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; not membrane-bound.

• Cell Wall: Rigid structure outside the plasma membrane 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.

• Capsule: Outer layer that protects against desiccation and immune attack (not always present).

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 proteins for secretion or membranes.

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

• Golgi Apparatus: Modifies, sorts, and packages proteins and lipids for delivery.

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

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

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

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

Transport Into and Out of the Nucleus

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

• Transported Molecules:

  • Into Nucleus: Proteins (e.g., histones, polymerases), nucleotides.

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

• Mechanism: Transport occurs via selective gates in the nuclear envelope; requires nuclear localization signals (NLS) for import and nuclear export signals (NES) for export.

Endomembrane System Organelles and Functions

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

• Golgi Apparatus: Protein modification and sorting.

• Lysosomes: Digestion and recycling (mainly in animals).

• Vesicles: Transport materials between organelles.

• Plasma Membrane: Secretion and uptake of materials.

Signal Hypothesis: Protein Targeting to the Endomembrane System

• Proteins destined for secretion or for organelles of the endomembrane system are synthesized with a signal sequence.

• 10 Steps (Summary):

  1. Translation begins on free ribosome.

  2. Signal sequence emerges from ribosome.

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

  4. SRP halts translation temporarily.

  5. SRP binds SRP receptor on ER membrane.

  6. Ribosome docks on ER membrane.

  7. SRP is released; translation resumes.

  8. Growing polypeptide is threaded into ER lumen.

  9. Signal sequence is cleaved off.

  10. Protein folds and undergoes modifications in ER.

Endocytosis and Autophagy

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

• Phagocytosis: Engulfment of large particles or cells ("cell eating").

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

• Purpose: Nutrient uptake, defense, recycling of cellular components.

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

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

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

• Plasmodesmata: Channels through plant cell walls that connect cytoplasm of adjacent cells, allowing molecule and signal transfer.

Cell-Cell Connections Facilitating Transfer

• Gap Junctions (Animals): Allow electrical and chemical signals to pass rapidly between cells.

• Plasmodesmata (Plants): Permit movement of water, ions, and signaling molecules.

Long-Distance Cell Signaling

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

• Reception:

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

  • Intracellular Receptors: Bind hydrophobic signals 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 inside the cell.

• Second Messengers: Small molecules that relay signals from receptors to target molecules 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 (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:

$ \Delta G = \Delta H - T \Delta S $

• If $ \Delta G < 0 $, the reaction is exergonic (spontaneous).

• If $ \Delta G > 0 $, the reaction is endergonic (non-spontaneous).

Redox Reactions and Phosphorylation in Metabolism

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

• Phosphorylation: Addition of a phosphate group to a molecule, often transferring energy.

• Coupling: Endergonic reactions are driven by coupling 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 increase reaction rates.

• Two Hurdles:

  • Reactants must collide in the correct orientation.

  • Reactants must have enough energy to break bonds.

• Enzyme Regulation:

  • Covalent Regulation: Enzyme activity is controlled by covalent modification (e.g., phosphorylation).

  • Noncovalent Regulation: Involves 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.

• Substrate Saturation: At high substrate concentrations, all enzyme active sites are occupied, and the reaction rate plateaus (Vmax).

Example: Enzyme Activity in Bamboo Shark

• Scientific studies may investigate how temperature, pH, or other factors affect enzyme activity in organisms such as the bamboo shark.

• Results typically show optimal conditions for enzyme function and how deviations reduce 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:

$ \mathrm{C_6H_{12}O_6} + 6\,\mathrm{O_2} \rightarrow 6\,\mathrm{CO_2} + 6\,\mathrm{H_2O} + \text{energy (ATP)} $

• Inputs: Glucose, oxygen

• Outputs: Carbon dioxide, water, ATP

Four Steps of Cellular Respiration

1. Glycolysis: Occurs in cytoplasm; glucose is split into pyruvate.

2. Pyruvate Processing: Occurs in mitochondrial matrix; pyruvate is converted to acetyl-CoA.

3. Citric Acid Cycle (Krebs Cycle): Occurs in mitochondrial matrix; acetyl-CoA is oxidized to CO2.

4. Electron Transport Chain and Oxidative Phosphorylation: Occurs in inner mitochondrial membrane; electrons are transferred to oxygen, generating ATP.

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, citrate) inhibit early steps to regulate pathway activity.

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 in Capturing Light Energy

• Chlorophyll: Main pigment in plants that absorbs light energy, exciting electrons for use in photosynthesis.

• Located in the thylakoid membranes of chloroplasts.

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 Production: Occurs during light-dependent reactions when water is split (photolysis).

• 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 first step of carbon fixation in the Calvin cycle.

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

• Consequence: Wastes energy and decreases sugar production, especially under hot, dry conditions.