The Chemistry of Microbiology: Foundations for Life and Cellular Function

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Chapter 2: The Chemistry of Microbiology

Atoms and Atomic Structure

The study of microbiology requires an understanding of the chemical foundations of life, beginning with atoms and their structure. Atoms are the smallest units of matter, and their arrangement determines the properties of elements and molecules.

Atom: The basic unit of matter, composed of a nucleus (containing protons and neutrons) and electrons orbiting in shells.
Element: A substance consisting of only one type of atom.
Atomic Number: The number of protons in the nucleus, defining the element.
Atomic Mass: The sum of protons and neutrons (electrons contribute negligibly).
Isotopes: Atoms of the same element with different numbers of neutrons; some are radioactive and undergo decay.
Electron Configuration: Electrons occupy shells around the nucleus; the outermost shell (valence shell) determines chemical reactivity.
Reactivity: Atoms with incomplete valence shells tend to gain, lose, or share electrons to achieve stability.
Common Elements of Life: Carbon, hydrogen, oxygen, nitrogen, phosphorus, sulfur, and others are essential for biological molecules.

Atomic structure diagram Carbon isotopes: C-12, C-13, C-14 Table of common elements of life

Chemical Bonds

Chemical bonds are formed when atoms interact to achieve stable electron configurations. The type of bond influences the properties of molecules and their biological functions.

Molecule: Two or more atoms held together by chemical bonds.
Compound: A molecule containing atoms of more than one element.
Types of Chemical Bonds:
- Nonpolar Covalent Bonds: Electrons are shared equally between atoms (e.g., O2).
- Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).
- Ionic Bonds: Electrons are transferred from one atom to another, forming charged ions (e.g., NaCl).
- Hydrogen Bonds: Weak attractions between a partially positive hydrogen and a partially negative atom (e.g., between water molecules, DNA base pairs).
Electronegativity: The tendency of an atom to attract electrons; differences in electronegativity drive bond formation.

Electron shell diagrams Bohr diagrams and periodic table Formation of molecules and compounds Types of chemical bonds Nonpolar covalent bond diagram Electronegativity and polar covalent bonds Polar covalent bond example Ionic bond formation Dissociation of ionic bonds in water Hydrogen bonds in DNA Hydrogen bonds are weak and easily broken

Type of Bond	Description	Relative Strength
Nonpolar covalent	Pair of electrons is nearly equally shared between two atoms	Strong
Polar covalent	Electrons spend more time around the more electronegative of two atoms	Strong
Ionic	Electrons are stripped from a cation by an anion	Weaker than covalent in aqueous environments
Hydrogen	Partial positive charges on hydrogen atoms are attracted to full and partial negative charges on other molecules or other regions of the same molecule	Weaker than ionic

Chemical Reactions

Chemical reactions involve the making or breaking of bonds, transforming reactants into products. These reactions are fundamental to metabolism and cellular processes.

Synthesis Reactions: Combine smaller molecules into larger, more complex ones. Dehydration synthesis releases water and stores energy. Also called anabolism.
Decomposition Reactions: Break down larger molecules into smaller components. Hydrolysis adds water and releases energy. Also called catabolism.
Exchange Reactions: Atoms or groups are transferred between molecules, breaking and forming new bonds.
Metabolism: The sum of all chemical reactions in an organism.

Dehydration synthesis reaction Hydrolysis reaction Glucose phosphorylation exchange reaction Exchange reaction equations

Water, Acids, Bases, and Salts

Inorganic molecules such as water, acids, bases, and salts are essential for life. Their properties influence cellular function, chemical reactions, and environmental adaptation.

Water: Makes up 50–99% of living organisms' mass. Cohesive due to hydrogen bonds, creating surface tension. Excellent solvent and participates in many reactions.
Acids: Dissociate to release hydrogen ions (H+).
Bases: Dissociate to release hydroxyl ions (OH–) and bind H+.
pH Scale: Measures the concentration of H+; organisms tolerate only a narrow pH range.
Buffers: Substances that prevent drastic changes in pH by absorbing excess H+ or OH–.
Salts: Compounds that dissociate into cations and anions in water; important for electrical gradients and electron transfer.

Hydrogen bonds between water molecules Surface tension in water pH scale with common substances Hydrogen ion concentration and pH Acid and base dissociation Dissociation of ionic salt in water

Organic Macromolecules

Organic macromolecules are large, complex molecules essential for metabolism and cellular structure. They are composed of carbon frameworks with functional groups and are classified into four main types.

Functional Groups: Specific arrangements of atoms that confer characteristic properties (e.g., hydroxyl, carboxyl, amino).
Monomers and Polymers: Macromolecules are built from monomers linked by covalent bonds to form polymers.
Types: Lipids, carbohydrates, proteins, nucleic acids.

Functional groups table

Lipids

Lipids are hydrophobic molecules composed mainly of carbon and hydrogen. They serve as energy storage, structural components, and signaling molecules.

Fatty Acids: Saturated (single bonds, solid, animal origin) and unsaturated (double bonds, liquid, plant origin).
Triglycerides: Glycerol + 3 fatty acids; most abundant lipid, high energy content.
Phospholipids: Glycerol + 2 fatty acids + phosphate; amphipathic, major component of cell membranes.
Steroids: Four-ring structure; includes cholesterol, hormones, and membrane components.
Cholesterol: LDL (bad, forms plaques) and HDL (good, removes cholesterol).

Saturated fatty acid structure Unsaturated fatty acid structure Triglyceride structure Phospholipid structure and bilayer Steroid structure (cholesterol) Lipoprotein particles (HDL, LDL) HDL removing cholesterol

Carbohydrates

Carbohydrates are composed of carbon, hydrogen, and oxygen in a 1:2:1 ratio. They provide energy, structural support, and are involved in cell recognition.

Monosaccharides: Simple sugars (glucose, fructose), usually cyclic, classified by number of carbons.
Disaccharides: Two monosaccharides linked by dehydration synthesis (e.g., sucrose, lactose).
Polysaccharides: Long chains of monosaccharides; storage (glycogen, starch) and structural (cellulose).

Glucose and acetylglucosamine structures Polysaccharide structures: starch, glycogen, cellulose Dehydration synthesis and hydrolysis of sucrose

Proteins

Proteins are polymers of amino acids and are the most complex macromolecules. They serve structural, enzymatic, transport, and defensive roles.

Amino Acids: Central carbon, amino group, carboxyl group, hydrogen, and variable side group (R).
Peptide Bonds: Link amino acids via dehydration synthesis.
Protein Structure: Primary (sequence), secondary (folding), tertiary (3D shape), quaternary (multiple polypeptides).
Denaturation: Loss of structure leads to loss of function.
Conjugated Proteins: Glycoproteins, lipoproteins, nucleoproteins.

Amino acid structure Amino acid side groups Peptide bond formation

Nucleotides and Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotides and carry genetic information. Nucleotides consist of a phosphate, pentose sugar, and nitrogenous base.

DNA: Double-stranded, antiparallel, held by hydrogen bonds (A-T, G-C).
RNA: Single-stranded, diverse functions in protein synthesis.
Function: Store and transmit genetic information, guide protein synthesis.

Nucleotide structure DNA double helix and base pairing Nucleic acid function

ATP (Adenosine Triphosphate)

ATP is the primary short-term energy storage molecule in cells, composed of adenine, ribose, and three phosphate groups. Hydrolysis of ATP releases energy for cellular processes.

ATP structure ATP function

Summary Table: Common Elements of Life

Element	Symbol	Atomic Number	Atomic Mass	Biological Significance
Hydrogen	H	1	1	Component of organic molecules and water; H+ released by acids
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 and organic molecules; O2 required for aerobic respiration
Phosphorus	P	15	31	Component of nucleic acids and ATP
Sulfur	S	16	32	Component of some amino acids and vitamins
Others	-	-	-	Trace elements required for enzyme function

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