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Amino
Acids
|
Peptide formation | Side
Chains | Covalent Modification | Optical
Rotation | Amino
Acids Grouped |
The
amino acids are the monomeric units from which proteins are derived.
The word protein is derived from the (Greek) word proteios which
means principal or prime. Proteins are, in fact, principal
components of biochemical systems. They serve in a structural
capacity, they are utilized as a source of energy, and they can
be catalysts - most enzymes that catalyze the reactions occurring
in living organisms are proteins. The
characteristics the amino acids are important to the structure
and functions of the polymers, the proteins.
The
most commonly occurring amino acids are shown in the table
below. They are usually characterized on the basis of the
fourth substituent (i.e., that in addition to the amino group,
the carboxyl group, and the hydrogen) that is bonded at C (2).
The trivial name of the amino acid is followed by its abbreviation
in parentheses. Next, the systematic name of the amino acid
is given. Common structure of amino acids is:
R--CH--COOH
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NH2
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In this structure the C in -COOH is
"carbon #1" and is attached to a -CH-,
which is called the "alpha" carbon or "carbon
atom #2", or C(2).
The amino group attached to alpha carbon is known as "alpha amino group".
The R group attached to
alpha carbon is known as side chain. |
Peptide Formation
The formation of a protein from amino acids entails a polymerization
process involving the amino group of one amino acid and the carboxyl
group of another, with the release of water and the formation of
a perptide bond.
 |
Practice
Exam on the Proteins Page (click
on the "practice exam" on the left, bottom), from
Seager/Slabagh's
Chemistry
Today [check out the additional information, too.] |
Importance
of side chains
The side chain bonded at C(2)
is not involved in forming the peptide bonds which create the
protein. But they may
be available to participate in the reactions
and processes in which the protein is involved. For example,
they may help form hydrogen bonds, or electrostatic and hydrophobic
interactions, or disulfide bonds.,
undergo covalent modification (phosphorylation,
methylation, adenylylation) that alter the chemical or physical
characteristics of the protein,
act as proton donors or proton acceptors
in a reaction mechanism when the protein is an enzyme,
influence the conformation of a structural element
and, thereby, alter the nature of its contribution to the structural
characteristics of the molecule (this is where secondary and tertiary
proptein structure may be developed).
Covalent
Modification
Certain functional groups at C(2)
of an aminoacyl group undergo enzymatic covalent modification
for the purpose of altering the behavior of the protein.
Such covalent modification is one of the principal ways in which
the catalytic activity of regulatory enzymes is modulated.
One of the most common types of covalent modification
for the purpose of regulation is phosphorylation of the hydroxyl
group of a serine, or a threonine, or a tyrosine unit of a protein.
This is one example in which the presence of a side-chain functional
group of an amino acid makes it possible for the protein containing
that amino acid to have an important role in regulating such fundamental
processes as cell development or cell proliferation.
Optical
Rotation
All amino acids except glycine
rotate the plane of polarized light because of the presence of
an asymetric center at C(2).
The definition of D and L depends on the position of -NH2 group
on C(2).
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COOH
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H - C - NH2
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R
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This is the D-form.
When the amino group is on the left of C(2), it is called L form. |
Grouping
of amino acids [see table
below]
| Acidic
and Basic |
Hydrophilic
and Hydrophobic |
Zwitter Ions |
|
At pH 7, the
amino acids are grouped as:
Acidic (negatively charged):
Glutamic acid (Glu) and Aspartic acid (Asp)
Basic (positively charged):
Lysine (Lys), Arginine (Arg), Histidine (His)
Neutral:
Rest of the amino acids have net zero charge at neutral
pH.
The
charge depends on the side chain.
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Hydrophilic: Ala, Arg, Asn (Asparagine),
Asp, Cys, Glu, Gln (Glutamine), Gly,His, Lys, Pro, Ser,
Thr. Sometimes Tyr is included in this group though Tyr
is more hydrophobic than hydrophilic.
Hydrophobic: Amino acid side chains other than those
above are hydrophobic.
This
property depends on whether the side chains like water
(hydrophilic) or hate water (hydrophobic).
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Any compound which has a net zero charge is called a zwitter
ion. Among amino acids, neutral amino acids have
net zero charge at pH 7 because their structure at this
pH is:
R-CH-COO-
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N+H3
The positive and negative charges neutralize
each other.
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Amino
Acid Table
| Amino acids in orange
have hydrophobic side chain R groups. Amino acids in green
are considered to be hydrophilic because they have electronegative
groups on the side chain except tyrosine which because of
the phenyl ring side chain is also hydrophobic in character.
Two amino acids in pink,
Glu and Asp, have two carboxylic acids in the side chain,
are hydrophilic and contribute one negative charge to a polypeptide
chain at neutral pH. The basic amino acids in light
blue are also very hydrophilic and are positively
charged at neutral pH. It should be clear from this that amino
acid side chains which contribute to overall charge on a protein
are either acidic or basic at neutral pH. |
The structure of amino acids shown
here are by Dr. Robert J. Huskey (retired) University
of Viginia. 
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