30 Prokarytoic Regulation Flashcards
1
Q
Levels of regulation of gene expression
A
- DNA and chromatin structure
- transcription
- mRNA processing
- RNA stability
- posttranslational modification
2
Q
structure genes
A
encode proteins that are used in metabolism or play a structural role in the cell
3
Q
regulatory genes
A
encode products that interact with other sequences and affect the transcription a/o translation of these sequences
4
Q
regulatory elements
A
DNA sequences that are not transcribed, but play a role in regulating other nucleotide sequences
5
Q
example of structural gene
A
genes that code for enzymes
6
Q
example of regulatory gene
A
genes that code for a repressor protein or for transcription factors
7
Q
example of regulatory elements
A
promotors and enhancers
8
Q
DNA binding domains of regulatory proteins include…
A
- helix-turn-helix
- zinc fingers
- leucine zipper
9
Q
what is the most common DNA binding domain in prokaryotes?
A
helix-turn-helix motif
10
Q
Regulatory mechanisms are important for…
A
making sure the correct genes are turned on at the proper times in the appropriate cells
11
Q
rapid turn on or off
A
a regulatory mechanism of transcription that provides the ability to respond rapidly to sudden changes
12
Q
sequential gene expression
A
cascades of gene expression
genes need to be expressed in a particular sequence
frequently cyclical
13
Q
constitutive expression
A
aka housekeeping genes
genes are turned on continuously during normal cell conditions
ex. genes for histones, genes for ribosomal RNA, genes for tRNA, etc.
14
Q
Positive vs Negative control
A
whether the biding of a regulatory protein increases or decreases transcription
15
Q
positive control
A
regulator protein binds to DNA to stimulate transcription
16
Q
the regulator protein in positive control is a …
A
activator
17
Q
negative control
A
regulator protein binds to DNA to prevent transcription
18
Q
the regulator protein in negative control is a …
A
repressor
19
Q
inducible vs repressible control
A
small molecules called effector molecules interact with regulatory protein and allow transcription to turn on or off
they do not interact with DNA
20
Q
inducible control
A
transcription is normally off and is turned on when an effector molecule binds the regulatory protein
21
Q
usually degradative process
A
inducible control of transcription
22
Q
repressible control
A
transcription is normally on and is turned off when an effector molecule binds the regulatory protein
23
Q
usually biosynthetic process
A
repressible control of transcription
24
Q
operon
A
the structural genes and the regulatory regions of DNA that control their expression
25
operons allow...
multiple genes to be under coordinated regulation
efficient way of obtaining gene products from genes several genes whose products are required at the same time
26
regulator regions
a gene that produces a regulatory proteins
27
operons consists of...
promotor
operator
structural gene(s)
28
polycistronic mRNA
transcribed by structural gene
then translated into multiple gene products which may work at multiple steps on the same biochemical pathway
29
negative inducible system
repressor = regulatory molecule
inducer = the small molecule
30
negative inducible system when inducer is not bound to the repressor
- repressor binds to the operator region of the DNA when NOT bound to the inducer blocking RNA polymerase so it does not bind the promotor and transcription is off
31
negative inducible system when inducer is bound to the repressor
- the binding causes a conformational change in the repressor so that it can not bind the operator of the DNA allowing RNA polymerase to bind the promotor and transcribe the structural genes
32
negative repressible system
the repressor cannot bind the DNA by itself - it is only effective when the small effector molecule or corepressor binds
33
negative repressible system when effector is absent
repressor doesn't bind the DNA
| RNA polymerase can bind the promotor and allow transcription
34
negative repressible system when effector is present
- effector complexes with the repressor and the combination binds the operator region of the DNA
- RNA polymerase cannot bind so transcription does not occur
35
positive inducible systme
regulatory molecule = activator
the activator must bind the DNA in order to allow transcription
36
positive inducible system with effector present
the complex binds to the DNA and facilitates the binding of RNA polymerase allowing transcription
37
positive inducible system without effector molecule present
the activator is not able to bind the DNA
| transcription does not occur
38
positive repressible system
activator can bind to the DNA on own
39
positive repressible system with effect molecule present
- effector binds the activator causing a conformation change preventing the activator form binding to the DNA
- RNA polymerase cannot bind and transcription does not occur
40
positive repressible system without effector molecule present
the activator can bind to DNA allowing RNA polymerase to bind and transcription to occur
41
Lac operon has aspects of what type of control systems?
- negative inducible
| - positive inducible
42
trp operon has aspects of what type of control systems?
negative repressible
43
lac operon
lactose is broken into galactose and glucose by E.coli in the mammalian gut
44
breakdown of lactose in ecoli
- has to be taken up into the cell which is facilitated by enzyme permease
- enzyme beta-galactosidase converts some of the lactose into allolactose and breaks these both down into galactose and glucose
45
enzyme that facilitates cellular uptake of lactose
permease
46
enzyme that facilitates breaking down lactose and allolactose into glucose and galactose
beta-galactosidase
47
lac operon regulatory gene
lacl
| codes for repressor
48
lac operon promotor
lacP
| binds RNA polymerase to allow transcription
49
lac operon operator
lacO
| interacts with repressor
50
lac operon structural genes
lacZ, lacY, and lacA
| transcribed and translated into proteins
51
lacZ
transcribed into beta-galactosidase
52
lacY
transcribed into permease
53
lacA
transcribed into transacetylase
54
polycistronic mRNA in lac operon
produced during transcription
| translated into 3 different products
55
the lac operon itself has...
a promotor, operator, and three structural genes
56
The three structural genes of lac operon are turned on/off at same time or different times? Why
same time
1 promotor for all three genes
57
normal operation of lac operon when lactose is not present
gene products not required - example of negative inducible regulation
the repressor bind the operator region blocking the RNA polymerase from binding promotor preventing gene transcription
58
lac operon genotype I+P+O+Z+Y+A+
normal
59
normal operation of lac operon when lactose is present
- allolactose will also be present
- this will bind the repressor causing conformational change so that it cannot bind the operator area of the lac operon
- RNA polymerase can bind the promotor and transcribe the 3 structural genes by making one polycistronic mRNA which is translated into 3 enzymes
60
allosteric change
the binding of the molecule causes a conformational change in the operator binding site of the repressor
61
Operon induced when...
lactose is present
62
Operon repressed when...
lactose is absent
63
cis acting
action of an element mutation affects only the genes adjacent to it
ex. mutations in operator and promoter elements
64
trans acting
diffusible product is produced - mutation does not have to be adjacent to other genes to affect them
ex. regulatory gene mutation
65
mutations in operator elements of lac operon are ___ acting
cis
66
mutations in promotor elements of lac operon are ___ acting
cis
67
mutations in regulatory gene of lac operon are ___ acting
trans
68
lac operon
| I+
normal repressor produced
69
lac operon
| I-
produces repressor that cannot bind to the operator as the binding site is defective
cannot block RNA polymerase
70
lac operon
| I^s
produces repressor that cannot bind allolactose
super repressor
stay bound to the operator all the time - assuming the operator is normal genotype
71
lac operon
| O^c
change in operator of the DNA
cannot bind any type of repressor
RNA polymerase cannot be blocked by repressor
constitutive operator
72
lac operon
| P-
promotor mutation abnormal sequence preventing RNA polymerase from binding and transcription from occuring
73
lac operon
| z- or y- or a-
structural gene mutation
| results in defective enzymes
74
lacI-
- repressor cannot bind operator
- RNA polymerase CAN bind and transcribe genes resulting in translation of appropriate enzyme
- operon is always on whether lactose is present or not - constitutive
75
LacO^c
- defective operative sequence cannot bind repressor so it is always on whether lactose is present or not
it is constitutive
76
Partial diploid of F' merozygote
| I+P+O+Z-Y+/I-P+O+Z+Y+
- first part regular bacterial chromosome, send part F factor
- Z- causes faulty beta-galactosidase
- I- causes faulty repressor protein
77
I+P+O+Z-Y+/I-P+O+Z+Y+
lactose absent
1. I+ produces good repressor
I- produces faulty repressor
Both are present - I- cannot bind but I+ can bind to both copies since it is diffusible and acts in a trans manner
2. the repressor binds the operator of both pieces of DNA and all genes are turned off
78
I+ allele is ____ to I- negative allele
transdominant
the I+ is dominant in a trans manner to I-
79
I+P+O+Z-Y+/I-P+O+Z+Y+
lactose present
1. allolactose binds the repressor causing allosteric change and preventing the repressor from binding the operator
2. RNA polymerase binds both promotors and transcription occurs
3. the first piece with Z- forms nonfunction bet galactosidase
4. the second piece with Z+ forms good beta galactosidase
5. all functional genes are produced
80
I^sP+O+Z+Y+/I+P+O+Z+Y+
- transcription does not occur as I^s repressor cannoth bind allolactose leaving it in place bound to the operator
the repressor is a diffusible protein and therefore binds both operators
this will be the case with lactose present or not present
81
I+P-O+Z-Y+A+/I+P+O+Z+Y-A+
lactose absent
repressor binds both operators and no transcription occurs
82
I+P-O+Z-Y+A+/I+P+O+Z+Y-A+
lactose present
allolactose binds the repressor and the repressor isn't bound to the dNA
RNA polymerase cannot bidn to the P- promotor so the gene products on that piece are not produced
The other strand can bind to the P+ promotor allowing beta galactosidase and transacetylase to be made. However no permease is made.
Permease is not made on either strand
83
the interactive of the repressor and allolatose and the regions of the lac operon can be described as...
negative inducible regulation
84
lac operon promoter is weak meaning...
the -10 and -35 regions are not ideal so RNA polymerase doesn't bind as well as it would if they were ideal
it requires an activator to help RNA polymerase bind better
85
CAP
cyclic AMP activator protein
binds to the promotor on lac operon to help RNA polymerase bind better
will only bind to promotor after complexing wit cyclic AMP
86
CAP and cyclic AMP activity is example of...
positive inducible control
87
In lac operon...
- CAP is...
- cAMP is...
CAP is activator
| cAMP is small effector molecule
88
catabolite repression
- glucose inhibits cAMP formation by inhibiting the enzyme that produces it
glucose works to limit its own production
prevents breakdown of lactose to produce glucose when there is already enough glucose
89
adenylcyclase
enzyme that produces cAMP
90
high glucose impact on lac operon
- high glucose means low cAMP
- low cAMP prevents CAP from binding
- no CAP bound prevents RNA polymerase from binding efficiently leading to little transcription of structural genes
91
low glucose impact on lac operon
- low glucose means plenty of cAMP
- CAP can complex with cAMP and then bind to DNA
- RNA polymerase can now bind well allowing structural genes to be efficiently transcribed
92
trp operon makes
the enzymes needed to synthesize tryptophan
93
trp operon is normally on or off
on
can be turned off if no additional tryptophan needed
94
trp operon is an example of ___ control
negative repressible
the repressor cannot bind to the DNA unless complexed with small effector molecule
95
corepressor in trp operon is...
tryptophan
96
leader sequence
area that is transcribed and translated prior to the first structural gene
important in regulation
97
allosteric action in trp operon
a change occurs in the conformation of the repressor when it bind to trp allowing it to bind the operator
98
R gene
gene that makes the repressor in the trp operon
99
R- mutant
makes a repressor that cannot bind to the DNA so trp operon is always on
100
O^c trp operon mutant
the sequence of the operator is bad so it cannot bind the repressor
the operon is always on
101
constitutive mutants in trp operon
R-
| O^c
102
feedback inhibtion
excess trp in cell decreases the production of the enzymes used to make trp
103
trp low
- cells need to make trp so produces enzymes to make it
repressore isn't bound to operator allowing RNA polymerase to bind and transcription then translation to occur
104
trp high
cell does not need trp
trp complexes with the repressor allowing it to bind the operator and preventing RNA polymerase binding and transcription/translation from occurring
105
structural genes in trp operon
```
A
B
C
D
E
```
106
attenuator
located in the leader sequence of trp operator
responsible for decreasing transcription when trp is present
107
action of attenuator
normally when trp is present, some RNA polymerase escapes repressor complex and begins transcribing however it ends after about 140 nts in the attenuator region
108
attenuator when trp low
- ribosome pauses when its gets to two trp codons in a row since there are not many tRNA with trp
- the polymerase keeps going and gets ahead of ribosome
- ribosome blocks region 1 of leader sequence, so 2 and 3 bind
- this is not a termination signal so transcription continues
109
attenuator when trp high
- transcription goes through leader with ribosome just behind polymerase
- when region 3 is transcribed the ribosome is blocking region 2
- still blocking when 4 is transcribed allowing 3 and 4 to bind forming the termination hairpin
- this stops transcription and RNA polymerase is released before structural genes are transcribed
110
Most regulation in prokaryotes is at the level of...
transcription
111
antisense RNA
small RNA molecules complementary to parts of the mRNA base pair to the mRNA to inhibit translation
112
OMP
produces protein in E.coli membrane that functions as a diffusion pore
when osmolarity low, ompF gene is transcribed
when osmolarity high, micF gene is activated, making antisense RNA which binds 5' end of ompF RNA and prevents ribsome from binding reducing ompF protein productions
113
riboswitches
rna sequences in the mRNA that affect the translation of the mRNA
blocks ribosome binding site
