AS Level Biology key facts

Cell structure

The microscope in cell studies

• magnification = image size ÷ actual size (M = I ÷ A)
• actual size = image size ÷ magnification; image size = actual size × magnification
• 1 mm = 1000 µm and 1 µm = 1000 nm, so 1 mm = 1 000 000 nm
• Scale bar: magnification = measured length of the bar ÷ length written on the bar
• Calibration: one graticule division = (number of stage divisions × length of one stage division) ÷ number of graticule divisions that line up with them
• Calibrate again for each objective lens: at a higher magnification each graticule division represents a smaller actual length
• Temporary slide: thin specimen in a drop of water or stain, coverslip lowered slowly at an angle to avoid air bubbles. Drawing: sharp pencil, clear continuous lines, no shading

Cells as the basic units of living organisms

• Nucleus: nuclear envelope (two membranes with pores) around chromatin; the nucleolus makes rRNA and ribosome subunits
• Rough ER has ribosomes and makes and transports proteins; smooth ER has no ribosomes and makes lipids and steroids
• Golgi body modifies proteins (for example into glycoproteins), packages them into vesicles and makes lysosomes, which contain hydrolytic enzymes
• Mitochondria (double membrane, cristae, matrix) make ATP in aerobic respiration; chloroplasts carry out photosynthesis; both contain small circular DNA and 70S ribosomes
• Ribosomes are 80S in the cytoplasm and on rough ER, 70S in mitochondria, chloroplasts and prokaryotes; ribosomes and centrioles have no membrane
• Plant cells only: cellulose cell wall, chloroplasts, large permanent vacuole with tonoplast, plasmodesmata. Animal cells only: centrioles
• Bacterium: unicellular, 1 to 5 µm, peptidoglycan cell wall, circular DNA free in the cytoplasm, 70S ribosomes, often plasmids. Virus: non-cellular, DNA or RNA core, protein capsid, sometimes a phospholipid envelope

Biological molecules

Testing for biological molecules

• Benedict's test (reducing sugar): heat with Benedict's solution in a water bath; blue → green → yellow → orange → brick-red precipitate
• Iodine test (starch): add iodine solution; orange-brown → blue-black
• Emulsion test (lipid): shake with ethanol, then pour into water; a milky white emulsion forms
• Biuret test (protein): add biuret reagent, no heating; blue → purple (lilac)
• Non-reducing sugar: after a negative Benedict's test, boil a fresh sample with dilute hydrochloric acid, neutralise with sodium hydrogencarbonate, then repeat the Benedict's test
• Semi-quantitative: same volumes, same temperature, same heating time, Benedict's in excess; compare with colour standards of known concentration, or time the first colour change

Carbohydrates and lipids

• α-glucose has the –OH on carbon 1 below the ring; β-glucose has it above the ring
• Maltose = α-glucose + α-glucose; sucrose = α-glucose + fructose. Glucose, fructose and maltose are reducing sugars; sucrose is non-reducing
• Amylose: α-glucose, 1,4 glycosidic bonds, unbranched helix. Amylopectin: 1,4 bonds with 1,6 branches. Glycogen: like amylopectin but more branched
• Starch and glycogen are compact and insoluble, so they store glucose without affecting water potential; many branch ends allow fast release of glucose
• Cellulose: β-glucose, 1,4 bonds, every second unit rotated 180°; straight chains held by hydrogen bonds into microfibrils with high tensile strength
• Triglyceride = glycerol + three fatty acids joined by three ester bonds (three water molecules released). Saturated fatty acids have no C=C bonds; unsaturated have one or more
• Phospholipid = glycerol + two hydrophobic (non-polar) fatty acid tails + one hydrophilic (polar) phosphate head

Proteins

• Amino acid: a central carbon joined to an amine group (–NH₂), a carboxyl group (–COOH), a hydrogen atom and an R group
• Peptide bond: condensation between the carboxyl group of one amino acid and the amine group of the next, releasing one water molecule; hydrolysis breaks it
• Secondary structure: α-helix or β-pleated sheet, held by hydrogen bonds between –C=O and –N–H groups of the backbone
• Tertiary structure is held by interactions between R groups: hydrogen bonds, ionic bonds, disulfide bonds (covalent, between two cysteines) and hydrophobic interactions
• Haemoglobin: two α-globin and two β-globin chains, each with a haem group containing one Fe²⁺ ion; each Fe²⁺ binds one O₂ reversibly, so one molecule carries up to four O₂
• Haemoglobin is soluble because hydrophilic R groups face outwards and hydrophobic R groups point inwards
• Collagen: three polypeptides in a triple helix with glycine as about every third amino acid; molecules are staggered and joined by covalent cross-links to form fibrils and fibres with high tensile strength

Water

• Solvent action: polar water molecules surround ions and polar molecules (glucose, amino acids), so these dissolve and can be transported and react in solution
• Non-polar molecules such as triglycerides do not dissolve in water
• High specific heat capacity (4.2 J g⁻¹ °C⁻¹): much energy is needed to raise the temperature, because energy is used to break hydrogen bonds; cells and habitats keep a stable temperature
• High latent heat of vaporisation (about 2400 J g⁻¹ at body temperature): evaporation removes a lot of heat, so sweating and transpiration cool the organism
• energy to change temperature = mass × specific heat capacity × temperature change
• energy to evaporate = mass × latent heat of vaporisation

Enzymes

Mode of action of enzymes

• Lock-and-key hypothesis: the active site has a fixed shape that fits the substrate exactly
• Induced-fit hypothesis: the active site changes shape slightly as the substrate binds, giving a closer fit
• Catalase: 2H₂O₂ → 2H₂O + O₂; follow the reaction by the volume of oxygen collected per unit time (product formed)
• Amylase: starch → maltose; follow the reaction by testing samples with iodine solution until it stays orange-brown (substrate gone)
• rate = change in amount ÷ time taken; compare initial rates, taken from the start of the reaction when the curve is steepest
• Colorimeter: measures absorbance of light by a coloured solution; a deeper colour gives a higher absorbance; set it to zero first with a blank

Factors that affect enzyme action

• Temperature: up to the optimum, more kinetic energy gives more successful collisions; above it, hydrogen and ionic bonds break and the enzyme is denatured
• pH: away from the optimum, the charges on R groups change and ionic bonds break; buffer solutions keep pH constant
• With substrate in excess, rate is directly proportional to enzyme concentration
• Michaelis-Menten constant (K_m) = the substrate concentration that gives half of V_max; a low K_m means a high affinity for the substrate
• Competitive inhibitor: similar shape to the substrate, binds to the active site; more substrate overcomes it; V_max unchanged, K_m increased
• Non-competitive inhibitor: binds away from the active site; more substrate does not overcome it; V_max lowered, K_m unchanged
• Immobilised enzymes (in alginate beads): reusable, product is free of enzyme, more stable to heat and pH changes; the rate may be slower because substrate must diffuse into the beads

Cell membranes and transport

Fluid mosaic membranes

• Phospholipids: form the bilayer; small non-polar molecules (oxygen, carbon dioxide) diffuse through it; ions and large polar molecules cannot
• Cholesterol: lies between the phospholipid tails; regulates fluidity, gives mechanical stability and reduces permeability to ions
• Channel proteins have a water-filled pore for specific ions; carrier proteins bind a specific molecule and change shape to move it across
• Glycoproteins and glycolipids have carbohydrate chains on the outer surface only; they act in cell recognition (cell surface antigens) and as receptors
• More unsaturated fatty acid tails (kinked, loosely packed) make a membrane more fluid
• Cell signalling: a cell secretes a ligand → the ligand is transported to target cells → it binds to a specific cell surface receptor → the target cell responds
• Only cells with a receptor of complementary shape to the ligand respond

Movement into and out of cells

• Simple diffusion: passive, directly through the phospholipid bilayer. Facilitated diffusion: passive, through channel or carrier proteins
• Active transport: against a concentration gradient, through carrier proteins, using ATP
• Endocytosis takes material into the cell in a vesicle made from the cell surface membrane; exocytosis releases material when a vesicle fuses with the membrane; both need ATP
• Osmosis: net movement of water from higher (less negative) to lower (more negative) water potential through a partially permeable membrane
• In a solution of higher water potential: an animal cell swells and bursts; a plant cell becomes turgid because the cell wall resists expansion. In a solution of lower water potential: an animal cell shrinks; a plant cell is plasmolysed
• No net change in mass or length of plant tissue means the solution has the same water potential as the tissue
• Cube: surface area = 6 × side², volume = side³, so surface area ÷ volume = 6 ÷ side; the ratio falls as size increases

The mitotic cell cycle

Replication and division of nuclei and cells

• Interphase: G₁ (growth, making proteins and organelles), S (DNA replication), G₂ (more growth and preparation for mitosis)
• The mass of DNA in a cell doubles during S phase and returns to the original value in each daughter cell
• Mitosis is needed for growth of multicellular organisms, replacement of damaged or dead cells, repair of tissues and asexual reproduction
• Telomeres are repeated non-coding DNA sequences at the ends of chromosomes; a little DNA is lost from the ends at each replication, and telomeres mean that no genes are lost
• Stem cells can divide by mitosis many times; some daughter cells stay as stem cells and others specialise to replace cells and repair tissue
• Tumour: mutations in genes that control the cell cycle → uncontrolled mitosis → a mass of abnormal cells

Chromosome behaviour in mitosis

• Prophase: chromosomes condense and become visible as two chromatids; the nuclear envelope breaks down; the spindle starts to form
• Metaphase: chromosomes line up along the equator of the cell, with spindle fibres attached to their centromeres
• Anaphase: centromeres divide; sister chromatids are pulled to opposite poles, centromere first, giving V shapes
• Telophase: chromatids reach the poles and uncoil; nuclear envelopes re-form; the spindle breaks down
• Cytokinesis in animal cells: the cell surface membrane pinches inwards. In plant cells: a cell plate forms across the middle and a new cell wall is built
• Animal cells have centrioles at the poles of the spindle; plant cells form a spindle without centrioles
• Count chromosomes by counting centromeres: once the centromere divides, each chromatid counts as a chromosome

Nucleic acids and protein synthesis

Structure of nucleic acids and replication of DNA

• Purines (double ring): adenine and guanine. Pyrimidines (single ring): cytosine, thymine and uracil.
• A pairs with T by 2 hydrogen bonds; C pairs with G by 3 hydrogen bonds.
• In double-stranded DNA, %A = %T and %C = %G, so purines are always 50% of the bases.
• DNA polymerase adds nucleotides only in the 5′ to 3′ direction.
• Leading strand: made continuously. Lagging strand: made in short fragments, which DNA ligase joins.
• Replication takes place in the S phase of the cell cycle.

Protein synthesis

• One triplet (codon) = 3 bases = 1 amino acid; a stop codon codes for no amino acid.
• mRNA is complementary to the template (transcribed) strand, with U in place of T.
• The tRNA anticodon is complementary to the mRNA codon.
• Gene mutation: a change in the sequence of base pairs in DNA, which may alter the polypeptide.
• Substitution: changes one triplet, so at most one amino acid changes (or none, or a stop codon forms).
• Deletion or insertion of one nucleotide: frameshift, so every triplet after it is changed.

Transport in plants

Structure of transport tissues

• Root: xylem in the centre in a star or cross shape, phloem between the arms, endodermis around the outside.
• Stem: vascular bundles in a ring, xylem on the inner side and phloem on the outer side.
• Leaf: in each vascular bundle, xylem towards the upper surface and phloem towards the lower surface.
• Lignin: strengthens xylem walls against collapse under tension and makes them waterproof.
• Pits: gaps in the lignin that let water move sideways between vessels.
• Companion cell: nucleus, dense cytoplasm, many mitochondria, joined to the sieve tube element by plasmodesmata.

Transport mechanisms

• Casparian strip: a band of waterproof suberin in the walls of endodermis cells.
• Cohesion: water molecules hold together by hydrogen bonds, so the column is pulled up unbroken.
• Adhesion: water molecules are attracted to the cellulose in the xylem walls.
• Loading: companion cells pump H⁺ out using ATP; H⁺ flows back in through cotransporter proteins, bringing sucrose with it.
• Sucrose lowers the water potential in the sieve tube, water enters by osmosis and the hydrostatic pressure rises.
• Source: where assimilates are loaded (such as a mature leaf). Sink: where they are removed (such as roots, seeds, growing buds).
• Xerophyte leaves: a thick cuticle reduces water loss through the surface; sunken stomata, hairs and rolled leaves trap humid air and lower the water potential gradient.

Transport in mammals

The circulatory system

• Pulmonary artery: deoxygenated blood from the heart to the lungs. Pulmonary vein: oxygenated blood from the lungs to the heart.
• Aorta: oxygenated blood from the left ventricle to the body. Vena cava: deoxygenated blood from the body to the right atrium.
• Elastic arteries (such as the aorta): much elastic tissue, which stretches and recoils to smooth the flow. Muscular arteries: more smooth muscle, to control flow to organs.
• Veins: thin wall, wide lumen and valves, for blood at low pressure.
• Capillaries: wall one endothelial cell thick, for a short diffusion distance.
• Tissue fluid is plasma without most of the proteins, which are too large to leave the capillary.
• Water in blood: a good solvent for transport, and a high specific heat capacity for carrying heat.

Transport of oxygen and carbon dioxide

• CO₂ + H₂O → H₂CO₃ → H⁺ + HCO₃⁻ (first step catalysed by carbonic anhydrase).
• H⁺ + haemoglobin → haemoglobinic acid, which keeps the pH steady.
• Chloride shift: HCO₃⁻ diffuses out of the red cell into the plasma and Cl⁻ moves in to keep the charge balanced.
• Carbon dioxide is carried mostly as HCO₃⁻ in the plasma, with a smaller part as carbaminohaemoglobin and a little dissolved in the plasma.
• Carbaminohaemoglobin: CO₂ bound to the amine groups of haemoglobin, not to the haem.
• Bohr shift: at high CO₂ the curve moves to the right, so haemoglobin has a lower affinity for oxygen.

The heart

• A valve opens when the pressure behind it is higher than the pressure in front, and closes when the pressure in front is higher.
• Atrial walls are thin (they pump only into the ventricles); ventricle walls are thick (they pump out of the heart).
• The left ventricle wall is thicker than the right: it pumps against the higher resistance of the systemic circulation.
• Sinoatrial node (SAN): starts the wave of excitation, which spreads over the atria.
• Atrioventricular node (AVN): passes the wave on after a short delay, so the atria empty first.
• Purkyne tissue: carries the wave down the septum to the apex, so the ventricles contract from the bottom up.
• Heart rate (beats per minute) = 60 ÷ time for one cardiac cycle in seconds.

Gas exchange

The gas exchange system

• Cartilage: C-shaped rings in the trachea, irregular plates in the bronchi, none in the bronchioles.
• Goblet cells and mucous glands secrete mucus, which traps dust and pathogens.
• Ciliated epithelial cells beat to sweep the mucus up towards the throat.
• Smooth muscle: contracts to narrow the airway and relaxes to widen it.
• Elastic fibres: stretch when breathing in and recoil when breathing out. They do not contract.
• Squamous epithelium: very thin, flat cells that give a short diffusion distance.
• Rate of diffusion is higher with a large surface area, a steep concentration gradient and a short distance.

Infectious diseases

Infectious diseases

• Cholera: the bacterium Vibrio cholerae; spread by water or food contaminated with faeces.
• Malaria: protoctists of the genus Plasmodium (falciparum, malariae, ovale, vivax); spread by the bite of a female Anopheles mosquito, the vector.
• TB: the bacteria Mycobacterium tuberculosis (airborne droplets) and Mycobacterium bovis (also from infected cattle, in unpasteurised milk or undercooked meat).
• HIV/AIDS: the human immunodeficiency virus; spread in body fluids by unprotected sex, shared needles, blood transfusion, and from mother to child across the placenta, at birth or in breast milk.
• Antibiotics can treat cholera and TB (bacteria) but not HIV (a virus).
• Vaccines: the BCG vaccine gives some protection against TB; there is no vaccine in use for HIV; a highly effective malaria vaccine is hard to make because the parasite has many stages and antigens, and the vaccines now used give only partial protection.

Antibiotics

• Penicillin inhibits the enzymes that form cross-links in the peptidoglycan cell wall; it acts only on growing bacteria.
• Human cells have no cell wall, so penicillin does not harm them.
• Resistance comes from a random mutation; the antibiotic is the selective agent and does not cause the mutation.
• Vertical transmission: resistance genes pass to daughter cells at division.
• Horizontal transmission: resistance genes on plasmids pass between bacteria, even of different species.
• To reduce resistance: use antibiotics only when needed, finish the course, do not use them for viral infections, and use more than one antibiotic together where suitable.

Immunity

The immune system

• Phagocytosis: attraction to the pathogen, attachment, engulfing into a phagocytic vacuole, fusion with lysosomes, digestion by enzymes.
• Neutrophils: short-lived, travel in the blood. Macrophages: long-lived, stay in tissues and present antigens to lymphocytes.
• T-helper cells release cytokines that stimulate B-lymphocytes to divide and macrophages to carry out more phagocytosis.
• T-killer cells attach to infected body cells and release toxins that kill them.
• Activated B-lymphocytes divide to form plasma cells, which secrete antibodies, and memory cells.
• Secondary response: shorter delay, faster rise and much higher antibody concentration than the primary response.

Antibodies and vaccination

• Antibody actions: agglutination (clumping pathogens), neutralising toxins, blocking pathogens from entering cells, and marking pathogens for phagocytes.
• Hinge region: gives flexibility, so the two sites can bind antigens at different distances apart.
• Hybridoma method: inject a mouse with the antigen, take plasma cells from its spleen, fuse them with myeloma cells, select and clone the hybridoma that makes the antibody wanted.
• Monoclonal antibodies in diagnosis: labelled antibodies show where an antigen is, as in pregnancy tests. In treatment: they bind to one target, such as a receptor on cancer cells.
• Active immunity: slow to start, memory cells made, long-lasting. Passive immunity: immediate, no memory cells, short-lived.
• Natural: by infection, or from mother across the placenta or in milk. Artificial: by vaccination or by injection of antibodies.
• Herd immunity: when most people are immune, the pathogen is rarely passed on, so the unvaccinated are protected too.