1. Which statement about mitochondria is CORRECT?bio240.chass.utoronto.ca/testExam/pastexams/1st...

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1. Which statement about mitochondria is CORRECT?

a) Mitochondria are passed from fathers to their offspring.

b) Mitochondria have a linear genome.

c) Mitochondria cannot synthesize proteins.

d) Mitochondrial genes do not use the standard eukaryotic genetic code.

e) Mitochondria probably arose from a free living bacteria specialized for life in anaerobic conditions.

2. What is the full length name of AMP?

a) Adenosine monophosphate

b) Adenine monophosphate

c) Adenylate monophosphate

d) Deoxyadenine monophosphate

e) None of the above

3. Which of these sequences is NOT likely to be part of a coiled-coil motif?

a) CPGDMY

b) CWISFPL

c) MHTVLI

d) ARREDK

e) AQTMLI 4. Which of the statements regarding DNA replication is CORRECT?

a) The leading strand is synthesized discontinuously from multiple primers. b) The polymerase enzyme caps the 5’ end of the nascent DNA strand.

c) The polymerase adds nucleotides onto the nascent DNA strand in a hydrolysis

reaction.

d) Okazaki fragments on the lagging strand are composed of a mixture of RNA and DNA.

e) The helicase responsible for unwinding DNA does NOT require ATP.


5. A eukaryotic DNA sequence of unknown origin contains 6 possible reading frames, 3 in the forward direction, and 3 in the reverse direction (on the complementary strand). An open reading frame is defined as the DNA sequence between two stop codons. How would you determine which open reading frame of an unknown eukaryotic DNA sequence codes for a protein?

a) The open reading frame must contain a TATA box.

b) The first codon following the stop codon must be an ATG.

c) The longest open reading frame always codes for a protein.

d) The open reading frame must contain a polyA sequence at the 3’ end.

e) Impossible to tell without additional evidence.

6. Which is a DIFFERENCE in the structure of RNA compared to DNA?

a) Uracil is present in DNA, not RNA.

b) RNA can never be double-stranded like DNA.

c) The base is attached to C1 in RNA, but not in DNA.

d) The 5’ end of RNA has a phosphate group, which is not true of DNA.

e) There is an hydroxyl group attached to the C2 in RNA, but not in DNA.

7. Which of the following statements concerning proteins is CORRECT?

a) Multi-subunit proteins are composed of a single polypeptide. 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 anti-parallel beta sheets, adjacent protein chains run in the same orientation.

e) The primary structure of proteins is determined by the sequence of nucleotides found in the mRNA coding for the protein.


8. What do gaps in a ClustalW alignment represent?

a) One or more sequences may have an insertion relative to the others.

b) One or more sequences may have a deletion relative to the others.

c) One or more sequences may have an intron relative to the others.

d) One or more sequences may have missing data relative to the others.

e) All of the above. 9. You perform a manual sequencing reaction and forget to add the

dideoxyribonucleoside triphosphate ddTTP. When the sequencing reactions are run on a gel, which of the following statements is TRUE?

a) None of the lanes will have bands because the polymerase cannot elongate

without all 4 nucleotides in the reaction mix. b) All of the lanes will have bands, but they will be incorrectly sized. c) The T lane will have no bands.

d) The T lane will have mostly longer fragments.

e) NONE of the above statements is TRUE.

10. Which statement concerning telomeres and telomerases is TRUE?

a) Telomeres are repetitive sequences that occur throughout the chromosome.

b) Telomere sequences tend to be GC-rich.

c) Telomerases use a DNA template to add repetitive sequences to 3’ ends of DNA.

d) It is not possible to regulate telomere length in cells.

e) Telomerases are related in structure and function to reverse transcriptases.


11. Which is NOT a concern of genome sequencing projects?

a) Capillary electrophoresis of sequencing reactions

b) Sequencing errors

c) Assembly of shotgun DNA sequence fragments

d) Gene prediction

e) Detection of radioactively labeled sequences

12. Which is TRUE of RNA transcription and processing?

a) RNA polymerase I transcribes protein-coding genes

b) Bacterial and eukaryotic RNA polymerases are NOT homologous

c) 5’ capping helps protect the ends of bacterial RNA

d) RNA polymerase II is activated by phosphorylation

e) The C-terminal tail of RNA polymerase II is important in proofreading

13. In an experiment that attempts to identify origins of replication in yeast, randomly

selected DNA fragments are introduced into a plasmid that has a selectable marker such as the HIS gene (histidine). Yeast that have plasmids with various DNA fragments introduced are then plated on a selective medium (i.e. without histidine). What would be expected in these experiments?

a) Yeast cells that have plasmids with DNA fragments without putative origins of

replication should grow on media without histidine. b) The strain of yeast used for these experiments should be able to grow in the

absence of histidine.

c) In order to replicate, the plasmids used for these experiments do not need a DNA fragment containing an origin of replication.

d) Yeast cells that have integrated the plasmid into their chromosome will be able to

grow on media without histidine, regardless of whether they have a putative origin of replication or not.

e) Yeast cells must be plated on medium with histidine to determine if they have

plasmids with DNA fragments containing putative origins of replication.


14. The following is a diagram of the replication forks during DNA replication in prokaryotes. What is WRONG with this diagram?

a) The 5’ and 3’ ends of the parental strand are labeled incorrectly.

b) The 5’ and 3’ ends of the Okazaki fragments are labeled incorrectly.

c) Bacterial chromosomes are not circular.

d) The number of replication forks is incorrect for a circular chromosome.

e) The positions of the RNA primers are incorrect.

15. The following is a gel showing the results of manual sequencing. What is the

sequence of the template strand in the 5’ to 3’ direction?

a) 5’ TCGCAAGCTGA 3’

b) 5’ ACGCTTGCAGT 3’

c) 5’ TCAGTTCGCGA 3’

d) 5’ TCAGCTTGCGA 3’

e) None of the above

A C G T - - - - - - - - - - -


Refer to the Codon Table below for Questions 16, 17 & 18

16. Which of the following statements concerning codons is FALSE?

a) Gly is four-fold degenerate. b) A change from a purine to pyrimidine (or vice versa) is required to convert a

codon from Asp to Glu.

c) The minimum number of mutational steps required to change a codon from Phe to Cys is 1.

d) The number of mutational steps required to change from one Ser codon to another

can be as high as 2.

e) The maximum number of mutational steps required to change a codon from Arg to Pro is 2.


17. A student would like to amplify using degenerate primers a gene from a family of sequences shown in the alignment below. The student is working with a species from which this gene has not yet been identified, and needs to design degenerate primers in order to amplify the gene. What region of the gene would be best for designing degenerate primers?

Chicken SPFLVPQTHLGSPGLFRAMAAFMFLLIALGVPINTLTIFCTARFRKLRSHLNYIMVNLALANLLVILVGSTTACYSFS Pigeon GPWDGPQYHIAPPWAFYLQTAFMGIVFAVGTPLNAVVLWVTVRYKRLRQPLNYIMVNISASGFVSCVLSVFVVFVASA Human GPFEGPNYHIAPRWVYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWIMVNLAVADLAETVIASTISIVNQV Macaque GPFEGPNYHIAPRWVYHLTSVWMIFVVIASVFTNGLVLAATMKFKKLRHPLNWIMVNLAVADLAETVIASTISVVNQV Chimp GPWDGPQYHIAPVWAFYLQAAFMGTVFLIGFPLNAMVLVATLRYKKLRQPLNYIMVNVSFGGFLLCIFSVFPVFVASC Xenopus SPFDGPQYHIAPKWAFTLQAIFMGMVFLIGTPLNFIVLLVTIKYKKLRQPLNYIMVNITVGGFLMCIFSIFPVFVSSS Zebrafish SPFLVPQDHLGGSGIFMIMTVFMLFLFIGGTSINVLTIVCTVQYKKLRSHLNYIMVNLAISNLLVSTVGSFTAFVSFL Goldfish SPFEGPQYHLAPKWAFYLQAAFMGFVFFVGTPLNAIVLFVTMKYKKLRQPLNYIMVNISLGGFIFDTFSVSQVFFSAL 1 2 3 4 5

a) 1

b) 2

c) 3

d) 4

e) 5

18. What is the fold degeneracy of a primer constructed for the following amino acid

sequence?

FWCVIM

a) 11-fold degenerate

b) 12-fold degenerate

c) 13-fold degenerate

d) 48-fold degenerate

e) 96-fold degenerate


19. Which of the following statements concerning protein synthesis is CORRECT?

a) A ribosomal protein provides the enzymatic activity of peptidyltransferase.

b) EF-Tu and EF-G are used in eukaryotes.

c) EF-Tu is active when it is bound to GTP.

d) Release factors are a special kind of tRNA that recognizes STOP codons.

e) EF-Tu is involved in the recognition and binding of the START codon.

20. What component is NOT involved in mRNA splicing?

a) snRNPs

b) Consensus sequences at the 5’ and 3’ ends of the intron

c) 2’OH group of the ribose sugar at splice site

d) Spliceosome

e) 28S rRNA


TigerSalRhXenopusRhRanaRh

HumanRhMacaqueRhDogRh

BovineRhRabbitRhMouseRh

RatRhHamstRh

ChickRhGatorRh

AnolisRhZebFishRhGoldfishRh

CarpRhAstyanaxRh

SandGobyRhMBerndtiRh

SkateRhLampreyRh

AnguillaRhCongerEelRh

SeaLampreyRh

21. Given the phylogeny depicted below, which statement concerning the relationships among these gene sequences is TRUE?

a) RanaRh is more closely related to XenopusRh than TigerSalRh.

b) TigerSalRh is more closely related to XenopusRh than RanaRh.

c) TigerSalRh is more closely related to ChickRh than RanaRh.

d) ChickRh is more closely related to HamstRh than AnolisRh.

e) CongelEelRh is more closely related to LampreyRh than SkateRh.


22. A student runs a PCR reaction in an attempt to amplify a gene from the genomic DNA of different vertebrates, and includes a positive control in which a completely unrelated gene is amplified from bacterial plasmid DNA. The following gel is obtained. All of the following are possible explanations for these results EXCEPT:

a) the gene of interest exists in the rabbit, but not the frog.

b) the primers used are not similar enough to the frog gene to amplify it.

c) the PCR conditions used for amplification were suitable for amplifying the rabbit, but not the frog gene.

d) the primers were poorly designed, do not amplify the gene of interest, and the

band in the rabbit lane is a contaminant (or otherwise unrelated gene).

e) the reason for nonamplification in the frog is that the Taq enzyme used in these reactions is too old and did not work.


23. Which of the following sequences would be found in a primary RNA transcript, but NOT in mature mRNA?

a) a poly A sequence

b) a stop codon

c) nucleotides upstream from the start codon

d) several branch-site A residues which form the base of the excised lariat

e) a start codon

24. You are interested in the pattern of expression of a specific gene called gene X in

different tissues from the same organism. You isolate RNA from the tissues, run the samples of the RNA in different lanes on an agarose gel, blot and probe with a radioactive probe complementary to the exon 2 of gene X. When you perform autoradiography on the blot, you find that the lanes each have a band of a different size and some lanes have no bands. What can you conclude with certainty from the results?

a) Gene X is NOT expressed in some tissues.

b) There is alternative splicing of the primary transcript of gene X in different tissues.

c) Within the same tissue, there is alternative splicing of the primary transcript of

gene X. d) Gene X does NOT code for protein.

e) Different introns of gene X are spliced out in different tissues.

25. Which statement concerning DNA replication or transcription in prokaryotes is

CORRECT?

a) Helicases have 6 subunits in order to stabilize single-stranded DNA during replication.

b) A sigma factor directs the DNA polymerase to the origin of replication.

c) RNA polymerase starts to transcribe from the start codon on the template strand.

d) A primer is required for the initiation of transcription.

e) DNA replication of bacterial chromosomes proceeds bidirectionally from one origin of replication.


26. Which of the following phenomena is NEVER associated with changes in chromatin structure?

a) Ubiquitination near the carboxyl termini of histone proteins.

b) Acetylation of leucine residues in the amino termini of histone proteins.

c) Methylation of cytosine residues in CG dimers in the DNA of vertebrates.

d) The subsequent recruitment of components of the general transcriptional machinery, such as TFIID.

e) Recruitment of histone deacetylase by sequence-specific transcriptional

repressors. 27. Which of the following statements is TRUE?

a) Histone proteins are small proteins, rich in leucine and arginine residues. b) The nucleosome is an octamer comprised of two of each of the following proteins:

H1, H2A, H2B and H3.

c) A segment of DNA, 120 nucleotides in length, wraps around each nucleosome.

d) The net result of chromatin formation is that in each mitotic chromosome, DNA is 10000 fold shorter than its extended length.

e) There are 3 million base pairs of DNA in the human genome, which means that

there are approximately 2 metres of DNA contained within the nucleus of a human cell.


28. Which of the following statements is FALSE?

a) Transcriptomics is the study of the transcriptome, and can include experimental approaches such as microarray analysis.

b) When microarrays are used to compare the transcriptome of two cells within the

same individual, many genes in the two cells show equivalence in transcript abundance, and this information is used to establish which genes show statistical differences in transcript abundance.

c) In microarray experiments that use red and green fluorescent dyes to label the two

different RNA populations, spots that appear yellow when the microarray is scanned indicate that the gene had equivalent transcript abundance in the two different RNA populations.

d) A clusterogram is a way of clustering microarray data to indicate which genes

show similar patterns of transcript abundance across multiple conditions.

e) In microarray experiments that use red and green fluorescent dyes to label the two different RNA populations, the scanned microarray reveals absolute levels of transcript abundance.

29. Which of the following statements is TRUE?

a) Sequence-specific DNA-binding proteins always bind to the minor groove in the DNA double helix.

b) The minor groove presents four different configurations of hydrogen-bond donor,

hydrogen-bond acceptor, hydrogen atom and methyl group; whereas, the major groove presents two.

c) Some gene regulatory proteins have DNA-binding motifs that are spaced by

3.4nm, as this places the motifs on the same side of the double helix.

d) Amino acids like asparagine and arginine can not participate in the interaction between proteins and DNA because of their charge.

e) Rigidity in the DNA molecule prevents conformational change when DNA-

binding proteins bind to DNA.


30. Through promoter (gene regulatory sequence) deletion analysis, it was found that deletion of a region of DNA resulted in the loss of gene expression. When this region was fused to a minimal promoter and a reporter gene, and the entire construct introduced by genetic engineering back into the same organism, there was no expression of the reporter gene. These experiments:

a) show that the region of DNA is unnecessary and sufficient for gene expression.

b) show that the region of DNA is unnecessary and insufficient for gene expression.

c) show that the region of DNA is necessary and insufficient for gene expression.

d) show that the region of DNA is necessary and sufficient for gene expression.

e) reveal nothing about the DNA sequence.

31. What does NOT happen in a binding site selection assay between a DNA-binding protein and DNA? a) Increasing concentrations of unlabelled competitor DNA are added to examine the

specificity of the interaction. b) The process starts by allowing a protein to interact with a pool of random

oligonucleotides that have been radioactively labelled.

c) Shifted bands are excised from the gel and the DNA used as template in a PCR reaction.

d) Following the final round of selection, the DNA is cloned into plasmids and the

inserts from many plasmids are sequenced.

e) The binding site is enriched in each round of selection, ultimately revealing the subset of DNA sites that the protein is most likely to bind.


32. In order to examine when the Arabidopsis thaliana gene encoding PHYTOCHROME A is expressed, you decide to use a reporter gene approach using GFP. In order to accomplish this, you need to genetically engineer Arabidopsis plants so that they contain a construct comprised of:

a) the protein coding sequence for the gene encoding PHYTOCHROME A fused to

the protein coding sequence for GFP. b) the gene regulatory region for the gene encoding PHYTOCHROME A fused to

the protein coding sequence for GFP.

c) the gene regulatory region for the gene encoding PHYTOCHROME A fused to the minimal promoter for GFP.

d) the protein coding sequence for the gene encoding PHYTOCHROME A fused to

the gene regulatory region for GFP.

e) the gene regulatory region for the gene encoding PHYTOCHROME A fused to the gene regulatory region for GFP.

33. When there is a high concentration of tryptophan, the following will occur at the E. coli trp operon: a) The RNA for trpC alone will be produced.

b) The trp repressor is unable to bind to the operator site.

c) RNA polymerase binds to the promoter, and transcribes genes in the trp operon.

d) Enzymes made by the trp operon will break down tryptophan.

e) Tryptophan functions as a co-repressing ligand that will be bound by the trp repressor.

34. A mutation in the lac operator sequence prevents the lac repressor from binding. What would you expect to see in bacteria harbouring this mutation?

a) The bacteria would have difficulty growing in media containing only lactose.

b) In the presence of glucose and lactose, the polycistronic message for the lac operon would accumulate to its maximum level.

c) The catabolite activator protein would no longer be able to bind.

d) cAMP levels would be constitutively high.

e) When both glucose and lactose are absent, lac permease activity would be higher in the mutant than in normal bacteria.


35. Which of the following statements do NOT account for the differences in complexity between eukaryotic transcriptional regulation and bacterial transcriptional regulation?

i. Eukaryotic DNA is packaged into chromatin.

ii. Eukaryotic RNA Polymerase II cannot activate transcription on its own.

iii. Eukaryotic Shine-Dalgarno sequences generate complex patterns of transcriptional regulation.

iv. Eukaryotic gene regulatory proteins act at a distance.

v. Eukaryotic gene regulatory proteins are not regulated by ligand binding.

a) i, ii, iii

b) ii, iv

c) iii, v

d) i, ii, iv

e) ii

36. Which of the following statements is FALSE?

a) Eukaryotic transcriptional activator proteins tend to be modular in structure, comprised of a DNA binding domain and an RNA polymerase domain.

b) Eukaryotic transcriptional activator proteins have only weak, non-specific

interactions with RNA polymerase.

c) Eukaryotic transcriptional activator proteins associate with a complex of proteins known as the mediator complex.

d) Eukaryotic transcriptional activator proteins working together tend to give rise to

transcriptional synergy.

e) Eukaryotic transcriptional activator proteins can compete for DNA binding sites with transcriptional repressor proteins.


37. What is the CORRECT order for the following steps in the Chromatin Immunoprecipitation Assay?

i. Break formaldehyde linkages.

ii. Cross-link proteins to DNA using formaldehyde.

iii. Break DNA into small fragments.

iv. Sequence DNA.

v. Precipitate transcription factor-DNA complexes using antibodies raised against the transcription factor.

vi. Lyse cells.

a) vi, ii, v, i, iii, iv

b) vi, ii, v, iii, i, iv

c) ii, vi, iii, v, i, iv

d) vi, ii, iii, v, i, iv

e) ii, vi, v, iii, i, iv

38. Which of the following statements about the bacterial ntrC gene product is TRUE?

a) NtrC is the third component of the trp polycistron.

b) NtrC is a galactose permease.

c) NtrC expression is controlled by a combination of the concentration of cAMP and lactose.

d) NtrC activates gene expression from a distance, involving the conversion of ATP

to ADP.

e) NtrC provides an example of a protein activity that is common in all bacterial cells.

39. Which of the following is NOT a feature of phytochrome?

a) Phytochrome is photointerconvertible between two stable forms.

b) Phytochrome is transported to the cytoplasm in the light.

c) Phytochrome contains a linear tetrapyrole chromophore.

d) Phytochrome functions as a homodimer.

e) Phytochrome has been shown to directly regulate gene expression.


40. What statement CORRECTLY completes the following sentence? The plant COP1 protein:

a) is found in the endoplasmic reticulum throughout growth and development.

b) directly activates genes that cause a plant to undergo skotomorphogenesis.

c) acts in the nucleus when the plant is in the light.

d) forms a heterodimer with phytochrome to activate genes involved in photomorphogenesis when the plant is in the light.

e) represses genes involved in photomorphogenesis when the plant is in the dark.

41. Which of the following ARE features of X chromosome inactivation?

i. XIST RNA induces heterochromatin formation.

ii. Hyperacetylation of histones associated with the X chromosome.

iii. DNA methylation of the X chromosome.

iv. Formation of Barr bodies in mammalian males, ensuring dosage compensation.

v. Seeding of euchromatin formation by the X-inactivation centre.

vi. Translation of XIST RNA into a DNA methylase.

a) i, ii, iv

b) i, ii, iii, v, vi

c) ii, iii, v

d) i, iii

e) ii, iii, vi

42. Which of the following statements about DNA methylation in vertebrates is TRUE?

a) Specific CG dinucleotides are methylated at the cytosine position.

b) Specific CC dinucleotides are methylated at the first cytosine position.

c) Specific CG dinucleotides are methylated at the cysteine position.

d) DNA methylation silences genes by inducing euchromatin formation.

e) DNA methylation locks genes in an epigenetic state that is always stably inherited from one generation of organisms to the next generation of organisms.


43. Which of the following statements about the 3’ end of mRNA is FALSE?

a) Cleavage of the 3’ UTR of the mouse CTN-RNA is important for the transit of the mRNA out of the cytoplasm and into the nucleus at times of stress.

b) The 3’ UTR can be important for localisation of the mRNA to specific regions of

the cell.

c) Proteins that bind to the 3’ UTR can negatively regulate translation.

d) A deadenylating nuclease can shorten the 3’ end of the mRNA by degrading the RNA in the 3’ to 5’ direction.

e) In most instances, the translation machinery requires the 3’ end of RNA to initiate

translation via interactions between poly-A binding proteins and eIF-4G.

44. A siRNA from humans was found and characterised. When the siRNA was

introduced as double-stranded RNA (dsRNA) back into an undifferentiated human cell line, the cells differentiated into blood cells. A siRNA with a different sequence did not have this effect; cells remained undifferentiated when dsRNA corresponding to this second siRNA was introduced into the cell line in an independent experiment. Together, these results indicate that: a) the second siRNA is not a good control for this experiment. b) the first siRNA activates a gene that is itself an activator of blood cell

differentiation.

c) the first siRNA represses a gene that is itself a repressor of blood cell differentiation.

d) the second siRNA competes with the first siRNA to regulate blood cell

differentiation.

e) the RISC is not involved in the recognition of the second siRNA to cause DNA methylation.

45. The gene cI of the bacteriophage lambda was mutated so that its gene product was no longer able to bind to DNA. What would you expect?

a) The helix-loop-helix domain of the cro protein would no longer bind to its target

DNA. b) The bacteriophage would not be able to sustain the lytic state.

c) The bacteria would always be in the lysogenic state.

d) The cI gene would always be turned off by the cro protein.

e) The cro protein would not be produced.


46. Which of the following statements about the synthesis of double-stranded cDNA in vitro is TRUE?

a) cDNA is made by the activity of an RNA-dependent RNA polymerase. b) The synthesis of the second strand takes place after the degradation of the original

RNA template by RNAse H.

c) The enzyme that is used to synthesise the first strand of the cDNA is derived from the bacterial virus, bacteriophage lambda.

d) The first strand of the cDNA is primed by a polyA primer that binds to the 3’ end

of the RNA template.

e) The first strand of the cDNA is primed by a polyT primer that binds to the 5’ end of the RNA template.

47. At the end of a western blot experiment, you detect two bands on the membrane. Why might this be?

a) The RNA in the sample contained two transcripts that hybridise with your probe.

b) The protein was able to bind to the DNA probe as a monomer or a dimer.

c) There are always two bands, which correspond to the two most prominent sizes of ribosomal RNA.

d) One band represents only the primary antibody, the other band represents only the

secondary antibody.

e) The primary antibody detected two very similar proteins; for example, the same protein with and without a post-translational modification.

48. Which of the following statements CORRECTLY completes the following phrase? During the process of ubiquitination (ubiquitylation), a) the carboxy terminus of ubiquitin is initially activated through a high-energy

thioester linkage to a cysteine side chain of the ubiquitin activating enzyme, E1. b) E1 and E2 proteins together form the ubiquitin ligase complex that binds to a

degradation signal on the target protein.

c) the amino terminus of ubiquitin is initially activated through a high-energy thioester linkage to a cysteine side chain of the ubiquitin activating enzyme, E1.

d) E2 and E3 proteins together form the ubiquitin activating enzyme that transfers

ubiquitin to E1 ligase before E1 ligase binds to the degradation signal on the target protein.

e) the carboxy terminus of ubiquitin is initially activated through a high-energy

thioester linkage to a cysteine side chain of the ubiquitin activating enzyme, E3.


49. In the yeast two-hybrid assay, what is the role of the GAL4 gene?

a) The GAL4 gene provides the upstream activating sequences that allow the expression of the LEU gene when the “bait” and “prey” fusion proteins have interacted.

b) The GAL4 gene is included on the bait plasmid as a selectable marker, as the yeast

strain that is used is gal-.

c) The GAL4 gene provides the coding sequences for the GAL4 protein DNA-binding domain that comprise part of the “bait” fusion protein, and the coding sequences for the GAL4 protein transcriptional activation domain that comprise part of the “prey” fusion protein.

d) The GAL4 gene encodes an enzyme that is a reporter that indicates when the

“bait” and “prey” fusion proteins have interacted and activated transcription.

e) The GAL4 gene is used to indicate the extent of transformation efficiency when the yeast strain has been transformed with the bait plasmid.

50. Which of the following statements is TRUE?

a) Gregor Mendel proved that a mutation in a DNA sequence encoding a starch biosynthetic enzyme caused the wrinkly pea phenotype.

b) The analysis of SNPs in humans suggests that, on average, there is one nucleotide

difference between the genomes of individuals every 100 000 bp.

c) Pelagibacter ubique is an ocean microbe that has the largest microbial genome.

d) Scientists now think that it will be possible to create a functional synthetic genome that has as few as 300 genes.

e) The only problem in creating Jurassic Park would be purifying enough dinosaur

DNA for PCR.


51. You have isolated a bacterium that is incapable of growing in medium lacking tryptophan. You hypothesize that there is a mutation in the trp operator sequence so that the trp repressor protein binds abnormally. Which of the following experiments would BEST confirm whether or not your hypothesis is correct?

a) Perform a luciferase assay to determine the activity of the tryptophan repressor.

b) Sequence the operator from your bacterium, perform a BLAST analysis, and

perform an EMSA (Gel-Mobility Shift Assay).

c) Perform a northern blot to determine the expression of tryptophan.

d) Create a recombinant bacterium containing the sequence for a trp repressor-GFP fusion protein and see whether GFP is detected in the nucleus.

e) Sequence the repressor protein from your bacterium, perform a BLAST analysis, and perform an EMSA (Gel-Mobility Shift Assay).

52. When using the P1000 micropipette to transfer 250µl of 20% SDS, the reading

on the pipette will be:

a)

b)

c) d) e)

2 5 0

0 2 50

0 2 5

2 5

µl

0 250 0


53. In the DNA Extraction Lab, which of the following statements BEST describes the purpose of NP40 and SDS?

a) NP40 disrupts bacterial chromosomes and SDS disrupts the cell wall. b) NP40 denatures histones and SDS disrupts the nuclear membrane.

c) NP40 disrupts chromatin structures and SDS disrupts the cell membrane. d) NP40 disrupts the nuclear membrane and denatures histones; SDS disrupts the

cell membrane.

e) NP40 disrupts the cell membrane; SDS disrupts the nuclear membrane and denatures histones.

54. Which of the following oligonucleotides will dissociate at the lowest

temperature?

a) ACGTACGTACGT TGCATGCATGCA b) TGCGACGCTGAG ACGCTGCGACTC c) ACTGCTGGACCT TGACGACCTGGA d) TGCATGCATGCA ACGTACGTACGT e) AATGCTTACTGTA TTACGAATGACAT

55. Assume that the following polypeptide forms an alpha helix. How many

COMPLETE turns would occur in the alpha helix of the following polypeptide? VAL-GLU-ALA-ALA-LYS-ASN-ALA-LEU-LYS-HIS-VAL-LEU-GLU-ALA-VAL-PRO-VAL-ASN

a) 3

b) 2

c) 6

d) 4

e) 5


56. Tris-EDTA (TE) is used to dissolve the RNA pellet before running the RNA on a gel. Which of the following is the BEST reason for using TE in the RNA lab?

a) Tris is a better solvent for RNA than DNA, so only the RNA is isolated.

b) TE is soluble in water and causes SDS-bound molecules to precipitate, further purifying the RNA.

c) Under alkaline conditions, Tris lyses any remaining membranes and organelles.

d) EDTA binds to loading dye and prevents the RNA from floating out of the well.

e) EDTA chelates Mg2+, thereby inactivating RNAses. 57. Ribosomal RNA is transcribed from multiple copies of a specific operon in

prokaryotes. Which of the following is the CORRECT order in descending size of the transcripts from that operon (from largest to smallest):

a) 16S rRNA 23S rRNA 5S rRNA tRNA

b) 23S rRNA 16S rRNA mRNA 5S rRNA tRNA

c) 23S rRNA 16S rRNA 5S rRNA tRNA

d) 16S rRNA 23S rRNA mRNA 5S rRNA tRNA

e) tRNA 16S rRNA 23S rRNA mRNA 5S rRNA


58. A 34kb linear piece of DNA was cut with the following restriction enzymes HindIII and BamH1.

HindIII: 14Kb, 20Kb BamHI: 4Kb, 12Kb, 18Kb HindIII + BamH1: 4Kb, 10Kb, 8Kb, 12Kb

Which of the following is the CORRECT restriction map?

BamHI HindIII BamHI

a) | | | 10Kb 12Kb 4Kb 8Kb

HindIII BamHI BamHI

b) | | | 12Kb 2Kb 8Kb 12Kb

BamHI BamHI HindIII

c) | | | 4Kb 10Kb 12Kb 8Kb

BamHI HindIII BamHI

d) | | | 4Kb 10Kb 8Kb 12Kb

HindIII BamHI HindIII

e) | | | 4Kb 10Kb 8Kb 12Kb

59. Which of the following would you add to a tube containing bacterial DNA if you

wanted to make many copies of a portion of the 16S rRNA gene using PCR?

a) dNTPs, lysozyme, buffer with Mg2+, RNA primers, and water

b) dNTPs, DNA polymerase, buffer with Mg2+, DNA primers, and water

c) ddNTPs, DNA polymerase, buffer with Mg2+, DNA primers, and water

d) dNTPs, DNA polymerase, buffer with Mg2+, RNA primers, and water

e) dNTPs, reverse transcriptase, buffer with Mg2+, DNA primers, and water


60. What is the BEST way to determine the size of a particular transcript in a specific cell type?

a) Perform a microarray analysis.

b) Perform a luciferase assay.

c) Perform a Northern blot.

d) Perform a Gel-Mobility Shift Assay (or EMSA)

e) Perform a Chromatin Immunoprecipitation assay.

61. In Lab 1 you decide to do a chloroform-isoamyl alcohol extraction. You decide to

repeat the chloroform-isoamyl alcohol extraction a total of 2 times on your wheat germ sample. Which of the following is most likely to be TRUE?

a) Your DNA will have less protein contamination than if you had only extracted

once with chloroform-isoamyl alcohol. b) Your DNA will have less salt contamination than if you had only extracted once

with chloroform-isoamyl alcohol.

c) The DNA will be more difficult to precipitate.

d) You will need to increase the volume of nuclear isolation buffer used.

e) You will need to add more NaCl. 62. You have just made two cDNA libraries from two different cell types within the

same individual organism. You have sequenced all the DNA of the clones in both libraries. Which of the following would be an EXPECTED result?

a) All sequences in both libraries should be identical.

b) Promoter sequences are common in both libraries.

c) The majority of clones contain coding sequences.

d) The majority of clones contain many intron sequences.

e) The majority of clones contain PolyU sequences.


63. From the following list, choose the CORRECT steps in the CORRECT order that you would perform them if you were going to do a Gel-Mobility Shift Assay (EMSA).

1. Restriction enzyme digest of genomic DNA.

2. Perform agarose gel electrophoresis.

3. Autoradiography.

4. Radioactive DNA fragments are mixed with proteins extracted from cells.

5. Add luciferin.

6. Short DNA fragments of specific length and sequence are synthesized and radioactively labelled.

7. Clone fragment into plasmid vector.

8. Polyacrylamide gel electrophoresis.

9. Agarose gel electophoresis.

10. Transfer fragments onto a nitrocellulose membrane and hybridise with probe.

a) 1, 2, 7, 9, 3

b) 6, 2, 7, 10, 3

c) 7, 8, 5, 3

d) 6, 4, 8, 3

e) 1, 7, 8, 10 64. When studying the three-dimensional structure of proteins, why is it necessary

to crystallize proteins prior to applying a beam of X-rays?

a) Single molecules of protein would not scatter enough X-rays to detect diffraction spots.

b) Protein crystals have a regular structure allowing all X-rays to pass through to the

detector without interference.

c) X-rays have a very short wavelength and will not pass through liquid protein samples.

d) Crystalline proteins emit more radiation and nuclear magnetic resonance, thereby

causing a spectral shift so that the distance between atoms can be determined. e) The synchrotron used to produce high energy X-rays would become plugged if

liquid protein samples were used.


65. The recognition sequence and cleavage site of the restriction enzyme Sal I is commonly shown as (the arrow indicates the cleavage site):

5’-GTCGAC-3’

Which of the following best describes the characteristics of the Sal I restriction enzyme when used to digest non-methylated DNA?

a) An enzyme that recognizes a 6-base sequence and when used to cut DNA will

produce fragments with sticky ends and a 3’ overhang. b) An enzyme that recognizes a 6-base sequence and when used to cut DNA will

produce fragments with blunt ends. c) An enzyme that recognizes a 5-base sequence and when used to cut DNA will

produce fragments with sticky ends and a 5’ overhang. d) An enzyme that recognizes a 6-base sequence and when used to cut DNA will

produce fragments with sticky ends and a 5’ overhang. e) An enzyme that recognizes a 5-base sequence and when used to cut DNA will

produce fragments with blunt ends.

66. In the “Virtual Bacterial ID lab” pre-lab preparation for Lab 4, you extracted bacterial DNA, used PCR to amplify the 16S rRNA gene sequence, and then purified the PCR product. You then performed PCR a second time using the purified PCR product as a template. Which of the following is a CORRECT reason for the second PCR step in the “Virtual Bacterial ID lab”?

a) You needed to make sure you had enough DNA to clone, so you performed the

PCR twice. b) You needed to use PCR the second time so that you could sequence the gene

using the chain termination method.

c) Some bacteria don’t grow well in culture, so you needed to use PCR twice to make more bacterial clones.

d) You needed to use PCR the second time so that you could sequence the gene

using the chemical degradation method.

e) Some primers do not anneal very well to the target, and a second PCR step is required to make sure that enough primer annealed to the target so that the hybridisation product can be detected.


67. Which of the following DO NOT contribute to the conformation or shape of proteins?

a) Disulfide bonds

b) Hydrophobic interactions

c) Hydrogen bonds

d) Phosphodiester bonds

e) Ionic bonds

68. Which of the following is the BEST description of the purpose of adding 5M

NaCl during the DNA purification lab?

a) To minimize fluctuations in pH so that nucleases do not degrade the DNA. b) To prevent premature lysis of the plasma membrane or nuclear envelope as a

result of osmotic shock.

c) To disrupt the ionic bonds between the negatively-charged DNA strands so that they do not attract each other.

d) To cause histones to dissassociate from DNA, thereby preventing the DNA from

precipitating out of solution with the protein. e) To react with potassium acetate, thereby causing all protein molecules previously

bound to sodium dodecyl sulphate to precipitate out of solution. 69. If you wanted to make a 1.5% agarose gel to use for electrophoresis of your

DNA from Lab 1, how much agarose would you add to 60 mL of TBE?

a) 1.5 g

b) 0.9 g

c) 0.15 g

d) 0.4 g

e) 90 mg


70. In Lab 4, you discovered that your bestrophin sequence had 5 transmembrane domains. What was the COMMON characteristic of the side chains of the majority of amino acids found within these transmembrane domains?

a) negatively charged

b) uncharged polar

c) positively charged

d) non polar

e) hydrophilic 71. Suppose that you want to compare your bestrophin amino acid sequence with

bestrophin sequences from other organisms to see how much variation there is in the amino acid sequence at the carboxy terminal end of the protein. Which of the following is the BEST way to do this?

a) Do a BlastN using your amino acid sequence, copy the sequences with the highest

Blast Scores and lowest E-values, and do a ClustalW alignment with all sequences including yours.

b) Do a BlastN using your amino acid sequence, copy the sequences with the highest

E-values, and do a ClustalW alignment with all sequences including yours.

c) Do a BlastP using your amino acid sequence, copy the sequences with the highest Blast Scores, and do a ClustalW alignment with all sequences including yours.

d) Do a BlastN using your amino acid sequence, copy the sequences with the highest

E-values, and do a ClustalW alignment with all sequences including yours. e) Do a BlastP using your amino acid sequence, copy the sequences with the highest

Blast Scores and lowest E-values, and do a ClustalW alignment with all sequences including yours.

72. Which of the following statements concerning the E-value is CORRECT?

a) The E-value is not related to the size of the database and therefore, for a given

sequence, will not change as sequences are added to the database. b) The higher the E-value, the more significant the Score. c) The E-value tells you the number of matches with Scores equivalent to or better

than a given Score that could occur in a database search by chance. d) The E-value is completely independent from the Score and is calculated using

probabilities. e) The E-value tells you the expected Score that could occur when searching a

database of a given size.

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73. You have discovered a new bacterial gene that plays a role in causing a rare skin disease in humans. Your lab has been given a new strain of bacterium isolated from a patient showing symptoms similar to patients with the rare skin disease. You have decided to do a Southern blot to see whether the new bacterial strain contains the new gene. What would be the best POSITIVE control for your Southern Blot?

a) A sample containing water only.

b) A DNA extract from a bacterium that you know contains the gene of interest.

c) An RNA extract from a bacterium that also causes the rare skin disease.

d) A sample containing only purified 16S rRNA gene sequences from a bacterium that contains the gene of interest.

e) A sample containing the purified protein from a recombinant bacterium that

contains the new gene. 74. You have digested a plasmid with EcoRI and expect to obtain fragments 5000 bp,

3000 bp, and 2000 bp in length. You want to clone the 2000 bp fragment into another vector and to be able to do this you need to obtain 1 µg of the desired 2000 bp fragment. Given that you will be using plasmid DNA at a concentration of 0.5 µg/µl, how many µl of plasmid DNA should you add to your EcoRI digest?

a) 2 µl

b) 5 µl

c) 10 µl

d) 4 µl

e) 8 µl

75. Which of the following amino acids contains an SH group in its side chain?

a) H

b) S

c) K

d) Y

e) C

END OF TEST

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