Chapter 2: The Chemistry of Microbiology Notes

Chapter 2: The Chemistry of Microbiology

Objectives

• State the number of protons, neutrons, and electrons in an atom using the periodic table or information from the table.

• List and describe the three types of chemical bonds.

• Read an equation for a chemical reaction and state the name of the type of reaction shown.

• Select and give examples of carbohydrates, proteins, lipids, and nucleic acids.

Atoms and Elements

Atomic Structure

• Atom: Smallest unit of matter that retains the properties of an element.

• Subatomic particles:

  • Protons: Positively charged, found in the nucleus.

  • Neutrons: No charge, found in the nucleus.

  • Electrons: Negatively charged, orbit the nucleus in electron shells.

• Element: Substance composed of a single type of atom (e.g., hydrogen, oxygen, carbon).

Atomic Number and Atomic Mass

• Atomic Number (Z): Number of protons in the nucleus of an atom. Determines the element's identity.

• Atomic Mass (A): Sum of protons and neutrons in the nucleus. Equation: $\text{Atomic Mass} = \text{Number of Protons} + \text{Number of Neutrons}$

Isotopes

• Atoms of the same element with different numbers of neutrons.

• Some isotopes are radioactive and release energy during decay.

Common Elements of Life

Element	Symbol	Atomic Number	Atomic Mass	Biological Significance
Hydrogen	H	1	1	Component of organic molecules and water; H+ essential for pH
Carbon	C	6	12	Backbone of organic molecules
Nitrogen	N	7	14	Component of amino acids, proteins, and nucleic acids
Oxygen	O	8	16	Component of water, organic molecules; required for aerobic respiration
Phosphorus	P	15	31	Component of nucleic acids, ATP, and phospholipids
Sulfur	S	16	32	Component of proteins and some vitamins

Electron Configuration and Chemical Bonds

Electron Configuration

• Electrons occupy electron shells around the nucleus.

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

Bohr Model

• Visual representation of electrons in shells around the nucleus.

• First shell holds up to 2 electrons; second shell up to 8, etc.

Chemical Bonds

• Covalent Bonds: Atoms share pairs of electrons.

  • Nonpolar covalent: Electrons shared equally (e.g., O2, H2).

  • Polar covalent: Electrons shared unequally, creating partial charges (e.g., H2O).

• Ionic Bonds: Electrons transferred from one atom to another, forming charged ions (e.g., NaCl).

• Hydrogen Bonds: Weak attraction between partially charged H+ and negative atoms (e.g., between water molecules, DNA base pairs).

Electronegativity

• Measure of an atom's ability to attract electrons in a bond.

• Differences in electronegativity determine bond type (nonpolar, polar, ionic).

Summary Table: Characteristics of Chemical Bonds

Type of Bond	Description	Relative Strength
Nonpolar covalent	Electrons shared equally	Strong
Polar covalent	Electrons shared unequally	Strong
Ionic	Complete transfer of electrons	Weaker than covalent in water
Hydrogen	Attraction between H+ and negative atom	Weaker than covalent or ionic

Chemical Reactions

Synthesis Reactions

• Form larger, more complex molecules from smaller ones.

• Often require energy input (endergonic).

• Dehydration synthesis: Water molecule formed as a product.

• General equation: $A + B \rightarrow AB$

Decomposition Reactions

• Break bonds in large molecules to form smaller atoms, ions, or molecules.

• Release energy (exergonic).

• Hydrolysis: Water is added to break bonds.

• General equation: $AB \rightarrow A + B$

Exchange Reactions

• Involve breaking and forming covalent bonds.

• Atoms move from one molecule to another.

• General equation: $AB + C \rightarrow AC + B$

Water, Acids, Bases, and Salts

Water

• Most abundant substance in organisms.

• Polar covalent bonds give water unique properties (e.g., surface tension, temperature stability).

Acids and Bases

• Acids: Release H+ ions in solution; lower pH.

• Bases: Bind H+ or release OH-; raise pH.

• pH scale: $\text{pH} = -\log_{10}[\text{H}^+]$

• pH 7 is neutral; lower is acidic, higher is basic.

Salts

• Compounds that dissociate in water into cations and anions other than H+ and OH-.

• Important for cellular functions and as electrolytes.

Organic Macromolecules

Functional Groups

• Specific groupings of atoms within molecules that have characteristic properties (e.g., hydroxyl, carboxyl, amino, phosphate).

Carbohydrates

• Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)n.

• Functions: Energy source, structural support (e.g., cell walls).

• Types:

  • Monosaccharides: Simple sugars (e.g., glucose).

  • Disaccharides: Two sugars (e.g., sucrose).

  • Polysaccharides: Many sugars (e.g., glycogen, cellulose).

Lipids

• Hydrophobic organic molecules; not composed of regular subunits.

• Types:

  • Fats (triglycerides): Energy storage, insulation.

  • Phospholipids: Major component of cell membranes.

  • Waxes: Waterproofing, structure.

  • Steroids: Hormones, membrane structure (e.g., cholesterol).

Proteins

• Composed of amino acids (contain C, H, O, N, sometimes S).

• Functions: Structure, enzymes, transport, regulation, defense.

• Peptide bonds: Link amino acids via dehydration synthesis.

• Levels of structure: Primary, secondary, tertiary, quaternary.

Nucleic Acids

• DNA and RNA are polymers of nucleotides.

• Nucleotide structure: Phosphate group, pentose sugar (deoxyribose or ribose), nitrogenous base (A, T/U, G, C).

• DNA: Double-stranded, genetic material of cells and viruses.

• RNA: Single-stranded, involved in protein synthesis and gene regulation.

ATP (Adenosine Triphosphate)

• Main energy currency of the cell.

• Energy released when phosphate bonds are broken: $\text{ATP} \rightarrow \text{ADP} + \text{P}_i + \text{energy}$

Summary

• Chemistry is fundamental to understanding microbial structure and function.

• Atoms, elements, and chemical bonds form the basis of biological molecules.

• Organic macromolecules (carbohydrates, lipids, proteins, nucleic acids) are essential for life.