Amino Acid Protein Chemistry

Amino Acid

To be able to write the amino acid, the C-H should be in the center, and they should get attached to CORN (CO is the Carboxyl group, R is the side chain, and N is the other functional group, which is the NH2 group). At the physiological pH of 7.4, the Amino acid is present as Zwitter Ion. 

To write amino acid in the Zwitter Ion form, the C and H should be in the center, and they should get attached to CORN (CO exists as COO- and N exists as NH3+), and the R is a functional group. The formation of the zwitter ion depends on the pKa of the group and the pH value of the amino acids. The pKa of the carboxyl group is 2, and of the amino group is 9.

In the surrounding pH 7.4, the carboxyl group will sense the surrounding as alkaline, giving the H+ to neutralize itself, leaving behind COO—, and the amino group will sense the surrounding as acidic, accepting the H+ to neutralize itself and become NH3+.

pKa

The pH at which 50% of the groups are ionized is known as pKa. The ionization or deionization of a functional group depends upon its pKa

• If a substance has pKa of 2 and another of pKa of 4.
• If they are put in the surroundings of pH 3.
• Therefore, the substance with higher pKa will start accepting the H+ from the surroundings to neutralize it. Similarly, the substance with lower pKa will release the H+ from the surroundings to neutralize it.

The lower the pKa, the stronger the acidic nature of the substance. A substance acts as an effective buffer when dropped in a medium of pH = pKa +/- 1. pKa is not a constant value.

Isoelectric pH

The pH at which the net charge carried by the particle is zero is known as Isoelectric pH. For a molecule with two ionizable groups, Pi= Pk1 + Pk2/2

At the isoelectric ph the particle has least electric mobility, Least solubility and Least buffering capacity.

Classification of Amino Acids

The classification is based on the functional groups, they are classified into two groups:

1. Polar: Such amino acids are only soluble in a polar solvent like water. They need to be charged to get dissolved. The Solute needs to interact with the solvent. If not charged, they must be of polar groups (OH / SH/ NH2) to bond hydrogen with water. Polar amino acid is further classified as
   • Charged Polar amino acid:
     • Positively charged/basic amino acids (Histidine / Lysine/arginine)
     • Negatively charged/ acidic amino acids (Aspartic Acid / Glutamic Acid)
   • Uncharged Polar amino acid:
     • OH (Serine / Threonine / Tyrosine)
     • SH (Cysteine)
     • NH2 (Asparagine / Glutamine)
2. Non-Polar: 
   • Aliphatic amino acid (Glycine / Alanine / Valine / Leucine / Isoleucine)
   • Aromatic amino acid (Phenylalanine / Tryptophan)
   • Imino acids (Proline)

Once you know the polar and non-polar amino acids, the protein folding will be easy to understand. The major function achieved by protein folding is solubility. 

Points to remember about Amino Acids:

• Histidine is the physiological buffer as its pKa is 6.
• Glycine is the simplest amino acid.
• Glycine has no asymmetric carbon atom.
• Glycine does not exhibit stereoisomerism.
• Glycine is optically inactive.
• Aromatic amino acids absorb UV light at 280nm. (Purines and pyrimidines absorb UV light at 260nm)
• Proline is an imino acid.
• Proline and Glycine disrupt the alpha helix.

Color Reactions

Biuret Reagent & Benedict’s Reagent

Peptide Linkage in Amino Acids 

Considering the 2 amino acids, both will have CH, a carboxyl group, an Amino Group, and the side chain. Once the bond occurs, the carboxyl group combines with the Amino Group to form water, leaving CONH and 2 C-alpha atoms behind. The CONH is the peptide linkage. The peptide linkage consists of 4 atoms. All the atoms in the peptide linkage are coplanar. At the physiological pH level of 7.5, the nitrogen will try to satisfy the valency of 4. Therefore, it gives the peptide linkage a partial double bond character. So, there is no freedom of rotation along the peptide linkage.

However, there is a freedom of rotation among the C-alpha atoms. The angle at which C-alpha & C can rotate is called Ѱ. The angle at which C-alpha & N can rotate is called . These angles are called the Ramachandra angle.

Structure of Protein

Primary Structure

Primary structure of the protein is defined by the number and sequences of the amino acid, which is linked by the peptide linkage. Sanger was the first person to sequence protein. Sanger’s reagent is 1fluro 24 DNB. The first protein that was sequenced was insulin.

Secondary Structure

It is defined by how adjacent segments of the polypeptide chain get organized to form ordered units. There are 2 types of ordered units:

• Alpha Helix
• Beta-Pleated Sheet

Difference Between Alpha Helix and Beta Pleated Sheet

Super Secondary Structures: 

These are the segments of polypeptide chains linked to the secondary structures. There are 2 types of super-secondary structures. 

• Turn / Bend (If limited numbers of amino acids link the adjacent structure.)
• Loop (If more amino acids are used to link the adjacent structure.)
  • These loops or turns can act as a binding domain. They have hydrogen bond linkages.

Proline and glycine are found in a super secondary structure. Therefore, super-secondary structures often form functional domains.

Quaternary Structure:

The protein that exists with more than one polypeptide chain can only have a quarternary structure. The Difference between myoglobin and hemoglobin is that Myoglobin consists of one polypeptide chain, whereas hemoglobin consists of multiple polypeptide chains. Therefore, hemoglobin can exist in a quaternary structure.

Difference between globular and fibrous protein

Also Read: Recombinant DNA Technology

Frequently Asked Questions

Q: Ninhydrin test gives purple color with all except

1. Glycine
2. Alanine
3. Glutamine
4. Proline

Answer: d. Proline

Q:Biuret test gives violet color with all except

1. Albumin
2. Glycoproteins
3. Glutathione
4. Dipeptide

Answer: Dipeptide

Q: The xanthoproteic acid test is answered by

1. Histidine
2. Arginine
3. Cysteine
4. Tyrosine

Answer:Tyrosine

Q: Which of the following is optically inactive?

1. Tryptophan
2. Tyrosine
3. Phenylalanine
4. Glycine

Answer:

Q: All of the following have hydroxyl groups except.

1. Cysteine
2. Tyrosine
3. Serine
4. Threonine

Answer:Cysteine

Q: All of the following are aromatic amino acids except.

1. Phenylalanine
2. Tyrosine
3. Tryptophan
4. Histidine

Answer:Histidine

Q: All of the following are basic amino acids except?

1. Lysine
2. Glutamate
3. Arginine
4. Histidine

Answer:Glutamate

Q: Which of the following is an imino acid?

1. Lysine
2. Glutamate
3. Arginine
4. Proline

Answer:Proline

Q: Which of the following is a polar but uncharged amino acid?

1. Serine
2. Glutamate
3. Arginine
4. Tryptophan

Answer:Serine

Q: All the following are true about Glutathione except.

1. It is a tripeptide.
2. It has 3 peptide linkages.
3. It has a pseudo-peptide linkage.
4. It is an antioxidant.

Answer:It has 3 peptide linkages.

Q: The primary structure of a protein is stabilized by

1. Peptide linkage
2. Hydrogen bond
3. Hydrophobic interaction
4. Disulphide bridges

Answer:Peptide linkage

Q: The tertiary structure of a protein is studied by

1. Sanger's method
2. Optical Rotatory dispersion
3. X-Ray crystallography
4. NMR Spectroscopy

Answer:X-Ray crystallography

Q: Which of the statement is true for Globular proteins.

1. Structural proteins
2. The axial ratio is more than 10.
3. Compact
4. More beta-pleated sheets

Answer:Compact

Q: A person presented with recurrent renal stones, which were hexagonal on microscopy. He was diagnosed with cystinuria. True about Cystine is:

1. It is an alpha amino acid.
2. It is a dipeptide.
3. it has a free sulfhydryl group.
4. It is an imino acid.

Answer: It is a dipeptide.

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