amino acid structure function protein structure

1. Amino acid

2. • Introduction
Amino acids are compounds containing carbon ,hydrogen ,oxygen and nitrogen.
They are a monomer(building block) of proteins and are composed of an amino
group , a carboxylic group, a hydrogen atom and ‘R’ group( a distinctive side chain),
all bounded to a carbon atom(α-carbon).
All 20 of the common acids are α -amino acids.
For all the standard amino acid except glycine, the α-carbon is bounded to those four
group.
They differ from each other in their side chains, or R groups, which vary in
structure, size, and electric charge, and which influence the solubility of the amino
acids in water.
In addition to these 20 amino acids there are many less common ones.
Some are residues modified after a protein has been synthesized; others are amino
acids present in organisms but not as constituents of proteins.

3. • The common amino acids of proteins have been assigned three letter abbreviations
and one-letter symbols , which are used as shorthand to indicate the composition and
sequence of amino acids polymerized in proteins.
General structure of amino acid :- this structure is common to all except proline, a
cyclic amino acid, so this is called core structure. The R group(side chain), attached to
the α -carbon is different in each amino acid.

4. • Features of amino acid:-
Four valency of α-carbon has satisfied by the four different groups.
Amino acids are diprotic in nature.
Amino acid are zwitterionic form at pI so it show amphoteric nature.
Amino acid except glycine have chiral center.
Configuration of chiral compound is defined as L and D amino acid.

5. • Classification
• On the basis of polarity:-
Polar
Uncharged – serine ,threonine, cysteine, glutamine , asparagine
Basic- lysine, arginine, histidine
Acidic – aspartic and glutamic acid
Nonpolar
Aliphatic – proline, leucine, isoleucine, alanine, valine, glycine, methionine
Aromatic – phenylalanine, tryptophan ,tyrosine

6. • On the basis of R group:-

9. Found in plant cell wall protein
Found in collagen protein
Found in fibrous protein of connective tissue
Found in collagen protein
Constitute of myosin,
contractile protein of muscle
Complex amino acid found in fibrous protein
elastin.
Derivative of four lysine residue.
Found in blood clotting protein prothrombin.
Uncommon amino acid

10. • General function of amino acids:-
Monomeric subunit of proteins:- all proteins are composed of some or all of 20
standard amino acid , so it is called building block of proteins.
Energy metabolite:- many amino acids are used as a essential nutrient (PVT TIM
HALL) and can be used as precursor.
Ex.-tyrosine is precursor of – dopamine, norepinephrine, epinephrine.
Tryptophan is precursor of – serotonin.
Chemical messenger:- many amino acids act as a neurotransmitters.
Ex.-glycine(inhibitory), glutamate and aspartate(excitatory).

11. • Peptides/protein
Peptides are macromolecules composed of amino acid linked together through
peptide bonds. They consisting of two or three to thousands of linked amino acid
residue.
When two amino acid molecules covalently joined through a peptide bond to yield
dipeptide.
Like this when many amino acid molecules covalently joined through a peptide
bond to yield a polypeptide, this polypeptide is called a protein.
Peptide bond:- it is a covalent bond formed between carboxyl group of one amino
acid and the amino group of its next amino acid with the elimination of one water
molecule.

12. • Properties of peptide bond:-
• Peptide bonds are backbone of protein . These bonds are very strong and stable.
• The peptide bond has a partial double bond character due to resonance.
• The partial double bond character keeps the peptide bond in a rigid planer
configuration. For a pair of amino acids linked by a peptide bond, six atoms
(Cα,C,O,N,H and Cα).
• Peptide bond formation is an endergonic process with ΔG˚≈+21kJ/mol.
• It has a high activation energy. As a result ,the peptide bonds in proteins are quite
stable, with an average half life of about 7 years under most intracellular
conditions.
• Due to the partial double bond character, two possible configurations, cis and
trans, are observed for a peptide bond in polypeptides. In the cis configuration,
successive α-carbon atoms are on the same side of the peptide bond. In the trans
configuration, the two successive α-carbon atoms are on opposite sides of the
peptide bond.

13. • Proteins
• Protein is a high molecular weighted nitrogenous complex organic compound. They are
polymer of L- α-amino acid.
• Some amino acid may occur only once or not at all in given type of protein, others may
occur in large numbers.
• Properties:-
• Physical properties
• State- usually these are colorless, tasteless, odorless, homogenous and crystalline.
• Shape- these are vary in shape from simple crystalloid spherical to long fibrillar structure.
• Molecular weight- great variation in the molecular weight of proteins usually between
5*103 to 1*106 Dalton.
• Colloidal nature- because of their giant size, charge the protein exhibit many colloidal
properties such as:-
• i) their diffusion rate are extremely slow.
• ii) it may produce considerable light scattering in solution thus resulting in visible
turbidity.

14. • Protein denaturation, renaturation, precipitation and coagulation:- the
process in which a protein losses its native confirmation under the treatment of
denaturants is referred to as protein denaturation. The denatured protein remained
its primary structure but no biological function.
• Chemical properties:-
• Hydrolysis:- proteins are hydrolyzed by a variety of hydrolytic agent such as
acidic agent, alkaline agent, proteolytic enzyme and yield amino acid.
• Reaction involving COOH group:-
i) salt formation- amino acid when reacts with alkaline form salt.
ii) esterification- amino acid when reacts with alcohol produce ester.
• Reaction involving NH2 group:-
i)Salt formation- amino acid when reacts with mineral acid like HCl form salt.

15. • Protein structure
• Protein has different level of structure according to their complexity.
• There are four level of protein structure:-
• Primary structure:- sequence of amino acid residue.
• Secondary structure:- refers to particularly stable arrangements of amino acid residues giving
rise to recurring structural patterns.
• Tertiary structure:- it describes all aspects of the three-dimensional folding of a polypeptide.
• quaternary structure:- When a protein has two or more polypeptide subunits, their
arrangement in space is referred to as quaternary structure.

16. • Primary structure
• The sequence and number of amino acid in protein is denotes the primary structure of
protein.
• It is also defined as linear sequence of amino acid joined together by peptide bond.
• secondary structure
Protein secondary structure describes the spatial arrangement of its main-chain atoms,
without regard to the positioning of its side chains.
These structures are stabilized by hydrogen bonds between the carbonyl oxygen and the
amide hydrogen in the polypeptide’s backbone.
Secondary structure may have repetitive and regular patterns or irregular and unique
structure.
The most common regular secondary structures are the α-helix and the β-pleated sheet. The
secondary structure without a regular pattern is sometimes referred to as coils. Sometimes
coil is referred to as ‘random coil’.

17. α-helix
The α-helix is a rigid , rod like structure that forms when a polypeptide chain twist into a
helical confirmation.
In this structure , the polypeptide backbone is tightly wound around an imaginary axis
drawn longitudinally through the middle of the helix, and the R group of amino acid residue
protrude outward from the helical backbone.
The screw sense of α-helix can be right handed(clockwise) or left handed(counter
clockwise).
Right handed helix are energetically more favorable because there is less steric clash
between the side chains and the backbone. Essentially all α-helices found in proteins are
right- handed.
In α-helix, there are 3.6 amino acid residues per turn of the helix and the pitch is 0.54nm.
Each residue is related to the next one by a rise of 1.5Å(0.15nm).

19. • β-pleated sheets
• β-pleated sheets form when polypeptide
chain segments line up side by side.
Each individual segment is referred to as
a β-strand.
• Each β-strand is fully extended. The
distance between adjacent amino acids
along a β-strand is approximately 3.5Å.
• β-pleated sheets are stabilized by
interchain hydrogen bonds that form
between the polypeptide backbone N-H
and carbonyl groups of adjacent strands.
• Adjacent strand can be parallel or anti-
parallel.

20. • β-turn
• Also know as reverse turns, hairpin bends or omega loops.
• In β-turns, H bonds form between the 1st amino acid and its 4th amino acid residue.
• The 3rd amino acid residue are changed in reverse direction and make loop or turn.
• Glycine and Proline residue often occur in β-turn as turn former because it is small and
flexible.

21. • Ramachandran plot
• Ramachandran plot was discovered by G.N.Ramachandran in1963.
• With the help of this plot, we can determine the protein structure.
• There are two dihedral angles in this method- i) ɸ-angle and ii) Ψ- angle
• ɸ and Ψ can raise value between -180˚ and +180˚ but many value are prohibited
by steric clashes between atoms in the polypeptide backbone and amino acid side
chain.
• The angle between 2 planes- dihedral angle.
• ɸ-angle- is the angle around the N- Cα bond.
• Ψ- angle – is the angle around the Cα- C bond.

24. • Tertiary structure
The overall three dimensional arrangement of all atoms in a protein is referred to as the
protein’s tertiary structure.
All information needed to fold the protein into its native tertiary structure is contained within
the primary structure of the peptide chain itself.
Secondary structure refers to the spatial arrangement of amino acid residues that are adjacent
in a segment of a polypeptide, whereas tertiary structure includes longer range aspects of
amino acid sequence.
Amino acids that are far apart in the polypeptide sequence and are in different types of
secondary structure may interact within the completely folded structure of protein.
There are various non-covalent and covalent interactions that stabilizes tertiary structure such
as
hydrophobic interaction(major form of non-covalent interaction)
Electrostatic interactions(salt bridges)
Hydrogen bonds
Van der Waals force of interaction.
Intrachain disulfide bond(covalent bond)

26. • Quaternary structure
• When proteins are composed of two or more polypeptide chains, it is called multimeric
proteins and each polypeptide chain is called a subunit.
• Polypeptide subunit assembled to form quaternary structure and are held together by non-
covalent interactions as well as covalent interactions.

27. Protein sequencing
• Protein sequencing refers to the method for determining the amino acid sequence of
protein in a peptide chain.
• Sanger’s method-
• Fredrick Sanger developed a reagent 1-fluoro-2,4 dinitro benzene(FDNB) for labeling and
identifying the amino terminal amino acid residue.
• FDNB reacts with the free amino acid of n-terminus residue of peptide chain in alkaline
solution and form yellow colored dinitrophenyl derivatives of amino acid.
• After the amino terminal residue is labeled with reagent, the polypeptide chain is partially
hydrolyzed by either acid (6M HCl) or enzyme(peptidase) to its constituent amino acids
and the labeled amino acid is identified.
• New free amino terminal yield in remain polypeptide . Similarly each amino acid is
identified by repeat the same procedure and determine the protein sequence.
• Similarly , Dansyl chloride reacts with a free amino group of the N-terminal amino acid
residue of a peptide in alkaline solution to form strongly fluorescent derivatives of free
amino acids and the labeled amino acid is identified.

29. Edman degradation:-
Edman degradation method for determining the sequence of peptides and proteins from
their N-terminus was developed by Pehr Edman. This chemical method uses
phenylisothiocynate (Edman reagent) for sequential removal of amino acid residues from
the N- terminus of a polypeptide chain.
Mechanism:-
• Phenylisothiocynate reacts with N-terminal amino group of polypeptide, under alkaline
conditions, to form the phenylcarbamyl-peptide derivative.
• Then, under the acidic condition in the presence of anhydrous trifluoroacetic acid , this
derivatives of the terminal amino acid is cleaved as a thiazolinone derivative.
• The thiazolinone amino acid is then selectively extracted into an organic solvent and
treated with aqueous acid to form the more stable phenylthiohydantoin-amino acid
derivative that can be identified by using chromatography or electrophoresis.