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Proteins
a. Linear polymers built of monomer units called amino acids which are linked end to
end
b. Contain a wide range of function groups
c. Can interact with one another and with other biological macromolecules to form
complex assemblies
d. Some proteins are quite rigid, whereas others display considerable flexibility
2. Levels of Protein Structure
a. Primary
b. Secondary
c. Tertiary
d. Quaternary
3. Basic Amino Acid Structure
a. -carbon is chiral (except G)
b. Primary amines (except P)
i. By convention, the amino end is taken to be the beginning of a polypeptide
chain, and so the sequence of amino acids in a polypeptide chain is written
starting with the amino-terminal residue
ii. Keep amine on the left side
c. Zwitterions
i. Charged ion, but overall is neutral
ii. Amino group weak base
iii. Carboxyl group weak acid
iv. Ionization state depends on pH
d. Tetrahedral structure
4. Stereoisomers
a. L vs. D
i. In living organisms, only L exists
5. Amino Acid Classification
a. Nonpolar/Hydrophobic
i. Aromatic, aliphatic and/or sulfur groups
ii. GAVLIMP TP
1. Glycine
2. Alanine
3. Valine
4. Leucine
5. Isoleucine
6. Methionine
7. Proline
8. Tryptophan
9. Phenylalanine
b. Polar
i. Neutral
1. OH- or an amide
a. SomeTimes Cats Try A Growl
i. Serine
ii. Threonine
iii. Cysteine
1. Forms disulfide bonds via oxidation
2. Insulin 2 peptide chains linked by disulfide bonds
iv. Tyrosine
v. Asparagine
vi. Glutamine
ii. Basic
1. N that can accept an H+
a. Life Always Has
i. Histidine
1. Histidine ionization histidine can bind or release
protons near physiological pH
ii. Arginine
iii. Lysine
iii. Acidic
1. CO2H that can donate H+
a. A Goal
i. Aspartate
ii. Glutamate
6. Titration Curves
a. pI (isoelectric point) the pH at which the number of positive and negative
charges on a population of molecules is equal (i.e. no net charge)
i. pI = (pK1 + pK2)/2
7. Bonds
a. Peptide bonds are planar, locked at those positions with no rotation
i. Planar because it is partially a double bond
ii. In cis and trans, trans is usually more favorable except for in proline
iii. The bond resonates between a single bond and a double bond; because of
this double-bond character, rotation about this bond is prevented and thus
the conformation of the peptide is constrained
b. Phi () and psi () can rotate freely about the N-C and C-carbonyl bond
respectively
i. The freedom of rotation about two bonds of each amino acid allows proteins
to fold in many different ways
c. Ramachandran diagram
i. Graphs all of the angles that they can rotate
8. Levels of Protein Structure
a. Primary Structure
i. Linear polypeptide chain
1. Backbone
a. Repeating
b. H-bonding potential
2. Side chains
ii. Size varies
1. 50-2000 amino acids27,000!
iii. Precisely defined amino acid sequence
1. Specified by gene
b. Secondary Structure & Strand
i. Non-linear
ii. 3-Dimensional
iii. Formed by a regular pattern of hydrogen bonds between the peptide N-H and
groups of amino acids that are near one another in the linear sequence Paul
& Corey
iv. -helix
1. Rod-like structure
2. A tightly coiled backbone forms the inner part of the rod and the side
chains extend outward in a helical array
3. It is stabilized by H-bonds between the NH and CO groups of the main
chain
4. H-bonding is very regular, repeating, and alternating
i. The surface for the overall process of protein folding can be visualized as a
funnel
ii. As the free energy of the population of protein molecule decreases, the
proteins move down into narrower parts of the funnel and fewer conformation
are accessible
iii. At the bottom is the folded state with its well-defined conformation
14.
15.
iv.
Cumulative selection
a. A monkey randomly poking at a key board could type a sentence from Shakespeare
in a few thousand keystrokes if the correct letters are retained
b. Protein folding occurs by cumulative selection
i. Partly correct folding intermediates are retained because they are slightly
more stable than unfolded regions
Energy Landscape
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Enzymes
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases