LOYOLA COLLEGE (AUTONOMOUS), CHENNAI – 600 034

M.Sc. DEGREE EXAMINATION – BIO TECHNOLOGY

VE 35

SECOND SEMESTER – April 2009

BT 2820 – STRUCTURAL BIOLOGY & BIOINFORMATICS

 

 

 

Date & Time: 27/04/2009 / 1:00 – 4:00  Dept. No.                                                   Max. : 100 Marks

 

 

                                                            SECTION A  (20 marks)

                                              Answer all the questions

1. Choose the best answer (5×1=5)
2. Alpha helix breakers are
3. a) Pro and Gly b) Asp and Asn c) Phe and Tyr d) Ala and His
4. Three dimensional structure of a protein is elucidated by
5. a) X ray crystallography b) NMR c) CD d) MS
6. In standard microarrays probes are attached to the chip coated with chemical matrix by
7. a) Covalent bonding b) van der waals forces
8. c) Hydrophobic forces d) ionic bonding
9. The most frequently used target for drugs are
10. a) GPCR and ion channels b) Ligands and small molecules
11. c) Kinases and esterase d) Sugars and lipids
12. Identify the type of isochore in which most of the house keeping genes are located?
13. a) L1 b) H1                         c) L2                            d) H3
14. State True or False; if false, give reasons (5×1=5)
15. Negatively supercoiled DNA runs faster in agarose gel electrophoresis.
16. Protein coding genes are transcribed by RNA polymerase I in eukaryotes.
17. RNA secondary structures can be predicted by software tool based on energy

minimization.

9. Protein signatures can be analysed by PRINTS.
10. KEGG and CaZy are enzyme databases.

 

III. Complete the following                                                                    (5×1=5)

11. Proteins present in silk fibre are called _______and _______.
12. UTR represents _________.
13. Energy required for protein folding is______kJ/mol.
14. GEO stands for___________.
15. DNA is stabilized by _________forces.

 

1. Answer the following questions each in about 50 words: (5×1=5)
2. Define alternative splicing
3. Explain folding funnel.
4. Differentiate Topoisomerase I and Topoisomerase II.
5. What are indels?
6. Write about NCBI.

 

SECTION B

  Answer any five of the following, each in about 350 words:                  (5 x 8 = 40)                     

 

21. Draw the structure of a gene and locate the ORF. What are the tools available to

analyze an ORF and CpG islands?

22. Explain how a hit compound succeeds to become a potential drug.
23. Write in detail about collagen and its biomedical significance and disorders.
24. What are the four levels of structures of the proteins?
25. Explain the different transition states of a folded protein.
26. Briefly write about Alpha and Beta Keratin.
27. Differentiate A, B and Z forms of DNA.
28. Write about Chou-Fasman, GOR and NN methods of protein prediction.

 

SECTION C

 Answer the following, each in about 1500 words:                                                (2 x 20 = 40)  

 

29.a)    i) Define steric collision and draw a planar peptide bond with Phi and Psi angle.

1. ii) Explain Ramachandran plot and show the allowable and disallowable quadrants for alpha

and beta structures.

(or)

1. Elaborate upon the Protein sequence and structural Databases and any five

proteomic tools.

30 a)    i) Detail gene expression analysis using Microarrays.

1. ii) Explain clustering approach and write about Mutation microarray analysis.

iii) List out the applications.

(or)

1. b) i)  Explain sequence alignment .
2. ii) Write about BLAST and its applications.

iii) Brief about the MSA tools available and interpret it using phylogenetic trees.

 

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