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MCGB - Exam 1 Material > E1L9 - RNA > Flashcards

E1L9 - RNA Flashcards

1
Q

Why do we need an RNA “middleman” between DNA and protein?

A

Amplification system

Flexibility

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2
Q

Why not use U instead of T in DNA? After all, T is just a methylated U!

A
  1. That methylation is protective.

2. The DNA repair machinery wouldn’t know the difference between authentic U and deaminated cytosine.

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3
Q

Why don’t we care about mistakes in RNA?

A

We make large quantities of RNA and it has a limited half-life; it will be degraded anyways. Therefore mutations in RNA are more tolerable than DNA mutations.

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4
Q

20-40%

A

The proportion of all RNA that, in a snapshot of the cell, will be mRNA

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5
Q

Similarities between transcription and replication

A
  1. BOth use DNA template strand
  2. Both make strand in 5’-3’ direction
  3. New base is added based on Watson-Crick complementarity at the 3’ end
  4. That nucleotide is linked via phosphodiester bond
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6
Q

Differences between transcription and replication?

A
  1. DNA Pol vs. RNA Pol
  2. need primer vs. don’t need primer
  3. replicate entire genome vs. only whats needed
  4. High fidelity required vs. lower fidelity
  5. 1 error in 10 million nucleotides vs. 1 error in 10 thousand nucleotides
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7
Q

How many RNA pol in eukaryotes vs prokaryotes?

A

Prok only has 1 RNA pol

Euk has 3 RNA pol

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8
Q

True about TATA

A. Promotor
B. Most common promoter
C. Not essential 
D. Near transcriptional start site
E. All of the above
A

E. All of the above

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9
Q

RNA pol TRANSVERSES the DNA in what direction?

A

3’ to 5’ direction. See slide 13.

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10
Q

Why do promotors need to be asymmetrical?

A

So that transcription only works in one direction; tells you which of the strands is the template.

Generally for TATA boxes: 5’-TATAA-3’
Double A towards 3’ end….

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11
Q

Which TFII is composed of TBP (TATA binding protein) and TAF’s

A

TFIID (1st to bind).

In cases with no TATA box is present, then TAF will force TFIID to interact with the DNA in a non-sequence dependent manner!

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12
Q

Unlike most proteins, TBP binds to which groove of DNA?

A

The minor groove! Slide 17

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13
Q

TFIIH

A

High yield (also TFIID)……

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14
Q

True or False: mRNA processing occurs after mRNA is transcribed.

A

FALSE. Factors associate with newly transcribed mRNA (eg. capping factors, splicing, polyA factors, etc.) while it is still elongating!

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15
Q

Function of 5’ cap? List 4

A
  1. Protects mRNA
  2. Identifies mRNA as an mRNA
  3. Aids export mRNA from nucleus to cytoplasm
  4. Stabilizes transcript while its being moved
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16
Q

Function of 3’ Poly AAA tail?

A
  1. Protect mRNA from cleavage
  2. Identifie mRNA as mRNA
  3. Aid in export out of the nucleus
  4. Help stabilize transcript

CAP AND TAIL DO SAME THING, ESSENTIALLY

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17
Q

About what % of genetic diseases are due to splicing problems?

A

50%

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18
Q

How many introns does one splice reaction remove?

A

1

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19
Q

Please rank mRNA, rRNA, and tRNA in order of increasing abundance in the cell.

A

tRNA: 10%
mRNA: 20-40%
rRNA: 50-70%

(trick: TuMoR)

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20
Q

What’s the function of siRNA, miRNA, and IncRNA?

A

REGULATE gene expression

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21
Q

Which of the Eukaryotic RNA polymerases binds to the TATA box?

A

RNA polymerase II

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22
Q

What region of a typical gene is likely to be found near the transcription start site?

A

Promoter.

Note: “Promoters can sit upstream, at, or in the coding region. As long as its close to the start site.” Slide 12

23
Q

What is the advantage of having multiple promoters?

A

If one is knocked out, then we have back up promoters for the gene.

24
Q

Consider the following double stranded DNA:

5’-CCCCC-3’
3’-GGGGG-5’

RNA pol II is transcribing this gene from RIGHT to LEFT. Which of the strands, the top or the bottom, contains the TATA box?

A

The top strand has the TATA box. Since the RNA pol II is moving to the left, that means that the top strand is the template. That’s the only orientation in which 5’ to 3’ synthesis of mRNA is going to the left.

Convince yourself of this!

25
Q

True or False: the promotor sequence can be palindromic

A

FALSE: since the promotor needs to by asymmetrical to impose directionality, then it can’t be read the same in both directions.

Hence 5’-TATAA-3’

See how there are two A’s in a row near the 3’ end?

26
Q

TFIID exhibits two elements. What are they, and what are their functions?

A

TBD: TATA binding protein - recognizes and binds TATA

TAFS: TATA binding protein associated factors - enables TFIID to bind DNA in the absence of a promoter

27
Q

What key functions of TFIIH did we discuss in class?

A
  1. Helicase activity (ATP consumed, initially), causing a conformational change and opening the DNA
  2. Kinase activity - phosphorylates C-terminal tail of Pol II, which activates transcriptional elongation

Note: repair mechanisms too, from previous lecture

28
Q

Which TF stabilizes the open conformation of the DNA double helix?

A

TFIIH

29
Q

What is significant about this number:

1 : 10,000

A

The rate of error for RNA pol II:

1 mistake per 10,000 bases, which is significantly more than DNA pol

30
Q

Why is it significant that the new mRNA is QUICKLY moved out of the RNA exit channel or RNA pol II?

A

A new RNA polymerase can bind and start the next mRNA copy, without having to wait for the previous mRNA transcript to finish….

31
Q

True or False: The termination sequence or structure for RNA polymerase II is clear and defined

A

False - there is no clear termination sequence…not well understood. Probably not on test!

32
Q

Where does the notable 5’ to 5’ linkage occur?

A

Post-transcriptional modification:

7-methylguanine cap binds to 5’ end of mRNA transcript via 5’ to 5’ triphosphate bridge

33
Q

What enzymes are involved in adding a 5’ cap to the mRNA transcript?

A
  1. Phosphotase: cleaves the 5’ triphosphate to a diphosphate
  2. Guanyl transferase
  3. Methyl transferase
34
Q

Is a template required to form the poly AAA tail?

A

No

35
Q

What factors are involved in cleavage and polyadenylation of the 3’ end of an mRNA?

Note: the answer is in more detail than I think was emphasized in class.

A

CPSF: cleavage and polyadenylation specificity factor
(binds to AAUAAA)

CSTF: cleavage stimulation factor
(binds to GU-rich or U-rich)

PAP: poly-A polymerase (needs no template)

Poly A binding proteins

36
Q

How do the snRNP’s recognize the mRNA transcript?

A

Base-pairing. the snRNP has base-pairs since it’s an RNA.

37
Q

What protein do all 3 RNA polymerases have in common?

A

TBP - its a universal TF that can either bind to TATA or in a sequence independent fashion.

38
Q

Because we need A LOT of rRNA, we have ______ rRNA genes per haploid genome spread out over 5 chromosomes!

A

200

39
Q

18S rRNA
5.8S rRNA
28S rRNA

Which go to the small ribosomal subunit, and which go to large?

A

18S - small subunit

5.8S and 28S - large subunit

40
Q

Whereas the 45S rRNA is a precursor for ________ , the 5S rRNA is a precursor for __________.

A

Ribosomal RNA; tRNA

41
Q

Which transcription factor changes the conformation of the dsDNA molecule?

A

TFIID bends the DNA after binding the minor groove, making it more accessible to transcription factors and RNA polymerase

Note: TFIIH pries the two strands apart.

42
Q

Match the following transcription termination strategies, to RNA pol I, II, and III:

A. Polymerase specific termination factor binds the DNA downstream of the transcription unit

B. Can terminate at multiple sites, 0.5-2 kB beyond poly A site. No clear termination sequence.

C. Terminates after a series of U residues

A

A. RNA Pol I
B. RNA Pol II
C. RNA Pol III

43
Q

True or False: while the most common termination signals in Eukaryotes is AAUAAA and AUUAAA, there are many other hexameric sequences that follow suite. Only testing in a lab can determine the other possibilities…

A

TRUE

44
Q

What releases the RNA Pol II from the TF’s, causing it to start transcribing?

A. Methylation of the C-terminal tail of RNA Pol II
B. Phosphorylation of the C-terminal tail by TFIIH
C. Phosphorylation of the C-terminal tail by TFIID
D. None of the above

A

B.

45
Q

Detail question: what’s the charge of the 5’-cap?

A

Positive (+)

46
Q

How does the cell tell the difference between mRNA and tRNA/rRNA, after it leaves the nucleus?

A. mRNA has a 5’-cap
B. mRNA has a 3’-poly AAA tail
C. mRNA has introns that indicate its identity
D. mRNA has a poly-phosphorylated C-terminus
E. Two of the above

A

E. Two of the above

A and B

47
Q

Which nucleotide bases are associated with the 5’ splice donor site?

A

GU

48
Q

Which nucleotide bases are associated with the 5’ splice acceptor site?

A

AG

49
Q

Two subsequent __________ reactions compose a typical mRNA splicing reaction.

A

Trans-esterification reaction

50
Q

What’s a lariat?

A

It’s a spliced out intron, looped on itself.

51
Q

Does rRNA gene contain a promotor?

A

No. TBP binds with the aid of TAF proteins.

52
Q

T/F: Even though rRNA genes have no promoter, TBP is still important for the “Pol II” initiation complex.

A

FALSE: everything is correct except “Pol II” which should be “Pol I”

53
Q

T/F: TBP is important for the transcription of tRNA, as a part of the RNA Pol III complex

A

TRUE.

MCGB - Exam 1 Material (6 decks)

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