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MCBM Exam 5 Kat > Transcription > Flashcards

Transcription Flashcards

0
Q

What kind of template is required for RNA synthesis?

A

A DNA template

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1
Q

What is RNA synthesized by?

A

By RNA polymerase

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2
Q

What direction is RNA synthesized?

A

5’ to 3’

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3
Q

Is a primer needed for RNA synthesis?

A

Nope

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4
Q

Do RNA polymerases proofread?

A

No, there are lots of mRNA copies, so occasional errors ok.

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5
Q

How many different RNA polymerases does E. Coli use for all transcript synthesis?

A

rRNA, tRNA and mRNA all use the same RNA polymerase

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6
Q

What are the 3 stages of RNA synthesis?

A

Initiation
Elongation
Termination

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7
Q

Where is transcription initiated?

A

At promoter regions on the template/coding strand

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8
Q

Which strand do we refer to when talking about the initiation site?

A

The sense strand even though the template strand is transcribed

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9
Q

Where is the site of transcription located in a gene?

A

5’ upstream of position of translational initiation codon of the sense strand

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10
Q

What is the transcriptional start site?

A

The first base on template transcribed/sense strand copied

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11
Q

Can promoter efficiency be increased or decreased?

A

Yes, by introducing mutations

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12
Q

How does RNA polymerase initially form a closed complex to DNA?

A

The holo enzyme binds weakly to the DNA, slides along the -35 site then binds closely.

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13
Q

What type of nt is almost always the first brought into the active site?

A

Purine

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14
Q

What is the sigma subunits required for?

A

Ensures specific, efficient recognition of the promoter

Once several bases incorporated the subunits is lost

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15
Q

What do different types of sigma subunits allow?

A

Different promoters to be used in transcription

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16
Q

When is the first phosphodiester bond created?

A

When the next nucleotide aligns with the template

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17
Q

How fast does RNA polymerase add bases?

A

About 50 bases/sec

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18
Q

What happens in the winding of DNA during elongation?

A

The DNA helix is unwound in front of the enzyme and rewound behind of the enzyme

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19
Q

What does rewinding do with RNA?

A

Displaces the growing RNA strand

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20
Q

Where does termination occur?

A

Some distance 3’ downstream of the translation termination codon

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21
Q

In termination, why does RNA polymerase dissociate?

A

Because once the nascent RNA chain is released the polymerase is no longer able to bind

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22
Q

What does DNA do when it goes through termination?

A

The helix rewinds

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23
Q

What are the two mechanisms of transcriptional termination?

A

Rho dependent

Rho independent

24
Q

What happens in Rho dependent termination?

A

The Rho protein binds to poorly characterized sequences in 3’ region of transcript and uses energy from ATP to break hydrogen bonds holding transcript to template.

25
Q

What is Rho independent termination driven by?

A

Secondary structure formation of RNA transcript and thermodynamics

26
Q

What happens in Rho independent termination?

A

Region of transcription folds into a U rich hairpin which reduces base pairing to just the template which has poor hydrogen bonding to template so favors DNA rewinding

27
Q

What does RNA polymerase I transcribe and where can it be found?

A

rRNA in the nucleolus

28
Q

What does RNA polymerase II transcribe and where can it be found?

A

mRNA and in the nucleus

29
Q

What does RNA polymerase III transcribe and where can it be found?

A

tRNA and 5S rRNA in the nucleus

30
Q

How sensitive is RNA polymerase I to alpha-amanitin?

A

Not

31
Q

How sensitive is RNA polymerase II to alpha-amanitin?

A

Super

32
Q

How sensitive is RNA polymerase III to alpha-amanitin?

A

Pretty sensitive

33
Q

Describe the core enzyme of RNA polymerase II?

A

It is a multisubunit protein and requires numerous additional proteins for efficient initiation of transcription.

34
Q

Where is the mRNA promoter TATA Box located?

A

25 bases upstream of +1 transcription start site

35
Q

What is required for efficient transcription to begin at the TATA box?

A

RNA polymerase II as well as numerous DNA sites(cis-acting elements, enhancers) and associated proteins that bind to these sites (transcription factors).

36
Q

What is the function of Pol II?

A

Catalyzes RNA synthesis

37
Q

What is the function of TBP?

A

Recognizes TATA box

38
Q

What is the function of TFIIA?

A

Stabilizes TFIIB and TBP binding to promoter

39
Q

What is the function of TFIIB?

A

Binds TBP; recruits pol II-TFIIF complex

40
Q

What is the function of TFIIE?

A

Recruits TFIIH; has ATPase and helicase activities

41
Q

What is the function of TFIIF?

A

Binds pol II; binds TFIIB and prevents nonspecific binding of pol II

42
Q

What is the function of TFIIH?

A

Unwinds DNA at promoter; phosphorylation pol II within CTD

43
Q

What is a newly synthesized RNA molecule called?

A

Primary transcript

44
Q

Does mRNA need to go through processing modification?

A

In prokaryotes no
In eukaryotes yes

All other transcripts other than mRNA in prokaryotes must go through processing.

45
Q

What sort of modifications do transcripts other than mRNA in prokaryotes go through?

A 
Base modifications (tRNA)
Cleavage of large primary transcript into functional fragments (rRNA)
46
Q

What happens in base modifications?

A

Bases are chemically modified

47
Q

Can primary transcripts be cleaved to produce functional fragments?

A

Yes they can!

48
Q

What are nucleoli?

A

Ribosomal factories

49
Q

What happens in the nucleolus?

A

rRNA and ribosomal proteins are arranged into large and small ribosomal subunits and shipped to the cytoplasm

50
Q

What happens to mRNA in eukaryotes when processed?

A

Introns are spliced, a 5’ cap and 3’ poly A tail are added

51
Q

What is mRNA splicing mediated by?

A

Small nuclear RNAs (snRNAs) called U1 to U6 and formation of a spliceosome complex

52
Q

How is the lariat structure formed in mRNA splicing?

A

OH groups serve as nucleophiles to form the structure then join the donor and acceptor junction.

53
Q

When are mRNAs edited before translation?

A

When the mRNA sequence does not precisely match complementary DNA sequence.

54
Q

What sort of editing does RNA undergo?

A

Addition, deletion and alteration of nucleotides

55
Q

When does addition/deletion of nucleotides occur?

A

In mitochondrial transcripts

56
Q

What does alteration usually involve?

A

Enzymatic deamination of A or C to form inosine (interpreted as g by translational machinery) or uridine.

57
Q

Why is protein produced in the intestine shorter than protein produced in the liver?

A

CAA (gln) is converted to UAA (stop)

58
Q

What are 4 inhibitors of transcription?

A

Rifamycin
Alpha-amanitin
Actinomycin D
Acridine

MCBM Exam 5 Kat (15 decks)

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