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BIO 2306 > Ch. 13 Transcription > Flashcards

Ch. 13 Transcription Flashcards

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Biology 101 flashcards
1
Q

The strand the RNA is transcribed from

A

template strand

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2
Q

The strand the RNA is not transcribed from

A

nontemplate strand

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3
Q

Compare the mRNA and template strand

A

antiparallel
complementary

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4
Q

Compare the mRNA and nontemplate strand

A

parallel
same sequence (except T/U)

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5
Q

What direction is mRNA made?

A

5’ to 3’

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6
Q

What are the 3 parts of the transcription unit?

A

promoter
RNA-coding region
terminator

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7
Q

Which parts of the transcription unit become mRNA?

A

RNA-coding region
terminator

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8
Q

The terminator is ___ to the transcription start site

A

downstream

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9
Q

The promoter is ___ to the transcription start site

A

upstream

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10
Q

What number is given to the transcription start site?

A

+1

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11
Q

The promoter includes ___ numbers

A

negative

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12
Q

What substrate is used to make mRNA?

A

NTP

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13
Q

True or False: RNA can form secondary structures

A

True

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14
Q

True or False: there is only one type of RNA

A

False

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15
Q

True or False: RNA polymerase can unwind, rewind and break hydrogen bonds

A

True

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16
Q

True or False: RNA polymerase requires a primer

A

False

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17
Q

The parts of the core RNA polymerase

A

alpha
beta
beta prime
omega

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18
Q

The parts of the holoenzyme

A

core RNA polymerase
sigma factor

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19
Q

Provides specificity of binding

A

Sigma factor

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20
Q

When does the sigma factor leave?

A

after initiation

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21
Q

What RNA polymerase makes mRNA in eukaryotes?

A

RNA polymerase II

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22
Q

True or False: Consensus sequences are highly conserved through evolution

A

True

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23
Q

How do you find consensus sequences?

A

find the most common nucleotide

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24
Q

What is a sequence found in the promoter of bacteria ?

A

pribnow box

25
Q

How many phosphates are on the first RNA nucleotide added?

A

3

26
Q

How many phosphates are on rest of the RNA nucleotides added?

A

1

27
Q

Rho-dependent termination:

A

rho factor binds to rho site
rho has helicase activity
RNA polymerase pauses at terminator

28
Q

Rho-independent termination:

A

inverted sequences from a hairpin
string of uracil causes RNA polymerase to pause
occurs in bacteria

29
Q

The holoenzyme is to bacteria as the ___ is to eukaryotes

A

basal transcription apparatus

30
Q

What is the important promoter sequence in eukaryotes?

A

TATA box

31
Q

What transcription factor has TBP?

A

TFIID

32
Q

What is TBP?

A

TATA binding protein

33
Q

Parts of the eukaryotic promoter

A

core promoter
regulatory promoter

34
Q

What does the core promoter do?

A

controls binding

35
Q

What does the regulatory promoter do?

A

controls rate of transcription

36
Q

What are the parts of the basal transcription apparatus?

A

RNA polymerase II
transcription factors
mediator

37
Q

This facilities communication between TAP’s and basal transcription apparatus

A

mediator

38
Q

Where can TAP’s be found?

A

regulatory promoter
enhancer

39
Q

True or False: enhancers increase transcription

A

True

40
Q

Rat1 termination…

A

RNA polymerase II doesn’t care about terminator
cleavage of mRNA
Rat1 does 5’ to 3’ exonuclease activity
happens in eukaryotes

41
Q

Describe the effect of the following mutations on DNA replication: DNA polymerase III no longer has 3’ to 5’ exonuclease activity

A

errors cannot be fixed and replication may not continue

42
Q

Describe the effect of the following mutations on DNA replication: DNA polymerase I can not do 5’ to 3’ exonuclease activity

A

there will be a mix of DNA and RNA

43
Q

Describe the effect of the following mutations on DNA replication: DNA polymerase III doesn’t have 5’ to 3’ exonuclease activity

A

no effect

44
Q

Describe the effect of the following mutations on DNA replication: DNA polymerase alpha is mutated to remove primase activity

A

DNA replication cannot happen

45
Q

Describe the effect of the following mutations on DNA replication: DNA polymerase III cannot perform 5’ to 3’ polymerase activity

A

the DNA will only have primers

46
Q

Describe the effect of the following mutations on DNA replication: DNA polymerase I loses 5’ to 3’ polymerase activity

A

primers will be removed and not replicated

47
Q

Identify what would happen if the following mutations in bacterial transcription occured: the rut site sequence is mutated

A

who will not bind, RNA polymerase cannot be removed

48
Q

Identify what would happen if the following mutations in bacterial transcription occured: RNA polymerase cannot break hydrogen bonds

A

mRNA cannot be built

49
Q

Identify what would happen if the following mutations in bacterial transcription occured: rho factor loses helicase activity

A

rho factor can bind out but can’t detach RNA polymerase

50
Q

Identify what would happen if the following mutations in bacterial transcription occured: the activate site of RNA polymerase can only bind to dNTP’s

A

single stranded DNA will be made

51
Q

A new bacteria is built in the laboratory. The researchers only add the Pribnow box at one location in the DNA because they only want one mRNA transcript to be produced. They begin analyzing the sequences of the mRNA being produced. They are all different and it appears to be random. What may be missing in this new bacteria?

A

sigma factor

52
Q

Rho-independent termination is being studied under a microscope. Each time, the results indicate that the hairpin results at a distance away from the RNA polymerase. Since it is too far away, the hairpin cannot destabilize the DNA-RNA pairing. Furthermore, RNA polymerase is continuing to transcribe without stopping at the termination sequence. What might have happened?

A

terminator sequence is mutated

53
Q

Identify what would happen if the following mutations in eukaryotic transcription occur: an enzyme degrades all transcriptional activator proteins (TAP’s)

A

transcription slows down

54
Q

Identify what would happen if the following mutations in eukaryotic transcription occur: TFIID is removed

A

RNA polymerase II won’t bind to TATA box

55
Q

Identify what would happen if the following mutations in eukaryotic transcription occur: Rat1 is mutated to only have 3’ to 5’ exonuclease activity

A

extra mRNA cannot be degraded

56
Q

Identify what would happen if the following mutations in eukaryotic transcription occur: the promotor sequence is moved to be 3 units upstream of the terminator

A

pre-mRNA will be very short

57
Q

When analyzing the number of proteins found in a liver cell in a mouse, it is found to be 80% less than normal protein amounts. Further analyzing is done, and it is found that 5% of the proteins found are transcriptional activator proteins. It is determined that the problem in protein levels lies with the speed that transcription is occurring. What could be added to the liver cell to increase transcription rates and protein concentrations?

A

mediator

58
Q

After continuously noticing different lengths of pre-mRNA strands, a geneticist decides to analyze the termination sequence. She finds that it is a transposon. Transposons can ‘jump’ to different locations in the DNA. In one location, the transposon is found to be 20 units downstream of its original location. How will this effect Rat1, the pre-mRNA length, and the activity of RNA polymerase II?

A

Rat1 is unaffected
pre-mRNA will be longer
RNA polymerase II will be unaffected

BIO 2306 (18 decks)

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