General Biology: Cell Structure, Biochemistry, and Membrane Function Study Guide

Introduction to Cell and Molecular Biology

Unity and Diversity of Cells

Cells are the fundamental units of life, displaying both remarkable diversity and underlying unity. All living cells share basic chemical processes and structures, despite differences in appearance and function.

• Cells vary in appearance and function: Cells can be specialized for different roles in multicellular organisms, such as muscle, nerve, or skin cells.

• Living cells have the same basic chemistry: All cells use DNA as genetic material and follow the central dogma: DNA → RNA → Protein.

Cells Under the Microscope

Microscopy has enabled scientists to observe cells and their internal structures, leading to the development of cell theory.

• Cell theory: All living things are composed of cells, and all cells arise from pre-existing cells.

Classification of Cells

Cells are classified into two main types based on structural differences.

• Prokaryotes: Cells without a nucleus (e.g., bacteria, archaea).

• Eukaryotes: Cells with a nucleus and membrane-bound organelles (e.g., plants, animals, fungi, protists).

The Eukaryotic Cell

Eukaryotic cells contain a nucleus and various organelles, each with specialized functions.

• Nucleus: Contains genetic material (DNA).

• Organelles and their purposes:

  • Cytosol: Fluid portion of the cell where metabolic reactions occur.

  • Mitochondria: Site of cellular respiration and ATP production.

  • Chloroplasts: Site of photosynthesis in plant cells.

  • Rough Endoplasmic Reticulum (ER): Studded with ribosomes; synthesizes proteins.

  • Smooth ER: Synthesizes lipids and detoxifies chemicals.

  • Golgi apparatus: Modifies, sorts, and packages proteins and lipids.

  • Lysosome: Contains digestive enzymes to break down waste.

  • Vesicles: Transport materials within the cell.

  • Endocytosis/Exocytosis: Processes for importing/exporting materials.

  • Cytoskeleton: Network of protein filaments for cell shape and movement.

Basics of Biological Chemistry

Atoms

Atoms are the basic units of matter, composed of subatomic particles.

• H, C, N, O significance: Hydrogen, carbon, nitrogen, and oxygen are the most abundant elements in living organisms.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Neutral particles in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus.

Chemical Bonds

Atoms combine to form molecules through different types of chemical bonds.

• Ionic bonds: Transfer of electrons from one atom to another.

• Covalent bonds: Sharing of electron pairs between atoms.

• Polar molecules: Molecules with uneven distribution of charge (e.g., water).

Four Types of Small Molecules in Cells

• Sugars:

  • Types: Monosaccharide, disaccharide, oligosaccharide, polysaccharide.

  • Bonds form through condensation reactions (removal of water).

  • Bonds broken by hydrolysis (addition of water).

• Fatty acids:

  • Unsaturated: Contain double bonds; liquid at room temperature.

  • Saturated: No double bonds; solid at room temperature.

  • Bonds form through condensation reactions.

• Amino acids:

  • Contain an amino group and a carboxylic acid group.

  • Side chain (R group) varies among 20 amino acids.

  • Classified as charged (acidic or basic), polar, or non-polar.

  • Bonds form through condensation (peptide bonds).

• Nucleotides:

  • Composed of a nitrogenous base, sugar (ribose or deoxyribose), and phosphate group.

  • Form DNA and RNA via phosphodiester bonds.

Proteins: Structure and Function

Protein Structure

Proteins are polymers of amino acids, and their function depends on their three-dimensional shape.

• Amino acids linked by peptide bonds: Form the polypeptide backbone.

• Polypeptide backbone: Repeating sequence of atoms along the protein chain.

• Amino terminus: The end of a polypeptide with a free amino group.

Levels of Protein Structure

• Primary: Amino acid sequence.

• Secondary: Local folding into alpha helices and beta sheets.

• Tertiary: Overall 3D conformation of a single polypeptide.

• Quaternary: Complex of more than one polypeptide chain.

Protein Folding and Stability

• Non-covalent bonds in proteins:

  • Electrostatic interactions (ionic bonds)

  • Hydrophobic interactions

  • Hydrogen bonds

  • van der Waals forces

• Disulfide bonds: Covalent bonds between cysteine residues stabilize structure.

• Chaperone proteins: Assist in proper folding of other proteins.

• Denaturation: Loss of structure due to pH, temperature, or chemicals.

• Misfolding can cause disease: Examples include amyloid structures and prions.

How Proteins Work

• Ligand: Molecule that binds to a protein.

• Binding site: Region on protein where ligand binds.

• Substrate: Molecule upon which an enzyme acts.

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

Proteins: Regulation and Methods of Study

How Proteins are Controlled

• Feedback inhibition: End product of a pathway inhibits an earlier step.

• Allosteric enzymes: Enzymes regulated by molecules binding at sites other than the active site.

• Phosphorylation: Addition of phosphate groups to regulate activity.

• Covalent modifications: Chemical changes to proteins that affect function.

• ATP hydrolysis and directed movements: Used by motor proteins for movement.

• Scaffolds: Proteins that organize groups of interacting proteins.

Methods of Protein Study

• Fractionation into sub-cellular compartments: Centrifugation separates cell components by size and density.

• Chromatography: Separates proteins based on properties such as affinity, ion-exchange, and size (gel-filtration).

• Gel electrophoresis: Separates proteins by size and charge.

• Mass spectrometry: Identifies proteins by mass and sequence.

• X-ray crystallography: Determines 3D structure of proteins.

• Extrapolation: Using data from experiments to infer protein function.

Membrane Structure and Function

The Phospholipid Bilayer

Biological membranes are primarily composed of a phospholipid bilayer, which forms a selective barrier around cells.

• Phospholipids: Amphipathic molecules with hydrophilic heads and hydrophobic tails.

• Spontaneous closure: Bilayers close on themselves to minimize exposure of hydrophobic regions to water.

• Fluidity: Phospholipids move within the plane of the membrane, influenced by hydrocarbon chain length, saturation, and cholesterol content.

Membrane Proteins

• Functions:

  • Transport substances across the membrane.

  • Detect and relay chemical signals.

  • Act as enzymes.

  • Anchor the membrane to other structures.

• Types:

  • Integral (span the membrane)

  • Peripheral (attached to membrane surface)

• Movement: Some proteins are mobile within the membrane; others are anchored.

• FRAP experiment: Fluorescence Recovery After Photobleaching measures protein mobility.

Membrane Transport

Principles of Membrane Transport

• Membranes as selective barriers: Only certain molecules can cross freely.

• Electrochemical gradient: Combination of concentration and electrical gradients across the membrane.

• Membrane potential: Voltage difference across the membrane.

• Active transport: Movement of substances against their gradient, requiring energy.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Hypertonic, hypotonic, isotonic: Terms describing relative solute concentrations and water movement.

• Aquaporins: Channel proteins that facilitate water movement.

Transporters and Their Functions

• Passive transport: Movement down a concentration gradient without energy input.

• Active transport: Movement against a gradient, requiring energy (e.g., Na+/K+ ATPase pump).

• Co-transport: Symport (same direction) and antiport (opposite direction) mechanisms.

• Example: Glucose and Na+ co-transport in intestinal epithelial cells.

Ion Channels and Membrane Potential

• Gated channels: Open or close in response to stimuli (ligand-gated, voltage-gated).

• Neuron signaling:

  • Structure: Axon, neuron terminal.

  • Action potential: Rapid change in membrane potential that travels along the axon.

  • Na+ channels inactivate temporarily; Na+/K+ ATPase restores ion gradients.

  • Synapse: Junction where neurotransmitters are released to signal the next cell.

Example Table: Types of Chemical Bonds in Biology

Bond Type	Description	Relative Strength
Ionic	Transfer of electrons between atoms	Strong (in dry conditions)
Covalent	Sharing of electron pairs	Very strong
Hydrogen	Attraction between H and electronegative atom	Weak
van der Waals	Transient attractions between molecules	Very weak

Example Table: Comparison of Prokaryotic and Eukaryotic Cells

Feature	Prokaryotes	Eukaryotes
Nucleus	Absent	Present
Organelles	Few or none	Many, membrane-bound
Size	Small (1-10 μm)	Larger (10-100 μm)
Examples	Bacteria, Archaea	Plants, Animals, Fungi, Protists

Key Equations

• Central Dogma of Molecular Biology: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Osmosis (Water Potential): $\Psi = \Psi_s + \Psi_p$ where $\Psi$ is water potential, $\Psi_s$ is solute potential, and $\Psi_p$ is pressure potential.

• Electrochemical Gradient: $\Delta G = RT \ln \left( \frac{[C]_\text{in}}{[C]_\text{out}} \right) + zF\Delta V$ where $\Delta G$ is free energy change, $R$ is gas constant, $T$ is temperature, $[C]$ is concentration, $z$ is charge, $F$ is Faraday's constant, and $\Delta V$ is membrane potential.

Additional info: Some explanations and tables were expanded for clarity and completeness based on standard General Biology content.