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Biochem BLOCK 3 > Transcription > Flashcards

Transcription Flashcards

1
Q

RNA polymerase action (general features of transcription)*

A
  • begins transcription without a ‘primer’
  • reads the template strand from 3’ to 5’
  • synthesizes the RNA transcript 5’ to 3’ using ribonucleotides (NTPs)
  • recognizes transcription termination signals
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2
Q

Transcription begins with

A
  • RNA polymerase identifying a gene’s promoter region
  • interacting with the DNA template strand
  • initiating synthesis of a complementary, antiparallel RNA transcript
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3
Q

When does transcription end

A

When a termination signal is reached

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4
Q

What strand is read during transcription?

A

Template strand

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5
Q

DNA coding strand sequence compared to RNA transcript sequence

A

Identical except RNA has Us instead of Ts

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6
Q

How are are base sequences (in DNA) numbered?

A

By giving the first base to be transcribed a +1 designation with +2, +3, etc. in the 3’ direction (downstream to the right)

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7
Q

How are the upstream DNA bases to the left, in the 5’ direction designated?

A

-1, -2, -3, etc

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8
Q

Holoenzyme

A

Core enzyme + sigma factor

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9
Q

Core enzyme

A 
4 subunits 
-two alpha subunits
-1 beta subunit
-1 beta-prime subunit 
  =a2BB
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10
Q

What kind of enzyme activity does core enzyme have?

A

RNA polymerase activity

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11
Q

What is sigma factor required for?

A

Recognizing and binding promoter sequences

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12
Q

Sigma factor

A
  • different sigma factors recognize different types of promoter sequences
  • recruits the core enzyme to the DNA promoter
  • dissociates from the core enzyme after the transcription begins
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13
Q

Initiation of transcription in prokaryotes

A

-scanning and recognition of promoter sequence cues by the holoenzyme trigger transcription initiation

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14
Q

Promoters

A

Contain two consensus sequences that are recognized by sigma factor

  • TATA box
  • -35 sequence
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15
Q

TATA box in prok

A

Consensus sequence of 6 nucleotides (TATAAT) sometimes called the pribnow box, ~7 nucleotides upstream from the +1 transcriptional start site (~-7)

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16
Q

-35 sequence in prok

A

Second consensus sequence (TTGACA) ~ 35 bases upstream (-35) from the +1 transcriptional start site

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17
Q

Elongation in transcription of prok

A

Transcription beings at the +1 transcriptional start site, sigma factor is released and the core enzyme continues

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18
Q

What does elongation create in transcription of prok

A

A temporary ‘melt’ between the double stranded DNA-forming a transcription bubble
-supercoils may be relieved by the action of topoisomerases

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19
Q

Net reaction of prok RNA synthesis (transcription)

A

Addition of a ribonucleotide to the growing RNA chain, and the release of pyrophosphate

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20
Q

What is pyrophospate cleaved by?

A

Pyrophosphatase

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21
Q

Cleaving of pyrophosphate by pyrophosphatase

A
  • irreversible coupled reaction

- 2 high energy bonds are cleaved

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22
Q

2 termination mechanisms of prokaryotic RNA synthesis (transcription)

A
  • Rho dependent termination

- Rho independent termination

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23
Q

Rho dependent termination

A

Requires an additional protein

-rho factor: displaces the DNA template strand from RNA polymerase

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24
Q

Rho factor

A

Displaces the DNA template strand from RNA polymerase

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25
Q

Rho independent termination

A

Requires G-C rich step loop followed by a poly-U stretch

-causes RNA polymerase to dissociate

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26
Q

Prokaryotic mRNA can be…

A

Polycistronic

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27
Q

Polycistronic

A

One mRNA can code for several proteins

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28
Q

Polycistronic mRNAs

A

Often code for multiple enzymes in the same biosynthetic pathway

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29
Q

Eukaryotic mRNAs are always

A

Monocistronic

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30
Q

Rifamipin (rifamyin)*

A
  • antibiotic
  • binds to prokaryotic RNA polymerase and prevents transcription initiation/elongation
  • used to treat tuberculosis
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31
Q

Prokaryotic synthesis of tRNA and rRNA

A

Similar to the model for eukaryotes, except in prokaryotes the same RNA polymerase produces all types of RNA

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32
Q

Why is eukaryotic DNA highly condensed (chromatin)

A

To allow gene transcription the genes must be exposed

33
Q

Euchromatin

A
  • Less condensed

- more accessible to RNA polymerases

34
Q

Acetlyation of histone H1

A

Causes the chromatin to revert to nucleosomes (bead on a string)

35
Q

Heterochromatin

A
  • appears more dense

- DNA is relatively inaccessible due to highly condensed structure

36
Q

DNA in herterchomatin

A

Highly methylated

37
Q

What is the foundation of epigenetics

A

DNA methylation

-twins with same genes, some mutations can result in the way its methylated in expressed between the twins

38
Q

RNA polymerase I (euk)

A

Transcribes precursors to rRNA in the nucleolus

39
Q

RNA polymerase II (euk)

A

Transcribes the precursor to mRNA (hnMRNA) in the nucleoplasm (some snRNAs as well)

40
Q

RNA polymerase III (euk)

A

Transcribes tRNA precursors (also small rRNA and some snRNAs)

41
Q

RNA pol II recognizes what two consensus sequences in eukaryotes

A
  • TATA box (Hogness box)

- CAAT box

42
Q

TATA box (Hogness box)

A
  • similar yo prokaryotic TATA box

- approximately 25 nucleotides upstream (-25)

43
Q

CAAT box

A
  • eukaryotes

- appproximately 70 nucleotides upstream (-70)

44
Q

Eukaryotic transcription elongation

A

Essentially the same as prokaryotic RNA syntheiss

45
Q

Termination of euk transcription

A

Requires a signal not well understood in euk

46
Q

rRNA synthesis and processing

A
  • not actually expressing a gene
  • three rRNAs are transcribed as a single larger precursor (by RNA pol I in the nucleolus)
  • individual rRNAs cleaved apart by RNases
  • prokaryotic rRNA synthesis is the same as in eukaryotes
  • instrumental in making ribosomes
47
Q

tRNA synthesis and processing

A

-RNA pol III in in the nucleoplasm

48
Q

RNA polymerase III in tRNA synthesis and processing

A
  • removal of intron loops
  • trimming of the 5’ and 3’ ends
  • base modifications
  • addition of the 3’-CCA sequence***
49
Q

Eukaryotic mRNA synthesis

A

Spatially and temporally separated from translation

50
Q

Transcription takes place (euk)

A

In the nucleus

51
Q

Translation takes place (euk)

A

In the cytoplasm

52
Q

Eukaryotic mRNA processing

A

Processed extensively (hnRNA to mRNA)

53
Q

When do prokaryotic mRNAs being translation?

A

Before transcription finishes

54
Q

Shine Delgarno sequence

A

Tells ribosome to start translation in prok

55
Q

Euk promoter regions

A 
CAAT box (-70)
TATA box (Hogness box) (-25)
56
Q

Prok promoter region

A 
TATA box (Pridnow) (-10)
-35 sequence
57
Q

Untranslated regions in prokaryotes and eukaryotes (UTRs)

A

Both have a 5’ and 3’ UTR

58
Q

Coding region in eukaryotes and prokaryotes

A

Eukaryotes have introns and exons (monocistronic)

Prokaryotes don’t have that

59
Q

5’ capping in eukaryotic mRNA

A
  • Addition of a 7-methylguanosine to the 5’ end of the mRNA-5’ to 5’ linkage
  • serves as a ribosome recognition signal and stabilizes mRNA (protects from nuclease degradation)***
60
Q

3’ poly A tail in Euk mRNA

A

The 3’ terminus contains a polyadenylation signal- a special enzyme (poly A polymerase) adds a variable stretch of adenin residues (~40-200)

61
Q

What kind of signal does the 3’ poly A tail of eukaryotic mRNA serve

A

Serves a signal for transport out of the nucleus, and stabilizes the mRNA from nuclease attack

62
Q

Is the 3’ poly A tail terminu encoded in the gene (of euk mRNA)

A

No, but the SIGNAL sequence is encoded, but the additional A’s are not

63
Q

Intervening sequences in euk RNA synthesis

A

Introns

64
Q

Expressed sequences in euk RNA synthesis

A

Exons

65
Q

Removal of introns

A

Must be removes from the coding region for proper translation

66
Q

Splicing

A

The removal of introns and the jointing of exons by snRNPs

67
Q

SnRNPs

A

Are composed of snRNAs and a group of proteins

68
Q

What are the snRNPs combined with?

A

Primary transcript from the spliceosome

-this is the molecular machine that performs the splicing reaction

69
Q

Lariat

A

Excised intron

70
Q

Splice sites

A

Have very specific sequences (mutations at these sites can cause incorrect splicing)

71
Q

Exons join together

A

During splicing to form mature mRNA

72
Q

How many intron sequences can eukaryotes contain?

A

Between 0 and 50

73
Q

Alternative splicing of hnRNAs

A

Joining of different exons together o form different mRNAs

74
Q

What does alternative splicing permit?

A

The production of proteins with some common domains, but the over all function of the protein is different
-gene is same though

75
Q

Systemic lupus erythematosus

A

Causes butterfly rash

  • observed in late-teen females
  • patient produces antibodies that recognize host proteins, including snRNPs
76
Q

After all processing events, mature eukaryotic mRNA is transported where?

A

Cytoplasm

77
Q

What mushroom genus accounts for 95% of all mushroom fatalities?

A

Genus amantia

78
Q

Amanita phalloides

A

The death cap mushroom

79
Q

Alpha-amanitin

A

From amanita phalloides mushroom

-binds to RNA polymerase II-inhibits mRNA synthesis

Biochem BLOCK 3 (12 decks)

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