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Flashcards in Exam 2 Deck (74):

Which RNA polymerase component is required for promoter recognition?

a. alpha (α)

b. beta (β)

c. beta prime (β’)

d. sigma (σ)

e. omega (ω)

d. sigma (σ)


Attenuation of the trp operon occurs when:

a. the trp repressor binds to the operator

b. the corepressor molecules are released from the repressor

c. specific stem-loop structures form in the RNA

d. the cell lacks charged tryptophan tRNA molecules

e. All of these

c. specific stem-loop structures form in the RNA


E. coli DNA replication and transcription are similar in that:

a. both use DNA Polymerase III

b. both use dNTPs

c. both require formation of an open bubble to initiate synthesis

d. both require primers to initiate synthesis

e. both make copies of each strand during synthesis

c. both require formation of an open bubble to initiate synthesis


 Which of the following is the small effector molecule that binds to CAP (catabolic activator protein)?

a. allolactose

b. glucose

c. tryptophan

d. cAMP

e. mediator

d. cAMP


What is a key structural feature, and the action performed by TFIID?

TFIID contains the TATA Binding Protien (TBP), and it binds to the TATA box early during the assembly of a transcription complex. RNA polymerase and other bidning factors attach to TFIID


Histone acetyltransferases act by:

a. adding phosphate groups to serines of histone proteins

b. adding acetyl groups to serines of histone proteins

c. adding phosphate groups to lysines of histone proteins

d. adding acetyl groups to lysines of histone proteins

e. moving acetyl groups from histone proteins to transcription factors

d. adding acetyl groups to lysines of histone proteins


Which of the following is not a domain found within transcription factors?

a. zinc finger

b. basic domain

c. cytosine zipper

d. helix-turn-helix

e. glutamine-rich domain

c. cytosine zipper


A single nucleosome is composed of:

a. Eight histone proteins, linker proteins, and about 146 bp of DNA

b. Eight histone proteins and about 146 bp of DNA

c. Six histone proteins and about 146 bp of DNA

d. Four histone proteins and about 146 bp of DNA

b. Eight histone proteins and about 146 bp of DNA


Which of the following processing events are not used with prokaryotic tRNAs:

a. endonucleolytic cleavage

b. exonucleolytic cleavage

c. base modifications

d. poly-A tailing

d. poly-A tailing


What does TFIIH do for RNA transcription?

What action allows Pol II to initate transcription?

TFIIH functions as a helicase, and binds late in the transctiption assembly. It also phosphorylates amino acids on the carboxy-terminal tail (CTD) of the RNA polymerase (Pol II) CTD, causing a change from initiating complex to elongating complex. 


This is because phosphorylation of the CTD allows Pol II to iniiate transcription. 



What cells contain Upstream Promoter elements?


What are they?


Eukaryotic promoters contain multiple Upstream Promoter Elements.


 They are DNA sequences that function as  binding sites for transcription factors that help recruit RNA polymerase II


4. Eukaryotic tRNA molecules have a CCA sequence at their 3’ terminus because:

a. that sequence is the anticodon sequence

b. that sequence is added by a nucleotidyl transferase

c. that sequence is a signal sequence for RNA polymerase binding

d. that sequence is a termination signal for the RNaseD exonuclease

e. that sequence is required for an internal hairpin to form

b. that sequence is added by a nucleotidyl transferase


How do repressors affect DNA regulation?

By binding to the DNA to INHIBIT transcription

(negative control)


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What is chromatin? 

Chromatin is a complex of DNA and proteins that forms chromosomes within the nucleus of eukaryotic cells. Nuclear DNA does not appear in free linear strands; it is highly condensed and wrapped around nuclear proteins in order to fit inside the nucleus.


How do activators affect gene regulation?

By binding to the DNA to INCREASE transcription

(positive control)


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What is a nucleosome?


How is it connected to histones?


A nucleosome the most fundamental subunit of chromatin.


Each nucleosome is composed of a little less than two turns of DNA wrapped around a set of eight proteins called histone


Inducers          1         transcription by      2         repressors and         3           activators.

1. increase

2. inhibiting

3. activating

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The most basic level of chromatin is the ___1___, which consists of __2__base pairs of DNA and __3__ copies of each of these four histones:  ____4____.

1) nucleosome

2) 146

3) two

4) H2A, H2B, H3, and H4

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Inhibitors        1         transcription by        2        activators.

1. decrease

2. inhibiting

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What is the function of the lacZ gene in the lac operon?

Encodes β-galactosidase



__1__ complexes and __2__proteins can reorganize nucleosomes to __3__ DNA sequences so that transcription factors can __4__.

1) Chromatin remodeling complexes

2) DNA binding proteins 

3) clear

4) bind



What is the function of the lacY gene in the lac operon?

Encodes lactose permease


Histone proteins can be covalently modified by ______ which leads to a change in their function.

The addition of:

1) phosphates

2) methyl groups

3) acetyl groups

4) the small protein ubiquitin


What is the function of the lacA gene in the lac operon?

Encodes transacetylase


What are the three structural genes of the lac operon?

lacZ, lacY, and lacA


What is the function of β-galactosidase?

 » Cleaves lactose and lactose analogues

» Also converts lactose into allolactose (an isomer)


___1___ tends to silence DNA while ___2___ can increase the transcription of DNA.

1) Methylation

2) acetylation and other modications


What is the function of lactose permease?

» Membrane protein required for transport of lactose and analogues into the cell


How can methylations and acetylations be reversed?

 By specific enzymes such as histone deacetylases.


What can microarray analysis monitor and why is this useful? 

Microarray analysis can monitor the expression of thousands of genes at once.

This is useful in understanding how a cell changes the expression of its genes in response to changes in its environment.

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What is the function of the lacP (promoter) on the lac operon?

lacP (the promoter) is the site where RNA Polymerase binds.

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What is the function of lacO (the operator site) on the lac operon?

This is the site where the repressor binds to.

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What are the non-coding segments that are added to messenger RNA called?


Why are they important?

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G - cap on the 5’ end,  poly(A) tail on the 3’ end.


 These are important in controlling the half life of mRNAs and are both required before mRNA can be translated.  

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When glucose levels are low, cAMP levels will be     1     ,

meaning the promoter (CAP) will bind/not bind to the CAP site

1. high

2. bind


What is the poly(A)-tail?




The poly(A) tail is a string of 150-250 A nucleotides added by a special enzyme: pol(A) polermerase. 




What is pol(A) polymerase?

A non-templated (aka, it's not coding for anything) RNA enzyme that places the poly(A) tail onto the end of the mRNA. 


1) What phosphorylizes RNA polymerase II CTC?


2) What does this accomplish? 



2) it allows binding by RNA processing factors, which makes RNA processing very efficient.  


1. CAP will bind to the         

2. RNA Polymerase will bind to the           

3. The lac repressor will bind to the            

1. CAP site

2. lacP/Promoter

3. lacO/Operator


___1___ requires cleavage of the pre-mRNA, followed by the addition of A’s, which are bound by the ___2___. The presence of this protein, along with the cap, are ___3___ for translation of the mRNA into protein: this system ensures that only ___4___ mRNAs are used to make proteins.

1) Polyadenylation

2) Poly(A) binding protein 

3) Required 

4) Intact


In the absence of both glucose and lactose, both the promoter and the repressor are  bound/unbound


If lactose is introduced, then the repressor will unbind.

If glucose is present, then the promoter will unbind.


What are introns? 



Portions of pre-mRNA that are removed by a complex called the spliceosome.  

(I would google RNA splicing to look at some good images)



Where do introns have conserved sequences?



1) At their beginning (the 5’ splice site).

2) At their ends (the 3’ splice site) along with a piece of A residue near the 3’ splice site (the branch site).  


Describe the steps of intron splicing:


1) Splicing begins when the branch site attacks the first nucleotide of the intron, forming a special 2’-5’ bond.

 2) The 5’ exon then attacks the 3’ splice site, resulting in precise joining of the exons and removal of the intron.  



When both glucose and lactose are absent, the promoter will be     1       and the repressor will be     2    

1. bound

2. bound

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When there is glucose present but no lactose, the promoter will be       1     and the repressor will be       2   

1. unbound

2. bound

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When there is lactose present but no glucose, the repressor will be    1     and the promoter will be     2   

1. unbound

2. bound

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When there is both glucose and lactose, the repressor will be     1      and the promoter will be      2       

1. unbound

2. unbound

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What is splicing?

 Splicing is a modification of the nascent pre-messenger RNA(pre-mRNA) transcript in which introns are removed and exons are joined.

(If you google RNA splicing and look at image results, the first two images are helpful)


1) What recognizes splice sites? 

2) What are they made of?

1) snRNP particles,

2) RNA and protein components.


What splice site does the U1 snRNP recognize? 

The 5' splice site


How does the U1 snRNP recognize the 5' splice site?

By base pairing with it. 


What happens after the U1 snRNP binds to the 5' splice site? 

snRNPs then bind to each other and rearrange to bring the spliceosome into a catalytically active configuration.


1) What is believed to catalyze mRNA splicing?

2) Why? 

 1) The RNA components of the snRNPs

2) Because similar sequences are found in the self-splicing introns, which can remove themselves in the absence of any proteins.


1) What characteristic of of mRNA is found in higher eukaryotes? 


2) What is the result? 

1) In higher eukaryotes, some mRNAs can be spliced in various ways.  


2) Alternative splicing lets one gene give rise to multiple protein products, which allows the proteome to be larger than the genome.



List all the ways that transcription is similar to replication

1) Both use DNA template to incorporate nucleotide triposphates into a polynucleotide strand

2) Both use an enzyme to synthesize polynucleoties in the 5' to 3' direction

3) Both need to unwind DNA

4) Both only begin at specific DNA sites

5) Both require stepwise assemply of a multiprotein complex to initiate


List the ways in which transcription is different from replication (Part 1) 

1) Transcription is asymmetric--only one DNA strand is ever copied

2) Only a small fraction of the chromosome is ever copied

3) Does NOT require a primer 

4) Only a small portion of the DNA unwound at any time

5) The RNA chain does not remain hydrogen bonded to the template strand


What are the two DNA strands called in transcription?

The strand that is copied is called the template strand. The strand that is NOT copied is called the sense strand, because it matches the RNA produced. 


List the ways in which transcription is different from replication (Part 2) 

6) Genes are expressed at different levels

7) Starts at Promoters instead of Origin or Replication

8) No proofreading activity

9) Extensively modified


Differences between eukaryotes and prokaryotes: RNA polymerase

Prokaryotes: 1 enzyme

Eurkaryotes: 3 ensymes

Pol I- rRNA

Pol II- mRNA

Pol III- tRNA, etc. 



Differences between Eukaryotes and Prokaryotes: Promoter

Prokaryotes: -35 box and  -10 box

Eukaryotes: TATA box, complex and variable set of DNA elements


Differences between Eukaryotes and Prokaryotes: Protein required for initiation 

Prokaryotes: sigma factor

Eurkaryotes: many basal transcription factors, many additional factors


This is the site for RNA polymerase binding; signals the beginning of transcription



What are promoter sequenes?

Promoter sequences (such as the -10 sequence and -35 sequence) are conserved sequences that are required for specific binding of RNA polymerase and transcription initiation


What are enhancers? 

DNA sequences located at a distance that greatly increase the expression of a gene. 


Where can enhancers be located?

1000’s of nucleotides upstream or downstream of a basal promoter. Enhancers can even lie within a transcription unit


How do enhancers work?

Enhancers provide additional sites for DNA binding proteins, which help to recruit RNA polymerase to the promoter. DNA binding proteins form lots of different protein-protein contacts to recruit RNA polymerase.


Rho dependent termination:

There is a rho recognition site (rut) that precedes the terminator. When that site is transcribed into the RNA strand, rho protein binds to it. It moves down the RNA strand in the 3' to 5' direction. When the RNA polymerase reaches the terminator, it slows down due the formation of a stem-loop structure. This allows the rho protein to catch up. When it reaches the open complex, it seperates it from the DNA strand. 


Intrinsic (rho independent) termination:

U to A bonds are very weak. When the RNA polymerase pauses at the terminator squence due to the formation of a stem-loop structure, the U-rich region (coded for by terminator) is not strong enough to hold the DNA-RNA complex together. 


What are the -10 and -35 sequences?

6 base-pair long regions in prokarytic RNA that are respectively 10 and 35 base pairs upstream from the start site.

Consensus sequence for each:

-10 sequence: TATAAT

-35 sequence: TTGACA


What is the eukaryotic equivalent of the Pribnow Box?

the TATA box


RNA polymerase can self-terminate by doing what?

Creating a stable hairpin structure with a stem and a loop; the polymerase pauses after it has synthesized the hairpin RNA, and then dissociates


When RNA polymerase isn't able to self-terminate, it may use       1        in which this helicase (       2    ) moves in the 5' to 3' direction, unwinding the RNA from the DNA template, releasing it

1. rho-dependent termination

2. rho factor


what is the purpose of the sigma factor in prokaryotic transcription?

The sigma factor converts the core RNA polymerase enzyme into a holoenzyme, and increases the affinity of this holoenzyme for the promoter while simultaneously decreasing its affinity for all other sites 

(basically: helps RNA polymerase bind to the promoter)


3 common DNA binding proteins

1.  helix-turn-helix motif

2. zinc finger motif

3. leucine zipper motif