BIO5 Essay - Key paragraphs

Glycolysis is the initial stage of both aerobic and anaerobic respiration. It occurs in the cytoplasm of all living cells and is the process in which glucose is split into pyruvate. It happens in four main stages;

• Activation of glucose by phosphorylation (addition of phosphate molecules to glucose)
• Splitting of the phosphorylated glucose (glucose is split into two molecules of triose phosphate)
• Oxidation of triose phosphate (hydrogen is removed and transferred to NAD to form reduced NAD)
• The production of ATP (triose phosphate is converted into pyruvate)

The overall yield from one glucose molecule is two molecules of ATP, two molecules of reduced NAD and two molecules of pyruvate.

The light dependent reaction involves the capture of light for photosynthesis.

• When a chlorophyll molecule absorbs light energy, it boosts the energy of electrons within the chlorophyll, raising them to a higher energy level.
• These electrons are in such an excited state, that they leave the chlorophyll molecule and taken up by electron carriers.
• These electrons are passed along a number of electron carriers in a series of oxidation-reduction reactions at a decreasing energy level.
• The energy lost at each stage is used to combine an inorganic phosphate molecule with an ADP molecule in order to make ATP.

Replacement electrons are provided from water molecules that are split using light energy. This process is known as photolysis. It also releases hydrogen ions that are taken up by NADP to form reduced NADP.

The light dependent reaction takes place in the thylakoids of chloroplasts as they provide a large surface area for the attachement of chlorophyll and enzymes.

The light independent reaction takes place in the stroma of chloroplasts. This is because the fluid of the stroma contains the enzymes, DNA and ribosomes necessary as well as being surrounded by grana where the products can readily diffuse.

It is referred to as the Calvin Cycle.

• Carbon dioxide combines with the 5-carbon compound Ribulose Bisphosphate (RuBP) using an enzyme
• This combination produces two molecules of the 3-carbon Glycerate 3-Phosphate (GP)
• ATP and reduced NADP from the light dependent reaction are used to reduce these molecules into Triose Phosphate (TP)
• Some triose phosphate molecules are converted to useful organic substances like Glucose, whilst others are used to regenerate Ribulose Biphosphate

This process requires the products of the light dependent reaction and so it rapidly ceases when light is not present.

Transcription is the process of making pre-mRNA using part of the DNA as a template.

• DNA helicase acts on a specific region of the DNA molecule to break the hydrogen bonds between the bases, causing the two strands to seperate
• The enzyme RNA polymerase moves along one of the template strands causing individual complementary nucleotides to join
• The exception is adenine links to uracil, rather than thymine
• When the RNA polymerase reaches a particular sequence of bases on the DNA that it recognises as a 'stop' triplet code, it detaches, and the production of pre-mRNA is complete.

The pre-mRNA is modified to mRNA by removing the introns by a process called splicing. These mRNA molecules leave via the nucleur pores.

The mRNA is used as a template to which complementary tRNA molecules attach and the amino acids that they carry are linked to form a polypeptide.

• A ribosome attaches to the starting codon at one end of the mRNA molecule.
• The tRNA molecule with the complementary anticodon sequence moves to the ribosome and pairs up with the sequence on the mRNA - carrying an amino acid
• The ribosome moves along the mRNA, bringing together two tRNA molecules at any one time
• By means of an enzyme and ATP, the two amino acids on the tRNA are joined by a peptide bond
• When another tRNA molecule joins, the first tRNA is released from its amino acid and is free to collect another amino acid
• This process continues until a complete polypeptide chain is built and when the ribosome reaches a stop codon

The codons on mRNA determine the order in which the tRNA molecules line up.

Individual nucleotides of DNA are made up of three components; deoxyribose sugar, phosphate group and organic bases. They are combined as a result of condensation reactions. The uprights of phosphate and deoxyribose sugar wind around one another to form a double helix and form the structural backbone of the DNA molecule. Adenine is said to be complementary to thymine and guanine is said to be complementary to cytosine. They are joined by hydrogen bonds.

Genes are sections of DNA that contain the coded information for making polypeptides. Amino acids have three bases coding for it and they are called a triplet code. The code is known as 'degenerate' because most amino acids have more than one triplet code. The code is non-overlapping and universal where it is the same in all organisms.

Semi-conservative replication is where one strand of DNA acts as a template to build a new strand. DNA helicase break the hydrogen bonds, causing the strands to seperate and individual complementary nucleotides are joined with DNA polymerase.

Substitution of bases is when a base in a nucleotide is replaced with another.

• A nonsense mutation occurs if the base change results in the formation of a stop codon and the protein would almost certainly be significantly different
• A mis-sense mutation arises when the base change results in a different amino acid being coded for. This may determine the tertiary structure of the protein and is may no longer function
• A silent mutation occurs when the substituted base still codes for the same amino acid due to its degenerative nature. This means the mutation has no effect

A gene mutation by deletion arises when a nucleotide is lost from a normal DNA sequence. This causes a frame shift in the triplet code.

Mutation is increased by outside factors known as mutanic agents, i.e. high energy radiation. It can disrupt cell division which is controlled by proto-onogenes (that stimulate cell division) and tumour supressor genes (which slows cell division).

Mitosis produces two daughter nuclei that results in each of them having an exact copy of the DNA of the parent cell. There are five main stages;

• Interphase (DNA is replicating and the cell is actively synthesising proteins)
• Prophase (Chromosomes become visible and the nuclear envelope disintegrates)
• Metaphase (Chromosomes arrange themselves at the equator of the cell and a spindle forms)
• Anaphase (Spindle fibres are attached to the chromatids which contract and cause the chromatids to be pulled towards their poles)
• Telophase (Nucleur envelope reforms and the spindle disintegrates)

Mitosis is important for growth as it ensures that the new cells possess the same genetic information, differentiation as they develop into groups of specialised cells and repair so that new cells are produced with identifcal structure and function to the ones that have been lost.

Meiosis produces four daughter nuclei, each with half the number of chromosomes as the parent cell. During this process, the chromosome pairs seperate so that only one chromosome from each pair enters each gamete. This is known as the haploid number of chromosomes which in humans is 23. When two haploid gametes fuse at fertilisation, the diploid number of chromosomes is restored. Meiosis involves two nucleur divisions;

• In meiosis 1, the homologous chromosomes pair up and their chromatids wrap around each other. The pairs are seperated, with one chromosome from each pair going into one of the two daughter cells.
• In meiosis 2, the chromatids move apart where four cells have been formed.

Meiosis produces genetic variation. Independent segregation of homologous chromosomes is when the homologous pairs are lined up at random, so that the combination of chromosomes that goes into the daughter cell in meiosis 1 is also random. Genetic recombination by crossing over is when the chromatids cross over one another many times and the broken off portions recombine with another.

Speciation is the evolution of new species from existing species. The environment creates a selection pressure where individuals with the advantegeous alleles are more likely to survive competition and successfully reproduce.

It depends on groups within a population becoming isolated in some way. An example of this is geographical isolation. This occurs when physical barriers prevent two populations from breeding with one another.

• A species can form a single gene pool and occupy a particular area.
• Climatic changes can reduce the size of the area to form two isolated regions in which the species cannot come into contact.
• Further climatic changes result in species from one area adapating to these new conditions and the same occurs with the other region - which environment can differ.
• Continued adaptaion leads to evolution of new species.
• The two groups of species are no longer capable of interbreeding as they have become two different species, each with its own gene pool.

Pyruvate is actively transported into the matrix of the mitochondria where the link reaction takes place. The molecule is oxidised by removing hydrogen which is then accepted by NAD to form reduced NAD. This new 2-carbon molecule, called an acetyl group, combines with a molecule called coenzyme A to produce a compound called acetylcoenzyme A. A carbon dioxide molecule is formed from each pyruvate.

During the Krebs Cycle, the following happens;

• The 2-carbon acetylcoenzyme A combines with a 4-carbon molecule to produce a 6-carbon molecule.
• It loses carbon dioxide and hydrogens to give a 4-carbon molecule and ATP is produced as a result of substrate-level phosphorylation.
• The 4-carbon molecule can now combine with a new acetylcoenzyme A.

For each molecule of pyruvate, the overall produce is reduced coenzymes, one molecule of ATP and three molecules of carbon dioxide.

The electron transport chain is a mechanism by which the energy of the electrons within the hydrogen atoms is converted into a form that cells can use - ATP. It occurs in the cristae of the mitochondria.

• Hydrogen atoms produced during Glycolysis and Kreb's cycle combine with coenzymes that donate the electrons of the hydrogen atoms they are carrying to the first molecule in the electron transport chain.
• This releases the protons from the hydrogen atoms and these are actively transported across the inner mitochondrial membrane.
• The electrons pass along a chain of electron transport carrier molecules in a series of oxidation-reduction reactions. The electrons lose energy as they pass down the chain. This energy is used to combine ADP and inorganic phosphate to make ATP.
• The protons accumulate in the space between the membranes before they diffuse back into the matrix.
• At the end of the chain, the electrons combine with these protons and oxygen to form water as oxygen is the final electron acceptor.

The main features of sensory reception are that they are specific to a single type of stimulus and that they are able to produce a generator potential by acting as a transducer.

Pacinian corpuscles respond to changes in mechanical pressure and are mainly located on our skin. When pressue is applied, it changes shape and the membrane  becomes stretched. This causes the stretch-mediated sodium channels to open and the influx of sodium ions changes the potential of the membrane, producing a generator potential.

Photoreceptors are found on the the retina of the eye. Rod cells show summation and convergence. There is a greater chance of the threshold being exceeded so they are sensitive to low light intensities. They have a low visual acuity as they share a single bipolar neurone. Each cone cell has its own connection to a single bipolar neurone so the brain can distinguish exactly where the light was hit on the retina. They do not show summation or convergence. Only light of high intensity will be able to exceed the threshold value for a generator potential to be created.

The resting potential is when the inside of the axon is negatively charged relative to the outside. In this condition, the axon is said to be polarised (-65mv). Sodium ions are actively transported out of the axon whilst potassium ions are actively transported into the axon by the sodium-potassium pumps. An equilibruim is reached where the chemical and electrical gradients are balanced and there is no net movement of ions.

When a stimulus is recieved by a receptor, it's energy causes a temporary reversal of the charges on the axon membrane. This is known as the action potential and the membrane is said to be depolarised. Sodium voltage-gated channels open and once the action potential of +40mv has been established, the voltage gates close. The potassium voltage-gated channels open and causes repolarisation of the axon. The refractory period consists of the cation pump using active transport to restore the membrane to a resting potential.

Nerve impulses are described as an all-or-nothing response where there is a certain level of stimulus, called the threshold value, which triggers an action potential. Passage is quicker along a myleinated axon due to saltatory conduction.

A synapse is the point where the axon of one neurone connects with the dendrite of another or with an effector. They transpit impulses by the means of neurotransmitters.

• The arrival of an action potential causes calcium channels to open.
• The influx of calcium ions causes the synaptic vesicles to fuse with the presynaptic membrane, releasing acetycholine into the synaptic cleft.
• Acetylcholine molecules fuse with receptor sites on the sodium ion channel in the membrane of the postsynaptic neurone.
• This causes sodium channels to open and the influx of sodium ions generates a new action potential in the postsynaptic membrane.
• Acetylcholinerase hydrolyses acetycholine into choline and ethanoic acid which diffuse back across the synaptic cleft where ATP is released by the mitochondria to recombine these substances into acetycholine.

A neuromuscular junction is the point where a neurone meets a skeletal muscle fibre. Their transmission of an impulse is the same process.

A synapse is the point where the axon of one neurone connects with the dendrite of another or with an effector. They transpit impulses by the means of neurotransmitters.

• The arrival of an action potential causes calcium channels to open.
• The influx of calcium ions causes the synaptic vesicles to fuse with the presynaptic membrane, releasing acetycholine into the synaptic cleft.
• Acetylcholine molecules fuse with receptor sites on the sodium ion channel in the membrane of the postsynaptic neurone.
• This causes sodium channels to open and the influx of sodium ions generates a new action potential in the postsynaptic membrane.
• Acetylcholinerase hydrolyses acetycholine into choline and ethanoic acid which diffuse back across the synaptic cleft where ATP is released by the mitochondria to recombine these substances into acetycholine.

A neuromuscular junction is the point where a neurone meets a skeletal muscle fibre. Their transmission of an impulse is the same process.

The process of contraction involves the actin and myosin filaments sliding past one another and is called the sliding filament mechanism. The evidence for this is due to that when the muscles are contracted, the sarcomere shortens and the I bands and H zone becomes narrower.

• Calcium ions released from the endoplasmic reticulum cause the blocking tropomyosin molecule to pull away from the binding sites on the actin molecule.
• The myosin head can now attach to the binding site and form cross-bridges.
• With the use of ATP, the head of the myosin changes angle (45 degrees), moving the actin filament along as it does so. ATP molecule fixes to the myosin head, causing it to detach from the actin filament.
• Hydrolysis of ATP to ADP by ATPase provides the energy for the myosin head to resume its normal position where it then reattaches to the binding site further along the actin filament and the cycle repeats.

Phosphocreatine can be used to regenerate ATP rapidly in anaerobic conditions.

The process of contraction involves the actin and myosin filaments sliding past one another and is called the sliding filament mechanism. The evidence for this is due to that when the muscles are contracted, the sarcomere shortens and the I bands and H zone becomes narrower.

• Calcium ions released from the endoplasmic reticulum cause the blocking tropomyosin molecule to pull away from the binding sites on the actin molecule.
• The myosin head can now attach to the binding site and form cross-bridges.
• With the use of ATP, the head of the myosin changes angle (45 degrees), moving the actin filament along as it does so. ATP molecule fixes to the myosin head, causing it to detach from the actin filament.
• Hydrolysis of ATP to ADP by ATPase provides the energy for the myosin head to resume its normal position where it then reattaches to the binding site further along the actin filament and the cycle repeats.

Phosphocreatine can be used to regenerate ATP rapidly in anaerobic conditions.

All membranes around and within cells have the same basic structure and are known as plasma membranes. It controls the movement of substances in and out of a cell. Phospholipids form a bilayer sheet which consists of the hydrophilic heads pointing inwards and the hydrophobic tails pointing inwards.

Proteins are embedded in the phospholipid bilayer in two main ways. Extrinsic proteins occur on the surface or partly embedded whilst intrinsic proteins completley span the phospholipid bilayer. The functions of these proteins in the membrane are;

• Provide structural support
• Act as carriers transporting water-soluble substances across the membrane
• Allow active transport across the membrane by forming ion channels
• Form recognition sites (glycolipids) e.g. cholera toxins
• Act as receptors (glycoproteins) e.g. hormones

The arrangement of these molecules is known as the fluid-mosaic model as it flexible and the proteins vary in shape, size and pattern. Cholesterol adds strength.

Diffusion is the net movement of molecules/ions from a region where they are more highly concentrated to one where their concentration is lower. Facilitated diffusion is where it occurs on a point on a plasma membrane and can involve carrier proteins. The factors that affect the rate of diffusion are the concentration gradient, surface area and thickness of the exchange surface.

Osmosis is the passage of water from a region where it has a higher water potential to a region where it has a lower water potential through a partially permeable membrane. A dynamic equilibrium is established when the water potentials are equal and there is no net movement of water. When a great amount of water enters a cell, it swells and burst whilst if a great amount leaves, the cells shrink. In plant cells however, they have a cell wall which means that they either become turgid or become plasmolysed.

Active transport is the movement of molecules/ions from a region of lower concentration to a region of higher concentration using ATP and carrier molecules. Examples of this process include the sodium-potassium pump/cation pump.

Mammals is a double circulatory system in which the blood is returned to the heart to increase its pressure before it is distrubuted to the rest of the body. It is essential that the oxygenated blood is seperated from the deoxygenated blood. Between each atrium and ventricle are valves that prevent the backflow of blood into the atria when the ventricles are contracting. Each of the four chambers are served by large blood vessels; the aorta, vena cava, pulmonary artery and the pulmonary vein. The heart muscle is supplied by its own blood vessels called coronary arteries. The cardiac cycle consists of three stages; diastole in which the the heart is relaxed, atrial systole where the atria contracts and ventricular systole where the atrioventricular valves close, the semi-lunar valves open and the ventricles contract.

Blood passed along narrow capillaries creates a hydrostatic pressure. It forces tissue fluid out of the blood plasma. This pressure only causes small molecules to leave the capillaries, leaving all cells and proteins in the blood. This is called ultrafiltration. Most tissue fluid returns to the blood plasma via capillaries. The remainder is carried back via the lymphatic system and these drain their contents back into the bloodstream via two ducts that join veins close to the heart.

Most gaseous exchange occurs in the leaves, which have certain adaptations for rapid diffusion. They have a thin, flat shape to provide a large surface area, they have many small pores called stomata and numerous interconnecting air-spaces.

Water moves via osmosis from the soil solution into the root-hair cells down a water potential gradient. After being absorbed into the root-hair cell, water continues its journey across the root in two ways. The symplastic pathway takes place across the cytoplasm of the cells of the cortex as a result of osmosis. A water potential gradient is set up across all the cells of the cortex, which carried water along the cytoplasm from the root-hair cell to the endodermis. Due to the cohesive properties of the water molecules, it creates a tension that draws water along the cell walls of the cells of the root cortex. This is known as the apoplastic pathway. It reaches a waterproof band that makes up the Casparian ***** which forces water to join the water that has arrived via the symplastic pathway. Active transport of salts is the mechanism in which water gets into the xylem as it creates a force called the root pressure. Water is pulled up the xylem as a result of transpiration. This is called the transpiration pull.

There are four main stages in the nitrogen cycle;

• Ammonification is the production of ammonia from organic ammonium-containing compounds. Saprobiotic microorganisms feed on these materials which release ammonia that forms ammonium ions in the soil.
• Nitrification is carried out by free-living soil microorganisms called nitrifying bacteria that convert the ammonium ions into nitrate ions. They require oxygen to carry out these conversions.
• Nitrogen fixation is a process by which nitrogen gas is converted into nitrogen-containing compounds. Free-living nitrogen-fixing bacteria reduce gaseous nitrogen to ammonia which they then use to manufacture amino acids. Nitrogen-rich compounds are released when they decay. Mutualistic nitrogen-fixing bacteria live in nodules on the roots of plants which fix the nitrogen, transforming it into a useful form.
• Denitrification is when soil nitrates are converted by anaerobic denitrifying bacteria into gaseous nitrogen which reduces its availability to plants.

The carbon cycle describes the flow of carbon between the living and non-living components of the environment. The process is described below;

• The carbon is taken up by producers for photosynthesis.
• When the producer is eaten, the carbon passes into consumers and then further along the food chain.
• The consumers respire, which releases carbon dioxide back into the atmosphere.
• When the producers and consumers die, their complex molecules are broken down by saprobiotic microorganisms.
• When these microorganisms decay, it releases carbon back into the atmosphere.
• If decay was prevented, fossil fuels are formed. However, when these are burnt by a process called combustion, carbon dioxide is also released back into the atmosphere and dissolved into the oceans.

The level of carbon dioxide has increased due to human activities, i.e. deforestation.

Succession is the term used to describe how ecosystems change over time as well as the species that occupy that area.

The first stage of sucession is the colonoisation of an inhospitable environment by organisms called pioneer species. They often have features that suit them to colonisation. Succession takes place in a series of stages where at each stage, certain species can be identified which change the environment and the soil. This makes it more suitable for other species. These other species may then out-compete the species in the existing community and so a new community is formed.

The environment eventually reaches a state where many species flourish and this is called the climax community. During any succession, there are a number of common features that emerge. The non-living environment becomes less hostile and as the soil forms, there are plentiful nutrients and plants provide shelter. This leads to a greater number and variety of habitats that in turn produce increased biodiversity, more complex food webs and an increased biomass.

The major parts of the digestive system are the oesophagus, stomach, small intestine, large intestine, rectum, salivary glands and the pancreas. Food is physically broken down by means of structures such as the teeth and is then churned by the muscles in the stomach wall. All digestive enzymes function by hydrolysis. Carbohydrases break down carbohydrates into monosaccharides. Lipases break down lipids into glycerol and fatty acids. Proteases break down proteins into amino acids

Salivary and pancreatic amylase hydrolyses starch into maltose. The epithelial lining of the small intestine produces the enzyme maltase which then hydrolyses maltose into alpha glucose. These molecules are then incorporated into bodies tissues to be used in processes within the body. This is called assimilation. Glucose can diffuse into the epithelial cells or it can be transported by co-transport. It is the process in which it entails glucose being drawn into the cells along with sodium ions that have been actively transported out by the sodium-potassium pump.  

Carbohydrates are made up of carbon, oxygen and hydrogen. When monosaccharides join, a water molecule is removed in a condensation reaction and a glycosidic bond is formed. When water is added to a disaccharide, it breaks the glycosidic bond and releases the monosaccharides. This is called hydrolysis. Reducing sugars can be tested by using Benedict's reagent where it is heated with an equal volume of food sample. If reducing sugar is present, the solution will turn orange-brown.

Starch is detected by iodine by a blue-black colouration. Starch is made up of a chain of alpha glucose monosaccharides linked by glyosidic bonds that are formed by condensation reactions. The unbranced chain is wound into a tight coil that makes the molecule very compact. The main role of starch is for energy storage and is never found in animal cells. Glycogen is very similar in structure to starch but has shorter chains and is more highly branched. It is the major storage product of animals. Cellulose has straight unbranched chains of beta glucose molecules that run parralel to each other, allowing hydrogen bonds to form cross-linkages. It is a major component of plant cell walls and provides rigidity.

Amino acids are the basic monomer units which combine to form a polypeptide. An amino acid is made up of four groups. These are an amino group, carboxyl group, hydrogen atom and R group. Through a series of reactions, many amino acid monomers can be joined together in a process called polymerisation.

• The primary structure of a protein is the sequence of amino acids found in its polypeptide chains. It determines its shape and properties.
• The secondary structure is the shape which the polypeptide chain forms as a result of hydrogen bonding - commonly a spiral known as an alpha helix.
• The tertiary structure is due to the bending and twisting of the polypeptide helix into a compact structure. Disulfide, ionic and hydrogen bonds contribute to the maintenance of the tertiarty structure.
• The quartenary structure arises from the combination of different polypeptide chains into a large, complex protein molecule.

Fibrous proteins have structural functions whilst globular functions carry out metabolic functions.

Cells can either be eukaryrotic or prokaryotic. An epithelial cell is an example of a eukayrotic cell and consists of the following organelles;

• Nucleus that acts as the control centre of the cell where mRNA is produced, and retains the genetic material in the form of DNA.
• The mitochondrion are the sites of certain stages of respiration. They are responsible for the production of ATP.
• Endoplasmic reticulum can either have ribosomes present on their membranes or lack ribosomes. The rough endoplasmic reticulum provides a large surface area for the synthesis of proteins and provide a pathway for the transport of materials. Smooth endoplasmic reticulum synthesise, store and transport lipids and carbohydrates.
• Golgi apparatus form glycoproteins and form lysosomes.
• Lysosomes are used in phagocytosis and digest worn out organelles.
• Ribosomes are important in protein synthesis.

These organelles can be seperated by ultracentrifugation.

Lipids contain carbon, hydrogen and oxygen. They are insoluble in water but are soluble in organic solvents. The main groups of lipids are triglycerides (fats and oils), phospholipids and waxes. The main role of lipids is in plasma membranes. Their other roles include;

• An energy source (when oxidised, they provide more energy)
• Waterproofing (can be useful in conserving water)
• Insulation (they are slow conductors of heat and can retain body heat)
• Protection (fats are often stored around delicate organs)

Triglycerides are so called because they have three fatty acids combined with glycerol. Each fatty acid forms a bond with glycerol in a condensation reaction. If the chain has no carbon double bonds, the fatty acid is described as saturated. If there is a single double bond, it is mono-unsaturated. Phospholipids are similar except that one fatty acid is replaced by a phosphate molecule.

The test for lipids is known as the emulsion test.

Enzymes are biological catalysts that work by lowering the activation energy level required to kickstart a reaction. Only a small region of an enzyme is functional and this is called the active site. When a substrate has a complementary shape to that of the active site, enzyme-substrate complexes can be formed. A model proposes that enzymes work in the way way as a key operates a lock; having a specific shape that fits and operates only one active site. This is known as the lock and key model. The induced fit model of enzyme action states that the enzyme is flexible and can change its shape in order to mould the substrate.

A rise in temperature increases the kinetic energy of molecules, so there are more frequent collisions and more enzyme-substrate complexes are formed. However, when the temperature reaches above the enzyme's optimum, it becomes denatured. A change in pH can alter the charges on the amino acids that make up the active site and cause the bonds that maintain the tertiary structure to break.

Competitive inhibitors bind to the active site of the enzyme whilst non-competitive inhibitors bind to the enzyme at a position other than the active site.

Exchange surfaces must have the following characteristics. They have a large surface area to volume ratio, they are very thin, partially permeable and that there is a movement of both the internal and environmental medium. The relationship between these factors can be described in an expression known as Fick's Law. In humans, breathing movements constantly ventilate the lungs and the action of the heart constantly circulates blood around the alveoli. This ensures that a steep concentration gradient of carbon dioxide and oxygen is maintained so that diffusion can take place.

In insects, the respiratory gases move in and out of the tracheal system along a diffusion gradient from the atmosphere along the tracheoles to the cells and by ventilation. Gases enter and leave trachae through tiny pores called spiracles that may be opened and closed with a valve. In fish, their gills made up of gill filaments where at right angles to these structures, are lamellae that increase the surface area. The flow of water and blood are in opposite directions and is known as a countercurrent flow. A constant rate of diffusion is able to be maintained across the length of the gill lamellae.

Our natural defences and phagocytosis make up our non-specific response where phagocytes engulf pathogens to form a phagosome and lysosomes release their lytic enzymes to break down the bacterium. However our specific response consists of two main ways;

• T lymphocytes respond to antigens that are attached to a body cell and this response is called cell-mediated immunity. Receptors on T helper cells fit onto the antigens that are placed on the enguled phagocyte's membrane and this stimulates cloned T cells to develop into memory cells, phagocytosis, division of B cells and it kills infected cells.
• Humoural immunity involves antibodies and they work within body fluids. Antibodies attach to complimentary antigens that stimulate B cells to divide by mitosis to form clones of identical cells. They also produce plasma cells that secrete antibodies directly and memory cells that circulate in preparation for another encounter.

Single types of antibodies can be isolated and cloned to form monoclonal antibodies.

Conduction occurs mainly in solids. Convection occurs in fluids. Radiation is the transfer of energy through electromagnetic waves. Ectotherms gain most of their heat from the environment and so their body temperature fluctuates with that of the environment. They can control their body temperature by exposing themselves to the Sun, taking shelter, gaining warmth from the ground, generating metabolic heat and colour variations.

Endotherms gain most of their heat from internal metabolic activities. In order to gain heat, vasconstriction takes place where the diameter of the aterioles near the surface of the skin is made smaller to reduce the volume of blood reaching through to the capillaries. We also use shivering, raising of hair and increase our metabolic rate. In order to lose, vasodilation takes place where the diameter of our arterioles become larger so that heat from blood can transferred to the environment via radiation. We also sweat, lower our body hair and use behavioural mechanisms. The hypothalamus monitors the temperature of our blood. Thermoreceptors send impulses along the autonomic nervous system to provide information to the heat gain or loss centre so that appropriate measures can take place to conserve or lose heat.

Germ-line gene therapy involves replacing or supplementing the defective gene in the fertilised egg. This is currently prohibited so we use somatic-cell gene therapy that targets just the effected tissues but has limited success. Its aim is to introduce cloned normal genes into epithelial cells of the lungs for cystic fibrosis sufferers.

Cystic fibrosis is caused by a deletion mutation. This deletion results is enough to make the protein unable to perform its role of transporting chloride ions across epithelial membranes. This prevents osmosis and leaves the membranes dry and the mucus that they produce remains viscous and sticky.

Adenoviruses can be used and are made harmless by interefering with a gene involved in their replication. The CFTR gene is incorporated and the viruses inject their DNA into the epithelial cells of the lungs. Genes can also be wrapped in lipid molecules as they can pass relatively easily into the phospholipid membrane. The recombinant plasmids are wrapped in lipid molecules and are used in a nasal spray.

Isolation - Reverse transcriptase is used to form complementary DNA from the mRNA produced fom the required gene. Resctriction endonucleases have recognition sequences that cut DNA to produce blunt or sticky ends.

Insertion - The fragment of DNA is placed into a plasmid which is a common vector. The same restriction endonucleases are used so that the sticky ends can join by DNA ligase to produce a recombinant plasmid.

Transformation - Plasmids and bacterial cells are placed in a medium containing calcium ions and the temperature is changed so that the membranes of the bacteria are made permeable and the plasmids can be taken up.

Idenfitication - The host cells that have successfully taken up the gene are identified by using gene markers. Antibitoic-resistance markers are used by a technique called replica plating. Fluroscent and enzyme markers are also used. Host cells are grown on a large scale by polymerase chain reaction.

A DNA probe is a short, single-stranded section of DNA that has some sort of label attached that makes it easily identifiable. They can be radioactive or fluroscent. It has complementary bases to the portion of DNA that we want to find and is involved in DNA hybridisation.

Sanger method is used to sequence the exact order of nucleotides in a section of DNA. Four different terminator nucleotides are used and depending on where the terminator nucleotide binds to the template, the DNA fragments will vary in lengths.

Gel electrophoresis is then used where these fragments are placed onto an agar gel and a voltage is applied across it. The resistance of the gel means that the larger the fragments, the slower that they move.

Larger genes must be cut into smaller fragments by restriction endonucleases and each fragment must be sequenced. This can be done using restriction mapping where the distance of the recognition sites can be determined by the patterns of fragments that are produced.

Genetic fingerprinting technique replies upon the fact that the genome of any organism contains many repetitive, non-coding bases of DNA. It consists of five main stages;

• Extraction is where the DNA is seperated by the rest of the cell and its quantity can be increased by using the polymerase chain reaction.
• Digestion is when the DNA is then cut into fragments by using restriction endonucleases.
• Seperation is when the fragments are seperated according to size by gel electrophoresis under the influence of an electrical voltage. It is immersed in alkali to seperate the strands into single strands. A technique called Southern blotting occurs where the single strands are transferred onto a nylon membrane.
• Hybridisation is when radioactive DNA probes are used to bind with the core sequences.
• Development is the final stage where an x-ray film is put over the nylon membrane and is series of bars are exposed which can be used to compare.

• Follicle-stimulating hormone (FSH) stimulates the development of follicles
• Luitenising hormone (LH) causes ovulation to occur
• Oestrogen causes the rebuilding of the uterus lining after menstruation
• Progesterone maintains the lining of the uterus in readiness for fertilisation

The menstrual cycle begins when the uterus lining is shed. The pituitary gland releases FSH into the blood which stimulates follicles in the ovary to grow. The growing follicles secrete small amounts of oestrogen. The level of oestrogen increases until a critical point is reached where it stimulates the pituitary gland to release more FSH and LH. This is an example of positive feedback. The surge in LH causes ovulation and it stimulates the empty follicle to develop into a corpus luteum. This structure secretes progesterone but inhibits the release of FSH and LH. This is an example of negative feedback. If the egg is not fertilised, the corpus luteum degenerates and progesterone is no longer produced. The uterus lining breaks down and FSH is no longer inhibited. It is released and the cycle repeats.

Pulmonary fibrosis arises when scars form on the epithelium of the lungs, causing them to become irreversibly thickened. This increases the diffusion pathway and it also reduces the elasticity of the lungs. It creates a shortness of breath, chronic cough, pain in the chest and fatigue. Asthma is a localised allergic reaction which causes white blood cells on the linings of the bronchioles to release histamine. The lining of these airways become inflamed and constricted and the epithelial cells secrete larger quantities of mucus. The symptoms of asthma are that there is a difficulty in breathing, wheezing, tight feeling in the chest and coughing.

Emphysema is caused by smoking and is when the elastin has become permanently stretched and the lungs are no longer able to force out all the air from the alveoli. The surface area is reduced and leads to shorteness of breath, chronic cough and a bluish skin colouration.

Pulmonary tuberculosis is a bacterium spread through the air by droplets and destroy the tissue of the lungs and results in cavities where the lung repairs itself.

Artheroma is a fatty deposit that forms within the wall of an artery. It is accumulations of white blood cells that have taken up low-density lipoproteins (LDL's). They bulge into the lumen, causing is to narrow so that the blood flow is reduced.If an artheroma breaks through the lining of the blood vessel, is may result in the formation of a blood clot or thrombus. This may block the vessel, reducing or preventing the supply of blood to tissues beyond it.

Artheromas that lead to a thrombus can weaken the artery walls. These weakened points swell to form a blood-filled structure called an aneurysm. They frequently burst, leading to haemorrhage. A blockage in the coronary artery can result in a myocardial infarction, or commonly known as a heart attack.

Coronary heart disease occurs in the coronary arteries and can be increased by a number of factors. Carbon monoxide in cigarettes combine easily with haemoglobin which reduces its oxygen-capacity and the nicotine stimulates adrenaline that increases heart rate and pressure. Diet and blood cholesterol can also impact.

The regulation of blood glucose is an example of how different hormones interact in achieveing homeostasis. They function in one way called the second messenger model where a hormone-receptor complexes activates an enzyme that produces a chemical that acts as a second messenger. The cells that produce hormones are known as islets of Langerhans. Alpha cells produce the hormone glucagon and beta cells produce the hormone insulin.

Blood glucose comes from diet, the breakdown of glycogen called glycogenolysis and from gluconeogenesis where glucose is produced from other sources. The beta cells detect a rise in blood glucose level and secrete insulin directly into the blood plasma. It is lowered by increasing the rate of absorption of glucose, increasing the respiratory rate, increasing the rate of conversion of glucose into glycogen by glycogenesis and increasing the rate of converstion of glucose to fat. The alpha cells detect a fall in blood glucose and secrete glucagon. They increase the amount of glucose in the blood by activating an enzyme that concerts glycogen to glucose and increasing the conversion of amino acids and glycerol into glucose by gluconeogenesis. Adrenaline can also raise the blood glucose level.

The stimulation of the sinoatrial node that determines the beat of the heart and is referred to as the pacemaker. A wave of electrical activity spreads out from the SAN and is recieved by the AVN. After a short delay, the AVN conveys a wave of electrical activity along the bundle of His which conducts the impulse through the Purkinje fibres. This is then released, causing the ventricles to contract.

Exercise has the following effects on cardiac output:

• Increased muscular contraction increases the production of carbon dioxide which lowers the blood pH
• Chemoreceptors in the walls of the carotid arteries that increases the frequency of impulses to the medulla oblongata
• The cardio-acceleratory centre increases the frequency of impulses to the sinoatrial node via the sympathetic nervous system
• The sinoatrial node increases to increase blood flow

Baroreceptors detect change in blood pressure.