General Biology Study Notes: Water, Chemical Reactions, Macromolecules, and Proteins

Water: Properties and Biological Importance

Hydrogen Bonding and Water Structure

Water's unique properties arise from its molecular structure and the hydrogen bonds that form between molecules.

• Hydrogen bonds: Weak attractions between an electronegative atom (like oxygen) and a hydrogen atom.

• Hydrogen bonds are crucial for maintaining the three-dimensional shapes of large biological molecules (e.g., proteins, DNA).

• Hydrogen bonds can form between water molecules and other polar molecules, making water an efficient solvent.

• Hydrophilic (water-loving) substances: Ions and polar molecules that dissolve easily in water due to hydrogen bonding.

• Hydrophobic (water-fearing) substances: Uncharged, nonpolar compounds that do not dissolve in water and interact through hydrophobic interactions.

Water: Polarity and Attraction

• Water molecules are polar, leading to strong intermolecular attractions (hydrogen bonds).

• Cohesion: Tendency of water molecules to stick together, resulting in high surface tension and contributing to capillary action.

• Adhesion: Attraction between water molecules and other substances, aiding in capillary action.

• Water is less dense as a solid (ice) than as a liquid due to the organization of hydrogen bonds, allowing ice to float and insulate aquatic environments.

Water's Capacity for Absorbing Energy

• Water has a high specific heat: the amount of energy needed to raise the temperature of 1 gram of water by 1°C.

• Extensive hydrogen bonding means water resists temperature changes, aiding in homeostasis.

• Heat of vaporization: Water requires a lot of energy to evaporate, helping organisms cool through sweating or transpiration.

Chemical Reactions and Energy

Acid-Base Chemical Reactions

Chemical reactions in biology often involve acids and bases, which affect the pH and function of biological systems.

• Acids: Substances that give up protons (H+) during chemical reactions, increasing hydronium ion concentration.

• Bases: Substances that acquire protons or reduce hydronium ion concentration.

• The chemistry of life is sensitive to acidic and basic conditions.

Chemical Reactions and Equilibrium

• Chemical reactions occur when bonds are broken and formed, often written as equations: $\text{Reactant(s)} \rightarrow \text{Product(s)}$

• Chemical equilibrium: The point at which the forward and reverse reactions occur at the same rate.

• Equilibrium can be disturbed by changing reactant/product concentrations or temperature.

Energy in Chemical Reactions

• Energy: The capacity to do work or supply heat.

• Exists as potential energy (stored in chemical bonds) and kinetic energy (energy of motion).

• In molecules, potential energy depends on the position of shared electrons in covalent bonds.

• The first law of thermodynamics: Energy is conserved; it can be transferred or transformed but not created or destroyed.

• The second law of thermodynamics: Entropy (disorder) always increases in a closed system.

Spontaneity of Chemical Reactions

• Spontaneous reactions proceed without continuous external input.

• Driven by two factors:

  • Products have lower potential energy than reactants.

  • Products are more disordered (higher entropy).

Metabolic Pathways

• A metabolic pathway is a series of chemical reactions, each catalyzed by a specific enzyme.

• Two types:

  • Anabolic pathways: Build complex molecules (require energy).

  • Catabolic pathways: Break down complex molecules (release energy).

• Metabolic pathways are regulated to meet the needs of the cell.

Carbon and Organic Molecules

Carbon: The Backbone of Life

• Carbon atoms form the backbone of most biological molecules.

• Can form four covalent bonds, allowing for branching, rings, and chains of various lengths.

• Forms polar bonds (C–O) and nonpolar bonds (C–H).

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical behavior of those molecules.

• Common functional groups: hydroxyl, carbonyl, carboxyl, amino, phosphate, sulfhydryl.

• Functional groups confer specific properties, such as acidity, basicity, or reactivity.

Macromolecules: Structure and Function

Polymers and Monomers

• Large biological molecules (macromolecules) are polymers made by linking smaller units called monomers.

• Condensation (dehydration) reactions: Join monomers by removing water.

• Hydrolysis reactions: Break polymers into monomers by adding water.

• Enzymes control these reactions in cells.

Proteins

Proteins are the most diverse biological molecules, involved in nearly every function in the body.

• Composed of amino acids (20 types), each with a core structure and a unique side chain (R group).

• The sequence of amino acids (primary structure) determines the protein's shape and function.

• Secondary structure: Local folding into alpha-helices and beta-pleated sheets, stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape formed by interactions between side chains.

• Quaternary structure: Association of multiple polypeptide chains.

• Denaturation: Loss of 3D structure (and function) due to heat, pH changes, or chemicals; some proteins can renature.

Protein Functions

• Enzymatic proteins: Catalyze chemical reactions (e.g., digestive enzymes).

• Defensive proteins: Protect against disease (e.g., antibodies).

• Storage proteins: Store amino acids (e.g., casein in milk).

• Transport proteins: Move substances (e.g., hemoglobin transports oxygen).

• Hormonal proteins: Coordinate activities (e.g., insulin regulates blood sugar).

• Receptor proteins: Respond to chemical stimuli (e.g., nerve cell receptors).

• Contractile and motor proteins: Movement (e.g., actin and myosin in muscles).

• Structural proteins: Support (e.g., collagen, keratin).

Nucleic Acids

Structure and Function

• Nucleic acids are polymers of nucleotides.

• Two types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

• Nucleotide monomers are joined by phosphodiester bonds.

• DNA is double-stranded (antiparallel), with complementary base pairing (A with T, C with G).

• RNA is usually single-stranded and can have various functions (e.g., mRNA, tRNA, rRNA).

Carbohydrates

Monosaccharides and Polysaccharides

• Carbohydrates are monomers or polymers of monosaccharides (simple sugars).

• General formula: multiples of CH2O.

• Monosaccharides (e.g., glucose, fructose) are a ready source of energy.

• Polysaccharides (e.g., starch, glycogen, cellulose) are formed by linking monosaccharides via glycosidic bonds.

• Functions: energy storage, structural support, precursors for other molecules.

Variation in Sugars

• Location of carbonyl group

• Number of carbons

• Spatial arrangement of atoms

• Linear and ring forms

Lipids

Structure and Function

• Lipids are hydrophobic molecules, including fats, phospholipids, and steroids.

• Fats store energy, phospholipids form cell membranes, and steroids serve as hormones.

• Phospholipid bilayers exhibit selective permeability, allowing some substances to cross while blocking others.

Types of Lipids

• Saturated fats: No double bonds between carbon atoms; solid at room temperature.

• Unsaturated fats: One or more double bonds; liquid at room temperature.

Summary Table: Macromolecules and Their Monomers

Macromolecule	Monomer	Bond Type	Main Functions
Proteins	Amino acids	Peptide bond	Enzymes, structure, transport, defense, signaling, movement
Nucleic acids	Nucleotides	Phosphodiester bond	Genetic information storage and transfer
Carbohydrates	Monosaccharides	Glycosidic bond	Energy storage, structure, cell recognition
Lipids	Glycerol and fatty acids (for fats)	Ester bond	Energy storage, membranes, signaling