Deck 13: RNA Processing and Post-Transcriptional Gene Regulation

Question 1

The ovalbumin gene is much longer than the mRNA produced by this gene. What causes this discrepancy?

A) The exons have been removed during mRNA processing.
B) The DNA represents a double-stranded structure and the RNA is single stranded.
C) There are more amino acids coded for by the DNA than the mRNA.
D) The introns have been removed during mRNA processing.

Answer 1

The introns have been removed during mRNA processing.

Question 2

RNA splicing is the process by which introns are removed from a primary RNA transcript at precisely defined splice points. Which statement is not true about introns?

A) Introns are that are joined together after splicing.
B) Introns are usually nonfunctional and are degraded, but some introns encode functionalRNA products
C) Introns are transcribed along with the exons.
D) Introns are larger on average than exons.

Answer 2

Introns are that are joined together after splicing.

Question 3

Some introns contain termination codons yet they do not interrupt the coding of a particular protein. Why?

A) The translation machinery recognizes and skips over introns.
B) These triplets cause frameshift mutations, not termination.
C) More than one termination codon is needed to stop translation.
D) Splicing occurs before translation.

Answer 3

Splicing occurs before translation.

Question 4

Group I intron self-splicing relies on

A) An external guanosine nucleotide as a cofactor.
B) A bulged internal guanosine nucleotide.
C) An external adenosine nucleotide as a cofactor.
D) A bulged internal adenosine nucleotide.

Question 5

The first nucleophilic attack in group II intron splicing is initiated by a

A) An external guanosine nucleotide as a cofactor.
B) A bulged internal guanosine nucleotide.
C) An external adenosine nucleotide as a cofactor.
D) A bulged internal adenosine nucleotide.

Question 6

The second transesterification step for group I and group II intron self-splicing is initiated by the

A) 3' end of the intron
B) 5' end of the intron
C) 3' end of the upstream exon
D) 5' end of the upstream exon

Question 7

Archael introns are

A) self-splicing.
B) spliced by an endoribonuclease.
C) spliced by the spliceosome.
D) require an external guanosine nucleotide as a cofactor.

Question 8

Which statement is true regarding eukaryotic nuclear tRNA genes?

A) There are no intron-containing nuclear tRNA genes in eukaryotes.
B) All eukaryotic nuclear tRNA genes contain at least one intron.
C) One of two classes of eukaryotic nuclear tRNA genes has introns.
D) Only yeast and plant nuclear tRNA genes have introns.

Question 9

Select three posttranscriptional modifications often seen in the maturation of nuclear pre-mRNA in eukaryotes.

A) 5'-capping; 3'-poly(A) tail addition; splicing
B) 3'-capping; 5'-poly(A) tail addition; splicing
C) 5'-capping, removal of exons; insertion of introns
D) 3'-capping, insertion of introns; 5'-poly(A) tail addition

Question 10

During maturation of nuclear pre-mRNA in eukaryotes, capping takes place at the

A) 5' end of the primary RNA transcript.
B) 3' end of the primary RNA transcript
C) 2' end of the primary RNA transcript
D) At either the 5' or 3' end, depending on the particular primary RNA transcript

Question 11

The 7-methylguanosine cap structure, the ribose of guanosine is connected to the 5' end of the mRNA by

A) phosphates
B) sulfates
C) glycerol
D) ethylene

Question 12

Which is not a function of the 7-methylguanosine cap?

A) protection from exonucleases
B) promoting mRNA nuclear export
C) stimulation of RNA polymerase elongation
D) stimulation of translation

Question 13

The process of polyadenylation is accomplished by

A) reverse transcriptase
B) the CTD domain
C) primase
D) poly(A) polymerase

Question 14

Which is not required for efficient mRNA polyadenylation?

A) a polyadenylation sequence in the mRNA
B) poly(A)-binding proteins
C) Xrn2 exonuclease
D) poly(A) polymerase

Question 15

To ensure that RNA polymerase is only released after it has transcribed a gene to its end, termination is mechanistically linked to

A) 5' capping
B) excision of the lariat RNA
C) alternative splicing
D) 3' end formation

Question 16

RNA polymerase is thought to be disengaged from the DNA template by

A) the Xrn2 exonuclease
B) cleavage and polyadenylation specific-factor (CPSF)
C) poly(A) polymerase
D) the spliceosome

Question 17

Nuclear pre-mRNA introns are

A) self-splicing
B) removed by an endoribonuclease
C) removed by the spliceosome
D) require an external guanosine nucleotide as a cofactor.

Question 18

RNA splicing of nuclear pre-mRNA involves removal of

A) introns from a primary RNA transcript by a series of two transesterification reactions.
B) exons from a primary RNA transcript by a series of two transesterification reactions.
C) introns from a primary RNA transcript by a series of polyadenylation reactions.
D) exons from a primary RNA transcript by a series of polyadenylation reactions.

Question 19

The spliceosome is composed of

A) U1, U2, U3, U4, and U5 snRNPs
B) five different U-rich snRNAs and more than 200 proteins
C) small ribosomal RNAs and associated proteins
D) more than 200 proteins

Question 20

Which snRNPs are thought to contribute to the catalysis of pre-mRNA splicing?

A) U1 and U2 snRNPs
B) U2 and U4 snRNPs
C) U5 and U6 snRNPs
D) U2 and U6 snRNPs

Question 21

The mechanism for nuclear pre-mRNA splicing is similar to the splicing mechanism of

A) Group I introns
B) Group II introns
C) Archael introns
D) nuclear tRNA introns

Question 22

It was once assumed that a count of the number of protein-coding genes in an organism would provide a reasonable estimate of the total number of gene products. This is now known to be incorrect, largely due to the discovery of widespread:

A) chromatin modification control
B) transcriptional initiation control
C) alternative splicing
D) translational control

Question 23

One way to detect alternative splicing of a given gene is to compare:

A) the relative rate of transcription of the alternatively spliced gene withanother gene
B) the sequence of the alternatively spliced gene to that of another gene.
C) the size and sequence of different pre-mRNAs transcribed from this gene.
D) the size and sequence of mature mRNAs produced from this gene.

Question 24

There is evidence supporting

A) that the spliceosome assembles in a step-wise fashion as the splicing reaction occurs
B) that the splicosome exists as a "pre-assembled" macromolecular complex
C) that the order of snRNP binding to a pre-mRNA varies between specific transcripts
D) A and B

Question 25

Which factors bind to pre-mRNA splice sites first?

A) U1 and U2AF
B) U2 and a DEXH helicase
C) U4/U6/U5
D) hnRNP proteins

Question 26

For some pre-mRNAs, splicing is regulated by

A) RNA polymerase stalling
B) splicing enhancer sequences
C) localization of the pre-mRNA to subnuclear "speckles"
D) transcription termination

Question 27

When an exon from one pre-mRNA joins to an exon from another pre-mRNA the process is called

A) trans-splicing
B) cis-splicing
C) alternative splicing
D) RNA editing

Question 28

RNA editing is a widespread mechanism for post-transcriptional modification of the base sequence of mRNA. In humans, RNA editing

A) is mediated by guide RNAs and a multiprotein complex called the "editosome" that inserts or deletes uridines.
B) occurs by deamination of adenosine to inosine, or cytidine to uridine.
C) is mediated by small nucleolar RNAs and base modification enzymes.
D) is mediated by the U12-type intron splicing pathway.

Question 29

RNA editing is a widespread mechanism for post-transcriptional modification of the base sequence of mRNA. In trypanosomes, RNA editing

A) is mediated by guide RNAs and a multiprotein complex called the "editosome" that inserts or deletes uridines.
B) occurs by deamination of adenosine to inosine, or cytidine to uridine.
C) is mediated by small nucleolar RNAs and base modification enzymes.
D) is mediated by the U12-type intron splicing pathway.

Question 30

The enzyme ADAR (adenosine deaminase acting on RNA) functions in

A) RNA interference
B) RNA editing
C) alternative splicing
D) formation of an alternative mRNA cap structure

Question 31

MicroRNAs are processed by the enzymes _______ and ______. One strand of the microRNA is loaded into a silencing complex named _________. The microRNAs target mRNA for ___________ or ___________.

A) RISC, Dicer, Drosha, mRNA degradation, translational repression
B) Drosha, Dicer, RISC, mRNA degradation, translational repression
C) Drosha, Dicer, RISC, alternative splicing, RNA editing
D) RISC, Dicer, Drosha, alternative splicing, RNA editing

Question 32

RNA interference is the process of

A) gene silencing at the transcriptional level.
B) gene silencing at the level of RNA splicing.
C) gene silencing at the post-transcriptional level.
D) gene silencing at the post-translational level.

Question 33

RNA interference is thought to have evolved to

A) downregulate cancer-causing genes
B) promote transposition
C) prevent spurious recombination
D) defend against viruses

Question 34

The target mRNA for a particular miRNA is cleaved by

A) RNA-directed RNA polymerase
B) Dicer
C) Drosha
D) RISC

Question 35

Which component of the RNAi pathway confers inheritance of siRNA-induced silencing?

A) Dicer
B) RISC (RNA induced silencing complex)
C) RdRP (RNA-directed RNA polymerase)
D) Drosha

Question 36

The targets of a microRNA are usually

A) viral mRNAs
B) bacterial dsRNAs
C) tissue-specific genes
D) "housekeeping" genes

Question 37

The nuclear exosome

A) degrades aberrant mRNAs
B) cleaves dsRNA into siRNAs
C) promotes nuclear export of mature mRNA complexes
D) facilitates spliceosome assembly

Question 38

Which aspect of an mRNA's life cycle serves as a key mRNA quality control mechanism?

A) 3' end cleavage
B) transcription termination
C) nuclear export
D) splicing

Question 39

Nuclear basket proteins Mlp1 and Mlp2 act as

A) nuclear exosomes
B) a sorting filter for unspliced transcripts
C) splicing factors
D) miRNA exportins

Question 40

When mRNAs lacking a poly(A) tail compete with polyadenylated mRNAs for
Limiting translational machinery

A) the polyadenylated mRNA is translated more efficiently.
B) the mRNA lacking a poly(A) tail is translated more efficiently.
C) the mRNAs are translated equally efficiently.
D) the efficiency of translation depends on the sequence of the mRNA, not the poly(A) tail.

Question 41

Failure of the ribosome to remove an exon-exon junction complex (EJC) leads to

A) degradation by nuclear exosomes
B) translation of the mRNA
C) storage of the mRNA in the cytoplasm
D) nonsense-mediated mRNA decay

Question 42

Describe the original observations that indicated the existence of "split genes."

Question 43

Define the terms "intron" and "exon."

Question 44

What is a snRNP ("snurp")?

Question 45

Discuss how the discovery of intron-encoded small nucleolar RNAs (snoRNAs) has added to the challenge of cloning "genes".

Question 46

Draw a diagram of the steps involved in self-splicing of an RNA containing a group I intron.

Question 47

You are characterizing an RNA transcript that contains an intron. List the key features you would need to analyze to determine whether the RNA is self-splicing and, if it is self-splicing, to classify the intron as a group I or group II intron.

Question 48

What is unusual about the phosphodiester bond forming a lariat intron?

Question 49

Compare and contrast the key features of "homing" and "retrohoming" by mobile group I and II introns, respectively.

Question 50

Diagram the Archael intron splicing pathway. Include a rough sketch of the conserved secondary structure of an archael intron.

Question 51

Diagram the tRNA splicing pathway of plants and fungi.

Question 52

a) Name the domain of RNA polymerase II that coordinates cotranscriptional processing of nuclear pre-mRNA. b) Name the post-translational modification that is required for function of this domain. c) Name the class of enzyme that carries out the post-translational modification in (b).

Question 53

Diagram a model showing how nuclear pre-mRNA processing is coupled to transcription.

Question 54

Diagram the structure of the 7-methylguanosine cap structure with sufficient detail to show how the cap is added in the "wrong" direction to the initial nucleotide of the mRNA.

Question 55

Describe and give the results of an experiment that showed that the carboxyl terminus of the RNA polymerase II carboxyl-terminal domain (CTD) is necessary and sufficient to enhance splicing.

Question 56

Diagram a two-step model for transcription termination in eukaryotes.

Question 57

Draw a diagram of the polyadenylation complex and the polyadenylation process.

Question 58

A friend of yours has been diagnosed with oculopharyngeal muscular dystrophy. Explain the genetic basis for this disease.

Question 59

Describe the composition and structure of the spliceosome, based on cryoelectron microscopy and biochemical analysis. Relate the structure to function.

Question 60

Suggest how DEXH/D-box RNA helicases might facilitate splicing.

Question 61

Describe and show the results of an experiment that demonstrates that U1 snRNP is the first snRNP to bind to the pre-mRNA.

Question 62

What process is thought to be defective in spinal muscular atrophy?

Question 63

Describe and show the results of an experiment to demonstrate that the survival of motor neurons (SMN) protein colocalizes with coilin in Cajal bodies.

Question 64

A friend of yours has been diagnosed retinistis pigmentosa. Explain the genetic basis for this disease.

Question 65

What are SR proteins and where are they located within cells?

Question 66

Is the spliceosome a ribozyme? Describe experimental evidence for the catalytic activity of U2 and U6 snRNAs.

Question 67

Define the term "alternative splicing." Describe a specific example of alternative splicing.

Question 68

Is alternative splicing within human genes common or uncommon? Explain your answer.

Question 69

Use a diagram to compare and contrast discontinuous group II trans-splicing with spliced leader trans-splicing. Discuss how the discovery of discontinuous group II trans-splicing in particular has added to the challenge of cloning "genes".

Question 70

When the genome of the only characterized member of the kingdom Nanoarchaeota (Nanoarchaeum equitans) was sequenced, it appeared to be missing genes encoding several tRNAs, yet the tRNAs themselves were all present in the organism. Provide an explanation.

Question 71

Define the term "RNA editing" and explain why its discovery shook the central dogma of molecular biology.

Question 72

Diagram the general mechanism for RNA editing in trypanosomes. You do not need to show a complete sequence for the pre-mRNA.

Question 73

In what cellular compartment does editing take place in trypanosomes? Are all the components required for editing produced in this compartment? Explain your answer.

Question 74

Diagram the process of apolipoprotein B (CU editing) in humans.

Question 75

Besides CU editing, what other type of editing occurs in humans?

Question 76

What unusual feature was revealed by X-ray crystallographic analysis of the structure of the adenosine deaminase ADAR?

Question 77

Describe evidence for a model in which a defect in RNA editing contributes to the onset of amyotrophic lateral sclerosis.

Question 78

You discover that a single gene can produce two different proteins. Provide possible explanations for your observation.

Question 79

Describe some of the experiments that led to the discovery of miRNAs in the nematode worm, Caenorhabditis elegans.

Question 80

Define the term RNA interference (RNAi). Compare and contrast key features of small interfering RNAs (siRNAs) and micro RNAs (miRNAs).