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1. Describe the principle as well as merits and demerits associated with---i. Cleavage of peptide bond by cyanogen bromide 2
ii. Cleavage of disulfide bonds in a polypeptide by performic acid 2
2.What happens when------------i. Chloroacetic acid is treated with excess trimethylamine 2
ii. Boc glycine is treated with HCl 2
iii.Tryptophan is treated with N-bromo succinimide 2.5
3. You generally titrate acids with bases but you cannot titrate amino acid (say glycine) directly with
NaOH------Explain why? What step you need to take before starting the titration? 2+2
4.Briefly explain how hydrophobic amino acids (and the rest) are distributed in the tertiary structure of
protein? 2
Hydrophobic amino-acid residues engage in van der Waals interactions only. Their tendency to avoid contact
with water and pack against each other is the basis for the hydrophobic effect. Alanine and leucine are strong
helix-favoring residues, while proline is rarely found in helices because its backbone nitrogen is not available for
the hydrogen bonding required for helix formation. The interior of a protein is generally a densely packed core of
hydrophobic amino acid side chains the aromatic side chain of phenylalanine can sometimes participate in weakly
Polar interactions.

5. Briefly explain with examples how amino acids are classified as hydrophobic or hydrophilic? 4
Amino acids are classified based on those with non-polar R group, uncharged polar R group, charged
polar R group. The non-polar side chain amino acids are called hydrophobic and the amino acid with
uncharged polar side chain is called hydrophilic. It also contain the acid side chains and basic side

Hydrophobic aminoacids(Non Polar Amino Acids)
Non Polar Amino Acids have equal number of amino and carboxyl groups and are neutral. These amino
acids are hydrophobic and have no charge on the 'R' group. The amino acids in this group are alanine,
valine, leucine, isoleucine, phenyl alanine, glycine, tryptophan, methionine and proline.

The amino acids which have positive charge on the 'R' group are placed in this category.Hydrophilic (Polar Amino Acids with Positive Charge) Polar amino acids with positive charge have more amino groups as compared to carboxyl groups making it basic. arginine and histidine. . They are lysine.

6. tyrosine. A mixture of Glutamine and Glycine is subjected to (i) anion exchange chromatography and (ii) gel fitration chromatography. What happens when you run an amino acid in an electric field through a pH gradient? 2 The amino acid tends to move in the electric field till their net charge become zero at a particular pH which is called the isoelectric point of the amino acid. glutamine and asparagine. The amino acids in this group are . Glycine elutes first since Glutamine is larger in size than glycine bearing an extra three . They are aspartic acid and glutamic acid. State with reasons which one amino acid willcome out first in each type of chromatography. The amino acids which have negative charge on the 'R' group are placed in this category. Polar Amino Acids with Negative Charge Polar amino acids with negative charge have more carboxyl groups than amino groups making them acidic. They are called as dicarboxylic mono-amino acids.Name briefly the possible secondary structure that occur in a given protein.Hydrophilic (Polar Amino Acids with no Charge) These amino acids do not have any charge on the 'R' group.serine. 8. cysteine. 2+2 (i) (ii) In the anion exchange chromatography the Glutamine being negatively charged binds to the anion and glycine being neutral elutes first. threonine. What secondary structure is likely to occur in a glycine rich region? 3+3 7. These amino acids participate in hydrogen bonding of protein structure.

How will you chemically convert---i. 3 19. What do you mean by the physical denaturation and re-naturation of a protein? 2 25. 3 24. Why turns are important in protein structure? 2 16. A protein has a pH less than 7. Cystine and methionine are separately heated with performic acid. 3 20. What will be the net charge on the tetrapeptide alanylglutamylglycyllysine at pH 7 to 10? 2 26. Alanine to acetic acid 2 ii. if you would like to purify this protein from impurities at neutral pH buffer. 3 22.0) lower than that of lysine (9. Write the advantages of using Dansyl chloride reagent in peptide analysis.BrCH2CO2Et to glycine 2 17. 4 10.P= 2. 2 21. what type of ion exchange chromatography would you use for purifying this protein at neutral pH buffer? 12.draw the acid base titration curve of the diprotic form (NH2-CH2-CO2-H).8) ? explain the answer indicating the structures of the amino acids.0) and aspartic acid (I.5) ? 3 14. How would you titrate the carboxyl group of an alpha amino acid? 2 15. Why isoelectric point of Arginine is greater than that of lysine? 2 18. Hydrogen bonds are important for protein secondary structure and hydrophobic groups are important for protein tertiary structure----explain. compare between paper chromatography and TLC.carbon amine side chain 9.0 containing alanine (I.Discuss the merits and demerits of using dicyclohexylcarbodiimide (DCC) in the peptide bond formation. (ii) hydrophobic bonds 2+2 13. Write down the structure of the . Why is the pH of aspartic acid (3. what information can be obtained from this titration curve? 3 23. Why is hemoglobin a globular protein? What are tha major structural differences between deoxyhemoglobin and oxyhemoglobin? 1+3 11. What happens when an electric current is passed through an aqueous solution buffered at pH 6.P= 6. Draw the structure of a dipeptide showing all bond angles and bonds. compare the energetics of the following in proteins---(i) H-bonds.

2 . How will you convert -COOH group of L-lysine to amide group? 3 29. State with examples that weak forces stabilize the protein structure? 3 30. Why is proline and glycine only found in protein? 2 28. Describe an experiment to isolate myoglobin and hemoglobin from a mixture. 3 27.product.