User:OldakQuill/Revision/Biology

10.1 - The cell is the basic unit of structure in prokaryotic and eukaryotic organisms

 * The main features of prokaryotic cells:
 * Cytoplasm, ribosomes (70S), nucleoid (no membrane), DNA (circular), plasmid, cell membrane, mesosome, cell wall (murein - gram stain), cell capsule, flagellum
 * One micrometre across, asexual and always unicellular
 * The structure of plant and animal cells as seen through an optical microscope:
 * Ten micrometres across
 * Can see organelles such as cell wall, cytoplasm, cell membrane, nucleus, vacuole, mitochondria, centriole, Golgi apparatus, chloroplast.

10.2 - The electron microscope and the technique of cell fractionation may be used to study ultrastructure

 * The principles and limitations of transmission and scanning electron microscopes:
 * Transmission EM fires beam through sample, Scanning EM shows surface
 * Works by beam of electrons being fired at sample, some are deflected and absorbed - density difference are noted as image reaches fluorescent screen. Vacuum is necessary
 * Disadvantages: sample needs to be dead, expensive, alteration through preservation, time consuming.
 * Resolution: 0.5 nm TEM, 5-20 nm in SEM.
 * Difference between magnification and resolution:
 * Magnification is how much larger something appears than in true life (mag = objective x eyepiece)
 * Resolution is ability to distinguish between two points
 * Interpreation of electron micrographs
 * Identification of principle features and organelles (and functions of) of a eukaryotic cell:
 * Cell wall: rigid to prevent bursting on osmosis. cellulose in plant, murein in prokaryote
 * Plasma membrane: partially permeable barrior controlling exchange
 * Nucleus: contains DNA, instructs protein synthesis and other activities.
 * Chloroplast: used in photosynthesis, produces sugars from light energy
 * Mitochondrion: produces energy. Site of cell respiration
 * Lysosome: breakdown of structures and molecules
 * Ribosome: protein syntehsis on endoplasmic reticulum
 * Endoplasmic reticulum: long structures. If rough covered in ribosomes. Transports protein.
 * Golgi apparatus: internal processing and transport system
 * Microvilli: increase surface area for absorbtion/secretion
 * Vesicles: enclosed packets involved in a variety of functions. Storage and transport.
 * Principle features of a bacterium
 * Cell wall: Murein, gram staining can test for type of wall.
 * capsule: outside cell wall - made of polysaccharides, protect.
 * genetic material: Not contained in nuclear envelope.
 * Principles of cell fractionation and ultracentrifugation as used to seperate cell components:
 * Place in cold (stop processes) isotonic (stop osmosis) buffer (maintain pH). Grind to open cells. Filter removes insoluble tissue. Centrifuge at 1000g for 10 minutes - nuclei, 10000g for 30 minutes - mitochondria and chloroplast, 100000g for 1 hour - ER, golgi, membrane; 300000g for 3 hour - ribosome.

10.3: The properties of plasma membranes are related to the passage of substances through them

 * Arrangement of phospholipids, proteins and carbohydrates in the fluid-mosaic model of membrane structure.
 * The hydrophilic head of phospholips faces outward (and is in contact with water; tails are hydrophobic and face toward centre. Two layers of these - proteins float in membrane - carbohydrates poke out from certain proteins. Proteins can be intrinsic (right through) or extrinsic - hydrophilic amino acids on outside, hydrophobic face lipids. Carbohydrates (glycoproteins when attached to protein) are involved in cell recognition and protection.
 * Diffusion and factors which determin it's rate. Fick's law - diffusion rate [proportional to] (surface area X difference in concentration)/thickness of exchange surface
 * Only lipid soluble molecules can - in very small amounts. It requires no energy and is uncontrollable
 * Osmosis as the movement of water from a solution of less negative water potential to a solution of more negative water potential through a partially permeable membrane.
 * Pure water has a water potential of 0psi - all solutions containing water "prefer" this. Water always falls from high to low water potential. The lower the water potential, the greater the osmotic pressure
 * The role of protein molecules and energy in active transport and facilitated diffusion
 * Active transport is requires a protein to "pump". Proteins are specific to molecules and the process requires energy. Only transport mechanism which can go up gradient
 * Facilitated diffusion, or passive transport, uses protein also - no energy is required. Only down concentration gradient. Channel (full of water) or carrier (bonding) proteins.
 * Endocytosis: Transport into cell by vesicle. For large ammounts of substance. Pinocytosis (for small substances) or phagocytosis may then occur.
 * Exocytosis: Transport out of cell by vesicle. Both require energy.

10.4: Large molecules are important in the structure and functioning of cells:

 * Biological molecules are based on a small number of chemical elements and frequently consist of monomers combined into polymers - carbon, oxygen, hydrogen, nitrogen. Also proteins are made of amino acids, which connect to form polypeptides. Nucleic acids are made of nucleotides which form polynucleotides. Carbohydrates are made of monosaccharides which form polysaccharides. Lipids are made of fatty acids and glycerol which form triglycerides.
 * Structure and properties of carbohydrates - sugars, monosaccharides are based on cyclohexane. Structural and storage. Famous include starch, glycogen, cellulose
 * Structures of [alpha]-glucose (cis) and [beta]-glucose (trans)
 * Glycosidic bonds - connect monosaccharides at hydroxyl groups
 * Benedict's reagent as a test for reducing sugars (2cm2 mixed with solution and heat to 95C - brick-red - green for little) and for non-reducing sugars (after acid hydrolysis - boiling with HCl, then same as above). Iodine or potassium iodide solution for starch (Orange -> blue-black)
 * Basic structure and function of:
 * Starch: plant storage - mix of amylose and amylopectine - amylase breaks down into maltose, then glucose
 * Glycogen: poly 1-4 glucose, storage in animals of energy. Highly branched - mobilised quickly.
 * Cellulose: plant cell walls - poly-1,4-[beta]-glucose. Can link to other chains to form rigid structure
 * Protein: made up of amino acid
 * General structure pf amino acids is: NH2CHRCOO
 * Linking together of aa by peptide bonds (between C and N). Primary structure (aa sequence), Secondary structure (a-helix and b-sheet), Tertiary structure (globular protein), and Quaternary structure (several protein chains linking).
 * Relationship between tertiary structure and globular protein - shape and function: via hydrogen bonds, ionic bonds and sulphur bridges.
 * Biuret test for proteins: 2cm2 of solution to protein - turns lilac.
 * Structure of lipids to include only saturated triglycerides (between 3 fatty acids and a glycerol by ester bond - used for insulation and storage), unsaturated triglycerides (where fatty acids are unsaturated), and phospholipids (2 fatty acids, a phosphate and glycerol - may form micille or bilayer).
 * Emulsion test for lipids: Shake with ethanol, decant into water - this should form cloudy precipitate. Sudan III will turn lipids red.
 * Chromatography to illustrate how milecules can be sepearated and identified - pour solvent into sealed chromotraphy tank - allow gases to build, place drop of substance on chromatography paper near end label with pencil, place sheet into solvent so origin just above solution, remove once near top of paper - may need to stain chromatogram to make clear (such us ninhydrin for amino acids to purple), measure distances of spots.
 * Calculation and use of Rf value = dist. moved by spot/dist moved by solvent.
 * Two-way chromatography: turn 90 degrees and repeat.

10.5 - Enzymes are proteins which control biochemical reactions in cells

 * Protein nature of enzymes: most acts as scaffolding to active site, amino acids at active site hold substrate in position.
 * Enzymes as catalysts lowering activation energy through the formation of an enzyme-substrate complex - lower activation energy by stabilising transition state
 * Lock and key enzyme model: Substrate exactly fits into active site, the site then changes altering molecule - lowering activation energy. For example, may pull bond making easier to brake - or increase pH.
 * Induced fit enzyme model: active site distorts and fits around substrate inducing transition state - lowering activation energy.
 * Effects of the following on enzyme activity:
 * Temperature: optimum temperature - steadily rises to this, dramatically drops due to denatureing of enzymes.
 * pH: optimum pH also - but rate at other pHs evenly fall around this,
 * Substrate concentration: Large linear increase initially - gets shallower after saturation point (though still gradually rises)
 * Enzyme concentration: Linear increase until flatens out (limitted by enzyme concentration - reacting with as many substrates per unit time possible).
 * Competitive inhibitors: Same structure of activation site as enzyme. So decreases rate.
 * Non-competitive inhibitors: Binds to another part of enzyme, so that active sites no longer fuse with substrate.

10.6 - Tissues contain similar cells, and organs are structures made of different tissues

 * Epithelial tissue: protective tissue for internal (and external) outer surface. A form of protection
 * Features of alveolar epithelium over which gas exchange takes place: Single cell thick, large surface area with blood vessels close by
 * Blood is specialised tissue containing a number of different cell types. Confined to recognition of:
 * Red blood cells: Nucleus-less cells with the purpose of carrying oxygen and other gases around the body. Contains haemoglobin - shape maximises surface area:volume.
 * Lymphocytes: a white blood cell, can be T cell or B cell. Play integral part in body defences.
 * Monocytes: A white cell with a single large nucleus - responsible for phagocytosis
 * Granulocytes: A white blood cell with a broken up nucleus - phagocytosis, allergic responses are some of their action
 * Structure of RBCs in relation to their transport function: RBCs do not have nuclei to maximise storage volume. Their surface is shaped to maximise surface:volume ratio. Haemoglobin attaches to oxygen to transport to muscle, etc. Shape means they can go through small capillaries.
 * Relationship between size and surface area to volume ratio: Shape is such that gas exchange is maximised with surroundings.
 * Blood vessels are organs
 * Structure of the following in relation to their function:
 * Arteries: Thick elastic tissue which allows for high pressure - carries blood from heart, small lumen, no valves, typically carries oxigenated blood, 0.1-10mm
 * Arterioles: Allows excahnge between tissues, single cell thick wall, low pressure, no valves - 8 micrometres
 * Veins: carry blood back to heart, thiner collagen-filled wall, lower pressure, many valves.

10.7 - The blood system is a mass flow system which moves substances from one part of the body to another. It is linked with exchange surfaces.

 * General pattern of blood circulation in a mammal - transport system, double circulatory system, veins and arteries.
 * Names of the following - carotid artery (head and neck), blood vessels entering and leaving the heart (vena cava to, aorta from), liver (hepatic artery and portal vein) and kidneys (renal vein and renal artery.
 * Structure of capillaries, importance in metabolic exchange - very thin cell walls with a lower pressure, many, pass through tight gaps.
 * Formation of tissue fluid and it's return ro the circulatory system. Details of lymphatic system not required. Substances exchanged between blood and cells. High hydrostatic pressure at artery end pushes plasma out - cells and large proteins stay in; substances are then exchanged between cells and tissue fluid; at vein end low pressure so water enters blood by osmosis - as well as solutes (gases, urea and salts) diffuse in; excess tissue fluid enters lymph vessels.
 * Gross structure of human gas-exchange system: double-circulatory, pulmonary artery and pulmonary vein, alveoli, bronchi, muscles
 * Exchange of respiratory gases in the lungs: Oxygen diffuses into blood, CO2 out of blood. Other gases are simply eejected. Steep conc. gradient due to blood flow
 * Fick's law provides an effective framework for consideration of how the maximum rate of diffusion of respiratory gases is achieved. Details of transport of oxygen and carbon diocide in the blood are not required.
 * Mechanism of ventilation and it's nervous control: Inspiration - diaphragm contracts and flattens outward, external intercostal muscles contract ribs out, incrase in volume of thorax, increase in alveolar volume, pressure drops (Boyle's law), air flows in to equalise pressure; Expiration - diaphragm relaxes and curves, external intercostal muscles relax, thorax volume decreases, alveolar volume decreases, pressure increases, air flows out.
 * Composition of inhaled air and exhaled air. Respiratory centre detects too low oxygen and too high carbon dioxide - chemoreceptors detect this (and accompanying pH change.
 * The role of the medulla and the phrenic nerves in generating a basic breathing rhythm - stretch receptors control exhalation by vagus nerve. Phrenic nerve controls diaphragm, intercostal nerve controls intercostal muscles. Medulla can tell when stretch receptors and chemoreptors stimulated.

10.8 - The functioning of the heart plays a central role in the circulation of blood and relates to the level of activity of an individual

 * Gross structure of the human heart and its relation to function: vena cava flows into right atrium which connects to right ventricle by tricuspid valve. Then enters pulmonary artery via pulmonary valve; reenters left atrium by pulmonary vein goes through mitral valve to left ventricle blood then flows to rest of body via aorta after passing though aortic valve.
 * Pressure and volume changes and associated valve movements during the cardiac cycle - Atrial systole occurs where the blood flow into the atria due to SAN contraction; ventricular systole occurs when ventricles contract due to atrioventricular node, distole occurs when all four chambers of the heart relax - allowing atra to fillwith blood.
 * Myogenic stimulation of the heart and transmission of a subsequent wave of electrical activity - from SAN to AVN
 * Roles of sinoastrial node, atrioventricular node and bundle of His - cause ventricle to contract.
 * Cardiac output as the product of heart rate and stroke volume.
 * Pulmonary ventilation as the product of tidal volume and breathing rate
 * Changes in cardiac output and pulmonary ventilation with exercise: all aspects are controlled (volume and rapidity) - allows greater speed of transport by cardiovascular centre - attached to temperature receptors, chemoreceptors, stretch receptors. Can control vasodilation and vasoconstriction. Synaptic nerve accelerates heart, parasynaptic nerve slows it.
 * Nervous control of heart rate in relation to changing demands - exercise -> increased muscle respirarion -> ^CO2 -> ^pH -> Chemoreceptors detect -> cardiovascular centre -> synaptic nerve -> SAN -> ^HR - same with breathing except to respiratory centre -> intercostal muscle and diaphragm.
 * Redistribution of blood flow in response to varying degrees of exercise - can be directed away from digestive system.
 * The relative stability of blood supply to the brain, kidneys and heart and the increase to skeletal muscle.

14.1 - Continuity is maintained by the transmission of genetic information from generation to generation

 * The process of meiosis emphasising the reduction in chromosome number (to 23) and the independent assortment of homologous chromosomes (pair of chromosomes seen during division, side-by-side), chiasma (a crossover) formation and the exchange of genetic material between homologous chromosomes.
 * Names of subdivisions of prophase I are not required.


 * Principles of Mendelian inheritance - solve problems involving any of the following four features presented as data derived from specific crosses or as pedigrees:
 * monohybrid crosses (TTxTt etc. 3:1) and dihybrid crosses (RrYy x RrYy, etc become RY|Ry|rY|ry and RY|Ry|rY|ry. 9:3:3:1)
 * multiple alleles - dominant and recessive in terms of phenotype
 * sex linkage (all genes along a chromosome are linked by chromosome - normally 500 to 1000 genes long)
 * codominance - where two alleles are expressed in phenotype - example is blood groups in humans
 * Autosomal linkage is not required.


 * Reasons why experimental results may be expected only to approximate Mendelian ratios: the allele is random - we can only predict ratio over large numbers. May be using too few samples.
 * Application of chi-squared test: X2 = [sumof](d2/x)

14.2 - Genetic and environmental factors influence variation between individuals

 * Need for random sampling and importance of chance in contributing to differences between samples: avoids bias towards pariticular traits, chance hopes to reflect actual numbers - all tries to reflect and be representative
 * Collection and display of data by means of appropriate graphical techniques: abiotic and biotic factors, standard deviation and index of diversity
 * Concept of normal distribution about the mean. Understanding of mean (average) and standard deviation (indication of spread of results) as a measure of variation in a sample
 * Calculation and interpretation of standard error (Standard errors provide simple measures of uncertainty in a value). Candidates will not be required to calculate standard deviation or standard error in answer to questions of written papers.
 * Variation exists between members of a species (due to random gene mutation)
 * Significance of meiosis in generating genetic variation (new combinations of genes)
 * Gene mutation. Restricted to substitution of base (triplet is replaced), addition of base (triplet is added) and deletion of base (triplet is removed).
 * Interaction of genetic and environmental factors resulting in the phenotype (produce continuous variation - a less well nourished individual will be shorter, for example)
 * Polygenic inheritance: (determined by a great number of genes, all interacting with each other)

14.3 - Selection can influence the frequency of alleles in a population

 * Gene pool: complete set of unique alleles in population or species
 * Hardy-Winberg equation and conditions under which it applies: infinite, randomly mating, diploid, no selection, no mutation, no migration (gene flow)
 * Calculation of allele, genotype and phenotype frequencies from equation (p2 + 2pq + q2 = 1)
 * Concept in change of allele frequency due to selection: abiotic factors favour certain traits - allowing them to fluorish
 * Following kinds of selection:
 * Directional selection: where one extreme is eliminated (giraffe necks) - moving to longer necks
 * Stabilising selection: both extremes are cut out, concentrating the mean
 * Disruptive selection: where mean is cut out, developing extremes (peppered moth?)
 * Examples of each - should include a study of the incidence of sickle-cell anaemia in relation to malaria and consideration of the evolution of resistance to pesticides and antibiotics as n example of the effect of human activities
 * Importance of reproductive isolation and speciation: latter caused by former - can be through geographic or sexual isolation - followed by seperating genotypes
 * Allopatric speciation: speciation by geographic isolation
 * Sympatric speciation: non-geographic isolation - behavioural/sexual, etc.

14.4 - Evolution has resulted in different species of organisms. They are classified into five kingdoms.

 * Difiniton of a species in terms of variation and potential for breeding: a related group of organisms which can interbreed to produce fertile offspring.
 * Recognition of kingdom, phylum, class, order, family, genus and species division
 * Five kingdom system, distinguishing features of each:
 * Prokaryotae: unicellular, auto- or heterotrophic, motile or non-motile
 * Protoctista: unicellular, eukaryote, ancestors of other eukaryotes - algae, mould, etc.
 * Fungi: heterotrophic, non-motile, external digestion
 * Plantae: autotrophic, non-motile
 * Animalia: heterotrophic, motile
 * Hierarchy should be illustrated with reference to the classification of familiar organisms. Candidates will not have to recall individual organisms

14.5 - The concept of the ecosystem

 * An understanding of the following:
 * ecosystem: community of organisms together with environment, functioning as a unit
 * community: group of interacting organisms living together in one place
 * population: group of organisms of one species occupying defined area and usually isolated from similar groups
 * environment: the abiotic factors in a specific area
 * habitat: describes the particular environment of a articular organism, population, community or ecosystem
 * niche: combines spatial habitat with functional relationships of an organism


 * A critical appreciation of some of the ways in which the numbers and distribution of organisms may be investigated (sampling techiques: quadrat, belt transect, capture, mark, release, recapture
 * Random sampling with quadrats and counting along transects to obtain quantitative data
 * The use of mark-release-recapture techniques for more mobile species


 * An understanding of diversity in the context of ecological stability: the more diverse the more stable the ecology
 * Calculation of the index of diversity using d = (N(N-1))/([sum of]n(n-1)) - where N = total number of organisms of all species; and n = total number of organisms in each species.
 * In extreme environments the diversity of organisms is usually low. THis may result in the unstable ecosystem in which populations are usually dominated by abiotic factors.
 * In less hostile environments the diversity of organisms is usually high. This may result in a stable ecosystem in which populations are usually dominated by biotic factors


 * Succession from pioneer species to climax community
 * Changes in abiotic factors resulting in a less hostile environment and increasing diversity.

14.6 - Photosynthesis uses energy from sunlight to synthesise organic molecules from inorganic sources

 * The following in a typical C3:
 * light-dependent reaction: in thylakoid membrane - including electron carrier system
 * light-independent reaction: in stroma - including Calvin's cycle
 * Only so much detail to show that
 * in the light-dependent reactions:
 * electrons in chlorophyll are excited by light energy
 * energy from these excited electrons generates ATP and reduced NADP
 * photolysis of water produces photons and electrons
 * oxygen is a valuable waste product of photolysis
 * in the light-independent reactions:
 * ribulose bisphosphate (RuBP) acts as a carbon dioxide acceptor leading to the formation of two molecules of glycerate 3-phosphate (GP)
 * ATP and reduced NADP are required for the reduction of GP to triose phosphate
 * RuBP is generated in the Calvin cycle
 * Triose phosphate is converted to useful carbohydrates, amino acids and lipids.
 * The role of chloroplasts in photosynthesis: occurs in chloroplast - contains crucial substances (chlorophyll, pigments, enzymes, and electron carrier proteins. Grana formed by stacked thylakoid membranes - connected by intergrana thylakoids with different pigments and proteins. Photosystem I an Photosystem II exist in thylakoids comprising of different pigments, enzymes and electron carrier proteins.

14.7 - Energy is transferred through food chains and webs in a community

 * Ecological pyramids (trophic pyramids) by number (usually a successive decrease in no., easy to collect; producers can be massive - tree is same as grass, range of numbers so great hard to draw pyramid to scale, trophic level of organism may be difficult to ascertain), biomass (harder to obtain, standing crop biomass may remain the same, small organisms may have small standing crop biomass while productivity is same as large, weight for weight one species can have higher energy) and energy (hardest to collect, takes into account rate of production, each bar represents the amount of energy per unit area or volume flowing through a trophic level in time period, compare ecosystems, inverted pyramids not obtained, input of solar energy may be added) - final is best representation (more true)
 * Trophic levels of a producer, primary consumer, secondary consumer and decomposer
 * A quantitative consideration of the transfer of energy between trophic levels and its relative efficiency.

14.8 - Respiration produces ATP which is the immediate form of energy for many cell activities

 * The use of different respiratory substrates (>1 anaerobic; 1 carboydrate; 0.9 protein; 0.7 fat) and the determination, calculation and interpretation of RQ (RQ = vol CO2/vol of O2)
 * RQ should be considered with reference to lipid, protein and carbohydrate.

Thes prcoess should only be considered in so much detail to show that:
 * The release of energy from carbohydrate by aerobic respiration. The production of ethanol or lactate and the regeneration of NAD in anaerobic respiration.
 * glycolysis involves the oxidation of glucose to pyruvate with the net gain of ATP and reduced NAD
 * acetylcoenzyme A is produced from pyruvate and coenzyme A in the link reaction
 * acetylcoenzyme A combines with a 4-carbon molecule to produce as 6-carbon molecule in the Krebs cycle
 * in a series of oxidation-reduction reactions, the Krebs cycle generates reduced coenzymes and ATP by substrate-level phosphorylation and carbon dioxide is lost
 * oxidative phosphorylation leads to the aerobic generation of ATP via a chain of electron carriers
 * aerobic respiration is more efficient than anaerobic respiration in terms of ATP production
 * The roles of the cytoplasm (glycolysis - glucose to pyruvate) and mitochondria (Krebs cycle) in these processes
 * ATP is an immediate source of energy in active transport, glycolysis, photosynthesis and other metabolic processes.

14.9 - Decomposition and recycling maintain the balance of nutrients in an ecosystem

 * The importance of respiration and photosynthesis in giving rise ot short-term fluctuations and in the long-term global balance of oxygen and carbon dioxide.
 * The passage of nutrients through various trophic levels and the role of microorganisms in converting organic molecules to inorganic substances which are made available to plants. Illustrated with reference to the carbon cycle and nitrogen cycle.

14.10 - Human activity can impose far reaching effects on an ecosystem. THere is a potential conflict of interest between production and conservation
Also, removing hedges means there is less for primary consumers to eat hence causing primary consumers numbers to deteriorate and hence less primary consumers can have widespread effects on the rest of the ecosytm.
 * Deforestation leading to the increase in land for agriculture. The influence of deforestation on diversity and on carbon and nitrogen cycling.
 * Conservation of forests allowing sustainable provision of resources
 * Specific knowledge will be required of this example only, although candidates may be required to interpret other material illustrating the general theme of this section.