Bio 3055 Practice Test

Student Number:

Directions: Click in the circle next to the option that BEST answers the question.
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 structure/function relationship?
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 protein.
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 file?
A. Actually hydrogen atoms are usually shown in crystal structures as long as the resolution is a least 5 angstroms.
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 SNP’s 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