Ch 2 and 3-BIOL201- Chemistry of Life- Organic compounds

A. Introduction to the Chemistry of Life

1. Definitions

  • Matter: Anything that occupies space; chemistry is the study of matter.

  • Substance: A distinct part of matter that has consistent properties regardless of its source.

    • Examples: Iron, water.

  • Element: A substance that cannot be broken down into simpler substances by chemical reactions; currently, 112 known elements.

    • Examples: Bromine, mercury, iodine, cadmium, phosphorus, copper.

  • Compound: A substance that can be broken down into simpler substances by chemical reactions; consists of two or more different elements.

    • Key feature: Has constant composition by weight (e.g., water is 11.19% hydrogen and 88.81% oxygen).

2. Atoms and Molecules

a. Atoms

  • The smallest particle of an element retaining its properties.

  • Composed of:

    • Electrons (negative charge)

    • Protons (positive charge)

    • Neutrons (neutral charge)

  • Atomic number is determined by the number of protons; atomic mass is determined by the sum of protons and neutrons.

b. Isotopes

  • Atoms of the same element with differing numbers of neutrons and atomic masses.

    • Examples: Hydrogen isotopes include 1H (no neutron), 2H (deuterium), and 3H (tritium).

  • Isotopes with excess neutrons may emit energy through radioactivity (radioisotopes).

c. Molecules

  • Formed when two or more atoms combine, representing units of all compounds.

  • Examples include water (H2O), glucose (C6H12O6), and elements like H2 and O2.

3. Chemical Bonds

  • Covalent Bonds: Involves sharing electrons to achieve full valence shells.

    • Types of covalent bonds: single (H2), double (O2).

b. Ionic Bonds

  • Formed when atoms gain or lose electrons, becoming ions; the attraction of these ions creates ionic bonds.

  • Example: Sodium chloride (NaCl).

c. Hydrogen Bonds

  • Weak interactions between hydrogen atoms and other electronegative atoms; significant in water.

B. Properties of Water

  • Water (H2O): Covers 70% of Earth's surface, crucial for life, constituent of many organisms (50-98%).

Key Properties

  1. Polarity: Water is a dipole, with partially positive hydrogen atoms and a partially negative oxygen atom.

  2. Hydrogen Bonding: Causes strong interactions between water molecules, contributing to its cohesive properties.

  3. High Specific Heat: Requires 1 calorie/gelsius to raise the temperature by 1°C; minimizes temperature fluctuations in organisms.

  4. Heat of Vaporization: Requires 540 calories/g to convert water from liquid to vapor, resulting in evaporative cooling.

  5. Cohesive and Adhesive Properties: Water molecules stick to themselves (cohesion) and to other substances (adhesion), with applications such as capillary action.

  6. High Surface Tension: Allows small animals to walk on water.

  7. Solvent Properties: Water dissolves many substances, forming hydration shells around ions.

C. Acids, Bases, and the pH Scale

1. Acids and Bases

  • Acids: Proton donors that release H+ in solution (e.g., HCl).

  • Bases: Proton acceptors that produce OH- in solution.

2. pH Scale

  • Ranges from 0 to 14 to indicate the H+ concentration.

    • pH < 7: acidic

    • pH > 7: basic

    • pH = 7: neutral

3. Buffers

  • Systems that maintain pH by minimizing changes in H+ concentration.

D. Organic Compounds

  • Contain carbon and hydrogen (examples: carbohydrates, proteins, lipids, nucleic acids).

1. Carbon Atom Chemistry

  • Carbon forms four bonds, allowing for chains or rings of molecules.

2. Functional Groups

  • Groups on carbon backbones (e.g., hydroxyl, carbonyl) provide unique properties to molecules.

E. Macromolecules and Polymers

1. Monomers and Polymers

  • Monomers: Small units (e.g., monosaccharides, amino acids).

  • Polymers: Larger molecules formed by linking monomers (e.g., polysaccharides, proteins).

2. Reactions

  • Condensation: Removes water to form linkages.

  • Hydrolysis: Adds water to break linkages.

F. Carbohydrates

1. Composition and Classification

  • Made primarily of carbon, hydrogen, and oxygen (CH2O).

  • Classes: Monosaccharides, disaccharides, polysaccharides.

2. Monosaccharides

  • Simple sugars containing 3-7 carbons; hexoses include glucose, fructose, and galactose.

3. Polysaccharides

  • Complex carbohydrates like starch, glycogen, cellulose, and chitin.

G. Lipids

  • Diverse group including fats, oils, steroids, and phospholipids.

1. Fats and Oils

  • Composed of glycerol and fatty acids; categorized into monoglycerides, diglycerides, and triglycerides.

2. Phospholipids

  • Form membranes due to their amphipathic nature (hydrophilic heads, hydrophobic tails).

3. Steroids

  • Characterized by a backbone of carbon rings, with cholesterol being a fundamental example.

H. Proteins

1. Functions

  • Serve as enzymes, structural elements, transport channels, and regulatory molecules.

2. Amino Acids

  • Building blocks of proteins, consisting of 20 standard types.

3. Protein Structure

  • Four levels:

    • Primary: Sequence of amino acids.

    • Secondary: Hydrogen bonding patterns (e.g., alpha helices, beta pleated sheets).

    • Tertiary: Overall folding of the protein due to R-group interactions.

    • Quaternary: Assembly of multiple polypeptide subunits.

I. Nucleic Acids

1. DNA

  • Composed of nucleotides (adenine, thymine, cytosine, guanine); double-stranded, forming a double helix.

    • Base pairing rules: A-T, C-G, with hydrogen bonds stabilizing the structure.

2. RNA

  • Single-stranded, containing ribose sugar and uracil instead of thymine.

3. ATP (Adenosine Triphosphate)

  • Primary energy carrier in cells.