Biology Note Cards

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  All living organisms are composed of cells. Multicellular organisms (example: humans) are composed of many cells while unicellular organisms (example: bacteria) are composed of only one cell. Cells are the basic unit of structure in all organisms.
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  Cells are the smallest unit of life. They are the smallest structures capable of surviving on their own.
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  Cells come from pre-exsisting cells and cannot be created from non-living material. For example, new cells arise from cell division and a zygote (the very first cell formed when an organism is produced) arises from the fusion of an egg cell and a sperm cell.

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  Take two containers and put food in both of these
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  Sterilize both of the containers so that all living organisms are killed
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  Leave one of the containers open and seal the other closed

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  Take a measurement of the drawing (width or length)
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  Take this same measurement of the specimen
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  Remember to convert units if needed to
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  Place your values into the equation
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  Magnification = length of drawing / length of actual specimen

Ribosomes: Found either floating free in the cytoplasm or attached to the surface of the rough endoplasmic reticulum and in mitochondria and chloroplast. Ribosomes are the site of protein synthesis as they translate messenger RNA to produce proteins.

Rough endoplasmic reticulum: Can modify proteins to alter their function and/or destination. Synthesizes proteins to be excreted from the cell.

Lysosome: Contains many digestive enzymes to hydrolyze macromolecules such as proteins and lipids into their monomers.

Golgi apparatus: Receives proteins from the rough endoplasmic reticulum and may further modify them. It also packages proteins before the protein is sent to it’s final destination which may be intracellular or extracellular.

Mitochondrion: Is responsible for aerobic respiration. Converts chemical energy into ATP using oxygen.

Nucleus: Contains the chromosomes and therefore the hereditary material. It is responsible for controlling the cell.

1. Prokaryotic cells have naked DNA which is found in the cytoplasm in a region named the nucleoid. On the other hand, eukaryotes have chromosomes that are made up of DNA and protein. These chromosomes are found in the nucleus enclosed in a nuclear envelope.

2. Prokaryotes do not have any mitochondria whereas eukaryotes do.

3. Prokaryotes have small ribosomes (70S) compared to eukaryotes which have large ribosomes (80S).

4. In prokaryotes there are either no or very few organelles bounded by a single membrane in comparison to eukaryotes which have many of them including the Golgi apparatus and the endoplasmic reticulum.

1. Animal cells only have a plasma membrane and no cell wall. Whereas plant cells have a plasma membrane and a cell wall.

2. Animal cells do not have chloroplasts whereas plant cells do for the process of photosynthesis.

3. Animal cells store glycogen as their carbohydrate resource whereas plants store starch.

4. Animal cells do not usually contain any vacuoles and if present they are small or temporary. On the other hand plants have a large vacuole that is always present.

5. Animal cells can change shape due to the lack of a cell wall and are usually rounded whereas plant cells have a fixed shape kept by the presence of the cell wall.

The plant cell wall gives the cell a lot of strength and prevents it from bursting under high pressure as it is made up of cellulose arranged in groups called microfibrils. It gives the cell its shape, prevents excessive water up take by osmosis and is the reason why the whole plant can hold itself up against gravity.

The animal cell contains glycoproteins in their extracellular matrix which are involved in the support, movement and adhesion of the cell.

Diffusion is the passive movement of particles from a region of high concentration to a region of low concentration.

Osmosis is the passive movement of water molecules, across a partially permeable membrane, from a region of lower solute concentration to a region of higher solute concentration.

During prophase the spindle microtubules grow and extend from each pole to the equator. Also chromosomes super coil and become short and bulky and the nuclear envelope breaks down.

During metaphase the chromatids move to the equator and the spindle microtubules from each pole attach to each centromere on opposite sides.

During anaphase the spindle microtubules pull the sister chromatids apart splitting the centromeres. This splits the sister chromatids into chromosomes. Each identical chromosome is pulled to opposite poles.

During telophase the spindle microtubules break down and the chromosomes uncoil and so are no longer individually visible. Also the nuclear membrane reforms. The cell then divides by cytokinesis to form two daughter cells with identical genetic nuclei.

Growth, embryonic development, tissue repair and asexual reproduction involve mitosis

Sulfur: Needed for the synthesis of two amino acids.

Calcium: Acts as a messenger by binding to calmodulin and a few other proteins which regulate transcription and other processes in the cell.

Phosphorus: Is part of DNA molecules and is also part of the phosphate groups in ATP.

Iron: Is needed for the synthesis of cytochromes which are proteins used during electron transport for aerobic cell respiration.

Sodium: When it enters the cytoplasm, it raises the solute concentration which causes water to enter by osmosis.

Thermal properties of water include heat capacity, boiling and freezing points and the cooling effect of evaporation.

Water has a large heat capacity which means that a considerable amount of energy is needed to increase it’s temperature. This is due to the strength of the hydrogen bonds which are not easily broken. This is why the temperature of water tends to remain relatively stable. It is beneficial for aquatic animals as they use water as a habitat.

Water has a high boiling and freezing point. It boils at 100 C because the strong hydrogen bonds. All these hydrogen bonds between the water molecules need to break for the liquid to change to gas. Water becomes less dense as it gets closer to the freezing point and so ice always forms on the surface first. The high boiling point of water is vital for life on earth as if water boiled at a lower temperature the water in living organisms would start to boil and therefore these organisms would not survive.
The fact that water becomes less dense as it freezes is beneficial to organisms as ice will always form at the surface of lakes or seas and by doing so it insulates the water underneath, maintaining a possible habitat for organisms to live in.

Water can evaporate at temperatures below the boiling point. Hydrogen bonds need to break for this to occur.

Cohesion is the effect of hydrogen bonds holding the water molecules together. Water moves up plants because of cohesion. Long columns of water can be sucked up from roots to leaves without the columns breaking. The hydrogen bonds keep the water molecules sticking to each other.

The solvent properties of water mean that many different substances can dissolve in it because of its polarity.

• Glucose, galactose and fructose are all monosaccharides.
• Maltose, lactose and sucrose are all disaccharides.
• Starch, glycogen and cellulose are all polysaccharides.

In animals, glucose is used as an energy source for the body and lactose is the sugar found in milk which provides energy to new borns until they are weaned. Finally, glycogen is used as an energy source (short term only) and is stored in muscles and the liver.

In plants, fructose is what makes fruits taste sweet which attracts animals and these then eat the fruits and disperse the seeds found in the fruits. Sucrose is used as an energy source for the plant whereas cellulose fibers is what makes the plant cell wall strong.

• Lipids can be used for energy storage in the form of fat in humans and oil in plants.
• Lipids can be used as heat insulation as fat under the skin reduces heat loss.
• Lipids allow buoyancy as they are less dense than water and so animals can float in water.

Enzyme activity increases with an increase in temperature and usually doubles with every 10 degrees rise. This is due to the molecules moving faster and colliding more often together. However at a certain point the temperature gets to high and the enzymes denature and stop functioning. This is due to the heat causing vibrations within the enzyme destroying its structure by breaking the bonds in the enzyme.

Enzymes usually have an optimum pH at which they work most efficiently. As the pH diverges from the optimum, enzyme activity decreases. Both acid and alkali environments can denature enzymes.

Enzyme activity increases with an increase in substrate concentration as there are more random collisions between the substrate and the active site. However, at some point, all the active sites are taken up and so increasing the substrate concentration will have no more effect on enzyme activity. As long as there are active sites available, an increase in substrate concentration will lead to an increase in enzyme activity.

As temperature increases, the rate of photosynthesis increases more and more steeply until the optimum temperature is reached. If temperature keeps increasing above the optimum temperature then photosynthesis starts to decrease very rapidly.

As light intensity increases so does photosynthesis until a certain point. At a high light intensities photosynthesis reaches a plateau and so does not increase any more. At low and medium light intensity the rate of photosynthesis is directly proportional to the light intensity.

As the carbon dioxide concentration increases so does the rate of photosynthesis. There is no photosynthesis at very low levels of carbon dioxide and at high levels the rate reaches a plateau.

Gene: a heritable factor that controls a specific characteristic.

Allele: one specific form of a gene, differing from other alleles by one or a few bases only and occupying the same gene locus as other alleles of the gene.

Genome: the whole of the genetic information of an organism.

Sickle cell anaemia is a genetic disease that affects red blood cells in the body. It is due to a mutation on the Hb gene which codes for a polypeptide of 146 amino acids which is part of haemoglobin (haemoglobin is an important protein component in red blood cells). In sickle cell anaemia the codon GAG found in the normal Hb gene is mutated to GTG. This is called a base substitution mutation as adenine (A) is replaced by thymine (T). This means that when the mutated gene is transcribed, a codon in the messenger RNA will be different. Instead of the normal codon GAG, the messenger RNA will contain the codon GUG. This in turn will result in a mistake during translation. In a healthy individual the codon GAG on the messenger RNA matches with the anticodon CUC on the transfer RNA carrying the amino acid glutamic acid. However, if the mutated gene is present then GUG on the messenger RNA matches with the anticodon CAC on the transfer RNA which carries the amino acid valine. So the base substitution mutation has caused glutamic acid to be replaced by valine on the sixth position on the polypeptide. This results in haemoglobin S being present in red blood cells instead of the normal haemoglobin A. This has an effect on the phenotype as instead of normal donut shaped red blood cells being produced some of the red blood cells will be sickle shaped. As a result these sickle shaped red blood cells cannot carry oxygen as efficiently as normal red blood cells would. However, there is an advantage to sickle cell anemia. The sickle cell red blood cells give resistance to malaria and so the allele Hb^s on the Hb gene which causes sickle cell anemia is quite common in parts of the world where malaria is found as it provides an advantage over the disease.

Summary of important steps:

Normal Gene

Mutated gene

Codon

GAG

GTG

Transcription

GAG on mRNA

GUG on mRNA

Translation

Anticodon CUC and amino acid glutamic acid on tRNA.

Anticodon CAC and amino acid valine on tRNA.

Haemoglobin

Hb^A

Hb^S

Phenotype

Normal donut shaped red blood cells.

Sickle cell shaped red blood cells.

Effects

Carry oxygen efficiently but are affected by malaria.

Do not carry oxygen efficiently but give resistance to malaria.

The first stage of meiosis I is prophase I. In prophase I the chromosomes pair up so that the chromosomes in each pair are homologous. Once the homologous chromosomes are paired up, crossing over occurs. Crossing over is the exchange of genetic material between non-sister chromatids. The nuclear membrane also starts to break down and the spindle microtubules stretch out from each pole to the equator.

The second stage is metaphase I. Here the paired up homologous chromosomes line up at the equator and the spindle fibbers attach to the chromosomes in a way that ensures that for each homologous pair, one chromosome moved to one pole and the other moves to the opposite pole.

The third stage is anaphase I. This is the stage where the homologous chromosomes are separated and pulled to opposite poles. This halves the chromosome number however each chromosome is still composed of two sister chromatids. The cell membrane starts to prepare for its separation at the equator to form two cells.

The fourth stage is telophase I. Here each chromosome from the homologous pair are found at opposite poles and the nuclear membrane reforms around each daughter nucleus. The membrane then divides through citokinesis.

There is a brief interphase stage before the start of meiosis II. This stage does not include the S phase.

Meiosis II
The first stage of meiosis II is prophase II. Here the cell has divided into two daughter haploid cells however the process does not end here as these two cells immediately start to divide again. The spindle microtubules stretch out from each pole again and the nuclear membrane breaks down as in prophase I.

The second stage is metaphase II. Here the chromosomes in each cell line up at the equator and the spindle microtubules attach to the centromere of each chromosome.

The third stage is anaphase II. Here the centromere devised as a result of the spindle microtubules pulling each sister chromatid to opposite poles in both cells. Each sister chromatid then becomes a chromosome.

The fourth stage is telophase II. Here the nuclear membrane reforms around the four sets of daughter chromosomes. Cytokinesis then follows to divide the cytoplasm of the two cells and so the result is four daughter cells each with a haploid set of chromosomes.

A number of problems can arise during meiosis. A common problem is non-disjunction. This is when the chromosomes do not separate properly during meiosis, either in meiosis I (in anaphase I) or meiosis II (in anaphase II). This leads the production of gametes that either have a chromosome too many or too few. Gametes with a missing chromosome usually die quite fast however gametes with an extra chromosome can survive. When a zygote is formed from the fertilization of these gametes with an extra chromosome, three chromosomes of one type are present instead of two. An example of this is Down syndrome. Down syndrome is a disease in which the chromosomes failed to separate properly during meiosis leading to three chromosomes of type 21 instead of two. A person with the condition therefore has a total of 47 chromosomes instead of 46. The non-disjunction can take place either in the formation of the egg or the sperm. Down syndrome leads to many complications and also the risk of having a child with the condition increases with age.

Karyotyping is performed using cells collected by chorionic villus sampling or amniocentesis, for pre-natal diagnosis of chromosome abnormalities.

Genotype: the alleles of an organism.

Phenotype: the characteristics of an organism.

Dominant allele: an allele that has the same effect on the phenotype whether it is present in the homozygous or heterozygous state.

Recessive allele: an allele that only has an effect on the phenotype when present in the homozygous state.

Codominant alleles: pairs of alleles that both affect the phenotype when present in a heterozygote.

Locus: the particular position on homologous chromosomes of a gene.

Homozygous: having two identical alleles of a gene.

Heterozygous: having two different alleles of a gene.

Carrier: an individual that has one copy of a recessive allele that causes a genetic disease in individuals that are homozygous for this allele.

Test cross: testing a suspected heterozygote by crossing it with a known homozygous recessive.

The ABO blood group is a good example of codominance and multiple alleles. There are three allele that control the ABO blood groups. If there are more than two allele of a gene then they are called multiple allele. The allele I^A corresponds to blood group A (genotype I^AI^A) and the allele I^B corresponds to blood group B (genotype I^BI^B). Both of these are dominant and so if I^A and I^B are present together they form blood group AB (genotype I^AI^B). Both allele affect the phenotype since they are both codominant. Codominant allele are pairs of allele that both affect the phenotype when present together in a heterozygote. The allele i is recessive to both I^A and I^B so if you have the genotype I^A i you will have blood group A and if you have the genotype I^B i you will have blood group B. However if you have the genotype ii then you are homozygous for i and will be of blood group O. Below is a table to summaries which genotypes give which phenotypes.

Phenotype Genotype

A I^AI^A or I^Ai

B I^BI^B or I^Bi

AB I^AI^B

O ii

Most of the time sex-linked genes are carried on the X chromosome. Since females have two X chromosomes they have two copies of the sex-linked gene whereas males only have one since they only have one X chromosome. Hemophilia and colour blindness are both examples of sex linkage.

Hemophilia
X^H is the allele for normal blood clotting and is dominate over X^h which is recessive and causes hemophilia. If a mother is heterozygous she is a carrier of the disease but does not have hemophilia as the dominate allele is present. She can however pass the disease on to her offspring. Below is a punnett showing how a carrier mother and an unaffected father can pass the disease on to their offspring.

From our four possible outcomes we can see that a female child cannot get hemophilia but can be a carrier. This is because the father will always pass on the dominate allele (X^H) on the X chromosome in females. Depending on whether the mother passes on the dominant or recessive allele will determine if the female child is a carrier or is unaffected by the hemophilia. If the child is a boy then the father has passed on the Y chromosome which does not contain the allele of the gene. So whether the child has the disease or is unaffected depends on which allele the mother had passed on. If she has passed on the recessive allele (X^h) then the male child will have hemophilia, however if she has passed on the dominate allele (X^H) then the child will be unaffected.

So there is a 50% chance of the child having hemophilia if it is male as half of the eggs produced by the mother will carry the recessive allele. The chance of a female offspring having hemophilia is 0% since the father always passes on the dominant allele on the X chromosome. Finally there is a 25% chance overall that the offspring will be affected.

• Squares represent males
• Circles represent females
• Shaded symbols represent affected individuals
• Unshaded symbols represent unaffected individuals.

• If most of the males in the pedigree are affected the disorder is X-linked.
• If it is a 50/50 ratio between men and women the disorder is autosomal.
• If the disorder is dominant, one of the parents must have the disorder.
• If the disorder is recessive than neither of the parents has to have the disorder as they can be heterozygous.

• It is now easier to study how genes influence human development.
• It helps identify genetic diseases.
• It allows the production of new drugs based on DNA base sequences of genes or the structure of proteins coded for by these genes.
• It will give us more information on the origins, evolution and migration of humans.

• The transfer of a gene for factor IX which is a blood clotting factor, from humans to sheep so that this factor is produced in the sheep’s milk.
• The transfer of a gene that gives resistance to the herbicide glyphosate from bacterium to crops so that the crop plants can be sprayed with the herbicide and not be affected by it.

It is quite common to see genetic modifications in crop plants. An example of this is the transfer of a gene that codes for a protein called Bt toxin from the bacterium Bacillus thuringiensis to maize crops. This is done because maize crops are often destroyed by insects that eat the corn and so by adding the Bt toxin gene this is prevented as the toxin kills the insects. However this is very controversial as even though it has many positive advantages, it can also have some harmful consequences. The table below summarizes the benefits and possible harmful effects of genetically modifying the maize crops.

Benefits

Harmful Effects

Since there is less damage to the maize crops, there is a higher crop yield which can lessen food shortages.

We are not sure of the consequences of humans and animals eating the modified crops. The bacterial DNA or the Bt toxin itself could be harmful to human as well as animal health.

Since there is a higher crop yield, less land is needed to grow more crops. Instead the land can become an area for wild life conservation.

Other insects which are not harmful to the crops could be killed. The maize pollen will contain the toxin and so if it is blown onto near by plants it can kill the insects feeding on these plants.

There is a reduction in the use of pesticides which are expensive and may be harmful to the environment, wild life and farm workers.

Cross pollination can occur which results in some wild plants being genetically modified as they will contain the Bt gene. These plants will have an advantage over others as they will be resistant to certain insects and so some plants may become endangered. This will have significant consequences on the population of wild plants.

Arguments for

Arguments against

Embryonic stem cells can be used for therapies that save lives and reduce pain for patients. Since a stem cell can divide and differentiate into any cell type, they can be used to replace tissues or organs required by patients.

Every human embryo is a potential human being and should be given the chance of developing.

Cells can be taken from embryos that have stopped developing and so these cells would have died anyway.

More embryos are generally produced than are needed and so many are killed.

Cells are taken at a stage when the embryos have no nerve cells and so they cannot feel pain.

There is a risk of embryonic stem cells developing into tumour cells.

Species: a group of organisms that can interbreed and produce fertile offspring.

Habitat: the environment in which a species normally lives or the location of a living organism.

Population: a group of organisms of the same species who live in the same area at the same time.

Community: a group of populations living and interacting with each other in an area.

Ecosystem: a community and its abiotic environment.

Ecology: the study of relationships between living organisms and between organisms and their environment.

Consumer: an organism that ingests other organic matter that is living or recently killed.

Detritivore: an organism that ingests non-living organic matter.

Saprotroph: an organism that lives on or in non-living organic matter, secreting digestive enzymes into it and absorbing the products of digestion.

The carbon cycle

There is strong evidence that shows that green house gases are causing global warming. This is very worrying as global warming has so many consequences on ecosystems. If nothing is done, and the green house gases are in fact causing the enhanced green house effect, by the time we realize it, it will probably be too late and result in catastrophic consequences. So even though there is no proof for global warming, the strong evidence suggesting that it is linked with an increase in green house gases is something we can not ignore. Global warming is a global problem. It affects everyone. For these reasons, the precautionary principle should be followed. Anyone supporting the notion that we can continue to emit same amounts or more of the green house gases should have to provide evidence that it will not cause a damaging increase in the green house effect.

Global warming could have a number of disastrous consequences largely affecting the arctic ecosystems:

• The arctic ice cap may disappear as glaciers start to melt and break up into icebergs.
• Permafrost will melt during the summer season which will increase the rate of decomposition of trapped organic matter, including peat and detritus. This in turn will increase the release of carbon dioxide which will increase the green house effect even further.
• Species adapted to temperature conditions will migrate north which will alter food chains and have consequences on the animals in the higher trophic levels.
• Marine species in the arctic water may become extinct as these are very sensitive to temperature changes within the sea water.
• Polar bears may face extinction as they loose their ice habitat and therefore can no longer feed or breed as they normally would.
• Pests and diseases may become quite common with rises in temperature.
• As the ice melts, sea levels will rise and flood low lying areas of land.
• Extreme weather events such as storms might become common and have disastrous effects on certain species.

Natality: increases population size as offspring are added to the population.

Immigration: increases population size as individuals have moved into the area from somewhere else and so this adds to the population.

Mortality: decreases the population as some individuals get eaten, die of old age or get sick.

Emigration: decreases the population as individuals have moved out of the area to go live somewhere else.

1. Shortage of resources (e.g. food)
2. Increase in predators
3. Increase in diseases and parasites

Antibiotic resistance in bacteria is a common problem. It results from the transfer of a gene that gives resistance to a specific antibiotic usually by means of a plasmid to a bacterium. Some bacteria will then have this gene and become resistant to the specific antibiotic while others will lack the gene and so will die if exposed to the antibiotic. Over time, the non-resistant ones will all die off as doctors vaccinate patients, but the resistant ones will survive. Eventually, the resistant ones will be the only ones left as a result of natural selection and so a new antibiotic must be created. However, this has to be done on a regular basis as the bacteria keep evolving and become resistant to multiple antibiotics.

The Peppered Moth is another example of evolution in response to environmental change. There are two types of these moths, one species has a light colour while the other one is darker. When Britain begun industrialising, the soot from the factories would land on trees and so the darker moths then had an advantage over the light ones as they could easily hide from predators. Before the soot, both types of moths were eaten by predators however now that the darker ones were able to hide the lighter ones got eaten more often.The population of the darker moths rapidly increased while that of the lighter ones rapidly decreased until only the dark moths were left. All the lighter moths were less adapted to the environmental change and so they could no longer survive in that new environment.

Amylase

Protease

Lipase

Enzyme

Salivary Amylase

Pepsin

Pancreatic Lipase

Source

Salivary Glands

Chief cells in stomach lining

Pancreas

Substrate

Starch

Proteins

Triglycerides such as fats and oils

Products

Maltose

Small polypeptides

Fatty Acids and Glycerol

Optimum pH

pH 7

pH 1.5 - 2

pH 7

The stomach is an important part of the digestive system. Firstly it secretes HCL which kills bacteria and other harmful organisms preventing food poisoning and it also provides the optimum conditions for the enzyme pepsin to work in (pH 1.5 - 2). In addition, the stomach secretes pepsin which starts the digestion of proteins into polypeptides and amino acids. Theses can then be absorbed by the villi in the small intestine.

The small intestine is where the final stages of digestion occur. The intestinal wall secretes enzymes and it also receives enzymes from the pancreas. However the main function of the small intestine is the absorption of the small food particles resulting from digestion. It contains many villi which increase the surface area for absorption.

The large intestine moves the material that has not been digested from the small intestine and absorbs water. This produces solid faeces which are then egested through the anus.

The structure of the villus is very specific. Firstly there is a great number of them so this increases the surface area for absorption in the small intestine. In addition the villi also have their own projections which are called microvilli. The many microvilli increase the surface area for absorption further. These microvilli have protein channels and pumps in their membranes to allow the rapid absorption of food by facilitated diffusion and active transport. Also, the villi contains an epithelial layer which is only one cell layer thick so that food can pass through easily and be absorbed quickly. The blood capillaries in the villus are very closely associated with the epithelium so that the distance for the diffusion of the food molecules is small. This thin layer of cells contains mitochondria to provide the ATP needed for the active transport of certain food molecules. Finally, there is a lacteal branch at the centre of the villus which carries away fats after absorption.

Arteries have a thick outer layer of longitudinal collagen and elastic fibers to avoid leaks and bulges. They have a thick wall which is essential to withstand the high pressures. They also have thick layers of circular elastic fibres and muscle fibres to help pump the blood through after each contraction of the heart. In addition the narrow lumen maintains the high pressure inside the arteries.

Veins are made up of thin layers with a few circular elastic fibres and muscle fibres. This is because blood does not flow in pulses and so the vein walls cannot help pump the blood on. Veins also have thin walls which allows the near by muscles to press against them so that they become flat. This helps the blood to be pushed forwards towards the heart. There is only a thin outer layer of longitudinal collagen and elastic fibres as there is low pressure inside the vein and so little chance of bursting. Finally, a wide lumen is needed to accommodate the slow flowing blood due to the low pressure.

Capillaries are made up of a wall that is only one cell layer thick and results in the distance for diffusion in and out of the capillary being very small so that diffusion can occur rapidly. They also contain pores within the their wall which allow some plasma to leak out and form tissue fluid. Phagocytes can also pass through these pores to help fight infections. In addition, the lumen of the capillaries is very narrow. This means that many capillaries can fit in a small space, increasing the surface area for diffusion.

The skin forms a physical barrier that prevents pathogens from entering the body as the outer layer is very tough. In addition the skin contains sebaceous glands which secret lactic acid and fatty acids which creates an acidic environment on the surface of the skin preventing the growth of pathogens.

Mucous membranes form another type of barrier against pathogens. Mucous membranes are soft and moist areas of skin found in the trachea, nose, vagina and urethra. These membranes are not strong enough to create a physical barrier but they do have mucus which contain lysozyme enzymes that digest the phagocytes. Also, the mucus can be sticky such as in the trachea, and trap the pathogens which are then expelled up the trachea and out of the body by muscles within the trachea.

Cause: HIV causes AIDS (acquired immunodeficiency syndrome). A syndrome is a group of symptoms that are found together. HIV destroys a type of lymphocyte which is vital for antibody production. Over the years, less active lymphocytes are produced which leads to a fall in the amount of antibodies. Pathogens that would normally be easily controlled by the body in healthy individuals can cause serious consequences and eventually lead to death for patients affected by HIV. The immune system is considerably weakened.

Transmission: HIV is transmitted through body fluids from an infected person to an uninfected one. This can occur through vaginal and anal intercourse as well as oral sex if there are cuts or tears in the vagina, penis, mouth or intestine. It can also be transmitted by hypodermic needles that are shared by intravenous drug abusers. The small amount of blood present on these needles after their use may contain the virus and is enough to infect another person. Another way of transmission is through the placenta from mother to child, or through cuts during childbirth or in milk during breast feeding. Finally there is a risk of transmission in transfused blood or with blood products such as Factor VIII used to treat hemophiliacs.

Social implications: Relatives and friends suffer grief. Families can also suffer from a loss of income as the person infected by HIV can lose their wage if they are unable to work and are refused life insurance. Also, HIV patients may find it hard to find partners, employment and even housing. Finally, AIDS can cause fear in a population and reduce sexual activity.

Ventilation is the process of bringing fresh air into the alveoli and removing the stale air. It maintains the concentration gradient of carbon dioxide and oxygen between the alveoli and the blood in the capillaries (vital for oxygen to diffuse into the blood from the alveoli and carbon dioxide out of the blood into the alveoli).

Gas exchange is the process of swapping one gas for another. It occurs in the alveoli of the lungs. Oxygen diffuses into the capillaries from the air in the alveoli and carbon dioxide diffuses out of the capillaries and into the air in the alveoli.

Cell respiration releases energy in the form of ATP so that this energy can be used inside the cell. Cell respiration occurs in the mitochondria and cytoplasm of cells. Oxygen is used in this process and carbon dioxide is produced.

Inhalation:

- The external intercostal muscles contract. This moves the ribcage up and out.
- The diaphragm contracts. As it does so it moves down and becomes relatively flat.
- Both of these muscle contractions result in an increase in the volume of the thorax which in turn results in a drop in pressure inside the thorax.
- Pressure eventually drops below atmospheric pressure.
- Air then flow into the lungs from outside the body, through the mouth or nose, trachea, bronchi and bronchioles.
- Air continues to enter the lungs until the pressure inside the lungs rises to the atmospheric pressure.

Exhalation:

- The internal intercostal muscles contract. This moves the ribcage down and in.
- The abdominal muscles contract. This pushes the diaphragm up, back into a dome shape.
- Both of these muscle contractions result in a decrease in the volume of the thorax.
- As a result of the decrease in volume, the pressure inside the thorax increases.
- Eventually the pressure rises above atmospheric pressure.
- Air then flows out of the lungs to outside of the body through the nose or mouth.
- Air continues to flow out of the lungs until the pressure in the lungs has fallen back to atmospheric pressure.

Resting potential: the electrical potential across the plasma membrane of a cell that is not conducting an impulse.

Action potential: the reversal and restoration of the electrical potential across the plasma membrane of a cell, as an electrical impulse passes along it (depolarization and repolarization).

Sodium is found in greater concentrations outside of the cell while potassium is found in greater concentrations inside the cell. Sodium-potassium pumps exist in the plasma membrane to maintain the the concentration gradients and the membrane potential. Nerve impulses have a domino effect. An action potential in one part of the neuron causes another action potential in the adjacent part and so on. This is due to the diffusion of sodium ions between the region of the action potential and the resting potential. It is the movement of sodium and potassium that reduce the resting potential.

If the resting potential rises above the threshold level, voltage gated channels open. Voltage gated sodium channels open very fast so that sodium can diffuse into the cell down its concentration gradient. This reduces the membrane potential and results in more sodium channels opening. Sodium ions are positively charged and so the inside of the cell develops a net positive charge compared to the outside of the cell. This results in depolarization as the potential across the membrane is reversed.

A short while after this, voltage gated potassium channels open and potassium ions flow out of the cell down the concentration gradient. Since potassium ions are positively charged, their diffusion out of the cell causes a net negative charge to develop again inside the cell compared to the outside. The potential across the membrane is restored. This is called repolarization.

Finally, the concentration gradients of both ions are restored by the sodium-potassium pump. Sodium is pumped out of the cell while potassium is pumped in. The resting potential is restored and the neuron is ready to conduct another nerve impulse.

A synapse is a junction that permits a neuron to pass an electrical or chemical signal to another cell. At a synapse, the plasma membrane of the signal passing neuron (presynaptic neuron) is closely related to the plasma membrane of the target cell (postsynaptic neuron). Between the two there is a narrow fluid filled space called the synaptic cleft. Chemical signals called neurotransmitters pass from the presynaptic neuron to the post synaptic neuron.

This is how a synaptic transmission occurs:
An action potential travels along the neuron and reaches the end of the pre-synaptic neuron. The depolarization of the pre-synaptic membrane results in the opening of voltage gated calcium channels. Calcium ions flow into the presynaptic neuron and cause vesicles with neurotransmitters inside the neuron to fuse with the plasma membrane and release the neurotransmitters into the synaptic cleft via exocytosis. These neurotransmitters then diffuse within the synaptic cleft and some will bind to specific receptors located on the postsynaptic plasma membrane. The receptors are transmitted-gated ion channels which open and let sodium and other positively charged ions into the postsynaptic neuron when the neurotransmitters bind. As these positively charged ions enter the postsynaptic neuron they cause its membrane to depolarize. This depolarization results in an action potential which passes down the postsynaptic neuron. The neurotransmitters in the synaptic cleft are then quickly degraded and the calcium ions are pumped back into the synaptic cleft from inside the presynaptic neuron.

he hypothalamus is responsible for monitoring the temperature of the blood which is normally close to 37 degrees. If there are significant fluctuations from this set point, the hypothalamus sends signals (messages carried by neurons) to different parts of the body to restore the temperature back to the set point. This is done through negative feedback.

If blood temperature significantly increases above the set point

If blood temperature significantly drops bellow the set point

Skin arterioles increase in diameter so that more blood flows to the skin. By doing so it transfers heat from the core of the body to the skin and this heat is then lost to the external environment, cooling down the body in the process.

Skin arterioles decrease in diameter so that less blood flows to the skin. The diameter of the capillaries in the skin cannot change but less blood flows through them. This prevents heat loss to the external environment as the temperature of the skin falls.

Skeletal muscle stays relaxed so that more heat is not generated.

Shivering occurs. This is when the skeletal muscle does many small rapid contractions to generate heat.

Sweat glands secrete large amounts of sweat which makes the surface of the skin moist. When water evaporates from the moist skin it cools down the body.

Sweat glands to not secrete sweat and so no water evaporation can occur as skin stays dry.

Blood glucose concentration does not have a specific set point like blood temperature. Blood glucose levels drop and rise through the day and so the body usually tries to keep blood glucose levels around 4 to 8 millimoles per dm³ of blood. Once again, negative feedback is used to do so. There are responses by target organs which affect the rate at which glucose is taken up from the blood or loaded into the blood.

Response to blood glucose levels above the set point

Response to blood glucose levels below the set point

β cells in the pancreatic islets produce insulin. Insulin stimulates muscle cells and the liver cells to take up glucose from the blood and convert it into glycogen. These are then stored in the form of granules in the cytoplasm of cells. Also, other types of cells are stimulated to take up glucose and use it for cell respiration instead of fat. All of these processes lower the levels of glucose in the blood.

α cells in the pancreatic islets produce glucagon. Glucagon stimulates the liver cells to convert glycogen back into glucose and release this glucose into the blood. This raises the glucose levels in the blood.

Type I diabetes

Type II diabetes

The onset is usually early, sometime during childhood.

The onset is usually late, sometime after childhood.

β cells do not produce enough insulin.

Target cells become insensitive to insulin.

Diet by itself cannot be used to control the condition. Insulin injections are needed to control glucose levels.

Insulin injections are not usually needed. Low carbohydrate diet can control the condition.

The menstrual cycle:

1. FSH is secreted by the pituitary gland and its levels start to rise. This stimulates the follicle to develop and the follicle cells to secret estrogen.
2. Estrogen then causes the follicle cells to make more FSH receptors so that these can respond more strongly to the FSH.
3. This is positive feedback and causes the estrogen levels to increase and stimulate the thickening of the endometrium (uterus lining).
4. Estrogen levels increase to a peak and by doing so it stimulates LH secretion from the pituitary gland.
5. LH then increases to its peak and causes ovulation (release of egg from the follicle).
6. LH then stimulates the follicle cells to secrete less estrogen and more progesterone. Once ovulation has occurred, LH stimulated the follicle to develop into the corpus luteum.
7. The corpus luteum then starts to secrete high amounts of progesterone. This prepares the uterine lining for an embryo.
8. The high levels of estrogen and progesterone then start to inhibit FSH and LH.
9. If no embryo develops the levels of estrogen and progesterone fall. This stimulates menstruation (break down of the uterine lining). When the levels of these two hormones are low enough FSH and LH start to be secreted again.
10. FSH levels rise once again and a new menstrual cycle begins.

Roles:

1. Stimulates the development of prenatal genitalia.
2. Stimulates the development of the male secondary sexual characteristics such as growth of the skeletal muscle and pubic hair.
3. During adulthood it maintains the sex drive.

Process:

1. For a period of three weeks, the women has to have a drug injected to stop her normal menstrual cycle.
2. After these three weeks, high doses of FSH are injected once a day for 10-12 days so that many follicles develop in the ovaries of the women.
3. HCG (another hormone) is injected 36 hours before the collection of the eggs. HCG loosens the eggs in the follicles and makes them mature.
4. The man needs to ejaculate into a jar so that sperm can be collected from the semen. The sperm are processed to concentrate the healthiest ones.
5. A device that is inserted through the wall of the vagina is used to extract the eggs from the follicles.
6. Each egg is then mixed with sperm in a shallow dish. The dishes are then put into an incubator overnight.
7. The next day the dishes are looked at to see if fertilization has happened.
8. If fertilization has been successful, two or three of the embryos are chosen to be placed in the uterus by the use of a long plastic tube.
9. A pregnancy test is done a few weeks later to find out if any of the embryos have implanted.
10. A scan is done a few weeks later to find out if the pregnancy is progressing normally.

Arguments for IVF

Arguments against IVF

Many types of infertility are due to environmental factors rather than genetic which means that the offspring would not inherit the infertility.

The infertility of the parents may be inherited by their offspring passing on the suffering to the next generation.

The embryos that are killed during the IVF process cannot feel pain or suffering as they do not have a developed nervous system.

More embryos are produced than needed and the ones that remain are usually killed which denies them the chance of a life.

Suffering caused by genetic diseases can be decreases by screening the embryos before placing them into the uterus.

Embryologists select which embryos will be placed into the uterus. Therefore they decide the fate of new individuals as they choose which ones will survive and which ones will die.

Since the IVF process is not an easy one emotionally and physically, is costly, takes time and there are no guarantees, parents who are willing to go through it must have a strong desire to have children and therefore are likely to be loving parents.

IVF is not a natural process which takes place in a laboratory compared to natural conception which occurs as a result of an act of love.

Infertility can cause emotional suffering to couples who want to have children. IVF can take away this suffering for some of those couples.

Infertility should be accepted as God’s will and to go against it by using IVF procedures would be wrong.

DNA is made up of two strands. At one end of each strand there is a phosphate group attached to the carbon atom number 5 of the deoxyribose (this indicates the 5' terminal) and at the other end of each strand is a hydroxyl group attached to the carbon atom number 3 of the deoxyribose (this indicates the 3' terminal). The strands run in opposite directions and so we say that they are antiparallel. One strand runs in a 5'-3' direction and the other runs in a 3'-5' direction. Adjacent nucleotides are attached together via a bond between the phosphate group of one nucleotide and the carbon atom number 3 of the deoxyribose of the other nucleotide.

The bases of each strand link together via hydrogen bonds. Adenine and Guanine are purines as they have two rings in their molecular structure. Thymine and Cytosine are pyrimidines as they only have one ring in their molecular structure. A purine will link with a pyrimidine. Adenine and thymine link together by forming two hydrogen bonds while Guanine and cytosine link together by forming 3 hydrogen bonds.

There are four levels of protein structure:

Primary Structure: The primary structure of a protein is its amino acid sequence. This amino acid sequence is determined by the base sequence of the gene which codes for the protein.

Secondary Structure: Secondary structures have α-helices and β-pleated sheets. These form as a result of hydrogen bonds between the peptide groups of the main chain. Therefore, proteins that contain secondary structures will have regions that are cylindrical (α-helices) and/or regions that are planar (β-pleated sheets).

Tertiary Structure: The tertiary structure of a protein is its three-dimensional conformation which occurs as a result of the protein folding. This folding is stabilised by hydrogen bonds, hydrophobic interactions, ionic bonds and disulphide bridges. These intramolecular bonds form between the R groups of different amino acids.

Quaternary Structure: A quaternary structure is formed when two or more polypeptide chains associate to form a single protein. An example is haemoglobin which consists of four polypeptide chains. In some cases, some proteins can have a non-polypeptide structure called a prosthetic group. These proteins are called conjugated proteins. The haem group in haemoglobin is a prosthetic group.

Amino acids have different R groups. Some of these R groups will be hydrophilic, making the amino acid polar, while others will be hydrophobic, making the amino acid non-polar. The distribution of the polar and non-polar amino acids in a protein influences the function and location of the protein within the body. Non-polar amino acids are found in the centre of water soluble proteins while the polar amino acids are found at the surface.

Examples of how the distribution of non-polar and polar amino acids affect protein function and location:

Controlling the position of proteins in membranes: The non-polar amino acids cause proteins to be embedded in membranes while polar amino acids cause portions of the proteins to protrude from the membrane.

Creating hydrophilic channels through membranes: Polar amino acids are found inside membrane proteins and create a channel through which hydrophilic molecules can pass through.

Specificity of active site in enzymes: If the amino acids in the active site of an enzyme are non-polar then it makes this active site specific to a non-polar substance. On the other hand, if the active site is made up of polar amino acids then the active site is specific to a polar substance.

Function

Example

Structural

Collagen strengthens bones, skin and tendons.

Movement

Myosin found in muscle fibers causes contraction of the muscle which results in movement.

Transport

Haemoglobin transports oxygen from the lungs to other tissues in the body.

Defense

Immunoglobulin acts as an antibody.

Initially the substrate does not fit perfectly into the active site of the enzyme. When the substrate binds to the active site, this changes the shape of the active site and only then does it perfectly fit the substrate. As the substrate binds it changes the shape of the active site and this weakens the bonds in the substrate and therefore reduces the activation energy. This model is a more precise version of the lock and key one. The reason for this is that it explains why some enzymes can bind to many different substrates. If the shape of the active site changes when a substrate binds, this allows many different but similar substrates to bind to the one enzyme.

Enzyme inhibitors are substances which inhibit enzyme activity. There are competitive enzyme inhibitors and non-competitive inhibitors.

Competitive Inhibitors

These are structurally similar to the substrate of the enzyme and bind to the active site. This means that when a competitive inhibitor binds to the active site of an enzyme, it prevents the substrate from binding to the active site. Only once the inhibitor has been released from the active site can the substrate bind. The inhibitor is called a competitive inhibitor as it competes with the substrate for the active site.

The effects of a competitive inhibitor can be reduced by increasing the substrate concentration. More substrate would successfully bind to the active site than inhibitor and therefore reducing the effect of the inhibition. The maximum rate of reaction or a level very close to the maximum rate of reaction can be reached.

An example of a competitive inhibitor is malonate. Malonate is structurally similar to the substrate succinate. Succinate is found in the Krebs cycle of aerobic respiration and binds to the active site of the dehydrogenase enzyme. Malonate can compete with succinate for the active site and in doing so it can prevent succinate from binding.

Non-Competitive Inhibition

These are not similar to the substrate and they do not bind to the active site of the enzyme. Instead they bind to a different site on the enzyme and change the conformation of the active site. The substrate may still be able to bind to the active site however the enzyme is not able to catalyse the reaction or can only do so at a slower rate.

Figure 7.6.5 - Non-competitive inhibition

In the presence of a non-competitive inhibitor, increasing the substrate concentration cannot prevent the inhibitor from binding to the enzyme as the two bind to different sites. Therefore, no matter how high the concentration of substrate is, some of the enzymes will still be inhibited. The maximum rate of reaction will always be lower in the presence of a non-competitive inhibitor.

An example of a non-competitive inhibitor is ATP. When ATP accumulates it binds to a site other than the active site on the enzyme phosphofructokinase. In doing so it changes the enzyme conformation and lowers the rate of reaction so that less ATP is produced.

Metabolic pathways are made up of many chemical reactions and these reactions are catalysed by enzymes. Often, the product of the last reaction in the pathway inhibits the enzyme that catalyses the first reaction of the pathway. This is called end-product inhibition and it involves non-competitive inhibitors.

The product of the last reaction of the metabolic pathway will bind to a site other than the active site of the enzyme that catalyses the first reaction. This site is called the allosteric site. When it binds to the allosteric site it acts as non-competitive inhibitor and changes the conformation of the active site. Therefore, it makes the binding of the substrate to the enzyme unlikely. Once the inhibitor is released from the allosteric site, the active site returns to its original conformation and the substrate is able to bind again.

There is a clear advantage in using end-product inhibition for controlling metabolic pathways. When there is an excess of end-product, the whole metabolic pathway is shut down as the end product inhibits the first enzyme of the pathway. Therefore less of the end product gets produced and by inhibiting the first enzyme it also prevents the formation of intermediates. When the levels of the end product decrease, the enzymes start to work again and the metabolic pathway is switched on.

Step 1 - Glucose is phosphorylated. Two phosphate groups are added to glucose to form hexose biphosphate. These two phosphate groups are provided by two molecules of ATP.

Step 2 - Lysis of hexose biphosphate. Hexose biphosphate splits into two molecules of triose phosphate.

Step 3 - Each triose phosphate molecules is oxidised. Two atoms of hydrogen are removed from each molecule. The energy released by the oxidation is used to add another phosphate group to each molecule. This will result in two 3-carbon compounds, each carrying two phosphate groups. NAD⁺ is the hydrogen carrier that accepts the hydrogen atoms lost from each triose phosphate molecule.

Step 4 - Two pyruvate molecules are formed by removing two phosphate groups from each molecule. These phosphate groups are given to ADP molecules and form ATP.

Glycolysis occurs in the cytoplasm of cells. Two ATP molecules are used and 4 ATP molecules are produced. Therefore there is a net yield of two ATP molecules. Also, two NAD⁺ are converted into NADH + H⁺ during glycolysis.

Aerobic Respiration

Glycolysis can take place without oxygen. This forms the anaerobic part of cell respiration and therefore is called anaerobic cell respiration. However, the pyruvate produced from glycolysis cannot be oxidised further without the presence of oxygen. The oxidisation of the pyruvate forms part of the aerobic respiration and therefore is called aerobic cell respiration. Aerobic respiration occurs in the mitochondria of cells. The first reaction to take place is the link reaction.

The Link Reaction

Mitochondria in cells take up the pyruvate which is formed from glycolysis in the cytoplasm. Once the pyruvate is in the mitochondrion, enzymes within the matrix of the mitochondrion remove hydrogen and carbon dioxide from the pyruvate. This is called oxidation (removal of hydrogen or addition of oxygen) and decarboxylation (removal of carbon dioxide). Therefore, the process is called oxidative decarboxylation. The hydrogen removed is accepted by NAD⁺. The link reaction results in the formation of an acetyl group. This acetyl group is then accepted by CoA and forms acetyl CoA.

Figure 8.1.3 - The link reaction

The Krebs Cycle

Step 1 - In the first stage of the Krebs cycle, the acetyl group from acetyl CoA is transferred to a four carbon compound. This forms a six carbon compound.

Step 2 - This six carbon compound then undergoes decarboxylation (CO₂ is removed) and oxidation (hydrogen is removed) to form a five carbon compound. The hydrogen is accepted by NAD⁺ and forms NADH + H⁺.

Step 3 - The five carbon compound undergoes decarboxylation and oxidation (hydrogen is removed) again to form a four carbon compound. The hydrogen is accepted by NAD⁺ and forms NADH + H⁺.

Step 4 - The four carbon compound then undergoes substrate-level phosphorylation and during this reaction it produces ATP. Oxidation also occurs twice (2 hydrogens are removed). The one hydrogen is accepted by NAD⁺ and forms NADH + H⁺. The other is accepted by FAD and forms FADH₂. The four carbon compound is then ready to accept a new acetyl group and the cycle is repeated.

The carbon dioxide that is removed in these reactions is a waste product and is excreted from the body. The oxidations release energy which is then stored by the carriers when they accept the hydrogen. This energy is then later on used by the electron transport chain to produce ATP.

The Electron Transport Chain

Inside the inner membrane of the mitochondria there is a chain of electron carriers. This chain is called the electron transport chain. Electrons from the oxidative reactions in the earlier stages of cell respiration pass along the chain. NADH donates two electrons to the first carrier in the chain. These two electrons pass along the chain and release energy from one carrier to the next. At three locations along the chain, enough energy is released to produce ATP via ATP synthase. ATP synthase is an enzyme that is also found in the inner mitochondrial membrane. FADH₂ also donates electrons but at a later stage than NADH. Also, enough energy is released at only two locations along the chain by electrons from FADH₂. The ATP production relies on energy release by oxidation and it is therefore called oxidative phosphorylation.

Figure 8.1.5 - Electron transport chain

The Role of Oxygen

Oxygen is important for cell respiration as at the end of the electron transport chain, the electrons are donated to oxygen. This occurs in the matrix at the surface of the inner membrane. At the same time oxygen binds with hydrogen ions and forms water.
If there is no oxygen then electrons can no longer pass through the electron transport chain and NADH + H⁺ can no longer be reconverted into NAD⁺. Eventually NAD⁺ in the mitochondrion runs out and therefore the link reaction and Krebs cycle no longer take place.

Figure 8.1.6 - Chemiosmosis

Figure 8.1.6 shows the movement of protons from the matrix into the space between the inner and outer membranes. This creates a concentration gradient. The energy used to pump these protons across the inner membrane comes from the energy released by the electrons passing through the electron transport chain.

The protons then move down the concentration gradient from the space between the inner and outer membranes back into the matrix. However, they can only move back across via an enzyme embedded in the inner membrane. This enzyme is called ATP synthase. The protons are transported back into the matrix through the channels of ATP synthase and as they do so they release energy. This energy is then used by ATP synthase to convert ADP into ATP. Since the electrons come from previous oxidation reactions of cell respiration and the ATP synthase catalyses the phosphorylation of ADP into ATP, this process is called oxidative phosphorylation. Chemiosmosis is necessary for oxidative phosphorylation to work.

Figure 8.1.7 shows the movement of protons down their concentration gradient. They can only travel through the inner membrane via ATP synthase and as they do so they release energy. This energy is used by ATP synthase to convert ADP into ATP.

Matrix: Watery substance that contains ribosomes and many enzymes. These enzymes are vital for the link reaction and the Krebs cycle.

Inner membrane: The electron transport chain and ATP synthase are found in this membrane. These are vital for oxidative phosphorylation.

Space between inner and outer membranes: Small volume space into which protons are pumped into. Due to its small volume, a high concentration gradient can be reached very quickly. This is vital for chemiosmosis.

Outer membrane: This membrane separates the contents of the mitochondrion from the rest of the cell. It creates a good environment for cell respiration.

Cristae: These tubular projections of the inner membrane increase the surface area for oxidative phosphorylation.

Photosynthesis occurs inside chloroplasts. Chloroplasts contain chlorophyll, a green pigment found inside the thylakoid membranes. These chlorophyll molecules are arranged in groups called photosystems. There are two types of photosystems, Photosystem II and Photosystem I. When a chlorophyll molecule absorbs light, the energy from this light raises an electron within the chlorophyll molecule to a higher energy state. The chlorophyll molecule is then said to be photoactivated. Excited electron anywhere within the photosystem are then passed on from one chlorophyll molecule to the next until they reach a special chlorophyll molecule at the reaction centre of the photosystem. This special chlorophyll molecule then passes on the excited electron to a chain of electron carriers.

The light-dependent reactions starts within Photosystem II. When the excited electron reaches the special chlorophyll molecule at the reaction centre of Photosystem II it is passed on to the chain of electron carriers. This chain of electron carriers is found within the thylakoid membrane. As this excited electron passes from one carrier to the next it releases energy. This energy is used to pump protons (hydrogen ions) across the thylakoid membrane and into the space within the thylakoids. This forms a proton gradient. The protons can travel back across the membrane, down the concentration gradient, however to do so they must pass through ATP synthase. ATP synthase is located in the thylakoid membrane and it uses the energy released from the movement of protons down their concentration gradient to synthesise ATP from ADP and inorganic phosphate. The synthesis of ATP in this manner is called non-cyclic photophosphorylation (uses the energy of excited electrons from photosystem II) .

The electrons from the chain of electron carriers are then accepted by Photosystem I. These electrons replace electrons previously lost from Photosystem I. Photosystem I then absorbs light and becomes photoactivated. The electrons become excited again as they are raised to a higher energy state. These excited electrons then pass along a short chain of electron carriers and are eventually used to reduce NADP⁺ in the stroma. NADP⁺ accepts two excited electrons from the chain of carriers and one H⁺ ion from the stroma to form NADPH.

If the light intensity is not a limiting factor, there will usually be a shortage of NADP⁺ as NADPH accumulates within the stroma (see light independent reaction). NADP⁺ is needed for the normal flow of electrons in the thylakoid membranes as it is the final electron acceptor. If NADP⁺ is not available then the normal flow of electrons is inhibited. However, there is an alternative pathway for ATP production in this case and it is called cyclic photophosphorylation. It begins with Photosystem I absorbing light and becoming photoactivated. The excited electrons from Photosystem I are then passed on to a chain of electron carriers between Photosystem I and II. These electrons travel along the chain of carriers back to Photosystem I and as they do so they cause the pumping of protons across the thylakoid membrane and therefore create a proton gradient. As explained previously, the protons move back across the thylakoid membrane through ATP synthase and as they do so, ATP is produced. Therefore, ATP can be produced even when there is a shortage of NADP⁺.

In addition to producing NADPH, the light dependent reactions also produce oxygen as a waste product. When the special chlorophyll molecule at the reaction centre passes on the electrons to the chain of electron carriers, it becomes positively charged. With the aid of an enzyme at the reaction centre, water molecules within the thylakoid space are split. Oxygen and H⁺ ions are formed as a result and the electrons from the splitting of these water molecules are given to chlorophyll. The oxygen is then excreted as a waste product. This splitting of water molecules is called photolysis as it only occurs in the presence of light.

The light-independant reactions of photosynthesis occur in the stroma of the chloroplast and involve the conversion of carbon dioxide and other compounds into glucose. The light-independent reactions can be split into three stages, these are carbon fixation, the reduction reactions and finally the regeneration of ribulose bisphosphate. Collectively these stages are known as the Calvin Cycle.

During carbon fixation, carbon dioxide in the stroma (which enters the chloroplast by diffusion) reacts with a five-carbon sugar called ribulose bisphosphate (RuBP) to form a six-carbon compound. This reaction is catalysed by an enzyme called ribulose bisphosphate carboxylase (large amounts present within the stroma), otherwise known as rubisco. As soon as the six-carbon compound is formed, it splits to form two molecules of glycerate 3-phosphate. Glycerate 3-phosphate is then used in the reduction reactions.

Glycerate 3-phosphate is reduced during the reduction reactions to a three-carbon sugar called triose phosphate. Energy and hydrogen is needed for the reduction and these are supplied by ATP and NADPH + H⁺ (both produced during light-dependent reactions) respectively. Two triose phosphate molecules can then react together to form glucose phosphate. The condensation of many molecules of glucose phosphate forms starch which is the form of carbohydrate stored in plants. However, out of six triose phosphates produced during the reduction reactions, only one will be used to synthesise glucose phosphate. The five remaining triose phosphates will be used to regenerate RuBP.

The regeneration of RuBP is essential for carbon fixation to continue. Five triose phosphate molecules will undergo a series of reactions requiring energy from ATP, to form three molecules of RuBP. RuBP is therefore consumed and produced during the light-independent reactions and therefore these reactions form a cycle which is named the Calvin cycle.

The stroma - Contains many enzymes, including rubisco, which are important for the reactions of the Calvin cycle.

The thylakoids - Have a large surface area for light absorption and the space within them allows rapid accumulation of protons.

The action spectrum of photosynthesis is a graph showing the rate of photosynthesis for each wavelength of light. The rate of photosynthesis will not be the same for every wavelength of light. The rate of photosynthesis is the least with green-yellow light (525 nm-625 nm). Red-orange light (625nm-700nm) shows a good rate of photosynthesis however the best rate of photosynthesis is seen with violet-blue light (400nm-525nm).

An absorption spectrum is a graph showing the percentage of light absorbed by pigments within the chloroplast, for each wavelength of light. An example is the absorption spectrum of chlorophyll a and b. The best absorption is seen with violet-blue light. There is also good absorption with red-orange light. However most of the green-yellow light is reflected and therefore not absorbed. This wavelength of light shows the least absorption.

As we can see, there is a close relationship between the action spectrum and absorption spectrum of photosynthesis. There are many different types of photosynthetic pigments which will absorb light best at different wavelengths. However the most abundant photosynthetic pigment in plants is chlorophyll and therefore the rate of photosynthesis will be the greatest at wavelengths of light best absorbed by chlorophyll (400nm-525nm corresponding to violet-blue light). Very little light is absorbed by chlorophyll at wavelengths of light between 525nm and 625 (green-yellow light) so the rate of photosynthesis will be the least within this range. However, there are other pigments that are able to absorb green-yellow light such as carotene. Even though these are present in small amounts they allow a low rate of photosynthesis to occur at wavelengths of light that chlorophyll cannot absorb.

A limiting factor is a factor that controls a process. Light intensity, temperature and carbon dioxide concentration are all factors which can control the rate of photosynthesis. Usually, only one of these factors will be the limiting factor in a plant at a certain time. This is the factor which is the furthest from its optimum level at a particular point in time. If we change the limiting factor the rate of photosynthesis will change but changes to the other factors will have no effect on the rate. If the levels of the limiting factor increase so that this factor is no longer the furthest from its optimum level, the limiting factor will change to the factor which is at that point in time, the furthest from its optimum level. For example, at night the limiting factor is likely to be the light intensity as this will be the furthest from its optimum level. During the day, the limiting factor is likely to switch to the temperature or the carbon dioxide concentration as the light intensity increases.

So how can these factors have an effect on the rate of photosynthesis? Lets start off with the light intensity. When the light intensity is poor, there is a shortage of ATP and NADPH, as these are products from the light dependent reactions. Without these products the light independent reactions can't occur as glycerate 3-phosphate cannot be reduced. Therefore a shortage of these products will limit the rate of photosynthesis. When the carbon dioxide concentration is low, the amount of glycerate 3-phosphate produced is limited as carbon dioxide is needed for its production and therefore the rate of photosynthesis is affected. Finally, many enzymes are involved during the process of photosynthesis. At low temperatures these enzymes work slower. At high temperatures the enzymes no longer work effectively. This affects the rate of the reactions in the Calvin cycle and therefore the rate of photosynthesis will be affected.

Monocotyledons

Dicotyledons

One cotyledon

Two cotyledons

Vascular bundles are randomly spread through out the stem

Vascular bundles are arranged in a ring

Parallel venation in leaves

Net-like venation in leaves

Floral organs are in multiples of 3

Floral organs are in multiples of 4 or 5

New roots form from the stem

New roots branch from pre-existing roots

Upper epidermis - Consists of a single layer of cells found on the upper surface of the leaf. It is covered by a thick waxy cuticle. The main function of the upper epidermis is water conservation. It prevents the loss of water from the upper surface where the light intensity and heat are the greatest.

Palisade mesophyll - Consists of tightly packed cylindrical cells. This tissue contains many chloroplasts as it is the main photosynthetic tissue. It is found on the upper half of the leaf (upper surface) where the light intensity is the greatest.

Spongy mesophyll - Made up of loosely packed cells. This tissue is found in the lower half of the leaf (lower surface) and has few chloroplasts. It provides gas exchange (CO₂ uptake and O₂release) and therefore needs to be close to the stomata found in the lower epidermis.

Vascular tissue - Consists of xylem and phloem which are found in the veins of the leaf. The veins in the leaf are positioned in the middle so that all the cells are in close contact with the vascular tissue. The xylem consists of xylem vessels (dead structure) which are long and tubular and transports water into the leaf to replace the water that has been lost through transpiration. The phloem is made up of living cells with pores in between them. It transports the products of photosynthesis out of the leaf.

Bulbs: These are modified leaf bases which serve as food storage and thereby enable the plant to survive adverse conditions.These leaf bases may look like scales or they may extend over and encircle the centre of the bulb (onion). At the base of the bulb, a modified stem can be seen. Roots grow from the underside of the base while the new stems and leaves arise from the upper side of the base. An example of a bulb is an onion bulb.

Stem Tubers: These are modified stems which serve as food storage. The stem extends into the ground and forms enlarged, swollen structures which we call stem tubers. Stem tubers are used to store nutrients and therefore allow the plant to survive winter as well as other adverse conditions. They also serve as a mean of asexual reproduction as new plants develop from these stem tubers. An example of a stem tuber is a potato.

Storage Roots: These are modified roots which serve as food storage. They also allow the plant to survive adverse conditions. An example of a storage root is a carrot.

Tendrils: These are modified leaves. They are slim and provide attachment as well as support. In doing so they allow plants to climb upwards. They will rotate in the air until they reach a solid structure to which they can attach to. An example of plants with tendrils are grape vines.

Tropisms are directional movement responses which occur due to external environmental stimuli. The direction of the stimulus affects the direction of movement. Tropisms can either be negative or positive. Positive tropisms are the directional movement towards the stimulus while negative tropisms are the directional movement away from the stimulus. Examples of stimuli causing tropisms in plants are gravity and light. Roots will grow towards gravity while the plant shoot will grow upwards in the opposite direction. The directional movement of plants in response to light is called phototropism. As seen with gravity, the plant's roots will grow away from the light, into the soil (negative phototropism) while the plant shoot will grow towards the light (positive phototropism). Positive phototropism seen at the tips of plant shoots is made possible due to plant hormones called auxins. Auxins are produced at the tips of plant shoots and then translocate to the darker side of the shoot tip and stem which is receiving less light. This translocation is made possible via auxin efflux carriers which are unevenly distributed in the plant tissue. Once auxins reach the shaded side of the plant, they cause the elongation of cells so that the shaded side grows faster than the brighter side, thereby promoting the bending of the plant shoot towards the light. Auxins do so by binding to auxin receptors on cells. The binding of auxin causes the transcription of certain genes within those cells and therefore the production of specific proteins which affect growth. Auxins allow the expelling of protons (hydrogen ions) into the cell walls of the cells on the shaded side, decreasing the pH inside the cells and in doing so activate specific enzymes which break down cellulose microfibrils within the cell wall. This loosens the cell wall and allows cell elongation. So to conclude, auxins are very important in the control of plant growth towards the light and thereby allow the plant to increase its rate of photosynthesis.

Four abiotic factors affect the rate of transpiration in a typical terrestrial plant:

Light - The rate of transpiration is much greater when light is available as the stomata close in the dark.

Humidity - Water diffuses out of the leaf, down its concentration gradient, from a high concentration gradient inside the leaf to a lower concentration gradient in the air. The lower concentration gradient in the air is vital for transpiration. Humidity is the water vapour in the air, therefore a rise in humidity means a larger concentration of water vapour in the air and results in a decrease in transpiration rate.

Temperature - As temperature rises, so does the rate of transpiration. This is because heat is vital for the evaporation of water vapour from the cell walls of spongy mesophyll cells. A rise in temperature leads to an increase in the evaporation rate thereby increasing transpiration rate. Higher temperatures also increase the rate of diffusion between air spaces inside the leaf and the air outside. Finally, an increase in temperature causes a reduction in humidity in the air outside the leaf which causes an increase in concentration gradient and therefore an increase in transpiration rate.

Wind - Wind increases the transpiration rate by removing the humidity around the leaf produced by transpiration.

1) Reduced surface area of the plant - reduced leaves such as spines in cacti (modified leaves)

2) Thick waxy cuticle covering the epidermis

3) Reduced numbers of stomata

4) Water storage tissues in roots, leaves and stems

5) CAM physiology - Stomata open during the evening/night instead of during the day (when the temperature is at its highest) as the transpiration rate will be lower during cooler hours.

Pollination - The process of pollen transfer from an anther to a stigma.

Fertilization - The fusion of a male gamete with a female gamete inside the ovule. This forms a zygote.

Seed dispersal - The movement/transport of seeds away from the plant. Fruits which develop from fertilised ovules, function as a mean of seed dispersal.

Germination is the emerging and growth of an embryonic plant from a seed. It requires certain conditions, such as water, heat and oxygen. If conditions are not favourable then the seed may remain dormant. This way the seed can survive adverse conditions and only start to germinate when conditions become more favourable.

Water is needed to rehydrate the cells of the seed. This is vital for the activation of certain enzymes which start the metabolism of the seed. Without water the embryo root and shoot are not able to grow. Also water causes the seed to swell and this leads to the bursting of the seed coat which enables the plant to emerge from the seed. In addition, heat is needed for germination as the enzyme activity inside the seed depends on it. However, appropriate temperatures are needed. If it is too hot or too cold the enzyme activity will be too low for germination. Therefore, seeds usually remain dormant if heat conditions are not favourable. Finally, oxygen is needed for metabolism. It is used in aerobic cell respiration to provide the energy for the growth of the plant until the first leaves emerge. Once the leaves emerge, photosynthesis can then provide the energy needed for growth.

Two divisions occure during meiosis, these are termed meiosis I and meiosis II. Each division involves the four stages of prophase, metaphase, anaphase and telophase.

Meiosis I

Prophase I

• Chromosomes coil up tightly and become visible under a light microscope
• Homologous chromosomes pair up and crossing over occures (the point of cross over is known as the chiasma)
• Nuclear membrane disintgrates and the centrioles travel to the poles of the cell

Metaphase I

• Microtubules form a spindle and the spindle fibers attach to the centromeres of the chromosomes
• Pairs of homologous chromosomes align along the equator

Anaphase I

• Spindle fibers shorten pulling paired homologous chromosomes in opposite directions
• Paired homologous chromosomes are seperated and pulled to opposite poles so that each pole contains one chromosome of each pair.

Telophase I

• A nuclear membrane forms around the chromosomes at each pole and chromosomes uncoil
• The cell undergoes cytokinesis to form two daughter cells
• Forms two haploid cells
• At the end of telophase I the cells may enter a short interphase period or proceed directly to meiosis II
• DNA is not replicated

Meiosis II

Prophase II

• Chromosomes coil up again
• Centrioles move to the cell poles
• Nuclear membrane disintergrates

Metaphase II

• Spindle fibers attach to the the centromeres
• Chromosomes align along the equator

Anaphase II

• Spindle fibers shorten
• Centromeres split
• Chromatids of each chromosome travel to opposite poles

Telophase II

• Nuclear membrane forms around the chromatids at each pole, once the membrane is formed, each chromatid is then called a chromosome.
• Both cells undergo cytokinesis to form four cells
• Chromosomes uncoil
• Nucleoli form

Two processes result in the infinite genetic variety in gametes. These are crossing over in prophase I and the random orientation of chromosomes in metaphase I.

Crossing over is important for genetic variety as it allows the exchange of genetic material between the maternal and paternal chromosomes. This forms chromatids with new combinations of alleles (recombination of linked genes). The chromatids which have a combination of allele different to that of either parent are called recombinants. It is also important to note that crossing over occures at a random point and more than one chiasma can form per homologous pair. This means that meiosis can result in almost an infinite amount of genetic variety.

The random orientation of homologous chromosomes at the equator in metaphase I also plays a vital role in genetic variety. Since the homologous pairs of chromosomes are orientated randomly at the equator, either maternal or paternal homolgue can orient towards either pole. The number of possible orientations is equal to 2 raised to the power of the number of chromosome pairs. For example, for a haploid number of n, 2ⁿ is the number of possible outcomes. Humans have a haploid number of 23. 2²³ gives a value of over 8 million. This means that there are over 8 million possible combinations just through the radom orientation of the homologous chromosmes. If we add the effects of crossing over, the number of combinations increases even further. Therfore, these two processes allow infinit genetic variety in gametes.

A dihybrid cross is a cross between first generation offspring of two individuals which have two different characteristics. These two characteristics are controled by two genes.

We can use dihybrid crosses to calculate and predict the genotypic and phenotypic ratio of offspring involving unlinked autosomal genes. For example: Let's say we cross two cats with two different characteristics such as fur colour and fur length. For this example we will be using the alleles as follows:

• S = allele for long fur
• s = allele for short fur
• B = allele for black fur
• b = allele for brown fur

Sex chromosomes are the ones that determine your gender. These are X and Y (XX in females, XY in males).

Autosomal chromosomes are the remaining chromosomes which are not sex chromosomes. There are 22 pairs of these in humans. This means that there is a total of 23 pairs of chromosomes in humans (22 autosomal pairs + 1 sex chromosome pair = 23 pairs of chromosomes).

Linkage group: A pair or set of genes on a chromosome which tend to be inherited together.