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!)
4) cohesiveness
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
B) Lipids:
1) Fatty acids = CH3(CH2)nCOOH (n is generally between 12 and
22), may be saturated
or unsaturated.
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
therefore stain
“acid fast”)
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’
e.g.
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
(ribosomes)
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
Return to previous page