Chapters 18

Question 1

What are the three levels at which prokaryotes can gene regulate?

Answer 1

1. Transcriptional control: Regulatory proteins alter the ability of RNA polymerase to bind to the promoter and initiate transcription.
2. Translational control: regulatory proteins interact with mRNA and affect it’s or interact with ribosomes to affect it’s stability, or interact with ribosomes to affect translation initiation or elongation.
3. Post-translational control: chemical modifications to protein ( e.g. phosphorylation) affect its activity.

Question 2

What are the pros/ cons of transcriptional control?

Answer 2

• least wasteful level of gene regulation, from the sense of if the cell no longer needs a protein then why waste ATP and other factors to transcribe the gene and translate the mRNA to make the protein in the first place.
• ——————————————————————————- negative: slowest way for a cell to change its behavior. because even if a cell stops transcribing a particular gene, any mRNA that were already made will continue to be translated for a while to make new proteins. Any protein that is made will continue to be active for some period of time.

Question 3

What are the pros/ cons of post- translational control?

Answer 3

Positive: allows the fastest change in cell behavior.
because any protein that is present, once it is modified can then be switched on or off.

Question 4

What is negative transcriptional control?

Answer 4

when some regulatory protein blocks transcription.

- a repressor protein binds to DNA and blocks RNA polymerase from initiating transcription.

Question 5

What is positive transcriptional control?

Answer 5

• when a regulator protein triggers transcription
• in the presences of a positive transcriptional protein (activator protein), RNA polymerase binds stable to it and can then begin transcription.

Question 6

What experiment test If every gene in the bacteria genome being constantly transcribed?
- what would you expect to happen?

Answer 6

Jaques Monod

• Escherichia coli, the most abundant e coli was studied in depth.
• They placed in different settings containing carbon, as that is coli’s primary food source.
• you would expect different forms of genes to be expressed in different arrays of carbohydrates to supply carbon energy.

Question 7

What is beta-galactosidase?

What is it’s purpose in this chapter?

Answer 7

• enzyme that cleaves the disaccharide of Lactose.
• Jaques Monod was interested in its expression, and if bacteria would express this gene all the time or just in the presences of lactose.

Question 8

Describe the experimental set up that Jaques Monod created?

- describe his results:

Answer 8

• He created three dishes, otherwise known as treatments, 1: glucose only, 2: glucose and lactose, 3: lactose only.
• the glucose and lactose serves as the carbon source.
• This allowed him to test the levels of beta-galactosidase expression in three different treatments.
  ——————————————————————————— Treatment 1: no beta-galactosidase
• Treatment 2: no beta-galactosidase
• Treatment 3: Production of beta-galactosidase
  PROVING: they can not only detect if lactose is in the environment, but a wide variety of other carbon sources so the can find the optimal one.

Question 9

How did Jacob and Jacques Mondo identify what proteins encoded for the lactase gene?

Answer 9

• Genetic screen: take a large population of organisms and expose them to a chemical or environmental factor that will randomly induce them to mutations in their genomes.
  2. ) - then you screen through that population to find individuals in the specific process you’re interested in.
• took a population of E Coli that had been exposed to a mutagen of some kind, and then grew those onto plates containing glucose as the only food source.
• they took a block with velvet (basically something to extract the E coli and place them on a new plate containing Lactose as the only food source.
• Following this growth on plate number two, they looked at which cells grew only on the glucose media and failed to grow in the presence of lactose.
• Thus, those cells genes had a mutation and made them unable to metabolize lactase.
• then they would go back to the original plate and study the cells from the colonies that grew in glucose but failed to grow in lactose.

Question 10

What is replica plating?

Answer 10

• you’re basically taking a copy of a plate via extracting cells from certain colonies that grew and placing on a different plate with a different media make up.

Question 11

What genes are important in lactose metabolism?

Answer 11

Galactoside permease: transports lactose into the cell.

- B-Galactosidase: breaks down lactose inside the cell.

Question 12

Describe the following genes in relation to the Jacques Mondo and Jacob experiment: lacZ, lacY, lacI:

Answer 12

lacZ: encodes B-Galactosidase
lacY: encodes Galactoside permease
lacI:
————————————————————————–
(mutant form:)
LacZ- : e-coli with a mutation that renders the LacZ gene inactive, so they don’t produce functional B-Galactosidase. ( Brings lactose in, but won’t be able to cleave it)
lacY- : renders Galactoside permease unfunctionable, and would fail to import lactose into the cell, in the first place, because it lacks Galactoside permease.
lacI- : expresses B-Galactosidase even if there is no lactose around,

Question 13

What are the observable phenotypes of lacI-,lacZ-, and lacY- ?

Answer 13

lacI- : cells cannot cleave lactose, even in the presence of inducer ( lactose)
lacZ- : cells cannot accumulate lactose.
lacY- : cells can cleave lactose even if lactose is absent as an inducer.

Question 14

what is the lac operon?

Answer 14

lacZ, lacY, lacA, Operator, promoter

Question 15

operon?

Answer 15

physically adjacent genes encoding functionally-related proteins, and under common regulatory control
- you turn one on you turn them all on type of relationship.
-

Question 16

What is the operator sequence?

Answer 16

• It sits in between the lacZ region and the promoter.

Question 17

what is true in the expression of the lac operon without the presence of lactose?
- Why does this happen??

Answer 17

• the lac operon isn’t expressed.
• The lacI gene, not in the operon is expressed all the time, which causes it to produce a suppressor protein.
• the repressor protein then binds to the operator sequence in the lac operon and prevents RNA polymerase from carrying out transcription.

Question 18

what is true in the expression of the lac operon in the presence of lactose?
- Why does this happen??

Answer 18

• lactose is an allosteric regulator of the repressor protein.
• so after the lacI gene synthesis the repressor protein and it binds to the lactose, which causes it it to change its shape and not bind to the operator.
• this allows for RNA polymerase to carry out transcription and express the gene.

Question 19

What is true in cells that lack a functional lacI gene?

Answer 19

• there is no repressor protein made.
• so these cells have their lac operon expressed all the time.
• Which is known as constitutive expression

Question 20

what is constitutive expression?

Answer 20

high levels of expression that are unregulated.

Question 21

Is the example of a cell not in the presence of lactose, thus causing the repressor protein to bind to the operator sequence and prevent expression of the lac operon a positive or negative transcriptional control?

Answer 21

• ## Negative: the regulatory protein is blocking transcription.

Question 22

What is an inducer and what is an example of an inducer?

Answer 22

• an environmental signal that causes a change in expression.
• lactose is an inducer of the lac operon

Question 23

how does the presence of glucose inhibit the expression of the lac operon?

Answer 23

• There are two key factors present:
• ## inducer exclusion and catabolite repression:
• inducer exclusion: high levels of the activity of the glucose transporter inhibit the activity of galactosidase permease. In other words, the more glucose is coming in, the less lactose.
  high levels of glucose outside the cell, it is difficult for galactosidase permease to bring lactose inside the cell .
  ——————————————————————————–
• catabolite repression: glucose inhibits transcription of the lac operon.
• catabolism: larger molecules are broken down into smaller pieces.
• ## i.e: B-Galactosidase breaking down lactose, meaning that glucose and galactose are catabolites of this reaction.
• It is important to understand Adenylyl cyclase’s role in this process: enzyme that takes ATP and strips it of two of the phosphate groups and uses that energy to sort of cyclize the molecule—-> cAMP.
• ## cAMP is a potent allosteric regulator of many kinds of proteins within the cell.pt2:
• there is a protein called cap and that binds to a regulatory sequence in the lac operon gene that is just infront of the promoter.
• when cap is bond to its regulatory sequence, cap site, then it promotes the stabile association of RNA polymerase with the promoter to make the transcription more likely, but cap only binds to the site when cAMP is present.
• ## cAMP is a allosteric regulator of cap, meaning it changes its shape so that CAP will bind to this other regulator site and in that configuration, cap helps to recruit RNA polymerase and stabilize it thus allowing RNA polymerase to be initiated.pt3:
• There is also an association between glucose and adenylyl cyclase.
• when glucose levels are high adenylyl cyclase levels are high, which means there is also very little cAMP inside the cell. Which also prevents the cap from binding to the cap site.
• So the inverse is true when glucose levels are low, thus low glucose = promotion of RNA transcription

Question 24

Are all bacterial genes arranged in operons?

Answer 24

No, but genes that encode proteins that are involved in a common process are.

Question 25

What is the ara operon?

Answer 25

• There are three genes encoded by the ara operon, the araB, araA, araD.
• Order of it: initator, araBAD promotor, araB, araA, araD.
• what is regulation of the ara operon a

Question 26

what controls the regulation of the ara operon?

Answer 26

protein called araC.

Structure/Order: left-right: araC–>Operator—>araC promotor.

Question 27

What are the proteins ara B, A, D of the ara operon involved with?

Answer 27

enzymes required for arabinose metabolism.

Question 28

T/F: araC can act as an activator or an inhibitor depending upon if it is bound to arabinose?

Answer 28

True: in the presence of arabinose, it binds to araC, which allows araC to dimerize and bind to the initator sequence for the ara operon.

• when the dimerized form is there and it is bound to the promoter sequence, RNA polymerase is stabilized and allows for efficient transcription.
• ——————————————————————————– In the absence of araC, it acts a repressor.
• araC proteins dimerize, but not side by side, but instead they dimerize head to head.
• one araC sits on the initiator and one sits on the Operator for the araC gene.

Question 29

What is a regulon?

Answer 29

• groups of distantly localized genes or operons that are under common regulatory control.