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MICROBIOLOGY CHAPTER 2 – The Chemistry of Microbiology
ATOMS
 Matter – anything that takes up space and has mass
 Atoms – the smallest chemical units of matter
 Atomic Structure
o Electrons – negatively charged subatomic particles circling a nucleus
o Nucleus – structure containing neutrons and protons
o Neutrons – uncharged particles
o Protons – positively charged particles
o Element – composed of a single type of atom
o Atomic number – equal to the number of protons in the nucleus
o Atomic mass (atomic weight) – sum of masses of protons, neutrons, and
electrons
 Isotopes
o Atoms of a given element that differ in the number of neutrons in their
nuclei
o Stable isotopes
o Unstable isotopes
 Radioactive isotopes
 Release energy during radioactive decay
 Electron Configurations
o Only the electrons of atoms interact, so they determine atom’s chemical
behavior
o Electrons occupy electron shells
o Valence electrons – electrons in outermost shell that interact with other
atoms
CHEMICAL BONDS
 Valence – combining capacity of an atom
o Positive if atom has electrons to give up
o Negative if atom has spaces to fill
o Stable when outer electron shells contain eight electrons

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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 bond – sharing of a pair of electrons by two atoms
Electronegativity – attraction of atom for electrons
o The more electronegative an atom, the greater the pull its nucleus exerts
on electrons
Nonpolar Covalent Bonds
o Shared electrons spend equal amounts of time around each nucleus
o Atoms with similar electronegativities
o No poles exist
o Carbon atoms form four nonpolar covalent bonds with other atoms
 Organic compounds contain carbon and hydrogen atoms
Polar Covalent Bonds
o Unequal sharing of electrons due to significantly different
electronegativities
o Most important polar covalent bonds involve hydrogen
 Allow for hydrogen bonding
Ionic Bonds
o Occur when two atoms with vastly different electronegativities come
together
o Atoms have either positive (cation) or negative (anion) charges
o Cations and anions attract each other and form ionic bonds (no electrons
shared)
o Typically form crystalline ionic compounds known as salts
Hydrogen Bonds
o Electrical attraction between partially charged H+ and full or partial
negative charge on same or different molecule
o Weaker than covalent bonds but essential for life
 Help to stabilize 3-D shapes of large molecules

Characteristics of Chemical Bonds
Type of Bond
Nonpolar Covalent
Bond
Polar Covalent Bond
Ionic Bond

Hydrogen Bond

Description
Pair of electrons is nearly equally shared
between two atoms
Electrons spend more time around the
electronegative of two atoms
Electrons are stripped from a cation by
an anion
Partial positive charges on hydrogen
atoms are attracted to full and partial
negative charges on other molecules or
other regions of the same molecule

Relative Strength
Strong
Strong
Weaker than
covalent in aqueous
environment
Weaker than ionic

CHEMICAL REACTIONS
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The making or breaking of chemical bonds
Involve reactants and products
Biochemistry involves chemical reactions of living things
Synthesis Reactions
o Involve the formation of larger, more complex molecules
o Require energy (endothermic)
o Common type is dehydration synthesis
 Water molecule formed
o All the synthesis reactions in an organism are called anabolism
 Decomposition Reactions
o Break bonds within larger molecules to form smaller atoms, ions, and
molecules
o Release energy (exothermic)
o Common type is hydrolysis
 Ionic components of water are added to products
o All the decomposition reactions in an organism are called catabolism
 Exchange Reactions
o Involve breaking and forming covalent bonds

o Have endothermic and exothermic steps
o Atoms are moved from one molecule to another
o Sum of all chemical reactions in an organism is called metabolism
WATER, ACIDS, BASES, and SALTS
 Water
o Most abundant substance in organisms
o Many special characteristics due to two polar covalent bonds
 Cohesive molecules – surface tension
 Excellent solvent
 Remains liquid across wide range of temperatures
 Can absorb significant amounts of energy without changing
temperature
 Participates in many chemical reactions
 Acids and Bases
o 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 int water; some dissociate
into cations and OHo Concentration of H+ in solution expressed using the pH scale
o Metabolism requires relatively constant balance of acids and bases
 Buffers prevent drastic changes in internal pH
o Microorganisms differ in their tolerance of various pH ranges
 Some microbes can change the pH of their environment
 Salts
o Compounds that dissociate in water into cations and anions other than
H+ and OHo Cations and anions of salts are electrolytes
 Create electrical differences between inside and outside of cell
 Transfer electrons from one location to another
 Form important components of many enzymes
ORGANIC MACROMOLECULES
 Functional Groups

o Contain carbon and hydrogen atoms
o Atoms often appear in arrangements called functional groups
o Macromolecules – large molecules used by all organisms
 Lipids
 Carbohydrates
 Proteins
 Nucleic acids
o Monomers – basic building blocks of macromolecules
o Lipids
 Not composed of regular subunits
 Are all hydrophobic
 Four groups
 Fats
 Phospholipids
 Waxes
 Steroids
 Waxes
 Contain one long-chain fatty acid covalently linked to longchain alcohol by ester bond
 Lack hydrophilic head
o Completely insoluble in water
 Monomers are the basic building blocks of macromolecules
 Monomers join to form chains called polymers
o Carbohydrates
 Organic molecules composed of carbon, hydrogen, and oxygen
(CH2O)n
 Functions
 Long-term storage of chemical energy
 Ready energy source
 Part of backbones of nucleic acids
 Converted to amino acids
 Form cell wall
 Involved in intracellular interactions between animal cells

 Types
 Monosaccharides
 Disaccharides
 Polysaccharides
o Proteins
 Mostly composed of carbon, hydrogen, oxygen, nitrogen, and
sulfur
 Functions
 Structure
 Enzymatic catalysis
 Regulation
 Transportation
 Defense and offense
 Amino acids
 The monomers that make up proteins
 Most organisms use only 21 amino acids in protein synthesis
 Side groups affect how amino acids interact with one another
and how a protein interacts with other molecules
 A covalent peptide bond is formed between amino acids
o Nucleic Acids
 DNA and RNA are the genetic material of organisms and viruses
 RNA also acts as enzyme, binds amino acids, and helps form
polypeptides
 Nucleotides and nucleosides
 Nucleotides
o Monomers that make up nucleic acids
o Composed of three parts
 Phosphate
 Pentose sugar – deoxyribose or ribose
 One of five cyclic nitrogenous bases
o Nucleosides are nucleotides lacking phosphate
 Nucleic acid structure
 Three H bonds form between C and G

 Two H bonds form between T and A (DNA) or U and A
(RNA)
 DNA is double stranded in most cells and viruses
o The two strands are complementary
o The two strands are antiparallel
 Nucleic acid function
 DNA is genetic material of all organisms and of many
viruses
 Carries instructions for synthesizing RNA and proteins
 Controls synthesis of all molecules in an organism
Comparison of Nucleic Acids
Characteristic
Sugar
Purine
nucleotides
Pyrimidine
nucleotides
Number of
strands
Function

DNA
Deoxyribose
A and G

RNA
Ribose
A and G

T and C

U and C

Double stranded in cells and in most
DNA viruses; single stranded in
parvoviruses
Genetic material of all cells and DNA
viruses

Single stranded in cells and in
most RNA viruses; double
stranded in parvoviruses
Protein synthesis in all cells;
genetic material of RNA
viruses



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