Cell Structure and Function

Prokaryotes vs. Eukaryotes

Cells are classified as either prokaryotic or eukaryotic based on their structural features. Understanding these differences is fundamental to cell biology.

• Prokaryotes (Domains: Bacteria and Archaea):

  • No membrane-bound nucleus; DNA is in a nucleoid region.

  • Circular DNA and plasmids present.

  • No membrane-bound organelles.

  • No histone proteins; DNA is not packaged with histones.

  • Cell wall contains peptidoglycan (in Bacteria).

  • Reproduce by binary fission.

  • Ribosomes: 70S (active), 50S (large subunit), 30S (small subunit), all in cytoplasm.

  • Some form endospores for survival.

• Eukaryotes (Domain: Eukarya):

  • Membrane-bound nucleus with linear chromosomes associated with histone proteins.

  • Contain membrane-bound organelles (e.g., mitochondria, ER, Golgi apparatus).

  • Ribosomes: 80S (active), 60S (large subunit), 40S (small subunit); found in cytoplasm or attached to rough ER.

  • Much larger in size compared to prokaryotes.

Example: Escherichia coli is a prokaryote; human cells are eukaryotic.

Key Theories in Cell Biology

• Cell Theory: All living things are composed of cells; all cells come from pre-existing cells.

• Theory of Evolution by Natural Selection: Explains the diversity of life and adaptation.

• Chromosomal Theory of Inheritance: Genes are located on chromosomes.

Endosymbiotic Theory

This theory explains the origin of mitochondria and chloroplasts in eukaryotic cells.

• Mitochondria originated from engulfed alpha-proteobacteria.

• Chloroplasts originated from engulfed cyanobacteria (in plants and algae).

• Evidence: Both organelles have their own circular DNA, double membranes, and ribosomes similar to prokaryotes.

Example: Maternal inheritance of mitochondrial DNA in humans.

Nucleus and Chromatin Structure

• Nucleus: Membrane-bound, contains linear chromosomes.

• Nucleolus: Site of rRNA synthesis.

• Chromatin:

  • Euchromatin: Loosely packed, actively transcribed.

  • Heterochromatin: Densely packed, transcriptionally inactive.

• Epigenetics: Chemical modifications (e.g., methylation) can regulate gene expression.

Nuclear Pore Complex

• Composed of ~30 different proteins.

• Regulates transport of molecules (e.g., mRNA, ribosomal subunits) in and out of the nucleus.

• Nuclear Localization Signal (NLS): Amino acid sequence that directs proteins to the nucleus.

The Endomembrane System

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

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; synthesizes and modifies proteins.

  • Smooth ER: Lacks ribosomes; synthesizes lipids.

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

  • Cis face: Receiving side.

  • Trans face: Shipping side.

  • Two models for protein movement: vesicle transport and cisternal maturation.

• Vesicles: Transport materials between organelles.

Example: Pulse-chase experiments track protein movement through the endomembrane system.

Protein Targeting and Signal Hypothesis

• Protein synthesis begins in the cytoplasm.

• Proteins destined for secretion or organelles have an ER signal sequence (17-20 amino acids).

• Signal Recognition Particle (SRP) binds the signal sequence, pauses translation, and directs the ribosome to the ER.

• After docking, translation resumes and the polypeptide is threaded into the ER.

• Proteins are folded (sometimes with chaperones) and modified in the ER and Golgi.

Lysosomes and Vacuoles

• Lysosomes: Animal cell organelles containing hydrolytic enzymes; degrade macromolecules and organelles.

• Primary lysosome: Contains inactive enzymes.

• Secondary lysosome: Formed by fusion with vesicles containing material to be digested.

• Vacuoles: Large, water-filled organelles in plants; store chemicals and maintain turgor pressure.

Mitochondria and Chloroplasts

• Mitochondria: Site of ATP production via oxidative phosphorylation; have their own DNA and ribosomes.

• Chloroplasts: (in plants) Site of photosynthesis; also have their own DNA and ribosomes.

Cytoskeleton

• Actin filaments: Two coiled strands; involved in cell movement and shape.

• Intermediate filaments: Rope-like; provide structural support.

• Microtubules: Hollow tubes of alpha and beta tubulin; involved in chromosome movement and cell division.

• All are dynamic and contribute to cell motility and structure.

Extracellular Structures

• Cilia and Flagella: Eukaryotic structures with a 9+2 microtubule arrangement; used for movement.

• Prokaryotic flagella are structurally simpler.

Cell Division and the Cell Cycle

Overview of Cell Division

• Cell Theory: All cells arise from pre-existing cells.

• Genome: The complete set of genetic material in a cell.

• Prokaryotes: Divide by binary fission (circular chromosome, origin of replication, septum formation).

• Eukaryotes: Divide by mitosis (somatic cells, 2n) or meiosis (gametes, n).

Karyotype and Chromosome Structure

• Karyotype: Visual representation of chromosomes.

• Homologous chromosomes: One from each parent; same genes, possibly different alleles.

• Centromere: Constriction point; site of kinetochore assembly.

• Sister chromatids: Identical copies held together by cohesion proteins.

The Eukaryotic Cell Cycle

• G1 phase: Cell growth and normal function (7-9 hours).

• S phase: DNA replication (3-6 hours).

• G2 phase: Organelle replication and preparation for mitosis (5-6 hours).

• M phase (Mitosis): Division of chromosomes and cytoplasm.

• Cytokinesis: Division of the cytoplasm.

• G0 phase: Resting state; some cells remain here permanently.

Stages of Mitosis

• Prophase: Chromosomes condense, nuclear envelope breaks down.

• Prometaphase: Microtubules attach to kinetochores.

• Metaphase: Chromosomes align at the metaphase plate; three types of microtubules (kinetochore, polar, astral).

• Anaphase: Sister chromatids separate and move to opposite poles.

• Telophase: Nuclear envelope reforms, chromosomes decondense.

• Cytokinesis: Cleavage furrow (animals) or cell plate (plants) divides the cell.

Cell Cycle Checkpoints

• G1/S Checkpoint: Checks for nutrients, size, DNA damage (p53 protein).

• G2/M Checkpoint: Ensures DNA replication is complete and undamaged; telomere length is monitored.

• Spindle (Metaphase) Checkpoint: Ensures all chromosomes are attached to spindle fibers.

Regulation of the Cell Cycle

• Growth factors: Signaling molecules that stimulate cell division.

• Cyclins and CDKs (Cyclin-dependent kinases): Regulatory proteins that control progression through the cell cycle.

• MPF (M-phase promoting factor): Cyclin-CDK complex that triggers mitosis.

• Retinoblastoma protein (RB): Inhibits cell cycle progression by binding E2F transcription factor.

• p53: Tumor suppressor gene; repairs DNA or induces apoptosis if damage is detected.

• Proto-oncogenes: Code for proteins that promote cell division; mutations can lead to cancer.

Metabolism: Energy, Enzymes, and Regulation

Basic Concepts of Metabolism

• Metabolism: All chemical reactions in a cell.

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of complex molecules from simpler ones.

Thermodynamics in Biology

• First Law (Conservation of Energy): Energy cannot be created or destroyed.

• Second Law: Entropy (disorder) increases in the universe.

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

• Enthalpy (H): Total energy in chemical bonds.

• Entropy (S): Energy unavailable due to disorder.

Gibbs Free Energy Equation:

• Endergonic reaction: Requires energy input ().

• Exergonic reaction: Releases energy ().

Enzymes and Catalysis

• Enzymes: Biological catalysts that lower activation energy.

• Active site: Region where substrate binds and reaction occurs.

• Induced fit: Enzyme changes shape to facilitate reaction.

• Enzyme complexes: Allow for efficient metabolic pathways and regulation.

• Factors affecting enzyme activity: Temperature, pH, substrate concentration, regulatory molecules.

Enzyme Regulation

• Cofactors: Inorganic ions (e.g., metals) required for enzyme activity.

• Coenzymes: Organic molecules (often vitamins) that assist enzymes.

• Prosthetic groups: Non-amino acid groups permanently attached to enzymes.

• Competitive inhibition: Inhibitor binds active site, blocking substrate.

• Noncompetitive inhibition: Inhibitor binds elsewhere, changing enzyme shape.

• Allosteric regulation: Effector molecules bind to sites other than the active site, activating or inhibiting the enzyme.

• Feedback inhibition: End product of a pathway inhibits an upstream enzyme.

• Covalent modification: Chemical changes (e.g., phosphorylation) alter enzyme activity.

ATP and Energy Coupling

• ATP: Main energy currency of the cell; hydrolysis releases energy ().

• Substrate-level phosphorylation: Direct transfer of phosphate to ADP by an enzyme.

• Oxidative phosphorylation: ATP synthesis driven by a proton gradient across the mitochondrial membrane.

Cellular Respiration

Overview

• Controlled release of energy from glucose to produce ATP.

• Involves redox reactions (oxidation and reduction).

• Stages: Glycolysis, Pyruvate Oxidation, Citric Acid Cycle, Electron Transport Chain & Oxidative Phosphorylation.

Stages of Cellular Respiration

Key Concepts

• Redox reactions: Transfer of electrons; oxidation is loss, reduction is gain.

• Substrate-level phosphorylation: Direct ATP synthesis in glycolysis and citric acid cycle.

• Oxidative phosphorylation: ATP synthesis via ATP synthase, powered by proton gradient.

• Maximum ATP yield per glucose: ~29 ATP (varies by cell type and conditions).

Anaerobic Respiration and Fermentation

• Anaerobic respiration: Uses inorganic molecules (e.g., sulfur, nitrate) as final electron acceptors.

• Fermentation: Uses organic molecules as final electron acceptors; produces less ATP.

• Ethanol fermentation: Occurs in yeast; produces ethanol and CO2.

• Lactic acid fermentation: Occurs in muscle cells; produces lactate.

ATP Synthase Structure

• F0 unit: Membrane-embedded, rotates as protons flow through.

• Stator: Anchors the complex.

• Rotor shaft: Transmits rotation to F1 unit.

• F1 unit: Catalyzes ATP synthesis.

Summary Table: Prokaryotes vs. Eukaryotes

Additional info: Some explanations and context have been expanded for clarity and completeness, including details on regulatory mechanisms, enzyme function, and cell cycle control.