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2) Biochemistry II > RNA Metabolism > Flashcards

RNA Metabolism Flashcards

1
Q

What is the first step in gene expression?

A

Transcribe a gene

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2
Q

How does RNA differ from DNA? (3)

A

o RNA contains a hydroxyl group on C2
o RNA contains Uracil, instead of Thymine in DNA
o RNA is mostly single-stranded

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3
Q

RNA is both a ______ and _______ molecule

A

genetic

catalytic

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4
Q

What are the three major classes of RNA?

A
  • mRNA (messenger)
  • tRNA (transfer)
  • rRNA (ribosomes)
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5
Q

RNA is the only macromolecule that functions as both an _______________ and ___________

A

information transmitter

catalyst

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6
Q

What is transcription?

A

DNA-dependent RNA synthesis (DNA template is needed to synthesize RNA)

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7
Q

What is translation?

A

RNA-dependent protein synthesis (mRNA)

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8
Q

What is transcriptome?

A

Collection of all transcripts (or mRNAs)

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9
Q

What is the function of mRNAs?

A

Encode the amino acid sequences of all the polypeptides found in the cell

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10
Q

What is the function of tRNAs?

A

Match specific amino acids to triplet codons in mRNA during protein synthesis

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11
Q

What is the function of rRNAs?

A

Constituents of ribosomes

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12
Q

What is the function of microRNAs? What must they have?

A
  • Regulate the expression of genes via binding to specific nucleotide sequences
  • Must have a complementary sequence for their target RNA
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13
Q

What are similarities between DNA replication and RNA synthesis? (3)

A

o Addition of complementary nucleotides
o Requirement of template
o Direction of synthesis: 5’ to 3’

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14
Q

What are differences between DNA replication and RNA synthesis?

A

o RNA synthesis does not require a PRIMER, unlike DNA synthesis
o While DNA replication includes the whole genome as a template, RNA synthesis only uses a SMALL SEGMENT of DNA as a template
o For any given segment of DNA, only ONE STRAND acts as a template in RNA synthesis

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15
Q

RNA must distinguish between which DNA strands?

A
  • DNA coding strand

- DNA template strand

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16
Q

Which DNA strand is the ALMOST the same as the RNA transcript? What is the minor difference?

A
  • DNA coding strand

- The Ts are replaced by Us

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17
Q

Where does RNA synthesis occur? What must be done for synthesis to occur?

A
  • At RNA polymerase

- DNA strand must be unwound, which creates a coding and template strand

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18
Q

What is created for a short period of time during RNA synthesis?

A

DNA/RNA hybrid

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19
Q

What did Watson and Crick determine in terms of complementarity of RNA?

A

Can either be:

  • 2 pyrimidines
  • 1 purine and 1 pyrimidine
  • 2 purines
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20
Q

What is the width of DNA? What is type of bonding between nucleotides?

A
  • Width: 1.08 nm

- Hydrogen bonding

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21
Q

During RNA synthesis, an incoming nucleotide arrives as a ________

A

triphosphate

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22
Q

What does RNA polymerase require?

A
  • DNA template
  • All 4 types of nucleotides
  • Magnesium (cofactor)
  • Zinc (cofactor)
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23
Q

What is the catalytic mechanism of RNA polymerase?

A
  • OH- group at the 3 position of the existing nucleotide attacks the first phosphate group (alpha phosphate)
  • Forms a 3’-> 5’ phosphodiester bond
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24
Q

The phosphate groups are always present at which carbon?

A

At the 5th carbon

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25
Q

Which strand of DNA becomes the coding strand?

A

The coding strand may be either; when one acts as a coding strand, the other is a template strand

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26
Q

In Prokaryotes, where are promoters located?

A

Upstream (left)

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27
Q

In Prokaryotes, what are -10 and -35 regions called? Why?

A
  • TATA boxes

- Mostly made of Thymine and Adenosine

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28
Q

What are the promoter regions composed of in Prokaryotes?

A
  • 2 TATA boxes

- 1 regulatory regions

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29
Q

What does RNA polymerase recognize?

A

The TATA boxes

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30
Q

What is the transcription cycle called in Prokaryotes?

A

Sigma cycle

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31
Q

What is the function of the Sigma domain?

A
  • Helps the RNA polymerase find the TATA box
  • Begins the unwinding of DNA (initiation of transcription)
  • Recognition and initiation
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32
Q

What happens once transcription begins in Prokaryotes?

A
  • Sigma domain leaves

- NusA subunit comes in

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33
Q

What is the function of the NusA subunit?

A
  • Helps the RNA polymerase move forward

- Elongation and termination

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34
Q

When is synthesis terminated in the transcription cycle of Prokaryotes?

A

When a terminator sequence is present, which causes the departure of NusA

35
Q

In Eukaryotes, what is upstream of the initiator sequence? And, what is upstream of that?

A

o Upstream: TATA box

o Upstream of the TATA box: several regulatory sequences (complex)

36
Q

Prokaryotes have ____ type of RNA polymerase, while Eukaryotes have _____

A

one

three

37
Q

What does “Y” mean in terms of nucleic acids? What does “N” mean?

A
  • “Y” means any pyrimidine (C or G)

- “N” means any of the four

38
Q

What is the function RNA polymerase I?

A

Synthesis of rRNA

39
Q

What is the function to RNA polymerase II?

A

Synthesis of mRNA and specialized RNA

40
Q

Which eukaryotic RNA polymerase is similar to the prokaryotic RNA polymerase? How many subunits does it contain in Eukaryotes?

A
  • RNA Pol II

- 12 subunits

41
Q

What is the function to RNA polymerase III?

A
  • Synthesis of tRNA
  • Synthesis of 5s rRNA
  • Synthesis of specialized RNA
42
Q

In Pol II, what binds to the TATA box? What is the TATA box often associated with?

A
  • TBP binds to the TATA box

- TATA box is often associated with TFIIA

43
Q

What happens when TBP binds to the TATA box?

A
  • TFIIB binds to the complex
  • RNA Pol II is brought in, which is bound to TFIIF
  • Recognizes the initiator sequence and binds
44
Q

Once Pol II binds to the initiator sequence, what is brought in?

A

TFIIE comes in, which causes TFIIH to enter

45
Q

What is important about the CTD domain in Pol II?

A
  • Contains heptad AA repeats (52 in humans)

- CTD needs to be phosphorylated to function

46
Q

What happens when the pre-initiation complex is formed?

A
  • When TFs are added, pre-initiation complex is formed
  • DNA unwinding beings
  • CTD domain of Pol II is phosphorylated
47
Q

The unwinding of DNA and the phosphorylation of the CTD domain is regulated by what?

A

TFIIH

48
Q

What allows promoter escape? What is the consequence?

A
  • When the CTD domain is phosphorylated (RNA Pol II can leave the promoter region)
  • Allows it to move forward into the gene region, while synthesizing RNA strands
49
Q

What happens when promoter escape takes place?

A
  • TFIIH and TFIIE leave

- Elongation factors arrive

50
Q

What happens when a termination sequence arrives?

A

Causes Pol II release and dephosphorylation

51
Q

What specifically recognizes the TATA box

A

TBP

52
Q

What stabilizes binding of TFIIB and TBP to the promoter?

A

TFIIA

53
Q

What unwinds DNA at the promoter and phosphorylates Pol II (within the CTD)?

A

TFIIH

54
Q

What recruits TFIIH?

A

TFIIE

55
Q

What binds to TBP and recruits Pol II-TFIIF complex?

A

TFIIB

56
Q

What binds tightly to Pol II and binds to TFIIB?

A

TFIIF

57
Q

What are three important processes on synthesized RNA?

A
  • 5’ capping
  • Intron deletion (splicing)
  • Polyadenylation (Poly-A tail) synthesis
58
Q

When does 5’ capping occur?

A

Very early in the synthesis of RNA (after 20-30 bases)

59
Q

What occurs in association with RNA polymerase?

A

5’ capping

60
Q

What is the unusual linkage in 5’ capping?

A
  • 5’ to 5’ phosphodiester bond

- 7-methyl-guanosine

61
Q

What is the function of the 5’ cap?

A

Protects from ribonuclease, which specifically cleave RNA

62
Q

Transcription always occurs with a ______ attached to RNA polymerase II

A

5’ cap

63
Q

Differentiate introns and exons.

A

Exons code for proteins, and introns are intermediate sequences

64
Q

What must be spliced out for an mRNA to be synthesized? What is the exception?

A
  • Introns

- Exception: histone genes do not have introns

65
Q

How do introns and exons differentiate in terms of length?

A

Exons are short (< 1000 bases); Introns are long (up to 20 000 bases)

66
Q

What are the two types of splicing?

A
  • Self-splicing mRNA

- Splicing by spliceosome

67
Q

Give an example of self-splicing mRNA.

A

Mitochondrial genes

68
Q

Do self-splicing mRNA require ATP?

A

No since it is non-enzymatic

69
Q

How do self-splicing mRNAs function? What is at the 5’ end and what is at the 3’ end?

A
  • 5’: UpA
  • 3’: GpU
    1) OH group of guanosine acts as a nucleophile and attacks the phosphate at the 5’ end
    2) The 3’ OH of the 5’ exon becomes a nucleophile, which completes the reaction
    3) pGpA - G-OH (spliced intron)
    UpU (exon)
70
Q

Group 1 and 2 introns are _________, while group 3 introns are ________

A

self-splicing

spliced by spliceosomes

71
Q

Group 3 introns occur in which types of mRNA?

A

Most types of mRNA

72
Q

What is a spliceosome? How many types are they?

A
  • RNA-proteins called snRNP’s (small nuclear RN proteins)

- 5 snRNPs: U1, U2, U4, U5, and U6

73
Q

Group 3 and 4 introns (ex: tRNA) require what?

A

ATP

74
Q

What is the typical sequence that forms boundaries in splicing by spliceosome?

A
  • 5’: GU

- 3’: AG

75
Q

Where is the splicing sequence in splicing by spliceosome?

A

Upstream of AG

76
Q

The snRNPs are complementary to what?

A

mRNA

77
Q

What are the steps to spliceosome splicing?

A

1) U1 and U2 bind to the sequence (energy dependent)
2) U4/U6 and U5 arrive, but the complex is still inactive
3) U1 and U4 leave, which frees up the GU at the 5’ end
4) G (5’) interacts with A (3’), which creates a loop

78
Q

The creation of a loop by a spliceosome is called what?

A

Lariat formation

79
Q

What is one of the cleavage signals in polyadenylation?

A

AAUAAA

80
Q

Which proteins assemble at cleavage sequences?

A
  • Polyadenylate polymerase

- Endonuclease

81
Q

What are the steps to polyadenylation (poly-A tail)?

A

1) Cleavage: endonuclease comes in and cleaves the long, extra sequence of mRNA
2) Synthesis of Poly-A tail: addition of a sequence of A-repeats

82
Q

What is the function of polyadenylation? When is it performed?

A
  • At the end of transcription
  • Protects the mRNA molecule from enzymatic degradation in the cytoplasm
  • Aids in transcription termination
83
Q

What does alternative splicing lead to?

A

Multiple mRNAs from one gene

2) Biochemistry II (23 decks)

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