Chapter 7: Inside the Cell

Major Components of Prokaryotic Cells

• Plasma Membrane: Phospholipid bilayer that controls the movement of substances in and out of the cell.

• Cytoplasm: Gel-like fluid inside the cell where metabolic reactions occur.

• Ribosomes: Structures responsible for protein synthesis; not membrane-bound.

• Nucleoid: Region containing the cell's circular DNA; not surrounded by a membrane.

• Cell Wall: Rigid structure providing support and protection; composed of peptidoglycan in bacteria.

• Flagella: Tail-like structures used for movement (motility).

• Pili/Fimbriae: Hair-like projections for attachment to surfaces or other cells.

• Capsule (sometimes present): Outer layer for protection and adherence.

Components of Eukaryotic Cells (Including Non-Animal Cells)

• Nucleus: Membrane-bound organelle containing DNA; site of transcription.

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; synthesizes and processes proteins.

  • Smooth ER: Lacks ribosomes; synthesizes lipids and detoxifies chemicals.

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for secretion or delivery to other organelles.

• Lysosomes: Contain digestive enzymes; break down macromolecules (mainly in animal cells).

• Peroxisomes: Break down fatty acids and detoxify harmful substances.

• Mitochondria: Site of cellular respiration; produces ATP.

• Chloroplasts (plants and algae): Site of photosynthesis.

• Vacuoles (plants, fungi, some protists): Storage of water, ions, and nutrients; structural support in plants.

• Cell Wall (plants, fungi, some protists): Provides structural support and protection.

• Cytoskeleton: Network of protein fibers (microtubules, microfilaments, intermediate filaments) for cell shape, movement, and transport.

Nuclear Transport

• Nuclear Envelope: Double membrane surrounding the nucleus; contains nuclear pores.

• Nuclear Pores: Protein complexes that regulate the movement of molecules between the nucleus and cytoplasm.

• Transported Molecules:

  • Into Nucleus: Proteins (with nuclear localization signals), nucleotides.

  • Out of Nucleus: mRNA, tRNA, ribosomal subunits.

• Mechanism: Transport is selective and often requires energy (GTP hydrolysis).

Endomembrane System Organelles and Functions

• Includes: Nuclear envelope, ER, Golgi apparatus, lysosomes, vesicles, plasma membrane.

• Function: Synthesis, modification, transport, and secretion of proteins and lipids.

Signal Hypothesis for Protein Targeting (10 Steps)

1. Protein synthesis begins on free ribosomes in the cytosol.

2. Signal sequence emerges from ribosome.

3. Signal recognition particle (SRP) binds to signal sequence.

4. SRP halts translation temporarily.

5. SRP binds to SRP receptor on ER membrane.

6. Ribosome docks onto translocon (protein channel) in ER membrane.

7. SRP is released; translation resumes.

8. Growing polypeptide is threaded into ER lumen.

9. Signal sequence is cleaved off by signal peptidase.

10. Protein folds and undergoes modifications in ER.

Endocytosis Types and Functions

• Receptor-Mediated Endocytosis: Specific uptake of molecules via receptor proteins; forms vesicles.

• Phagocytosis: "Cell eating"; engulfment of large particles or cells.

• Autophagy: Digestion of the cell's own damaged organelles or macromolecules.

Chapter 11: Cell-Cell Interactions

Extracellular Matrix (ECM) in Animals vs. Plants

• Animal ECM: Composed mainly of proteins (collagen, elastin) and polysaccharides; provides structural support, cell signaling, and anchorage.

• Plant ECM (Cell Wall): Made of cellulose, hemicellulose, and pectin; provides rigidity, protection, and mediates cell growth.

• Comparison: Both provide support and regulate cell behavior, but differ in composition and flexibility.

Types of Cell-Cell Connections

• Tight Junctions (animals): Seal cells together, preventing leakage of extracellular fluid.

• Desmosomes (animals): Anchor cells together via intermediate filaments; provide mechanical strength.

• Gap Junctions (animals): Channels that allow ions and small molecules to pass directly between cells; enable communication.

• Plasmodesmata (plants): Channels through cell walls that connect cytoplasm of adjacent cells; allow transport and communication.

Cell-Cell Connections for Molecule and Signal Transfer

• Gap Junctions: Permit direct transfer of ions and signaling molecules between animal cells.

• Plasmodesmata: Allow movement of water, ions, and signaling molecules between plant cells.

Long-Distance Cell Signaling

• Process: Signaling molecules (hormones) are released, travel through the organism, and bind to receptors on target cells.

• Reception:

  • Cell-Surface Receptors: Bind hydrophilic signaling molecules (e.g., G-protein-coupled receptors).

  • Intracellular Receptors: Bind hydrophobic molecules that cross the membrane (e.g., steroid hormones).

• G-Protein-Coupled Receptors (GPCRs): Activate G-proteins, which then trigger production of second messengers (e.g., cAMP) to amplify the signal.

• Second Messengers: Small molecules that relay signals inside the cell, leading to a cellular response.

Chapter 8: Energy and Enzymes

Potential Energy, Enthalpy, Entropy, and Gibbs Free Energy

• Potential Energy: Stored energy due to position or structure (e.g., chemical bonds).

• Enthalpy (H): Total energy of a system, including heat content.

• Entropy (S): Measure of disorder or randomness in a system.

• Gibbs Free Energy (G): Energy available to do work; determines spontaneity of reactions.

Gibbs Free Energy Equation:

• If , the reaction is exergonic (spontaneous).

• If , the reaction is endergonic (non-spontaneous).

Redox Reactions and Phosphorylation in Metabolism

• Redox Reactions: Transfer of electrons; oxidation (loss of electrons) and reduction (gain of electrons).

• Phosphorylation: Addition of a phosphate group to a molecule, often making it more reactive.

• Coupling: Cells drive endergonic reactions by coupling them to exergonic reactions (e.g., ATP hydrolysis).

Enzyme Function and Regulation

• Activation Energy: Energy barrier that must be overcome for a reaction to proceed.

• Enzymes: Biological catalysts that lower activation energy and speed up reactions.

• Two Hurdles: (1) Reactants must collide in the correct orientation; (2) Sufficient energy to break/form bonds.

• Enzyme Regulation:

  • Covalent Regulation: Enzyme activity modified by covalent attachment of chemical groups (e.g., phosphorylation).

  • Noncovalent Regulation: Temporary binding of regulatory molecules (e.g., allosteric inhibitors or activators).

  • Competitive Inhibition: Inhibitor binds to active site, blocking substrate.

  • Allosteric Regulation: Inhibitor or activator binds to a site other than the active site, changing enzyme shape and activity.

Enzyme Activity and Substrate Saturation

• As substrate concentration increases, reaction rate increases until the enzyme is saturated (all active sites occupied).

• At saturation, increasing substrate further does not increase rate.

Example: Enzyme Activity in Bamboo Shark

• Scientific studies may investigate how temperature, pH, or other factors affect enzyme activity in specific organisms.

Chapter 9: Cellular Respiration and Fermentation

Catabolic vs. Anabolic Processes

• Catabolic Pathways: Break down molecules to release energy (e.g., cellular respiration).

• Anabolic Pathways: Build complex molecules from simpler ones, requiring energy (e.g., protein synthesis).

Cellular Respiration: Inputs, Outputs, and Steps

• Overall Equation:

• Inputs: Glucose, oxygen

• Outputs: Carbon dioxide, water, ATP

Four Steps of Cellular Respiration

1. Glycolysis: Occurs in cytosol; glucose → pyruvate, ATP, NADH.

2. Pyruvate Processing: Occurs in mitochondrial matrix; pyruvate → acetyl-CoA, CO₂, NADH.

3. Citric Acid Cycle (Krebs Cycle): Mitochondrial matrix; acetyl-CoA → CO₂, ATP, NADH, FADH₂.

4. Electron Transport Chain & Oxidative Phosphorylation: Inner mitochondrial membrane; NADH/FADH₂ donate electrons, O₂ is final electron acceptor, ATP produced.

Redox Chemistry, Phosphorylation, and Feedback Inhibition in Respiration

• Redox: Electrons transferred from glucose to oxygen via NAD⁺/NADH and FAD/FADH₂.

• Phosphorylation: ATP produced by substrate-level and oxidative phosphorylation.

• Feedback Inhibition: End products (e.g., ATP) inhibit enzymes early in the pathway (e.g., phosphofructokinase in glycolysis).

Importance of Oxygen

• Oxygen is the final electron acceptor in the electron transport chain; without it, the chain stops and ATP production drops.

Fermentation

• Occurs when oxygen is scarce; cells regenerate NAD⁺ by transferring electrons to pyruvate or derivatives.

• Produces less ATP than aerobic respiration.

Chapter 10: Photosynthesis

Role of Chlorophyll

• Chlorophyll: Pigment in chloroplasts that absorbs light energy, initiating photosynthesis.

• Transfers energy to reaction centers, driving electron transport.

Locations of Photosynthetic Reactions

• Light-Dependent Reactions: Occur in thylakoid membranes; produce ATP and NADPH, release O₂.

• Light-Independent Reactions (Calvin Cycle): Occur in stroma; use ATP and NADPH to fix CO₂ into sugars.

Oxygen Production and Carbon Fixation

• Oxygen Produced: During light-dependent reactions, from splitting water.

• Carbon Fixed: During Calvin cycle, when CO₂ is incorporated into organic molecules.

Photosynthesis vs. Cellular Respiration

Rubisco and Photorespiration

• Rubisco: Enzyme that catalyzes CO₂ fixation in the Calvin cycle; most abundant enzyme on Earth.

• Photorespiration: Occurs when Rubisco binds O₂ instead of CO₂, reducing photosynthetic efficiency.

• Consequences: Wastes energy and reduces sugar production, especially under hot, dry conditions.