Study Guide: Biology Unit 2 for CAPE - Vocabulary Flashcards

ENERGY AND CARBON IN LIVING SYSTEMS

• Energy and Carbon Requirements: All living organisms necessitate a source of energy to perform work and a source of carbon to build biological molecules.

• Sources of Energy:

  • Phototrophs: Gain energy by absorbing light. This group includes plants, some prokaryotes (e.g., blue-greens), and some protoctists (e.g., seaweeds and algae).

  • Chemotrophs: Acquire energy from chemical reactions involving elements, simple inorganic compounds, or complex organic compounds.

• Sources of Carbon:

  • Autotrophs: Use inorganic carbon, specifically carbon dioxide ($CO_2$), and convert it into complex organic compounds like glucose, starch, and proteins. This process of converting inorganic carbon to organic forms is called carbon fixation.

  • Heterotrophs: Obtain carbon from pre-existing complex carbon-based compounds by consuming food.

• Nutritional Categories:

  • Photoautotrophs: Use light for energy and $CO_2$ for carbon (e.g., trees in Dominican elfin forests, Barbadian sugar cane).

  • Chemoautotrophs: Use chemical reactions for energy and $CO_2$ for carbon. Examples include nitrifying bacteria and vent communities in the Cayman Trench (found at depths below light reach) that utilize sulfur, iron, or nitrogen compounds.

  • Photoheterotrophs: Use light for energy but complex carbon compounds for carbon (e.g., purple non-sulfur bacteria).

  • Chemoheterotrophs: Use chemical reactions for energy and complex organic compounds for carbon (e.g., fungi, animals, many bacteria).

• Energy Flow Dynamics:

  • Energy flows linearly through systems and is not recycled. It enters from the Sun and is eventually radiated into space as infrared radiation.

  • Energy transfer is inefficient; much is lost as heat. Endotherms (birds and mammals) use some of this heat to maintain constant body temperature.

• Biological Energy Uses:

  • Active transport and movement.

  • Biosynthesis: Production of biological molecules.

  • Growth, reproduction, and raising compound energy levels for reactions.

ADENOSINE TRIPHOSPHATE (ATP)

• Basic Definition: ATP is the universal energy currency within the cells of all organisms.

• Structure: ATP is a phosphorylated nucleotide. It consists of the base adenine and ribose sugar (together forming the nucleoside adenosine) plus three phosphate groups.

• Characteristics:

  • It is small and soluble, allowing easy diffusion throughout the cell.

  • Phosphate bonds are unstable and break easily by hydrolysis, releasing energy in manageable "packets" suitable for anabolic reactions.

  • The total quantity in a human is about $50\,g$, which is turned over in seconds. Turnover is estimated at $8000\,g/h$.

• ATP Production Methods:

  • Substrate-linked Phosphorylation: Direct synthesis on an enzyme surface during glycolysis or the Krebs cycle.

  • Chemiosmotic Phosphorylation: ATP synthetase (or synthase) uses a proton ($H^+$) gradient established by active transport (pumping protons). The gradient is powered by oxidation/reduction (redox) reactions in mitochondrial and chloroplast membranes.

LEAF STRUCTURE AND ADAPTATIONS FOR PHOTOSYNTHESIS

• Tissue-Specific Functions:

  • Upper Epidermis: Secretes waxy cuticle; transparent to allow light through.

  • Palisade Mesophyll: Cylindrical cells packed with chloroplasts to maximize light absorption. Vacuoles push organelles to the cell edge.

  • Spongy Mesophyll: Large air spaces allow rapid diffusion of $CO_2$ and act as a reservoir.

  • Xylem and Phloem: Xylem supplies water and ions; phloem transports sucrose and amino acids (assimilates).

  • Lower Epidermis: Contains pairs of guard cells managing stomata for gas exchange ($CO_2$, $O_2$) and water vapor release.

• Chloroplast Structure:

  • Envelope: Outer and inner membranes controlling export of triose phosphate.

  • Stroma: Protein-rich region containing $70S$ ribosomes, DNA loops, and enzymes for carbon fixation.

  • Grana/Thylakoids: Membranous sacs providing surface area for light absorption and the electron transport chain (ETC).

THE MECHANISM OF PHOTOSYNTHESIS

• Summary Equation: $nCO_2 + nH_2O \xrightarrow{\text{light energy/chlorophyll}} (CH_2O)_n + nO_2$.

• Light-Dependent Stage (Grana):

  • Photolysis: Splitting of water into protons, electrons, and oxygen: $2H_2O \rightarrow 4H^+ + 4e^- + O_2$.

  • Photophosphorylation: Light excites electrons in Photosystem II ($P_{680}$) and Photosystem I ($P_{700}$). Non-cyclic flow moves electrons to NADP to form reduced NADP. Protons are pumped into the thylakoid space, driving ATP synthesis through ATP synthetase.

• Light-Independent Stage (Calvin Cycle) (Stroma):

  1. Carboxylation: Carbon dioxide ($1C$) combines with ribulose bisphosphate (RuBP, $5C$) catalyzed by the enzyme rubisco (ribulose bisphosphate carboxylase/oxygenase).

  2. This forms two molecules of glycerate 3-phosphate (GP or PGA, $3C$).

  3. Reduction: GP is reduced to triose phosphate (TP, $3C$) using ATP and reduced NADP from the light-dependent stage.

  4. Regeneration: Out of every $12$ TP, $10$ are used to regenerate $6$ molecules of RuBP via ATP. $2$ TP are used to make hexoses, starch, fatty acids, or amino acids.

CELLULAR RESPIRATION

• Overview: Respiration is the stepwise enzymatic breakdown of organic molecules (carbohydrates, fats, proteins) to transfer chemical energy to ATP and heat.

• Energy Density: Carbohydrate $16\,kJ/g$; lipid $39\,kJ/g$; protein $17\,kJ/g$.

• Stages of Aerobic Respiration:

  1. Glycolysis (Cytosol): Glucose ($6C$) is phosphorylated using $2$ ATP, lysed into two triose phosphates ($3C$), oxidized to produce $2$ reduced NAD, and undergoes substrate-linked phosphorylation to produce a net of $2$ ATP and $2$ Pyruvate.

  2. Link Reaction (Mitochondrial Matrix): Pyruvate ($3C$) is decarboxylated (removes $CO_2$) and dehydrogenated (removes $H$ to reduce NAD) to form Acetyl Coenzyme A ($2C$).

  3. Krebs Cycle (Mitochondrial Matrix): Acetyl CoA combines with oxaloacetate ($4C$) to form Citrate ($6C$). Reactions produce $2$ $CO_2$, $3$ reduced NAD, $1$ reduced FAD, and $1$ ATP per turn.

  4. Oxidative Phosphorylation (Cristae): Reduced NAD and FAD deliver electrons to the ETC. Energy from electron flow pumps protons into the intermembrane space. Protons flow back through ATP synthetase (chemiosmosis). Oxygen is the final electron acceptor ($O_2 + 4H^+ + 4e^- \rightarrow 2H_2O$). Total net ATP yield of aerobic respiration is approximately $30$.

ANAEROBIC RESPIRATION AND ECOLOGY

• Anaerobic Pathways:

  • Mammals: Pyruvate is reduced to lactate to recycle NAD, allowing glycolysis to continue. This creates an oxygen deficit and subsequent oxygen debt.

  • Yeast: Pyruvate is decarboxylated to ethanal and reduced to ethanol and $CO_2$. Used commercially in brewing and bread making.

• Ecology Concepts:

  • Trophic Levels: Producers (autotrophs), Consumers (heterotrophs), and Decomposers.

  • Pyramids: Numbers, Biomass (dry mass), and Energy ($kJ\,m^{-2}\,year^{-1}$). Energy pyramids are never inverted.

  • Nitrogen Cycle:

    • Nitrogen Fixation: $N_2 \rightarrow NH_3$ (via Rhizobium or lightning).

    • Nitrification: Ammonia ($NH_3$) oxidized to Nitrite ($NO_2^-$) by Nitrosomonas, and Nitrite to Nitrate ($NO_3^-$) by Nitrobacter.

    • Denitrification: Nitrate converted back to $N_2$ by Pseudomonas.

MAMMALIAN TRANSPORT AND HOMEOSTASIS

• Circulatory System: Closed, double circulation (pulmonary and systemic).

  • Red Blood Cells: Biconcave discs with no nucleus; transport oxygen via haemoglobin ($Hb + 4O_2 \rightleftharpoons HbO_8$).

  • Blood Vessels: Arteries (thick walls, high pressure), Capillaries (one-cell thick, exchange), and Veins (valves, low pressure).

  • Heart Control: Myogenic. SAN (pacemaker) initiates impulse; delayed at AVN; spreads via Purkyne tissue to ventricles.

• Homeostasis: Maintenance of steady internal state (negative feedback).

  • Blood Glucose: Controlled by Pancreas islets. Insulin ($\beta$ cells) lowers blood glucose via glycogenesis. Glucagon ($\alpha$ cells) raises it via glycogenolysis and gluconeogenesis.

  • Osmoregulation: Hypothalamus monitors water potential. ADH (Antidiuretic Hormone) from posterior pituitary increases collecting duct permeability to reabsorb water.

  • Kidney Function: Ultrafiltration in the glomerulus; selective reabsorption in the PCT (glucose, amino acids); water reabsorption in the Loop of Henle and Collecting Duct.

THE NERVOUS SYSTEM

• Transmission: Resting potential ($-70\,mV$) is maintained by the sodium-potassium pump. Action potential ($+40\,mV$) involves rapid $Na^+$ influx and subsequent $K^+$ efflux.

• Synapse: Cholinergic. Action potential triggers $Ca^{2+}$ entry, release of acetylcholine by exocytosis, and activation of post-synaptic receptors. Enzyme acetylcholinesterase breaks down the neurotransmitter to stop the signal.

HUMAN HEALTH APPLICATIONS

• Infectious Diseases:

  • Dengue Fever: RNA virus transmitted by the Aedes aegypti mosquito vector.

  • HIV/AIDS: Retrovirus infecting helper T-cells (CD4 proteins); transmitted via blood, sex, or birth.

• Chronic Diseases:

  • Atherosclerosis: Build-up of atheroma (plaques) in artery walls; leads to hypertension, CHD, and strokes.

  • COPD: Chronic obstructive pulmonary disease (bronchitis and emphysema) primarily caused by smoking.

• Immunology:

  • Active Immunity: Long-term; memory cells formed (natural via infection; artificial via vaccine).

  • Passive Immunity: Short-term; provides immediate antibodies (natural via placenta/milk; artificial via serum injection).