Chapter 12 Flashcards
(114 cards)
1
Q
how is most gene expression regulated in bacteria
A
transcriptional regulation
2
Q
what are the three types of transcriptional regulation
A
inducible transcription
repressible transcription
attenuation
3
Q
what are the two types of posttranscriptional regulation
A
mRNA destruction
translation blockage
4
Q
what is negative control
A
- always has repressor protein present
- prevent transcription
5
Q
what is positive control
A
- binding of activator protein
- initiate transcription
6
Q
what is the job of repressor protein
A
repress activity of operon and bind in way of transcription
7
Q
what are repressor proteins
A
regulatory proteins that exert negative control of transcription
8
Q
what do activated repressors bind to
A
operators
9
Q
can be repressor proteins be activated and inactivated
A
yes by other compounds
10
Q
what are the two active sites of repressors
A
- DNA binding domain: has to bind directly to DNA
- allosteric binding domain: binds additional molecule to turn repressor on
11
Q
allostery
A
allosteric binding molecule that causes a change in conformation of DNA binding domain that turns on or off repressor protein
12
Q
when inducer binds to repressor, what happens
A
operator released and allows RNA polymerase to bind and allow for transcription
13
Q
if corepressor is not present, what occurs
A
repressor does not bind and transcription can occur
14
Q
are inducers and corepressors positive or negative control
A
negative
15
Q
what causes positive control of transcription to occur
A
activator proteins that bind regulatory DNA sequences called activator binding sites
16
Q
what are the two modes of positive control
A
- DNA binding domain inactive until allosteric effector binds allosteric domain and induces conformational change
- DNA binding domain inactive by binding of inhibitor to allosteric domain
17
Q
when allosteric effector compound bonds to activator protein, what happens
A
increases ability if RNA polymerase to bind and allow transcription to occur
18
Q
when the allosteric inhibitor compound bonds to activator protein, what happens
A
no transcription occurs
19
Q
when the allosteric inhibitor is not present, what happens
A
transcription occurs
20
Q
what is the common secondary structure in regulatory DNA binding proteins
A
a helixes
21
Q
what are the two types of protein segments that contact DNA
A
- single polypeptide fold and forms two domains that bind target DNA sequences
- regulatory protein that consist of two+ proteins
22
Q
two
A
dimeric
23
Q
three
A
trimeric
24
Q
four
A
tetrameric
25
can polypeptides be both identical or different
yes
26
why do bacteria have inverted or direct repeats of regulatory DNA
each polypeptide of regulatory homodimer interacts with one repeat
27
what is the most common structural feature of bacterial regulatory DNA
helix-turn-helix motif
28
helix-turn-helix motif
two a regions interact with the inverted repeats
29
what separates recognition and stabilizing helix
turn in each polypeptide
30
inducible operon
keep it turned off unless we need it
31
is the lac operon inducible
yes
32
operons in bacteria
series of related genes related to the same function and share the same promoter
33
what is the job of the lac operon
produce three polypeptides needed for use of lactose
34
characteristics of lactose
- disaccharide
- consists of glucose and galactose
- joined by B-galactoside linkage
35
lac+ phenotype
bacteria can grow on medium containing lactose
36
job of permease
enzyme protein channel that brings lactose in
37
job of enzyme B-galactosidase
break the B-galactosidase linkage
38
what makes up the lac operon
regulatory region and 3 strutural genes
39
what are the 3 parts of the regulatory region
1. promoter
2. lac o (operator sequence)
3. CAP binding site
40
what are the three parts of the structural genes
1. lacZ (break down lactose into monosaccharide)
2. lacY (allows lactose to come in)
3. lacA (encodes transacetylase)
41
what is not apart of the lac operon
lacI
42
why is lacI contionioulsy expressed
keeping lactose pathway turned off most of the time
43
when is the lac operon transcriptionally silent
no lactose is available or glucose is available
44
when does the lac repressor bind to lacO and what is the outcome
when there is no allolactose in cell and this prevents transcription (negative control)
45
lactose unavailable and glucose available
lac repressor protein bins to operator and inhibits transcription
46
what structure alters DNA binding domain of repressor and prevents binding operator
inducer-repressor complex
47
what would happen if we stopped at negative control and what is this called
transcription would not be efficient; basal transcription would not
48
lactose available and glucose unavailable
repressor protein inactivated by allolactose binding so transcription occurs
49
what does cAMP need to bind to
CAP
50
what complex cannot form when glucose is present in a cell
CAP-cAMP
51
catabolite repression
transcription limited since CAP-cAMP is not bound to lac promoter
52
lactose and glucose available
some transcription but not a lot
53
lacI product
repressor protein
54
lacZ product
B-galactosidase
55
lacY product
permease
56
lacA product
transacetylase
57
lacO product
operator
58
lacP product
promoter
59
constitutive mutants
genes are transcribed continuously whether or not lactose is available
60
cis acting
influence transcription of genes only on same chromosome
- lac operator mutations
61
what can work in cis and trans
lacI-
62
in an Is mutation, where does the mutation occur
allosteric binding site
63
what is the result of a noninducible operon
- Z and Y genes not expressed
- allolactose cannot bind to allosteric domain
- unresponsive cell to presence of lactose
64
when should active transcription of lac operon take place
only when glucose is absent from cell and lactose is available
65
what do promoter mutations reduce
transcription of lacZ and lacY (cis)
66
what are the four things that will happen in operon transcription when glucose is absent and lactose is present
1. cAMP levels rise
2. CAP-cAMP complex forms and binds to CAP site
3. allolactose forms in side reaction of lactose metabolism
4. repressor protein binds allolactose and releases from operator
67
what type of pathway is the lac operon
catabolic
68
what supports the idea that repressor protein block RNA polymerase binding
the repressor protein binding region overlaps with promoter binding region for RNA polymerase
69
what are the three segments of operator DNA sequence
O1
O2
O3
70
O1
primary repressor binding
71
what operator follows O1
O3
72
homotetramer
4 polypeptides joined by their C-terminal ends
73
what do the ends of each bundle form
- one end forms operator DNA binding domain
- other end forms regulatory domain
74
what does the DNA loop in combination of the position of the overlapping with RNA polymerase prevent
transcription
75
what will bind if inducer molecule of present
allosteric domains
76
what induces the formation of the DNA loop
repressor binds O1 and O3
77
if O1 doesn't bind, what happens
O3 can't bind
78
what operons are anabolic pathways
repressible operons
79
what is attenuation
- second regulatory capability
- fin tune transcription to match immediate needs of cell
80
promoter of tryptophan
trpP
81
operator of tryptophan
trpO
82
what is the leader region of tryptophan
- trpL
- contains attenuator region
83
what is responsible for tryptophan synthesis
products of the structural genes
84
what does tryptophan acts as
corepressor
- binds Trp repressor and activates it
85
if tryptophan is absent, what happens
repressor protein can't bind operator so transcription occurs
86
if tryptophan is present, what happens
repressor activated by tryptophan and binds operon, blocking transcription
87
which has higher rates of operon transcription in presence of tryptophan, trpR- or trpR+
trpR-
88
what is the second mechanism controlling trp operon expression
attenuation
89
what controls attenuation
folding of mRNA from 162-bp trpL region
90
in TrpL mRNA, why is there two Trp sequences in region 1
going to help determine whether or not tryptophan is present in adequate amounts
91
tryptophan present in high amount
tRNA available
92
tryptophan present in low amount
ribosome has to wait until correct tRNA shows up with tryptophan
93
what are the four structures that can be formed from trpL attenuation in mRNA transcript
1. TrpL mRNA
2. pause stem loop
3. antitermination stem loop
4. termination stem loop
94
what structure doesn't terminate and makes more tryptophan
antitermination stem loop
95
how does the antitermination stem loop work
region 2 base pairs with region 3, so region 3 can't base pair to region 4, so translation moves all the way through
96
tryptophan abundance
- termination
- ribosome completes translation
- regions 3 and 4 pair
- transcription terminates
97
tryptophan starvation
- antitermination
- ribosome stalls at region 1
- regions 2 and 3 pair
- transcription continues
98
what happens if one of two codons is mutated
alters responsiveness to tryptophan
99
what happens if both codons are mutated
abolishes attenuator's ability to sense tryptophan
100
what happens if regions 3 and 4 are mutated
prevents stable binding and reduces efficiency of attenuation
101
what are the two ways translation regulation takes place
1. binds protein to mRNA to prevent translation
2. uses complementary antisense RNA to block mRNA translation
102
how do translation repressor proteins work
interfere with interaction between mRNA and small ribosomal subunit
103
what is antisense RNA and how does it work
- produce reverse complement to mRNA
- create a double stranded RNA through binding mRNA and its antisense RNA
104
what two promoters does IS10 regulation have
- Pin: weak and low production of mRNA
- Pout: strong and high production of mRNA
105
how does a riboswitch work
segment of mRNA binds a small regulatory molecule
106
what is the job of a riboswitch
regulate transcription and translation and alter mRNA stability
107
TPP
acts as a regulatory molecule to bind to riboswitch
108
in bacillus, what are the 2 outcomes of riboswitch mRNA regulation
1. low TPP concentration
2. high TPP concentration
109
low TTP
- TPP amounts too low for riboswitch binding
- leads to antitermination stem loop formation
- leads to transcription
110
high TPP
- TPP binds to riboswitch
- generates stem loop followed by poly U sequence
- prevents transcription
111
what secondary structure does low TPP form
Shine Dalgarno antisequestor stem loop
112
what happens when this atisequestor stem loop forms
shine-Dalgarno bonds to small subunit so start codon can initiate translation
113
low GlcN6p concentration
- riboswitch not active
- transcription of glmS can occur
- translation of its mRNA occurs
- sugar produced
114
high GlcN6p concentration
- GlcN6p binds to riboswitch
- mRNA is cleaved
