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BIOL 112 > 3.6 gene regulation and operons > Flashcards

3.6 gene regulation and operons Flashcards

1
Q

A Gene is said to be expressed when …

A

the gene product is actively being synthesized and used in a cell (recall the transcriptome)

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2
Q

constitutively expressed gene

A

A gene that is expressed ALL the time because its gene product is needed all the time

  • rRNA, tRNA
  • RNA polymerase
  • Ribosomal proteins
  • Amino acyl tRNA
  • synthetases (enzymes)
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3
Q

Are constitutively regulated/expressed genes always made at the same level?

A

No! Gene products of constitutively expressed genes are NOT needed in the same amounts in cells

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4
Q

Common control mechanisms of constitutively gene products:

A

Promoter “strength” i.e. how effectively RNA Pol & transcription factors bind to the promoter
* Determines how frequently transcription is initiated.
* This determines how many RNA molecules are made.

mRNA half-life can affect
* How quickly the mRNA is degraded after it is made.
* The longer the mRNA lasts, the more protein copies can
be translated per unit time.
* Only applies to protein encoding genes i.e. mRNA

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5
Q

Gene and Gene Product Expression can be Controlled at Three Levels

A
  1. transcriptional
  2. translational
  3. post- (protein activation or inactivation)
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6
Q

operon

A

region of DNA consisting of promoter, operator, and coding sequence for the structural gene

share a promoter and termination sequence but have multiple coding regions. One mRNA is produced yet multiple proteins are translated.

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7
Q

examples of Transcriptional level of control

A
  1. Promoter Strength – how strongly
    RNA Pol + Transcription Factors bind to
    the promoter
  2. Operons – regulatory proteins binding
    to a regulatory region “operator”
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8
Q

transcriptional level of control

A

gene organization where polycistronic mRNA results from transcription of a group of functionally related genes location in tandem along the DNA and transcribed as a single unit from one promoter

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9
Q

the genes organized into operons are those whose products are:

A
  • products needed for successive steps in
    the synthesis of an essential small molecule
  • amino acid
  • successive steps in the breakdown of a
    source of energy - complex carb
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10
Q

example of translational level of control

A

mRNA – adding poly A tails extends the life of the mRNA (i.e. longer tails are known to last longer)

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11
Q

operator

A
  • found in operons
  • regulatory region
  • can be found either upstream or downstream (and sometimes overlapping) the promoter.
  • regulatory protein binds here… turn on or off the protein
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12
Q

basal

A

means base, minimal.

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13
Q

Positive regulation:

A

regulatory protein binds a region by the promoter (operator) and increases transcription

main players are: - DNA
- RNA polymerase complex
- regulatory protein called a transcriptional activator

DNA has 2 important binding sites:
- one for the activator protein
- one for the RNA polymerase complex

binding site for the activator may be upstream,
downstream, or overlap the promoter

Regulatory protein called an “activator” protein
* Example: MalT

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14
Q

Negative regulation:

A

regulatory protein binds to a region by the promoter (operator) and decreases transcription
- DNA in its native state can recruit the RNA polymerase complex
- transcription takes place at a constant rate unless something turns it off
- repressor!
- binding site for the repressor can be upstream,
downstream, or overlap the promoter
* Regulatory protein called a “repressor” protein
* Example: LacI

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15
Q

features of the operon: promoter region

A

RNA polymerase binds to this region

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16
Q

features of the operon: operator region

A

upstream and close to the malPQ promoter region. where regulator binds

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17
Q

INDUCTION:

A

genes are expressed due to a signal molecule
- transcribed and translated
- proteins synthesized are usually involved in catabolism (degradation)

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18
Q

REPRESSION

A

genes are repressed due to the signal molecule
- not expressed
- proteins synthesized are usually involved in anabolism (synthesis)

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19
Q

CATABOLIC GENES

A

breaks down stuff… normally requires an inducer

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20
Q

ANABOLIC GENES

A

creates stuff from smaller things…
- if the signalling molecule is in the environment, there is no need to make these enzymes
- presence of this signalling molecule leads to blocking gene expression…

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21
Q

SYSTEMS THAT REGULATE TRANSCRIPTION IN RESPONSE TO ENVIRONMENTAL CONDITIONS INVOLVE AT LEAST 3 COMPONENTS

A

DNA regulatory regions
a regulatory protein/genes
small signal molecule, often an environmental chemical

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22
Q

DNA regulatory regions

A
  • operator
  • specific nucleotide sequence near to, or partially overlapping, the promoter
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23
Q
  • a regulatory protein/genes for transcription
A
  • bind to the regulatory regions near the promoter
  • influences whether or not RNA polymerase can initiate transcription at the promoter - bind to specific sequences on the dsDNA
  • for most operons, these are NOT part of the operon whose expression they control - usually constitutively expressed at low levels
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24
Q

small signal molecule, often an environmental chemical in the regulation of transcription

A
  • affect binding of the regulatory proteins to the regulatory regions of a gene
  • binding of regulatory proteins to regulatory regions is dependent on the signal molecule binding to the regulatory proteins
  • are allosteric proteins
  • can be inducers or co-repressors
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25
Q

allosteric proteins

A
  • adopt different shapes depending on whether or not the signal molecule is bound to them
  • shape affects whether or NOT it can bind efficiently to DNA
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26
Q

what kind of operons are mal and lac operons an example of and what do they do

A
  • catabolic operons
  • Bacterial cells metabolize sugars.
  • Some cells use lactose (or maltose) as a source of energy and carbon.
  • The cells ONLY need to synthesize the proteins in the mal (or lac) operons IF those sugars are present. The proteins produced in these operons function to break down (catabolize ) the sugars.
27
Q

writing genes vs writing proteins

A

Genes
- 3 or 4 letter abbreviation (no caps) written in italics or underlined

Proteins (= gene “product”)
- 3 or 4 letter abbreviation with caps
- Different genes / proteins involved in the same cellular process often given the same 3 letter abbreviation.

28
Q

The Mal Operon structure

A
  • the mal operon shares a promoter and termination sequence but has 2 coding regions.
  • One mRNA is produced yet multiple proteins are translated.
  • The mal operon has the coding region for 2 proteins; malP and malQ.
29
Q

MalT

A
  • regulator protein that regulates the mal operon
  • The gene malT has its own promoter, terminator, coding region and is constitutively expressed.
  • malT is found upstream from the mal Operon - - The protein is involved in the regulation of the malPQ operon BUT not part of the operon… is a separate transcription unit
30
Q

MalT is a ___ regulator of the malPQ operon

A

POSITIVE!

31
Q

promoter for the malPQ operon is a ___

A

weak
on its own, it initiates very little to almost no transcription

32
Q

the promoter binds sigma/RNA polymerase ____

A

weakly

33
Q

absence of maltose on the MalPQ operon

A
  • Do not need to make the enzymes MalP and MalQ
  • RNA polymerase doesn’t bind the promoter strongly
  • Therefore there is very little or no transcription of malPQ operon
  • Low/no production of MalP and MalQ enzymes.
34
Q

What promotes transcription of malP and malQ?

A
  • MalT can help out when bound to maltose
  • a form of MalT binds to a region near the promoter (called the operator) and helps RNA POL (i.e. sigma + RNA Pol) to bind and remain on the promoter
35
Q

what happens to malT when maltose is in the cell?

A
  • A form of MalT binds to operator and helps recruit RNA POL to bind
  • When maltose is taken up by the cell, the molecule maltose can bind to MalT protein.
  • This changes the shape of MalT and allow MalT –mal to bind to the operator.
36
Q

what happense to the Mal operon when there’s maltose in the cell?

A

Need to make lots of the enzymes MalP and MalQ

37
Q

what genes does the lac operon contain

A

LacZ
LacY
LacA

38
Q
  1. LacZ protein
A

beta-galactosidase (cleaves lactose into glucose and galactose)

39
Q
  1. LacY protein
A

This is a transporter- transport protein that transport lactose into the cell.

40
Q
  1. LacA protein
A

This is a trans-acetylase – not clear what its role in the lac operon is and is found NOT to be necessary for lactose metabolism.
Often, the lacA gene is not shown on the operon!

41
Q

lacI gene purpose and where to find

A

A separate gene lacI, can be found upstream of lac operon. This gene produces the regulatory protein, LacI

42
Q

Lacl is a ____ regulator/regulatory protein of the lac operon

A

NEGATIVE

43
Q

the promoter for the lac operon is a ___

A

strong

44
Q

the promoter for the lac operon binds sigma/RNA polymerase _____

A

strongly

45
Q

where is the operator region found in the lac operon

A

The operator region is found downstream but overlapping the promoter.

A regulatory protein LacI can bind to the operator.

46
Q

Where is lacI gene found relative to the operon?

A

The gene, lacI, for the regulatory protedin, LacI, can be found upstream of the lac operon

47
Q

when is the lacl gene expressed

A

constitutively

48
Q

LacI in the absence of lactose

A

This “form” of LacI can bind to the operator.
- prevents/blocks RNA POL from binding. No transcription = Repressor

49
Q

Lacl in the prescence of lactose

A

This form of LacI cannot bind to the operator
i.e. no repression RNA Pol can bind.

Transcription of lacZYA operon!

50
Q

In the lac Operon, when lactose is in the cell, lactose…

A

binds to LacI proteins which then results in promoting transcription.

51
Q

How does lactose get into the cell if the lac operon is repressed and LacY (transport protein) is not being synthesized?

A

The transport protein LacY is already present

52
Q

Catabolic operons

A

produce proteins that are involved in the
catabolism (breakdown) of the signal molecule.

53
Q

Both lactose & maltose are…

A
  • signal molecules
  • INDUCERS
54
Q

signal molecule

A

presence determines whether the operons are expressed at high levels.

55
Q

inducers

A

when present, the lac and mal operons are expressed at high levels.

56
Q

co-repressor”.

A

If the presence of a signal molecule results in low levels (to zero) of operon expression

57
Q

Both LacI and MalT are:

A

Regulatory proteins

58
Q

Anabolic operons

A
  • produce proteins that are involved in the synthesis (anabolism) of the signal molecule.
  • the operon are expressed (transcribed) in the absence of the signal molecule (negatively regulated), the signal molecule is a co-repressor.
  • helps the Repressor protein repress the expression of the operon.
59
Q

Three levels of Transcription for Regulated Genes (environmentally regulated):

A
  • high levels
  • basal/low levels
  • zero levels
60
Q

high levels of transcription

A

Gene/Operon is transcribed at high levels
i.e. RNA Pol (& transcription factors) bind strongly/tightly and often to the promoter to initiate transcription.

61
Q

Basal /Low Levels

A

Gene/Operon is minimally (sometimes rarely) transcribed
i.e. RNA Pol binds weakly and rarely to the promoter and transcription is not
initiated very often.

62
Q
  • Zero levels
A
  • no transcription /not possible. Not functional.
  • Usually due to some deletion mutation (e.g. promoter deletion) that prevents transcription from initiation.
63
Q

Why would the lac operon be expressed at basal/low levels when the repressor protein (LacI) is bound to the operator (i.e. why not ZERO)?

A
  • Regulatory proteins such as Repressors make non-covalent interactions with the operator region (sequence of DNA bases).
  • Remember that the lac operon promoter is a STRONG promoter!
  • Occasionally, LacI can fall off the DNA allow RNA Pol to bind and transcribe
  • benefit to the cell bc some LacZ and LacY is needed to transport lactose inside the cell

BIOL 112 (25 decks)

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