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CHEMICAL PRINCIPLES Chapter 2, pp 17-38
Review the following: matter, subatomic particles, atoms, atomic number and weight (mass), isotopes, acids, bases, and pH, and electronic configurations of elements in Table 2-1, p 18; Fig 2-1, p18
I. Chemistry background.
A) Chemical bonds - involves valence electrons; how atoms in molecules are held
together. Type formed depends on electronegativity of the atoms involved.
1) Ionic = transfer of electrons, Fig 2-4, p21 (weak in aqueous solution)
2) Covalent = sharing of electrons, Fig 2-2, p19; Fig 2-3, p20; Table 2-2 p20
a) nonpolar = equal sharing (generally hydrophobic)
b) polar = unequal sharing resulting in charge differences across the molecule
B) Transient bonds holding molecules together (weak compared to the above).
1) Hydrogen bonds (H bonds), (Fig 2-7, p22)
2) Electrostatic attractions = between oppositely charged groups (like ionic)
3) Hydrophobic interactions = between nonpolar regions of macromolecules
C) Moles (a way of expressing how many molecules you have)
1) 1 mol = molecular weight of that substance expressed in grams
e.g. 1 mol of water = 18g
(molecular weight Hydrogen = 1, Oxygen = 16)
2) Molarity is a way of expressing solute strength in a solvent (usually aqueous)
D) Water - has unique properties making it essential for life. These properties are due
to its polarity and resulting hydrogen bonding capacity.
1) high boiling point
2) heats and cools slowly
3) ice is less dense than water (it floats!)
5) excellent solvent for polar substances
E) pH Fig 2-10, p23
F) Organic compounds = containing carbon (and hydrogen)
1) Basic functional groups ( determine how molecules interact)
methyl, hydroxyl, carboxyl, amino, keto, aldehyde, sulfhydryl (know these!)
II. Biological Molecules and macromolecules (Table 2-3, p36)
Polymers formed by dehydration synthesis (removal of water) Fig 2-12, p 25
(breakdown = hydrolysis)
A) carbohydrates (CnH2nOn) = glucose, ribose, fructose, galactose, etc. are monosaccharides
1) monosaccharides = generally polyhydroxy aldehydes or polyhydroxy ketones. Figs 2-19, 2-20, p30
2) disaccharides: common ones include:
maltose = 2 glucoses
sucrose = glucose-fructose
lactose = galactose-glucose
3) polysaccharides: starch (amylose or amylopectin), glycogen, cellulose. Fig 2-21,p 31
1) Fatty acids = CH3(CH2)nCOOH (n is generally between 12 and 22), may be saturated
2) fats = 3 fatty acids esterified to glycerol (again may be saturated or unsaturated).
Fig 2-26, p34 (function = energy storage)
3) Phospholipids = 2 fatty acids and one phosphate esterified to glycerol (again may be
saturated or unsaturated and degree of saturation effects membrane fluidity.
Function = membrane structure; Fig 2-29, p35 for phospholipid structure
(Mycobacterium contain high amounts of a lipid (mycolic acid) and
4) Steroids such as cholesterol (a sterol), Fig 2-28, p34; important component of
membranes in animal cells, generally absent form procaryotes except Mycoplasmas.
5) Lipoproteins and lipopolysaccharides
C) Amino acids - proteins
1) basic structure Fig 2-13, p25; differ according to nature of R, see Fig 2-14, p26
2) protein = composed of amino acids joined by peptide bonds (Fig 2-16, p27), can also have glycoproteins, lipoproteins, nucleoproteins.
3) levels of protein structure (Fig 2-17, p 28)
a) Primary (1°)
b) Secondary (2°)
c) Tertiary (3°)
d) Quatenary (4°)
4) denaturation = loss of shape and therefore function. Protein shape is affected by
temperature, pH, salt concentration
D) Enzymes = globular proteins, require a specific shape to function.
1) active site = where substrate binds; composed of amino acids from different parts of the protein e.g. lysozyme active site = amino acids 59,62,63,101,107
2) show high degree of specificity.
3) cofactors, coenzymes sometimes required for activity.
4) mechanism of action - they lower the activation energy required allowing reactions to occur under physiological conditions. Fig 6-6, p133
E + S ---> [ES] ---> E + P
Factors affecting reactions see Chapter 6
1) vary enzyme concentration: substrate in excess
2) vary substrate concentration: enzyme amount constant
3) vary Temperature and pH (Fig 6-12, p140)
4) competitive inhibitors = similar to substrate, competes for active site; can outcompete with excess substrate.
5) noncompetitive inhibitors = bind to enzyme at a spot different from the active site and effects enzyme activity; cannot outcompete with excess substrate.
E) Nucleic acids = RNA, DNA are polynucleotides
1) nucleotide = nitrogenous base, pentose, phosphate Fig 2-22, p32
a) nitrogenous bases = adenine, thymine, guanine, cytosine, uracil
purines = A,G; pyrimidines = C,T,U; RNA = AUCG; DNA = ATCG (Fig 2-23, p32)
b) pentose = ribose (RNA); deoxyribose (DNA)
2) structure = RNA single stranded; DNA double stranded and have complementary base pairing = hydrogen bonding between bases on paired strands, A=T (U in RNA); G=C
In double stranded DNA, duplex strands are antiparallel (Fig 2-25, p33)
one runs 5 ---> 3
other runs 3 ---> 5
5 A-G-G-C-T-A-C-T-G 3 note: sugar - phosphate backbone has been omitted
3 T-C-C-G-A-T-G-A-C 5'
3) Types of RNA
a) ribosomal (rRNA) plus proteins make up ribosomes
b) transfer (tRNA) carries amino acids to site of protein synthesis
c) message (mRNA) transcript of gene, translated during protein synthesis
into the specific amino acid sequence
4) other uses of nucleic acids
a) ATP = energy currency of cell (Fig 2-11, p24)
b) coenzymes NAD and FAD are derivatives of nucleic acids and vitamins
Macromolecules summarized Table 2-3 p36
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