General Biology I: Exam 3 Study Guide (Chapters 8–11) – Metabolism, Cellular Respiration, Photosynthesis, and Cell Communication

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Chapter 8: An Introduction to Metabolism

Metabolism and Energy

Metabolism refers to all chemical reactions that occur within a living organism to maintain life. These reactions are organized into metabolic pathways, which can be classified as catabolic (breaking down molecules) or anabolic (building molecules).

Metabolism: The sum of all chemical reactions in an organism.
Catabolic pathway: Pathways that release energy by breaking down complex molecules into simpler compounds (e.g., cellular respiration).
Anabolic pathway: Pathways that consume energy to build complex molecules from simpler ones (e.g., protein synthesis).
Bioenergetics: The study of how organisms manage their energy resources.

Forms of Energy

Kinetic Energy: Energy associated with motion.
Potential Energy: Stored energy due to position or structure.
Thermal Energy: Kinetic energy associated with random movement of atoms or molecules.
Heat: Transfer of thermal energy from one object to another.
Chemical Energy: Potential energy available for release in a chemical reaction.

Thermodynamics in Biology

Thermodynamics: The study of energy transformations.
First Law of Thermodynamics: Energy cannot be created or destroyed, only transformed ().
Second Law of Thermodynamics: Every energy transfer increases the entropy (disorder) of the universe.
Entropy (S): A measure of disorder or randomness.

Free Energy and Spontaneity

Gibbs Free Energy (G): The energy in a system available to do work at constant temperature and pressure.
Equation:
Spontaneous Process: Occurs without energy input; (negative free energy change).
Non-spontaneous Process: Requires energy input; .
Higher free energy = less stable; lower free energy = more stable.

ATP and Energy Coupling

ATP (Adenosine Triphosphate): Main energy currency of the cell.
ATP hydrolysis releases energy ().
Energy Coupling: Using exergonic reactions to drive endergonic reactions.
ATP is used in transport work (e.g., pumping ions), mechanical work (e.g., muscle contraction), and chemical work (e.g., synthesis of macromolecules).
The ATP cycle involves continual regeneration of ATP from ADP and inorganic phosphate.

Enzymes and Regulation

Enzyme: Biological catalyst that speeds up reactions by lowering activation energy.
Substrate: The reactant an enzyme acts on.
Enzyme-Substrate Complex: Temporary complex formed when enzyme binds substrate.
Induced Fit: Enzyme changes shape to better fit the substrate.
Activation Energy (E_a): The energy required to start a reaction.
Competitive Inhibition: Inhibitor binds to active site; can be overcome by more substrate.
Noncompetitive Inhibition: Inhibitor binds elsewhere, changing enzyme shape; cannot be overcome by more substrate.
Cofactors: Non-protein helpers (may be inorganic or organic—coenzymes).
Allosteric Regulation: Regulatory molecules bind to a site other than the active site, affecting enzyme activity.
Cooperativity: Substrate binding increases enzyme activity at other active sites (seen in multi-subunit enzymes).

Table: Types of Enzyme Inhibition

Type	Binding Site	Effect	Overcome by Substrate?
Competitive	Active site	Blocks substrate	Yes
Noncompetitive	Allosteric site	Changes enzyme shape	No

Chapter 9: Cellular Respiration and Fermentation

Overview of Cellular Respiration

Cellular respiration is the process by which cells extract energy from glucose and other fuels to produce ATP. It can be aerobic (using oxygen) or anaerobic (without oxygen).

Cellular Respiration: Catabolic pathway for the production of ATP, with oxygen as the final electron acceptor.
Aerobic Respiration: Uses oxygen; most efficient ATP production.
Anaerobic Respiration: Uses other molecules as final electron acceptors.
Fermentation: Partial degradation of sugars without oxygen; produces less ATP.

Redox Reactions

Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Oxidizing Agent: Accepts electrons.
Reducing Agent: Donates electrons.
NAD+/NADH: Electron carrier; NADH is the reduced form.

Stages of Cellular Respiration

Glycolysis: Occurs in cytosol; splits glucose into 2 pyruvate, produces 2 ATP (substrate-level phosphorylation) and 2 NADH.
Pyruvate Oxidation: Pyruvate transported into mitochondria, converted to Acetyl CoA, producing NADH and CO2.
Citric Acid Cycle (Krebs Cycle): Completes breakdown of glucose; produces ATP, NADH, FADH2, and CO2.
Electron Transport Chain (ETC): Series of proteins in inner mitochondrial membrane; electrons from NADH and FADH2 pass through, creating H+ gradient.
Oxidative Phosphorylation: ATP synthase uses H+ gradient to make ATP (chemiosmosis).

Fermentation

Alcohol Fermentation: Pyruvate converted to ethanol; used by yeast (e.g., brewing, baking).
Lactic Acid Fermentation: Pyruvate reduced to lactate; used by muscle cells and some bacteria (e.g., yogurt production).

Key Molecules and Enzymes

Kinase: Enzyme that transfers phosphate groups.
Reductase: Enzyme that catalyzes reduction reactions.
Isomerase: Enzyme that rearranges molecules.
Phosphofructokinase: Key regulatory enzyme in glycolysis; inhibited by ATP and citrate.

Table: Summary of Cellular Respiration Steps

Process	Location	ATP Produced	NADH Produced	FADH2 Produced	CO2 Produced	O2 Required?
Glycolysis	Cytosol	2	2	0	0	No
Pyruvate Oxidation	Mitochondrial matrix	0	2	0	2	Yes
Citric Acid Cycle	Mitochondrial matrix	2	6	2	4	Yes
ETC & Chemiosmosis	Inner mitochondrial membrane	~26-28	0	0	0	Yes

Additional info: The total ATP yield per glucose is typically 30–32 ATP, but this can vary due to leaky membranes and shuttle systems.

Chapter 10: Photosynthesis

Overview and Structure

Photosynthesis is the process by which plants, algae, and some bacteria convert light energy into chemical energy stored in glucose. It occurs in chloroplasts, primarily in the mesophyll cells of leaves.

Chloroplast: Organelle where photosynthesis occurs.
Stomata: Pores for gas exchange (CO2 in, O2 out).
Thylakoid: Membranous sacs containing chlorophyll; site of light reactions.
Grana: Stacks of thylakoids.
Stroma: Fluid surrounding thylakoids; site of Calvin cycle.

Light and Pigments

Electromagnetic Spectrum: Range of all wavelengths of light; visible light is used in photosynthesis.
Chlorophyll a: Main pigment; absorbs blue-violet and red light.
Chlorophyll b and Carotenoids: Accessory pigments; broaden spectrum and provide photoprotection.
Photoprotection: Carotenoids dissipate excess energy as heat.
Light can be reflected, transmitted, or absorbed by pigments.

Stages of Photosynthesis

Light Reactions: Occur in thylakoid membranes; convert light energy to chemical energy (ATP, NADPH), release O2 from H2O.
Calvin Cycle: Occurs in stroma; uses ATP and NADPH to fix CO2 into G3P (a sugar).

Photosystems and Electron Flow

Photosystem II (PSII): Functions first; absorbs light, splits water, releases O2.
Photosystem I (PSI): Functions second; produces NADPH.
Linear Electron Flow: Produces ATP, NADPH, and O2.
Cyclic Electron Flow: Produces ATP only; no NADPH or O2.

Calvin Cycle and Carbon Fixation

Three phases: Carbon fixation, reduction, regeneration of RuBP.
Rubisco: Enzyme that fixes CO2; most abundant protein on Earth.
Three turns of the cycle produce one G3P; six turns for one glucose.
Consumes 9 ATP and 6 NADPH per G3P.

Adaptations in Plants

C3 Plants: Use Calvin cycle directly; susceptible to photorespiration.
C4 Plants: Use PEP carboxylase to fix CO2 in mesophyll cells, then Calvin cycle in bundle-sheath cells; reduces photorespiration.
CAM Plants: Open stomata at night, fix CO2 into organic acids; Calvin cycle during day.

Table: Comparison of C3, C4, and CAM Plants

Type	CO2 Fixation	Photorespiration	Adaptation
C3	Direct (Calvin cycle)	High	Cool, moist climates
C4	PEP carboxylase, then Calvin cycle	Low	Hot, dry climates
CAM	Night: organic acids; Day: Calvin cycle	Low	Arid environments

Chapter 11: Cell Communication

Types of Cell Signaling

Paracrine Signaling: Local signaling; cells secrete molecules affecting nearby cells.
Synaptic Signaling: Nerve cells release neurotransmitters across synapses.
Endocrine (Hormonal) Signaling: Long-distance; hormones travel via bloodstream to target cells.

Signal Reception and Transduction

Ligand: Signaling molecule that binds to a receptor.
Receptor: Protein that detects a signal molecule and initiates a response.
Transduction: Conversion of signal to a cellular response via a signal transduction pathway.
Response: Cellular activity triggered by the signal (e.g., gene expression, enzyme activation).

Types of Receptors

G Protein-Coupled Receptors (GPCRs): Activate G proteins, which relay signals to other proteins.
Receptor Tyrosine Kinases (RTKs): Dimerize and autophosphorylate, activating multiple pathways.
Ligand-Gated Ion Channel Receptors: Open or close in response to ligand binding, allowing ion flow.
Intracellular Receptors: Located in cytoplasm or nucleus; bind nonpolar hormones (e.g., steroids), often act as transcription factors.

Signal Transduction Pathways

Protein Kinases: Enzymes that phosphorylate proteins, often in a cascade (phosphorylation cascade).
Protein Phosphatases: Remove phosphate groups (dephosphorylation), turning off the signal.
Second Messengers: Small molecules (e.g., cAMP, Ca2+, IP3, DAG) that relay signals inside the cell.
Amplification: One signal molecule can activate many molecules in the pathway.
Specificity: Different cells respond differently to the same signal due to different proteins/pathways.
Termination: Signals are terminated by removal of ligand, dephosphorylation, or degradation of second messengers.

Table: Major Second Messengers

Second Messenger	Produced By	Main Effect
cAMP	Adenylyl cyclase	Activates protein kinase A
Ca2+	Released from ER	Activates various proteins
IP3	Phospholipase C	Releases Ca2+ from ER
DAG	Phospholipase C	Activates protein kinase C

Examples and Applications

Yeast cells use signaling to coordinate mating.
Neurons use synaptic signaling for rapid communication.
Hormones regulate processes like growth and metabolism via endocrine signaling.

Additional info: Signal transduction pathways allow for branching (one signal triggers multiple responses) and cross talk (integration of signals from different pathways).