Amino acids presentation by Atif Nauman(University of Gujrat)

1. Amino Acid
By Atif Nauman (University of Gujrat)

2. Roadmap
• What are amino acids?
• Structure of amino acids.
• Classification of Amino acid.
• Optical Properties of Amino Acids.
• Acid-Base properties.
• Buffer characteristic.
• Standard and Non Standard Amino acids.
• Difference between essential and non-essential amino acids.
• Discussion.

3. What are Amino acids?
• They are molecules containing an amine group, a carboxylic acid
group, and a side-chain that is specific to each amino acid.
• The key elements of amino acid are carbon, hydrogen, oxygen,
and nitrogen.
• Amino acids are the basic structural building units of protein and
other biomolecules, they are also utilized as an energy source.

4. Structure of Amino Acids
Each amino acid (except for proline) has:
1. A carboxyl group (-COO-) .
2. An amino group (-NH3+) .
3. Side chain ("R-group") bonded to the α-carbon atom.
These carboxyl and amino groups are combined in peptide linkage.

5. Structure of Amino Acids

6. Classification of Amino acids
They classified according to the side chain:
• Amino acids with nonpolar side chains.
• Aromatic R Groups.
• Amino acids with uncharged polar side chains.
• Positively Charged (Basic) R Groups.
• Amino acids with acidic side chains.

7. Classification of Amino acids

8. Nonpolar Side Chains
• The side chains cluster in the interior of the protein due to
hydrophobicity.
• The side chain of proline and its α-amino group form a ring
structure.
• Proline gives the fibrous structure of collagen, and interrupts
the α-helices found in globular proteins.
• For Example: alanine, cysteine, glycine, isoleucine, leucine,
methionine, phenylalanine, proline, tryptophan, tyrosine and
valine.

9. Aromatic (R) Groups
• Their aromatic side chains, are nonpolar so that participate in
hydrophobic interactions.
• Tyrosine is an important in some enzymes.
• Most proteins absorb light at a wavelength of 280 nm due to
aromatic groups.
• A property exploited by researchers in the characterization of
proteins.
• For Example:Phenylalanine (Phe),tyrosine (Tyr),
and tryptophan (Trp) .

10. Uncharged polar side chains
• More hydrophilic because they form hydrogen bonds with
water.
• includes serine, threonine, cysteine, asparagine, and
glutamine.
• Cysteine contains a sulfhydryl group (-SH), an important
component of the active site of many enzymes.
• Two cysteines can become oxidized to form a dimmer cystine,
which contains a covalent cross-link called a disulfide bond (-
S-S-).
• For Example: serine, cysteine, threonine, tyrosine, asparagine,
and glutamine.

11. Basic (R) Groups
• The R groups have significant positive charge.
• Lysine has a second positive amino group at the ε position on
its (R) chain.
• Arginine has a positively charged guanidino group.
• Histidine has a positive imidazole group facilitates the enzyme-
catalyzed reaction by serving as a proton donor/acceptor.
• For Example: arginine (Arg), lysine (Lys), and histidine (His).

12. Acidic Side Chains
• Aspartic and glutamic amino acids are proton donors.
• At neutral pH, the side chains of these amino acids are fully
ionized.
• They have a negatively charged carboxylate group (COO-).
• For Example: aspartate (Asp) and glutamic acid or glutamate
(Glu) amino acids.

13. Optical Properties of Amino Acids.
• The α-carbon is
attached to four
different chemical
groups called optically
active carbon atom.
• Glycine is the exception
amino acids exist in two forms, D and L, that are mirror images of each
other.
• All amino acids found in proteins are of the L-configuration.

14. Acidic and Basic Properties of Amino Acids
• Amino acids in aqueous solution contain weakly acidic α-carboxyl groups
and weakly basic α-amino groups.
• Each of the acidic and basic amino acids contains an ionizable group in its
side chain.
• Thus both free and some of the combined amino acids in peptide linkages
can act as buffers.
• The concentration of a weak acid (HA) and its conjugate base(A-) is
described by the Henderson-Hasselbalch equation.

15. Buffer characteristic of amino acid.
• Amino acids have the capability of reacting with both acid and base, they
naturally act as buffers.
• The carboxylate ion group act as a base and the amine group act as a acid.
• e.g. Aspartic acid is one of two acidic amino acids. Aspartic acid and
glutamic acid play important roles as general acids in enzyme active
centers, as well as in maintaining the solubility and ionic character of
proteins.

16. Standard Amino Acids
• Amino acids join together to form short polymer chains called peptides or
longer chains called either polypeptide proteins.
• These polymers are linear and unbranched, with each amino acid within
the chain attached to two neighboring amino acids.
• Twenty-two amino acids are naturally incorporated into polypeptides and
are called proteinogenic or natural amino acids. Of these 20 are encoded by
the universal genetic code. The remaining 2 are incorporated into proteins
by unique synthetic mechanisms.

18. Non-standard amino acids
• Aside from the 22 standard amino acids, there are many other amino acids
that are called non-proteinogenic or non-standard.
• They are either not found in proteins (for example carnitine, GABA), or
are not produced directly.
• Non-standard amino acids that are found in proteins are formed by post-
translational modification, which is modification after translation during
protein synthesis.
• These modifications are often essential for the function or regulation of a
protein. For example, the carboxylation of glutamate allows for better
binding of calcium cations.

19. In Human Nutrition
• When taken up amino acids into the human body from the diet, the 22
standard amino acids either are used to synthesize proteins and other
biomolecules or are oxidized to urea and carbon dioxide as a source of
energy.
• The oxidation pathway starts with the removal of the amino group by a
transaminase, the amino group is then fed into the urea cycle. The other
product of transamination is a keto acid that enters the citric acid cycle.
• Glucogenic amino acid can also be converted into glucose.

20. Difference between essential and non-
essential amino acids
• There are 20 different amino acid that make up all proteins in the human
body.
• These amino acids required in tissue, red blood cells, enzymes, and other
substances.
• 9 – 12 amino acids can be manufactured by the body. Non-essential amino
acids are not obtained from the diet.
• The remaining 8 to 11 essential amino acids, must be obtained from the
diet.