DNA is the genetic material in bacteria as well as in most other organisms. Mutations are changes in DNA and result in different characteristics. Mutations in bacteria may result in resistance to antibiotics. Resistance to antibiotics may be passed to subsequent generations by vertical gene transmission. Resistance may also be passed from one species to another when DNA is transferred during conjugation. This is horizontal gene transmission. Antibiotic resistance in terms of the difficulty of treating tuberculosis and MRSA.Candidates should be able to • apply the concepts of adaptation and selection to other examples • evaluate methodology, evidence and data relating to antibiotic resistance • discuss ethical issues associated with the use of antibiotics • discuss the ways in which society uses scientific knowledge relating to antibiotic resistance to inform decision-making.

Bacteria carry DNA both as circular chromosome and as plasmids (little rings of DNA).

Mutations are random changes that occur to the DNA sequence. A change in DNA results in different protein being produced, this changes the characteristics of an organism.

Variation is caused by two things: mutations; recombination of existing DNA.

Conjugation
Bacteria do not sexually reproduce, so until recently it was unknown how bacteria were so diverse without recombination of existing DNA, however, now we know that there is recombination of existing DNA but not from two parents to an offspring, it happens from one existing bacteria to another: plasmids are transferred between them in a process known as conjugation:

• One bacteria starts to grow a tube called a pilus or conjugation tube
• It also starts to replicate a plasmid
• The tube reaches another bacteria and the DNA starts to move through it as a line
• It enters the new bacteria and forms a ring (the new plasmid)
• The tube is broken down

This process takes a matter of seconds and allows the transfer of genetic material from one existing bacteria to another- this is known as horizontal gene transmission (because it occurs across a generation). In this way a mutation could be passed between the same type of bacteria, to a different strain, or even to a different species. Like this resistance to an antibiotic could be gained by a species.

Bacteria also pass DNA on by asexual reproduction, this is known as vertical gene transmission as DNA is passed down from one generation to another.

Conjugation discovery

In 1946 Lederberg and Tatum designed an experiment to prove that DNA was transferred horizontally between bacteria:

• Take two strains of E. coli, one that can synthesise everything but methionine and biotin and one that could synthesise everything but threonine and leucine
• This meant that when they were placed in a medium without the nutrients neither strain could grow
• They mixed the two together and left them for several hours
• They put the mixture back onto a medium with no nutrients
• Some bacteria were able to survive
• This meant that there must have been DNA exchanged so that the strains had the ability to synthesise the nutrients they needed to survive

Antibiotic resistance

Most of the time mutations are not beneficial to an organism, they stop it from being able to function properly, however, occasionally a mutation happens that can increase the success of an organism.

In bacteria mutations can occur that make them resistant to antibiotics, this means that if they are in an infected person who is taking antibiotics then all the other, non mutated bacteria will die off, the one with the mutation will survive and replicate passing on the resistant gene and making the resistant bacteria more common.

This will only occur because of the presence of antibiotics giving the resistant strains an advantage, therefore the more antibiotics are used, the more resistance happens.

An example of this is the mutation of an enzyme in a bacteria that changed an enzyme to make one which could break down penicillin (an antibiotic) before it could harm the bacteria. This meant that it was not destroyed by the antibiotic and lived on to reproduce successfully. The gene was then passed on to future generations of the bacteria to make a resistant population, but it was also transferred horizontally so that other species were also resistant.

Discovering resistance

A bacteria is placed in a Petri dish with an antibiotic. If the bacteria is not resistant then it will not be able to grow near the antibiotic, and it will be visible everywhere apart from near the antibiotic. It the bacteria is resistant it will grow even in the area of the antibiotic and therefore will be visible over the whole dish.

Tuberculosis

To treat the bacterial infection of tuberculosis (TB) you have to take a 6-9 month course of antibiotics. Often people start to feel better a little way into the course because a lot of bacteria has been killed off so they stop taking the antibiotic. However, even though a lot of bacteria had been killed off, some would not yet have died- this is the more resistant stuff that is harder to kill. As a consequence the resistant bacteria are left in the body, free to multiply and spread. This is known as selection pressure.

As a result, TB is resistant to most known antibiotics- the definition of a super bug.

MRSA

Methicillin-resistant staphylococcus aureus (MRSA) is also a super bug. It is found in hospitals where: people tend to be ill anyway, making them more susceptible to infection; people are in close proximity; there is a lot of contact (doctors patients); there are a lot of antibiotics being taken (which make resistant strains more successful.

Antibiotics may be used to treat bacterial disease. One way in which antibiotics function is by preventing the formation of bacterial cell walls, resulting in osmotic lysis.

Bacteria in the body may cause disease, this can be treated by the use of antibiotics.

These work in a variety of ways to kill off bacteria. One way in which this can be one to cause osmotic lysis:

• Antibiotics can prevent the formation of the proteins for peptide cross linkages in cell walls
• This means that the cell wall which regulates water movement cannot be formed
• As a result, water moves by osmosis into the cell
• Eventually the cell will become too full and burst, this is called osmotic lysis

Diversity may relate to the number of species present in a community. The influence of deforestation and the impact of agriculture on species diversity

Community- all the different species living in an area.

Diversity is the variation in species living in an area: it is important to look at the amount of different species but it is also important to look at the size of each of the species.

This is because there could be many species, but some could be very unsuccessful or endangered and others could be successful and dominant.

An example of where this is important is in an agricultural setting where a certain crop is cultivated. For example in a wheat field, there will be some insects and mammals so potentially lots of species, but they will all have a relatively small number of members compared to the wheat which will have a huge number of individuals. Here, even though there are many species the biodiversity is low.

Deforestation causes disruption to the relationships in a community by removing on species (trees) and decreasing the biodiversity. Important things such as food and habitat are lost which can cause a decrease in the population of other species.

The structure of arteries, arterioles and veins in relation to their function. The structure of capillaries and their importance in metabolic exchange. The formation of tissue fluid and its return to the circulatory system.

All the blood vessels have a lining or endothelial layer which prevents friction.

Arteries

• Carry blood away from the heart
• Blood inside is high pressure to push blood all the way round the body
• Thick muscle layer so the amount of blood going through can be controlled
• Thick elastic lining to maintain pressure
• Having thick walls also helps prevent it from bursting
• Small lumen keeps the pressure high

Arterioles

• Are in between arteries and veins to decrease the pressure before the blood reaches the capillaries so they don't burst
• Thick muscle layer so that it can control the blood flow into the capillaries
• Thinner elastic layer as pressure is not so high

Veins

• Carry blood back to the heart
• Doesn't need a thick elastic layer because the blood pressure is low (no danger of bursting)
• Thin elastic and muscle layers make it easy to compress so that blood can be pushed through
• Valves make sure blood doesn't flow in the wrong direction

Capillaries

• Thin lining layer and no muscle or elastic layer so there is a small diffusion distance
• It is also small so that it can get in between tissues so cells are close, decreasing the diffusion distance again
• Spaces in lining to let white blood cells through
• There are lots of them and they are small to increase the surface area

Large surface area and small diffusion distance are key to aiding fast diffusion, this is key because it is through the capillaries that crucial metabolic substances like oxygen are delivered to the cells of the body

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Tissue fluid
At the arteriole end of capillaries there is a lot of blood pressure (hydrostatic pressure), this forces substances out by pressure filtration. Water and some other substances are pushed out of the capillaries into what is know as the tissue fluid (however large molecules like proteins cannot fit through the gaps); this surrounds cells and delivers substances to them like glucose, amino acids and oxygen.

Because a lot of water moved out of the capillary but the proteins remained, at the venous ends of the capillary, the water potential is very low: this causes water in the tissue fluid move back into the blood by osmosis. Some of the liquid enters the lymphatic system, but most then renters the blood at the neck.

Similarities and differences between organisms may be defined in terms of variation in DNA. Differences in DNA lead to genetic diversity. The influence of the following on genetic diversity • selection for high-yielding breeds of domesticated animals and strains of plants • the founder effect • genetic bottlenecks. Candidates should be able to discuss ethical issues involved in the selection of domesticated animals.

Genetic diversity is the level of variation between organisms, the more differences in DNA (nucleotides, genes of genomes) the larger genetic diversity. It can also be defined as the number of different allels present in a population.

Genetic variation is seen as a good thing because it reduces the inheritance of genetic diseases from recessive alleles. It also means that if a disaster occurred (e.g. a change of atmosphere or the introduction of a new predator) some of the species may be able to survive because of their differences.

Selective breeding
This is where humans choose animals or plants with desired characteristics and breed and nurture them. The selected ones will be more successful at reproducing as they are encouraged by the humans and therefore be a successful species.

A prime example is the breeding of dogs, which was occurring even in the Roman times when wolves with the ability to read human behaviour were selected to breed and keep as pets.

Another species that this can be seen in is the pig, where wild boar were captured and farmed. Characteristics such as being fat (more food) and having small legs (can't run away) meant the animals would be selected to have offspring to pass on the traits. Years of selective breeding have left us with the domestic pig, too fat and disproportionate to walk properly- it raises ethical issues about weather it is fair to manipulate the DNA of animals for domestic qualities as it does not benefit a species and can reduce their chances of survival in the wild.

The founder effect
When some of a population moves to start a new colony, only some of the alleles will be taken. This means that in the new community there a smaller variety of different DNA so genetic diversity is decreased. This can cause problems, for example in the Amish community, people suffer from many genetic disorders because they are more likely to have two parents with the same genotype who are both carriers.

Bottle necks
A similar thing can happen when the size of a population suddenly drops- some alleles may be completely lost (either by chance or because their characteristic was vulnerable), decreasing the genetic diversity. When cheetahs died in the ice age, the population sank to around just fifty, of the survivors a very high proportion had fertility issues, this meant the characteristic was passed on to a high proportion of the offspring and that even as the population began to expand again the percentage with fertility issues remained high.

Comparisons of amino acid sequences in specific proteins can be used to elucidate relationships between organisms. Immunological comparisons may be used to compare variations in specific proteins. Candidates should be able to interpret data relating to similarities and differences in base sequences in DNA and in amino acid sequences in proteins to suggest relationships between different organisms.

Genes code for amino acids to make proteins. So if we look at a protein in two different species and examine its amino acids, we can see how similar or different their genes are.

For example, (arbitrary data used) if we took heamaglobin from a gorilla and a human and looked at the amino acids and they looked like this:
Human: Ser; Val; Ser; Glu; Ile; Gln; Leu; Met; His; Asn
Gorilla: Ser; Val; Val; Ser; Ile; Gln Leu; Met; His; Asn
then we could see they are relatively genetically similar with  7/10 amino acids are the same.

One way to compare proteins is by comparing antigens on the body cells of a specie. This is immunological comparison:

• Extract blood serum from a species
• Put it in a second species
• This species will produce antibodies that are complimentary to the antigens of the first species
• Extract the antibodies
• Mix them with the blood serum of a third species
• A precipitate will form if the antibodies respond to the antigens of that specie

If the antibodies that were created for the antigens of the first specie can respond to antigens of the third then that means it must be complimentary to both. That means that both antigens had a similar tertiary structure, which means they had a similar primary structure, which means they had a similar sequence of amino acids which means that had a similar base sequence which means they are genetically similar. Therefore antibody can respond to both= more precipitate= more genetically similar.

If there is not very much precipitate its because the antibody can respond to the antigens in the third species because it is not sufficiently similar to the first, this shows us that they are genetically dissimilar.

Comparison of DNA base sequences is used to elucidate relationships between organisms. These comparisons have led to new classification systems in plants. Similarities in DNA may be determined by DNA hybridisation.

If two species have recently shared a common ancestor, then they are closely related. If this is the case, then they will have much of the same DNA because when one species gives rise to another they initially have similar DNA.

Over time mutations will render the DNA very different through the accumulation of mutations. This means that species that have not shared a common ancestor recently will have very different DNA.

So by looking at DNA scientists can determine what other species a species is related to and therefore what type it should be classified as.

A recent example of where this has been useful is in the classification of plants. Before genetic comparison plants had been categorised due to physical characteristics, however when the DNA was examined, scientists found that some plants that looked very different had more similar genes than ones that looked similar. The whole plant kingdom had to be re-classified.

DNA hybridisation is one method of comparing the base sequence of DNA:

• Heat the DNA of two species, this will break the hydrogen bonds holding together the two sides of the chromosome
• Leave them to cool and reform hydrogen bonds between complimentary base pairs
• Some of the DNA will have formed with one strand from each species
• This 'hybrid' DNA is then heated in stages to see at what temperature it separates into single strands

A higher temperature means more energy was required because there are more hydrogen bonds, this means that there were many complimentary base pairs made, and that means that the DNA from both species was similar.

If the DNA was not similar there would not be very many complimentary base pairs, so the hybrid DNA would have few hydrogen bonds and not take very much energy to break them all. This means that hybrids strands that separate at a low temperature come from two species that are not genetically similar.

Genetic comparisons can be made between different species by direct examination of their DNA or of the proteins encoded by this DNA.

Genetic comparisons are made to find out the classification of a living thing, i.e. what its ancestors are.

Comparing DNA will show what characteristics two species have in common, and what mutations have been made to make them different.

This can also be done by looking at proteins because DNA codes for amino acids which make up proteins. Therefore looking at one protein from two species and seeing the similarities and differences in amino acids equates to seeing similarities and differences in their genetics.

The basic structure and functions of starch, glycogen and cellulose and the relationship of structure to function of these substances in animals and plants.

Starch is the form of carbohydrate which plants store energy as: in small grains especially in the seeds and storage organs.
It is a polysaccharide made up of α-glucose to make a long straight chain which then winds up tight (unbranched helical chain).
Being wound up so tight means you can fit a lot of it in a small space and therefore a convenient way to store energy.
It is also a positive that it is made up of α-glucose, because this means when it is hydrolysed (broken down) that will be the molecule produced and it is easy to transport and use in respiration reactions.
Starch is also insoluble, this is good for two reasons: one, it does not tend to diffuse out of cells; two, it doesn't tend to draw water into cells by osmosis.

Glycogen is the form of carbohydrate which animals store energy as: in small granules especially in the muscles and liver.
It is a polysaccharide made up of α-glucose to make a short and very branched chain which winds up tight (branched helical chain).
Like starch it is insoluble, fits a lot of energy into a small space and makes α-glucose when hydrolysed, but because it is shorter is is hydrolysed more quickly.

Cellulose is found in plant cell walls.
It is a polysaccharide made up of β-glucose. If you have two β-glucose molecules and perform a condensation reaction, one of the molecules will have to turn up side down; this is because the order of the OH and the H is reversed on one side, so to match up it has to be turned round. This fact means that in a chain of β-glucose the 'CH2OH' group will alternate between being at the top and the bottom of the chain. The importance of this is that it can't coil up.
So, the chain is straight and unbranched which means several chains can lie next to each other; hydrogen bonds will form between these chains creating a strong 'microfibril' (what fibres are made of).

Beta glucose forming a glycosidic bond

Chain of cellulose

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The structure of b-glucose as... b-glucose and the linking of b-glucose by glycosidic bonds formed by condensation to form cellulose.

β-glucose has the same chemical formula as α-glucose, and the other hexose sugars (C6H12O6), but a different structure:

In a condensation reaction, the following will be formed:

Water is formed from the OH of the one glucose and the H of the others OH, the left over O forms a glycosidic (between sugars) bond.

Many β-glucose joined together in this way a polysaccharide called cellulose will be formed. 

There are fundamental differences between plant cells and animal cells. The structure of a palisade cell from a leaf as seen with an optical microscope. The appearance, ultrastructure and function of • cell wall • chloroplasts. Candidates should be able to apply their knowledge of these and other eukaryotic features in explaining adaptations of other plant cells.

Plant cells and animal cells share some of the same organelles, but there are some that differ. Cell walls and chloroplasts are examples of things that plant cells have which animal cells don't. Bother can have vacuoles but plants almost always have large central ones and animals rarely have them, and when they do they are small and scattered. Another difference is that plants store glucose as starch and animals store it as glycogen.

A palisade cell is traps sunlight with chlorophyll, it is found in the leaf.

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Cell wall
This is needed in a plant cell to offer structural support, stop cells bursting and provide the symplastic pathway for water movement. They are made up of polysaccharides, like cellulose, and have a middle lamella which holds adjacent cells together.

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Chloroplasts
These are needed in plant cells as they need the suns energy to carry out photosynthesis.
They are made up of three parts:

• The chloroplast envelope- double plasma membrane to control the movement of substances in and out of the cell.
• The grana- stacks of disks (thylakoids) which contain chlorophyll and have a large surface area for the first stage of photosynthesis. Tubular extensions can link them.
• The stoma- matrix with the enzymes needed for the second stage of photosynthesis
• DNA and ribosomes to manufacture proteins for photosynthesis

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Root hair cells adaptations

• Carrier proteins for active transport
• Lots of mitochondria to produce ATP for active transport
• Long thin shape to increase surface area for diffusion
• Large vacuole containing a high proportion of ions to decrease the water potential and encourage osmosis into the cell

Xylem vessel adaptations

• Thick walls to cope with the negative pressure of transpiration
• Thickening happens in a spiral so the plant is still flexible
• They are hollow and elongated so that water can move up them
• They are dead so that water does not need to diffuse through anything and can go quickly through
• Have a substance called lignin in their walls to offer strength and make it water proof (so water doesn't move out by osmosis)

The general pattern of blood circulation in a mammal. Names are required only of the coronary arteries and of blood vessels entering and leaving the heart, liver and kidneys.

Mammals have a double circulatory system, this means that there are two different sides of the heart pumping to two different places (the lungs and the rest of the body.)

We need a system like this because mammals are so large and so things need to be transported long distances and we are have a fairly high metabolic rate so we need a lot of oxygen transported.

Heart
The vein that brings blood into the heart from the body is called the vena cava.
The artery that takes blood out of the heart and to the lungs is the pulmonary artery.
The vein that brings blood into the heart from the lungs is the pulmonary vein.
The artery that takes blood out of the heart is called the aorta.

Liver
The hepatic artery brings blood in.
The hepatic vein takes blood out.
The vein that brings blood to the liver from the stomach is the hepatic portal vein.

Kidneys
The renal artery brings blood in.
The renal vein takes blood out.

The haemoglobins are a group of chemically similar molecules found in many different organisms. Haemoglobin is a protein with a quaternary structure. The role of haemoglobin in the transport of oxygen. The loading, transport and unloading of oxygen in relation to the oxygen dissociation curve. The effects of carbon dioxide concentration.Candidates should be aware that different organisms possess different types of haemoglobin with different oxygen transporting properties. They should be able to relate these to the environment and way of life of the organism concerned.

Haemoglobins are molecules consisting of four polypeptide chains and four haem groups. Different ones are found in different organisms.

There is a primary level of four polypeptide chains, two alpha and two beta, which turn into helices at the secondary level and fold up at the tertiary level much like any other protein. The difference is an additional quaternary structure in which the four chains are bonded to each other and four haem groups (iron).

Because the haem groups can form temporary bonds with oxygen, this means that the haemoglobin is able to carry four molecules of oxygen.

The dissociation curve shows the concentrations of oxygen at which the haem groups bind to oxygen.
On this graph we see the four points at which oxygen binds to the haemoglobin molecule.

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The curve can be moved left or right depending on the type of haemoglobin and conditions.

Moving right means it has a lower affinity to oxygen and means it will give up oxygen more easily. High concentrations of CO2 will move the curve to the right. This means that near the muscles where there is a high concentration of CO2 (because it is a waste product of respiration that happens there) the molecule will easily give oxygen to the muscles that need it.

Moving to the left will mean the molecule has a greater affinity for oxygen and give it up less easily. In the lungs there are low amounts of CO2 because it is being removed by the lungs, this means the curve is moved to the left and haemoglobin easily picks up the oxygen it needs to.

This is called the Bohr effect. The movement happens because the shape of the molecule effects how it binds to oxygen, PH effects the shape and so CO2 which has a low PH will cause these changes.

Different organisms need different affinities of their haemoglobin because of the environment they live in and their metabolic rates.

By moving the curve to the left, an organism in an environment with a low partial pressure of oxygen can still fully load its haemoglobin.

An organism with a high metabolic rate needs oxygen frequently to respire and provide ATP (energy) to cells, this is achieved by moving the curve to the right so that oxygen dissociates easily even at higher partial pressures.

The use of monoclonal antibodies in enabling the targeting of specific substances and cells. • evaluate methodology, evidence and data relating to the use of vaccines and monoclonal antibodies • discuss ethical issues associated with the use of vaccines and monoclonal antibodies.

So... what are monoclonal antibodies?
Monoclonal just means a group of the same thing, so when we talk about monoclonal antibodies we mean a whole load of antibodies that are exactly the same. This is significant because inside the body, you find many different types of antibodies: this is because B cells which produce antibodies are induced to clone by antigens on the surface of a pathogen, there are many different antigens on a single cell, so many different B cells are produced and hence many different antibodies (polyclonal).

How are they made?
There now several ways to produce monoclonal antibodies, the one below is Milstein and Kohlers method (1975):

1. Introduce a pathogen (with complimentary antigens to the antibody you want) to a mammal.
2. The antigen will induce the cloning of the B cell that produces the right antigen. However, it will also produce others, giving B cells that will produce polyclonal antibodies.
3. The B cells are taken out of the body and fused with tumour cells. The result is a hydribomas which is a cells that produces antibodies but can live for a longer time and divide outside the body.
4. Different hybridoma are separated off and left to divide until it forms a group (a clone).
5. Each clone is screened for the antibody that is needed- if it is being produced then it is grown on an industrial scale.
6. Antibodies are extracted from the clone.

What are they used for?

Monoclonal antibodies are useful in the treatment of illness and the application of science because they allow the targeting of specific cells due to the fact that they will only bind with one antigen.

• Separation techniques.
• Immunoassay: when you take a pregnancy, drugs or HIV test, there are complimentary monoclonal antibodies in the test which will form an antigen-antibody complex with the protein that is being looked for which triggers a colour change.
• Cancer therapies: trigger the immune system to attack cancer cells; carry radiation to the cancer cells; block signals that tell the cancer cells to divide.
• Preventing rejection of transplanted organs: by targeting the T cells involved with destroying the foreign tissue.
• Diabetes treatment.

What are the associated ethical issues?

• You have to give cancer and illness to mammals (mice).
• You have to make transgenic mammals (giving the properties of humans to make the antibodies suitable to use in the treatment of people).
• Testing on humans caused organ failure.
• Some people with MS have died as a cause.