Chemistry of Life

Electrons and Energy

Atoms consist of a nucleus surrounded by electrons in energy levels called shells. The arrangement of electrons in these shells determines the atom's chemical behavior.

• First shell: Lowest energy level, closest to the nucleus.

• Second shell: Higher energy level than the first.

• Third shell: Highest energy level among the three.

Electronegativity is the measure of how strongly an atom's nucleus attracts its orbiting electrons. This property influences the type of chemical bonds atoms form.

Covalent and Ionic Bonds

• Covalent Bonds: Electrons are shared between atoms.

  • Non-polar covalent: Electrons are shared equally (e.g., O2).

  • Polar covalent: Electrons are shared unequally due to differences in electronegativity (e.g., H2O).

• Ionic Bonds: Electrons are transferred from one atom to another, resulting in charged ions (e.g., NaCl). Occurs when electronegativity differences are large.

Polarity

• Non-polar bonds: Equal sharing of electrons.

• Polar covalent bonds: Unequal sharing of electrons.

• Ionic bonds: Complete transfer of electrons.

Properties of Water

Structure and Polarity

Water's unique properties arise from its molecular structure and polarity. Each water molecule contains two polar covalent bonds, forming a bent shape. Multiple water molecules interact via hydrogen bonds, creating a network.

Hydrogen Bonding and Properties

• Cohesion: Attraction between water molecules due to hydrogen bonding. Responsible for surface tension and the movement of water in plants.

• Adhesion: Attraction between water molecules and other substances.

• Capillary Action: Movement of water within narrow spaces, resulting from cohesion and adhesion.

Water and Temperature

• High Specific Heat: Water absorbs a lot of heat before increasing in temperature.

• High Heat of Vaporization: Requires significant energy to convert water from liquid to gas.

• Evaporative Cooling: As water evaporates, it removes heat, cooling the surface.

Density of Ice

• Ice is less dense than liquid water because hydrogen bonds form a stable lattice, spacing molecules farther apart.

• In liquid water, hydrogen bonds constantly break and reform.

Water as a Solvent

• Hydrophilic substances: Ionic or polar molecules that dissolve in water (e.g., salt, sugar).

• Hydrophobic substances: Nonpolar molecules that do not dissolve in water (e.g., oil).

pH Scale

• Measures the concentration of H+ ions in a solution.

• Scale ranges from 0 (most acidic) to 14 (most basic).

• Pure water has a neutral pH of 7 (equal amounts of H+ and OH-).

Introduction to Biomolecules

Why Carbon?

Carbon is the backbone of biological molecules due to its ability to form four covalent bonds, allowing for diverse structures such as chains, rings, and complex branching.

• Can form single, double, or triple bonds.

• Can assemble into various organic compounds.

Functional Groups

Chemical groups attached to carbon skeletons that determine molecular behavior and reactivity.

Macromolecule Structure

• Monomers: Small, repeatable subunits (e.g., monosaccharides, amino acids, nucleotides).

• Polymers: Large molecules made from chains of monomers (e.g., polysaccharides, proteins, nucleic acids).

Dehydration Synthesis and Hydrolysis

• Dehydration Synthesis: Builds polymers by removing a water molecule (one monomer loses a hydroxyl group, another loses a hydrogen).

• Hydrolysis: Breaks polymers into monomers by adding water (enzymes add a hydroxyl group and hydrogen atom).

Carbohydrates

Structure and Function

• Composed of carbon, hydrogen, and oxygen (1:2:1 ratio).

• Functions: energy source, structural support, energy storage, and transport.

Types of Carbohydrates

• Monosaccharides: Simple sugars (e.g., glucose, fructose, galactose); soluble in water; can be linear or ring-shaped.

• Disaccharides: Two monosaccharides joined by a glycosidic bond (e.g., sucrose, lactose).

• Polysaccharides: Long chains of monosaccharides; can be branched or unbranched (e.g., cellulose, chitin, starch, glycogen).

Lipids

Structure and Function

• Long-term energy storage and structural components of cell membranes.

• Nonpolar and hydrophobic; includes fats, oils, waxes, and steroids.

Fatty Acids

• Consist of a hydrophilic carboxyl group and a hydrophobic hydrocarbon tail (4–36 carbons).

Saturated vs. Unsaturated Fatty Acids

• Saturated: Only single bonds; straight, flexible tails; solid at room temperature (e.g., butter).

• Unsaturated: One or more double bonds; bent tails; liquid at room temperature (e.g., vegetable oils).

Types of Lipids

• Fats: Glycerol bonded to one, two, or three fatty acids (e.g., triglycerides, phospholipids).

• Waxes: Long fatty acid tails bonded to alcohols or rings; water-resistant and firm.

• Steroids: Four fused carbon rings; no fatty acid tails (e.g., cholesterol, estrogen, testosterone).

Proteins

Structure and Function

• Most diverse macromolecules; involved in nearly all cellular processes.

Types of Proteins and Functions

Amino Acids and Protein Structure

• 20 different amino acids, each with an amine group, carboxyl group, and variable R group.

• Proteins are polymers of amino acids (polypeptides) linked by peptide bonds.

• Sequence and arrangement of amino acids determine protein structure and function.

Levels of Protein Structure

• Primary: Linear sequence of amino acids.

• Secondary: Local folding into alpha helices or beta sheets via hydrogen bonds.

• Tertiary: Overall 3D shape due to R group interactions (hydrogen bonds, hydrophobic interactions, disulfide bridges, ionic bonds).

• Quaternary: Association of multiple polypeptide chains (e.g., hemoglobin has four subunits).

Denaturation

• Loss of protein's three-dimensional structure, resulting in loss of function.

• Caused by changes in temperature, pH, salts, or detergents.

Nucleic Acids

Structure and Function

• DNA and RNA are polymers of nucleotides.

• Each nucleotide consists of a phosphate group, a 5-carbon sugar (deoxyribose in DNA), and a nitrogenous base (A, T, C, G).

DNA Structure

• Deoxyribose sugar has five carbon atoms.

• DNA strands are antiparallel (run in opposite directions: 5'→3' and 3'→5').

• Hydrogen bonds hold complementary bases together: A=T (2 bonds), G≡C (3 bonds).

• Phosphodiester bonds link nucleotides along the backbone.

Base Pairing Rules

• Pyrimidines (T, C; single rings) always pair with purines (A, G; double rings).

Example: In DNA, the sequence 5'-ATCG-3' pairs with 3'-TAGC-5'.

Additional info: Understanding the chemistry of life is foundational for all biological processes, as the structure and interactions of molecules determine the function of cells and organisms.