Biological Molecules

Carbon Chemistry

Carbon is the fundamental element in biological molecules due to its ability to form four covalent bonds, creating diverse molecular structures essential for life.

• Versatility: Carbon forms straight chains, branched chains, and rings.

• Valence: Carbon (4), Oxygen (2), Nitrogen (3), and Hydrogen (1) determine molecular structure.

• Backbone: Carbon's bonding forms the backbone of biomolecules.

Macromolecules: Synthesis and Breakdown

Macromolecules are large biological molecules built from smaller units (monomers). They are synthesized via dehydration reactions (removal of H2O) and broken down via hydrolysis (addition of H2O).

• Four classes: Carbohydrates, Lipids, Proteins, Nucleic Acids.

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components.

• Monomers: Monosaccharides (e.g., glucose, fructose, galactose, ribose).

• Disaccharides: Sucrose, lactose, maltose (formed by glycosidic bonds).

• Polysaccharides:

  • Starch: Plant storage, mostly unbranched.

  • Glycogen: Animal storage (liver, muscle), highly branched.

  • Cellulose: Plant cell walls, structural, unbranched.

  • Chitin: Fungal cell walls, insect exoskeletons (contains N-acetylglucosamine).

• Functions:

  • Immediate energy (glucose).

  • Energy storage (starch, glycogen).

  • Structural support (cellulose, chitin).

  • Components in other biomolecules (ribose in RNA/DNA).

Lipids

Lipids are hydrophobic molecules that include fats, phospholipids, and steroids. They play roles in energy storage, membrane structure, and signaling.

• Types:

  • Fats (triglycerides): Glycerol + 3 fatty acids.

    • Saturated: No double bonds, solid at room temperature (e.g., animal fat).

    • Unsaturated: 1+ double bonds, liquid at room temperature (e.g., plant oils).

  • Phospholipids: 2 fatty acids + phosphate head; amphipathic, form bilayers in membranes.

  • Steroids: Four fused rings; includes cholesterol, sex hormones, vitamins A/D/E/K, bile acids.

• Functions:

  • Energy storage (2x carbohydrates).

  • Membranes (phospholipids).

  • Hormones, insulation, organ protection, waterproof coatings.

Proteins

Proteins are polymers of amino acids that perform a vast array of functions in cells, including catalysis, structure, transport, and defense.

• Monomers: 20 amino acids, each differing by their R group.

  • Nonpolar (hydrophobic), polar, charged.

• Bonds: Peptide bonds link amino acids into polypeptides.

• Structure:

  1. Primary: Amino acid sequence.

  2. Secondary: α-helix, β-sheet (hydrogen bonds).

  3. Tertiary: 3D folding (R group interactions).

  4. Quaternary: Multiple polypeptides.

• Key principle: Sequence → structure → function.

• Functions: Enzymes, storage, hormones, movement, structure (collagen), transport, defense (antibodies).

Nucleic Acids

Nucleic acids store and transmit genetic information. DNA and RNA are the two main types.

• Monomers: Nucleotides = phosphate + pentose sugar + nitrogenous base.

• Polymers: Polynucleotides (DNA, RNA) linked by phosphodiester bonds.

• DNA: Deoxyribose, double-stranded, bases A-T / G-C, hydrogen bonds.

• RNA: Ribose, single-stranded, bases A-U / G-C.

• Sequence: Encodes genetic information, mutations = nucleotide sequence change.

• Central dogma: DNA → RNA → Protein.

Membrane Structure & Transport

Membrane Structure

Biological membranes are primarily composed of a phospholipid bilayer with embedded proteins, providing selective permeability and compartmentalization.

• Fluid Mosaic Model: Phospholipid bilayer (hydrophilic heads, hydrophobic tails) + proteins + carbohydrates.

• Fluidity factors:

  • Temperature: Higher temperature = more fluid; lower temperature = more rigid.

  • Unsaturated fatty acids: Increase fluidity.

  • Cholesterol: Stabilizes; reduces fluidity at moderate temps, prevents freezing at low temps.

Membrane Proteins

Proteins embedded in the membrane perform transport, signaling, and structural functions.

• Integral proteins: Penetrate bilayer (e.g., transmembrane proteins).

• Peripheral proteins: Attached to membrane surface.

• Functions: Transport, cell recognition, enzymatic activity, signal transduction.

• Examples:

  • HIV infection requires CCR5 receptor.

  • CFTR mutation blocks Cl- transport → cystic fibrosis.

Membrane Carbohydrates

Carbohydrates attached to membrane proteins and lipids play roles in cell-cell recognition and signaling.

• Glycolipids/glycoproteins: Short chains (<15 sugars).

• Cell-cell recognition: Immune system, blood types (AB/ABO).

Transport Mechanisms

Transport across membranes can be passive (no energy required) or active (requires ATP).

• Passive (no ATP, down gradient):

  1. Simple diffusion: Small/nonpolar (O2, CO2), some H2O.

  2. Facilitated diffusion: Transport proteins for hydrophilic molecules/ions (e.g., aquaporins for water).

  3. Osmosis: Water diffusion across semipermeable membrane.

     • Hypotonic: Water enters (endosmosis).

     • Hypertonic: Water exits (exosmosis, plasmolysis).

     • Isotonic: Equilibrium.

• Active (requires ATP, against gradient):

  • Pumps: e.g., Na+/K+ pump (maintains gradients), proton pumps.

  • Cotransport: Coupling diffusion of one molecule (H+) with active uptake of another (sucrose).

• Bulk Transport (ATP required):

  • Exocytosis: Vesicles fuse, release contents.

  • Endocytosis: Engulfing particles.

    • Phagocytosis: "Cell eating" solids.

    • Pinocytosis: "Cell drinking" liquids.

Comparison of Membrane Transport Mechanisms

Key Equations

• Osmotic Pressure: where i = van 't Hoff factor, M = molarity, R = gas constant, T = temperature (K)

Additional info:

• Definitions, comparisons, and application scenarios (e.g., plasmolysis in hypertonic solutions) are essential for exam preparation.

Chapter 3 – Water and Life

Hydrogen Bonding & Polar Covalent Bonds

• Water = polar covalent molecule (O more electronegative than H → unequal electron sharing).

• Polarity → partial negative charge on O, partial positive charges on H.

• Leads to hydrogen bonds (weak bonds between δ+ hydrogen and δ– oxygen of nearby water molecules).

• Hydrogen bonding explains unique water properties essential for life.

Four Emergent Properties of Water (from hydrogen bonding)

1. Cohesion & Adhesion

• Cohesion = attraction of water molecules to each other (via H-bonds).

• Adhesion = attraction of water molecules to other surfaces/materials.

• Together enable capillary action → water transport from roots to leaves in plants.

• Cohesion also contributes to surface tension (resistance to breaking surface of water).

• Examples: insects walking on water, floating plants.

2. Universal Solvent

• Water dissolves many compounds:

  • Hydrophilic substances (polar molecules, ions) dissolve easily.

  • Hydrophobic substances (nonpolar, e.g., oils) repel water.

• Water dissolves salts, sugars, proteins with ionic/polar regions.

• Essential for metabolism, chemical reactions, cleaning transport.

3. Moderation of Temperature

• High specific heat: absorbs/releases large amounts of heat with little temperature change.

  • Heat absorbed when H-bonds break; heat released when H-bonds form.

• Stabilizes environments: oceans regulate climate, organisms maintain stable internal temperatures.

• Evaporative cooling: evaporation removes heat → regulates temperature in organisms (e.g., sweating, elephants spraying water).

4. Expansion Upon Freezing

• Solid ice = less dense than liquid water (due to stable H-bond lattice → more open structure).

• Ice floats → insulates bodies of water below, prevents freezing solid.

• Makes aquatic life possible in winter.

Acids, Bases, and pH

• Dissociation of water: H₂O ⇌ H⁺ + OH⁻.

  • [H⁺] in pure water = 10⁻⁷ M → pH 7 (neutral).

• Acids = release H⁺ (low pH).

  • Example: HCl → H⁺ + Cl⁻.

• Bases = release OH⁻ or bind H⁺ (high pH).

  • Example: NaOH → Na⁺ + OH⁻.

• pH scale = −log[H⁺]; each unit = 10× difference in H⁺ concentration.

• Buffers = substances that minimize pH changes.

  • Carbonic acid–bicarbonate buffer important in blood: CO₂ + H₂O ⇌ H₂CO₃ ⇌ HCO₃⁻ + H⁺.

Threats to Water Quality

• Normal rainwater: pH ≈ 5.6 (due to CO₂ forming carbonic acid).

• Acid precipitation: pH < 5.6.

  • Caused by burning fossil fuels → release SO₂ & NOₓ → react with water → H₂SO₄, HNO₃.

• Impacts of acid rain:

  • Soil: kills nitrogen-fixing bacteria, leaches nutrients (Ca, Mg, K).

  • Water: releases toxic aluminum → kills fish.

  • Plants: tree/forest decline.

  • Infrastructure: corrodes buildings, bridges, statues.

• Eastern U.S. rainwater often pH 4–5 (much more acidic than normal).

Chapter 6 – A Tour of the Cell

General Overview

• Cell theory: cells are the basic units of structure and function of life.

• Two main types: prokaryotic vs. eukaryotic.

Prokaryotic vs. Eukaryotic Cells

• Prokaryotes:

  • Small, older.

  • No membrane-bound organelles.

  • DNA is “naked” (not in nucleus, no histones).

  • Small ribosomes.

  • Domains: Bacteria, Archaea.

• Eukaryotes:

  • Larger, younger evolutionarily.

  • Membrane-bound organelles.

  • DNA in chromosomes inside nucleus.

  • Large ribosomes.

  • Kingdoms: Plants, Animals, Fungi, Protists.

Common Structures (Both Cell Types)

1. Cell/Plasma Membrane

   • Phospholipid bilayer + proteins + sugars.

   • Hydrophilic heads, hydrophobic tails.

   • Functions: selective barrier (semipermeable), communication, defense.

2. Cytoplasm

   • Gel-like fluid (water, salts, biomolecules).

   • Site of many chemical reactions.

   • Provides shape, storage, and turgidity in plants.

3. Ribosomes

   • Smallest organelle.

   • Made of rRNA + proteins; two subunits.

   • Free in cytoplasm or attached to ER.

   • Function: protein synthesis.

   • Present in both prokaryotes and eukaryotes.

4. Cytoskeleton

   • Network of microtubules & proteins.

   • Provides structural support, cell shape, organelle anchoring, transport.

5. Cell Wall

   • Strong protective layer (not in animals).

   • Plants → cellulose, pectin, lignin.

   • Fungi → chitin, glucans, glycoproteins.

   • Bacteria → peptidoglycan.

   • Function: support, protection.

Eukaryotic-Only Structures

Nucleus

• Nuclear envelope with pores.

• Contains DNA as chromosomes + nucleolus (makes ribosomes).

• Functions: genetic info storage, control center, RNA synthesis.

Mitochondria

• “Powerhouse of cell.”

• Double membrane; inner folds = cristae; interior = matrix.

• Site of cellular respiration → ATP production.

Endoplasmic Reticulum (ER)

• Rough ER: ribosomes attached; protein synthesis.

• Smooth ER: lipid synthesis; detoxification.

• Both: storage, processing, transport.

Golgi Apparatus

• Stacks of flattened sacs.

• Modifies, sorts, packages proteins/lipids from ER → secretion/transport.

Vacuoles

• Fluid-filled sacs.

• Large central vacuole in plants (stores pigments, toxins, water, nutrients).

• Functions: storage, turgor pressure.

Chloroplasts (plants & algae only)

• Photosynthesis.

• Double membrane + thylakoid system.

• Thylakoids stacked = grana; contain pigments (chlorophyll, carotenoids).

• Stroma = fluid interior.

Lysosomes (animals only)

• Vesicles with digestive enzymes.

• Function: digestion of waste, pathogens, old organelles.

Centrioles / Centrosomes (animals only)

• Barrel-shaped microtubule structures.

• Organize spindle during cell division.

• Form cilia & flagella.

Cilia & Flagella

• Extensions made of microtubules.

• Function: movement, fluid flow across cells.

Differences Between Plant & Animal Cells

• Plant cells: cell wall, chloroplasts, large central vacuole.

• Animal cells: lysosomes, centrioles.

• Both: plasma membrane, cytoplasm, ribosomes, nucleus, mitochondria, ER, Golgi, small vacuoles.

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