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).

Transport Into and Out of the Nucleus

• Nuclear Pores: Large 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 (with nuclear export signals).

• Mechanism: Transport is selective and energy-dependent, often involving transport proteins (importins/exportins).

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.

• Plasma Membrane: Secretion and uptake of materials.

Signal Hypothesis: Protein Targeting to the Endomembrane System (10 Steps)

1. Protein synthesis begins on free ribosomes in the cytosol.

2. Signal sequence emerges from ribosome.

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

4. SRP halts translation temporarily.

5. SRP binds to SRP receptor on ER membrane.

6. Ribosome docks onto ER membrane.

7. SRP is released; translation resumes.

8. Growing polypeptide is threaded into ER lumen through a translocon.

9. Signal sequence is cleaved off.

10. Protein folds and undergoes modifications in the 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 that fuse with lysosomes.

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

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 regulates cell growth.

• Comparison: Both provide support and mediate cell signaling, but differ in composition and mechanical properties.

Types of Cell-Cell Connections

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

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

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

• Plasmodesmata: Channels in plant cell walls that connect cytoplasm of adjacent cells, allowing transport of molecules and signals.

Cell-Cell Connections Facilitating Molecular and Signal Transfer

• Gap Junctions (Animals): Permit passage of ions, nutrients, and signaling molecules.

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

Long-Distance Cell Signaling

• Process: Signaling molecules (hormones, neurotransmitters) are released, travel through extracellular fluid or bloodstream, and bind to receptors on target cells.

• Reception: Target cells detect signals via specific receptors.

• Transduction: Signal is relayed and amplified inside the cell, often involving second messengers.

• Response: Cell changes behavior (gene expression, metabolism, etc.).

Types of Receptors and Signal Reception

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

• Second Messengers: Small molecules (e.g., cAMP, Ca2+) that relay signals from receptors to target molecules inside the cell.

• Other Receptors: Ion channel-linked, enzyme-linked, and intracellular receptors (for lipid-soluble signals).

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 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 (e.g., ATP hydrolysis).

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

Biological Reaction Hurdles and Enzyme Function

• Activation Energy: Energy barrier that must be overcome for a reaction to proceed.

• Proper Orientation: Reactants must be correctly aligned for reaction.

• Enzymes: Biological catalysts that lower activation energy and increase reaction rates without being consumed.

Enzyme Activity and Regulation

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

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

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

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

• Allosteric Regulation: Inhibitor or activator binds to 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:

• Inputs: Glucose, oxygen

• Outputs: Carbon dioxide, water, ATP

Four Steps of Cellular Respiration

1. Glycolysis: Occurs in cytosol; glucose → pyruvate, ATP, NADH.

2. Pyruvate Processing: Occurs in 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 and Oxidative Phosphorylation: Inner mitochondrial membrane; NADH/FADH2 → ATP, H2O.

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

• Oxygen is the final electron acceptor in the electron transport chain; without it, the chain stops and ATP production decreases.

Fermentation

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

• Produces less ATP than aerobic respiration.

• Examples: Lactic acid fermentation (animals), alcoholic fermentation (yeast).

Chapter 10: Photosynthesis

Role of Chlorophyll in Capturing Light Energy

• Chlorophyll: Main pigment in plants that absorbs light energy, primarily in blue and red wavelengths.

• Excited electrons from chlorophyll are used to drive the synthesis of ATP and NADPH.

Locations of Photosynthetic Reactions

• Light-Dependent Reactions: Occur in the thylakoid membranes of chloroplasts; produce ATP, NADPH, and O2.

• Light-Independent Reactions (Calvin Cycle): Occur in the stroma of chloroplasts; 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. Aerobic Cellular Respiration

Rubisco and Photorespiration

• Rubisco: Enzyme that catalyzes the fixation of CO2 in the Calvin cycle; most abundant enzyme on Earth.

• Photorespiration: Occurs when Rubisco binds O2 instead of CO2, reducing photosynthetic efficiency and leading to loss of fixed carbon.

Additional info: Photorespiration is more likely under high temperatures and low CO2 concentrations.