Microbiology: Chemical Principles

Chemical Principles

The Structure of Atoms

• Chemistry studies interactions between atoms and molecules.
• An atom is the smallest unit of matter that cannot be further subdivided without losing its properties.
• Atoms interact to form molecules.
• Atoms are composed of:
  • Electrons
  • Protons
  • Neutrons

Chemical Elements

• Atoms sharing the same number of protons are classified as the same chemical element.

The Elements of Life

• Key elements in living organisms include:
  • Hydrogen (H): Atomic number 1, approximate atomic mass 1.
  • Carbon (C): Atomic number 6, approximate atomic mass 12.
  • Nitrogen (N): Atomic number 7, approximate atomic mass 14.
  • Oxygen (O): Atomic number 8, approximate atomic mass 16.
  • Sodium (Na): Atomic number 11, approximate atomic mass 23.
  • Magnesium (Mg): Atomic number 12, approximate atomic mass 24.
  • Phosphorus (P): Atomic number 15, approximate atomic mass 31.
• Hydrogen, carbon, nitrogen, and oxygen are the most abundant elements in living organisms.

How Atoms Form Molecules: Chemical Bonds

• Atoms combine to form molecules by filling their outermost shells.
• Valence electrons form attractive forces called chemical bonds.
• Types of chemical bonds:
  • Covalent
  • Ionic
  • Hydrogen

Molecules and Compounds

• A molecule is a group of two or more atoms held together by chemical bonds.
• A compound is a molecule containing two or more kinds of atoms.
• Example: Water (H₂O) consists of two hydrogen atoms and one oxygen atom.

Ionic Bonds

• Ions are charged atoms that have gained or lost electrons.
  • Cations: Positive ions.
  • Anions: Negative ions.
• Ionic bonds are attractions between ions of opposite charge.

Covalent Bonds

• Covalent bonds form when two atoms share one or more pairs of electrons.

Hydrogen Bonds

• Hydrogen bonds form when a hydrogen atom covalently bonded to an oxygen or nitrogen atom is attracted to another nitrogen or oxygen atom in another molecule.

Chemical Reactions

• Chemical reactions involve the making or breaking of bonds between atoms.
• Types of chemical reactions:
  • Synthesis
  • Decomposition
  • Exchange

Synthesis Reactions

• Occur when atoms, ions, or molecules combine to form new, larger molecules.
• Anabolism is the synthesis of molecules in a cell.

Decomposition Reactions

• Occur when a molecule is split into smaller molecules, ions, or atoms.
• Catabolism includes the decomposition reactions in a cell.

Exchange Reactions

• Are part synthesis and part decomposition.
• Reactants recombine to form products: AB + CD \rightarrow AD + BC

Important Biological Molecules

• Organic compounds always contain carbon and hydrogen and are often structurally complex.
• Inorganic compounds typically lack carbon-hydrogen bonds and are usually small and structurally simple.

Water

• Water is an inorganic compound.
• It is a polar molecule with an unequal distribution of charges.
• Water characteristics:
  • Excellent solvent: Polar and ionic substances undergo dissociation in water, forming solutes.
  • Excellent temperature buffer.

Acids, Bases, and Salts

• Acids:
  • Substances that dissociate into one or more hydrogen ions and one or more negative ions.
  • Referred to as a proton donor.
• Bases:
  • Substances that dissociate into one or more hydroxide ions and one or more positive ions.
  • Referred to as a proton acceptor.
• Salts:
  • Substances that dissociate into cations and anions, neither of which is H+ or OH-.

Acid–Base Balance: The Concept of pH

• The concentration of H+ in solution is expressed as pH.
• pH = -log_{10}[H^+]
• pH scale extends from 0 to 14:
  • pH=7: Neutral
  • pH<7: Acid
  • pH>7: Alkaline (basic)

Structure and Chemistry of Organic Compounds

• Organic compounds commonly contain hydrogen, oxygen, and/or nitrogen in addition to carbon.
• The chain of carbon atoms in an organic molecule is the carbon skeleton.

Representative Functional Groups

• Functional groups bond to carbon skeletons and are responsible for most of the chemical properties of a particular organic compound.

Macromolecules

• Small organic molecules can combine into large macromolecules.
• Macromolecules are polymers consisting of many small repeating molecules called monomers.
  • Nucleic acids from nucleotides
  • Carbohydrates from monosaccharides
  • Proteins from amino acids

Carbohydrates

• Serve as cell structures and cellular energy sources.
• Include sugars and starches.
• Consist of C, H, and O with the formula (CH2O)n
• Types:
  • Monosaccharides
  • Disaccharides
  • Polysaccharides

Proteins

• Made of C, H, O, N, and sometimes S.
• Essential in cell structure and function.
  • Enzymes speed up chemical reactions.
  • Transporter proteins move chemicals across membranes.
  • Flagella aid in movement.
  • Some bacterial toxins.
  • Structural components.

Amino Acids

• Proteins consist of subunits (monomers) called amino acids.
• Amino acids contain an alpha-carbon that has an attached:
  • Carboxyl group
  • Amino group
  • Side group

Peptide Bond Formation

• Peptide bonds are formed by dehydration synthesis, linking the carboxyl group of one amino acid to the amino group of another, with the removal of water.

Levels of Protein Structure

• Primary structure: Polypeptide strand (amino acid sequence) held together by peptide bonds.
• Secondary structure: Alpha-helix and beta-pleated sheets stabilized by hydrogen bonds.
• Tertiary structure: Overall 3D shape formed by folding of helixes and pleated sheets, stabilized by disulfide bridges and other interactions.
• Quaternary structure: The relationship of several folded polypeptide chains forming a protein.

Protein Denaturation

• Proteins can undergo denaturation.
• Denaturation occurs when proteins encounter hostile environments (high temperature, unfavorable pH) and lose their shapes and functions.

Nucleic Acids

• Carry genetic information.
• Include DNA and RNA.
• Consist of nucleotides.
• Nucleotides consist of:
  • A five-carbon (pentose) sugar
  • Phosphate group
  • Nitrogen-containing (purine or pyrimidine) base

DNA

• Deoxyribonucleic acid
• Contains deoxyribose.
• Exists as a double helix.
• Adenine (A) hydrogen bonds with Thymine (T).
• Cytosine (C) hydrogen bonds with Guanine (G).
• The order of nitrogen-containing bases forms the genetic instructions of the organism.

RNA

• Ribonucleic acid
• Contains ribose.
• Is single-stranded.
• Contains Adenine (A), Uracil (U), Cytosine (C), and Guanine (G).

Adenosine Triphosphate (ATP)

• Principle energy-carrying molecule of all cells.
• Stores energy released by some chemical reactions.
• Provides energy for reactions that require energy.
• Releases phosphate groups by hydrolysis to liberate useful energy for the cell.

Lipids

• Consist of C, H, and O.
• Are nonpolar and insoluble in water.
• Lipid functions:
  • Primary structural component of cell membranes
  • Energy storage

Simple Lipids

• Fats or triglycerides
• Contain glycerol and fatty acids; formed by dehydration synthesis
  • Saturated: no double bonds.
  • Unsaturated: one or more double bonds.

Complex Lipids

• Include phospholipids and steroids.
• Cell membranes are made of complex lipids called phospholipids
  • Glycerol, two fatty acids, and a phosphate group
• Phospholipids have polar as well as nonpolar regions

Steroids

• Four carbon rings with an -OH group attached to one ring
• Part of membranes that keep the membranes fluid
  • Cholesterol
  • Ergosterol