Chemical Principles in Microbiology: Structure and Function of Biological Molecules

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Chemical Principles of Microbiology

Introduction to Chemical Principles

Chemical principles are foundational to understanding the structure and function of microorganisms. Atoms, molecules, and their interactions form the basis for all biological processes in microbiology.

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 in electron shells around the nucleus.

Structure of an atom with labeled nucleus, protons, neutrons, and electron shells

Chemical Elements and Isotopes

Elements and Atomic Number

Chemical element: Defined by the number of protons in the nucleus (atomic number).
Atomic mass: The sum of protons and neutrons.
Isotopes: Atoms of the same element with different numbers of neutrons.

Hydrogen, carbon, nitrogen, and oxygen are the most abundant elements in living organisms.

Electronic Configurations

Electron Shells and Reactivity

Electrons are arranged in shells with specific energy levels.
The valence shell (outermost shell) determines an atom's chemical reactivity.
Atoms are most stable when their outermost shell is full.

Electronic configuration of carbon atom Electronic configuration of nitrogen atom Electronic configuration of oxygen atom Electronic configuration of magnesium atom Electronic configuration of phosphorus atom Electronic configuration of sulfur atom

Chemical Bonds and Molecules

Types of Chemical Bonds

Ionic bonds: Formed when electrons are transferred from one atom to another, creating ions (cations and anions) that attract each other.
Covalent bonds: Formed when two atoms share one or more pairs of electrons. These are stronger and more common in biological molecules.
Hydrogen bonds: Weak attractions between a hydrogen atom covalently bonded to O or N and another O or N atom. Important for stabilizing large molecules like DNA and proteins.

Ionic bond formation between sodium and chlorine Ionic bond formation resulting in sodium chloride Covalent bond formation in hydrogen molecule Covalent bond formation in methane molecule Hydrogen bond formation in water

Molecular Mass and Moles

Calculating Molecular Mass

Molecular mass: The sum of the atomic masses of all atoms in a molecule, measured in daltons (Da) or atomic mass units (amu).
Mole: The molecular mass of a substance expressed in grams.

Calculation of molecular mass for water

Chemical Reactions

Types of Chemical Reactions

Synthesis reactions: Atoms, ions, or molecules combine to form larger molecules. Anabolism refers to synthesis in cells.
Decomposition reactions: Molecules are split into smaller components. Catabolism refers to decomposition in cells.
Exchange reactions: Involve both synthesis and decomposition.
Reversible reactions: Can proceed in both directions under suitable conditions.

Water and Its Importance

Properties of Water

Water is a polar molecule, making it an excellent solvent for ionic and polar substances.
Hydrogen bonding gives water unique properties such as high heat capacity and surface tension.
Water participates in many chemical reactions, including hydrolysis and dehydration synthesis.

Polarity of water molecule Hydrogen bonding between water molecules Water dissolving sodium chloride

Acids, Bases, and Salts

Definitions and Biological Importance

Acids: Substances that dissociate into hydrogen ions (H+) and anions; proton donors.
Bases: Substances that dissociate into hydroxide ions (OH-) and cations; proton acceptors.
Salts: Substances that dissociate into cations and anions, neither of which is H+ or OH-.

Acid dissociation in water Base dissociation in water Salt dissociation in water

Acid–Base Balance: The Concept of pH

pH Scale and Biological Relevance

pH: Measures the concentration of hydrogen ions in solution.
pH < 7 is acidic, pH = 7 is neutral, pH > 7 is basic (alkaline).
Organisms must maintain a stable pH for optimal biochemical function; buffers help maintain pH balance.

The pH scale with examples of acidic, neutral, and basic solutions

Organic Molecules and Functional Groups

Structure and Diversity of Organic Compounds

Organic compounds contain carbon and hydrogen, often with oxygen and nitrogen.
The carbon skeleton forms the backbone of organic molecules.
Functional groups (e.g., hydroxyl, carboxyl, amino, phosphate) determine the chemical properties and reactivity of organic molecules.

Hydroxyl group in alcohols

Structure	Name of Group	Biological Importance
R-OH	Alcohol	Lipids; carbohydrates
R-CHO	Aldehyde	Reducing sugars, polysaccharides
R-CO-R'	Ketone	Metabolic intermediates
R-CH3	Methyl	DNA; energy metabolism
R-NH2	Amino	Proteins

Table of representative functional groups (part 1)

Structure	Name of Group	Biological Importance
R-COO-R'	Ester	Bacterial and eukaryotic plasma membranes
R-O-R'	Ether	Archaeal plasma membranes
R-SH	Sulfhydryl	Energy metabolism; protein structure
R-COOH	Carboxyl	Organic acids, lipids, proteins
R-PO4	Phosphate	ATP; DNA

Table of representative functional groups (part 2)

Macromolecules: Structure and Synthesis

Monomers and Polymers

Macromolecules are large polymers made of repeating monomers.
Monomers join via dehydration synthesis (removal of water) and are broken down by hydrolysis (addition of water).

Dehydration synthesis reaction

Carbohydrates

Structure and Function

Carbohydrates serve as energy sources and structural components.
General formula: (CH2O)n
Monosaccharides: Simple sugars (e.g., glucose, fructose, deoxyribose).
Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., maltose, sucrose, lactose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

Dehydration synthesis and hydrolysis of disaccharides

Lipids

Types and Biological Roles

Lipids are nonpolar molecules, insoluble in water, and serve as energy storage and membrane components.
Simple lipids (fats/triglycerides): Composed of glycerol and fatty acids.
Saturated fats: No double bonds; unsaturated fats: One or more double bonds (cis or trans configuration).
Complex lipids: Include phospholipids (major component of cell membranes) and steroids (e.g., cholesterol).

Structural formulas of simple lipids Saturated and unsaturated fatty acids in simple lipids Phospholipid structure and orientation in membranes Cholesterol structure as a steroid

Proteins

Structure and Function

Proteins are polymers of amino acids and are essential for cell structure, function, and regulation.
Functions include enzymes, transport, movement, toxins, and structural support.
Amino acids have a central (alpha) carbon, amino group, carboxyl group, and variable side chain (R group).
There are 20 different amino acids, each with a unique side group.

Generalized amino acid structure Table of amino acids (part 1) Table of amino acids (part 2)

Amino acids exist as L- or D-isomers; L-forms are most common in nature.

L- and D-isomers of amino acids

Amino acids are joined by peptide bonds formed via dehydration synthesis.

Peptide bond formation by dehydration synthesis

Levels of Protein Structure

Primary structure: Sequence of amino acids in a polypeptide chain.
Secondary structure: Local folding into alpha helices or beta sheets, stabilized by hydrogen bonds.
Tertiary structure: Overall 3D shape, stabilized by disulfide bridges, hydrogen bonds, ionic bonds, and hydrophobic interactions.
Quaternary structure: Association of two or more polypeptide chains.
Denaturation: Loss of protein structure and function due to environmental changes.
Conjugated proteins: Proteins combined with other organic molecules (e.g., glycoproteins, nucleoproteins).

Primary structure of protein Secondary structure of protein Tertiary structure of protein Quaternary structure of protein Summary of protein structure levels

Nucleic Acids

DNA and RNA Structure and Function

Nucleic acids store and transmit genetic information.
Composed of nucleotides (pentose sugar, phosphate group, nitrogenous base).
DNA: Double helix, deoxyribose sugar, bases A-T and C-G.
RNA: Single-stranded, ribose sugar, bases A-U and C-G; includes mRNA, rRNA, tRNA.

Structure of DNA double helix Structure of a uracil nucleotide in RNA

Adenosine Triphosphate (ATP)

ATP as the Energy Currency of the Cell

ATP is the main energy-carrying molecule in cells.
Composed of adenine, ribose, and three phosphate groups.
Energy is released by hydrolysis of the terminal phosphate bond.

Structure of ATP molecule ATP hydrolysis releases energy

Additional info: This summary covers the chemical principles essential for understanding microbial structure and function, including atomic structure, chemical bonding, macromolecules, and the role of water, acids, bases, and energy molecules in cellular processes.