Lecture 7- Intro & Prokaryotic Transcription

Question 1

What is transcription?

Answer 1

Process of copying DNA -> RNA

Question 2

In what direction does the coding strand run?

Answer 2

5’ -> 3’

Question 3

In what direction does the Template Strand run?

Answer 3

3’ -> 5’

Question 4

What is another name for the non-coding strand?

Answer 4

Template Strand

Question 5

RNA Polymerase runs in what direction?

Answer 5

5’ -> 3’

Question 6

RNA Polymeras’s template runs in what direction?

Answer 6

3’ -> 5’

Question 7

What direction does Polypeptides run in?

Answer 7

Amino Terminus -> Carbonyl Terminus

Question 8

_________- encodes the amino acids sequences of all the poly peptides found in the cell

Answer 8

mRNA (messenger)

Question 9

_________- matches specific amino acids to triplet codons in mRNA during protein synthesis

Answer 9

tRNA (transfer)

Question 10

________- the RNA component of the ribosome, interacts with tRNA during translation

Answer 10

rRNA (ribosomal)

Question 11

_________- post-transcriptionally regulate the expression of genes by binding to mRNA nucleotide seq.

Answer 11

miRNA (micro)

Question 12

True or False

Ribonucleic Acids act as genomic material in viruses.

Answer 12

True; also called ribosymes

Question 13

RNA Polymerase elongates in which direction?

Answer 13

5’ -> 3’

Question 14

How does RNA Polymerase attack/elongate?

Answer 14

Using the 3’ OH to attack the alpha phosphorous atom of the incoming nucleotide and release PPi

Question 15

How large is the initiation footprint?

Answer 15

100 base pair

Question 16

How large is the elongation footprint?

Answer 16

35 base pair

Question 17

True or False

RNA Polymerase’s footprint gets larger as it transcribes.

Answer 17

False; it gets smaller

Question 18

Which DNA strand travels through the RNA Polymerase’s Active Site?

Answer 18

Template Strand/Non-Coding strand

Question 19

True or False

DNA strand that serves as a template for RNA Synthesis is the non-template/coding strand?

Answer 19

False; Template Strand/Non-Coding strand

Question 20

True or False

Coding Strand is the complementary to the new RNA sequenced strand

Answer 20

True

Question 21

True or False

Genes can be encoded on either of the two DNA strands

Answer 21

True

Question 22

True or False

During Transcription, there is continuous winding/unwinding about RNA polymerase

Answer 22

True

Question 23

What size is the transcription bubble

Answer 23

17 base pair

Question 24

What size is the RNA/DNA Hybrid

Answer 24

8 base pair

Question 25

Is the 5’end ever on the Active Site

Answer 25

No, it is always outside the Active Site

Question 26

What happens if the wrong ribonucleotide attempts to enter the Active site and how does it enter?

Answer 26

It enters through the NTP channel and the channel rejects any ribonucleotide that is incorrect.

Question 27

What happens to NTP’s KD when an incorrect ribonucleotide attempts to enter the NTP channel.

Answer 27

Decreased Affinity

Question 28

How many basepair of RNA-DNA are completed during elongation?

Answer 28

8

Question 29

Elongation at the Active Site occurs at a rate of___.

Answer 29

50-90 pair

Question 30

How many subunits are in RNA Polymerase’s core?

Answer 30

5

Question 31

How many total subunits are there?

Answer 31

6

Question 32

What is the fx of alpha subunits?

Answer 32

Assembly & Binding of UP elements

Question 33

What is the fx of Beta subunits?

Answer 33

Catalytic Subunit

Question 34

What is the fx of Beta’ subunits?

Answer 34

DNA Binding

Question 35

What is the fx of omega subunits?

Answer 35

Protect RNA Polymerase from denaturation

Question 36

What is the fx of sigma subunits?

Answer 36

directs enzyme to promoter “Brains”

Question 37

True or False once transcription is started, the sigma subunit remains on the core complex.

Answer 37

False; once started, sigma subunit will release from the subunit

Question 38

True or False; RNA Polymerase is able to proofread its mistakes

Answer 38

False; it lacks a proofreading ability

Question 39

Are mistakes in RNA synthesis critical? Why yes or no?

Answer 39

No; many RNA copies are made from a single gene and they are rapidly degraded and replaced.

Question 40

What happens if there is a mistake made during RNA synthesis?

Answer 40

The RNA is rapidly degraded and replaced

Question 41

Upon Transcription Initiation, RNA Polymerase binds to how many DNA nucleotides? What bp upstream and downstream are they?

Answer 41

100 bp
-70 (upstream)
30 (downstream)

Question 42

Which Promotor Region bind at the:

-10

Answer 42

-10-Tata Box

sigma

Question 43

Which Promotor Region bind at the:

-40

Answer 43

-40- UP Element

alpha

Question 44

Which Promotor Region bind at the:

-60

Answer 44

-60- UP Element

alpha

Question 45

Which Promotor Region bind at the:

-35

Answer 45

-35- Nameless Region

sigma

Question 46

True or False

Single base pair chains in promotor sequences can affect the rate of transcription by orders of magnitude

Answer 46

True

Question 47

What is the RNA initiation region

Answer 47

+1

Question 48

True or False

RNA needs a primer

Answer 48

False; RNA does NOT need a primer

Question 49

Is upstream positive or negative?

Answer 49

Negative

Question 50

What forms when the polymerase (subunit) binds to the promoter?

Answer 50

Closed complex

Question 51

What forms the open complex?

Answer 51

DNA partially unwinds at the -10 sequence (TATA box)

Question 52

What happens immediately after Transcription begins?

Answer 52

Complex is converted into a conformationally distinct elongation form

Question 53

Does RNA Polymerase require a primer for synthesis?

Answer 53

No

Question 54

What are a few ways of controlling Transcription?

Answer 54

Changing promoter sequences;
Change binding preferences
using Accessory Proteins

Question 55

What are accessory proteins

Answer 55

Proteins that can either repress or activate transcription.

Question 56

Accessory Proteins are synonymous to _____.

Answer 56

Transcription Factors

Question 57

Does Accessory Help sites by increasing or decreasing kD?

Answer 57

Lowering

Question 58

If you want to keep a gene turned off, what can you do with sigma for gene affinity.

Answer 58

Use an accessory protein to prevent sigma from recognizing the promoter.

Question 59

What is the difference between activator and repressor in terms of kd?

Answer 59

activator- lowers kD

repressor- increases kD

Question 60

Which enzyme prevents “Supercoiling”

Answer 60

Topoisomerase

Question 61

RNA elongation occurs in which direction?

Answer 61

5’ -> 3’

Question 62

What can you do to take a photo of RNA Polymerase?

Answer 62

Give it a nucleotide that lacks 3’OH because it will stop transcribing and not have anything else to bind to.

Question 63

True or False

While Transcribing, RNA polymerase can stop at any moment.

Answer 63

False; it cannot stop until all DNA has been transcribed.

Question 64

Many RNA polymerases may transcribe the same gene at once

Answer 64

True

Question 65

What are the two types of RNA Transcription Termination in prokaryotes?

Answer 65

p- dependent/-independent

Question 66

Which type of Termination forms a Hairpin?

Answer 66

p-independent

Question 67

Explain the mechanism of p-independent termination?

Answer 67

• Self-complementary sequence of RNA near end of transcript forms a hairpin.
• DNA sequence is followed by a string of 3-A Uridylates at 3’ end
• Polymerase then pauses at this point, hangs up, disassociates and terminates.

Question 68

Explain the mechanism of p-dependent termination?

Answer 68

Sequence of A-residues is missing but there is usually a CA-rich region.

Polymerase pauses

P protein (Helicase) uses ATP hydrolysis to move along RNA strand.

P jumps on and tries to catch and can only catch it when it stalls, when it stalls p catches and termination occurs.

Question 69

Which type of Termination involves ATP Hydrolysis?

Answer 69

p-dependent

Question 70

What type of enzyme is P? (Termination)

Answer 70

Helicase`

Question 71

Which of the following is (are) characteristic of rho-independent termination of RNA transcription in E. coli?

Answer 71

The RNA transcript contains self-complementary sequences.

Three conserved A’s in the template strand near the end of the transcript.

Question 72

Which of the following statements about E. coli RNA polymerase is false?

A) Core enzyme selectively binds promoter regions, but cannot initiate synthesis without a sigma factor.
B) RNA polymerase holoenzyme has several subunits.
C) RNA produced by this enzyme will be completely complementary to the DNA template.
D) The enzyme adds nucleotides to the 3’ end of the growing RNA chain.
E) The enzyme cannot synthesize RNA in the absence of DNA.

Answer 72

A

Question 73

Which one of the following statements about the reverse transcriptases of retroviruses and the RNA replicases of other single-stranded RNA viruses, such as R17 and influenza virus, is correct?

A) Both enzymes can synthesize either RNA or DNA from an RNA template strand.
B) Both enzymes can utilize DNA in addition to RNA as a template strand.
C) Both enzymes carry the specificity for the RNA of their own virus.
D) Both enzymes have error rates similar to those of cellular RNA polymerases.
E) Both enzymes require host-encoded subunits for their replication function.

Answer 73

D

Question 74

Which one of the following statements about E. coli RNA polymerase (core enzyme) is false?

A) It can start new chains de novo or elongate old ones.
B) It has no catalytic activity unless the sigma factor is bound.
C) It uses nucleoside 5’-triphosphates as substrates.
D) Its activity is blocked by rifampicin.
E) Its RNA product will hybridize with the DNA template.

Answer 74

B

Question 75

Which of these polymerases does not require a template?

A) RNA pol I
B) RNA pol II
C) Reverse transcriptase
D) Polyadenylate polymerase
E) RNA replicase

Answer 75

D

Question 76

Splicing of introns in nuclear mRNA primary transcripts requires:

A) a guanine nucleoside or nucleotide. 
B) endoribonucleases. 
C) polynucleotide phosphorylase. 
D) RNA polymerase II. 
E) small nuclear ribonucleoproteins (snRNPs).

Answer 76

E

Question 77

Which of the following is not usually essential for the catalytic activity of ribozymes?

A) Correct base pairing 
B) Correct base sequence 
C) Correct interaction with protein 
D) Correct secondary structure 
E) Correct three-dimensional structure

Answer 77

C

Question 78

RNA polymerase:

A) binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed.
B) can synthesize RNA chains without a primer.
C) has a subunit called lambda, which acts as a proofreading ribonuclease.
D) separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them.
E) synthesizes RNA chains in the 3’—>5’ direction.

Answer 78

B

Question 79

“Footprinting,” or DNase protection, is a technique used to identify:

A) a region of DNA that has been damaged by mutation.
B) E. coli cells that contain a desired, cloned piece of DNA.
C) the position of a particular gene of a chromosome.
D) the position of internally double-stranded regions in a single-stranded DNA molecule.
E) the specific binding site of a repressor, polymerase, or other protein on the DNA.

Answer 79

E

Question 80

Which of the following statements about the synthesis of rRNA and tRNA in E. coli is true?

A) Both rRNA and some tRNAs are part of the same primary transcript.
B) Each rRNA sequence (16S, 23S, 5S) is transcribed as a separate primary transcript.
C) Primary tRNA transcripts undergo methylation, but rRNA sequences are not methylated.
D) The tRNA sequences all lie at the 3’end of the rRNA transcripts.
E) There is a single copy of the rRNA genes.

Answer 80

A

Question 81

After binding by E. coli RNA polymerase, the correct order of events for transcription initiation is:

A) closed complex formation, open complex formation, promoter clearance, start of RNA synthesis.
B) closed complex formation, open complex formation, start of RNA synthesis, promoter clearance.
C) open complex formation, closed complex formation, start of RNA synthesis, promoter clearance.
D) start of RNA synthesis, closed complex formation, open complex formation, promoter clearance.
E) start of RNA synthesis, open complex formation, closed complex formation, promoter clearance.

Answer 81

B

Question 82

Which of the following is not involved in mRNA processing in vertebrates?

A) 30S pre-rRNA
B) The nucleoleus
C) Ribonucleases
D) snoRNAs.
E) snoRNPs

Answer 82

A

Question 83

Which of the following statements about E. coli RNA polymerase (core enzyme) is false?

A) In the absence of the subunit, core polymerase has little specificity for where initiation begins.
B) The core enzyme contains several different subunits.
C) The core enzyme has no polymerizing activity until the subunit is bound.
D) The RNA chain grows in a 5’ 3’ direction.
E) The RNA product is complementary to the DNA template

Answer 83

C

Question 84

The 5’-terminal cap structure of eukaryotic mRNAs is a(n):

A) 7-methylcytosine joined to the mRNA via a 2’,3’-cyclic linkage.
B) 7-methylguanosine joined to the mRNA via a 5’ 3’ diphosphate linkage.
C) 7-methylguanosine joined to the mRNA via a 5’ 5’ triphosphate linkage.
D) N6-methyladenosine joined to the mRNA via a 5’ 5’ phosphodiester bond.
E) O6-methylguanosine joined to the mRNA via a 5’ 5’ triphosphate linkage.

Answer 84

C

Question 85

AZT (3’-azido-2’,3’-dideoxythymidine), used to treat HIV infection, acts in HIV-infected cells by:

A) blocking ATP production. 
B) blocking deoxynucleotide synthesis. 
C) inhibiting reverse transcriptase. 
D) inhibiting RNA polymerase II. 
E) inhibiting RNA processing.

Answer 85

C

Question 86

Which of the following is not a known function of TFIIH?

A) DNA helicase activity.
B) Hydrolysis of ATP.
C) Formation of an open complex
D) Termination of transcription
E) Nucleotide excision repair

Answer 86

D

Question 87

Can utilize only RNA templates.
B) has a 3’ 5’ proofreading exonuclease but not a 5’ 3’ exonuclease.
C) is activated by AZT.
D) is encoded by retroviruses.
E) synthesizes DNA with the same fidelity as a typical DNA polymerase

Answer 87

D

Question 88

Aptamers are:

A) double-stranded RNA products of nuclease action on hairpin RNAs.
B) repeat sequence elements at the ends of transposons.
C) small RNA molecules selected for tight binding to specific molecular targets.
D) the RNA primers required for retroviral replication.
E) the short tandem repeat units found in telomeres

Answer 88

C

Question 89

Which of the following is not a characteristic of the -terminator in E. coli?

A) The rho-terminator has an ATP-dependent RNA-DNA helicase activity.
B) The rho-terminator migrates in the 3’-5’ direction along RNA.
C) The rho-terminator causes RNA polymerase release at a CA-rich sequence near the end of the transcript.
D) ATP is hydrolyzed by the rho-terminator during the termination process.
E) All of the above are characteristics of the rho-terminator.

Answer 89

B

Question 90

Which of the following is not true about telomerase?

A) Telomerase is a reverse transcriptase.
B) Telomerase utilizes a tRNA template.
C) The primer for telomerase is the 3’-end of the DNA chromosomes.
D) Telomerase synthesizes DNA in the 5’ 3’ direction.
E) Telomerase consists of both RNA and protein.

Answer 90

B

Question 91

Compared with DNA polymerase, reverse transcriptase:

A) does not require a primer to initiate synthesis.
B) introduces no errors into genetic material because it synthesizes RNA, not DNA.
C) makes fewer errors in synthesizing a complementary polynucleotide.
D) makes more errors because it lacks the 3’ 5’ proofreading exonuclease activity.
E) synthesizes complementary strands in the opposite directionfrom 3’ 5’.

Answer 91

D

Question 92

Which of the following is not a post-transcriptional modification in mRNA or tRNA?

A) 4-thiouridine
B) Pseudouridine
C) Dihydrouridine
D) Ribouridine
E) Ribothymidine

Answer 92

D

Question 93

A branched (“lariat”) structure is formed during:

A) attachment of a 5' cap to mRNA. 
B) attachment of poly(A) tails to mRNA. 
C) processing of preribosomal RNA. 
D) splicing of all classes of introns. 
E) splicing of group II introns.

Answer 93

E

Question 94

Which of the following is (are) characteristic of rho-independent termination of RNA transcription in E. coli?

A) The RNA transcript contains self-complementary sequences.
B) Three conserved A’s in the template strand near the end of the transcript.
C) A CA-rich sequence near the end of the transcript.
D) Both A and B
E) Both A and C

Answer 94

D

Question 95

RNA polymerase:
A) binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed.
B) can synthesize RNA chains de novo (without a primer).
C) has a subunit called lambda, which acts as a proofreading ribonuclease.
D) separates DNA strands throughout a long region of DNA (up to thousands of base pairs),
then copies one of them.
E) synthesizes RNA chains in the 3’ → 5’ direction.

Answer 95

B

Question 96

The sigma factor of E. coli RNA polymerase:
A) associates with the promoter before binding core enzyme.
B) combines with the core enzyme to confer specific binding to a promoter.
C) isinseparablefromthecoreenzyme.
D) is required for termination of an RNA chain.
E) will catalyze synthesis of RNA from both DNA template strands in the absence of the
core enzyme.

Answer 96

B

Question 97

After binding by E. coli RNA polymerase, the correct order of events for transcription initiation is:
A) closed complex formation, open complex formation, promoter clearance, start of RNA synthesis.
B) closed complex formation, open complex formation, start of RNA synthesis, promoter clearance.
C) open complex formation, closed complex formation, start of RNA synthesis, promoter clearance.
D) start of RNA synthesis, closed complex formation, open complex formation, promoter clearance.
E) start of RNA synthesis, open complex formation, closed complex formation, promoter clearance.

Answer 97

B

Question 98

Which one of the following statements about E. coli RNA polymerase (core enzyme) is false?
A) It can start new chains de novo or elongate old ones.
B) It has no catalytic activity unless the sigma factor is bound.
C) Itusesnucleoside5’-triphosphatesassubstrates.
D) Its activity is blocked by rifampicin.
E) Its RNA product will hybridize with the DNA template.

Answer 98

B

Question 99

Processing of a primary mRNA transcript in a eukaryotic cell does not normally involve:
A) attachment of a long poly(A) sequence at the 3’ end.
B) conversion of normal bases to modified bases, such as inosine and pseudouridine.
C) excision of intervening sequences (introns).
D) joining of exons.

Answer 99

B

Question 100

The excision (splicing) of many group I introns requires, in addition to the primary transcript RNA:
A) a cytosine nucleoside or nucleotide and a protein enzyme.
B) a guanine nucleoside or nucleotide (only).
C) aproteinenzymeonly.
D) asmallnuclearRNAandaproteinenzyme.
E) ATP, NAD, and a protein enzyme.

Answer 100

B

Question 101

Splicing of introns in nuclear mRNA primary transcripts requires:
A) a guanine nucleoside or nucleotide.
B) endoribonucleases.
C) polynucleotidephosphorylase.
D) RNApolymeraseII.
E) small nuclear ribonucleoproteins (snurps).

Answer 101

E

Question 102

Which one of the following is not true of the mRNA for ovalbumin?
A) Exons are used for polypeptide synthesis.
B) Introns are complementary to their adjacent exons and will form hybrids with them.
C) The mature mRNA is substantially shorter than the corresponding region on the DNA.
D) The mRNA is originally synthesized in the nucleus, but ends up in the cytoplasm.
E) The splicing that yields a mature mRNA occurs at very specific sites in the RNA primary
transcript.

Answer 102

B

Question 103

Which of the following is not usually essential for the catalytic activity of ribozymes?
A) Correctbasepairing
B) Correctbasesequence
C) Correct interaction with protein
D) Correct secondary structure
E) Correct three-dimensional structure

Answer 103

C

Question 104

The reverse transcriptase of an animal RNA virus catalyzes:
A) degradation of the RNA strand in a DNA-RNA hybrid.
B) insertion of the viral genome into a chromosome of the host (animal) cell.
C) RNA formation in the 3’ → 5’ direction.
D) RNA synthesis, but not DNA synthesis.
E) synthesis of an antisense RNA transcript.

Answer 104

A

Question 105

Reverse transcriptase:
A) can utilize only RNA templates.
B) hasa3’5’proofreadingexonucleasebutnota5’3’exonuclease.
C) is activated by AZT.
D) is encoded by retroviruses.
E) synthesizes DNA with the same fidelity as a typical DNA polymerase.

Answer 105

D

Question 106

Compared with DNA polymerase, reverse transcriptase:
A) introduces no errors into genetic material because it synthesizes RNA, not DNA.
B) makes fewer errors in synthesizing a complementary polynucleotide.
C) makesmoreerrorsbecauseitlacksthe3’→5’proofreadingexonucleaseactivity.
D) synthesizes complementary strands in the opposite direction → from 3’ →
5’.

Answer 106

C

Question 107

Which one of the following statements about the reverse transcriptases of retroviruses and the RNA replicases of other single-stranded RNA viruses, such as R17 and influenza virus, is correct?
A) Both enzymes can synthesize either RNA or DNA from an RNA template strand. B) Both enzymes can utilize DNA in addition to RNA as a template strand.
C) Both enzymes carry the specificity for the RNA of their own virus.
D) Both enzymes have error rates similar to those of cellular RNA polymerases.
E) Both enzymes require host-encoded subunits for their replication function.Short Answer Questions

Answer 107

D

Question 108

What is alternative splicing?

Answer 108

One way to obtain multiple proteins from one gene

Question 109

True or False

rRNA are methylated

Answer 109

True

Question 110

On which end are tRNA’s processed 3’ or 5’ and what nucleases are found there?

Answer 110

3’ end; CCA

Question 111

_____ degrade mRNA. In eukaryotes this usually starts with ____ of poly (A) tail, followed by ______.

Answer 111

Ribonuclease
Shortening
Recapping