L211 Final

the list of events below describes intron removal and splicing during pre-mrna processing. what is the order that the events occur. 1. attachment of snRNP U1 to the 5' splice site 2. U1 and U4 snRNPs released 3. attachment of snRNP U2 to branch point 4. transesterification reactions at the branch point adenine 5. splicing together of exons, release of lariat structure

1, 3, 2, 4, 5

During the process of eukaryotic mRNA degradation by different mechanisms, all of the following can occur EXCEPT one of the options below: A. lengthening of the poly-A tail B. Removal of 5' cap by decapping enzymes C. Degradation of mRNA by exonucleases D. Binding of regulatory proteins to 3' UTR sequences that can influence stability

a

In absence of repair and after replication the UG mispair will become a TA. The overall change that has occurred is C:G to T:A. This is an example of A. Transition B. Transversion

a

Understanding the mechanism of HMG1a mediated alternative splicing is an important first step towards potential therapies for Alzheimer's disease. One way in which this can be done is by looking for interactions between HMG1a proteins and other proteins of interest such as splicing factors. Which of the following methods would allow you to test if HMG1a protein is interacting with proteins in the splicing factor U1snRNP? A. Co-immunoprecipitation B. EMSA C. DNA footprinting D. PCR

a

What role does the Shine-Dalgarno sequence found within prokaryotic mRNA sequence play? A. Recruitment of ribosomes to the 5` end of the mRNA transcript. B. Recruitment of splicing proteins to the intron-exon junction. C. Recruitment of translation termination factors to the 3` end of the mRNA transcript. D. Recruitment of translation elongation factors.

a

Which of the following is not one of the many functions of the RNA-induced silencing complex (RISC)? A. primary miRNA transcript conversion to precursor miRNA B. inhibit translation of mRNA C. facilitation of base pairing between mature miRNA and its complementary sequence in an mRNA D. cleavage of the mRNA transcript targeted by siRNA

a

Which of the following is the LEAST likely way in which a eukaryotic repressor would repress transcription? A. By binding to a site that overlaps the core promoter B. By binding to a site that overlaps an activator's binding site C. By blocking an activator's activating domain D. By binding to a component of the preinitiation complex to prevent transcriptional initiation E. By recruiting a histone modifier that will condense DNA

a

Which of these processes involved in translation is most important to the fidelity of protein synthesis? A. formation of aminoacyl-tRNAs B. initiation of translation at an AUG codon C. translocation of the peptidyl-tRNA from the A site to the P site during elongation D. termination of translation at a STOP codon

a

based on your viewing of the videos regarding alternative splicing and spinal muscular atrophy (sma), which of the following statements is false? a. the cause of sma is unregulated transcription and translation of a second gene SMN2 due to loss of SMN1 gene resulting in excess SMN2 protein b. in the general population, individuals who have a normal SMN1 genes do not require SMN2 gene c. splicing is involved in sma in 2 ways; the smn protein itself is needed for assembly of splicing components and the smn2 gene has a mutation that results in an alternatively spliced transcript d. the principle behind antisense oglionucleotide therapy for sma is to obscure or prevent the rna splicing repressor proteins from associating with the rna, thus promoting utilization of critical exon

a

if you were interested in studying the order of assembly of transcription factors on a eukaryotic gene promoter to form the preinitiation complex, which of the following methods would you use? a. electrophoretic mobility shift assay (EMSA) b. dnase footprinting c. dna microarray d. reporter gene fusions

a

In the CRISPR/Cas9 nuclease system, what is the role of the sgRNA (guide RNA)? A. The sgRNA is required to pair the CRISPR/Cas9 with its intended target site in the RNA and to activate the CRISPR nuclease domains for cleavage. B. The sgRNA is required to pair the CRISPR/Cas9 with its intended target site in the DNA and to activate the CRISPR nuclease domains for cleavage. C. The sgRNA is required to pair the CRISPR/Cas9 with its intended target site in the DNA and then cleaves one or both of the CRISPR nuclease domains. D. The sgRNA is required cleave both of the CRISPR nuclease domains so it will then bind the intended target site in the DNA.

b

Protein synthesis in cells during times of stress (starvation, hypoxia) is often shut down, with translation initiation steps being targeted. One factor that regulates this step involves ___________of the eIF2 factor. A. glycosylation B. phosphorylation C. esterification D. dephosphorylation

b

Scientists were able to show that HMG1a was needed for the alternative splicing. Which of the following would you predict is the role of HMGA1a protein? [Note: Remember for every intron a 5' splice site and 3' splice site pair is selected] A. HMG1a acts a splice site enhancer protein, promoting the recognition of the underlined 5' and 3' SS. B. HMG1a acts as a splice site silencer protein, preventing the recognition of underlined 5' and 3' splice site that is underlined.

b

Tetracyclines are broad - spectrum antibiotics. Structural studies have revealed that Tetracycline associates with the small ribosomal subunit such that its binding site overlaps with the position of the anticodon stem loop of the A-site tRNA, interfering with delivery of aa-tRNA's. What stage of protein translation would tetracycline inhibit? A. Initiation B. Elongation C. Termination D. Recycling and release of ribosomes

b

What is the main difference between siRNA and miRNA? A. siRNAs are involved in RNA interference; miRNAs are not. B. miRNAs are encoded by the genome; siRNAs are not. C. miRNAs are processed by Dicer; siRNAs are not. D. siRNAs are double-stranded; miRNAs are not.

b

You identify a disease of epidermal cells in mice in which Gene A is not transcribed. Further analyses reveals that the sequence of Gene A in affected and normal mice is the SAME. Which of the following choices below could be likely explanation of why Gene A is NOT transcribed in the epidermal cells of affected mice... 1. Mature mRNA corresponding to Gene A lacks the 5 methyl Cap and 3' Poly A- X 2. Histones around the promoter region of Gene A are de-acetylated. [YES) 3. Epidermal cells of affected mice lack the transcription factors (TF) associated with Gene A. [YES] 4. The Ribosome binding site in mature mRNA transcript corresponding to Gene A is mutated- X A. One of the choices is correct. B. Two of the choices are correct. C. Three of the choices are correct. D. All of the options are possible explanations.

b

a transcriptional fusion was made such that the core promoter plus the upstream UAS was fused to the reporter gene lacz. which of the following statements regarding domain swapping experiments using wild type gal4 or mutant versions of gal4 is correct? a. wild type gal4 will turn lacz transcription off b. a mutant gal4 lacking the activation domain will turn lacz transcription off c. a mutant gal4 lacking the dna binding domain will turn lacz transcription on d. all of the above e. none of the above

b

based on your reading of the article "a decade of iPS cells", which of the following statements is false? a. iPS cells are created by adding a cocktail of 4 genes, that code for transcription regulators, to a fibroblast b. unlike other cell lines, ips cell lines show a remarkable consistency with no changes in genetic background or gene expression between strains c. since ips cells represent cells early in human dev. they have been used to create mini brain tissues to study effects of zika virus d. ips cells provide a patient-derived source of cell for testing experimental drugs

b

pre-mrna splice sites are recognized by the spliceosome through: a. splicing proteins that use alpha helix structures to recognize unique sequences within the mRNA b. snRNAs embedded within the splicing proteins that form complementary base pairing with the different splice sites on the mRNA transcript c. methylation of the 3 splice sites recruits the splicing machinery to the mRNA transcript d. as rna pol II transcribes the 3 splice sites, it momentarily stalls and recruits the splicing machinery to the correct positions on the mRNA transcript

b

the generate an intron-free version of an animal gene so that it may be expressed in e. coli, it is first necessary to convert its mRNA into a ______________ a. tRNA b. complimentary dna c. gene encoding fusion protein d. expression vector

b

which of the following is an accurate statement regarding eukaryotic promoters? a. regulatory sequences are usually with the 200 base pairs upstream of the start site b. the more complex the organism, the more complex the promoters c. promoters are under the control of a single regulatory sequence d. rna poly II exhibits high intrinsic affinity for promoter sequences

b

A function of which initiation factor is to prevent premature joining of the large and small ribosomal subunits in bacteria? A. IF-1 B. IF-2 C. IF-3

c

Because the genetic code is nonoverlapping, a missense mutation (from a single nucleotide change) results in the alteration of ______________, and the resulting protein has ______________. A. only one codon / at least three amino acid changes B. three codons / a single amino acid change C. only one codon / a single amino acid change D. three codons / three amino acid changes

c

Which of the following is a false statement regarding the process of translation? A. In eukaryotes, the 5` end of the mRNA is brought into contact with the 3` end thereby forming a circular transcript, which protects against degradation. B. Each mRNA transcript can be bound simultaneously by multiple ribosomes thereby increasing the amount of protein that is produced. C. The ribosome starts translating the mRNA transcript at the first three nucleotides of the 5` end. [ALSO BASIS OF QUESTION 31!] D. In prokaryotes transcription and translation are occurring simultaneously while in eukaryotes these processes are separated in both time and space.

c

Which of the following is not true of the function of iron response elements (IREs)? A. Iron reduces the affinity of iron response proteins (IRPs) for IREs. B. IREs are located at either the 3' or 5' UTRs of mRNAs. C. Iron regulates translation by binding directly to the IREs. D. iron response proteins bind to IREs within 5' UTR of some messages and inhibits translation.

c

Which one of the following statements is a feature of the wobble hypothesis? A. An amino acid-specific tRNA molecule can recognize only one codon. B. The wobble occurs only in the third base of the anticodon. C. When inosine (I) is the first nucleotide of an anticodon, at least three different codons for the same amino acid can be recognized. D. tRNA molecules can recognize codons that specify two different amino acids.

c

basal transcription factors are: a. necessary only for initiation of transcription of housekeeping genes b. factors that bind to other proteins, not to dna directly c. required at every pol II promoter d. factors that bind to enhancers

c

how does the phosphorylation state of RNA pol II affect the process of transcription? a. rna pol II must be phosphorylated in order for it to physically interact with the general transcription factors b. the binding of rna pol II to the lnr element requires phosphorylation of the c-terminal tail of the protein c. phosphorylation of rna pol II c-terminal tail is required for it to be released from the core promoter and for transcription to be initiated d. in order for RNA pol II to terminate transcription it must be dephosphorylated

c

A reporter gene: A. can reveal when a gene is expressed. B. can reveal where a gene is expressed. C. is a gene whose activity can be easily monitored. D. All of the above

d

From the genes they identified using the method above, one was known to code for a splicing regulator HMG1a. Since alternative splicing of presinilin transcript occurs only under conditions of hypoxia, researchers wanted to check if levels of HMG1a protein under these conditions were elevated. Which of the following methods would allow you to assess protein abundance of HMG1a. A. Microarray of hypoxia-exposed brain cells versus normal (no hypoxia) cells. B. DNAse foot printing of presenilin gene in hypoxia-exposed cells versus normal cells. C. Replacing endogenous HMG1a gene with reporter gene construct using GFP. D. Western blot using antibodies against HMG1a protein (anti-HMG1a) in hypoxia exposed cells and normal cells.

d

The enzyme that catalyzes the activation of tRNA molecules is: A. the ribosome. B. RNA polymerase. C. tRNA isomerse. D. aminoacyl-tRNA synthetase

d

Transcription is similar to DNA replication in that ___________________. A. an RNA transcript is synthesized discontinuously and the pieces are then joined together. B. it uses the same enzyme as that used to synthesize RNA primers during DNA replication. C. the newly synthesized RNA remains paired to the template DNA. D. nucleotide polymerization occurs only in the 5ʹ-to-3ʹ direction.

d

What role do release factors (RF) play in the process of translation? A. Release factors (RF) recognize the transcription termination site and stimulate the release of the mRNA transcript from RNA polymerase thereby allowing for translation to initiate. B. Release factors (RF) recognize the Shine-Dalgarno and Kozak sequences and stimulate the release of the ribosome from the 5` end of the mRNA transcript. C. Release factors (RF) recognize the intron-exon junction and stimulate the removal of introns from the mRNA transcript. D. Release factors (RF) recognize stop codons and stimulate the release of the polypeptide chain from the ribosome.

d

Which of the following signals for Nonsense Mediated Decay (NMD) activation of decapping to initiate degradation of mRNA? A. The absence of Poly(A) Binding Protein (PABP) on the poly(A) tail. B. The absence of Exon Junction Complexes (EJCs) in the exon ahead. C. The presence of Poly(A) Binding Protein (PABP) on the poly(A) tail. D. The presence of Exon Junction Complexes (EJCs) in the exon ahead.

d

during the process of transcription, sequence specific transcription factors are known to interact with which one of the following types of proteins? a. general transcription factors and rna poly b. histone modifying enzymes and chromatin remodeling proteins c. the mediator complex d. all of the above

d

what would happen if a mutation inactivated the ability of poly-a-polymerase to add a stretch of adenine nucleotides to the 3' end of a cleaved mRNA transcript? a. the polyadenylation factors would not be able tot cleave the nascent mrna transcript b. rna pol II would not recognize the end of the gene and transcription would fail to be terminated c. the ribosome would be unable to bind to and initiate translation from the 3' end of the transcript d. the poly A binding proteins would not be bound and the transcript would be quickly degraded by cellular nucleases

d

which of the following is an example of post-transcriptional gene repression? a. the amount of rna transcribed from a gene is reduced because the dna is methylated b. the amount of rna is reduced because it is rapidly degraded c. the amount of protein made is reduced by action of an mrna d. the amount of rna is reduced because it is rapidly degraded, and the amount of protein is reduced by action of an miRNA

d

which of the following provides the best explanation for why a methylated guanine and a poly-A-tail are added to the 5' and 3' ends of the eukaryotic mRNA transcript? a. splicing machinery will be recruited to the mRNA transcript only after these 2 modifications have been made to the transcript b. special cellular proteins recognize the modifications at the 5' and 3' ends of the transcript in the cytoplasms. these proteins, in turn, interact with each other thus generating a circular rna molecule c. these modifications protect the coding portion of transcript from being degraded by rna nucleases d. b and c e. all of the above

d

which of the following statements based on the article "the second coming of rnai" and the follow up article "gene silencing drug approved" is true? a. inhibiting the expression of proteins by rnai is more specific than targeting them with small molecule drugs b. early problems with rnai therapies resulted form degradation of sirna in the bloodstream c. many rnai therapies were focused on liver diseases, as most sirna in lipid nanoparticles ended up in the liver d. all of the above

d

In DNA editing by CRISPR, the function of CRISPR associated proteins (for example Cas 9) is to: A. Bind CRISPR RNA B. Transcribe CRISPR RNA C. Translate CRISPR RNA D. Cleave target DNA E. A and D

e