COMPUTATIONAL MOLECULAR BIOLOGY ONLINE BITS 4 UNIT VII

Introduction to proteins

1. _______ bond binds two amino acids together (S)

a. peptide

b. ionic

c. Vander wall force

d. no bond ans- a

2. A peptide bond is formed between the (S)

a. Carboxyl & amino group of same amino acid residue

b. Carboxyl & carboxyl group of adjacent amino acid residue

c. Carboxyl & amino group of adjacent amino acid residue

d. Carboxyl & hydrogen group of adjacent amino acid residue ans- c

3. The word protein comes from the Greek word _______and it means______(M)

a. proteios, primary

b. proteios, nutritious

c. primary, nutritious

d. proteome, nutritious ans- a

4. Tertiary structure is generally not stabilized by (M)

a. salt bridge

b. hydrogen bond

c. disulfide bonds

d. covalent bonds ans- d

5. ________ experimental methods produce information at atomic resolution(M)

a. NMR spectroscopy

b. cryo electron microscopy

c. electron crystallography

d. electron microscopy ans- a

6. The set of proteins expressed in a particular cell or cell type is know as it's (S)

a. proteios

b. proteome

c. protein

d. prosito ans- b

7. ________ enzyme is specific for specific amino acid (S)

a. amino synthase

b. amino transferase

c. amino acyl tRNA synthetase

d. amino specific tRNA ans- c

8. Antibodies are protein components of _______ immune system whose main function is to bind antigens (S)

a. natural

b. adaptive

c. captive

d. acquired. ans- b

9. An example of a ligand binding protein is (H)

a. insulin

b. amylase

c. hemoglobin

d. prolin ans-c

10. _______ allows the detection of the relative levels of a large number of proteins present in a cell (H)

a. 2D electrophoresis

b. mass spectrometry

c. structural genomics

d. protein micro arrays ans-d

Protein identification ,structure and function determination

1. The first atomic resolution structure of proteins were solved by X-ray crystallography in the year (M)

a. 1980's

b. 1970's

c. 1950's

d. 1960's ans- d

2. The first atomic resolution structure of proteins were solved by NMR in the year(M)

a. 1980's

b. 1970's

c. 1950's

d. 1960's ans- a

3. The various types of secondary structure of protein are stabilized by_______ bonds mainly(M)

a. amide-amide hydrogen

b. water-amide hydrogen

c. ionic hydrogen

d. amino carboxy bond ans- b

4. An amino,carboxyl group ,hydrogen and side chain are specific for any a amino acid but with an exception in______ (S)

a. glycine

b. valine

c. prolin

d. serien ans-c

5. Achiral amino acid is(S)

a. glycine

b. valine

c. prolin

d. serien ans-a

6. ________ type of hydrogen bond is formed between

N-Ca peptide bond (H)

a. O-H--------O-H

b. N-H--------O=C

c. O-H--------O=C

d. O=C-------O=C ans- c

7. The sequence of a protein can be determined by a method like

a. tandem mass spectrometry(S)

b. transcription

c. reverse transcription

d. cloning ans- a

8. The part of the backbone that is not in a regular secondary structure of protein is said to be________(H)

a. coil

b. perfect coil

c. junk coil

d. random coil ans- d

9. Tertiary structure of protein are held together by________ &________(S)

a. glycosidic

b. glycosidic & covalent

c. electromeric & vanderwall forces

d. hydrogen bond & ionic bonds ans- b

10. Among Ca , Cb , Cg , Cd ……. Is usually considered as part of the protein back bone(S)

a. Cb

b. Cg

c. Ca

d. Cd ans- c

Structure comparision methods prediction of secondarz structures from sequences

1. Prediction of a- helices , b strands & other secondary structures are studied under (S)

a. protein formation

b. sequence analysis

c. amino acid basic structures

d. amino acid functional structures ans- b

2. The main types of secondary structures that are examined for sequence variations are

a. a- helices and b strands (S)

b. a- helices

c. delta strands

d. gamma strands ans- a

3. The basic assumption in all secondary structure prediction is that there should be a correlation between (S)

a. amino acid and secondary structure

b. secondary & tertiary structures

c. tertiary & quaternary structures

d. amino acid & nucleic acid structures ans- a

4. __________ is the most accurate and comprehensive structure prediction method

a. statistical thermodynamics (S)

b. comparative modeling

c. quantum mechanics

d. sequencing ans- c

5. The basic assumption in all secondary prediction is that (S)

a. there should be a correlation between amino acid sequence and secondary structure

b. there should be a correlation between amino acid sequence and proteins

c. there should be a correlation between amino acid sequence and tertiary structure

d. there should be a correlation between proteins and nucleic acids ans- a

6. Chou and fosman and GOR methods are based on (M)

a. local amino acid composition of single sequences

b. local amino acid composition of double sequences

c. evolution only

d. mutational sequences ans-a

7. _________ method is uses the principles of information theory to derive predictions

a. Chou and fosman (M)

b. GOR

c. COR

d. CFL ans-b

8. __________ method is based on analyzing the frequency of each of the amino acid in a- helices, b sheets and turns (M)

a. Chou and fosman

b. GOR

c. COR

d. CFL ans-a

9. ___________ are neural network predictions(H)

a. FM

b. PHD and NNPREDICT

c. CFMT

d. NJ ans-b

10. __________ is a machine learning method (H)

a. GOR

b. CFM

c. Nearest-neighbor-predictions

d. CFL ans-c

CATH, SCOP, CASP and yearly updates

1. CATH and SCOP are (S)

a. 1^o structural database

b. 1^o sequence database

c. 2^o structural database

d. 2^o sequence database ans-c

2. Expand CASP (S)

a. critical assessment of techniques for gene structure prediction

b. critical assessment of techniques for protein structure prediction

c. critical assignment of technical for protein structure prediction

d. critical assessment of techniques for RNA structure prediction ans-b

3. In CASP _________ method focus on building structure with no prior information(S)

a. homology modeling

b. threading

c. ab-initio prediction

d. milling ans-c

4. Homology based prediction as per sequence alignment is detecting meaningful sequence homology in the Twilight zone below _________ % sequence homology (M)

a. 25

b. 50

c. 75

d. 100 ans-a

5. Which of the following database describes structural and evolutionary relationships between proteins of known structures (S)

a. CATH

b. SCOP ans-b

c. DALI

d. CE

6. De-novo structure prediction is now referred as_______________ (S)

a. old fold

b. keen fold

c. new fold

d. modern fold ans-c

7. ________ is a community wide experiment for protein structure prediction taking place every two years since 1994 (M)

a. CASP

b. CATH

c. SCOPE

d. SAL ans-a

8. ________ provides research groups with an opportunity to assess the quality of their methods for protein structure prediction from the primary structure of the protein (H)

a. CASP

b. CATH

c. SCOPE

d. SAL ans-a

9. Evaluation of the results for domain boundary prediction is carried out at _______ prediction categories (H)

a. starting CASP 7

b. starting CASP 6

c. dropped after CASP 5

d. starting CASP 4 ans-b

10. If the given sequence is found to be similar to a protein sequence of known structure, may be used to predict the tertiary structure (M)

a. non-comparative modeling

b. de-novo modeling

c. functional modeling

d. comparative protein modeling ans-d

1. Till 2008 how many CASP experiments have been conducted (M)
a. 5
b. 6
c. 7
d. 8 ................................ans(c)

2. The first CASP experiment was conducted in the year (H)
a. 1992
b. 1994
c. 2000
d. 2006 ..................................ans(b)

3. CASP was developed by the idea of (M)
a. David lip man
b. John moult
c. Pearson
d. Smith and Waterman ............................ans(b)

4. CASP is a kind of (S)
a. An instrument
b. a compitition
c. an online tool
d. Sequence aligning tool ..........................ans(b)

5. Murzin and Bateman used _________ database, which organizes all known protein folds according to their structural and evolutionary relation ships for manual predictions (S)

a. NCBI

b. DDBY

c. SWIS PROT

d. SCOP ans-d

6. The next CASP experiment is going to be held in _______ 2008 at ________ .(H)
a. December, Italy
b. November, U.S
c. December, Australia
d. November, India ........................ans(a)

7. The CASP experiments that are conducted by Protein Structure Prediction Center is sponsored by (M)
a. Swiss Institute
b. Kyoto Institute
c. UNISCO
d. NIH, NLM ..............................ans(d)

8. Expand CATH (S)

a. class /architecture /topology / homology

b. classification of proteins at thermophilic stage

c. structural classification of amino acids

d. classification of alignment of threading ans-a

9. Which of these can be seen in all CASPS (S)
a. Tertiary structure prediction
b. Domain boundary prediction
c. function prediction
d. Structure complexes ....................................ans(a)

10. ________ is a protein sequence secondary database (S)

a. CATH

b. SCOP

c. NCBI

d. PROSITE ans-d