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Biochem Module 8 > RNA Synthesis, Processing & Modification > Flashcards

RNA Synthesis, Processing & Modification Flashcards

0
Q

RNA is a polymer composed of ribonucleotides connected through what bond?

A

3’-5’ phosphodiester bond

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1
Q

The central dogma of molecular biology:

A

DNA replication (DNA repair gentic recombination) –> RNA synthesis (transcription) –> protein syntesis (translation)

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2
Q

Ribonucleotides contain:

A

Hydroxyl groups on 2’- carbon of ribose sugar

Uracil (in place of thymine)

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3
Q

It is 80% of total RNA.

A

Ribosomal RNA (rRNA - rampant)

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4
Q

Involved in mRNA splicing and gene regulation.

A

small RNA (1%)

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5
Q

Working copies

A

The RNA are considered as _______ of DNA and it expresses the master plan contained in DNA.

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6
Q

It is the smallest of RNA species, excluding small RNA, and make up about 15%.

A

Transfer RNA (tRNA - transient/tiny)

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7
Q

Most heterogenous in terms of size and base sequence.

A

Messenger RNA (mRNA - massive) 2-5%

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8
Q

Measure of size based on molecular sedimentation rate during ultracentrifugation.

A

Svedberg unit

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9
Q

Prokaryotic rRNA:

A

23s
16s
5s

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10
Q

Give the type and stability of micro (miRNA - <1% total).

A

100’s-1000’s, stable

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11
Q

Stability of mRNA.

A

May vary from unstable to very stable (rRNA & tRNA are both very stable)

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12
Q

T or F: only DNA adhere to Watson-Crick base-pairing rules.

A

FALSE (both DNA & RNA)

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13
Q

Is a primer involved in RNA synthesis?

A

No (bec RNA polymerase have the ability to initiate synthesis de novo)

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14
Q

Which requires the entire genome to be replicated? RNA or DNA

A

DNA (RNA - only a portion is copied)

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15
Q

T or F: there is no proofreading function during RNA transcription.

A

TRUE

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16
Q

The template strand is always read in what direction?

A

3’ to 5’ direction

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17
Q

What do you call the opposite strand of the template?

A

Coding strand (non-template strand)

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18
Q

What is the enzyme responsible for polymerization of ribonucleotides into a sequence complementary to the template strand of the gene?

A

DNA-dependent RNA polymerase

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19
Q

The DNA-dependent RNA polymerase will attach to the ________ on the template strand, then initiation of RNA synthesis occurs.

A

Promoter

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20
Q

The ___________ of transcription corresponds to the 5’ nucleotide of the mRNA and is designated position +1.

A

Starting point of transcription

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21
Q

The nucleotide in the promoter adjacent to the transcription initiation site will be designated what number?

A

-1

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22
Q

Positive numbers will increase as sequence go ___________.

A

Downstream

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23
Q

_________ numbers will increase as sequence proceeds upstream, away fron the initiation site.

A

Negative

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24
Q

What are the 3 signals for transcription?

A

Initiation
Elongation
Termination

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25
Q

It is the RNA product, synthesized in 5’ to 3’ direction:

A

Primary transcript

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26
Q

It is defined as the region of DNA that includes initiation, elongation & termination:

A

Transcription unit

27
Q

3 components of a transcription unit:

A

Promoter
Coding-region
Terminator

28
Q

The enzyme responsible for 5’ -> 3’ RNA polymerase activity; has 4 subunits (plus an omega subunit):

A

Core enzyme

29
Q

The core enzyme lacks _______. It cannot recognize the promoter on the DNA template.

A

Specificity

30
Q

It enables RNA polymerase to recognize promoter regions on DNA:

A

Sigma subunit/factor contained in holoenzyme

31
Q

Some regions of DNA that signal the termination of transcription are recognized by _______________.

A

RNA polymerase

32
Q

On the other hand, termination of RNA synthesis in bacteria is signaled by a sequence in temolate strand, this signal is recognized by what termination protein?

A

rho factor

33
Q

It is an auxiliary lrotein of RNA polymerase:

A

Termination factor

34
Q

Primary transcripts generated by RNA polymerase II are promptly capped by:

A

7-methylguanosine triphosphate

35
Q

Why are caps for transcripts necessary? Give 3 reasons.

A

For subsequent processing of primary transcript to mRNA
For translation of mRNA
For protection of mRNA against exonucleolytic attack

36
Q

Binding of the RNA polymerase holoenzyme to a promoter region:

A

Initiation

37
Q

It is a stretch of 6 nucloetides (5’-TATAAT-3’) centered around 8 to 10 nucleotides to the left of the transcription start site that codes for the initial base of mRNA:

A

Pribnow box

38
Q

Consensus (general agreement/idea) of nucleotide sequences:

A

Pribnow box & -35 sequence
Highly conserved
Recognized by prokaryotic RNA polymerase sigma factors

39
Q

Centered around 35 bases to the left of the transcription start site

A

-35 sequence

40
Q

What is the possible effect of a mutation in Pribnow box or -35 sequence?

A

Can affect the transcription of the gene controlled by mutant promoter

41
Q

T or F: Unlike DNA polymerase, RNA polymerase has no endo or exonuclease activity. (No repair capability)

A

TRUE

42
Q

When would the RNA polymerase begin to synthesize a transcript of DNA sequence, and release signa subunit? (ELONGATION)

A

Once promoter has been recognized by holoenzyme

43
Q

In elongation, the ribonucleotides are added to ________.

A

3’-OH end

44
Q

T or F: the mechanism of RNA synthesis is NOT the same as that used for elongation of a DNA strand.

A

FALSE (same mechanism)

45
Q

3’-OH acts as a _________, attacking -phosphate of incoming ribonucleoside triphosphate & releasing pyrophosphate.

A

Nucleophile

46
Q

A rho factor protein is required for release of RNA product:

A

Rho dependent termination

47
Q

Rho factor binds to a _____ region near 3’ end of newly synthesized RNA, migrate behind RNA polymerase in the _____ direction until termination is reached.

A

C-rich region, 5’-3’ direction

48
Q

At termination, rho factor displaces DNA template strand thus facilitating ________ of RNA molecule.

A

Dissociation

49
Q

Activity of Rho factor that allows it to hydrolyze ATP thus able to unwind the 3’ end of transcript from the template:

A

ATP-dependent RNA-DNA helicase activity

50
Q

Give the 5 steps of Rho-dependent transcriptional termination:

A
  1. RNA polymerase transcribes DNA
  2. Rho attaches to recognition site on RNA
  3. Rho moves along RNA, following polymerase which would pause at terminator allowing rho to catch up
  4. Rho unwinds the DNA:RNA hybrid in transcription bubble
  5. Termination: RNA polymerase, rho & RNA are released
51
Q

In Rho-INDEPENDENT termination, a stable ___________ slows down progress of RNA polymerase & causes it to pause temporarily.

A

Hairpin turn

52
Q

A hairpin turn complementary to a region of DNA template near the termination region that exhibits 2-fold symmetry is due to _______.

A

Palindrome

53
Q

A rho-independent terminator contains an ______________, which are transcribed into RNA and would fold into a hairpin loop which would cause RNA polymerase to pause.

A

Inverted repeat

54
Q

In rho-independent termination, a transcription will terminate when inverted repeat form a ______ followed by a string of_________.

A

Hairpin, string of uracils

55
Q

In transcription of eukaryotic genes, aside from RNA polymerase recognizing the promoter, supplemental _____________ bind to DNA in eukaryotes.

A

Transcription factors

56
Q

How will RNA polymerase & transcription factors recognize & bind to specific DNA sequence?

A

Double helix must assume loose conformation & dissociate temporarily from nucleosome core

57
Q

Most actively transcribed genes are found in a relaxed form of chromatin called:

A

Euchromatin

58
Q

Refers to the interconversion of active & inactive forms of chromatin:

A

Chromatin remodeling

59
Q

Most inactive segmenta are in highly condensed:

A

Heterochromatin

60
Q

Acetylated histones would result to:

A

Looser chromatin structure

61
Q

Inactive genes contain more:

A

Methylated DNA (5-methylcytosine)

62
Q

T or F: mitochondrial RNA resembles bacterial RNA polymerase.

A

TRUE

63
Q

________ promoters utilize a small number of ybiquitous transcription factors while ________ uses a latge variety of specific ones.

A 
Pol I and III (small number)
Pol II (large variety)
64
Q

Fatal disease that results from autoimmune response where Px produces Abs against host proteins, including snRNPs:

A

Systemic lupus erythematosus

65
Q

Mutation causing incorrect splicing of beta-globin mRNA:

A

Beta thalassemia

Biochem Module 8 (4 decks)

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