Module 8 Flashcards
Regulation (96 cards)
1
Q
define: replication
A
DNA copies itself
2
Q
define: transcription
A
DNA converts to RNA
3
Q
define: translation
A
proteins are synthesized from RNA
4
Q
how does RNA polymerase recognize the genes it will transcribe
A
has both a core enzyme and a sigma factor
5
Q
describe the modularity of sigma factors
A
- they can be exchanged for one another
- each sigma factor is responsible for a number of relevant genes
6
Q
what is the purpose of sigma factors
A
they recognize and initiate transcription of genes, guide RNA polymerase to promoter regions
7
Q
define: holoenzyme
A
RNA polymerase + sigma factor
8
Q
what are the two mechanisms of transcription termination in bacteria
A
- rho-dependent
- rho-independent
9
Q
describe rho-dependent termination
A
- a rho protein follows RNA pol
- when the protein catches up it removes RNA pol from the DNA strand
- happens when the pol reaches the GC-rich termination sequence
10
Q
describe rho-independent termination
A
- termination sequence leads to RNA hairpin loop formation, causing RNA pol to disassociate from the DNA
- hairpin duplex restricts forward movement of RNA pol
- hairpin made of guanines & cytosines
11
Q
what is the high-GC hairpin region followed by
A
a row of adenosines
12
Q
what does the Shrine-Dalgarno sequence do
A
orients the ribosome on the mRNA strand
13
Q
what does it mean for a mRNA strand to be polycistronic
A
it can code for more than one gene
14
Q
what allows an mRNA strand to be polycistronic
A
multiple Shrine-Dalgarno sequences
15
Q
why can transcription and translation occur simultaneously in bacteria
A
there’s no nucleus separation
16
Q
why do genes need to be regulated
A
expressing all genes is too expensive, allows microorganisms to respond to environmental stimuli
17
Q
define: inducible genes
A
genes subject to regulation
18
Q
define: constitutive genes
A
genes that are always on
19
Q
what are some levels of regulation
A
- level of mRNA production
- conversion of mRNA to proteins during translation
- level of protein activity (modifications to proteins)
20
Q
what are 2 modifications at the post-translational level
A
- covalent modifications
- allosteric regulation
21
Q
describe how covalent modifications work
A
- proteins can be phosphorylated, acetylated, methylated, or glycosylated
- their conformations get changed
22
Q
how does allosteric regulation work
A
- involves an effector molecule binding to a protein and changing its activity
- binds to a second site of the enzyme, not the active site
- can either activate or inhibit
23
Q
which form of post-translational protein regulation are multi-step synthesis pathways usually associated with
A
allosteric regulation
24
Q
what often serves as an effector molecule in multi-step synthesis pathways
A
end product of the pathway, inhibits the first enzyme of the pathway
25
what parts of the bacterial mRNA are regulatory elements
- activator binding site
- promoter
- operator
26
what regions are in an operon aside from the regulatory elements
structural genes
27
what is the relationship between an operon and mRNA
an operon is a DNA structure that gives rise to mRNA
28
what does negative control of transcription involve
- allosteric protein preventing mRNA synthesis
- blocking RNA polymerase from proceeding
- repression or induction of transcription
29
what does repression of transcription look like
- repressor protein is "ON"
- repressor protein binds to the operator
- RNA pol is blocked
30
what enzymes are usually associated with repression of transcription
anabolic enzymes (e.g. amino acid synthesis) [minority of enzymes]
31
what does induction of transcription look like
- repressor protein can't bind to the operator
- repressor is removed
32
what enzymes are usually associated with induction of transcription
catabolic enzymes
33
define: co-repressor
effector molecule that changes repressor shape to enable it to bind to the operator
34
define: co-inducer
effector molecule that changes repressor shape so that it falls off the operator
35
which region of the operon does postivite control of transcription involve
activator binding site
36
describe the process of positive control of transcription
- effector molecule binds to an allosteric activator protein
- activator binds to activator binding site
- transcription is initiated
37
where is positive control located on the operon
upstream of the promoter, doesn't have to be directly upstream
38
what is an example where positive control would be used
use of an alternative carbon source (e.g. maltose)
39
why are an activator and activator binding site required for positively controlled promoters
the promoters only weakly bind RNA polymerase, the activate changes DNA structure to inscrease the binding affinity
40
since activator proteins are allosteric proteins, what do they require
co-activate effector molecule
41
can bacterial genes and operons use multiple methods of regulation
yes, they can use either one or both
42
what does the lac operon encode
the ability to use lactose as a carbon source
43
define: diauxic growth
two phases of growth
44
why is the lac operon regulated
the use of glucose is favored above the use of lactose
45
what does the lacZ gene encode
the β-galactosidase that cleaves lactose into glucose and galactose
46
what does the lacY gene encode
a permease, enables lactose to enter the cell
47
what does the lacA gene encode
β-galactoside transacetylase, function unknown
48
what is the repressor protein involved in negative control of the lac operon
Lacl
49
what happens with the lac operator under "normal" conditions - sufficient glucose
Lacl repressor is bound to the lac operator
50
what is produced in addition to glucose & galactorse when β-galactosidase cleaves lactose
allolactose, an isomer of lactose
51
what type of effector molecule does allolactose act as in terms of negative control of transcription
a co-inducer, binds to Lacl & removes it from the operator or prevent binding in the first place
52
when is cyclic AMP prevented from being produced
when glucose is present
53
what type of effector molecule does cAMP act as and what does it act on
acts as a co-activator to the lac operon's activator protein (cAMP receptor protein, CRP)
54
describe the conditions needed for both controls of the lac operon to be activated
negative control - presence of lactose
positive control - absence of glucose
55
what is an example of negative control - repression
the tryptophan (trp) operon which is responsible for make the amino acid tryptophan
56
what acts as the co-repressor for the trp operon
tryptophan itself
57
define: attenuation
a form of transcriptional regulation that interrupts transcription after it starts but before its termination
58
in the tryptophan operon, what's the first region transcribed
the leader sequence (trpL)
59
why can't attenuation occur in eukaryotes
the ability for transcription and translation to occur simulatenously is required
60
what happens when there sufficient tryptophan in the cell [attenuation]
- region 1 is rapidly processed by ribosome (requires tryptophan)
- regions 1 and 2 are occupied by the ribosome
- regions 3 and 4 form a stable "hairpin" - terminator loop for rho-independent termination
- RNA polymerase falls off
61
what happens when there is not enough tryptophan in the cell [attenuation]
- the ribosome is stalled in region 1
- region 2 and 3 form a stronger hairpin
- this hairpin prevents terminator loop from forming
- RNA polymerase continues to transcribe structural genes
62
define: quorum sensing
how a group of individuals assess whether there are sufficient individuals (i.e. a quorum) in order to carry out some process of interest
63
how do bacteria assess sufficient population density
through chemical signalling
64
define: autoinducer molecules
chemicals released for quorum sensing purposes that act as co-activator effector molecules
65
describe how quorum sensing is positive feedback
detecting autoinducers => increase of some autoinducers by increased gene expression of signalling genes
66
what is the purpose of quorum sensing
to coordinate expensive processes
67
what is an example of the use of quorum sensing
Bobtail Squid and Aliivibrio fischeria
68
what are the components in two-component regulatory systems
- sensing component
- response component
69
what is the purpose of the sensing component [two-component regulatory systems]
membrane-associated protein that detects environmental signals
70
what does the response component do [two-component regulatory systems]
changes gene expression & possibly other phenotypic behaviours in response to the signal
71
what is the mechanism of signalling in two-component regulatory systems
via chemical signal transduction
72
what type of protein are membrane-associated sensor proteins
histidine protein kinase (HPK)
- "kinase" - adds phosphate groups to itself or has phosphate groups added
- "histidine" - the histidine residue is phosphorylated
73
what is the signal in a two-component regulatory system
phosphorylation event
74
what does the response regulator receive from the HPK
it receives a phosphate, attached to an aspartate residue
75
how is the ability of the response regulator limited
the phosphate group can be removed
76
what is autophosphatase activity
ability for a protein to desphosphorylate themselves [context or response regulators]
77
what are ways to remove phosphate groups
- autophophatase activity
- instability of the phophate-aspartate bond
- use of other proteins
78
what form of transcription regulation are two-component regulatory systems responsible for
negative control, positive control, or both
79
what does Agrobacterium tumefaciens regulate through a two-component regulatory system
it's virulence
80
when are vir genes found on the Ti plasmid expressed [Agrobacterium tumefaciens]
conditions similar to a plant wound site
81
what proteins are required for expression of the other virulence genes in Agrobacterium tumefaciens
VirA - sensor kinase
VirG - response regulator
82
what is chemotaxis an example of in terms of regulation
modification of a two-component regulatory system
83
what are the 3 steps to chemotaxis
1. response to an attractant or repellant signal
2. control of flagellar rotation
3. adaptation
84
what are the membrane-associated proteins in chemotaxis
methyl-accepting chemotaxis proteins (MCPs)
they aren't kinases themselves, instead they're associated with sensor kinases
85
define: regulon
set of genes that are coordinated together and respond to the same regulatory system
86
define: catabolite repression
shutdown of several systems that utilize various nutrients when glucose is present
87
define: SOS response system
multigene system for wide-scale DNA repair in response to serious DNA damage
88
what are the most important proteins regulating the SOS response regulon
RexA and LexA
89
describe: LexA
- repressor protein responsible for negative control of transcription
- normally bound to different genes & operons (over 40 different inducible genes)
- normally present at low levels sufficient to prevent the transcription of these genes
90
describe: RecA
- always present at low concentrations in a cell
- binds to single-stranded DNA
- has the ability to cleave LexA
91
what happens when LexA is cleaved by RecA
- LexA can no longer bind to operators
- results in high levels of SOS-gene expression that produces repair proteins and polymerases
92
what is DNA polymerase made up of (holoenzyme)
the polymerase enzyme and its associate sigma factors
93
what is the default sigma factor of RNA polymerase in E. coli
sigma-70, recognizes most of the promoters
94
what is the purpose of sigma-54
regulation of nitrogen utilization genes
95
what is the purpose of sigma-32
heat shock protein gene regulator
96
what is the purpose of sigma-38
general stress response gene regulator
