Amino acids and
proteins
Dr Una Fairbrother
Amino acids and proteins
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Proteins are composed of amino acids
When a protein is hydrolysed e.g. with
hydrochloric acid then about 20 different
amino acids can be detected
When a protein is sequenced it may be
found that it is composed of hundred
amino acids
Therefore each of the different amino
acids is occurring more than once
Each protein has unique
sequence
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Think of coloured beads in a necklace
One necklace may differ from another by
the order of the beads and the frequency
with which they occur
Different amino acid content and
sequence alters the properties of proteins
Illustration of the 20 amino
acids
Amino acid game

http://www.wiley.com/legacy/college/boyer/0470003790/animations/
animations.htm
General Structure of an alpha
amino acid
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A 'free' amino acid (a
single amino acid) always
has:
An amino group -NH2,
A carboxyl group -COOH
A hydrogen -H
A chemical group or side
chain -"R".
These are all joined to a
central carbon atom, the
a -carbon
Only L Amino Acids Are Found in
Proteins.
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The L and D Isomers
of Amino Acids.
R refers to the side
chain.
The L and D isomers
are mirror images of
each other.
R groups
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Differences between
amino acids due to
differing R group
structures
The R group or side
chain can be
aliphatic, hydroxyl or
sulphur containing,
aromatic, basic or
acidic
Features of the R group
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The aliphatic amino acids have hydrocarbon
side chains which are hydrophobic.
They do not like to be in contact with water
molecules in an aqueous solution.
These allow hydrophobic bonding in proteins to
occur.
For this reason, they are often located in the
core of the protein, surrounded by the rest of the
protein, and "shielded" by them from the
aqueous surroundings.
Properties of the aliphatics
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Glycine (Gly; G)
 simplest and smallest of all, has a single hydrogen as it's side chai
Alanine (Ala; A)
 has a methyl group as it's sidechain.
Valine (Val; V)
 Longer sidechain with a branch. As the aliphatic side chains get
longer they are also more hydrophobic.
Leucine (Leu; L)
 has another methyl group attached to the sidechain.
Isoleucine (Ile; I)
 similar to L and V but orientation of sidechain atoms is different.
Isoleucine also has two centers of asymmetry
Proline (Pro; P)
 Different- the sidechain is bonded to the a-carbon and the amino
group. Marked effects on the architecture of proteins. Less
hydrophobic than the others.
Proline
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Proline is a special case
Due to its structure it causes bends in
proteins
It is a feature which contributes to the
compactness of globular proteins
Neutral Polar Amino Acids
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These amino acids are not charged at
physiological pH.
Serine and threonine, asparagine and glutamine
have polar hydroxyl groups in their side chains
These can contribute to hydrogen bonding in
proteins
For this reason the amino acids are classed as
hydrophillic.
Sulphur containing amino acids
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Cysteine (Cys; C)
 contains a thiol or sulphydryl group (-SH).
 This is extremely reactive, and can form hydrogen
bonds.
 But the long aliphatic part of the side chain makes it
quite hydrophobic.
 The (-SH) group of cysteine can be oxidised with
another cystein -SH to give a -S-S-disulphide bridge
Methionine (Met; M)
 is a very special amino acid in that it is the "start"
amino acid in the process of translation (protein
synthesis).
 sulphur atom in a thioether linkage, and is relatively
unreactive.
 Has a highly hydrophobic sidechain.
Aromatic amino acids
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Two of the aromatic amino acids, tryptophan and
tyrosine are useful in quantitative protein
determination.
They are detected in the Lowry assay: a
biochemical test to measure the amount of
protein in a sample.
Copper(II) ion in alkaline solution reacts with
protein to form complexes, which react with a
Folin-phenol reagent. The product becomes
reduced and can be detected colourimetrically
by absorbance at 650 nm.
Aromatic amino acids
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Contain an aromatic ring as part of their sidechains.
Because of the aromatic rings, they are highly
hydrophobic
Phenylalanine (Phe; F)
 Contains a phenyl ring attached to a methylene group
Tyrosine (Tyr; Y)
 contains a hydroxyl group on the phenyl ring
 makes it less hydrophobic than F. It is also a reactive
group
Tryptophan (Trp; W)
 has a slightly different ring attached to the methylene
group.
 This is an indole ring and it is highly hydrophobic.
Charge
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The basic and acidic amino acids can exist
in charged forms either -ve (with acidic
aas) or +ve (with basic aas).
Attraction between oppositely charged
amino acids in proteins produces ionic
bonds.
Acidic Amino Acids
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These amino acids are highly polar, and are nearly
always negatively charged at physiological pH.
Aspartate (Asp; D)
 is really aspartic acid.
 It is called aspartate because it is usually negatively
charged at physiological pH and so it is named for the
carboxylate anion.
Glutamate (Glu; E)
 is also called glutamic acid.
 The side chain of glutamate also has a carboxylate
group which has a negative charge at physiological
pH
Basic Amino Acids
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Contain side chains which are postively charged at physiological pH.
Lysine (Lys; K)
 one of the longest side chains
 it is very polar because of the terminal amino group and is a
hydrophillic amino acid.
Arginine (Arg; R)
 the largest of all sidechains
 Bacause of the guanidino group on the sidechain it is postively
charged at physiological pH.
Histidine (His; H)
 has an imidazole ring which often sits inside the active site of an
enzyme and helps bonds to be broken or made.
 It can do this because it can exist in two states -uncharged, or
positively charged.
Ion Pairs
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When amino acid sidechains of opposite charge are in
close proximity, they can form an ion pair (also called a
salt bridge).
If they can form a salt bridge, they will usually be buried.
Since charge is affected by pH, so is the formation and
the breakage of these ion pairs.
Salt bridges increase the stability of the tertiary structure.
Features of the a-amino and acarboxyl group
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In solution amino acids can exist in
different charged forms depending on pH.
At the most acid pH values they are fully
protonated with two weakly acidic groups.
Dissociation constant (pKa)
values
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If we know the pKa value for a protein titratable group, we
can predict the charge present on this group if the protein
is in solution at a given pH value, since pH=-log([H3O+])
Glycine contains two ionisable groups: an a-carboxyl
group and a protonated a-amino group.
As base is added, these two groups are titrated.
The pKa of the a-COOH group is 2.4, whereas that of the
a-NH3+ group is 9.8.
The pKa values of these groups in other amino acids are
similar.
Some aas, such as aspartic acid, have an ionisable side
chain.
The pKa values of ionizable side chains in amino acids
range from 3.9 (aspartic acid) to 12.5 (arginine).
Zwitterion
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At a neutral pH, both the
amino and the carboxyl
groups are ionised
giving what is termed the
zwitterionic form of the
molecule (or dipolar ion).
Titration of the a-Carboxyl and aAmino Groups of an Amino Acid.
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First the carboxyl group then the protonated
amino group loses its proton as the pH
increases.
Ionisation State as a Function of
pH: the graph
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The ionisation state of amino acids is altered by a
change in pH.
The zwitterionic form predominates near
physiological pH.
Titration with NaOH
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The curve produced is really two curves
added together. On the left-hand side is the
curve from the titration of the carboxyl
group. On the right-hand side is the curve
from the titration of the amino group.
One equivalent of NaOH is required to
titrate each acidic group.
When the first equivalent has been added
the amino acid is in its dipolar form.
Question
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What are the relative
amounts of structure I
and structure II when
0.5 equivalents have
been added?
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There are equal
amounts of each
Hydrogen Bonds
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When unfolded, all polar/hydrophillic sidechains can interact via Hbonds with water.
When the protein folds, they must H-bond to each other and exclude
much of the water.
All groups capable of forming a hydrogen bond MUST, hence Hbonding in the backbone (C=O to N-H) by way of helices and sheets
is an efficient way of ensuring maximum H-bonding.
Sidechains can either accept (as in C=O) or donate (as in N-H, or OH) an H-bond.
The capacity of proteins to form hydrogen bonds is an important
determinant of protein stability.
Hydrogen bonds can be:
 between backbone groups, as in helices and sheets;
 between side chains, such as serine or threonine O-H groups and
carbonyl carbons of side chains (-C=O);
 and between backbone groups and side chain groups.
Summary
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General features
Aliphatic amino acids
Neutral polar amino acids
Sulphur containing amino acids
Aromatic amino acids
Charge:
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Acidic amino acids
Basic amino acids
Ion pairs
pKa values
Titration with NaOH
Hydrogen bonds
Question
Reading
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Biochemistry, 5th edition, Berg, Tymoczko
and Stryer

http://www.wiley.com/legacy/college/boyer/0470003790/animations/
animations.htm