From Atoms to Macromolecules

Atoms and Their Structure

Atoms are the fundamental units of elements, which are pure substances that compose all ordinary matter. The atomic nucleus contains protons (positively charged) and neutrons (neutral), while electrons (negatively charged) orbit the nucleus in electron shells.

• Atom: Smallest unit of an element.

• Proton: Positive charge, found in nucleus.

• Neutron: No charge, found in nucleus.

• Electron: Negative charge, found in electron cloud.

Ions and Isotopes

Ions are atoms with unequal numbers of protons and electrons, resulting in a net charge. Isotopes are variants of elements with the same number of protons but different numbers of neutrons.

• Cation: Atom that has lost electrons, positive charge.

• Anion: Atom that has gained electrons, negative charge.

• Isotope: Same element, different neutron number.

Molecules and Compounds

Molecules form when two or more atoms bond. Compounds are molecules made of more than one type of element. Molecular formulas indicate the ratio of elements (e.g., for water).

• Molecule: Two or more atoms bonded.

• Compound: Molecule with different elements.

Organic vs. Inorganic Molecules

Organic molecules contain both carbon and hydrogen. Inorganic molecules may contain carbon but lack associated hydrogen. Functional groups are specific molecular groups that participate in chemical reactions.

• Organic: Contains carbon and hydrogen.

• Inorganic: May contain carbon, lacks hydrogen.

• Functional group: Shared chemical properties, reactive.

Acids, Bases, and Salts

Acids, bases, and salts are important in cellular chemistry, which often occurs in aqueous solutions.

• Solvent: Dissolving agent (e.g., water).

• Solute: Substance dissolved.

• Salt: Formed when acids and bases react.

• Acid: Adds hydrogen ions ().

• Base: Adds hydroxide ions ().

pH: A Measure of Acidity

The pH scale (0–14) measures acidity and alkalinity. Pure water is neutral (pH 7). Most microbes grow best at pH 6.5–8.5. Buffers stabilize pH by absorbing or releasing ions.

• Acidosis: Blood pH lower than normal.

• Alkalosis: Blood pH higher than normal.

• Buffer: Compound that stabilizes pH.

Chemical Bonds

Valence Electrons and Bonding

Valence electrons are in the outermost shell and participate in chemical reactions. Atoms with full valence shells are stable and nonreactive; those without are reactive.

• Valence electron: Electron in outer shell.

• Stable: Full valence shell (e.g., noble gases).

• Reactive: Not full, can gain, lose, or share electrons.

Ionic Bonds

Ionic bonds are formed by the electrostatic attraction between oppositely charged ions, resulting from electron transfer. Dissolved ionic compounds release electrolytes.

• Ionic bond: Attraction between cation and anion.

• Electrolyte: Free ions in solution.

Covalent Bonds

Covalent bonds form when atoms share electrons. Carbon is central to organic molecules.

• Covalent bond: Shared electron pairs.

Polar Covalent Bonds and Hydrogen Bonds

Polar covalent bonds involve unequal sharing of electrons, creating dipoles. Hydrogen bonds are noncovalent attractions between molecules or within large molecules.

• Polar covalent bond: Unequal sharing, partial charges.

• Hydrogen bond: Noncovalent electrostatic attraction.

Hydrophobic, Hydrophilic, and Amphipathic Molecules

• Hydrophilic: Water-loving, dissolves in water.

• Hydrophobic: Water-fearing, does not dissolve.

• Amphipathic: Both hydrophilic and hydrophobic properties (e.g., phospholipids).

Chemical Reactions

Reactants, Products, and Catalysts

Chemical reactions make or break bonds. Reactants are ingredients; products are results. Catalysts (e.g., enzymes) speed up reactions.

• Reactant: Starting material.

• Product: Resulting substance.

• Catalyst: Increases reaction rate.

Synthesis, Decomposition, and Exchange Reactions

• Synthesis: Builds substances (e.g., dehydration synthesis releases water).

• Decomposition: Breaks substances (e.g., hydrolysis adds water).

• Exchange: Swaps components between compounds.

Activation Energy

Activation energy is the minimum energy required to start a reaction. Catalysts lower activation energy.

• Activation energy: Minimum energy for reaction.

Biologically Important Macromolecules

Four Main Classes of Biomolecules

• Carbohydrates: Sugars, energy and structure.

• Lipids: Fats, oils, waxes, steroids, hydrophobic.

• Nucleic acids: DNA and RNA, genetic material.

• Proteins: Enzymes, structural, transport, communication.

Polymerization and Functional Groups

Macromolecules are built by polymerization (joining monomers) and broken down by decomposition. Functional groups contribute to chemical properties.

Carbohydrates

• Monosaccharide: Single sugar unit.

• Disaccharide: Two monosaccharides linked by glycosidic bond.

• Polysaccharide: Many monosaccharides (e.g., glycogen).

• Glycosidic bond: Formed by dehydration synthesis, broken by hydrolysis.

Functions: Energy, structure, adhesion, communication, environmental sensing.

• Cellulose: Structural in plant/algal cell walls.

• Glycogen: Energy reserve.

• Chitin: Structural in fungal cell walls.

• Peptidoglycan: Bacterial cell wall component.

• Capsules: Protection and adhesion in bacteria.

Lipids

• Saturated: No double bonds, solid at room temperature.

• Unsaturated: Double bonds, liquid at room temperature.

• Monounsaturated: One double bond.

• Polyunsaturated: Multiple double bonds.

• Ester bond: Joins glycerol and fatty acids.

• Triglyceride: Glycerol + three fatty acids.

Functions: Energy, cell structure, signaling.

• Phospholipids: Membrane structure, amphipathic.

• Glycolipids: Lipid + carbohydrate.

• Lipoproteins: Lipid + protein.

• LPS: Gram-negative bacterial cell wall, toxic.

• Mycolic acid: Acid-fast bacterial cell wall, pathogenicity.

• Cholesterol: Animal cell membranes.

Nucleic Acids

• DNA: Double-stranded, deoxyribonucleotides (adenine, guanine, cytosine, thymine).

• RNA: Single-stranded, ribonucleotides (adenine, guanine, cytosine, uracil).

• Nucleotide: Five-carbon sugar, phosphate group(s), nitrogenous base.

• Phosphodiester bond: Joins nucleotides, forms backbone.

Functions: DNA is genetic blueprint; RNA directs protein synthesis and can catalyze reactions (ribozymes); ATP is an energy source.

Proteins

• Amino acid: Amine group, carboxyl group, side (R) group.

• Peptide bond: Joins amino acids.

• Peptide: Short chain of amino acids.

• Polypeptide: Long chain of amino acids.

Protein Structure:

• Primary: Linear sequence of amino acids.

• Secondary: Alpha-helices (spirals), beta-pleated sheets (folds).

• Tertiary: 3D folding, noncovalent and covalent interactions.

• Quaternary: Two or more polypeptide chains combined.

Functions: Structure, enzymes, transport, recognition, communication.

Example:

Enzymes are proteins that catalyze biochemical reactions, lowering activation energy and increasing reaction rates.

Additional info:

Polymerization, functional groups, and macromolecule structure are foundational for understanding microbial cell structure and function, relevant to microbiology.