Chemical Principles in Microbiology: Atoms, Bonds, and Biological Macromolecules

Chapter 2: Chemical Principles

The Atom

An atom is the smallest unit of matter that can participate in a chemical reaction. Atoms are composed of a dense nucleus containing protons and neutrons, surrounded by electrons in shells. The types of atoms are called elements, and there are about 90 naturally occurring elements. The nucleus contains nearly all the atom's mass, while the electron cloud occupies most of its volume.

• Proton (p+): Positively charged particle in the nucleus.

• Neutron (n0): Neutral particle in the nucleus.

• Electron (e-): Negatively charged particle in shells around the nucleus.

Nuclear symbols are written as $^{A}_{Z}\mathrm{X}$, where Z is the atomic number (number of protons), and A is the mass number (protons + neutrons). Atoms of the same element with different numbers of neutrons are called isotopes. Atoms are electrically neutral unless they gain or lose electrons, forming ions.

The Periodic Table and Elements Essential for Life

The most important elements for life are represented by the acronym CHNOPS: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur. These elements are fundamental to the structure and function of biological molecules.

Element	Diagram	Valence Electrons	Unfilled Spaces	Max Bonds
Hydrogen	1	1	1	1
Carbon	4	4	4	4
Nitrogen	5	3	3	3
Oxygen	6	2	2	2

Chemical Bonds

Atoms combine to form compounds through chemical bonds. The electrons in the outermost shell, called valence electrons, are involved in bonding.

• Ionic Bonds: Formed when electrons are transferred from one atom (usually a metal) to another (usually a nonmetal), resulting in oppositely charged ions that attract each other. Example: NaCl (table salt).

• Covalent Bonds: Formed when two atoms (usually nonmetals) share electrons. Covalent bonds can be single, double, or triple, depending on the number of shared electron pairs. Covalent compounds are called molecules.

• Hydrogen Bonds: Weak attractions between polar molecules, especially those containing hydrogen bonded to oxygen or nitrogen. These bonds are crucial for the structure of water, DNA, and proteins.

Acids, Bases, and Salts

When dissolved in water, acids, bases, and salts dissociate into ions. The pH scale measures the concentration of hydrogen ions (H+) in solution:

• Acids: pH 0–6; high H+ concentration.

• Bases: pH 8–14; low H+ concentration.

• Neutral: pH 7; equal H+ and OH- concentrations.

Most microbes prefer environments with pH between 6.5 and 8.5, but some can tolerate more extreme conditions.

Organic Chemistry and Biological Macromolecules

Carbon Chemistry

Organic chemistry is the study of carbon-containing compounds. Carbon atoms can form four covalent bonds, allowing them to create chains and rings that serve as the backbone for large biological molecules.

Carbohydrates

Carbohydrates are essential for energy storage and structural components in cells. They are composed of carbon, hydrogen, and oxygen, typically in a 1:2:1 ratio.

• Monosaccharides: Simple sugars (e.g., glucose, fructose, ribose). They are water-soluble and serve as monomers for larger carbohydrates.

• Disaccharides: Formed by joining two monosaccharides (e.g., sucrose = glucose + fructose) via dehydration synthesis.

• Polysaccharides: Long chains of monosaccharides. Examples include starch (plants), glycogen (animals), cellulose (plants/algae), peptidoglycan (bacteria), and chitin (fungi).

Lipids

Lipids are hydrophobic molecules that include fats, oils, waxes, phospholipids, and steroids. They are primarily composed of carbon and hydrogen, with few oxygen atoms.

• Triglycerides: Consist of one glycerol and three fatty acids. Fatty acids can be saturated (no double bonds, solid at room temperature) or unsaturated (one or more double bonds, liquid at room temperature).

• Phospholipids: Composed of glycerol, two fatty acids, and a phosphate group. They are the main component of cell membranes, forming a bilayer with hydrophilic heads and hydrophobic tails.

• Steroids: Characterized by four fused carbon rings. Cholesterol is a key steroid in animal cell membranes and a precursor for hormones and vitamins.

Proteins

Proteins are polymers of amino acids and perform a vast array of functions, including catalysis (enzymes), structure, transport, movement, and immunity. Each amino acid contains an amino group, a carboxyl group, and a unique side chain (R group).

• Primary structure: Sequence of amino acids.

• Secondary structure: Local folding (alpha helices, beta sheets) stabilized by hydrogen bonds.

• Tertiary structure: Overall 3D shape of a single polypeptide.

• Quaternary structure: Arrangement of multiple polypeptide chains.

Nucleic Acids

Nucleic acids (DNA and RNA) store and transmit genetic information. Their monomers are nucleotides, each consisting of a sugar, a phosphate group, and a nitrogenous base.

• DNA: Double helix, bases are adenine (A), thymine (T), cytosine (C), guanine (G); sugar is deoxyribose. Stores genetic information.

• RNA: Single-stranded, bases are adenine (A), uracil (U), cytosine (C), guanine (G); sugar is ribose. Functions in protein synthesis and gene regulation.

ATP: The Energy Currency of the Cell

Adenosine triphosphate (ATP) is the primary energy carrier in all cells. It consists of adenosine (adenine + ribose) and three phosphate groups. Hydrolysis of ATP releases energy for cellular processes.

ATP is produced mainly from glucose metabolism and is continually recycled in living cells.