CAPE Biology Unit 2 Complete Study Guide

Modules and Topics Overview (Sperwin Zinger - CAPE Biology Unit Two)

• Module One: Bioenergetics and Conservation

  • Topic 1: Photosynthesis and ATP Synthesis.

  • Topic 2: Cellular Respiration and ATP Synthesis.

  • Topic 3: Energy Flow and Nutrient Cycling.

  • Topic 4: Ecological Systems, Biodiversity, and Conservations.

• Module Two: Biosystems Maintenance

  • Topic 1: The Uptake and Transport of Water and Minerals.

  • Topic 2: Transport in the Phloem.

  • Topic 3: The Circulatory System of Mammals.

  • Topic 4: Homeostasis and Hormonal Action.

  • Topic 5: The Kidney, Excretion, and Osmoregulation.

  • Topic 6: Nervous Coordination.

• Module Three: Applications of Biology

  • Topic 1: Health and Disease.

  • Topic 2: Immunology.

  • Topic 3: Social and Preventative Medicine.

  • Topic 4: Substance Abuse.

Topic 1: Photosynthesis and ATP Synthesis

• Photosynthesis Definition: A process where autotrophs (producers) take in inorganic molecules to produce organic substances, such as carbohydrates. These contain trapped energy released via respiration.

• ATP (Adenosine Triphosphate): The intracellular energy currency in all organisms. Structure includes a nitrogenous base (adenine), a ribose sugar, and three inorganic phosphate groups ($Pi$).

• The Photosynthesis Equation:

  • Word: Carbon dioxide + Water (in the presence of light/chlorophyll) $\rightarrow$ Glucose + Oxygen.

  • Chemical: $6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$

• Stages of Photosynthesis:

  • Light-Dependent (Thylakoids): Uses light to break water molecules (photolysis). Oxygen diffuses out. Hydrogen combines with CO2.

  • Light-Independent (Stroma): Also known as the Calvin Cycle. Fixes carbon dioxide into glucose.

• The Dicotyledonous Leaf Internal Structure:

  • Upper Epidermis: Transparent thin layer coated with a watertight waxy cuticle. Reduces water loss and allows sunlight penetration.

  • Lower Epidermis: Contains guard cells forming stomata. Walls are unevenly thickened; they absorb water via osmosis to curve and open stomata for diffusion and transpiration.

  • Spongy Mesophyll: Loosely packed with air spaces for gas exchange between stomata and palisade cells.

  • Palisade Mesophyll: Cylindrical, upright cells containing a large number of chloroplasts. Features a large vacuole to push chloroplasts to the outer edges (maximizing light exposure). Cells have thin walls for efficient gas diffusion.

• Chloroplast Structure: Double-membraned organelle containing inner membranes (lamellae) and sac stacks (grana) made of thylakoids. The thylakoid lumen holds $H^+$ ions for ATP production.

• Photophosphorylation:

  • Defined as using light energy to attach a phosphate group to ADP, creating ATP ($ADP + Pi \rightarrow ATP$).

  • Involves an Electron Transport Chain (ETC) in thylakoids. Energy comes from photons caught by the antenna complex of a Photosystem (PSI and PSII).

• Cyclic vs. Non-Cyclic Photophosphorylation:

  • Cyclic: Involves only PSI. Electrons return to the original chlorophyll. Produces ATP only. Predominates in anaerobic conditions.

  • Non-Cyclic: Involves PSI and PSII. Requires an electron donor (water). Produces both ATP and reduced NADP (NADPH). Releases Oxygen due to photolysis. Predominates in aerobic conditions.

• The Calvin Cycle Stages:

  1. Carbon Fixation (Carboxylation): $CO_2$ combines with the pentose sugar RuBP ($5C$) catalyzed by the enzyme RUBISCO (ribulose biphosphate carboxylase) to form a $6C$ intermediate that breaks into two $3C$ acids (phosphoglyceric acid or PGA).

  2. Reduction: ATP and NADPH convert PGA into G3P (triose phosphate). NADPH donates electrons.

  3. Regeneration: ATP is used to recycle unused G3P back into RuBP.

  • Purpose: To create glucose ($C_6H_{12}O_6$), fructose, or sucrose.

• Limiting Factors:

  • Light Intensity: Reaches a saturation point where all chlorophyll molecules are occupied.

  • $CO_2$ Concentration: Limited concentration slows the Calvin Cycle.

  • Temperature: Optimal at $25\text{-}35^{\circ}C$. Excessive heat causes denaturation of RUBISCO, leading to photorespiration (wastefully combining RuBP with Oxygen).

Topic 2: Cellular Respiration and ATP Synthesis

• Glycolysis (Cytosol): The "breaking apart of glucose."

  1. Phosphorylation: Glucose is phosphorylated to Glucose-6-P ($uses\,1\,ATP$), then isomerized to Fructose-6-P, then phosphorylated to Fructose Biphosphate ($uses\,1\,ATP$).

  2. Lysis: Fructose Biphosphate splits into two $3C$ sugars: G3P and DHAP (which rearranges into G3P).

  3. Oxidation: Two G3P molecules are oxidized by dehydrogenase enzymes using NAD as a coenzyme (catcher's mitt for $H$) to form NADH. This generates $4\,ATP$ via substrate-level phosphorylation.

  • Net Yield: $2\,ATP$ and $2\,NADH$ per glucose.

• Mitochondrion Structure:

  • Matrix: Fluid-filled space for Krebs cycle and Link reaction.

  • Inner Membrane: Contains ATP synthase and ETC carriers.

  • Cristae: Inward folds increasing surface area for ATP production.

• Aerobic Respiration Stages Post-Glycolysis:

  • Link Reaction (Oxidative Decarboxylation): Pyruvate ($3C$) enters the matrix, loses $CO_2$, and is oxidized (forming NADH) to become Acetyl CoA ($2C$).

  • Krebs Cycle: Acetyl CoA ($2C$) joins Oxaloacetate ($4C$) to form Citrate ($6C$). Through steps losing $2\,CO_2$, it reforms Oxaloacetate. Produces $3\,NADH$, $1\,FADH_2$, and $1\,ATP$ per turn (x2 per glucose).

  • Oxidative Phosphorylation: NADH ($yields\,2.5\,ATP$) and $FADH_2$ ($yields\,1.5\,ATP$) release electrons to the ETC. Energy pumps $H^+$ into the intermembrane space creating an electrochemical gradient. $H^+$ flows back through ATP synthase (chemiosmosis) to make ATP. Oxygen is the final electron acceptor, forming $H_2O$.

  • Total Energy Yield: Net $32\,ATP$ per glucose (Max $34\,ATP$).

• Anaerobic Respiration:

  • In Humans: Pyruvate is converted to Lactate to regenerate NAD. Excess leads to cramps; cleared by the liver via "Oxygen Debt."

  • In Yeast (Fermentation): Pyruvate is decarboxylated to Ethanal, then reduced to Ethanol ($C_2H_5OH$) and $CO_2$.

Topic 3: Energy Flow and Nutrient Cycling

• Ecological Terms:

  • Habitat: Where an organism lives.

  • Population: Same species group.

  • Community: Multiple species group.

  • Niche: Role in the environment.

  • Ecosystem: Dynamic of biotic and abiotic factors.

• Energy Transfer: Only $10\%$ of energy is transferred between trophic levels (Producer, Primary/Secondary/Tertiary/Quaternary Consumer).

• Productivity:

  • GPP (Gross Primary Productivity): Total chemical energy converted from sunlight.

  • NPP (Net Primary Productivity): $GPP - R\text{ (Respiration)}$. Represents stored biomass.

• Pyramids:

  • Pyramid of Numbers: Can be inverted (e.g., one tree supporting many insects).

  • Pyramid of Biomass: Measured in $g\,m^{-2}$.

  • Pyramid of Energy: Always standard shape due to energy loss.

• The Nitrogen Cycle:

  • Nitrogen Fixation: Rhizobium in legume nodules converts $N_2$ gas into reactive forms ($NH_4^+$).

  • Nitrification: Nitrosomonas and Nitrobacter convert Ammonium to Nitrites ($NO_2^-$) and then Nitrates ($NO_3^-$).

  • Denitrification: Bacteria return Nitrates to Nitrogen gas.

Topic 4: Ecological Systems and Biodiversity

• Biotic Interactions: Predation, Competition, Symbiosis (Parasitism, Commensalism, Mutualism, Altruism).

• Abiotic Factors: Light intensity, Temperature, pH, Salinity, Humidity, Wind speed, Topography, Edaphic (soil) factors.

• Case Study: Aripo Savannah Scientific Reserve (Trinidad):

  • Environment: Annual rainfall $2500\,mm$, humidity $>50\%$, acidic pH soil due to runoff, impermeable clay layer causing flooding/drying cycles.

  • Plants: Over 250 species. Cassytha (parasitic vine), Drosera capillaris (carnivorous sundew), Epiphytes, Rhizobium in legumes. Xerophytic adaptations (succulent tissue, stilted roots).

  • Threats: Squatting, poaching, quarrying, illegal timber removal (Galba, Cocorite palms).

• Biodiversity Maintenance:

  • Species Diversity: Variety of species in a biome.

  • Genetic Diversity: Variation in the gene pool.

  • Ecosystem Diversity: Variation in habitats (e.g., savannah, palm marsh, forest).

  • Conservation: In situ (on-site: National Parks) vs. Ex situ (off-site: Zoos, Seed banks).

Topic 5: Transport in Plants (Xylem and Phloem)

• Water Uptake: Inorganic ions (nitrates/magnesium) enter via active transport (using ATP) or facilitated diffusion. Water follows via osmosis due to a water potential gradient.

  • Symplast Pathway: Through cytoplasm and plasmodesmata.

  • Apoplast Pathway: Through cell walls. Blocked at the endodermis by the waterproof Casparian strip.

• Xylem Structure: Elements made of dead polymer lignin (annular or reticulated). Unsegmented tubes with pits.

• Ascent of Sap: Facilitated by capillarity (cohesion/adhesion), root pressure, and transpirational pull.

• Stomata Mechanics: Guard cells become turgid with $K^+$ influx, curving to open pores. Closed at night or when flaccid.

• Phloem Structure: Sieve tube elements (lacking many organelles) and companion cells (rich in mitochondria for loading).

• Translocation: High hydrostatic pressure at the source (leaves) pushes sucrose through the phloem to sinks (roots/fruits). Loading involves $H^+$ pumping to co-transport sucrose.

Topic 6: Mammalian Circulatory System

• Heart Structure: Double circulation (Pulmonary and Systemic). Valves: Atrioventricular (Tricuspid/Bicuspid) and Semi-lunar (Pulmonary/Aortic).

• Blood Vessels:

  • Arteries: Thick walls (tunica media density), small lumen, high pressure.

  • Veins: Thin walls, large lumen, valves to prevent backflow, low pressure.

  • Capillary: Single endothelial layer, $0.8\mu m$ diameter.

• Blood Cells: Erythrocytes ($7\mu m$ biconcave), Leucocytes (Lymphocytes, Neutrophils, Monocytes), Platelets.

• Cardiac Cycle Initiation:

  • SAN (Sino-atrial node) acts as the myogenic pacemaker.

  • Signal travels to AVN (Atrioventricular node), followed by a $0.3\,s$ delay for atrial emptying.

  • Impulse travels through Bundles of His and Purkyne fibres to ventricles.

• Haemoglobin ($Hb$): Sigmoidal dissociation curve. Exhibits positive cooperativity (allosteric effect). Bohr Effect: right-shift in high $CO_2$/low $pH$ (lower affinity, higher unloading).

Topic 7: Homeostasis and Coordination

• Homeostasis: Regulation of internal environment. Uses Negative Feedback (correcting to set point, e.g., body temp $37.5^{\circ}C$) and Positive Feedback (straying further, e.g., oxytocin in labor).

• Hormonal Action:

  • Steroid: Lipid-soluble, diffuses through membranes.

  • Non-steroid: Lipid-insoluble, binds to receptors, uses second messengers like $cAMP$.

• Pancreatic Action: Islets of Langerhans contain $\alpha\text{-cells}$ (Glucagon increases glucose via gluconeogenesis) and $\beta\text{-cells}$ (Insulin decreases glucose, activates GLUT4 transporters).

• Ripening: Ethylene ($C_2H_4$) is a gaseous plant hormone. Increases respiration rate and converts chloroplasts to chromoplasts.

• Nerve Impulse (The Neurone):

  • Resting Potential: $\approx -70\,mV$. Maintained by Sodium-Potassium pump ($3\,Na^+\text{ out}, 2\,K^+\text{ in}$).

  • Action Potential:

    1. Depolarization: $Na^+\text{ influx}$ takes potential to $+30\,mV$.

    2. Repolarization: $K^+\text{ efflux}$ lowers potential.

    3. Hyperpolarization: Potential dips below $-70\,mV$, entering the refractory period.

  • Saltatory Conduction: In myelinated axons, impulses "leap" between Nodes of Ranvier.

  • Synapse: Action potential reaches the bulb, $Ca^{2+}$ triggers neurotransmitter (Acetylcholine) release across the synaptic cleft ($20\text{-}50\,nm$). ACh is broken down by Acetylcholinesterase (AChE).

Topic 8: Excretion and Immunology

• Kidney Function:

  • Ultrafiltration: Glomerulus filters blood into Bowman’s capsule due to pressure (afferent lumen $>$ efferent).

  • Reabsorption (PCT): Glucose/ions reabsorbed via active transport ($Na/K\,\text{pump}$ and symport).

  • Osmoregulation: Loop of Henle uses a counter-current multiplier. ADH from pituitary adds aquaporins to collecting ducts to conserve water.

• Immunology:

  • Humoral Response: B-lymphocytes produce specific antibodies ($immunoglobulins$). Structure: Light/Heavy chains joined by disulphide bonds; constant and variable regions.

  • Cell-Mediated Response: T-lymphocytes (Killers and Helpers). Helpers secrete cytokines.

  • Monoclonal Antibodies: Formed from Hybridomas (B-cell fused with Cancer cell). Used in MabThera (Rituximab) for cancer and pregnancy tests.

  • Vaccines: Artificially acquired active immunity (e.g., attenuated, inactivated, mRNA).

Topic 9: Disease and Substance Abuse

• Disease Data: Incidence (new cases) vs. Prevalence (current cases). Mortality rate (deaths per year).

• Viral Infections:

  • Dengue: Vector is female Aedes aegypti mosquito.

  • HIV/AIDS: Invades CD4 T-cells. AIDS defined as $<200\,cells/mm^3$. No vaccine; AZT (azidothymidine) is a common treatment.

• Lifestyle Diseases: Obesity ($BMI \ge 30$). Hypertension ($>140/90\,mm\,Hg$). CHD and Atherosclerosis (LDLs and plaques).

• Substance Abuse:

  • Alcohol: Depressant. Ethanol converted to ethanoate in liver (hepatocytes). Long-term: Liver Cirrhosis.

  • Tobacco: components include Tar (emphysema), Carbon Monoxide (carboxyhaemoglobin), Nicotine (stimulant/addictive), and Particulates.

  • Nicotine: Resembles ACh; causes tachycardia and constricts vessels. Increases insulin resistance. Relaxes lower oesophageal sphincter.

  • Drug Dependency: Physical (strong withdrawal/anxiety) vs. Psychological (cravings based on mood).