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 (not present in all prokaryotes).

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

• Capsule: Outer polysaccharide layer for protection and adhesion (in some species).

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 plant cells 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).

Nuclear Transport

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

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

• Transported Molecules:

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

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

• Mechanism: Transport is selective and often requires nuclear localization signals (NLS) or nuclear export signals (NES).

Endomembrane System and Protein Targeting

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

• Functions: Synthesis, modification, transport, and degradation of proteins and lipids.

• Signal Hypothesis (10 Steps): Describes how proteins are directed into the ER for secretion or membrane insertion.

  • 1. mRNA binds to ribosome

  • 2. Signal peptide emerges from ribosome

  • 3. Signal recognition particle (SRP) binds signal peptide

  • 4. SRP halts translation

  • 5. SRP-ribosome complex binds SRP receptor on ER membrane

  • 6. Ribosome docks on translocon (protein channel)

  • 7. SRP is released; translation resumes

  • 8. Growing polypeptide is threaded into ER lumen

  • 9. Signal peptide is cleaved

  • 10. Protein folds and undergoes modifications in ER

Endocytosis and Autophagy

• 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.

• Purpose: Nutrient uptake, defense, cellular maintenance.

Chapter 11: Cell-Cell Interactions

Extracellular Matrix (ECM) in Animals vs. Plants

• Animal ECM: Composed 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 allowing direct transfer of ions and molecules between animal cells.

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

Connections Facilitating Molecular Transfer

• Gap Junctions: Allow ions, nutrients, and signaling molecules to pass between animal cells.

• Plasmodesmata: Enable cytoplasmic exchange in plant cells.

Long-Distance Cell Signaling

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

• Reception:

  • G-Protein-Coupled Receptors (GPCRs): Activate intracellular G-proteins, triggering signaling cascades.

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

• Other Receptors: Ion channel-linked, enzyme-linked receptors.

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.

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

Gibbs Free Energy Equation:

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

• Exergonic/Spontaneous: $ \Delta G < 0 $

• Endergonic/Non-spontaneous: $ \Delta G > 0 $

Redox Reactions and Phosphorylation

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

• Phosphorylation: Addition of phosphate group; often activates molecules.

• 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 correct orientation and possess enough energy.

• Enzyme Regulation:

  • Covalent Regulation: Chemical modification (e.g., phosphorylation).

  • Noncovalent Regulation: Binding of regulatory molecules (reversible).

  • Competitive Inhibition: Inhibitor binds active site.

  • Allosteric Regulation: Inhibitor or activator binds site other than active site, changing enzyme shape.

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

Example: Enzyme Activity in Bamboo Shark

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

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

Chapter 9: Cellular Respiration and Fermentation

Catabolic vs. Anabolic Processes

• Catabolic: Breakdown of molecules to release energy (e.g., cellular respiration).

• Anabolic: Synthesis of complex molecules from simpler ones (requires energy).

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: 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

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

• 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 severely limited.

Fermentation

• Occurs when oxygen is scarce; regenerates NAD+ so glycolysis can continue.

• Produces less ATP than aerobic respiration.

• Example: Lactic acid fermentation in muscles, alcoholic fermentation in yeast.

Chapter 10: Photosynthesis

Role of Chlorophyll

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

• Transfers energy to reaction centers, driving electron transport.

Photosynthesis: Locations and Reactions

• Light-Dependent Reactions: Thylakoid membranes; produce ATP, NADPH, and 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.

Comparison: Photosynthesis vs. Cellular Respiration

Rubisco and Photorespiration

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

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

• Importance: Rubisco is essential for carbon fixation but is inefficient due to photorespiration.