Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIO 315 > Module 6 - Regulation of Gene Expression > Flashcards

Module 6 - Regulation of Gene Expression Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

What is gene expression?

A

A process where information from a gene is used in the synthesis of a functional gene product (often a protein)

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

How do cells conserve energy?

A

Not all the genes are expressed all the time

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

What are constitutive genes?

A

Genes that are constantly on

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

What are some examples of constitutive genes?

A

Genes involved in glycolysis, transcription, and translation

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

What are inducible genes?

A

Genes that are needed when a substrate is present

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

What are the three levels of gene expression?

A

Transcriptional, translational, and post-translational

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is transcriptional control of gene expression?

A

Binding of RNA polymerase to the promoter and initiating transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is translational control of gene expression?

A

Binding of the ribosome to mRNA for continued translation

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

What is post-translational control of gene expression?

A

Modification of the protein to activate, inhibit, or degrade it

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

What are enzymes?

A

Biological catalysts

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

How can the activity of an enzyme be altered?

A

By changing its confirmation due to modifications, or by using inhibitors

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

What modifications can be done to an enzyme to alter its function?

A

Phosphorylation, acetylation, methylation, and glycosylation

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

What is a competitive inhibitor?

A

An inhibitor that competes directly with the substrate for the active site of the enzyme

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

What is a non-competitive inhibitor?

A

An inhibitor that binds to an allosteric site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is an allosteric site?

A

A site other than the active site on the enzyme

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is another name for allosteric inhibition?

A

Feedback inhibition

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

What happens when the enzyme activity is modified?

A

The biochemistry of the cell is changed

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

True or false: modifying an enzyme is a conservative process

A

False: it does not save much energy

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

How come modifying an enzyme is not a conservative process?

A

It still takes a lot of energy to create the enzyme in the first place

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

What is a better way for the cell to save energy?

A

By only producing the enzyme when it is needed

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

How do most of the control mechanisms in bacteria work?

A

By preventing transcription (and thus translation) of genes when not required

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What does the operon mechanism suggest?

A

A method where regulatory genes can direct cell metabolism by altering rates of transcription of functional genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is an operon?

A

A transcriptional unit with a series of structural genes and their transcriptional regulatory elements

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

If a cell requires three proteins for a single process, how should they be regulated?

A

They should either all be produced or not produced at the same time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

When was the first eukaryotic operon found?

A

In the 1990s

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

True or false: operons are only found in prokaryotes

A

False: while this was originally thought to be true, eukaryotic operons have been discovered

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What does expression of prokaryotic operons lead to?

A

Polycistronic mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What is polycistronic mRNA?

A

mRNA that encodes for 2 or more proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the majority of mRNA in eukaryotic cells?

A

Monocistronic mRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What is monocistronic mRNA?

A

mRNA that encodes for one protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What are the structural genes of the lac operon?

A

lacZ, lacY, and lacA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is another name for LacY?

A

Permease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What does LacY do?

A

Facilitates the uptake of lactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What is another name for LacZ?

A

Beta-galactosidase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What does LacZ do?

A

Breaks down lactose enzymatically

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is another name for LacA?

A

Beta-galactosidase transacetylase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What does LacA do?

A

It is not well understood currently

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Where does RNA polymerase bind to?

A

The promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

Where do regulatory proteins bind to?

A

The operator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What do regulatory proteins do?

A

Modulate the ability of RNA polymerase to bind to the promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What does LacI do?

A

Inhibits the lac operon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

What is negative control?

A

When regulatory proteins inhibit operon transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

What is positive control?

A

When regulatory proteins facilitate operon transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What happens when lactose enters the cell?

A

It gets metabolized to glucose and galactose by beta-galactosidase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What two simple sugars make up lactose?

A

Glucose and galactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

What is allolactose?

A

An isomer of lactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

What reaction produced allolactose?

A

Beta-galactosidase converts lactose into allolactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What does allolactose do?

A

It acts as an inducer of the lac operon (it turns it on)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

What is a promoter?

A

The site on the DNA bound by RNA polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

What is an activator?

A

A protein that binds to a site on the DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

What does a promoter do?

A

It directs initiation of transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

What does an activator do?

A

It assists binding of RNA polymerase to the promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What is an activator binding site?

A

A site on the DNA bound by an activator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is a repressor?

A

A protein that binds to the operator site to inhibit transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What is an operator?

A

A site on the DNA bound by a repressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What is an effector?

A

A small molecule that binds to an activator or a repressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What does an effector do?

A

Modifies gene regulation activity by being an inducer or corepressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What is an inducer?

A

An effector than increases transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

How does an inducer work?

A

It either enables an activator or disables a repressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

What is a corepressor?

A

An effector that decreases transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

How does a corepressor work?

A

By enabling a repressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

What is LacI?

A

A repressor molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What does LacI do?

A

Binds to the operator as a dimer to interfere with the binding of RNA polymerase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

What is the effector of the lac operon?

A

Allolactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What type of proteins are usually effectors?

A

Intermediates of the related metabolic pathway

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What happens to the lac operon in the absence of lactose?

A

Transcription is off due to LacI binding to the operator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

What happens to the lac operon in the presence of lactose?

A

Allolactose acts as an inducer by inhibiting LacI, thus promoting transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

What type of effector is allolactose?

A

An inducer (it inhibits LacI)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

How does allolactose work?

A

It inactivates LacI by changing its shape so it can’t bind to the operator

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

What types of reactions are usually done by negative control?

A

Catabolic pathways in the absence of substrates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

How many structural genes are in the trp operon?

A

6

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

What happens to the trp operon in the absence of tryptophan?

A

The repressor cannot bind to the operator, and the structural genes are transcribed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

What happens to the trp operon in the presence of tryptophan?

A

Tryptophan acts a corepressor to allow the repressor to bind to the operator region

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

What is the effector molecule in the trp operon?

A

Tryptophan

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

What type of effector is tryptophan?

A

A corepressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

What type of control is the lac operon (considering lactose)?

A

Negative control

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
77
Q

What type of control is the lac operon (considering glucose)?

A

Positive control

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
78
Q

What type of control is the trp operon?

A

Negative control

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
79
Q

True or false: the activator protein always binds directly to the activator site

A

False: there could be another protein involved

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
80
Q

What is the activator protein in the lac operon?

A

CRP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
81
Q

What does CRP stand for?

A

cAMP receptor protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
82
Q

What is the co-activator of CRP?

A

cAMP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
83
Q

How does CRP work?

A

When bound to cAMP, it binds to the activator site to promote binding of RNA polymerase to the promoter

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
84
Q

What do E. coli cells grow best in?

A

Glucose (as opposed to lactose)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
85
Q

How come E. coli cells grow better in glucose than lactose?

A

Glucose can enter glycolysis directly, while lactose must first be converted into glucose and galactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
86
Q

What is needed for the lac operon to be transcriped?

A

The repressor (LacI) must be unbound, and the activator (CRP) must be bound

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
87
Q

When there is glucose present, what are the cAMP levels?

A

Low

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
88
Q

Where glucose is absent, what are the cAMP levels?

A

High

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
89
Q

What is catabolite repression?

A

When a catabolite is preferred over another, so there is repression of the catabolism of the nonpreferred catabolite

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
90
Q

What happens when glucose is absent and lactose is present in a cell?

A

The operon has the activator, and there is transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
91
Q

What happens when glucose and lactose is absent in a cell?

A

The operon has the activator and the repressor, so there is low transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
92
Q

What happens when glucose is present and lactose is absent in a cell?

A

The operon has the repressor, so there is no transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
93
Q

What happens when glucose and lactose is present in a cell (in terms of the operon)?

A

The operon has no repressor or activator, so there is low transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
94
Q

What happens when glucose and lactose are available (in terms of sugar availability)?

A

Glucose is used first, and then lactose is used

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
95
Q

What is a diauxic growth curve?

A

A growth curve caused by the use of two metabolites

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
96
Q

When does a diauxic growth curve occur?

A

When a cell has both glucose and lactose available

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
97
Q

What is the shape of a diauxic growth curve?

A

Logistic (steep at the ends, flat in the middle)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
98
Q

What happens when glucose becomes depleted in diauxic growth?

A

Beta-galactosidase and permease must be produced before the cells can use lactose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
99
Q

What does the flat region on the diauxic growth represent?

A

The cells not growing because they have to produce the enzymes of the lac operon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
100
Q

What happens during the lag phase of diauxic growth?

A

The cells are not growing because they are producing LacZ and LacY

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
101
Q

What did scientists use to understand the role of LacI?

A

Mutants that constitutively expressed beta-galactosidase (even in absence of lactose)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
102
Q

What does I- refer to?

A

Inducer negative mutants (mutants that constitutively expressed beta-galactosidase)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
103
Q

What happened when a wild type copy of the lac region was inserted as a plasmid in I- mutants?

A

They could now be induced for expression of beta-galactosidase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
104
Q

What was the conclusion of putting a wild type copy of the lac region in I- mutants?

A

LacI was diffusable

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
105
Q

How was it discovered that LacI was diffusable?

A

It was able to complement a lac mutant, even on a separate piece of DNA (plasmid)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
106
Q

What does O- refer to?

A

Mutants that had a mutation at the operator site

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
107
Q

What happened when a wild type copy of the lac region was inserted as a plasmid in O- mutants?

A

There was still constitutive expression of beta-galactosidase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
108
Q

What was the conclusion of putting a wild type copy of the lac region in O- mutants?

A

LacI binds to the operator to stop transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
109
Q

How was it discovered that LacI binds to the operator?

A

When the operator was mutated and LacI was expressed, the system remained constitutively active

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
110
Q

What happens when a cell is under stressed conditions (such as high temperature)?

A

Heat shock proteins are produced to help the cell survive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
111
Q

What are regulons?

A

Groups of operons coordinated to respond to the same regulatory systems

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
112
Q

What is an example of global control?

A

Regulation by glucose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
113
Q

How does glucose act as a global control?

A

It is involved in catabolite repression to shut down other pathways

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
114
Q

In E. coli, how many operons does CRP regulate?

A

100

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
115
Q

What environmental stresses can damage DNA?

A

UV radiation and chemicals

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
116
Q

What is the SOS response?

A

A regulon that allows the cell to recognize and respond to serious DNA damage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
117
Q

What was used for the experimental evidence for the existence of regulons?

A

Bacteriophages treated with UV light

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
118
Q

What two E. coli cultures were used to prove the existence of regulons?

A

One that was preexposed to UV, and another that was untreated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
119
Q

What happened when E. coli untreated with UV were mixed with the phages?

A

There was a low number of phages, and no increase in mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
120
Q

What happened when E. coli treated with UV were mixed with the phages?

A

There was a greater number of phages, with an increase in phage mutations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
121
Q

What did the experiments with UV light on E. coli show?

A

That DNA repair is error prone (generates mutations)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
122
Q

What does chloramphenicol do?

A

It is an antibiotic that blocks protein synthesis in bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
123
Q

What happened when chloramphenicol was added to E. coli?

A

DNA repair was also blocked

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
124
Q

What was the conclusion from adding chloramphenicol to E. coli?

A

DNA repair required protein synthesis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
125
Q

How were the genes expressed for DNA repair identified?

A

Through a lacZ promoter probe transposon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
126
Q

What is a lacZ promoter probe transposon?

A

A promoter-less lacZ reporter gene that can insert into DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
127
Q

How does lacZ get expressed in a lacZ promoter probe transposon?

A

It must insert within an actively transcribed gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
128
Q

How can the lacZ in the lacZ promoter probe transposon be identified?

A

By using X-gal to see if there is LacZ activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
129
Q

What happens if LacZ inserts into an active gene?

A

It will show up blue in the presence of X-gal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
130
Q

What happens if LacZ inserts into an inactive gene?

A

It will show up white in the presence of X-gal

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
131
Q

What DNA damaging agent was used to study the SOS regulon?

A

Mitomycin C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
132
Q

In the experiments with Mitomycin C, which cells had genes that were part of the SOS regulon?

A

Those that were blue in the presence of Mitomycin C, but white in the absence of Mitomycin C

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
133
Q

What does din stand for?

A

Damage induced gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
134
Q

What are din genes?

A

Genes part of the SOS regulon that respond to DNA damage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
135
Q

How do cells sense DNA damage?

A

They detect single stranded DNA (a result of damage)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
136
Q

Which genes can alter the SOS response?

A

lexA and recA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
137
Q

What is recA involved in?

A

Recombination

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
138
Q

What does RecA do?

A

Binds to single stranded DNA to regulate the SOS regulon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
139
Q

What is RecA activated?

A

When it is bound to single stranded DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
140
Q

What does LexA do?

A

It is a repressor that binds to the operator of the SOS regulon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
141
Q

What does RecA do when it is bound to single stranded DNA?

A

It cleaves LexA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
142
Q

What happens when LexA is cleaved?

A

It can no longer bind to the operator, so the SOS genes are expressed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
143
Q

How many genes in E. coli are part of the SOS regulon?

A

40

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
144
Q

Besides regulons, how can global gene regulation be achieved?

A

Through alternative sigma factors

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
145
Q

What is a sigma factor and what does it do?

A

A polypeptide that allows RNA polymerase to identify promoter for initiation of transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
146
Q

What is a primary sigma factor?

A

The sigma factor responsible for recognizing the most promoters

147
Q

What is the primary sigma factor in E. coli?

A

Sigma-70

148
Q

What does Sigma-54 do?

A

Regulates nitrogen utilization genes

149
Q

What is required for Sigma-54 to function?

A

An activating protein and ATP to initiate transcription

150
Q

True or false: Sigma-70 requires an activating protein and ATP to initiate transcription

A

False: Sigma-54 requires this, not Sigma-70

151
Q

What does Sigma-32 do?

A

Regulates heat shock proteins

152
Q

What does Sigma-38 do?

A

It is a general stress response gene regulator

153
Q

Which sigma factor is a general stress response gene regulator?

A

Sigma-38

154
Q

Which sigma factor regulates heat shock proteins?

A

Sigma-32

155
Q

Which sigma factor regulates nitrogen utilization?

A

Sigma-54

156
Q

What RNAs are encoded in the genome?

A

rRNA, tRNA, and regulatory RNAs

157
Q

What is sRNA?

A

Small noncoding RNAs

158
Q

How big are sRNAs?

A

50-400 nt

159
Q

What do sRNAs do?

A

Affect gene expression by interacting with existing mRNA

160
Q

How do sRNAs silence a gene?

A

By preventing transcription from completing or by blocking translation

161
Q

What are some types of sRNA?

A

miRNA, siRNA, and asRNA

162
Q

What does miRNA stand for?

A

MicroRNA

163
Q

What does siRNA stand for?

A

Small interfering RNA

164
Q

What does asRNA stand for?

A

Antisense RNA

165
Q

What is another name for Sigma-38?

A

rpoS

166
Q

What does rpoS stand for?

A

RNA polymerase S

167
Q

How do asRNAs work?

A

They use complementary base pairing to interact with specific mRNA molecules

168
Q

What does rpoS do in the absence of asRNA?

A

It inhibits translation through its 5’ leader sequence

169
Q

What is the structure of rpoS?

A

A 5’ leader sequence that forms a hairpin stem loop structure

170
Q

What happens when cells are exposed to different stresses?

A

They accumulate different sRNAs

171
Q

What is DsrA?

A

A sRNA

172
Q

When is DsrA produced?

A

When the cell is exposed to low temperatures

173
Q

What does DsrA do?

A

It binds with Hfq, which binds to rpoS

174
Q

What is Hfq?

A

An RNA-binding protein for DsrA

175
Q

What happens when DsrA and Hfq bind to RpoS?

A

They disrupt the inhibitory secondary structure, which allows translation to proceed

176
Q

What are riboswitches?

A

Regulatory molecules that bind to RNA and alter its shape

177
Q

What is quorum sensing?

A

A chemical signaling system used to detect presence and number of other organisms in a population

178
Q

What is a quorum?

A

The number of members that must be present at a meeting to conduct business

179
Q

What does quorum sensing involve?

A

Release of specific signaling molecules called autoinducers

180
Q

What does an autoinducer do?

A

It acts as a signaling molecule that increases in concentration as density of bacterial population increases

181
Q

How can bacteria assess population density?

A

By detecting autoinducer concentration

182
Q

What happens when population density changes?

A

Gene expression may also change

183
Q

What is special about Vibrio fischeri?

A

They can produce light

184
Q

Which organism does Vibrio fischeri live inside?

A

The Hawaiian bobtail squid

185
Q

What does the light organ in bobtail squid do?

A

It luminesces when colonized by V. fischeri

186
Q

What was the first quorum sensing system described?

A

The lux system

187
Q

What does luciferase do?

A

Produces light

188
Q

When do V. fischeri cells emit light?

A

When they are at a high density

189
Q

What is the autoinducer in the lux system?

A

AHL

190
Q

What does AHL stand for?

A

N-acyl-homoserine lactone

191
Q

True or false: AHL is only used for intracellular signaling in V. fischeri

A

False: it is seen in many other types of bacteria

192
Q

What protein synthesizes AHL?

A

LuxL

193
Q

What does LuxL do?

A

Synthesizes AHL

194
Q

At low cell density, what is the concentration of AHL?

A

Low

195
Q

How come AHL concentration is low at low cell density?

A

It diffuses away from the cell

196
Q

At high cell density, what is the concentration of AHL?

A

High

197
Q

What happens when there is a high concentration of AHL?

A

It binds to LuxR

198
Q

What is LuxR?

A

A transcriptional activator protein

199
Q

What happens when LuxR is activated?

A

It binds to the lux box to promote transcription

200
Q

What is the lux box?

A

A regulatory DNA site for the lux operon

201
Q

What is encoded by the lux operon?

A

LuxA, LuxB, and LuxL

202
Q

What does LuxA and LuxB do?

A

Encode luciferase

203
Q

True or false: the lux system is a positive feedback mechanism

A

True: LuxL is produced, which creates more AHL

204
Q

How is the lux system a positive feedback loop?

A

LuxL is produced, which creates more AHL to regulate the lux operon further

205
Q

What processes can be controlled by quorum sensing?

A

Motility, conjugation, biofilm formation, pathogenesis, and secondary metabolite production

206
Q

How can quorum sensing control pathogenesis?

A

By producing cholera toxin when enough cells are present (V. cholera)

207
Q

How can autoinducers play a role in competition?

A

They may interrupt or inhibit a control pathway in other organisms in the environment

208
Q

How to cells commonly react to the environment?

A

Through a two component regulatory system

209
Q

What are the components of a two component regulatory system?

A

A sensor protein, and a protein that regulates transcription

210
Q

What happens when the two components of a two component regulatory system interact?

A

It creates signal transduction

211
Q

What are the most common regulatory systems in bacteria?

A

A two component system

212
Q

What is a commonly used sensor?

A

HPK

213
Q

What does HPK stand for?

A

Histidine protein kinase

214
Q

What does RR stand for?

A

Response regulator

215
Q

What does HPK do?

A

It becomes phosphorylated and phosphorylates RR

216
Q

What happens when RR is phosphorylated?

A

It changes confirmation and regulates gene expression

217
Q

What is chemotaxis?

A

The movement of motile bacteria in response to a chemical stimulus

218
Q

Why is chemotaxis important in bacteria?

A

It is important to swim towards the highest concentration of food or run away from detrimental chemicals

219
Q

In which organism is regulation of chemotaxis best understood?

A

In E. coli

220
Q

What is the flagella structure of E. coli?

A

Peritrichous (several flagella all around the cell)

221
Q

What happens during counterclockwise rotation?

A

The cell propels forward

222
Q

What happens during clockwise rotation?

A

It causes a tumble (change of direction)

223
Q

What happens to flagellar rotation in the absence of an attractant or repellant?

A

It alternates between clockwise and counterclockwise rotation

224
Q

What is the rate of rotation switching in E. coli?

A

Once per sec

225
Q

What happens to flagellar rotation in the presence of an attractant or repellent?

A

The ratio of clockwise to counterclockwise rotation changes

226
Q

What did researchers use to understand chemotaxis?

A

Mutants where chemotaxis was disrupted

227
Q

How were mutants where chemotaxis was disrupted isolated?

A

By using a capillary tube with semi-solid agar and higher concentration of attractant than surrounding media

228
Q

In the apparatus to isolate chemotaxis mutants, where would wild-type E. coli be found?

A

In the capillary tube

229
Q

How come wild type E. coli would be in the capillary tube?

A

There is a higher concentration of attractant there

230
Q

In the apparatus to isolate chemotaxis mutants, where would the mutants be?

A

In the surrounding media

231
Q

How come chemotaxis mutants would be in the surrounding media?

A

Because they would not move to the capillary tube with higher concentration

232
Q

Mutations in which genes result in counterclockwise rotation?

A

cheA, cheY, cheW, or cheR

233
Q

Mutations in which genes result in clockwise rotation?

A

cheB or cheZ

234
Q

What happens if cheA is mutated?

A

Counterclockwise rotation

235
Q

What happens if cheY is mutated?

A

Counterclockwise rotation

236
Q

What happens if cheW is mutated?

A

Counterclockwise rotation

237
Q

What happens if cheR is mutated?

A

Counterclockwise rotation

238
Q

What happens if cheB is mutated?

A

Clockwise rotation

239
Q

What happens if cheZ is mutated?

A

Clockwise rotation

240
Q

What does the regulation of chemotaxis involve?

A

Protein switches

241
Q

What proteins are found in all chemotactic bacteria?

A

CheA and CheY

242
Q

What does CheA do?

A

Acts as the sensor kinase in the system

243
Q

How does CheA work?

A

It is phosphorylated at a histidine residue in response to the presence or absence of a particular attractant or repellant

244
Q

What does CheY do?

A

Acts as a RR in the system

245
Q

What does pCheA do?

A

It phosphorylates CheY at a specific aspartic residue

246
Q

What does pCheY do?

A

It interacts with the flagellar motor to determine direction of rotation

247
Q

True or false: phosphorylation circuit is typical in a 2 component regulatory system

A

True: phosphorylation is very common in cell signaling

248
Q

In the absence of an attractant, what state is CheA in?

A

Phosphorylated state

249
Q

What phosphorylates CheA?

A

CheW

250
Q

What does CheW do?

A

Phosphorylates CheA in the absence of an attractant

251
Q

What direction does pCheY lead to?

A

Clockwise rotation (tumble)

252
Q

When does a cell tumble?

A

Clockwise rotation

253
Q

What does a cell run?

A

Counterclockwise rotation

254
Q

What happens when pCheY is dephosphorylated?

A

It cannot interact with the flagellar motor, leading to counterclockwise rotation (run)

255
Q

How does CheY get dephosphorylated?

A

By CheZ

256
Q

What does CheZ do?

A

Dephosphorylates CheY

257
Q

In the presence of an attractant, what state is CheA in ?

A

Dephosphorylated state

258
Q

What happens to CheY in the presence of an attractant?

A

It cannot be phosphorylated by CheA, so it stays dephosphorylated

259
Q

What is the result of CheY being dephosphorylated in the presence of an attractant?

A

The cell run towards that attractant (counterclockwise rotation)

260
Q

True or false: the chemotaxis system is a two component regulatory system

A

True: it has a sensor kinase (CheA) and an RR (CheY)

261
Q

True or false: the chemotaxis system involves transcriptional or translation regulation

A

False: it involves protein switches

262
Q

What is the most common promoter sequence?

A

The consensus sequence

263
Q

What is the least common method of gene expression?

A

Controlling mRNA expression (after transcription, before translation)

264
Q

What does virB do?

A

Has virulence genes involved in DNA transfer form bacteria to plant

265
Q

How many structural genes are in the virB operon?

A

11

266
Q

What bacteria has virB?

A

Agrobacterium

267
Q

What does nifHDK do?

A

Nitrogenase enzyme involved in nitrogen fixation

268
Q

How many structural genes are in the nifHDK operon?

A

3

269
Q

What bacteria has nifHDK?

A

Klebsiella pneumoniae

270
Q

What does S10 do?

A

Ribosome structure

271
Q

How many structural genes are in the S10 operon?

A

11

272
Q

What bacteria has S10?

A

Conserved throughout bacteria

273
Q

Where are the genes encoding regulatory proteins for the operon found?

A

They can be adjacent to the operon, or located elsewhere on the chromosome

274
Q

How did researchers figure out what genes did what in the lac operon?

A

By using radioactive lactose

275
Q

What happens if lacA is mutated?

A

There is no effect on lactose utilization or transport

276
Q

What mutations defined the promoter of the lac operon?

A

Mutations where no LacZ or LacY was produced

277
Q

Who investigated lambda phages and E. coli in the DNA damage pathway?

A

Jean-Jacques Weigle

278
Q

What correlation was seen in the E. coli and lambda phage UV experiments?

A

A correlation between infectivity and mutagenesis

279
Q

What was the conclusion of the UV experiments on E. coli and lambda phages?

A

UV treatment of host cells enhanced their ability to repair UV-induced damage of lambda phages, but this system was error-prone

280
Q

What does the cell detect to determine DNA damage?

A

Single stranded DNA

281
Q

What does the SOS repair system use to repair DNA?

A

An alternative DNA polymerase that lacks proof-reading ability

282
Q

How come the SOS repair system is error prone?

A

The DNA polymerase used lacks the ability to proofread to fill in the missing DNA

283
Q

What does umuDC do?

A

Error-prone DNA polymerase V

284
Q

What are some genes in the E. coli SOS regulon?

A

umuDC, dinB, polB, uvrA, uvrB, uvrD, sbmC, ruvAB, lexA, recA, dinI, recN, ssb, dinG, sulA, ftsK, and pcsA

285
Q

What does dinB do?

A

Error-prone DNA polymerase IV

286
Q

What does polB do?

A

DNA polymerase II, repair of DNA interstrand crosslinks

287
Q

What does uvrA do?

A

Nucleotide excision repair

288
Q

What does uvrB do?

A

Nucleotide excision repair

289
Q

What does uvrD do?

A

DNA helicase, involved in DNA repair

290
Q

What does sbmC do?

A

DNA gyrase inhibitor

291
Q

What does ruvAB do?

A

Homologous recombination, Holliday junction resolution

292
Q

What does dinI do?

A

DNA damage inducible protein, regulation of RecA protease activity

293
Q

What does recN do?

A

DNA recombinational repair protein

294
Q

What does ssb do?

A

Single stranded DNA binding protein

295
Q

What does dinG do?

A

ATP-dependent DNA helicase

296
Q

What does sulA do?

A

SOS cell division inhibitor

297
Q

What does ftsK do?

A

Cell division protein

298
Q

What does pcsA do?

A

Phosphatidylcholine synthesis

299
Q

What is another name for sigma-70?

A

RpoD

300
Q

How many alternative sigma-70 family members does E. coli have?

A

6

301
Q

How many alternative sigma-70 family members does Streptomyces coelicolor have?

A

60

302
Q

What is another name for sigma-54?

A

RpoN

303
Q

True or false: sigma-54 can recognize promoter regions at different distances from the initiation of transcription

A

True: sigma-70 cannot do this

304
Q

True or false: sigma-70 can recognize promoter regions at different distances from the initiation of transcription

A

False: sigma-54 can, not sigma-70

305
Q

What is another name for sigma-32?

A

RpoH

306
Q

What happens to sigma-32 under normal conditions?

A

It is degraded very rapidly

307
Q

What happens to sigma-32 under higher temperatures?

A

Other proteins unfold and compete with sigma-32 for proteases. This increases the concentration of sigma-32

308
Q

What are some examples of situations where rpoS would be activated?

A

High cell density, nutrient starvation, low temperature, high osmolarity, and oxidative stress

309
Q

What are some genes that respond to RpoS?

A

Protein processing, general stress adaptation, membrane stability and transport, and metabolism

310
Q

What do anti-sigma factors do?

A

They bind to the sigma factor to prevent RNA polymerase from binding to the promoters (thus turning off genes it controls)

311
Q

What are anti-sigma factors useful for?

A

Controlling the timing of global gene expression

312
Q

What is an example of an anti-sigma factor?

A

FlgM

313
Q

What does FlgM interact with?

A

Sigma-28

314
Q

What does sigma-28 do?

A

It is responsible for the timing of expression of the genes involved with the assembly of the flagella

315
Q

What asRNAs regulate RpoS?

A

DsrA and RprA

316
Q

When is DsrA activated?

A

When there are low temperatures

317
Q

When is RprA activated?

A

Where there are high cell surface stresses

318
Q

What is attenuation?

A

Regulatory mechanisms that involve interacts between transcription and translation

319
Q

How was attenuation first discovered?

A

By deletion mutations in the upstream regulatory region of the trp operon

320
Q

What happened when there were deletion mutations in the upstream regulatory region of the trp operon?

A

There was an increase in transcription, regardless of whether repressor was activated or not

321
Q

When does regulation by attenuation occur?

A

After the initiation of transcription, but before transcription of the operon has been completed

322
Q

What causes attenuation in the trp operon?

A

A short translated leader sequence of the mRNA coded by trpL

323
Q

Where is trpL found?

A

Following the operator, but before the 5 structural genes

324
Q

How come the 5’ end of the leader sequence can be translated before the transcript is finished?

A

Transcription and translation is coupled in bacteria and archaea

325
Q

What is the consequence of transcription and translation being coupled for attentuation?

A

The 5’ end of the leader sequence can be translated before the transcript is finished

326
Q

What does the leader sequence of trpL contain?

A

Tryptophan codons, and base pair complementary

327
Q

What happens if tryptophan is abundant for the leader sequence?

A

The leader will be translated completely

328
Q

What happens if tryptophan is scare for the leader sequence?

A

It is difficult for the leader to be translated completely

329
Q

What region of trpL has the tryptophan codons?

A

Region 1

330
Q

What is the consequence of base pair complementary in trpL?

A

It can form stem loops

331
Q

Which regions of trpL can form stem loops?

A

Region 2 and Region 3, and Region 3 and Region 4 (not both)

332
Q

In trpL, what is after Region 4, and what does it do?

A

A uracil-rich attenuator sequence that can interact with the 3-4 stem loop

333
Q

What happens if the attenuator interacts with the 3-4 stem loop in trpL?

A

It will form a transcription termination structure, causing termination to occur before reaching the structural genes

334
Q

If tryptophan is plentiful, how will trpL stop transcription?

A

The ribosome will reach the stop codon, blocking formation of the stem loop between Region 2 and 3. Thus, the 3-4 stem loop is formed, terminating transcription

335
Q

If tryptophan is scare, how will trpL continue transcription?

A

The ribosome pauses at Region 1, which allows Region 2 to bind to Region 3. This prevents the attenuator from interacting with the 3-4 stem loop, continuing transcription

336
Q

What can riboswitches bind to to regulate gene expression?

A

Effector molecules, such as vitamins and amino acids

337
Q

True or false: riboswitches can affect both transcription and translation

A

True: they can be involved in either process

338
Q

Which phylum uses AHL as an autoinducer?

A

Proteobacteria

339
Q

What do Gram-positive bacteria use for quorum sensing?

A

Small peptides

340
Q

How do small peptides function in quorum sensing?

A

They are transported outside the cell, and can bind to specific cell-surface receptors, triggering a cell-signaling pathway that affects gene expression

341
Q

How can organisms use multiple quorum sensing signals?

A

By using AHLs with different lengths and chemical modifications

342
Q

True or false: quorum sensing can only affect one particular species

A

False: they may also affect gene expression in other species (biofilms)

343
Q

What is signal transduction?

A

A cellular response to an external stimulus

344
Q

True or false: two-component systems can have several HPK and RR proteins

A

True: this is seen in Bacillus subtilis endospore formation

345
Q

What does the transfer of tDNA from the bacterium to the plant require?

A

vir genes

346
Q

When are the vir genes activated in agrobacterium?

A

In conditions similar to the plant wound site (acidic pH, and certain phenolic compounds like acetosyringone)

347
Q

What is the HPK for the vir genes?

A

VirA

348
Q

What is the RR for the vir genes?

A

VirG

349
Q

What happens when VirA senses the phenolic compounds?

A

It becomes phosphorylated (activated)

350
Q

What happens when VirA is phosphorylated?

A

It phosphorylates VirG

351
Q

What happens when VirG is phosphorylated?

A

It is an activate transcription factor

352
Q

What happens to VirA when VirG is phosphorylated?

A

VirA becomes dephosphorylated

353
Q

What system uses phosphotransfer mechanisms?

A

The vir system

354
Q

What do MCPs do in the chemotaxis pathway?

A

Sensory proteins or transducers, methylated by CheR

355
Q

What does MCP stand for?

A

Methyl-accepting chemotaxis protein

356
Q

What does CheR do?

A

Methylates MCP

357
Q

What does CheA do?

A

Sensor kinase

358
Q

What does CheY do?

A

Response regulator, controls direction of flagellar movement

359
Q

What does CheB do?

A

Response regulator, demethylates MCP

360
Q

What does CheZ do?

A

Dephosphorylates pCheY

361
Q

What does CheW do?

A

Involved in the transduction of signal from MCP to CheA

362
Q

What does methylation of MCP result in?

A

Adaptation

363
Q

What does methylation of MCP do?

A

Decreases ability to respond to attractant

364
Q

When does CheB demethylate MCP?

A

What is is phosphorylated by pCheA

BIO 315 (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions