Amino acid

Dr.K.RAJARAJAN.M.Sc;M.Phil;Ph.D.
Assistant prof. of chemistry,
Rajah Serfoji Govt. College,
Thanjavur-613 005.

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Amino acid, any of a group of organic molecules that
consist of a basic amino group (NH2), an acidic carboxyl
group (COOH), and an organic R group (or side chain)
that is unique to each amino acid. The term amino acid
is short for -amino [alpha-amino] carboxylic acid.
Each molecule contains a central carbon (C)
atom, called the -carbon, to which both an amino and a
carboxyl group are attached. The remaining two bonds
of the -carbon atom are generally satisfied by a
hydrogen (H) atom and the R group. The formula of a
general amino acid is:
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The amino acids differ from
each other in the particular
chemical structure of the R
group.

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Group I: Nonpolar amino acids
Group I amino acids are glycine, alanine, valine,
leucine, isoleucine, proline, phenylalanine,
methionine, and tryptophan. The R groups of these
amino acids have either aliphatic or aromatic
groups.
This makes them hydrophobic (water
fearing). In aqueous solutions, globular proteins
will fold into a three-dimensional shape to bury these
hydrophobic side chains in the protein interior. The
chemical structures of Group I amino acids are:

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amino acid classification.
Most of the amino acids we are familiar with are known as
standard amino acids. These are amino acids that are formed from
universal genetic coding. Standard amino acids (also known as
canonical amino acids) are protein building-blocks. These are the
amino acids that together with DNA help organism to form and
function.

Non-standard amino acids do not help to build proteins. There are

only three exceptions to this rule. Selenocysteine, pyrrolysine, and
N-formylmethionine are non-standard amino acids that can still be
naturally incorporated into proteins.
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They do this by exploiting genetic code that has not been
used or in a certain position within an amino acid chain. Non-
standard amino acids can also be modified forms of standard
amino acids. Many non-standard amino acids are used in
genetic engineering.

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Proteinogenic and non-proteinogenic amino acid
classification
Proteinogenic amino acids are broadly defined as the
amino acids that are used to form proteins. Many of
these are naturally produced by the body. However,
there are proteinogenic amino acids that must be
sourced from diet. In all cases, proteinogenic amino
acids are necessary for healthy body function. You can
read about these in greater detail in our article The
20 Proteinogenic Amino Acids.

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 Non-proteinogenic amino acids are not required to build
proteins. However, this doesnt mean that they are not
important. These amino acids have a vital role as
metabolic intermediates.
There are approximately 700 known non-protein
amino acids, of which around 300 are plant derived. Their
routes of origin include modification of an existing amino
acid or pathway, or their own novel pathways.

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Amino acid classification based on human nutrition

One of the most common ways to classify amino acids is

based on human health requirements. Some amino acids can
be synthesised by the body. These are classified as non-
essential amino acids.
There are eleven non-essential amino acids. Conversely,
essential amino acids must be acquired from food sources. A
balanced diet usually ensures that the body acquires enough
essential amino acids

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There is also a third category of amino acids classified based
on nutrition. These are called semi-essential amino acids.
These are amino acids that are normally considered as non-
essential although during periods of stress they may become
semi-essential.
For example, if the immune system is compromised the
body may struggle to produce certain amino acids.
Consequently diet becomes a necessary source of these
amino acids.

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Amino acid classification based on chemical properties

There are many different chemical properties of amino acid

side chains that can be classified. These variations can help to
order and classify amino acids into groups with common
characteristics.

Some of the common chemical properties used to classify

amino acids include the charge of the side chain, whether it is
acid or basic, and whether it has hydrogen bonding ability.
Broadly, the twenty common amino acids can be split into
non-polar amino acids (hydrophobic) and polar amino acids
(hydrophilic). 12
Non-polar amino acids can be further split into alkyl or
aromatic, while the polar amino acids can be split into
neutral, acid, or basic.
The following video goes into more detail about the
various chemical properties that help to classify different
amino acid groups:

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Amino acid classification based on chemical properties.
There are many different chemical properties of amino acid
side chains that can be classified. These variations can help to
order and classify amino acids into groups with common
characteristics.

Some of the common chemical properties used to classify

amino acids include the charge of the side chain, whether it is
acid or basic, and whether it has hydrogen bonding ability.
Broadly, the twenty common amino acids can be split into non-
polar amino acids (hydrophobic) and polar amino acids
(hydrophilic). 14
Non-polar amino acids can be further split into alkyl or
aromatic, while the polar amino acids can be split into
neutral, acid, or basic. The following video goes into
more detail about the various chemical properties that
help to classify different amino acid groups:

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THE ACID-BASE BEHAVIOUR OF AMINO ACIDS
Zwitterions in simple amino acid solutions
An amino acid has both a basic amine group and an acidic
carboxylic acid group. There is an internal transfer of a
hydrogen ion from the -COOH group to the -NH2 group to
leave an ion with both a negative charge and a positive
charge.
This is called a zwitterion.

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This is the form that amino acids exist in even in the solid
state. If you dissolve the amino acid in water, a simple solution
also contains this ion.

A zwitterion is a compound with no overall electrical charge,

but which contains separate parts which are positively and
negatively charged.

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the amino acid now existed as a negative ion using
electrophoresis.
Adding an acid to an amino acid solution. If you
decrease the pH by adding an acid to a solution of an
amino acid, the -COO- part of the zwitterion picks up
a hydrogen ion.

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Protein structure
Primary structure
The simplest level of protein structure, primary
structure, is simply the sequence of amino acids in a
polypeptide chain. For example, the hormone insulin has
two polypeptide chains, A and B, shown in diagram below.
Each chain has its own set of amino acids,
assembled in a particular order. For instance, the sequence
of the A chain starts with glycine at the N-terminus and
ends with asparagine at the C-terminus, and is different
from the sequence of the B chain.

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 The sequence of a protein is determined by the DNA of
the gene that encodes the proteinA change in the gene's DNA
sequence may lead to a change in the amino acid sequence
of the protein. Even changing just one amino acid in a
proteins sequence can affect the proteins overall structure
and function.
For instance, a single amino acid change is associated with
sickle cell anemia, an inherited disease that affects red blood
cells. In sickle cell anemia, one of the polypeptide chains that
make up hemoglobin, the protein that carries oxygen in the
blood, has a slight sequence change.

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The glutamate that is normally the seventh amino
acid of the hemoglobin chain is replaced by a
valine. This substitution is shown for a fragment of
the chain in the diagram below.

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 What is most remarkable to consider is that a
hemoglobin molecule is made up of two chains and
two chains, each consisting of about 150 amino
acids, for a total of about 600 amino acids in the whole
protein.
The difference between a normal hemoglobin
molecule and a sickle cell molecule is just 2 amino
acids out of the approximately 600.

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Secondary structure
The next level of protein structure, secondary structure,
refers to local folded structures that form within a polypeptide
due to interactions between atoms of the backbone
The most common types of secondary structures are the
helix and the pleated sheet. Both structures are held in shape by
hydrogen bonds, which form between the carbonyl O of one
amino acid and the amino H of another.

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 In an helix, the carbonyl (C=O) of one amino
acid is hydrogen bonded to the amino H (N-H) of an
amino acid that is four down the chain. (E.g., the
carbonyl of amino acid 1 would form a hydrogen
bond to the N-H of amino acid 5.)
This pattern of bonding pulls the polypeptide
chain into a helical structure that resembles a curled
ribbon, with each turn of the helix containing 3.6
amino acids. The R groups of the amino acids stick
outward from the helix, where they are free to
interact

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 In a pleated sheet, two or more segments of a
polypeptide chain line up next to each other, forming a
sheet-like structure held together by hydrogen bonds. The
hydrogen bonds form between carbonyl and amino groups
of backbone, while the R groups extend above and below
the plane of the sheet start superscript, 3, end superscript.
The strands of a pleated sheet may be
parallel, pointing in the same direction (meaning that their
N- and C-termini match up), or antiparallel, pointing in
opposite directions (meaning that the N-terminus of one
strand is positioned next to the C-terminus of the other).

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Certain amino acids are more or less likely to be
found in -helices or pleated sheets.
For instance, the amino acid proline is
sometimes called a helix breaker because its
unusual R group creates a bend in the chain and is
not compatible with helix formation.
Proline is typically found in bends,
unstructured regions between secondary structures.

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 Similarly, amino acids such as tryptophan,
tyrosine, and phenylalanine, which have large ring
structures in their R groups, are often found in
pleated sheets, perhaps because the pleated sheet
structure provides plenty of space for the side chains
Many proteins contain both helices and
pleated sheets, though some contain just one type
of secondary structure

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Tertiary structure
The overall three-dimensional structure of a
polypeptide is called its tertiary structure. The tertiary
structure is primarily due to interactions between the R groups
of the amino acids that make up the protein.
R group interactions that contribute to tertiary
structure include hydrogen bonding, ionic bonding, dipole-
dipole interactions, and London dispersion forces basically,
the whole gamut of non-covalent bonds.

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 For example, R groups with like charges repel one
another, while those with opposite charges can form an ionic
bond. Similarly, polar R groups can form hydrogen bonds and
other dipole-dipole interactions.
Also important to tertiary structure are hydrophobic
interactions, in which amino acids with nonpolar,
hydrophobic R groups cluster together on the inside of the
protein, leaving hydrophilic amino acids on the outside to
interact with surrounding water molecules.

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 Finally, theres one special type of covalent
bond that can contribute to tertiary structure: the
disulfide bond.

Disulfide bonds, covalent linkages between

the sulfur-containing side chains of cysteines, are much
stronger than the other types of bonds that contribute to
tertiary structure.
They act like molecular "safety pins," keeping
parts of the polypeptide firmly attached to one another.

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Quaternary structure
Many proteins are made up of a single polypeptide
chain and have only three levels of structure.
However, some proteins are made up of multiple
polypeptide chains, also known as subunits.
When these subunits come together, they give the
protein its quaternary structure. Haemoglobin carries
oxygen in the blood and is made up of four subunits,
two each of the and types.
Another example is DNA polymerase, an enzyme that
synthesizes new strands of DNA and is composed of ten
subunits
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 In general, the same types of interactions
that contribute to tertiary structure (mostly
weak interactions, such as hydrogen bonding
and London dispersion forces) also hold the
subunits together to give quaternary structure.

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Peptide Synthesis : Protecting groups
Protein synthesis is important for several reasons
including:
confirming the structure of natural proteins (e.g. for
medical research etc.)
to investigate how protein structure and function are
controlled by the amino acid sequence.
However, it is not as straight forward as mixing the amino
acids together to form the amides.
For example, a mixture of alanine, A and glycine, G would
give a mixture of amides : A-G, G-A, A-A and G-G, plus
higher polypeptides...)
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 In order to control the coupling reaction, it is
necessary to use protecting groups.
By protecting the amine group of one
component and the carboxylic acid group of the
other, a specific amide bonds can be formed.

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Therefore the sequence required is to:
protect the amino group in the N-terminal amino
acid and the carboxyl group in the C-terminal amino
acid couple the two amino acids by forming the new
amide bond deprotect the termini of the new peptide
(as and if required)
By repeating the process, polypeptides can be
grown one amino acid residue at a time, or by building
pieces and then joining those together.

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