Amino Acids

Protein Roles
1. Many proteins function as enzymes, the biochemical catalysts. Enzymes
catalyse nearly all reactions that occur in living organisms.
2. Some proteins bind other molecules for storage and transport. For
example, myoglobin binds oxygen in skeletal and cardiac muscle cells, and
haemoglobin binds and transports oxygen and carbon dioxide in red blood
cells.
3. Some proteins, such as tubulin, actin and collagen provide support and
shape to cells and hence to tissues and organisms.
4. Assemblies of proteins can do mechanical work, such as the movement of
flagella, the separation of chromosomes at mitosis and the contraction of
muscles.
5. Many proteins play a role in decoding information in the cell. Some are
involved in translation, whereas others play a role in regulating gene
expression by binding to nucleic acids.
6. Some proteins are hormones, which regulate biochemical activities in target
cells or tissues; other proteins serve as receptors for hormones.
7. Some proteins have highly specialised functions. For example, antibodies
defend vertebrates against bacterial and viral infections, and toxins, produced
by bacteria, can kill larger organisms.
These roles fall into four major functional groups:
Binding carrier protein or enzyme bind a ligand or a substrate. Nearly all
proteins have a binding function
Catalysis enzymes
Switching many proteins, especially in cell membranes, that bind things
that come from the outside of the cell. Receptors then change shape and
contact something inside the cell which switching something on inside the
cell which sends a signal to the nucleus
Structural hold cells in 3d shape

Proteins are made of Amino Acids

Amino acids can condense together to
form peptides. Once you form a peptide
bond/amide bond, it is very difficult to
break very strong. If the string of
amino acids is larger than 30, it is
capable of starting to fold up into a 3d
shape, and so it is called a protein. If it
is less than 30 amino acids, it is not
capable of forming a 3d shape, and so
is called a peptide.

General Structure of Amino Acids

There is commonality in all amino acids
they all have:

a central carbon
an amino group
an carboxylate group
a hydrogen atom
an R group

The difference between amino acids is the

R group. The chemical character of the
amino acid is therefore given by the R
group.

Acid/Base Chemistry of Amino Acids

The acidity of the carboxylic acids is due to the
stability of the carboxylate anion relative to the
acid. The charge of the carboxylate resides on two
equivalent electronegative oxygen atoms. This is
represented by a weighted average of the simple
structures, resonance or canonical forms.
The relationship between these two canonical forms can be shown using curly
arrows which are used in organic chemistry to denote the movement of pairs of
electrons. The negative charge is shared between the two oxygen atoms.
Amino acids are zwitterionic they have both an acidic group and a basic
group. An acid donates protons and a base accepts protons. A carboxylate
group is an acidic group (it has a tendency to lose its H to become COO -) and an
amino group is a basic group (it has a tendency to accept an H to become NH 3+).
This occurs in a pH dependant manner:
At pHs above the pK of an acidic side chain, the side chain is always
negatively charged.
At pHs below the pK of a basic side chain, the side chain is always
positively charged.
pK is a dissociation constant. Anything that is capable of ionisation has a pK.
The carboxylate group has a pK of about 2.5. This means that at a pH of 2.5, the
carboxylate group is 50% COOH and 50% COO - and H+ - it has dissociated by
50%. The pH scale is logarithmic so if we go from pH 2.5 to pH 3.5, there is a
tenfold change in the ionisation of the side chain, 4.5 is a one hundredfold
change etc. So at pH 7, there will be 100 000 fewer protons around than there
would be at 2.5. Hence, it remains 99.999% COO - at pH 7 as there are so few
protons around. The converse is true of a basic group at pH 7 (when the amino
group has a pK of 9.5) there are more protons around. So, under physiological
conditions, an amino acid never has COOH and NH2 groups it always has COO and NH3+ groups. At pH 7 the acid has lost a proton and the base has gained a

proton they are charged (although the charges cancel each other out) and are
therefore zwitterions.
Some R groups are also capable of being ionised. This is important in the role of
R groups in protein structure and function. For example, histones bind DNA
because DNA is strongly negatively charged and histones contain a lot of
lysine which is a basic amino acid it has a side chain that is positively
charged at pH 7 so the positive charge of the histone binds the negative charge
of the DNA.

pKa values vary somewhat depending on the

precise molecular structure and the environment in
which the acid-base chemistry is taking place.
For example, the carboxylic acid group of glycine is
more acidic than a simple carboxylic acid since the
corresponding carboxylate anion is more stable in
the presence of the adjacent, positively charged,
ammonium ion.
The effect of environment on pKa is particularly
important in non-polar conditions such as the
interior of a protein.
The table on the right (do not need to learn) shows
that every amino acid has an amino group and an
carboxylate group. The pKs of these groups are all
very similar (between 1.8 and 2.5 for acidic
carboxylate group and between 8.7 and 10.7 for
basic amino group). Only some amino acids are
capable of having their side chains ionised. Under
physiological conditions, the acidic amino acids,
with a pK less than 7 (aspartic acid & glutamic acid)
will be negatively charged and the basic ones,
with a pK greater than 7 (e.g. lysine and arginine)
will be positively charged. Histidine has a pK which varies between pH 6 and pH
7, therefore it can be either basic or acidic at neutral pH which makes it very
special. It is often present in the binding sites of enzymes where it plays a role in
acid/base chemistry.
When put into a protein, the amino group and the carboxylate group form
the peptide bond and therefore there charge can be ignored there is no
charge associated with a peptide bond. The only charge that has any significance
for a protein in solution is the charge on the R groups.

Stereochemistry of Amino Acids

Amino acids exhibit stereochemistry they can either be the D or the L form
(D isomer rotates the plane of polarised light to the right, an L to the left). The
two forms are non-superimposable mirror images of each other
(stereoisomers).

In nature, almost all amino

acids are in the L form. This
means that it is easy for the
protein to fold up when they are
all in the same configuration.

A Survey of the -Amino Acids of Proteins

The following paragraphs take a look at the structure of the amino acids by
group, and also some of the important amino acid derivatives used in the body.
Amino Acids can be divided into a number of chemically distinct groupings. The
side chains have differing reactivity and differing roles in proteins. The groups
are:

hydrocarbon side chains

carboxylic acid side chains
amide side chains
acyclic with basic N containing side chains
hydroxyl functional groups
sulphur containing side chains
nitrogen heterocycles and proline

Amino Acids with Aliphatic R Groups

These are:

GLYCINE
ALANINE
VALINE
LEUCINE
ISOLEUCINE

These amino acids build in complexity. The simplest is glycine and it has a very
important role to play in proteins. It is very small so is found at points in the
polypeptide where there is a turn. Small amino acids such as glycine are found
in these regions as large amino acids with bulky side chains would restrict the
ability of the protein to turn. All these amino acids, particularly the larger ones
(with longer hydrocarbon side chains) are hydrophobic. So, if there was a
stretch of these amino acids in the primary sequence of a protein, and the
protein folded up, these would be found on the inside of the protein, away from
the water. If they were on the outside of a protein, they could be forming a
binding site for something else that is hydrophobic.

Because both the and carbon atoms of isoleucine are asymmetric it has two
chiral centres and therefore four possible stereoisomers:

Acidic R Groups and their Amide Derivatives

These are:
ASPARTATE
GLUTAMATE

 ASPARGINE
GLUTAMINE
Aspartate and glutamate confer negative charge on proteins because their
side chains are ionised at pH 7. Under physiological conditions acidic side
chains exist as the conjugate base, hence the suffix
-ate.
These amino acids have either acidic side chains or polar side chains. Aspartate
and glutamate have a tendency to lose an electron so they are negatively
charged at pH 7. This means they are basic at pH 7. If there is one of these
groupings in the active site of an enzyme it acts as a base it would want to
grabs protons back or attract a positive charge. It could also be involved in base
catalysis where it abstracts a proton from something to make that group
nucleophilic so it can attack a susceptible bond. If there is an appropriately
positioned basic group next to water, it can take one of the protons from water,
forming the nucleophile OH-.
Asparagine and glutamine are not charged they are polar and can form
hydrogen bonds. This means they are very important structurally they can
form hydrogen bonds to other groups, forming a network. A single hydrogen
bond is very weak, but hundreds become a significant force.
Amino Acids with Basic R Groups

These are:
HISTDINE
LYSINE
ARGININE
The side chains of both lysine and arginine are positively charged at
physiological pH contributing basicity to proteins, arginine is the most basic of
the 20 amino acids.
They are positively charged because they have a pK which is higher than the pH
at which they sit. As you take the pH down, they are protonated and positively
charged. If they were in the active site, they could bind a negatively charged
group or could be involved in acid catalysis.

Histidine is very important it has the

capability of losing a proton and gaining
a proton it can act as an acid or a base.
In some enzyme active sites, histidine
sits there and in one part of a reaction
mechanism it donates a proton and in
another part it will, once it has lost a
proton, it will become a base and can
accept a proton. It is therefore involved
in acid/base chemistry in the active sites
of enzymes. Histidine can also bind metal ions. It particularly likes to bind zinc.
About 30% of all of the proteins in your body require zinc or a metal ion to work.
Haemoglobin wouldnt carry oxygen without iron in its active centre. Enzymes
that hydrolyse proteins wouldnt be able to do this without zinc in their active
site. This is because zinc loves to bind water and if zinc binds water, it reduces
the pK of water from 14.7 to 7, so water can be ionised at a much lower pH. This
makes water a really good nucleophile in the presence of zinc it is 50% OH (and H+). This means it can take part in hydrolysis reactions.
Protonated and neutral forms of histidine are both physiologically important. This
evenly balanced equilibrium underpins histidines key role in biological acid/base
chemistry.
Side Chains with Alcohol and Sulphur Groups

These are:
METHIONINE
CYSTEINE

 SERINE
THREONINE
Cysteine is important as if there are two close
together in a peptide, they can form strong
covalent (disulphide bridges) between the SH
groups. This gives the protein stability. Proteins
that exist in extremely nasty environments like hot
sulphur springs can survive at 100c due to the
strong disulphide bridges that gives them tight
structures. The disulphide bond is the ONLY
covalent bond that exists in the tertiary
structure of proteins between R groups. All
the other R groups interact non-covalently.
Methionine is always found as the first amino
acid in proteins. In bacteria it is formylmethionine (it has a functional group on it that
gives it polarity). As it is aliphatic (and hence
hydrophobic) it is found buried deep inside proteins, away from water. It has a
thiol group (sulphur), protected by methylation. In some metabolic
processes, this amino acid becomes very important.
Serine and threonine have a free hydroxyl group in their side chain. They are
important in metabolic processes as that hydroxyl group is capable of
phosphorylation (being phosphorylated) it loses the H and becomes OP. This
is very important when it comes to activating enzymes for metabolic
processes. Because of this, and because they are hydrophobic, they tend to be
exposed on the outside of proteins.
Side Chains containing Nitrogen Heterocycles

These are:
PROLINE

 PHENYLALANINE
TYROSINE
TRYPTOPHAN
These amino acids with aromatic side chains are
very hydrophobic. They are found on the inside
of proteins. The hydrophobic effect results in
hydrophobic amino acids such as these being
sequestered away from water it is the driving
force for protein folding.
Proline is a special amino acid it has no free
amino group. The R group makes contact
covalently with the amino group. This forms a
ring structure. This is very important in protein
structure it is called a helix breaker at the
end of a helix there is always a proline as this
stops helix formation between free amino and
carboxylate groups. The presence of an extra alkyl
group rather than a hydrogen atom on the amide
nitrogen of proline not only precludes formation of
a stabilising hydrogen bond with the usual
carbonyl group but it also introduces a steric
repulsion with that group. Proline often acts to terminate -helices and is
therefore called a helix breaker.

Hydrophobic Character of Amino Acids

The more hydrophobic amino acids have a tendency to be sequestered away
from the solvent towards the centre of protein molecules. This provides one of
the major driving forces for protein folding.

Hydrophilic residues tend to interact with the

solvent more easily via hydrogen bonding and thus
can be on the outside of proteins.
The table on the right (do not need to learn) shows
the hydrophobicity of the amino acids the larger
the number, the more hydrophobic the amino acid.
The group at the top are very hydrophobic and are
therefore found on the inside of proteins. The group
in the middle can be found either in the middle or
outside they are neither strongly hydrophobic nor
strongly hydrophilic. Finally, the group at the
bottom are very hydrophilic and are likely to be
found on the outside of proteins, towards the
water.

The Peptide Bond

Proteins are linear polymers of L-amino acids linked via a peptide

(amide) bond. They can form
hydrogen bonds which affects
secondary structure the ONLY bond that affects secondary structure.
The nitrogen of the peptide bond forms a planar trigonal shape because a
partial double bond is formed with the adjacent carbon.
The stereochemistry requires that the carbonyl carbon, nitrogen, oxygen,
hydrogen atoms and the two neighbouring -carbons are all constrained to lie in
a plane.
Under physiological conditions this effectively restricts the peptide bond to one
of two configurations: cis or trans.
To minimise steric crowding due to close proximity of bulky groups on the
carbonyl carbon and the nitrogen the trans form is favoured, except where
proline is involved.

Proline is a Unique Amino Acid

The steric preferences of proline are different from the other amino acids.
It has an alkyl chain rather than a hydrogen atom as the second substituent
on nitrogen.
For amide bonds except those involving the nitrogen of proline there is a
thermodynamic preference for the trans configuration (-carbon substituents to
be as far apart as possible) the peptide therefore has a slight curve to it. As
they are all the same form, they are flexible and can fold logically.
In amides containing proline the cis form is not dramatically disadvantaged.
In proteins about 10% of all peptide bonds involving proline are cis. This can
induce quite sharp kinks in protein structure

The Shape of Polypeptides is defined by the Rotation about the

C-N & C-C bonds
All atoms around the peptide bond lie in a planar conformation. There is no
rotation around the peptide bond

Therefore, the shape of the polypeptide is defined

by rotation about the C-N and C-C bonds.
This rotation is described by the torsion angles
phi between
C-N and psi between C-C.
If all psi and phi angles are the same, the peptide
assumes a repeated structure.
For certain combinations of angles this can take
the form of a helical structure (-helix) or a
beta sheet structure.
Clearly, the peptide structure exhibits flexibility
and this is important for the complex structure of
proteins.
The R groups are on alternating sides (opposite
directions) as we go down the chain as otherwise
the protein would not be able to fold correctly due
to steric hindrance.

The Ramachandran Plot

The physical size of atoms and groups of
atoms limits the possible psi and phi
torsion angles that the backbone of the
polypeptide chain can adopt without
causing protruding R groups to bump into
each other. Ramachandran devised a way
of plotting these allowed psi and phi
angles. The red patches on the right are
those combinations of psi and phi angles
that are allowed as they do not result in
steric hindrance. The pink areas are
allowed with a little relaxation of steric
hindrance.