Lecture 7- Intro & Prokaryotic Transcription Flashcards
(111 cards)
1
Q
What is transcription?
A
Process of copying DNA -> RNA
2
Q
In what direction does the coding strand run?
A
5’ -> 3’
3
Q
In what direction does the Template Strand run?
A
3’ -> 5’
4
Q
What is another name for the non-coding strand?
A
Template Strand
5
Q
RNA Polymerase runs in what direction?
A
5’ -> 3’
6
Q
RNA Polymeras’s template runs in what direction?
A
3’ -> 5’
7
Q
What direction does Polypeptides run in?
A
Amino Terminus -> Carbonyl Terminus
8
Q
_________- encodes the amino acids sequences of all the poly peptides found in the cell
A
mRNA (messenger)
9
Q
_________- matches specific amino acids to triplet codons in mRNA during protein synthesis
A
tRNA (transfer)
10
Q
________- the RNA component of the ribosome, interacts with tRNA during translation
A
rRNA (ribosomal)
11
Q
_________- post-transcriptionally regulate the expression of genes by binding to mRNA nucleotide seq.
A
miRNA (micro)
12
Q
True or False
Ribonucleic Acids act as genomic material in viruses.
A
True; also called ribosymes
13
Q
RNA Polymerase elongates in which direction?
A
5’ -> 3’
14
Q
How does RNA Polymerase attack/elongate?
A
Using the 3’ OH to attack the alpha phosphorous atom of the incoming nucleotide and release PPi
15
Q
How large is the initiation footprint?
A
100 base pair
16
Q
How large is the elongation footprint?
A
35 base pair
17
Q
True or False
RNA Polymerase’s footprint gets larger as it transcribes.
A
False; it gets smaller
18
Q
Which DNA strand travels through the RNA Polymerase’s Active Site?
A
Template Strand/Non-Coding strand
19
Q
True or False
DNA strand that serves as a template for RNA Synthesis is the non-template/coding strand?
A
False; Template Strand/Non-Coding strand
20
Q
True or False
Coding Strand is the complementary to the new RNA sequenced strand
A
True
21
Q
True or False
Genes can be encoded on either of the two DNA strands
A
True
22
Q
True or False
During Transcription, there is continuous winding/unwinding about RNA polymerase
A
True
23
Q
What size is the transcription bubble
A
17 base pair
24
Q
What size is the RNA/DNA Hybrid
A
8 base pair
25
Is the 5'end ever on the Active Site
No, it is always outside the Active Site
26
What happens if the wrong ribonucleotide attempts to enter the Active site and how does it enter?
It enters through the NTP channel and the channel rejects any ribonucleotide that is incorrect.
27
What happens to NTP's KD when an incorrect ribonucleotide attempts to enter the NTP channel.
Decreased Affinity
28
How many basepair of RNA-DNA are completed during elongation?
8
29
Elongation at the Active Site occurs at a rate of___.
50-90 pair
30
How many subunits are in RNA Polymerase's core?
5
31
How many total subunits are there?
6
32
What is the fx of alpha subunits?
Assembly & Binding of UP elements
33
What is the fx of Beta subunits?
Catalytic Subunit
34
What is the fx of Beta' subunits?
DNA Binding
35
What is the fx of omega subunits?
Protect RNA Polymerase from denaturation
36
What is the fx of sigma subunits?
directs enzyme to promoter "Brains"
37
True or False once transcription is started, the sigma subunit remains on the core complex.
False; once started, sigma subunit will release from the subunit
38
True or False; RNA Polymerase is able to proofread its mistakes
False; it lacks a proofreading ability
39
Are mistakes in RNA synthesis critical? Why yes or no?
No; many RNA copies are made from a single gene and they are rapidly degraded and replaced.
40
What happens if there is a mistake made during RNA synthesis?
The RNA is rapidly degraded and replaced
41
Upon Transcription Initiation, RNA Polymerase binds to how many DNA nucleotides? What bp upstream and downstream are they?
100 bp
-70 (upstream)
30 (downstream)
42
Which Promotor Region bind at the:
| -10
-10-Tata Box
sigma
43
Which Promotor Region bind at the:
| -40
-40- UP Element
alpha
44
Which Promotor Region bind at the:
| -60
-60- UP Element
alpha
45
Which Promotor Region bind at the:
| -35
-35- Nameless Region
sigma
46
True or False
| Single base pair chains in promotor sequences can affect the rate of transcription by orders of magnitude
True
47
What is the RNA initiation region
+1
48
True or False
| RNA needs a primer
False; RNA does NOT need a primer
49
Is upstream positive or negative?
Negative
50
What forms when the polymerase (subunit) binds to the promoter?
Closed complex
51
What forms the open complex?
DNA partially unwinds at the -10 sequence (TATA box)
52
What happens immediately after Transcription begins?
Complex is converted into a conformationally distinct elongation form
53
Does RNA Polymerase require a primer for synthesis?
No
54
What are a few ways of controlling Transcription?
Changing promoter sequences;
Change binding preferences
using Accessory Proteins
55
What are accessory proteins
Proteins that can either repress or activate transcription.
56
Accessory Proteins are synonymous to _____.
Transcription Factors
57
Does Accessory Help sites by increasing or decreasing kD?
Lowering
58
If you want to keep a gene turned off, what can you do with sigma for gene affinity.
Use an accessory protein to prevent sigma from recognizing the promoter.
59
What is the difference between activator and repressor in terms of kd?
activator- lowers kD
| repressor- increases kD
60
Which enzyme prevents "Supercoiling"
Topoisomerase
61
RNA elongation occurs in which direction?
5' -> 3'
62
What can you do to take a photo of RNA Polymerase?
Give it a nucleotide that lacks 3'OH because it will stop transcribing and not have anything else to bind to.
63
True or False
| While Transcribing, RNA polymerase can stop at any moment.
False; it cannot stop until all DNA has been transcribed.
64
Many RNA polymerases may transcribe the same gene at once
True
65
What are the two types of RNA Transcription Termination in prokaryotes?
p- dependent/-independent
66
Which type of Termination forms a Hairpin?
p-independent
67
Explain the mechanism of p-independent termination?
- 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.
68
Explain the mechanism of p-dependent termination?
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.
69
Which type of Termination involves ATP Hydrolysis?
p-dependent
70
What type of enzyme is P? (Termination)
Helicase`
71
Which of the following is (are) characteristic of rho-independent termination of RNA transcription in E. coli?
The RNA transcript contains self-complementary sequences.
Three conserved A's in the template strand near the end of the transcript.
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.
A
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.
D
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.
B
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
```
D
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).
```
E
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
```
C
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.
B
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.
E
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.
A
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.
B
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
```
A
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
C
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.
C
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.
```
C
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
```
D
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
D
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
C
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.
B
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.
B
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'.
D
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
```
D
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.
```
E
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
D
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.
B
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.
B
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.
B
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.
B
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.
B
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.
B
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).
E
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.
B
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
```
C
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.
A
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.
D
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'.
C
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
D
108
What is alternative splicing?
One way to obtain multiple proteins from one gene
109
True or False
| rRNA are methylated
True
110
On which end are tRNA's processed 3' or 5' and what nucleases are found there?
3' end; CCA
111
_____ degrade mRNA. In eukaryotes this usually starts with ____ of poly (A) tail, followed by ______.
Ribonuclease
Shortening
Recapping
