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1.Explain how cDNA microarray technique can be used to study cellular response to the environment? Support your answer with a flowchart for the same.

2.(a) Which information can be retrieved from the following databases:

          (i) EMBL

          (ii) PDB

          (iii) PALI (b) Give two reasons for completely sequencing a genome.

3. Define SNPs. Describe a possible use of this technique in medicine. How do the physicians decide our susceptibility or resistance to a particular disease through this technique? Explain with the help of an example.

4. Gene prediction by computers is different from number of genes identified by experimental methods. Why is it so? Is there any correlation between the complexity of an organism and the total number of genes in its genome? Justify.

5. What kind of analysis can be done using Bioinformatics tools for DNA and proteins?

6. Expand BLAST. Discuss the steps involved in comparison of DNA sequences using this tool. Differentiate between paralogs and homologs.

7. Name the two methodologies used for genome sequencing. Present a comparative account.

8. CML patients have the ‘Philadelphia Chromosome”. How is this chromosome detected? Explain the technique with a diagram.

9. Breast cancer cells often exhibit abnormal expression of certain genes which are too many to study individually. Describe a method that you would use to compare the gene expression in the breast cancer cells and a normal cell.

10. Name four major databases for bioinformatics with their respective information contents. Name any database retrieval tool and its application.

1. Name any three resources available from the NCBI and their uses.
2. Explain how DNA “microarray” technique can be used to study cellular response to environment. Also depict major steps diagrammatically.                                                                            
3. A  Chronic Myelogenous Leukemia (CML) patient has been put on a combination drug therapy for the past 2 months. How can the FISH technique be used to monitor the effect of chemotherapy?
4. Based on Genomic studies, why do people say that different species and organisms had a common ancestor 100 million years ago.                                                                    
5. The publication of ‘Atlas of Protein Sequences and Structure” under the editorship of Margaret O” Dayhoff was a pioneering effort. Why?
6. Suggest any four reasons why complete genome sequencing projects should be undertaken? Describe the advantage of using bacterial artificial chromosomes (BAC) in such sequencing programmes. 
7. Expand BLAST. Differentiate between homologues and paralogs.         
8. Name four major databases for bioinformatics with their respective information contents. Name any database retrieval tool and its application.          
9. A scientist determines the complete genome and proteome of a liver cell and a muscle cell from the same person. Would you expect bigger differences in the genome or proteome of these two cell types? Explain.
10. What are DNA chips and how they are used in functional genomics?
11. Expand BLAST. Discuss the steps involved in comparison of DNA sequences using this tool. Differentiate between paralogs and homologs
12. A scientist determines the complete genome and proteome of a liver cell and a muscle cell from the same person. Would you expect bigger differences in the genome or proteome of these two cell types? Explain.
13. There is no simple correlation between the intuitive complexity of an organism and the number of genes in its genome. Do you agree with the statement? Justify your answer.
14. It is believed that each person’s genome is 99.8% is identical to everyone else’s. Discuss the basis of this 0.2% difference in DNA sequence of  individuals. Does it always occur in coding regions of the genome? Suggest the usefulness of studying such variations using two examples.
15. As a student of bioinformatics you want to produce a data set which can be compare easily and uniformily around the world. What features would you consider?
16. SNPs can be used to understand genomic variations in responses to medicines. Explain. Name a disease caused due to single gene mutation.
17. How are fluorescent colors introduced into chromosomes? Give a possible use of this technique. Draw a suitable diagram of the same
18. (a) Human population vary greatly in their susceptibility to diseases. Why?

(b)Which present day approach can assist physicians in predicting with confidence the risk of developing a disease.

19.Name the two methodologies used for genome sequencing. Present a comparative account.

20.Enlist any three database retrieval tools available at NCBI. Does similarity between two sequences always indicate their homology? Explain.

21.CML patients have the ‘Philadelphia Chromosome”. How is this chromosome detected? Explain the technique with a diagram.

22. Do you think ‘in silico’ based prediction techniques are accurate in genomics? Support your answer with reasoning

23. What are the various types of DNA sequences which can be deposited into databases? Suggest at least 3 commonly used database retrieval tools and their uses.

24. How does genome sequencing can be done? Suggest, any four reasons why these should be undertaken.

25. Interpret possible use of nick translation in detecting chromosomal translocation. Draw a suitable diagram.

26. The human genome contains twice as many genes as the simple organisms Drosophila. Give one explanations to how just double the number of genes can give rise to the complexity required for a human being.

27. DNA microarray permits an investigator to monitor simultaneously, the level of mRNA production from every gene in an eukaryotic organism:

(a) Why might such an analysis is not give an accurate estimate of the level of protein expressed in an organism?

(b) Which alternative technique will be better suited for the above mentioned analysis?

1. What is the IUPAC code for T or C? Write the complementary sequence of the following sequence:                                                 5′ – A T G A Y C G B T – 3′        
2. C.elegans is a eukaryotic organism with a genome of 97 Mb and about 20,000 genes. What organizational features of this genome are unusual when compared to the genomes of other eukaryotes, such as yeast and Drosophila?
3. Annotation of human genome sequence reveals that our genome contains 30000- 33000 genes. Proteomic  analysis indicates that human cells are capable of synthesizing more than 30,000 different proteins. How           can this discrepancy be reconciled?
4. Differentiate between structural and functional genomics.
5. The number of genes predicted by computational biology is different from the number of genes identified by experimental methods in a genome. Justify.
6. How can ‘Expression Proteomics” be useful in the identification of disease specific proteins.
7. What kind of analysis can be done using Bioinformatics tools for DNA and proteins?
8. How can a CML patient be identified by the FISH technique?
9. As a student of bioinformatics you want to produce a data set which can be compare easily and uniformily around the world. What features would you consider?
10. (a) Human population vary greatly in their susceptibility to diseases. Why?

(b)Which present day approach can assist physicians in predicting with confidence the risk of developing a disease.

1. Why is it useful to search a database to identify sequences that are homologous to a newly determined sequence?
2. Why is it useful to search a database to identify newly determined DNA sequence? Give two reasons.

             How can a CML patient be identified by the FISH technique?

1. What is the information coded by the following set – DEGWYVBZXR
2. (a) Human population vary greatly in their susceptibility to diseases. Why?

(b)Which present day approach can assist physicians in predicting with confidence the risk of developing a disease.

1. Given below is the table of genome size and gene numbers of the weed Arabidopsis thaliana and Homo sapiens:

Organism	No. of chromosomes	Genome size (bp)	Predicted genes
Arabidopsis	5	15,70,00,000	25,498
Homo sapiens	23	3,00,00,00,000	25,000

Derive two observations with explanation of the table.

1. In DNA sequence readouts occasionally a S symbol appears. What does this means?
2. What is the IUPAC code for A or G? write the complementary sequence of the following:-

5′ – GYTWASGA-3′

GENOMICS AND BIOINFORMATICS

(1 Mark Questions)

1. Why is a DNA sequence always listed in the direction 5’to 3′?
2. What are ESTs? How are they useful in genome analysis?
3. How can SNPs be used to predict susceptibility to diseases?
4. Proteome of a given cell is dynamic. Why?
5. When aligning two or more genetic sequences, it is sometimes necessary to insert gaps, why?
6. Why there is a need to create bioinformatics databases?
7. Name a disease caused due to single gene mutation.
8. Indicate which one of the two broad areas of genomics addresses the biological functions of genes.
9. Human population vary greatly in their susceptibility to diseases. Why?
10. Which were the two first genomes to be sequenced? Name the organization which achieved this feat.
11. Suppose you are a planning a large scale hybridization programme in maize. How can this task be made less labour intensive?
12. In DNA sequence readouts occasionally a S symbol appears. What does this means?
13. What are ESTs? How are they useful in genome analysis?
14. Who is curator? What is curation?
15. Name the database which was created to manage to redundancy in ESTs.

https://www.learnhowtobecome.org/science-technology-careers/biotechnology/

Click to access biotechnologyms.pdf

https://cdn.aglasem.com/schools/cbse/class-12/sample-paper/2019/sample-paper/biotechnologysp.pdf

Unit-V Protein and Gene Manipulation 

Chapter-1: Recombinant DNA Technology

Introduction, Tool of rDNA technology, Making rDNA, Introduction of recombinant DNA into host cells, Identification  of  Recombinants, Polymerase Chain Reaction  (PCR), Hybridization Techniques, DNA Library, DNA Sequencing, Site-directed Mutagenesis.

Chapter-2: Protein Structure and Engineering

Introduction to the world of proteins, 3-D shape of proteins, Structure-Function Relationship in Proteins, Purification  of  Proteins,  Characterization  of  Proteins,  Protein  Based  Products, Designing Proteins (Protein Engineering).

Chapter-3: Genomics, Proteomics and Bioinformatics

Introduction, Genome, Sequencing Projects, Gene prediction and counting, Genome  Similarity, SNPs and Comparative Genomics, Functional Genomics, Proteomics, History of Bioinformatics, Sequences and nomenclature, Information Sources, Analysis using Bioinformatics tools.

Unit-VI Cell Culture and Genetic Manipulation (30 Marks, 80 Periods)

Chapter-1: Microbial Cell Culture and Its Applications

Introduction, Microbial Nutrition and Culture Techniques, Measurement and Kinetics of Microbial Growth,   Scale-up   of  Microbial   Process,  Isolation   of   Microbial   Products,  Strain   Isolation  and Improvement, Applications of Microbial Culture Technology, Biosafety Issues in Microbial Technology.

Chapter-2: Plant Cell Culture and Applications

Introduction,  Cell  and  Tissue  Culture  Techniques,  Applications  of  Cell  and  Tissue  Culture,  Gene Transfer Methods in Plants, Transgenic Plants with Beneficial Traits, Biosafety of Transgenic Plants.

Chapter-3: Animal Cell Culture and Applications

Introduction, Animal Cell Culture Techniques, Characterization of Cell lines, Methods of Gene Delivery into Cells, Scale-up of Animal Culture Process, Applications of Animal Cell Culture, Stem Cell Technology, Tissue Engineering.

Practicals (30 Marks)

Note: Every student will be required to do the following experiments during the academic session.

List of Experiments

1. Use of special equipment in biotechnology experiments.

2. Isolation of bacterial plasmid DNA

3. Detection of DNA by gel electrophoreses

4. Isoloation of Genomic DNA (CTAB method)

5. Estimation of DNA

6. Bacterial transformation using any plasmid

7. Restriction digestion of plasmid DNA & its analysis by gel electrophoreses

8. Isolation of bacterial grom curd & staining of bacteria

9. Cell viability assay

10. Data retreival and data base search using internet site NCBI and download a DNA and protein sequence from internet, analyse it and comment on it

11. Reading of a DNA sequencing gel to arrive at the sequence

12. Project work

Scheme of Evaluation (Practicals):

Time 3 Hours | Maximum marks 30

A	Two experiments	6+6 (only one computer based practical)
	Practical record	04
	Viva on Practicals	04
B	Project work
	Write up	05
	Viva on project	05
	Total	30

https://www.google.com/url?sa=t&source=web&rct=j&url=http://cbseacademic.nic.in/web_material/CurriculumMain20/SrSecondary/BioTechnology.pdf&ved=2ahUKEwjv2bWj-6DjAhX8_XMBHeDWCRkQFjAPegQIBhAB&usg=AOvVaw1t63cFV5qOY2choOyXp0Vn&cshid=1562439191106

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