Chapter 2: The Chemistry of Microbiology

Atoms and Atomic Structure

Atoms are the fundamental units of matter, forming the basis of all chemical substances. Understanding their structure is essential for grasping the chemical processes that underpin microbiology.

• Matter: Anything that occupies space and has mass.

• Atoms: Smallest chemical units of matter, composed of a nucleus (containing protons and neutrons) and electrons orbiting in shells.

• Protons: Positively charged particles in the nucleus.

• Neutrons: Uncharged particles in the nucleus.

• Electrons: Negatively charged particles circling the nucleus.

Atomic Number and Mass

• Element: Substance composed of a single type of atom.

• Atomic Number: Number of protons in the nucleus.

• Atomic Mass: Sum of protons, neutrons, and electrons (electrons contribute minimally).

Isotopes

Isotopes are variants of elements with differing numbers of neutrons. Some are stable, while others are radioactive and release energy during decay.

• Stable Isotopes: Do not undergo radioactive decay.

• Unstable/Radioactive Isotopes: Undergo decay, releasing energy.

Electron Configuration

Electron shells determine chemical behavior. Only the outermost (valence) electrons interact with other atoms.

• Valence Electrons: Electrons in the outer shell, responsible for chemical bonding.

• Electron Shells: Energy levels where electrons reside.

Chemical Bonds

Chemical bonds are formed when atoms share or transfer valence electrons, resulting in molecules and compounds.

• Molecule: Two or more atoms held together by chemical bonds.

• Compound: Molecule composed of more than one element.

• Valence: Combining capacity of an atom, positive if electrons are given up, negative if spaces are filled.

Covalent Bonds

Covalent bonds involve the sharing of electron pairs between atoms. Electronegativity determines the distribution of shared electrons.

• Electronegativity: Atom's attraction for electrons; higher values mean stronger pull.

• Nonpolar Covalent Bonds: Electrons shared equally; no charge separation.

• Polar Covalent Bonds: Electrons shared unequally, creating partial charges.

Ionic Bonds

Ionic bonds form when atoms with very different electronegativities transfer electrons, resulting in charged ions (cations and anions) that attract each other.

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

• Salts: Crystalline ionic compounds.

Hydrogen Bonds

Hydrogen bonds are weak attractions between partially charged hydrogen and other electronegative atoms. They stabilize large molecules and are essential for life.

• Hydrogen Bond: Electrical attraction between H+ and negative charges.

• Important in stabilizing DNA, proteins, and water properties.

Chemical Reactions

Chemical reactions involve the making or breaking of bonds, transforming reactants into products. Biochemistry studies these reactions in living organisms.

• Synthesis Reactions: Form larger molecules; require energy (endothermic). Example: dehydration synthesis.

• Decomposition Reactions: Break down molecules; release energy (exothermic). Example: hydrolysis.

• Exchange Reactions: Involve both breaking and forming bonds; atoms move between molecules.

• Metabolism: Sum of all chemical reactions in an organism.

Water, Acids, Bases, and Salts

Water is the most abundant substance in organisms, with unique properties due to its polar covalent bonds. Acids, bases, and salts are vital for cellular function and homeostasis.

• Cohesion: Water molecules stick together, generating surface tension.

• Solvent: Water dissolves many substances.

• Temperature Stability: Water absorbs heat without changing temperature rapidly.

• Acids: Dissociate to release H+.

• Bases: Bind H+ or release OH-.

• pH Scale: Measures H+ concentration; buffers maintain pH stability.

• Salts: Dissociate into ions other than H+ or OH-; important for electrical gradients and enzyme function.

Organic Macromolecules

Organic macromolecules are large, carbon-based molecules essential for life. They include lipids, carbohydrates, proteins, and nucleic acids, each with unique structures and functions.

• Functional Groups: Specific atom arrangements that confer properties to molecules.

• Monomers: Basic building blocks of macromolecules.

Lipids

Lipids are hydrophobic molecules not composed of regular subunits. They include fats, phospholipids, waxes, and steroids.

• Fats (Triglycerides): Energy storage; formed by dehydration synthesis of glycerol and fatty acids.

• Phospholipids: Major component of cell membranes; amphipathic structure.

• Waxes: Long-chain fatty acid linked to alcohol; water-insoluble.

• Steroids: Four-ring structure; important in membrane fluidity and signaling.

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources, structural components, and are involved in cell interactions.

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

• Disaccharides: Two monosaccharides joined (e.g., sucrose).

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

Proteins

Proteins are polymers of amino acids, performing diverse functions such as catalysis, regulation, transport, and defense.

• Amino Acids: Monomers of proteins; 21 types used in organisms.

• Peptide Bond: Covalent bond linking amino acids via dehydration synthesis.

• Protein Structure: Four levels – primary, secondary, tertiary, quaternary.

Nucleic Acids and Nucleotides

Nucleic acids (DNA and RNA) are polymers of nucleotides, carrying genetic information and participating in protein synthesis.

• Nucleotide: Monomer composed of phosphate, pentose sugar, and nitrogenous base.

• Nucleoside: Nucleotide lacking phosphate.

• DNA: Double-stranded, antiparallel, complementary strands; genetic material.

• RNA: Single-stranded; involved in protein synthesis and enzymatic functions.

• Base Pairing: C-G (three H bonds), A-T (DNA, two H bonds), A-U (RNA, two H bonds).

ATP (Adenosine Triphosphate)

ATP is the main short-term energy supply for cells. Energy is released when its phosphate bonds are broken.

• ATP: Adenosine triphosphate; energy currency of the cell.

• ADP: Adenosine diphosphate; formed when ATP loses a phosphate.

• AMP: Adenosine monophosphate; formed when ADP loses a phosphate.