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Biology Lecture Notes: Cell Structure and Function

Basic Cell Types

  • Two fundamental cell types: prokaryotic and eukaryotic

  • Prokaryotes: domains Bacteria and Archaea

  • Eukaryotes: protists, fungi, animals, plants

Prokaryotic vs Eukaryotic Characteristics

  • Prokaryotic cells: no nucleus, DNA in a nucleoid, no membrane-bound organelles, cytoplasm bounded by plasma membrane

  • Eukaryotic cells: DNA in a nucleus with a nuclear envelope, membrane-bound organelles, cytoplasm between plasma membrane and nucleus; generally larger

Microscopy and Image Quality (Key Concepts)

  • Light microscopy (LM): visible light passes through specimen and lenses; magnification ~ up to ~1000x; resolution and contrast affect image quality

  • Electron microscopy (EM): TEM (internal structure) and SEM (surface/3D view)

  • Techniques to enhance contrast: staining, labeling; confocal microscopy offers sharper 3D images

  • Lateral movement of membrane proteins: ~10^7 movements per second; flip-flop across bilayer is rare (~once per month)

  • Most subcellular structures are too small to resolve with LM

Size, Surface Area, and Volume

  • Surface area to volume (S:V) ratio is critical for exchange with environment

  • Smaller cells have a greater S:V; higher S:V supports faster exchange

  • Formula (conceptual): rac{S}{V} = rac{ ext{surface area}}{ ext{volume}}

Membrane Structure and Function

  • Plasma membrane is a boundary with selective permeability

  • Phospholipid bilayer: hydrophilic heads face outward, hydrophobic tails inward

  • Fluid mosaic model: membrane is a dynamic lipid bilayer with embedded proteins

  • Lipids: fats (triacylglycerols), phospholipids, steroids

  • Phospholipids are amphipathic: hydrophobic tails, hydrophilic heads

  • Fatty acids: saturated (no double bonds) vs unsaturated (one or more double bonds)

  • Steroids (e.g., cholesterol) are lipids with four fused rings; cholesterol helps modulate membrane fluidity

Lipid Details and Membrane Components

  • Fats are nonpolar and separate from water; triglycerides = glycerol + 3 fatty acids

  • Phospholipids: two fatty acids + phosphate group attached to glycerol; hydrophilic head, hydrophobic tails

  • Cholesterol in membranes helps maintain fluidity at different temperatures

Proteins and Carbohydrates in Membranes

  • Six major functions of membrane proteins: transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to cytoskeleton/ECM

  • Peripheral proteins: bound to membrane surface; Integral proteins: penetrate hydrophobic core

  • Carbohydrates in membranes: glycoproteins and glycolipids on exterior; important for cell-cell recognition

  • ECM in animal cells: composed of glycoproteins (collagen, proteoglycans, fibronectin) linked to plasma membrane via integrins

Organelles: Nucleus and Endomembrane System

  • Nucleus: houses most genes; enclosed by double membrane nuclear envelope with pore complexes; contains chromatin and nucleolus (rRNA synthesis)

  • Nuclear envelope: outer and inner membranes; nuclear pores regulate traffic

  • Endoplasmic Reticulum (ER): Rough ER (ribosomes on surface) synthesizes proteins; Smooth ER lacks ribosomes, synthesizes lipids, detoxifies, stores calcium, and produces glycoproteins

  • Golgi apparatus: cis (receiving) and trans (shipping) faces; modifies, sorts, and packages proteins and lipids into vesicles

  • Lysosomes: hydrolytic enzymes for digestion; autophagy recycles cellular components; can digest ingested materials

  • Vesicles and transport between organelles

Energy and Metabolism Organelles

  • Mitochondria: sites of cellular respiration; ATP production; double membrane with cristae; own DNA

  • Chloroplasts (plants/algae): photosynthesis; thylakoids, granum, stroma; own DNA; part of plastids

  • Peroxisomes: degrade fatty acids; detoxify poisons; produce hydrogen peroxide and convert it to water

Other Organelles and Concepts

  • Ribosomes: protein synthesis; free ribosomes (cytosol) and bound ribosomes (ER/nuclear envelope)

  • Cytoskeleton: network of protein fibers

    • Microtubules: hollow tubes (~25 nm) made of tubulin; maintain shape, track vesicle movement, separate chromosomes during division, cilia/flagella movement

    • Microfilaments (actin filaments): ~7 nm; support shape, enable muscle contraction, cytoplasmic streaming, and cell movement

    • Intermediate filaments: 8–12 nm; provide structural support and anchor organelles

  • Cytoplasmic streaming and amoeboid movement driven by actin-myosin dynamics

  • Extracellular matrix (ECM): network of glycoproteins; provides support and regulates cell behavior

  • Cell walls (plants, fungi, some protists): cellulose in plants; provide protection, shape, and water balance

  • Plasmodesmata (plants): channels through cell walls for transport between plant cells

Intercellular Junctions (Animal Cells) and Plant Junctions

  • Tight junctions: prevent leakage between cells

  • Desmosomes: anchor cells into strong sheets

  • Gap junctions: allow cytoplasmic exchange between adjacent cells

  • In plants: plasmodesmata connect cytoplasm of neighboring cells through cell walls

Protein Structure Basics

  • A protein is one or more polypeptides folded into a unique shape

  • Polypeptides are polymers of amino acids linked by peptide bonds

  • Amino acids: amino group, carboxyl group, and distinctive side chain (R group)

  • Protein structure levels:

    • Primary: amino acid sequence (determined by genes)

    • Secondary: α-helix and β-pleated sheet formed by backbone hydrogen bonds

    • Tertiary: interactions among R groups (hydrogen bonds, ionic, hydrophobic, van der Waals, disulfide bonds)

    • Quaternary: association of two or more polypeptide chains

  • Sickle-cell example: a single amino acid substitution can alter structure and function

  • Denaturation: loss of native structure due to pH, salt, or temperature changes; biologically inactive

Protein Folding in Cells

  • Protein folding is hard to predict from primary structure

  • Many proteins fold through intermediate stages; chaperonins assist proper folding

  • Misfolded proteins are linked to diseases (e.g., Alzheimer’s, Parkinson’s, prions)

Transport Across Membranes

  • Diffusion: movement down a concentration gradient; passive

  • Osmosis: diffusion of water across a selectively permeable membrane

  • Isotonic, hypertonic, hypotonic solutions determine net water movement and cell turgor

  • Facilitated diffusion: through channel or carrier proteins; still passive

  • Active transport: requires energy (ATP); pumps (e.g., proton pump, Na+/K+ pump); may involve cotransport mechanisms

  • Primary vs secondary (indirect) active transport

  • Bulk transport: endocytosis and exocytosis

  • Endocytosis types: phagocytosis, pinocytosis, receptor-mediated endocytosis

Endomembrane and Vesicle Transport Overview

  • Endocytosis brings in large macromolecules via vesicles; exocytosis releases materials via vesicles

  • Receptor-mediated endocytosis involves ligand binding to receptors to trigger vesicle formation

Cell Fractionation (Organelles by Density)

  • Cell fractionation separates organelles to study function

  • Differential centrifugation: stepwise increasing speeds isolates nuclei, mitochondria, microsomes, ribosomes

Plant vs Animal Cells: Water Balance and Walls

  • Plant cells rely on cell wall to maintain turgor in hypotonic solutions

  • Isotonic: no net water movement; Hypotonic: water influx; Hypertonic: water efflux

Quick Reference Summary

  • Cell types, organelles, and their primary functions

  • Key membrane properties: fluid mosaic, amphipathic lipids, lateral mobility, rare flip-flop

  • Major cytoskeletal components and roles in shape, transport, and movement

  • Intercellular junctions and ECM roles in tissue organization

  • Core principles of diffusion, osmosis, and active transport

  • Protein structure levels and folding concepts

  • Endomembrane system: ER, Golgi, lysosomes, and related trafficking

  • Plant cell walls and water balance mechanisms