Deck 8: Rna: Transcription and Processing

Question 1

Which of the following is/are TRUE about functional RNA?

A)Functional RNAs do not encode proteins and are active as RNA.
B)Some functional RNAs encode proteins.
C)Examples of functional RNA include mRNA,tRNA,and rRNA.
D)Examples of functional RNA include tRNA,rRNA,snRNA,and miRNA.
E)Functional RNAs do not encode proteins,and examples include tRNA,rRNA,snRNA,and miRNA.

Answer 1

E

Question 2

The "RNA World" theory suggests that:

A)RNA is the intermediate between DNA and proteins.
B)RNA was the genetic material in the first living cells.
C)many RNAs are capable of self-splicing.
D)eventually,RNA will become the genetic material of most living organisms.
E)RNA viruses are more dangerous than DNA viruses.

Answer 2

B

Question 3

If the DNA template 5′-ATGCATGC-3′ were transcribed to RNA,the RNA would read:

A)3′ TACGTACG 5′.
B)5′ AUGCAUGC 3′.
C)5′ UACGUACG 5′.
D)3′ UACGUACG 5′.
E)5′ATGCATGC 3′.

Answer 3

D

Question 4

In a chromosome,which of the following is TRUE?

A)RNAs of different genes can be transcribed off either DNA strand,but always 5' to 3'.
B)RNAs of different genes can be transcribed off either DNA strand,but always 3' to 5'.
C)The RNAs of all genes are synthesized 5' to 3' off the same DNA strand.
D)The RNAs of all genes are synthesized 3' to 5' off the same DNA strand.
E)Different genes can be transcribed off either strand,some in the 5' to 3' direction and some in the 3' to 5' direction.

Question 5

RNA polymerase can transcribe in different directions on a chromosome.This is enabled because:

A)genes and their associated promoters can be oriented in either direction along a chromosome.
B)RNA polymerase can transcribe from either strand of DNA,synthesizing RNA in the 5′ to 3′ direction.
C)the chemistry of RNA synthesis is identical regardless of which strand is transcribed.
D)the 3′ end of a gene is always the template strand.
E)All of the answer options are correct.

Question 6

Which of the following is/are TRUE for RNA compared to DNA?

A)RNA has ribose sugar in its nucleotides,rather than the deoxyribose found in DNA.
B)RNA is usually single stranded and can make more complex three-dimensional molecular shapes than double-stranded DNA.
C)RNA contain the bases A,G,C,and U,whereas DNA contain the bases A,G,C,and T.
D)RNA can catalyse biological reactions,but DNA cannot.
E)All of the answer options are correct.

Question 7

The experimental value of a "pulse-chase" cellular labeling experiment using radioactive uracil is that:

A)all RNAs within a cell are labeled and easily detected.
B)the radioactivity allows for easy purification of cellular nucleic acids.
C)all RNAs created during the pulse are labeled and detectable,revealing their stability and localization.
D)the spliceosome function is easily seen with radiolabeled RNAs in the cellular cytosol.
E)cells adapt to the pulse of radioactivity,revealing nucleic acid repair mechanisms.

Question 8

These functional RNAs function to regulate protein production of specific genes.

A)transfer RNA (tRNA)
B)small nuclear RNAs (snRNAs)
C)micro RNAs (miRNAs)
D)small interfering RNAs (siRNAs)
E)ribosomal RNAs (rRNAs)

Question 9

Before the completion of the human genome project,it was generally estimated that human DNA would contain up to 100,000 genes.We now know humans contain only around 25,000 individual genes within our genomes.This "gene count" is so surprising because:

A)simple roundworms have over 10,000 genes,so humans should have many more.
B)experimental analysis of mRNA diversity generated estimates of ~100,000 genes.
C)humans have a large genome size (3.3 $\times$ 10⁹ base pairs).
D)the diverse types of tissue in humans require many thousands of genes.
E)All of the answer options are correct.

Question 10

Which of the following mRNA codons would form a codon-anticodon base pairing interaction with the 3′-UAG-5′ tRNA anticodon?

A)3'- ATC-5'
B)5'- GAU-3'
C)5'-ATC-3'
D)3'-AUC-5'
E)5'-AUC-3'

Question 11

Template strand DNA and encoded RNA are:

A)complimentary of one another with antiparallel orientation.
B)complimentary of one another but share the same 5′-3′ orientation.
C)identical sequences with the exception of U substituted for T.
D)different with regard to the inclusion of introns.
E)interconverted via nucleic acid remodeling.

Question 12

RNA synthesis is always 5' to 3' because:

A)the unwinding of the double-stranded DNA can only move one direction.
B)nucleotides can only be added to an available 3'-OH group on the transcript terminus.
C)nitrogenous bases cannot pair up in the 3' to 5' direction.
D)the structure of ATP restricts 3' to 5' polymerization into RNA.
E)RNA synthesis can move in the 3' to 5' direction.

Question 13

The -10 and -35 boxes found in most bacterial promoter elements were discovered by:

A)comparing the DNA sequences in front of highly expressed genes and determining nucleic acids that were common (consensus).
B)the finding that RNA polymerase begins translation when a 10-nucleotide followed by a 35-nucleotide repeat of guanine ("G")are encountered.
C)comparing bacterial promoters to known eukaryotic promoters.
D)examining data from the human genome project.
E)Robert Koch as he characterized the microbe that causes tuberculosis.

Question 14

The role of tRNA is to:

A)serve as an intermediate in the decoding of genes.
B)act as transporters bringing amino acids to the site of protein synthesis.
C)serve as general translational components of the ribosome.
D)facilitate splicing of pre-messenger RNAs.
E)facilitate protein trafficking in protein secretion.

Question 15

The spliceosome includes both protein and a functional type of RNA known as:

A)transfer RNA (tRNA).
B)small nuclear RNAs (snRNAs).
C)micro RNAs (miRNAs).
D)small interfering RNAs (siRNAs).
E)ribosomal RNAs (rRNAs).

Question 16

Which of the following is evidence that RNA was a message-carrying intermediary between DNA and protein?

A)A hydroxyl group is present on ribose.
B)RNA is single stranded and thus cannot be copied by semiconservative replication in a manner similar to DNA.
C)RNA structure includes a molecular code,proving that it carries a genetic message.
D)RNA is produced in the nucleus (with DNA)and then migrates to the cytosol,the location of protein synthesis.
E)Pulse-chase experiments revealed RNA to be exclusively localized to the nucleus.

Question 17

In what cellular compartment are introns removed from pre-mRNA to make mature mRNA?

A)cytoplasm
B)endoplasmic reticulum
C)nucleus
D)mitochondria
E)Golgi apparatus

Question 18

Pulse-chase experiments provided evidence that:

A)RNA is made of ribose sugars rather than deoxyribose.
B)RNA is an information-transfer intermediary between DNA and protein.
C)many viruses have RNA genomes.
D)RNA is capable of catalyzing biological reactions.
E)RNA is synthesized in short pulses of transcriptional activity.

Question 19

The spliceosome functions to:

A)insert introns into mRNA sequences before translation.
B)create noncoding sequences in genes to enhance gene stability.
C)remove noncoding introns from transcribed RNAs.
D)control translation,ensuring that only exons are translated.
E)inhibit transcription of noncoding DNA regions.

Question 20

Which of the following acts before the others?

A)tRNA alignment with mRNA
B)aminoacyl-tRNA synthetase
C)RNA polymerase
D)ribosome movement to the next codon
E)amino acid chain elongation

Question 21

The initial discovery of the spliceosome resulted from experiments focused on:

A)autoimmunity in Lupus patients.
B)the isolation of large RNA/protein complexes from cells.
C)careful analysis of electron microscopy images from the cell nucleus.
D)RNAs from plant cells.
E)the cell biology of Huntington's disease.

Question 22

For protein-encoding genes,six general transcription factors (GTFs)function to:

A)identify a gene's promoter,facilitating RNA polymerase II binding.
B)terminate transcription at the end of an open reading frame.
C)assemble the RNA polymerase subunits.
D)arrest DNA replication.
E)recruit the ribosome to newly synthesized RNAs.

Question 23

siRNAs are distinct from microRNAs (miRNAs)in that siRNAs:

A)silence their own expression.
B)are smaller than microRNAs.
C)are derived from rRNA sequences.
D)silence gene expression.
E)are made of double-stranded DNA.

Question 24

The role of most microRNAs within a eukaryotic cell is to:

A)regulate the splicing of primary transcripts to mRNAs.
B)bind with other RNAs to stabilize their secondary structure.
C)associate with ribosomal proteins to facilitate translation.
D)regulate RNA polymerase activity in the nucleus.
E)repress the expression of genes by destroying mRNAs.

Question 25

Why does E.coli have several different sigma factors?

A)They allow different RNA polymerases to bind to the promoters.
B)They allow the different subunits of the RNA polymerase holoenzyme to bind to each other.
C)There is no good reason.They all perform the same function.
D)One is needed to transcribe mRNA.A second is needed to transcribe tRNA.And a third is needed to transcribe rRNA.
E)They allow RNA polymerase to recognize and bind to a different subset of promoters.

Question 26

The -10 and the -35 boxes found in bacterial gene promoters function to:

A)recruit DNA polymerase activity for DNA replication before cell division.
B)activate transcription at the -35 region of a gene.
C)orient RNA polymerase at a gene's transcription start site.
D)identify the boundaries between introns and exons.
E)identify the boundaries for DNA unwinding during transcription.

Question 27

The carboxyl tail domain of RNA polymerase II plays a key role in:

A)capping of the 5′ end of a new transcript.
B)recruiting capping enzymes to the RNA polymerase enzyme.
C)addition of a poly(A)tail at the 3′ end of a transcript.
D)splicing of introns out of RNA transcripts.
E)All of the answer options are correct.

Question 28

What is the function of the TATA binding protein?

A)aids in the removal of introns from eukaryotic pre-mRNA
B)allows prokaryotic RNA polymerase to bind to the promoter of genes
C)allows eukaryotic RNA polymerase II to bind to the promoter of genes
D)helps termination factors bind and terminate transcription.
E)All of the answer options are correct.

Question 29

In eukaryotic species,three separate RNA polymerases transcribe different categories of genes.RNA polymerase I is known to primarily transcribe:

A)messenger RNAs.
B)protein-encoding genes.
C)most ribosomal RNAs.
D)transfer RNAs and small nuclear RNAs.
E)genes responsible for DNA replication.

Question 30

Following splicing,the conserved adenosine nucleotide within the intron displays an unusual array of bonds,including:

A)a phosphate attached to the 4-carbon of the adenine nitrogenous base.
B)phosphodiester bonds attached at three places on the ribose (2′,3′,5′).
C)additional methyl (-CH₃)groups added to the adenine.
D)a DNA strand attached to the spliced RNA.
E)attachment to an arginine amino acid.

Question 31

A key characteristic of bacterial RNAs that is not observed with eukaryotic RNAs is that:

A)transcription generates RNAs that contain both introns and exons.
B)transcription can occur in the same cellular region as translation.
C)a prerequisite for translation initiation is RNA processing.
D)the genetic code used by bacteria is different from other organisms.
E)bacterial RNAs are generated as double stranded.

Question 32

In eukaryotic species,three separate RNA polymerases transcribe different categories of genes.RNA polymerase III is known to primarily transcribe:

A)messenger RNAs.
B)protein-encoding genes.
C)most ribosomal RNAs.
D)transfer RNAs and small nuclear RNAs.
E)genes responsible for DNA replication.

Question 33

Shown below is the structure of a Drosophila gene,divided into 10 segments,designated A-J.The gene contains three exons,two introns,a promoter,and a site in I for poly(A)addition.
a)What segment or segments of the gene will be represented in the initial RNA transcript? List the appropriate letter or letters.

b)What segment or segments of the gene will be found in the completely processed transcript?

c)What segment or segments of the gene in the processed transcript will have additional nucleotides added to them?

d)What segment or segments of the gene contain the CCAAT box and TATA box elements?

e)What segment or segments of the gene will possess the translation initiation codon?

f)In a large sample of null alleles,would mutant sites be expected in segments C and D,at the boundary of G-H,or both? If mutant sites exist,would the transcript be detected? Would a polypeptide chain be observed?

Question 34

Why is transcription in eukaryotes more complex than in prokaryotes?

A)Compared to a few thousand genes in prokaryotes,eukaryotes have larger genomes and tens of thousands of genes to be transcribed.
B)Transcription and translation takes place in the same cellular compartment in prokaryotes but in different compartments in eukaryotes.
C)The template for transcription in prokaryotes is simple and exists as naked DNA,whereas the eukaryotic template is organized into a highly condensed chromatin structure.
D)All of the answer options are correct.
E)Eukaryotes have larger genomes and more genes than prokaryotes,and their genomes are organized into a highly condensed chromatin structure.

Question 35

In what cellular compartment are introns removed from pre-mRNA to make mature mRNA?

A)cytoplasm
B)endoplasmic reticulum
C)nucleus
D)mitochondria
E)Golgi apparatus

Question 36

The sigma factor protein's role in transcription in E.coli includes which of the following?

A)forms part of the core enzyme required for transcription initiation
B)helps the holoenzyme to bind to the promoter
C)contributes to the proof reading activity of RNA polymerase
D)plays a role in transcription termination
E)All of the answer options are correct.

Question 37

The conserved adenine nucleotide in introns serves as the:

A)site for intron recognition for the spliceosome.
B)branch point for the formation of the intronic "lariat."
C)key point for ribosome assembly and initiation of translation.
D)initial site of intronic RNA digestion and removal.
E)molecular signal for RNA splicing.

Question 38

The functional equivalent of the TATA binding protein in prokaryotes is:

A)a sigma subunit.
B)a holoenzyme.
C)the Rho factor.
D)TFIID.
E)hairpin loops.

Question 39

Which of the following is/are role(s)of the 5′ cap?

A)The cap helps the RNA polymerase find the promoter and initiate transcription.
B)The cap plays a role in the removal of introns.
C)The cap acts as a binding site for the ribosome.
D)The cap protects the RNA from degradation.
E)The cap acts as a binding site for the ribosome and protects the RNA from degradation.

Question 40

Which of the following statement/s about RNA pol II is/are FALSE?

A)RNA pol II transcribes protein-encoding genes.
B)General transcription factors (GTFs)help RNA pol II to position at the promoter start to initiate transcription.
C)RNA pol II adds new nucleotides to the 3′ end of the transcript.
D)The CTD domain of RNA pol II coordinates cotranscriptional modifications.
E)RNA pol II reads the template DNA strand in a 5′-to-3′ direction during transcription.

Question 41

A segment of DNA from Drosophila melanogaster has the sequence:
5′ TCA AGC TTA AGA AGG CAT TTT 3′
a)Assuming that this is the template strand,what is the sequence of the encoded mRNA (make sure to denote 5′ and 3′ ends of the transcript)?
b)If this sequence is the coding strand,what is the sequence of the encoded mRNA?

Question 42

The following table contains a list of statements that may apply to mRNA,tRNA,snRNA,or rRNA.For each class of RNA molecule,put a check mark if the statement applies to that type of RNA.
$\begin{array}{|l|l|l|l|l|}\hline& \text { MRNA } & \text { tRNA } & \text { snRNA } & \text { rRNA } \\\hline \text { Contains a 5'UTR } & & & & \\\hline \text { Translated into protein } & & & & \\\hline \text { Contains an anticodon } & & & & \\\text { Classified as functional RNA } & & & & \\\hline \text { Transcribed in the } 5^{\prime}-3^{\prime} \text { direction } & & & & \\\hline \text { Major component of ribosomes } & & & &\\\hline \text { Component of spliceosomes } & & & & \\\hline \text { Transcribed by RNA polymerase II in eukaryotes } & & & & \\\hline \text { Have a functional role in translation } & & & &\\\hline\end{array}$

Question 43

The following sequence was identified at the 3′ end of a transcribed RNA in prokaryotes.
a)What is the name of the structure shown below?
b)What is its function in transcription?
c)What is the probable base composition of the region marked by the A arrow?
d)What is the probable base composition of the region marked by the B arrow?
e)In the original gene encoding this RNA sequence,the B region was mutated to GGCCGGTGC.How might this mutation of B affect transcription of this gene?

Question 44

You generated a eukaryotic cell line that expresses an RNA polymerase II subunit that is missing the repeated sequences (seven amino acids per repeat)near the
C-terminus.These repeated sequences are known to be important in the regulation of gene expression in eukaryotes.Define how expression of this RNA polymerase might affect the cell line.Define how these repeated sequences are regulated within a normal RNA polymerase II enzyme.

Question 45

Pulse-chase experiments were vital for showing that RNA acts as an information-transfer intermediary between DNA and protein.Describe the basic steps of a pulse-chase experiment,and explain in your own words how the results suggested that RNA is the intermediate.

Question 46

Name the three major modifications of mRNA in eukaryotes before it is transported to the cytoplasm.In addition,tell why each of the modifications is necessary.

Question 47

A major difference between eukaryotes and prokaryotes is that eukaryotes have a nucleus,whereas prokaryotes do not.Discuss the impact of having a nucleus on the creation of mature mRNA.

Question 48

Of the three classes of functional RNAs,rRNA and tRNA exist in both eukaryotes and prokaryotes.However,snRNAs exist only in one of these types of organisms.Do snRNAs exist in prokaryotes or eukaryotes? Explain why they are only found in that type of organism.

Question 49

Consider the following piece of messenger RNA:
5'-AUGGAGUCGUUAAUUAAACCGGUGCGGAUCGUAUUUAGUCCCCAC-3'
a)Draw both strands of the segment of DNA that this mRNA was transcribed from.
b)State which of the DNA strands the RNA synthesizing enzyme used as template for the transcription process.
c)Using the codon chart,give the amino acid sequence of the protein that would be produced by translation of the mRNA,assuming the ribosome moved along the mRNA from left to right.

Question 50

Suppose that you have sequenced five genes,including the putative promoter region of each gene,that are involved in the cold acclimation process in Arabidopsis.Each of the five genes is expressed only when the temperature falls below a certain temperature.You know that a specific transcription factor (CBF1)binds somewhere between -200 and -250 of these genes to initiate transcription.How could you use the sequences to determine the DNA sequence motif that is bound by CBF1?

Question 51

What are the three major classes of functional RNAs? Briefly describe the role of each class of functional RNA.

Question 52

The following table contains a list of statements that apply to replication,transcription,both,or neither.In each empty box,put a check mark if that statement applies to replication or transcription.
$$\begin{array} { | l | l | l | } \hline & \text { Replication } & \text { Transcription } \\\hline \text { The new strand is made 5' to 3'. } & & \\\hline \text { The new strand is made 3' to 5'. } & & \\\hline \begin{array} { l } \text { The new strand is identical to the termplate strand, with } \\\text { the exception of U's replacing T's. }\end{array} & & \\\hline \text { The new strand is complennentary to the ternplate strand } & & \\\hline \text { The termplate strarnd is RNA } & & \\\hline \text { The product is DNA } & & \\\hline \text { The product is RNA } & & \\\hline \text { An RNA priner is required to iritiate synthesis. } & & \\\hline \text { Synthesis of the new strand is initiated at a pronoter. } & & \\\hline \begin{array} { l } \text { The process is done only during the S-phase of the cell } \\\text { cycle. }\end{array} & & \\\hline \begin{array} { l } \text { The process is done only during the Gl -phase of the cell } \\\text { cycle. }\end{array} & & \\\hline\end{array}$$

Question 53

What would the minimum word (codon)size be if the number of different bases in the mRNA were a)two;b)three;c)five.Give your reasoning.Assume that all other features of the translation of mRNA into protein are the same as what we now know.