2.1.1 Outline the cell theory (2).

Outline: To give a brief account or summary. All living things are made of cells. Cells are the smallest unit of life. Existing cells have come from other cells.

2.1.2 Discuss the evidence for the cell theory (3).

Discuss: Give an account including, where possible, a range of arguments for and against the relative importance of various factors, or comparisons of alternative hypotheses. a. All living things are made of cells: When living things are observed under the microscope they consistently appear to be composed of cells. However, there are a number of examples that do not conform to the standard notion of what a cell looks like at the microscopic level. Exceptions that test the rule of cell theory: b. Cells are the smallest unit of life. The cell is the smallest unit of organisation that can show all the characteristics of living processes. Organelles often require the cooperation of other organelles for their successful function. Interested students should research the concept of endosymbiont theory. c. Cells come only from other cells. where do cells come from? Cells carry out a form of cell division to form new cells. This process of cell replication in eukaryotes is called mitosis and in prokaryotes is called binary fission. The parental cell divides to produce identical daughter cells. This aspect of cell theory suggests that all cells therefore have a common ancestor, the original ancestral cell form which all other cells have arisen by descent. (origin of cellular life). This relationship of common ancestor suggest thereof re that all organisms are related.

2.1.3 State that unicellular organisms carry out all the functions of life (1).
State:means to give a specific name, value or other brief answer without explanation or calculation. These organisms are able to carry out all the processes which are characteristic of living things such as: a. metabolism which includes respiration the synthesis of ATP. b. response to a change in the environment c. homeostasis the maintenance and regulation of internal cell conditions. d. growth which for a unicellular organism means an increase in cell size and volume. e. reproduction which for the unicellular organism is largely asexual through cell division to form a clone. f. nutrition which means either the synthesis of organic molecules or the absorption of organic matter.

2.1.4 Compare the relative sizes of molecules, cell membrane thickness, viruses, bacteria, organelles and cells, using the appropriate SI unit (3)
Compare: means to Give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout. We depend on the microscope for our observation of cellular structures. Observations of this type are for the most part dependable but we must consider the introduction of 'artifacts' by those processes that prepare the material for microscopy. These artifacts are a consequence of specimen dehydration, contrast enhancement (staining), radiation and microscope function. These artifacts can lead to image or data distortions and misinterpretation. Relative sizes: 1. molecules (1nm). 2. cell membrane thickness (10nm). 3. virus (100nm). 4. bacteria (1um). 5. organelles (less 10um). 6. cells (<100 um). 7. generally plant cells are larger than animal cells.

Molecules of Biological significance are around 1 nm in size where as the cell membrane is about ten times thicker at 10nm. Where as a virus is ten times larger again at around 100nm. where as a bacteria is ten times larger again at around 1 um. where as a eukaryotic animal cell is is ten time larger again at around 10 um. where as a eukaryotic plant cell is ten times larger again at around 100 um.

2.1.5 Calculate the linear magnification of drawings and the actual size of specimens in images of know magnification (2).
Calculate means find a numerical answer showing the relevant stages in the working (unless instructed not to do so). On an image of a specimen it is useful to show how much larger/smaller the image is than the real specimen. This is called magnification. Exercise 1: Find a leaf, any leaf around 10-15 cm in length. Magnification = measured length of the image /measured length of the specimen Length of the actual specimen = length on the image/ magnification ( e.g. rose leaf = image length 4.2cm/ magnification 0.82 = 5cm real length

2.16 Explain the importance of the surface area to volume ratio as a factor limiting cell size (3).
Explain means to give a detailed account of causes, reasons or mechanisms. As the size of a structure increases the surface area to volume ratio decreases. Reasoning: This can be seen by performing some simple calculations concerning differentsized organisms. The rate of exchange of substances therefore depends on the organism's surface area that is in contact with the surroundings. Reason: as organisms get bigger their volume and surface area both get bigger, but not by the same amount. The volume increases as the cube but the area of the surface only increases by the square. Conclusions: As the organism gets bigger its surface area : volume ratio decreases This rule is a limiting factor for cell size. As the cell gets bigger the ratio decreases If the ratio decreases the rate of exchange decreases Example: gas exchange of oxygen for respiration. A cell which respires aerobically demands oxygen for the process. Oxygen is obtained form the surrounding environment such as water or blood (depends on the cell). Oxygen diffuses across the cell membrane. More membrane more diffusion (Surface area= increases by the 2). Bigger cell (Volume = increases by the 3). However the ratio of surface area2 : volume 3 is decreasing Therefore the volume of oxygen obtained for each unit of cell volume is actually decreasing Cells must not get too big because they cannot obtain sufficient oxygen to satisfy the demands of the cell. why cells are small (reasoning): Size as a limiting Factors for cell because: A big cell needs more oxygen than a little cell Big cells need to have more oxygen diffusion across the cell membrane. But the big cell has relatively small surface area compared to its volume i.e. the surface area: volume ratio is small. What ever other benefits a cell might gain from being big, it cannot become larger than is limited by the rate of gas exchange. This reasoning can be applied to nutrients and to waste, anything that is exchanged across the cell surface. Try preparing a reason why size is a limiting factor for: Obtaining nutrient (glucose)

Excretion of waste molecules ( urea, ammonia, carbon dioxide).

2.1.7 State that multicellular organisms show emergent properties (1).

State:means to give a specific name, value or other brief answer without explanation or calculation. syllabus: 'Emergent properties arise from the interaction of the component parts; the whole is greater than the sum of the parts'. As a model consider the electric light bulb. The bulb is the system and is composed of a filament made of tungsten, a metal cup, and a glass container. We can study the parts individually how they function and the properties they posses. These would be the properties of : Tungsten Metal cup Glass container.

2.1.8 Explain that cells in multicellular organisms differentiate to carry out specialized functions by expressing some of their genes but not others (3).
Explain means to give a detailed account of causes, reasons or mechanisms. An interesting parallel with economic theories is that the larger collective economic group the greater the number of specialisms, (Adam Smith) a rough guide which is found to hold true in living systems. As a general principle then we find that the larger a multicellular organisms become the more diversity and differentiated specialisms there are within the organism. Rather than all cells carrying out all functions, tissues and organs specialise to particular functions. These organs and systems are then integrated to give the whole organism (with its emergent properties). Differentiation: Cells within a multi cellular organism specialise their function. Specialised cells have switched on particular genes (expressed) that correlate to these specialist functions. These specific gene expressions produce particular shapes, functions and adaptations within a cell. Therefore a muscle cell will express muscle genes but not those genes which are for nerve cells. What is the benefit of differentiation and specialisation of tissues rather than all tissues carrying out all functions? In a multi cellular organism specialisation is more efficient than the generalised plan when competing for a specific resource. Consider the role of water transport through the plant: 1. In higher plants we have specialisation to for a tubular system called the xylem. 2. This is more efficient way of water transport than simply been passed by the mass movement of water from cell to cell. 3. In the xylem water can be moved very efficiently from underground to the canopy of the highest trees at very little cost to the plant. 4. If there is no specialised tissue for carrying water then the plant would rely on the movement of water by mass flow of diffusion which is very slow. The plant is therefore limited in size and therefore cannot compete with larger species.

2.1.9 State that stem cells retain the capacity to divide and have the ability to differentiate along different pathways(1).
State:means to give a specific name, value or other brief answer without explanation or calculation. A stem cell retains the capacity to divide and has the ability to differentiate along different pathways. A stem cell is able to divide but has not yet expressed genes to specialise to a particular function. Under the right conditions stem cells can be induced to express particular genes and differentiate into a particular type of cell. Stem cells can be obtained from a variety of different places including the blastocyte. Adults still posses stem cells in some organs but much less so than a child. Even the placenta can be a useful source of stem cells.

2.1.10 Outline one therapeutic use of stem cells (2).

Outline means to give a brief account or summary. 1.Non-Hodgkins Lymphoma is a cancerous disease of the lymphatic system. Outline of the disease. 1. patient requires heavy does of radiation and or chemotherapy. This will destroy health blood tissue as well as the diseased tissue. 2. Blood is filtered for the presence of peripheral stem cells. Cells in the general circulation that can still differentiate into different types of blood cell otherwise known as stem cells. 3. Bone marrow can be removed before treatment. 4. Chemotherapy supplies toxic drugs to kill the cancerous cells. 5. Radiation can be used to kill the cancerous cells. In time however the cancerous cells adapt to this treatment so that radiation and chemotherapy are often used together. 6. Post radiation/ chemotherapy means that the patients health blood tissues is also destroyed by the treatment. 7. Health stem cells or marrow cells can be transplanted back to produce blood cells again 2. Embryonic Stem cell 3. Therapeutic cloning

2.2.1 Draw and label a diagram of the ultrastructure of Escherichia coli (E. coli) as an example of a prokaryote (1)
Draw: To represent by means of pencil lines. The general size of a prokaryotic cell is about 1-2 um. Note the absence of membrane bound organelles There is no true nucleus with a nuclear membrane The ribosome's are smaller than eukaryotic cells The slime capsule is used as a means of attachment to a surface Only flagellate bacteria have the flagellum Plasmids are very small circular pieces of DNA that maybe transferred from one bacteria to another.

2.2.2 Annotate the diagram from 2.2.1 with the functions of each named structure.
Annotate: to add brief notes to a diagram or graph. Cell Wall: Made of a murein (not cellulose), which is a glycoprotein or peptidoglycan (i.e. a protein/carbohydrate complex). There are two kinds of bacterial cell wall, which are identified by the Gram Stain technique when observed under the microscope. Gram positive bacteria stain purple, while Gram negative bacteria stain pink. The technique is still used today to identify and classify bacteria. We now know that the different staining is due to two types of cell wall Plasma membrane: Controls the entry and exit of substances, pumping some of them in by active transport. Cytoplasm: Contains all the enzymes needed for all metabolic reactions, since there are no organelles. Ribosome: The smaller (70 S) type are all free in the cytoplasm, not attached to membranes (like RER). They are used in protein synthesis which is part of gene expression. Nucleoid:

Is the region of the cytoplasm that contains DNA. It is not surrounded by a nuclear membrane. DNA is always a closed loop (i.e. a circular), and not associated with any proteins to form chromatin. Flagella: These long thread like attachments are generally considered to be for movement. They have an internal protein structure that allows the flagella to be actively moved as a form of propulsion. The presence of flagella tends to be associated with the pathogenicity of the bacterium. The flagella is about 20nm in diameter. This structure should not be confused with the eUkaryotic flagella seen in protoctista. Pilli: These thread like projections are usually more numerous than the flagella. They are associated with different types of attachment. In some cases they are involved in the transfer of DNA in a process called conjugation or alternatively as a means of preventing phagocytosis. Slime Capsule: A thick polysaccharide layer outside of the cell wall, like the glycocalyx of eukaryotes. Used for sticking cells together, as a food reserve, as protection against desiccation and chemicals, and as protection against phagocytosis. In some species the capsules of many cells in a colony fuse together forming a mass of sticky cells called a biofilm. Dental plaque is an example of a biofilm. Plasmids: Extra-nucleoid DNA of up to 400 kilobase pairs. Plasmids can self-replicate particularly before binary fission. They are associated with conjunction which is horizontal gene transfer. It is normal to find at least one anti-biotic resistance gene within a plasmid. This should not be confused with medical phenomena but rather is an ecological response to other antibacterial compounds produced by other microbes. Commonly fungi will produce antibacterial compounds which will prevent the bacteria replicating and competing with the bacteria for a resource. conjugation Direct contact between bacterial cells in which plasmid DNA is transferred between a donor cell and a recipient cell. There is no equal contribution to this process, no fertilisation and no zygote formation. It cannot therefore be regarded as sexual reproduction.

2.2.4 State that prokaryotic cells divide by binary fission (1).

State:means to give a specific name, value or other brief answer without explanation or calculation. Prokaryotic cells divide by binary fission. This is an asexual method of reproduction in which a 'parental' cell divides into two smaller but equally sized cells. The cells are genetically identical and form the basis of a reproductive clone. The process of binary fission takes place in four stage: (a). Reproduction signal: The cell receives a signal, of internal or external origin that initiates the cell division. E.coli replicates about once every 40 minutes when incubated at 37o C. If however we increase the concentration of carbohydrate nutrients that the cell is supplied with then the division time can be reduced to 20 minutes. There is a suggestion here that an external signal (nutrient concentration) is acting as the reproductive signal. (b). Replication of DNA: bacterial cells have a single condensed loop of DNA. This is copied by a process known as semi-conservative replication to produce two copies of the DNA molecule one for each of the daughter cells The replication begins at a single point (ori)on the loop of DNA. The process proceeds around the loop until two loop have been produced, each a copy of the original. The process finishes at a single point on the loop of DNA called the ter position. (c). Segregation of DNA: One DNA loop will be provided for each of the daughter cells.

As the new loops form the ori site becomes attached to some contractile proteins that pull the two ori sites, and therefore the loops, to opposite ends of the cell. This is an active process that requires the bacteria to use energy for the segregation. (d). Cytokinesis: Cell separation. This occurs once the DNA loop replication and segregation is complete. The DNA completes a process of condensing whilst the plasma membrane begins to form a 'waist' or constriction in the middle of the cell. As the plasma membrane begins to pinch and constrict the membrane fuses and seals with additional new membrane also being formed.

2.3.1.Draw and label a diagram of the ultrastructure of a liver cell as an example of an animal cell (1).
Draw: To represent by means of pencil lines.

N:Nucleus PM: plasma membrane M: mitochondria rER: Rough endoplasmic reticulum GA: Golgi apparatus L: Lysosome MV: Microvilli

2.3.2 Annotate the diagram from 2.3.1 with the functions of each named structure.
Annotate: to add brief notes to a diagram or graph. Nucleus: This is the largest of the organelles. The nucleus contains the chromosomes which during interphase are to be found the nucleolus. The nucleus has a double membrane with pores(NP). The nucleus controls the cells functions through the expression of genes. Some cells are multi nucleated such as the muscle fibre Plasma membrane: controls which substances can enter and exit a cell. It is a fluid structure that can radically change shape. The membrane is a double layer of water repellant molecules. Receptors in the outer surface detect signals to the cell and relay these to the interior. The membrane has pores that run through the water repellant layer called channel proteins. Mitochondria: location of aerobic respiration and a majot synthesis of ATP region.. Double membrane organelle. Inner membrane has folds called cristae. This is the site of oxidative phosphorylation. Centre of the structure is called the matrix and is the location of the Krebs cycle. Oxygen is consumed in the synthesis of ATP on the inner membrane The more active a cell the greater the number of mitochondria. Rough endoplasmic reticulum (rER): protein synthesis and packaging into vesicles. rER form a network of tubules with a maze like structure. In general these run away from the nucleus The 'rough' on the reticulum is caused by the presence of ribosomes. Proteins made here are secreted out of the cell Ribosomes: the free ribosome produces proteins for internal use within the cell. Golgi apparatus: modification of proteins prior to secretion. proteins for secretion are modified possible addition of carbohydrate or lipid components to protein packaged into vesicles for secretion Lysozyme: Vesicles in the above diagram that have formed on the golgi apparatus. Containing hydrolytic enzymes.

Functions include the digestion of old organelles, engulfed bacteria and viruses.

2.3.4 Comparison of prokaryotic and eukaryotic cells (3).

compare means to give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout.

2.3.5 State three differences between plant and animal cells (1).
State:means to give a specific name, value or other brief answer without explanation or calculation. Only three differences from this list are required.

2.3.6 Outline two roles of extracellular components(3).

Outline means to give a brief account or summary. a) Plant cell wall. Found around all plant cells Composed of cellulose. Maintains the shape of the cell. Provides structural support against the force of gravity. prevents excessive uptake of water by the cell b) Animal extracellular matrix i) Basement membrane: a secretion formed from collagen and glycoproteins joined together by a third 'linkage' protein. Their exact composition varies form tissue to tissue. Support: the membrane surrounds the tissues of lines ducts. It provides structural support for the integrity of the tissue or organ. Usually found as the basal lamina or basement membrane of epithelial cells. Filter : The basement membrane of the kidney glomerulus provides the effective barrier for ultrafiltration Vascular niche : Interestingly cells often require a base on which to organise before they will form proper tissue. There are implications here for developmental biology, tissue repair, stem cell therapies and cancer treatment. ii) Interstitial matrix: Bone has a matrix which includes collagen with a calcium phosphate.

Other tissues are surrounded by a matrix composed of a kind of gel that provides support for the tissue.

2.4.1 Draw and label a diagram to show the structure of membranes (1).
Draw: To represent by means of pencil lines.

2.4.2 Explain how the hydrophobic and hydrophilic properties of phospholipids help to maintain the structure of the cell membranes (3)
Explain means to give a detailed account of causes, reasons or mechanisms. This model of the bilayer's has the proteins removed for clarity. The 'head's have large phosphate groups, thus they are hydrophilic (attract water) or polar. These section are suited to the large water content of the tissue fluid and cytoplasm on opposite sides of the membrane. The fatty acid tails are non-charged, hydrophobic meaning they repel water. This creates a barrier between the internal and external 'water' environments of the cell. The 'tails' effectively create a barrier to the movement of charged molecules The individual phospholipids are attracted through their charges and this gives some stability. They can however move around in this plane The stability of the phospholipid can be increased by the presence of cholesterol molecules.

2.4.3 List the functions of membrane proteins (1).

List means to give a sequence of names or other brief answers with no explanation.

2.4.4 Define diffusion and osmosis (1).

define means to give the precise meaning of a word, phrase or physical quantity. Diffusion: passive movement of particles from a region of high concentration to a region of low concentration. Osmosis is the passive movement of water molecules from a regions of lower solute concentration to a region of higher solute concentration DIffusion ideas: This model illustrates the main features of the process of diffusion. The movement of particles is caused by the kinetic energy possessed by the particle. The direction of movement is random. Observing groups of particles it emerges that they move from regions of high concentration to regions of low concentration. Alternatively the statement can be in terms of pressure. Movement from a region of high pressure to a region of low pressure. However, most biological diffusion takes place through membranes and involves sources,sinks and diffusion gradient. This model shows diffusion through a membrane: The region that supplies and maintains the high concentration of particles are called thesource. The place where the substances is continually removed (or changed) is called the sink. Maintaining the concentration gradient between the two areas is a feature of biological systems. A concentration gradient maintains the movement of the substance. e.g. Source = blood oxygen. Sink= respiring cell Osmosis ideas: water moves(because they have kinetic energy) through plasma membranes pores called aquaporin. The water molecules have kinetic energy like other molecules. The water molecules move randomly and will if they come into contact with the membrane pass straight through. The tendency is for water to pass from lower solute (left) to higher solute (right) concentrations.

2.4.5 Explain passive transport across membranes by simple diffusion and facilitated diffusion (3).
Explain means to give a detailed account of causes, reasons or mechanisms. The passive movement implies that there is no expenditure of energy in moving the molecules from one side of the membrane to the other: However the molecules themselves possess kinetic energy which accounts for why they are in movement. The membrane therefore 'allows' the molecules to pass through without needing to add any additional energy to the kinetic energy already possessed by the particles.

Particles will in fact pass in both directions but over all the emerging pattern is that molecules move from a region of their high concentration to a region of their low concentration. Some molecules are so small that they pass through the membrane with little resistance This includes Oxygen and Carbon Dioxide Lipid molecules (even though very large) pass through membranes with very little resistance also. Larger molecules (red) move passively through the membrane via channel proteins These proteins(grey) have large globular structures and complex 3d-shapes The shapes provide a channel through the middle of the protein, the 'pore' The channel 'shields' the diffusing molecule from the non-charged/ hydrophobic/ non-polar regions of the membrane.

2.4.6 Explain the role of protein pumps and ATP in active transport across membranes(3).
Explain means to give a detailed account of causes, reasons or mechanisms. Molecules are moved against the concentration gradient from a region of their low concentration to a region of their high concentration. Active mean that the membrane protein 'pump' requires energy (ATP) to function The source of energy is ATP is produced in cell respiration Transported molecules enter the carrier protein in the membrane. The energy causes a shape change in the protein that allows it to move the molecule to the other side of the membrane. The sodium-potassium, pump that creates electro-chemical gradient across the cell membrane of all cells. Cells are -ve charged on the inside relative to the outside. This pump is modified in the nerve cell to create some of the electrochemical phenomena seen in nerve cells.

2.4.7 Explain how vesicles are used to transport materials within a cell between the rough endoplasmic reticulum , Golgi apparatus and plasma membrane(3).
Explain means to give a detailed account of causes, reasons or mechanisms. Cells will manufacture molecules for secretion outside of the cell. Some of these secretion molecules are complex combinations of proteins, carbohydrates and lipids. The base protein is coded for by a gene whose expression begins the process. 1. Protein is already synthesised and present in the rER. 2. The protein is moved through the rER and modified. 3. A spherical vesicle is formed form the end of the rER with the protein inside. 4. The vesicle migrates to the golgi apparatus. 5. Vesicle and golgi membranes fuse. The protein is released into the lumen of the golgi apparatus. 6. The golgi modifies the protein further by adding lipid or polysaccharides to the protein. 7. A new vesicle is formed from golgi membrane which then breaks away. The vesicles migrates to the plasma membrane. 8. The vesicle migrates to the plasma membrane fuses and secretes content its contents out of the cell. A process called exocytosis.

2.4.8 Describe how the fluidity of the membrane allow s it to change shape, break and re-form during endocytosis and exocytosis(2).
a) Exocytosis: vesicle membrane fuses with the plasma membrane. b) Endocytosis:a vesicle is formed by the infolding of the plasma membrane Membrane fluidity: (a) The phospholipid molecules can change places in the horizontal plane. This creates the so called fluid property of the membrane. (b) Molecule exchange in the vertical plane does not occur. This maintains the integrity of the membrane. (c) Cholesterol embedded in the membrane reduces its fluidity.

2.5.1 Outline the stages in the cell cycle, including interphase (G1, S, G 2), mitosis and cytokinesis (2).
outline means to give a brief summary The cell cycle describes the major phases of activity in the division of a cell. The length of the cell cycle depends on the particular function of the cell. For example bacterial cells can divide every 30 minutes under suitable conditions, skin cells divide about every 12 hours on average, liver cells every 2 years, and muscle cells never divide at all after maturing. The total length of a cell cycle varies depending on the specialised function of a cell. Interphase (grey) is the longest phase which itself occurs in three stages. G1 The cell performs its normal differentiated function. Protein synthesis/ mitochondria replication/ chloroplast replication. S DNA replication. At this point the mass of DNA in the cell has doubled. G2 Preparation for cell division Phases of mitosis Cytokinesis: division of the cytoplasm to form two daughter cells.

An appreciation of mitosis only comes when you have studied the structure of nucleic acids, DNA replication and some gene expression. At that point you will understand better the significance of the S phase= DNA replication.

2.5.2 State that tumours (cancers) are the result of uncontrolled cell division and that these can occur in any organ or tissue(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Tumours (cancers) are a cell mass formed as a result of uncontrolled cell division. They can occur in any tissue. Stomach cancer

2.5.3 State that interphase is an active period in the life of a cell when many metabolic reactions occur, including protein synthesis, DNA replication and an increase in the number of mitochondria and/or chloroplasts (1).
State means to give a specific name, value or other brief answer without explanation or calculation. The cell specialises to a particular function in a process called differentiation. Through gene expression and protein synthesis there is a specialisation of cell structure and function. During this interphase the cell carries out this specialist function. The length of the interphase varies from one type of cell to another. G1 follows cytokinesis. The cell is involved in the synthesis of various proteins which allow the cell to specialise. S-phase involves the replication of DNA molecules which takes place prior to the phases of mitosis. G2 preparation for the phases of mitosis which involves the replication of mitochondria and in the case of plants, the chloroplast.

2.5.4 Describe the events that occur in the four phases of mitosis (prophase, metaphase, anaphase and telophase (2).
Describe means to give a detailed account. Super coiling: Eukaryotic DNA is combined with histone proteins and non-histone proteins to form chromatin. The method of folding of chromatin is specific to each chromosome leaving genes in predictable positions and a distinctive overall chromosome shape. The human cell has a DNA length of about 1.8 m this has to be packed into a nucleus which has only a 5 um diameter.

a)The cell membrane is intact during this the interphase. The chromosomes cannot be seen during G1,S and G2. b) G1,Within the nucleus, genes on the chromosome are being expressed to carry out normal cell function (interphase). Remember you cannot see chromosomes at this stage. The diagram has a 'see's through' the nuclear membrane so you can see inside. In reality it would look just like cell a). c) S-phase in which DNA replication occurs and the chromosomes are copied. The copies called sister chromatids are held together by a protein to form the centromere. It is still not possible to see this happen with an intact cell. d) Early Prophase in which the sister chromatids have condensed by super coiling. Note the formation of the spindle microtubules and their attachment to centrioles. The nuclear membrane will now break down to reveal sister chromatids. The internal arrangements of chromosomes can now be seen with a light microscope. e) Metaphase the chromosomes arranged on the equator of the cell each attached to a spindle microtubule at the centromere f) Anaphase: The spindle microtubules contract and pull apart the sister chromatids one to each pole of the cell. The centromere splits allowing the sister chromatids to be separate. g) Telophase: at each pole there are separate groups of the replicated chromosomes the spindles is degenerating h) Cytokinesis: the cell membrane begins to separate, dividing the cell into two new cells. The nuclear membrane is reforming around each cell. i) Two daughter cells are formed. They are genetically identical to each other and in effect the basis of a clone.

2.5.5 Explain how mitosis produces two genetically identical nuclei (3).
Explain means to give a detailed account of causes, reasons or mechanisms. The process of cell division produces genetically identical daughter cells. Conservation of chromosome number. The chromosome number in each of the daughter cells is the same as that of the original parental cell During the S-phase, each chromosome is copied exactly. The two copies of each chromosome are held together by a protein structure called a centromere. Therefore just prior to the beginning of the phases of mitosis there is actually double the number of chromosomes present in a cell. Each chromosome in this state is represented by a pair of sister chromatids. These give the now classic cross image of the DNA

2.5.6 State that growth, embryonic development, tissue repair and asexual reproduction involve mitosis(1).
State means to give a specific name, value or other brief answer without explanation or calculation. Growth: multicellular organisms increase their size through growth. This growth involves increasing the number of cells through mitosis. These cells will differentiate and specialise their function. Embryonic development is when the fertilised egg cell (zygote) divides to form the multicellular organism. Each cell in the organisms is identical (genetically) to all the other cells. However, each cell will express only a few of its genes to determine its overall specialisms, a process called differentiation. In this way a stem cell may becomes a muscle, or it may become a nerve cell or any one of the many different kinds of cells found in a complex multicellular organism. The best book about this process for the interested reader is Tissue Repair: As tissues are damaged they can recover through replacing damaged or dead cells. This is easily observed in a skin wound. More complex organ regeneration can occur in some species of amphibian. Asexual Reproduction: This the production of offspring from a single parent using mitosis. The offspring are therefore genetically identical to each other and to their parent- in other words they are clones. Asexual reproduction is very common in nature, and in addition we

humans have developed some new, artificial methods. Bacteria DO NOT asexually reproduce by mitosis but rather by a process called Binary Fission.

3.1.1State that the most frequently occurring chemical elements in living things are carbon, hydrogen, oxygen and nitrogen.
State means to give a specific name, value or other brief answer without explanation or calculation. Carbon............ Symbol C Oxygen ...........Symbol O Hydrogen ........Symbol H Nitrogen...........Symbol N

3.1.2 State that a variety of other elements are needed by living organisms, including sulphur, calcium , phosphorus, iron and sodium
State means to give a specific name, value or other brief answer without explanation or calculation. Here we only need to read and recall the syllabus statement itself.

3.1.3 State one role for each of the elements

State means to give a specific name, value or other brief answer without explanation or calculation. Sulphur which is an important element in some amino acids. Calcium which is found in bones / Teeth Iron which is to be found in haemoglobin (animal) Sodium which is needed for a nerve impulse Phosphorus found in cell membrane structures

3.1.4 Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation.
draw means to represent by means of pencil lines and labels means to add labels to a diagram. Water show the covalent bonds between oxygen and two hydrogen atoms. The nuclei of oxygen is significantly larger and greater charge (+8) than the hydrogen nuclei (+1). Consequently the electron pair in the covalent bond is found 'closer' to the oxygen than the hydrogen nuclei. This creates a polar molecule in which the oxygen carries and additional small negative dipole and each hydrogen a small positive dipole.

3.1.5 Outline the thermal, cohesive and solvent properties of water (2).
Outline means to give a brief account or summary. Due to the polarity of the water molecules, the small negative charge on each oxygen atoms is attracted the hydrogen atoms of other water molecules. These attractions are called HYDROGEN BONDS. A hydrogen bond in water has a typical strength of 5.0 kcal/mol but these vary in strength in solutions. Hydrogen bonds can occur between water molecules and with other types of polar molecule. The hydrogen bond does not change the chemical properties of water but does accounts for physical properties. The three of the more important properties for biological systems include: 1. Cohesive properties 2.Thermal properties. 3. Solvent properties. Cohesive properties:

The water molecules 'sticking together' or the cohesion has a number of effects on living systems. Cohesion of water molecules is critical in the way plants transport water through their tissues in the process known as transpiration. Solvent Properties: The polar water molecules are attracted to the strong ionic charges of the ions in solution. Often the ion, in this instance the Na+ , exert a strong enough attraction on water molecules that they form shells around the ion. Here there appears to be concentric shells of water molecules around the sodium ion. This has the effect of isolating one ion form another which is essentially what is known as solubility. Osmosis: A reduced tendency of the water molecules to move in a solution is another way to explain processes such as osmosis. Transport and reactions: Water of course is the solvent of blood, tissue fluid and the cytoplasm. It therefore allows the transport of the soluble minerals, carbohydrates, amino acids etc that are required to be transported around the body. Thermal properties of water. You will be familiar with the concept of the phases of matter, solid, liquid and gas. The transition form one phase to another (in the above sequence) requires energy to be added. From the structure of any molecules we can predict the energy required to make each transition e.g. liquid to a gas. The predictions made for water (based on the empirical formula) turn out to be too low. With experiments showing higher values than predicted. To make the phase transition from a liquid to a gas requires that extra energy be added to overcome the hydrogen bonding. Water is described as having a high specific heat capacity. The biological consequences include using water as a coolant. Body heat can be absorbed by the water molecules before entering the gas phase evaporating and in so doing reducing body temperature. A body of water such as a pond, lake or ocean tend to be thermostable with considerably less variation in daily temperatures than land. This has consequences for the ecology and evolution of aquatic organisms.

3.1.6 Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium for metabolic reactions and transport medium .
Explain means to give a detailed account of causes, reasons or mechanisms. Thermal Properties Heat capacity is a measure of the energy input required for a certain rise in temperature. It is important to define what is meant by temperature at this point. Temperature is the average kinetic energy possessed by a particle in a substance. For substances of large molecules, a certain mass of that substance consists of fewer molecules than a substance with smaller molecules. This means that for a certain energy input, the substance of larger molecules with receive more energy per molecule, than a substance of smaller molecules. Thus the temperature of the substance of larger molecules should increase more than the substance of smaller molecules. Following this argument through would lead to the explanation that water has a high specific heat capacity because its molecules are small, which compared to most other (more complex) substances is true. The hydrogen bonding in water also provides another means of storing both KE and PE. Water absorbs a lot of heat before there is a change in temperature Therefore water is a useful substance for living things both physiologically and ecologically. Physiology: Cooling effects

 The heat generated by the body needs to be removed to prevent a denaturation of enzyme systems. Water absorbed a great deal of energy before entering the vapour phase. This makes it an effective agent for the removal of heat and the maintenance of body temperature. Blood which is mainly water can absorb and carry heat away from hot parts of the body to the cooler parts. Ecological effects: Oceans, lakes and ponds have fairly stable temperature (since it can absorb alot of heat without a temperature change) which means that poikilothermic organisms need not waste energy on thermoregulation. Surrounding air temperatures may show marked changes but water water in the same vicinity will remain relatively stable. Medium for metabolic reactions: Most biochemical reactions take place in solution where water is the solvent. The basis of this ability of water molecules to act as a solvent in covered in section 3.1.5. Remember that the cytoplasm is largely water and all cells exist in a medium which is water based e.g. tissue fluid, blood, pond. Transport Medium: Transport systems require something to do the 'transporting', carrying of material from one place to another. Blood carries nutrient, gases and waste all of which are dissolved in the water of blood. Once more this is achieved by taking advantage of the solubility of water.

3.2.1 Distinguish between organic and inorganic compounds (2).

Distinguish means to give the differences between two or more different items. Organic compounds are based on carbon and are found in living things. There are a number of exceptions including hydrogen carbonate (HCO3- ), carbon dioxide (CO2 )and Carbon monoxide (CO). Inorganic compounds are by default all the molecules other than those in the category above.

3.2.2 Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure(2).
Identify means to find an answer from a given number of possibilities. Monosaccharide sugars. These are the monomers from which larger polymer molecules are constructed. Molecules like glucose and fructose are metabolically active molecules usually stored in an inactive, insoluble polysaccharide form. Glucose: C6H12O6 this is a hexose sugar (six carbons) most commonly found in this ring structure. Glucose will be known to most students as a product of photosynthesis or the substrate molecule for respiration. Glucose is also found in a polymer as starch, glycogen or cellulose. All bonds are covalent. Glucose is a reducing sugar and will give positive (Brick red) precipitate in a Benedicts test. Glucose is metabolically active compound Ribose: Pentose (5 carbon sugar). Ribose is part of one the important organic molecules in photosynthesis, ribulose bisphosphate. (RUBP) A modified version of ribose, deoxyribose is perhaps best known for its role in Deoxyribonucleic acid or DNA where it forms part of the sugar phosphate backbone. The chemical properties of deoxyribose are very different from the properties of ribulose Both Ribose and Glucose will attract water molecules (hydrogen bonding ) to form solutions.

Amino Acids: There are 20 common amino acids found in the protein structures of living things. Amino acids are monomers which combine to form the larger polypeptides. In turn polypeptides combine to form proteins. Proteins molecules are the basis of enzymes and many cellular and extra cellular components. This model shows the structure of the general amino acid. If you build one in a molecular kit you will appreciate better the 3D structure. Each of the common amino acids has the same structure as the one shown except that the R group is different. Amino acids are soluble

This is an alternative way to draw the general amino acid structure. This diagram illustrates the 'amino' group which is -NH2 There is also the acidic group -COOH which ionizes in solution to form an -COO-and H+groups This acid group is known as a carboxylic acid group . This is an illustration of the smallest of the amino acids, Glycine. Notice that Glycine has an amino group, carboxylic acid group and a R group = H A common source of glycine is sugar cane. This image shows a common amino acids, Alanine Note the similarity in structure with glycine but this time the R group is -CH3 Students are not required to know the structure of all 20 common amino acids

Fatty Acids: These molecules are the basis of triglycerides and many other types of lipid. These molecules are also the basis of the phospholipid molecules that form the bilayer of the cell membrane.

The image shows a basic saturated (no double bonds) fatty acid. There is a methyl group (-CH3) at one end of the chain. Chain is the formed from a series of covalently bonded carbons saturated with hydrogens. The chain is non-polar and hydrophobic The carbonyl group is polar making this ends of the molecule hydrophilic.

3.2.3 List three examples each of monosaccharides, disaccharides and polysaccharides(1)

List means to Give a sequence of names or other brief answers with no explanation.

3.2.4 State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants(1)

State means to give a specific name, value or other brief answer without explanation or calculation.

3.2.5 Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides and polysaccharides; between fatty acids, glycerol and triglycerides; and between amino acids and polypeptides(2).
Outline means to give a brief account or summary. Polymer: consisting of large molecules made up of a linked series of repeated simple molecules called monomers Monomers: simple molecular units Model of polymerisation through condensation reaction. (1) Dimers a) Two monomers are bonded together to form a dimer. b) Water (H + OH) are removed to form water. c) The dimer can be split by hydrolysis but needs water adding (2) Polymerisation a) In this example six monomers are joined together b) Polymers normally form more complex shapes than suggested in this model c) The polymer can be 'digested' back to monomers by hydrolysis reaction Formation of a disaccharide a) Two molecule of glucose will polymerise to form maltose b) The condensation reaction will take place between C1 of the first glucose and C4 of the second glucose. c) A condensation reaction takes place between the glucose 1 (-OH on C1) and Glucose (-H on C4). d) The bond formed is a covalent bond between C1 -O-C4 , called a 1, 4 glycosidic bond. e) The disaccharide molecule formed is called Maltose which like glucose is a reducing sugar. f) Hydrolysis; The diagram can be reversed so that the disaccharide can be split into two glucose monosaccharides. g) Hydrolysis is the type of reaction catalysed by the digestive enzymes. Formation of a polysaccharide The above chain of glucose molecules represent the polysaccharide formed by many glucose monomers joining together to form this polysaccharide called amylose. The molecule to the left represents the helical structure of the polypeptide, amylose. Amylose is a polymer of glucose. Intramolecular hydrogen bonding causes the chain molecule to twist into a helical shape. Amylose is one of two molecules found in starch, the other being a branching polymer of glucose called amylopectin. Amylopectin Starch: Starch is composed of two polysaccharides, Amylose and amylopectin Starch is metabolically un-reactive and insoluble and hence an excellent storage carbohydrate. Formation of a dipeptide and a polypeptide a) Two amino acid monomers of glycine aligned to form a peptides bond by condensation reaction.

b) The peptide bond can form between the carboxyl group of the first amino acid and the amino group of the second amino acid. c) H-OH or water is removed in the reaction hence the term condensation reaction. d) Dipeptide is formed (naming system not required) with the characteristic -C-N- bond between the two monomers. e) Notice that in the dipeptide there is still an amino group at one end and a carboxylic group at the other end. f) The above pattern is true of all polypeptides and known as the amino terminal and carboxyl terminal of the polypeptide. Polypeptide chains do not remain as linear (straight) chains. Instead they fold up into the complex yet specific shapes of the protein as seen in this image. The shape of a protein is determined by intra-molecular hydrogen bonding and some covalent bonding between R groups (-S-S-, disulphide bridges). Polypeptides can be hydrolysed in the same way as polysaccharides with by incubating with acids. Naturally polypeptides are digested by a group of enzymes called Peptidases which hydrolyse the chain into amino acids. Formation of a triglyceride: Chemically all fats and oils are triglycerides (simple lipids). Fats are those lipids which are solid state at 20oC. Oils are those lipids which are liquid at 20oC. Oils with unsaturated fatty acids have bends in their tail structure which reduces the density of the molecule and lowers its melting point. Oil also tend to have short fatty acid tails. Conversely fats tend to have longer fatty acids with saturated bonds. This makes their structure densely packed and raises the melting point. The formation of a triglyceride or any lipid is not a polymerisation like the previous examples. Instead three fatty acids chains (usually of different length) are bonded to the molecule glycerol. Ester bonds (-O-) are formed between an -OH group on the glycerol molecule and the carboxylic acid group (-COOH) of the fatty acid. The triglyceride formed is insoluble. (Hydrophobic). Fatty acid tails can vary in length and may contain unsaturated bonds Animals fats have saturated fatty acids which are straight molecules and very compact. This is gives them a higher melting point than the plant oils Plant oils have unsaturated and polyunsaturated fatty acid chains that tend to branch and make the molecule less dense and with a lower melting point. Phospholipids are the principle molecule in the cell membrane they form the 'bilayer' that is the cell membrane. Phospholipid structure: Very similar to the triglyceride except one fatty acid chain is replaced by a polar phosphate group. The molecule is in two parts a) Polar hydrophilic phosphate heads. b) 2 Non polar hydrophobic tails

3.2.6 State three functions of lipids(1).

State means to give a specific name, value or other brief answer without explanation or calculation.

3.2.7 Compare the use of carbohydrates and lipids in energy storage(3).

Compare means to give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout.

3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate(2)
Outline means to give a brief account or summary. . Sugar is deoxyribose which differs from ribose in having one less oxygen on carbon 2. Phosphate is the PO4-3 group. Bases are nitrogen based ring structures of which there are 4 different kinds.

3.3.2 State the names of the four bases in DNA (1).

State means to give a specific name, value or other brief answer without explanation or calculation. Nucleosides are the combination of sugar and base only and are not required for the syllabus. You will however see the terms used in the literature. These are the four bases which are universally found in living things. In 1950 Edwin Chargaff determined that within an organism there was same approx the same amount of A as T and the same amount of G=C. Chargaff surveyed a wide variety of organsims and found in the ratio of A:T, G:C consistently across the range of his specimens These ratios became known as Chargaff's ratio's and would later prove to be a significant clue to the structure of DNA.

3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand (2).
Outline means to give a brief summary. DNA is composed of two polynucleotides chains. Nucleotides are covalently bonded between the phosphate of one nucleotide to the C3 of the second nucleotide. The phosphate group creates a bridge connecting C5 on one pentose with the C3 on the next pentose. The bond is a phosphodiester bond which indicates that there are two covalent bonds formed between the

-OH and the acidic phosphate group.

3.3.4 Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds (3).
Complementary means matching, is different from complimentary, which means being nice.

Explain means to give a detailed account of causes, reasons or mechanisms. The complementary bases are formed (A-T, G-C) when hydrogen bonded occur between the two bases in a pair. Refer to the diagram and notes in the next section..

3.3.5 Draw and label a simple diagram of the molecular structure of DNA(1) .
Draw means to be able to represent by means of pencil lines. This image of DNA shows the arrangement of the two polynucleotide chains but not the helical shape which can be seen in the space filled model below. This is image shows: Two polynucleotide chains. Two anti-parallel chains. a)The number followed by the prime (') determined the carbon in deoxyribose free from bonding to another nucleotide. b) Note that the two chains are in opposite directions 3' to 5' is parallel to 5' to 3' chain. The anti-parallel chains have a uniform distance (2nm) between the outside of the two sugar phosphate backbones Complementary base pairs: Inside the double helix bases form one strand hydrogen bond to bases on the opposite strand but always in the following way: a) Adenine hydrogen binds to Thymine b) Cytosine hydrogen bonds to Guanine

3.4.1 Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands by DNA polymerase.(3)
Explain means to give a detailed account of causes, reasons or mechanisms. 1. The original double helix molecule. 2. Helicase enzyme breaks the hydrogen bonds between complementary base pairs. This unzips the double helix at a position called the replication fork. 3. There is an abundant supply of nucleotides in the nucleus for the formation of the new polynucleotides. 4. Nucleotides base pair to the bases in the original strands. 5. DNA polymerase joins together the nucleotides together with strong covalent phosphodiester bonds To form a new complementary polynucleotide strand. 6. The double strand reforms a double helix under the influence of an enzyme. 7 Two copies of the DNA molecule form behind the replication fork. These are the new daughter chromosomes.

3.4.2 Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.(3)
Explain means to give a detailed account of causes, reasons or mechanisms. The significance of the mechanism outlined above is that the DNA molecule is copied precisely from one cell generation to the next. In a unicellular organism this means that the total genome is successfully copied into each new generation. In the multi-cellular organism all cells contain an exact copy of the total genome (even though not fully expressed). Genes (base sequences) are faithfully passed from one generation to the next. The genes (base sequences) which the reader possess have been passed from generation to generation until they arrived in you now. With minor and rare modification the base sequences copied by DNA replication and successfully passed on through sexual reproduction.

3.4.3. State that DNA replication is semiconservative.(1)

State means to give a specific name, value or other brief answer without explanation or calculation. The mechanism of semi-conservative replication produces two descendent double helices that each contain one of the original polynucleotide chains. This need not have been the case as there are 3 possible mechanism for replication: Conservative replication in which the original molecule is completely retained an a new molecule (two new polynucleotide chains are combined). Semi-conservative replication in which each of the new double helices contains one of the original polynucleotide chains. Dispersive replication in which fragment of the original double helix serve as templates for the new DNA . The fragments are randomly arranged.

3.5.1Compare the structure of RNA and DNA.(3).

Compare means to give an account of similarities and differences between two (or more) items, referring to both (all) of them throughout.

3.5.2 Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase.(2).
Outline means to give a brief account or summary. The DNA helix is opened at the position of the gene. The helix is unwound by RNA polymerase RNA nucleotides are found in the nucleus space. One of the polynucleotide chains act as a template for mRNA Free nucleotides base pair with DNA nucleotides The phosphodiester bonds on the mRNA chain are formed by RNA polymerase mRNA is a single polynucleotide chain but the base thymine is replaced by Uracil. After the mRNA is complete the molecule detach's from the DNA and leaves the nucleus for the cytoplasm ribosomes. The DNA helix reforms.

3.5.3 Describe the genetic code in terms of codons composed of triplets of bases.(2)
Describe means to give a detailed account. The genetic code: A polynucleotide is a sequence of bases Bases are either A T G or C There are 4 bases which operate in sets of 3 (a triplet).= 43possible triplets of DNA =64 triplets There are 20 common amino acids Therefore 64 triplets are mapped to 20 amino acids However there is a 'punctuation' triplets. Therefore the mapping of the code is 64: 21 The genetic code is first transcribed into mRNA The mRNA codons can be mapped to a specific amino acid. The mapping is 64 triplets: 64 codons: 21 Degenerate code:

DNA is a degenerate code since there are more than one triplet or codon that maps to an amino acid or punctuation. mRNA codon AUG codes for Methionine and is a START signal for translation. mRNA codon UAA, UAG, UGA are all stop codons punctuating the code. GGU, GGC, GGA and GGG all code for amino acid glycine.

3.5.4 Explain the process of translation, leading to polypeptide formation.(3)

Explain means to give a detailed account of causes, reasons or mechanisms. mRNA is translated into an amino acid sequence (mapping above) The location of translation is the ribosomes in the cytoplasm. Ribosomes are also composed of RNA (rRNA) which acts as a catalyst for the translation of the mRNA. Free ribosomes form polypeptides (proteins ) for internal cell use. Ribosomes on the endoplasmic reticulum synthesis proteins for secretion. mRNA from the nucleus locates onto the ribosome. The start codon (initiation codon) AUG occupies one of two rib some site. In this image the second site is occupied by CUG codon. The ribosome moves along the mRNA One mRNA can have many ribosomes (polysome) which accelerates protein synthesis. Activation is a process in which Transfer RNA (tRNA) molecules attach to specific amino acids. The tRNA molecule an anti-codon, three bases that are complementary to the codons on mRNA. In heterotrophs the amino acids for activation come form consumed protein in the diet. The first codon (AUG) bonds to the tRNA anti-codon UAC. This tRNA carried the amino acid Methionine. The second tRNA (GAC) binds to the second site with mRNA codon CUG The second tRNA carried the amino acid Leucine. Note that codon-anticodon binding is antiparallel The link between the tRNA and the amino acid Methionine is broken. The bond energy is transferred to form a peptide bond between methionine and Leucine. The first tRNA is released form the ribosome first site. This tRNA molecule moves away to pick up more methionine. The ribosome move one mRNA codon to the right (in this image). mRNA now occupied site one on the ribosome The mRNA codon is UGC which has the complementary tRNA of ACG and is charged with Serine. This occupied site site on the ribosome. The bond between tRNA and Leucine is broken. The bond energy is transferred to form a peptide bond between Leucine and Serine. The tRNA for leucine is released form site one. Then ribosome shift to the right and the process repeats itself until the stop codon is encountered. As the amino acid chain is built the polypeptide self assembles into the correct shape. It essentially folds up due to intra-molecular forces such as hydrogen bonds.

3.5.5 Discuss the relationship between one gene and one polypeptide.(3)
Discuss means to Give an account including, where possible, a range of arguments for and against the relative importance of various factors, or comparisons of alternative hypotheses. Theory: One gene is transcribed and translated to produce one polypeptide. Some proteins are composed of a number of polypeptides and in this theory each polypeptide has its own gene. e.g. haemoglobin is composed of 4 polypeptides (2 of each type) and there is a gene for each type of polypeptide. This theory, like so many in biology has exceptions. e.g. 1) Some genes code for types of RNA which do not produce polypeptides. 2) Some genes control the expression of other genes.

3.6.1 Define enzyme and active site.(1)

Define means to give the precise meaning of a word, phrase or physical quantity. globular proteins catalysts which speed up biological reactions unchanged by the reaction specific to their substrate active site is the position on the enzyme occupied by the substrate affected by temperature and pH

3.6.2 Explain enzymesubstrate specificity. (3)

Explain means to give a detailed account of causes, reasons or mechanisms. a) Large globular protein enzyme b) Active Site where the substrate combines to the enzyme c)Substrate which fits the active site d) Activated complex. The substrate is weakened to allow the reaction. e)Unchanged enzyme/ re-used at low concentrations f) Product of the reaction

3.6.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity.(3)
Explain means to give a detailed account of causes, reasons or mechanisms. Effect of temperature on the rate of an enzyme catalysed reaction: (a) As the temperature increases enzyme stability decreases. The kinetic energy of the enzyme atoms increases causing vibrations in the enzyme molecule that lead to the hydrogen bonds to breaking, shape changes in the active site. (b) As the temperature increases the kinetic energy of the substrate and enzyme molecules also increases. Therefore more collisions of the substrate with the active site and the formation of activated complex's and product. The rate of reaction is increasing. (c) The optimal temperature (X) is the highest rate of reaction. Compromise between decreasing enzyme stability and kinetic energy of the reactants. (d) Higher temperature increases the kinetic energy of the enzyme atoms so much that they break bonds, change shape of the active site. The effect of pH on the rate of an enzyme catalysed reaction: pH also affects the rate of reaction of an enzyme catalysed reaction. At the optimal pH (a) or (b) the maximum rate of reaction is achieved. Above or below the optimal pH the rate decreases. The change in rate is because bonds are made and broken which change the shape of the active site and therefore decrease the rate of reaction.

The two enzyme shown in the image illustrate the fact that different enzymes can have very different optimal pH.

Effect of substrate concentration on the rate of an enzyme catalysed reaction: (a) As the substate concentration is increased the rate of reaction increases. There are more collisions between the substrate and the enzyme such that more activated complex's are formed and therefore product per unit time. (b) Further increases in substrate also increase the rate but proportionately less than previously. The number of occupied active site is increasing and there is competition for the active site. (c) The rate is constant. The enzyme active site is fully saturated with substrate such that adding more substrate does not increase the rate of reaction. The enzymes molecules are fully occupied converting substrate to product and any substrate must await a free active site before conversion to product.

3.6.4 Define denaturation.(1)

Define means to give the precise meaning of a word, phrase or physical quantity. Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties. Temperature: Temperature rises cause the average kinetic energy of the enzyme atoms to increase. This vibration breaks the weakest bonds first, which in the enzyme are the hydrogen bonds. The breaking of bonds, changes the shape of the enzyme. Change the shape of the enzyme changes the shape of the active site. Change the shape of the active site prevents substrate from entering. The rate of reaction reduces or stops. pH: At pH lower than the optimal pH the concentration of H+ in the solution will be higher than normal. The hydrogens will tend to be attracted to electronegative regions of the enzyme protein. Bonds are formed or changed as a consequence of the additional H+ which changes the shape of the enzyme molecule. Changes in shape, change the active site shape. Changes in active site shape reduces the ability of the substrate to bind with the active site. This reduces the rate of reaction that changes substrate to product. The rate of reaction reduces. For pH values above the optimum breaks bonds in the same way and have the same reductions in the rate of reaction

3.7.1 Define cell respiration. (1)

Define means to give a the precise meaning of a word, phrase or physical quantity. Syllabus definition: Cell respiration is the controlled release of energy from organic compoundsin cells to form ATP. ATP or Adenosine triphosphates is the molecule which directly fuels the majority of biological reactions. Everyday each person will hydrolyse (reduce) 1025 ATP molecules to ADP. The ADP is reduced back to ATP using the free energy from the oxidation of organic molecules.

3.7.2 State that, in cell respiration, glucose in the cytoplasm is broken down by glycolysis into pyruvate, with a small yield of ATP.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Location: Cytoplasm Process: Glycolysis Substrate: Glucose Products: 2 Pyruvate and a small amount ATP Glycolysis does not use oxygen.

of

3.7.4 Explain that, during aerobic cell respiration, pyruvate can be broken down in the mitochondrion into carbon dioxide and water with a large yield of ATP. (3)
Explain means to give a detailed account of causes, reasons or mechanisms. Location: Mitochondria Substrate: Pyruvate Products: ATP, Carbon dioxide, water and heat. The production of ATP in the aerobic pathway is much greater than in either glycolysis or the anaerobic alternatives. The oxygen breathed in during ventilation is sent form the lung into the blood and then transported to the cell. The oxygen diffuses into the cell and then into the mitochondria for aerobic respiration. Cellular respiration: This diagram is a summary of the complete aerobic pathway. The by-product carbon dioxide is excreted and of course the heat produced is important in thermoregulation.

3.8.1 State that photosynthesis involves the conversion of light energy into chemical energy.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Location: chloroplast or prokaryotic equivalent. Reaction: Traps light energy (photons) and converts it into chemical energy. Organisms: Prokaryotic and Eukaryotic Substrate: Inorganic CO2 and H2O Products: Organic compounds (sugars) and O2 Environments: Aquatic environments with light, terrestrial environments with light. There are even extremophiles that can photosynthesis at some extreme latitudes and altitudes. At extreme high temperatures we see photosynthesis in geothermal active regions.

3.8.2 State that light from the Sun is composed of a range of wavelengths (colours).(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Light form the sun is composed of a range of wavelengths (colours). The visible spectrum to the left illustrates the wavelengths and associated colour of light. Combined together these wavelengths give the 'white' light we associate with full sunlight. The shortest wavelengths are the 'blues' which have more energy. The longer wavelengths are the 'reds' which have less energy.

3.8.3 State that chlorophyll is the main photosynthetic pigment.(1)

State means to give a specific name, value or other brief answer without explanation or calculation. Chlorophyll is the main photosynthetic pigment. This is where light energy is trapped and turned into chemical energy.

The head of the molecule is polar and composed of a ring structure. At the heart of this ring structure is the inorganic ion magnesium. This is the light trapping region of the chlorophyll molecule. The tail of the molecule is non polar and embeds itself in membranes in the chloroplast. There are other pigments, reds, yellows and browns but these are only usually seen in the experimental chromatography or if you have been lucky enough to witness the autumnal colours of deciduous trees in a temperate climate.

3.8.4 Outline the differences in absorption of red, blue and green light by chlorophyll.(2)
Outline means to give a brief account or summary The 'peaks' show which wavelength of light are being absorbed. Look at the x-axis for colours of light absorbed at the 'peaks'. The main colour of light absorbed by chlorophyll is red and blue. The main colour reflected (not absorbed) is green. Hence why so many plants are seen as green, the light is reflected from the chlorophyll to your eye.

3.8.5 State that light energy is used to produce ATP, and to split water molecules (photolysis) to form oxygen and hydrogen.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. (a) Light is absorbed by chlorophyll molecules (green) on membranes inside the chloroplast. This is the light trapping stage in which photons of light are absorbed by the chlorophyll and turned into chemical energy (electrons). (b) The chemical energy (electrons) is trapped in making ATP. Photolysis(c): Water used in photosynthesis is split which provides: hydrogen for the formation of organic molecules. (C6H12O6) oxygen gas is given off.

3.8.6 State that ATP and hydrogen (derived from the photolysis of water) are used to fix carbon dioxide to make organic molecules.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. H+ from the splitting of water are combined with carbon dioxide to form organic compounds like sugar. Bonds are formed between the carbon, hydrogen and oxygen using the energy from ATP (which came form the sun). C, H, O are enough to form lipids and carbohydrates. With a Nitrogen source amino acids and therefore proteins can be made. Plants have this remarkable ability to manufactory all their own organic molecules and by definition all the basic organic molecules required by all life forms.

3.8.7 Explain that the rate of photosynthesis can be measured directly by the production of oxygen or the uptake of carbon dioxide, or indirectly by an increase in biomass.(3)
Explain means to give a detailed account of causes, reasons or mechanisms. Processes like photosynthesis and respiration can be measured by either: Depletion of substrate. Accumulation of products Investigation: Photosynthesis: Carbon dioxide + water ----> Organic molecule + Oxygen The rate of photosynthesis can therefore be measured by:

Depletion of substrate which includes measuring how much carbon dioxide has been used or how much water is used. Accumulation of product which might include measuring how much oxygen is produced or organic molecules (biomass) produced.

3.8.8 Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis.(2)
Outline means to give a brif account or summary. The effect of temperature on the rate of photosynthesis: Photosynthesis is a biological reaction and like all other such reactions there are steps that require the presence of enzymes. Temperature as we have already met is a change in the average kinetic energy of the particle. The graph the left should look familiar as this is the same one covered in the section on the effect of temperature on the rate of an enzyme catalysed reaction. (a) Increasing rate of photosynthesis as the kinetic energy of reactants increases. (b) Maximum rate of reaction of photosynthesis at the 'optimal' temperature. (c) Decrease in rate of photosynthesis as the enzymes become unstable and denature.

The effect of carbon dioxide concentration on the rate of photosynthesis: Carbon dioxide is one of the reactants of the reaction so this graph is very much like the effect of substrate on the rate of reaction. (a) O2 is used up as the plant is not photosynthesising but only respiring. (b) As the concentration of the carbon dioxide (substrate) increases the rate of reaction increases. (c) The atmospheric levels of carbon dioxide and the associate rate photosynthesis. (d) Maximum rate of photosynthesis (see section e). (e) The is a range of values for different plants reaching their saturation level with carbon dioxide. One the saturation level has been reached there is no further increase in the rate of photosynthesis.

The effect of light intensity on the rate of reaction. Light energy absorbed by chlorophyll is converted to ATP and H+ see section 3.8.5. At very low light levels (a) the plant will be respiring only not photosynthesising. As the light intensity increases then the rate of photosynthesis increases. At high light intensities the rate becomes constant, even with further increases in light intensity there are no increases in the rate. The plant is unable to harvest the light at these high intensities and indeed the chlorophyll system can be damaged by very intense light levels.

4.1.1 State that eukaryote chromosomes are made of DNA and proteins.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. The chromosome is composed of two main molecules. a) DNA b) Proteins called histones. This image was taken shortly after DNA a replication but before the prophase. It is composed of two daughter chromatids joined at the centromere. The chromosome is super coiled by a factor around x16,000. The DNA molecule is about 1.8m long but is located in the nucleus which is only 10um in diameter!

4.1.2 Define gene, allele and genome. (1)

Define means to give the precise meaning of a word, phrase or physical quantity. Gene:a heritable factor that controls a specific characteristic. Allele: one specific form of a gene, differing form other alleles by one or a few bases only and occupying the same gene locus as other alleles of that gene. Genome: the whole genetic information of the organism.

4.1.3 Define gene mutation. (1)

Define means to give the precise meaning of a word, phrase or physical quantity. Gene mutation is a change in the base sequence of an allele. The changed base sequence may produce a different amino acid sequence in the protein translated. The changed base sequence may not change the protein because of the degenerate nature of the genetic code. The expression of the mutated gene may or may not be beneficial to the organism. Substances that cause mutation are called mutagens and include chemicals and radiation.

4.1.4 Explain the consequence of a base substitution mutation in relation to the processes of transcription and translation, using the example of sickle-cell anemia.(3)
Explain means to give a detailed account of causes, reasons or mechanisms. Sickle cell anaemia is a genetic disease. Sickle cell anaemia at the tissue level: (a) Normal haemoglobin has two of four proteins changed in the mutation. (b) The normal biconcave disc shape of the red blood cell is changed to a 'sickle' shape. (c) In addition to not carrying oxygen correctly (anaemia) the cells also causes local clots (infarctions) such as is shown in the kidney tubules. This leads to necrosis (death) of the tubules, kidney damage, kidney failure and possible to death.

4.2.1 State that meiosis is a reduction division of a diploid nucleus to form haploid nuclei.(1)
State means to give a specific name, value or other brief answer without explanation or calculation.

Meiosis is a reduction division of a diploid nucleus(2n) to form a haploid nucleus (n). For clarity the nuclear membrane has been omitted from the diagram. (a) The cell is in G1 of the interphase and has a total of 2 chromosomes, 2n=2. (b) The S phase of the interphase is DNA replication. (c) In G2 of the interphase the cell has two daughter chromatids per chromosome, the cell mass of DNA has doubled. (d) Meiosis occurs in a series of phases similar to mitosis ut with significant differences. (e) The diploid cell has divided to form haploid gamete cells (n=1). (f) The homologous pair of chromosomes has been separated (red from blue). One diploid cell which undergoes meiosis produces four haploid gametic cells.

4.2.2 Define homologous chromosomes. (1)

Define means to give the precise meaning of a word, phrase or physical quantity. Homologous chromosomes form pairs within the nucleus and during cell division. The name suggest that both members of the pair share certain structural characteristics. They are the same length of chromosomes. They have the same shape of chromosomes. They carry the same genes in the same gene loci. The forms of the gene found on the homologous pairs are the alleles of the gene that an individual may posses. Note that for every gene there are normally two alleles in the individual.

4.2.3 Outline the process of meiosis, including pairing of homologous chromosomes and crossing over, followed by two divisions, which results in four haploid cells. (2)
Outline means to give a brief account or summary. Meiosis is a form of cell division that produces gametes. It takes place in the reproductive organs and shows variation in how long the process occurs. Although meiosis can produce millions of gametes in a short period of time in comparison to mitosis in the body it is relatively rare. The stages of meiosis are shown below but begins with some diagrams about Interphase as a reminder. In the diagrams homologous pairs are shown in different colours ((red with blue), (purple with green)). The organism shown is an animal cell with a diploid number (2n)= 4. Therefore we expect to see four gametes each with a haploid number (n) =2. Meiosis I: This is the first of two sets of divisions. In meiosis one the prophase, metaphase, anaphase and telophase will divide the cell into two and separate the homologous pairs. This is perhaps the most significant step in terms of genetics. Interphase: (a) The nuclear membrane is intact and the chromosomes inside cannot be seen. At this stage the chromosomes are not greatly coiled or condensed which allows genes to be expressed. Each DNA molecule is about 1.8m long but still wound sufficiently such that it can be contained inside a 10um nucleus. (b) In the G1 stage of the Interphase each chromosome is a single DNA molecule (+histones). Here we can see (although in-reality you cannot since the nucleus is intact) that there are four chromosomes and the diploid number of the cell is 2n=4. Red and blue are a homologous pair as are green and purple. (c) In S1 of the interphase the DNA molecules replicate. Each copy (sister chromatids) are held together at the centromere (black dot). The cell is now preparing for the meiotic division in which: Chromosome number will be halved and the Homologous chromosomes will be separated (d):Early prophase, the nuclear membrane is breaking down. The spindle of microtubules is forming from opposite ends of the cell.

Centrioles organise the spindle construction at the poles of the cell. (e) The pairs of sister chromatids attach to the spindle microtubules at the centromere. The DNA is condensing by super coiling, this will reach it peak in the metaphase. (f) The pairs of chromatids will move up and down the between the poles but gradually move towards the equatorial plate (centre) of the cell. The nucleus has now disappeared and the chromosomes are dense enough to be seen with a light microscope. Note that the red and blue homologous pair are 'crossing over' , see metaphase for details. (g) The metaphase is marked by all pairs of sister chromatids aligned on the equator. The chromosomes are at their most condensed and therefore most visible at the metaphase. (h) Cross-over. Notice that the chromosome of one homologous chromosome is exchanging with the chromosome of the parallel non-sister chromosome. Cross-over is the exchange of genetic material between non-sister chromatids during Prophase I but is most readily seen during the metaphase. The point at which the chromosomes exchange genetic information is called the chiasma. (i) Early anaphase with the homologous pairs are aligned together on the equatorial plate of the cell. The spindle microtubules contract and pull the homologous pairs (alleles) apart. The homologous pairs separate one to either pole. This is the case with all homologous pairs. (j) Late anaphase the pairs of chromatids are moving to the poles. Notice that there has been an exchange of genetic material on the 'arm' of the red and blue homologous pair. New combinations of genes are not found on the same chromosome. (K) Illustrates how to identify anaphase by the 'arrow' shape make by the pair of sister chromatids points towards the poles. (l) chromosomes are now in two sets at opposite ends of the cell. Each set contains one from each of the homologous pairs. In some species a nuclear membrane may form, in others there is a progression straight into Prophase II. The cell membrane 'pinches' towards the centre in a 'cleavage furrow' the membrane will fuse at a central point and the cell will have divided in half. This marks the end of meiosis one (reduction division) in which the homologous pairs have been separated. Meiosis II: involves the separation of the sister chromatids and looks very like mitosis. (m) The nuclear membrane breaks down if present. Spindles reform ( shown here in the vertical plane only to distinguish from the diagrams above). Centrioles begin the organisation of the spindle microtubules. Pairs of sister chromatids will attach one to each spindle microtubule set. (n) All Pairs of sister chromatids aligned on the equatorial plate of the cell. (o) The spindle fibres contract and the pairs of sister chromatids separate. Each pole receives one of the chromosomes ( one chromatid). (p) Nuclear membranes form around each of the tetrad of haploid game cells. Notice that each cell contains two chromosomes n=2 (haploid). Notice that the homologous pairs are separated (no red with blue, no purple with green) There are some unusual chromosomes with exchanged genetic material due to cross-over.

4.2.4 Explain that non-disjunction can lead to changes in chromosome number, illustrated by reference to Down syndrome (trisomy 21). Objective level (3)
Explain means to give a detailed account of causes, reasons or mechanisms. Non-disjunction is an error in meiosis produce cells with unusual combinations of chromosomes. (a) This is the diploid parental cell (2n=2) (b) S-phase involves DNA replication during the interphase. (c) Pairs of sister chromatids are formed during the interphase (d) meiosis should separate; i) Homologous pairs ii) sister chromatids, so that each cell contains one chromosome (in this example). (e) Has an extra red chromosome so that sister chromatids have failed to separate during meiosis II. This games has one extra chromosomes (f) This gamete has one less chromosome that it should have (none in this case). (g) These gametes are normal Non-disjunction can also occur during meiosis I in which case all the tetrad are affected.

4.2.7 Analyse a human karyotype to determine gender and whether nondisjunction has occurred.(3)
Analyse means to interpret data to reach conclusions. karyotyping can be carried out when: Chromosomes from the metaphase are available. Appropriate staining techniques are used to reveal characteristic banding patterns. Count the number of chromosomes. Size of the sister chromatids can be compared to find the homologous pairs Position of centromeres. Human Karyotyping exercise. The human karyotype has already been organised for you. Try to spot the abnormal condition and then try to identify its name and the symptoms of the condition.

4.3.1 Define genotype, phenotype, dominant allele, recessive allele, codominant alleles, locus, homozygous, heterozygous, carrier and test cross.(1)
Define means to give the precise meaning of a word, phrase or physical quantity.

4.3.2 Determine the genotypes and phenotypes of the offspring of a monohybrid cross using a Punnett grid.(3)
Determine means to find the only possible answer. It is possible using genetic crosses to determine the genotype and phenotype of the offspring. The method used is called the Punnett square which is a simple grid which allows the genotypes and phenotypes to be determined methodically. When you begin genetic crosses it is worth writing out in full the calculation and only later start to abbreviate your calculations. This may seem very time consuming but it will prepare you properly for the questions asked in the examination. In the following example a very long hand form is used that includes images of chromosomes and alleles to help us track what it taking place. I strongly advise that students always think about what is taking place in the stages of meiosis and fertilisation. Monohybrid genetic crosses: genetics involving one gene. Example: Pea plants and the texture of their seed coats. The characteristic of seed coat texture is controlled by by one gene with two alleles. The seed coat can be either smooth or rough. Smooth coat is dominant to rough coat. One parent is homozygous dominant and the other is homozygous recessive.

4.3.3 State that some genes have more than two alleles (multiple alleles).(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Some genes have more than two alleles. An individual can only possess two alleles.

The population may contain many alleles for a given gene. Multiple alleles increases the number of different phenotypes. Multiple alleles can be dominant, recessive or co-dominant to each other.

4.3.4 Describe ABO blood groups as an example of codominance and multiple alleles. (2)
Describe means to a detailed account The ABO blood group system is an example of both a multiple allele and codominance condition. There are three alleles the base letter = I stands for immunoglobulin IA and IB are codominant to each other. Both these alleles are dominant to i The Allele hierarchy is IA = IB > i

4.3.6 State that some genes are present on the X chromosome and absent from the shorter Y chromosome in humans.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Male: Some genes are present on the X-chromosome but missing on the shorter Y-chromosome. The image of the male 23rdpair of homologous chromosomes represent the size difference in the two chromosomes. In the non-homologous region of the Xchromosome a male will only have one allele for any gene in this region. Genes in the homologous region have two alleles per gene and function just as other genes already described. Female: The complete length of the X-chromosome has a homologous pair on the other Xchromosome. Genes on the x-chromosome of female therefore have two alleles just like another gene on the other chromosomes.

4.3.7 Define sex linkage.(1)

Define means to give a precise meaning of a word, phrase or physical quantity. Genes on the non-homologous region of the X - chromosome are said to be sex linked. Females have two such chromosomes (therefore two alleles) and males only one. Phenotypes associated with recessive alleles are more common in males than in females. Assuming that this plant species is dioecious The recessive allele (a) is found on the non-homologous region of the X-chromosome. Males only get one allele for this gene. Males have a 50% chance of being recessive. Female have a lower risk (33.3 %) since they always receive 2 alleles. 'Recessive' males can pass on this condition( X-chromosome) to the 'daughter'. Cannot pass these conditions to the 'sons' as they pass the y-chromosome with no alleles.

4.3.8 Describe the inheritance of colour blindness and hemophilia as examples of sex linkage.(2)
Describe means to give a deatiled account Red Green colourblindness is a sex linked condition. The gene loci is on the non-homologous region of the X-chromosomes. Red Green colour blindness is more common in males than in females.

Males always inherit the colourblind allele form their mothers. Males cannot pass on colourblindness to their sons since the Y-allele does not have any of the colourblindness alleles. Inheritance of colourblindness: Calculation: Calculate the phenotypic ratio of a cross between a female carrier for red green colour blindness and a normal vision male. Haemophilia Haemophilia is a recessive, sex-linked genetic disorder. Persons suffering from haemophilia are unable to produce clotting factor. The haemophiliac allele (Xh)is recessive to the normal allele (XH). The gene is located on the non-homologous region of the x-chromosome. Haemophilia is more common in men than women. Males inherit the allele from their mother and develop the disease. Since (until recently) the prognosis for survival was poor and haemophiliac males did not survive to pass on the allele to their daughters (its on the X-chromosome). Therefore female haemophilia where rare. Haemophilia can occur in the children where the mother is a carrier and a normal male. The mother is heterozygous for the allele (XH Xh) . The father carries the normal allele on the x-chromosome and none on the Y chromosomes (XH Y). We can see that from such a cross the probability of being a haemophiliac male is P=0.25 ( 25% or 1 in 4). Today with treatment haemophiliac males can survive until sexual maturity but they cannot have daughters who are normal for this condition, why? Historically the haemophiliac allele has played a significant role in history and not least amongst the royal families of europe.

4.3.9 State that a human female can be homozygous or heterozygous with respect to sex-linked genes.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Females can be homozygous or heterozygous for the sex-linked alleles

4.3.10 Explain that female carriers are heterozygous for X-linked recessive alleles.(3)
Explain means to give a detailed account of causes, reasons or mechanisms. Carrier are individuals that are heterozygous for the allele. The have both the dominant and the recessive (disease) allele. Females have two long x chromosomes (two alleles) but males have only one such chromosome (one allele). Heterozygous famales can carry the disease causing allele but are normal as they also have the dominant allele. To carry a disease causing allele in the heterozygote and be normal is called a ' Carrier'.

4.3.12 Deduce the genotypes and phenotypes of individuals in pedigree charts.(3)

Deduce means to give reach a conclusion from the information given. Often geneticists will carry out planned experiments in which breeding pairs are selected and the offspring phenotypes counted. However this is not acceptable or possible when working with humans. Instead geneticists have to collect information form about individuals and relatives within a family and construct diagrams of inheritance(family trees) called pedigrees. The chart show the typical symbol found in a pedigree chart.

Circles are female(1),(3),(5), (6). Squares are male (2), (4), (7). Black means that the individual is affected by the condition,(3). White indicates that the individual is unaffected by the condition. Mating: Female 1 and male 2 (Horizontal line) Children: Female (3) and male (4) are the children of (1) and (2). Individuals (6) and (7) are the paternal grandchildren of (1) and (2).

4.4.1 Outline the use of polymerase chain reaction (PCR) to copy and amplify minute quantities of DNA. (2)
Outline means to give a brief account or summary PCR is the cloning of DNA (amplification). Copies are made and the amount of DNA can be rapidly increased. Useful if the source of DNA is small. Temperature is used instead of enzymes like helicases (95oC ). DNA polymerase is thermostable to protect it against the reaction temperatures. This is an automated process and can produce sufficient DNA in 20 cycles.

4.4.2 State that, in gel electrophoresis, fragments of DNA move in an electric field and are separated according to their size.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Sample of fragmented DNA is placed in one of the wells on the gel. An electrical current is passed across the gel. Fragment separation is based on charge and size. Large fragments move slowly. Negative fragments are moved to the right. Gel after staining: This diagram shows the separation of 6 separate mixtures of DNA. The dark bands to the left are those with a large molecular mass or a positive charge (a) contains 5 fragments of DNA. Each bands corresponds to a group of DNA molecules of the same size and charge. (b) and (c) have the same bands. They are identical

4.4.3 State that gel electrophoresis of DNA is used in DNA profiling.(1)

State means to give a specific name, value or other brief answer without explanation or calculation. Gel electrophoresis is used in DNA profiling. Satellite (Tandem repeating) DNA are highly repetitive sequences of DNA from the non coding region of DNA. Different individuals have a unique length to their satellite regions. These can be used to differentiate between one individual and another. There are different types of 'DNA fingerprinting' for different circumstance (a) The mothers chromosome provides a DNA STR cutting the chromosome with particular restriction enzymes. (b)The fathers chromosome provides the same fragment using the same restriction enzymes. (c) The mother DNA fragment placed in the well of the gel. (d) The mother DNA fragment placed in the well of the gel.

(e) Mothers fragment produces 5 STR and moves a short distance along the electrophoresis gel. (f) fathers fragment produces 2 STR and moves a longer distance along the electrophoresis gel. (g) The child is heterozygous for the fragment having on homologous chromosome form the father and one form the mother. The technique can be used in: Forensic crime investigations Parentage Issues Animal breeding pedigrees Disease detection

4.4.4 Describe the application of DNA profiling to determine paternity and also in forensic investigations.(2).
Describe means to give a detailed account. Paternity Investigation: Trying to determine who are the biological parents of a child. The DNA fragments in the child comes from the mother and father. A band present in the child must come either from the mother or from the father Comparing male 1 with the child then male 2 with the child. Interpretation: The bands on the child's fragments are either found on the mother or the male1. Male 1 therefore is this father of this child. None of the Male 2 bands appear in the child Forensic Investigation: A specimen of DNA is taken from the victim or the crime scene. DNA samples are taken from the 3 suspects. The bands are compared to associate the suspects but to eliminate the victims DNA from the specimens Interpretation: Note that the bands on the specimen are matched by the bands on the Suspect 1. This means that Suspect 1 was present at the crime scene. The law will still require to prove a crime was committed and then that Suspect 1 committed the crime

4.4.6 Outline three outcomes of the sequencing of the complete human genome. (2)
Outline means to give a brief account or summmary. identify all the approximate 30,000 genes in human DNA. determine the sequences of the 3 billion chemical base pairs that make up human DNA. store this information in database. improve tools for data analysis. transfer related technologies to the private sector. address the ethical, legal, and social issues (ELSI) that may arise from the project. To help achieve these goals, researchers also are studying the genetic makeup of several nonhuman organisms. These include the common human gut bacterium Escherichia coli, the fruit fly, and the laboratory mouse.

4.4.7 State that, when genes are transferred between species, the amino acid sequence of polypeptides translated from them is unchanged because the genetic code is universal.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. The genetic code is universal All known organisms use the same genetic code. Therefore in principle if we transfer a gene from one species to another it should still be transcribed and translated into the same protein.

4.4.8 Outline a basic technique used for gene transfer involving plasmids, a host cell (bacterium, yeast or other cell), restriction enzymes (endonucleases) and DNA ligase. (2)
Outline means to give a brief account of summary. Stage 1: obtaining the gene for transfer: Restriction enzymes are used to cut out the useful gene that is to be transferred. Note the 'sticky ends' of unattached hydrogen bonds. Stage 2. Preparing a vector for the transferred gene: Plasmids are small circular DNA molecules found in bacteria. These can be cut with the same restriction enzyme as above. This leaves the same complementary 'sticky ends' in the plasmid The plasmid can be cut at particular sites. These are called restriction sites and some are named in the diagram. Stage3. Recombinant DNA (a) plasmid that will be the vector (b) plasmid cut at restriction site Pstl (c) Source DNA cut with same restriction enzyme as plasmid to (d) (e) Recombinant DNA (f) unaffected plasmid Expression vectors: usually if a eukaryotic gene is inserted into the genome of a prokaryote it make very little of the desired gene product. Therefore additional factors are included in the vector plasmid 'package' which includes types of RNA. The final plasmid as outlined above containing these additional factors is called an' Expression vector'. Stage4. Isolation of transformed cells Recombinant DNA is introduced into the host cells Many cells remain untransformed Some cells are transformed to contain the recombinant DNA. These transformed cells must be separated from untransformed Stage 5. Product manufacture. The transformed bacterial cells are isolated. They are introduced into a Fermenter to be cloned. The bacterial population grows by asexual reproduction. The Recombinant DNA is copied along with the rest of the bacterial genome. In a fermenter the conditions for growth and reproduction are controlled. Once the bacteria express the transformed gene the product is produced. The next (long ) step is to isolate and purify the product. This is called downstream processing.

4.4.9 State two examples of the current uses of genetically modified crops or animals.(1)
State means to give a specific name, value or other brief answer without explanation or calculation. Genetically modified organism (GMO) is an organism containing a transplanted gene. The organism will express the gene and synthesis the protein. Factor IX : A human clotting factor is produces by genetically modified sheep. The protein (factor IX) is expressed in milk from which it must be isolated before use by haemophiliacs. A ewe is treated with fertility drugs to create super-ovulation. Eggs are inseminated. Each fertilised egg has the transgene injected. A surrogate ewe has the egg implanted for gestation. Lambs are born which are transgenic, GMO for this factor IX gene.

Each Lamb when mature can produce milk. The factor IX protein is in the milk and so must be isolated and purified before use in human.

4.4.10 Discuss the potential benefits and possible harmful effects of one example of genetic modification.(3)
Discuss means to give an account including, where possible, a range of arguments for and against the relative importance of various factors, or comparisons of alternative hypotheses. The advantages and disadvantages of GMO is a controversial topic with wide political, environmental, health and social effects. The following issues can be applied specifically to the above examples of GMO. The benefits of GMO include: Increased yields particularly in regions of food shortage. Yields of crops with specific dietary requirement such as vitamins and minerals. Crops that do not spoil so easily during storage. GM animals produce similar effect including higher meat yields. The disadvantages or concerns about GMO usually can be found: The foods (animal and plant) are considered un-natural and unsafe for human consumption. There is a risk of the escape of 'genes' into the environment where they may be passed to other organisms with unknown effects.

4.4.11 Define clone.(1)

define means to give the precise meaning of a word, phrase or physical quantity. Syllabus statement: ' Clone: a group of genetically identical organisms or a group of cells derived from a single parent'.

4.4.12 Outline a technique for cloning using differentiated animal cells.(2)

Outline means to give a brief account or sumarry. Somatic cells are differentiated that is specialised to a particular function. In the case of Dolly (1996) the cell was taken from the udder of the original sheep (1) that was to be cloned. Sheep (2) provides the egg cell after being stimulated to superovulated by the use of the hormone FSH. The nucleus is removed from the egg cell. This removes the genetic information of sheep (2). The cells are fused combining the nucleus of sheep (1) with the egg cell from sheep(2). The egg cell retains its ability to replicate chromosomes and divide by mitosis. The cell is grown 'in-vitro' until it reaches the16 cell stage this will then be implanted into a surrogate mother sheep. Sheep (3) is the surrogate mother sheep and is not related to any of the other sheep. There is a normal gestation period before the 'Clone lamb' is born. Lamb (4) is dolly the clone of sheep (1). They are genetically identical. However they will experience a different set of environmental conditions.It should be noted that this technique was tried many times before it was successful.

7.1.1 Describe the structure of DNA, including the antiparallel strands, 35 linkages and hydrogen bonding between purines and pyrimidines.(2)
DNA has a double stranded helix which has uniform diameter along its entire length. Both helices are right handed which allows it to fit within a defined three dimensional space. Two polynucleotide chains are 'anti-parallel', running in opposite directions The polynucleotides are form around the outside of the helix with the bases extending into the centre. Polynucleotide chains are held together by the bases (in centre) hydrogen bonding with bases on the opposite polynucleotide. The hydrogen bonding is specific and known as complementary base pairing.

7.1.2 Outline the structure of nucleosomes. (2)

The double helix has major and minor groves on its outer diameter. These groves expose chemical groups that can form hydrogen bonds. These chemical groups within DNA are bonded to by proteins. DNA is bonded to proteins called HISTONES. The diagram to the left is of a nucleosome: DNA is wound around and hydrogen bonded to eight histones. 146 DNA bases or 1.65 turns of the helix are associated with the 8 histones The combination of DNA and histones is secured by the 'H1 linker' protein.

7.1.3 State that nucleosomes help to supercoil chromosomes and help to regulate transcription.(1)
Supercoiling condenses the DNA molecule by a factor of X 15,000 Histones are responsible for the packaging of DNA at the different levels (diagram left). The metaphase chromosome is an adaptation for mitosis and meiosis. The fibre must be less condensed for transcription to occur during the interphase. Condensing controls if the genes are transcribed or not.

7.1.4 Distinguish between unique or single-copy genes and highly repetitive sequences in nuclear DNA.(2)
The 'gene coding region' (about 1.5 % of our DNA) codes for a polypeptide (around 25, 000 proteins). Around 3% of the human genome is regulatory coding for genetic switches which control development. The non-coding region function remains unclear but can be as much as 5-45% of the total genome. These regions are often made of highly repetitive sequences of bases each some 5-300 bases long. These are referred to as satellite regions. Due to the combination of bases in the repeating regions they tend to create dense and less dense DNA regions. These are the parts of DNA used in finger print technologies.

7.1.5 State that eukaryotic genes can contain exons and introns.(1)
Eukaryotic organisms have DNA which differs from prokaryotic organism Eukaryotic organism have non-coding regions within the gene called introns. These are copied when the gene is transcribed to produce pre-mRNA. The intron-RNA is edited out to form mature mRNA.

7.2.1 State that DNA replication occurs in a 5 3 direction.(1)

DNA replication has been outlined in section. The 5' (prime) end of the free nucleotide is added to the 3' (prime) end of the nucleotide chain that is already formed. (a) Shows a nucleotides in isolation. The 5 ' is orientated to the 3' so that DNA polymerase enzyme can form the phosphodiester bond between carbon 5 and carbon 3. (b) There is a polynucleotide chain already in place. Note the position of the free 3' on the left end of this chain. The free nucleotide 5' end is bonded covalently to the 3' end on the alreadyformed polynucleotide chain.

7.2.2 Explain the process of DNA replication in prokaryotes, including the role of enzymes (helicase, DNA polymerase, RNA primase and DNA ligase), Okazaki fragments and deoxynucleoside triphosphates. (3)
Ori is the point of origin (start) for DNA replication. Ter is the point at which the replication will finish. The DNA replication takes place under the control of a number of different proteins and enzymes here indicated as replication complex. In E. coli five such polymerases have been identified with DNA polymerase III being associated with most polymerisation of the pentose-phosphate backbone. Humans have as many as fourteen polymerases. Until recently it was thought that the replication complex moved over the DNA. New evidence now suggests that the replication complex is static and that the DNA is moved. (c) DNA molecule Shows the two anti-parallel polynucleotide chains. Note the position of the 5' and 3' ends of the chains but remember when working out the direction of replication we focus on the NEW strand. The parent strands of polynucleotide are coded red and blue in this diagram for clarity. New strands will be coloured green for ease of identification. (d) DNA Helicase enzyme The enzyme is unwinding the chain and breaking the bonds between the complementary base pairs (A-T, G-C). The position of the helicase and the opening of the DNA helix is called areplication fork. The helicase has parted the two polynucleotide chains. (e) This red original 'parent' strand is polymerised at the same time as the one below but for the purposes of this diagram is left till later in our model. The diagrams follows the building of the new polynucleotide chain on the blue side first. 3' prime to 5' prime on the original DNA strand. A free nucleotide (Green 1) complementary base pairs with the first 'blue' nucleotide in the parent strand. The free nucleotide (Green 2) complementary base pairs. DNA polymerase III joins the 5' to the 3' of the NEW STRAND. Prokaryotic DNA polymerases can work at around 1000 bases per second which means the whole circular (loop) can replicated between 20 and 40 minutes. (g) The nucleotide sequence is building up as a new polynucleotide using the original as a template. Specificity is maintained through complementary base pairing of A-T, G-C. The next nucleotide (Green 3) has base paired and is being polymerised by DNA polymerase III. The helicase is progressing just ahead of the DNA polymerase III creating the replication fork. Errors do occur in the replication process but there are biochemical proof reading, repairing and removal mechanisms. Retuning to the other parent polynucleotide (red). Since this was anti-parallel to the blue strand the template nucleotides (red) have the opposite direction to the blue ones. (h) Free nucleotides have complementary base paired with the first two template bases. Notice that the nucleotides cannot be joined as DNA polymerase is specific to joining 5' to 3'. DNA polymerase III like all enzymes has an active site that is specific to the 5' to 3' orientation of the two nucleotides to be joined. The chain is not polymerised at this stage. The bases continue to add working in behind the DNA helicase enzyme. (Upper Green 1-4). Below we have the polymerisation of the new strand on the 'blue' template as previously described in part (g).

(L) The red strand in which the nucleotides do not immediately polymerise is called the Lagging strand (since it lags behind) it forms on the "5 to 3' original DNA template. (m) Note that there are now a number of bases already in position forming the lagging strand (in reality this is about 100-200 nucleotides). DNA polymerase III can now work 'backwards' towards the ori joining the sugar phosphate backbone of the polynucleotide. On the lagging strand the DNA polymerase is working away from the replication fork. (n) On the Leading strand (new strand building on the blue template) the DNA polymerase III works towards or follows the helicase. The important point to note here is that the DNA polymerase only works by joining 5' nucleotides to 3' nucleotides on the established chain. The lagging strand is therefore made up of a number of short polynucleotide chains that need joining together. The short chains are called Okazaki fragments after the Japanese Biochemist Reiji Okazaki. Summary: This diagram is the usual version used to describe the process of leading and lagging strand polymerase activity. ( p) shows the orientation of the DNA helix (with helicase) for the diagram below. (q) Note the position of the replication fork with the DNA helicase opening the DNA chain. (r) The leading strand forming with DNA polymerase III On the lagging strand (top green) the new strand is presented as a number of Okazaki fragments. (s) The DNA polymerase III on this strand has to work from the beginning of each fragment towards the 3' free end of the lagging strand (away from the replication fork). DNA ligase is the enzyme that joins the fragments. Primers: In fact all polymerisation both leading and lagging strands actually begin with the addition of 'priming' RNA nucleotides. (u) RNA nucleotides (yellow) attach to the first few bases on the template through the action of a Primase enzyme. DNA polymerase III then adds DNA nucleotides to the Primer (v). Later the RNA primer is broken down and removed by DNA polymerase I DNA nucleotides are added to replaced the removed RNA nucleotides. The Pentose -phosphate backbone is joined by DNA ligase.

7.2.3 State that DNA replication is initiated at many points in eukaryotic chromosomes. (1)
Prokaryotic DNA polymerase can work at around 1000 bases per second which means the whole circular (loop) can replicated between 20 and 40 minutes. The eukaryotic DNA polymerase works much slower around 50 bases per second. With as many as 80 million bases to replicate the job is achieved in about one hour by having many replication forks

7.3.1 Transcription direction on the DNA molecule.

mRNA is composed of nucleotides based on Ribose sugar and four bases Uracil, , Adenine, Guanine and Cytosine. The 5' end of the nucleotide is added to the 3' of the already existing mRNA chain. This is a key point to learn in the interpretation, drawing and understanding of transcription.

7.3.2 Sense and anti sense strands of DNA.

The sense strand has the same base sequence as the transcribed mRNA except that the base thymine is replaced by the base uracil. The anti-sense strand acts as the template for the transcription of mRNA. The RNA nucleotides are polymerised along the sugar phosphate backbone by RNA polymerase.

7.3.3 Transcription in prokaryotes.

Initiation: The Promoter region allows the binding of RNA polymerase. The RNA polymerase is then able to: Find the anti-sense strand.

Find the start for transcription. Know the direction of transcription. The hydrogen bonds between the bases of the DNA helix are opened up by DNA helicase. The bases of the anti-sense strand ('3 to 5' for DNA) are exposed progressively. RNA nucleotides complementary base pair with the anti-sense nucleotide bases. The free nucleotides (nucleoside triphosphates) are based on RNA. The sugar is the pentose ribose and there are four different nitrogen bases. The nucleotides are adenine, guanine, cytosine and uracil.

Elongation: The RNA polymerase forms covalent bonds between the nucleotides. Free energy is released from the oxidation of the nucleoside triphosphates to form the bond. The bonds are formed by joining the 5' of the free nucleotide to the 3' end of the nucleotide already part of the mRNA chain. The RNA polymerase works along the nucleotides completing the pentose-phosphate backbone. The mRNA builds up with the RNA polymerase moving along the anti-sense strand joining the nucleotides. As with the other biochemical processes considered in the syllabus there are additional factor involved in transcription. These are not required for the examination. Termination: The RNA polymerase reaches the terminator and the RNA polymerase stops. The mRNA is complete Various factors result in the RNA polymerase being released and will return to catalyze another mRNA. The mRNA itself is released from the antis-sense strand. The mRNA strand in prokaryotes can be use straight away unlike the eukaryotic mRNA which requires further modification (see below).

7.3.4 Post transcriptional modification in eukaryotes.

Pre-mRNA has been produced through transcription of the anti-sense strand as described for prokaryotic transcription. (a) The non coding introns are spliced out of the mRNA. The introns are broken down in the nucleus. (b) The remaining mRNA is called mature mRNA and is exported from the nucleus to the cytoplasm for translation into the polypeptide.

7.4.1 Activation tRNA.

a) Amino acid which is specific to each tRNA. (b) CCA base sequence to which the amino acid is attached by the 'Activating Enzyme'. (c) Complementary base pairing sequence. Helical in shape. (d) 8 free bases non-pairing giving one loop of RNA. (e) 7 free bases non-pairing giving second loop of RNA. (f) Small open loop of RNA which is variable in shape between different tRNA. (g) Anti-codon (3 bases) which binds to the mRNA codon (3 bases) this is specific to the amino acids being carried. The anti-codon is complementary to the sense DNA. Activation specificity:how does the tRNA attach to the correct amino acid. shape of each tRNA is different. shape of the tRNA is defined by the loop and the helical sections. shape of the tRNA selects a specific enzyme (aminoacyl-tRNA synthetase). the enzyme adds a specific amino acid to the CCA base sequence (at 3' end of the tRNA) this requires ATP (energy). each amino acid has one or more tRNA molecules this again is an example of a degenerate code.

7.4.2 Ribosome structure.

 Proteins and Ribosomal RNA combine in the structure Large sub-unit and a small sub-unit Large sub-unit has three binding sites for tRNA molecules ( E, P and A site). Small sub-unit has a binding site for mRNA Ribosome Function: Ribosomes are enzymes. The catalyse the translation of mRNA into a polypeptide. Their substrate is mRNA. Each ribosome can catalyse the transcription of different mRNA.

7.4.3 Stages of translation.

There are three stages in translation ( just as in transcription) Initiation: In which the ribosome, tRNA and mRNA come together to begin the translation of the mRNA. Elongation: tRNA molecules attach to the mRNA based on the codon-anticodon recognition. Amino acids are brought together and polymerised into the primary structure of the polypeptide. Termination: mRNA and the ribosomes detach from one another. The polypeptide is released and the tRNA return to be charged with more amino acid.

7.4.4 Translation direction.

Translation of the mRNA takes place from the 5' free end to the free 3' end. Ribosomes move along the mRNA in this direction. The genetic code is translated from the 5' free end to the 3' free end.

7.4.5 Peptide bonds between amino acids.

During translation amino acids are joined together to form polypeptides. The specific sequence of amino acids is called the primary structure. Between each amino acid a peptide bond forms to join them together. In this example the amino acids are both Alanine in which the R group is a single hydrogen. The carboxyl acid end on the first amino acid is orientated to the amino group of the second amino acid. The -OH group and -H are removed to form water (condensation reaction). The bond forms between the terminal carbon on the first amino acid and the nitrogen on the second amino acid. The backbone of the molecule has the sequence N-C-C-N-C-C Polypeptides maintain this sequence no matter how long the chain. The R groups project from the backbone. As the amino acids are added in translation the polypeptide folds up into it specific shape.

7.4.6 Translation process.

The tRNA charged with Methionine has the anti-codon UAC. This is complementary to the start codon (mRNA) of AUG. The small sub unit of the ribosome associates with the Methionine tRNA. The small unit of the ribosome moves over the START codon. The large unit of the ribosome moves over the mRNA. There are three binding sites for tRNA on the large sub unit. A-(Amino acid) is the position which the new tRNA codon-anticodon binds making sure that the correct amino acid is in position. P-(Polypeptide) is the position in which the amino acid on the tRNA adds to the polypeptide. E-( Exit) is the position the tRNA (without amino acid) locates and is the released from the ribosome to become re-activated. The START codon (AUG) occupies the P site. The A site is free for the complementary tRNA to bind. Specificity is maintained by the codon-anticodon binding which is a major feature of the ribosome function.

 Both

In this sequence the A site has the codon CCG. The tRNA anticodon GGC which carried Proline hydrogen bonds with the codon bases. The codon -anticodon binding has placed the two amino acids methionine and proline beside each other. (a)The bond between the tRNA and methionine is broken. This releases free energy. (b)The free energy is used to form the peptide bond between methionine and proline. The large sub-unit then moves to three bases (one codon) towards the 3' end of the mRNA. units of the ribosome are now located over the second and third codons (a) The tRNA for methionine is on the E site and is released from the ribosome. It will beceom recharged with methionine in the cell cytoplasm. The tRNA for proline is in the P site. (b) The A site for the next tRNA is free and holds the codon base sequence GCU. The tRNA for Alanine has the anti-codon CGA which is complementary to the codon on the A site. The anticodon tRNA for Alanine complementary base pairs with the A site codon. The ribosome checks that this is the correct tRNA and therefore amino acid. The bond between the tRNA and Proline is broken. Free energy is released. A peptide bond is formed between Proline and Alanine. The peptide chain will be folding and shaping. The end of the codon sequence in mRNA has been reached. The ribosome encounters a termination sequence signaling the end of translation. The ribosome moves the alanine tRNA to the P site. The polypeptide is released from the translation process. The ribosome has no new codons read. The two sub units move and separate. The protein will now be further modified in either the endoplasmic reticulum, golgi or secreted in a vesicle.

7.4.7 Free and membrane bound ribosomes

Free ribosomes: Free ribosomes in the cytoplasm are associated with the synthesis of proteins for internal use in the cell. Ribosomes which are attached to the wall of the endoplasmic reticulum are associated with proteins which will ne placed into vesicles and secreted form the cell.

7.5.1 Levels of protein structure.

Proteins structures are describe on four levels: Primary Structure: The order/ number of amino acids in a polypeptide chain. This forms a -N-C-C-N-C-C-N-C-C- backbone to the molecules The primary structure is read from the NH2-- terminal to the --COOH terminal. Each amino acid is identified by its specific R group Met-Gly-Ala-Pro is a four amino acid polypeptide beginning with Methionine-GlycineAlanine-Proline Most polypeptides are between 50- 1000's amino acids long. (Insulin =51, Titin= 26, 926) There are 20 different amino acids in living things. It is therefore possible to have an incredible diversity of primary structures. In reality on a small fraction of these polypeptides are found in living things. Indeed it is one of the revelations of molecular biology that the diversity of polypeptides within the cells of different types of organism is relatively low. Secondary Structure: The primary structure of a polypeptide has group projecting from the N-C-C backbone. These groups can attract each other and through hydrogen bonding cause a folding of the amino acid chain. There are three noted forms of secondary structure: 1. Alpha Helix:

Formed from Hydrogen Bonds There are 3.6 amino acid residues per turn of the helix. Notice the regular helix shape. This is drawn as a helix that follows the -N-C-C-N-C- backbone of the polymer Alpha helices are often the basis of fibrous polymers (see below). Right handed helix.

2. Beta-pleated sheet Beta-pleated sheets are so called because of the 'pleated' or folds when view form the side. The polypeptide chain is much more stretched out in comparison to the alpha helix. This 'sheet' often has twists that increase the strength and rigidity of the structure. (Try twisting a sheet of paper to see this effect). 3. Open Loops Alpha helices and beta-pleated sheets are often connected together by short chains of amino acids which form neither of the previous structures but simply link other sections together (see tertiary). These loops often connect the more recognisable helices and pleated sheets. They are in fact often important regions of proteins including the active sites of enzymes. Tertiary Structures: Tertiary structure is the three-dimensional conformation of a polypeptide. In other words there are folds in a polypeptide chain. The polypeptide folds just after it is formed in translation. The shape is maintained by intra-molecular bonds Hydrogen bonds Ionic Bonds Disulphide Bridges Quaternary Structure: A number of tertiary polypeptides joined together. Haemoglobin is a quaternary structure. It is composed of four different polypeptide chains. Each chain forms a tertiary structure called a haem group.

7.5.2 Fibrous and globular proteins.

Fibrous proteins are water insoluble, long and narrow proteins. They are associated with providing strength and support to tissues. Collagen is the basis of the connective tissue and is composed of three left handed helices. This is the most common protein in animals. Keratin is another common fibrous protein which is composed of seven helices. keratin is the major protein in hair and nail structure. Globular proteins are near soluble (colloids). They have more compact and rounded shapes. They are associated with functions such as: pigments and transport proteins( haemoglobin, myoglobin, lipoproteins) immune system (Immunoglobulins). There is now a more sophisticated method of describing protein structure called structural motifs. Examples are haemoglobin and Immunoglobulin (antibodies).

7.5.3 Polar and non polar amino acids in protein structures.

Cell membrane proteins: Those sections of the molecule that contain polar amino acids are hydrophilic and can exist in contact with water. Polar amino acids allow the positioning of proteins on the external and internal surface of a cell membrane. Both cytoplasm and tissue fluid are water based regions. The non-polar amino acids allow the same protein to site within the phospholipid bilayer. The lining of the channel itself will be of polar amino acids to allow the diffusion of charged molecules and ions.

Enzymes: Polar amino acids within the active site of an enzyme allow a chemical interaction between the substrate and the enzyme to form an activated complex. This transitional state allows the weakening of internal molecular structure and therefore the reduction of the activation energy.

7.5.4 Examples of proteins.

Hormones: Insulin is a 51 amino acid single polypeptide. Produced in the beta-cells of the pancreas islets. main target tissues is muscle cells and liver cells. Function: bring about the uptake of glucose across the cell membrane and the storage of glucose as the insoluble polymer glycogen. Immunoglobulin: Immunoglobulins are otherwise known as antibodies. Produced by the plasma cells in an immune response to an infectious antigen. Great variation exists in the heavy chains which allows a response to virtually any possible antigen surface. Due to their high specificity in identifying antigen they are used in a wide variety of bio technologies. Enzyme: Enzymes reduce the energy of activation and allows a biochemical reaction to reach equilibrium more quickly. Enzymes are large globular proteins often with prosthetic groups. This image shows catalase which is a very large molecule. The maximum number of substrate molecules that can be converted into product per second (excess substrate) is called the 'turn-over rate'. Liver catalase has a turnover rate of around 4x107s-1 which is quick fast! Gas transport: Haemoglobin molecules transport oxygen to respiring tissues. They are contained within the erythrocytes (red cells ) of the circulatory system. Composed of four haem groups each associated with a prosthetic Fe2+ion. Each haem group can carry an oxygen atom.

7.6.1 Metabolic pathways.

Chemical changes in living things often occurring with a number of intermediate stages. Each stage has its own enzyme. Catabolic pathways breakdown molecules Anabolic pathways build up molecules Linear Chain Pathways: Enzyme (1) is specific to substrate 1. This is changed to product 1. Enzyme (2) is specific to product1 which becomes the substrate and converted to product 2. Enzyme (3) is specific to products which becomes the substrate and converted to product 3. Product 3 is called the 'End product'. e.g. Glycolysis Cyclic Pathways: The initial substrate is fed into the cycle. Enzyme (1) combines the regenerated 'intermediate 4' with the initial substrate to catalyses the production of intermediate 1. Enzyme (2) is specific to intermediate 1 and converts intermediate 1 to intermediate 2 Enzyme (3) is specific to intermediate 2 and catalyses it conversion to product and intermediate 3. Enzyme (4) is specific to intermediate 3 and catalyses its conversion to intermediate 4. The difference is the regeneration of the intermediate, in this case intermediate 4. Examples Krebs cycle and Calvin cycle.

7.6.2 Induced-fit model.

The lock and Key hypothesis does not explain the broad specificity of some enzymes. Also the molecular shape of active sites is not always complementary to that of the substrate. The induced fit attempts to over come these difficulties.

a) Note the active site is not complementary to the substrate b) At the complexing of the enzyme and substrate the active site changes to accommodate the substrate. The structure of the enzyme allows a certain amount of adaptation to the substrate. hence the broad specificity of some enzymes. States (c), (d) and (e) happen in the same way as the lock and key hypothesis.

7.6.3 Activation energies.

Exergonic reactions: Enzymes lower the activation energy of the chemical reaction that they catalyse. In the activated complex or transition state energy is put into the substrate to weaken the structure. This allow the reaction to occur with a minimal amount of additional energy required. Normal activation energy would cause damage to the proteins of the cell. Thus reduced activation energy make these reactions possible in a cell. After the product is formed energy is released. Exergonic reactions release more energy than the activation energy. .

7.6.4 Competitive and non-competitive inhibition.

Inhibitors are substances that reduce or completely stop the action of an enzyme Inhibition can act on the active site (competitive) or on another region of the enzyme molecule(non-competitive). The competition in the former being for the active site of the enzyme. Competitive inhibition: The substrate and inhibitor are chemically very similar in molecular shape. The inhibitor can bind to the active site Enzyme-inhibitor complexing blocks substrate from entering the active site. This blockage reduces the rate of reaction. If the substrate concentration is increased it occupies more active sites than the inhibitor. Therefore the substrate out-competes the inhibitor for the active site. The rate of reaction will increase again. Non-competitive Inhibition: The substrate and the inhibitor are chemically different in molecular structure. The inhibitor cannot bind to the active site. The inhibitor can bind to another region of the enzyme molecule. The bonding of the inhibitor with the enzyme causes structural changes in the enzyme molecule. The active site changes shape. The substrate cannot bind therefore the rate of reaction decreases.

7.6.5 End product inhibition of enzyme pathway

Enzyme pathways can be controlled by concentration of products from the end of the pathway. The principle is illustrated by the transamination (change R group) of the amino acid threonine to isoleucine Isoleucine the end product, this molecule can inhibit the enzyme Threonine Deaminase The inhibition occurs at an inhibition site on the enzyme but not the active site An excess of end product (Isoleucine) switches off any more production of that product, isoleucine. At high concentrations, Isoleucine attaches to the inhibition site of Threonine deaminase. This attachment causes the active site of the enzyme to change blocking any further reaction. Isoleucine is used up in cellular processes that require this particular amino acid. The isoleucine concentration in the cell falls and so the Isoleucine that is attached to the enzyme detaches. This amino acid is also used up in the various cellular processes. With the inhibitor removed the the active site then becomes active again and the pathway switches back on. The isoleucine is again in production but once high concentrations are reached the pathways is once more inhibited. The process then cycles on in alternating stages of production and inhibition

Notice the similarity with non-competitive inhibition. This mechanism makes the pathway self-regulating in terms of product manufacture.

8.1.1 Forms of oxidation and reduction.

In respiration the oxidation of organic compounds is coupled to the reduction of ADP to ATP. The oxidation of ATP is then coupled to biological processes such as muscle contraction of protein synthesis. Oxidation: often associated with the release of energy Reduction: often associated with the gain of energy

8.1.2 Glycolysis.
Location: Cytoplasm of all cells Outline: Oxidation of Glucose (6 carbons) to two Pyruvate (3 carbons) is coupled to the reduction of ADP to ATP In the following models the hydrogen and oxygen are not shown. The models show the number of carbons in each molecule not the structural formula. The first stage actually begins by phosphorylating glucose to a hexose diphosphate. The phosphate groups allow a stronger interaction between the hexose and its enzyme. This stage involves the breaking of the hexose diphosphate into two triose phosphate molecules. The triose phosphate is an intermediate in many biochemical reactions. The phosphate group allows the sugar to form stronger interaction with the next enzyme in the pathway. This is the main oxidative stage of glycolysis which results in the formation of ATP and NADH + H+ Each Triose phosphate is oxidised to a 3 carbon molecule called Pyruvate Each TP has hydrogen removed (oxidation) to reduce one NAD+ to NADH Each TP adds a phosphate to Adenosine Diphosphate reducing this to ATP (substrate level phosphorylation) Note that each Triose phosphate releases enough energy for the formation of two ATP Glycolysis takes place in the cytoplasm of the cell. It does not require oxygen. The hexose sugar (glucose) is converted into two 3C atoms compounds called pyruvate. Two ATP are consumed but four are produced making a net gain of 2 ATP Two NADH + H+ are produced which will yield more ATP when they are transferred to the mitochondria and oxidative phosphorylation. Yield: 2 Pyruvate + 2 ATP + 2NADH + 2H+

8.1.3 Structure of the mitochondria.

Location of aerobic respiration Pyruvate, the product of glycolysis can be further oxidised here to release more energy. Mitochondria are only found in eukaryotic cells. Cells that need a lot of energy will have many mitochondria ( liver cell) or can develop them under training (muscles cells). There is a double membrane. The inner membrane is folded to form 'cristae'. There is a space between the two membranes which is important for creating a place to concentrate H+ The inner space is called the matrix. Mitochondria contain some of their own DNA (mDNA).

8.1.4 Aerobic respiration.

Stages in the Aerobic respiration: Link Reaction: Pyruvate is transported into the matrix of the mitochondria

Krebs cycle: carbon fragments (C2) are progressively decarboxylated to yield ATP and reduced coenzymes Electron Transport System: reduced coenzymes are used to generate more ATP. Link Reaction: Pyruvate(3C) is transported to the matrix of the mitochondria A large Co-enzyme A joins with the 3 carbon fragment pyruvate. Pyruvate is decarboxylated removing a single carbon as carbon dioxide. The remaining fragment is an Acetyl group and temporarily forms Acetyl CoA. NAD+ is reduced to NADH + H+. Acetyl (2C) is already transported into the matrix. Krebs Cycle: oxidative decarboxylation of the C2 Acetyl group (CH3CO). This cycle has been broken down into 4 steps. The carbons from the original glucose molecule are shown in purple and those of mitochondria molecules in blue. Acetyl CoA joins with the C4(acceptor)group CoA is released to transport more pyruvate into the matrix A C6 fragment is formed (citric acid) C6 (Citric Acid) is oxidatively decarboxylated. A C5 group is formed. The Carbon is given off as Carbon Dioxide NAD+ is reduced to NADH + H+ The C5 fragment is oxidised and decarboxylated further to a C4 compound. Again the carbon removed forms carbon dioxide. NAD+ is further reduced to NADH + H+. The final stage in the cycle has the C4 acceptor regenerated. There is a reduction of NAD+ to NADH + H+. FAD (Coenzyme)is reduced to FADH2 . ADP is reduced to ATP

8.1.5 Oxidative phosphorylation in terms of chemiosmosis.

On the inner membrane of the mitochondria (Cristae) there are membrane proteins. The oxidation of reduced coenzymes (NADH + H+and FADH2) allows these membrane proteins to pump protons (H+) into the space between the outer and inner mitochondrial membranes. The electrons released from the reduced coenzyme flows along the electron transfer chain of proteins. These H+ form a high concentration (low pH) within this space. They diffuse back to the matrix through a channel in a membrane protein called an ATP synthetase. This flow of H+ through the ATP synthetase drives an enzyme reaction that brings about the phosphorylation of ADP to ATP. The membrane shown is only the inner mitochondrial membrane folded into the cristae. The NADH is oxidised and the reduced proteins transport H+from the matrix into the space between both mitochondrial membranes. There is electron transfer down the chain of proteins in a series of oxidation and reductions. For each NADH, 3 Moles of H+ are pumped into the space. Oxygen supplied by the respiratory/ circulatory system acts as the final H+acceptor forming water. The FADH2 is oxidised and the reduced membrane proteins pump H+into the space between the mitochondrial membranes. The H+diffuse back to the matrix driving the ATP Synthetase to produce ATP. One FADH2 produces two moles of hydrogen ions. Again, the H+ are accepted by oxygen to form water. A concentration gradient has been created between the high concentration of H+ between the mitochondrial membranes and the lower concentration in the matrix. ATP synthetase is an enzyme embedded in the cristae membrane. H+create an electrochemical gradient (chemical potential energy). The H+pass through a channel in the enzyme driving the motor. The motor spins bringing together ADP and Pi to produce ATP

8.1.6 Relationship between the structure and function of the mitochondria.

1. Cristae folds increase the surface area for electron transfer system. 2. The double membrane creates a small space into which the H+ can be concentrated. 3. Matrix creates an isolated space in which the krebs cycle can occur.

8.2.1 Chloroplast Structure.

(a) Cell wall (b) Double membrane (c) Starch grain (d) Grana (e) Thylakoid (f) Stroma

Internal membranes called thylakoids which is the location of the light dependent reaction Stroma surrounding the thylakoids and inside the double membrane. This is the location of the light independent reaction that includes the Calvin cycle. The stroma often contains starch grains and oil droplets both products of photosynthesis

8.2.2 Stages of photosynthesis.

Photosynthesis occurs in two main phases: Light Dependent Reaction in which 1. Energy of sun is trapped by chlorophyll molecules (oxidation) 2. Photon energy is used to raise the energy of electrons which escape the chlorophyll (oxidation) 3. This energy is coupled to the reduction of ADP to ATP and the coenzyme NADP+ is reduced to NADPH + H+ . 4. The reaction must have light to take place. 5. This reaction takes place on the thylakoid membranes. The Light Independent Reaction 1. which uses the chemical energy from the LDR to fix atmospheric carbon into organic molecules such as glucose. 2. The process does not require light and can occur in both the light and dark periods. 3. This reaction takes place in the stroma

8.2.3 Light-dependent reaction.

Light energy is converted into chemical energy. Chlorophyll molecules are attached to the thylakoid membranes. They are often associated with accessory pigments and other proteins to form Photosystem. At the centre of all photosystem are forms of chlorophyll a each of which is specialised to absorb a particular wavelength of light. Electrons within the chlorophyll absorb the energy from photons and this raises them to higher 'excited' states. Excited electrons are more easily lost from the chlorophyll which is a form of oxidation Summary of Cyclic Photophosphorylation: Non-cyclic photophosphorylation has the following feature: 1. Light energy is trapped in two Photosystem. 2. ATP is produced. 3. The co-enzyme NADP+is reduced Breakdown of Non-cyclic photophosphorylation: Light is absorbed by chlorophyll a in Photosystem II (number of different chlorophyll's working together). PSII absorbs light best at 680nm and is designated as P680 The chlorophyll absorbs the light energy and converts this to chemical energy in the form of electrons.

Photosystem II is oxidised, releasing electrons. The electrons from PS II pass along membrane proteins in a series of redox reactions(in thylakoids) The reduced membrane protein pumps H+from the stroma into the space inside the thylakoids.

At the same time as a), Photosystem I (different chlorophyll combination) absorbs light with a peak absorption of 700 nm. The chlorophyll molecule releases electrons in the oxidation of PS I PS I is now oxidised. The electrons pass from PSI to other membrane proteins named here as ferrodoxins These proteins bring about the reduction of NADP+ to NADPH + H+ NADPH is found in the stroma and is used in the light independent reaction PS I has been oxidised and lost its electron. To continue absorbing light PSI must be reduced back to its 'ground state' The source of electrons for this reduction are those passed to cytochrome from PSII PS II must also be reduced and returned to its 'ground state' to maintain light absorption The source of electrons is water. Electrons are removed form water for PS II which leaves a source of H+and Oxygen Oxygen is a waste product of photosynthesis but very important to aerobic organisms There is a high concentration of H+ in the thylakoid lumen The H+diffuse back to the stroma through the channel pore of the ATP Synthetase This drives the phosphorylation of ADP to ATP Non-Cyclic Photophosphorylation: When the ratio of NADPH + H+: NADP+ is high then only ATP is produced in a cyclic process. PS I does not generate NADPH + H+ but sends its 'excited' electron to a proton pump. 1. PS I is oxidised releasing an 'excited' electron. 2. The electron reduces the membrane proton pump. Protons are pumped into the thylakoid space. This generates ATP. 3. The electrons are cycled back to PS I for its own reduction.

8.2.4 Photophosphorylation.
Photophosphorylation in terms of chemiosmosis. Chemiosmosis theory is based on: Accumulation of a high concentration of H+ which is due to proton pumping. There being a concentration difference between two places which is the high concentration of H+in the thylakoid space and a lower concentration in the stroma. The protons diffuse through the core of the ATP synthetase. This drives the motor mechanism of the structure resulting the in the reduction of ADP to ATP. Note how the same mechanism was seen on the cristae membranes in respiration.

8.2.5 Light-Independent reaction.

The energy trapped from sunlight in the light dependent reaction (ATP and NADPH) is used to fix carbon from carbon dioxide into organic molecules. The reaction called the Calvin Cycle takes place in the stroma and is controlled by enzymes. Ribulose Bisphosphate Carboxylase (Rubisco) allows carbon (carbon dioxide) to be fixed into an initial organic molecule RBCase therefore can be seen as a link between inorganic(non-living) and the organic (living) e.g. Primary productivity

Step by Step: Carbon Fixation: The single carbon in carbon dioxide is first trapped by Ribulose bisphosphate (5C) to form a 2 molecules of Glycerate-3-phosphate (GP). Reduction:

GP is reduced to a Triose-phosphate(TP) in the process NADPH and ATP are oxidised to provide the energy TP is used to manufacture a variety of organic molecules including Glucose-phosphate Regeneration: Some of the TP is used to regenerate Ribulose Bisphosphate. This will allow more carbon dioxide to be fixed from the atmosphere.

8.2.6 Structure and function of the chloroplast.

8.2.7 Action spectrum and absorption spectrum.

White light from the sun is a short section of the much larger electromagnetic spectrum. White light is made up of a range of wavelengths that correspond to the colours we can see. Longer wavelength have less energy (red light) whilst shorter wavelengths have more energy include blue light. Absorption spectra are obtain from samples of pigment. Using a colorimeter different wavelengths of light are passed through and the absorption is measured. This absorption spectra for chlorophyll shows: absorption of blue light absorption of red light green light is reflected. Notice the Y-axis is rate of photosynthesis The rate of photosynthesis is measured at different wavelengths. The maximum rate are at the blue end and red end of the visible spectrum. The lowest rates are in the yellow greens. Chlorophylls are absorbing blue and red light well but not green.

8.2.8 Limiting factors on the rate of photosynthesis.

Light Intensity Carbon dioxide concentration Temperature However here we consider the concept of the limiting factor. The rate of complex biochemical pathways like respiration and photosynthesis are affected by a number of factors. The rate of photosynthesis can be affected by light intensity, carbon dioxide concentration and temperature. Under a given set of conditions only one factor will affect the rate of photosynthesis this factor is at its minimum and is called the limiting factor. As has been shown photosynthesis is a process with many individual steps or stages. The overall rate of photosynthesis is determined by the step that is proceeding most slowly (rate-limiting step). Therefore each factor e.g.. light, temperature etc can become the limiting factor in any on the rate-limiting steps.

10.1.1 Chromosome behaviour during the phases of meiosis.

Meiosis has a number of overall functions Reduce the chromosome number by half from diploid(2n) to haploid(n). Each gamete nuclei will contain one chromosome from every homologous pair. Increase genetic diversity.

This section assumes that the information in section 4.2. Student should review that work before adding the following details. Additional notes are provided for HL students. Meiosis consists of two rounds of cell division. M1 : Reduction division which separates the chromosomes of a homologous pairs. Each gametic cell will contain one of the two chromosomes from every homologous pair. This has great genetic significance since it separates the alleles for every gene. M2: Separation of the 'sister chromatids'. After M1 the gametic cells contain a pairs of 'sister chromatids'. The separation of the 'sister chromatids' also produces variation in gametes since this will isolate the 'recombinants alleles' due to cross-over in a gamete cell. Meiosis is proceeded by the interphase which includes the replication of DNA (S-Phase) so that when meiosis begins, it starts with each chromosome represented by a pair of 'sister chromatids' held together by a centromere.

M1 Separation of the homologous Pairs (a-d).

a) Prophase I : Chromatin begins to condense with super coiling reaching it peak(x16, 000) in metaphase I. A process called synapsis which brings together the chromosomes of a homologous pair (do not confuse with sister chromatids) begins. This only lasts until cross-over has occurred. After cross-over has completed in metaphase I the homologous pairs are held together only at the chiasmata. The chiasmata are the positions of DNA exchange which is called cross-over. The non-sister chromatids of a homologous pair adhere along the length of the chromosomes. The four chromatids from each pair of homologous chromosomes are called a tetrad or bivalents. Cross-over occurs during the prophase but is not visible until the final condensation at metaphase. During the condensation of the chromosomes, a point is reached when the homologous pair seems to repel each other except at regions called chiasma. The centromere's of one pair of 'sister chromatids' particularly repels the centromere region of the other in the homologous pair. Crossing over increases the genetic diversity of the gametes and therefore increases variation in successful fertilizations. Nuclear membrane breaks down and the nucleoli disintegrates. In animal cells the centrioles are placed at either pole of the cell and serves as a focal point for the organisation of the spindle microtubules. Microtubules attach to the centromere's of each pair of homologous chromosomes. (b) Metaphase I: Homologous pairs are aligned on the equatorial plate. Homologous pairs have been held together by the chiasmata but this is not shown for clarity. Each 'pair of sister chromatids' in a homologous pair is attached to microtubule. Each half of the spindle is attached to the opposite poles. (c) Anaphase I: The spindle microtubules contract pulling the pair of 'sister chromatids' to one pole and the other pair of 'sister chromatids' for the same homologous pair to the other pole. It seems that this process is a combination of spindle contraction (75%) and a centromere motor (25%) pulling the pairs of chromatids along the spindle. At this point the chiasmata break down and the exchange of lengths of DNA including alleles of genes is complete. (d) Telophase I: The genetic material is now organised at the two pole of the cell. Each pole contains a pair of 'sister chromatids' , one from each homologous pair. In some species the nuclear envelop re-forms whilst in others there is an immediate progression to M2 and prophase II.

M2 Separation of the 'Sister Chromatids (e-i).

(e) Prophase II: Chromosomes condense again if required. There has been no chromosome replication but each chromosome is represented by a pair of 'sister chromatids'. The spindle forms in a new plane for each of the two cells. The positioning of the plane for the spindle is critical for later development. The 'sister chromatids' attach to the spindle microtubule at the region of their centromere. The 'pairs' then move around, beginning to align for the metaphase II. (f) Metaphase II: The pairs of sister chromatids line up at the equator of each cell. The are now very condensed and at their most visible. The cohesin joining together the arms of the chromatids has broken down except at the centromere. The chromosome takes on the characteristic open X -shape. Each of the chromatids will separate at the next stage. (g) Anaphase II: The combination of spindle contraction and the centromere 'motor' pulling on the spindle microtubule, pulls the sister chromatids apart. One chromatid from each pair goes to each pole. Each chromatids can now be referred to as a chromosomes again. The chromosomes from the pair of 'sister chromatids' are not identical due to the exchange of DNA during cross-over (not shown in diagram). (h) Telophase II : The chromosomes gather at opposite pole and form the new haploid nuclei. The nuclear envelope material that has remained within the cytoplasm re-forms around the sets of chromosomes. There are now two nuclei per cell, each is haploid. (i) Cytokinesis: The cells divide to form a tetrad of four haploid nuclei. The type of division depends on this being an animal or plant cell. In the sexually mature human male the process of meiosis and the production of mature motile sperm cells (haploid) takes over a month. In the human female the process begins during embryonic development but then undergoes a period of 'dormancy'. The cell still diploid is held at prophase I until ovulation many years later. Other species have refined this process in different ways as an adaptation to their own ecology.

10.1.2 Outline the formation of chiasmata in the process of crossing over.

(a) Interphase: During the interphase each of the chromosomes in a homologous pair replicates. The two copies of a chromosome are held together by a centromere. The replicated chromosome pair are described as 'sister chromatids'. (b) Prophase I: Molecules, 'cohesin's', hold the homologous pairs close together. This facilitates the homologous pair joining to the same spindle microtubule. The exchange of DNA between parallel arms of the non-sister chromatids takes place. (c) Prophase I -Metaphase I: Still in prophase the DNA molecule exchanges length of DNA. In metaphase the chiasmata are more obvious as the 'cohesin's' are broken down. The homologous pairs seem to repel each other particularly at the centromere. However they remain linked together at the chiasma. This is also the peak phase of condensation. (d) Anaphase I: The separation of the homologous pairs in the anaphase finally breaks the chiasma connections. The DNA exchange on the arms of the chromosomes is complete. (e) Anaphase II: In anaphase II the 'sister chromatids' are separated into different cells. Some of the chromosomes are new recombinants of DNA containing part maternal and part paternal chromosomes. In effect this has created new combinations of linked genes.

10.1.3 Genetic variation due to cross over and random orientation in metaphase 1.
Genetic variation in gametes: 1 Crossover. Increasing genetic diversity in gametes which in turn increases genetic diversity of the populations. Crossover as described in the previous section creates new combinations of linked genes. This creates new genotypes for the gametes that are not due to random assortment.

10.2.1 Calculate and predicting the genotype and phenotype of offspring of dihybrid crosses involving unlinked autosomal genes.
Terminology: Dihybrid crosses involve two genes which control two characteristics. There are complications of these patterns as illustrated in the calculations that follow. Unlinked genes are found on different chromosomes and can be segregated by random assortment of meiosis/ metaphase II Autosomal are those chromosomes other than the XY gender determining chromosomes (not sex linked).

10.2.2 Distinguish between autosomes and sex chromosome.

In some species there is one homologous pair which carry genes that determine gender. This work has already been covered in the section on sex chromosomes. There are other genetic conditions (also covered in topic 4) associated with the so called 'sex linked" conditions.

10.2.3 How crossing over between non-sister chromatids of a homologous pair in prophase I results in an exchange of alleles.
Read the next section 10.2.4 first and understand the concept of a linkage group which is key to understanding of this particular assessment statement. The alleles A is linked to B, a is linked to b. The homologous pairs are held together like this during prophase I. The crossover point occurs above the loci for gene A and below the gene loci for A. The position at which the exchange occurs is called the chiasma. The recombinants will form between non-sister chromatids which are crossing over. The homologous pairs remain attached at the chiasma until anaphase I when they are pulled apart. After anaphase II, the chromatids are separated. The linked genes are: A with B a with b recombinant a with B recombinant A with b Genetic crosses: The genotype of the gametes from meiosis above would be AB and ab. After cross over there would also be Ab and aB. However most cells of the cell undergoing meiosis to form a gamete will not cross over between these two points. Therefore: Gametes Ab and ab will be high frequencies. Gametes Ab and aB will be low frequency. When cross over occurs there will be low frequency of recombinants produced.

10.2.4 Define linkage group.

The genotypes of an organism is AaBb. This looks like a dihybrid such as those in the sections above. The two genes would be on separate homologous pairs, however there is an alternative and this is known as linkage. These two genes are actually on the same chromosome. The A allele is linked to the B allele along the length of DNA. The a allele is linked to the b allele along the length of DNA. In the image take after S-phase, the homologous pair is aligned as it would be found in Prophase I of meiosis.

It might be predicted that during gamete formation of fertilisation that the A allele will be followed by the B allele. This would be more like carrying out two simultaneous monohybrid crosses.

10.2.5 Crosses between two linked genes.

Example: Sweat Peas (Lathyrus odoratus) This famous example comes from the work of W. Batson who rediscovered the work of Mendel and carried out his own experiments in the early 20 Century. Allele Key: Flower colour Purple (P) and Red (p) Pollen grain shape, Long (L) and short (l) A cross was made between a plants that where heterozygotes at both gene loci (PpLl).

When dealing with linked genes the linkage group is drawn on the horizontal with a line representing the chromosome. Using the above cross the cross would be represented. Parental phenotypes are the same PpLl being heterozygous at both gene loci. If the gene for flower colour and pollen grain shape are linked then the genotypes are shown as left. The gamete genotypes are shown to the left with the alleles for flower colour and pollen grain shape shown linked by the horizontal line. The possible recombinants from cross over are shown for one parent only. These recombinant gametes will be at low frequency. Cross: The grid shows the cross with the possible fertilisations in the boxes. There four expected genotypes. There are four recombinant genotypes but cannot be observed from phenotypes. There are two recombinant phenotypes which would be actually observed during the experiment. Batson's results: The result of W Batson's cross showed that the result are neither dihybrid and unlinked (9:3:3:1)or linked with no linkage (3:1) The result shows a rough 3:1 ratio of Purple/Long : Red/Short There are also recombinant phenotypes at much lower frequency.

10.2.6 Identification of offspring as recombinants in a dihybrid cross involving linked genes.

Recombinants are recognised by: Unpredicted combinations of characteristics. (Red Long, Purple Short). Low frequency of new combinations of phenotype. Statistical significant difference from ratios expected from either dihybrid and unlinked (9:3:3:1)or linked with no linkage (3:1)

10.3.1 Define Polygenic inheritance

Definition: 'A single characteristic that is controlled by two or more genes' Each allele of a polygenic character often contributes only a small amount to the over all phenotype. This makes studying the individual alleles difficult. In addition environmental effects smooth out the genotypic variation to give continuous distribution curves.

10.3.2 Polygenic inheritance contribution to continuous variation.

a) Is the genotypic variation in the population. The more genes involved with the characteristic the greater the number of phenotypic classes. (b) Phenotypic variation = genotypic variation + environmental variation. The environmental component smooth the genotypic category differences. example of polygenic effect is human skin colour. This is controlled by as many as 4 genes each with its own alleles. As the number of genes increases the amount of phenotypic variation increases. The alleles control the production of melanin which is a pigment that colours skin. In this example the calculation is performed with 2 genes each with 2 alleles. The cross is between two individuals heterozygous at both alleles Allele Key A= add melanin (with a nominal value of 1 unit)

a= no melanin added (with a nominal value of 0 units) B= adds melanin (with a nominal value of 1 unit) b= no melanin added (with a nominal value of 0 units)