CAPE Biology Unit 2 Complete Study Guide

Energy and Carbon in Living Systems

Sources of Energy and Carbon

• All organisms require both a source of energy and an carbon source for survival.

• Phototrophs: Organisms that obtain energy by absorbing light.

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

• Autotrophs: Organisms that absorb carbon dioxide ($CO_2$) and convert it into complex organic compounds (glucose, starch, proteins). Most use light energy to drive anabolic reactions.

• Heterotrophs: Organisms that obtain carbon by eating complex carbon-based organic compounds produced by others.

Types of Nutrition (Functional Categories)

• Photoautotrophs: Use light as energy and $CO_2$ as carbon. Examples include plants, algae, and blue-green bacteria.

• Chemoautotrophs: Use chemical reactions for energy and $CO_2$ as carbon. Found in deep-sea vent communities using sulfur/iron compounds or nitrifying bacteria in soil.

• Photoheterotrophs: Use light as energy but obtain carbon from organic compounds (e.g., purple non-sulfur bacteria).

• Chemoheterotrophs: Use chemical reactions for energy and obtain carbon from organic compounds. Includes all fungi, animals, and many bacteria/protoctists.

• ## Energy Flow and Transfer

  • Energy flow is unidirectional: Energy flows through living systems and is NOT recycled. It enters from the Sun and eventually leaves as heat radiated into space.

  • Respiration: The transfer of energy from complex organic compounds to ATP and heat. ATP ($Adenosine \, Triphosphate$) is the universal energy currency.

  • Endotherms: Birds and mammals that can retain some respiratory heat to maintain a constant body temperature.

  • Uses of Energy: Active transport, movement, biosynthesis (production of biological molecules like protein/DNA), growth, and reproduction.

ATP (Adenosine Triphosphate)

Structure and Properties

• ATP is a phosphorylated nucleotide.

• Composed of:

  • Adenine (nitrogenous base).

  • Ribose (5-carbon sugar).

  • Three phosphate groups.

• Adenosine: Adenine + Ribose.

• AMP/ADP/ATP: Based on 1, 2, or 3 phosphate groups respectively.

• It is small, soluble, and can diffuse easily through cells.

Production of ATP

• Produced via two main methods:

  1. Substrate-linked phosphorylation: Direct synthesis during a chemical reaction where energy in bonds is reorganized (occurs in glycolysis and Krebs cycle).

  2. Chemiosmotic phosphorylation: Uses a proton ($H^+$) gradient across a membrane (mitochondria/chloroplasts). Protons diffuse through ATP synthetase (also known as ATP synthase), which provides the energy to combine ADP and $P_i$.

• ## Fates of ATP

  • It is not stored. Cells maintain very little ATP and must constantly recycle it from ADP and $P_i$.

  • It is not transported between cells; it is produced locally within each cell.

  • Function: Provides energy for muscle contraction, active transport via carrier proteins, and activation of molecules (e.g., phosphorylating glucose in glycolysis).

Leaf Structure and Photosynthesis

Tissue Adaptations

• Upper Epidermis: Waxy cuticle reduces water loss; transparent to allow light through.

• Palisade Mesophyll: Cylindrical cells at right angles to the surface; contains many chloroplasts; large vacuoles push chloroplasts to cell edges for maximum light absorption.

• Spongy Mesophyll: Large air spaces allow fast diffusion of $CO<em>2$; also stores $CO</em>2$ when stomata are closed.

• Vascular bundle: Xylem supplies water/ions; Phloem transports sucrose/amino acids (assimilates) away.

• Lower Epidermis: Contains pairs of guard cells controlling stomata (pores) for gas exchange and transpiration.

Chloroplast Structure

• Envelope: Inner and outer phospholipid membranes.

• Stroma: Protein-rich fluid containing enzymes for the light-independent stage (Calvin cycle), DNA loops, and 70S ribosomes.

• Grana: Stacks of membranous sacs called thylakoids providing a large surface area for light absorption.

• Thylakoid membranes: Contain photosynthetic pigments, electron carriers, and ATP synthetase.

• ## The Process of Photosynthesis

  • General Equation: $nCO<em>2 + nH</em>2O \xrightarrow{light, \, pigments, \, enzymes} (CH<em>2O)</em>n + nO_2$

  • Light-Dependent Stage:

    • Occurs in the grana (thylakoids).

    • Involves photolysis of water: $2H<em>2O \to 4H^+ + 4e^- + O</em>2$.

    • Transfers light energy to chemical energy in ATP and reduced NADP.

  • Light-Independent Stage (Calvin Cycle):

    • Occurs in the stroma.

    • Fixes $CO_2$ into triose phosphate (TP) using ATP and reduced NADP.

    • RuBP (5C) + $CO_2$ $\xrightarrow{rubisco}$ 2x GP (3C) $\to$ 2x TP (3C).

Respiration

Introduction and Glycolysis

• Respiration: Stepwise breakdown of organic molecules catalyzed by enzymes to produce ATP.

• Glycolysis:

  • Occurs in the cytosol.

  • Converts glucose (6C) to pyruvate (3C).

  • Net gain: 2 ATP (via substrate-linked phosphorylation) and 2 reduced NAD.

Aerobic Respiration (In Mitochondria)

• Link Reaction: Pyruvate is decarboxylated ($CO_2$ removed) and dehydrogenated ($H$ removed) to form acetyl coenzyme A.

• Krebs Cycle: Occurs in the matrix. Acetyl CoA + Oxaloacetate (4C) $\to$ Citrate (6C). Series of reactions produce: $3 \, reduced \, NAD, 1 \, reduced \, FAD, 1 \, ATP \, and \, 2 \, CO_2$ per turn.

• Oxidative Phosphorylation: Occurs on the inner membrane (cristae). Reduced NAD/FAD release electrons to the Electron Transport Chain (ETC). Energy released pumps protons into the intermembrane space. Protons flow back through ATP synthetase to make ATP. Oxygen is the final electron acceptor, forming water ($H_2O$).

• ## Anaerobic Respiration

  • In Mammals: Pyruvate is reduced to lactate by lactate dehydrogenase to recycle NAD so glycolysis can continue. Creates an oxygen debt.

  • In Yeast: Pyruvate is decarboxylated to ethanal, then reduced to ethanol. Used in bread making (to produce $CO_2$) and brewing (to produce ethanol).

Ecosystems and Energy Flow

Trophic Levels

• Producers: Autotrophs (usually plants).

• Primary Consumers: Herbivores.

• Secondary/Tertiary Consumers: Carnivores.

• Decomposers: Break down dead matter to recycle nutrients ($N, \, P, \, S$).

Ecological Pyramids

• Pyramid of Numbers: Can be inverted if a single tree supports many insects.

• Pyramid of Biomass: Measures dry mass. Can be inverted in marine systems (phytoplankton vs zooplankton).

• Pyramid of Energy: Shows energy flow over time (units: $kJ \, m^{-2} \, y^{-1}$). Can never be inverted because energy is lost as heat at each level ($1^{st}$ and $2^{nd}$ Laws of Thermodynamics).

• ## Nitrogen Cycle

  • Fixation: $N_2$ gas $\to$ ammonia (by bacteria like Rhizobium in root nodules).

  • Nitrification: Ammonia $\to$ Nitrite $\to$ Nitrate (by bacteria like Nitrosomonas and Nitrobacter).

  • Denitrification: Nitrate $\to$ $N_2$ gas (by bacteria like Pseudomonas in anaerobic soils).

Transport in Plants

Xylem and Water Movement

• Xylem: Composed of dead vessel elements. Walls are thickened with lignin (provides support and prevents collapse).

• Transpiration Pull: Driven by evaporation of water from leaves. This creates tension that pulls a column of water up due to cohesion (hydrogen bonding between water molecules) and adhesion (bonding to cell walls).

• Apoplast Pathway: Water moves through cell walls.

• Symplast Pathway: Water moves through cytoplasm and plasmodesmata.

• ## Phloem and Translocation

  • Phloem: Transports assimilates (sucrose/amino acids). Living tissue made of sieve tube elements and companion cells.

  • Pressure Flow Mechanism:

    1. Loading: Sucrose actively pumped into sieve tubes at the source (leaves).

    2. Osmosis: Water follows by osmosis, creating high hydrostatic pressure.

    3. Flow: Sap flows down the pressure gradient to the sink (roots/fruits).

    4. Unloading: Sucrose removed at the sink, water follows by osmosis, lowering pressure.

The Mammalian Heart and Circulation

Double Circulation

• Pulmonary circulation: Heart to lungs to heart.

• Systemic circulation: Heart to body body to heart.

• Advantage: Allows blood to be pumped at higher pressure to the body and lower pressure to the lungs.

Cardiac Cycle

1. Atrial Systole: Atria contract, pushing blood into ventricles.

2. Ventricular Systole: Ventricles contract; AV valves (bicuspid/tricuspid) close (making the 'lub' sound); semi-lunar valves open; blood forced into aorta/pulmonary artery.

3. Diastole: Heart relaxes; semi-lunar valves close (making the 'dub' sound); heart fills with blood.

• ## Control of the Heart beat

  • Myogenic: Heartbeat starts in the muscle itself at the Sino-atrial node (SAN) (the pacemaker).

  • Impulse path: $SAN \to atria \to Atrioventricular node (AVN) \to Purkyne fibres \to base of ventricles$.

  • AVN imposes a delay to allow atria to finish contracting before ventricles start.

Homeostasis and Excretion

Principles

• Homeostasis: Maintaining a near-constant internal environment (e.g., temperature, blood glucose).

• Negative Feedback: A change in a factor triggers a response that reverses the change toward the set point.

Blood Glucose Control

• High glucose: $\beta$-cells in pancreas secrete insulin. Target cells (liver/muscle) increase glucose uptake and convert it to glycogen (glycogenesis).

• Low glucose: $\alpha$-cells in pancreas secrete glucagon. Liver converts glycogen to glucose (glycogenolysis) and makes new glucose from fats/proteins (gluconeogenesis).

• ## The Kidney and Excretion

  • Ultrafiltration: Occurs in the glomerulus. High blood pressure forces small molecules into the Bowman's capsule (forming filtrate).

  • Selective Reabsorption: Occurs in the Proximal Convoluted Tubule (PCT). Glucose and amino acids are reabsorbed into the blood via active transport.

  • Osmoregulation: Controlled by Anti-diuretic Hormone (ADH). High blood concentration triggers ADH release. ADH makes the collecting duct more permeable to water by inserting aquaporins, so more water is reabsorbed and urine becomes more concentrated.