CAPE Biology Unit 2 - Exhaustive Study Notes and Solution Bank

MODULE 1: BIOENERGETICS AND ECOLOGY

Photosynthesis: Light-Dependent and Light-Independent Reactions

• Transition from Light to Dark Reactions: The electrons from non-cyclic photophosphorylation pass into the Calvin cycle via the electron carrier $NADP$, which is reduced to $NADPH$.
• Photosystem II ($P_{680}$): During photosynthesis, $Ps_{680}$ emits electrons that will eventually generate reduced $NAD$ (specifically $NADPH$ in plants).
• The Thylakoid Membrane: This structure consists of membranes and is explicitly involved in the light-dependent reactions of photosynthesis.
• Antenna Complex: The role of the antenna complex in Photosystems I and II is to collect light energy and funnel it toward the reaction center.
• Photophosphorylation Products: The primary products of the light-dependent phase are $ATP$ and $NADPH$.
• Chloroplast Structure and Localisation:     * Ribulose bisphosphate carboxylase (Rubisco): This enzyme is found in the stroma (Region II in typical chloroplast diagrams).     * Photosystems: These are located in the thylakoid membranes (often labelled as structure Y or Z depending on the diagram).
• The Calvin Cycle (Light-Independent Reaction):     * Temperature Dependence: The cycle is temperature-dependent because the enzymes involved in the enzymatic reactions (like Rubisco) are affected by temperature changes.     * Carbon Fixation: Carbon dioxide is incorporated into the cycle at the stage where it reacts with Ribulose bisphosphate ($RuBP$) to form Glycerate phosphate ($GP$ or $PGA$).     * Intermediate Compounds: After about 20 seconds of the dark reaction, the sequence of intermediates identifies $X$ as Phosphoglyceric acid ($GP$) and $Y$ as Triose phosphate ($TP$).     * ATP Utilization: Energy in the form of $ATP$ enters the cycle at two points: the reduction of $GP$ to $TP$ (Triose Phosphate) and the regeneration of $RuBP$.     * Oxygen Inhibition: High oxygen concentration can limit photosynthesis because oxygen competes with carbon dioxide to combine with $RuBP$ (photorespiration), preventing the formation of glycerate phosphate.
• Limiting Factors:     * On a warm, sunny day, photosynthesis is most likely limited by carbon dioxide availability.     * On a graph of light intensity vs. rate, light is a limiting factor only during the initial steep, linear phase of the curve.     * Main factors affecting the rate: Light intensity, temperature, and carbon dioxide concentration.

Cellular Respiration: Aerobic and Anaerobic Pathways

• Glycolysis:     * Final products: Pyruvate, $ATP$, and $NADH$.     * Sequence: Glucose $\rightarrow$ Glucose-6-phosphate $\rightarrow$ Fructose-6-phosphate $\rightarrow$ Triose phosphate $\rightarrow$ Pyruvate.     * Location: Occurs in the cytoplasm.
• Mitochondrial Processes:     * Cristae Oxidation: NADH and FADH molecules enter the mitochondrial cristae to be oxidized.     * Matrix Substances: The matrix contains $ADP$, $ATP$, and Acetyl CoA.     * Mitochondrial Adaptations: Mitochondria in muscle cells have more cristae than skin cells to provide more $ATP$-ase (ATP synthase) for increased $ATP$ production.
• Krebs Cycle (Citric Acid Cycle):     * Main products include $FADH_2$, $ATP$, and reduced $NAD$.     * It is the pathway that contributes the most electrons to the electron transport chain ($ETC$).     * Decarboxylation occurs within the matrix during these reactions.
• Oxidative Phosphorylation and the ETC:     * The Role of Oxygen: Oxygen acts as the final electron acceptor in the electron transport chain, accepting hydrogen ions to form water ($H_2O$).     * Main Products: The two main products of oxidative phosphorylation in the mitochondrion are $ATP$ and water.     * Cofactors: Vitamin B acts as a cofactor in the electron transport chain.
• ATP Yield: In aerobic respiration, the maximum theoretical yield of $ATP$ from one molecule of glucose is $38$.
• Anaerobic Respiration:     * In Muscle Tissue: Strenuous contractions lead to lactate formation due to a low concentration of oxygen.     * In Yeast: Pyruvic acid is converted to ethanol and $CO_2$ with a net gain of $2\ ATP$. Decarboxylation occurs during the conversion of pyruvate to ethanal.     * Substrates and Products: The substrate is glucose; products are ethanol and $CO_2$ (in plants/yeast) or lactic acid (in animals).     * Yield: The maximum net $ATP$ produced per glucose molecule is $2$.

Ecology: Energy Flow and Nutrient Cycling

• Ecosystem Definitions:     * Ecosystem: The sum of producers + consumers + decomposers + non-living (abiotic) components.     * Ecological Niche: The specific way in which an organism exploits its environment.     * Dynamic Ecosystem: Represented by pioneer species interacting with the environment to colonize a new area.
• Trophic Levels and Energy Flow:     * Primary Production: Net primary production ($NPP$) is the new organic matter remaining after respiration and metabolism have been fueled.     * Energy Transfer Calculation: If total light is $1 \times 10^6\ kJ\,m^{-2}\,yr^{-1}$, and 1% is trapped in production, and 10% of that is transferred to primary consumers: $(1 \times 10^6) \times 0.01 \times 0.1 = 1 \times 10^3\ kJ\,m^{-2}\,yr^{-1}$.     * Energy Loss: Most energy is lost at the stage between sunlight and the primary producer (grass).
• Biological Pyramids:     * Pyramids of Numbers: Can be inverted (e.g., one tree supporting many insects/parasites).     * Pyramids of Energy: These are never inverted and provide the most accurate representation of energy flow.     * Limitations: It is difficult to assign omnivores to a single level; representative samples require time-consuming combustion; a single grass plant is technically given the same status as a large tree.
• Nutrient Cycling:     * Energy flows through an ecosystem (it is not recycled).     * Nutrients cycle within an ecosystem.     * Decomposition is the critical stage for nutrient cycling back to the abiotic environment.
• Nitrogen Cycle:     * Nitrification: Ammonium compounds $\rightarrow$ Nitrites $\rightarrow$ Nitrates ($NH_4^+ \rightarrow NO_2^- \rightarrow NO_3^-$).     * Denitrification: Conversion of nitrates back to atmospheric nitrogen gas ($N_2$).     * Nitrogen Fixation: Splitting nitrogen molecules to form ammonium or nitrates (done by bacteria like Rhizobium).
• Biodiversity and Conservation:     * Biodiversity: The variety of different life forms on earth, defined at genetic, species, and ecosystem levels.     * Methods of Conservation: Protected reserves, sperm banks, and botanic gardens.     * Values: Direct value (tourism income); Indirect value (erosion protection and removal of $CO_2$ from the atmosphere).     * Deforestation Risks: Leads to flooding due to soil erosion, loss of canopy (which breaks rain force), and disruption of the water cycle.     * Competitive Exclusion (Gause's Principle): No two species can coexist if they occupy the same niche.

Respirometer Experiments

• Calculating Respiration Rate:     * Formula: $\text{Rate} = \frac{\text{Volume of } O_2}{\text{time} \times \text{mass}}$.     * $Volume = \pi r^2 L$ where $r = 0.2\ mm$ (radius) and $L = 85\ mm$ (distance moved).     * Volume $\approx 10.68\ mm^3$.     * $\text{Rate} = \frac{10.68\ mm^3}{50\ s \times 1\ g} = 0.21\ mm^3\,g^{-1}\,s^{-1}$.
• Potassium Hydroxide ($KOH$) / Soda Lime: Used in respirometers to absorb carbon dioxide ($CO_2$) produced by the organisms, so that movement of the fluid indicates only oxygen ($O_2$) uptake.
• Equilibration: Apparatus is left in water for several minutes before readings to stabilize the temperature and pressure.
• Control: Glass beads are used in a control tube to ensure changes are due to biological respiration and not physical pressure fluctuations.

MODULE 2: MULTICELLULAR ORGANISMS

Plant Transport Systems

• Xylem Structure:     * Made of dead cells with lignified walls (annular, spiral, or pitted patterns).     * Facilitates the ascent of water via capillarity (narrow vessels) and transpiration pull.
• Phloem Structure and Function:     * Sieve Tube Elements: Lack a nucleus at maturity; have peripheral cytoplasm.     * Companion Cells: Connected to sieve tubes by plasmodesmata; rich in mitochondria and rough endoplasmic reticulum ($RER$) to provide energy/nutrients for loading.     * Loading: Sucrose is loaded into phloem vessels via active transport.     * Mass Flow Hypothesis: Sucrose moves in phloem down a hydrostatic pressure gradient from source to sink.
• Stomatal Mechanics: Influx of Potassium ions ($K^+$) into guard cells lowers water potential, causing water to enter by osmosis, making guard cells turgid and opening the pore.
• Water Pathways:     * Symplastic: Through cytoplasm and plasmodesmata.     * Apoplastic: Through cell walls (blocked by the Casparian strip in the endodermis).

Mammalian Circulatory System

• Blood Vessels:     * Arteries: Thick walls, many elastic fibres, and collagen to withstand high pressure; no valves.     * Veins: Thinner walls, fewer elastic fibres, have valves to prevent backflow.     * Tunica Externa: Made mainly of collagen fibres.
• The Heart:     * Sinoatrial Node (SA node): The pacemaker, located in the right atrium.     * Atrioventricular Node (AV node): Delays the electrical impulse to allow atria to empty before ventricles contract.     * Cardiac Cycle:         * The first heart sound ("lub") is the closure of AV valves.         * The second heart sound ("dub") is the closure of semilunar (aortic/pulmonary) valves.         * Pulse: A direct measure of heart rate, caused by ventricular systole.
• Blood Components:     * Erythrocytes: Red blood cells.     * Neutrophils: Phagocytic white blood cells with lobed nuclei.     * Lymphocytes: Non-granular white blood cells involved in specific immunity.     * Haemoglobin and Bohr Effect:         * Bohr Effect: Higher partial pressures of carbon dioxide ($pCO_2$) cause haemoglobin to release oxygen ($O_2$) more readily.         * Fetal haemoglobin has a higher affinity for oxygen than adult haemoglobin.

Homeostasis and Excretion

• Feedback Loops:     * Negative Feedback: Corrects deviations from a set point (e.g., blood glucose, temperature).     * Positive Feedback: Increases the deviation (e.g., generation of an action potential, child birth/labour).
• Control Center: Acts as a reference point to determine the action of the effector.
• Blood Glucose Regulation:     * When glucose is low: Glucagon is secreted by $\alpha$-cells in the pancreas; promotes glycogenolysis in the liver.     * When glucose is high: Insulin is secreted by $\beta$-cells; increases cell permeability to glucose and promotes glycogenesis.
• The Kidney and Nephron:     * Ultrafiltration: Occurs in the Bowman's capsule; the basement membrane prevents molecules larger than $68,000$ molecular mass from passing.     * Proximal Convoluted Tubule ($PCT$): Site of selective reabsorption; cells have a brush border (microvilli) and many mitochondria.     * Loop of Henlé: Descending limb is permeable to water (water potential of fluid becomes more negative as it descends).     * Distal Tubule and Collecting Duct: Target for Antidiuretic Hormone ($ADH$). $ADH$ increases permeability to water.     * Urine Volume: If $180\ L$ of filtrate is produced and $178.4\ L$ reabsorbed, urine volume is $1.6\ L$.
• Osmoregulation: Drinking large amounts of pure water causes a decrease in $ADH$ release and makes urine water potential less negative (more dilute).

Nervous Coordination

• Neurone Structure:     * Dendrites: Receive impulses.     * Axon: Transmits impulses.     * Myelin Sheath: Fatty insulation that speeds up transmission by allowing saltatory conduction ("jumping" between Nodes of Ranvier).
• Resting Potential: Inside is negative ($-70\ mV$) relative to outside. Maintained by the Sodium/Potassium ($Na^+/K^+$) pump (pumps $3\ Na^+$ out for every $2\ K^+$ in).
• Action Potential: Rapid influx of Sodium ions ($Na^+$) causes depolarization.
• Synapse: Transmission is one-way. Calcium ions ($Ca^{2+^{}}$ ) enter the presynaptic bulb to trigger neurotransmitter (e.g., Acetylcholine) release from vesicles into the synaptic cleft.

MODULE 3: HEALTH AND DISEASE

The Immune System

• Antigens: Cell surface proteins or substances that trigger an immune response.
• Leucocytes:     * T-lymphocytes: Mature in the thymus; involved in cell-mediated immunity.     * B-lymphocytes: Mature in bone marrow; differentiate into plasma cells that produce antibodies (humoral response).     * Phagocytes: Neutrophils and Macrophages; engulf and digest pathogens.
• Antibodies (Immunoglobulins):     * Structure: Two heavy chains, two light chains, variable region (binding site), hinge region (flexibility), and disulphide bridges.     * Types: $IgM$ is primary in the first response; $IgG$ is high in secondary responses.
• Immune Response:     * Primary Response: Slow; low concentration of antibodies.     * Secondary Response: Fast and intense due to activation of Memory Cells.
• Immunity Types:     * Natural Active: Result of an infection (e.g., Chicken Pox).     * Natural Passive: Maternal antibodies passing to the fetus.     * Artificial Active: Vaccination with attenuated pathogens; body makes its own antibodies.     * Artificial Passive: Injection of pre-made antibodies (e.g., tetanus antitoxin). Short-term because antibodies are broken down and no memory cells are made.
• Monoclonal Antibodies: Purified antibodies from a single B-cell clone. Used in pregnancy tests (detecting $HCG$), diagnosing diseases (AIDS, Dengue), and cancer treatment.

Infectious Diseases

• HIV/AIDS:     * Causative agent: Retrovirus (contains $RNA$ and reverse transcriptase).     * Target: Infected T-helper cells.     * Transmission: Blood, semen, vaginal fluids, breast milk.     * Resistance: Small percentage of people are resistant due to a mutation preventing HIV binding to T-cells.
• Dengue Fever:     * Causative agent: Virus.     * Vector: Aedes aegypti mosquito.     * Prevention: Cover water drums, use insect repellent, introduce fish to ponds (to eat larvae).

Non-Infectious and Lifestyle Diseases

• Definitions:     * Chronic: Develops slowly and persists for a long time.     * Degenerative: Gradual loss of function (e.g., Stroke).
• Obesity and Diet:     * Body Mass Index (BMI): $\frac{\text{Mass (kg)}}{\text{Height (m)}^2}$.     * Ranges: Normal ($18.6-24$); Overweight ($25-30$); Obese ($>30$).
• Diabetes:     * Type I: Insulin cannot be produced.     * Type II: Physiological disorder where cells become resistant to insulin; often dietary-linked.
• Cardiovascular Disease:     * Atherosclerosis: Build-up of plaque (cholesterol) in the artery walls.     * Hypertension: High blood pressure; can be caused by atherosclerosis or high aldosterone levels.
• Smoking Effects: Tar is a mutagen/carcinogen; causes increased mucus secretion; linked to lung cancer and emphysema.
• Alcohol Effects:     * Liver Disease: Fatty liver and inflammation are reversible; Cirrhosis (fibrous scar tissue) is irreversible.     * Neurological: Alcohol inhibits $ADH$ release (leading to dehydration), causes demyelination, and impairs judgment.
• Exercise Benefits: Increases stroke volume and cardiac output; increases $VO_{2}\ max$ (maximum oxygen uptake); improves resistance to infection.

Social and Statistical Factors in Health

• Incidence Rate: The rate of new cases in a population over a specific period.     * Calculation: If cases grow from $5000$ to $5600$ in a population of $456,600$, the incidence of new cases is $600$.     * Rate: $\frac{600}{456,600} \approx 0.13\%$.
• Health (WHO Definition): A state of complete physical, mental, and social/spiritual well-being, not just the absence of disease.
• Viral Disease Sprawl: Factors such as rural-urban migration causing overcrowding lead to the rapid spread of respiratory and other viral diseases in developing countries.