Illustrate and explain the general structure of amino acid.

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 α-amino [alpha-amino] carboxylic acid. Each
molecule contains a central carbon (C) atom, called the α-carbon, to which
both an amino and a carboxyl group are attached. The remaining two bonds of
the α-carbon atom are generally satisfied by a hydrogen (H) atom and

the R group. The formula of a general amino acid is:

The amino acids differ from each other in the particular chemical structure of
the R group.
Illustrate the stereochemistry of amino acid.

The amino acids are all chiral, with the exception of glycine, whose side chain is H. As
with lipids, biochemists use the L and D nomenclature. All naturally occuring proteins
from all living organisms consist of L amino acids. The absolute stereochemistry is
related to L-glyceraldehyde, as was the case for triacylglycerides and phospholipids.
Most naturally occurring chiral amino acids are S, with the exception of cysteine. As the
diagram below shows, the absolute configuration of the amino acids can be shown with
the H pointed to the rear, the COOH groups pointing out to the left, the R group to the
right, and the NH3 group upwards. You can remember this with the anagram CORN.

Figure:  Stereochemistry of Amino Acids.

[ CITATION Die20 \l 1033 ]

Differentiate L-amino acid from D-amino acid.

The main difference between L and D amino acids is that the amine group of L-
amino acids occurs in the left-hand side when drawn in the Fischer projection,
keeping the carboxylic acid group on top and the carbon chain in the bottom,
whereas the amine group of the D-amino acids occurs in the right. 
L- and D-amino acids are the two isomeric forms of amino acids which occur in
nature. L-amino acids are the form used by the cells to synthesize proteins.

L-amino acid refers to a stereoisomer of a particular amino acid whose amino group is on

the left side in its Fisher projection while D-amino acid refers to the other stereoisomer of
the amino acid whose amino group is on the right side in its Fisher projection. This explains
the basic difference between L and D amino acids[ CITATION Lak18 \l 1033 ]

What are the three classifications of amino acids based on the general properties and chemical
structures of their side chains? Draw their structures and indicate their respective 1-letter and 3-letter
abbreviations. [Tabular Form]
Amino acids can be classified based on the characteristics of their distinctive side
chains as nonpolar, 
polar
 but uncharged, negatively charged, or positively charged.

What is a zwitterion? Give one example.

A zwitterion is a molecule with functional groups, of which at least one has a

positive and one has a negative electrical charge. The net charge of the entire
molecule is zero.

Amino acids are the best-known examples of zwitterions. They contain an amine
group (basic) and a carboxylic group (acidic). The -NH 2 group is the stronger
base, and so it picks up H+ from the -COOH group to leave a zwitterion (i.e. the
amine group de-protonates the carboxylic acid)[ CITATION aqi18 \l 1033 ]

Using a chemical equation, illustrate the behavior of amino acid in acid and base solution, respectively.

When an amino acid dissolves in water, the situation is a little bit more complicated than
we tend to pretend at this level. The zwitterion interacts with water molecules - acting as
both an acid and a base.

As an acid:

The -NH3+ group is a weak acid and donates a hydrogen ion to a water molecule.
Because it is only a weak acid, the position of equilibrium will lie to the left.

As a base:
The -COO- group is a weak base and takes a hydrogen ion from a water molecule.
Again, the equilibrium lies to the left.

When you dissolve an amino acid in water, both of these reactions are happening.

But . . .

The positions of the two equilibria aren't identical - they vary depending on the influence
of the "R" group. In practice, for the simple amino acids we have been talking about, the
position of the first equilibrium lies a bit further to the right than the second one.

That means that there will be rather more of the negative ion from the amino acid in the
solution than the positive one.

In those circumstances, if you carried out electrophoresis on the unmodified solution,

there would be a slight drift of amino acid towards the positive electrode (the anode).

To stop that, you need to cut down the amount of the negative ion so that the
concentrations of the two ions are identical. You can do that by adding a very small
amount of acid to the solution, moving the position of the first equilibrium further to the
left.

Typically, the pH has to be lowered to about 6 to achieve this. For glycine, for example,
the isoelectric point is pH 6.07; for alanine, 6.11; and for serine, 5.68. [ CITATION Jim16 \l
1033 ]

Differentiate acidic amino acid from basic amino acid and neutral amino acid.

Neutral amino acids are the amino acids that possess equal number of carboxylic acid groups
and amino groups. The groups attached to the amino acid, apart from the carboxylic acid
groups and amino acid groups, may be non-polar or polar. The non-polar amino acids contain
alkyl groups as side chains and the polar amino acids contain a functional group.

The neutral amino acids can be divided into two types: 

 Non-polar amino acids: These amino acids contain an equal number of carboxylic and

amino group along with an R group which can be aliphatic or aromatic. Due to the
presence of R groups, these amino acids are hydrophobic in nature. The globular proteins
will undergo folding to form a shape such that the hydrophobic groups will be in the
interior of the protein. The examples of non-polar amino acids are alanine, valine,
leucine, glycine, isoleucine, methionine, tryptophan, phenylalanine and proline. 

 Polar uncharged amino acids: In this type of neutral amino acids, the side chains
contain functional groups which possess atoms like nitrogen, sulfur and oxygen. These
atoms possess a lone pair of electrons that help in the formation of hydrogen bonds with
 water or other molecules. The examples of polar uncharged amino acids are serine,
cysteine, asparagine, glutamine, threonine and tyrosine. 

The pka of neutral amino

acid is moderate, Free amino acids can never occur as neutral nonionic molecules: ... they exist
as neutral zwitterions that contain both positively and negatively charged groups.
What is an isoelectric point? Show the complete solution in determining the isoelectric point of glycine.

These amino acids are characterised by two pKas : pKa1 and pKa2 for the
carboxylic acid and the amine respectively.
The isoelectronic point will be halfway between, or the average of, these two
pKas, i.e.   pI = 1/2 (pKa1 + pKa2). This is most readily appreciated when you
realise that at very acidic pH (below pKa1) the amino acid will have an overall
+ve charge and at very basic pH (above pKa2 ) the amino acid will have an
overall -ve charge.  For the simplest amino acid, glycine, pKa1= 2.34 and
pKa2 = 9.6, pI = 5.97.

isoelectric point is defined as the pH at which no net migration takes

place in an electric field, while the isoionic point is defined as the pH at
which there is no net charge on the molecule. In a deionized solution,
the isoelectric and isoionic points are for most purposes identical.
[ CITATION PHa03 \l 1033 ]

Differentiate peptide bond and amide formation.

The main difference between amide and peptide bond is in the molecules involved in the
bond formation. An amide bond is a chemical bond that occurs between a hydroxyl
group of a carboxylic group (-COOH) of one molecule and a hydrogen of an amino
group (-NH2) of another molecule. Whereas, the peptide bond is a type of amide bond
which occurs between two amino acids during the synthesis of a polypeptide chain.
[CITATION Lak181 \l 1033 ]

Explain in detail the formation of peptide bond.

A peptide bond is a chemical bond formed between two molecules when the
carboxyl group of one molecule reacts with the amino group of the other
molecule, releasing a molecule of water (H2O). Polypeptides and proteins are chains
of amino acids held together by peptide bonds, as is the backbone of PNA. [ CITATION enc21 \l 1033 ]

Differentiate N-terminal from C-terminal of a polypeptide.

In the molecule of a peptide, the amino acid residue on one end has an amine group on the alpha carbon. This amino
acid residue is called the N-terminal of the peptide. The amino acid residue on the other end has a carboxylic acid
group on the alpha carbon. This amino acid is called the C-terminal.

eg:
When the structure of a peptide is drawn horizontally, by convention, the N-terminal is placed on the left and the C-
terminal on the right.

[ CITATION Gam20 \l 1033 ]

-Illustrate the general backbone of a polypeptide. Indicate the N-terminal and C-terminal and the
direction of the peptide chain.

If the amine and carboxylic acid functional groups in amino acids join together to form amide
bonds, a chain of amino acid units, called a peptide, is formed. A simple tetrapeptide structure
is shown in the following diagram. By convention, the amino acid component retaining a free
amine group is drawn at the left end (the N-terminus) of the peptide chain, and the amino acid
retaining a free carboxylic acid is drawn on the right (the C-terminus). As expected, the free
amine and carboxylic acid functions on a peptide chain form a zwitterionic structure at their
isoelectric pH.
By clicking the "Grow Peptide" button, an animation showing the assembly of this peptide will be
displayed. The "Show Structure" button displays some bond angles and lengths that are
characteristic of these compounds.

The conformational flexibility of peptide chains is limited chiefly to rotations about the bonds
leading to the alpha-carbon atoms. This restriction is due to the rigid nature of the amide
(peptide) bond. As shown in the following diagram, nitrogen electron pair delocalization into the
carbonyl group results in significant double bond character between the carbonyl carbon and
the nitrogen. This keeps the peptide links relatively planar and resistant to conformational
change. The color shaded rectangles in the lower structure define these regions, and identify
the relatively facile rotations that may take place where the corners meet (i.e. at the alpha-
carbon). This aspect of peptide structure is an important factor influencing the conformations
adopted by proteins and large peptides.
[ CITATION Wil13 \l 1033 ]

Glutathione is a tripeptide compound consisting of glutamic acid attached via its side chain to
the N-terminus of cysteinylglycine. It has a role as a skin lightening agent, a human metabolite,
an Escherichia coli metabolite, a mouse metabolite, an antioxidant and a cofactor. It is a
tripeptide, a thiol and a L-cysteine derivative. It is a conjugate acid of a glutathionate(1-).

Aspartame is a dipeptide obtained by formal condensation of the alpha-carboxy group of L-

aspartic acid with the amino group of methyl L-phenylalaninate. Commonly used as an artificial
sweetener. It has a role as a sweetening agent, a nutraceutical, a micronutrient, a xenobiotic, an
environmental contaminant, an apoptosis inhibitor and an EC 3.1.3.1 (alkaline phosphatase)
inhibitor. It is a dipeptide, a carboxylic acid and a methyl ester. It derives from a L-aspartic
acid and a methyl L-phenylalaninate.
Oxytocin is a neuropeptide containing nine amino acids produced by paraventricular and
supraoptic nuclei of hypothalamus. Oxytocin is derived from a Greek word ‘oxutokia’ meaning
sudden delivery and it is well known for its role in parturition and lactation. In addition oxytocin
performs a wide spectrum of functions. Oxytocin is a hormone with great potential and it is a great
facilitator of life. The purpose of this review is to cover almost all the functions of oxytocin -
reproductive functions, social functions, role in human behaviour and other biologically significant
functions.
Vasopressin, also called antidiuretic hormone, hormone that plays a key
role in maintaining osmolality (the concentration of dissolved particles, such
as salts and glucose, in the serum) and therefore in maintaining the volume of
water in the extracellular fluid (the fluid space that surrounds cells). This is
necessary to protect cells from sudden increases or decreases in water content,
which are capable of interfering with proper cell function.