RIP BIO CLASS OF 2K17 Biology Study Notes: 1 Cell Biology 1.1 Introduction to cells The Cell Theory: I. II. III. All living organisms are composed of one or more cells. The cell is the basic unit of structure and organisation in organisms. All cells come from pre-existing cells. Exceptions to the Cell Theory: I. Fungi: consists of narrow thread-like structures called hyphae, which have both a cell membrane and cell wall. Many are divided by cross wall like structures called septa. Aseptate hyphae don’t have septa and are long uninterrupted tubes with many nuclei spread along it. Algae: Unicellular and some types (giant algae) can grow to be very large (up to 100mm). Striated muscle: Much larger than normal animal cells and have an average length of 30 mm in humans. They are multi-nucleated. II. III. Functions of unicellular organisms: Metabolism: chemical reactions inside the cell (respiration etc.). Response: Ability to react to stimuli Growth: irreversible increase in size. Reproduction: producing offspring either sexually or asexually. Excretion: getting rid of the waste products of metabolism Nutrition: obtaining food to provide energy and the materials needed for growth. ● Homeostasis: keep internal conditions within tolerable limits. ● ● ● ● ● ● Paramecium as an example of a unicellular organism: ● Nucleus contains genetic material and divides asexually by mitosis.. ● Food vacuoles contain smaller organisms, which are slowly digested; the products are expelled to the cytoplasm where they are assimilated for energy and growth. RIP BIO CLASS OF 2K17 ● Contractile vacuoles store water and expel it to the extracellular to maintain internal water levels. ● Metabolic reactions are enzyme-regulated and occur in the cytoplasm. ● Cilia control movement of the cell and can be controlled by the cell as a regulated response to environment stimuli. ● Cell membrane controls movements of substances in and out. ● Excretion occurs by diffusion of substances to the extracellular. Chlamydomonas as an example of a unicellular organism: ● Nuclear can divide via mitosis. Nuclear can also fuse and divide to carry out sexual reproduction. ● Metabolic reactions occur in the cytoplasm with the enzymes present. ● Cell wall is freely permeable; cell membrane controls what enters/exists the cell. Oxygen, waste product, diffuses out of the cell. ● Contractile vacuole maintains internal water levels by expelling water into the extracellular. ● Photosynthesis occurs in the chloroplasts. Carbon Dioxide is absorbed from carbon compounds of other organisms. ● Light sensitive eyespot enables detection of light and flagellum facilitates movement towards light. Limitations to cells size: ● Surface area to volume ratio is important to be maintained because a small ratio would slow down the rate of exchange between substances in the extra/intracellular. ● Waste products would be expelled too slowly and products needed for cellular reactions would be absorbed too slowly. ● This would result in a built up of waste products as they would be excreted slower than produced. ● Heat production and loss would also be affected as the cell may over heat, as it would produce heat faster than it loses it over the cell’s surface. Multicellular organisms: ● Cells in multicellular organisms can be regarded as cooperative groups. ● Individual cells in a group can work together to form distinctive overall properties called emergent properties. These arise from the interaction of the component parts of a complex structure. Cell differentiation in multicellular organisms: ● Specialised tissues can develop by cell differentiation in multicellular organisms. RIP BIO CLASS OF 2K17 ● A group of cells to specialise in the same way to perform the same function are called a tissue. This allows them to be more efficient. ● There are 220 highly specialised cell types in humans (that have been recognised so far). Gene expression and cell differentiation: ● Differentiation involves the expression of some genes and not others in a cell’s genome. ● All tissues have the same genes, however specialisation involves the ‘turning on’, or expression, of particular genes, which define a specific function. Differentiation occurs because different sequences of genes are expressed in different cell types. Stem cells: ● The capacity of stem cells to divide and differentiate along different pathways is necessary in embryonic development. It also makes them suitable for therapeutic uses. ● Therapeutic uses of stem cells include replacing damaged skin tissue and non-therapeutic uses include formation of striated muscle for human consumption. ● Stem cells can be found in the bone marrow, skin and liver and can be used for self-repair. Use of stem cells to cure Stargardt’s macular dystrophy: ● Stargardt’s macular dystrophy is a genetic disease that develops in children ages 6-12 years old. ● Recessive mutation of ABCA 4 gene and results in the malfunctioning of a membrane protein responsible for active transport in retina cells. ● Photoreceptor cell degenerate and vision decays. ● Stem cells are injected into the eye and attach themselves to damaged cells resulting in improved vision. Use of stem cells to cure Leukaemia: ● Involves the production of lots of white blood cells at an uncontrollable rate. ● Chemotherapy kills the dividing cells. ● Adult stem cells are extracted from the bone marrow with a large needle and then frozen. ● Chemotherapy is then executed and kills cells in the bone marrow. ● Stem cells are then returned to the patient’s body. RIP BIO CLASS OF 2K17 Sources of stem cells and the ethics of using them: Embryonic stem cells Cord blood stem cells ● Can differentiate into any type of cell. ● Likely to be genetically different from the adult patient. ● Removal of stem cells kills the embryo. ● Easily obtained and stored. ● Limited differentiation capacity and develops into blood cells only. ● Umbilical cord is discarded regardless. Adult stem cells ● Difficult to obtain because they are buried deep in tissues. ● Less differentiation potential than embryonic stem cells. ● Does not kill the adult from which they are taken. 1.2 Ultrastructure of cells: The resolution of electron microscopes: ● Electron microscopes have a much higher resolution than light microscopes. ● Resolution is making separate parts of an object distinguishable by the eye. Light microscopes are inhibited by the wavelength of visible light (400-700nm). Electrons have shorter wavelengths so electron microscopes have higher resolution. ● Electron microscopes can see viruses and objects up to 1 nm. ● Light microscopes can see objects up to 200 nm. Prokaryotic cell structure: ● ● ● ● ● ● ● ● Prokaryotes have no nucleus. They contain a nucleoid with naked DNA. They have no compartmentalisation and contain only 70s ribosomes. They have no other cytoplasmic organelles (besides plasmids). The entire body is filled with cytoplasm, which has several enzymes. DNA is not associated with proteins (naked). Peptidoglycan cell wall. - for eubacteria, not for archaeans. Contains cell membrane. Contains flagellum and cilia. Cell division in prokaryotes: RIP BIO CLASS OF 2K17 ● Occurs through binary fission. Asexual reproduction. ● DNA replicates (as it does in eukaryotes). ● Copies of DNA move to opposite ends of the cell and then cytoplasm divides each cell get identical DNA. Eukaryotic cell structure: ● ● ● ● ● ● ● ● ● ● ● ● ● Complicated internal structure due to compartmentalisation. Single/double membrane partitions. Contains organelles. Compartmentalisation allows: o Enzymes and substrates to be concentrated to a specific region. o Damaging substances can be kept within the membrane of an organelle (lysosome). o pH levels can be maintained at an ideal level for particular processes. o Organelles can be moved around with their contents. Nucleus: Nuclear membrane is double and has pores (nuclear pores) through it. Chromosomes within are tightly coiled DNA around histones. Chromatin is uncoiled chromosome. DNA replication and transcription occurs in the nucleus. Rough endoplasmic reticulum (rER): Contains cisternae, which are flat membranous sacs upon which 80S ribosomes are attached. Protein synthesis occurs here. Proteins pass into cisternae and are carried by vesicles to the Golgi. Golgi Apparatus: Also contains cisternae. Processes and packages proteins from the rER. Carried in vesicles to the plasma membrane for secretion. Contents that are being packaged move from CIS to TRANS end. Lysosomes: Single membrane. Formed by Golgi vesicles. Contain digestive enzymes that can break down ingested food or dysfunctional organelles. Mitochondrion: Double membrane. Inner membrane invaginated to form cristae. Fluid inside called matrix. Produce ATP out of glucose/lipids by aerobic respiration. Ribosomes (80S): Synthesise proteins and release them into cytoplasm. Ribosomes are constructed in the nucleolus, which is present in the nucleus. Chloroplasts: Double membrane. Thylakoids are flattened sacs of membrane. Produce glucose by photosynthesis. Starch grains may be present. Stroma is the cytoplasm of chloroplasts. Vacuoles and vesicles: Single membrane. Plant cells have large vacuoles to store starch Contractile vacuoles expel excess water. Vesicles are small vacuoles for transport. Microtubules and centrioles: Cylindrical fibres, which move chromosomes during cell division. Centrioles are two groups of nine triple microtubules. Centrioles form an anchor point for microtubules during cell division. RIP BIO CLASS OF 2K17 ● Cilia and flagella: Contain a ring of nine double microtubules plus two central ones. One flagellum is usually present. Many cilia are present. Used for locomotion. Cilia can be used to create a current in extracellular fluid. Exocrine gland cells of the pancreas: ● Exocrine glands secrete hormones into ducts and endocrine glands secrete them into the bloodstream. ● Exocrine gland cells have organelles for protein synthesis. Contain plasma membranes, Golgi Apparatuses, Mitochondrion, Vesicles, Nuclei, Lysosomes and rER’s. ● Since the exocrine gland cells need to synthesise proteins and then release them into the blood, they need all the organelles required to synthesise, package and transport proteins. Palisade mesophyll cells: ● Contain chloroplasts and vacuoles. ● Chloroplasts are important for the absorption of light for photosynthesis and vacuoles are important for the temporary storage of some produced glucose (as starch). 1.3 Membrane Structure: Phospholipid bilayers: ● Phosphate heads, which are hydrophilic; and hydrocarbon tails, which are hydrophobic. ● Since they have both hydrophilic/phobic properties, they are amphipathic. ● The arrangement of the bilayer is with the tails facing each other and the heads facing the water on the intra/extra cellular. ● This is the formation observed in all cell membranes. ● When mixed with water, the phosphate heads are more attracted to each other than they are to the water and therefore are attracted, whilst the hydrocarbon tails are less attracted to the water and thus are hydrophobic. ● Phospholipids are similar in structure to triglycerides, but instead of having 3 fatty acids to glycerol, phospholipids have 2 fatty acids bonded to the glycerol and a phosphate group instead of the 3rd fatty acid. Membrane proteins: RIP BIO CLASS OF 2K17 ● ● ● ● ● ● ● Hormone binding sites. Channels for passive transport of hydrophilic/charged molecules. Immobilised enzymes. (Small intestine) Matrix for intercellular adhesion. Pumps for active transport. Cell-to-cell communication. (Neurotransmitters) Types of membrane proteins: o Integral: Trans-membrane and have a hydrophobic part. They generally project through the phosphate heads on each side. They are imbedded in the hydrocarbon chains. o Peripheral: Generally hydrophilic and are embedded on the surface of the integral proteins. They are not fixedly attached. They sometimes have a hydrocarbon chain that anchors them onto the membrane surface. o More protein content means more active membranes. Cholesterol in membranes: ● Cholesterol is mostly hydrophobic but has a hydroxyl group on one end that is partly hydrophilic. Resultantly it is situated in between the bilayer. It is a type of steroid. Amount of cholesterol in the bilayer varies. ● In the bilayer the phosphate heads usually behave like solids and hydrocarbon tails usually behave like liquids. o Cholesterol regulates the extent to which the membrane bilayer is solid/liquid and also controls the permeability of it. ● Due to its irregular placement within the bilayer it disrupts the arrangement of the hydrophobic tails and prevents them from crystallizing. ● Also restricts molecular motion to prevent the bilayer from being overly permeable and provides rigidity to its structure. Permeability reduction to hydrophilic particles such as hydrogen ions and sodium ions. ● Cholesterol also gives a curved shape, which is usually useful in the formation of vesicles during endocytosis. 1.4 Membrane Transport Endocytosis: ● The fluidity of membranes allows materials to be taken into cells by endocytosis or released by exocytosis. ● Formation of a vesicle occurs when a small region of a membrane is pulled from the rest of the membrane and pinched off. Forms on the inside of the plasma membrane and contains the material that was outside of the cell. RIP BIO CLASS OF 2K17 o Phagocytosis is endocytosis of a solid o Pinocytosis is endocytosis of a liquid/fluid o Receptor mediated endocytosis is for specific substances - bind to receptors then pinching occurs. ● Contains water, solutes and larger molecules that can’t pass through the bilayer. Vesicle movement in cells: ● Vesicles can be use to move materials around cells. However sometimes it is the proteins on the membrane of the vesicles that need to be moved. ● Cell growth occurs with the help of vesicles. Phospholipids are synthesised near the rER and then embed themselves on the rER membrane. Ribosomes on the rER synthesise membrane proteins, which then embed themselves on the rER membrane. Both phospholipids and membrane proteins are transported via vesicles to the plasma membrane. They fuse with it and increase its size. Exocytosis: ● Vesicle carries substance and binds with the plasma membrane. ● Contents are then expelled to the extracellular. ● Plasma membrane then flattens out. Simple diffusion: ● Particles, due to random movement, spread out in a volume. This occurs via a net movement from area of high concentration to low concentration. ● Does not require ATP expenditure. ● Can occur across the bilayer however large/polar molecules are unlikely to cross in this fashion, because the centre of the bilayer is hydrophobic. ● Oxygen and small polar molecules can diffuse easily. Facilitated diffusion: ● Large polar particles and other that are unable to diffuse through the phospholipid bilayer directly, diffuse through channel proteins. ● Channel proteins allow one type of particle to pass through; adds another dimension of selectiveness to permeability. Osmosis: ● Osmosis is the net movement of water molecules across a partially permeable membrane. This is caused by the difference in concentration of solute, not solvent. RIP BIO CLASS OF 2K17 ● Substances dissolve by forming intermolecular bonds with water, which restrict water movement. Hence areas with high solute concentration will see reduced movability of water. As a result water moves from low solute concentration to high solute concentration - hypotonic to hypertonic. ● This is a passive process. Water molecules are small, but hydrophilic. However they still pass through the bilayer. Active Transport: ● Occurs when a particle moves against the concentration gradient and is an active process (requires ATP). ● Carried out by pump proteins, which are within the plasma membrane. ● Substance enters the pump and goes to the central chamber, which elicits a conformational change. ATP then joins and causes the substance to be released on the other side. Active transport of sodium and potassium pumps in axons: 1. Three sodium ions enter the pump on the inside of the axon and attach the their binding sites. 2. ATP transfers a phosphate group to the pump, causing a conformational change and the three ions to be released. 3. Two potassium ions from the extracellular then attach to their binding sites. 4. Binding of potassium causes release of the phosphate group and causes the pump to open back to the inside, enabling the potassium ions to enter the ion. Facilitated diffusion of potassium in axons: ● Potassium ions naturally form bonds with water and have a shell of water molecules surrounding them. ● In order to pass through a potassium voltage gated channel these bonds need to be broken and bonds need to be made with amino acids inside the channel. The voltage-gated channel opens during repolarization, when there are more positive charges inside the axon than outside. ● Voltage gated channels quickly close with the help of a globular protein attached to a flexible amino acid chain, which plugs the opening of the channel. ● This voltage-gated channel allows for facilitated diffusion of potassium in axons. Preventing osmosis in excised tissues and organs ● In a hypertonic solution (high osmolarity), water leaves cells by osmosis RIP BIO CLASS OF 2K17 (to enter solution), causing crenellations (indentations) in their plasma membrane. ● In a hypotonic solution the opposite occurs and the cells swell up, causing them to lyse. ● Hence cells need to be bathed in a solution with the same osmolarity (isotonic) during medical procedures. Saline (Sodium Chloride solution) is normally used with an osmolarity of 300 milliOsmoles (mOsm). 1.5 The Origin of cells: Origin of the first cells: ● First cells must have arisen from non-living material. ● Miller and Urey experiment where they passed steam through a mixture of methane, hydrogen and ammonia. They then passed electrical discharges to simulate lightning. This formed amino acids and some carbon compounds. ● These carbon compounds could have been assembled into polymers in deep-sea vents, which have gushing hot water carrying reduced inorganic chemicals like iron sulphide, which would’ve provided the energy to assemble carbon compounds into polymers. ● The formation of membranes would have naturally occurred due to hydrophobic and hydrophilic properties of certain carbon compounds. This would’ve allowed internal chemistry to develop. ● Mechanisms for inheritance rely on genes. RNA could have been the genetic information and is both self-replicating and can act as a catalyst (enzyme). Endosymbiosis and eukaryotic cells: ● Smaller prokaryotes would’ve developed certain characteristics and then been absorbed by larger prokaryotes. This would’ve created a mutualistic relationship between them. ● Smaller cells would’ve supplied larger ones with aerobic respiration and larger ones would’ve supplied smaller ones with food. ● Chloroplasts and Mitochondria both support this theory: o They have their own circular DNA molecule. o Own 70S ribosomes of a size and shape typical of some prokaryotes. o Transcribe their own DNA and use mRNA to synthesize some proteins. o Can only be produced through division of pre-existing mitochondria and chloroplasts. o They have double membranes, which suggests they have the RIP BIO CLASS OF 2K17 membrane from the cell's vesicle in addition to their own membrane. 1.6 Cell division: The role of mitosis: ● Mitosis is division of the nucleus into two genetically identical daughter nuclei. ● DNA replicates during interphase. The cytoplasm then splits and both daughter cells have one set of DNA each. Interphase: ● G1: Mitochondria grow and divide. Similarly chloroplasts also grow and divide. ● S: DNA replication occurs. ● G2: Further growth occurs in preparation for mitosis. ● G0: entered by cells that do not undergo mitosis, like nerve cells. The G0 phase comes after G1, as cells that do not undergo mitosis do not need to replicate DNA. Supercoiling of chromosomes: ● Chromosomes condense by supercoiling during mitosis. Need to package them into shorter structures. Occurs during the first stage of mitosis. Histones are associated with DNA in eukaryote chromosomes and help with supercoiling. Phases of mitosis: ● Prophase: Chromosomes condense. Nucleolus breaks down. Microtubules grow and link the poles of the cell. Nuclear envelope disintegrates. ● Metaphase: Microtubules attach to the centromere of each chromosome. Attach onto opposite ends of the centromere to ensure that each chromatid is attached to a microtubule from a different pole. The chromosomes are then aligned along the cell equator. Microtubules pull slightly with equal force to ensure proper attachment has occurred. ● Anaphase: Microtubules shorten after chromosomes divide at the centromere, quickly pulling sister chromatids to opposite sides. ● Telophase: At each pole the chromosomes are pulled near the MTOC (MicroTubule Organising Centre) and a nuclear membrane reforms around them. Chromosomes uncoil and nucleolus is reformed. ● Mitotic index = Number of cells in mitosis/total number of cells. RIP BIO CLASS OF 2K17 Cytokinesis: ● Animal: Cleavage furrow forms at the equator due to contractile proteins actin and myosin. Cleavage furrow extends along the equator and the cell is finally pinched off the form two genetically identical daughter cells. ● Plant: Vesicles line up at the equator and merge to form a continuous tube like structure which acts as the plasma membrane. Vesicles carrying pectin then move towards the plasma membrane and release the pectin between the two plasma membranes of the two cells to form the lamella, which would bind the cellulose for the cell wall. The vesicles then carry cellulose and release it to the extracellular via exocytosis completing the formation of the cell wall. Cyclins and the control of the cell cycle: ● Cyclins are proteins that bind to cyclin dependant kinases. ● Kinases attach phosphate groups to other proteins and activate them at specific times. ● The proteins carry out tasks specific to the cell cycle. ● Cyclins need to reach a threshold concentration for the cell cycle to proceed to the next stage. o Cyclin D triggers cells to move from phase to phase in interphase. o Cyclin E prepares cell for DNA replication o Cyclin A activates DNA replication o Cyclin B prepares cell for mitosis RIP BIO CLASS OF 2K17 Tumour formation and cancer: ● Tumours are either benign, and remain as primary tumours, or malignant, and undergo metastasis to set up secondary tumours in other parts of the body. Metastasis is the movement of cells from a primary tumour to set up secondary tumours in other parts of the body. ● Mutations are random changes to the base sequences of genes. Genes that become cancer causing after being mutated are called oncogenes. These cells are called proto-oncogenes before being mutated. Proto-oncogenes are involved with cell cycle and division; hence they lead to rapid division of cells and tumour formation (if mutated). ● Mutations that occur to proto-oncogenes can result in these genes not properly regulating cell division and resulting in the uncontrollable division of cells. ● Carcinogens, including some viruses and high-energy radiation, can cause mutations. 2 Molecular Biology 2.1 Molecules to metabolism Molecular biology: ● Reductionist approach in coming to conclusions. Can’t explain everything by breaking down complex systems into small parts and studying them individually. Need to study emergent properties as well, which only occur when the organisms are studied as a whole. Synthesis of Urea: ● Ammonia + Carbon Dioxide => Ammonium Carbonate => urea + water ● Synthesised in the liver due to excess amino acids (deamination). ● Excreted in urine. Vitalism: ● Origin of all life comes due to a “vital principle”, which is different to life being composed purely of chemical + physical forces. Production of Urea by Fredrich Wohler in 1828, disproved this theory. First organic compound, which was synthesised artificially; hence without a vital principle. RIP BIO CLASS OF 2K17 Carbon Compounds: ● Carbon atoms can form 4 covalent bonds. These can be single or double bonds. ● Can form chains/rings of any length. Classifying Carbon atoms: ● Carbohydrates: Carbon, Hydrogen, Oxygen. H:O => 2:1 ● Amino acids: Carbon, Hydrogen, Oxygen, Nitrogen, 2 Amino acids also contain sulphur. ● Lipids: Insoluble in water. Triglycerides are fats if solid at room temperature and oils if liquid. Also contain Carbon Hydrogen and Oxygen. ● Nucleic Acids: Chains of nucleotides. Carbon, Hydrogen, Oxygen, Nitrogen and Phosphate. Form DNA and RNA. Drawing molecules: Amine group: NH2 Carboxyl group: COOH Methyl group: CH3 Hydroxyl group: OH Ribose: C5H10O5. OH groups on Carbons 1, 2 and 3. Point up, down, down respectively. ● Glucose: C6H12O6. OH groups on Carbons 1, 2, 3, 4. Point down, down, up, down respectively (alpha). On beta glucose, found in cellulose, OH group on carbon 1 points up. ● ● ● ● ● ● Saturated fatty acids: Carbon atoms form an un-branched chain of about 14-20 atoms, no double bonds. ● Amino Acids: Contain Amine group; Carboxyl group; Hydrogen atom; and R variable group. RIP BIO CLASS OF 2K17 ● Lipids contain less oxygen than carbohydrates. Proteins usually contain sulphur. Carbohydrates have a H:O ratio of 2:1. Metabolism: ● Web of all enzyme catalysed reactions in a cell or organism. Most reactions are enzyme catalysed and generally occur in cell cytoplasm. ● Anabolism: Synthesis of complex molecules from simpler ones. Monomers => Macromolecules by condensation reactions. Photosynthesis is an anabolic process. ● Catabolism: Breakdown of complex molecules into simpler ones including the hydrolysis of macromolecules into monomers. Digestion, respiration and decomposition are catabolic processes. 2.2 Water Hydrogen bonding in water: ● Water molecules are polar and hydrogen bonds form between them. ● Bonds between hydrogen and oxygen involve the unequal sharing of electrons because oxygen nuclei are more attracted to electrons than hydrogen nuclei. Hence hydrogen atoms are partially positive and oxygen atoms are partially negative, forming two poles. ● Adjacent water molecules are therefore attracted to one another (hydrogen to oxygen) forming hydrogen bonds. ● In general a hydrogen bond forms when a hydrogen atom in one polar molecule is attracted to a partially negative atom of another polar covalent molecule. Water properties: ● Cohesive properties: the binding together of two-like molecules. Water to water. Hydrogen bonds enable this binding. Used in capillary action. ● Adhesive properties: Hydrogen bonds between water and other polar molecules. Useful in leaves where water adheres to cellulose molecules in cell walls. Maintains dampness for diffusion of CO2. RIP BIO CLASS OF 2K17 ● Thermal properties: High specific heat capacity; restricts temperature of water in varying environment. This is due to water requiring large amounts of energy to change by 1˚C. Allows for stability of water, but also means it is a large store for heat energy, hence serving as a coolant. ● Solvent properties: Polar nature of water means that it forms shells around other polar molecules. As a result solutes to clump together. Both positive and negative ions dissolve. ● Hydrophilic and Hydrophobic properties: All chemical substances that dissolve in water are hydrophilic. Substances that water adheres to are also hydrophilic. Substances that are insoluble are hydrophobic: uncharged and non-polar particles, like lipids. When hydrophobic substances enter water, hydrogen bonds form between water molecules but not between water and hydrophobic substances. This is because hydrophobic substances are non-polar and are therefore immune to hydrogen bonds. Instead hydrophobic interactions occur, as the substances are more attracted to themselves than they are to water, and so they end up clumping together. ● Water vs. Methane: Both small molecules linked by single covalent bonds and have similar masses. However methane is nonpolar and doesn’t form hydrogen bonds. Water has a higher specific heat capacity, latent heat of vaporisation and thus a higher boiling point. Methane is liquid over a range of 22˚C whereas water is liquid over a range of 100˚C. ● Sweat as a coolant: Heat needed for the evaporation of water in sweat is taken from the tissues of the skin, reducing their temperature. Solutes are left on the skin. Hypothalamus controls sweat secretion. Adrenaline can cause the body to sweat even when cold because it anticipates a period of intense activity. Transport in blood plasma: Blood transports a variety of substances. ● Sodium Chloride: Dissolves in water to form Na+ and Cl-. ● Amino Acids: Both negative and positive charges. Solubility depends on R group. All amino acids, however, are soluble enough to dissolve in blood plasma. ● Glucose: Freely soluble because it is polar. ● Oxygen: Non-polar molecule. Dissolves due to its small size but saturates blood at low levels. Higher temperature blood plasma results in lower bandwidth of absorption. Hence Haemoglobin, an oxygen carrier, is present in red blood cells. ● Fatty molecules: Entire nonpolar and large. Completely insoluble. Carried in micelles, which are lipoprotein complexes. Phospholipids act as a vesicle, with hydrophobic fatty tails on the insides, facing the fatty molecule. Single layer of phospholipid. ● Cholesterol: Mainly hydrophobic: Insoluble in water. Transported in lipoprotein complexes. Positioned within the phospholipid monolayers RIP BIO CLASS OF 2K17 with the hydrophilic part facing outwards with the phosphate heads. 2.3 Carbohydrates and Lipids: Carbohydrates: Monosaccharide monomers are linked together by condensation reactions to form disaccharides and polysaccharide polymers. ● Monosaccharides: Glucose, fructose, galactose and ribose. Single sugar units. ● Disaccharides: Two monosaccharides linked together. Maltose: glucose + glucose. Sucrose: glucose + fructose. Lactose: glucose + galactose. ● Polysaccharides: Starch and Glycogen are examples. ● Monosaccharides combine in a condensation reaction. Loss of OH group from one molecules and hydrogen from another. OH and H form H 2O. This anabolic process requires energy. Link between two monosaccharides is called a glycosidic bond. Polysaccharides: Cellulose and starch in plants. Glycogen in humans. ● OH groups on Carbon 1, 4 and 6 are used to make links. OH on Carbon 6 is usually for side branches. ● In alpha glucose the OH points downwards and in beta, it points upwards. ● Cellulose: Linking beta glucose in a 1-4 structure makes cellulose. OH groups point in opposite directions therefore each glucose molecule is positioned 180˚to the previous one. Hence the beta glucose molecules alternate ‘up and down’. This results in a straight chain. Un-branched chains allow them to form bundles, connected by hydrogen bonds and created cellulose micro-fibrils. These give cellulose its high tensile strength. Used in cell walls. ● Starch: Made by linking alpha-glucose molecules. Made by 1-4 glycosidic bonds. All –OH molecules point downwards, hence all molecules have a similar orientation, which results in a curved structure. This forms two types: amylose and amylopectin. Due to insolubility of both molecules, despite them being hydrophilic, they are used as a storage molecule as they do not cause an influx of water into cells. ● Glycogen: Similar to amylopectin in structure; but has more branching. The molecule is more compact. Stored in the liver and some muscles. Stores energy in the form of glucose because large stores of dissolved glucose would cause osmotic problems. Easy to add/remove glucose molecules on either branched/unbranched sides of glycogen/starch. Amylose Amylopectin RIP BIO CLASS OF 2K17 Branched Unbranched Alpha helix Globular Hydrophilic but insoluble due to size Hydrophilic but insoluble due to size Has only 1-4 linkages Has some 1-6 linkages in addition to 14 linkages Lipids: ● Triglycerides are formed by condensation from three fatty acids and a glycerol. ● All lipids are insoluble. ● Triglycerides are the fat in adipose cells and oils in sunflower seeds. ● Fats are liquid at body temperature (37˚C) but solid at room temperature (20˚C). ● Oils are always liquid. Triglycerides: ● 3 fatty acids + glycerol => triglyceride + 3H2O. ● Fatty acids form ester bonds with glycerol, which are generally formed when an acid reacts with the OH group in alcohol. Energy from triglyceride can be released from aerobic cell respiration. Energy storage: ● Lipids are more suitable for long-term energy storage than carbohydrates. ● Adipose tissue is located directly beneath the skin and round some organs including the kidneys. RIP BIO CLASS OF 2K17 ● Amount of energy released in cell respiration per gram of lipids is double that of carbohydrates. Therefore it adds half the body mass as carbohydrates. ● Fats store as pure droplets whereas glucose stores with two grams of water (per gram of glucose). ● Effectively lipids are 6 times more efficient in energy storage than carbohydrates. ● Lipids are insulators as they are poor conductors of heat. This is why adipose tissue is subcutaneous. ● They can also act as shock absorbers because they are liquid at body temperature. ● However fat cannot be rapidly used and therefore can only be used in aerobic respiration. Body Mass Index (BMI): BMI = Mass (kg)/(Height (m))2. Units are in kg/m2 Causes of being overweight/underweight vary.. Obesity and anorexia nervosa are both eating disorders, which amount to unhealthy body composition. ● Can use a nomogram to calculate BMI (its a cross of 2 scales). ● ● ● ● Fatty Acids: Can be mono/polyunsaturated or saturated. Most fatty acids have 14-20 carbon atoms. Carbon atoms with a double bond can only link to two hydrogen atoms. Fatty acids without any double bonds are saturated and those with double bonds are mono/poly unsaturated, depending on the number of double bonds present. ● Unsaturated fatty acids: o Can be ‘cis’ or ‘trans’ isomers. o Fatty acids are cis if the hydrogen atoms are on the same side of the double bond. If they are on opposite sides they are trans. o In cid fatty acids there is a kink at the double bond, which causes the fatty acid to bend. This contributes to cis’s ability to pack tightly in regular arrays; far more efficiently stored than saturated fatty acids. Tight packing also lowers their melting point. o Trans-fatty acids have no kinks because they have been artificially hydrogenated in a factory. ● ● ● ● Health risks: ● Main concerns is CHD (Coronary Heart Disorder) . RIP BIO CLASS OF 2K17 ● Coronary arteries getting partially blocked resulting in clotting and damage. Positive correlation between saturated fats and CHD. ● Cis monosaturated fatty acids are claimed to be good fats. ● Trans fats are the biggest contributors to heart disease. 2.4 Proteins Amino acids and polypeptides: ● Amino acids are linked together by condensation to form polypeptides. The linking together occurs on ribosomes during translation. ● Dipeptides: Two amino acids. ● Polypeptide: 20 or more amino acids. ● Oligopeptide: between 2 and 20 amino acids. Diversity of amino acids: ● 20 different amino acids in polypeptides. ● By changing an amino acid, you essentially get an entirely different protein. In collagen, the change of one amino acid from proline to hydroproline, results in a stronger structure. ● 20n , where n is the number of amino acids in the chain. ● Three bases of DNA code for one amino acid. These ‘codons’ are triplet bases. Proteins and polypeptides: ● Protein may consist of two single polypeptides or more than one polypeptide linked together. ● Lysozyme: 1 polypeptide. ● Integrin: 2 polypeptides. ● Collagen: 3 polypeptides. ● Haemoglobin: 4 polypeptides. RIP BIO CLASS OF 2K17 Protein conformations: ● Amino acid sequence determines the 3D shape of the polypeptide. Fibrous Globular Elongated, structure with a repeating Intricate shape with parts that are helical or sheet-like. No folding up, amino acid prevents Polypeptide folds up as amino acids it. are added on. Have bonds between the R groups of the amino acids. Hydrophobic groups on the inside and hydrophilic groups on the outside. Denaturation of protein: Heat/pH extremes (causes). Bonds in 3D structure of protein are susceptible to breakage. This breakage in bonds results in denaturation. Denatured protein does not normally return back to its former structure. Soluble proteins become insoluble and form a precipitate because hydrophobic groups become exposed to water. ● Heat breaks intermolecular bonds or interactions. ● pH changes affect charge on the R groups, breaking ionic bonds with the protein or causing new ones to form. ● ● ● ● Protein functions: ● ● ● ● ● ● ● ● ● ● ● Catalysis. Muscle contractions. Cytoskeletons. Tensile strengthening. Blood clotting. Transport of nutrients and gases. Cell adhesion. Membrane transport. Hormones and receptors. DNA packing. Immunity. RIP BIO CLASS OF 2K17 Examples of proteins: ● Rubisco: Ribulose phosphate carboxylase. Catalyses the reactions for carbon fixation. ● Insulin: Signal to cells to absorb glucose. Reduces blood glucose. Shape and chemical properties correspond to binding site on the receptor. Secreted by beta cells in pancreas. ● Immunoglobulin: Antibody. Binding sites for bacterial antigens has a different binding cite – specific immunity. ● Collagen: Rope-like protein made of three polypeptides wound together. They are located in the skin, blood vessel walls to prevent tearing and allow for tensile strength. ● Rhodopsin: Pigments of rhodopsin, membrane proteins of rod cells in the retina are light sensitive molecules surrounded by an opsin polypeptide. Changes in shape when it absorbs light, triggers opsin and abuses the rod cell to send an impulse to the brain. ● Spider silk: Polypeptide forms parallel arrays very resistant to breaking. Proteomes: ● All of the proteins produced by a cell, tissue or organism. Genome of an organised is fixed but a proteome is not because different cells make different proteins. Proteomes reveal what is happening in a cell at the time, not what could happen. Proteomes differ due to differences in amino acid sequences. 2.5 Enzymes: Active site and enzymes: ● Enzymes have active sites to which specific substrates bind. ● Enzymes are globular proteins that work as catalysts. ● Enzyme substrate specificity: one enzyme can facilitate one particular substrate only. ● Shape and chemical properties of active site and substrates match each other. ● Enzyme catalysts require molecular motion and the collision of substrates with the active site. o Substrate binds to enzyme. o Substrate changes in chemical structure. o Products separate from active site. ● Collision: when enzyme and substrate come together. Collisions occur because of random movements and are successful when the substrate and active site are correctly lined up to each other. Factors affecting enzyme activity RIP BIO CLASS OF 2K17 ● Temperature: Higher kinetic energy leads to greater rate of collision and an increased chance of a successful collision as the energy could exceed the activation energy needed for the reaction to proceed. However, bonds in enzyme vibrate more and change of breakage increases. Breaking of bonds changes shape of active site and this is called denaturation. As temperature increases and more enzymes denature, the rate of collision decreases. ● pH: Enzymes have an optimum pH for functionality. Change in pH, or deviation from the optimum pH, results in reduced rate of reaction. When the H+ ion concentration is higher/lower than the optimum, enzymes activity is hindered and the structure of the enzyme is altered – another example of denaturation. Not all enzymes have the same optimum pH. ● Substrate concentration: Increased substrate concentration would mean more frequent collisions between enzyme and substrate. After binding substrate to active site it is unavailable to other substrates until the products have been created and released. As substrate concentration rises, active sites are increasingly occupied at a given moment; hence the rate of reaction will stagnate. Immobilised enzyme: ● Widely used in industry. Enzymes are immobilised by attaching them to other substances or into aggregations to restrict movement. Enzymes can be attached to a glass surface, trapped in alginate gel or bonded together. ● Advantages: o Easily separated from products of reaction, preventing contamination of products. o Recycling of enzymes: more cost efficient. o Increases durability of enzymes to temperature/pH change o Higher enzyme concentration can be used for increased reaction rate. ● Lactose free milk: Lactose is broken down into glucose and galactose with the help of lactase, an enzyme. o After extracting the lactase from yeast it is used commercially. o Lactose intolerant individuals benefit off this. o Galactose + glucose is sweeter so less sugar needs to be used. o Glucose + galactose are more soluble and hence give a smoother texture in icecream. o Bacteria ferment glucose + galactose faster, so it is easily digested. 2.6 Structure of RNA and DNA: Nucleic acids and nucleotides: RIP BIO CLASS OF 2K17 ● Nucleic acids, DNA and RNA, are polymers of nucleotides. ● Linking together nucleotides forms nucleic acids. ● They consist of three parts: o A sugar: Ribose/deoxyribose. Both are five carbon atoms (pentose). o Phosphate group: Acidic, negatively charged part of the nucleic acid. o Nitrogenous base: Made of nitrogen. Either two/one rings of atoms in its structure (purine (AG)/pyrimidine (CT)). o Base and phosphate are linked to the sugar by covalent bonds. o Covalent bonds are also formed between the phosphate of one nucleotide and the sugar of the next - phosphate with no3 Carbon. o Creates a backbone of alternating sugar and phosphate groups. o Base sequence can vary, and this is how information is stored, through sequencing of 4 bases. Differences between DNA and RNA: DNA RNA Deoxyribose - 2nd Carbon has no Ribose hydroxyl group Two polymers of nucleotides (double One polymer of nucleotide (single stranded) stranded) Thymine Uracil Structure of DNA: ● Double helix. ● Made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs. ● Each strand consists of a chain of nucleotides linked by covalent bonds. ● Antiparallel strands: One strand runs in the opposite direction to the other. ● Two strands are wound together to form a double helix and are held together by hydrogen bonds between the nitrogenous bases. 2 hydrogen bonds between A and T, 3 hydrogen bonds between C and G. ● Complementary base pairing: Adenine with Thymine (Uracil in RNA) and Cytosine with Guanine. 2.7 Transcription, Translation and Replication: RIP BIO CLASS OF 2K17 Semi-conservative replication of DNA: New strands of DNA are formed upon the template strand. The original strand divides. The free nucleotides are added upon the template strand. As a result, two new strands are formed, both having 50% pre-existing DNA. ● Base sequence of the template strand determines the base sequences on new strand, due to complementary base pairing. ● A hydrogen bond would not form with a non-complementary nucleotide. ● ● ● ● DNA Helicase: ● Unwinds the double helix and separates the two strands by breaking the hydrogen bonds. Groups of enzymes that use energy from ATP are required to break the Hydrogen bonds. ● Globular (6) polypeptides arrange around a string of DNA. ● Causes unwinding of the DNA, which separates the strands. DNA polymerase III: ● Links nucleotides together to form a new strand, using pre-existing strand as a template. ● Each of the two strands after helicase splits the DNA molecule, are used as templates. ● DNA polymerase moves from the 5’ to 3’ direction, adding a nucleotide at a time. ● Nucleotides must be complementary to the base position on the template strand. ● Hydrogen bonds are formed between nucleotides. ● After hydrogen bonds, DNA polymerase links the nucleotide to the existing end of a new strand. This is done by making covalent bonds between the phosphate groups of the new nucleotide on the new strand the sugar group of the existing nucleotide on the new strand. ● Very high degree of fidelity is maintained. Polymerase chain reaction (PCR): ● Use of Taq DNA polymerase to produce multiple copies of a specific DNA sequence. ● Very small quantity of DNA is needed at the start. ● Three stages: RIP BIO CLASS OF 2K17 o DNA molecule is heated to 95˚C for 15 seconds to break the hydrogen bonds between the two strands and separate the strands. o DNA molecule is then cooled to 54˚C for 25 seconds during which multiple DNA primase enzymes bind RNA primers bind on the parent strands. This stops them from re-annealing with each other and also provides a starting point for replication. o Reaction mixture then heated to 72oC, the temperature at which Taq DNA polymerase works and adds complementary nucleotides to template strands. ▪ Taq DNA polymerase is extracted from bacteria, Thermusaquaticus, and can withstand very high temperatures. It is used because it will not denature at 95˚C. Reaction mixture is heated to 72˚C for 80 seconds, during which 1,000 nucleotides are added per minute. Transcription: ● Synthesis of mRNA from the DNA base sequence using RNA polymerase. ● Proteins are what determine observable characteristics in an organism. ● Transcription occurs along the antisense strand. RNA polymerase binds to it at the start of a gene and then moves along to separate the two DNA strands. Concurrently it pairs RNA nucleotides with complementary bases. ● Uracil replaces thymine and is complementary to Adenine. ● RNA polymerase forms covalent bonds between RNA nucleotides and then separates from the DNA. Transcription stops at the end of the gene, the enzyme is then released and the mRNA molecule as well. Ribosomes: ● Synthesis of polypeptides on ribosomes: ribosomes consist of a small and a large subunit. Have binding sites for each molecule that partakes in the process. ● Large subunit makes peptide bonds between amino acids to link the, together into a polypeptide. Messenger RNA and genetic code: ● mRNA determines all sequences of polypeptides according to genetic code. ● Length of mRNA is usually 2000 nucleotides. ● Only certain genes will be transcribed, depending on which protein is required to be made. ● Cells that need or secret large amounts of a particular polypeptide will RIP BIO CLASS OF 2K17 contain large amounts of the specific mRNA needed to create it. Codons: ● ● ● ● Genetic code converts base sequence on mRNA into amino acid sequence. Sequence of three bases is called a codon. 64 possible codons. Genetic code is degenerate - many codons specify the same amino acid. Each amino acid is carried by a transfer RNA. Contains a 3 base anticodon complementary to the mRNA codon for that particular amino acid. Codons and anticodons: ● Translation depends on complementary base pairing between mRNA codons and tRNA anticodons. ● Ribosomes act as the binding site for both mRNA and tRNA. They catalyse assembly of polypeptide. ● Translation follows the following process: o mRNA binds to small subunit. o tRNA binds to ribosome. Has anti codon complementary to first mRNA codon. o 2nd tRNA binds. Maximum of two tRNA can be bound to a ribosome at one time. o Amino acids from first tRNA goes to second tRNA and joins by a peptide bond. 2nd tRNA carries dipeptide. o Ribosome moves along mRNA and tRNA is removed leaving one space for new tRNA molecule. o Similar process continues until a stop codon is reached. o Polypeptide is released and ribosome complex breaks down. Human insulin production: ● Occurs in bacteria and is a manifestation of how universal the genetic code is; allowing gene transfer between species. ● Human insulin is produced synthetically using E. coli bacteria. ● Gene that codes for insulin production is transferred to bacteria. ● Transcription and translation then occur to produce harvestable quantities of bacteria. ● Earlier bovine insulin was used. Despite slight genetic difference they still bound to insulin receptors properly. 2.8 Cell Respiration: RIP BIO CLASS OF 2K17 Cell respiration: ● Controlled release of energy from organic compounds to produce ATP. ● ATP from cell respiration is immediately available as a source of energy in the cell. ● The 3 main ATP-requiring activities are: o Synthesising large molecules: DNA, RNA proteins. o Pumping molecules/ions across membranes: active transport. o Moving things around in a cell/ muscle contraction. ● ATP is used by splitting ATP into ADP + P. This is an exothermic reaction and releases energy. This energy is used by cells and then converted into heat energy, which is not reusable/recyclable. As a result all energy is eventually lost to the environment, thus creating a continuous need to obtain energy through ingestion and then respiration. Anaerobic respiration: ● Gives a small yield of ATP from glucose, which is broken down without oxygen. ● Required when a short burst of ATP is needed. ● When oxygen supplies are internally low and in oxygen deficient environments. ● In humans, glucose is converted into lactic acid. However in yeast and plants it converts to ethanol and carbon dioxide. Both lactate and ethanol are toxic. Use of yeast in baking: ● Release of carbon dioxide due to anaerobic respiration causes lighter texture in bread. ● Carbon dioxide cannot escape and forms bubbles. ● Ethanol evaporates during baking. ● Bioethanol is produced by Yeast converting sugar into ethanol. Only sugars, mono/di saccharides can be converted. This is an enzymecatalysed reaction. This ethanol is distilled and can be used in vehicles. Lactate production in humans: ● Used to maximise the power of muscle contractions. ● ATP is created anaerobically when the body requires quick powerful movements. ● Weight lifters, short distance runners are examples of sportsmen who anaerobically respire during their events. ● Muscles cannot tolerate lactate past a certain extent. It results in oxygen debt and so must be broken down. RIP BIO CLASS OF 2K17 Aerobic respiration: ● Requires oxygen and produces large yield of ATP from glucose. Over 30 ATP produced from a single glucose molecule. ● Molecules of ATP per molecule of glucose. ● Glucose + Oxygen => Carbon Dioxide + Water. ● Most of the reactions happen inside the mitochondria. 2.9 Photosynthesis: Photosynthesis: ● Production of carbon compounds in cells using light energy. Photosynthesis is an example of energy conversion. Light energy is converted to chemical energy in carbon compounds. Produces carbohydrates, proteins and lipids. Wavelengths of light: ● Visible light has a range of wavelengths with violet the shortest and red the longest. This is the spectrum of electromagnetic radiation. ● Visible light ranges between 400-700 nm. Sunlight is a mixture of different wavelengths. Light absorption by Chlorophyll: ● Absorbs red/blue light. Reflects green light. ● When drawing an action spectrum for photosynthesis or an absorption spectrum for chlorophyll, the x-axis should be from 400-700 nm. ● For an action spectrum, the y-axis should be ‘relative rate of photosynthesis’ from 0-100%. ● On an absorption spectrum the y-axis should be ‘% absorption’ from 0100%. Oxy gen pro duct ion in phot RIP BIO CLASS OF 2K17 osynthesis: ● Caused by photolysis of water. Light energy splits molecules of water to release electrons needed in other stages. ● 2H2O => 4e-+4H++O2. Oxygen is therefore a waste product and diffuses away. Effects of photosynthesis on Earth: ● Changes to Earth’s atmosphere, oceans and rock deposition due to photosynthesis. ● Causes rising oxygen concentration in atmosphere, known as the Great Oxidation Event. o Glaciation occurred due to reduction of greenhouse effect – fall in methane and carbon dioxide concentrations. o Oxidation of iron deposits in the water result in precipitation on the sea-bed called banded iron formation – iron ores. Production of Carbohydrates: ● Energy is needed to produce carbohydrates and other carbon compounds from carbon dioxide. ● Endothermic reaction to make carbohydrates from carbon dioxide. This energy is derived from light absorption. ● Light energy is therefore converted to chemical energy. Limiting factors: ● Temperature, light intensity and carbon dioxide concentrations. ● Can limit photosynthesis if below the optimal level. ● Under any combination of limiting factors only one actually limits the rate of photosynthesis: the one furthest from its optimum. ● In order to test for effects of limiting factors, two will have to be constant by controlling them. The third would be the independent variable and would change by stead increments. RIP BIO CLASS OF 2K17 3 Genetics 3.1 Genes What is a gene? ● A gene is a heritable factor that consists of a length of DNA and influences a specific characteristic. ● Genes consist of a much shorter length of DNA than a chromosome and each chromosome carries many genes. Comparing numbers of genes ● ● ● ● ● E. coli has 3200 genes. Gut bacterium. Prokaryote group. T. vaginatis has 60,000 genes. Unicellular parasite. Protoctista group. S cerevisiae has 6,000 genes. Unicellular fungus. Fungi group. O. sativa has 41,000 genes. Rice. Plant group. H. sapiens has 23,000 genes. Humans. Animal group. Where are genes located? ● A gene occupies a specific position on one type of chromosome. ● The number of groups of linked genes = the number of chromosomes. For example humans have 23 linked genes and 23 chromosomes. ● The specific position of a gene on a chromosome is called the locus. RIP BIO CLASS OF 2K17 What are alleles? ● Alleles are the various specific forms of a gene. They are alternate forms of the same gene. ● There can be two or more alleles per gene and they occupy the same position on one type of chromosome. ● There can only be one allele of a particular gene at a specific locus. Differences between alleles: ● Different alleles of a gene have variations in their base sequence. ● A position in a gene that has the option of being filled by more than one nitrogenous base is known as a single nucleotide polymorphism (SNP). ● These SNPs are ultimately what allow for the formation of alleles as they allow for variation in the base sequence of the gene. Mutation: ● New alleles are formed by mutation. ● Most common type: base substitution – one base replaces another, which gives rise to a new allele. ● Most mutations are either neutral or harmful, because organisms have already developed over millions of years. ● Mutations in the body cells can’t be inherited, but mutations in gametes can. Sickle cell anaemia: ● Sickle cell anaemia is caused by a base substitution in the Hb gene that codes for alpha-globin polypeptide. ● A base substitution on the sixth codon ‘GAG’ of the Hb gene gives rise to a new allele ‘GTG’, which translates to the amino acid valine instead of glutamic acid. ● Valine causes the Haemoglobin groups to stick together in red blood cells and induce the formation of a rigid sickle cell shape in low oxygen concentrations. ● Sickle cells block blood capillaries and reduce blood flow, causing damage to tissues. ● Eventually the plasma membranes and the haemoglobin cells are damaged and the red blood cells die; their lifespans are shortened to 4 days. ● The body cannot replenish red blood cells at the rate at which they die, so there is a shortage of red blood cells – anaemia. ● HbS genes code for sickle cells. HbA genes code for the normal red blood RIP BIO CLASS OF 2K17 cell. Genome: ● Whole of the genetic information of an organism. ● Human genome consists of 23 pairs of chromosomes in the nucleus plus the DNA molecule in the mitochondria. ● Plant species are similar, however the chromosomes of the chloroplasts must be accounted for too. ● Prokaryote genomes consist of DNA in the circular chromosome plus plasmid DNA. ● Most of the genome is not transcribed. These sections are called junk DNA. ● Some of this junk DNA affects gene expression and some, highly repetitive sequences, are called satellite DNA. 3.2 Chromosomes: Bacterial chromosomes: ● DNA in bacteria is not associated with proteins and is therefore naked. ● Prokaryotic DNA consists of one chromosome of circular DNA, which is double stranded. Plasmids: ● Eukaryotes don’t have plasmids. ● They also consist of circular and naked DNA. ● Do not contain genetic information that is useful for basic life processes but contain the information for antibiotic resistance, for example. ● Aren’t replicated at the same time or same rate as chromosomes, and therefore aren’t always passed down during cell division. Plasmids can be transferred laterally between cells. ● There may be multiple plasmids in a cell. Measuring the length of DNA molecules using Cairns’ technique by autoradiography: ● Cell were grown for two generations in a culture medium containing tritiated thymidine. o Thymidine consists of the base thymine linked to deoxyribose and is used by E. coli cells to make nucleotides that it used in DNA replication. Since tritiated thymidine contains the radioactive isotope of hydrogen, tritium, the DNA produced by DNA replication would be radioactively labelled. RIP BIO CLASS OF 2K17 ● Cells are then placed into a dialysis membrane and their cells walls are digested by the enzyme lysozyme. This releases their DNA onto the surface of the dialysis membrane. ● A photographic emulsion film was placed onto the surface of the membrane and left in the darkness for two months. Atoms of tritium in the DNA decayed emitting high energy electrons which reacted with the film. ● Film was then developed and at each point where the tritium atom decayed was a dark grain, which indicated the position of the DNA. Eukaryotic DNA: ● Is associated with histone proteins, which are globular proteins. Differences between chromosomes: Chromosomes supercoil during mitosis/meiosis and can be seen then. 23 types of chromosome in humans. Genes are arranged in a standard sequence along a type of chromosome. Different chromosomes can be of different lengths and can also vary in the positioning of the centromeres. ● Each chromosome carries a specific sequence of genes arranged along the linear DNA molecule. ● ● ● ● Homologous chromosomes: ● Carry the same sequence of genes but not necessarily the same alleles of those genes. ● They are therefore differentiated by the fact that different alleles of the genes occupy a particular locus, even though they have the same genetic sequence. Genome sizes: ● Genome sizes are correlated with the complexity of the organism but aren’t directly proportional. ● This is because the proportion of DNA that acts as function genes is very variable and the amount of gene duplication varies. ● Humans have a genome size of 3,000 (million base pairs). Whereas E.coli have a genome size of 5 (million base pairs). Haploid nuclei: ● Haploid nuclei have one chromosome of each pair. ● Human haploid nuclei, as found in gametes, have 23 chromosomes, rather RIP BIO CLASS OF 2K17 than 23 pairs of chromosomes. Diploid nuclei: ● Diploid nuclei have pairs of homologous chromosomes. ● They are created when haploid nuclei fuse together as a result of fertilization. ● Having two copies of each gene means that the harmful effects of recessive mutations can be avoided if a dominant allele is also present. Chromosome numbers: ● The number of chromosomes is a characteristic feature of members of a species. ● Organisms with a different number of chromosomes are unlikely to be able to interbreed. ● The number of chromosomes can change during the evolution of a species, however chromosome numbers tend to remain unchanged over millions of years. ● Humans have 46 chromosomes (23 pairs) whereas Dogs have 78 chromosomes (39 pairs). Sex determination: ● X and Y-chromosomes determine sex. Small part of the Y chromosome has the same sequence of genes as a small part of the X chromosome. ● Genes on the remainder of the Y chromosome are not found on the X chromosome and are not needed for female development. ● X chromosomes don’t contain the TDF (test determining factor) gene; hence ovaries develop instead of testes, in women. ● All offspring inherit the X chromosome. Karyograms: ● A karyogram shows the chromosomes of an organism in homologous pairs of decreasing length. ● Stains have to be used to make the chromosomes visible. ● The banding pattern allows chromosomes that are of a different type but similar size to be distinguished. ● As most cells are diploid, the chromosomes are generally in homologous pairs. ● A trisomy on chromosome 21 signifies Down syndrome. ● Karyotypes can also suggest whether an organism is male or female. RIP BIO CLASS OF 2K17 3.3 Meiosis Meiosis in outline: Meiosis includes two nuclear divisions: Meiosis I and II. Nucleus undergoing first division of meiosis is diploid. Daughter cells are haploid. Halving the chromosome number occurs in the first division, but each cell still consists of two sister chromatids until after the second division. ● Final gametes are haploid. ● ● ● ● Meiosis and sexual life cycles: ● The halving of the chromosome number allows a sexual life cycle with fusion of gametes. ● In an asexual life cycle, the offspring have the same chromosomes as the parent, so are genetically identical. ● In a sexual life cycle there is variation between the chromosomes of the offspring and the parents. ● Fertilization doubles the number of chromosomes each time it occurs, hence if the gamete number was not halved, there would be a doubling effect on chromosomal number every generation. ● Meiosis occurs during the process of creating the gametes. ● Body cells are diploid; sex cells are haploid. Replication of DNA before meiosis: ● DNA is replicated during the interphase before meiosis so that all chromosomes consist of two sister chromatids. ● Two chromatids that make up each chromosome are genetically identical. ● Replication does not occur again before the second meiotic division, which results in the halving effect. ● One diploid nucleus divides twice to produce four haploid nuclei, which each chromosome consisting of one chromatid. 0Formation of bivalents and crossing over: ● Pair of homologous chromosomes: bivalents. This complex is also known as a tetrad. The pairing of homologous chromosomes occurs through a process called synapsis. ● Crossing over occurs at the same loci between bivalents. Points at which crossing over occurs are called chiasmata. ● Crossing over can occur at random positions. ● Chromatids with new combinations of alleles are produced. Random orientation of bivalents: RIP BIO CLASS OF 2K17 ● Random orientation is caused by the random positioning of the bivalents during meiosis I. The poles to which the bivalents are pulled to would dependent on which way they are facing. ● The orientation of the bivalent is random, but due to the genetic diversity between bivalents, the different positions would impact the offspring’s genotype differently. Halving the chromosome number: ● In meiosis I the centromere does not divide and whole chromosomes move to opposite poles. Instead disjunction occurs, during which the bivalents are split at the chiasmata that form between them. ● Disjunction is the splitting of homologous chromosomes. ● This halves the chromosome number of a cell, thus meiosis I is a reduction division. Obtaining cells from a foetus: ● Amniocentesis: passes a needle through the mother’s abdomen wall to withdraw a sample of amniotic fluid containing fetal cells. ● Chorionic villus sampling: sampling tool obtains cells from the chorionic villi, a membrane from which the placenta develops. ● Risk of miscarriage is 2% using CVS but 1% using amniocentesis. Divisions of meiosis: ● Prophase I: Cell has 2n chromosomes: n is haploid number of chromosomes. Double chromatids. o Homologous chromosomes pair (synapsis). o Crossing over occurs (at chiasmata). ● Metaphase I: Spindle microtubules move homologous pairs to equator of the cell. o Orientation of paternal and maternal chromosomes on either side of equator is random and independent of other homologous pairs. ● Anaphase I: o Homologous pairs are separated. One chromosome of each pair moves to each pole. ● Telophase I: o Chromosomes uncoil. During the interphase that follows no replication occurs. o Reduction of chromosome number from diploid to haploid completed. o Cytokinesis occurs. ● Prophase II: Chromosomes, which still consist of two chromatids, condense and become visible. RIP BIO CLASS OF 2K17 ● Metaphase II: Spindle fibres attach to centromeres. ● Anaphase II: Centromeres separate and chromatids are moved to opposite poles. ● Telophase II: Chromatids reach opposite poles. Nuclear envelope reforms. Cytokinesis occurs, forming 4 haploid gametes. Meiosis and genetic variation: ● Crossing over and random orientation promotes genetic variation. ● Random orientation of bivalents: o 2n number of random orientations of bivalents, where ‘n’ is the number of chromosomes possessed by a haploid nucleus of an organism. Humans have 223~8 million different ways to place chromosomes. ● Crossing over: o Allows linked genes to be reshuffled to produce new combinations, called recombinants. ● Fertilization and genetic variation: o Fusion of gametes is random. Non-disjunction and Down syndrome: ● Occurs during anaphase I and results in a chromosome excess or deficiency in a gamete. ● This can lead to trisomy 21 after fertilisation, also known as down syndrome. ● Maternal age is positively correlated with the occurrence of trisomy 21. 3.4 Inheritance: Mendel and the principles of inheritance: ● Male and females contribute equally. ● Inheritance is discrete; characteristics that are shown in one generation don’t necessarily appear in the next. ● Some characteristics show a stronger tendency than others. Gametes: ● ● ● ● Gametes are haploid so contain one allele of each gene. Male gamete is smaller than the female one. It is motile, whilst the female is immobile/restricted in its movement. Male and females make an equal contribution because each gamete is haploid and come together to form a diploid cell, zygote. RIP BIO CLASS OF 2K17 Zygotes: ● Zygotes have two alleles of each gene. ● These may be the same alleles or different alleles ● The zygote could contain various combinations of alleles, depending on the number of available alleles. Separation: ● Segregation of alleles into different nuclei. ● Allows new combinations to form in the offspring. ● During meiosis if the parent cell contained two copies of the same allele, each haploid cell would receive one copy of the allele. ● If PP, all gametes would receive a P. If Pp, 50% of gametes would receive P and 50% would receive p. Dominant, recessive and co-dominant alleles: ● Dominant alleles mask the effects of recessive alleles but co-dominant alleles have joint effects. ● Dominant alleles would be expressed in the phenotype. ● Co-dominant alleles: Cw – White flowers. Ck – Red flowers. CwCk – Pink flowers. ● Dominant alleles code for an active protein whereas recessive alleles code for non-functional proteins. Punnett grids: ● Parent generation consists of two pure breeds (two of the same allele). ● They then breed to form a hybrid, usually heterozygous. This forms the F1 generation. ● These hybrids self-pollinate to form 1 homozygous dominant, two heterozygous and 1 homozygous recessive. This forms the F2 generation. ABO blood groups: ● IA is dominant because it codes for an active protein. This active protein alters the glycoprotein by adding N-acetyl-galactosamine. Those without IA would not have N-acetyl-galactosamine and would produce anti-A antibodies. ● IB is dominant because it alters the glycoprotein by the addition of galactose. Those without this allele would produce anti-A antibodies. ● IAIB causes the glycoprotein to be altered by the addition of both N-acetylgalactosamine and galactose. Anti-A antibodies aren’t produced. ● Allele ‘i’ is recessive because it does not alter the glycoprotein. The presence of either IA or IB would result in the addition of galactosamine or RIP BIO CLASS OF 2K17 galactose respectively. ● IA codes or blood group A, IB codes for blood group B, ii, codes for blood group O and IAIB codes for blood group AB. Genetic diseases due to recessive alleles: Most genetic diseases are caused by a recessive allele. Will not show symptoms if heterozygous. Both parents must be carriers of the disease. Cystic fibrosis is an example of a genetic disease caused by a recessive allele. ● Genetic diseases caused by chromosomes, besides the sex chromosomes, are called autosomal diseases. ● ● ● ● Other causes of genetic diseases: ● Red-green colorblindness and haemophilia are examples of sex-linked diseases. ● Huntington’s disease is caused by a dominant allele, and is autosomal. ● Sickle cell anaemia is caused by recessive allele HbS ● Genetic diseases are very rare to inherit and only 75 to 200 alleles among 25,000 genes in the human genome code for any known genetic diseases. Cystic fibrosis: ● Cystic fibrosis is caused by the recessive allele of the CFTR gene, on chromosome 7. ● Produces a chloride ion channel involved in sweat secretion, mucus and digestive juices. ● Recessive allele codes for dysfunctional chloride ion channel, causing reactions like mucus to be low in NaCl, thus little water moves into the mucus and they become viscous and sticky. ● The sticky fluid builds up in the lungs and in the pancreatic duct, causing infections and hindering digestive processes. ● Digestive processes are inhibited because the pancreatic duct is usually blocked by the mucus so digestive enzymes cannot reach the small intestine. Huntington’s disease: ● ● ● ● ● Caused by the dominant allele of the HTT gene on chromosome 4. Codes for a protein named huntingtin. Causes degenerative changes in the brain, onset is around 30-50 years. Causes changes in behaviour and emotion. Life expectancy is 20 years after onset. RIP BIO CLASS OF 2K17 Sex linkage: ● When inheritance patterns are different in males and females, it is presumable that the inheritable feature is located on a sex chromosome. ● Males have one copy of chromosome X and females have two copies. Since X is so much larger than Y, most sex -linked diseases are located on the X chromosome. Red-green colorblindness: Genes are located on the chromosome. Caused by a recessive allele for a photoreceptor protein-coding gene. Cone cells in retina are coded for by these. Detects specific wavelength ranges of visible light. If males inherit a chromosome carrying this recessive allele, they will be colour-blind. ● Females are less likely to inherit colour blindness unless both their parents are either carriers or affected. ● ● ● ● ● Haemophilia: ● Stems from an inability to make clotting Factor VIII. ● The gene that codes for this protein are on the X chromosome, and the allele that causes haemophilia is recessive. ● Males would be more likely than females to inherit it. Causes of mutation: ● High-energy radiation can be mutagenic as it can cause chemical changes to DNA. Gamma rays, short-wave ultraviolet radiation and X rays. ● Some chemical substances like nitrosamines found in tobacco smoke are also mutagenic. Benzene. ● Nuclear bombs and accidents at nuclear power stations contribute to the excess amount of radiation of in some areas and massively increase the number of mutations that occur within organisms in the surrounding areas. 3.5 Genetic modification and biotechnology: Gel electrophoresis: ● Separates charged molecules in an electric field according to size and charge. RIP BIO CLASS OF 2K17 ● Gel is immersed in conducting fluid and an electric field is applied. ● Negatively and positively charged molecules will move in opposite directions. Proteins can be separated according to charge. ● DNA are all negatively charged but are too long to move through the gel so are broken up into smaller fragments by restriction endonucleases. ● Smaller fragments will move further than larger ones in a set amount of time, as they move faster. ● Hence electrophoresis can distinguish molecules by size. DNA profiling: ● ● ● ● ● ● DNA is obtained from a known individual. Highly repetitive sequences sequences are selected and copied by PCR. Copied DNA is then split by restriction endonucleases. Fragments then undergo gel electrophoresis. Banding pattern produced is the individual’s profile. Profiles of different individuals can be compared. Genetic modification: ● Is carried out by transferring genes between species. It is only possible because the genetic code is universal. ● This makes it possible to transfer the genes for insulin coding to bacteria to produce large quantities of insulin for the treatment of diabetics. Methods of gene transfer: ● Endonucleases cut a section of a plasmid, and cut the desired genes from a larger DNA molecule. ● The cutting process, leave single stranded sticky ends on both the plasmid and on the genes from the DNA. ● Hydrogen bonds can form between the bases of the DNA genes and the plasmid. ● DNA ligase seals the nicks in the sugar phosphate backbone after the hydrogen bonds between bases have been formed. Risks of GM crops: ● Environmental benefit of GM crops: o Use of GM crop varieties reduces the need for ploughing and spraying crops, so less fuel is needed for farm machinery. ● Health benefits of GM crops: o Nutritional value of crops can be enhanced by increasing the vitamin content/ removing allergens that may be present in the crop naturally. RIP BIO CLASS OF 2K17 ● Agricultural benefits of GM crops: o Varieties resistant to drought, cold and salinity can be produced, expanding the range over which crops can be produced and increasing yields. ● Environmental risks of GM crops: o Non-target organisms could be affected by toxins that are intended to control pests. ● Health risks of GM crops: o Antibiotic resistance genes used as markers during gene transfer could spread to pathogenic bacteria. ● Agricultural risks of GM crops: o Pests may become resistant to toxins used in GM crops, exacerbating the issue. Analysing risks to monarch butterflies of Bt corn: ● Gene transferred to corn from Bacillus thuringiensis that codes for Bt toxin. ● This kills butterflies, moths, flies, beetles and ants. ● Larvae of the Monarch butterfly feed on milkweed that often grows close to corn, ● This milkweed could be dusted with the toxic pollen of Bt corn and the larvae might be poisoned. Cloning: ● Production of genetically identical organisms is called cloning. A group of genetically identical organisms is called a clone. ● Identical twins are not clones because they have different fingerprints, for example. ● A single garlic bulb can clone itself to form several garlic bulbs that are generally genetically identical. ● Strawberry plants grow long stems with plantlets at the end. These plantlets grow roots into the soil and become independent of the parent plant. These are identical to the parent plant. Cloning animal embryos: ● Process of splitting an embryo is called fragmentation. ● It can be done because embryos are pluripotent. o Totipotent – Can form any cell type, as well as extra-embryonic (placental) tissue (e.g. zygote) o Pluripotent – Can form any cell type (e.g. embryonic stem cells) o Multipotent – Can differentiate into a number of closely related cell types (e.g. hematopoietic adult stem cells) RIP BIO CLASS OF 2K17 o Unipotent – Can not differentiate, but are capable of self renewal (e.g. progenitor cells, muscle stem cells) ● This has been observed to occur in coral embryos. ● Each individual embryo would then be placed in a surrogate mother. ● This is most successful at the eight-cell stage of the blastocyst. Cloning adult animals using differentiated cells: ● Cloning by somatic cell nuclear transfer: o Adult cells are taken from the udder of a sheep. o In order to make the genes inactive and lose differentiation patterns, the cells are grown in a medium of low nutrients. o Unfertilised eggs are taken from another sheep and the nuclei are removed. o Cultured cells from the first sheep are placed inside the zona pellucida around the egg and using an electric pulse they are fused together. o With a 10% success rate, the new embryo is then injected into a surrogate mother using IVF. 4 Ecology 4.1 Species, communities and ecosystems Species: ● Species are groups of organisms that interbreed to produce fertile offspring. ● When two members of the same species mate and produce offspring they are interbreeding. ● Crossbreeding is when members of different species breed together. ● Offspring of crossbreeding tend to be infertile. ● Interbreeding maintains recognizable characteristics of species Populations: ● Members of a species may be reproductively isolated in separate populations. ● Population is a group of organisms of the same species that live in the same area at the same time. ● Two populations may live in different areas but are still have the same RIP BIO CLASS OF 2K17 species as long as they could interbreed to produce fertile offspring. ● If they never interbreed it is likely that they may develop differences. Autotrophs, heterotrophs and mixotrophs: ● Autotrophs make their carbon compounds from carbon dioxide and other simple substances – self-feeding. ● Photosynthetic plants are an example of autotrophs. ● Parasites are exceptions to autotrophs because they evolved from them (divergent evolution). ● Heterotrophs obtain carbon compounds from other organisms. ● Mixotrophs can have both auto/heterotrophic tendencies depending on environmental circumstance. Organisms such as Euglena gracillis can photosynthesis but also feed on detritus that they ingest by endocytosis. Consumers: ● Consumers are heterotrophs that feed on living organisms by ingestion. ● They ingest their food; take in undigested material from other organisms, digest it and absorb the products of digestion. ● Divided into primary, secondary and tertiary ● Many don’t fit into one specific trophic level because their diet includes material from a variety of trophic groups. Detritivores: ● ● ● ● Obtain organic nutrients by internal digestion. Organic matter – dead leaves, feathers, dead animal parts, feces. They ingest the dead matter and then absorb the products of digestion. Unicellular organisms ingest it into food vacuoles whilst multicellular ingest into gut. Saprotrophs: ● Saprotrophs are heterotrophs that obtain organic matter by external digestion. ● They secrete digestive enzymes into dead organic matter. ● Bacteria and fungi are common examples. ● Known as decomposers because they break down dead matter and release elements such as nitrogen back into the soil. Community: ● Populations of different species co-existing. ● All species are dependent on relations with other species, which is why no RIP BIO CLASS OF 2K17 population of one species can live in isolation --- except humans, because we're independent af. Quadrat sampling: Base line marked around habitat using measuring tape. Random numbers are generated using a number generator. First number is used to determine distance along the measuring tape. Second is used to determine a distance out across the habitat at right angles to the tape. ● Quadrat is placed precisely at the distance determined by the two random numbers. ● Only suitable for immotile species. ● Results: o Positive associations: two species occur in the same parts of a habitat and are therefore associated. o Negative associations: two species occur in different parts of a habitat thus tend to not grow around each other and are therefore associated. o Independent distribution: no association between species (forms null hypothesis during chi squared test). ● ● ● ● Ecosystems: ● Community forms an ecosystem by its interactions with the abiotic environment ● Organisms cannot live in isolation as they depend on their non-living surroundings of air, water, soil or rock ok yea so maybe humans aren't independent. Inorganic nutrients: ● Autotrophs and heterotrophs obtain inorganic nutrients from the abiotic environment. ● Elements such as Carbon, Hydrogen and Oxygen are needed to make monomers and polymers of the macronutrients we consume. ● Nitrogen and Phosphates are also needed (for DNA and proteins). ● These are obtained from the abiotic environment. ● Heterotrophs obtain such nutrients from carbon compounds in their food. They can, however, obtain Calcium, Sodium and Potassium from their abiotic environment. Nutrient cycles: ● Supply of inorganic nutrients is maintained by nutrient cycling. ● Carbon cycle and nitrogen cycle are examples. RIP BIO CLASS OF 2K17 ● Nutrients refer to elements that an organism needs. Ecosystem sustainability: ● Ecosystems have the potential to be sustainable over long periods of time. ● Three requirements of nutrient sustainability: o Nutrient availability o Detoxification of waste products. o Energy availability. ● Nutrients are often recycled and the waste products of one organism can be used by another. ● Energy comes in continuous supply from the sun. 4.2 Energy flow Sunlight and ecosystems: ● Most ecosystems rely on a supply of energy from sunlight. ● Three groups of autotrophs: plants, eukaryotic algae and cyanobacteria. o not all plants are autotrophs like the dodder, which feeds on the stems of other plants. ● Autotrophs rely on sunlight directly. ● Heterotrophs rely on sunlight indirectly. ● All energy in the carbon compounds will originally have been harvested by photosynthesis in producers. ● Amount of sunlight absorbed/available for use, varies around the world. Energy conversion: ● Light energy is converted to chemical energy in carbon compounds by photosynthesis. ● Producers can release energy from their carbon compounds by cell respiration and then use it for cell activities. ● This energy is eventually lost as waste heat. ● Large parts of carbon compounds remain in the cells and tissues of producers and are available to heterotrophs. Energy in food chains: ● Chemical energy in carbon compounds flows through food chains by means of feeding. ● Consumers obtain energy from the carbon compounds in the organisms on which they feed. RIP BIO CLASS OF 2K17 Respiration and energy release: ● Energy released by respiration is used in living organisms and converted to heat. o Need energy for synthesising large molecules (DNA RNA proteins). o Active transport across membranes also consumes large amounts of energy. o Moving things around inside the cell, such as chromosomes or vesicles or muscle fibres. ● Energy comes from ATP. o Carbohydrates and lipids are oxidised during cell respiration. o Oxidation is exothermic and therefore energy releasing – the energy released is stored in ATP. ● Second law of thermodynamics states that energy transformations are never 100% efficient. o Energy that isn’t transferred from glucose to ATP is converted to heat. o Heat is also produced during cellular activities. (ATP => heat) Heat energy in ecosystems: ● Heat energy cannot be converted to any other form of energy; hence when it is produced it is generally lost to the environment. ● Heat makes living organisms warmer. It is therefore used as a mechanism of homeostasis. ● Heat passes from hotter bodies to cooler bodies which is why it is eventually lost to the abiotic environment. Energy losses from ecosystems: ● Only about 10% of the energy at each tropic level becomes part of the biomass of the organism in the next trophic level. o As a result there is less and less bioavailable energy in each trophic level. o This limits the number of trophic levels in food chains. o Energy in faeces does not pass along the food chain and instead passes to ‘decomposers’ like saprotrophs and detritivores. o There is a lot of uneaten material, bones or hair, which passes to decomposers and gets excluded from the energy chain. o A large part of energy is lost to heat, due to respiration and other cellular activities. The only energy available to organisms is the RIP BIO CLASS OF 2K17 chemical energy in carbon compounds. ● Biomass, measured in grams, also diminishes along food chains due to loss of carbon dioxide and water from respiration and uneaten/undigested parts of food. o Biomass therefore decreases in higher trophic levels. 4.3 Carbon cycling: Carbon fixation: ● Autotrophs convert carbon dioxide into carbohydrates and other carbon compounds via carbon fixation. ● This reduces carbon dioxide concentrations in the air. Carbon dioxide in solution: ● Carbon dioxide is present as a dissolved gas or hydrogen carbonate ions in aquatic habitats. ● Disassociation of carbon dioxide to form H+ and HCO3- causes acidity. ● Aquatic plants to make carbohydrates and other carbon compounds absorb carbon dioxide and HCO3- ions. Absorption of carbon dioxide: ● Carbon dioxide taken in by autotrophs. ● Since carbon dioxide is used to produce carbon compounds within autotrophs, there is a continuous debt of carbon dioxide causing a concentration gradient with the atmosphere. ● This may happen through stomata on leaves or pores on stems. Release of carbon dioxide from cell respiration: ● Release of carbon dioxide from cell respiration through diffusion. ● Non-photosynthetic cells in producers for example root cells in plants; animal cells; saprotrophs and other decomposers of dead organic matter. ● Diffuses into water or atmosphere. Methanogenesis: RIP BIO CLASS OF 2K17 ● Methane is produced from organic matter in anaerobic conditions by methanogenic archaeans and some diffuses into the atmosphere. ● Methane is a waste product of anaerobic respiration. o Bacteria convert organic matter into a mixture of organic acids, alcohol, hydrogen and carbon dioxide. o Bacteria use the organic acids and alcohol to produce acetate, carbon dioxide and hydrogen. o Archaeans produce methane from carbon dioxide, hydrogen and acetate. ▪ CO2 + 4H2 = CH4 + 2H2O ▪ CH3COOH = CH4 + CO2 ● Archaeans are methanogenic. They carry out this process in mud along shores, swamps, mires, mangroves, guts of animals, peat deposits and landfill sites. Essentially anywhere that is predominantly considered as an anaerobic environment. Oxidation of methane: ● Methane is oxidised to carbon dioxide and water in the atmosphere. ● Monatomic oxygen and highly reactive hydroxyl radicals are involved in methane oxidation. ● Results in low atmospheric concentrations despite large production on earth. Peat formation: ● Forms when organic matter is not fully decomposed because of anaerobic conditions in waterlogged soils. ● Saprotrophs obtain oxygen that they need for respiration from air spaces in the soil. ● Waterlogged soil is anaerobic so saprotrophs can’t respire as completely,, so dead organic matter is left partially decomposed. ● Acidic conditions develop which further inhibit saprotrophs and methanogens from breaking down the organic matter. ● This results in peat. Fossilised organic matter: ● Partially decomposed organic matter was converted into oil and gas in porous rocks/coal. ● Large deposits are a result of incomplete decomposition of organic matter and its burial in sediments that became rock. ● Coal is formed when peat is buried under other sediments. Peat is compressed and heated, turning into coal. ● Oil and natural gas is formed in the mud at the bottom of seas and lakes. RIP BIO CLASS OF 2K17 o Caused by incomplete decomposition in aerobic environments o Compression and heating due to sedimentation causes chemical changes to occur. o Porous rocks hold methane and the sedimentation is formed by impervious rocks placed above and below that prevent the deposit’s escape. Combustion: ● Carbon dioxide is produced by the combustion of biomass and fossilised organic matter. ● Heating to ignition in the presence of oxygen causes combustion. ● Products are carbon dioxide and water. ● Combustion of forest/grassland is natural but can also be artificially induced for agricultural purposes. ● Coal, oil and natural gas are burned as fuels. Limestone: ● Animals such as reef-building corals and molluscs have hard parts that are composed of calcium carbonate. o These can be fossilized in limestone. ● Post mortem, in neutral/alkaline conditions, these exoskeletons form deposits on the seabed or can precipitate to form limestone rock. ● 12% of calcium carbonate is carbon; it is therefore a large carbon sink. Pool versus flux: ● Pool is a reserve of an element whilst flux is the transfer of an element from one pool to another. ● Carbon cycle features the flux of carbon from one pool to another. RIP BIO CLASS OF 2K17 4.4 Climate Change: Greenhouse gases: ● Gases in the atmosphere retain heat, similar to how glass retains heat in greenhouses. ● Water vapour and carbon dioxide are the two most potent greenhouse gases. ● Water in clouds continues to retain heat and radiate it back to the earth’s surface. ● Also reflects heat energy back from the Earth’s surface. Other greenhouse gases: ● Methane: o Released during extraction of fossil fuels and from melting ice. o Also released from methanogens. ● Nitrous oxide: o Released by bacteria and by agricultural processes/vehicle exhausts. ● Greenhouse gases absorb longer wave radiation. Assessing the impact of greenhouse gases: ● Two factors that determine the warming impact of a gas are: o Their ability to absorb longer-wave radiation. o The concentration of the gas in the atmosphere. RIP BIO CLASS OF 2K17 Long-wavelength emissions from Earth: ● Earth absorbs short-wave energy and re-emits longer wavelengths in the form of infrared radiation. ● Solar radiation is short length. Greenhouse gases: ● 30% of solar radiation is absorbed by ozone (UV rays). ● 80% of light reaching earth is radiated back towards atmosphere. ● Greenhouse gases capture 85% of remitted light; some of this energy is radiated back to earth as it is scattered in all directions when re-emitted. Global temperatures and carbon dioxide concentrations: ● Carbon dioxide concentrations from ice cores are consistent with the positive correlation between carbon dioxide concentration and global temperature. ● There seems to have a large fluctuation in global temperatures over the span of Earth’s lifetime. These fluctuations, when analysed, reveal that higher global temperatures are usually preceded by higher concentrations of carbon dioxide in the atmosphere. ● This shows that an increase in greenhouse gases could result in increasing global temperatures. ● The consequences in any rise in global average temperature, however, would not be evenly spread, and some areas would experience different changes (like getting colder or experience more rain etc.). Industrialisation and climate change: ● Industrialisation has caused the combustion of fossil fuels and biomass on a wider and more profound level. ● This increases atmospheric concentration of carbon dioxide rapidly, which as affected and will continue to affect rising average global temperatures. ● Releasing sinks of carbon stored as fossil fuels into the atmosphere. Coral reefs and carbon dioxide: ● Ocean acidification will increase as carbon dioxide concentrations in the atmosphere increase. RIP BIO CLASS OF 2K17 ● Marine animals, such as reef-building corals, that deposit calcium carbonate in their skeletons, need to absorb carbonate ions from seawater. ● Carbon dioxide, when dissolved in water, makes carbonate ion concentrations lower due to the reduction of carbonate to form HCO3. ● This reduces carbonate levels, which are crucial to the survival of corals. o Carbonates are used by corals to make their skeletons. o Also if the seawater ceases to be saturated with carbonate ions, existing calcium carbonate tends to dissolve, putting existing skeletons of corals at threat. 5 Evolution and biodiversity 5.1 Evidence for evolution: Evolution in summary: ● Evolution only concerns heritable characteristics. ● Occurs when heritable characteristics of a species change. Evidence from fossils: ● Fossil records show the sequence in which organisms evolved and can link together existing organisms with their likely ancestors. ● Sequence in which fossils appear matches the sequence in which they would be expected to evolve. ● The sequence also fits in with the ecology of the groups (plant fossils before animal fossils) etc. ● Many sequences of fossils are known, which link together existing organisms with their likely ancestors. Evidence from selective breeding: ● Selective breeding through artificial selection provides evidence for evolution. ● Considerable changes have occurred. ● However this only proves that selection has caused evolution, not that evolution occurs naturally. Evidence from homologous structures: RIP BIO CLASS OF 2K17 ● Evolution of homologous structures by adaptive radiation explains similarities in structures when there are differences in function. ● Analogous structures: different origins but have diverged due to the performance of a similar function. Convergent evolution. ● Homologous structures: Look superficially different and perform different functions but are similar in structure. E.g. pentadactyl limb. Same origin but have diverged due to use/function. Adaptive radiation. ● Vestigial structures: structures that have no function and have slowly diminished over time. Appendix; pelvic bone in whales. Pentadactyl limbs: ● ● ● ● Humerus/femur: single bone in the proximal part. Radius+ulna/tibia+fibia: two bones in the distal part. Carpals/Tarsals: group of wrist/ankle bones. Metacarpals+Phalanges/metatarsals+phalanges: series of bones in each of five digits. Speciation: ● Populations of a species can gradually diverge into separate species by evolution. ● The characteristics of the two populations will gradually diverge to the extent where they will no longer be able to interbreed to produce fertile offspring. ● Endemic species: one found only in a certain geographical area. Occurs by migration and subsequent divergence. Evidence from patterns of variation: ● Continuous variation across the geographical range of related populations matches the concept of gradual divergence. ● Decision to lump populations together or split them into separate species remains arbitrary. Industrial melanism: ● Dark varieties of light insects are called melanistic. ● Biston Betularia, peppered moth. ● Melanic moths are better camouflaged in polluted areas as sulphur dioxide blackens bark of trees and kills light coloured lichens. ● Example of evolution by natural selection as melanism affects survival rates. RIP BIO CLASS OF 2K17 5.2 Natural selection: Variation: ● Natural selection occurs when variation amongst members of the same species occurs. ● This way specific characteristics can be favoured over others, resulting in higher chances of those characteristics becoming predominant in a gene pool. Sources of variation: ● Mutation: base-shift or base substitution. Produces new alleles, due to base substitution at SNPs, enlarging the gene pool. ● Meiosis: New combination of alleles by breaking up existing combinations. Every new cell created by meiosis is likely to carry a different combination of alleles. Crossing over (recombination), independent orientation. ● Sexual reproduction. Gametes come from different parents – combination of alleles from two individuals. Allows mutations in different individuals to be brought together. Adaptations: ● Characteristics that make an individual suited to its environment. ● These occur over time by natural selection. ● Acquired characteristics develop during the lifetime of an individual but these are considered to be non-inheritable. Overproduction of offspring: ● Overproduction of offspring means more offspring produced than supportable by the environment. This is a selection pressure. ● This leads to a struggle for existence in which only the fittest and most well adapted would survive. Differential survival and reproduction: ● Well-adapted individuals survive and reproduce whereas less welladapted die or fail to reproduce. ● Favourable characteristics are therefore inherited by offspring as they allow their ancestors to survive and reproduce successfully. ● This is therefore the process of natural selection. RIP BIO CLASS OF 2K17 Inheritance: ● Individuals that reproduce pass on characteristics to their offspring. ● These are significant to evolution. ● Acquired characteristics are not. Progressive change: ● Natural selection increases the frequency of characteristics that make individuals better adapted and decreases the frequency of other characteristics. ● This causes change within species towards adapting to the demands of their environment. Antibiotic resistance: ● Causes: o Widespread use of antibiotics. o Bacteria reproduce rapidly. o Large populations of bacteria mean higher chance of gene mutation forming resistance. o Bacteria can pass genes between each other laterally using plasmids. ● Process: o Resistance gene either formed by mutation or received by another bacterium. o Use of antibiotic provides environment for natural selection to occur (it is a selection pressure). o Bacteria with resistance survive and reproduce rapidly forming more resistant organisms in the population. ● This is why high risk patients are given a cocktail of antibiotics - to kill off the bacteria that become resistant to one type of antibiotic with another antibiotic. 5.3 Classification of biodiversity: The binomial system: ● Genus species: o Genus name, upper case. o Species name, lower case. ● Can be abbreviated to G. species after first use. Hierarchy of taxa: RIP BIO CLASS OF 2K17 ● Domain, Kingdom, phylum, class, order, family, genus, species. o Delicious Katy Perry Came Over For Great Sex. ● Each taxon includes more species with fewer commonalities. The three domains: ● Eukaryota: o Histones in DNA. o Lots of introns. o Cellulose cell walls/ not present. o Glycerol-ester lipids, d-form glycerol. ● Eubacteria: o No histones. o No introns (rare). o Peptidoglycan cell wall. o Glycerol-ester lipids; d-form glycerol. ● Archaea: o Histone like proteins in DNA. o Occasional presence of introns. o Cell wall not made of peptidoglycan. o Glycerol-ester lipids; I-form glycerol. ● Archaeans are found in extreme habitats of salinity/temperature/acidity. Methanogens are an example. ● Viruses aren’t considered living and are therefore not classified in any of the three domains. Examples of classification: ● Grey wolf: o Eukaryota, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, lupus. ● Date palm: o Eukaryota, Plantae, Angiospermophyta, Monocotyledoneae, Palmales, Araceae, Phoenix, dactylifera. Natural classification: ● All members of a genus or higher taxon should have a common ancestor. ● This is called natural classification. ● Natural groups share many characteristics. Reviewing classification: ● Evidence sometimes shows that members of a group do not actually have a common ancestor. ● This results in splitting the group into two/more taxa. ● The opposite can also occur, uniting taxa. RIP BIO CLASS OF 2K17 Advantages of natural classification: ● Identification of species is easier. Dichotomous keys can be used to help with this process. They can be assigned to a specific kingdom, phylum class, etc. and therefore be identified relative to other known species. ● Because all of the members of a group in a natural classification have evolved from a common ancestral species, they inherit common characteristics. This allows prediction of characteristic within a group. Plants: ● ● ● ● Bryophyta: mosses. Filicinophyta: ferns. Coniferophyta: conifers. Angiospermophyta: flowering plants. Bryophyta Filicinophyt a Coniferophyt a Angriospermophyt a Vegetativ e organs – parts concerne d with growth Rhizoids but Root’s stems and leaves are present. no true roots. Some have simple stems/leaves. Vascular tissue No xylem/phloem . Cambium No cambium. Present in confers and most angiosperms. Allows secondary thickening of stems Pollen No pollen produced Produced in Produced male cones anthers. by Ovules No ovaries/ovules Produced in Enclosed female cones ovaries. inside Seeds No seeds Seeds are produced and dispersed Fruits No fruits Xylem and phloem are both present. Fruits produced for dispersal of seeds. RIP BIO CLASS OF 2K17 Animals: Porifera: Sponges. Cnidaria: Jelly fish, sea anemone. Platyhelminthes: Tapeworms. Mollusca: Squid. Annelids: Leeches. Arthropoda: Insects, crabs. Phylum Mouth/anus Symmetry Skeleton Other external features Porifera No None Internal spicules Surface pores draw in water. Cnidaria Mouth Radial Soft; hard Tentacles corals around secrete mouth. CaCO3 Platyhelminthe s Mouth Bilateral Soft, skeleton Mollusca Both Bilateral Most have Mantle shell made of secretes CaCO3. shell. Annelids Both Bilateral Internal Ring-shaped cavity with segments, fluid under with bristles pressure Arthropoda Both Bilateral External skeleton made pates chitin. no No blood system/ gas exchange system. Segmented bodies and of legs/other of appendages. RIP BIO CLASS OF 2K17 Vertebrates: ● ● ● ● ● Bony ray-finned fish. Amphibians/ Repitles Birds. Mammals. Bony ray-fish Amphibians Reptiles Scales Skin Impermeable Skin with permeable to skin, in scales feathers made water and of keratin. of keratin gases Gills covered Simple lungs Lungs with by an with small extensive operculum folds and folding to moist ksin increase surface area No limbs Birds Mammals Skin has follicles with hair made of keratin. Lungs with parabronchial tubes. Lungs with alveoli ventilated using ribs and diaphragm. Two legs/ two wings, hollow wings adapted for flight Four legs or two legs/two are or two legs/two wings Pentadactyl limbs Fins Four legs Four legs supported by when adult rays Eggs and sperm released for Sperm passed into the female for internal external fertilization fertilization. Remain in Larval in Female lays Female lays water water, adult eggs with soft eggs with through their on land. shell hard shells life cycle Swim bladder Eggs coated in Teeth protective jelly No constant body temperature 5.4 Cladistics: No teeth have beak) Most give birth to live young. Have mammary glands ( Teeth different types. Constant body temperature of RIP BIO CLASS OF 2K17 Clades: ● A group of organisms that have evolved from a common ancestor. Identifying members of a clade: ● Members of a particular clade can be identified by their base or amino acid sequence. ● Species that diverged from a common ancestor long ago are likely to have many differences. Molecular clocks: ● Differences in base/amino acid sequences accumulate gradually. ● Positive correlation between number of differences between two species and the time since they diverged from a common ancestor. ● Number of differences can be used to deduce when species split. ● Molecular clocks basically show how often a mutation occurs. Analogous and homologous traits: ● Homologous is due to similar ancestry. E.g. pentadactyl limb. ● Analogous structures are similar due to convergent evolution. Evolve independently and have similar uses/functions for the limb in question. Cladograms: ● Show probable sequence of divergence in clades. ● Principle of parsimony: computer programmes show how clades could have evolved based on differences in their base sequences. Indicates sequence of evolution. ● Branching point on a cladogram is called a node. Cladograms and reclassification: ● Cladistics highlights that classifications made by structure are not always accurate depictions of how the organism actually evolved. Classification by morphology: ● Classification based on physical characteristics/anatomical characteristics rather than base sequence/amino acid sequence. ● Inaccurate. 6 Human Physiology RIP BIO CLASS OF 2K17 6.1 Digestion and absorption: Structure of the digestive system: ● Mouth: chewing (mechanical digestion). Saliva contains amylase (enzyme) and lubricants. ● Oesophagus: Peristalsis from mouth to stomach. ● Stomach: Churning into chime. Water and acid kills bacteria and pathogens. Protein digestion. ● Small intestine: Digestion of lipids, carbohydrates, proteins, and nucleic acids. Neutralisation of stomach acid and absorption of nutrients through villi. ● Pancreas: Secretes lipase, amylase and protease. ● Liver: Secretion of surfactants in bile break up lipid droplets. ● Gall bladder: Stores/releases bile. ● Large intestine: reabsorbs water; carbohydrates are digested further by symbiotic bacteria; formation/storage of faeces. Structure of the wall of the small intestine: ● Serosa – Outer coat. ● Muscle layers – Longitudinal/circular muscle. RIP BIO CLASS OF 2K17 ● Sub-mucosa – Tissue containing blood/lymph vessels. ● Mucosa – Lining of small intestine, epithelium absorbs nutrients on its inner surface. Peristalsis: ● Contraction of circular and longitudinal muscle layers of the small intestine translocates food and mixes it with enzymes. ● Circular and longitudinal muscle in the wall of the gut is smooth muscle. ● Consists of short cells. ● Exerts continuous moderate force and short periods of forceful contraction. ● These contractions are called peristalsis. ● Circular muscles contract to prevent backflow of food - narrowing the lumen behind the food. ● Contraction of longitudinal muscle assists movement forward - dilating the lumen at and slightly ahead of the food. ● Controlled by the enteric nervous system. ● Unidirectional movement of food, away from the mouth. ● Main function of peristalsis in the intestine is churning of semi-digested food to mix with enzymes. Pancreatic juice: ● Secretes enzymes into the lumen of the small intestine. ● Two types of gland tissue: o Cells responsible for sugar control (cells in the islets of Langerhans - your alpha and beta cells) and; RIP BIO CLASS OF 2K17 ● ● ● ● ● o Cells responsible for digestive enzymes. Controlled by enteric nervous system and hormones secreted by stomach.. Enzymes are secreted into ducts. Enzymes synthesised on the rough endoplasmic reticulum (rER) of pancreas. Processed by the Golgi apparatus (GA) and secreted by exocytosis. Amylase, lipases and proteases. Digestion in the small intestine: ● Enzymes digest most macromolecules in food into monomers in the small intestine. ● Enzymes secreted by pancreas carry out hydrolysis reactions. o Starch => Maltose (amylase). o Triglycerides => fatty acids and glycerol (lipase). o Phospholipids => fatty acids, glycerol and phosphate (phospholipase). o Proteins/polypeptides => shorter peptides (protease). ● Walls of small intestine produce other enzymes. o Gland cells secrete enzymes into the intestinal juice, however most enzymes are immobilised in the plasma membrane of the epithelium. o Types of enzymes are: nucleases, maltase, lactase, sucrase, exopeptidases (break peptide chains into dipeptides) and dipeptidases (break dipeptides into amino acids). o These break all the nutrients down until they are reduced to the monomers. ● Some substances (like cellulose) remain undigested because humans are unable to synthesise the necessary enzymes. Villi and the surface area for digestion: ● Villi increase the surface area of the epithelium (mucosa) over which absorption is carried out. They are finger-like projections of the mucosa. ● Increase surface area by a factor of 10. They have microvilli, which increases the surface area even more. Absorption by villi: ● Absorb monomers formed by digestion as well as mineral ions and vitamins. o Any monosaccharides, amino acids, fatty acids, monoglycerides, glycerol and nitrogenous bases are absorbed. ● The liver detoxifies harmful substances that pass through the villi; un- RIP BIO CLASS OF 2K17 harmful but unwanted substances are also absorbed by the liver but are later excreted through urination. ● Bacteria passes through are eliminated through phagocytosis. Methods of absorption: ● Methods of membrane transport are required to absorb different nutrients. ● Nutrients move from the lumen of the small intestine, through the plasma membrane, through the epithelium and into the lacteal/blood capillaries of the villus. ● Fats: o Triglycerides: ▪ Glycerol diffuse into villus epithelium. They can pass through phospholipids. ▪ Fatty acids require facilitated diffusion (fatty acid transporters) in the microvilli membrane). ▪ Fatty acids and Glycerol combine to form triglycerides once inside the epithelium. o Triglycerides coalesce with cholesterol to form larger droplets. o Lipoproteins are released by exocytosis through the plasma membrane on the inner side of the villus and either enter the lacteal, or enter the blood capillaries. ● Glucose: o Glucose cannot pass through simple diffusion because it is polar and hydrophilic. o Sodium-Potassium pumps in the inner part of the plasma membrane pump sodium ions out from the cytoplasm into the interstitial spaces of the villus and potassium ions in the opposite direction. o Creates low sodium concentration in the villus epithelium. o Sodium-glucose co-transporter proteins in microvilli transport one molecule of sodium and glucose together into the epithelium. o Due to the low concentration of sodium into the villus epithelium, and the relatively high concentration of sodium in the lumen of the small intestine, the movement into the villus epithelium is passive, through facilitated diffusion. Even though glucose is moving against its concentration gradient, it moves into the epithelium because sodium is moving down its own conc gradient. o Glucose channels allow movement by facilitated diffusion into the blood capillaries in the villus. Starch digestion in the small intestine: ● Starch is a macromolecule composed of alpha glucose monomers linked RIP BIO CLASS OF 2K17 ● ● ● ● ● ● together. It is too large to be absorbed. The breakdown of starch is exothermic but is too slow without enzymes. Consists of two molecules: o Amylose (1,4) unbranched o Amylopectin (1,6) branched. Amylase breaks down any 1,4 bonds in starch. o Amylose is therefore broken down into maltose and maltotriose. o Amylase cannot break down 1,6 bonds due to its active site specificity. o Fragments containing 1,6 bonds are called dextrins. Enzymes in microvilli on villi epithelium cells (maltase, glucosidase and dextrinase) digest the three products of amylase digestion (maltose, maltotriose and dextrin) into glucose. The glucose is then co-transported with sodium ions into the villus epithelium and into the blood capillaries, where it is sent to the liver via the hepatic portal vein and any excess is turned into glycogen. 6.2 The blood system: Arteries: ● Arteries convey blood at high pressure from the ventricles to the tissues of the body. ● Elastic tissue contains elastin fibres. o These fibres store energy to stretch them. o The subsequent recoil of the fibres releases the energy and forces the blood down the artery. ● Smooth muscle controls the diameter of the lumen and overall blood flow. ● Both elastic and smooth tissues prevent aneurysm (swelling of artery). ● Blood’s movement through arteries is pulsatile, reflecting each heartbeat. Artery walls: ● ● ● ● Have muscle and elastic fibres in their walls. Tunica externa – tough outer layer. Tunica media – thick layer with smooth/elastic fibres Tunica intima – smooth endothelium. Arterial blood pressure: ● Smooth and elastic fibres maintain blood pressure between pump cycles. o Systolic pressure (peak pressure reached in an artery). ▪ Stores potential energy in elastin due to high pressure. o Diastolic pressure (lowest pressure in arteries). RIP BIO CLASS OF 2K17 Elastin fibres squeeze blood in the lumen when pressure in the lumen falls at the end of a heartbeat. ● Blood flow remains continuous, although pulsating, due to maintenance of relative high pressure. ● Vasoconstriction: contraction of circular muscles. o Form a ring so during vasoconstriction, the circumference reduces and lumen is narrowed. o Blood pressure is increased as a result. o Arterioles have more circular muscles that control blood flow that is usually hormone/neutrally regulated. o Vasoconstriction restricts blood flow and vasodilation increases it. ▪ Capillaries: ● Allow the exchange of materials between cells in tissue and blood in the capillary. ● Supply blood to every tissue except cornea and lens. ● Capillary wall consists of a layer of endothelial cells. o Single cell structure makes it very permeable. o Permeability does however vary, and depends on the needs of the tissues they perfuse. ● Blood cells are suspended in plasma. o Some plasma leaks out of capillaries to become tissue fluid that contains oxygen, glucose, etc. but not large protein molecules, which can’t pass out of capillaries. o Tissue fluid flows between cells so they can absorb nutrients and oxygen and excrete metabolic waste into it. o Tissue fluid then re-enters the capillaries. Veins: ● Collect blood at low pressure from body tissue and return it to the atria from capillary networks. ● Much lower pressure (than arteries). Have thinner walls than arteries. ● Have fewer smooth/elastic fibres. ● Much larger lumen, hold more blood. ● Blood flow in veins is increased by contraction of muscles (muscles that are not part of the blood vessel) in any activity. ● Most body parts are linked to more than one vein. ● Non pulsatile flow of blood. Valves in veins: ● Ensure circulation by preventing backflow. ● Due to low blood pressure in veins, backflow is possible. Hence pocket RIP BIO CLASS OF 2K17 ● ● ● ● valves prevent this. Flaps of pocket valves catch blood, fill with it, and block the vein’s lumen. This increases pressure and past a certain pressure threshold the blood pushes through the flaps and continues flowing towards the heart. This allows for unidirectional blood flow. Maximises the use of intermittent pressures by muscular and postural changes. Artery Diameter Larger um Capillary than 10 Around 10 um Relative thickness Relatively thick Extremely thin of wall and wall and narrow diameter of lumen lumen Vein Much larger than 10 um Thin wall wide lumen but Number of layers Three layers, One layer, tunica Three layers in wall which are sub- intima. (same as artery) divided into more layers. Muscle and elastic Abundant fibres in the wall Valves None None Small amounts None Present in most Double circulation: ● Lungs are supplied with blood by a separate circulation. ● Blood is pumped to lungs at a lower pressure (which is why the right ventricle is smaller than the left). ● Pulmonary circulation: to and from the lungs. ● Systemic circulation: to and from all other organs. RIP BIO CLASS OF 2K17 ● Pulmonary artery carries deoxygenated blood and pulmonary vein carries oxygenated blood. Atherosclerosis: ● Caused by fatty tissue (atheroma) developing adjacent to the endothelium in artery walls. o Low-density lipoproteins (LDL) accumulate, and phagocytes are attracted due to signals from endothelial cells. The combination of LDL and phagocytes forms the atheroma. ● Smooth muscle cells form a tough cap on the atheroma, causing artery wall to bulge and impeding blood flow. ● Coronary occlusion: o Narrowing of blood arteries that supply the heart with oxygen. ● Causes angina, which impairs ability to contract – faster heart beat. ● Fibrous cap covering atheromas sometimes rupture, causing blood clots. ● Caused by: o High LDL intake, diabetes, high blood pressure, production of trimethylamine N-oxide by microbes in intestine. Sinoatrial node: ● Initiates heartbeat and located in the right atrium. ● Myogenic; does not require stimulation from motor neurons. ● Contraction of cell depolarises the membrane causing surrounding cells to depolarise too (due to local currents and impulse propagation). ● Have proteins that offset contraction also have most extensive membranes to affect surrounding cells (depolarise). ● First to depolarise in a cardiac cycle. RIP BIO CLASS OF 2K17 Initiating the heartbeat: ● SA node acts as a pacemaker. ● Initiates each heartbeat, therefore setting the pace for the heart beat. ● Can be replaced by an artificial pacemaker (placed under the skin with electrodes attached to wall of the heart). Atrial and ventricular contraction: ● SA node’s electrical signals stimulate contraction in walls of atria and ventricles. ● Electrical signal spreads through adjacent fibres in the heart and reach atria in less than 1/10 of a second. ● Left and right walls of atria contract first. ● 0.1 seconds later the ventricles contract, once the electric impulse reaches them. Changing the heart rate (HR): ● HR can be increased/decreased. This is caused by impulses brought the heart through two nerves from the medulla of the brain (parasympathetic to increase heart rate, sympathetic to decrease heart rate) ● SA node responds to signals from outside the heart, including two nerves from medulla. Specific part of the brain – cardiovascular centre in the medulla. ● One nerve increases frequency of heartbeats (parasympathetic) and the other nerve decreases frequency (sympathetic). ● Cardiovascular centre in brain responds to blood pressure, pH and oxygen concentrations in the body. Epinephrine: ● ● ● ● Increases HR to prepare for vigorous physical activity. SA node also responds to epinephrine (adrenaline). Increases HR. Produced by adrenal glands, which sit on top of kidneys. “Fight or flight” hormone. NOTE: Notes are a bit weak with the cardiovascular system, specifically the cardiac cycle. Look through study guide for this. 6.3 Defence against infectious diseases: RIP BIO CLASS OF 2K17 Skin as a barrier to infection: ● Skin and mucous membranes form a primary defence against pathogens that cause infectious disease. o Tough outer layer provides physical barrier. o Sebaceous glands, associated with hair follicles, secrete sebum, moisture and lowers pH. ▪ Inhibits growth of bacteria. ● Mucous membranes are found in nasal passages, penis, and vagina. o Secrete sticky solution of glycoproteins, which acts as a physical barrier by trapping pathogens. Goblet cells in the esophagus do this. o Enzyme lysozyme gives anti-bacterial properties. Cuts and clots: ● Cuts in the skin are sealed by blood clots. ● Blood changes from being liquid to a semi-solid gel. ● Clots prevent entry of pathogens. Platelets and blood clotting: ● Clotting factors are released from platelets. ● Platelets aggregate at the cut, forming a plug and then release clotting factors. Fibrin production: ● Conversion of fibrinogen to fibrin by thrombin, which is activated by prothrombin activator from prothrombin to thrombin. ● Release of clotting factors from platelets results in thrombin being produced. ● Converts soluble protein fibrinogen into insoluble fibrin. ● Mesh of fibrin traps platelets and blood cells, increasing the clot. Coronary thrombosis: ● Coronary arteries supply blood to the walls of the heart – oxygen and glucose for cell respiration. ● Blood clot is called a thrombus in medical terms. ● Blood clot in the coronary arteries can result in heart being deprived of molecules required for respiration. o Cardiac muscles are unable to contract properly with the shortage of ATP and become irregular and uncoordinated. o Results in fibrillation. ● Occlusion in the coronary arteries occurs when an atheroma develops, RIP BIO CLASS OF 2K17 hardening the artery and damaging them. ● Lesions occur when the atheroma ruptures. ● These ruptures trigger the clotting process and results in fibrillation. ● Caused by smoking, high blood cholesterol concentration, and high blood pressure. Phagocytes: ● White blood cells that give non-specific immunity. ● After skin and mucous membranes, the WBC gives a secondary line of defence. ● They engulf pathogens by endocytosis and digest them with enzymes from lysosomes. ● Infection of wounds results in pus – large amount of phagocytes aggregating at the infected site. Antibody production: ● Lymphocytes produce antibodies providing specific immunity. ● Proteins on the surface of the pathogen (antigens) are recognised as foreign bodies and trigger a specific immune response. ● Antibodies bind to the antigen. ● Each lymphocyte produces one type of antibody. ● Few of these, but the antigens on the pathogens stimulate cell divisions that produce the appropriate type of antibody. ● Plasma cells, clones of the antibody producing lymphocytes, then secrete antibodies to control the pathogen. Antibodies: ● Have a hyper-variable region that binds to an antigen. ● Have another region that prevents viruses from docking to host cells and makes pathogens more recognisable to phagocytes. ● Antibodies and plasma cells don’t remain after the infection. o Some of the lymphocytes, instead of becoming plasma cells, become memory cells, which remain inactive until the body is invaded by the pathogen again. Human immunodeficiency virus (HIV): ● HIV invades and destroys helper T cells and as a result antibodies cannot be produced. ● HIV positive if body begins making antibodies against HIV ● Retrovirus uses reverse transcriptase to make DNA copies of its genes. RIP BIO CLASS OF 2K17 o Antiretroviral drugs can slow destruction of T helper cells. o Results in weak immune system due to acquired immune deficiency syndrome (AIDS). o Occurs due to sex or sharing of hypodermic needles. Antibiotics: ● Antibiotics block metabolic processes in prokaryotic cells, resulting in their death o These metabolic processes are not present in viruses (they don't have metabolic processes as they rely on the host cells to carry out their metabolic processes for them. This is why antibiotics don't affect viruses. ● Does not affect human cells. ● Block DNA replication, transcription, translation, ribosomal function and cell wall formation. Viruses and antibiotics: ● Viral diseases cannot be treated using antibiotics because they lack a metabolism. ● Live off the chemical processes of a host cell. ● Do not synthesise proteins and depend on a host for ATP synthesis. ● Using antibiotics to treat viral infections are redundant, and contribute to the overuse of antibiotics, which contributes to antibiotic resistance. ● Antivirals can target viral enzymes (neuraminidase and hemagglutinin) without affecting host cells. Resistance to antibiotics: ● Bacteria have evolved with genes that confer resistance to antibiotics. ● Natural selection results in resistance. Some strains have developed such as MRSA - methicillin resistant staphylococcus aureus. ● Doctors must prescribe antibiotics for serious bacterial infections only. ● Antibiotics courses must be completed. ● High standards of hygiene in hospitals. ● Animal feeds should not contain antibiotics. 6.4 Gas exchange: Ventilation: ● Maintains concentration gradients of oxygen and carbon dioxide between air in alveoli and blood flowing in adjacent capillaries. RIP BIO CLASS OF 2K17 ● Gas exchange happens by diffusion between air in alveoli and blood in capillaries. ● Air in alveoli has higher oxygen concentration than in blood capillaries. ● Ventilation is the maintenance of this concentration gradient by supplying the alveoli with fresh air. WE DON'T NEED TO KNOW THIS ^ Ventilation rate: ● Number of times air is drawn in/expelled in a minute. ● Tidal volume: volume of air drawn in and expelled with each inhalation or exhalation. Type I pneumocytes: ● Type I pneumocytes are extremely thin alveolar cells that are adapted to carrying out gas exchange. ● Make up a large part of the epithelium. ● Thinness of the cells means shorter diffusion pathways. Type II pneumocytes: ● Type II pneumocytes secrete a solution containing surfactant. ● Creates moist surface inside the alveoli to prevent the sides from sticking RIP BIO CLASS OF 2K17 together; this reduces surface tension. ● The fluid also dissolves oxygen, which can then diffuse to the blood in the alveolar capillaries. ● Pulmonary surfactant: contained within fluid released by Type II pneumocytes. o Monolayer on the surface of the moisture lining the alveoli; hydrophilic heads face the moisture and hydrophobic tails face the air. o Reduces surface tension and prevents water from adhering to the sides of the alveoli during exhalation. Airways for ventilation: ● Air is carried to the lungs in the trachea and bronchi and then to the bronchioles, which have alveoli. ● Rings of cartilage in trachea keep it open even when pressure is low or surrounding tissue pressure is high. Pressure changes during ventilation: ● Muscle contractions cause the pressure changes inside the thorax that force air in and out of the lungs to ventilate them. ● Muscle contractions cause the pressure inside the thorax to drop below atmospheric pressure, which results in inspiration (movement of atmospheric air into thoracic cavity). ● The opposite leads to expiration (movement of air into the atmosphere from the thoracic cavity). Antagonistic muscles: ● Muscles are required for inspiration and expiration. ● Muscles are pulled into an elongated state by the contraction of another muscle. ● Contraction and relaxation of muscles to cause movement are known as antagonistic pairs. Antagonistic muscle action in ventilation during inspiration (opposite occurs during expiration): ● Diaphragm: downwards and flattens (contracts). ● Ribcage: Moves upwards and outwards. o External intercostal muscles contract. o Internal intercostal muscles relax. ● Abdominal muscles relax. RIP BIO CLASS OF 2K17 ● This allows volume inside the thorax to increase; internal pressure decreases as a result. Causes of lung cancer: ● ● ● ● ● ● Smoking: Tobacco smoke contains mutagenic chemicals. Passive smoking: non-smokers inhale tobacco smoke exhaled by smokers. Air pollution: diesel exhaust fumes, nitrogen oxides. Radon gas: radioactive gas that leaks out of certain rocks. Asbestos: contained in dust and other particles that can be inhaled. Silica. Emphysema: Results in larger air sacs with thicker walls. Longer diffusion pathways lead to more inefficient gas exchange. Less surface area for gas exchange. Ventilation is therefore more difficult because lungs are less elastic. Cilia that line the airways and get rid of mucus are damaged and stop functioning. Mucus builds up as a result and causes infections. White blood cells that combat these infections are damaged (inflamed and damaged) by toxins in cigarette smoke, causing these WBCs and surrounding cells to release trypsin, which breaks down the elastic fibres in the lungs. ● Results in low oxygen saturation in the blood. ● ● ● ● ● 6.5 Neurons and synapses Neurons: ● Neurons transmit electrical impulses. A nerve impulse is an electrical signal. ● Cell body (cytoplasm + nucleus) and nerve fibres, along which impulses travel. ● Dendrite: short branched nerve fibres. ● Axons: Elongated nerve fibres. Myelinated nerve fibres: ● Myelinated nerve fibres: myelinations allows for saltatory conduction. ● Basic structure of a nerve fibre: RIP BIO CLASS OF 2K17 o Fibre is cylindrical in shape. o Plasma membrane surrounds cytoplasm. o One micrometre diameter. o Conducts nerve impulses at a speed of 1 meter per second. ● Myelination is the formation of many layers of phospholipid bilayers, created by Schwann cells. o Each time a Schwann cell goes around the nerve fibre, a double layer of phospholipid bilayer is deposited. ● Node of Ranvier is the gap between two myelinations. o Nerve impulses jump from one node to the next – saltatory conduction. o Much quicker than continuous conduction. o Rate of 100 meters per second. Resting potential: ● Maintenance of a resting potential by pumping of sodium ions out of the axoplasm and potassium ions into the axoplasm. ● Sodium-potassium pumps transfer ions across the membrane in ratio of 3/2. ● Potassium is pumped into axoplasm and sodium is pumped out of axoplasm. ● Membrane is more permeable to potassium than sodium, so more potassium ions leak back than sodium. ● Negatively charged proteins/chlorine ions inside nerve fibre increases charge imbalance. ● All factors contribute to creating a -70mV resting potential. Action potential: ● Consists of depolarization and repolarization of the neuron. ● Depolarization is the change from negative to positive charge and repolarisation is the change from positive to negative charge. ● Depolarization: Opening of sodium channels allowing sodium ions to diffuse into the neuron. This raises membrane potential to +30mV. ● Repolarization: closing of the Sodium voltage gated channels and the subsequent opening of the potassium voltage gated channels. o Potassium ions then diffuse out down their concentration gradient. o Membrane potential falls below resting potential -90mV. ● Refractory period: restoration of resting potential. This is hyperpolarization, where the potential changes from -90mV to -70mV by the action of the sodium potassium pump. RIP BIO CLASS OF 2K17 Propagation of action potentials: ● Occurs because the ion movements that depolarise one part of the neuron trigger depolarization in the neighbouring part of the neuron (local currents of Na+ ions moving diffusing to other areas of the axoplasm). ● Impulse propagation is unidirectional and moves along the axon. ● Refractory period prevents backwards propagation. Local currents: ● Cause each successful part of the axon to reach the threshold potential. ● Depolarisation results in the influx of sodium ions. o This results in there being a different sodium concentration at the part of the axon where influx occurred, than a neighbouring part of the axon. o So, sodium ions diffuse between these regions both inside and outside the axon. ● Movement of sodium ions between polarised parts to depolarised parts (and vice versa) are known as local currents. ● By decreasing the concentration gradient (of sodium ions) in the part that is still polarised, the membrane potential rises from -70mV to -50mV, which is the threshold potential required to open the sodium voltage gated channels and cause depolarisation. o Thus local currents increase the membrane potential to the RIP BIO CLASS OF 2K17 threshold potential. Synapses: ● Junctions between neurons and other neurons/receptor/effector cells. ● Neurotransmitters are used to send the electrical impulse across the synapse in chemical form. ● Presynaptic and postsynaptic cells make this occur. ● Gap is called the synaptic cleft – 20 nanometres wide. Synaptic transmission: ● Nerve impulse reaches the end of a neuron and depolarises the presynaptic membrane. ● This results in the release of calcium ions to diffuse in, through channels, into the membrane. ● This triggers vesicles with neurotransmitters to fuse with the presynaptic membrane and the neurotransmitters to be released by exocytosis. ● Neurotransmitters then diffuse across the synaptic cleft and bind to receptors on postsynaptic membrane. ● Triggers sodium ion channels to open and sodium ions to diffuse into the postsynaptic neuron. o Causes it to reach threshold potential and an action potential to be triggered. ● Neurotransmitters are then broken down and removed from the synaptic cleft. Acetylcholine: ● Used as a neurotransmitter. ● Produced by combining choline with an acetyl group. ● Loaded into vesicles and released into the synaptic cleft during synaptic transmission. ● Bind the specific receptors on postsynaptic membrane. ● Acetylcholinesterase rapidly breaks acetylcholine into acetyl and choline. ● Choline is then reabsorbed into the presynaptic neuron. Neonicotinoids: ● Block synaptic transmission at cholinergic synapses in insects by binding of neonicotinoid pesticides to acetylcholine receptors. ● Acetylcholinesterase does not break down neonicotinoids, so the binding is irreversible. ● Synaptic transmission is therefore prevented. ● Not very effective on humans, however concerns regarding honeybees RIP BIO CLASS OF 2K17 have been raised. Threshold potentials: ● Nerve impulses follow an all-or-nothing principle. ● If the threshold potential is reached then an action potential is triggered, if not then it isn’t. ● If threshold potential is reached there will always be full depolarization. ● If the threshold potential is not reached in postsynaptic membrane, sodium potassium pumps pump out the sodium ions that have entered the postsynaptic neuron. o The postsynaptic membrane returns to the resting potential. ● Most postsynaptic neurons in the brain have synapses with many presynaptic neurons. ● Many of these release neurotransmitters at the same time so the threshold potential will be reached. 6.6 Hormones, homeostasis and reproduction: Control of blood glucose concentration: ● Insulin and glucagon are secreted by beta and alpha cells in the pancreas to control blood glucose concentration. ● The maintenance levels of glucose in the body are 5 mmol/L. Variation from this triggers a homeostatic response. ● Pancreas: exocrine (into ducts)and endocrine (release straight into blood). Insulin and glucagon are released directly into the blood (endocrine). ● Islets of Langerhans contain alpha and beta cells. ● Glucagon increases blood glucose concentration by turning glycogen into glucose. o Stimulates the liver cells to break glycogen down into glucose and release the glucose. This increases blood glucose level. ● Insulin reduces blood glucose concentration. o Stimulates uptake of glucose by various tissues (eg liver and muscle cells) and for these cells to convert glucose to glycogen. o Broken down by the cells it acts upon, so requires continuous production o Insulin stimulates other cells to use glucose in cell respiration instead of fat. Diabetes: RIP BIO CLASS OF 2K17 ● Consistently elevated blood glucose levels. Damages tissues; decreases reabsorption of water from urine, resulting in dehydration. ● Type I: early onset. o Inability to produce insulin. Autoimmune disease arising from the destruction of beta cells. ● Type II: late onset. o Inability to process/respond to insulin due to deficiency of insulin receptors or glucose transporters. o Caused by sugary or fatty diets, lack of exercise and genetic factors. ● Treatments: o Type I: Constant blood sugar tests and insulin injections. Done before a meal to prevent spikes in blood sugar. Implanted devices that release insulin into blood as necessary. Stem cells can become fully functional beta cells. o Type II: Adjusting diet to reduce peaks and troughs of blood glucose. Small frequent amounts of food. No sugary foods; only low glycaemic carbs (slow digesting). Exercise and weight loss. Thyroxin: ● Secreted by thyroid gland to regulate metabolic rate and control body temperature. ● Contains four atoms of iodine. Iodine is therefore important to the diet. ● Targets all body cells. ● Most metabolically active cells (liver, brain and muscle) are main targets. ● High metabolic rates = more protein synthesis and growth. Increases body heat generation. ● Cooling triggers increased thyroxin secretion. ● Thyroxin deficiency: o Lack of energy, forgetfulness and depression, weight gain, constipation. ● Tries to maintain normal body temperature by regulating metabolic processes of the body → negative feedback. o Less thyroxin secreted when body temp is too high= reduced metabolic rate, reduced respiration and vasodilation of skin arterioles. o More thyroxin secreted when body temp is too low = increased metabolic rate, increased respiration and vasoconstriction of skin arterioles. Leptin: ● Secreted by cells in adipose tissue and acts on the hypothalamus of the brain to inhibit appetite. ● Blood leptin concentrations are controlled by: food intake and adipose RIP BIO CLASS OF 2K17 ● ● ● ● tissue amount in the body. Targets group of cells in the hypothalamus that control appetite. Binds onto them. As adipose tissue increases, leptin concentrations rise, inhibiting appetite. Obese mice had two copies of a recessive allele, ob. Those with homozygous recessive could not produce leptin. In obese humans, however, cells seem to have developed resistance to leptin. Increased leptin levels, therefore, have no/reduced effect on appetite restriction. Melatonin: ● Is secreted by the pineal gland to control circadian rhythms. ● Circadian rhythms are controlled by suprachiasmatic nuclei cells (SCN) in the hypothalamus. ● Control secretion of melatonin from the pineal gland. ● Secretion increases in the evening and decreases at dawn. ● Melatonin release results in falling core body temperature. ● Melatonin receptors in the kidney lead to decreased urine production at night. ● Ganglion cells that detect whether it is light or dark and pass impulses to the SCN, which allows it to adjust to the 24hr day and night cycle. ● Jet lag: o SCN and pineal gland continue to set a circadian rhythm for the point of departure rather than destination. o Impulses sent by ganglion help regulate body to point of destination. o Melatonin tablets prevents onset of jetlag by promoting deeper sleep etc. Sex determination in males: ● Gene on Y chromosome causes embryonic gonads to develop as testes and secrete testosterone. ● In the presence of the SRY gene, which codes for the TDF, testes develop. ● This gene is only found on the Y chromosome. ● TDF is not produced in girls, as they don’t have Y-chromosomes. ● TDF stimulates expression of genes for testis development. Testosterone: ● Causes prenatal development of male genitals and both sperm production and development of male secondary sexual characteristics during puberty. o Testes develop in the 8th week. RIP BIO CLASS OF 2K17 o Until the 15th week, testosterone-secreting cells produce testosterone, during which genitalia develop. o At puberty, primary sexual characteristics (sperm) develop. o Testosterone causes onset of secondary sexual characteristics during puberty: enlargement of penis, pubic hair, deepening of voice. Sex determination in females: ● Oestrogen and progesterone cause prenatal development of female reproductive organs and female secondary sexual characteristics during puberty. ● SRY gene is not present so embryonic gonads develop as ovaries. ● Oestrogen and progesterone are secreted by the mother’s ovaries and then placenta. ● In the absence of fetal testosterone, the maternal oestrogen and progesterone will contribute to the development of ovaries. ● Oestrogen causes the prenatal development of female reproductive organs such as the fallopian tubes, uterus and vagina. ● Puberty causes the development of breasts and growth of pubic and underarm hair. o Also results in increased oestrogen and progesterone production. o Positive feedback, as raised levels of oestrogen during puberty cause development of female secondary sexual characteristics. Reproductive systems of males and females: Testis Produce sperm and testosterone Scrotum Hold testes at lower than core body temperature. Epididymis Store sperm until ejaculation Seminal vesicle Secrete fluid containing alkali, proteins and fructose that is added to sperm to make semen and make it sticky. Prostate Gland Secretes alkaline fluid that is added to sperm at the start of ejaculation and helps sperm to swim. Sperm duct/Vas eferens Transfer sperm during ejaculation. Urethra Transfer semen during ejaculation and urine during urination. Penis Penetrate the vagina for ejaculation of RIP BIO CLASS OF 2K17 semen near the cervix. Ovary Produce eggs, progesterone. oestrogen and Oviduct/Fallopian Tubes Collect eggs at ovulation, provide a site for fertilization then move the embryo to the uterus. Uterus Provide for the needs (protection, food, oxygen and removal of waste products) of the embryo and then fetus during pregnancy. Cervix Protect the fetus during pregnancy and then dilate to provide a birth canal. Vagina Stimulate penis to cause ejaculation and provides a birth canal. Vulva Protect internal parts of the female reproductive system. Menstrual cycle: ● Is controlled by negative and positive feedback mechanisms involving ovarian and pituitary hormones. ● Follicular phase: follicles develop in ovary. o An egg is stimulated to grow in each follicle. Endometrium is repaired and thickens. o Most developed follicle breaks open, egg is released into oviduct, RIP BIO CLASS OF 2K17 ● ● ● ● ● and other follicles degenerate. Luteal phase: Corpus luteum formed from wall of follicle that released ovum. o Endometrium continues to develop for implantation. If fertilisation doesn’t occur, corpus luteum breaks down. Endometrium also sheds. Towards the end of the menstrual cycle, FSH rises to a peak and follicle development is stimulated. o Secretion of oestrogen from follicle wall is also stimulated. Oestrogen peaks at the end of a follicular phase and stimulates the repair and thickening of the endometrium. o Also increases FSH receptors, making follicles more receptive to FSH and further stimulating the secretion of oestrogen (positive feedback). At high levels, oestrogen then inhibits FSH. LH rises suddenly at the end of follicular phase and stimulates: o Completion of meiosis I in the oocyte and; o Partial digestion of follicle wall so it can burst open at ovulation. o Assists development of follicular wall into corpus luteum postovulation. o This (Corpus Luteum) secretes more oestrogen and progesterone. Progesterone levels rise at the beginning of the luteal phase and drop back down by the end of the phase. o Promotes thickening and maintenance of the endometrium and inhibits FSH and LH secretion by the pituitary gland. READ THROUGH OXFORD STUDY GUIDE FOR THIS ^. EXPLAINED MORE CLEARLY THERE WITH GRAPHS AND DIAGRAMS. In vitro fertilisation IVF: ● Drugs are taken to stop FSH and LH secretion. o Allows external control of menstrual cycle. o Intramuscular injections of FSH and LH are administered for 10 days to stimulate follicle development. o High concentration of FSH results in around 12 developed follicles (superovulation). ● HCG is then administered to stimulate maturation of follicles. o Each egg is then mixed with 100000 sperm cells and incubated for 37˚C. ● After fertilization, eggs are placed in the uterus. o Progesterone tablet placed in the vagina to ensure uterus lining is maintained. ALSO READ THROUGH OXFORD STUDY GUIDE FOR THIS ^ RIP BIO CLASS OF 2K17 7 Nucleic Acids 7.1 DNA structure and replication: The Watson and Crick model suggested semi-conservative replication: ● DNA structure suggested a mechanism for DNA replication. ● Pyrimidine paired with purine. ● Bases are upside down in relation to one another as strands are antiparallel. ● Adenine has a surplus positive charge and Thymine has a surplus negative charge. o They are therefore electrically compatible. ● Cytosine paired with Guanine forms three hydrogen bonds, enhancing stability. The role of nucleosomes in DNA packing: ● Nucleosomes help to supercoil DNA. ● 2 copies of 4 types of histones linked together by linker DNA. o Connects one nucleosome to the next. o H1 (histone number 9) serves to bind DNA to the core particle of 8 histones. ● Process is supercoiling. o Tails of histone proteins interact with tails from histone proteins in other nucleosomes to tighten and supercoil the chromosome. ● H1 histone bins to form structure called the 30nm fibre that facilitates further packing. ● Packed together in the nucleosome. The leading strand and the lagging strand: ● Replication is continuous on the leading strand along the replication fork as it opens; and discontinuous on the lagging strand moving away from the replication fork. ● Replication occurs anti-parallel. ● Fragments on the lagging strand are called Okazaki fragments. Proteins involved in replication: ● Proteins are involved as enzymes at each stage but also serve several RIP BIO CLASS OF 2K17 ● ● ● ● ● ● other functions. DNA is unwound by DNA Helicase at the replication fork. The strain developing ahead of helicase is released for unwinding by DNA Gyrase (this is a specific class of DNA Topoisomerases). The two strands are kept apart by single stranded binding proteins to allow the template strand to be copied. Multiple RNA primers on lagging strand but only one on leading strand. o Necessary to start replication. o These are created by DNA primase. o Initiates activity of DNA polymerase III. o DNA polymerase I replaces the primer with complementary nucleotides. DNA Polymerase III covalently links deoxyribonucleotide-triphosphates to the 3’ end of the growing strand. DNA ligase links Okazaki fragments - specifically, creates sugar phosphate bonds between the fragments. Direction of replication: ● Replication begins at the origin of replication, where the RNA primer is placed by DNA primase. ● Replication occurs in the 5’ to 3’ direction (nucleotides are added to the 3’ end of the primer) ● Non-coding regions of DNA have important functions: ● Non-coding DNA has some function. o Regulate gene expression. o Produce tRNA and rRNA. o Called introns. ● Repetitive sequences: o 60% of human genome. ● Telomeres: o Occur at the ends of eukaryotic chromosomes. o Serve to protect DNA. o Genes at the end of chromosomes would be lost if replication continued to the end of a chromosome without a telomere. o Telomere’s highly repetitive sequences are sacrificed. DNA profiling: ● Variable number tandem repeats (VNTR) distinguishes individuals based on the number of times this short sequence of DNA repeats. ● Inherited as an allele and is analysed in DNA profiling. ● Sections of VNTR allele combinations are cut from DNA using restriction enzymes and analysed using gel electrophoresis. RIP BIO CLASS OF 2K17 ● Two individuals can be compared in this way. ● Paternal lineage can be deduced by analysing alleles of VNTR from the Y chromosome. ● Maternal lineage can be deduced by analysing variations in mitochondrial DNA at specific hyper-variable region. DNA sequencing: ● Copies of DNA are placed into test tubes with deoxyribonucleotides and enzymes for replication. ● Small quantities of fluorescent dideoxyribonucleotides are added which will stop replication upon being added. o Dideoxyribonucleotides have H instead of OH on the 3rd carbon, which prevents the binding of a phosphate group to it, hence stopping the DNA replication process. ● Fragments created will be analysed through gel electrophoresis and sequences will be determined through colour pattern of fluorescent markers. o New technology allows for the fluorescent dideoxyribonucleotides to be detected by computers and quick interpretation of results. 7.2 Transcription and gene expression: Regulation of gene expression by proteins: ● Promoter: non-coding DNA to which RNA polymerase binds. Not transcribed. ● There are unregulated proteins that are necessary for survival and regulated proteins that are only produced in certain amounts. ● Prokaryotic cells: o Environmental factors influence regulation of gene expression. o Specific genes are expressed to breakdown lactose but an absence of lactose activates repressor proteins that repress the expression of lactose metabolism genes. ● Eukaryotic gene expression is regulated in response to environmental conditions: o Regulation of gene expression is crucial during embryonic development and cellular differentiation. ● Three types of regulatory sequences on DNA: o Enhancers: speed up transcription rates. o Silencers: slow down transcription rates. o Promoter-proximal elements: near to the promoter region. Binding of proteins to them is essential for the start of transcription. RIP BIO CLASS OF 2K17 The impact of the environment on gene expression: ● Human behaviour or phenotype should be attributed to environment or to heredity. ● Production of skin pigmentation in sunlight. ● Morphogens: impact gene expression in the embryo depending on where the embryo cells are placed (endo/meso/ectoderm). ● Selective breeding and temperature can also impact gene expression. Nucleosomes regulate transcription: ● Tails of histones are chemically modified to impact transcription. ● Acetylation, methylation or phosphorylation impact transcription. ● Acetylation neutralises positive charges that stops binding of lysine (on DNA) to other negatively charged DNA therefore stopping tight packaging and allowing for higher transcription levels. ● Chemical modification increases the accessibility of genes to transcription factors. ● Direct methylation of DNA reduces transcription as it aids in supercoiling. ● These chemical modifications are called epigenetic tags and impact phenotype/genotype. ● Epigenome: sum of all epigenetic tags. Can be inherited. Environment affects inheritance. o Most of the epigenome, however, is erased during reprogramming during fertilisation. o 1% survives – this is called imprinting. The direction of transcription: ● Transcription occurs in a 5’ to 3’ direction. ● RNA polymerase binds to promoter region and unwinds RNA. ● Slides across it synthesising a single strand of RNA. Post-transcriptional modification: ● Does not occur in prokaryotes. o Impacts gene expression. o Prokaryotic expression occurs during transcription, not after. o No nuclear membrane around genetic material in prokaryotes hence translation and transcription occur concurrently. ● Compartmentalisation in eukaryotes enables post-transcriptional modification. o Removal of introns. o Pre-mRNA is spliced leaving the mature mRNA with exons only, o 5’ cap and poly A tail to 3’ end are added. RIP BIO CLASS OF 2K17 mRNA splicing: ● Impacts number of proteins an organism can produce, ● Alternatively spliced mRNAs will differ in their AA sequence and biological functions because particular exons may not be included in the mature mRNA. ● Tropomyosin is spliced differently in different tissues resulting in five forms of the protein. o Exon 2 is missing from mRNA of skeletal muscle whilst exons 3 and 10 are absent from mRNA in smooth muscle. 7.3 Translation: The structure of the ribosome: ● Two subunits: o Large and small. ● Three binding sites: o Aminoacyl. o Peptidyl o Exit ● tRNA: o loops of seven unpaired bases. ▪ Three form an anticodon. o Two other loops. o CCA at 3’ end is site for AA attachment. o Have hydrogen bonds. tRNA-activating enzymes: ● Activation of the tRNA occurs when tRNA activating enzyme adds an amino acid to the 3’ terminal. ● 20 different tRNA activating enzymes o Active site of each is specific to an amino acid and a tRNA. ● Energy from ATP is needed to attach the amino acid onto the active site of the enzyme. o Once ATP and amino acid are attached, the amino acid is activated by the formation of a bond between the enzyme and AMP (adenosine monophosphate). Release of two phosphate groups causes this. o Activated amino acid is then covalently attached to tRNA. ● Energy from covalent bond later links amino acid to growing polypeptide chain. Initiation of translation: RIP BIO CLASS OF 2K17 ● Initiation of translation involves assembly of the components that carry out the process. o mRNA binds to small ribosomal subunit at the binding site. o tRNA molecule carrying methionine binds to start codon (AUG). ● Large ribosomal subunit binds to the small one. ● Initiator tRNA is in the P site, another tRNA binds to the A site. o Peptide bond forms between the amino acids in the P and A sites. Elongation: ● Synthesis of the polypeptide involves a repeated cycle of events o Ribosome translocates three bases along the mRNA. o tRNA moves to E site and is released; subsequent tRNA binds to P site, with growing polypeptide chain and a new tRNA binds to A site. o This cycle repeats. Termination: ● Disassembly of the components follows termination of translation. o Stop codon is reached. o Free polypeptide is released. ● Occurs in 5’ to 3’ direction. Free ribosomes: ● Proteins for use primarily within the cell. ● Proteins destined for use in the cytoplasm, mitochondria and chloroplasts are synthesised by ribosomes free in the cytosol. Bound ribosomes: ● Synthesise proteins primarily for secretion or use in lysosomes. ● Destined for use in the endoplasmic reticulum, Golgi apparatus, lysosomes, plasma membrane, extracellular. ● Signal sequence present of polypeptide determines whether a ribosome is bound or free. o This is translated first. o Once the section is translated it is bound to a signal recognition protein that stops the translation until it can bind to a receptor on the surface of the endoplasmic reticulum. o In the absence of the signal sequence, the polypeptide will continue to be translated in a free ribosome. Transcription and translation: RIP BIO CLASS OF 2K17 ● Occurs concurrently in prokaryotes due to absence of nuclear membranes. As soon as transcription ends translation begins. ● Polysomes represent multiple ribosomes attached to a single mRNA molecule. ● Polysomes are present in eukaryotes as well. Primary structure: ● Number and sequence of amino acids in a polypeptide is the primary structure. ● Huge diversity of proteins. ● 20^n, where n is the number of amino acids in a polypeptide. Secondary structure: ● Secondary structure is the formation of alpha helices and beta-pleated sheets stabilised by hydrogen bonds. ● Amino acids in a polypeptide have polar covalent bonds in their backbones; they fold in a way that allows for hydrogen bonds between carboxyl groups and amino acids. Tertiary structure: ● 3D shape of a protein. ● Interaction of R groups with each other and with the surrounding water medium. ● Positively charged R groups interact with negatively charged R groups. ● Hydrophobic amino acids orient themselves towards the centre whilst hydrophilic orient themselves outwards. ● Polar R groups form hydrogen bonds amongst each other. ● Disulphide bridge formed by covalent bonds between R groups of cysteine. Quaternary structure: ● Exists in proteins with more than one polypeptide chain. ● Insulin is made of two chains and haemoglobin of four. ● Addition of non-polypeptide components is present; haemoglobin consists of four chains and four haem groups. ● pH and temperature can distort the structure. 8 Metabolism, Cell respiration and RIP BIO CLASS OF 2K17 Photosynthesis 8.1 Metabolism: Metabolic pathways: ● Metabolic pathways consist of chains and cycles of enzyme-catalysed reactions. ● Small sequence of steps. ● Some metabolic pathways are chain reactions whilst some are cycles. Enzymes and activation energy: ● Enzymes lower the activation energy of the chemical reactions that they catalyse. ● Energy is required for substrates to reach a transition state, this is called the activation energy (breaks or weakens bonds). ● Enzymes bind to the active site and are altered by this. ● This binding reduces activation energy and therefore elicits higher efficiency and speed. ● Net amount of energy released by the reaction is unchanged by the enzyme; only the activation energy is reduced, therefore increasing rate of reaction. Types of enzyme inhibitors: ● Competitive inhibition: o Inhibitor binds to active site so substrates cannot bind. o Increasing substrate concentration can overpower inhibitor and restore full capacity. o Sulfadiazine binds to dihydropteroate synthetase and in doing so blocks para-aminobenzoate. ● Non competitive inhibition: o Inhibitor binds to the allosteric site distorting the active site. o Increasing substrate concentration will have a slight positive effect; however since some enzymes are rendered dysfunctional by the inhibitor, rate of reaction will still be lowered overall. o Xylital-5-phosphate binds to allosteric site; disallows fructose-6phosphate from binding to active site of phosphofructokinase. ● End-product inhibition: o Substance that binds to the allosteric site is the end product of the pathway (in some cases); this acts as an inhibitor so the pathway can be switched off to stop excess product generation. RIP BIO CLASS OF 2K17 o Reactions are therefore monitored by equilibrium, measured by a ratio between product and substrate. o Concentration of product increasing means reaction will slow down and stop to maintain a balance. o End product inhibition therefore stops excess final product and also excess build up of intermediate products. o Threonine dihydretase => Isoleucine. ▪ Isoleucine acts as a non-competitive inhibitor by binding to the active site of the first enzyme in the chain – threonine dehydratase. 8.2 Cell respiration: Oxidation and reduction: Oxidation is the loss of electrons. Reduction is the gain of electrons. NAD + 2H => NADH + H+ Gaining oxygen is oxidation because oxygen has a high affinity for electrons so draws electrons away from other parts of the molecule or ion. ● Nitrifying bacteria oxidise nitrite ions to nitrate. o NO2+0.5O2 => NO3 ● ● ● ● Phosphorylation: ● Phosphorylation makes the phosphorylated molecule unstable. ● Adds phosphate group (PO4)3 – ‘activates’ the molecule. ● Addition of phosphate group is endergonic (energy absorbing) and requires energy from hydrolysis of ATP, which is exergonic (energy releasing). RIP BIO CLASS OF 2K17 ● Glucose => (ATP to ADP) => Glucose-6-phosphate. Glycolysis and ATP: ● Glycolysis gives a small net gain of ATP without the use of oxygen. ● Metabolic pathway: o Glucose. o Glucose-6-phosphate (requires ATP=>ADP). o Fructose-6-phosphate. o Fructose-6-bisphosphate (requires ATP=>ADP). o 2 x triose phosphate. ▪ Oxidised by removal of hydrogen atoms. ▪ Hydrogen atom accepted by NAD+ which because NAD++H+. o Glycerate-3-phosphate. ▪ Created by oxidation of triose phosphate. ▪ The oxidation of triose phosphates provides the energy to dephosphorylate them. ▪ Dephosphorylated to change ADP to ATP. The link reaction: ● Pyruvate is converted into acetyl coenzyme A. ● Decarboxylation occurs first, ridding the three-carbon pyruvate of one carbon, which is released along with oxygen as carbon dioxide. RIP BIO CLASS OF 2K17 ● Then the pyruvate is oxidised, resulting in the reduction of NAD+ ● The energy from these oxidations is used to associate the pyruvate with a carrier molecule, resulting in the formation of acetyl CoA. The Krebs cycle: ● Final breakdown of glucose molecule. Oxidation of acetyl groups is coupled to the reduction of hydrogen carriers. ● Most of the energy is released in oxidations and the link reaction and the Krebs cycle are used to reduce hydrogen carriers. This allows energy, instead of being lost as heat, to remain in chemical form and be used in oxidative phosphorylation. ● For 2 turns of every cycle, 6 NADH are produced, 4 decarboxylations occur, 2 FADH are produced and 2 ATP are produced. ● Outline of the Krebs cycle: o Acetyl CoA carboxylates oxaloacetate to form a 6 carbon compound (citric acid/citrate) o Citrate is decarboxylated, forming carbon dioxide, and oxidised to create a molecule of reduced NAD. o The five-carbon compound is decarboxylated, forming carbon dioxide, and oxidised to reduce a molecule of NAD. o On molecule of ADP is phosphorylated to form ATP and one molecule of FAD is reduced to form FADH2. Reduction of FAD provides energy for the phosphorylation of ADP. o The four-carbon compound undergoes further oxidation and one molecule of NAD+ is reduced to NAD. ● All the reduced NAD and FAD provide energy for oxidative phosphorylation during the electron transport chain. RIP BIO CLASS OF 2K17 Electron transport chain: ● ETC – transfer of electrons between carriers of differing electron affinities. ● As electrons are transferred hydrogen ions are pumped into the intermembrane space from the matrix and across the inner membrane, ● They then diffuse through ATP synthase to provide the energy for ADP phosphorylation to ATP. RIP BIO CLASS OF 2K17 Chemiosmosis: ● NADH+H+ supplies pairs of hydrogen atoms to the first carrier in the chain. o These hydrogen atoms donate their electrons to the electron transport chain and move into the inner membrane space as hydrogen ions. (Oxidation of hydrogen atoms). o Concentration gradient of protons forms as a result and is a store of potential energy. ● To maintain to the energy gradient between each electron carrier, the electrons are transferred to a terminal electron acceptor, oxygen, which then combines with two H+ ions from the matrix to become water. o This is one of the waste products of respiration, and contributes to the proton gradient and H+ ions are being removed from the matrix. Thus there is also a need to refresh H+ ion supply. ● Energy released by protons moving through ATP synthase is used to phosphorylate ATP. This is oxidative phosphorylation. The role of oxygen: ● Oxygen is needed to bind with the free protons to form water to maintain the hydrogen gradient. ● H+ ions in the matrix need to be used up to maintain concentration for the RIP BIO CLASS OF 2K17 diffusion of H+ ions through ATP synthase. Structure and function of mitochondria: ● Semi-autonomous organelle. Grows and reproduces independently. ● 70S ribosomes and naked loop of DNA. ● Outer mitochondrial membrane compartmentalises the cell especially for biochemical reactions of aerobic respiration. ● Oxidative phosphorylation occurs in the inner mitochondrial membrane. ATP synthase and electron transport chain are contained here. ● Cristae increase surface area of inner membrane. ● Proteins build up in the inner membrane space. o Volume of space is small so concentration gradient builds up rapidly. o Matrix site of Krebs cycle and link reaction. ▪ Contains enzymes for these reactions. 8.3 Photosynthesis: Location of light-dependent reactions: ● Chloroplast has inner and outer membrane. ● Inner membrane encloses thylakoid membranes. o Within this exists the thylakoid space. ● Light dependent reactions take place in the thylakoid space and across the thylakoid membranes. Products of the light-dependent reaction: ● NADP and ATP are produced in the LDR. ● Light energy => chemical energy (ATP) and NADPH+H+ Location of the light-independent reactions: ● ● ● ● ● Light independent reactions take place in the stroma. Inner membrane of the chloroplast encloses the stroma Like cytoplasm it contains enzymes for the LIR. LIR therefore occurs in the stroma. Calvin cycle (LIR) is endergonic (creation of larger molecule fuelled by the hydrolysis of ATP and oxidation of reduced NADP). Photoactivation: ● Absorption of light by photosystems generates excited electrons. RIP BIO CLASS OF 2K17 ● Photosystems: chlorophyll and accessory pigments groups together. Called light harvesting arrays. ● Located in thylakoids; two photosystems – PSI and PSII. ● Besides the light harvesting arrays they contain reaction centres. ● When chlorophyll molecules absorb light, an electron within them gets excited (photoactivation). ● These chlorophylls donate excited electrons to a central special chlorophyll molecule, which donates the excited electrons to an electron acceptor. ● LDR begins at PSII. o First electron acceptor: plastoquinone. ▪ Collects two excited electrons from PSII and then moves to another position for the ETC. ▪ Hydrophobic – stays within the membrane. ▪ Is reduced by the electrons. o This processes occurs twice so PSII loses 4 electrons and two reduced plastoquinones are created Photolysis: ● Photolysis of water provides electrons for use in the LDR. o Chlorophyll in the reaction centres, after reducing plastoquinone, are oxidised by inducing photolysis. o Nearby water molecules split and give up electrons. o 2H2O => O2+4H+4e-. o Photolysis leads to the production of oxygen. ▪ Waste product diffuses away. Electron transport chain: ● Transfer of excited electrons occurs between carriers in thylakoid membranes. ● Production of ATP from energy derived from light photophosphorylation. ● Carried out by thylakoids (stacks of membranes). Photon gradient: ● Excited electrons from PSII are used to generate a proton gradient. ● Protons are pumped into thylakoid space as electrons pass from carrier to carrier. ● Concentration of protons develops in thylakoids spaces, store of potential energy. ● 4H+ from photolysis also contributes to the proton gradient. Chemiosmosis: ● ATP synthase in thylakoids generates ATP using the proton gradient. RIP BIO CLASS OF 2K17 ● Protons pass through ATP synthase, providing energy for the photophosphorylation of ADP. ● Plastocyanin is the final electron acceptor (water soluble) needed for next stage. Reduction of NADP: ● Excited electrons from PSI reduce NADP. ● Reduced NADP carries pairs of electrons that can carry out reduction reactions ● Chlorophyll molecules in PSI undergo photoactivation and the same process with the ETC occurs. ● However the final electron acceptor is called ferredoxin. ● Two molecules of reduced ferredoxin reduce NADP to form reduced NADP. ● Electrons carried by plastocyanine from PSII replace lost electrons in PSI. ● Sometimes, when NADP runs out, electrons carried by plastocyanin to PSI go back to the start of the ETC and are used to phosphorylate ADP again ● This is known as cyclic photophosphorylation. Carbon fixation: ● In the LIR, a carboxylase catalyses the carboxylation of ribulosebiphosphate. ● Occurs in the stroma. ● Produces Glycerate-3-phosphate. ● Rubisco (Rubp carboxylase) catalyses carboxylation of Rubp (5C) to form a 6C compound that breaks down into 2 x 3C compound (G3P). ● G3P is converted into triose phosphate by: o 2 x ATP => 2 x ADP + P o 2 x reduced NADP => 2 x NADP READ OXFORD STUDY GUIDE FOR THIS ^ RIP BIO CLASS OF 2K17 The fate of triose phosphate: Triose phosphate regenerates RuBP and produces carbohydrates. 1 RuBp molecule is carboxylated in one turn of the Calvin cycle. 2 triose phosphates produced. 5 carbons out of six used to regenerate RuBP, so only one contributes to formation of hexose (starch). ● Therefore 6 turns of the Calvin cycle create one carbohydrate hexose. ● ● ● ● RuBP regeneration: ● RuBP is reformed using ATP. ● 5 triose phosphates ((3ATP=>3(ADP+P))=3RuBp. Chloroplast structure and function: ● ● ● ● ● ● ● Structure of the chloroplast is adapted to its function in photosynthesis Double membrane forming outer chloroplast envelope. Internal membranes (thylakoids). Fluid filled thylakoids space. Stroma, surrounding thylakoids, containing enzymes. Stacks of thylakoids called grana Starch grains/lipid droplets if photosynthesis happens at a fast rate. Chloroplast’s structure-function relationship: ● Contain light absorbing arrays/ photosystems/ chloroplasts. Deep grana RIP BIO CLASS OF 2K17 increase light absorption. ● ATP by photophosphorylation. ● Proton gradient develops in small volume inside thylakoids. ● Chemical reactions of the Calvin cycle. Stroma contain all the enzymes required. READ OXFORD STUDY GUIDE FOR THIS TOO ^ 9 Plant Biology 9.1 Transport in the xylem of plants: Transpiration: ● Inevitable consequence of gas exchange in the leaf. ● Exchange of oxygen and carbon dioxide must occur to sustain photosynthesis. ● Carbon dioxide is absorbed and Oxygen is released through stomata on epidermis (underside) of the leaf. ● However the opening of the stomata to absorb CO2 and release O2 results in the loss of water vapour (transpiration). ● Guard cells minimise water loss, which controls the aperture of the stoma. Xylem structure helps withstand low pressure: ● Cohesive property of water and the structure of xylem vessels allow transport under tension. ● Xylem: long continuous tubes, walls thickened with lignin, which strengthens the wall to withstand very low internal pressures. ● Xylem vessels are arranged end-to-end. ● Mature xylem vessels are non-living so water flow is passive (cohesion and adhesion). ● Internal pressures are much lower than atmospheric pressure. ● Cohesion: o Formed due to hydrogen bonding in water, due to its polar structure. ● Adhesion: o Water is attracted to hydrophilic parts of the xylem. RIP BIO CLASS OF 2K17 ● Cohesion and adhesion allow for passive movement of water up the xylem (capillary action). Tension in leaf cell walls maintains the transpiration stream: ● Adhesive property of water and evaporation generate tension forces in leaf cell walls. The cohesion of water molecules to other water molecules propagates this tension. ● The evaporation of water in the leaf causes water to be drawn into the leaf from the xylem vessels in the veins of the leaf. ● This is caused by adhesion. ● The pressure in the xylem is already low, so for water to move out from a low pressure environment would mean the force of adhesion between water and the cell walls in the leaf is very strong. ● Movement of water out of the xylem reduces its pressure further and causes a pulling force (movement from high pressure to low pressure) that facilitates water movement. o This is called the transpiration pull. o IT depends on cohesion between water molecules to work. Active transport of minerals in the roots: ● Active uptake of mineral ions in the roots causes absorption of water by osmosis. ● Osmosis between root cell and soil occurs because solute concentration in root cells is greater (100 times). ● Active transport establishes these concentration gradients. o Mineral pumps in the plasma membrane of root cell. o Each mineral ion has a specific protein pump. o Mineral ions come in contact with protein pumps due to diffusion/mass flow alongside water movement. ● Fungi facilitate the movement of mineral ions into the root hair cell. o Create a symbiotic relationship with the plant. o Fungi grow on the surface of the roots and into the cells of roots. o Mineral ions are absorbed into the thread-like hyphae of the fungi and are supplied to the plant. o In exchange the plant proved the fungi with sugars. o Example of a mutualistic relationship. ● Water movement from roots into xylem o Apoplast pathway: through the cell walls. o Symplast pathway: through the cytoplasm. ▪ Easy way to remember this - SYMPlast, ie simple - through cytoplasm. RIP BIO CLASS OF 2K17 Replacing losses from transpiration: ● Plants transport water from roots to leaves to replace losses from transpiration. ● Soil => roots (osmosis) =>Xylem (apoplast/symplast way is from roots or other cells to xylem) => leaves. Adaptations for water conservation: ● Xerophytes (desert plants): o Increase rate of water uptake from the soil and reduced rate of water loss by transpiration. o Ephemeral: short life cycle, only alive during rainfall. o Perennial: Store water in specialised leaves, stems/ roots. o Cacti: Leaves are reduced in size. They have a thick waxy cuticle. ▪ Stoma are sparsely placed. Open at night to prevent water loss. ▪ Carbon dioxide is absorbed at night and stored as malic acid, which then released carbon dioxide slowly during the day to be used for photosynthesis whilst stoma are kept closed. ▪ Called crassulacean acid metabolism (CAM). o Small hairs near stoma stop air from increasing transpiration rate. o Stoma sit buried deep into epidermis. o Film of water surrounding stoma reduces transpiration by decreasing the concentration gradient of water. ● Halophytes (saline soil plants): o Has salt concentration higher than in the saline soils surrounding it. ▪ This cannot be done just by increasing Na+ conc as this would have adverse effects on cell activities such as protein synthesis. ▪ Other solutes such as K+ and sugars are maintained at high concs in the cytoplasm. ▪ Na+ can be maintained at high conc in vacuoles. o Saline soils contain high salt concentrations. o Leaves are small. o Leaves shed during water scarcity. o Stem becomes green and photosynthesises. o Water storage structures in leaves. o Thick waxy cuticle, multiple layer epidermis (longer diffusion pathway for water). o Sunken stoma. o Long roots search for water. RIP BIO CLASS OF 2K17 o Structures to remove salt build-up. RIP BIO CLASS OF 2K17 RIP BIO CLASS OF 2K17 9.2 Transport in the phloem of plants: Translocation occurs from source to sink: ● Phloem is composed of sieve tubes, which are made up of specialised sieve tube cells. ● Sieve tube cells are separated by perforated walls called sieve tube plates. ● Plants transport organic compounds from source to sink in a process called translocation. ● Sugars and solutes are translocating. ● Phloem can transport biochemical in both directions. ● Pressure gradients caused movement of fluid. ● Energy is required to generate pressures (active process). Sources Sinks Photosynthetic tissues: ● Mature green leaves. ● Green stems. Storage organs that are unloading their stores: ● Storage tissues in germinating seeds. ● Tap roots or tubers at the start of growth season Roots that are growing or absorbing mineral ions using energy from cell respiration. Parts of the plant that are growing or develop food stores: ● ● ● ● Fruits. Seeds. Leaves. Tap roots. RIP BIO CLASS OF 2K17 Phloem loading: ● Active transport is used to load organic compounds into phloem sieve tubes at the source. ● Sucrose is the most prevalent solute in phloem sap. ● Makes a good transport form of carbohydrate because it is not readily available to be metabolised. ● Phloem loading is the process by which sugars are brought into the phloem. ● Apoplast route: o Sucrose travels from cell walls of mesophyll cells to cell walls of companion cells. o Transport proteins then actively transport sugar into the phloem. Hydrogen ions are pumped out of the companion cells into the interstitial spaces of the cell wall of the companion cell. o They then flow back into the cell through a co-transport protein, which provides the energy to carry sucrose into the companion cell-sieve tube complex. ● Symplast route: o Sucrose travels through plasmodesmata, which run between cells. o This is down a concentration gradient. o Sucrose converted to oligosaccharide in the companion cell to maintain the sucrose concentration gradient. Pressure and water potential differences play a role in translocation: ● Incompressibility of water allows transport by hydrostatic pressure gradients. ● Build up of sucrose in phloem draws water into the companion cell through osmosis from the xylem. ● Rigidity of cell walls plus incompressibility of water results in hydrostatic pressure build up. ● Water flows down pressure gradient. ● Sucrose is withdrawn from phloem at the sink end of the phloem and used as an energy source or converted to starch. ● Loss of solute results in reduction in osmotic pressure and water is drawn back into the transpiration stream (xylem). Phloem sieve tubes: ● Sieve tubes consist of sieve tube cells. ● They have a nucleus and cytoplasm. ● They are living and depend on living cells to establish sucrose/organic molecule concentrations through active transport. RIP BIO CLASS OF 2K17 ● Sieve tube cells and companion cells share the same parent cell. ● Companion cells perform the genetic and metabolic functions of the sieve tube cells. ● Companion cells contain large amounts of mitochondria for active transport of H+ ions for sucrose co-transport. ● Infolds of plasma membrane in companion cells increases the loading capacity of phloem using the apoplastic route. ● Plasmodesmata link cytoplasm of companion cells with sieve tube cells. ● Rigidity of cell walls of the sieve tube cell allow for establishment of a pressure gradient. ● Perforated walls (sieve plates) plus reduced cytoplasm means that phloem sap will move easier. 9.3 Growth in plants Growth in plants: ● Undifferentiated cells in the meristems of plants allow indeterminate growth. ● Plant growth is indeterminate, cells continue to divide indefinitely. ● Some plant’s cells, unlike animal cells, are totipotent. ● Meristems are composed of undifferentiated cells. ● Primary meristems are at the tips of stems/roots (apical meristems). ● Dicotyledonous plants also have lateral meristems. Role of mitosis in stem extension and leaf development. ● Mitosis and cells division in the shoot apex provide cells needed for extension of the stem and development of leaves. ● Cells in the meristem are small but increase in volume by absorbing nutrients and water. ● With each division one cell remains as a meristem whilst the other increases in size and differentiates. ● Apical meristem can give rise to specialised cells: procambium (vascular tissue), protoderm (epidermis) and ground tissue (pith). ● Young leaves are produced at the sides of the shoot apical meristems, known as leaf primordia. Plant hormones affect shoot growth: ● Plant hormones control growth in the shoot apex. ● Auxins have a broad range of functions: initiating growth of roots, development of fruits and regulating leaf development. ● IAA (indole-3-acetic acid). RIP BIO CLASS OF 2K17 ● Controls growth in the shoot apex through elongation of cells in stems. ● Synthesised in the apical meristem and transported down the stem to stimulate growth, but can inhibit growth in very high concentrations. ● Axillary buds grow at the node between stem and base of leaf. ● Meristems are left behind at the node as shoot apical meristems grow and form leaves. ● Auxin produced by shoot apical meristem inhibits growth at these nodes (apical dominance). o The further the distance between the node and the shoot apical meristem, the lower the concentration of auxin at the node and the less likely growth at the node will be inhibited. o Cytokinins, produced in the root, promote axillary bud growth. o Ratio between cytokinins and auxin determine whether development in the axillary bud will occur. o Gibberellins will contribute to stem elongation. Plant tropisms: ● Plants respond to the environment by tropisms. ● Light and gravity influence growth directionality. ● Phototropism and gravitropism (geotropism). Auxin influences gene expression: ● Auxin influences cell growth rates by changing the pattern of gene expression. ● Phototropins absorb light in the first stage of phototropism. ● Light of a specific wavelength (blue light) alters their structure to trigger off movements of auxin by active transport. This is carried out by auxin pumps in the plasma membrane. ● Once the auxin is pumped out of the membrane into the cell wall of the next cell it binds to a proton and diffuses into a cell through the plasma membrane. ● It is then pumped out by an efflux pump again after it loses its proton. ● The auxin efflux pumps are moved around in accordance to light intensity differences, so they set up a conc gradient of auxin from lower conc on the lighter side to higher conc on the darker side. ● Auxin binds to auxin receptor, promoting the transcription of specific genes. The expression of these genes causes the secretion of hydrogen ions into the cell wall, which interacts with the cellulose fibres and loosens them, allowing cell expansion. Intracellular pumps: ● Auxin efflux pumps set up concentration gradients of auxin in plant tissue. RIP BIO CLASS OF 2K17 ● Auxin is transported to the shaded area during phototropism. ● Higher concentrations of auxin in the shaded area cause growth here, so the stem curves towards the brighter light. ● Gravitropism: o Gravity causes cellular organelles caused statoliths to accumulate at the tip of roots. o PIN3 transporter proteins direct auxin transport to the cells. o Therefore downward growth occurs here. Micropropagation of plants: In vitro procedure that produces large numbers of identical plants. Depends on the totipotency of plant tissue. Tissues are cut into pieces called explants. Least differentiated tissue serves as the source tissue (meristem). Placed into growth media that includes plant hormones, cytokinins and auxins. ● This creates an undifferentiated mass called a callus. ● If growth media contains a 10:1 ratio of auxins to cytokinins then roots develop (rooting media). If less than 10:1 then shoots develop (shoot media). Cloned parts can be transferred to soil. ● ● ● ● ● Micropropagation is used for rapid bulking up: ● Viruses are transported within a plant from cell-to-cell through vascular tissue and via plasmodesmata. ● Micropropagation can be used to produce virus free strains of plants. ● Can also be used to produce plants with specific characteristics. ● Also being used to preserve species of orchids. ● Micropropagated plants can be stored in liquid nitrogen (cryopreservation). Differences between monocots and dicots: RIP BIO CLASS OF 2K17 9.4 Reproduction in plants: Flowering and gene expression: ● Flowering involves change of gene expression in the shoot apex. ● Vegetative structures: roots, stems and leaves. o These form during seed germination during the vegetative phase. ● The productive phase causes flower growth. o Meristems produce flowers instead of leaves. ● Flowers allow for sexual reproduction; are produced by the shoot apical meristem and are a reproductive shoot. ● Temperature plays a role in transforming leaf-producing shoot into flower-producing shoot. ● Light plays a role in producing inhibitors/ activators of genes that control flowers. ● Long day: o Activation of pigment phytochrome results in transcription of FT gene (flowering time). o FT mRNA then transported to shoot apical meristem and translated into FT protein that binds to a transcription factor and causes the consequential activation of many flowering genes. o This transforms leaf-producing apical meristems into reproductive meristems Photoperiods and flowers: ● Switch to flowering is a response to the length of light and dark periods in many plants. ● Long day plants (LDP) flower when nights are shorter. ● Shorter day plants (SDP) flower when nights are long. RIP BIO CLASS OF 2K17 ● Length of darkness is the trigger for flowering, not length of daylight. ● Pr is converted to Pfr with 660nm sunlight, this happens in abundance because sunlight mostly comprises of this wavelength (red). ● Pfr is converted to Pr in 730 nm. Less important because sunlight contains little of this wavelength (far red). ● In darkness, however, Pfr gradually changes into Pr because Pr is a more stable form. ● Pfr is the active form of phytochrome and binds to receptor proteins present in the cytoplasm which control for the transcription of genes (FT gene) needed for flowering. ● In long-day plants large amounts of Pfr remain to bind to the receptor and therefore transcription is promoted. ● In short-day plants the binding of Pfr to a receptor inhibits flowering. However because there is such little Pfr remaining at the end of a long night, the inhibition fails and flowering proceeds. Inducing plants to flower out of season: ● Plants can be induced to flower out of season. ● This can be done by manipulating the length of days and nights. Animal pollinated flowers: ● Carpel: o Stigma o Style. ● Stamen: o Anther o Filament ● Sepal ● Ovary Mutualism between flowers and pollinators: ● Most flowering plants use mutualistic relationships with pollinators in sexual reproduction. ● Sexual reproduction requires the transfer of pollen from one plant’s stamen to another plant’s style. ● Wind pollination and water pollination exist, however animals are most common pollinators. ● Birds, bats, insects and bees. ● Pollinators gain food from nectar and plants gain a means to reproduce – hence mutualism. Pollination, fertilization and seed dispersal: RIP BIO CLASS OF 2K17 Fertilization: Each pollen grain on the stigma grows a tube down the style to the ovary. Carries the male gametes to fertilise the ovary. Located inside the ovule. Ovule develops into seed and ovary into fruit. Seed dispersal reduces competition between offspring and parent, and spreads species geographically. ● Means of seed dispersal varies depending on the type of seed. ● ● ● ● ● ● Structure of seeds: ● Seed consists of: o Embryo plant: ▪ Embryo root. ▪ Embryo shoot (plumute). ▪ One/two cotyledons. o Food reserves o Protective seed coat. ● Cotyledons are the embryo leaves and contain the food reserves of the seed. ● In some plants endosperm store food. ● Seed coat is known as testa. ● Micropyle is a small hole through the testa. Germination experiment design: ● Dormancy: o Non-germination even when provided with favourable conditions. o Water is required for germination, either for rehydration or to wash out a hormone that inhibits germination. o Growth of embryo root/shoot also requires water. ● Germination: o After absorption of water, metabolic rate of seed increases, and energy is released by aerobic respiration. o Oxygen is also required. o Warmth is required for enzyme functionality during germination. ● Synthesis of gibberellin occurs at the start of germination. o This hormone stimulates mitosis and cell division in the embryo and stimulates amylase production, which breaks down starch in the food reserves into maltose, which is then converted into glucose/sucrose. ● Sucrose/glucose can be transferred via the phloem to where they are needed (translocation). ● Embryo root/shoot require sugars for growth and glucose for aerobic respiration. RIP BIO CLASS OF 2K17 10 Genetics and Evolution 10.1 Meiosis: Chromosome replication: ● Protein based structure forms between the homologous chromosomes called the synaptonemal complex. ● Crossing over occurs between non-sister homologous chromatids. Exchange of genetic materials: ● Crossing over is the exchange of DNA material between non-sister homologous chromatids. ● Non-sister chromatids “invade” a homologous sequence on a non-sister chromatids and bind to the region. ● They continue to adhere to the point, and these points of connection are called chiasmata. Chiasmata formation: ● Breaks occur in chromosomes and non-sister chromosomes invade a homologous sequence and bind to its region. ● Connected points are called chiasmata. ● Serves to stabilise bivalents. ● Increases genetic variability. ● Exchange of DNA between maternal and paternal chromosomes. ● Independent assortment arises because linked alleles can be decoupled. ● Crossing over can occur multiple times between different chromatids within the same homologous pair. New combinations of alleles: ● Crossing over produces new combinations of alleles on the chromosomes of the haploid cells. RIP BIO CLASS OF 2K17 ● Occurs because genes are linked. Meiosis I: ● Sister chromatids remain associated with each other. ● Homologous chromosomes behave in a coordinated fashion in prophase. ● Homologous chromosomes exchange DNA leading to genetic recombination. ● Meiosis I is a reduction division in that it reduces the chromosome number by half. Independent assortment: ● Occur due to random orientation of pairs of homologous chromosomes in meiosis I. ● Random movement to poles during anaphase I is caused by independent orientation: direction in which chromosomes face does not affect the direction in which any other chromosomes are facing. ● There is an equal probability of a particular combination being produced. Meiosis II: ● Interphase does not reoccur between meiosis I and II. ● Mitosis and Meiosis II both separate a replicated chromosome into chromatids. ● However these sister chromatids are likely to be non-identical sister chromatids due to crossing over. 10.2 Inheritance: Segregation and independent assortment: ● Unlinked genes segregate independently as a result of meiosis. ● Segregation is the separation of two alleles of a particular gene. ● Genes that are unlinked – exist on different chromosomes – will segregate independently because the chromosomes will be pulled to opposite poles. ● Genes on the same chromosome are linked. ● These will not segregate independently. Genes that are on the same chromosome but are placed far apart have a higher change to form an exception. ● They may be separated during crossing over and therefore will function as unlinked genes. Punnett squares for dihybrid traits: RIP BIO CLASS OF 2K17 ● Used to predict the occurrence of a particular geno/phenotype. ● The Mendelian ratio for independently assorted traits is 9:3:3:1. o This is for the F2 generation. ● The chance of a particular gamete of the F1 generation containing an allele is ½, if there are two alleles and inheritance is independent. ● Hence, a particular combination of alleles would be (1/2*1/2)=1/4. ● This corresponds to the law of independent assortment, where unlinked genes segregate independently from each other. Linked genes: Group of genes were all located on the X chromosome of Drosophila. These genes were arranged in a linear sequence. Locus of a gene: specific position of a gene on one chromosome type. Homologous: two chromosomes with the same sequence of genes. o They vary in the alleles of genes present at a particular point. ● 8 chromosomes in a diploid Drosophila. o Males have an XY and females have an XX. o The other 6 are autosomes and are common to both. o 3 autosomal pairs. ● Two types of gene linkage: o Autosomal and sex. ● Sex linkage means the genes are located on the X chromosomes. ● ● ● ● Polygenic characteristics: ● Polygenic characteristics tend to show continuous variation. ● Two or more genes have an additive effect hence affecting the same phenotypic characteristic. ● This additive effect is caused by co-dominant alleles that are unlinked. ● The F2 generation would show ratios based on alternating levels of Pascal's triangle. ● Number and frequency of variants would be affected by the number of codominant alleles for a particular gene – an increasing number of which would bring the distribution close to the normal distribution. ● Height/intelligence in humans are all examples of polygenic inheritance. Environmental influence: ● Environmental factors blur the differences in phenotype to make them undetectable. ● Sunlight stimulates the production of black pigment melanin in the skin. ● Skin colour is also influence by several genes and is therefore polygenic. Identifying recombinants: RIP BIO CLASS OF 2K17 ● Linked genes are part of the same chromosomes and therefore do not follow the laws of independent assortment (9:3:3:1). o Alleles of such genes would pass together into a gamete. o Results in a higher frequency of the parental combinations than predicted from Mendelian ratios. ● Linkages between pairs of genes are not complete and therefore new combinations are formed as a result of crossing over. o Formation of new combinations is called recombination. o An individual with a recombinant chromosome is called a recombinant. RIP BIO CLASS OF 2K17 10.3 Gene pools and speciation: Gene pools: ● Gene pools consist of all possible genes and alleles of an interbreeding population. ● Some populations of the same species are geographically isolated so it is possible for multiple gene pools to exist for the same species. ● Gene equilibrium: all members of a population have an equal chance of contributing to the future gene pool. Allele frequency and evolution: ● Evolution requires that allele frequencies change with time in populations. ● Occurs due to: o Mutations. o Selection pressures favouring certain traits. o Barriers to gene flow between different populations. Patterns of natural selection: ● Fitness of geno/phenotype: Likelihood that it will be found in the next generation. ● Three patterns of natural selection: o Stabilizing: Extremities are removed e.g. preference of the average over the extreme. o Disruptive: Favour extremes over intermediate varieties. Longer necks in giraffes are preferred. o Directional: Population changes, as one extreme of a range is better adapted. There are different categories of reproductive isolation: ● Reproductive isolation can be temporal behavioural or geographic. ● Allopatric speciation: speciation that occurs due to geographic separation. ● Sympatric speciation: isolation within the same geographic area; isolation is behavioural. Different mating practises/ courtship behaviour. ● Temporal speciation: Occurs as species are only active during specific seasons etc. therefore don’t reproduce. Gradualism versus punctuated equilibrium in speciation: ● Speciation due to divergence of isolated populations can be gradual. RIP BIO CLASS OF 2K17 ● Gradualism states that species change through many intermediate forms. ● Countered by punctuated equilibrium which states that speciation can occur abruptly. o Stability is punctuated by periods of rapid evolution. o This explains that gaps in the fossil record are simply evidence for this punctuation. o Allopatric speciation can lead to rapid speciation. o Rapid change is more common in organisms with short generation times. Polyploidy can lead to speciation: ● Can lead to sympatric speciation. ● Polyploidy can only mate with each other. ● Caused by hybridization events between different species/nondisjunction in meiosis. Polyploidy has occurred frequently in Allium: ● Around 50 to 70% of angiosperms have experienced a polyploidy. ● Allium genus includes onions. ● Allium reproduces asexually and polyploidy may confer an advantage over diploidy under certain selection pressures. 11 Animal physiology 11.1 Antibody production and vaccination: Antigens in blood transfusion: ● Every organism has unique molecules on the surface of their cells. ● Molecules that trigger a foreign response are called antigens and are found on the surface of cells. ● Immune systems function based on recognising foreign antigens from self. ● Antigens on the surface of RBC stimulate antibody production in a person with a different blood group. ● Antigen B: galactose. Antigen A: n-acetyl-galactosamine. Antigen AB: both. ● Wrong blood type results in agglutination followed by haemolysis o Antibodies clump incompatible RBC (agglutination) and then destroy them (haemolysis). RIP BIO CLASS OF 2K17 The specific immune response: ● B-lymphocytes are activated by T lymphocytes. ● Pathogens ingested by macrophages and antigens (from the pathogens) are displayed on the plasma membrane of the macrophages on the antigen presenting cells. ● T helper cells bind to antigens displayed by macrophages and are activated. ● T helper cells then bind to B-lymphocyte cells. o Specific B-lymphocytes are selected depending on whether they have the receptor protein for the antigen that the T helper cell presents. ● B cells are activated accordingly and become mature B cells The role of plasma cells: ● Plasma cells secrete antibodies. ● They are mature B-lymphocyte cells and secrete antibodies during immune response. ● Cell’s cytoplasm contains lots of rER to produce antibodies (specific to antigen). ● Range of genes expressed is much lower, since only a specific antibody is produced. Clonal selection and memory cell formation: ● Activated B cells multiply to form a clone of plasma cells but also some memory cells. ● Division by mitosis occurs to form plasma cells with a specific antibody type; this is called clonal selection. ● Antibodies last in the body for a few weeks and are quite short term. ● Hence memory cells are produced and this forms immunity. The role of antibodies: ● Opsonization: makes pathogens more recognisable. ● Neutralisation of viruses and bacteria: prevents viruses from docking to host cells. ● Neutralisation of toxins: binds to toxins to prevent them from affecting cells. ● Activation of complement: Complement creates a perforation in the membranes of pathogens. Antibodies activate a complement cascade which forms a membrane attack complex. Water and ions then enter the pathogen and cause it to burst. ● Agglutination: causes sticking together of pathogens so they are prevented from entering cells/ easier for phagocytes to ingest. RIP BIO CLASS OF 2K17 Immunity: ● ● ● ● ● Immunity depends on the persistence of memory cells. Antibodies present + memory cells present = immunity. These need to be specific to the antigen. Immunity develops once the immune system is challenged. Reaction is much quicker during the secondary response, due to immunity. Vaccines lead to immunity: ● Contain antigens that trigger immunity but do not cause the disease. ● Attenuated version of the disease therefore does not cause problems. ● Stimulates a primary immune response and results in the creation of memory B cells. ● Injecting attenuated strain of pathogen is a form of artificial active immunity. ● Tetanus shots are artificial, but a passive form of immunity because the antibodies are being injected. Zoonosis is a growing global health concern: ● Pathogens can be species-specific although others can cross species barriers. ● Pathogens are generally highly specialised, however there are some which can affect a large number of hosts. ● Zoonosis is a pathogen which can cross a species barrier. ● Such diseases have increased due to growing contact between animals and humans. The immune system produces histamines: ● White cells release histamine in response to allergens. ● Mast cells are immune cells found in connective tissue. o They release histamine, which causes the dilation of small blood vessels. o This allows more blood flow to infected area, carrying antibodies and WBCs, resulting in specific and nonspecific responses. Effects of histamines: ● Cause allergic symptoms: o Cells in many tissues have membrane bound histamine receptors. o Brings symptoms of allergens in the nose. o Itching, inflammation of tissues, mucus secretion and sneezing. ● Plays a role in formation of rashes and dangerous swelling (anaphylaxis). RIP BIO CLASS OF 2K17 ● Antihistamines can be taken to avoid these effects. The process for creating hybridoma cells: ● Tumour cell fused with an antibody-producing plasma cell creates a hybridoma cell. ● Monoclonal antibodies are highly specific and are derived from a single cell and recognise only one antigen. ● Myeloma cells (cancer cells) are fused with B-plasma cells from the spleen of a rat, forming hybridoma. Production of monoclonal antibodies: ● Hybridomas are tested to find the one that contains the specific antibody. ● The selected hybridomas are then allowed to divide. o Multiplication occurs in a fermenter. ● The super-specific hybridomas are called monoclonal antibodies. Monoclonal antibodies are used to test for human chorionic gonadotropin (HCG) in pregnancy tests: ● Antibodies to HCG are immobilised in the strip and dye bearing antibodies that cause colour change in the presence of HCG. ● HCG is present in high amounts during pregnancy. 11.2 Movement: Bones and exoskeletons anchor muscles and act as levers: ● Exoskeletons surround and protect the body surface of animals. ● Bones and exoskeletons facilitate movement. ● Levers can change the size and direction of forces. o Effort force o Pivot force. o Resultant force. ● First class lever: fulcrum between effort and load. ● Second class lever: fulcrum before effort and load, at edge o Load closer to fulcrum than effort is. ● Third class lever: fulcrum before effort and resultant forces. o Effort closer to fulcrum than load is. Skeletal muscles are antagonistic: ● Antagonistic muscles occur in pairs. RIP BIO CLASS OF 2K17 ● When one contracts, the other relaxes. ● This is true for skeletal muscles. ● Opposite movements are produced at a joint. Example of a synovial joint: ● Articulation: o Movement of bones in relation to one another. ● Joint: o Point where bones meet. ● Cartilage prevents contact between bones, preventing friction. o Also absorbs shock. ● Synovial fluid fills cavity between cartilages on the ends of bones. o Lubricates the joint, to prevent friction. ● Joint capsule seals the joint and holds synovial fluid. o Prevents dislocation. ● Ligaments are tough cords of tissue that connect bones on opposite sides of a joint. THey restrict movement and help to prevent dislocation. Different joints allow for different ranges of movement: ● Synovial joints allow for certain movements. ● Knees act as hinge joints, for flexion and extension. ● Hip joints are ball and socket joints. o They can flex, extend, rotate and abduct (sideways)/adduct (backwards). Structure of muscle fibres: ● Skeletal muscle fibres are multinucleated and contain specialised endoplasmic reticulum (sarcoplasmic reticulum). ● Striated muscle is composed of bundles of cells called muscle fibres. ● Single plasma membrane called the sarcolemma surrounds each muscle fibre. ● Many nuclei present and are much longer than normal cells. ● Embryonic muscle cells fuse together to form muscle fibres. ● Endoplasmic reticulum wraps around myofibrils, conveying contraction signals to all part of the muscle fibres at once. ● Sarcoplasmic reticulum stores calcium. ● Mitochondria provide the ATP needed for contractions and are found between the myofibrils. Myofibrils: ● Muscles fibres contain many myofibrils. RIP BIO CLASS OF 2K17 ● Parallel elongated structures. ● Alternating light and dark bands, which give striated muscle its stripes. ● In the centre of each light band is the ‘Z’ line. Structure of myofibrils: ● Made up of contractile sarcomeres. ● Part of a myofibril between one ‘Z’ line and the next is called a sarcomere, which is the functional unit of a myofibril. ● Actin filaments at the end of the sarcomeres (light bands) and myosin + actin filaments in the middle (dark bands). Mechanism of skeletal contraction: ● Sliding of actin and myosin filaments causes contraction of skeletal muscle. ● Myosin filaments pull actin filaments towards the centre of the sarcomere, shortening the sarcomere and overall length of muscle fibres. ● Myosin heads bind to special binding sites on actin filaments, creating cross bridges. ● Regular spacing of heads and binding sites allows many to bind at once. ● ATP gives energy for sliding. The control of skeletal muscle contractions: ● Calcium ions and the proteins tropomyosin and troponin control muscle contractions. ● Tropomyosins block binding sites on actin. ● When motor neurons send impulses to muscle fibres, sarcoplasmic reticulum releases calcium ions which bind to troponin and cause tropomyosin to move ● Myosin heads then bind. The role of ATP in the sliding of filaments: ● ATP hydrolysis and cross-bridge formation are necessary for the filaments to slide. ● ATP attach to myosin heads, resulting in cross bridges to break. ● ATP is hydrolysed into ADP+P, which releases energy for myosin heads to swivel into a ‘cocked’ position, storing potential energy. ● New cross bridges form to binding sites, each head binding to one position further from the centre of the sarcomere. ● ADP is released, which allows for energy stored as potential energy to then used to swivel the myosin heads inwards towards the centre of the sarcomere and move the actin filament accordingly. RIP BIO CLASS OF 2K17 ● This continues until a motor neuron stops sending signals to muscle fibres. ● Calcium ions are pumped back into the sarcoplasmic reticulum and tropomyosin re-covers the myosin-binding site. 11.3 The kidney and osmoregulation: Different responses to changes in osmolarity in the environment: ● Animals are either osmoregulators or osmoconformers. o Osmoregulators maintain a constant internal solute concentration. o Osmoconformers’ internal solute concentration tends to be the same as the concentration of solutes in the environment. The Malphighian tubule system: THIS IS BASICALLY JUST USING WATER AS A SOLVENT THAT CAN MOVE AROUND THE SOLUTES TO THE HIND GUT. ● Arthropods have a circulating fluid known as hemolymph, which combines characteristics of tissue fluid and blood. ● Osmoregulation is a form of homeostasis that maintains the concentration of hemolymph within a specific range. ● Nitrogenous waste in animals is produced from the breakdown of amino acid (uric acid/urea). ● Malpighian tubules branch off from intestinal tract. ● Cells lining the tubules are responsible for actively transporting ions and uric acid into the lumen of the tubules. ● Water the moves into the lumen by osmosis. All contents in the tubules are emptied into the gut. ● Contents then move to the hindgut where most of the water and salts are RIP BIO CLASS OF 2K17 reabsorbed while the nitrogenous waste is excreted with the faeces. Drawing the human kidney: Comparing the composition of blood in the renal artery and the renal vein: ● Kidneys remove substance from the blood that are unnecessary or harmful. Hence blood that enters the kidney is different from that which leaves the kidney. ● 1/5th of blood plasma is filtered in the kidney (all substance in plasma besides large protein molecules). Specific substances are then actively reabsorbed. Unwanted substances pass out through urine. Renal Artery Renal Vein Enters the kidney Leaves the kidney Higher concentration of toxins that have noT been completely metabolised (drugs/pigments). Nitrogenous waste. Carbon Dioxide is a waste product of respiration and will be present in higher amounts in the renal vein. Blood in the renal artery will Blood in the renal vein will have a RIP BIO CLASS OF 2K17 contain a variable amount of water/salt. fixed amount of water and salt. Oxygenated blood. Deoxygenated blood because metabolic activity in the kidneys will require blood oxygen. High concentrations of glucose Low concentrations of glucose, since it would have been broken down by metabolism in the kidneys. Plasma proteins are present in equal amounts in both renal vein and artery. The ultrastructure of glomerulus and Bowman’s capsule facilitate ultrafiltration: ● Glomerular filtrate is formed because: o Blood pressure in capillaries is exceptionally high in the glomerulus. o Capillary walls are particularly permeable, resulting in large amounts of tissue fluid forming. ▪ Tissue fluid forms when blood plasma is pushed out of capillaries due to high internal pressure. o Most solutes are filtered out freely alongside blood plasma, except large protein molecules. o Ultrafiltration is the separation of molecules based on size. ● Fenestration: o Allow fluid to escape but not blood cells. ● Basement membrane: o Prevents plasma proteins from being filtered out. Made of negatively charged glycoproteins and therefore repels negatively charged protein molecules. ● Podocytes: Inner wall of Bowman’s capsule – wrap around capillaries of glomerulus with foot processes. Gaps between foot processes prevent certain small molecules being filtered out of blood in the glomerulus. The foot processes make a fibrous mesh. The role of the proximal convoluted tubule: ● Selectively reabsorbs useful substances by active transport. ● Glomerular fluid contains 1.5kg of salt and 5.5 kg of glucose and is around 180 dm^-3 in volume. Volume of urine is only 1.5 dm^3, hence a very large part of glomerular filtrate is selectively reabsorbed in the PCT. ● PCT reabsorbs all glucose, amino acids and 80% of water, sodium and RIP BIO CLASS OF 2K17 mineral ions Sodium ions Actively transported from filtrate to space outside tubule by pump proteins located on the outer membrane of the tubule. Ions are then passed on to peritubular capillaries. Chloride ions Active transport of sodium ions sets up a charge gradient that causes chloride ions to simply move down this charge gradient from filtrate to space outside the tubule. Glucose ions Glucose is co-transported using specific proteins. Movement of Sodium ions down concentration gradient from outside tubule to inside provides energy to proteins for glucose to move to space outside tubule. Water Pumping of solutes to space outside the solute sets up a solute concentration gradient. Therefore reabsorption of water occurs through osmosis. The nephron and the Bowman’s capsule: ● Bowman’s capsule: Collects the fluid filtered from the blood. ● PCT: Has many mitochondria to provide ATP for active transport of ions. ● Loop of Henlé: Descending limb carries filtrate into medulla and ascending limb brings it back out to cortex. ● Distal convoluted tubule (DCT): Fewer microvilli and fewer mitochondria (than PCT). Collecting duct: Carries filtrate back through cortex and medulla to renal pelvis. ● Blood flows through vessels in this order: o Afferent arteriole (blood from renal artery into kidney); o Glomerulus (high pressure capillary bed during which ultrafiltration occurs); o Efferent arteriole (Narrow vessel which generates high pressure in glomerulus); o Peritubular capillaries (low pressure capillary bed which absorbs fluid from convoluted tubules; o Vasa recta (unbranched capillaries with a descending limb and ascending limb); Venules (carry blood to the renal vein) RIP BIO CLASS OF 2K17 The role of the loop of Henlé: ● The loop of Henlé maintains hypertonic conditions in the medulla. o Loop of Henlé creates a gradient of solute concentration in the medulla. In the ascending limb, sodium ions are pumped out of the filtrate to the fluid in the medulla (interstitial fluid). ● Wall of ascending limb is impermeable to water, so water is retained in the filtrate. ● Interstitial concentration of 500 mOsm is achieved. ● Cells in the wall of the descending limb are permeable to water, the highly hypertonic interstitial fluid in the medulla causes water to be drawn out of filtrate in the descending limb until the volume of water = volume of interstitial fluid. ● This results in the ascending limb being able to pump out more sodium ions into interstitial fluid raising concentration to 700 mOsm. This process can continue until the interstitial fluid reaches a concentration of around 1200 mOsm (in humans). This is an example of a countercurrent multiplier system. Counter current because the fluid flows in opposite direction and a multiplier because it allows a steeper concentration gradient to develop than would develop with a concurrent system. Some animals have relatively long loops of Henlé: ● Length of loop of Henlé is positively correlated with the need for water conservation in animals. ● The longer the loop, the more water will be acquired. Thicker medullas will accommodate longer loops of Henelé. Function for ADH: ● ADH controls reabsorption of water in the collecting duct. Solute concentration is hypotonic in DCT, because proportionately more solutes than water passed out of filtrate in the loop of Henlé. Low solute concentration means little water can be reabsorbed into filtrate. Hence large volume of urine is produced with low solute concentration and blood solute concentration is increased (as interstitial fluid contains high solute concentration). This is not favourable. 1) If solute concentration of the blood is too high, ADH is released from the pituitary gland, which causes the walls of the DCT and collecting duct to become more permeable to water. 2) As a result, most of the water in the filtrate is reabsorbed into the blood. 3) Filtrate passing down collecting duct deep into medulla where solute concentration of interstitial fluid is high creates concentration gradient for water to be continually to reabsorbed into the blood. RIP BIO CLASS OF 2K17 4) The filtrate, as a result, becomes a small volume of concentrated urine. Animals vary in the types of nitrogenous waste they produce: ● The type of nitrogenous waste in animals is correlated with evolutionary history/habitat. ● Ammonia is produced due to the breakdown of amino acids and nucleic acids. Highly basic and alters pH balance. o Highly reactive chemical (hence toxic). ● In freshwater habitats, organisms can release waste as ammonia as it can be diluted in the environment. Amphibians release waste as ammonia during larval form and then switch to urea. This is to save energy expenditure. ● Terrestrial organisms expend energy to convert ammonia to less toxic forms (urea/uric acid). o Birds and insects release waste as uric acid (requires the most energy to create) but does not require water to be released. o For birds not carrying water for excretion means saving energy during flight. o Uric acid is released as it is not soluble and crystallises rather than building up to toxic concentrations within the egg. Dehydration and overhydration: ● Dehydration: high solute concentration in filtrate results in darker urine. o Water is necessary to remove metabolic waste so lethargy and tiredness are symptoms due to decreased muscle functionality at being exposed to metabolic waste. o Blood pressure falls resulting in increased heart rate. o Body temperature regulation is affected due to inability to sweat. ● Overhydration is less common: results in body fluids becoming hypotonic and swelling of cells. Headache and nerve function disruption. Treatment options for kidney failure: ● Blood in tubing flows through dialysis fluid. o Tubing is partially permeable and allows small molecules to pass through into dialysis fluid but not blood cells and protein molecules. o Purified blood is returned to patient via a vein. ● Kidney transplant is also a viable option. o Donors can be deceased or alive. o Only one kidney needed to survive. 11.4 Sexual reproduction: RIP BIO CLASS OF 2K17 Similarities between oogenesis and spermatogenesis: ● Both involve mitosis, cell growth, two divisions of meiosis and differentiation. ● Oogenesis: o Production of egg cells in the ovaries. o Germinal epithelium cells in the fetal ovary divide by mitosis and distribute themselves through the cortex of the ovary. o At 4/5 months (foetus), the cells grow and start to divide by meiosis. o By 7 months they are in the first division of meiosis and follicle cells form around them. o This is called the primary follicle of which there are 400,000 at birth. o No more primary follicles are produced, but at the start of each menstrual cycle a small batch are stimulated to develop and one becomes a mature follicle containing a secondary oocyte. ● Spermatogenesis: o Production of sperm and occurs in the testes. o Testes are composed of narrow tubes (seminiferous tubules) with groups of cells filling the gaps between the tubules. o The cells are called interstitial cells. o Outer layer of cells in the seminiferous tubules are called he germinal epithelium, where sperm production begins. o Cells in the germinal epithelium that are closer to lumen (fluid filled centre) of seminiferous tubules are more mature. o Spermatogonium are at the outermost part of the germinal epithelium. o Spermatozoa are cells that have developed tails (flagella). o Sertoli cells are nurse cells and exist in the walls of the seminiferous tubule. o Spermatogenesis follows the following sequence of events: ▪ Germinal epithelium cells (2n) divide by mitosis. ▪ Diploid cells grow larger to become primary spermatocytes (2n). ▪ Each primary spermatocyte carries out first division of meiosis to produce two secondary spermatocytes (n). ▪ Each secondary spermatocyte carries out the second division of meiosis to produce two spermatids (n). ▪ Spermatids associate with Sertoli cells to develop flagellum and become spermatozoa. ▪ Sperm detach from Sertoli cells and are carried out by the fluid in the seminiferous tubule. RIP BIO CLASS OF 2K17 Diagrams of sperm and egg: ● ● ● ● ● ● ● Haploid nucleus. Two centrioles. First polar cell. Plasma membrane. Layer of follicle cells. Zona pellucida. Cortical granules. Sperm cells consist of: ● Head: o Haploid nucleus. o Centriole. o Plasma membrane. ● Mid-piece: o Helical mitochondria. ● Flagella: o Protein fibres to strengthen tail. o Microtubules. Differences in the outcome of spermatogenesis: ● Processes in spermatogenesis and oogenesis result in different numbers of gametes with different amounts of cytoplasm. ● Each mature sperm consists of different parts to a mature egg. ● Each meiotic division results in four spermatids. ● Sperm differentiation eliminates most of the cytoplasm, whereas the egg increases its cytoplasm. ● First meiotic division in eggs produces one large egg cell and one polar body and the second meiotic division produces a similar result, therefore only one egg is produced per meiotic division. ● Egg is much larger than sperm. ● Sperm are produced continuously whilst only a few hundred mature eggs are produced during the lifetime of a female. Preventing polyspermy: ● Acrosome reaction: Sperm binds to egg and enzymes from acrosome digest the zona pellucida. ● Penetration of egg membrane: Sperm and egg fuse together and sperm nucleus enters the egg cell (fertilisation). RIP BIO CLASS OF 2K17 ● Cortical reaction: Acrosome reaction exposes area on tip of the sperm that has proteins that bind to egg membrane. Sperm activates egg. Contents of cortical granules are released from the egg by exocytosis. o Cortical vesicle enzymes digest binding proteins so that no further sperm can bind. Enzymes also harden zona pellucida and make it impermeable to other sperm. Internal and external fertilization: ● Fertilization in animals can be internal or external. ● Aquatic animals release gametes directly into water and have behaviours that bring eggs into proximity with sperm. This is dangerous as it is prone to predation and environmental fluctuation. ● Terrestrial animals generally display internal fertilization as gametes may dry out. Sperm and ova are placed in close proximity to each other. Marine mammals still use internal fertilization. Developing embryos can be protected inside the female. Implantation of the blastocyst: ● ● ● ● ● ● ● ● ● Blastocyst forms after pregnancy. Upon fertilization, mitotic division occurs to form a 2-cell embryo. Occurs again to form a four cell embryo by 48 hrs. This continues slowly, alongside the migration of other cells, which gives the embryo the shape of a hollow ball (blastocyst). By 7 days the blastocyst is 125 cells and has reached the uterus after being brushed down the oviduct by the cilia of cells in the oviduct wall. Zona pellucida then breaks down and blastocyst sinks into the endometrium (implantation). Finger like projections on blastocyst allows it to penetrate uterus lining. Exchanges materials with mother’s blood (food and oxygen). By 8 weeks, begins to develop bone tissue and is considered a foetus. Role of HCG in early pregnancy: ● HCG (Human chorionic gonadotropin) stimulates the ovary to secrete progesterone during early pregnancy. ● This helps maintain the uterus lining during pregnancy. ● HCG stimulates the corpus luteum to continue to secrete progesterone and oestrogen. Materials exchange by the placenta: ● Placenta facilitates the exchange of materials between the mother and embryo. RIP BIO CLASS OF 2K17 ● Humans are placental mammals. ● Two other groups of mammals include: o Monotremes (egg laying) and; o Marsupials (offspring develop inside a pouch). ● Placenta is needed because the body surface area to volume ratio becomes smaller as the foetus grows. ● Foetal tissues with contact to maternal tissues in the uterus wall. Foetus develops membranes that form the amniotic sac, which encompasses the amniotic fluid for the support and protection of the foetus. ● Placental villus increase in number during pregnancy and assist in the exchange of materials with the mother. o Maternal blood flows in the inter-villous spaces around the villi (not confined to blood vessels/capillaries). o Foetal blood circulates in capillaries close to the surface of each villus. o Distance between foetal and maternal blood is small, and cells that separate them form the placental barrier. o This barrier is selectively permeable. Release of hormones by the placenta: ● The placenta secretes oestrogen and progesterone. ● This means that the corpus luteum is no longer needed for this role. ● Switch over from corpus luteum to placenta occurs. The role of hormones in parturition: ● Birth is mediated by positive feedback involving oestrogen and oxytocin. ● Progesterone inhibits secretion of oxytocin by the pituitary gland and inhibits contraction of the myometrium. ● The foetus (at the end of pregnancy) produces hormones to that cause the placenta to stop secreting progesterone and oxytocin is therefore secreted which stimulates contraction of the myometrium. ● Stretch receptors detect contractions, which signal for greater oxytocin secretion, and more vigorous contractions as a consequence. ● This is an example of positive feedback, which gradually increases myometrium contractions. ● Relaxation of muscle fibres cause cervix to dilate and uterine contractions then burst the amniotic sac. ● Further uterine contractions then push the baby out. Gestation times, mass and growth, and development strategies: ● Altricial species (born weak and defenceless and immobile). Short gestation period. RIP BIO CLASS OF 2K17 ● Precocial: born with open eyes, hair, mobile, and are often able to defend themselves. Long gestation period. Option A: Neurobiology and Behaviour A.1 Neural development: Development of the neural tube: ● Infolding of ectoderm followed by elongation of the tube forms neural tube of embryonic chordates. ● Process is called neurulation. ● An area of the ectoderm cells on the dorsal surface develops into the neural plate. ● Cells in the neural plate change shape causing the plate to fold inwards. ● This forms a groove on the ectoderm. ● The neural plate eventually separates from the rest of the ectoderm and forms the neural tube. ● The neural tube elongates as the embryo develops. Development of neurons: ● Neurons are initially produced by differentiation in the neural tube. ● Part of the ectoderm develops into neuro-ectodermal cells in the neural plate. ● The nervous system is formed from these. ● Continuing proliferation of cells and differentiation in the neural plate forms the neural tube. ● Neural tube is therefore comprised of functioning neurons. ● To form the mature CNS proliferation of neurons continues in the developing spinal cord and brain. Neurulation in Xenopus: ● ● ● ● ● Ectoderm, mesoderm and endoderm: Day 13. Formation of neural tube: Day 18.5. Wall of developing gut and cavity: Day 20. Notocord: Day 22. Developing dorsal fin: Day 36. Spina bifida: RIP BIO CLASS OF 2K17 ● Centrum provides support to the vertebrae. ● These develop on the ventral side of the neural tube ● Tissue migrates from both sides of the centrum to form the vertebral arch but in some cases the arch never fuses together properly. ● This is called spina bifida. ● Symptoms can vary from mild to severe. Migration of neurons: ● Immature neurons migrate to a final location. ● This occurs by moving the cytoplasm and organelles from the trailing end to the leading edge by contractile actin filaments. ● It is an important occurrence in brain development as neurons may grow in one part but are needed in another part. ● Mature, functional neurons don’t usually move but their axons and dendrites can regrow if damaged. Growth and development of axons: ● An axon grows from each immature neuron in response to chemical stimuli. ● Immature neurons consist of a cell body with cytoplasm and a nucleus. ● One axon develops on each neuron. ● Smaller dendrites that bring impulses from other neurons also develop. ● Chemical stimuli determine neuron differentiation and the growth directionality. ● Some axons extend beyond the neural tube to reach other parts of the body. ● Axons can be more than a meter long in humans. ● They carry impulses to other neurons or effector cells. ● If the cell body remains intact the axon can grow if damaged. ● Recovery depends on correct connections being re-established between the axon and the cell with which it should be communicating. ● Developing neurons forms multiple synapses. ● Growth of axons or dendrites are directed so that they reach the cell with which they interact. ● A synapse forms between the neuron and the other cell. ● Synapse development involves special structures being assembled in the membranes on either side of the synapse and in the synaptic cleft. ● In practise neurons develop many synapses but the smallest number is 2. Elimination of synapses: ● Synapses that are not used do not persist. ● New synapses can be formed at any stage of life. RIP BIO CLASS OF 2K17 ● Transmission occurs at a synapse chemical markers are left that strengthen the synapse. ● When the synapse isn’t used these chemical markers aren’t made and so the synapse becomes weaker and weaker until it is eventually eliminated. Neural pruning: ● ● ● ● Involves the loss of unused neurons. More neurons in new-born babies’ brains than in adults. Apoptosis is the process by which neurons destroy themselves. Elimination of part of a neuron or the whole cell is known as neural pruning. Plasticity of the nervous system: ● Plasticity of the nervous system allows it to change with experience. ● Connections between neurons can be changed by growth of axons/dendrites, establishment of new synapses and pruning, ● Stimulus for change comes with how the person’s nervous system is used. ● It is important in repairing damage to the brain and spine. Strokes: ● Ischemic stroke is a disruption of the supply of blood to a part of the brain. Bleeding from a blood vessel is another cause. ● Brain is deprived of oxygen and glucose and therefore neurons become irreparably damaged and die. ● 1/3 of sufferers make full recovery and another 1/3 survive but with disability. A.2 The human brain: Development of the brain: ● ● ● ● ● Anterior part of the neural tube expands to form the brain. This process is called cephalisation. Human brain contains around 86 billion neurons. Brain is the central control centre for the body. Directly from cranial nerves and indirectly via the spinal cord and hormones. Roles of the parts of the brain: ● Medulla oblongata: autonomic control of gut muscles, breathing, blood RIP BIO CLASS OF 2K17 ● ● ● ● vessels and heart muscle. Cerebellum: coordinates unconscious functions – posture, non-voluntary movement and balance. Hypothalamus: Interface between brain and pituitary gland. Synthesises the hormones secreted by the posterior pituitary. Regulates secretion of hormones by anterior pituitary. Pituitary gland: posterior lobe stores and releases hormones and anterior lobe produces and releases hormones. Cerebral hemispheres: carry out high complex functions such as learning, memory and emotions. Methods of brain research: ● Lesions have been analysed via autopsy and relating the position of the lesion to observed changes in behaviour ● MRI is used to investigate the internal structure of the body. ● FMRI allows the identification of activated parts of the brain as these parts receive increased blood flow. o The scans can show which part of the brain responds to a specific stimulus. Examples of brain functions: ● Both cerebral hemispheres have a visual cortex. ● Visual signals from light sensitive rod and cone cells in the retina are processed here. o Information is first projected in region called V1, the information is then analysed by V2 to V5. ● Broca’s are is a part of the left cerebral hemisphere. o Damage to this area inhibits the production of meaningful words and sentences; even if the individual knows what they want to say, they can’t. say it. ● Nucleus Accumbens is in each of the cerebral hemispheres which is the pleasure or reward centre of th brian. o Variety of stimuli including food and sex cause the release of dopamine that cuses feelings of satisfaction. The autonomic nervous system: ● Autonomic nervous system controls involuntary processes in the body using centers located in the medulla oblongata. ● The peripheral nervous system comprises all of the nerves outside the central nervous system. ● Divided into voluntary and autonomic. ● Autonomic has two parts: sympathetic and parasympathetic. RIP BIO CLASS OF 2K17 o Parasympathetic nerves cause an increase of blood flow to the gut wall during digestion and absorption. o Sympathetic nerves cause a decrease in blood flow during fasting. ● Therefore parasympathetic and sympathetic nerves have contrary effects to each other. Activities coordinated by the medulla: ● Activities coordinated by the medulla are swallowing, breathing and heart rate. Passing down of food from the pharynx to stomach via the oesophagus is involuntary and controlled by the medulla oblongata. ● Two centres in the medulla control breathing. One controls the timing of inspiration and the other controls the force of inspiration and active voluntary expiration. o This is controlled by chemoreceptors in the medulla that monitor blood pH. Co2 concentration increases acidity of blood and therefore a fall in pH results in deeper/more frequent breathing. ● Cardiovascular centre of the medulla regulates the rate of heartbeat. o Receptor cells monitor Blood pH and pressure. o Heart rate will be adjusted according to these factors, to maintain a constant state of blood pH and pressure. Signals are sent to the SA node (pacemaker). o Signals carried by the sympathetic system speed up heart rate and those carried by the parasympathetic system slowdown the heart rate. The cerebral cortex: ● Use of pupil reflex to evaluate brain damage. o Impulses carried to radial muscle fibres cause them to contract/dilate the pupil; impulses carried by parasympathetic system cause contraction. o When bright light is shone into the eyes photoreceptive ganglion cells send impulses to the mid brain, which trigger the parasympathetic system to contract the radial cells and the pupil to be constricted. o If the pupils do not constrict at once the medulla oblongata is probably damaged. ● The cerebral cortex forms a larger proportion of the brain and is more highly developed in humans that other animals. o It is the outer layer of the cerebral hemisphere with up to 6 different layers of neurons. o Processes the most complex tasks of the brain. In birds and reptiles the cells are organised in clusters instead of layers. RIP BIO CLASS OF 2K17 The evolution of the cerebral cortex: ● Human cerebral cortex has become enlarged by an increase in total area with extensive folding to accommodate it. ● Most of the surface area of the cerebral cortex is in the folds rather than on the outer surface. Functions of the cerebral hemispheres: ● Cerebral hemispheres are responsible for high order functions. o Learning memory speech and emotion. ● Most sophisticated processes occur in the frontal and prefrontal lobes. ● They use stimuli from different sources, eyes ears and also memory. o Rely on complex network of neurons. Sensory inputs to the cerebral hemispheres: ● The left cerebral hemisphere receives sensory input from sensory receptors in the right side of the body and the right side of the visual field in both eyes and vice versa for the right hemisphere. ● Inputs from the eyes pass to the visual area of the occipital lobe (visual cortex). Motor control by the cerebral hemispheres: ● Motor control by the cerebral hemispheres: Left cerebral hemisphere controls muscle activity in the right side of the body and vice versa for the right hemisphere. ● Posterior part of the frontal lobe called the primary motor cortex controls muscles throughout the body. Homunculi: ● Homunculi basically represent how much of the brain is used to control a certain part of the body – motor homunculus. ● It also shows how much of each part is devoted to sensory inputs from the brain – sensory homunculus. Energy of the brain: ● Brain metabolism requires large energy inputs. ● Energy is required to maintain resting potential in neurons. ● Also needed for synthesis of neurotransmitters and other signal molecules. ● Brain contains lots of neurons therefore requires large amounts of glucose and oxygen to generate this energy. RIP BIO CLASS OF 2K17 ● 10% of the energy consumed by basal metabolism is in the brain. A.3 perception of stimuli: Sensory receptors: ● Receptors detect changes in the environment. Nerve endings of sensory neurons act as receptors. ● Body also has specialised receptor cells that pass impulses to sensory neurons (light sensitive rod and cones). o Mechanoreceptors. o Chemoreceptors. o Thermoreceptors. o Photoreceptors. Olfactory receptors: ● Detection of chemicals in the air by the many different olfactory receptors. ● Located inside the epithelium of the nose. ● Membrane contains odorant receptor molecules, which detect chemicals in the air. ● Volatile chemicals can be smelled. ● Odorants from food can pass through mouth and nasal cavities to reach the nasal epithelium. ● A different gene encodes each odorant receptor protein. Each receptor cell has one type of odorant receptor in its membrane. But there are several of each receptor cell type. Photoreceptors: ● Photoreceptors: rods and cones are photoreceptors located in the retina. Light is focussed on the retina by the cornea and the lens. ● Many nocturnal mammals have only rods and cant distinguish colours. Rods and cones convert the light into neural signals. Differences between rods and cones: ● Rods and cones differ in their sensitivities to light intensities and wavelengths. ● Rods are: o Sensitive to light (work well in dim light). o Are bleached by bright light. o Absorb a wide range of visible wavelengths. RIP BIO CLASS OF 2K17 o Can’t respond selectively to different colours. ● Cones are: o Red Blue and Green. o Each absorbs a different range of light. o Relative stimulation of each cone type produces signal carrying specific colour. o Stimulated by bright light and colour vision fades in dim light. Red-green colour-blindness: ● Red green colour blindness as a variant of normal trichromatic vision. ● Absence of gene for photoreceptor pigments essential in either red or green cone cells. ● Sex linked condition. ● Normal alleles are dominant so it’s a recessive disorder. ● Much commoner among males. Structure of a retina: Bipolar cells: ● Bipolar cells send the impulses from rods and cones to ganglion cells. ● If rods and cones don’t receive light they send a inhibitory neurotransmitter to the bipolar cell (with which they synapse), which hyperpolarises it to stop it from transmitting impulses. ● When rods or cones absorb light, they become hyperpolarised. RIP BIO CLASS OF 2K17 ● As a result they stop sending inhibitory neurotransmitters to the bipolar cells and allow the bipolar cells to depolarise and activate ganglion cells. Ganglion cells: ● Ganglion cells have cell bodies with dendrites that form synapses with bipolar cells. ● Long axons along which impulses pass to brain at a low frequency when ganglion cells aren’t being activated and at an increased rate when ganglion cells are stimulated. ● Pass across the front of the retina to form a bundle at the blind spot. This area has no rods and cones. Axons of ganglion cells pass via the optic nerve to the optic chiasma in the brain. Vision in the right and left fields: ● The information from the right field of vision from both eyes is sent to the left part of the visual cortex and vice versa. ● Stimuli from both sides of one eye are integrated by the axons of ganglion cells. ● Crossover of axons between left and right sides happens at the optic chiasma. Structure of the ear: ● Outear: o Pinna. ● Middle ear: o Incus o Malleus o Stapes ● Inner ear: o Round window. o Oval window. o Semi-circular canals. o Auditory nerve. o Cochlea. The middle ear: ● Middle ear transmits and amplifies sound. ● It’s an air-filled chamber between the outer ear and the inner ear, separated by the eardrum. ● Tiny bones (malleus, incus and stapes) form connections between the eardrum and oval window. RIP BIO CLASS OF 2K17 ● Ossicles (three bones) transmit vibrations from eardrum to oval window, which amplifies them 20 times. ● This occurs because oval window is so much smaller than the eardrum. ● Contraction of muscles in the ossicles during loud sounds weakens connections between the ossicles and dampens the vibrations. The cochlea: ● ● ● ● ● ● ● ● ● Sensory hairs of the cochlea detect sounds of specific wavelengths. Cochlea is where vibrations are transduced into neural signals. Layers of tissue (membranes) to which sensory cells are attached. Bundle of hairs stretch from one membrane to another. Vibrations from the oval window resonate with the hair bundles, stimulating the sensory cells and activating them. Selective activation results into distinguishing between different pitches. Fluid in cochlea is incompressible. The round window is therefore a thin sheet that allows movement of the oval window. When oval window pushes fluid in the cochlea inwards, the round window moves outwards. The auditory nerve: ● Impulses caused by sound perception are transmitted to the brain via the auditory nerve. ● Hair cells in the cochlea depolarise by vibrations and release neurotransmitters across a synapse, which triggers a sensory neuron. ● An action potential is triggered and an impulse is propagated to the brain along the auditory nerve. Cochlear implants: ● Cochlear implants in deaf patients. ● If hair cells in the cochlea are defective then a cochlear implant is necessary. ● External parts are a microphone to detect sounds, speech processor which selects specific frequencies of speech and filters out others. ● Internal parts include a receiver that picks up sound signals, a stimulator that converts the signals to electrical impulses and electrodes that carry impulses to the cochlea that stimulate auditory nerve directly. Directing head movements: ● Hair cells in the semi-circular canals detect movement of the heads. ● Fluid-filled semi-circular canals have a swelling at one end in which there RIP BIO CLASS OF 2K17 ● ● ● ● are sensory hair cells. The hair cells are embedded in gel, forming the cupula. Every time the head moves in a specific direction, the fluid flows past the cupula, which is detected by hair cells and sends impulses to the brain. Three semi-circular canals are at right angels to each other so each is in a different plane. Brain can deduce the direction of movement by the relative amount of stimulation of the hair cells in each of the semi-circular canals. A.4 Innate and Learned Behaviour: Innate behaviour: ● Innate behaviour is inherited from parents and so develops independently of the environment. ● It is unaffected by external influences (like experience) and develops independently of environmental factors. ● Palmar grasp reflex (babies grabbing onto objects). ● It is genetically programmed and inherited. ● Can change through evolution if natural selection favours one behaviour pattern over others. Invertebrate behaviour experiments: ● ‘Taxis’ is movement towards or away from a directional stimulus. ● Kinesis is movement as a response but is non-directional in nature. o Speed of movement is measure/ number of turns. Reflexes: ● Autonomic and involuntary responses are referred to as reflexes. ● Stimulus is a change in the environment that is detected by a receptor and elicits a response. ● Response can be a change carried out by muscle or gland (usually). ● Involuntary responses are carried out by the autonomic nervous system, known as reflexes – a rapid response to a stimulus (involuntary). ● Pupil reflex, in response varying light conditions, controlled by the radial muscles. Reflex arcs: ● Reflex arcs comprise the neurons that mediate reflexes. ● Receptor perceives the stimulus and eventually relays the impulse to the effector, which is a muscle or gland and carried a response. ● The sequence of neurons that links the two is known as the reflex arc. RIP BIO CLASS OF 2K17 Sensory neuron and motor neuron. ● Most reflex arcs contain more than two neurons (more than one relay neuron connects the sensory neuron to the motor neuron. Withdrawal reflex: ● Withdrawal reflex of the hand from a painful stimulus. ● Innate response to pain. o Activate sensory neurons (thermoreceptors to heat) and carry impulses from the finger to the spinal cord via the dorsal root of the spinal nerve. o Impulses ravel to the grey matter of the spinal cord in which there are synapses with relay neurons. o Relay neurons have synapses with motor neurons that then carry impulses out of the spinal cord via the ventral root to the muscles in the arm. o Muscle fibres contract and pull the arm away. RIP BIO CLASS OF 2K17 Learned behaviour: ● ● ● ● Learned behaviour develops as a result of experience. Acquisition of new patterns of behaviour. Language is a learned behaviour. Ability to make sense of vocal patterns and make them oneself is innate but the specific language spoken is learned. Development of birdsong: ● Partly innate and partly learned. ● All members of a bird species share innate aspects of song; that means each individual recognises other members of the species. Many species learn mating calls from their father. Learned aspects causes slight differences to the song and some species mates are chosen based on the quality of singing. Reflex conditioning: ● Reflex conditioning involves forming new associations. ● Establishes new neural pathways in the brain. ● Conditioned reflexes are used extensively in animal behaviour and can greatly increase survival chances. ● Innate reflex to dislike bitter foods, but learned behaviour to know which foods have that taste. ● Insect with yellow and black stripes having a bitter taste would mean that all insects of that type would have a bitter taste and would therefore be avoided. ● The colour is associated with a taste, in this case. Pavlov’s experiments: ● Rang a bell every time it was dinnertime. ● Unconditioned stimuli were that the dog salivated at the smell of food. ● The bell ringing every time food was served posed as the conditioned stimuli. ● After a while, the dog would salivate even with the ringing of the bell, even if no food were present. Imprinting: RIP BIO CLASS OF 2K17 ● Imprinting is learning occurring at a particular life stage and is independent of the consequences of behaviour. ● It is the establishment of preference of stimulus that elicits behaviour patterns of trust and recognition. ● For example, the mother is the first big large moving object that the hatchlings see, so they follow her around for a few weeks of their life and are protected and fed. ● If they do not see their mother, they follow another large object that they see. ● This occurs regardless of whether they may be put in danger by following that object. ● Hence imprinting is independent of the consequences of behaviour. Operant conditioning: ● Operant conditioning is a form of learning that consists of trial and error experiences. ● The environment imposing a stimulus on an animal initiates reflex conditioning, whereas an animal testing out a behaviour pattern to become aware of the consequences initiates operant conditioning. ● If the behaviour pattern is positive in consequence then it is reinforced, otherwise it is inhibited. ● For example, lambs don’t touch electric fencing due to operant conditioning; the pain from carrying out an action inhibits them from displaying that behaviour. Learning: ● Learning is the acquisition of skill or knowledge. ● Could be the acquisition of behavioural patterns or the loss of them. ● These are often the result of growth and maturation, however growth and maturation is generally supplemented, or instigated, by learning. ● Motor skills such as walking, talking, or playing the violin are learned. ● Knowledge has to be learned. ● Useful things for survival etc. need to be learned. ● Higher order function, so humans have a greater capacity of doing it because of their larger frontal and prefrontal cortex. ● Social animals are likely to learn from each other. Memory: ● Process of encoding, storing and accessing information. ● Higher order function. ● Encoding is the process of converting information into a storable form (by the brain). ● Accessing is the recall of information so that it can be used actively in thought processes. RIP BIO CLASS OF 2K17 ● Hippocampus is related to memory. o Removal of the hippocampus can result in the inability to make new memories, besides from procedural ones. o Synapses in the hippocampus can be pruned. A.5 Neuropharmacology: Excitatory and inhibitory neurotransmitters: ● Some neurotransmitters are excitatory (they excite nerve impulses in post-synaptic neurons) and others are inhibitory (they inhibit nerve impulses in the post-synaptic neuron). ● Excitatory neurotransmitters excite the post-synaptic neuron by depolarising it. ● Ones that inhibit the formation of action potentials make the membrane potential more negative (rather than positive, which is required to depolarise) and therefore hyperpolarise it. ● As a result post-synaptic neurons cannot reach the threshold potential. ● Inhibitory neurotransmitters are small molecules that are inactivated by specific enzymes in the membrane of the post-synaptic neuron. Summation: ● Nerve impulses are initiated or inhibited in post-synaptic neurons as a result of summation of all excitatory and inhibitory neurotransmitters received from pre-synaptic neurons. ● Single release of an excitatory neurotransmitter from one pre-synpatic neuron is insufficient to trigger an action potential. ● As a result excitatory neurotransmitters need to be released repeatedly from one pre-synaptic neuron or from several adjacent pre-synaptic neurons (since many can synapse with one post-synaptic neuron). ● This additive effect is called summation. ● Summation involves combining the effect of excitatory and inhibitory neurotransmitters. ● Formation of an action potential depends on the balance between the two. ● Integration of different sources is the basis of decision making in the CNS. Slow and fast neurotransmitters: ● Many different slow-acting neurotransmitters modulate fast synaptic transmission in the brain. ● Fast-acting neurotransmitters are the ones which cause the opening or closing of voltage gated ion channels. ● Slow acting ones take several hundreds of milliseconds and generally RIP BIO CLASS OF 2K17 diffuse through liquid in synaptic cleft to affect a group of neurons. ● Dopamine, non-adrenaline and serotonin are examples. ● They do not affect ion movement but release secondary messengers inside post-synaptic neurons, which essentially regulate fast synaptic transmission (opening/closing of voltage gated channels). Memory and learning: ● Memory and learning involve changes in neurons caused by slow-acting neurotransmitters. ● Slow acting neurotransmitters cause the release of secondary messengers within the post-synaptic neurons and increase the number of receptors in the post-synaptic membrane which result in an increased rate of ion movement when a neurotransmitter binds (fast acting). o These secondary messengers cause long-term potentiation, which is central to synaptic plasticity that is necessary for memory and learning. ● Learning of new skills results in formation of new synapses in the hippocampus and elsewhere in the brain. Endorphins: ● Pain receptors in the skin and other parts of the body detect stimuli. ● These receptors are the endings of sensory neurons that convey impulses to the CNS. ● When the impulse reaches a sensory area of the cerebral cortex, we experience pain. ● Endorphins are oligopeptides that are secreted by the pituitary gland and act as painkillers. ● Bind to the receptors in synapses in the pathways used in the perception of pain, inhibiting synaptic transmission and preventing pain from being felt. Psychoactive drugs: ● Affect the brain by either increasing or decreasing post-synaptic transmission. ● Over a hundred different neurotransmitters are known. ● Psychoactive drugs alter the functioning of some synapses. ● Some drugs are excitatory and some are inhibitory. o Nicotine, cocaine and amphetamines are excitatory. o Benzodiazepines, alcohol and tetrahydrocannabinol (THC) are inhibitory. Anaesthetics: RIP BIO CLASS OF 2K17 ● Anaesthetics act by interfering with neural transmission between areas of sensory perception and the CNS. ● Cause a reversible loss of sensation in part or all of the body. ● Local anaesthetics cause an area to be numbed and general anaesthetics result in unconsciousness. Anaesthetics and awareness: ● Patients under general anaesthesia are completely unaware. ● Sometimes it is undesirable or unnecessary for this level of unconsciousness. o For example, a spinal block is used during a caesarean section so that the mother stays alive and breathing normally but pain cannot be felt below the spinal cord. Stimulant drugs: ● Stimulant drugs mimic the stimulation provided by the sympathetic nervous system. o Make a person more alert. o Increased heart rate, blood pressure and body temperature. ● This is basically what the sympathetic nervous system does, so stimulants mimic it. ● Caffeine and cocaine are examples of stimulants. Examples of stimulants and sedatives: ● Pramipexole mimics dopamine and binds to dopamine receptors in postsynaptic membranes at dopaminergic synapses. o Has the same effect as dopamine when it binds. Used in early stages of Parkinson’s and can be used as an anti-depressant. ● Cocaine acts at synapses that use dopamine. o Binds to dopamine reuptake transporters which pump dopamine back into the pre-synaptic neuron. o Cocaine blocks these transporters so dopamine builds up in the synaptic cleft and the post-synaptic neuron is continuously excited. ● Diazepam (valium) binds to an allosteric site on GABA receptors in postsynaptic membranes. o GABA is an inhibitory neurotransmitter and causes the hyperpolarization of the post-synaptic neuron by opening chloride ion channels. o Diazepam causes chloride ions to enter at a greater rate therefore causes greater hyperpolarisation. It is therefore a sedative RIP BIO CLASS OF 2K17 (diazepam). ● THC binds to cannabinoid receptors in pre-synaptic membranes. o This inhibits the release of neurotransmitters that cause excitation of post-synaptic neurons. o It is therefore inhibitory. o Cannabinoid receptors are found in the cerebellum, hippocampus and cerebral hemispheres. o Hence they result in stimulation of appetite, psychomotor behaviour and short-term memory impairment. Drug addiction: ● Addiction can be affected by genetic predisposition, social environment and dopamine secretion. ● Some people are far more susceptible to addiction than others (genetic predisposition). o DRD2 codes for dopamine receptor protein. People with A1 allele consumed less alcohol than those homozygous for the A2 allele. ● Social environment can greatly affects the likelihood of taking drugs. o Peer pressure, poverty and social deprivation, traumatic life experiences and mental health. ● Addictive drugs affect dopamine-secreting synapses. o This is attractive to the drug user and they find it difficult to abstain. A.6 Ethology: Ethology: ● Ethology is the study of animal behaviour in natural conditions. ● Animals won’t display the same behaviour in zoos as they would in their natural habitat because the stimuli would be different. Natural selection and animal behaviour: ● ● ● ● ● Natural selection can change the frequency of observed animal behaviour. House finches are generally sedentary (native population in California). Small number were released and spread throughout eastern US. Within 20 years migratory behaviour was observed. This change in behaviour was likely due to natural selection. The mechanism of natural selection: ● Behaviour that increases the chances of survival and reproduction will RIP BIO CLASS OF 2K17 become more prevalent in a population. ● However only genetically determined behaviour can be inherited. ● Parus major is an example of how behaviour evolves by natural selection, especially in response to environmental changes. o Availability of food rises to a peak in spring. o Due to global warming peak availability has become earlier and so a birds that lay their eggs a few days earlier than the mean date had a greater chance of survival when they were young. o As a result, mean date of egg-laying evolved to become earlier. Breeding strategies in salmon: ● Coho salmon die after breeding and the young live in the river for a year before migrating to the ocean. ● They return to spawn. ● Breeding strategies: o Hooknoses fight each other for access to females laying eggs (winer sheds sperm over the eggs to fertilise them). o Jacks sneak up on females and attempt to shed sperm over their eggs before being noticed. o Whether a male becomes a jack or hooknose depends on his growth rate. o Larger fish are hooknoses whilst Jacks are smaller and can therefore go unnoticed. Synchronised oestrus: ● Oestrus is a period of increased sexual receptivity. ● Synchronised oestrus in female lions in a pride is an example of innate behaviour that increases the chances of survival and reproduction of offspring. o Males can only breed if they overcome the dominant male in another pride by fighting. o When a new male takes over a pride, he kills all the suckling cubs causing the females to come into oestrus more quickly so that he can mate with them. o Two or more closely related males may fight together for dominance. o Females can only breed when they come into oestrus, which enables them to have their cubs at the same time so they are all lactating together. o This means they can suckle each other’s cubs when they are hunting, increasing the cubs’ chances of survival. o Also, a group of male cubs can seek dominance more effectively if they all leave the pack at the same time. RIP BIO CLASS OF 2K17 Blackcap migration: ● Migratory behaviour in blackcaps is an example of the genetic basis of behaviour and its change by natural selection. ● Until recently almost all blackcaps migrated to Spain and Portugal for the winter. ● However recently some were found to be migrating to Britain and Ireland (10%). ● Winters in Britain are now warmer due to global warming and it is much closer than Spain. ● Also people in Britain feed wild birds, which increases survival of offspring. ● Britain, minimum day length is shorter so birds are prompted to go back to Germany (breeding grounds) quicker and can dominate the best territories. Vampire bats: ● Blood sharing in vampire bats is an example of the evolution of altruistic behaviour by natural selection. ● Vampire bats regurgitate blood for those who have not fed. ● This blood sharing is altruistic because: o The blood sharing is not a kin-selection; o And giving blood to an individual who has not fed incurs a cost to the giver because their daily diet is lost. o Blood sharing is an example of reciprocal altruism because if Individual A feed B then on a later night when A can’t feed, B may be able to feed A. If B died, then B would not be able to feed A when A needs it. Hence it aids the chances of survival. Foraging in shore crabs: ● Foraging behaviour in shore crabs is an example of increased chances of survival by optimal prey choice. ● Foraging is searching for food. ● Prey chosen by animals is that which gives the highest rate of energy return. ● Hence crabs choose to eat mussels of intermediate size because they are the most profitable in terms of the energy yield per second of time spent breaking open the shells. Courtship in birds of paradise: ● Courtship in birds of paradise is an example of mate selection. RIP BIO CLASS OF 2K17 ● Plumage and courtship displays of male birds are reasons for exaggerated traits. ● The traits are of no benefit in terms of flight but are there only to attract female attention. ● Males gather at a site called a lek and females select mates depending on who has the best display. o The plumage and courtship dances help the female identify whether the male belongs to her species. o Exaggerated traits could also suggest overall fitness – if the male had enough energy to grow and maintain the elaborate plumage, it must have fed very efficiently. o The male would therefore be better adapted to living and surviving. Changing learned and innate behaviour: ● Learned behaviour can spread through a population or be lost from it more rapidly than innate behaviour. ● Innate behaviour can be modified by natural selection slowly because there needs to be variation in the alleles that affect such behavioural patterns. o Changes in allele frequencies in populations need to occur. ● Learned patterns take longer to develop in an individual. o However since they don’t require genetic modification and changes in allele frequencies, they can spread relatively rapidly. o However they can also be forgotten quickly. Blue tits and cream: ● Feeding on cream from milk bottles in blue tits is an example of the development and loss of learned behaviour. ● Blue tits peck through the aluminium foil to drink the cream from milk bottles. ● This behaviour caused their migration far further than usual. ● German occupation of the Netherlands stopped deliveries of milk for eight years; however soon after the resumption of deliveries blue tits throughout the Netherlands were pecking through bottle tops. ● This shows that this behavioural pattern is learned. Since milk has been delivered to doorsteps less, and a lot of it is skimmed (without cream), blue tits have stopped displaying such behaviour.