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 for protein synthesis, smooth ER is involved in lipid synthesis and detoxification.

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

• Lysosomes: Contain digestive enzymes for breaking down macromolecules (mainly in animal cells).

• Vacuoles: Large storage organelles in plant and fungal cells; store water, ions, and nutrients.

• Mitochondria: Site of cellular respiration and ATP production.

• Chloroplasts: Site of photosynthesis in plant and algal cells.

• 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 structural support (cellulose in plants, chitin in fungi).

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 (such as histones, polymerases) and nucleotides (into nucleus).

• Mechanism: Transport occurs via selective gates; small molecules diffuse freely, larger molecules require nuclear localization signals (NLS) and transport proteins.

Endomembrane System Organelles and Functions

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

• Golgi Apparatus: Protein modification and sorting.

• Lysosomes: Macromolecule digestion.

• 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 halts translation temporarily.

5. SRP binds to 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; forms vesicles.

• Phagocytosis: Engulfment of large particles or cells; forms phagosomes.

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

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, cell signaling, and anchorage.

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

Types of Cell-Cell Connections

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

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

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

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

Cell-Cell Connections for Molecule and Signal Transfer

• Gap Junctions (Animals): Permit direct cytoplasmic exchange of ions and small molecules.

• Plasmodesmata (Plants): Allow movement of water, ions, and signaling molecules between cells.

Long-Distance Cell Signaling

• Signaling Molecules: Hormones or other ligands travel through the bloodstream or plant vascular tissue to reach distant cells.

• Reception: Target cells detect signals via specific receptors.

• G-Protein-Coupled Receptors (GPCRs): Membrane receptors that activate G-proteins, which then trigger 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 (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

• 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.

• 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 reaction rates under different conditions to determine optimal enzyme function.

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:

• 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, citrate) inhibit enzymes early in the pathway to regulate flux.

Importance of Oxygen and Fermentation

• Oxygen: Final electron acceptor in the electron transport chain; essential for maximal ATP yield.

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

Chapter 10: Photosynthesis

Role of Chlorophyll in Capturing Light Energy

• Chlorophyll: Pigment in chloroplasts that absorbs light energy, exciting electrons for use in photosynthesis.

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 (photolysis).

• Carbon Fixation: Occurs during the Calvin cycle; 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.

Additional info: Rubisco's dual affinity for CO2 and O2 is a major limitation for plant productivity, especially under hot, dry conditions.