Download Bioc 462a Lecture Notes

Biochemistry 462a – Amino Acids
Reading - Chapter 4
Practice problems - Chapter 4 - 4,5,14; Proteins extra problems
Basics
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Proteins are polymers of -amino acids.
There are 20 different amino acids found in proteins and they differ by the nature of the R
group.
The nonionic form shown above does not occur in water, rather the zwitterion occurs.
Note that the-carbon is asymmetric (has four different substituents) meaning that amino
acids occur as enantiomers. L-amino acids are the naturally occurring enantiomers
found in all proteins.
Properties of Amino Acid Side Chains
Side chain classes
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The side chains of the amino acids play an essential role in determining the properties of
proteins.
There is a wide diversity in the chemical properties of amino acid side chains, but they can be
grouped into 6 classes (you are expected to know which class each amino acid belongs to).
Side Chain Class
Aliphatic
Hydroxyl- or Sulfur-Containing
Aromatic
Basic
Acidic and Their Amides
Cyclic
Amino Acids
glycine, alanine, valine, leucine, isoleucine
serine, cysteine, threonine, methionine
phenylalanine, tyrosine, tryptophan
histidine, lysine, arginine
aspartic acid, glutamic acid, aspargine, glutamine
proline
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Proline does not fit nicely into any class because it is cyclic. Proline shares many properties
with the aliphatic group. The rigidity of the ring plays a critical role in protein structure, as
we shall see later.
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The side chain sulfhydryl groups of cysteine can undergo a
reversible oxidation reaction to form cystine, which contains a
disulfide bond. The presence of disulfide bonds in proteins is
often a critical structural feature.
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Proteins contain several classes of weak acid groups. The ionization state of the side chain
weak acid groups controls the charge on the protein.
Group
-Carboxyl
Asp, Glu
His
Cys (SH)
Tyr (OH)
-Amino
Lys
Arg
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pKa Range
1.8-2.6
4.0-4.8
6.5-7.4
8.5-9.0
9.5-10.5
8.0-9.0
9.8-10.4
12.0-12.5
The aromatic amino acids, tryptophan, tyrosine and phenylalanine absorb light in the
ultraviolet region of the spectrum (250-300 nm). Tryptophan has the highest molar
absorptivity, followed by tyrosine, with phenylalanine making only a small contribution.
In some proteins the side chains of a few amino acids are modified. For example,
O-Phosphoserine
4-Hydroxyproline
Hydroxylysine
-carboxyglutamate
The Peptide Bond
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In proteins, amino acids are joined together via the peptide
bond, which is formed by the reaction of the -carboxyl
group of one amino acid with the -amino group of another
amino acid.
If this process is repeated many times, then a long linear
chain of amino acids is produced - a polypeptide.
By convention the sequence of the polypeptide is written
beginning with the residue containing the free -amino
group (the N-terminal or amino terminal) and ending with
the residue containing the free -carboxyl group (the Cterminal or carboxyl terminal), e.g. NH2-Glu-Gly-Ala-LysCOOH.
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Due to the partial double bond character of the peptide bond, the O, C, N and H atoms are
nearly planar and there is no rotation about the peptide bond. As we shall see
later, the planarity of these elements has important consequences for the three
dimensional structure of proteins.
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Generally, the two C groups are in a trans configuration, which minimizes steric interaction.
Chemical Reactions of Amino Acids
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All amino acids have at least two reactive groups - the amino and -carboxyl groups and
these groups can react with a variety of reagents. Here are two examples:
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A particularly interesting example is the green fluorescent protein (GFP) from the Pacific
Northwest jellyfish Aequorea victoria, which has generated intense interest as a marker for
gene expression and localization of gene products. The chromophore, results from the
spontaneous cyclization and oxidation of the sequence -Ser65-Tyr66-Gly67-is unusual
because it does not involve a non-protein chromophore, as is usually the case for colored
proteins. The chromophore is buried in the interior of the protein.
Amino Acid Analysis
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Because the side chains of the amino acids have different properties, it is possible to separate
and quantitate all 20 amino acids using a variety of chromatographic techniques.
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