Chemical Principles of Microbiology

Introduction to Chemical Principles

Chemistry is fundamental to understanding microbiology because all living organisms are composed of atoms and molecules. The interactions between these atoms and molecules underlie the structure and function of microbial cells.

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 regions called electron shells around the nucleus.

Chemical Elements and Isotopes

• Chemical element: Defined by the number of protons in the nucleus (atomic number).

• Atomic mass: The sum of protons and neutrons in an atom.

• 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

Electrons are arranged in shells around the nucleus, and their arrangement determines the chemical reactivity of the atom.

• First shell: up to 2 electrons

• Second shell: up to 8 electrons

• Third shell: up to 8 electrons (if outermost)

• The valence shell (outermost shell) determines how atoms interact with each other.

How Atoms Form Molecules: Chemical Bonds

Chemical Bonds and Valence

Atoms form molecules by combining to fill their outermost electron shells. The number of electrons needed to fill the valence shell determines the atom's valence and its combining capacity.

• Chemical bonds are attractive forces that hold atoms together in molecules.

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

Ionic Bonds

• Ions: Atoms that have gained or lost electrons, resulting in a charge.

• Cations: Positively charged ions (lost electrons).

• Anions: Negatively charged ions (gained electrons).

• Ionic bonds: Attractions between oppositely charged ions.

Covalent Bonds

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

• Single, double, or triple covalent bonds are possible depending on the number of shared electron pairs.

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

Hydrogen Bonds

• Hydrogen bonds: Weak attractions between a hydrogen atom covalently bonded to O or N and another O or N atom.

• Hydrogen bonds do not form molecules but stabilize large molecules (e.g., DNA, proteins).

• They break and reform readily, serving as bridges between molecules or within large molecules.

Comparison of Bond Types

Molecular Mass and Moles

Calculating Molecular Mass

• Molecular mass: The sum of the atomic masses of all atoms in a molecule (unit: dalton or atomic mass unit).

• Mole: The molecular mass of a substance expressed in grams.

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 molecules, ions, or atoms. Catabolism refers to decomposition in cells.

• Exchange reactions: Involve both synthesis and decomposition.

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

Activation Energy and Energy Changes

• Activation energy: The energy required to break bonds and initiate a reaction.

• Endergonic reactions: Absorb energy.

• Exergonic reactions: Release energy.

Water and Its Importance

Properties of Water

• Water is an inorganic compound essential for life.

• It is a polar molecule, allowing it to form hydrogen bonds and act as an excellent solvent.

• Water participates in many chemical reactions, including hydrolysis and dehydration synthesis.

Acids, Bases, and Salts

Definitions and Properties

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

• Bases: Substances that dissociate into one or more hydroxide ions (OH-) and one or more positive ions; proton acceptors.

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

Acid–Base Balance: The Concept of pH

• pH: A measure of hydrogen ion concentration in a solution.

• pH scale ranges from 0 (acidic) to 14 (basic), with 7 being neutral.

• Organisms must maintain a stable pH for optimal biochemical reactions; buffers help maintain this balance.

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 are specific groups of atoms that confer characteristic chemical properties to organic molecules.

Representative Functional Groups

Amino Acids and Macromolecules

• Amino acids contain an amino group, a carboxyl group, and a variable side chain (R group).

• Macromolecules are polymers formed by joining monomers through dehydration synthesis (removal of water).

Carbohydrates

Structure and Function

• Carbohydrates serve as energy sources and structural components in cells.

• Composed of carbon, hydrogen, and oxygen (general formula: (CH2O)n).

• Isomers: Molecules with the same chemical formula but different structures.

Monosaccharides, Disaccharides, and Polysaccharides

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

• Disaccharides: Formed by joining two monosaccharides via dehydration synthesis (e.g., maltose, sucrose, lactose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).

Lipids

Structure and Types

• Lipids are nonpolar molecules composed of carbon, hydrogen, and oxygen.

• Functions include energy storage and forming cell membranes.

• Simple lipids: Fats or triglycerides (glycerol + fatty acids).

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

Complex Lipids and Steroids

• Complex lipids: Contain additional elements (P, N, S); phospholipids are major components of cell membranes.

• Steroids: Four carbon rings with functional groups; cholesterol is found in animal cell membranes, ergosterol in fungi.

Proteins

Structure and Function

• Proteins are polymers of amino acids and are essential for cell structure and function.

• Functions include enzymes, transport, movement, toxins, and structural roles.

Amino Acids and Peptide Bonds

• Each amino acid has a central (alpha) carbon, an amino group, a carboxyl group, and a side chain (R group).

• There are 20 different amino acids, each with a unique side group.

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

• Peptide bonds link amino acids via dehydration synthesis.

Levels of Protein Structure

• Primary structure: Sequence of amino acids in a polypeptide chain.

• Secondary structure: Folding into alpha helices or beta sheets, stabilized by hydrogen bonds.

• Tertiary structure: Irregular folding into a 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).

Nucleic Acids

Structure and Function

• Nucleic acids store and transmit genetic information.

• Two main types: DNA (deoxyribonucleic acid) and RNA (ribonucleic acid).

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

DNA and RNA

• DNA: Double helix, deoxyribose sugar, bases A-T and C-G (A pairs with T, C pairs with G).

• RNA: Single-stranded, ribose sugar, bases A-U and C-G (A pairs with U, C pairs with G).

• Types of RNA: mRNA (messenger), rRNA (ribosomal), tRNA (transfer).

Adenosine Triphosphate (ATP)

Structure and Role

• ATP: The main energy-carrying molecule in cells.

• Composed of ribose, adenine, and three phosphate groups.

• ATP stores energy released from exergonic reactions and provides energy for endergonic reactions.

• Hydrolysis of ATP releases energy by removing phosphate groups.