1. How is ancient drug designing different from modern drug designing methods?

2. What do you mean by rational drug designing. Enlist the steps in rational drug
designing?
3. What do you mean by molecular mimicry . How is it useful for rational drug
designing?
4. How does diseased physiological mechanism help in identification of lead
compound?
5. Explain the follwing terms:
a. Receptor
b. Pharmacophore
6. What do you mean by ADME ? Why are such type of studies carried out?
QSAR
7. What do you mean by QSAR. Illustrate with an example the relationship of
activity and structure of any compound.
8. Discuss advantages and disadvantages of QSAR studies.
9. What is 3-D QSAR . What are advantages of 3-D QSAR over old QSAR?
10. Define the following terms:
a. QSAR
b. QSPR
c. Molecular descriptors

11. What is logP . How is it related to biological activity of the drug?

12. Discuss Hansch contribution to QSAR?
13. Enlist the steps for developing QSAR model?

14. What do you mean by CADD? What are limitations of this method?

15. What is QSAR? Give basic principle behind Hansch QSAR equation?

16. Give main step in QSAR analysis?

17. What are descriptors ? Give two exaples of : structural descriptors ,

thermodynamic descriptors, topological descriptors, Internal energy descriptors,
Receptor descriptors, Intranenergy descriptors,

Quntam Mechnics:
18. Define the term free energy? How is it calculated and discuss its significance?
19. Expalin Quantum Mechanical method. How is it different from quantum chemical
approach?
20. Differentiate between Uniform and Non-uniform methods?
21. Explain Schrondiger’s equation. What questions does it address?
22. How do abinitio and semi-emperical method differ for solving Schrondiger
equation?
23. Explain the following:
a. CNDO
 b. MNDO
c. EHT method.

24. Explain any one method for geometry optimization.

25. What are principles behind quantum chemical method ?
26. Expalin SCF theory model?
27. Expalin Hartree Forck method?
28. Discuss Huckel method?

INTRODUCTION TO PROTEIN MODELLING:

29. What is difference between structure assignment and structure prediction
methods? Explain any one method for structure assignment in detail.
30. What are different methods for structure prediction. Explain Chou-Fasman
method for structure prediction.
31. Explain GOR method for Structure prediction. What are the advantages of this
method over Chou-Fasman method?
32. What do you mean by neural network. How does this method help in predicting
secondary structure of protein?
33. Enlist main steps for comparative protein modeling.
34. What is the last step in Homology modeling.?
35. What is threading . Discuss advantages and limitations of this method?
36. Discuss any one approach for solving structure alignment problem.
37. Name any two softwares freely available for threading or fold recognition .
Discuss steps for fold recognition for any one of the softwares?
38. Describe in short different approaches for prediction of secondary structure of
proteins. List three programs to predict secondary structure of proteins.
39. Describe problems associated with docking a ligand in the active site of target
molecule.
40. Enumerate main steps in docking a ligand in active site of a target molecule.
41. Discus any one method for abintio structure prediction.
42. Explain the following terms:
a. WhatIF
b. WhatCheck

Module 2 Nucleic acid Structures Five hours

1. Describe Historical developments that led to discovery of Watson Crick’s

model of DNA Structure
2. Describe in short Watson and Crick’s DNA structure
3. Describe Biological importance of Watson & Crick’s DNA structure
4. Draw a nucleotide unit for purine and pyrimidine with IUPAC-IUB nomenclature
for atoms. And define backbone torsional angles
 5. Describe five torsional angles in deoxyribose sugar. Give the formula for
calculating Pseudo rotational angle P
6. Draw a nucleotide unit with IUPAC-IUB nomenclature, show the cgycosydic
angle χ. Define C2’ and C3’ endo sugar pucker

7. Illustrate the main differences between Fiber X-ray photographs of A and B form
of DNA. Define the conditions under which these were obtained and give the
names of scientists
8. Discuss major structural differences between A and B- form of DNA
9. What is the historic importance of left handed structure of CGCGCG by Wang et
al
10. Give the main characteristics of left handed or Z DNA structure
11. Compare structural features of A,B and Z form of DNA
12. Describe the conditions under which B DNA goes to A or Z DNA
13. Write short note on
a. DNA polymorphism
b. Left handed DNA

14. Describe main structural features of structure of DNA dodecamer

CGCGAATTCGCG by Dickerson
15. Draw a DNA base pair CG and define terms Roll, twist, tilt and propellar twist
16. Describe different models for binding of Drugs to DNA. Give one example of
minor groove binding and intercalation binding to DNA
17. Write a short note on:
a. Drug-DNA interaction,
b. Regulatory protein-DNA interaction

Module 3 Structural features of proteins

18. Distinguish between L and D amino acids
19. Describe five classes of amino acids
20. Describe four levels of protein structure
21. Draw a tri peptide Ala-Ser-Ala with IUPAC-IUB nomenclature and define
torsional angles φ and ψ
22. Draw a tripeptide, define torsional angles φ and ψ. Innumerate main features of
Ramachandran Plot
23. Compare the main structural features of for alpha 3.6 13, 3.010 , 2.27, helices
24. What are reverse turns? What is their importance?
25. Write short notes on
a. Structural motifs
b. Greek Key structure
c. β hairpin
26. Give one example of αα topologies, αβ topologies, structural domains
27. What is meant by tertiary structure?
28. Give one example of all α proteins and all β proteins
 29. Describe main structural features of:
a. Rossman fold
b. Immunoglobin fold
c. Disulphide fold
d. Toxin fold
30. What is a quaternary structure?
31. Give example of covalently connected structural subunits
32. Give example of homo and hetero multimers
33. Describe in short subunit arrangement in:
a. Photosynthetic reaction center,
b. F1-ATPase,
c. P- Lectins,
d. GroEL

Module 4 Structural features of lipids and carbohydrates 4 hours

34. Give reasons why it is difficult to determine lipid structures using single crystal
X-ray diffraction
35. Give list of techniques which can be used to analyse structural organization of
lipids. Write three sentenses on each method
36. Explain how ESR spectroscopy is useful for analysis of lipid structures

37. Describe structural arrangement in dry lipids

38. Describe phase behaviour of hydrated phospholipids. What is a Kraft point?
39. Distinquish between: Hexagonal, lamellar and micellar phases of lipid water
system
40. Write an essay on membrane models
41. Describe historical developments that led to discovery of Singer Nicolsons Fluid
Mosaic model
42. Describe current view of membrane structure
43. What is the importance of carbohydrates?
44. What are amino sugars? Give structure for NAG and NAM
45. Give the basic chemical formulas for aldose and ketose. Describe what is ment by
cyclic monosaccharides
46. Describe by giving example structure of mono, di and polysaccharide
47. Describe conformational features of monosaccharides

Module 5 Use of X-ray crystallography to study Biomolecular Structure 4 hours

48. Discuss in short problems associated with protein crystallization
 49. Describe hanging drop method for protein crystallization
50. Describe methods of used to obtain phase factor
51. How can one avoid:
a. Damage of crystal due to over heating
b. Ice formation
52. Describe general methodology for obtaing X-ray diffraction patterns of a protein
crystal
53. What are the methods used for analysis of X-ray pattern

Module 6 Use of NMR spectroscopy for structure determination 3 hours

54. Describe various parameters from NMR spectroscopy
55. Discuss importance of measurement of NMR line width and height in
determination of relaxation times T1 and T2
56. What is meant by chemical shift of a NMR line. What is its use
57. What is the reason for splitting of the NMR lines? What is the application of
line splitting in NMR
58. What is meant by coupling constants?
59. What is Karplus equation? Explain its use in analysing peptide conformation
60. What is a multidimensional NMR?
61. Explain terms: NOESY, COSY, SECSY, DQS-COSY, TOCSY
62. Explain the practical applications of 2D NMR in understanding protein
conformation

NMR
Explain the NMR spectra of the compound containing Flourine and Phosphorous.
Give construction of continuous wave spectrometer.
What is anisotropic effect? Explain with suitable example.
What is nuclear Over Hauser effect? What is its application?
What is coupling constant? How is Karplus equation related to coupling constant?
What is chemical shift? How will you prove that it is independent of instrument
frequency?
What is spin splitting? Explain formation triplet, quartet and quinent splitting of NMR
peaks?

What are the sugars involved in the structure of high mannose type N-linked
oligosaccharides? Give structures of any four sugars in their pyranose ring forms.

Wite the chair conformation of β-D-glucopyranose, β-D-mannopyranose & α-D-

galactopyranose.
How N-glycosidic bonds and O- glycosidic bonds are formed?

What is N-linked oligosaccharide? Write the structure of N-linked oligosaccharides.

Wite the structure of sucrose and lactose in their pyranose /furanose ring forms.

Write the structures of β-D-N-Acetylgalactosamine and β-D-N-Acetymuramic acid.

Explain the role of α-(1,4),α-(1,6) and β-(1,4) glycosidic likages present in starch,
glycogen and cellulose.

Give the structures of β-D-Xylopyranose, 2’-D-β-D-Ribofuranose & α-D-Lyxofuranose.

What is the envelope form of furanose? Give the difference between the C-3’-endo and
C-2’ endo conformation of ribose. Wirte the structure of any one.

Explain the role of antifreeze glycoproteins.Write the structure recurring unit present in
their structure.

Give the general structure of common O-linked glycan present in all blood group
antigens. Mention the terminal sugars present in A & B oligosaccharide antigen.

Write the structure of amylose and cellulose in their pyranose ring forms.

What are types of lipids? Give example of each one.

Give the systematic (IUPAC) names and structures of Lauric acid, Palmitic acid, and
Stearic acid.
Give the systematic (IUPAC) names and structures of Palmitoleic acid, Oleic acid and
Linoleic acid.

Explain:Unsaturated fatty acids have lower melting point than saturated acids..

Write the systematic (IUPAC) name and structure of Arachidonic acid.

Write the structure of lecithin and it’s parental compound. What are the polar and
nonpolar entities involved inLecithin.

Give the structure of Cholesterol along with numbering system for carbon atoms. Write
the polar and non polar entities involved in the structure.

Enlist the techniques used to study lipid organization.

Differentiate between active transport and facilitated diffusion.

Explain: Active transport reouires a coupled input of energy.

If the transport of an uncharged molecule from C-1 (10 -4 mM) to C-2 (10 -1 mM) occurs.
Then calculate Δ G. (T= 250 C, R= 1.99 )

What are perme ses ? Explain facilitated diffusion with a diagram.

What is Tc (kraft point)? Explain Lα phase of lipids.

What is Pβ’ phase of lipids.Explain with a diagram.

What are dry phase lipids? Explain with a diagram.

Explain Micellar, Lamellar and Gel phase with a suitable diagram.