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.

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).

• Vacuoles: Storage organelles; large central vacuole in plant cells stores water and nutrients.

• Mitochondria: Site of cellular respiration; produces ATP.

• 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 structure and movement.

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

Transport Into and Out of the Nucleus

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

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

• Exported: mRNA, tRNA, ribosomal subunits.

• Mechanism: Transport occurs via selective gates in the nuclear envelope called nuclear pore complexes.

Endomembrane System Organelles and Functions

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

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

Signal Hypothesis: Protein Targeting to the Endomembrane System

• Describes how proteins are directed to the ER for secretion or membrane insertion.

• 10 Steps (Summary):

  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 to translocon (protein channel).

  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 Types and Functions

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

• 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 support, adhesion, and signaling.

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

• Comparison: Both provide structural support, but composition and flexibility differ.

Types of Cell-Cell Connections

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

• Desmosomes: Anchor cells together via intermediate filaments (animal cells).

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

• Plasmodesmata: Channels through plant cell walls for transport and communication.

Connections Facilitating Molecular and Signal Transfer

• Gap Junctions (Animals): Allow ions and small molecules to pass directly between cells.

• Plasmodesmata (Plants): Enable cytoplasmic exchange and signaling 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 signals (e.g., G-protein-coupled receptors).

  • Intracellular Receptors: Bind hydrophobic signals that cross the membrane.

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

• Second Messengers: Small molecules that amplify and relay signals 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.

• Equation: Where is the change in free energy, is the change in enthalpy, is temperature in Kelvin, and is the change in entropy.

Predicting Reaction Spontaneity

• Exergonic/Spontaneous: ; releases energy.

• Endergonic/Non-Spontaneous: ; requires energy input.

Redox Reactions and Phosphorylation in Metabolism

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

• Phosphorylation: Addition of phosphate group to a molecule, often activating it.

• Coupling: Endergonic reactions are driven by coupling to exergonic reactions (e.g., ATP hydrolysis).

Enzyme Function and Reaction Hurdles

• Hurdle 1: Reactants must collide in the correct orientation.

• Hurdle 2: Activation energy barrier must be overcome.

• Enzymes: Lower activation energy and increase reaction rate without being consumed.

Enzyme Activity: Example Study

• Scientific studies (e.g., in bamboo sharks) measure enzyme activity under different conditions to understand optimal function and adaptation.

Substrate Saturation and Enzyme Rate Limits

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

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 elsewhere, changing enzyme shape and 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 and Outputs

• Inputs: Glucose, oxygen.

• Outputs: Carbon dioxide, water, ATP.

Four Steps of Cellular Respiration and Locations

1. Glycolysis: Cytoplasm; glucose → pyruvate, ATP, NADH.

2. Pyruvate Processing: 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 → ATP, H2O.

Redox Chemistry, Phosphorylation, and Feedback Inhibition in Respiration

• Redox: Electrons transferred from glucose to oxygen via NADH/FADH2.

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

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

Importance of Oxygen

• Oxygen is the final electron acceptor in the electron transport chain; without it, ATP production is greatly reduced.

Fermentation in Low Oxygen Conditions

• Cells switch to fermentation to regenerate NAD+ when oxygen is scarce, allowing glycolysis to continue.

• Products: Lactic acid (animals), ethanol (yeast).

Chapter 10: Photosynthesis

Role of Chlorophyll in Capturing Light Energy

• 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: Thylakoid membranes; produce ATP and NADPH, release O2.

• Light-Independent Reactions (Calvin Cycle): 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 by enzyme Rubisco.

Photosynthesis vs. Aerobic Cellular Respiration

Rubisco and Photorespiration

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

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