LOYOLA COLLEGE (AUTONOMOUS), CHENNAI – 600 034

B.Sc. DEGREE EXAMINATION – PLANT BIOLOGY & PLANT BIO-TECH.

VE 10

FOURTH SEMESTER – April 2009

PB 4208 – BIOINFORMATICS – II (GENOMICS & PROTEOMICS)

 

 

 

Date & Time: 27/04/2009 / 9:00 – 12:00  Dept. No.                                               Max. : 100 Marks

 

 

PART A

Answer all the questions                                                                              (20 marks)

 

I      Choose the correct answer                                                                  (5 x1  = 5)

 

1. C score determines the ______
2. a) signal peptide b) signal peptide cleavage site score
3. c) mature protein d) protein secondary structure.

 

2. ______ is a database of interacting proteins.
3. a) Protein blast b) DIP           c) proteomedb               d) ncbi

 

3. _______is a database of metabolic pathways
4. a) kegg b) ncbi            c) enzymedb                d)TIGR

 

4. _____ is the software used to identify splice sites.
5. a) nebcutter b) BDGP         c) spliceview    d) mapviewer.

 

5. _____are GC rich regions in genomes.
6. a) CpG islands b) splice sites   c) restriction sites      d) promoter regions

 

 

 

II State True or False                                                                                    (5 x 1  =5)

 

6. CATH is a database of protein structures.
7. Genomic blast can be used to compare proteins.
8. Genscan is used to predict restriction sites.
9. Any number of init exons can be present in genes.
10. DIP is used in protein protein interaction studies.

 

III  Complete the following                                                                (5 x 1 = 5)

 

11. _____is the region present 100 bp upstream the genes.
12. CpG islands can be used as a clue in _________.
13. Chemical method of DNA sequencing was done by _____ and ______.
14. ______ is used for gene
15. ______ is used to identify intron exon boundaries..

 

 

IV Define the following                                                          .             (5 x  1 = 5)

 

16. What is Genome ?.
17. What are Donor sites ?.
18. What is INTR .
19. Define :Y score.
20. Explain DIP-blast.

PART B

 

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

 

21. Write short notes on the types of exons..
22. Discuss about CpG islands and their importance.
23. Explain promoter 2.0 and its output format.
24. Give a brief note on BDGP analysis tool and its applications.
25. Discuss the role of computers in the field of biology.
26. Explain the database of drugs and metabolic pathways.
27. Discuss about electrophoresis and its applications.
28. Explain mapviewer and its applications.

PART C

 

Answer  the following  in about 1500 words.         (2 x 20 = 40)

Draw diagrams / flowcharts wherever necessary.

 

 

29.a) Explain the DNA sequencing method.

Or

1. b) Explain the Database of interacting proteins and its applications

 

30.a) Discuss the software used to predict the signal used for transfer of proteins to

their site of action.

Or

b). Discuss about Genscan and its output format and interpret the following results.

 

Gn.Ex Type S .Begin …End .Len Fr Ph I/Ac Do/T CodRg P…. Tscr..—– —- – —— —— —- — — —- —- —– —– ——  1.00 Prom +    658    697   40                              -3.65 1.01 Init +   2877   3004  128  2  2   74   37    96 0.196   2.78 1.02 Term +   8092   8218  127  1  1   67   42   102 0.105   0.27 1.03 PlyA +   8929   8934    6                               1.05

 

 

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LOYOLA COLLEGE (AUTONOMOUS), CHENNAI – 600 034

B.Sc. DEGREE EXAMINATION – PLANT BIOLOGY & PLANT BIO-TECH.

FOURTH SEMESTER – APRIL 2012

PB 4208 – BIOINFORMATICS – II (GENOMICS & PROTEOMICS)

 

 

Date : 19-04-2012              Dept. No.                                        Max. : 100 Marks

Time : 1:00 – 4:00

 

PART –A (20 Marks)

Answer all the questions

1. Choose the best answer:               (5×1= 5 marks)

 

1. Which of the following nucleotide database belongs to Europe?

1. GenBank b. EMBL      c. DDBJ      d.       UniProt

1. What is the total number of genetic codes in a codon usage table?

1. 20 b. 24    c. 60                d. 64

1. Among the following post translational modifications, which is the most important?

1. Acetylation b. Methylation        c. Phosphorylation      d. Glycosylation

1. The following are protein family databases EXCEPT

1. pfam b. PROSITE c. PRINTS        d. BiNGO

1. The size of the spots in a microarray chip is

1. 800microns b. 600 microns c. 400 microns d. 200 microns

 

1. State whether the following are True or False (5×1= 5 marks)

 

1. Psuedogenes are fully functional genes.
2. Promoters are found only on the upstream of a gene.
3. The set of proteins secreted by an organism is a proteome.
4. PDB is a structure based database.

10. The human genome project was completed in 1991.

 

     

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

 

 

1. The size of human genome is__________________.
2. The 5’ splice site is also called _________________.
3. The web based tool used for the prediction of N-glycosylated sites is ________.
4. The biological pathway database is ____________________.
5. Gene ontology refers to ____________ and ______________ function of a gene.

 

1. Answer the following each in about 50 words.      (5×1= 5 marks)

 

1. Restate the definition of a genome.
2. List any one use of DNA sequencing.
3. Give an example of a protein family database.
4. What is a secondary database?
5. Define a clade.

                                                        

 

 

 

 

PART-B                        

Answer the following, each in about 500 words; Draw diagrams wherever necessary.                                                                                              (5×8=40 marks)

 

1. a. Explain about any two nucleotide databases.

(OR)

1. Write about the different stages in DNA coiling.

 

1.   a. What is a genetic code? Explain the significance of Codon Usage Bias.

(OR)

1.   Define:
2. Promoter ii. Enhancer iii. TSS   iv.  Core promoter.

 

1. a. Discuss about any two protein family databases.

(OR)

1. Provide your understanding on glycosylation and phosphorylation of

proteins.

 

1. a. Describe SCOP as a domain structure database.

(OR)

1. How will you study protein- protein interactions?

 

1. a. List the goals and advantages of Human genome project.

(OR)

1.   Comment on Gene Ontology resources.

 

 

PART-C                        

Answer any TWO of the following, each within 1500 words; Draw diagrams wherever necessary                                                                  (2×20= 40 marks)

                                                           

• Elaborate on any two ab initio gene prediction programs.
• Explain the post translational modifications of proteins and add a note on signal

peptides.

• Outline the different levels of protein structure and describe a protein structure

database.

• Examine the different steps involved in Phylogenetic tree building with

illustrations.

 

 

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