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Biochemistry > Chapter 26: RNA Metabolism > Flashcards

Chapter 26: RNA Metabolism Flashcards

1
Q

DNA-dependent synthesis of RNA (process of copying a piece of DNA (a gene) as RNA)

A

Transcription

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2
Q

Which DNA strand is the template strand for transcription?

A

non-coding strand

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3
Q

Which Ribonucleic Acid encodes amino acid sequences of all the polypeptides found in the cell?

A

Messenger RNAs (mRNA)

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4
Q

Ribonucleic Acids?

A 
Messenger RNAs (mRNA)
Transfer RNAs (tRNA)
Ribosomal RNAs (rRNA)
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5
Q

post-transcriptionally regulate the expression of genes, by binding to mRNA nucleotide sequences

A

miRNA

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6
Q

Transfer RNAs (tRNA)

A

During protein synthesis, match specific amino acids to triplet codons in mRNA

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7
Q

RNA component of the ribosome, interact with tRNA during translation

A

Ribosomal RNAs (rRNA)

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8
Q

Less understood RNA function in eurkaryotes?

A

micro RNA (miRNA)

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9
Q

Four ribonucleotide 5’-triphosphates

A

ATP, UTP, GTP, CTP

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10
Q

DNA-dependent RNA polymerase requires:

A
  • DNA template, all
    four ribonucleotide 5’-triphosphates (ATP, UTP, GTP, CTP)
    -Mg2+
    -*In transcription, UTP is used in place of TTP.
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11
Q

RNA polymerase elongates an RNA strand in what direction?

A

5’ to 3’ direction

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12
Q

3’ hydroxyl attack the alpha-phosphorous atom of the incoming nucleotide and release PPi.

A

RNA Polymerase elongation mechanism

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13
Q

What is “NTP”?

A

nucleoside triphosphate (NTP) molecule containing a nucleoside bound to 3 phosphate groups.

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14
Q

The DNA strand that serves as the template for RNA synthesis

A

Template strand (DNA non-coding region)

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15
Q

TRUE/FALSE:

DNA non-template (coding) strand sequence as the newly made RNA molecule (RNA transcript)

A

TRUE

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16
Q

RNA-DNA duplex of approximately 8 bp are created during elongation

After elongation, RNA peels away allowing the DNA duplex to reform.

A transcription bubble forms with about 17 bp of DNA unwound.

A

Polymerization

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17
Q

Large complex with 5 sub-units, alpha, alpha, Beta, Beta prime, and omega (core units), and a sixth subunit , sigma.

A

E. coli RNA polymerase

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18
Q

In E.Coli RNA Polymerase, the assembly and binding to UP elements (sequence upstream of promoter)

A

Two alpha subunits function

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19
Q

In E.Coli RNA Polymerase, main catalytic subunit in the large complex

A

Beta subunit

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20
Q

In E.Coli RNA Polymerase, responsible for DNA-binding in the large complex

A

Beta prime subunit

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21
Q

In E. Coli RNA Polymerase, protect the

polymerase from denaturation (structural but no catalytic function) in the large complex.

A

Omega subunit

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22
Q

In E. Coli RNA Polymerase, directs enzyme to the promoter (“the brains”) in the large complex.

A

Sigma subunit

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23
Q

What subunit directs the core complex to specific binding sites on the DNA and released from core complex once transcription started?

A

Sigma subunit

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24
Q

Why aren’t mistakes in RNA synthesis are

generally not critical?

A

many RNA copies are made from a single gene and they are rapidly degraded and replaced.

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25
Q

Which phase of transcription is:

RNA polymerase binds to specific sequences of DNA known as promoters.

A

Intiation

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26
Q

RNA polymerase binds to how many DNA nucleotides,?

A

about 100

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27
Q

70 bp upstream of the start site has what numbers?

A

Designated by negative numbers

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28
Q

30 bp downstream of start site has what numbers?

A

Designated by positive numbers

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29
Q

In Transcription Initiation, two important promoter regions?

A

-10 position, -35 position

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30
Q

The Pribnow box, or TATA sequence, is found at what position?

A

-10 position

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31
Q

The UP element is located at what position?

A

-40 to -60 position

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32
Q

3 AT rich regions in Initiation?

A

-10
-35
UP element

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33
Q

Transcript Initiation

A

Polymerase binds to the promoter (forms closed complex)

DNA is partially unwound near the -10 sequence (forming the open complex)

Transcription is initiated and the complex is converted into a conformationally distinct elongation form.

complex then moves away from the promoter, releasing the sigma subunit

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34
Q

Examples of controlling Transcription

A

Differences in promoter sequences, requiring several sigma proteins with different sequence binding preferences.

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35
Q

Accessory proteins can either be _____ or ______ of transcription (transcription factors)

A

Activators, Repressors

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36
Q

Which Transcription step?

  • RNA chain elongation occurs in the 5’ to 3’ direction
  • RNA polymerase moves the transcription bubble along the DNA strand, creating positive supercoiling ahead of transcription and negative supercoiling behind.

-Entirely processive (Cannot let go of
DNA until it has finished making the complete RNA
transcript)

A

Elongation

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37
Q

Require a pausing of RNA polymerase on the
DNA transcript, which allows time for
termination to occur.

A

Transcript Termination

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38
Q

What are :

Rho-independent termination
Rho-dependent termination

A

Types of Transcript Termination

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39
Q

What type of transcript termination?

  • Self-complementary DNA sequence of RNA near the end of the transcript is usually followed by a string of three A residues (transcribed into
    uridylates) at the 3’ end of the RNA strand.
  • Forms a stable hairpin structure.
  • The polymerase pauses at this point,
    possibly because of the “hairpin” (affects
    associations between the RNA
    polymerase and the RNA transcript)
A

Rho-independent

40
Q

What type of transcript termination?

  • Sequence of repeated A residues is missing but there’s usually a CA-rich region. The polymerase pauses at this site.
  • The Rho protein binds to RNA at specific binding sites and migrates in the 5’ to 3’ direction until it catches up with the polymerase.
  • The Rho protein can only catch up to the polymerase if it is paused on the RNA transcript, hairpin structure also occurs in the RNA transcript in this form of termination.
A

Rho-dependent termination

41
Q

TRUE/FALSE:

The Rho protein is a helicase, and uses ATP hydrolysis to migrate along the RNA strand.

A

TRUE

42
Q

Eukaryotes have ____ types of RNA polymerases which form distinct complexes, although they do share some subunits.

A

3

43
Q

Which Eukaryotic RNA Polymerase?

Synthesizes mRNA precursors. Can recognize
thousands of promoters of varying sequence, through associated proteins.

A

RNA Polymerase II

44
Q

Eukaryotic RNA Polymerases have how many subunits?

A

at least 12.
{Requires an additional array of transcription factors (accessory proteins) to form an active transcription
complex.}

45
Q

Which subunit of Eukaryotic RNA Polymerase is similar to a Prokaryote RNA Polymerase subunit?

A

Eukaryote’s RBP1 subunit is similiar to bacteria’s Beta prime subunit

46
Q

Why are extra subunits required in eukaryotic transcription?

A

Because the packaging of DNA is far more complex in eukaryotes

47
Q

What is contained in RBP1 subunit long tail?

A

repeats of a “–YSPTSPS-“ sequence that

is important for regulation.

48
Q

Transcription from RNA polymerase II

can be divided into 4 steps:

A

– assembly
– initiation
– elongation
– termination

49
Q

Which step of Eukaryotic Transcription?

TATA-binding protein (TBP) binds to the TATA box. TFIIB, TFIIF-RNA Polymerase II, TFIIE, and TFIIH are recruited

A

Assembly

50
Q

Eukaryotic Transcription Initiation factor:

Binds tightly to RNA PolI and guides it to the correct DNA sequences (complex)
Binds to TFIIB.

A

TFIIF

51
Q

Binding of what completes the closed complex and starts to unwind the DNA to create the open complex?

A

TFIIH

52
Q

Which step of Eukaryotic Transcription?

TFIIH is also responsible for phosphorylating
RNA Pol II numerous times in its C-terminal
domain, causing a structural change and

A

Initiation

53
Q

What’s released as RNA Pol II synthesizes the first 60-70 nucleotides and enters the elongation phase?

A

TFIIE and TFIIH

54
Q

Which step of Eukaryotic Transcription?

Dephosphorylation of RNA Pol II

A

Termination

55
Q

Eukaryotic Transcription Initiation factor:

recognizes the TATA box

A

TBP (TATA-binding protein)

56
Q

Eukaryotic Transcription Initiation factor:

stabilizes the binding of TFIIB and TBP

A

TFIIA

57
Q

Eukaryotic Transcription Initiation factor:

Binds to TBP
Recruits TFIIF-Pol II complex

A

TFIIB

58
Q

Eukaryotic Transcription Initiation Factor:

Recruits TFIIH; has ATPase and helicase activties

A

TFIIE

59
Q

Eukaryotic Transcription Initiation factor:

Unwinds DNA at promoter (helicase activity); Phosphorylates Pol II I(within CTD); recruits nucleotide-excision repair

A

TFIIH

60
Q

Eukaryotic RNA molecules are called what?

A

Primary transcripts

61
Q

Eukaryotic transcripts generally contain information for how many genes?

A

A single gene

62
Q

Eukaryotic transcripts have intervening non-coding sequences that have to be what?

A

spliced out of the RNA transcrip

63
Q

In post-transcriptional processing, a cap consisting of a ________ residue is added to the _____ end of mRNA transcripts. The ___ end has to be cleaved and a poly(A) tail of 80-250 nucleotides is added.

A

7-methylguanosine , 5’, 3’

64
Q

In Capping of the 5’ end, what is added to the first and possibly the second nucleotide of the mRNA?

A

methyl group

65
Q

help protect the mRNA from ribonucleases and participates in binding to the ribosome.

A

The Cap

66
Q

When is the “cap” added and where does it come from?

A

early in transcription and comes from a molecule of GTP

67
Q

Is the “cap” methylated?

A

Yes. Cap is methylated at N-7 after it has been

added to the mRNA.

68
Q

TRUE/FALSE:

Cap is bound to the polymerase complex by
the cap-binding complex.

A

TRUE

69
Q

Capping likely marks the completion of what?

A

RNAP II’s switch from transcription initiation to elongation.

70
Q

Enzymes involved in the Cap-Synthesizing complex of process for “Capping the 5’ End”?

A
  • Phosphohydrolase
  • Guanylyltransferase
  • Guanine-7-methyltransferase
  • 2’ O-Methyltransferase
71
Q

TRUE/FALSE:

Mature eukaryotic mRNAs have poly(A)
tails of 80-250 nucleotides appended to their 3’ ends

A

TRUE

72
Q

TRUE/FALSE:

Poly A tails protect eukaryotic mRNAs (also interacts with ribosome), but they cause degradation of bacterial
mRNAs.

A

TRUE

73
Q

Endonuclease

A

Trims the Eukaryotic mRNA molecule back to within ~20 nucleotides

74
Q

TRUE/FALSE:

The poly(A) tail shortens over time and transcripts that
lack poly(A) tails are degraded in <30 minutes.
A

TRUE

75
Q

Coding part of a gene

A

Exon

76
Q

Non-coding part of a gene

A

Introns

77
Q

TRUE/FALSE:

Introns must be removed from the final
mRNA product before it is transported to the cytosol

A

TRUE

78
Q
  • Are self splicing
  • Interrupt mRNA, tRNA and rRNA genes
  • Found within nuclear, mitochondrial, and chloroplast genomes
  • Common in fungi, algae, and plants, also found in bacteria
A

Group I and II Introns

79
Q
  • Spliced by spliceosomes
  • Most common introns
  • Frequent in protein-coding regions of eukaryotic genomes
A

Splicesomal introns

80
Q
  • Spliced by protein-based enzymes
  • Found in certain tRNAs in eukaryotes and archae
  • Primary transcript cleaved by endonuclease
  • Exons are joined by ATP-dependent ligase
A

tRNA introns

81
Q

TRUE/FALSE:

Poly(A) site is ~15 to 20 nucleotides past a conserved AAUAAA sequence

A

TRUE

82
Q

Group I Intron

A

Use guanylate (GMP, GDP, or GTP) to initiate the splicing process.

Nucleotide attacks the 3’-end of the first exon, generating a 3’-OH that will then attack at the 5’-end of the second exon.

3’ OH of a specific guanosine in the intron acts as nucleophile attacking phosphate at the 5’ splice site to form lariat structure

Intron is then released and eventually degraded

83
Q

Group II Intron

A

Use an adenosine residue within the intron to initiate
splicing.

2’ OH of a specific adensosine in the intron acts as nucleophile attacking 5’ splice site to form lariat structure

A branched lariat
structure is formed as an
intermediate, and then
released.

84
Q

Most introns require help to be spliced or removed by what large protein complex

A

spliceosome

85
Q

Spliceosome contains five RNA-protein complexes involving small nuclear RNA proteins (snRNPs). What are they?

A

U1, U2, U4, U5, U6,

86
Q

What is required to bring the spliceosome
together, but it is not needed for the
cleavage reaction?

A

ATP

87
Q

What splicing generates alternative mRNAs from a single gene?

A 
Alternative Splicing
(intron could be spliced out by itself or spliced out along with an intervening exon)
88
Q

Encoded as one or two long genes that are transcribed by RNA Pol I and then get spliced into the individual
rRNA molecules.

rRNA molecules also get methylated.

Some prokaryotes have tRNAs located in the sequences between
the rRNA genes.

A

Ribosomal RNAs

89
Q

RNase P

A

a ribozyme

90
Q

RNase D

A

a protein

91
Q

Nucleotides are removed from both the 5’ and 3’-
ends of the initial transcript: the 5’ end is cut by RNase P (a ribozyme) and the 3’ end is cut by RNase D (a protein).

Base modification

5’ cleavage

3’ cleavage

“CCA” tail is added.

Additional splicing and base modifications occur

A

Transfer RNAs (tRNA)

92
Q

Cellular level where cell can regulate the expression of proteins

A

mRNA is one way

93
Q

TRUE/FALSE:

Bacterial mRNAs have an average half life of only 1.5
minutes.

A

TRUE

94
Q

mRNA is degarded by what?

A

Ribonucleases

95
Q

TRUE/FALSE:

In eukaryote, mRNA degradation usually starts with shortening of Poly A tail, then decapping

A

TRUE

96
Q

TRUE/FALSE:

Average half life of a vertebrate mRNA is 3 hours, but it
can be degraded in seconds or days.

A

TRUE

Biochemistry (5 decks)

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