COMPUTATIONAL MOLECULAR BIOLOGY ONLINE BITS 4 UNIT V

Sequence assembly and gene identification

1. A gene is not sequenced for for acquiring PhD and fame

2. Availability of gene sequences provides the sequences of all the genes of an organism so that important genes like genes influencing the metabolism, cellular differentiation,& disease processing in plants and animals can be identified and the relevant genes are manipulated.

3. Mus musculus is a genetic model for human beings

4. When a gene that specifies an important biological function is not identified ,then it can be traced in individuals using sequence variations that occur among individuals in a population called sequence polymorphism

5.Example of sequence polymorphism SNP's

6.Proteome- by -proteome comparisons identifies orthologs

7.Genome sequences are assembled from DNA sequence fragments of approximate length 500bp

8.Dispersed tandem repeats includes mini & macro satellite

9.Microarray method says which genes are expressed at a particular stage of the cell cycle or developmental cycle of an organism or genes that respond to a given environmental signal to the same extent (H)

10.Which of the following detects translation products.Two dimensional gel protein analysis

Homology based gene prediction

1.In homology modeling it has been reported that sequence identity of greater than 40% usually implies more than 90% of 3D structure

2.In 2002 best results were obtained by CASP4 by . rosetta package overlap

3.Homology modeling and threading are comparative methods

4.Methods that specifically address the problem of predicting side chain geometryinclude dead end elimination & self consistent minefield methods

5.swiss model provide an automated web server for basic homology modeling

6.The original method of homology modeling relied on the assembly of a complete model from structural fragments identified in closely related solved structures (S)

a. conserved

b. non conserved

c. complex

d. simple ans-a

7. A force field specifically constructed for model assessment is known as the effective force field and is based on atomic parameters from (H)

a. CHARM

b. CARM

c. CHARAM

d. CHARMM ans-d

8. One newer method for model assessment relies on machine learning techniques such as ______(H)

a. DOPE

b. PROSA

c. PDB

d. Neural nets ans-d

9. EXPAND RMSD (M)

a. Root -Mid-Square derivation

b. Root -Mean -Square deviation

c. Root -Mid-Sequence derivation

d. Route-Mid-Square derivation ans- b

10. _____ method is used for assessment of homology models (S)

a. RMSD

b. RASMOL

c. CAFAST

d. EVA ans- a

Restriction Mapping analysis coding region identification

1. ________ is a map of known restriction sites with in a sequence of DNA (S)

a. restriction map

b. chromosomal linkage

c. cytological

d. HMR ans- a

2. Restriction map along with ________ &________ are used to determine the genetic relationships between two or more subjects often different species at the molecular level (S)

a. DNA & RNA sequence analysis

b. DNA-DNA hybridization & DNA/RNA sequence analysis

c. DNA-RNA hybridization

d. DNA-RNA hybridization & RNA-RNA analysis ans-b

3. Restriction enzymes are called(S)

a. catalysts

b. restriction exo nucleases

c. restriction endo nucleases

d. biocatalyst ans- c

4. Generally restriction enzymes will cut DNA at specific base sequences ____________ long (M)

a. 4-8 base pairs

b. 20 base pairs

c. 500 base pairs

d. 2 base pairs ans- a

5. Restriction mapping is more practical for comparing smaller segments of DNA usually a few _______ nucleotides long(S)

a. 10

b. 100

c. 500

d. 1000 ans- d

6. Several laboratories have used restriction maps to compare _______ for eukaryotic organisms(M)

a. chromosomal

b. mitochondrial DNA

c. plasmid DNA

d. Nuclear RNA ans- b

7. Mitochondrial DNA changes by mutation about _______ times faster than the nuclear genome (M)

a. 10

b. 20

c. 40

d. 50 ans- a

8. __________ segments containing related inverted repeats were isolated from D. melanogaster & analyzed by electron microscopy & restriction mapping (H)

a. Bam H1

b. SAL

c. Eco R1

d. 5 Bam H1 ans- d

9. Restriction mapping of YAC indicates that it contains both __________&_______ genes in addition to DXST (H)

a. MAOA & DXS7

b. MAOA & MAOB

c. MAOB & DXS7

d. DXS7 & DXS6 ans- b

10. Using an oligo nucleotide probe to the E1 glycoprotein region and limited restriction endo nuclease mapping , the resulting amplified products were shown to be specific for _______ viruses (S)

a. rubella

b. polio

c. siemen

d. measles ans- a

SNP's Applications

1. ________ is a DNA sequence variation occurring when a single nucleotide in the genome differs between members of a species (S)

a. SNP

b. GNP

c. GTP

d. EST ans- a

2. Two of every three SNP's involve the replacement of (S)

a. Guanine with adenine

b. Cytosine with thyamine

c. Adenine with cytosine

d. Cytosine with guanine ans- b

3. SNP's with in a coding sequence will not necessarily change the amino acid sequence of the protein that is produced due to ___________ (S)

a. Degeneracy of the amino acid

b. Wobbling process

c. Degeneracy of the genetic code

d. Removal of introns ans- c

4. A SNP in which both forms lead to the same polypeptide sequence is termed (S)

a. non synonymous

b. synchrony

c. hybrids

d. synonymous ans- d

5. A special subset of SNP's is one where the base change alters the sensitivity of a sequence to cleavage by a restriction endonuclease is called (S)

a. Snip-SNP's

b. Silent mutations

c. SNP's

d. EST's ans- a

6. Which of the following is a component of the SNP arrays (M)

a. one or more labeled probes

b. The array that contains immobilized amino acid sequences

c. Receiver

d. Monitor ans-a

7. A human genome has ___ SNP's approximately (M)

a. 1-2 million

b. 1-20 million

c. 5-10 million

d. 10-20 million ans- c

8. research has shown that an individual who inherits at least one ________ allele will have a greater chance getting Alzheimer's (M)

a. E₂

b. E₁

c. E₃

d. E₄ ans-d

9. The pattern of SNP's in a stretch of DNA is known as (H)

a. haplotype

b. diplotype

c. triplotype

d. monotype ans-a

10. Single box variants in CDNA's (CSNP's) are usually called as SNP's because most of these will reflect underlying genomic DNA variants although they could result from________ (H)

a. DNA editing

b. RNA editing

c. Amino acid editing

d. Protein editing

Methods of studying gene expression EST approach

1. Expand EST (S)

a. Expressed sequence tag

b. Expression of sequence of thiamine

c. Expand sequence tag

d. Expression of sequence tags ans-a

2. ______ is a partial sequence of a clone, randomly selected from a CDNA library and used to identify genes expressed in a particular tissue (M)

a. EST

b. GST

c. micro array

d. gene chip ans-a

3. while analyzing ESTs, EST alphabet is _____________characters (S)

a. 5

b. 4

c. 3

d. 2 ans-a

4. First step in EST is________ (S)

a. CDNA library in constructed from a tissue or cell line of interest

b. it takes amino acid

c. it takes proteins

d. it takes introns from library ans-a

5. Atypical EST has _____basis in length (M)

a. 200 to 500

b. 500 to 1000

c. 100 to 200

d. 200 to 800 ans-a

6. In EST production process uses_______ system to read sequenced gels (M)

a. florescent lazar

b. anti body

c. enzyme based

d. light ray ans-a

7. Which of the following statement is not correct while analyzing EST (H)

a. EST alphabet is 5 characters

b. EST will often be a subsequence of any other sequence in the data banks

c. EST may not represent part of the CDS of any genes

d. EST alphabet is 2 characters ans-d

8. Expand ORF (S)

a. open reading frame

b. orient restriction fragment

c. open restriction sites fragment

d. orient reading fragment ans-a

9. If the EST results are not similar to the library sequence we can not immediately assume that as new gene because (S)

a. EST represents DNA

b. EST represents non-coding sequences for a known gene that is not in data base

c. EST represents RNA

d. EST represents enzymes ans-b

10. Many MRNA's (especially humans) have long un translated regions at ______ends of the CDS (H)

a. 3^|

b. 5^|

c. 3^| and 5^|

d. 2^| and 6^| ans-c