Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

3382 > Prokaryotic Regulation of Transcription > Flashcards

Prokaryotic Regulation of Transcription Flashcards

1
Q

bacteria can respond quickly to environmental changes because

A

transcription or repression of genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

strand of DNA that is read by RNAP is called

A

template strand

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

The strand that is not used to transcribe is called

A

the coding/non-template strand (identical to transcript except T-> U)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are the units of the core enzyme of bacterial RNAP?

A

alpha2, beta, beta prime, omega

can function without omega

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is found in the active site of RNAP?

A

Mg2+, wich interacts with negatively charged bb

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Steps of Transcription (bacteria)?

A
  1. binding
  2. initiation
  3. elongation
  4. termination
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How does RNAP bind to DNA?

A
  • sigma subunit (holoenzyme) recognizes promoter sequences
  • RNAP binding protects nucleotide sequence from -70 to +20 where +1 is TSS. but binds to -10 and -35 region
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

is the transcription and translation start site the same?

A

NO

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

How does the Kd of the holoenzyme binding to DNA compre when DNA is wound vs unwound?

A

closed promoter complex (wound): 10^-9 M
open promoter complex (unwound): 10^-14 M

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are bacterial promoters?

A

defined nucleotide sequences that determine the site of transcription initiation (~40 nts on 5’ end)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are the 2 consensus elements in bacterial promoters?

A

Pribnow bow (-10 region -> AT rich)
-35 region (variable – more AT rich = more efficient transcription = prob more necessary gene)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Is the sequence between -10 and -35 region important?

A

no – number of bases between are important otherwise RNAP would cover other important regions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Why are there different sigma factors?

A

each one recognizes a different -35 region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What are the steps of bacterial transcription initiation and elongation?

A
  1. sigma factor of RNAP recognizes DNA promoter
  2. formation of RNAP:closed promoter complex
  3. DNA begins to unwind at promoter -> open complex formation
  4. RNAP adds two NTPs (at initiation site and elongation site)
  5. 3’ OH of first NTP attacks a-phosphate of second forming phosphodiester bond
  6. elongation begins and sigma subunit dissociates
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What are the two types of termination of bacterial transcription?

A
  1. Rho-independent/intrinsic termination
  2. Rho-dependent
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How does Rho-independent/intrinsic termination work?

A
  • inverted repeat sequence rich in G-C bases form stable stem loop structure in RNA transcript
  • then a stretch of As in the DNA template (Us in the RNA) destabilizes RNAP bindind

termination sites present in DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How does Rho-dependent termination work?

what is Rho?

A
  • Rho translocates along RNA transcript until it reachs the transcription bubble
  • RNAP stalls in a G:C rich region of template DNA
  • Rho catches up and cause termination by allosterically changing RNAP and unwinding RNA from template DNA like a helicase

ATP-dependent helicase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Where do repressors and activators bind in bacteria?

A

repressors - operators (overlaps with promoter)
activator - enhancer (upstream of promoter)

repressors bind to silencers in eukaryotes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How does negative of gene expression work when induced or repressed?

A

induced: repressor always binds until an inducer inactivates repressor
repressed: repressor always binds and a corepressor promotes repression

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

How does positive of gene expression work when induced or repressed?

A

induced: activator always binds and an inducer promotes induction
repressed: activator always binds until a corepressor inactivates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is the lac operon?

A

several genes under same promoter
translates into B-galactosidase transacetylase:
- transfer acetyl group from acetyl-CoA to B-galactosides

22
Q

What are the genes in the lac operon? What do they do?

A

LacY: translates to Galactosidate permease: channel for lactose to enter cell
LacZ: B-galactosization: hydrolyzes lactose to galactose or isomerizes to allolactose
LacI: represser

23
Q

What is glucose repression or catabolite repression?

A

preventing wasteful duplication of energy-producing enzymes by repressing transcription of lac and other operons

24
Q

What is the relationship between glucose and cAMP in glucose metabolism?

A

high glucose = low cAMP
and vice versa

cAMP increases when glucose runs out in a media

25
the lac operon is under -- regulation?
negative (repressed unless lactose is present and glucose is absent)
26
Where exactly does LacI bind?
1. strong operator site: O1, upstream of lacZ 2. weak operator site: O3 upstream 3. weak operator site: O2 downstream | there are 3 operator site for lac operon O1, O2, O3
27
How does LacI binding affect RNAP?
LacI is a tetramer that can bind to 2 operator sequences at once bind to 2 operators creates a loop in the DNA loop prevents RNAP binding
28
How is lac operon induced?
- allolactose induces LacI so it can't bind (changes its affinity for DNA)
29
lacI mRNA is extremely...
unstable (1/2 life of 3 minutes, allows induction to be rapidly reversed to basal state)
30
What are the 3 functional regions of LacI?
- recognize and bind operator sequence - bind inducer at a site different from DNA binding site - oligomerization region that forms its 4º repressor structure
31
since the Lac promoter is weak (weak interaction of sigma factor to -35 region) how is latose metabolism better induced?
catabolite activator protein (CAP) increases recruitment of RNAP - CAP bound to CAP site on promoter - RNAP's **a-subunit interacts** with CAP to **stabilize RNAP's interaction** with the promoter
32
What is CAP regulated by?
cAMP! adenylate cyclase is inhibited when glucose enters cell when no glucose adenylate cylcase makes cAMP cAMP binds to CAP which binds to enhancer sequence and to RNAP
33
How is the arabinose operon (araBAD) regulated? When is it on and off?
genes/proteins: AraA, B, D AraC = repressor - no arabinose = OFF - arabinose and glucose = OFF - arabinose only = ON
34
Where on the operon does AraC bind?
O2, O1, I2, I1 site throughout araBAD operon
35
What does the araBAD operon look like?
- has a promoter that works in 2 directions, one for araC and one for araB, A, D - O2, O1, I2, I1 sites for araC repression
36
In the absence of L-arabinose, the AraC protein forms a
dimer that is stable when bound to I1 and O2 operator sites
37
why is AraC dimer stable when bound to I1 and O2 operators? | when is it unstable?
forms a loop structure of ~210 bp between in the DNA that prevents RNAP binding | adding 5 bp to 210 = DNA in a half turn = binding site faces other way
38
What happens to AraC when L-arabinose is present? How does it affect RNAP?
- arabinose binds to AraC causing conformational change - this does NOT change protein-DNA affinity of AraC - this now makes AraC more stable when bound to I2 and I1 operators sites which are next to each other - this allows RNAP to bind but has to compete with AraC
39
What is the activator of the araBAD operon? Why is it needed?
- weak promoter - requires CAP-cAMP to activate when glucose levels are low
40
How is AraC an autoregulator (along with a repressor) of its own transcription?
if a high level of AraC protein bind to O1 site, RNAP can't RNAP is prevented from accessing the promoter for araC
41
What is attenuation?
intrinsic terminators of transcription
42
What does the trp operon look like?
- attenuator sequence - each gene in the operon has its own stop codon before the next gene - each gene has a RBS at its start - each gene builds a small molecule in the trp making pathway | we need stop codons & RBSs otherwise erroneously make one long gene
43
How is the trp operon regulated?
- TrpR repressor - Tryptophan is a co-repressor - Tryptophan binds to TrpR which binds to *trp* operator | Transcription is not completely off!
44
How is trp operon different from arabinose and lac operons?
default is ON because loss of regulation = Trp is still being made in excess
45
What is transcribed by trp operon when high Tryptophan levels?
makes a leader (TrpL) 139-nt segment
46
What does the sequence of TrpL tell us?
- encodes for 2 Trps in a row (Trp is rare, 2 in a row is very unusual) - started looking at other other amino acid synthesis operons and saw a similar pattern of multiple of its own AA in a row
47
What structures do the trpL transcript make?
- "terminator" (1:2 pause structure; 3:4 **terminator**) - "antiterminator" (2:3) - no terminator | 2 different secondary structures from 4 regions ## Footnote PAUSE STRUCTURE has Trp Trp and stop codon for leader peptide
48
What does the terminator secondary structure of trpL look like?
an intrinsic terminator! GC content stem loop structure and a poly(U) follows
49
What happens in low tryptophan conditions?
- ribosome binds to RBS and starts translating trpL - ribosome stalls when it gets to 2 successive trp codons in trpL -> incomplete leader peptide - ribosome sits ontop of sequence 1 (of 4) - ribosome pause = occlude seq 1 - antiterminator forms where 2:3 seq makes hairpin loop - RNA polymerase continutes transcribing to make all trp genes which will make more tryptophan
50
What happens in high tryptophan conditions?
- ribosome translates trpL gene making a full leader peptide - no ribosome pause = occludes seq 1&2 - 3:4 terminator bp structure forms - short transcript of just trpL gets made - transcription is teminated
51
does the pause structure actually form?
no because the ribosome pauses on seq 2 -- its just hypothetically what would form in ribosome wasn't there
52
which structure, antiterminator or terminator forms preferentially?
2:3 (antiterminator) has the chance to form first compared to 3:4 (in terminator) also cell is default to ON to actually make trp

3382 (20 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions