Chapter 2 - Chemical Principles in Microbiology: Structure and Function of Atoms, Molecules, and Macromolecules

Chemical Principles in Microbiology

Introduction

Chemical principles are foundational to understanding microbiology, as all microbial processes are governed by the interactions of atoms and molecules. This chapter explores the structure of atoms, types of chemical bonds, and the properties of important biological molecules essential for microbial life.

The Structure of Atoms

Atomic Structure and Subatomic Particles

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

• Subatomic particles: Atoms are composed of protons (positively charged), neutrons (neutral), and electrons (negatively charged).

• Protons and neutrons form the nucleus, while electrons move around the nucleus in electron shells.

Chemical Elements

• Elements are defined by the number of protons in their nucleus (atomic number).

• Atomic mass is the sum of protons and neutrons.

• Isotopes are atoms of the same element with different numbers of neutrons.

Element	Symbol	Atomic Number	Approximate Atomic Mass
Hydrogen	H	1	1
Carbon	C	6	12
Nitrogen	N	7	14
Oxygen	O	8	16
Sodium	Na	11	23
Magnesium	Mg	12	24
Phosphorus	P	15	31
Sulfur	S	16	32
Chlorine	Cl	17	35
Potassium	K	19	39
Calcium	Ca	20	40
Iron	Fe	26	56
Iodine	I	53	127

Electronic Configurations

• Electrons are arranged in shells around the nucleus, each corresponding to a different energy level.

• The chemical properties of an atom are largely determined by the number of electrons in its outermost shell (valence electrons).

Chemical Bonds and Molecules

How Atoms Form Molecules

• Atoms combine to fill their outermost electron shells, forming chemical bonds.

• The number of missing or extra electrons in the outer shell is called the valence.

• A compound is a molecule that contains two or more different kinds of atoms (e.g., H2O).

Ionic Bonds

• Ions are atoms that have gained or lost electrons, acquiring a charge.

• Cations are positively charged ions (lost electrons); anions are negatively charged ions (gained electrons).

• Ionic bonds are attractions between oppositely charged ions.

Covalent Bonds

• Covalent bonds form when two atoms share one or more pairs of electrons.

• Covalent bonds are stronger and more common in living organisms than ionic bonds.

Hydrogen Bonds

• Hydrogen bonds form when a hydrogen atom covalently bonded to an O or N atom is attracted to another O or N atom in a different molecule.

• Hydrogen bonds are weaker than covalent and ionic bonds but are important in stabilizing biological molecules (e.g., DNA, proteins).

Molecular Mass and Moles

• The molecular mass is the sum of the atomic masses of all atoms in a molecule (unit: dalton, da).

• One mole of a substance is its molecular mass in grams.

Chemical Reactions

Types of Chemical Reactions

• Synthesis reactions: Atoms, ions, or molecules combine to form new, larger molecules. Anabolism refers to synthesis reactions in cells.

• Decomposition reactions: A molecule is split into smaller molecules, ions, or atoms. Catabolism refers to decomposition reactions in cells.

• Exchange reactions: Involve both synthesis and decomposition.

• Reversible reactions: Can proceed in either direction under suitable conditions.

Water and Its Importance

• Water is an inorganic, polar molecule with an unequal distribution of charges.

• It is an excellent solvent, temperature buffer, and is involved in many chemical reactions.

• Polar substances dissociate in water, forming solutes.

Acids, Bases, and Salts

Definitions

• Acids: Substances that dissociate into one or more hydrogen ions (H+) and one or more negative ions.

• Bases: Substances that dissociate into one or more hydroxide ions (OH–) and one or more positive ions.

• Salts: Substances that dissociate into cations and anions, neither of which is H+ or OH–.

Acid-Base Balance: The Concept of pH

• The pH scale expresses the concentration of H+ in a solution.

• Increasing H+ increases acidity; increasing OH– increases alkalinity.

• Most organisms grow best between pH 6.5 and 8.5.

Organic Compounds and Functional Groups

Structure and Chemistry of Organic Molecules

• Organic compounds contain carbon and hydrogen, often with oxygen and nitrogen.

• The carbon skeleton forms the backbone of organic molecules.

• Functional groups attach to the carbon skeleton and determine the chemical properties of the molecule.

Structure	Name of Group	Biological Importance
–OH	Alcohol	Lipids, carbohydrates
–CHO	Aldehyde	Reducing sugars, polysaccharides
–CO–	Ketone	Metabolic intermediates
–CH3	Methyl	DNA, energy metabolism
–NH2	Amino	Proteins
–COO–	Ester	Bacterial and eukaryotic plasma membranes
–O–	Ether	Archaeal plasma membranes
–SH	Sulfhydryl	Energy metabolism, protein structure
–COOH	Carboxyl	Organic acids, lipids, proteins
–PO4	Phosphate	ATP, DNA

Amino Acids and Functional Groups

• Amino acids contain both an amino group (–NH2) and a carboxyl group (–COOH).

Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic Acids

Carbohydrates

• Serve as cell structures and energy sources.

• General formula: (CH2O)n.

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

• Disaccharides: Formed by joining two monosaccharides via dehydration synthesis; can be broken down by hydrolysis.

• Polysaccharides: Large molecules composed of many monosaccharides (e.g., starch, glycogen, cellulose).

Lipids

• Primary components of cell membranes; nonpolar and insoluble in water.

• Simple lipids (fats/triglycerides): Composed of glycerol and fatty acids, formed by dehydration synthesis.

• Saturated fats: No double bonds; unsaturated fats: One or more double bonds (cis or trans configuration).

• Complex lipids: Contain additional elements (P, N, S); phospholipids are essential for membrane structure.

• Steroids: Four carbon rings with functional groups; maintain membrane fluidity.

Proteins

• Composed of C, H, O, N, and sometimes S; essential for cell structure and function.

• Functions include enzymes, transport, movement (flagella), and toxins.

• Amino acids are the building blocks of proteins, joined by peptide bonds (dehydration synthesis).

• Protein structure has four levels: primary, secondary, tertiary, and quaternary.

• Denaturation: Loss of protein structure and function due to environmental changes.

• Conjugated proteins: Contain amino acids plus other organic molecules (e.g., glycoproteins, lipoproteins).

Nucleic Acids

• Composed of nucleotides (pentose sugar, phosphate group, nitrogenous base).

• DNA (deoxyribonucleic acid): Double helix, contains deoxyribose, bases A-T and C-G; stores genetic information.

• RNA (ribonucleic acid): Single-stranded, contains ribose, bases A-U and C-G; involved in protein synthesis.

Adenosine Triphosphate (ATP)

• ATP is the primary energy carrier in cells, composed of ribose, adenine, and three phosphate groups.

• ATP stores energy released from chemical reactions and releases it by hydrolysis of phosphate bonds.

Additional info: Understanding chemical principles is essential for studying microbial metabolism, genetics, and physiology, as all cellular processes depend on the structure and function of atoms, molecules, and macromolecules.