Answers: 1A; 2C; 3E; 4E; 5D; 6A; 7B; 8C; 9E; 10A; 11B; 12A; 13E; 14C; 15D; 16B; 17B; 18A; 19D; 20C; 21C; 22A; 23E; 24B; 25B; 26E; 27A; 28D; 29C; 30ABCDE(any); 31DorE; 32A; 33D; 34E; 35E; 36B; 37C; 38C; 39A; 40C; 41E; 42B; 43D; 44B; 45D; 46B; 47D; 48A; 49C; 50C; 51C; 52B; 53B; 54A; 55E; 56C; 57B; 58B; 59C; 60A; 61C; 62B; 63D; 64BorC; 65C; 66B; 67D; 68C; 69A; 70C; 71E; 72B; 73B; 74D; 75E.

Questions 1 through 50 are based on lecture sections I and II: 1. What is the function of the nucleolus?

a) The site where cellular rRNA is made.

b) The site of transcription by RNA polymerase II.

c) The region in prokaryotic cells where DNA is found.

d) The region in eukaryotic cells where simple sequence DNA is found.

e) The region in the eukaryotic nucleus where RNA splicing occurs.

2. DNA is held together by hydrogen bonds, hydrophobic interactions, ionic bonds and van der Waals interactions. What is a van der Waals interaction?

a) A noncovalent bond in which one atom donates and electron to another atom.

b) A covalent bond in which there is a sharing of electrons in the outer shell.

c) A noncovalent bond involving oppositely charge dipoles.

d) An aggregation of nonpolar molecules surrounded by highly ordered water molecules.

e) A covalent bond involving a hydrogen atom and a carbon atom.

3. Which of the following statements describes a SIMILARITY between the structure of

DNA and RNA?

In both DNA and RNA,

a) the nitrogenous base uracil is found.

b) there is a hexose sugar.

c) the carbon 3’ is bound only to hydrogen.

d) the carbon 2’ has an hydroxyl group.

e) the nitrogenous base is attached to carbon 1’.

Continued… Page 1

4. Guanosine

a) is used by DNA polymerase for the synthesis of DNA.

b) consists of guanine, deoxyribose, and one or more phosphates.

c) is used by RNA polymerase in the synthesis of RNA.

d) can also be called guanylate.

e) consists of guanine and ribose.

5. Proteins of interest are frequently tagged with green fluorescent protein. In many cases

addition of GFP does not alter the function of protein of interest. What is the most likely explanation for this observation?

a) GFP consists of a helix-loop-helix motif that binds to DNA when it enters the nucleus.

b) GFP only has primary protein structure, so the tertiary structure of the protein of interest

is not altered.

c) GFP is always attached to the N-terminal end of the protein of interest.

d) Proteins consist of functional and structural domains that fold and function as modular

units.

e) GFP-tagged proteins can be made and can act in living cells.

6. Which of the following concerning DNA replication in prokaryotes is CORRECT?

a) DNA polymerase III moves towards the 5’ end of the template strand.

b) Telomerase is required to add nucleotides to the 3’end of the lagging-strand template.

c) Deoxyribonucleoside monophosphates are used as substrates.

d) The hydrogen on carbon 2’ of deoxyribose reacts with the nucleotide.

e) The synthesis of the leading strand is discontinuous.

Continued… Page 2

7. Which one of the following amino acid sequences is most likely to be found on the

surface of a protein that circulates in the bloodstream?

a) MYAVI

b) KNSKT

c) VFYLE

d) WIIHM

e) FMLLV

8. Which of the following BEST explains the conclusion of the experiment in which cells

where grown in medium containing [3H]-thymidine with high radioactivity and then switched to medium containing [3H]-thymidine with low activity?

a) DNA replication is semi-conservative.

b) DNA replication always starts from the same origin of replication.

c) DNA replication is bidirectional.

d) The chromosomes of E. coli are circular.

e) DNA replication of the lagging strand is discontinuous.

9. What is the percentage of adenines in a piece of RNA if the percentage of cytosine is 30%?

a) 30%

b) 20%

c) 60%

d) 40%

e) Unable to calculate with the information provided.

Continued… Page 3

10. In diagram below illustrating DNA replication which numbers represent the 5’ end of the single-stranded DNA. X = origin of replication.

a) 1, 3, 4

b) 2, 4

c) 3, 4, 5

d) 2, 5

e) 1, 2

11. Which of the following statements concerning the origin of replication in E. coli (oriC) is

CORRECT?

a) DnaA binds to the 13 mers of the oriC causing melting of the 9 mers.

b) There is one oriC found in the E. coli chromosome.

c) The sequence of the oriC is not like sequences found in other bacteria.

d) T antigen binds to the oriC to unwind the DNA.

e) The oriC is a protein that is required to start DNA replication.

Continued… Page 4

12. The following are steps involved in DNA replication of eukaryotic genes. Put the steps in

the CORRECT order.

1) Primase synthesizes primers composed of RNA. 2) MCM helicases unwind double-stranded DNA 3) DNA polymerase α synthesizes DNA. 4) Replication protein A (RPA) proteins bind. 5) Replication factor C (Rpc) binds. 6) T antigen unwinds double-stranded DNA. 7) DNA polymerase δ synthesizes DNA. 8) Ribonuclease I and FENI remove RNA.

a) 2, 4, 1, 3, 5, 7, 8

b) 6, 5, 1, 3, 4, 7, 8

c) 1, 2, 3, 4, 5, 6, 8

d) 2, 5, 1, 7, 4, 3, 8

e) 6, 5, 1, 7, 4, 3, 8

13. Which of the following statements concerning DNA replication in prokaryotes and

eukaryotes is CORRECT?

a) Discontinuous DNA synthesis of the lagging strand occurs in prokaryotes but not in eukaryotes.

b) Single-strand binding protein and replication factor C (Rfc) both bind to single-stranded NA to prevent complementary base pairing. D

c) In both prokaryotes and eukaryotes only one type of DNA polymerase is required to

synthesize the daughter strands.

d) The τ-subunit of DNA polymerase III and PCNA in eukaryotes make DNA polymerase rocessive. p

e) DNA polymerase I in prokaryotes and DNA polymerase δ in eukaryotes fill in the gap

left by removal of RNA.

Continued… Page 5

14. A sequence of an RNA template found in telomerase is: 5’UAGGGUAGGGUAGGG3’

Which diagram represents the correct sequence of one of the ends of a chromosome taken from the same cell as the telomerase? The “---” represents the middle part of the chromosome.

a) --------------------TAGGGTAGGGTAGGG3’

-----------------------ATCCCATCCCATCCC5’

b) -------------------- ATCCCATCCCATCCC 3’

-----------------------TAGGGTAGGGTAGGG 5’

c) -------------------- CCCTACCCTACCCTA3’

----------------------GGGATGGGATGGGAT5’

d) -------------------- GGGATGGGATGGGAT3’

---------------------- CCCTACCCTACCCTA 5’

e) none of the above.

15. Which CORRECT statement can be made concerning DNA replication or transcription

in prokaryotes?

a) A DNA primer is required for DNA replication of the bacterial chromosome.

b) RNA polymerase starts to transcribe from the TAC triplet on the template strand.

c) A helicase is used to unwind DNA into single strands in transcription.

d) A sigma factor directs the core RNA polymerase to the start site of transcription.

e) The entire chromosome is copied in DNA replication and in transcription.

Continued… Page 6

16. You perform a sequencing reaction using the manual Sanger (Dideoxy) chain method. You

have 4 tubes and add ddATP to tube A, ddCTP to tube C, ddGTP to tube G and ddTTP to tube T along with the other reagents. By mistake you also add ddATP to tube C. What would be the pattern on the sequencing gel if the primer used was 5’CTCAGG3’ and the DNA that you sequenced was:

5’CTCAGGTTCAACGT3’ 3’GAGTCCAAGTTGCA5’

17. Which of the following statements is CORRECT?

a) Prokaryotic genomes have lots of spacer DNA.

b) Many genes devoted to a single metabolic pathway are found within complex

transcriptional units in prokaryotes.

c) Once the sequence of the human genome was known the function of all human proteins

became known.

d) Eukaryotic chromosomes consisting of DNA and proteins are circular.

e) Genes in prokaryotes and eukaryotes always code for proteins.

Continued… Page 7

18. Rho-dependent termination of transcription is used to terminate transcription of some prokaryotic genes. What occurs in this process?

a) Rho moves in the 5’ to 3’ direction along the newly formed mRNA.

b) A stem loop forms between C and G bases in the mRNA, followed by a poly U sequence.

c) Rho forms positive supercoils making the DNA hard to transcribe.

d) Rho attaches to the DNA template and rewinds the DNA.

e) A poly U sequence is detected by the rho protein.

19. Which of the following is NOT a function of RNA?

a) It acts a peptidyltransferase during translation.

b) It is required for RNA splicing.

c) It is essential for the structure of ribosomes.

d) It attaches the correct amino acid to tRNA.

e) It recognizes the Shine-Dalgarno sequence.

20. Which reading frame on the following mRNA would code for the longest full-length

peptide?

5’CCUGAUGCAUGCCUAGAUGCCAUAACGGGCUUAAAUAGAUGA3’

a) First.

b) Second.

c) Third.

d) First and second.

e) Second and third.

Continued… Page 8

21. What is the name of the region between the start codon and 5’ end of prokaryotic

mRNA?

The a) 3’ untranslated region.

b) start site for translation.

c) 5’ untranslated region.

d) polyadenylation signal.

e) promoter.

22. Which of the following is required for the initiation of translation in prokaryotes?

a) Hydrolysis of GTP bound to initiation factor 2 (IF2).

b) The addition of a methyl group to the methionine attached to tRNAimet.

c) The Shine Dalgarno sequence base pairs with the 5’ end of the mRNA.

d) The binding of RF1 to the stop codon on the mRNA.

e) f-met- tRNAimet binding to the A site on the ribosome.

23. During the elongation phase of protein synthesis,

a) aminoacyl tRNA synthetase adds the correct amino acids to the tRNA already positioned on the P site.

b) he transfer RNA with an amino acid attached to it is called peptidyl-transfer RNA. t

c) eptidyltransferase activity is found in elongation factors. p

d) the function of EF-G is to help to replace GDP bound to EF-Tu with GTP.

e) EF-Tu bound to GTP brings the aminoacyl-transfer RNA to the A site.

Continued… Page 9

24. Which of the following statements concerning aminoacyl-tRNA synthetase is correct?

a) The activity of these enzymes is enhanced in the presence of EF-Tu.

b) These enzymes have proofreading activity to ensure that the correct amino acid is

attached to tRNA.

c) These enzymes are responsible for removing the polypeptide from the tRNA at the end of

translation.

d) These enzymes also have peptidyltransferase activity and are found in the large subunit

of the ribosome.

e) These enzymes attach amino acids to the C1’ hydroxyl group of the ribose at the 3’ end

of tRNA.

25. What is the most direct technique to determine if cells express RNA that codes for a

specific protein?

a) Purify RNA from the cells, cut the RNA with a restriction enzyme, run the digest on a gel nd look for a band of the appropriate size. a

b) Purify RNA from the cells, run it on a gel, transfer the RNA to a membrane and probe

with DNA complementary to the RNA you are interested in.

c) Purify the specific RNA from the cells and do a polymerase chain reaction with specific primers.

d) Purify RNA from the cells, run it on a gel and look for a band of the appropriate size.

e) Purify DNA from the cells, run it on a gel, do a Southern blot and probe with DNA

complementary to the RNA you are interested in. 26. If the region of DNA immediately upstream from the lac promoter was mutated so that it

catabolite activator protein could not bind, what would you expect to see in bacteria carrying this mutation?

a) Positive regulation of the lac operon would occur normally.

b) The lac repressor in the presence of allolactose would bind to the lac operator.

c) RNA polymerase would not be able to bind to the lac promoter.

d) cAMP concentrations would be low even in the absence of glucose.

e) The bacteria would have difficulty growing in medium containing only lactose.

Continued… Page 10

27. Which of the following would be observed when normal bacteria are grown in medium

containing glucose only?

a) The lac repressor is bound to the lac operator.

b) β-galactosidase concentrations are at maximal levels.

c) Allolactose induces transcription of the lac operon.

d) CAP is bound to the lac promoter.

e) cAMP concentration in the cell in high.

28. You are hired to work in a lab in the summer. Your professor would like you to determine

both where and when a specific protein (protein Y) is expressed in mouse embryos. Which of the following describes the best experiment to determine this information?

a) Attach the protein-coding region of the gene for protein Y in frame with the DNA for

green fluorescent protein and introduce this DNA into fertilized mouse embryos. Look for green fluorescence in mouse embryos at different days of development.

b) Perform an immunoprecipitation followed by a western blot on protein extracts from

whole mouse embryos taken at different days of development.

c) Attach the protein-coding region of the gene for protein Y to the promoter region of green fluorescent protein and introduce the DNA into fertilized mouse embryos. Look for green fluorescence in mouse embryos at different days of development.

d) Attach the promoter and proximal promoter region of the gene for protein Y to the lac Z

gene and introduce the DNA into fertilized mouse embryos. Look for β galactosidase activity by incubating mouse embryos at different days of development in X-gal.

e) Sequence the gene for protein Y and compare the sequence with other genes that are

expressed in the mouse embryo.

29. Why is antibiotic added to agar plates when blue/white selection is used to identify cloning vectors containing the DNA of interest?

a) To inhibit lac repressor binding to the bacterial chromosome and cloning vector.

b) To eliminate the need to add glucose to the culture medium.

c) So that bacteria without cloning vectors will die.

d) To inhibit the expression of the lac repressor so that the α peptide will be produced.

e) Because antibiotics turn blue in the presence of β-galactosidase.

Continued… Page 11

30. Which of the following would be produced upon transcription and translation of the following operon? SD = DNA coding for the Shine Dalgargo sequence.

a) One mRNA with one start codon and one stop codon and 3 polypeptides.

b) One mRNA with three start codons and three stop codons and 3 polypeptides.

c) Three mRNAs each with a start and stop codon and 3 polypeptides.

d) Three mRNAs with one start and one stop codon and 1 polypeptide.

e) None of the above.

31. You have just identified a previously unknown protein, which you call protein A, and you

would like to do an experiment to determine if the intracellular localization of protein A changes upon stimulation of the cell. Which of the following pieces of DNA would you introduce into cells in your experiment?

a) The promoter region of the gene for protein A and the promoter region of gene for green

luorescent protein. f

b) The promoter region of the gene for protein A and the protein-coding region of the gene for green fluorescent protein.

c) The protein-coding region of the gene for protein A and the promoter region of the gene or green fluorescent protein. f

d) The protein-coding region of the gene for protein A ligated in frame with the protein-

coding region of the gene for green fluorescent protein.

e) None of these DNA pieces would be appropriate.

Continued… Page 12

32. You would like to clone a piece of DNA into a plasmid and use blue/white selection to identify bacteria containing a plasmid with an insert. By mistake you used bacteria that have the complete lac operon in their genome. What would you observe the next day?

a) Blue colonies with plasmids containing the DNA insert.

b) White colonies with plasmids containing the DNA insert.

c) White colonies containing plasmids without the DNA insert.

d) Both white and blue colonies on the plate.

e) No colonies on the plate.

33. Why do ribosomes pause at the trp codons in the leader sequence of trp operon mRNA

when trp is low in the culture medium?

a) The levels of aminoacyl-tRNA synthetase are low inside the cell.

b) The trp repressor blocks the movement of the ribosome along the mRNA.

c) The trp leader mRNA forms a stem loop between regions 2 and 3 inhibiting translation.

d) The levels of trp-tRNAtrp are low inside the cell.

e) The trp leader mRNA forms a stem loop between regions 3 and 4 inhibiting translation.

34. What happens when tryptophan levels are high in bacteria?

a) Transcription of the trp operon is prematurely terminated by the binding of rho proteins.

b) The trp repressor dissociates from the trp operator.

c) The trp leader mRNA forms a stem loop between regions 2 and 3.

d) RNA polymerase transcribes the trp operon and dissociates after transcribing the E gene.

e) The leader peptide is synthesized.

Continued… Page 13

35. Which of the following describes a SIMILARITY in the processes that occur during the

polymerase chain reaction and DNA replication?

In both cases, a) deoxyribonucleotides are added to the 3’ end of RNA primers.

b) the double-stranded DNA separates due to the action of helicases.

c) all of the DNA present in the sample or in the cell is copied.

d) polymerization of nucleotides occurs at 95 C.

e) the synthesis of DNA is semi-conservative.

36. Which of the following statements concerning transcription of the pre-rRNA gene in eukaryotes is CORRECT?

a) To make sufficient rRNA, transcription is carried out by all three types of RNA

polymerases.

b) Ribonucleases cleave pre-RNA to produce 18S, 5.8S and 28S.

c) rRNA is translated by ribosomes.

d) The pre-rRNA gene contains introns with GU at the 5’ end and AC at the 3’ end.

e) The pre-rRNA gene contains three open reading frames.

37. The diagram below depicts a simple transcriptional unit with two control regions

labelled “a” and “b” and three exons and two introns. What would happen if a mutation occurred in the middle of intron #2, which introduced a 5’ end of a splice site?

a) This transcriptional unit would not be transcribed.

b) The mRNA that was produced would not bind to the small ribosomal subunit.

c) An mRNA encoding a non-functional protein may be produced.

d) Intron #1 would remain in the mature mRNA.

e) The regulation of transcription termination would be lost.

Continued… Page 14

38. The following is the restriction map of regions of the maternal and paternal chromosomes #1 from an individual. What would be the correct pattern of bands on an autoradiogram if the genomic DNA from this individual was isolated, divided into two tubes, cut with Eco RI and Bam HI, run on a gel and a Southern blot was performed? Note that probe used is complementary to the minisatellite DNA found in the rectangular region drawn on the chromosomes. E = Eco RI and B = Bam HI

39. Eukaryotic primary RNA transcripts undergo cleavage and polyadenylation during the

formation of mRNA. Which statement concerning the process is CORRECT?

a) Polyadenylation is coupled to transcription because factors involved associate with the

CTD domain of RNA polymerase II.

b) Cleavage stimulatory factor (CStF) binds to the AAU AAA site at the 3’ end of the newly

formed primary transcript.

c) Polyadenylation binding protein (PAPB II) adds the poly A tail using a DNA template.

d) Cleavage and polyadenylation specificity factor (CPSF) binds to the GU or U rich region

at the 3’ end of the newly formed primary transcript.

e) Polyadenylated mRNA is more susceptible to degradation than mRNA without a poly A tail.

Continued… Page 15

40. The primary RNA transcript in eukaryotes is spliced. Which of the following statements

concerning this process is CORRECT?

a) The branch A is found in the exon downstream from the intron to be spliced.

b) Exons are removed from the primary transcript to produce mRNA.

c) U2, U5, U6 directly participate in the two transesterification reactions.

d) U1 snRNA forms complementary base pairs with the branch point.

e) The lariat structure that is produced is immediately translated.

41. Which of the following is a feature of chromatin?

a) Moderate digestion of chromatin with DNases yields amino acids and deoxyribonucleotides.

b) DNA that is actively being transcribed exists in cells as heterochromatin.

c) Histones are the only proteins found in chromatin.

d) Chromatin is found in its most condensed form in interphase.

e) Regions of DNA that contain methylated cytosine are less likely to be transcribed.

42. What is meant by the histone code?

It refers to a) the sequence of ribonucleotides that code for each type of histone. b) histone modifications to which specific proteins bind, thereby altering transcription.

c) the high degree of homology between all types of histones.

d) the observation that the genes coding for histones are tandemly repeated genes.

e) the specific sequence of deoxyribonucleotides that code for each type of histone.

43. In yeast transcriptional control, which of the following is observed?

a) Gnc4 recruits Sin3 and Rpd3.

b) Ume6 binds to the UAS sequence.

c) The repressor domain of Ume6 binds to the URS1 sequence.

d) Gnc5 has histone acetylase activity.

e) The UAS sequence is downstream from the TATA box.

Continued… Page 16

44. Which of the following concerning the molecular mechanisms of gene regulation is CORRECT?

a ) SWI/SNF complexes phosphorylate histones to increase the rate of gene transcription.

b) Mediators interact with general transcription factors and transcription factors.

c) SWI/SNF are only involved in the activation of transcription and not in gene repression.

d) Mediators and SWI/SNF complex act independently of one another.

e) Gal4 is an example of a coactivator that possesses enzymes that modify histone residues.

45. What is the purpose of the TRP gene in the hybrid #1 or bait plasmid of the yeast two-hybrid system?

a) To show that there is an interaction between the protein of interest and the protein

xpressed by the “fish” construct. e

b) o ensure that the yeast also have both the fish and the bait plasmid. T

c) To show that there is an interaction between the DNA binding domain of the “bait” construct and the activation domain of the “fish” construct.

d) o ensure that yeast with the plasmid will live in medium without trp. T

e) To bind to the DNA binding domain of the bait fusion protein. 46. What is produced upon transcription and translation of the hybrid #2 or “fish”

construct?

a) A fusion protein of Gal4 with a protein of interest.

b) A fusion protein of the Gal4 activation domain and an unknown protein.

c) A fusion protein of the Gal4 DNA binding domain and Gal4 activation domain.

d) Full-length Gal4 protein.

e) A fusion protein of the Gal4 DNA binding domain and a known protein.

Continued… Page 17

47. In the regulation of gene transcription by glucocorticoids,

a) glucocorticoids increase the transcription of all genes in the cell.

b) receptors for glucocorticoids bind to the TATA box.

c) the GRE (glucocorticoid response element) is a zinc finger protein.

d) CBP possesses histone acetylase activity.

e) hsp90 binds to glucocorticoid receptors in the nucleus to activate transcription.

48. Which of the following concerning in the regulation of gene transcription by thyroid hormones is CORRECT?

a) Thyroid hormone response elements exist as direct repeats.

b) In the presence of thyroid hormone, histone deacetylation is observed.

c) The binding of thyroid hormone to its receptor is required for receptor binding to DNA.

d) The thyroid hormone receptor is a homodimer.

e) The thyroid hormone receptor without bound thyroid hormone associates with hsp90.

49. A scientist would like to determine whether a newly identified protein is a transcription

factor that binds to a UASGAL4 sequence to activate gene transcription. Which of the following procedures would be the first step in the best experiment to investigate this activity? (Assume that the yeast cells have a mutation in the GAL4 gene.)

a) Transform yeast cells with a plasmid containing DNA coding for the transcription factor

and a plasmid containing the UAS GAL4 sequence downstream of DNA coding for β-alactosidase. g

b) Transform yeast cells with a plasmid coding for the DNA binding domain of the

transcription factor and a plasmid containing the UAS GAL4 sequence upstream of DNA oding for β-galactosidase. c

c) Transform yeast cells with a plasmid containing DNA coding for the transcription factor

and a plasmid containing the UAS GAL4 sequence upstream of DNA coding for β-galactosidase.

d) Transform yeast cells with a plasmid containing DNA coding for the promoter region of the transcription factor and a plasmid containing the UAS GAL4 sequence upstream of

NA coding for β-galactosidase. D

e) Transform yeast cells with a plasmid containing DNA coding for Gal4 and a plasmid containing DNA coding for β-galactosidase.

Continued… Page 18

50. In the technique called chromatin immunoprecipitation, chromatin is isolated and

mechanically sheared (broken into pieces), and then incubated with antibodies. The pieces that are bound to antibodies can then be isolated and the DNA contained in the chromatin can be amplified by PCR and then sequenced. If the antibody used in the chromatin immunoprecipitation recognized acetylated histones, which of the following would be observed?

a) The immunoprecipitate contains repressor transcription factors.

b) The immunoprecipitated chromatin would represent the 3’ end of protein-coding genes.

c) Nuclear receptor response elements may be found in the immunoprecipitated DNA.

d) The immunoprecipitated chromatin would be in the most condensed form.

e) DNA sequences representing the control regions of all genes would be detected.

Questions 51 through 75 are based on labs 1 to 6: 51. Which is the best description of the underlying principle behind the DNA and RNA

extraction protocols used in labs 1 and 3?

a) A series of steps designed primarily to protect RNA and DNA from RNAses present within the cell and in the external environment. b) A series of steps designed primarily to take advantage of the different centrifugal

properties of cellular components and molecules in order to separate the target (RNA or DNA) molecules from the non-target (undesired) components.

c) A series of steps designed primarily to take advantage of the different size, stability,

solubility, biochemical and physical characteristics of cellular components and molecules in order to separate the target (RNA or DNA) molecules from the non-target (undesired) components.

d) A series of steps designed primarily to prevent osmotic shock of the cells. e) A series of steps designed primarily to solubilize all of the non-target (undesired) cellular

components simultaneously and leave the target (RNA or DNA) molecules as a pellet in the bottom of the tube.

Continued… Page 19

52. What is the purpose of adding ethanol during DNA isolation?

a) It denatures proteins so that they are not precipitated with DNA at the end. b) It replaces the water molecules near the DNA, and as a result of hydrophobic interactions,

the DNA becomes insoluble in an aqueous solution and can be precipitated c) It maintains the osmotic pressure and pH of the solution. d) It neutralizes the ionic interactions between DNA and histones so the DNA does not

precipitate out of solution with the protein. e) It chelates Mg2+ ions thereby reducing the activity of many nucleases and preventing

DNA degradation. 53. The RNA that you isolated in the lab could have been used in a Northern blot to look for the presence of a specific mRNA transcript. Once the RNA was isolated, what would be the next step in a Northern Blot procedure? a) Cut the RNA with a restriction enzyme b) Run the RNA on an agarose gel c) Transfer the RNA from the gel to a special membrane

d) Isolate RNA and use polymerase chain reaction with appropriate primers to amplify RNA.

e) Incubate the RNA with a DNA probe made from the gene whose expression is being studied

Continued… Page 20

54. The following picture represents the volume setting of a P1000 micropipettor. What volume of fluid will be delivered if the pipettor is used correctly?

0 3 5

a) 350 µl b) 35 µl

c) 3.5 µl d) None, setting the volume as shown will break the pipettor. e) An indeterminate amount since this setting is outside of the range of this pipettor.

55. Which of the following statements concerning the structure of DNA is CORRECT?

a) Thymine is a purine that makes three hydrogen bonds with adenine.

b) The nitrogen 1 of purines is bonded to the carbon 1’ of deoxyribose.

c) The free carbon 3’ end of DNA has a phosphate group attached.

d) Uracil is covalently attached to the carbon 1’ of deoxyribose.

e) Guanine is a purine that makes three hydrogen bonds with cytosine.

56. Which of the following statements describing the function of the chloroform in the chloroform:isoamyl alcohol step during DNA extraction is correct?

a) It prevents osmotic shock and premature lysis of the plasma and nuclear membranes.

b) It chelates Mg2+ thereby reducing the activity of DNAses that degrade DNA.

c) It denatures protein and results in large insoluble aggregates that are not precipitated with DNA. d) It separates the cytoplasm from the nucleus during DNA isolation. e) It reduces the frictional drag of DNA in solution so that the DNA can be spooled onto the

glass rod.

Continued… Page 21

Use the following output to answer questions #57 and #58 1: U10867. Cryptococcus neof...[gi:508700] Links

LOCUS FNACTIN 2274 bp DNA linear PLN 01-FEB-2001 DEFINITION Cryptococcus neoformans var. grubii strain H99 actin gene, complete cds. ACCESSION U10867 VERSION U10867.1 GI:508700 KEYWORDS . SOURCE Cryptococcus neoformans var. grubii ORGANISM Cryptococcus neoformans var. grubii Eukaryota; Fungi; Basidiomycota; Hymenomycetes; Heterobasidiomycetes; Tremellomycetidae; Tremellales;

Tremellaceae;Filobasidiella. REFERENCE 1 (bases 1 to 2274) AUTHORS Cox,G.M., Rude,T.H., Dykstra,C.C. and Perfect,J.R. TITLE The actin gene from Cryptococcus neoformans: structure and phylogenetic analysis JOURNAL J. Med. Vet. Mycol. 33 (4), 261-266 (1995) MEDLINE 96034426 PUBMED 8531025REFERENCE 2 (bases 1 to 2274) AUTHORS Cox,G.M. TITLE Direct Submission JOURNAL Submitted (15-JUN-1994) Gary M. Cox, Medicine/Infectious Diseases, Duke University Medical Center, Durham, NC 22710, USA FEATURES Location/Qualifiers source 1..2274 /organism="Cryptococcus neoformans var. grubii" /mol_type="genomic DNA" /strain="H99" /variety="grubii" /db_xref="taxon:178876" /clone_lib="Crypto1EMBL3"

CDS (887..899,951..1032,1077..1145,1192..1955,2007..2147, 2199..2257) /codon_start=1 /product="actin" /protein_id="AAC49074.1" /db_xref="GI:508701" /translation="MEEEVAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVM VGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEDDP VLLTEAPLNPKQNREKMTQIMFESFNAPAFYVSIQAVLSLYASGRTTGIVLDSGDGVT HTVPIYEGFSLPHAILRIDLAGRDLTDYLVKILMERGYLFTTSAEREIVRDIKEKLCY VALDCEQELQTAAQSSQLEKSYELPDGQVITIGNERFRCPEALFQPSLLGLEAAGIHE TTYNSIMKCDLDIRKDLYGNIVMSGGTTMYNGIADRMQKEITALAPSSMKVKIVSPPE RKYSVWIGGSILASLSTFQQMWIAKSEYDESGPSIVHRKCF" BASE COUNT 488 a 662 c 543 g 581 t

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57. The output above is an example of which of the following? a) BLAST Search b) GenBank Record c) ClustalW Alignment d) PubMed Search Output e) Entrez Search Output 58. Which of the following would NOT be indicated on the output above? a) authors b) BLASTN score c) the length of the nucleotide sequence d) literature reference e) coding regions and introns 59. What would be the best tool to use if you wanted to look for conserved and variable regions in the amino acid sequence of the actin protein of 4 different organisms? a) BLASTN b) Southern c) ClustalW d) Northern e) Entrez

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60. Analysis of your RNA gel with UV light in Laboratory 5 indicated that the 23S rRNA band was almost twice as bright as the 16S rRNA band. Which of the following statements offers the best explanation for this observation? a) 23S rRNA is nearly twice as long as 16S rRNA. b) There are twice as many copies of 23S rRNA compared with 16S rRNA. c) 23S rRNA is less double-stranded than 16S rRNA, therefore it binds much more eithidium bromide d) 23S rRNA is about twice as sensitive to degradation by RNAses compared with 16S rRNA e) 23S rRNA is about twice as sensitive to UV light compared with 16S rRNA 61. Restriction enzymes have been isolated from bacteria, algae, fungi and other organisms and act as a defense system against foreign DNA. How are the genomes of these organisms protected against their own restriction enzymes?

a) The restriction enzymes are produced in the cytoplasm and do not have access to nuclear DNA.

b) The specific sequences recognized by the restriction enzymes are not found in the

genome of the organism.

c) Bases in the DNA of the organisms are methylated and methylated bases are not recognized by the restriction enzymes.

d) DNA in the organisms is packaged with proteins that protect the DNA from cleavage by the restriction enzymes.

e) An inhibitor protein binds to the restriction enzymes keeping the enzyme inactive until it

encounters foreign DNA.

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62. A 17 kb linear piece of DNA was cut with the restriction enzymes EcoRI and BamHI alone and in combination. Which of the following is the CORRECT restriction map given the following results.

EcoRI: 7 Kb, 10 Kb BamHI: 2 Kb, 6 Kb, 9 Kb EcoRI + BamHI: 2 Kb, 5 Kb, 4 Kb, 6 Kb

a) b) c) d) e)

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63. The following peptide is part of a larger protein that folds into two closely linked alpha- helices. What residue must be in the region separating the two helices?

HAVVVLSGPYAAMVTH

a) L

b) S

c) G

d) P

e) A

64. A helix-loop-helix motif is what kind of protein structure? a) primary b) secondary c) tertiary d) quaternary e) supramolecular 65. Which group of amino acids shares a common property?

a) Valine, Asparagine, Glutamic acid.

b) Tryptophan, Phenylalanine, Threonine.

c) Alanine, Valine, Isoleucine.

d) Histidine, Arginine, Methionine.

e) Cysteine, Glutamic acid, Tyrosine.

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66. There is no coding sequence (CDS) for the 16S rRNA gene in E. coli because it is

a) not transcribed.

b) not translated.

c) found only in eukaryotes.

d) rapidly degraded by RNAses.

e) produced as a larger RNA transcript.

67. Which of the following statements concerning the synthesis of 16S, 23S, and 5S rRNA is CORRECT?

a) Transcription of the RNA operon yields a 2:1 ratio of 16S rRNA to 23S rRNA.

b) Three Shine-Dalgarno sequences in each operon direct rRNA synthesis.

c) These rRNAs are the least abundant type of RNA found in the cell.

d) There are several RNA operons in the E. coli genome.

e) The nucleic acid sequences of each of these rRNAs are identical in all species of bacteria.

68. A scientist isolates DNA from a pathogenic bacterium that he would like to identify. He

performs PCR using genomic DNA and primers complementary for a portion of the 16S rRNA gene. What is the purpose of the PCR step?

a) To determine the open reading frame of the 16S rRNA.

b) To make many copies of 16S rRNA so that its function can be tested.

c) To make many copies of the portion of the 16S rRNA gene for subsequent sequencing.

d) To clone the 16S rRNA gene into a plasmid to determine if a mutant protein is produced.

e) To determine the sequence of the portion of the 16S rRNA gene.

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69. The recognition and cleavage site of the restriction enzyme BamHI is commonly shown as (the arrow indicates the cleavage site): 5’-GGATCC-3’ 3’-CCTAGG-5’ Which of the following best describes the characteristics of the BamHI restriction enzyme when used to digest non-methylated DNA? a) An enzyme that has a 6-base recognition site and when used to cut DNA will produce

fragments with sticky ends and a 5’ overhang.

b) An enzyme that has a 6-base recognition site and when used to cut DNA will produce fragments with sticky ends and a 3’ overhang. c) An enzyme that has a 6-base recognition site and when used to cut DNA will produce blunt-ended fragments. d) An enzyme that has a 4-base recognition site and when used to cut DNA will produce fragments with sticky ends and a 5’ overhang. e) None of the above. 70. Which of the following describes a CORRECT relationship that allowed you to determine the size of an unknown fragment of DNA in the restriction enzyme lab?

a) Linear DNA fragments migrate at rates that are proportional to the log10 of their

molecular weights.

b) Linear DNA fragments migrate at rates that are inversely proportional to the percentage of agarose in the gel.

c) Linear DNA fragments migrate at rates that are inversely proportional to the log10 of their

molecular weights.

d) Linear DNA fragments migrate at rates that are proportional to their molecular weights.

e) Linear DNA fragments migrate at rates that are inversely proportional their molecular weights.

71. A Western blot is best described by which of the following statements?

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a) A multi-step method to detect a specific protein in its natural subcellular location. b) A multi-step method using an RNA probe to detect a specific protein in a complex

mixture. c) A multi-step method using a DNA probe to detect the expression of a specific gene in a complex mixture. d) A multi-step method for assaying the expression of a specific gene in its natural subcellular location. e) A multi-step method using 2 different antibodies to detect a specific protein in a complex mixture. 72. When a type of mutant bacteria are grown in medium containing glucose and lactose, the expression of β-galactosidase is greater than normal. What is a possible explanation for this observation?

There may be a a) mutation in the lac repressor which causes it to bind more strongly to the operator.

b) mutation in the lac promoter which converts it from a weak to a strong promoter.

c) defect in the production of cAMP so that less cAMP is made by the mutant bacteria.

d) mutation in the lac repressor so that it is not able to bind to allolactose.

e) mutation in the I gene which causes an increase in the production of the lac repressor.

73. In prokaryotic cells, RNA polymerase binds directly to the promoter. In eukaryotic cells,

what is required for the binding of RNA polymerase II?

a) The binding of T antigen.

b) The binding of a number of general transcription factors.

c) The binding of MCM helicases.

d) A start codon.

e) The phosphorylation of the CTD domain of RNA polymerase II.

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74. PCR reactions were performed to amplify a region of the 16S rRNA gene from a pathogenic bacterium. Which of the following reagents would be found in the negative control tube in addition to buffer, salts, water, Taq polymerase, and forward and reverse primers? a) dNTPs and DNA from the pathogenic bacterium. b) dNTPs and DNA from a normal bacterium. c) dNTPs and RNA from the pathogenic bacterium. d) dNTPs and no DNA from any type of bacterium. e) ddNTPs and DNA from the pathogenic bacterium. 75. Which of the following is NOT a key characteristic of the gene cloning process?

a) The use of restriction enzymes that cleave double-stranded DNA at specific sites b) Analysis of DNA fragment sizes, sequences and the production of restriction maps

c) Preparation of pure samples of DNA

d) Joining of DNA molecules together (ligation)

e) The use of lambda strains containing multiple recognition sequences for every restriction

endonuclease

END OF TEST

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