Bio 3055 Practice Test
|1. Which of the following websites would be best to go to when you
want to do a search for a recent scientific publication, you want to find
a DNA sequence given a gene name or you want to find a protein sequence
given a protein name?
- A. ClustalW
- B. OMIM
- C. KEGG
- D. NCBI
- E. SwissProt
|2. Which of the following programs DO NOT use pdb files to create a
picture of a three-dimensional molecule?
- A. RasMol
- B. Chime
- C. Swiss-PdbViewer/DeepView
- D. Protein Explorer
- E. BLAST
|3.When a nucleotide is changed in a gene, it ____________leads to an
amino acid change in protein encoded by that gene. If two nucleotides are
changed in a gene, it _____________leads to at least one amino acid change
in the protein encoded by that gene. Which of the following is the best
choice for filling in the blanks above?
- A. always, sometimes
- B. sometimes, sometimes
- C. sometimes, always
- D. always, always
- E. never, sometimes
|4. Which of the following statements is true regarding the protein
A. The structure of most
proteins is extremely rigid and cannot tolerate even a small change of one
aspartate for one glutamate residue.
B. Most proteins lose activity
if conservative amino acid changes are made in loop regions.
C. The function of a protein
will change only if the amino acid that is changed is in the active site.
D. Proteins are more likely to
tolerate non-conservative amino acid substitutions in alpha helix regions
than loop regions.
E. Changing just one amino
acid can have effects on protein folding and lead to an unfolded, inactive
|5. To make a muliple sequence alignment, the sequences are saved in FASTA format in a text document, then copy and pasted into what program?
- A. BLAST
- B. ClustalW
- C. PSIPRED
- D. Swiss Pdb Viewer
- E. Sequence Manipulation Site
|6. Which of the following best describes the scoring pattern by homology
search programs such as BLAST?
- A. identical residue = 10 pts, gap = 0 pts
- B. identical residue = 10 pts, conservative substitution = 5 pts, gap = 0 pts
- C. identical residue = 10 pts, conservative substitution = 1 9 pts, gap = - 3 pts
- D. identical residue = 10 pts, conservative subsitution = 1 9 pts, gap = 0 pts
- E. identical residue = 10 pts, conservative substitution = 10 pts, gap = - 3 pts
|7. You have just performed a BLAST search and are analyzing the
results. Which of the following E-values would you choose if you wanted
to select the sequence with the highest homology to your search sequence?
- A. le-90
- B. le-175
- C. 0.0
- D. 0.002
- E. 0.001
|8. The correct FASTA format for a multiple sequence alignment is best explained by which of the following statements:
- A. Use one-letter amino acid code, all capital letters, spaces separating each letter, and a return separating each line. Headings are put in quotation marks.
- B. Use one-letter amino acid code, no spaces between letters, returns separate different sequences and headings. Heading lines are marked with a >.
- C. Use one-letter amino acid code, no spaces between letters, returns separate each line of the sequence. Headings are put in all capital letters, followed by a return.
- D. Use three-letter amino acid code, capitalize the first letter of each amino acid, with a space between each amino acid.
- E. Use one letter amino acid code, put spaces every ten amino acids, put the numbering system above each line of amino acids.
|9. Why are hydrogen atoms not usually part of a crystal structure data
- A. Actually hydrogen atoms are
usually shown in crystal structures as long as the resolution is a least 5
- B. Hydrogen atoms are left
out of the data file to keep the file from getting too large to work with.
- C. Hydrogen atoms don't need
to be part of the data file because the structure-viewing program can
accurately predict where they will be located in the crystal structure and
add them to the structure display.
- D. The resolution of the
crystal structure is usually too low to accurately predict the location of
the hydrogen atoms.
- E. It is assumed that everyone
knows where the hydrogen atoms are.
|10. Which of the following sets of information is NOT usually found in a SwissProt entry?
- A. The three dimensional coordinates for the crystal structure
- B. Tissue and subcellular localization
- C. Amino acids in the active site
- D. Alternate names for the protein
- E. The E.C. number for an enzyme
|11. Which of the following databases would you select for a BLAST search if you would like to obtain the most homologous protein sequence to your search sequence that has its three dimensional structure solved?
- A. nr
- B. swissprot
- C. pdb
- D. month
- E. pat
|12. Which of the these search sites combine the following information for a particular gene: RefSeq files, KEGG links, PubMed articles, OMIM entries, and dbSNP entries?
- A. GenBank
- B. ExPASy
- C. LocusLink
- D. RCSB
- E. PSIPRED
|13. Why is GenBank called a redundant database?
- A. Because it contains two versions of every entry
- B. Because it is saved in multiple locations for safety
- C. Because it contains similar sequences for different organisms
- D. Because it contains a historical record of sequence discoveries which sometimes includes multiple versions of the same sequence
- E. Because it is re-read many times to check for mistakes
|14. RefSeq files are useful to researchers for what reason?
- A. RefSeq files have been editted and contain the most up-to-date sequence information for a particular locus
- B. RefSeq files are editted to contain just the most biologically interesting sequence information
- C. RefSeq files are generated solely by a computer so contain no mistakes
- D. RefSeq files contain sequence information generated only from the Human Genome Project
- E. RefSeq files are the only sequence files that have been obtained experimentally
|15. Approximately how close together should two atoms be in a crystal structure to assume hydrogen bonding?
- A. 0.25 angstroms
- B. 0.5 angstroms
- C. 3 angstroms
- D. 6 angstroms
- E. 20 angstroms
|16. Which of the following BEST describes the KEGG database?
- A. A database of all macromolecular structure files
- B. A database of metabolic pathways
- C. A database of genetic disease genes
- D. A database of phylogenetic trees
- E. A database of enzyme substrates
|17. Which of the following terms describes SNPs that result in an amino acid change in the protein?
- A. synonymous change in the non-coding region
- B. synonymous change in the coding region
- C. non-synonymous change in the non-coding region
- D. non-synonymous change in the coding region
- E. mutation in the promoter region
|18. A conservative mutation means:
- A. An amino acid change in a conserved region of the protein
- B. An amino acid change in a non-conserved region of the protein
- C. An amino acid change from acidic to basic
- D. An amino acid change from hydrophobic to hydrophilic
- E. An amino acid change to an amino acid with similar size and chemical properties
|19. If you were interested in reading a referenced summary about the research done on sickle cell anemia, which website would be best to go to?
- A. KEGG
- B. LocusLink
- C. Sequence Manipulation Site
- D. OMIM
- E. SwissProt