult distinguish between a strain and a species.

 

New species usually develop by reproductive isolation (e.g. Albert and Kaibab squirrels of the Grand Canyon).

  1. Start with an interbreeding population of one species.

  • The population becomes divided by a physical barrier such as water, mountains, desert, or just a large distance. This can happen when some of the population migrates or is dispersed, or when the geography changes catastrophically (e.g. earthquakes, volcanoes, floods) or gradually (erosion, continental drift).
  • If the two environments (abiotic or biotic) are different (and they almost certainly will be), then the two populations will experience different selection pressures and will evolve separately. Even if the environments are similar, the populations may change by random genetic drift, especially if the population is small.
  • Even if the barrier is removed and the two populations meet again, they are now so different that they can no longer interbreed. They are therefore reproductively isolated and are two distinct species. They may both be different from the original species, if it still exists elsewhere.
  • It is meaningless to say that one species is absolutely better than another species, only that it is better adapted to that particular environment. A species may be well-adapted to its environment, but if the environment changes, then the species must adapt or die. In either case the original species will become extinct. Since all environments change eventually, it is the fate of all species to become extinct (including our own).

     

    Classification

    There are some 10 million species of living organisms (mostly insects), and many more extinct ones, so they need to be classified in a systematic way. In 1753 the Swede Carolus Linnaeus introduced the binomial nomenclature for naming organisms. This consists of two parts: a generic name (with a capital letter) and a specific name (with a small letter), e.g. Panthera leo (lion) and Panthera tigris (tiger). This system replaced non-standard common names, and is still in use today.

    A group of similar organisms is called a taxon, and the science of classification is called taxonomy. In taxonomy groups are based on similar physical or molecular properties, and groups are contained within larger composite groups with no overlap. The smallest group of similar organisms is the species; closely related species are grouped into genera (singular genus), genera into families, families into orders, orders into classes, classes into phyla (singular phylum), and phyla into kingdoms. So you need to remember KPCOFGS.

    This shows how the seven taxons are used to classify humans. As we go through the taxon hierarchy from kingdom to species, the groups get smaller and the animals are more closely related.

     

    Kingdom

    Animalia

    Phylum

    Chordata

    Class

    Mammalia

    Order

    Primates

    Family

    Hominidae

    Genus

    Homo

    Species

    sapiens

    Sponge

    4

    Earthworm

    4

    Insect

    4

    Fish

    4

    4

    Dinosaur E

    4

    4

    Bird

    4

    4

    Mouse

    4

    4

    4

    Cat

    4

    4

    4

    Elephant

    4

    4

    4

    Lemur

    4

    4

    4

    4

    Monkey

    4

    4

    4

    4

    Orang-utan

    4

    4

    4

    4

    Gorilla

    4

    4

    4

    4

    4

    Chimpanzee

    4

    4

    4

    4

    4

    Australopithecus E

    4

    4

    4

    4

    4

    Homo Habilis E

    4

    4

    4

    4

    4

    4

    Neanderthal Man E

    4

    4

    4

    4

    4

    4

    4

    Modern Human

    4

    4

    4

    4

    4

    4

    4

    E = Extinct

    This shows the complete classification of some other species:

     

    Earthworm

    Mushroom

    Garlic

    Kingdom

    Phylum

    Class

    Order

    Family

    Genus

    Species

    Animalia

    Annelida

    Oligochaeta

    Terricolae

    Lumbricidae

    Lumbricus

    terrestris

    Fungi

    Mycota

    Basidiomycota

    Agaricales

    Agaricacae

    Agaricus

    campestris

    Plantae

    Angiospermophyta

    Monocotyledonea

    Liliales

    Liliaceae

    Allium

    sativum

    The aim of taxonomists today is to develop phylogenies, family trees representing true evolutionary relationships. Historically classification was based on easily observable structures, and gradually this was extended to microscopic and electron-microscopic detail. The recent advances in embryology and molecular biology have given new tools such as patterns of life cycle, larval development, and gene sequences. These have often led to radically different phylogenies (e.g. humans should really be the "third chimpanzee").

    The Five Kingdoms

    Until the middle of this century, life was divided into two kingdoms, plants and animals. With the greater understanding gained from new techniques this has been revised, and modern classifications recognise far more diversity and are less zoocentric. The classification system used today is that of Whittaker (1959, modified by Margulis), and contains five kingdoms: prokaryotae, protoctista, fungi, plantae and animalia. The greatest division now recognised is not between plants and animals (which are relatively similar), but between the prokaryotes (cells without nuclei) and eukaryotes (cells with nuclei). The three "higher" kingdoms are distinguished by their ecological strategies: absorption (fungi), consumption (animals) and production (plants).