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Biochemistry 2 > RNA Metabolism > Flashcards

RNA Metabolism Flashcards

1
Q

What is the 1st step in gene expression?

A

To transcribe a gene

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2
Q

How is RNA different from DNA?

A

RNA has

  1. a hydroxyl group (on ribose at C2)
  2. Uracil (replaces thymine)
  3. is a single strand
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3
Q

What are 2 characteristics of RNA? Is it the only macromolecule that acts as both….

A

catalytic and genetic

Acts as an information transmitter and a catalyst

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4
Q

What are the 3 major classes of RNA?

A

mRNA (messenger)
tRNA (transfter)
rRNA (ribosomal)

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5
Q

What is transcription?

A

DNA-dependent RNA synthesis - need DNA template to make RNA

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6
Q

What is translation?

A

RNA-dependent protein synthesis (making proteins using code in mRNA)

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7
Q

What is a transcriptome?

A

The sum of all RNA molecules produced in a cell under a given set of conditions

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8
Q

What is the role of mRNA?

A

encodes the AA sequences of one or more polypeptides specified by a gene or set of genes

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9
Q

What is the role of tRNA?

A

reads the information encoded in the mRNA and transfers the appropriate AA to a growing polypeptide chain during protein synthesis

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10
Q

What is rRNA?

A

Constituents of ribosomes which synthesize proteins

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11
Q

What do microRNAs do?

A

they regulate the expression of genes via binding to specific nucleotide sequences - they don’t code for protein, but they regulate gene expression

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12
Q

What does RNA act as in some viruses?

A

Genomic material

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13
Q

What are the similarities between DNA replication and RNA synthesis?

A

Both

  1. Involve addition of complementary nucleotides
  2. Require a template
  3. Same direction of synthesis
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14
Q

What are the differences between DNA replication and RNA synthesis?

A
  1. transcription & RNA synthesis doesn’t require a primer
  2. A segment of DNA is used as a template for RNA
  3. There is only one template strand for RNA synthesis
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15
Q

What is the direction of the coding strand?

A

5’–>3’

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16
Q

What is the direction of the template strand?

A

3’–>5’

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17
Q

How is the new RNA strand created from the template strand different from the template strand?

A

U instead of T

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18
Q

How many subunits is RNA polymerase?

A

up to 12

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19
Q

What must happen to the DNA strand in order for RNA polymerase to synthesize it?

A

unwound

20
Q

How many DNA base pairs are unwound for RNA synthesis?

A

17-20

21
Q

how long are RNA-DNA hybrids that form as RNA is synthesized from the template strand?

A

~8-10 base pairs

22
Q

What is bound to RNA polymerase that aids in the dephosphorylating of the alpha-phosphate of an incoming nucleoside tri-phosphate?

A

Mg(2+)

23
Q

What is required in the catalytic mechanism of DNA-dependent RNA synthesis?

A
  1. DNA template
  2. all 4-rivo-NTPs
  3. Mg2+ (in 3D structure of protein)
  4. Zn2+ (in 3D structure of protein)
24
Q

Where does the Mg2+ attach the incoming NTP? On what side of the growing RNA chain?

A

alpha phosphate

By the 3’ hydroxyl of the growing RNA chain

25
Q

Which of the DNA strand is the coding strand?

A

EITHER one can be the coding strand!!!!! When one acts as coding strand, the other one does not.

26
Q

What is a promoter?

A

A specific sequence in the DNA that RNA-polymerase binds to

27
Q

Where does RNA polymerase begin?

A

at promoter

28
Q

What is upstream of the transcription start site in promoters?

A

TATA boxes

29
Q

How do sigma domains help RNA polymerase function?

A

They help RNA polymerase find the TATA box in the promoter sequence and bind to it, allowing the unwinding of DNA (initiation of transcription)

30
Q

What happens to the sigma subunit once transcription has begun?

A

It leaves

31
Q

What replaces the sigma subunit once transcription has begun? What is the function of this new subunit?

A

NusA, which helps move the polymerase forward (elongation)

32
Q

When does elongation stop in DNA dependent RNA synthesis? What leaves the complex at this point?

A

Once the terminator sequence has been reached.

The new mRNA & NusA leaves the complex. The RNA polymerase is now free to go bind to another sigma subunit which can then bind to a new promoter.

33
Q

What is the cycle involving the sigma and the NusA subunits?

A

Sigma Cylce

34
Q

What 2 characteristics of promoter sequences in eukaryotes?

A

Complex and very long (up to 1-2 kbp)

35
Q

What are the 3 types of RNA polymerases? What does each do?

A
  1. Pol I: synthesis of rRNA
  2. Pol II: synthesis of mRNA and specialized RNA
  3. Pol III: synthesis of tRNA, 5s rRNA and specialized RNA
36
Q

What is the major assembly point for the proteins of the preinitiation complexes of Pol II?

A

TATA box

37
Q

In promoters recognized by eukaryotic RNA polymerase 2, where is the DNA unwound?

A

At the initiator sequence: lnr

38
Q

Where is the TATA box relative to lnr?

A

upstream

39
Q

How many types of polymerases do prokaryotes have? Eukaryotes?

A

Prokaryotes: 1
Eukaryotes: 2

40
Q

Transcription at Pol II promoter: What initially binds to the TATA box? What comes in next and what does it do?

A

TBP with or without TFIIA.

TFIIB the comes in and binds into the complex, this brings in RNA Pol II

41
Q

Transcription at Pol II promoter: what does RNA polymerase II come in attached to?

A

TFIIF–Pol II

42
Q

What two following TFII(?) come in?

A

TFIIE, TFIIH

43
Q

What needs to be phosphorylated in order for Polymerase 2 to function? What is it made up of?

A

CTD (Carboxyl terminal domain). Repeats of 7 AAs

44
Q

What is the preinitiation complex made up of?

A

TBP, TFIIA/B/F/E/H, CTD, Pol 2, etc.

45
Q

What happens once the preinitiation complex is assembled?

A

DNA unwinding begins

46
Q

What happens as DNA unwinding begins?

A

The CTD domain is phosphorylated

47
Q

What enzyme both unwinds DNA and phosphorylates CTD?

A

TFIIH

Biochemistry 2 (8 decks)

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