Microbiology Lecture Notes Chapter 2

The Chemistry of Microbiology

I.                     Basic review of Atom - subatomic particles, orbitals, and reactivity

A.     Anatomy of an Atom – 02-01_bohrmodel_1.jpg

1.      Nucleus contains protons + charge  and neutrons 0 charge

2.      Orbitals pathway of electrons  - charge

3.      Periodic Table - http://www.webelements.com/webelements/scholar/ and text link

4.      Basic atoms of Life – CHNOSP

B.     Atomic number = the number of protons

C.    Ions - Electrolytes - charged atoms that have given up or adopted an electron

D.    Inert atoms - atoms that have full outer orbitals and are non-reactive

E.     Isotopes - same electrons and protons, different number of neutrons Radioactivity - the loss of subatomic particles degradation of atoms


II.                   Bonds

A.     Valence - number of electrons an atom must gain or lose to fill its outer orbit


B.     Periodic Table organization- http://www.webelements.com/webelements/scholar/

text link

C.    Molecule bonds of a single atom e.g. H2 or O2

D.    Compounds – bonds between different atoms

1.      Chemical formulas - C6H12O6 = either glucose or fructose

2.      Chemical structures -

glucose                        Glucose                                                                        Fructose




E.     Types of Bonds - Nature of bonds and energy - In biological systems (where water is present) covalent bonds are the strongest, followed by ionic, and hydrogen

1.      Non-polar covalent bonds – Atoms having equal electronegativity sharing electrons e.g. H2, O2, CH4

Carbon – a unique atom single, double, triple bonds, Organic



See questions on pages 32 & 33

2.      Polar covalent bonds - atoms, within a molecule, have unequal attraction for electrons e.g. H2O



Water a unique molecule – cohesion, surface tension, solvent, temperature (liquid longer), reactive


3.      Ionic bonds- - atoms that are attracted due to opposite charges vastly different electronegativity e.g. NaCl


4.      Hydrogen bonds- slight charge of atom results in weak bonds e.g. Cytosine and Guanine DNA bases


III.                  Chemical Reactions

A.     Reactants (Substrate) -> Products

B.     Decomposition - catabolic – hydrolysis – exothermic –


Solubility of substances

C.    Dehydration – synthesis – anabolism – endothermic

D.    Exchange Reactions – Redox (Reduction (gains electron): Oxidation (substances losses electron) – metabolism Energy transfers - cytochrome system, Kreb's cycle

E.     Acids and Bases

1.       Molar concentration of hydrogen


2.       Factor of 10


3.       Buffers - Helps to prevent rapid pH changes

4.       Neutral - relate to bacteria, media etc

a.      acidophiles - organisms that "love" an acid environment. (Helicobacter pylori)

b.      alkalophiles - organisms that "love" a basic environment

IV.               Major Organic Substances - Macromolecules - polymers

A.     Lipids –hydrophobic, non-polar bonds

1.      Composed of monomers of alcohol (glycerol) & fatty acids

2.      Functions energy storage, cell membrane permeability & diffusion, signaling






Glycerol & 3 fatty acids

Energy Storage







Glycerol, 2 fatty acids, & Phosphate


Hydrophilic end with P

Hydrophobic end



Alcohol & 1 fatty acid

Water repellent, cell wall protection (mycobacteria)

Water insoluble


Lipids fused in rings (cholesterol)

Message & membrane fluidity

Testosterone etc


B.     Carbohydrates (CH2O) N   C6H12O6

1.      Components = Monosaccharides (Same components [d-glucose] different bonds yield varied structures and functions)

2.      Dehydration synthesis= polysaccharides

3.      Examples; Glucose, cellulose, starch 

4.      Functions - rapid energy source, cell structure (recognition markers A, B, O blood types), part of nucleic acids (deoxyribose sugar)


C.    Proteins – Most complex molecules composed of CHONS

1.      Components - amino acids - amino and carboxyl groups cause protein to have a positively charged end and a negatively charged end --> peptide bonds 

2.      Protein Structure

a.       primary – sequence of amino acids (one change = sickle cell)

b.       secondary - amino acid arrangement beta sheets or coils

c.       tertiary - 3D shape due to hydrophobic reactions of R groups

d.       quaternary - (e.g. globular and fibrous) interaction of polypeptide chains

3.      Denatured = change of structure due to temperature, pH, or salt changes. Reversible and non-reversible denaturing can occur.

4.      Function - Most structurally diverse of all organic molecules

a.      Structure

b.      Catalysts  - enzymes

c.      Regulation - hormones- messengers

d.      Transport

e.      Defense – antibodies

D.    Nucleic Acids – 

1.      Components = Phosphate, sugar, nucleic acid base = nucleotides

2.      Examples: DNA, RNA, ATP

3.      Function - informational molecules – heredity/genetic  information and interpretation, protein synthesis, and energy

Chapter 2 The Chemistry of Microbiology

1.      Define matter, atom, element, atomic number, atomic mass or weight molecule, compound, and valence.

2.      Draw and label an atom when given the atomic number or identified on the periodic table including the nucleus (and components), orbitals, and electrons.

3.      Give an example of and describe the relevance in medicine of: ions, electrolytes, isotopes, and inert atoms.

4.      Using examples describe the relative strength and advantages of each of the four main types of chemical bonds.

5.      Compare and contrast synthetic chemical reactions (also called dehydration reactions or anabolic reactions) with decomposition reactions (also called hydrolytic, catabolic, or exothermic reactions) and exchange or transfer reactions.

6.      Define, use, and interpret data regarding pH particularly with relation to living systems.

7.      Describe the unique qualities and importance of water as a compound and Carbon as an atom in making bonds and in chemical reactions.

8.      Identify in living systems and by analyzing chemical structures the four classes of organic molecules.

9.      Describe the monomer, structure and function of

·         carbohydrates

·         lipids

·         nucleic acids

·         proteins

10.  Give examples of and explain the chemical basis of biochemical tests to identify bacteria.

Chapter 2 Chemistry

1. Describe the structure and function of the subatomic particles discussed in class.

2. Draw and label an atom when given the atomic number or identified on the periodic table..

3. Give an example and describe: ions, isotopes and inert atoms.

4. Using examples describe the relative strength and advantages of each of the three main  types of bonds.

5. Be prepared to use and interpret data regarding pH.

6. Describe the importance of Carbon.

7. List the 4 classes of organic molecules

8. Describe the monomer, structure and function of

9. Give examples of and explain the chemical basis of biochemical tests to identify bacteria.




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