Chemistry of Life

Atoms, Ions, Chemical Bonds, and Chemical Reactions

The chemistry of life forms the basis for understanding microbial structure and function. This section introduces the fundamental concepts of matter, elements, atomic structure, chemical bonds, and reactions, all of which are essential for microbiology.

• Matter: Anything that occupies space and has mass. Exists in solid, liquid, or gaseous forms.

• Elements: Pure substances that cannot be broken down by natural forces. Common elements in living cells include oxygen, carbon, hydrogen, nitrogen, phosphorus, and sulfur.

• Atoms: The smallest unit of an element, consisting of a nucleus (protons and neutrons) and electrons in orbitals.

• Atomic Nucleus: Contains positively charged protons and neutral neutrons.

• Electrons: Negatively charged particles found in orbitals/shells around the nucleus.

• Atomic Weight: The sum of protons and neutrons in an atom.

• Atomic Number: The number of protons in an atom.

• Valence Electrons: Electrons in the outermost shell; determine chemical reactivity and bonding.

• Isotopes: Atoms of the same element with different numbers of neutrons; same atomic number, different atomic weight.

• Ions: Electrically charged atoms or molecules formed by loss (cation, +) or gain (anion, –) of electrons.

• Electrolytes: Free ions in solution, important for cellular function.

Types of Chemical Bonds

• Covalent Bonds: Formed by sharing electrons between atoms. Can be nonpolar (equal sharing) or polar (unequal sharing).

• Ionic Bonds: Formed by transfer of electrons, resulting in charged ions.

• Hydrogen Bonds: Weak bonds involving a hydrogen atom attracted to oxygen or nitrogen; important in DNA and water.

• van der Waals Forces: Weakest intermolecular forces, dependent on distance; important for molecular recognition (e.g., antibody-antigen).

Types of Chemical Reactions

• Synthesis (Dehydration Synthesis): Formation of larger molecules from smaller ones, with removal of water.

• Hydrolysis: Breakdown of large molecules, requiring water.

• Endergonic Reactions: Require energy input (e.g., synthesis).

• Exergonic Reactions: Release energy (e.g., hydrolysis).

• Redox (Reduction-Oxidation): Involves electron transfer; reduction is gain of electrons, oxidation is loss of electrons.

Chemical Notation Rules

• Element abbreviations represent one atom (e.g., H for hydrogen).

• Numbers before symbols indicate quantity (e.g., 2H).

• Subscripts after symbols show number of atoms in a molecule (e.g., H2O).

• Superscripts (+/–) indicate ions (e.g., Na+).

• Chemical reactions rearrange atoms; they do not create or destroy them.

Inorganic Compounds and Organic Molecules

Microbial cells are composed of both inorganic and organic compounds. Understanding their properties is essential for studying cell structure and metabolism.

• Inorganic Compounds: Do not contain carbon (exceptions: CO2, CO).

• Acids: Substances that release hydrogen ions (H+) in water.

• Bases: Substances that release hydroxyl ions (OH–).

• Salts: Substances that dissociate in water but do not release H+ or OH–.

pH Scale and Buffers

• pH Scale: Measures acidity/alkalinity based on H+ concentration; ranges from 0 (acidic) to 14 (basic), with 7 as neutral.

• Buffers: Chemicals that absorb H+ or OH–, stabilizing pH in biological fluids.

Properties of Water

• Water: Essential solvent for life, held together by hydrogen bonds; polar molecule.

• States: Exists as solid, liquid, or gas depending on temperature.

• Solutions: Mixtures of solute (dissolved substance) and solvent (liquid, usually water).

• Isotonic: Equal solute concentration inside and outside the cell.

• Hypertonic: Higher solute concentration outside the cell.

• Hypotonic: Higher solute concentration inside the cell.

• Hydrophilic: Water-loving, soluble in water.

• Hydrophobic: Water-repelling, insoluble in water.

Organic Molecules

Organic molecules are built on a carbon backbone and are essential for cellular structure and function. They include carbohydrates, proteins, lipids, and nucleic acids.

• Monomer: Basic unit or building block (e.g., glucose).

• Polymer: Chain of monomers (e.g., starch).

Carbohydrates

• Monosaccharides: Simple sugars (glucose, fructose, galactose, ribose, deoxyribose).

• Disaccharides: Two monosaccharides joined covalently (sucrose = glucose + fructose, lactose = glucose + galactose, maltose = glucose + glucose).

• Polysaccharides: Many monosaccharides linked (starch, glycogen, cellulose).

• Functions: Energy storage (starch, glycogen), structural support (cellulose).

Proteins

• Amino Acids: Monomers of proteins; 20 naturally occurring types.

• Structure: Each amino acid has an amino group, carboxyl group, and variable side chain (R group).

• Dipeptide: Two amino acids joined by a peptide bond.

• Polypeptide: Chain of 10 or more amino acids.

• Structural Arrangements:

  • Primary: Sequence of amino acids.

  • Secondary: α helix or β sheet.

  • Tertiary: Three-dimensional globular shape.

  • Quaternary: Multiple tertiary proteins combined.

Lipids

• Triglycerides: Fats and oils; glycerol + fatty acids; saturated (solid) or unsaturated (liquid).

• Phospholipids: Glycerol, two fatty acids, phosphate group; polar head, nonpolar tail; main component of cell membranes.

• Steroids: Includes anabolic, sex, mineralocorticoids, glucocorticoids, phytosterols; important for metabolism and immune function.

• Cholesterol: Precursor for steroids and vitamin D.

• Prostaglandins: Local hormones involved in defense mechanisms (blood clotting, inflammation).

Nucleic Acids

• Nucleotides: Monomers of nucleic acids; consist of pentose sugar, phosphate, and nitrogen base.

• DNA (Deoxyribonucleic Acid): Stores genetic information.

• RNA (Ribonucleic Acid): Directs protein synthesis.

• ATP (Adenosine Triphosphate): Energy transfer molecule.

• Bases: Purines (adenine, guanine), pyrimidines (cytosine, thymine, uracil).

• Complementary Base Pairing: Hydrogen bonds form between specific bases (A-T, G-C in DNA; A-U, G-C in RNA).

Table: Types of Chemical Bonds

Table: Carbohydrate Types and Functions

Key Equations

• Atomic Weight:

• pH Calculation:

• Dehydration Synthesis:

• Hydrolysis:

Example: Complementary Base Pairing in DNA

• In DNA, adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C) via hydrogen bonds.

• This ensures accurate replication and transcription in microbial cells.

Additional info: The notes expand on basic chemistry concepts to provide context for their importance in microbiology, including cell structure, metabolism, and genetic information.