Cell Structure and Function

Cell Theory

The cell theory is a fundamental concept in biology, describing the properties and significance of cells in living organisms.

• Historical Observations:

  • Robert Hooke (17th century): Observed compartments in cork, naming them "cells."

  • Antonie van Leeuwenhoek: Improved the microscope and observed single-celled microorganisms.

• Development of Cell Theory:

  • Matthias Schleiden: All plant tissues are composed of cells.

  • Theodor Schwann: All animal tissues are composed of cells; together with Schleiden, postulated the cell theory.

  • Rudolf Virchow: Added that all cells arise only from preexisting cells.

• Principles of Cell Theory:

  • All organisms consist of one or more cells.

  • The cell is the basic unit of structure for all organisms.

  • All cells arise only from preexisting cells.

The Emergence of Modern Cell Biology

Modern cell biology integrates three main strands of scientific inquiry:

• Cytology: Focuses on cellular structure, emphasizing optical techniques.

• Biochemistry: Studies cellular structure and function at the molecular level.

• Genetics: Examines information flow and heredity, including genome sequencing.

Early Biochemistry

• Wöhler: Demonstrated that organic compounds can be synthesized in the laboratory.

• Pasteur: Showed that yeasts ferment sugar into alcohol.

• Buchners: Demonstrated that yeast extracts can catalyze fermentation, leading to the discovery of enzymes.

Biochemistry Methods

• Separation Techniques:

  • Subcellular Fractionation: Uses centrifugation to separate cellular structures and macromolecules.

  • Ultracentrifugation: Achieves very high speeds (>100,000 rpm) for fine separation.

  • Chromatography: Separates molecules based on size, charge, or chemical affinity.

  • Electrophoresis: Uses an electric field to move proteins, DNA, or RNA through a medium based on size or charge.

• Identification Techniques:

  • Mass Spectrometry: Determines the size and composition of proteins.

  • X-ray Crystallography: Determines the 3D structure of molecules and complexes.

The Genetic Strand

• Inheritance: Study of how characteristics are passed from generation to generation.

• Key Discoveries:

  • 19th century: Discovery of genes.

  • 1953: Watson, Crick, and Rosalind Franklin proposed the double helix structure of DNA.

  • 1960s: Advances in understanding DNA replication, RNA production, and the genetic code.

Central Dogma of Molecular Biology

The central dogma describes the flow of genetic information within a cell:

• DNA Replication: Nuclear DNA is copied once per cell division.

• Transcription: DNA directs the synthesis of specific mRNA molecules.

• Translation: Ribosomes synthesize proteins encoded by mRNA.

Working with DNA

• Recombinant DNA Technology: Uses restriction enzymes to cut and recombine DNA from different sources.

• DNA Cloning: Generation of many copies of a specific DNA sequence.

• DNA Transformation: Introduction of DNA into cells.

Bioinformatics and "Omics"

• Bioinformatics: Merges computer science and biology to analyze large datasets.

• Genomics: Study of all genes in an organism.

• Proteomics: Study of all proteins and their interactions in a cell.

• Transcriptomics: Study of all genes transcribed in a cell.

• Metabolomics: Analysis of all metabolic reactions in a cell at a given time.

• Lipidomics: Study of all lipids in a cell.

• Ionomics: Study of all ions in a cell.

Macromolecules of the Cell

Proteins

Proteins are polymers of amino acids and perform a wide variety of cellular functions.

• Monomeric Components: Amino acids are the building blocks of proteins.

• Classes of Proteins:

  • Enzymes: Catalysts for biochemical reactions.

  • Structural Proteins: Provide support and shape.

  • Motility Proteins: Involved in contraction and movement.

  • Regulatory Proteins: Control and coordinate cell functions.

  • Transport Proteins: Move substances across membranes.

  • Signaling Proteins: Facilitate communication between cells.

  • Receptor Proteins: Respond to chemical stimuli.

  • Defensive Proteins: Protect against disease.

  • Storage Proteins: Store amino acids.

• Monomeric vs. Multimeric Proteins:

  • Monomeric: Single polypeptide chain.

  • Multimeric: Multiple polypeptide chains (dimers, trimers, etc.). Most functional proteins are multimeric.

• Bonds and Interactions in Protein Structure:

  • Covalent Bonds: Peptide bonds (backbone), disulfide bonds (stabilization).

  • Noncovalent Interactions: Hydrogen bonds, ionic bonds, van der Waals forces, hydrophobic interactions.

• Levels of Protein Structure:

  • Primary: Amino acid sequence (covalent peptide bonds).

  • Secondary: Local folding (α-helix, β-sheet) via hydrogen bonds.

  • Tertiary: 3D folding of a single polypeptide (various bonds/interactions).

  • Quaternary: Association of multiple polypeptides (subunit interactions).

• Fibrous vs. Globular Proteins:

  • Fibrous: Extensive secondary structure, highly ordered (e.g., collagen).

  • Globular: Compact, unique tertiary structure; most enzymes are globular.

• Protein Domains: Functional regions within proteins; proteins with multiple functions often have multiple domains.

Nucleic Acids

Nucleic acids store, transmit, and express genetic information. DNA and RNA are linear polymers of nucleotides.

• Types:

  • DNA: Deoxyribonucleic acid.

  • RNA: Ribonucleic acid.

• Nucleotide Components: Phosphate group, pentose sugar (deoxyribose or ribose), nitrogenous base (adenine, guanine, cytosine, thymine, uracil).

• Nomenclature:

  • Nucleoside monophosphate: One phosphate group.

  • Adenosine diphosphate (ADP): Two phosphate groups.

  • Adenosine triphosphate (ATP): Three phosphate groups.

• Bases:

  • Purines: Adenine (A), Guanine (G).

  • Pyrimidines: Cytosine (C), Thymine (T), Uracil (U).

• Polymerization: Nucleotides are linked by 3',5' phosphodiester bonds, forming a backbone with directionality (5' to 3').

• Nucleic Acid Synthesis: Requires a template for correct base pairing and sequence.

Polysaccharides and Lipids

Polysaccharides

• Long-chain polymers of sugars; serve structural and storage roles.

• May consist of one type of sugar or alternating types.

• Oligosaccharides (short chains) are often attached to cell surface proteins.

• Sugar Classification:

  • Aldosugars: Terminal carbonyl group (aldehyde).

  • Ketosugars: Internal carbonyl group (ketone).

  • Classified by carbon number: trioses (3), tetroses (4), pentoses (5), hexoses (6), heptoses (7).

• Disaccharides: Two monosaccharides linked by a glycosidic bond (formed by water elimination).

• Storage Polysaccharides:

  • Starch (plants): Amylose (unbranched), amylopectin (branched).

  • Glycogen (animals, bacteria): Branched.

  • Both consist of α-D-glucose units linked by α(1-4) glycosidic bonds; α(1-6) bonds create branches.

• Structural Polysaccharides:

  • Cellulose (plants): β-glycosidic bonds, forms rigid rods and microfibrils.

  • Starch/glycogen: α-glycosidic bonds, form loose helices.

Lipids

• Hydrophobic molecules, not formed by linear polymerization.

• Functions: Energy storage, membrane structure, signaling.

• Some are amphipathic (polar and nonpolar regions).

• Fatty Acids: Long, unbranched hydrocarbon chains with a carboxyl group; can be saturated (no double bonds) or unsaturated (cis/trans double bonds).

• Triacylglycerols: Storage lipids; saturated forms are solid at room temperature, unsaturated (plant oils) are liquid.

• Glycolipids: Lipids with carbohydrate groups; found mainly on the outer plasma membrane.

• Steroids: Four-ringed hydrocarbon skeleton; cholesterol is the precursor for other steroids.

Enzymes: The Catalysts of Life

General Properties of Enzymes

• Enzymes increase reaction rates by lowering activation energy.

• They form transient, reversible complexes with substrates.

• Enzymes change the rate at which equilibrium is achieved, not the equilibrium position.

• Most enzymes are proteins, but some RNA molecules (ribozymes) also have catalytic activity.

Major Classes of Enzymes

• Oxidoreductases

• Transferases

• Hydrolases

• Lyases

• Isomerases

• Ligases

Active Site and Cofactors

• The active site is a cluster of amino acids where substrates bind and catalysis occurs.

• Cofactors (prosthetic groups) are nonprotein components required for activity; can be metal ions or coenzymes (often vitamin derivatives).

Enzyme Specificity and Mechanisms

• Enzymes are highly specific for their substrates.

• Induced fit: Substrate binding induces conformational changes in the enzyme, optimizing catalysis.

• Mechanisms of substrate activation:

  • Bond distortion

  • Proton transfer

  • Electron transfer

Enzyme Inhibition

• Irreversible Inhibitors: Bind covalently, permanently inactivating the enzyme (e.g., heavy metals, some drugs).

• Reversible Inhibitors:

  • Competitive: Inhibitor binds active site, blocking substrate.

  • Noncompetitive: Inhibitor binds elsewhere, altering enzyme conformation and reducing activity.

Enzyme Regulation

• Substrate-Level Regulation: Direct interaction of substrates and products with the enzyme; increased substrate increases rate, increased product decreases rate.

• Allosteric Regulation: Enzymes have two conformations; regulated by molecules other than substrates/products (allosteric effectors).

• Feedback Inhibition: Final product of a pathway inhibits an earlier step.

• Covalent Modification: Enzymes can be regulated by addition/removal of chemical groups (e.g., phosphorylation, proteolytic cleavage).

Cells and Organelles

Origin and Characteristics of Cells

• Cell theory: All organisms are composed of cells; cells arise from preexisting cells.

• Origin of cells involved:

  1. Abiotic synthesis of simple organic compounds

  2. Abiotic polymerization into macromolecules

  3. Emergence of self-replicating macromolecules

  4. Encapsulation within a membrane

• Stanley Miller Experiment: Simulated early Earth conditions, demonstrating abiotic synthesis of organic molecules.

• RNA World Hypothesis: RNA may have been the first information molecule; ribozymes can catalyze reactions (e.g., peptide bond formation).

General Characteristics of Cells

• Organizational complexity

• Diverse molecular components

• Variety in size and shape

• Specialization for different functions

Three Domains of Life

• Bacteria

• Archaea

• Eukarya

Cell Size and Diffusion

• Molecules move by diffusion (from high to low concentration).

• As cell size increases:

  • Molecular concentration falls

  • Reaction rates slow down

Eukaryotic Strategies for Large Cell Size

• Cytoplasmic streaming: Active movement of cytoplasmic contents.

• Vesicular transport: Movement of molecules in vesicles along protein fibers.

• Internal organelles: Localize and concentrate molecules for specific functions.

Eukaryotic Cell Overview

• Typical eukaryotic cells have:

  • Plasma membrane

  • Nucleus

  • Membrane-bounded organelles

  • Cytosol interlaced by cytoskeleton

  • Plant and fungal cells: Rigid cell wall and extracellular matrix

Table: Comparison of Major Macromolecules

Key Equations

• Phosphodiester Bond Formation (Nucleic Acids):

• Peptide Bond Formation (Proteins):

• General Enzyme-Catalyzed Reaction:

Additional info: Some explanations and examples have been expanded for clarity and completeness, including the table and equations.