Amino acids, peptides and proteins

Chemical Nature of the Amino Acids

All peptides and polypeptides are polymers of α-
amino acids. There are 20 α-amino acids that are
relevant to the make-up of mammalian proteins .
Several other amino acids are found in the body
free or in combined states (i.e. not associated with
peptides or proteins).
These non-protein associated amino acids perform
specialized functions. Several of the amino acids
found in proteins also serve functions distinct from
the formation of peptides and proteins, e.g.,
tyrosine in the formation of thyroid hormones or
glutamate acting as a neurotransmitter.
The α-amino acids in peptides and proteins
(excluding proline) consist of a carboxylic acid
(–COOH) and an amino (–NH2) functional
group attached to the same tetrahedral carbon
atom. This carbon is the α-carbon.
Distinct R-groups, that distinguish one
amino acid from another, also are attached to
the alpha-carbon (except in the case of glycine
where the R-group is hydrogen). The fourth
substitution on the tetrahedral α-carbon of
amino acids is hydrogen.
 α-Amino Acids Found in Proteins

Amino Acid Symbol Structure

Amino Acids with Aliphatic R-Groups

Glycine Gly – G

Alanine Ala – A

Valine Val – V

Leucine Leu – L

Isoleucine Ile – I
Amino Acid Symbol Structure
Non-Aromatic Amino Acids with Hydroxyl R-Groups

Serine Ser – S

Threonine Thr – T
Amino Acids with Sulfur-Containing R-Groups

Cysteine Cys – C

Methionine Met – M
Amino Acid Symbol Structure
Acidic Amino Acids and their Amides

Aspartic Acid Asp – D

Asparagine Asn – N

Glutamic Acid Glu – E

Glutamine Gln – Q

Basic Amino Acids

Arginine Arg – R

Lysine Lys – K

Histidine His – H
 Amino Acid Symbol Structure

Amino Acids with Aromatic Rings

Phenylalanine Phe – F

Tyrosine Tyr – Y

Tryptophan Trp – W

Imino Acids

Proline Pro – P
Acid-Base Properties of the Amino Acids
The α-COOH and α-NH2 groups in amino acids are
capable of ionizing (as are the acidic and basic R-groups
of the amino acids). As a result of their ionizability the
following ionic equilibrium reactions may be written:
R-COOH <——> R-COO– + H+
R-NH3+ <——> R-NH2 + H+
The equilibrium reactions, as written, demonstrate that
amino acids contain at least two weakly acidic groups.
However, the carboxyl group is a far stronger acid than
the amino group. At physiological pH (around 7.4) the
carboxyl group will be unprotonated and the amino
group will be protonated. An amino acid with no
ionizable R-group would be electrically neutral at this
pH. This species is termed a zwitterion.
Like typical organic acids, the acidic strength of the
carboxyl, amino and ionizable R-groups in amino acids
can be defined by the association constant, Ka or more
commonly the negative logrithm of Ka, the pKa. The net
charge (the algebraic sum of all the charged groups
present) of any amino acid, peptide or protein, will
depend upon the pH of the surrounding aqueous
environment. As the pH of a solution of an amino acid
or protein changes so too does the net charge. This
phenomenon can be observed during the titration of
any amino acid or protein. When the net charge of an
amino acid or protein is zero the pH will be equivalent
to the isoelectric point: pI.
 Functional Significance of
Amino Acid
R-Groups
In solution it is the nature of the amino acid R-groups
that dictate structure-function relationships of
peptides and proteins. The hydrophobic amino acids
will generally be encountered in the interior of
proteins shielded from direct contact with water.
Conversely, the hydrophilic amino acids are generally
found on the exterior of proteins as well as in the
active centers of enzymatically active proteins.
Indeed, it is the very nature of certain amino acid R-
groups that allow enzyme reactions to occur.
The imidazole ring of histidine allows it to act as
either a proton donor or acceptor at physiological pH.
Hence, it is frequently found in the reactive center of
enzymes. Equally important is the ability of histidines
in hemoglobin to buffer the H+ ions from carbonic
acid ionization in red blood cells.
It is this property of hemoglobin that allows it to
exchange O2 and CO2 at the tissues or lungs,
respectively.
The primary alcohol of serine and threonine as well as
the thiol (–SH) of cysteine allow these amino acids to
act as nucleophiles during enzymatic catalysis.
Additionally, the thiol of cysteine is able to form a
disulfide bond with other cysteines:
Cysteine-SH + HS-Cysteine <——> Cysteine-S-S-Cysteine

This simple disulfide is identified as cystine.

The formation of disulfide bonds between
cysteines present within proteins is important
to the formation of active structural domains in
a large number of proteins. Disulfide bonding
between cysteines in different polypeptide
chains of oligomeric proteins plays a crucial role
in ordering the structure of complex proteins,
e.g. the insulin receptor.
.
 . Reactions of Amino Acids

1. Reactions due to the amino

group
a. Salt formation with strong inorganic acid

Salts are water insoluble

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 b. Nucleophilic reactions

Practical application:
• Used to determine the N-terminal amino acid in a
peptide
• In the synthesis of peptides

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Nucleophilic reactions cont…

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Nucleophilic reactions cont…

e.g.Acylation

• The amino group is converted to amide not the

carboxylic group. Why???
• Acid chlorides and anhydrides are the acylating agents.
• Benzyl chloroformate, PhCH2OCOCl, is commonly used
because it is easily removed.

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 c. Reaction with nitrous acid

• Application: by measuring the nitrogen evolved one can

estimate the amino acid content of a given sample (Van-
Slyke estimation of amino acids).

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 2. Reactions due to the carboxylic acid group

• Generally exits as carboxylate (in water) and unreative.

– It is not liable to nucleophilic attack nor a nucleophile itself since the
charge is spread out

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 a. Esterification

• Use a large excess of alcohol and an acidic catalyst.

• Esters are often used as protective derivatives.
• Aqueous hydrolysis regenerates the acid.

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 b. Formation of acid chloride

• Note: the amino group should first be "protected" (blocked) as amide by

treating it with acetyl chloride or acetic anhydride.

Application: to make the carboxylic acid group

highly reactive (to activate it)
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 c. Decarboxylation

• aas can be decarboxylated by heat, acids, bases (e.g. BaOH) or specific

enzymes

Examples:
• Histamine (from histidine)
• Cadaverine (from lysine)
• Putrescine from (ornithine)
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d. Salt formation with alkali

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e. Reduction to alcohols

amino alcohol

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 3. Reactions due to the carboxylic acid and amino group

a. Reactions with salts of heavy metals

• Amino acids form chelate compounds with the salts of
heavy metals e.g. copper salts

•The reaction deactivates both functional groups

• Application: used to selectively modify the side group
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Synthesis of α-Amino Acids
1) Amination of alpha-bromocarboxylic acids,
provides a straightforward method for preparing
alpha-aminocarboxylic acids.

The bromoacids, in turn, are conveniently prepared from

carboxylic acids by reaction with Br2 + PCl3. Although this direct
approach gave mediocre results when used to prepare simple
amines from alkyl halides, it is more effective for making amino
acids, by reducing nucleophilicity of the nitrogen atom in the
product.
2) By modifying the nitrogen as a phthalimide salt, the
propensity of amines to undergo multiple
substitutions is removed, and a single clean
substitution reaction of 1º- and many 2º-alkylhalides
takes place.

This procedure, known as the Gabriel synthesis, can be

used to advantage in aminating bromomalonic esters, as
shown in the upper equation of the following scheme.
Since the phthalimide substituted malonic ester has an
acidic hydrogen (colored orange), activated by the two
ester groups, this intermediate may be converted to an
ambident anion and alkylated.
Finally, base catalyzed hydrolysis of the
phthalimide moiety and the esters, followed by
acidification and thermal decarboxylation,
produces an amino acid and phthalic acid .
3) An elegant procedure, known as the Strecker
synthesis, assembles an alpha-amino acid from
ammonia (the amine precursor), cyanide (the carboxyl
precursor), and an aldehyde. This reaction (shown
below) is essentially an imino analog of cyanohydrin
formation. The alpha-amino nitrile formed in this way
can then be hydrolyzed to an amino acid by either acid
or base catalysis.
4) Resolution   The three synthetic procedures
described above, and many others that can be
conceived, give racemic amino acid products. If pure L
or D enantiomers are desired, it is necessary to resolve
these racemic mixtures. A common method of resolving
racemates is by diastereomeric salt formation with a
pure chiral acid or base.
The Peptide Bond
Peptide bond formation is a condensation reaction leading
to the polymerization of amino acids into peptides and
proteins. Peptides are small consisting of few amino acids. A
number of hormones and neurotransmitters are peptides.
Additionally, several antibiotics and antitumor agents are
peptides. Proteins are polypeptides of greatly divergent length.
The simplest peptide, a dipeptide, contains a single peptide
bond formed by the condensation of the carboxyl group of one
amino acid with the amino group of the second with the
concomitant elimination of water. The presence of the carbonyl
group in a peptide bond allows electron resonance stabilization
to occur such that the peptide bond exhibits rigidity not unlike
the typical –C=C– double bond. The peptide bond is, therefore,
said to have partial double-bond character.

Resonance stabilization forms

of the peptide bond
 Protein
Proteins have a complex three dimensional structure which is
important because the function of a protein is closely tied to its
three dimensional structure.  This nature of this structure is
usually explained in terms of a structural hierarchy, from
primary to quaternary. 
Primary Structure
The primary structure of a polypeptide or protein is the
sequence of amino acids in the protein. In the case of insulin
shown here there are two polypeptide chains in the primary
structure.Human Insulin Primary structure. Each three letter
abbreviation stands for one of the twenty basic amino acids
found in living things: 
Chain 1 GLY- ILE -VAL- GLU -GLN -CYS -CYS -THR- SER -ILE -CYS- SER -LEU -
TYR -GLN -LEU -GLU -ASN -TYR -CYS -ASN  

Chain 2 PHE -VAL -ASN-GLN -HIS -LEU -CYS- GLY- ASP -HIS -LEU- VAL- GLU-
ALA -LEU- TYR -LEU- VAL- CYS- GLY- GLU- ARG -GLY- PHE -PHE -TYR - THR -
PRO -LYS -THR  
Secondary Structure   

Secondary structure refers to the folding of the chain of amino acids into a helix or
a pleated sheet. 
This structure is a pleated sheet formed by parallel chains of amino acids. These
sheets are important in many structural proteins. Many proteins have sheets and
helices. Secondary structure arises from the geometry of the bond angle between
amino acids as well
Tertiary Structure
Tertiary structure refers to a higher level of folding in which the helices and
sheets of the secondary structure fold upon themselves. This higher level
folding arises for several reasons. First, different regions of the amino acid
chain are hydrophilic or hydrophobic and arrange themselves accordingly
in water. Second different regions of the chain bond with each other via
hydrogen bonding or disulfide linkages. 
This kind of structure is most important in globular proteins such as this
insulin molecule, shown in cartoon form by RasMol to indicate the folding of
helices.
Quaternary structure Quaternary structure arises when
polypeptide chains are bound together usually by hydrogen bonds. For
example hemoglobin the oxygen carrying protein in blood has four
subunits hydrogen bonded together. Most proteins with a molecular
weight of 50,000 or more are made of such units. 
Sometimes quaternary structure maybe very complex. For example, beef
glutamate dehydrogenase is an enzyme with a molecular weight of
2,200,000. Each enzyme molecule consists of eight large subunits. In
turn, each of these consists of numerous smaller units.