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Transcription Flashcards

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1
Q

What are the three classes of RNA?

A

rRNA
mRNA
tRNA

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2
Q

What is transcription?

A

The process that is responsible for synthesizing the three major classes of RNA

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3
Q

The synthesis of RNA is under the direction of a ______ template.

A

DNA

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4
Q

Each type of RNA participates in the synthesis of proteins by what other process?

A

translation

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5
Q

What is the first step in gene expression?

A

transcription

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6
Q

Transcriptional control is important in gene expression for _____ genes.

A

many

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7
Q

Do transcriptional mechanisms differ between prokaryotes and eukaryotes?

A

yes

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8
Q

Prokaryotes have _______ of RNA polymerase(s) and eukaryotes have ________ of RNA polymerase(s).

A

a single type

3 different types

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9
Q

How many subunits does the prokaryotic RNA polymerase consist of?

A

4 subunits

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10
Q

What are the holoenzyme subunits and the core polymerase subunits of the prokaryote RNA polymerase?

A

holoenzyme- alpha 2, beta, beta prime, sigma

core polymerase- alpha 2, beta, beta prime

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11
Q

What is the sigma subunit and what does it do?

A

It is the specificity factor and it directs the core enzyme to transcribe specific genes

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12
Q

How does the sigma subunit direct the core enzyme to transcribe specific genes? and what does this stimulate?

A

It causes tight binding between RNA polymerase and the regions of DNA known as the promoters. This stimulates the initiation of transcription.

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13
Q

What does the tight binding of the RNA polymerase to the DNA depend on?

A

localized melting

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14
Q

What is the open-promoter complex?

A

the complex that is formed when the RNA polymerase is allowed to tightly bind tot the DNA template

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15
Q

The melting of DNA and the tight binding of RNA polymerase can only occur in the presence of what?

A

sigma

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16
Q

How does sigma promote the binding of multiple RNAPs to the template DNA?

A

Once it has successfully allowed the RNAP to bind to the template DNA it then disassociates from the RNAP leaving it tightly bound to the DNA and the sigma is free to participate in the binding of another RNAP at another location.

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17
Q

Promoter regions have specific base sequences that attract what to bond?

A

RNA polymerase

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18
Q

What is the -10 box?

A

A promotor sequence that is 6-7bp long and located 10 base pairs upstream of the start of transcription.

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19
Q

WHat was the -10 box originally called?

A

Pribnow box

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20
Q

What is the -35 box?

A

a second promoter sequence that is found 35 base pairs upstream form the transcription start site.

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21
Q

How far does RNA polymerase extend when it binds in an open-promotor complex?

A

at least -44 to +3

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22
Q

what are UP elements?

A

sometimes very strong promoters contain another region located between -40 and -60 to which the RNA polymerase is additionally added to. This region is known as the Up elements.

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23
Q

What other region is the promotor region also associated with?

A

Three Fis sites between -60 and -150

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24
Q

What is the Fis protein and what are its binding sites?

A

transcription activator and the 3 Fis sites

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25
Do the Fis sites bond to RNA polymerase?
no
26
What do the Fis sites represent?
A group of transcription activating elements that help activate transcription without the direct binding to RNA polymerase
27
what are enhancers?
group of transcription activating elements that help activate transcription without the direct binding of RNA polymerase
28
What antibiotics are inhibitors of prokaryotic transcription and what organism do they come from?
Rifamycin B ---> Streptomyces mediterranei Rifamycin ---> synthetic form of Rifamycin B
29
Does Rifamycin B and Rifamycin inhibit initiation in eukarotes as well?
No
30
Does Rifamycin B and Rifamycin inhibit elongation in prokaryotes?
No
31
When does the termination of transcription occur?
When the bacterial RNA polymerase reaches a terminator at the end of a gene being transcribed
32
What are the two types of E coli. terminators? and what is the relative abundance of each type?
1. intrinsic terminators-Rho independent 2. Rho-dependent terminator Equal numbers of both
33
What does Rho independent termination depend on in prokaryotes?
It depends on the presence of an inverted repeat that is immediately followed by a T-rich region in the nontemplate strand.
34
What does the inverted repeat allow that terminates transcription?
It creates a hairpin structure
35
A model strong efficient terminator includes what two things and how does it trigger termination?
The hairpin structure along with the associated poly (U) tail work together to trigger termination by causing the RNA polymerase to dissociate from the template.
36
What is the difference between Rho-independent and Rho-dependent termination in E.coli?
Rho-dependent and Rho-independent lack any resemblance to one another and Rho-dependent termination is unable to form hairpin structures.
37
What is the protein factor that is required for termination in the Rho-dependent sites?
Rho protein
38
What is the structure of the Rho protein and what does it do?
It is a helicase that unwinds the RNA-DNA and RNA-RNA double helices
39
Where must the specific recognition sequence for the Rho protein to recognize and terminate transcription be located?
On the newly synthesized RNA strand
40
How does Rho go about terminating the transcription of RNA?
It binds to the recognition sequence on the RNA and then migrate towards the RNA polymerase that is paused at the termination site and then proceeds to unwind the RNA-DNA duplex at the transcription bubble.
41
All cells do not express their genes continuously and this is die to what?
The excessive energy expenditure would be required
42
Cells will only express certain genes when those spefic gene products are required. true or false?
true
43
How do bacteria maximize the efficiency of gene expression?
functionally related genes are grouped together
44
grouping together functionally related genes allows for what to occur?
The regulation of the gene groups as a unit
45
What forms an operon?
A group of contiguous coordinately controlled genes
46
What is the classic example of the operon theory?
The lac operon
47
Who put forth the hypothesis of the operon and based on what?
jacob and monod | based on the inducibility of lactose metabolism in E coli.
48
What does E coli perfer as a carbon source and what of this carbon source is unavailable?
E coli prefers glucose as a carbon source however when unavailable the cells are able to induce the enzymes to metabolize lactose
49
What three genes does the lac operon contain whose gene products are required for the utilization of lactose?
1. galatoside permease (lac Y) 2. Beta-galatosidase (lac Z) 3. galatoside transactylase (lac A)
50
What two genes are definitely absolutely required for utilization of lactose?
lac y and lac Z
51
What is the function of lac y?
transport of lactose int the cell
52
What os the function of lac z?
cleaves lactose to form galactose and glucose
53
What os the function of lac A?
Uses acetyl CoA to transfer acetyl to beta-galactose not a step required for the utlization of lactose by the cell and is expressed at a lower level than the other two genes
54
All 3 genes that make up the lac operon are transcribed together to form what from what?
form a single RNA molecule from a single promoter
55
What is polycistronic RNA? Give an example
information comes from more than one gene for example the lac operon
56
What does it mean that the lac operon is under negative control?
The lac operon is "turned on" unless there is something present keep the operon "shutoff"
57
What is the lac operon kept turned off by?
The presence of the lac repressor(the product of the lacI gene)
58
cistron=what?
gene
59
What is the regulatory gene of the operon?
The lacI gene
60
The lac repressor is a homotetramer. what is a homotetramer?
a protein made of 4 identical polypeptide subunits
61
The repressor protein binds to what region on the lac operon?
operator region
62
Where is the operator located?
downstream of the promoter region
63
what does the presence of the bound repressor hinder on the lac operon?
It hinders the bonding and processivity of the RNP
64
When the repressor is bound to the lac operon what is repressed?
the lac operon-it is turned off
65
If the glucose is unavailable but lactose is available what binds to the lac repressor?
The inducer
66
Binding of the inducer to the repressor causes what to occur?
conformational change in the repressor that makes it lose affinity for the operator region and then falls off the lac operon
67
What does the removal of the repressor allow?
It allows RNAP to bind to the promoter and the lac operon can be transcribed
68
What is the inducer mol for the lac operon?
allolactose
69
How is lactose rearranged to form allolactose?
A side reaction of Beta galactosidase- lactose is beta 1-4 linkage and allolactose is beta 1-6 linkage
70
If the operon is in a repressed state how is it that lactose and beta galactosidase are available to the cell to make the inducer?
Repression is leaky and it does not result in total repression of the operon so very low levels of lactose and lac operon products are always present
71
The lac operon is normally in what state under what control?
repressed state under negative control
72
What is the role of lacI?
in the absence of lactose it is the info repressor protein that blocks RNAP from binding to the promoter
73
If lactose is available and glucose is unavailable What series of events occurs in depression/induction?
beta galactosidase rearranges lactose into allolactose. allolactose then induces transcription of the gene by binding to the repressor proteins causeing conformational changes that makes them fall off freeing the region RNAP binds to transcribe gene.
74
What is the role of permease?
to transport lactose into the cell
75
WHat is catabolite repression?
It is a control mechanism that keeps operon turned off when glucose concentration is high and can sense when glucose levels are low and stimulates the activity of the lac operon
76
The lac operon is also under positive control. what is the mechanism control name for this?
catabolite repression
77
WHat molecule mediates the positive control of the lac operon?
CAP-cAMP complex
78
What does CAP stand for?
catabolite activator protein
79
what does cAMP stand for?
cyclic adenosine monophosphate
80
What is the effect of an abundance of glucose in the cell on cAMP concentrations?
It depresses cAMP
81
Glucose and cAMP have what kind of relationship?
inverse
82
Low amount of glucose do what to cAMP concentrations?
raises
83
How is the transcription of the lac operon stimulated with regards to CAP-cAMP?
The CAP-cAM complex bonds to an activator site next to the promoter and facilates the binding of RNAP to the promotor.
84
What does the binding of CAP-cAMP complex to the actovator result in?
It increases the rate at which the open promotor complex is formed and makes facilates the binding of rnap
85
WHat are the relative positions of all the binding site in the positive control?
lacI--activator site---promotor site----operator---lacZ
86
The activator site is where what binds in lac operon catabolite repression?
CAP-cAMP
87
The promoter site is where what bonds in lac operon catabolite repression?
RNAP
88
WHat does the trp operon encode for? how is this different from the lac operon?
The trp operon encodes for anabolic enzymes that synthesize tryptophan. The lac operon encodes for catabolic enzymes that break down lactose.
89
High levels of tryptophan stimulate or suppress trp activity?
suppress
90
low tryptophan results in what
no repression
91
WHat controls the trp operon?
attenuation
92
Why does the trp operon need to be controlled by attenuation?
WHen the trp operon is fully repressed the degree of transcription that continues to occur is only 70-fold less than it is at the fully unrepressed level
93
What is the relative strength of the trp operon compared to the lac operon?
weak
94
Attenuation allows for how many fold increase of control of the trp operon activity
10-fold
95
WHat range os the trp operon controlled over?
700-fold range
96
The control of the trp operon is extremely costly?
yes
97
What two gene loci are present in the trp operon?
trp leader locus | trp attenuator locus
98
What is the prupose of the leader-attentuator's?
to weaken (attentuate) transcription of the trp structural genes when tryptophan is abundant
99
How the attentuator function?
by causing the premature termination of transcription
100
Transcription that manages to get started in the presence of high tryptophan levels is how likely to terminate in the attenuator region?
90%
101
What does the attentuator region contain?
inverted repeat followed by a series of 8 AT pairs in a row
102
How does the inverted repeat lead to premature termination of the transcript?
The transcript tends to for hairpin structures that destabilized the transcript binding to the DNA
103
When tryptophan is in short supply the cell needs a way to override attenuation so that what can be activated to do what?
SO the trp operon can be activated to transcribed genes required for the synthesis of tryptophan.
104
Who created the hypothesis of how attenuation is overridden?
Charles Yanofsky
105
What does the overriding of attentuation in prokaryotes depend on?
The fact that transcription and translation occur simultaneously and about the same rate-unlike in eukaryotes

Molecular Final (4 decks)

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