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Biochemistry 2 > RNA Metabolism > Flashcards

RNA Metabolism Flashcards

(47 cards)

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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?

20
Q

How many DNA base pairs are unwound for RNA synthesis?

21
Q

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

Study These Flashcards
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?

23
Q

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

Study These Flashcards
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?

Study These Flashcards
A

alpha phosphate

By the 3’ hydroxyl of the growing RNA chain

25
Which of the DNA strand is the coding strand?
EITHER one can be the coding strand!!!!! When one acts as coding strand, the other one does not.
26
What is a promoter?
A specific sequence in the DNA that RNA-polymerase binds to
27
Where does RNA polymerase begin?
at promoter
28
What is upstream of the transcription start site in promoters?
TATA boxes
29
How do sigma domains help RNA polymerase function?
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
What happens to the sigma subunit once transcription has begun?
It leaves
31
What replaces the sigma subunit once transcription has begun? What is the function of this new subunit?
NusA, which helps move the polymerase forward (elongation)
32
When does elongation stop in DNA dependent RNA synthesis? What leaves the complex at this point?
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
What is the cycle involving the sigma and the NusA subunits?
Sigma Cylce
34
What 2 characteristics of promoter sequences in eukaryotes?
Complex and very long (up to 1-2 kbp)
35
What are the 3 types of RNA polymerases? What does each do?
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
What is the major assembly point for the proteins of the preinitiation complexes of Pol II?
TATA box
37
In promoters recognized by eukaryotic RNA polymerase 2, where is the DNA unwound?
At the initiator sequence: lnr
38
Where is the TATA box relative to lnr?
upstream
39
How many types of polymerases do prokaryotes have? Eukaryotes?
Prokaryotes: 1 Eukaryotes: 2
40
Transcription at Pol II promoter: What initially binds to the TATA box? What comes in next and what does it do?
TBP with or without TFIIA. | TFIIB the comes in and binds into the complex, this brings in RNA Pol II
41
Transcription at Pol II promoter: what does RNA polymerase II come in attached to?
TFIIF--Pol II
42
What two following TFII(?) come in?
TFIIE, TFIIH
43
What needs to be phosphorylated in order for Polymerase 2 to function? What is it made up of?
CTD (Carboxyl terminal domain). Repeats of 7 AAs
44
What is the preinitiation complex made up of?
TBP, TFIIA/B/F/E/H, CTD, Pol 2, etc.
45
What happens once the preinitiation complex is assembled?
DNA unwinding begins
46
What happens as DNA unwinding begins?
The CTD domain is phosphorylated
47
What enzyme both unwinds DNA and phosphorylates CTD?
TFIIH

Biochemistry 2 (8 decks)

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