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Biochem Block 3 > Transcription > Flashcards

Transcription Flashcards

1
Q

RNA polymerase action in prokaryotes

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

What does transcription begin with?

A
  • RNA polymerase identifying a genes promoter region
  • interacts with DNA template strand
  • initiates 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 synthesis?

A

-genes are described by the sequence of the CODING STRAND, but the TEMPLATE STRAND is the one read during synthesis by RNA polymerase

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5
Q

Coding strand of DNA and RNA transcript sequence

A
  • they are the exact same, but there are U’s instead of T’s in the RNA transcript
  • both are 5’ to 3’
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6
Q

numbering and base sequence

A
  • the first base to be transcribed is +1
  • downstream(to the right in the 3’ direction) goes up in plus direction
  • upstream(to the left in the 5’ direction) goes down in the negative direction
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7
Q

promoter

A

-always upstream of the +1 position

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8
Q

what direction does the template strand run?

A

3’ to 5’

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9
Q

holoenzyme

A
  • core enzyme+sigma factor
  • prokaryotic RNA polymerase construction
  • scanning and recognition or promoter sequence cues by holoenzyme initiate RNA transcription
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10
Q

core enzyme subunits

A
  • 2 alpha subunits
  • 1 beta subunit
  • 1 beta’ subunit
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11
Q

core enzyme

A

-has RNA polymerase activity for nucleotide elongation

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12
Q

sigma factor

A
  • required for recognizing and binding promoter sequences
  • different sigma factors recognize different promoter sequences
  • recruits core enzyme to DNA promoter
  • dissociates from core enzyme after transcription begins
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13
Q

prokaryotic promoters

A
  • 2 consensus sequences
  • TATA box
  • -35 sequence
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14
Q

prokaryotic TATA box

A
  • prinbnow box
  • sequence of 6 nucleotides
  • 7 nucleotides upstream from the +1 transcriptional start site
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15
Q

-35 sequence

A
  • consensus sequence in prokaryotes

- 35 bases upstream from +1 transcriptional start site

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16
Q

elongation in prokaryote RNA synthesis

A
  • transcription begins at the +1 start site
  • sigma factor must be released first, then core enzyme continues
  • generated in the 5’ to 3’ direction
  • creates a temporary “melt” of dsDNA to form transcription bubble
  • results in supercoiling
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17
Q

Net reaction of prokaryote RNA synthesis

A
  • addition of a ribonucleotide to the growing RNA chain

- release of a pyrophosphate

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18
Q

what do DNA polymerases and RNA polymerases have in common?

A
  • both release a pyrophosphate which is further cleaved by pyrophosphatase
  • provides energy to drive reaction
  • makes reaction irreversible
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19
Q

What are the two termination mechanisms for prokaryotic RNA sequences?

A
  • Rho-dependent termination

- Rho-independent termination

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20
Q

rho

A

-displaces the DNA template strand from RNA polymerase

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21
Q

rho-dependent termination

A

-requires an additional protein to displace DNA template from RNA pol

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22
Q

rho-independent termination

A
  • requires a G-C rich stem loop followed by a poly-U stretch
  • causes RNA pol to dissociate
23
Q

Shine-dalgarno sequence

A
  • translation
  • right before a gene
  • tells ribosome to begin at that point to start translation
  • the next time you see a start codon, you should start translation
  • new shine-dalgarno sequence right before each new gene
24
Q

polycistronic

A
  • only prokaryotes
  • one mRNA codes for several proteins(multiple genes on one transcript
  • code for multiple enzymes in the same biosynthetic pathway
25
Q

rifampin

A
  • antibiotic
  • binds to prokaryotic RNA pol to prevent transcription
  • used to treat TB
  • interact with core enzyme and cause conformational change so it cannot read template strand
  • ONLY PROKARYOTIC
26
Q

prokaryotic RNA polymerase

A

-RNA pol I produces ALL types of RNA

27
Q

Euchromatin

A
  • less condensed DNA

- more accessible to RNA polymerase for transcription

28
Q

Acetylation of histone H1

A

-causes chromatin to revert to nucleosomes,beads on a string, so it is more exposed

29
Q

Heterochromatin

A
  • appears more dense DNA
  • DNA is relatively inaccessible due to its highly condensed structure
  • highly methylated which determines epigenetics/phenotype
30
Q

Eukaryotic RNA polymerase I

A

-transcribes precursors to rRNA in the nucleolus

31
Q

RNA polymerase II

A
  • transcribes precursor to hnRNA in nucleoplasm

- eventually hnRNA becomes mRNA

32
Q

RNA polymerase III

A

-transcribes tRNA precursors

33
Q

Eukaryotic consensus sequences

A
  • TATA box

- CAAT box

34
Q

Eukaryotic TATA box

A
  • Hogness box
  • 25 nucleotides UPstream from start site
  • recognized by RNA pol II
35
Q

CAAT box

A
  • 70 nucleotides UP stream from start site

- recognized by RNA pol II

36
Q

rRNA synthesis in Eukaryotes

A
  • three rRNAs are transcribed as a single large precursor
  • large precursor cut to three by RNA pol I
  • individual rRNA are cleaved apart by RNases
37
Q

tRNA synthesis in Eukaryotes

A
  • RNA pol III
  • removal of intron loops
  • trimming of 5’ and 3’ ends
  • base modifications at 3’ end
  • addition of 3’CCA sequence(important for adding amino acids)
38
Q

where does eukaryotic transcription take place?

A

nucleus

39
Q

Where does eukaryotic translation take place?

A

cytoplasm

40
Q

Eukaryotic mRNA and prokarotic mRNA

A

Eukaryotic: extensively processed from hnRNA to mRNA
Prokaryotic: begin mRNA translation before transcription is over

41
Q

5’ capping

A
  • addition of 7-methylguanosine to 5’ end of eukaryotic mRNA

- ribosome recognition signal AND protect from nuclease degradation

42
Q

3’ poly-A tail

A
  • 3’ terminus of eukaryotic mRNA contains a polyadenylation signal
  • site for addition of adenine residues
  • the additional A’s are not encoded in the gene
  • serves are a signal for transport out of the nucleus and stabilizes mRNA from nuclease degradation
43
Q

introns

A

intervening sequences

44
Q

exons

A

expressed sequences

45
Q

Why must introns be removed?

A

-they are not exressed, so they must be removed for proper translation

46
Q

Splicing

A

-the removal of introns and the joining of exons by snRNPs

47
Q

snRNPs

A
  • composed of snRNA and a group of proteins

- form lariot, clip it out, join exons

48
Q

lariat

A

-the excised intron

49
Q

alternative splicing

A
  • joining of different exons together to form different mRNAs
  • produces proteins with SOME common domains, but the overall function is different
50
Q

Who is primarily affected by systemic lupus erythematosus?

A

-onset is in late-teen females

51
Q

systemic lupus erythematosus

A
  • produce antibodies that recognize host proteins, including snRNPs
  • results in butterfly rash
52
Q

where is mature mRNA transported after processing events are complete?

A

cytoplasm

53
Q

Amanita phalloides

A
  • death cap mushroom

- contains alpha-amanitin

54
Q

alpha amanitin

A

-binds to RNA pol II and inhibits mRNA synthesis

Biochem Block 3 (10 decks)

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