BIOCHEM!!!!
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.
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.
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
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.
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 DNAbinding 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 DNAbinding 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.
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
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 isTRUE?
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.
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.