Proteomic / 52b Biotech
Subject: Protein structure
Test: HUS - Protein structure wer. 1.0.3
1. N-glycosylation sites of a protein can be localized with the aid of the program:
A) WebLab Viewer Lite
B) Antheprot
C) BLAST
D) Predict7
2. By dot matrix analysis it is possible to detect:
A) the greek keys and beta barrels
B) the dissulfide bridges topology
C) the hairpins and helical bundles
D) the insertions/deletions and repeated sequence segments
3. The amino acids that stabilize alpha-helical structure are:
A) L, V and I
B) G, E and Y
C) S, R and L
D) W, E and F
4. CD (circular dichroism) spectra are used to predict
A) amino acid sequence
B) secondary structures contribition
C) protein concentration in the sample solution
D) amino acid composition
5. The low expect value in BLAST package means that: ???
A) compared sequences are long
B) sequence identity/similarity is low
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C) compared sequences are short
D) sequence identity/similarity is high
6. Amino acid is:
A) an organic compound containing amino group and carboxyl goup
B) an organic compound containing amino group and acidic goup
C) an organic compound containing alpha amino group and alpha acidic goup
D) an organic compound containing alpha amino group and alpha carboxyl goup
7. The protein primary structure is:
A) amino acid composition
B) amino acid sequence and disulfide bridges topology
C) amino acid sequence
D) sequence (distribution) of helices, beta-chains and turns
8. The CPK protein visualization shows:
A) secondary structure of the protein chain
B) all atoms of the molecule with considering their Van der Waals radii
C) all atoms of the molecule and the chemical bonds between them
D) the protein backbone folding
9. The protein surface can be visualized by:
A) WebLab Viewer Lite and VMD
B) VMD and Rasmol
C) Rasmol and WebLab Viewer Lite
D) only Rasmol
10. The program BLAST gets the data about the proteins from:
A) protein sequences databases
B) protein sequence databases and Protein Data Bank
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C) Protein Data Bank
D) only from UniProt database
11. In CPK representation the hydrogen atoms are marked as:
A) white
B) blue
C) red
D) yellow
12. The program HCA Plot is used for:
A) analysis of the antigenic properties of a protein
B) drawing the hydrophobicity and hydrophilicity profiles
C) protein hydrophobic cluster location and analysis
D) protein sequence multiple alignment
13. The bundle structure is composed by:
A) four beta chains
B) the turns as the only regular structures
C) four helices
D) two helices and two beta chains
14. Helical wheel can be drawn and analysed with the aid of the program:
A) HCA Plot
B) BLAST
C) Antheprot
D) Predict7
15. The amino acids that can strongly destabilize alpha-helical structure are:
A) P, S and G
B) W, E and F
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C) S, R and L
D) G, E and Y
16. In peptide bond formation there are involved:
A) 4 atoms
B) 6 atoms
C) 2 atoms
D) 3 atoms
17. X-ray crystallography provides the data
A) about the amino acid composition of the protein
B) about only one possible structure of the protein
C) about many possible structures of the protein
D) about the amino acid sequence of the protein
18. The replication and transcription repressor proteins have usually the structure of:
A) greek key
B) helical bundle
C) hairpin
D) beta-barrel
19. Protein secondary structure can be predicted with the aid of the programs:
A) ClustalX, Predict 7 and Antheprot
B) HCA Plot, WebLab Viewer Lite and Antheprot
C) Predict7, HCA Plot and BLAST
D) Antheprot, Protein Sequence Analyzer and Predict 7
20. Hairpin structure is composed of:
A) four helices
B) two turns and one helix
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C) two beta-chains and one helix
D) two helices and one turn
21. Many disulfide bridges can:
A) cause the insertion/deletion in the protein sequence
B) change the amino acid sequence
C) destabilize the regular helical structure
D) destabilize the primary structure of a protein
22. Helical bundle is composed of:
A) two helices and one turn
B) four helices
C) two turns and two helices
D) two beta-chains and two helices
23. Protein secondary structure can be predicted by four independent methods with the
aid of the program:
A) Predict 7
B) Antheprot
C) ClustalX
D) HCA Plot
24. Alpha helix is mainly stabilized by:
A) hydrogen bonds in amino acid 1-5 hyrdophobic pairs
B) hydrogen bonds between peptide bonds, amino acid 1-5 hydrophobic pairs and disulfide
bridges
C) hydrogen bonds between every four peptide bonds and amino acid 1-5 hydrophobic pairs
D) dissulfide bridges and amino acid 1-5 hydrophobic pairs
25. The protein tertiary structure can be visualized by:
A) VMD, Predict7 and WebLab Viewer Lite
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B) Rasmol, VMD and HCA Plot
C) Antheprot, HCA Plot and Predict7
D) WebLab Viewer Lite, Rasmol and VMD
26. In CPK representation the sulphur atoms are marked as:
A) yellow
B) red
C) white
D) green
27. Disulfide bridges play very important role in stabilization of a protein:
A) supersecondary and domain structure
B) tertiary and quarternary structure
C) primary and tertiary structure
D) secondary and supersecondary structure
28. The Van der Walls surface representation of a molecule shows:
A) the possible molecular dynamics of the protein
B) the single molecule shape in water solution
C) the single molecule shape in any solution
D) the single molecule shape in vacuum
29. The most preferred secondary structure in a protein is
A) beta-chain
B) alpha-helix
C) random coil
D) turn
30. By dot matrix (dot plot) procedure it is NOT possible to identify:
A) deletions/insertions in the compared sequences
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B) secondary structure of the protein chain
C) the repeated sequence resulting from gene duplication/multiplication
D) putative homology of the compared sequences
31. The examples of domain structure (motifs) are:
A) hairpin and helical bundle
B) beta-sheet and greek key
C) greek key and beta-sandwich
D) beta-chain and hairpin
32. Atoms involved in peptide bond formation are situated: ???
A) semitetrahedrally
B) tetrahedrally
C) planary
D) trigonally
33. The main experimental methods of protein teriary structure analysis are:
A) Circular dichroism spectrophotometry and X-ray diffraction
B) X-ray diffraction and NMR analysis
C) High performance liquid chromatography and circular dichroism spectrophotometry
D) UV spectrophotometry and NMR analysis
34. Transmembrane proteins which for the transmembrane channels often contain
structural motifs of:
A) beta-barrels
B) hairpins
C) helical bundles
D) greek keys
35. The acidic amino acids OR their amide derivatives have the symbols:
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A) Q and N
B) E and D
C) E, D, Q and N
D) B and Z
36. The minimum input data to run the Swiss Modeller is:
A) amino acid sequence and the topology of disulfide bridges
B) amino acid sequence
C) amino acid composition
D) amino acid composition and secondary structure
37. The estimated radius of a water molecule in protein surface modeling in water solution
is: ???
A) 2 Angstroms
B) 1 Angstrom
C) 1.2 Angstroms
D) 1.4 Angstroms
38. Beta-chain is stabilized by the interaction between side chains of the amino acids which
make a pair:
A) 1-3
B) 1-5
C) 1-2
D) 1-4
39. Dot matrix (dot plot) is the graphical representation of the comparison of:
A) only multiple sequences
B) two sequences or more
C) not more than two different sequences
D) exactly two different sequences
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40. The examples of supersecondary structure are:
A) hairpin and helical bundle
B) beta-sheet and greek key
C) greek key and beta-barrel
D) beta-chain and hairpin
41. One periodical turn of alpha-helix contains:
A) 6 amino acid residues
B) 4 amino acid residues
C) 3.6 amino acid residues
D) 3.2 amino acid residues
42. Swiss Modeller is a program to:
A) analyse hydropathy profile of a protein
B) analyse the hydrophobic clusters in a protein
C) predict the tertiary structure of a protein
D) analyse the protein-protein interactions
43. Antigenic determinants (epitopes) can be localized with the aid of the program:
A) WebLab Viewer Lite
B) Antheprot
C) Predict7
D) BLAST
44. Dot plot application is available in:
A) Predict7
B) BLAST
C) HCA Plot
D) Antheprot
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45. According to Creighton's classiffication there are:
A) 3 structural levels of the proteins
B) 4 structural levels of the proteins
C) 2 structural levels of the proteins
D) 6 structural levels of the proteins
46. Immunoglobulins contain structural motifs known as:
A) helical bundles
B) hairpins
C) beta-barrels
D) greek keys
47. UniProt, TrEMBL and PDB are the names of: ???
A) biological databases
B) bioinformatics online services
C) software
D) the stochastic matrices of the amino acid replacements in homologous proteins
48. Tryptophane often forms antihelical hydrophobic pair and cannot stabilize alpha-helix
because of its:
A) flexibility
B) big size
C) amphipatic properties
D) charge
49. ExPASy is:
A) a database of protein sequences
B) a bioinformatics software
C) Swiss service of bioinformatics resources and tools
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D) a database of protein structures
50. In CPK representation the carbon atoms are marked as:
A) gray
B) white
C) blue
D) green
51. Which sentence is true?
A) All proteins have dissulfide bridges
B) Proteins that do not have cysteines, do not have tertiary structure
C) Dissulfide bridges topology describe the protein tertiary structure
D) Some proteins do not have quarternary structure
52. The amino acid which is a specific helix destabilizer is:
A) P
B) W
C) G
D) S
53. In CPK representation the nitrogen atoms are marked as:
A) blue
B) red
C) yellow
D) white
54. The Markov model is:
A) the theoretical model of the changes independent on the past occurences
B) the program for protein structure prediction
C) an approach of analysis the genetic relations between amino acids
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D) the model of dissulfide bridges topologies
55. In CPK representation the oxygen atoms are marked as:
A) blue
B) white
C) red
D) yellow
56. The peptide bond is planar because of: ???
A) aromatic character
B) the delocalized electron pair
C) the planar character of every C-N bond
D) the same reasons as in the amide group
57. The shortest possible alpha-helical fragment in a protein consists of: ???
A) 10 amino acid residues
B) 4 amino acid residues
C) 8 amino acid residues
D) 6 amino acid residues
58. Proteins are biologically active because they are:
A) flexible
B) destroyed at high temperature
C) antigenic agents
D) large molecules
59. The alpha-helical fragment must contain:
A) at least two overlapping hydrophobic pairs 1-5
B) at least four overlapping hydrophobic pairs 1-5
C) at least six overlapping hydrophobic pairs 1-5
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D) at least eight overlapping hydrophobic pairs 1-5
60. NMR studies provide the data
A) about only one possible structure of the protein
B) about many possible structures of the protein
C) about the amino acid sequence of the protein
D) about the amino acid composition of the protein
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