Fourth Semester M.Sc. Degree Examination, September 2019BotanyBO 241: BIOINFORMATICS(2013 Admission onwards)

Reg. No.......

Name:........

G-5262

Fourth Semester M.Sc. Degree Examination, September 2019

Botany

BO 241: BIOINFORMATICS

(2013 Admission onwards)

Time: 3 Hours

I. Answer the following questions:

1. Contiguous sequences

2.Protein Motif

3.INDEL

4. DOTPLOT

5. J PRED

6. Phylogram

7.EST

8. Query sequence

9. TIGR

10. CLUSTAL

(10 x 1 = 10 Marks)

II. Answer the following questions in not more than 50 words:

11. (a) Describe protein atlas and its significance in the development of bioinformatics.

(b) Contribution of Frederick Sanger in advancement of proteomics.

12. (a) Describe Entrez with its significance.

(b) Describe the advantages of EST search in gene sequencing programme.

13. (a) What are the salient features of UniProt KB (SWISSPROT).

(b) Describe the features GenBank.

14. (a) Describe the concept of evolutionary tree.

(b) Describe RasMol.

15. (a) Significance of BioPerl software in Human Genome project

(b) Describe boutique databases.

(5 x 2 = 10 Marks)

III. Answer the following questions in not more than 150 words.

16. (a) Describe the major DNA databases.

(b) Describe the major protein databases.

17. (a) Describe the concept of molecular docking.

(b) Describe the relevance of mass spectrometry in proteomics.

18. (a) What is the relevance of metabolomics?

(b) Describe functional genomics with its application.

19. (a) Describe homology modeling with its significance.

(b) Describe SNPs with its role in bioinformatics.

20. (a) Describe protein secondary structure database.

(b) Describe how CADD is important in pharmaceutics

21. (a) Explain genome annotation.

(b) Explain the role of DNA microarray in genomics.

22. (a) Describe BLAST algorithm used in alignment.

(b) Briefly describe the contribution of Craig Venter in genomics.

(7 x 5= 35 Marks)

IV. Answer the following questions in not more than 250 words.

23. (a) Describe comparative genomics with its application in phylogeny.

(b) Enumerate the role of pharmacogenomics in healthcare.

24. (a) Describe the methods and tools used in protein structure prediction.

(b) Describe the milestones and achievements of human genome project.

(2 x 10 = 20 Marks)

Comments

❥NORTHERN BLOTTING

NORTHERN BLOTTING – 30 MARK DETAILED NOTES 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞❥ 𓆞 ❥ 𓆞❥ 𓆞❥ Northern blotting is a molecular biology technique used to detect specific RNA molecules in a complex mixture. It provides information about gene expression, RNA size, and transcript abundance by hybridizing RNA with a labeled complementary DNA or RNA probe. 📌 Named by analogy to Southern blotting (DNA detection). 2. Principle The principle of Northern blotting is based on: Separation of RNA molecules by size using denaturing agarose gel electrophoresis Transfer (blotting) of separated RNA onto a nylon or nitrocellulose membrane Hybridization of membrane-bound RNA with a labeled complementary probe Detection of RNA–probe hybrids by autoradiography or chemiluminescence ✔ Only RNA sequences complementary to the probe will be detected. 3. Types of RNA Analyzed mRNA (most common) rRNA tRNA miRNA and siRNA (with modified protocols) 4. Requirements / Materials Total RNA or poly(A)+ RNA Denaturing agarose ...

Single Nucleotide Polymorphisms (SNPs) – Detailed Notes

Single Nucleotide Polymorphisms (SNPs) – Detailed Notes 1. Definition SNPs are single base-pair variations in the DNA sequence that occur at a specific position in the genome among individuals of a species. Example: At a specific locus, one individual may have A while another has G: Copy code Individual 1: …A T C G A T… Individual 2: …A T C G G T… SNPs are the most common type of genetic variation in most organisms. 2. Characteristics of SNPs Single base change: Involves substitution of one nucleotide for another (A↔G, C↔T). Biallelic nature: Most SNPs have only two alleles in a population. Widespread in the genome: Found in coding regions (exons), non-coding regions (introns, promoters, intergenic regions). Stable inheritance: Passed from generation to generation like other genetic markers. Frequency: Occur approximately every 100–300 bp in the human genome. 3 . Types of SNPs SNPs are categorized based on location or effect on gene function: A. Based on genomic location Cod...

SCAR (Sequence Characterized Amplified Region) Markers

SCAR (Sequence Characterized Amplified Region) Markers Introduction SCAR markers are PCR-based DNA markers derived from RAPD, AFLP, or other random markers. Developed by Paran and Michelmore in 1993 to convert dominant, less reproducible markers into specific, reproducible, co-dominant markers. SCAR markers are locus-specific, reproducible, and sequence-characterized, making them ideal for marker-assisted selection (MAS). Principle SCAR markers are designed based on known DNA sequences obtained from cloned RAPD/AFLP fragments. Specific primers (18–24 bp) are synthesized to amplify a single, defined locus. The PCR amplification of this region generates a distinct band, which is highly reproducible and can distinguish homozygotes from heterozygotes if designed as co-dominant. Key idea: Random marker (e.g., RAPD) → Cloning & sequencing → Design specific primers → PCR → SCAR marker Materials Required Genomic DNA from the organism Specific primers (18–24 bp) designed from sequence...

❃HPLC – High Performance Liquid Chromatography

HPLC – High Performance Liquid Chromatography ┏━━━━━ •❃°•°❀°•°❃•━━━━•━━━┓ 1. Introduction High Performance Liquid Chromatography (HPLC) is an advanced analytical technique used for the separation, identification, and quantification of components present in a mixture. It is based on the differential distribution of analytes between a stationary phase and a liquid mobile phase under high pressure. HPLC is widely used in biochemistry, biotechnology, pharmaceuticals, food analysis, environmental studies, and clinical diagnostics. 2. Principle of HPLC The principle of HPLC is based on partition, adsorption, ion-exchange, or size-exclusion mechanisms, depending on the type of column used. A liquid mobile phase is pumped at high pressure through a column packed with fine stationary phase particles Sample components interact differently with the stationary phase Components with stronger interaction elute slower Components with weaker interaction elute faster Separated components are detec...

Microbial Production of PharmaceuticalsSomatostatin, Humulin and Interferons

Microbial Production of Pharmaceuticals Somatostatin, Humulin and Interferons 1. Introduction Advances in recombinant DNA technology have enabled microorganisms to produce human therapeutic proteins safely, economically and in large quantities. Microbial systems such as Escherichia coli and yeast (Saccharomyces cerevisiae) are widely used for the production of pharmaceuticals that were earlier isolated from human or animal tissues. Important microbial-derived pharmaceuticals include somatostatin, human insulin (Humulin) and interferons. 2. Advantages of Microbial Production of Pharmaceuticals High yield and rapid production Cost-effective and scalable Free from animal pathogens Consistent product quality Easy genetic manipulation 3. General Steps in Microbial Production of Recombinant Pharmaceuticals Isolation of target gene Construction of recombinant DNA Insertion into suitable vector Transformation into host microorganism Expression of protein Downstream processing and purification ...

Intellectual Property Rights (IPR) – Detailed Notes

Intellectual Property Rights (IPR) – Detailed Notes 1. Introduction Intellectual Property Rights (IPR) are legal rights granted to creators and inventors over their creations or inventions. They protect innovation and creativity, providing the owner exclusive rights to use, sell, or license their creation. IPR encourages research, development, and economic growth by rewarding creativity. 2. Importance of IPR Protects inventions, designs, and creative work. Prevents unauthorized use, copying, or commercialization. Encourages innovation and research. Provides financial benefits to inventors through licensing or royalties. Supports economic growth and competitiveness. Safeguards traditional knowledge and biodiversity. 3. Types of Intellectual Property Rights A. Patents Definition: Exclusive right granted to an inventor for a new invention for a limited period (usually 20 years). Requirements: Novelty – must be new and not published. Inventive step – non-obvious to someone skilled in the f...

••CLASSIFICATION OF ALGAE - FRITSCH

MODULE -1 PHYCOLOGY CLASSIFICATION OF ALGAE - FRITSCH ❖F.E. Fritsch (1935, 1945) in his book“The Structure and Reproduction of the Algae”proposed a system of classification of algae. He treated algae giving rank of division and divided it into 11 classes. His classification of algae is mainly based upon characters of pigments, flagella and reserve food material. Classification of Fritsch was based on the following criteria o Pigmentation. o Types of flagella o Assimilatory products o Thallus structure o Method of reproduction Fritsch divided algae into the following 11 classes 1. Chlorophyceae 2. Xanthophyceae 3. Chrysophyceae 4. Bacillariophyceae 5. Cryptophyceae 6. Dinophyceae 7. Chloromonadineae 8. Euglenineae 9. Phaeophyceae 10. Rhodophyceae 11. Myxophyce...

Suspension culture and development - methodology, kinetics of growth and production formation, elicitation methods, hairy root culture. Detailed notes

Suspension culture and development - methodology, kinetics of growth and production formation, elicitation methods, hairy root culture. Detailed notes 1. Introduction Suspension culture is a type of plant tissue culture in which single cells or small cell aggregates are grown in liquid nutrient medium under continuous agitation. It is mainly used for: Large-scale biomass production Secondary metabolite production Cell physiology and biochemical studies Genetic manipulation and selection. 2. Methodology of Suspension Culture 2.1 Source of Explant Usually initiated from friable callus Callus derived from: Leaf Stem Root Hypocotyl Friable callus is preferred as it disintegrates easily into single cells. 2.2 Preparation of Cell Suspension Friable callus is transferred into liquid MS medium Medium contains: Carbon source (usually sucrose) Auxins (2,4-D commonly used) Culture maintained in: Conical flasks Orbital shaker (100–150 rpm) 2.3 Culture Conditions Parameter Requirement Temperature ...

Protoplast culture covering isolation, fusion, somatic hybrid & cybrid production, preferential chromosome elimination, role in CMS, and genetic transformation.

Protoplast culture covering isolation, fusion, somatic hybrid & cybrid production, preferential chromosome elimination, role in CMS, and genetic transformation. Protoplast Culture 1. Introduction A protoplast is a plant cell without a cell wall, surrounded only by the plasma membrane. Protoplast culture allows direct access to the plasma membrane and genome, making it a powerful tool for: Somatic hybridization Cybrid production Genetic transformation Cytoplasmic trait transfer (e.g., CMS) 2. Isolation of Protoplasts 2.1 Source of Protoplasts Young leaves (mesophyll cells) Callus tissue Cell suspension cultures Roots or hypocotyls Young, actively dividing tissues are preferred due to high viability. 2.2 Methods of Protoplast Isolation A. Mechanical Method Cell walls removed by cutting and plasmolysis Rarely used Causes low yield and high damage B. Enzymatic Method (Most Common) Cell wall digested using enzymes: Enzyme Function Cellulase Degrades cellulose Pectinase Degrades mi...

Notethepoint 43official Previous Question Paper Updates2.0

Search This Blog