The Chemistry of Microbiology

Introduction

Chemistry forms the foundation for understanding the structure and function of microorganisms. This chapter explores the atomic and molecular principles essential for microbiology, including the nature of atoms, chemical bonds, reactions, and the properties of water, acids, bases, and salts.

Atoms

Basic Concepts

• Matter: Anything that takes up space and has mass.

• Atoms: The smallest chemical units of matter.

Atomic Structure

• Electrons: Negatively charged subatomic particles circling a nucleus.

• Nucleus: Central structure containing neutrons and protons.

• Neutrons: Uncharged particles.

• Protons: Positively charged particles.

Example: The Bohr model illustrates electrons in shells around a nucleus composed of protons and neutrons.

Elements and Atomic Properties

• Element: Composed of a single type of atom.

• Atomic number: Number of protons in the nucleus.

• Atomic mass (atomic weight): Sum of masses of protons, neutrons, and electrons.

Table: Common Elements of Life

Additional info: Other elements such as magnesium, iron, zinc, and iodine are also essential in trace amounts for enzyme function and metabolic processes.

Isotopes

• Atoms of a given element that differ in the number of neutrons in their nuclei.

• Stable and unstable (radioactive) isotopes exist.

• Radioactive isotopes: Release energy during radioactive decay.

Example: Carbon-12, Carbon-13, and Carbon-14 are isotopes of carbon with 6, 7, and 8 neutrons, respectively.

Electron Configurations

• Only electrons interact during chemical reactions, determining an atom’s chemical behavior.

• Electrons occupy electron shells.

• Valence electrons: Electrons in the outermost shell that interact with other atoms.

Chemical Bonds

Valence and Bonding

• Valence: Combining capacity of an atom, determined by the number of electrons in the outer shell.

• Atoms are stable when their outer electron shells contain eight electrons (octet rule).

• Chemical bonds: Atoms combine by sharing or transferring valence electrons.

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

• Compound: A molecule composed of more than one element.

Covalent Bonds

• Covalent bond: Sharing of a pair of electrons by two atoms.

• Electronegativity: Attraction of an atom for electrons; higher electronegativity means a stronger pull on electrons.

Types of Covalent Bonds

• Nonpolar covalent bonds: Shared electrons spend equal time around each nucleus; atoms have similar electronegativities; no poles exist.

• Polar covalent bonds: Unequal sharing of electrons due to significantly different electronegativities; most important in biology involve hydrogen, allowing for hydrogen bonding.

Ionic Bonds

• Formed when two atoms with vastly different electronegativities come together.

• Atoms become cations (positive) or anions (negative).

• Cations and anions attract each other, forming ionic bonds (no electrons shared).

• Typically form crystalline ionic compounds known as salts.

Hydrogen Bonds

• Electrical attraction between partially charged H+ and full or partial negative charge on the same or different molecule.

• Weaker than covalent or ionic bonds but essential for life.

• Help stabilize 3-D shapes of large molecules (e.g., DNA, proteins).

Table: Characteristics of Chemical Bonds

Chemical Reactions

Overview

• Involve the making or breaking of chemical bonds.

• Reactants are transformed into products.

• Biochemistry: The study of chemical reactions in living things.

Synthesis Reactions

• Formation of larger, more complex molecules.

• Require energy (endothermic).

• Common type: dehydration synthesis (water molecule formed).

• All synthesis reactions in an organism are called anabolism.

Decomposition Reactions

• Break bonds within larger molecules to form smaller atoms, ions, and molecules.

• Release energy (exothermic).

• Common type: hydrolysis (ionic components of water are added to products).

• All decomposition reactions in an organism are called catabolism.

Exchange Reactions

• Involve breaking and forming covalent bonds.

• Have both endothermic and exothermic steps.

• Involve atoms moving from one molecule to another.

• The sum of all chemical reactions in an organism is called metabolism.

Water, Acids, Bases, and Salts

Water

• Most abundant substance in organisms.

• Special characteristics due to two polar covalent bonds:

  • Cohesive molecules—generate surface tension.

  • Excellent solvent.

  • Remains liquid across a wide range of temperatures.

  • Can absorb significant amounts of heat energy without changing temperature.

  • Participates in many chemical reactions.

Acids and Bases

• Dissociated by water into component cations and anions.

• Acid: Dissociates into one or more H+ and one or more anions.

• Base: Binds with H+ when dissolved in water; some dissociate into cations and OH-.

• Concentration of H+ in solution is expressed using the pH scale:

• Metabolism requires a relatively constant balance of acids and bases.

• Buffers prevent drastic changes in internal pH.

• Many microbes grow best between pH 6.5 and 8.5.

• Microorganisms can change the pH of their environment by using or producing acids and bases.

Salts

• Compounds that dissociate in water into cations and anions other than H+ and OH-.

• Cations and anions of salts are electrolytes that:

  • Create electrical differences between inside and outside of cells.

  • Transfer electrons from one location to another.

  • Form important components of many enzymes.

Summary Table: Types of Chemical Bonds

Key Equations

• pH calculation:

Conclusion

Understanding the chemical basis of life is essential for microbiology. Atoms, chemical bonds, and the properties of water, acids, bases, and salts all play critical roles in the structure and function of microorganisms.