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VERSION 11 Page 1 of 24

1D 2D 3E 4E 5C 6A 7C 8B 9C 10CE 11B 12B 13D 14E 15D 16C 17C 18A 19D 20A 21D 22B 23E 24C 25C 26E 27A 28B 29B 30D 31A 32D 33B 34C 35D 36C 37C 38A 39A 40ABCDE 41B 42D 43B 44E 45B 46D 47B 48ABCDE 49A 50C 51B 52D 53E 54B 55C 56D 57D 58C 59C 60E 61C 62A 63E 64D 65E 1. Which of the following statements concerning proteins is CORRECT?

a. Proteins cannot be composed of multiple polypeptides. b. Alpha helical structures are stabilized by hydrogen bonding between the carbonyl

oxygen and the amide hydrogen of amino acids on adjacent strands. c. Formation of a peptide bond is via a hydrolysis reaction. d. In parallel beta sheets, adjacent protein chains run in the same orientation. e. Covalent bonds can be created from Van der Waals forces.

2. What is the CORRECT order of events during DNA replication on the lagging

strand?

(1) RNA primer synthesized by DNA primase. (2) Separation of double-stranded DNA by helicase. (3) Exonucleolytic proofreading by DNA polymerase. (4) Excision of RNA, replaced by DNA. (5) Nick sealing. (6) Formation of a new phosphodiester bond by DNA polymerase. (7) Binding of single-strand DNA binding proteins.

a. 2, 1, 7, 6, 3, 5, 4 b. 2, 1, 6, 3, 4, 7, 5 c. 1, 2, 7, 6, 3, 4, 5 d. 2, 1, 7, 6, 3, 4, 5 e. 2, 1, 4, 7, 6, 3, 5

3. Which statement is FALSE concerning mechanisms that ensure accuracy during

translation?

a. As it escorts an incoming aminoacyl tRNA to the ribosome, EF-Tu checks whether the tRNA-amino acid match is correct.

b. At the A-site, if the codon-anticodon match between the tRNA and mRNA template is correct, EF-Tu dissociates from the tRNA.

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c. Aminoacyl tRNA’s are in a bent conformation when bound to the GTP-form of EF-Tu, which does not allow for incorporation of the amino acid into the growing polypeptide chain.

d. At the A-site, rRNA in the small subunit of the ribosome forms a series of hydrogen bonds with the codon-anticodon pair between the incoming tRNA, and the mRNA template to determine if the basepairing is correct.

e. Incorrectly matched tRNA’s at the A-site whose anti-codon/codon interactions are weaker tend to dissociate more slowly from the mRNA template than those which are correctly basepaired.

4. Which of the following statements concerning hemoglobin is FALSE?

a. The same mutation causing sickle cell anemia is thought to be advantageous (in heterozygotes) against malaria infection.

b. Each subunit of hemoglobin contains a heme group in the site that binds O2. c. The disease sickle cell anemia is the result of a point mutation in the hemoglobin

gene. d. Hemoglobin is composed of 4 subunits. e. None of the above.

5. Which of the following statements concerning the ribosome is FALSE?

a. The ribosome is composed of a large and a small subunit. b. The ribosome is composed of 2/3rds RNA and 1/3rd protein. c. Ribosomal proteins are generally located in the interior, and rRNA’s on the

exterior of the ribosome. d. The secondary structure of 23S rRNA is composed of 6 domains. e. The entire 3D conformation of the large and small subunits have been

determined. 6. Which is NOT an example of splice site mutations causing abnormal processing of

the beta-globin primary RNA transcript in humans with the disease beta-thalassemia?

a. Mutations that cause exon rearrangements due to translational shifting of cryptic

splice sites. b. Mutations that cause exon skipping due to destruction of a splice site. c. Mutations that cause incorporation of new exons by the creation of new splice

sites. d. Mutations that cause extensions of exons due to activation of cryptic splice sites. e. None of the above.

7. What is TRUE concerning protein folding?

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a. Protein folding only occurs after the polypeptide has dissociated from the ribosome.

b. The molten globule state does not have any of the secondary structures contained in the final tertiary protein structure.

c. Molecular chaperones help proteins fold correctly. d. Heat shock proteins tend to have an affinity for exposed hydrophilic patches on

incompletely folded proteins. e. None of the above.

8. Which statement is FALSE concerning the processing and export of mature mRNA’s from the nucleus?

a. Nuclear pore complexes are aqueous channels through the nuclear membrane

connecting nucleoplasm and cytosol through which successfully processed mRNA’s are exported.

b. Improperly processed mRNA’s are retained in the nucleus where they are degraded in nuclear endosomes.

c. Properly processed mRNA molecules can be distinguished by the lack of any proteins involved in processing, such as snRNP’s.

d. Properly processed mRNA molecules have acquired cap-binding complexes, exon junction complexes, and poly-A-binding proteins.

e. Initiation factors for protein synthesis do not associate with mRNA’s until after they are exported from the nucleus.

9. This question refers to transcriptional activation of a target gene by the estrogen receptor. Place the following transcriptional activation events in the correct order:

(1) Recognition of the TATA promoter element by TFIID. (2) Estradiol stabilizes the interaction between the estrogen receptor and the ERE. (3) The interactions between core histones and promoter DNA are loosened. (4) Recruitment of histone modifying enzymes. (5) Phosphorylation of the C-terminal domain of RNA Polymerase II by TFIIH. (6) Recruitment of RNA Polymerase II to the promoter.

a. 2, 3, 4, 1, 6, 5 b. 3, 1, 2, 4, 5, 6 c. 2, 4, 3, 1, 6, 5 d. 1, 2, 3, 4, 5, 6 e. 1, 2, 4, 3, 6, 5

10. In an experiment, the gene encoding the lac repressor protein was mutated so that it encoded an abnormal repressor. The abnormal repressor was able to bind to the

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lac operator both in the presence or in the absence of allolactose. What effect would you expect to see in bacteria carrying this mutation?

a. The bacteria would have difficulty growing in medium containing only glucose. b. The lac operon would be induced in medium containing lactose but no glucose. c. The CAP binding protein would bind to the CAP binding site when glucose was

absent. d. In glucose and lactose, β-galactosidase levels would be higher than normal. e. RNA polymerase would not be able to bind to the lac promoter.

11. A researcher isolated mRNA from 2 different cell types (hair follicle stem cells and neural stem cells). The two transcriptomes were compared using the microarray technique. The following graph summarizes the microarray data:

Which of the following statements is NOT a valid conclusion based on the data shown in this graph?

a. There are fewer “gene 1” transcripts in neural stem cells than in hair follicle stem

cells. b. “Gene 3” is expressed at a significantly higher level in hair follicle stem cells than

in neural stem cells. c. Varying the expression level of “gene 2” potentially affects the developmental

fate of stem cells. d. “Gene 3” could be a housekeeping gene such as TFIID. e. The difference in transcript abundance for “gene 2” in these 2 cell types is

statistically significant.

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12. Which of the following would NOT be observed when normal bacteria are grown in medium containing only lactose as a carbon source?

a. CAP protein would be bound to CAP binding site. b. The cAMP concentration in the cell would be low. c. Lac permease concentration would be at a high level. d. Allolactose would induce transcription of the lac operon. e. The lac repressor would not be bound to the lac operator.

13. Which of the following is NOT a true statement about chromatin?

a. The positive charge of histones partially neutralizes the negative charge of DNA. b. Heterochromatin is observed in interphase and tends to be transcriptionally

inactive. c. Nucleosome structure is stabilized by hydrogen bonding between histones and

DNA. d. Adjacent nucleosomes in euchromatin are tightly packed to prevent access of

basal transcription factors to DNA. e. A nucleosome core consists of 8 core histone proteins and approximately 147

base pairs of DNA. 14. In a region of chromatin containing “gene X”, H3 N-terminal tails have been

covalently modified as shown in the figure below. Which of the following statements about the effects of these modifications is NOT true?

a. It is more likely that RNA polymerase II will be recruited to the promoter of gene

X. b. Covalent modification of lysine residues has reduced the positive charge of the

H3 tail. c. It is likely that the chromatin in this region exists as euchromatin. d. A code “reader-writer” complex likely transferred these modifications to adjacent

nucleosomes. e. A histone kinase code “writer” was recruited to gene X by a gene regulatory

protein.

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15. If the antibody used in a chromatin immunoprecipitation (ChIP) experiment recognized the glucocorticoid receptor, and the cells had been stimulated with cortisol, which of the following components would NOT be expected in the results of the ChIP analysis? a. H2A b. Histone acetyltransferase (HAT) c. Glucocorticoid response element (GRE) d. Hsp90 e. TFIID

16. You would like to identify all of the possible protein targets of a specific E3 ubiquitin ligase. Which of the following techniques would provide this information?

a. Chromatin immunoprecipitation b. 2-dimensional polyacrylamide gel electrophoresis c. Yeast 2-hybrid assay d. Western blot e. Electrophoretic mobility shift assay

17. You would like to observe the sub-cellular localization of the p53 protein (a tumor

suppressor protein) in live cells. To do this, you decide to make a transgenic mouse. What pieces of DNA should you ligate together to form the transgene that will be injected into a mouse zygote?

a. The gene-specific control region of the p53 gene, a basal promoter, and the

protein-coding region of the GFP gene. b. A basal promoter, the protein-coding region of the p53 gene, and the protein-

coding region of the GFP gene. c. The gene-specific control region of the p53, a basal promoter, the protein-coding

region of the p53 gene, and the protein-coding region of the GFP reporter gene. d. The gene-specific control region of the p53 gene, a basal promoter, and the

protein-coding region of the p53 gene. e. The gene-specific control region of the GFP gene, a basal promoter, and the

protein-coding region of the p53 gene. 18. What is the purpose of the GAL4 sequence included in the “bait” construct in the

yeast two-hybrid system? a. To bind to the UAS sequence of the reporter gene. b. To select for yeast that contain the reporter plasmid. c. To provide a site for RNA polymerase II to bind. d. To stimulate transcription of the reporter gene.

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e. To select for yeast that contain the bait and prey plasmids. 19. Transcriptional control of the Tryptophan (Trp) operon in E. coli is an example of

which class of gene regulation?

a. Positive regulation with an inactivating ligand. b. Negative regulation with a de-repressing ligand. c. Negative regulation with an inactivating ligand. d. Negative regulation with a co-repressing ligand. e. Positive regulation with a co-activating ligand.

20. A researcher uses a binding site selection assay to identify the consensus DNA

sequence of the estrogen response element (ERE). The researcher then uses a BLAST search to identify a list of genes that are responsive to estrogen. Which of the following is not a concern with this method?

a. Only the ERE sequences within 500 base pairs of the basal promoter of a gene

are likely to be functional as transcriptional regulatory elements. b. Some genes on the list could be due to random chance occurrence of the

consensus sequence in the genome. c. Deletion analysis should be performed to test whether each predicted ERE is

necessary. d. The list of genes could be incomplete because of nucleotide sequence variation

in the consensus ERE. e. Sufficiency of each predicted ERE should be tested with a gain-of-function

experiment.

21. You extract nucleic acids from embryonic hindlimbs and forelimbs in order to investigate Tbx4 expression in the embryo. Using a radioactively labeled DNA probe that can hybridize with both Tbx4 RNA and DNA, you perform a Southern blot and a northern blot. For the northern blot, you also perform an α-Tubulin (α-Tub) loading control. The results are illustrated below. From the following list, choose the possible explanation that is NOT supported by these results:

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a. The Tbx4 gene is present in cells of the forelimb and hindlimb. b. A microRNA gene with sequence complementarity to Tbx4 mRNA is transcribed

in forelimb cells but not hindlimb cells. c. In the hindlimb, two Tbx4 transcripts are present because of alternative splicing. d. Tbx4 transcripts exist in the forelimb, but you used the promoter sequence from

the Tbx4 gene for your probe instead of the coding region. e. In forelimb cells, the region of DNA including the Tbx4 gene contains methylated

CG dinucleotides. 22. A researcher obtains a set of target DNA sequences using a binding site selection

assay. However, the sequences appear random and cannot be aligned to define a consensus binding site. Which one of the following is a possible explanation for this result?

a. The antibody did not cross react with any proteins in the mixture containing

proteins and their bound DNA. b. The radioactive DNA that migrated farthest toward the positive electrode of the

gel was excised and cloned. c. The researcher forgot to add formaldehyde prior to lysing the cells. d. The PCR reaction at the end of the procedure failed. e. The protein that is precipitated by the antibody is not selective in the DNA

sequences it binds. 23. Which of the following statements does NOT accurately complete the following

sentence? X-chromosome inactivation:

a. involves a repressive chromatin state that can be passed on to daughter cells epigenetically.

b. involves specific covalent modifications to both the core histones and the DNA itself.

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c. is a dosage compensation mechanism in females that ensures that genes from

only one X chromosome are expressed. d. originates at the X-inactivation centre (XIC), which seeds and facilitates the

spread of heterochromatin over the length of the chromosome. e. involves the synthesis of XIST proteins that coat the inactive X-chromosome and

promote the formation of heterochromatin. 24. Which of the following statements about packaging the bacterial genome into the

bacterial cell is TRUE? a. Negatively charged polyamines neutralize the positive charge of the DNA. b. Polyamines and other small proteins form nucleoids along the length of the

DNA. c. The circular chromosome is condensed by DNA supercoiling. d. Operons are regulated in part by chromatin state. e. The genome is packaged into a 30nm structure.

25. Which of the following statements about packaging the human genome into chromatin is NOT true?

a. ATP-dependent chromatin remodeling complexes can slide nucleosomes along

the DNA. b. Active and inactive genes tend to occupy discrete territories within the interphase

nucleus. c. A nucleosome consists of an octameric histone core and 147 nucleotides of

DNA. d. Relatively unstructured N-terminal tails of histones protrude from nucleosomes. e. Histone H1 and the positive charges of core histones are important to stabilize

chromatin structures. 26. In a microarray experiment, red and green fluorescent dyes were used to label the

mRNA populations isolated from two different eukaryotic cell types. mRNA from neurons was labeled red and mRNA from epithelial cells was labeled green. The two labeled mRNA populations were mixed and hybridized to a single microarray chip. Which of the following is true of the data obtained from DNA microarray analysis?

a. Microarray spots that appear green indicate that the gene had equivalent

transcript abundance in the two RNA populations. b. The proteomes of the two cell populations can be inferred from the microarray

data.

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c. The microarray analysis will likely reveal that the transcriptome is static and

identical in the two cell types. d. Genes with increased transcript abundance in epithelial cells relative to neural

cells could be recognized by their red fluorescence on the chip. e. This technique can potentially monitor differences in the level of mRNA

corresponding to every gene in the genome.

27. Which of the following statements about the histone code is NOT true?

a. Specific lysine residues can be monoacetylated, diacetylated or triacetylated. b. Specific serine residues are targets of histone kinases. c. Specific lysine residues can be either acetylated or methylated, but not both. d. All of the core histones contain lysine residues that are targets for acetylation. e. Both the globular domain and N-terminal tails of core histones are targets for

covalent modifications.

The following figure represents a pair of silver-stained 2-dimensional gels. For simplicity, most of the proteome is not illustrated. For the 2D gel on the left, proteins were isolated from a tumor cell line, and for the 2D gel on the right, the proteins were isolated form a normal control cell line. Use this figure to answer the following two questions.

28. Which of the following is NOT a valid conclusion based on the 2D gel on the left.

a. Proteins were separated by isoelectric focusing in dimension 1. b. Protein Y migrated toward the positive pole in both dimensions 1 and 2. c. Protein X has a higher molecular weight than protein Y.

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d. At low pH, protein Y is more positively charged than protein X. e. In dimension 2, negatively charged SDS molecules caused protein Y to unfold.

29. Which of the following possibilities is NOT supported by the 2D gels shown above?

a. Protein Z is poly-ubiquitinated in normal cells, but not tumor cells. b. Protein Z is sequestered in the cytoplasm of normal cells by Hsp90, but its

conformation allows nuclear import in tumor cells. c. The mRNA encoding protein Z forms a stem loop in its 3’ UTR that is recognized

by nuclear retention proteins, and this stem loop is cleaved in tumor cells. d. A micro-RNA that represses translation of Z in normal cells is not expressed in

tumor cells. e. In normal cells, the poly-A tail of the mRNA encoding gene Z has been removed

by endonucleolytic cleavage. 30. Which of the following potential targets for mutation are LEAST likely to alter the

phenotype of a cell, tissue or organism?

a. Nucleotide substitution in the splicing branch point of an intron. b. Single nucleotide insertion in the protein coding region. c. Nucleotide substitution in a consensus transcription factor binding site that

changes one of the invariant bases. d. Nucleotide substitution in the DNA linking the basal promoter and the gene

regulatory region. e. Deletion of a nearby chromatin barrier sequence.

31. A grad student makes a new antibody by expressing a protein kinase in E.coli,

purifying the protein, and injecting this antigen into a rabbit. The grad student performs a western blot on proteins isolated from cultured neural cells using the new antibody for the first time. The grad student identified three proteins with different molecular weights that were clearly labeled on the western blot. Which of the following explanations for this result is NOT possible?

a. The protein kinase mRNA was the target of a small interfering RNA. b. The antigen recognized by the primary antibody is not specific to the protein

kinase. c. Post-translational modifications of the protein kinase affect its migration in the

polyacrylamide gel. d. The new antibody was not tested using immunoprecipitation.

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e. Various isoforms of the protein kinase are formed by alternative splicing. 32. A scientist is characterizing chromatin organization from a novel organism from outer

space. From the following list of results from the alien, choose the item that is the most similar to the majority of eukaryotes on earth.

a. The alien genome is condensed approximately 1000-fold through the action of

topoisomerases. b. The alien nuclosome core is an octamer comprising pairs of histones H1, H2,

H3A and H3B. c. Wrapping of alien DNA 1.7 times around the histone core is stabilized by 142

covalent bonds between the DNA and histone core proteins. d. Some alien histone core proteins can be covalently modified on their N-terminal

or C-terminal tails. e. Acetylation of alien DNA is associated with a euchromatic chromatin state.

33. You are analyzing the differences and similarities between chromatin isolated from a

euchromatic region of an active X-chromosome compared to a heterochromatic region of an inactivated X-chromosome. Both X chromosomes are from a female mammal. Which of the following would you NOT expect to observe?

a. Chromatin from the inactive X-chromosome contains hypoacetylated core

histone H3 and H4 tails. b. The X-inactivation center (XIC) of the inactive X-chromosome is transcriptionally

repressed. c. Chromatin from the inactive X-chromosome contains XIST RNA. d. Methylated DNA was isolated from chromatin from the inactive X-chromosome. e. A specific Lysine residue is methylated in the tail of core histone H3 isolated from

the inactive X-chromosome. 34. Which of the following statements is FALSE?

a. The DNA recognition motif of some gene regulatory proteins consists of a beta-

sheet secondary structure that fits into the major groove of the DNA. b. DNA-protein interactions generally consist of about 20 weak interactions that

together ensure specificity and strength of the interaction. c. Gene regulatory proteins “read” the DNA minor groove because it provides the

maximum amount of information from functional groups in the DNA. d. R-groups of gene regulatory proteins interact with hydrogen bond donors and

acceptors, hydrogen atoms, and methyl groups of DNA bases. e. Many gene regulatory proteins recognize DNA as dimers.

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35. A researcher identified a short DNA sequence matching the consensus

glucocorticoid response element (GRE) by in silico analysis. The GRE consensus sequence is located 500 nucleotides upstream of an uncharacterized gene (gene B). Which of the following statements is TRUE?

a. The researcher can conclude that Gene B transcription is activated when the

GRE is bound by a glucocorticoid receptor dimer in the presence of cortisol. b. The DNA region containing the predicted GRE should be deleted from a reporter

transgene to test whether it is sufficient for reporter gene transcription. c. The DNA region containing the predicted GRE should be ligated to a reporter

transgene containing a basal promoter to test whether it is necessary for reporter gene transcription.

d. The DNA region containing the predicted GRE should be used in an electrophoretic mobility shift assay with glucocorticoid receptor proteins that have been treated with cortisol.

e. The predicted GRE is too close to the basal promoter to easily form the DNA loop involved in transcriptional activation.

36. Which of the following statements concerning DNA binding motifs is FALSE?

a. The Trp repressor contains two helix-turn-helix DNA binding motifs that recognize a two segment recognition motif separated by a short nucleotide spacer.

b. A C2H2 zinc-finger motif consists of two Cysteine residues and two Histidine residues coordinated by a single zinc ion.

c. Zinc finger motifs interact with the major groove using specific R-groups from their antiparallel beta sheet.

d. The Helix-loop-helix motif is responsible for both dimerization and DNA binding. e. Leucine zippers consist of two α-helices that each bind to one half of a symmetric

DNA sequence. 37. You want to isolate proteins from a cell lysate that are able to bind to the short DNA

sequence “GGGCCC”. You used a two-step DNA affinity chromatography method, as discussed in lecture. At the end of the protocol, you expected the final eluate to contain proteins that recognized your DNA sequence, but no proteins were present in the final eluate. Why might this be the case?

a. The missing proteins are still bound to the second column because the final

buffer should have been low-salt and you used high-salt instead. b. You conducted the protocol properly, but your DNA fragment contains a

sequence only recognized by a basal transcription factor. c. Your DNA fragment does contain a gene regulatory sequence, but the cells you

used to isolate total cellular proteins did not express the relevant gene regulatory protein.

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d. You conducted the protocol properly, but none of the proteins used at the beginning of the assay are able to bind to DNA.

e. All of the above are correct. 38. Which of the following statements about nuclear import of proteins is FALSE?

a. The hydrolysis of ATP to ADP is part of the cycle related to the transport of

proteins into the nucleus. b. Nuclear localization signals are rich in the positively charged amino acids Lysine

and Arginine. c. Gene regulatory proteins can be sequestered in the cytoplasm by inhibitor

proteins such as Hsp70. d. Cells contain various nuclear import receptor proteins that recognize the nuclear

localization elements of a subset of cargo proteins. e. The nuclear pore complex blocks the passive diffusion of large macromolecules.

39. Which of the following statements about eukaryotic transcriptional activator or

repressor proteins is FALSE?

a. Eukaryotic gene repressor proteins prevent transcription by physically competing with RNA Polymerase for binding to the promoter region.

b. Eukaryotic gene repressor proteins can recruit histone methyltransferase to modify histones.

c. Eukaryotic gene repressor proteins can mask the activation surface of a gene activator protein by direct protein interaction.

d. Eukaryotic gene activator proteins can lead to histone code modifications that recruit TFIID to the basal promoter.

e. Eukaryotic gene activator proteins can recruit histone acetyltransferases to modify histones.

40. Because of its sequence similarity to the fly Eyeless transcription factor, you

hypothesize that the vertebrate Pax-6 protein acts as an eye selector gene (or master control gene) in mice. Assuming your hypothesis is CORRECT, which of the following predictions is TRUE?

a. Deleting the Pax-6 gene from the mouse genome should cause loss of eyes,

since Pax-6 is expected to be necessary for eye development. b. The Pax-6 promoter region should contain regulatory DNA sequences that are

necessary for reporter gene expression in the embryo where eyes will develop. c. Pax-6 protein is expected to be cytoplasmic in the embryonic cells that will

develop into the eyes. d. Expressing the Pax-6 gene in mouse limb buds should cause extra eyes to

develop, since Pax-6 is expected to be sufficient for eye development.

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e. Pax-6 gene regulatory sequences should be sufficient to drive GFP expression from a basal promoter in embryonic eyes.

41. Adding a polyubiquitin chain to a target protein to mark it for proteasomal

degradation is a multi-step process. Which of the following is part of that process?

a. An E2 ubiquitin-activating enzyme primes itself with ubiquitin using energy released by ATP hydrolysis.

b. E1 transfers ubiquitin onto the cysteine side chains of E2 ubiquitin conjugating enzymes.

c. An E2/E3 ubiquitin ligase recognizes an E1 protein and attaches a single ubiquitin molecule to E1.

d. E1 ubiquitin ligase begins a new polyubiquitin chain on the target protein to be degraded.

e. The carboxy terminus of ubiquitin is initially activated though a high-energy phosphodiester linkage to an R-group from the ubiquitin activating enzyme E2.

42. Which of the following is an example of epigenetic inheritance?

a. Gene A has a mutation that changes the amino acid sequence of its nuclear

localization signal. b. Monozygotic twins have the same eye color because they inherited the same

alleles. c. Embryonic stem cells can be forced to differentiate into various cell types by

exposing them to different extracellular signals. d. The promoter region of gene A is methylated, and this methylated state is

maintained in both daughter cells following mitosis. e. Allelic variation can affect phenotype by altering the function of enzymes.

43. Which of the following statements about post-transcriptional regulation of gene

expression is FALSE?

a. In Drosophila females, the Sex-lethal protein blocks a regulated splice site in the transformer mRNA.

b. The poly-A tail of an mRNA can be shortened by a deacetylating nuclease (DAN), increasing mRNA stability.

c. A single transcript can produce two different protein isoforms by skipping an optional exon during splicing.

d. Ribosomes can use different AUG codons in a single mRNA to translate proteins with different N-termini.

e. A sequence in the 3’ untranslated region of some transcripts results in their retention in the nucleus, preventing translation.

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44. The influenza virus has a single-stranded RNA genome. Which tests could be

performed by Health Canada to determine if the flu virus is present in cells isolated from the respiratory tract of a pig that shows flu symptoms?

a. A western blot to detect viral RNA-dependent RNA polymerase. b. A northern blot to detect transcripts encoding viral Hemagglutinin. c. A Southern blot to detect the viral genome after it inserts into a host

chromosome. d. The tests described in a, b, and c would show the presence of the virus. e. The tests described in a and b (i.e. not c) would show the presence of the virus.

45. Which of the following statements regarding dsRNA-mediated gene silencing or

RNA interference is FALSE?

a. The presence of double stranded RNA in a cell recruits a protein complex containing the Dicer RNase enzyme.

b. Perfect base pairing between a micro-RNA and target mRNA is required for translational inhibition and mRNA degradation.

c. The RISC complex uses a single-stranded small interfering RNA to identify and repress target RNAs.

d. Dicer cleaves double stranded RNA into small interfering RNAs that are about 23 nucleotides in length.

e. Small RNA molecules can target DNA methylation to genes in the nucleus and silence transcription.

46. Which of these statements regarding protein folding is FALSE? a. Misfolded proteins can be recognized by the E3 component of ubiquitin ligases. b. Denatured or abnormal proteins are degraded by the proteasome. c. Repeated cycles of Hsp70 binding and release help the target protein to re-fold. d. Incorrectly folded proteins are isolated in the capped hydrophilic barrel of Hsp70

chaperones. e. Refolding of proteins by Hsp60 is an energy-dependent process involving

hydrolysis of ATP.

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47. Which of the following statements concerning the yeast 2-hybrid system is TRUE?

a. The Leu gene encodes an enzyme that acts as a reporter indicating when the

“bait” and “prey” fusion proteins interact and activate transcription. b. If two proteins that normally interact in vivo are unable to enter the nucleus in

yeast cells, this is likely to give rise to a false negative result. c. A false positive result may arise if the prey protein has a transcriptional activation

domain and it does not normally interact with the bait protein in vivo. d. The His gene is used as a reporter gene to indicate the efficiency of

transformation of the “prey” plasmid. e. A Gal4 protein containing a DNA-binding domain and a transcriptional activation

domain is expressed from a plasmid containing the Trp gene as a selectable marker.

48. Which of the following definitions is TRUE?

a. The “proteome” is the entire complement of proteins expressed by a cell, tissue

or organism; proteomes can be characterized with 2D gel electrophoresis. b. The “genome” refers to the complete, unique set of hereditary material in a cell;

genomes can be characterized by whole-genome shotgun sequencing. c. The “metabolome” describes the complete and very dynamic set of small-

molecule metabolites produced by a cell, tissue or organism. d. The “transcriptome” is the complete set of RNA transcripts that can possibly be

expressed in a cell; transcriptomes can be inferred from genome sequences. e. All of the above are correct.

49. You have joined a lab as a new summer research student and have been asked to

purify DNA from D. melanogaster (fruit fly). You decided to use two different protocols that yielded the following results:

• Protocol A gave an A260:A280 ratio of 1.9 • Protocol B gave an A260:A280 ratio of 1.2

Which of the two protocols resulted in a more pure DNA sample (the sample least contaminated with proteins), and according to what you have learned in BIO240, which step may have been used/removed to obtain this result?

a. A chloroform-isoamyl alcohol step was used in Protocol A to yield a purer DNA

sample. b. A chloroform-isoamyl alcohol step was removed in Protocol A to yield a purer

DNA sample.

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c. A chloroform-isoamyl alcohol step was used in Protocol B to yield a purer DNA sample.

d. A chloroform-isoamyl alcohol step was removed in Protocol B to yield a purer DNA sample.

e. An A260:A280 ratio can only be used to determine DNA concentration and cannot be used to determine DNA purity.

50. You need to perform a PCR reaction but realized that you have run out of Taq DNA

polymerase. Out of desperation, you decided to use a different polymerase, Baq DNA polymerase. Baq DNA polymerase functions most efficiently at 78ºC instead of the regular 72ºC for Taq DNA polymerase. Which step(s) of the PCR protocol do you need to change in order for Baq DNA polymerase to function most efficiently?

The temperature(s) of:

a. denaturation needs to be changed to 78ºC. b. annealing needs to be changed to 78ºC. c. extension needs to be changed to 78ºC. d. denaturation and extension need to be changed to 78ºC. e. denaturation and annealing need to be changed to 78ºC.

51. A 21Kb linear piece of DNA was cut with the restriction enzymes BamHI and HindIII alone and in combination, and produced the following fragments. Which of the following is the CORRECT restriction map? BamHI: 6Kb, 7Kb, 8Kb

HindIII: 10Kb, 11Kb BamHI + HindIII: 3Kb, 4Kb, 6Kb, 8Kb

a. 8Kb 4Kb 6Kb 3Kb b.

6Kb 4Kb 3Kb 8Kb c.

3Kb 4Kb 8Kb 6Kb

BamHI BamHI HindIII

BamHI HindIII BamHI

HindIII BamHI HindIII

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d. 6Kb 3Kb 4Kb 8Kb e.

8Kb 3Kb 6Kb 4Kb 52. Which of the following is TRUE?

a. Nucleosides have three major components: a base, a sugar, and a phosphate

group. b. In double stranded DNA there are three hydrogen bonds between the bases,

adenosine and thymine. c. A-DNA is the most common DNA helix structure found in human cells. d. Amphiphilic beta sheets contain sequences of alternating hydrophobic and

hydrophilic amino acids. e. The primary structure of a protein is dictated by the hydrogen and disulfide bonds

between amino acids. 53. Which of the following is true about bioinformatic tools?

a. ClustalW compares one known sequence against a data base of sequences. b. The BLASTn query sequence must be a protein sequence in Fasta format. c. When performing a BLAST search, a subject sequence with a high E value is

desirable. d. BLAST and ClustalW are different graphical user interfaces that were designed

to perform the same bioinformatic task. e. In a BLAST search, the E value of a subject sequence can increase as the size

of the data base increases.

BamHI HindIII BamHI

HindIII BamHI HindIII

Answer Key


54. What is the correct order of DNA isolation steps to be used with wheat germ?

i. Deproteinize DNA ii. Acetylate histones iii. Rupture nuclear envelope and dissociate histone and non-histone proteins iv. Separate nuclei from cellular components v. Rupture cell wall and plasma membrane vi. Chelate divalent cations needed by DNAses vii. Precipitate DNA

a. v, iii, v, iv, ii, vi, vii b. v, iv, iii, vi, i, vii c. iii, v, iv, i, vi, ii, vii d. iii, iv, ii, vi, v, i, vii e. v, i vi, iii, iv, ii, vii

55. Which of the following is TRUE concerning detergents?

a. Detergents are less soluble than lipids in water. b. Detergents are large amphiplastic molecules. c. Their polar ends can be either ionic or non-ionic. d. At high concentrations above a threshold, they form monomeric micelles. e. SDS is an example of a weak uncharged detergent.

56. Which of the following statements regarding A, B and Z-DNA is CORRECT?

a. A-DNA has a right-handed helix formed under high salt conditions. b. The major and minor grooves of all three forms of DNA are identical. c. B-DNA has a right-handed helix formed under dehydrating conditions. d. Z-DNA is characterized by a left-handed helix formed under high salt conditions. e. Z-DNA is a right-handed helix formed when there are many C-G pairs.

57. Loading dye is added to DNA samples before loading the sample onto an agarose

gel. Which of the following is NOT a function of the loading dye?

a. The loading dye makes the sample more dense than the running buffer and thus “pulls” the sample into the wells.

b. The loading dye helps visualize the sample while loading.

Answer Key


c. The loading dye can be used as a reference point while running the gel. d. The loading dye contains ethidium bromide that will enable the nucleic acids to

be visualized with UV light. e. The bromophenol blue in the loading dye will travel towards the positive end of

the gel. 58. The accession number:

a. summarizes the number of occurrences of each base code in the subject sequence.

b. cites all the literature containing data reported in a GenBank entry. c. is the unique and unchanging code assigned to each GenBank entry. d. is dependent on the length of the matched portion of the query sequence. e. changes as newer sequences are added to the PubMed database.

59. Which of the following statements regarding DNA, RNA and protein stabilizing forces

is INCORRECT?

a. Hydrogen bonding stabilizes formation of alpha-helices and B-sheets in proteins. b. DNA and RNA backbones are negatively charged and can form ionic bonds with

positively-charged ions. c. Van der Waals forces are not involved in stacking interactions between DNA and

RNA base pairs. d. Hydrogen bonding occurs between complementary base pairs of DNA double

helices. e. Hydrophobic interactions stabilize DNA, RNA and protein structures because

water forces non-polar surfaces together to minimize their disruptive effects on hydrogen bonding of water.

60. If you were making a 50 µl PCR reaction using 5X PCR buffer, how much PCR

buffer should you add to the tube?

a. 2.5 µl b. 5.0 µl c. 25 µl d. 1 U e. 10 µl

Answer Key


61. There are several reasons for comparing a protein sequence of unknown function with protein sequences of known function. All of the following statements are true EXCEPT:

a. X-ray crystallography has already revealed the structure of many proteins. b. Proteins with the same structure often perform the same biochemical function. c. Discovery of homologous sequences and structures via bioinformatic analysis

means that direct experimentation is unnecessary. d. Predictions of protein structures have been based on data from NMR

spectroscopy and our knowledge of the physical forces that act on atoms. e. Bioinformatic analyses can make the design of experiments on proteins of

unknown function more efficient. 62. A sample of DNA is digested using Xba1 and BamH1. The sample is then run on a

gel along with a molecular weight (MW) ladder. Possible restriction maps using bp units are shown below.

Answer Key


Which of the following restriction maps shown above could represent the DNA sample?

a. 1 and 4 only b. 2 and 3 only c. 4 only d. 3 only e. 1, 2, 3, and 4

Xba

Xba

BamH

500 500 1500

Xba

BamH

1000 500 1500

500

Xba

Xba

BamH

500 500 1000 500

Xba

500 1500

2000bp

1500bp

500 bp

1000 bp

MW Ladder

Sample

500 (1)

(2)

(3)

(4)

Answer Key


63. What mechanism have bacteria evolved to prevent the digestion of their own DNA by restriction nucleases?

a. Bacterial DNA is a single stranded, circular plasmid that is glycosylated at the

restriction sites to prevent cleavage. b. Bacteria produce enzymes that chelate divalent cations that are required for

nuclease activity. c. Bacterial DNA is circular therefore they do not possess the palindromic

sequences recognized by the restriction nucleases. d. Bacteria evolved restriction nucleases that only produce staggered cuts, while

their DNA only has blunt ended recognition sites that are acetylated. e. Bacterial DNA is methylated at or near restriction sites to prevent cleavage.

64. Which of the following statements regarding restriction enzymes used in Lab 5 is

CORRECT?

a. A restriction buffer is used together with the enzyme to provide a chelating medium necessary for optimal nuclease function.

b. The recognition sequences are similar to palindromes because the sequence is the same for the Okazaki fragments used for synthesis of the leading and lagging strands.

c. The CITES database contains a listing of restriction enzyme recognition sites. d. The majority of restriction enzymes recognize either four or six base pair

sequences. e. The restriction enzymes used in Lab 5 are commonly referred to as restriction

exonucleases because they cleave nucleic acids from the ends of DNA. 65. All of the following could affect migration of a nucleic acid fragment within an

agarose gel EXCEPT:

a. Mass of the fragment. b. Percentage agarose in the gel. c. Voltage and/or current used. d. Whether the fragment was single or double-stranded. e. Whether the fragment originated from a prokaryote or a eukaryote.

END OF TEST

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