Advanced Higher Biology Course Specification PDF

Cells and protein Key area Depth of knowledge required Suggested learning activities 1 Laboratory techniques for biologists (a) Health and safety Substances, organisms, and equipment in a Hazards in the lab include toxic...

Cells and protein Key area Depth of knowledge required Suggested learning activities 1 Laboratory techniques for biologists (a) Health and safety Substances, organisms, and equipment in a Hazards in the lab include toxic or corrosive Become familiar with standard laboratory laboratory can present a hazard chemicals, heat or flammable substances, rules and with risk assessment. pathogenic organisms, and mechanical equipment. Hazard, risk, and control of risk in the lab by Risk is the likelihood of harm arising from risk assessment exposure to a hazard. Risk assessment involves identifying control measures to minimise the risk. Control measures include using appropriate handling techniques, protective clothing and equipment, and aseptic technique. (b) Liquids and solutions Method and uses of linear and log dilution Dilutions in a linear dilution series differ by an Become familiar with the use of measuring equal interval, for example 0·1, 0·2, 0·3 and cylinders, pipettes, burettes, autopipettes, so on. and syringes. Dilutions in a log dilution series differ by a constant proportion, for example 10-1, 10-2, 10-3 and so on. Version 4.1 44  Cells and protein Key area Depth of knowledge required Suggested learning activities Production of a standard curve to determine Plotting measured values for known an unknown concentrations to produce a line or curve allows the concentration of an unknown to be determined from the standard curve. Use of buffers to control pH Addition of acid or alkali has very small Practise making solutions using buffers and effects on the pH of a buffer, allowing the pH measuring the pH with a meter or an of a reaction mixture to be kept constant. indicator. Method and uses of a colorimeter to quantify Calibration with appropriate blank as a Use a colorimeter or spectrophotometer to concentration and turbidity baseline; use of absorbance to determine calibrate a known solution and determine an concentration of a coloured solution using unknown using, for example, Bradford protein suitable wavelength filters; use of percentage assay. transmission to determine turbidity, such as cells in suspension. (c) Separation techniques Use of centrifuge to separate substances of More dense components settle in the pellet; differing density less dense components remain in the supernatant. Paper and thin layer chromatography can be The speed that each solute travels along the used for separating different substances such chromatogram depends on its differing as amino acids and sugars solubility in the solvent used. Details of how to carry out these procedures are not required. Version 4.1 45  Cells and protein Key area Depth of knowledge required Suggested learning activities Principle of affinity chromatography and its A solid matrix or gel column is created with use in separating proteins specific molecules bound to the matrix or gel. Soluble, target proteins in a mixture, with a high affinity for these molecules, become attached to them as the mixture passes down the column. Other non-target molecules with a weaker affinity are washed out. Principle of gel electrophoresis and its use in Charged macromolecules move through an Use protein electrophoresis to identify separating proteins and nucleic acids electric field applied to a gel matrix. different muscle proteins. Native gels separate proteins by their shape, Native gels do not denature the molecule so size and charge that separation is by shape, size and charge. SDS–PAGE separates proteins by size alone SDS–PAGE gives all the molecules an equally negative charge and denatures them, separating proteins by size alone. Proteins can be separated from a mixture IEP is the pH at which a soluble protein has Determine the isoelectric point of a soluble using their isoelectric points (IEPs) no net charge and will precipitate out of protein, such as casein. solution. If the solution is buffered to a specific pH, only the protein(s) that have an IEP of that pH will precipitate Proteins can also be separated using their Soluble proteins can be separated using an IEPs in electrophoresis electric field and a pH gradient. A protein stops migrating through the gel at its IEP in Version 4.1 46  Cells and protein Key area Depth of knowledge required Suggested learning activities the pH gradient because it has no net charge. Further details of electrophoresis are not required. (d) Detecting proteins using antibodies Immunoassay techniques are used to detect and identify specific proteins These techniques use stocks of antibodies Knowledge of monoclonal antibody Research the use of monoclonal antibodies with the same specificity, known as production is not required. in the diagnosis and detection of disease. monoclonal antibodies An antibody specific to the protein antigen is The ‘label’ is often a reporter enzyme Use the ELISA technique to identify the linked to a chemical ‘label’ producing a colour change, but presence of specific antigens. chemiluminescence, fluorescence and other reporters can be used. In some cases the assay uses a specific antigen to detect the presence of antibodies. Western blotting is a technique, used after SDS–PAGE electrophoresis The separated proteins from the gel are transferred (blotted) onto a solid medium Version 4.1 47  Cells and protein Key area Depth of knowledge required Suggested learning activities The proteins can be identified using specific antibodies that have reporter enzymes attached (e) Microscopy Bright-field microscopy is commonly used to Refresh skills in the use of microscopes and observe whole organisms, parts of making slides. organisms, thin sections of dissected tissue or individual cells Discuss the ethics of dissection in an educational context. Fluorescence microscopy uses specific fluorescent labels to bind to and visualise certain molecules or structures within cells or tissues (f) Aseptic technique and cell culture Aseptic technique eliminates unwanted Aseptic technique involves the sterilisation of Investigate methods of sterilisation of microbial contaminants when culturing micro- equipment and culture media by heat or containers, equipment, and materials. organisms or cells chemical means and subsequent exclusion of microbial contaminants. A microbial culture can be started using an Many culture media exist that promote the Culture bacterial, yeast, and algal cells using inoculum of microbial cells on an agar growth of specific types of cells and aseptic technique. medium, or in a broth with suitable nutrients microbes. Version 4.1 48  Cells and protein Key area Depth of knowledge required Suggested learning activities Animal cells are grown in medium containing Growth factors are proteins that promote cell Investigate some of the different types of growth factors from serum growth and proliferation. Growth factors are culture media and their uses. essential for the culture of most animal cells. In culture, primary cell lines can divide a limited number of times, whereas tumour cells lines can perform unlimited divisions Plating out of a liquid microbial culture on solid media allows the number of colony- forming units to be counted and the density of cells in the culture estimated Serial dilution is often needed to achieve a suitable colony count Method and use of haemocytometer to Use a haemocytometer to make an estimate estimate cell numbers in a liquid culture of cell count. Vital staining is required to identify and count viable cells 2 Proteins (a) The proteome The proteome is the entire set of proteins expressed by a genome The proteome is larger than the number of genes, particularly in eukaryotes, because Version 4.1 49  Cells and protein Key area Depth of knowledge required Suggested learning activities more than one protein can be produced from a single gene as a result of alternative RNA splicing Not all genes are expressed as proteins in a Genes that do not code for proteins are particular cell type called non-coding RNA genes and include those that are transcribed to produce tRNA, rRNA, and RNA molecules that control the expression of other genes. The set of proteins expressed by a given cell Some factors affecting the set of proteins type can vary over time and under different expressed by a given cell type are the conditions metabolic activity of the cell, cellular stress, the response to signalling molecules, and diseased versus healthy cells. (b) The synthesis and transport of proteins (i) Intracellular membranes Eukaryotic cells have a system of internal Because of their size, eukaryotes have a membranes, which increases the total area of relatively small surface area to volume ratio. membrane The plasma membrane of eukaryotic cells is therefore too small an area to carry out all the vital functions carried out by membranes. The endoplasmic reticulum (ER) forms a network of membrane tubules continuous with the nuclear membrane The Golgi apparatus is a series of flattened membrane discs Version 4.1 50  Cells and protein Key area Depth of knowledge required Suggested learning activities Lysosomes are membrane-bound organelles containing a variety of hydrolases that digest proteins, lipids, nucleic acids and carbohydrates Vesicles transport materials between membrane compartments (ii) Synthesis of membrane components Lipids and proteins are synthesised in the ER Rough ER (RER) has ribosomes on its cytosolic face while smooth ER (SER) lacks ribosomes. Lipids are synthesised in the smooth endoplasmic reticulum (SER) and inserted into its membrane The synthesis of all proteins begins in cytosolic ribosomes The synthesis of cytosolic proteins is completed there, and these proteins remain in the cytosol Transmembrane proteins carry a signal A signal sequence is a short stretch of amino sequence, which halts translation and directs acids at one end of the polypeptide that the ribosome synthesising the protein to dock determines the eventual location of a protein with the ER, forming RER in a cell. Version 4.1 51  Cells and protein Key area Depth of knowledge required Suggested learning activities Translation continues after docking, and the protein is inserted into the membrane of the ER (iii) Movement of proteins between membranes Once the proteins are in the ER, they are transported by vesicles that bud off from the ER and fuse with the Golgi apparatus As proteins move through the Golgi Molecules move through the Golgi discs in Research post-translational modification and apparatus they undergo post-translational vesicles that bud off from one disc and fuse activity in trypsinogen and trypsin. modification to the next one in the stack. Enzymes catalyse the addition of various sugars in multiple steps to form the carbohydrates. The addition of carbohydrate groups is the major modification Vesicles that leave the Golgi apparatus take proteins to the plasma membrane and lysosomes Vesicles move along microtubules to other membranes and fuse with them within the cell Version 4.1 52  Cells and protein Key area Depth of knowledge required Suggested learning activities (iv) The secretory pathway Secreted proteins are translated in ribosomes Peptide hormones and digestive enzymes on the RER and enter its lumen are examples of secreted proteins. The proteins move through the Golgi apparatus and are then packaged into secretory vesicles These vesicles move to and fuse with the plasma membrane, releasing the proteins out of the cell Many secreted proteins are synthesised as Proteolytic cleavage is another type of post- inactive precursors and require proteolytic translational modification. Digestive enzymes cleavage to produce active proteins are one example of secreted proteins that require proteolytic cleavage to become active. Specific names of digestive enzymes are not required. (c) Protein structure, ligand binding and conformational change (i) Amino acid sequence determines protein Use amino acid chromatography to structure distinguish between different amino acids. Proteins are polymers of amino acid monomers Version 4.1 53  Cells and protein Key area Depth of knowledge required Suggested learning activities Amino acids are linked by peptide bonds to Recognise the chemical structure of a form polypeptides peptide bond from a diagram. Amino acids have the same basic structure, R groups of amino acids vary in size, shape, differing only in the R group present charge, hydrogen bonding capacity and chemical reactivity. Amino acids are classified according to their Classify amino acids according to the R Determine the isoelectric point of a protein R groups: basic (positively charged); acidic group present. and explain the result using understanding of (negatively charged); polar; hydrophobic protein structure. Names and structures of individual amino acids are not required. The wide range of functions carried out by Carry out molecular modelling, for example proteins results from the diversity of R groups computer-aided drug design. The primary structure is the sequence in Carry out primary structure comparisons of which the amino acids are synthesised into enzymes from different evolutionary the polypeptide backgrounds, for example alcohol dehydrogenase from different organisms. Hydrogen bonding along the backbone of the protein strand results in regions of secondary structure — alpha helices, parallel or anti- parallel beta-pleated sheets, or turns Version 4.1 54  Cells and protein Key area Depth of knowledge required Suggested learning activities The polypeptide folds into a tertiary structure This conformation is stabilised by interactions between R groups: hydrophobic interactions; ionic bonds; London dispersion forces; hydrogen bonds; disulfide bridges Disulfide bridges are covalent bonds between R groups containing sulfur. Quaternary structure exists in proteins with Quaternary structure describes the spatial two or more connected polypeptide subunits arrangement of the subunits. A prosthetic group is a non-protein unit tightly The ability of haemoglobin to bind oxygen is Analyse haemoglobin dissociation curves. bound to a protein and necessary for its dependent upon the non-protein haem group. function Interactions of the R groups can be Increasing temperature disrupts the influenced by temperature and pH interactions that hold the protein in shape; the protein begins to unfold, eventually becoming denatured. The charges on acidic and basic R groups are affected by pH. As pH increases or decreases from the optimum, the normal ionic interactions between charged groups are lost, which gradually changes the conformation of the protein until it becomes denatured. Version 4.1 55  Cells and protein Key area Depth of knowledge required Suggested learning activities (ii) Ligand binding changes the conformation of a protein A ligand is a substance that can bind to a protein R groups not involved in protein folding can allow binding to ligands Binding sites will have complementary shape and chemistry to the ligand As a ligand binds to a protein-binding site the conformation of the protein changes This change in conformation causes a functional change in the protein Allosteric interactions occur between spatially The binding of a substrate molecule to one distinct sites active site of an allosteric enzyme increases the affinity of the other active sites for binding of subsequent substrate molecules. This is of biological importance because the activity of allosteric enzymes can vary greatly with small changes in substrate concentration. Many allosteric proteins consist of multiple subunits (have quaternary structure) Version 4.1 56  Cells and protein Key area Depth of knowledge required Suggested learning activities Allosteric proteins with multiple subunits show co-operativity in binding, in which changes in binding at one subunit alter the affinity of the remaining subunits Allosteric enzymes contain a second type of Investigate the action of aspartate site, called an allosteric site transcarbamoylase as an example of an allosteric enzyme of biological importance. Modulators regulate the activity of the enzyme when they bind to the allosteric site Following binding of a modulator, the Positive modulators increase the enzyme’s conformation of the enzyme changes and this affinity for the substrate, whereas negative alters the affinity of the active site for the modulators reduce the enzyme’s affinity. substrate The binding and release of oxygen in Changes in binding of oxygen at one subunit haemoglobin shows co-operativity alter the affinity of the remaining subunits for oxygen. The influence and physiological importance A decrease in pH or an increase in of temperature and pH on the binding of temperature lowers the affinity of haemoglobin oxygen for oxygen, so the binding of oxygen is reduced. Reduced pH and increased temperature in actively respiring tissue will reduce the binding of oxygen to haemoglobin promoting increased oxygen delivery to tissue. Version 4.1 57  Cells and protein Key area Depth of knowledge required Suggested learning activities Effects of DPG are not required. (iii) Reversible binding of phosphate and the control of conformation The addition or removal of phosphate can cause reversible conformational change in proteins This is a common form of post-translational modification Protein kinases catalyse the transfer of a phosphate group to other proteins The terminal phosphate of ATP is transferred to specific R groups Protein phosphatases catalyse the reverse reaction Phosphorylation brings about conformational Research examples of proteins regulated by changes, which can affect a protein’s activity phosphorylation, such as glycogen phosphorylase. The activity of many cellular proteins, such as enzymes and receptors, is regulated in this way Version 4.1 58  Cells and protein Key area Depth of knowledge required Suggested learning activities Some proteins are activated by Adding a phosphate group adds negative phosphorylation while others are inhibited charges. Ionic interactions in the unphosphorylated protein can be disrupted and new ones created. 3 Membrane proteins (a) Movement of molecules across membranes Knowledge of the fluid mosaic model of cell Research the history of evidence-based membranes models of membrane structure as an example of refinement of scientific ideas. Regions of hydrophobic R groups allow Integral membrane proteins interact strong hydrophobic interactions that hold extensively with the hydrophobic region of integral membrane proteins within the membrane phospholipids. phospholipid bilayer Some integral membrane proteins are transmembrane proteins Peripheral membrane proteins have hydrophilic R groups on their surface and are bound to the surface of membranes, mainly by ionic and hydrogen bond interactions Many peripheral membrane proteins interact with the surfaces of integral membrane proteins Version 4.1 59  Cells and protein Key area Depth of knowledge required Suggested learning activities The phospholipid bilayer is a barrier to ions and most uncharged polar molecules Some small molecules, such as oxygen and carbon dioxide, pass through the bilayer by simple diffusion Facilitated diffusion is the passive transport of substances across the membrane through specific transmembrane proteins To perform specialised functions, different cell types have different channel and transporter proteins Most channel proteins in animal and plant Channels are multi-subunit proteins with the cells are highly selective subunits arranged to form water-filled pores that extend across the membrane. Some channel proteins are gated and Research CFTR mutation and cystic fibrosis. change conformation to allow or prevent diffusion Ligand-gated channels are controlled by the binding of signal molecules, and voltage- gated channels are controlled by changes in ion concentration Version 4.1 60  Cells and protein Key area Depth of knowledge required Suggested learning activities Transporter proteins bind to the specific Transporters alternate between two Research glucose transporters in mammalian substance to be transported and undergo a conformations so that the binding site for a cells. conformational change to transfer the solute solute is sequentially exposed on one side of across the membrane the bilayer, then the other. Active transport uses pump proteins that Pumps that mediate active transport are transfer substances across the membrane transporter proteins coupled to an energy against their concentration gradient source. A source of metabolic energy is required for active transport Some active transport proteins hydrolyse ATPases hydrolyse ATP. ATP directly to provide the energy for the conformational change required to move substances across the membrane (b) Ion transport pumps and generation of ion gradients For a solute carrying a net charge, the A membrane potential (an electrical potential concentration gradient and the electrical difference) is created when there is a potential difference combine to form the difference in electrical charge on the two electrochemical gradient that determines the sides of the membrane. transport of the solute Ion pumps, such as the sodium-potassium pump, use energy from the hydrolysis of ATP to establish and maintain ion gradients Version 4.1 61  Cells and protein Key area Depth of knowledge required Suggested learning activities The sodium-potassium pump transports ions against a steep concentration gradient using energy directly from ATP hydrolysis It actively transports sodium ions out of the cell and potassium ions into the cell The pump has high affinity for sodium ions For each ATP hydrolysed, three sodium ions inside the cell; binding occurs; are transported out of the cell and two phosphorylation by ATP; conformation potassium ions are transported into the cell. changes; affinity for sodium ions decreases; This establishes both concentration gradients sodium ions released outside of the cell; and an electrical gradient. potassium ions bind outside the cell; dephosphorylation; conformation changes; potassium ions taken into cell; affinity returns to start The sodium-potassium pump is found in most animal cells, accounting for a high proportion of the basal metabolic rate in many organisms In the small intestine, the sodium gradient In intestinal epithelial cells the sodium- created by the sodium-potassium pump potassium pump generates a sodium ion drives the active transport of glucose gradient across the plasma membrane. The glucose transporter responsible for this Sodium ions enter the cell down their glucose symport transports sodium ions and concentration gradient; the simultaneous Version 4.1 62  Cells and protein Key area Depth of knowledge required Suggested learning activities glucose at the same time and in the same transport of glucose pumps glucose into the direction cell against its concentration gradient. Details of the apical and basal membranes are not required. 4 Communication and signalling (a) Co-ordination Multicellular organisms signal between cells Steroid hormones, peptide hormones, and using extracellular signalling molecules neurotransmitters are examples of extracellular signalling molecules. Receptor molecules of target cells are proteins with a binding site for a specific signal molecule Binding changes the conformation of the receptor, which initiates a response within the cell Different cell types produce specific signals Signalling molecules may have different Research examples of degenerative that can only be detected and responded to effects on different target cell types due to diseases. by cells with the specific receptor differences in the intracellular signalling molecules and pathways that are involved. In a multicellular organism, different cell types may show a tissue-specific response to the same signal Version 4.1 63  Cells and protein Key area Depth of knowledge required Suggested learning activities (b) Hydrophobic signals and control of transcription Hydrophobic signalling molecules can diffuse directly through the phospholipid bilayers of membranes, and so bind to intracellular receptors The receptors for hydrophobic signalling Transcription factors are proteins that when molecules are transcription factors bound to DNA can either stimulate or inhibit initiation of transcription. The steroid hormones oestrogen and testosterone are examples of hydrophobic signalling molecules Steroid hormones bind to specific receptors in the cytosol or the nucleus The hormone-receptor complex moves to the The hormone-receptor complex binds to Research sex hormone disorders. nucleus where it binds to specific sites on specific DNA sequences called hormone DNA and affects gene expression response elements (HREs). Binding at these sites influences the rate of transcription, with each steroid hormone affecting the gene expression of many different genes. Version 4.1 64  Cells and protein Key area Depth of knowledge required Suggested learning activities (c) Hydrophilic signals and transduction Hydrophilic signalling molecules bind to Peptide hormones and neurotransmitters are transmembrane receptors and do not enter examples of hydrophilic extracellular the cytosol signalling molecules. Transmembrane receptors change conformation when the ligand binds to the extracellular face; the signal molecule does not enter the cell, but the signal is transduced across the plasma membrane Transmembrane receptors act as signal transducers by converting the extracellular ligand-binding event into intracellular signals, which alters the behaviour of the cell Transduced hydrophilic signals often involve G-proteins relay signals from activated G-proteins or cascades of phosphorylation by receptors (receptors that have bound a kinase enzymes signalling molecule) to target proteins such as enzymes and ion channels. Details of G- proteins subunits are not required. Phosphorylation cascades allow more than Phosphorylation cascades involve a series of one intracellular signalling pathway to be events with one kinase activating the next in activated the sequence and so on. Phosphorylation cascades can result in the phosphorylation of many proteins as a result of the original signalling event. Version 4.1 65  Cells and protein Key area Depth of knowledge required Suggested learning activities Binding of the peptide hormone insulin to its Binding of insulin to its receptor causes a Research data from glucose tolerance tests. receptor results in an intracellular signalling conformational change that triggers cascade that triggers recruitment of GLUT4 phosphorylation of the receptor. This starts a glucose transporter proteins to the cell phosphorylation cascade inside the cell, membrane of fat and muscle cells which eventually leads to GLUT4-containing vesicles being transported to the cell membrane. Diabetes mellitus can be caused by failure to Research health effects associated with type produce insulin (type 1) or loss of receptor 2 diabetes and the success rate of treatment function (type 2) programmes. Type 2 is generally associated with obesity Write a review of data from studies of health and wellbeing, considering the importance of Exercise also triggers recruitment of GLUT4, publishing negative results. so can improve uptake of glucose to fat and muscle cells in subjects with type 2 (d) Nerve impulse transmission (i) Generation of a nerve impulse Resting membrane potential is a state where there is no net flow of ions across the membrane The transmission of a nerve impulse requires changes in the membrane potential of the neuron’s plasma membrane Version 4.1 66  Cells and protein Key area Depth of knowledge required Suggested learning activities An action potential is a wave of electrical excitation along a neuron’s plasma membrane Neurotransmitters initiate a response by Neurotransmitter receptors are ligand-gated binding to their receptors at a synapse ion channels. Depolarisation of the plasma membrane as a Depolarisation is a change in the membrane Carry out Daphnia heart rate investigation. result of the entry of positive ions triggers the potential to a less negative value inside. The action of chemical agonists can be opening of voltage-gated sodium channels, assessed. This could provide an opportunity and further depolarisation occurs to focus on aspects of experimental design associated with pilot studies, measurement accuracy, sample size and replication. Inactivation of the sodium channels and the Binding of a neurotransmitter triggers the opening of potassium channels restores the opening of ligand-gated ion channels at a resting membrane potential synapse. Ion movement occurs and there is depolarisation of the plasma membrane. If sufficient ion movement occurs, and the membrane is depolarised beyond a threshold value, the opening of voltage-gated sodium channels is triggered and sodium ions enter the cell down their electrochemical gradient. This leads to a rapid and large change in the membrane potential. A short time after opening, the sodium channels become inactivated. Voltage-gated potassium channels then open to allow potassium ions to move out of the cell to restore the resting membrane potential. Version 4.1 67  Cells and protein Key area Depth of knowledge required Suggested learning activities Depolarisation of a patch of membrane causes neighbouring regions of membrane to depolarise and go through the same cycle, as adjacent voltage-gated sodium channels are opened When the action potential reaches the end of the neuron it causes vesicles containing neurotransmitter to fuse with the membrane — this releases neurotransmitter, which stimulates a response in a connecting cell Restoration of the resting membrane potential allows the inactive voltage-gated sodium channels to return to a conformation that allows them to open again in response to depolarisation of the membrane Ion concentration gradients are re- Following repolarisation the sodium and established by the sodium-potassium pump, potassium ion concentration gradients are which actively transports excess ions in and reduced. The sodium-potassium pump out of the cell restores the sodium and potassium ions back to resting potential levels. (ii) Initiation of a nerve impulse in response to Investigate vision experimentally. an environmental stimulus: the vertebrate eye Version 4.1 68  Cells and protein Key area Depth of knowledge required Suggested learning activities The retina is the area within the eye that Rods function in dim light but do not allow Carry out a fish eye dissection. detects light and contains two types of colour perception. Cones are responsible for photoreceptor cells: rods and cones colour vision and only function in bright light. In animals the light-sensitive molecule retinal is combined with a membrane protein, opsin, to form the photoreceptors of the eye In rod cells the retinal-opsin complex is called rhodopsin Retinal absorbs a photon of light and rhodopsin changes conformation to photoexcited rhodopsin A cascade of proteins amplifies the signal Photoexcited rhodopsin activates a G- A single photoexcited rhodopsin activates protein, called transducin, which activates the hundreds of molecules of G-protein. Each enzyme phosphodiesterase (PDE) activated G-protein activates one molecule of PDE. PDE catalyses the hydrolysis of a molecule Each active PDE molecule breaks down called cyclic GMP (cGMP) thousands of cGMP molecules per second. The reduction in cGMP concentration as a result of its hydrolysis affects the function of ion channels in the membrane of rod cells. Version 4.1 69  Cells and protein Key area Depth of knowledge required Suggested learning activities This results in the closure of ion channels in the membrane of the rod cells, which triggers nerve impulses in neurons in the retina A very high degree of amplification results in rod cells being able to respond to low intensities of light In cone cells, different forms of opsin combine with retinal to give different photoreceptor proteins, each with a maximal sensitivity to specific wavelengths: red, green, blue or UV 5 Protein control of cell division (a) The cytoskeleton and cell division The cytoskeleton gives mechanical support and shape to cells It consists of different protein structures Microtubules are hollow cylinders composed Research and consider the effects of including microtubules, which are found in all of the protein tubulin. They radiate from the colchicine and paclitaxel on the cytoskeleton. eukaryotic cells microtubule organising centre (MTOC) or centrosome. Knowledge of other cytoskeleton proteins is not required. Version 4.1 70  Cells and protein Key area Depth of knowledge required Suggested learning activities Microtubules control the movement of membrane-bound organelles and chromosomes Cell division requires remodelling of the cytoskeleton Formation and breakdown of microtubules involves polymerisation and depolymerisation of tubulin Microtubules form the spindle fibres that are active during cell division (b) The cell cycle The cell cycle consists of interphase and Interphase involves growth and DNA Stain actively dividing plant meristem tissue mitotic (M) phase synthesis including G1, a growth phase; S and calculate a mitotic index. phase, during which the DNA is replicated; and G2, a further growth phase. Mitotic phase involves mitosis and In mitosis the chromosomal material is cytokinesis separated by the spindle microtubules. This is followed by cytokinesis, in which the cytoplasm is separated into two daughter cells. Version 4.1 71  Cells and protein Key area Depth of knowledge required Suggested learning activities Mitosis consists of prophase, metaphase, Prophase — DNA condenses into anaphase and telophase chromosomes each consisting of two sister chromatids. Nuclear membrane breaks down; spindle microtubules extend from the MTOC by polymerisation and attach to chromosomes via their kinetochores in the centromere region. Metaphase — chromosomes are aligned at the metaphase plate (equator of the spindle). Anaphase — as spindle microtubules shorten by depolymerisation, sister chromatids are separated, and the chromosomes are pulled to opposite poles. Telophase — the chromosomes decondense and nuclear membranes are formed around them. (c) Control of the cell cycle Progression through the cell cycle is Checkpoints are mechanisms within the cell Use an online simulation of mitotic controlled by checkpoints that assess the condition of the cell during checkpoint control. the cell cycle and halt progression to the next phase until certain requirements are met. Version 4.1 72  Cells and protein Key area Depth of knowledge required Suggested learning activities Cyclin proteins that accumulate during cell Cyclins combine with and activate cyclin- Investigate cell cycle mutation in yeast growth are involved in regulating the cell dependent kinases (CDKs). Active cyclin- Schizosaccharomyces pombe. cycle CDK complexes phosphorylate proteins that regulate progression through the cycle. If sufficient phosphorylation is reached, progression occurs. At the G1 checkpoint, retinoblastoma protein (Rb) acts as a tumour suppressor by inhibiting the transcription of genes that code for proteins needed for DNA replication Phosphorylation by G1 cyclin-CDK inhibits This allows transcription of the genes that the retinoblastoma protein (Rb) code for proteins needed for DNA replication. Cells progress from G1 to S phase. At the G2 checkpoint, the success of DNA replication and any damage to DNA is assessed DNA damage triggers the activation of several proteins including p53 that can stimulate DNA repair, arrest the cell cycle or cause cell death Version 4.1 73  Cells and protein Key area Depth of knowledge required Suggested learning activities A metaphase checkpoint controls At the metaphase checkpoint, progression is progression from metaphase to anaphase halted until the chromosomes are aligned correctly on the metaphase plate and attached to the spindle microtubules. An uncontrolled reduction in the rate of the Research the role of cell cycle regulators in cell cycle may result in degenerative disease degenerative diseases such as Alzheimer’s and Parkinson’s. An uncontrolled increase in the rate of the Research the types of mutations associated cell cycle may result in tumour formation with cancer, for example the influence of environmental factors and viruses, the A proto-oncogene is a normal gene, usually conversion of proto-oncogenes into involved in the control of cell growth or oncogenes, and mutations in division, which can mutate to form a tumour- tumour-suppressing genes. promoting oncogene (d) Control of programmed cell death (apoptosis) Apoptosis is triggered by cell death signals The production of death signal molecules that can be external or internal from lymphocytes is an example of an external death signal. DNA damage is an example of an internal death signal. External death signal molecules bind to a surface receptor protein and trigger a protein cascade within the cytoplasm Version 4.1 74  Cells and protein Key area Depth of knowledge required Suggested learning activities An internal death signal resulting from DNA damage causes activation of p53 tumour- suppressor protein Both types of death signal result in the activation of caspases (types of protease enzyme) that cause the destruction of the cell Apoptosis is essential during development of Research and consider apoptosis in an organism to remove cells no longer development of tetrapod limbs. required as development progresses or during metamorphosis Cells may initiate apoptosis in the absence of Research the challenges in overcoming growth factors apoptosis in maintaining animal cell culture lines. Version 4.1 75  Organisms and evolution Key area Depth of knowledge required Suggested learning activities 1 Field techniques for biologists (a) Health and safety Aspects of fieldwork can present a hazard Hazards in fieldwork include adverse weather Discuss standard rules for fieldwork safety. conditions, difficult terrain, problems associated with isolation, and contact with harmful organisms. Hazard, risk, and control of risk by risk Risk is the likelihood of harm arising from assessment exposure to a hazard. Risk assessment involves identifying control measures to minimise risk. Control measures include appropriate equipment, clothing, footwear, and means of communication. (b) Sampling of wild organisms Sampling should be carried out in a manner Participate in fieldwork, using a variety of that minimises impact on wild species and techniques. habitats Consideration must be given to rare and Research protected species in Scotland. vulnerable species and habitats that are protected by legislation Version 4.1 76  Organisms and evolution Key area Depth of knowledge required Suggested learning activities The chosen technique, point count, transect A point count involves the observer recording or remote detection must be appropriate to all individuals seen from a fixed point count the species being sampled location. This can be compared to other point count locations or with data from the same location gathered at other times. Quadrats, of suitable size and shape, or transects are used for plants and other sessile or slow-moving organisms Capture techniques, such as traps and nets, are used for mobile species Elusive species can be sampled directly using camera traps or an indirect method, such as scat sampling (c) Identification and taxonomy Identification of an organism in a sample can In the context of fieldwork, sample organisms be made using classification guides, from a variety of habitats and attempt to biological keys, or analysis of DNA or protein classify and catalogue them using keys, guides, and other materials. Organisms can be classified by both taxonomy and phylogenetics Version 4.1 77  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Taxonomy involves the identification and Classic taxonomy classification is based on Research the taxonomic groups. naming of organisms and their classification morphology. into groups based on shared characteristics Visit a botanic garden to learn more about the major divisions of plants. Visit a zoological park to learn more about the animal phyla. Phylogenetics is the study of the evolutionary Phylogenetics uses heritable traits such as Read excerpts from Bryan Sykes’s book, The history and relationships among individuals morphology, DNA sequences, and protein Seven Daughters of Eve. or groups of organisms structure to make inferences about an [Sykes B. (2001), The Seven Daughters of organism’s evolutionary history and create a Eve, New York: W. W. Norton & Company] Phylogenetics is changing the traditional phylogeny (or phylogenetic tree) — a classification of many organisms diagrammatic hypothesis of its relationships Research the evolution of the pentadactyl to other organisms. Genetic evidence can limb. reveal relatedness obscured by divergent or convergent evolution. Familiarity with taxonomic groupings allows Nematodes, arthropods and chordates are predictions and inferences to be made about examples of taxonomic groups. the biology of an organism from better-known (model) organisms Version 4.1 78  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Model organisms are those that are either Model organisms, such as the bacterium easily studied or have been well studied E. coli; the flowering plant Arabidopsis thaliana; the nematode C. elegans; the arthropod Drosophila melanogaster (a fruit fly); mice, rats, and zebrafish, which are all chordates, have been very important in the advancement of modern biology. Information obtained from them can be applied to other species that are more difficult to study directly (d) Monitoring populations Presence, absence or abundance of indicator Identify relevant indicator species to classify species can give information of a habitat, using the British National environmental qualities, such as presence of Vegetation Classification. a pollutant Susceptible and favoured species can be Absence or reduced population indicates a used to monitor an ecosystem species is susceptible to some factor in the environment. Abundance or increased population indicates it is favoured by the conditions. Version 4.1 79  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Procedure for the mark and recapture A sample of the population is captured and Carry out a mark and recapture experiment technique as a method for estimating marked (M) and released. After an interval of using a wild species. population size using the formula time, a second sample is captured (C). If MC some of the individuals in this second sample Carry out a mark and recapture simulation in N= are recaptured (R), then the total population R the laboratory. MC N= R This method assumes that all individuals have an equal chance of capture, that there is no immigration or emigration, and that individuals that are marked and released can mix fully and randomly with the total population. Methods of marking animals such as: banding, tagging, surgical implantation, painting and hair clipping The method of marking and subsequent observation must minimise the impact on the study species (e) Measuring and recording animal behaviour Some of the measurements used to quantify Latency is the time between the stimulus animal behaviour are latency, frequency and occurring and the response behaviour. duration Version 4.1 80  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Frequency is the number of times a behaviour occurs within the observation period. Duration is the length of time each behaviour occurs during the observation period. An ethogram of the behaviours shown by a An ethogram lists species-specific Use an ethogram and time sampling to species in a wild context allows the behaviours to be observed and recorded in compare the behaviour of different individuals construction of time budgets the study. Recording the duration of each of of a species. the behaviours in the ethogram, together with the total time of observation, allows the proportion of time spent on each behaviour to be calculated in the time budget. The importance of avoiding Anthropomorphism can lead to invalid anthropomorphism when analysing behaviour conclusions. 2 Evolution (a) Drift and selection Evolution is the change over time in the proportion of individuals in a population differing in one or more inherited traits During evolution, changes in allele frequency occur through the non-random processes of natural selection and sexual selection, and the random process of genetic drift Version 4.1 81  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Natural selection acts on genetic variation in Variation in traits arises as a result of populations mutation. Mutation is the original source of new sequences of DNA. These new sequences can be novel alleles. Most mutations are harmful or neutral, but in rare cases they may be beneficial to the fitness of an individual. Populations produce more offspring than the environment can support Individuals with variations that are better Selection results in the non-random increase suited to their environment tend to survive in the frequency of advantageous alleles and longer and produce more offspring, breeding the non-random decrease in the frequency of to pass on those alleles that conferred an deleterious alleles. advantage to the next generation Sexual selection is the non-random process involving the selection of alleles that increase the individual’s chances of mating and producing offspring Sexual selection may lead to sexual dimorphism Version 4.1 82  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Sexual selection can be due to male-male Male-male rivalry: large size or weaponry rivalry and female choice increases access to females through conflict. Female choice involves females assessing the fitness of males. Genetic drift occurs when chance events cause unpredictable fluctuations in allele frequencies from one generation to the next Genetic drift is more important in small populations, as alleles are more likely to be lost from the gene pool The importance of bottleneck and founder Population bottlenecks occur when a effects on genetic drift population size is reduced for at least one generation. Founder effects occur through the isolation of a few members of a population from a larger population. The gene pool of the new population is not representative of that in the original gene pool. A gene pool is altered by genetic drift because certain alleles may be under- represented or over-represented and allele frequencies change Version 4.1 83  Organisms and evolution Key area Depth of knowledge required Suggested learning activities Where selection pressures are strong, the Selection pressures are the environmental Study cladograms of MRSA and primate rate of evolution can be rapid factors that influence which individuals in a evolution to compare the effect of generation population pass on their alleles. time on rates of evolution. They can be biotic: competition, predation, disease, parasitism; or abiotic: changes in temperature, light, humidity, pH, salinity. The Hardy-Weinberg (HW) principle states The conditions for maintaining the HW that, in the absence of evolutionary equilibrium are: no natural selection, random influences, allele and genotype frequencies mating, no mutation, large population size in a population will remain constant over the and no gene flow (through migration, in or generations out). The HW principle can be used to determine Use the HW principle to calculate allele, Research the application of the HW principle whether a change in allele frequency is genotype and phenotype frequencies in in medical research. occurring in a population over time populations. p 2 + 2 pq + q 2 = 1 Changes suggest evolution is occurring p = frequency of dominant allele q = frequency of recessive allele p2 = frequency of homozygous dominant genotype 2pq = frequency of heterozygous genotype q2 = frequency of homozygous recessive genotype Version 4.1 84  Organisms and evolution Key area Depth of knowledge required Suggested learning activities (b) Fitness Fitness is an indication of an individual’s Fitness is a measure of the tendency of some ability to be successful at surviving and organisms to produce more surviving reproducing offspring than competing members of the same species. It refers to the contribution made to the gene pool of the next generation by individual genotypes Fitness can be defined in absolute or relative terms Absolute fitness is the ratio between the frequency of a particular genotype frequency of individuals of a particular after selection genotype after selection, to those before frequency of a particular genotype selection before selection If the absolute fitness is 1, then the frequency of that genotype is stable. A value greater than 1 conveys an increase in the genotype and a value less than 1 conveys a decrease. Relative fitness is the ratio of the number of number of surviving offspring per surviving offspring per individual of a individual of a particular genotype particular genotype to the number of number of surviving offspring per individual of the most successful genotype surviving offspring per individual of the most successful genotype Version 4.1 85  Organisms and evolution Key area Depth of knowledge required Suggested learning activities (c) Co-evolution Co-evolution is the process by which two or more species evolve in response to selection pressures imposed by each other A change in the traits of one species acts as a selection pressure on the other species Co-evolution is frequently seen in pairs of Symbiosis: co-evolved intimate relationships Research examples of co-evolved symbiotic species that have symbiotic interactions between members of two different species. relationships. The impacts of these relationships can be positive (+), negative (-) or neutral (0) for the individuals involved Mutualism, commensalism, and parasitism Mutualism: both organisms in the interaction are types of symbiotic interactions are interdependent on each other for resources or other services. As both organisms gain from the relationship, the interaction is (+/+). Commensalism: only one of the organisms benefits (+/0). Parasitism: the parasite benefits in terms of energy or nutrients and the host is harmed as the result of the loss of these resources (+/-). Version 4.1 86  Organisms and evolution Key area Depth of knowledge required Suggested learning activities The Red Queen hypothesis states that, in a Read excerpts from Matt Ridley’s book, The co-evolutionary relationship, change in the Red Queen: Sex and the Evolution of Human traits of one species can act as a selection Nature. pressure on the other species [Ridley M. (2003), The Red Queen: Sex and the Evolution of Human Nature, London: Harper Perennial] This means that species in these relationships must adapt to avoid extinction 3 Variation and sexual reproduction (a) Costs and benefits of sexual and asexual reproduction Costs of sexual reproduction: males unable Research how the evolutionary importance of to produce offspring; only half of each sexual reproduction influences experimental parent’s genome passed onto offspring, design in the life sciences. The natural disrupting successful parental genomes variation generated means that biologists have to take care when sampling a population and analysing data to make sure that they can distinguish this ‘noise’ from any experimental result or ‘signal’. Investigate the paradox of the existence of males. Benefits outweigh costs due to an increase in genetic variation in the population Version 4.1 87