Protein Chemistry

Proteins
General  Proteins are the basis of structure and functions of life.
Information  Proteins are organized into primary, secondary, tertiary and quaternary
structures.
 Proteins are classified as simple, conjugated and derived proteins.
 Proteins are made in the ribosome. They are polymers composed of 20 amino
acids.

General  Each amino acid (Except GLYCINE, which is achiral) has both D & L forms. These
Structure of stereoisomers have the same chemical properties.
AMINO  ALL the amino acids incorporated by organisms into proteins are in the L Form.
ACIDS

L- Amino Acids General Structure

Classifications of Amino Acids:

Amino acids can be classified according to

Structure of the side Polarity of the Side

Nutritional Requirement Metabolic Fate
chain (R) chain

Non-Polar Essential Non-

Aliphatic Aromatic Polar
Amino Amino Essential
Amino Amino Amino Glucogenic Ketogenic Both
Acids Acids Amino
acids acids acids
Acids
 1. Classification of Amino Acids according to the Structure of the Side Chain (R):
Name Abbv. And Structure
Letter
Glycine Gly - G

Simple
Amino
Acids Alanine Ala - A

Valine Val - V

Branched
Amino Leucine Leu - L
Acids

Isoleucine Ile - I

Serine Ser - S

Amino
Acids with
Threonine Thr - T
HYDROXYL
R-groups

Cysteine Cys - C
Amino
Acids with
SULFUR- Methionine Met - M
containing
R-groups

Aspartic Asp - D
Acid

Acidic Asparagine Asn – N

Amino
Acids
 Glutamic Glu - E
Acid

Glutamine Gln - Q

Arginine Arg - R

Basic Lysine Lys - K

Amino
Acids

Histidine His - H

Phenyl Phe – F
Alanine

Aromatic
Tyrosine Tyr - Y
Amino
Acids

Tryptophan Trp - W

Proline Pro - P
 2. Classification of Amino Acids according to THEIR POLARITY:

Polar Amino Acids Non-Polar Amino Acids

CAN form H-bonds with H2O Can NOT form H-bonds with H2O
Acidic a.a Between Neutral a.a Between Basic a.a 1. Alanine (Ala)
Acidic Neutral 2. Leucine (Leu)
and and Basic 3. Isoleucine (Il)
Neutral a.a 4. Valine (Val)
a.a 5. Methionine (Met)
9. Aspartic Tyrosine 1. Asparagine Histidine 1. Arginine 6. Phenylalanine (Phe)
Acid (Asp) (Tyr) (Asn) (His) (Arg) 7. Proline (Pro)
10. Glutamic 2. Serine (Ser) 2. Lysine 8. Tryptophan (Trp)
Acid (Glu) 3. Cysteine (Cys) (Lys)
4. Glutamine (Gln)
5. Threonine (Thr)
Between Polar and Non-polar amino acids
Glycine

3. Classification of Amino Acids according to nutritional requirement:

Essential Amino Acids Non-Essential Amino Acids
Body cannot synthesize them Body synthesizes them endogenously from
intermediates of glycolysis or the TCA cycle.
Valine Alanine
Isoleucine Asparagine
Lysine Aspartate
Leucine Cysteine
Arginine (CHILDREN ONLY) Glutamate
Histidine Glutamine
Methionine Glycine
Tryptophan Proline
Threonine Serine
Phenylalanine Tyrosine
Mnemonic: VILLA HM = Ten Thousand Pounds Mnemonic: A (except Arginine) P C G ST
 4. Classification of Amino Acids based on metabolic fate:
Type Glucogenic Amino Acids Ketogenic Amino Acids
Carbon Pyruvate Acetyl Co-A
skeleton Fumarate Acetoacetate
is Alpha-Ketoglutarate
converted Oxaloacetate (OAA)
to Succinyl-CoA
Mnemonic: PFKOS (‫)بفكس‬

Biological Value of Proteins:

High Biological Value Proteins Low Biological Value Proteins
Content Contains all the essential amino Deficient in one or more essential amino acid.
acids.
Digestibility Digestible Not Digestible
Example Animal Proteins Plant Protein
e.g. milk, meat and eggs protein e.g. 1. Zein of Maize
2. Gliadine of Wheat

Properties of Amino Acids

I. Physical Properties of Amino Acids:
A. Due to the presence of multiple charged groups on amino acids, they are:
1. Readily solvated by water and hence soluble in polar solvents and insoluble in non-polar
solvents.
2. On adding alcohols to their solutions  they ppt.
3. Of high melting points (>200oC) [G.R]  Due to the high energy needed to disrupt the ionic
forces that stabilizes their crystal lattice.
B. Amino acids have different tastes:
1. Sweet  e.g. Glycine, Alanine, Valine, Tryptophan, Histidine and Proline.
2. Tasteless  e.g. Leucine
3. Bitter  e.g. Isoleucine and arginine.
4. Flavoring agent  e.g. Sodium glutamate.
5. Artificial sweeteners e.g. Aspartame contains aspartic acid + phenylalanine.
C. Isoelectric Point (pl) of amino acids:
Definition  PH at which the majority of the amino acid molecules in solution have no net charge.

 At the isoelectric point, the amino acid carries NO

net charge even though all the groups are ionized.
Therefore, there is NO mobility in the electric field
of the amino acid, which causes the solubility and
the buffering capacity to be at a minimum.
 pK1 (Acid dissociation constant of the COOH gp)
 the p.H at which 50% of the molecules are in the cationic state, while the other 50% are in the
zwitterion state.
 pK2 (Acid dissociation constant of the NH2 gp)   the p.H at which 50% of the molecules are in
the anionic state, while the other 50% are in the zwitterion state.

Calculation of Isoelectric point of different Amino Acids:

 Isoelectric point of monoamine monocarboxylic amino acids (neutral) =

 Isoelectric point of amino acids with Acidic Side chains (Acidic R-groups):
 Isoelectric point of amino acids with Basic Side chains (Basic R-groups):

Notes:

 At the physiological pH of the body (7.4), plasma proteins and hemoglobin have a buffering
capacity [G.R]  mainly due to the Histidine residue present in their polypeptide chain [G.R] 
because at this pH histidine is at its isoelectric point. The present imidazole group of histidine can be
ionizied.
 The buffer action of histidine lies between pH of 6-8.
 II. Chemical Properties of Amino Acids:
Quantitative Principle Ninhydrin is a powerful oxidizing agent that causes oxidative decarboxylation of
Determination alpha-amino acids in alkaline medium producing CO2 and Ammonia.
-- Ninhydrin Reaction Alpha amino acid + Ninhydrin  CO2 + NH3 + Aldehyde (1 less carbon) + reduced
Test Ninhydrin
Result Blue complex (Reduced Ninhydrin + NH3 + Ninhydrin)
Reactions of A. Decarboxylation:
the Carboxylic  Examples:
group Glutamic Acid  Gamma amino butyric acid (GABA) + CO2
Histidine  Histamine + CO2
Tyrosine  Tyramine + CO2
Tryptophan  Tryptamine + CO2
B. Amide Formation:
 Done only to acidic amino acids.
 The –COOH group of dicarboxylic amino acids (other than the alpha-carboxyl) combines with
ammonia to form the corresponding amide.
 Examples:
Aspartic Acid + NH3  Asparagine
Glutamic Acid + NH3  Glutamine
Reactions of A. Transamination:
the Amino An important reaction for the synthesis of non-essential amino acids.
groups B. Oxidative deamination:
In the body, Glutamic acid is the most common amino acid to undergo oxidative deamination

C. Formation of Carbamino compounds:

CO2 attaches to the amino gp of amino acids to form Carbamino compound

This reaction serves as a mechanism for the transport of CO2 from the tissues to the lungs by
hemoglobin.
Reactions due A. Transmethylation:
to the Side Methionine + acceptor  Methylated acceptor + homocysteine
Chain (R) B. Ester formation by the OH groups:
Hydroxyl amino acids can form esters with phosphoric acid.
Example: Serine and Threonine are involved in the formation of phosphoproteins.
C. Reactions of the SH groups:
Formation of peptide bonds by dehydration:

Peptide bond formation may be:

1. Di-peptide formation
2. Tri-peptide formation
3. Poly-peptide formation
4. N and C terminals of a polypeptide chain

Examples of naturally occurring polypeptides:

1. Glutathione (GSH):
It is a tripeptide formed of Gamma-glutamyl-cysteinyl-glycine.

It is a reduced glutathione but when two molecules of GSH combine by a disulfide bond, they form
oxidized glutathione.

Glutathione is an important anti-oxidant.

2. Adrenocorticotrophic Hormone (ACTH):

It is a polypeptide hormone containing 39 amino acids.

3. Bradykinin:
It is a short polypeptide. It works as a smooth muscle relaxant.
 Levels (Organization) of protein structures

1. Primary Protein Structure:

It is the number, type and sequence of linear structure of amino acids in the protein.

The primary structure determines the biological activity of protein molecules, for example:

A. Insulin:
Insulin has two polypeptide chains that are held together by disulfide bonds:

1. The A – Chain (glycine chain) with 21 amino acids

2. The B – Chain (phenylalanine chain) with 30 amino acids

The species variation is restricted to:

1. Amino acids 8,9,10 in the A – Chain (glycine chain)

2. C – Terminal of the B – Chain (phenylalanine chain)  Pig and Human insulin differ in the C –
terminal in which threonine in human is replaced by alanine in pigs.

Pig insulin produced antibodies in human by repeated injection. But, de-alaninated pig insulin bear no
antigenic response difference from human insulin.

N.B. Insulin is produced by recombinant DNA technology nowadays.

B. Sickle-cell hemoglobin (HbS):

It is an inherited blood disease, which results from a single amino acid substitution. In the protein
hemoglobin, the 6th amino acid (glutamic acid) in the B – Chain is replaced by valine.
2. Secondary protein structure:
A. Alpha helix:
Keratins are fibrous proteins that are nearly alpha-helical. They are a component of hair
and skin. Disulfide bonds between the polypeptide chain constituents determine their
rigidity. It is stabilized by IntrAmolecular H-Bonds.

B. Pleated-Sheet Structure:

It is stabilized by IntrEmolecular H-Bonds.

3. Tertiary Protein Structure:

Tertiary structures are stabilized by:

A. Disulfide bonds:

It is a covalent linkage formed between the sulfhydryl (-SH) groups of each two-cysteine molecules
to produce cystine residue.

These bonds are strong and help protect the protein from denaturation in the extracellular
environment.

B. Hydrophobic interactions (Van der waal’s forces):

They occur due to the attraction between non-polar hydrophobic chains (R) of amino acids like
valine and leucine.

These forces attract when the atoms are at a certain distance from each other but repel when the
atoms are more closely.

These interactions are usually present in the interior of the molecule.

C. Hydrogen Bonds:

Polar side chains of amino acids may form H-bonds with water or other polar groups.

D. Ionic attractions (Salt bridges or ionic bonds):

 Negatively charged groups (COO-) in the side chains of aspartate or glutamate may interact with the
positively charged groups (NH3+) in the side chains of Lysine.

4. Quaternary Protein Structure:

These structures are made of multiple similar or dissimilar subunits.

These units are NOT united by covalent bonds (Not disulfide or peptide bonds). They are united by
Hydrogen bonds and Ionic bonds.

These structures are essential to the activity of a protein such as enzyme proteins.

Some of the enzymes consist of subunits that has different functions, some of the subunits act as
regulatory subunits and the others act as catalytic subunits.

E.g. Hemoglobin has four subunits (2 alpha and 2 beta chains).