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.

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

• Ribosomes: Structures responsible for protein synthesis; smaller than eukaryotic ribosomes.

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

• Flagella: Tail-like structures used for movement (not present in all prokaryotes).

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

Components of Eukaryotic Cells (Including Non-Animal Cells)

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

• Endoplasmic Reticulum (ER): Network of membranes; rough ER has ribosomes (protein synthesis), smooth ER (lipid synthesis, detoxification).

• 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).

• Vacuoles: Storage organelles; large central vacuole in plant cells for water and solute storage.

• Mitochondria: Site of cellular respiration; produces ATP.

• Chloroplasts: Site of photosynthesis in plants and algae.

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

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

• Cell Wall: Found in plants, fungi, and some protists; provides structure and protection.

Nuclear Transport

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

• Transported Molecules: mRNA, tRNA, ribosomal subunits (out of nucleus); proteins (into nucleus).

• Mechanism: Transport is selective and often requires nuclear localization signals (NLS) on proteins.

Endomembrane System Organelles and Functions

• Endoplasmic Reticulum (ER): Protein and lipid synthesis.

• Golgi Apparatus: Protein modification and sorting.

• Lysosomes: Digestion and recycling.

• Vesicles: Transport materials between organelles.

Signal Hypothesis: Protein Targeting to the Endomembrane System

1. Protein synthesis begins on free ribosomes.

2. Signal sequence emerges from ribosome.

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

4. SRP binds to SRP receptor on ER membrane.

5. Ribosome docks on ER membrane.

6. Protein synthesis resumes; polypeptide enters ER lumen.

7. Signal sequence is cleaved.

8. Protein folds and undergoes modifications in ER.

9. Protein is packaged into vesicles.

10. Vesicles transport protein to Golgi for further processing.

Endocytosis and Autophagy

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

• Phagocytosis: Engulfment of large particles or cells by the plasma membrane.

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

Chapter 11: Cell-Cell Interactions

Extracellular Matrix (ECM) of Animal vs. Plant Cells

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

• Plant ECM (Cell Wall): Composed of cellulose, hemicellulose, and pectin; provides rigidity and protection.

Types of Cell-Cell Connections

• Tight Junctions: Seal cells together to prevent leakage (animal cells).

• Desmosomes: Anchor cells together, providing mechanical strength (animal cells).

• Gap Junctions: Channels that allow direct communication and transfer of ions/molecules between animal cells.

• Plasmodesmata: Channels in plant cell walls for transport and communication between adjacent cells.

Cell-Cell Connections for Molecule and Signal Transfer

• Gap Junctions: Permit direct transfer of ions and small molecules in animal cells.

• Plasmodesmata: Permit direct transfer of substances in plant cells.

Long-Distance Cell Signaling

• Signaling Molecules: Hormones or other ligands travel through the bloodstream or extracellular fluid to target cells.

• Reception: Target cells detect signals via receptors (membrane-bound or intracellular).

• G-Protein-Coupled Receptors (GPCRs): Membrane receptors that activate G-proteins, triggering intracellular signaling cascades.

• Second Messengers: Small molecules (e.g., cAMP, Ca2+) that amplify and propagate the signal inside the cell.

Chapter 8: Energy and Enzymes

Potential Energy, Enthalpy, Entropy, and Gibbs Free Energy

• Potential Energy: Stored energy due to position or structure.

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

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

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

The change in Gibbs free energy is given by:

• If , the reaction is exergonic (spontaneous).

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

Redox Reactions and Phosphorylation

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

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

• Cells couple exergonic reactions (e.g., ATP hydrolysis) to drive endergonic processes.

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 increase reaction rates.

• Substrate Saturation: At high substrate concentrations, enzyme activity plateaus as all active sites are occupied.

• Regulation:

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

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

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

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

Example: Enzyme Activity in Bamboo Shark

• Enzyme activity can be affected by temperature, pH, and substrate concentration.

• Scientific studies may measure enzyme rates under different conditions to determine optimal activity.

Chapter 9: Cellular Respiration and Fermentation

Catabolic vs. Anabolic Metabolism

• 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:

• Four Steps:

  1. Glycolysis (cytoplasm)

  2. Pyruvate Processing (mitochondrial matrix)

  3. Citric Acid Cycle (mitochondrial matrix)

  4. Electron Transport Chain & Oxidative Phosphorylation (inner mitochondrial membrane)

Redox Chemistry, Phosphorylation, and Feedback Inhibition in Respiration

• Redox: NAD+ and FAD are reduced to NADH and FADH2 as they accept electrons.

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

• Feedback Inhibition: End products (e.g., ATP) inhibit enzymes early in the pathway to regulate metabolism.

Importance of Oxygen and Fermentation

• Oxygen: Final electron acceptor in the electron transport chain; essential for efficient ATP production.

• Fermentation: Occurs when oxygen is scarce; regenerates NAD+ but produces less ATP.

Chapter 10: Photosynthesis

Role of Chlorophyll in Light Capture

• 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 the thylakoid membranes; produce ATP and NADPH, release O2.

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

Oxygen Production and Carbon Fixation

• Oxygen Production: Occurs during the light-dependent reactions when water is split.

• Carbon Fixation: Occurs during the Calvin cycle when CO2 is incorporated into organic molecules.

Comparison: Photosynthesis vs. Cellular Respiration

Rubisco and Photorespiration

• Rubisco: Enzyme that catalyzes the fixation of CO2 in the Calvin cycle.

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

Additional info: Rubisco is the most abundant enzyme on Earth but is relatively slow and can catalyze a wasteful reaction with O2 (photorespiration), especially under hot, dry conditions.