Cell Structure and Function

Prokaryotic Cell Components

Prokaryotic cells, such as bacteria and archaea, have a simpler structure compared to eukaryotic cells. Understanding their components is essential for distinguishing cell types and their functions.

• Plasma Membrane: A phospholipid bilayer that controls the movement of substances into and out of the cell.

• Cell Wall: Provides structural support and protection; composed of peptidoglycan in bacteria.

• Cytoplasm: Gel-like substance where cellular processes occur.

• Ribosomes: Sites of protein synthesis; smaller than eukaryotic ribosomes.

• Nucleoid: Region containing the cell’s circular DNA; not membrane-bound.

• Flagella: Tail-like structures used for movement (motility).

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

Eukaryotic Cell Components

Eukaryotic cells (animals, plants, fungi, protists) have membrane-bound organelles, each with specialized functions.

• Nucleus: Contains DNA; site of transcription and ribosome assembly.

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; synthesizes proteins for secretion or membranes.

  • Smooth ER: Synthesizes lipids, 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 of water, ions, and nutrients; large central vacuole in plant cells.

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

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

Nuclear Transport

The nucleus is separated from the cytoplasm by the nuclear envelope, which contains nuclear pores for selective transport.

• What is transported: mRNA, tRNA, ribosomal subunits (out); proteins, nucleotides (in).

• How transport occurs: Nuclear pore complexes recognize nuclear localization signals (NLS) on proteins, allowing regulated passage.

• Directionality: Import and export are energy-dependent and highly selective.

Endomembrane System

The endomembrane system is a group of organelles involved in protein and lipid synthesis, modification, and transport.

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

• Functions: Synthesis, processing, and transport of proteins and lipids.

Signal Hypothesis (Protein Targeting to the Endomembrane System)

The signal hypothesis explains how proteins are directed to the ER for secretion or membrane insertion.

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 onto translocon (protein channel).

7. SRP is released; translation resumes.

8. Growing polypeptide is threaded into ER lumen or membrane.

9. Signal sequence is cleaved off (if necessary).

10. Protein is folded and modified in ER.

Endocytosis and Autophagy

• Receptor-mediated endocytosis: Specific uptake of molecules via receptor binding and vesicle formation.

• Phagocytosis: Engulfment of large particles or cells by the plasma membrane.

• Autophagy: Degradation of the cell’s own components via lysosomes.

Cell-Cell Interactions and Communication

Extracellular Matrix (ECM)

The ECM provides structural and biochemical support to surrounding cells.

• Animal ECM: Composed of proteins (collagen, elastin) and polysaccharides; provides support, regulates cell behavior.

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

Cell-Cell Connections

Cells connect to each other via specialized structures for communication and adhesion.

• Tight Junctions: Seal cells together, preventing passage of materials between them (animals).

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

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

• Plasmodesmata: Channels through plant cell walls for cytoplasmic exchange.

Transfer of Molecules and Signals: Gap junctions (animals) and plasmodesmata (plants) facilitate direct communication between adjacent cells.

Cell Signaling

Cells communicate over long distances using signaling molecules (ligands) and receptors.

• Reception: Target cell detects signaling molecule via receptor (membrane-bound or intracellular).

• Transduction: Signal is relayed and amplified inside the cell, often via second messengers (e.g., cAMP, Ca2+).

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

G-Protein-Coupled Receptors (GPCRs): Membrane receptors that activate G-proteins, which then trigger second messenger pathways.

Second Messengers: Small molecules that relay signals inside the cell (e.g., cAMP, IP3).

Energy, Enzymes, and Metabolism

Thermodynamics in Biology

• Potential Energy: Stored energy due to position or structure.

• Enthalpy (H): Total energy of a system.

• Entropy (S): Measure of disorder or randomness.

• Gibbs Free Energy (G): Energy available to do work.

Gibbs Free Energy Equation:

• Exergonic/Spontaneous:

• Endergonic/Non-spontaneous:

Redox Reactions and Phosphorylation

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

• Phosphorylation: Addition of phosphate group to a molecule, often to activate or deactivate proteins.

• 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 (Vmax).

• Regulation:

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

  • Noncovalent: Binding of regulatory molecules (competitive or allosteric inhibition).

  • Competitive Inhibition: Inhibitor binds active site.

  • Allosteric Regulation: Inhibitor or activator binds elsewhere, changing enzyme shape.

Example: Enzyme activity in bamboo sharks can be studied under different temperatures or pH to determine optimal conditions.

Cellular Respiration and Fermentation

Metabolic Pathways

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

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

Cellular Respiration Overview

• Inputs: Glucose, O2

• Outputs: CO2, H2O, ATP

Four Steps of Cellular Respiration:

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: NAD+ and FAD are reduced to NADH and FADH2.

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

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

Importance of Oxygen: Final electron acceptor in the electron transport chain; without O2, the chain stops and ATP production drops.

Fermentation: Occurs in low oxygen; regenerates NAD+ for glycolysis but produces less ATP.

Photosynthesis

Role of Chlorophyll

Chlorophyll is the main pigment in plants that absorbs light energy for photosynthesis, primarily in the blue and red wavelengths.

Photosynthesis Reactions

• Light-dependent reactions: Occur in thylakoid membranes; produce ATP, NADPH, and O2.

• Light-independent reactions (Calvin cycle): Occur in stroma; use ATP and NADPH to fix CO2 into sugars.

Oxygen Production: Produced during light-dependent reactions when water is split.

Carbon Fixation: Occurs during the Calvin cycle, catalyzed by the enzyme Rubisco.

Comparison: Photosynthesis vs. Cellular Respiration

Rubisco and Photorespiration

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

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

• Consequences: Wastes energy and reduces sugar production in plants, especially under hot, dry conditions.