AQA A-level Biology Paper 1 Comprehensive Study Notes

Biological Molecules

Monomers and Polymers: - Monomers are smaller units from which larger molecules (polymers) are made (e.g., amino acids, nucleotides, and monosaccharides). - Polymers are molecules made from a large number of monomers joined together. - A condensation reaction joins two molecules together with the formation of a chemical bond and involves the elimination of a molecule of water. - A hydrolysis reaction breaks a chemical bond between two molecules and involves the use of a water molecule.
Carbohydrates: - Monosaccharides are the monomers from which larger carbohydrates are made. Common examples include glucose, galactose, and fructose. - Glucose has two isomers: $\alpha$ -glucose and $\beta$ -glucose. In $\alpha$ -glucose, the hydroxyl group ( $-OH$ ) on carbon-1 is below the plane of the ring; in $\beta$ -glucose, it is above. - Glycosidic bonds are formed by condensation reactions between monosaccharides. - Disaccharides: - Maltose: formed by condensation of two glucose molecules. - Sucrose: formed by condensation of a glucose molecule and a fructose molecule. - Lactose: formed by condensation of a glucose molecule and a galactose molecule. - Polysaccharides: - Starch: Composed of $\alpha$ -glucose. Contains amylose (unbranched, helical 1,4-glycosidic bonds) and amylopectin (branched 1,4 and 1,6-glycosidic bonds). Function: Insoluble energy storage in plants. - Glycogen: Composed of $\alpha$ -glucose. Highly branched (many 1,6-glycosidic bonds). Function: Energy storage in animals and bacteria; branching allows for rapid hydrolysis to glucose. - Cellulose: Composed of $\beta$ -glucose. Long, straight, unbranched chains. Chains run parallel to each other and are linked by hydrogen bonds to form strong microfibrils. Function: Structural support in plant cell walls.
Lipids: - Triglycerides: Formed by the condensation of one molecule of glycerol and three molecules of fatty acids, forming three ester bonds. Their fatty acid R-groups can be saturated (no $C=C$ double bonds) or unsaturated (contain $C=C$ double bonds). - Phospholipids: Formed by the condensation of one molecule of glycerol, two fatty acids, and a phosphate group. They feature a hydrophilic head (phosphate) and hydrophobic tails (fatty acids). - Identification: The emulsion test (add ethanol, then water; a white/milky emulsion indicates presence).
Proteins: - Amino Acids: The monomers of proteins. Structure includes an amine group ( $-NH_2$ ), a carboxyl group ( $-COOH$ ), a hydrogen atom, and a variable R-group attached to a central carbon. - Peptide bond: Formed by condensation between the amine group of one amino acid and the carboxyl group of another. - Structure levels: - Primary: The sequence of amino acids in a polypeptide chain. - Secondary: The folding or coiling into $\alpha$ -helices or $\beta$ -pleated sheets, held by hydrogen bonds. - Tertiary: Further folding to create a specific 3D shape, stabilized by ionic bonds, disulfide bridges, and hydrogen bonds. - Quaternary: Multiple polypeptide chains linked together. - Enzymes: Biological catalysts that lower activation energy ( $E_a$ ). The induced-fit model describes how the active site changes shape slightly to fit the substrate, putting strain on bonds.
Nucleic Acids: - DNA and RNA are polymers of nucleotides. A nucleotide consists of a pentose sugar, a nitrogen-containing organic base, and a phosphate group. - DNA: Deoxyribose sugar, bases Adenine ( $A$ ), Cytosine ( $C$ ), Guanine ( $G$ ), Thymine ( $T$ ). Double helix structure with two antiparallel strands held by hydrogen bonds between complementary bases ( $A-T$ and $C-G$ ). - RNA: Ribose sugar, bases $A$ , $C$ , $G$ , and Uracil ( $U$ ). Usually a shorter, single-stranded polynucleotide. - Semi-Conservative Replication: DNA helicase breaks hydrogen bonds to unwind the double helix. Free nucleotides align with complementary bases and DNA polymerase joins them via phosphodiester bonds.
ATP (Adenosine Triphosphate): - Structure: Ribose, adenine, and three phosphate groups. - Hydrolysis: $ATP + H_2O \rightarrow ADP + P_i + \text{energy}$ (catalyzed by ATP hydrolase). The released inorganic phosphate ( $P_i$ ) can phosphorylate other compounds to make them more reactive. - Resynthesis: Condensation of $ADP$ and $P_i$ during respiration or photosynthesis (catalyzed by ATP synthase).
Water and Inorganic Ions: - Water: A metabolite in condensation/hydrolysis; a solvent; high high specific heat capacity (buffers temperature); high latent heat of vaporization (cooling effect); cohesive (supports columns of water in plants). - Inorganic Ions: Occur in solution in the cytoplasm and body fluids. Examples: $Fe^{2+}$ in hemoglobin, $Na^{+}$ in co-transport, $PO_4^{3-}$ in DNA/ATP, and $H^{+}$ determining pH.

Cell Structure and Transport

Eukaryotic Cells: - Nucleus: Contains genetic material; nucleolus produces ribosomes; pores allow mRNA exit. - Mitochondria: Site of aerobic respiration ( $ATP$ production). Features cristae (inner folds) and the matrix. - Chloroplasts: Site of photosynthesis in plants/algae. Contains thylakoids (stacked as grana) and stroma. - Endoplasmic Reticulum (ER): Rough ER (ribosomes for protein synthesis); Smooth ER (lipid synthesis). - Golgi Apparatus: Modifies and packages proteins/lipids into vesicles. - Lysosomes: Contain lysozymes (digestive enzymes).
Cell Fractionation: - Step 1: Homogenization (breaking cells in a cold, isotonic, buffered solution). - Step 2: Filtration (removing large debris). - Step 3: Ultracentrifugation (spinning at increasing speeds). The order of sediment (pellet) formation: Nuclei, then Mitochondria/Chloroplasts, then Lysosomes, then Ribosomes.
Microscopy: - Magnification Formula: $M = \frac{\text{Image Size (I)}}{\text{Actual Size (A)}}$ . - Optical (Light) Microscope: Lower resolution due to long wavelength of light; can view live specimens. - Electron Microscope (TEM/SEM): High resolution due to short wavelength of electrons. TEM (Transmission) shows internal structures (requires thin specimens); SEM (Scanning) shows 3D surface images.
Cell Membrane: - Fluid Mosaic Model: Phospholipid bilayer with embedded proteins, glycoproteins, glycolipids, and cholesterol. - Transport Mechanisms: - Simple Diffusion: Net movement of small/non-polar molecules down a concentration gradient. - Facilitated Diffusion: Movement via channel or carrier proteins. - Osmosis: Diffusion of water from an area of higher water potential (closer to $0\,kPa$ ) to lower water potential across a selectively permeable membrane. - Active Transport: Movement against a concentration gradient using carrier proteins and $ATP$ . - Co-transport: e.g., sodium/glucose transport. Sodium is actively pumped out of ileum cells to create a gradient; sodium then diffuses back in through a co-transporter protein, bringing glucose with it.

The Immune Response

Non-Specific Defense: - Phagocytosis: A phagocyte recognizes foreign antigens on a pathogen, engulfs it into a phagosome, and fuses with a lysosome which releases enzymes to hydrolyze the pathogen.
Specific Defense: - Antigen-Presenting Cells (APCs): Cells like phagocytes present foreign antigens on their surface. - T-lymphocytes (Cellular Response): Helper T-cells ( $T_H$ ) bind to APCs and release cytokines to activate B-cells and Cytotoxic T-cells ( $T_C$ ). $T_C$ cells kill infected cells by secreting perforin to create holes in cell membranes. - B-lymphocytes (Humoral Response): B-cells are activated by $T_H$ cells. Clonal selection leads to the production of Plasma cells (which secrete specific antibodies) and Memory cells (which provide long-term immunity).
Antibodies: - Proteins with a quaternary structure consisting of four polypeptide chains (two heavy, two light). - They have a constant region and a specific variable region (antigen-binding site). - Function: Agglutination (clumping pathogens together) and acting as markers for phagocytes.
Vaccines and Immunity: - Vaccines contain dead or inactive pathogens to trigger a primary response and create memory cells without causing disease. - Passive Immunity: Introduction of antibodies from an outside source (short-term, no memory). - Active Immunity: Immune system produces its own antibodies after exposure to antigen (long-term, memory formed).
HIV and ELISA: - HIV structure: Lipid envelope, attachment proteins, capsid, RNA, and reverse transcriptase. - HIV replication: Infects Helper T-cells; reverse transcriptase converts RNA to DNA, which is inserted into host DNA. - ELISA Test: Uses monoclonal antibodies to detect the presence of specific antigens or antibodies in a sample (indicated by a color change).

Exchange and Transport Systems

Gas Exchange: - Surface Area to Volume Ratio ( $SA:V$ ): Smaller organisms have a larger $SA:V$ , allowing for simple diffusion. Larger organisms require specialized systems. - Fish: Counter-current system where blood and water flow in opposite directions across the lamellae. This maintains a concentration gradient for oxygen across the entire length of the gill. - Insects: Spiracles lead to tracheae and tracheoles, delivering oxygen directly to tissues. - Plants: Gas exchange occurs via stomata controlled by guard cells. - Humans: Alveoli provide a large surface area, short diffusion pathway (one cell thick), and steep concentration gradient (via ventilation and blood flow).
Digestion and Absorption: - Amylase (salivary/pancreatic) hydrolyzes starch to maltose; membrane-bound disaccharidases hydrolyze disaccharides to monosaccharides. - Lipids: Emulsified by bile salts into micelles; lipase hydrolyzes triglycerides into monoglycerides and fatty acids. Micelles transport these to the ileum membrane for absorption. - Proteins: Endopeptidases (hydrolyze internal bonds), exopeptidases (hydrolyze terminal bonds), and dipeptidases (hydrolyze dipeptides).
Mass Transport in Animals: - Hemoglobin: Protein with four heme groups that binds oxygen. High affinity in lungs (loading); low affinity in tissues (unloading). - Bohr Effect: High $CO_2$ concentration reduces hemoglobin's affinity for oxygen, shifting the dissociation curve to the right. - Cardiac Cycle: Atrial systole (atria contract, AV valves open), Ventricular systole (ventricles contract, AV valves close, SL valves open), Diastole (heart relaxes). - Cardiac Output: $\text{Cardiac Output} = \text{Heart Rate} \times \text{Stroke Volume}$ .
Mass Transport in Plants: - Xylem (Transpiration): Cohesion-tension theory. Water evaporates from leaves (transpiration), creating tension. Hydrogen bonding (cohesion) pulls a continuous column of water up the xylem. - Phloem (Translocation): Mass flow hypothesis. Sugars are actively loaded into the phloem at the source, lowering water potential and causing water to enter from the xylem. This creates high hydrostatic pressure, forcing the sap toward the sink.