Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MICR Final > RNA Synthesis and Regulation from DNA Templates: DNA virus and Retroviruses > Flashcards

RNA Synthesis and Regulation from DNA Templates: DNA virus and Retroviruses Flashcards

1
Q

Where does transcription, translation, and genome replication of RNA viruses occur?

A

Transcription: Cytoplasm
Translation: Cytoplasm
Replication: Cytoplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Where does transcription, translation, and genome replication of DNA viruses occur?

A

Transcription: Nucleus
Translation: Cytoplasm
Replication: Nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Where does transcription, translation, and genome replication of retroviruses and para-retroviruses occur?

A

Transcription: Nucleus
Translation: Cytoplasm
Replication: Nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is special about Orthomyoxiviridae’s transcription and genome replication?

A

Transcription: Nucleus
Replication: Nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is special about Poxviridae’s transcription, translation and genome replication?

A

Everything is in the cytoplasm

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the four key features of transcription in eukaryotes?

A

1) Confined to the nucleus
2) Three distinct types of RNA polymerases and associated factors
3) RNA processing
4) Combinatorial regulation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are three types of RNA polymerases and their dependency?

A

1) RNA POL I –> DNA-dependent RNA polymerase I
2) RNA POL II –> DNA- dependent RNA polymerase II
3) RNA POL III –> DNA-dependent RNA polymerase III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is special about RNA POL II?

A

Most viruses use POL II

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the composition or core polymerases of RNA POL I? (5)

A

RPA1, RPA2, RPC5/RPC9, RPB6, and 9 others

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the composition or core polymerases of RNA POL II? (5)

A

RBP1, RBP2, RPB3, RPB6, and 7 others

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the composition or core polymerases of RNA POL III? (5)

A

RPC1, RPC2, RPC5, RPB6, and 11 others

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What cellular RNAs are synthesized from RNA POL II?

A

Pre-mRNAs, pre-miRNAs, four snRNAs (U1, U2, U4,U5)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What cellular RNAs are synthesized from RNA POL III?

A

Pre-tRNAs, 5srRNA, snRNA (U6)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What viral RNAs are synthesized from RNA POL I?

A

None identified

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What viral RNAs are synthesized from RNA POL II?

A

Pre-mRNAs, mRNAs, pre-miRNAs, and genomic RNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What viral RNAs are synthesized from RNA POL III?

A

Ad2 VA-RNAs, EBV EBER RNAs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What does it mean for mRNA transcription in eukaryotes to be combinatorial?

A

1) Ensures a gene is transcribed only when it needs to be (avoid accidental transcription from off-target gene)
2) Sharing of a finite set of transcription activators among many genes
3) Offers fine tuning and regulation of gene expression via the combinatorial effects of different combinations of transcription factors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are the common DNA binding motifs?

A

Zinc finger
Helix-turn- helix
Basic helix-loop-helix
Homeodomain

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the DNA dimerization domain?

A

Leucine zipper helix

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the features of a DNA activation domain?

A

Acidic
Rich in glutamate
Proline and isoleucine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is the limiting step in transcription?

A

Initiation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What was the dilemma with RNA splicing?

A

Precursors of mRNAs are heterogenous in size (hnRNAs) and these hnRNAs are much longer than mature mRNAs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What do hnRNAs have?

A

They have preserved sequences at both the 5’ and the 3’ ends after treatment with RNAse1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What happened when viral genomic DNA was hybridized with hexon mRNA?

A

Produces three loops in the mRNA (introns)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is mRNA splicing?

A

Introns are spliced out of pre-mRNA to get mature mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Why is alternative splicing important (4)?

A

1) Allows multiple mynas and proteins to be produced from a single gene
2) Different isoforms of proteins have different functions, which are important for gene regulation
3) Enables the mix and match of sequence modules and functional domains
4) Maximize the coding capacity of limited genomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What does HSV1 produce?

A

The protein VP16

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are the functions and properties of HSV1 ? (2)

A

1) Stimulates transcription from IE promoters via its potent acidic activation domain
2) Achieves promoter specificity by interacting with two cellular factors, Oct-1 and Hcf

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What does SV40 produce?

A

The LT antigen

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are the functions and properties of SV40? (4)

A

1) Stimulates late gene transcription
2) Binds to Top, TfIIB, and Tef-1 via different domains
3) no activation domain
4) May stabilize initiation complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is the transcription activator for HSV-1?

A

ICP4

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is the function of ICP4 in HSV-1?

A

1) Induces transcription from E and L promoters

2) Represses IE transcription (auto-repression)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What does HSV-1 contain? (5)

A

IE, EE, LE, LL, TL genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is expressed as late genes in HSV-1?

A

Essential proteins required for entry and DNA replication are expressed as late genes and packaged into the virion.
These are the tegument proteins: VP16, VHS, ICP27

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What happens when HSV-1 enters the cell?

A

When HSV-1 enters the nucleus of the host cell, the linear genome is circulated by cellular enzymes

36
Q

What is special about the viral transcripts in HSV-1?

A

They lack introns, so individual genes need to be transcribed individually
ICP27 can actually block the splicing of host pre-mRNA because they lack introns, so no splicing occurs

37
Q

What is the cycle of infection for HSV-1?

A

Switches between latency and lytic infection

38
Q

In latency of viruses what happens?

A

In latency, viral mRNAs are not produced, so no viral DNA replication and no virion formation
There are three latency associated transcripts detected in infected neuronal cells
Research demonstrates the production of 16 miRNAs, most of which are derived from the LAT region

39
Q

What are the RNA POL III transcriptions for HAV-2? What is the function?

A

VA-RNA1, VA-RNAII

Prevent activation of dsRNA-dependent protein kinase

40
Q

What are the RNA POL III transcriptions for EBV? What is the function?

A

EBER-1 and EBER-2

Always made in latently infected cells and maintain latency

41
Q

What are the RNA POL III transcriptions for Herpes salmiri-2? What is the function?

A

HSVR 1- 5

Degrade certain cellular mRNAs

42
Q

What are the RNA POL III transcriptions for Moloney murine leukaemia virus? What is the function?

A 
Let 
Stimulates transcription of specific cellular genes (CD4 and class I MHC genes
43
Q

What is the TATA Box?

A

Binding by TBP, followed by the assembly of the pre-initation complex, basal transcription

44
Q

What is +1?

A

This is the transcription start site the first nucleotide being synthesized. It will always be a purine

45
Q

What is the coding DNA strand?

A

5’ –> 3’ and is the strand that has the same sequence as its transcript RNA

46
Q

What is the template DNA strand?

A

3’ –> 5 and is the strand used as the template to make RNA copies

47
Q

What are transcription regulators?

A

Activators, co-activators, and repressors

They bind regulatory sequences and modulate transcription through a mediator complex (looping model of transcription)

48
Q

What are the distant regulatory sequences?

A

Enhancers and silencers

Far from transcription start site

49
Q

What makes up the core promoter?

A

TATA sequence and the initiator sequence

50
Q

What is the initiator sequence?

A

Where transcription starts

51
Q

What makes up the promoter?

A

core promoter and local regulatory sequences

52
Q

What makes up the transcriptional control region?

A

Distant regulatory sequences and the promoter

53
Q

What happens in the RNA polymerase during transcription and after?

A

During transcription there is a bend in DNA, and DNA re-anneals after transcription

54
Q

How does DNA enter and exit the polymerase?

A

DNA enters the polymerase downstream and exits upstream

55
Q

What makes up the RNA polymerase?

A

A wall, a pore, a funnel, ribonucleoside enter site and a groove

56
Q

What are the commonly used inhibitors of transcription?

A

Antinomycin D

alpha- Amanitin

57
Q

What is guanylyl-transferase associated with and why?

A

Guanylyl transferase is associated with CTD of Pol II to ensure each mRNA is capped as it is transcribed

58
Q

How is 5’ capping carried out?

A

On a short (20-30 nt) nascent pre-mRNA transcribed by POL II

59
Q

What is the 5’ cap?

A

It is a special molecule of 7 methyl-guanosine linked to the 5’ terminal nucleotide of pre-mRNA via a 5’- 5’ triphosphate linkage

60
Q

What is the 5’ cap’s function?

A

To signal and protect mRNAs for translation

61
Q

How was the 5’ cap discovered?

A

In 1970 in a reovirus and vaccinia virus

62
Q

What is the 5’ cap bound by?

A

The 5’ cap is bound by the cap-binding complex.

Once the cap is added, the guanylyl-transferase dissociates and CBC joins

63
Q

What and where are the promoters for adenovirus transcription and RNA splicing?

A

5 on the top strand: E1A, E1B, E3, IX, and major late

3 on the bottom strand: E4, E2A/E2B, and IVa2

64
Q

How does adenovirus transcription work?

A

11 polyadenylation sites
13 families of viral genes, encoding 50 proteins
The major late promoter is present and very active during late infection

65
Q

How does adenovirus transcription termination occur?

A

There are 5 late promoters, and transcription can terminate anywhere from L1 to L5

66
Q

What proteins do each of the late promoters encode?

A 
L1: IIIa, 52/55k
L2: V, PVII, penton (III)
L3: 23K (protease), hexon (II), PVI 
L4: pVIII, 33K, 100K 
L5: fiber (IV)
67
Q

How are sequences of introns recognized for splicing of pre-mRNAs?

A

1) 5’ splice site in exon 1: A/G A G
2) 3’ splice site in exon 2: G
3) Branchpoint in in the intron which is an A

68
Q

What is constitutive splicing?

A

Let’s say you have exon 1 intron 1 exon 2 intron 2 exon 3.

Constitutive splicing you get: exon1-exon-2-exon 3

69
Q

What is alternative splicing?

A

Let’s say you have exon 1 intron 1 exon 2 intron 2 exon 3
Exon skipping: exon1-exon 2
Alternative 5’ splice sites
Alternative 3’ splice sites

70
Q

What is special about viral transcription control regions?

A

They resemble those of eukaryotic genes

71
Q

What do the SV40 early, Ad2 early, and Ad2 late genes have in common?

A

They all contain the TATA box to ensure assembly of the POL II holoenzyme
Each promoter contains upstream DNA binding sites for multiple transcription activators encoded by the host cell

72
Q

What do the early promoters for SV40 and Ad2 have?

A

They contain repeats of the same DNA sequences, even in reverse direction, to allow binding of multiple copies of the transcription activator

73
Q

Where can transcription initiation begin?

A

Multiple positions in the Inr sequence

74
Q

Explain the SV40 early gene

A

Has many Sp1 sequences (stimulatory protein 1) and a TATA box, and transcription initiation can start from many sites within the promoter region

75
Q

Explain the Ad2 early gene

A

Has an Atf (activating transcription factor), two E2F sequences (E2 factor, which binds to the E2 gene promoter in adenoviruses) and a TATA box, and transcription initiation can start from many sites within the promoter region

76
Q

Explain Ad2 late genes

A

Has a CpI site, and a Usf sequence (upstream stimulatory factor), and a TAT box. Transcription can only begin from one position in the promoter region

77
Q

How does 289R and 243R stimulate RNA transcription?

A

1) Both isoforms recruit HAT (p300/Cpb), loosening up nucleosomes for transcription
2) Both isoforms bind pRb, releasing transcription activator E2F, activating expression of a wide range of genes, forcing cell entry to S phase
3) E2F activates E2 expression, producing proteins required for genome replication
4) 289R binds Med23 (part of mediator complex), Atf-2 and Sp1, inducing E3 and E4 transcription.

78
Q

Why is VP16 important and where does it come from?

A

VP16 activates transcription in HSV and is an abundant tegument protein in the virion

79
Q

How does VP16 activate transcription

A

VP16 activates transcription of IE genes through interaction with two cellular transcription factors: Oct-1 and HCF
Oct1 binds at the octane sequence (TAAT-GARAT) in promoters of IE genes
HCF binds VP16 in the cytoplasm and transports VP16 to the nucleus
VP16 bound with HCF associates with Oct-1, stimulating transcription via two mechanisms: assembly of initiation complex, and chromatin remodelling

80
Q

How do retroviruses transcribe proviral DNA

A

Transcription control elements are located in the U3 region of LTR
No viral transcription factors, total reliance on the host cell factors
Transcription control regions are recognized by various common transcription factors in both avian and mammalian species
Avian and mammalian factors are homologs of each other

81
Q

What is each region in proviral DNA and what do they produce in avian cells?

A 
CArG region (2): EfII
Y region (2): Yb-1
82
Q

What is each region in proviral DNA and what do they produce in mammalian cells?

A 
CArG region (2): Srf
Y region (2): Cbf, Nf-y
83
Q

What is each region in proviral DNA and what do they produce in third option?

A 
CArG region (2): MADS box
Y region (2): Cbf, Y box
84
Q

Where are the retroviruses promoters and enhancers?

A

Promoter downstream from -100 bp
Enhancer upstream of -100 bp
If confused there is a figure

85
Q

What is the domain structure of TAT? What does each domain structure do?

A

N-terminal - Cytosine rich - Core - Basic - C terminal
N terminal and Cytosine rich and Core: Stimulation of activation domain
Basic: RNA binding in vitro (NLS)

86
Q

How does HIV-1 undergo transcription?

A

1) TAT enhances transcription of full length viral RNA through binding at TAR
2) TAR forms a SL structure in short nascent RNA transcript, impeding elongation of transcription
3) TAT recruits p-Tefb (cyclin T and Cdk9) and phosphorylates CTD of POL II, increasing full length viral RNA by 100-fold

87
Q

How is Ad2 VA-1 RNA transcribed by RNA POL III?

A

A and B boxes are essential for efficient transcription of VA-1 gene

1) TfIIIC1 and TFIIIc2 bind to the intragenic promoter
2) TfIIIb binds TFIIIc- DNA complex and recruits RNA POL III
3) Transcription termination resembles that of tRNA genes

MICR Final (13 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions