I. Basic review of Atom - subatomic particles, orbitals, and reactivity
A. Anatomy of an Atom
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
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/
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 -
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
Glycerol, 2 fatty acids, & Phosphate
Hydrophilic end with P
Alcohol & 1 fatty acid
Water repellent, cell wall protection (mycobacteria)
Lipids fused in rings (cholesterol)
Message & membrane fluidity
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
b. Catalysts - enzymes
c. Regulation - hormones- messengers
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
· nucleic acids
10. Give examples of and explain the chemical basis of biochemical tests to identify bacteria.
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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Date last updated 08/07/2011