Ch. 13 Transcription Flashcards by Emily Burks

The strand the RNA is transcribed from

template strand

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The strand the RNA is not transcribed from

nontemplate strand

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Compare the mRNA and template strand

antiparallel
complementary

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Compare the mRNA and nontemplate strand

parallel
same sequence (except T/U)

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What direction is mRNA made?

5’ to 3’

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What are the 3 parts of the transcription unit?

promoter
RNA-coding region
terminator

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Which parts of the transcription unit become mRNA?

RNA-coding region
terminator

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The terminator is ___ to the transcription start site

downstream

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The promoter is ___ to the transcription start site

upstream

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What number is given to the transcription start site?

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The promoter includes ___ numbers

negative

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What substrate is used to make mRNA?

NTP

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True or False: RNA can form secondary structures

True

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True or False: there is only one type of RNA

False

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

True

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True or False: RNA polymerase requires a primer

False

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The parts of the core RNA polymerase

alpha
beta
beta prime
omega

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The parts of the holoenzyme

core RNA polymerase
sigma factor

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Provides specificity of binding

Sigma factor

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When does the sigma factor leave?

after initiation

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What RNA polymerase makes mRNA in eukaryotes?

RNA polymerase II

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True or False: Consensus sequences are highly conserved through evolution

True

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How do you find consensus sequences?

find the most common nucleotide

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What is a sequence found in the promoter of bacteria ?

pribnow box

How many phosphates are on the first RNA nucleotide added?

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

Rho-dependent termination:

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

Rho-independent termination:

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

The holoenzyme is to bacteria as the ___ is to eukaryotes

basal transcription apparatus

What is the important promoter sequence in eukaryotes?

TATA box

What transcription factor has TBP?

TFIID

What is TBP?

TATA binding protein

Parts of the eukaryotic promoter

core promoter regulatory promoter

What does the core promoter do?

controls binding

What does the regulatory promoter do?

controls rate of transcription

What are the parts of the basal transcription apparatus?

RNA polymerase II transcription factors mediator

This facilities communication between TAP's and basal transcription apparatus

mediator

Where can TAP's be found?

regulatory promoter enhancer

True or False: enhancers increase transcription

True

Rat1 termination...

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

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

errors cannot be fixed and replication may not continue

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

there will be a mix of DNA and RNA

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

no effect

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

DNA replication cannot happen

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

the DNA will only have primers

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

primers will be removed and not replicated

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

who will not bind, RNA polymerase cannot be removed

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

mRNA cannot be built

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

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

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

single stranded DNA will be made

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?

sigma factor

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?

terminator sequence is mutated

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

transcription slows down

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

RNA polymerase II won't bind to TATA box

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

extra mRNA cannot be degraded

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

pre-mRNA will be very short

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?

mediator

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?

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