Biochemistry Basics

Atoms and Elements

All living organisms are composed of matter, which in turn is made up of atoms. Understanding atomic structure is fundamental to biochemistry and microbiology.

• Atoms are the smallest units of elements and consist of subatomic particles:

  • Protons: Positively charged; number defines the element (atomic number).

  • Neutrons: No charge; contribute to atomic mass.

  • Electrons: Negatively charged; orbit the nucleus in shells.

• Protons and neutrons have nearly identical mass (measured in daltons); electrons are much lighter and usually ignored in mass calculations.

• Atomic mass is the sum of protons and neutrons in an atom.

• Isotopes are atoms of the same element with different numbers of neutrons (e.g., 12C, 13C, 14C).

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

Electron Shells and Valence Electrons

Electron arrangement determines chemical behavior.

• Electron shells surround the nucleus and hold electrons.

• Valence electrons are in the outermost shell and dictate reactivity.

• Atoms with full valence shells are chemically inert; those without are reactive and tend to gain, lose, or share electrons to achieve stability.

Chemical Bonds

Atoms interact through chemical bonds to form molecules.

• 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, forming charged ions (cations and anions) that attract each other.

• Electronegativity: An atom's tendency to attract electrons in a bond; higher electronegativity means stronger pull.

• Hydrogen bonds: Weak, noncovalent attractions between partially charged regions of molecules.

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

Bond Strength (from strongest to weakest): Covalent > Ionic > Hydrogen > Van der Waals

Solutions, Acids, Bases, and Salts

Understanding solutions and pH is essential for microbiological experiments and cellular processes.

• Concentration is the amount of solute in a given volume of solvent.

• Molarity (mol/L) measures moles of solute per liter of solution.

• Weight-volume proportion (e.g., mg/mL) expresses mass of solute per volume of solvent.

• Acids release hydrogen ions (H+); bases release hydroxide ions (OH-).

• Salts form when acids and bases react; acids contribute anions, bases contribute cations.

• pH measures hydrogen ion concentration:

  • Formula:

  • pH scale ranges from 0 (acidic) to 14 (basic); pH 7 is neutral.

  • Pure water: [H+] = [OH-], pH = 7.

  • Acidic: pH < 7; Basic (alkaline): pH > 7.

• pH indicators (e.g., phenol red) are used in microbiology to detect metabolic by-products.

Properties of Water

Water is the universal solvent in biological systems due to its polarity.

• Polar covalent bonds make water an excellent solvent for polar substances.

• Hydrophilic substances dissolve readily in water; hydrophobic substances do not.

• Amphipathic molecules have both hydrophilic and hydrophobic regions (e.g., phospholipids).

Chemical Reactions

Chemical reactions involve making or breaking bonds, essential for metabolism.

• Reactants: Starting materials; products: Substances formed.

• Synthesis reactions: Build larger molecules from smaller ones (often release water in dehydration synthesis).

• Decomposition reactions: Break down molecules (often require water in hydrolysis).

• Exchange reactions: Swap components between molecules.

• Activation energy: Minimum energy required to start a reaction.

• Catalysts: Substances that speed up reactions without being consumed (can be organic or inorganic).

Organic and Inorganic Molecules

Organic molecules contain both carbon and hydrogen; inorganic molecules may contain carbon but lack hydrogen.

• Example of inorganic molecule: Carbon dioxide (CO2).

• Functional groups determine the chemical properties and classification of organic molecules.

Carbohydrates

Carbohydrates are essential biomolecules serving as energy sources and structural components.

• Monosaccharides: Simple sugars (C, H, O); basic formula:

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

• Polysaccharides: Long chains of monosaccharides.

• Functions: Energy storage, structural support, cellular adhesion, communication, environmental sensing.

Examples:

• Cellulose: Main structural polysaccharide in 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 with diverse structures and functions.

• Types: Fats, oils, waxes, steroids.

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

  • Monoglyceride: One fatty acid.

  • Diglyceride: Two fatty acids.

  • Triglyceride: Three fatty acids.

• 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; sterols are steroids with an alcohol group (e.g., cholesterol).

• Phospholipids: Amphipathic; major component of cell membranes, form bilayers.

• Glycolipids: Lipids linked to carbohydrates.

• Lipoproteins: Lipids linked to proteins.

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

• Mycolic acid: Found in acid-fast bacterial cell walls; increases pathogenicity.

• Cholesterol: Abundant in animal cell membranes.

• Functions: Energy storage, cell structure, cell signaling.

Nucleic Acids

Nucleic acids store and transmit genetic information in cells and viruses.

• Types: Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).

• DNA: Double-stranded helix; contains deoxyribose sugar and bases adenine, guanine, cytosine, thymine.

• RNA: Single-stranded; contains ribose sugar and bases adenine, guanine, cytosine, uracil.

• Nucleotides: Building blocks; each has a five-carbon sugar, 1-3 phosphate groups, and a nitrogenous base.

• Nucleotides are linked by phosphodiester bonds to form the sugar-phosphate backbone.

• Functions: DNA is the genetic blueprint; RNA directs protein synthesis; some RNAs (ribozymes) catalyze reactions; ribonucleotides (e.g., ATP) serve as energy carriers.

Proteins

Proteins are polymers of amino acids and perform most cellular functions.

• Amino acids: 20 standard (genetically encoded), 2 nonstandard (selenocysteine, pyrrolysine).

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

• Amino acids are joined by peptide bonds (between amine and carboxyl groups).

• Peptides: Short chains; polypeptides: long chains.

• Protein folding determines function and involves four levels of structure:

  • Primary: Linear sequence of amino acids.

  • Secondary: Local folding into alpha-helices (spirals) and beta-pleated sheets (accordion folds).

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

  • Quaternary: Association of multiple polypeptide chains.

• Functions: Structural support, enzymes, transporters, cell recognition, communication.

Summary Table: Major Biomolecules

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