This document contains 29 questions related to amino acids and protein structure. The questions cover topics such as the cleavage of peptide bonds and disulfide bonds, classification of amino acids as hydrophobic or hydrophilic, secondary protein structures like helices and sheets, chromatographic techniques for separating amino acids, and factors that stabilize protein structure such as hydrogen bonds and hydrophobic interactions. The document provides background information on how hydrophobic amino acids are distributed in protein tertiary structure and how amino acids are classified.
This document contains 29 questions related to amino acids and protein structure. The questions cover topics such as the cleavage of peptide bonds and disulfide bonds, classification of amino acids as hydrophobic or hydrophilic, secondary protein structures like helices and sheets, chromatographic techniques for separating amino acids, and factors that stabilize protein structure such as hydrogen bonds and hydrophobic interactions. The document provides background information on how hydrophobic amino acids are distributed in protein tertiary structure and how amino acids are classified.
This document contains 29 questions related to amino acids and protein structure. The questions cover topics such as the cleavage of peptide bonds and disulfide bonds, classification of amino acids as hydrophobic or hydrophilic, secondary protein structures like helices and sheets, chromatographic techniques for separating amino acids, and factors that stabilize protein structure such as hydrogen bonds and hydrophobic interactions. The document provides background information on how hydrophobic amino acids are distributed in protein tertiary structure and how amino acids are classified.
This document contains 29 questions related to amino acids and protein structure. The questions cover topics such as the cleavage of peptide bonds and disulfide bonds, classification of amino acids as hydrophobic or hydrophilic, secondary protein structures like helices and sheets, chromatographic techniques for separating amino acids, and factors that stabilize protein structure such as hydrogen bonds and hydrophobic interactions. The document provides background information on how hydrophobic amino acids are distributed in protein tertiary structure and how amino acids are classified.
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AMINO ACIDS QUESTIONS:
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 chains.
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.
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. The amino acids which have positive charge on the 'R' group are placed in this category. They are lysine, arginine and histidine.
Hydrophilic (Polar Amino Acids with no Charge)
These amino acids do not have any charge on the 'R' group. These amino acids participate in hydrogen bonding of protein structure. The amino acids in this group are - serine, threonine, tyrosine, cysteine, glutamine and asparagine.
Polar Amino Acids with Negative Charge
Polar amino acids with negative charge have more carboxyl groups than amino groups making them acidic. The amino acids which have negative charge on the 'R' group are placed in this category. They are called as dicarboxylic mono-amino acids. They are aspartic acid and glutamic acid.
6.Name briefly the possible secondary structure that occur in a given protein. What secondary structure is likely to occur in a glycine rich region? 3+3 7. 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. 8. A mixture of Glutamine and Glycine is subjected to (i) anion exchange chromatography and (ii) gel fitration chromatography. State with reasons which one amino acid willcome out first in each type of chromatography. 2+2 (i) (ii)
In the anion exchange chromatography the Glutamine being negatively charged binds to the anion and glycine being neutral elutes first. Glycine elutes first since Glutamine is larger in size than glycine bearing an extra three
carbon amine side chain
9. Hydrogen bonds are important for protein secondary structure and hydrophobic groups are important for protein tertiary structure----explain. 4
10. Why is hemoglobin a globular protein? What are tha major structural differences between deoxyhemoglobin and oxyhemoglobin? 1+3 11. A protein has a pH less than 7. if you would like to purify this protein from impurities at neutral pH buffer, what type of ion exchange chromatography would you use for purifying this protein at neutral pH buffer? 12. compare the energetics of the following in proteins---(i) H-bonds, (ii) hydrophobic bonds 2+2 13. Why is the pH of aspartic acid (3.0) lower than that of lysine (9.5) ? 3 14. How would you titrate the carboxyl group of an alpha amino acid? 2 15. Why turns are important in protein structure? 2 16. How will you chemically convert---i. Alanine to acetic acid 2 ii.BrCH2CO2Et to glycine 2 17. Why isoelectric point of Arginine is greater than that of lysine? 2 18. What happens when an electric current is passed through an aqueous solution buffered at pH 6.0 containing alanine (I.P= 6.0) and aspartic acid (I.P= 2.8) ? explain the answer indicating the structures of the amino acids. 3 19.Discuss the merits and demerits of using dicyclohexylcarbodiimide (DCC) in the peptide bond formation. 3 20. Write the advantages of using Dansyl chloride reagent in peptide analysis. 2 21. compare between paper chromatography and TLC. 3 22.draw the acid base titration curve of the diprotic form (NH2-CH2-CO2-H). what information can be obtained from this titration curve? 3 23. Draw the structure of a dipeptide showing all bond angles and bonds. 3 24. What do you mean by the physical denaturation and re-naturation of a protein? 2 25. What will be the net charge on the tetrapeptide alanylglutamylglycyllysine at pH 7 to 10? 2 26. Cystine and methionine are separately heated with performic acid. Write down the structure of the
product.
27. Why is proline and glycine only found in protein?
28. 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. Describe an experiment to isolate myoglobin and hemoglobin from a mixture.
