Biochemistry Basics for Microbiology

Biochemistry Basics

Atoms and Elements

All living organisms are composed of matter, which is made up of atoms. Understanding the structure and properties of atoms is fundamental to the study of biochemistry and microbiology.

• Atoms are the smallest units of elements and consist of subatomic particles: protons (positive charge), neutrons (no charge), and electrons (negative charge).

• The number of protons in an atom defines the element and is equal to its atomic number.

• Atoms can vary in their number of neutrons (isotopes) and electrons (ions), but the number of protons remains constant for a given element.

• Atomic mass is the sum of protons and neutrons in an atom. Electrons have negligible mass (about 1/2000th of a dalton).

• Elements are organized in the periodic table by their atomic number.

Isotopes are atoms of the same element with different numbers of neutrons. For example, carbon has three naturally occurring isotopes: C-12, C-13, and C-14.

Electron Shells and Valence Electrons

Electrons are arranged in shells around the nucleus. The chemical behavior of an atom is largely determined by the electrons in its outermost shell, known as valence electrons.

• Atoms with a full valence shell are chemically inert.

• Atoms without a full valence shell are reactive and tend to gain, lose, or share electrons to achieve stability.

Chemical Bonds

Atoms interact to form molecules through chemical bonds, which involve the sharing or transfer of valence electrons.

• Covalent bonds: Sharing of electron pairs between atoms.

• Nonpolar covalent bonds: Equal sharing of electrons.

• Polar covalent bonds: Unequal sharing of electrons, leading to partial charges.

• Ionic bonds: Transfer of electrons from one atom to another, resulting in oppositely charged ions (cations and anions) that attract each other.

• Hydrogen bonds: Weak, noncovalent attractions between a hydrogen atom and an electronegative atom (e.g., oxygen or nitrogen).

• Van der Waals interactions: Weak attractions due to temporary dipoles in molecules.

Electronegativity is an atom's attraction for electrons in a covalent bond. Higher electronegativity means a stronger pull on electrons.

Solutions, Acids, Bases, and Salts

Many biochemical reactions occur in aqueous solutions. The concentration of a solution can be expressed in different ways:

• Molarity (mol/L): Moles of solute per liter of solution.

• Weight/volume proportion (mg/mL): Mass of solute per volume of solvent.

Acids release hydrogen ions (H+), bases release hydroxide ions (OH-), and salts are formed when acids and bases react.

• The pH of a solution measures its acidity or basicity:

$\mathrm{pH} = -\log [\mathrm{H}^+]$

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

• pH indicators (e.g., phenol red) can be used to detect changes in acidity or basicity in microbial growth media.

Properties of Water

Water is the universal solvent in biological systems due to its polar covalent bonds, making it excellent for dissolving polar substances.

• Hydrophilic substances dissolve readily in water.

• Hydrophobic substances do not dissolve in water.

• Amphipathic molecules have both hydrophilic and hydrophobic regions.

Chemical Reactions

Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products.

• Synthesis reactions: Combine two or more reactants to form a larger product (often via dehydration synthesis, which releases water).

• Decomposition reactions: Break down molecules into simpler components (often via hydrolysis, which adds water).

• Exchange reactions: Swap components between molecules.

• Activation energy is the minimum energy required to initiate a reaction.

• Catalysts (organic or inorganic) increase the rate of chemical reactions without being consumed.

Macromolecules in Microbiology

Organic vs. Inorganic Molecules

• Organic molecules contain both carbon and hydrogen (e.g., glucose).

• Inorganic molecules may contain carbon but lack hydrogen (e.g., carbon dioxide).

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

Carbohydrates

Carbohydrates are organic molecules consisting of one or more sugar monomers (monosaccharides). They serve as energy sources, structural components, and play roles in cell adhesion and communication.

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

• Disaccharides: Two monosaccharides linked by a glycosidic bond (formed by dehydration synthesis, broken by hydrolysis).

• Polysaccharides: Long chains of monosaccharides (e.g., cellulose, chitin, peptidoglycan).

Examples of Polysaccharides:

• Cellulose: Major structural component of plant and algal cell walls.

• Chitin: Structural polysaccharide in fungal cell walls.

• Peptidoglycan: Component of bacterial cell walls.

• Capsules: Carbohydrate-based structures in some bacteria for adhesion.

Lipids

Lipids are hydrophobic or amphipathic molecules, including fats, oils, waxes, and steroids. They are important for energy storage, cell structure, and signaling.

• Fats and oils: Built from glycerol and up to three fatty acids (ester bonds).

• Fatty acids: Long hydrocarbon chains with a carboxylic acid group.

• Monoglycerides: One fatty acid chain.

• Diglycerides: Two fatty acid chains.

• Triglycerides: Three fatty acid chains.

• Saturated fatty acids: No double bonds; solid at room temperature (e.g., butter).

• Unsaturated fatty acids: One or more double bonds; liquid at room temperature (e.g., olive oil).

• Waxes: Fatty acids linked to long-chain alcohols.

• Steroids: Four fused hydrocarbon rings (e.g., cholesterol).

• Sterols: Steroids with an alcohol group.

• Phospholipids: Amphipathic molecules, major components of cell membranes, form lipid bilayers.

• Glycolipids: Lipids linked to carbohydrates.

• Lipoproteins: Lipids linked to proteins.

• Lipopolysaccharide (LPS): Toxic component of Gram-negative bacterial cell walls.

• Mycolic acid: Component of acid-fast bacterial cell walls, increases pathogenicity.

Nucleic Acids

Nucleic acids are macromolecules that store and transmit genetic information. There are two main types: DNA and RNA.

• DNA (Deoxyribonucleic acid): Double-stranded helix, contains deoxyribose sugar and the bases adenine, guanine, cytosine, and thymine.

• RNA (Ribonucleic acid): Single-stranded, contains ribose sugar and the bases adenine, guanine, cytosine, and uracil.

• Nucleic acids are polymers of nucleotides, each consisting of a five-carbon sugar, 1-3 phosphate groups, and a nitrogenous base.

• Nucleotides are linked by phosphodiester bonds, forming a sugar-phosphate backbone.

Functions:

• DNA serves as the genetic blueprint for all cells.

• RNA directs protein synthesis and can act as a catalyst (ribozymes).

• Some ribonucleotides (e.g., ATP) serve as energy carriers.

Proteins

Proteins are polymers of amino acids and are essential for virtually all cellular processes.

• There are 20 standard amino acids and 2 nonstandard (selenocysteine and pyrrolysine).

• Each amino acid contains an amine group (NH2), a carboxyl group (COOH), and a variable side chain (R group).

• Amino acids are linked by peptide bonds (between the amine group of one and the carboxyl group of another).

• Peptides: Short chains of amino acids.

• Polypeptides: Long chains of amino acids.

Levels of Protein Structure:

• Primary structure: Linear sequence of amino acids.

• Secondary structure: Local folding into alpha-helices and beta-pleated sheets.

• Tertiary structure: Overall 3D shape, stabilized by noncovalent interactions (ionic bonds, hydrogen bonds, van der Waals forces) and covalent bonds (disulfide bridges).

• Quaternary structure: Association of two or more polypeptide chains.

Functions of Proteins:

• Structural support in cells

• Enzymes (catalyze biochemical reactions)

• Transporters

• Cell recognition and communication

Summary Table: Biological Macromolecules

Macromolecule	Monomer	Bond Type	Main Functions	Examples
Carbohydrates	Monosaccharides	Glycosidic bonds	Energy, structure, adhesion, communication	Cellulose, chitin, peptidoglycan
Lipids	Fatty acids & glycerol	Ester bonds	Energy, membranes, signaling	Triglycerides, phospholipids, steroids
Nucleic Acids	Nucleotides	Phosphodiester bonds	Genetic information, energy transfer	DNA, RNA, ATP
Proteins	Amino acids	Peptide bonds	Structure, enzymes, transport, signaling	Enzymes, antibodies, transporters
Waxes	Long-chain fatty acid & alcohol	Ester bonds	Protection, waterproofing	Cutin, beeswax

Example: The bacterial cell wall contains peptidoglycan (a carbohydrate), while the plasma membrane is composed mainly of phospholipids (a type of lipid). Enzymes (proteins) catalyze the synthesis and breakdown of these macromolecules, and DNA (nucleic acid) encodes the instructions for their production.

Additional info: This summary expands on the original notes by providing definitions, examples, and a comparative table for clarity and completeness.