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Pharm 411: fundamentals of molecular bio > Pharm 411: Regulation of Gene Expression > Flashcards

Pharm 411: Regulation of Gene Expression Flashcards

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1
Q

What are the stages that regulation of gene expression can occur?

A

Before making the RNA -Transcriptional regulation
Before making the protein - translational regulation
After making the protein - post translational regulation (could be like phosphylation to activate or not)

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2
Q

Do all genes get regulated?

A

No, some genes are always on and its called constituively active
Something like a ribosome would fall into this because we use it so often we always need to make them

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3
Q

What is the most common type of regulation and why?

A

Its transcriptional regulation
This is because its the most energy economical meaning that regulate it before you make it you dont waste the energy in building it and then not using it

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4
Q

What are the two ways in which transcriptional regulation can occur in prokaryotes?

A

Cis-acting elements

trans-acting factors

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5
Q

What are cis-acting elements for prokaryotes in transcriptional regulation

A

Sections of DNA near the gene which control transcription
Normally found in noncoding regions of the genome
Known as promoters, operators, silencers, enhancers and hormone response elements

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6
Q

What are trans-acting factors for prokaryotes in transcriptional regulation

A

Proteins or other molecules which bind to the DNA
They interact with the DNA and activate or repress transcription
They usually bind to cis-acting elements

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7
Q

What is the prokaryotic operon

A

A cluster of genes only in porkaryotes with related functions acting as a coordinated unit controlled by a common regulatory sequence
*they all respond to the same control mechs

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8
Q

What is an operon composed of?

A
  1. structural genes which code for the proteins for desired function
  2. Promoter region which influences the efficiency of transcription
  3. An operator which is a sequence of DNA which can bind a repressor and/or an activator
  4. Repressor gene which codes for a protein which inhibits transcription when bound to DNA
  5. Activator gene which codes for a protein which enhances transcription when bound to DNA
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9
Q

What is the prokaryotic promoter?

A

A sequence of DNA that influences how frequently a gene is transcribed
Usually found upstream (towards 5’ end) from the gene

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10
Q

What is meant by the promoter regions have consensus sequence of DNA?

A

A consensus sequence is the sequence of bases that are most commonly found
*If a promotor is more similar to the consensus sequence, the better the promoter and the more often the gene will be transcribed

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11
Q

What is the prokaryotic operators?

A

Sequence of DNA to which regulatory proteins (repressors and activators) bind

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12
Q

What is different about the operators compared to the promotors in terms of where they bind?

A

They dont need a consensus sequence

They dont have a common location and can bind upstream or down stream to the promoter

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13
Q

What kind of control do prokaryotic operators exert?

A

Negative control

Positive control

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14
Q

What is negative control of the prokaryotic operator?

A

A repressor protein binds directly to the operator blocking RNA polymerase turning OFF the gene

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15
Q

What is positive control of the prokaryotic operator?

A

activator protein binds directly to the operator stimulating RNA polymerase BINDING which turn ON the gene expression

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16
Q

What are effectors?

A

They are small molecules or signaling peptides that exert control on transcription thro operators

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17
Q

What are the two types of control that an effector can have?

A

Inducible control

Repressive control

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18
Q

What is inducible control caused by an effector

A

Binding of and effector turns ON transcription

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19
Q

What is repressible control caused by an effector?

A

Binding of effector shuts OFF transcription

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20
Q

What is Negative Inducible control?

A

A repressor protein binds to the operator and block transcription WITHOUT effector. An inducer can then bind to the repressor causing it to leave the operator and turn on transcription

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21
Q

What is negative repressible control?

A

Repressor protein WONT BIND the operator without an effector. A corepressor BINDs to the repressor and causes it to bind to the operator turning OFF transcription

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22
Q

What is positive inducible control?

A

Activator protein wont bind to operator without an effector. An inducer binds to the activator and causes it to bind to the operator turning on transcription

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23
Q

What is positive repressible control?

A

Activator protein binds to the operator and activates transcription without effector. An inhibitor bind to the activator causing it to leave the operator turning off transcription

24
Q

What is a Catabolic operon?

A

Codes for enzymes used in pathways to break down substances

  • kept off until the substance is present
  • Usually under inducible control
25
Q

What is an Anabolic operon?

A

Code for enzymes used in pathways to synthesize substances

  • Kept on until there is too much substance
  • usually under repressible control
26
Q

What is the lac operon?

A

Its a catabolic operon that codes for three proteins that are necessary for the breakdown and utilization of lactose
*lac (lactose)

27
Q

What are the two mechanisms which control the lac operon?

A
  1. A repressor which binds to an operator region

2. Inducers which bind to an operator ( CAP-binding site)

28
Q

What is the status of the repressor protein on the mRNA for the lac operon?

A

It is always transcribed (uncontrolled) this means the repressor is always available

  • the repressor bound to the operator block RNA polymerase
  • The genes needed to breakdown lactose are not normally produced
29
Q

What does control of the lac operon depend upon?

A

Both the levels of glucose and lactose

30
Q

What is the signal for glucose levels?

A

cAMP, When glucose levels are high it blocks the production of cAMP
When glucose levels fall you activate glyogen to bind the the Adenylate cylclase system which will produce cAMP
**TLDR: High glucose = no cAMP, low glucose = cAMP

31
Q

What do cAMP levels have to do with the lac operon?

A

If glucose levels are lower there is an increase in cAMP production. This causes cAMP to bind to the cAMP receptor protein (CRP) which allows it to bind to the CRP activator site of the operon.

32
Q

What kind of control does the CRP have on the lac operon?

A

Its a positive inducer. It must be bound to the gene in order to get RNA polymerase to bind

33
Q

What does lactose and allolactose have to do with the effects of the lac operon?

A

Lactose and allolatose act as inducers of the lac operon which bind the the repressor and induce transcription.
*inducer binds and caused repressor to release and transcription is on

34
Q

In what environment does the lac operon turn on?

A

When glucose is low (allows for cAMP to bind CRP, which binds to operon and promotes RNA polymerase to bind)
When lactose levels are high (means there is enough lactose to induce the repressor and remove it so RNA polyermase can run)
*TLDR: Low glucose and high lacotse = transcription on!

35
Q

What kind of operon is the trp operon?

A

An anabolic operon

36
Q

What does tryptophans role within the trp operon?

A

It acts as a co-repressor and binds to the trp repressor
*if tryptophan levels are low, there is little repressor/trypohan complex, and the repressor WONT bind the operator so transcription is ON

37
Q

What happens when tryptophan levels are high?

A

The tryptophan/repressor complex binds to the operator and turns OFF transcription

38
Q

What kind of control is the trp operon based off of?

A

Negative repressor

*Neg means it will bind and shut it off, but since its a repressor it will NOT bind unless that repressor is bound

39
Q

How do histones effect gene regulation in eukaryotes?

A

We regulate expression of DNA thro packaging or condensing the DNA (histones pack DNA)
When DNA is wound around a histone its not available for RNA polymerase

40
Q

What is chromatin remodeling?

A

We change the condensation state (the winding of the DNA around a histone) and its required for allowing gene expression
*Wound DNA can not be expressed so we must unwind it to express it

41
Q

How does acetylation work as a control mechanism for controlling chromatin condensation?

A

The histone proteins have a lot of lysine residues (+ charged AA) This charge allows it to interact with the negatively charged phophate backbone of DNA to hold it in place.
*When you acetylate the lysine residues it removes this charge and the DNA can no longer interact with the phosphate back bone causing it unwind from the histone

42
Q

What is the main purpose of the acetylation?

A

Its to make the DNA more neutral by binding to its basic N-terminus which has a positive charge by interacting with an actyl group with has a negative charge

Give DNA no charge or neutral

43
Q

What is histone acetyltransferase (HAT)?

A

It will cause histones to be acetylated which allows access to DNA
*More HAT means more DNA and leads to an increase in transcription

44
Q

What are Histone deacetylase (HDAC)?

A

This removes the acetyl groups from DNA causing it have condensation and stops access to DNA
**More HDAC means more DNA condensation and less access to DNA so less transcription

45
Q

What is an HDAC inhibitor?

A

This is inhibit HDAC which means it will cause less condensation of DNA meaning DNA will be unwound and moving around more.

46
Q

What are HDAC inhibitors used for and why do they work?

A

They are used to treat cancer.
They do this because most cancers are due to DNA replicating itself to much. These will cause less DNA to be not condensed meaning ti cant go thro cell division.

47
Q

How does receptor control effect gene expression?

A

Molecules binding to cell surface receptors modulate gene expression by initiating a bicochemical signal
* will involve second messengers such as cAMP, or kinase cascades
Something like kinase cascade could phosphorlayte something causing activation or inactivation

48
Q

What are silencers?

A

A place on the DNA sequence where a repressor will bind

49
Q

What are enhancers?

A

A DNA sequence where an activator will bind

50
Q

What is a hormone response element?

A

A sequence on the DNA where a hormone receptor complex will bind
**this is cis-element because it is Incorporated into the DNA sequence

51
Q

What are Peroxisome Proliferator-Activated Receptors (PPARs)

A

They are ligand-activated transcription factors located in the nucleus
They are targeted by TZDs
When a TZD binds to PPAR, they change the transcription of genes which control metabolism of glucose and lipids
This means that they increase insulin sensitivity, reduce stored triglycerides in muscle and liver, and lower plasma glucose levels

52
Q

What is post-transcriptional control in eukaryotes?

A

Its when you change the protein after it has already by transcribed
Ex: splicing, GTP caps, Poly-a tail
Post-transnational protein modification = adding phosphates to things to turn them on/off

53
Q

What is mRNA editing?

A

Only happens in eukaryotes
When you change one base into another; most common type of RNA editing
changing a C to a U with cytidine deaminase to get a uricil
changing an A to I

54
Q

What is the point of mRNA editing?

A

Allows us to change the size of a protein if needed. We can change it to a stop codon and get a different protein which has a different effect

55
Q

What is RNA interference (RNAi)?

A

Method of silencing the translation of certain genes by controlling the mRNA for those genes
A double stand of RNA is used as the “drug” which it turned into small RNA pieces in the cell which bind to mRNA
Since these strands are not know to the body we cut up the mRNA and render it nonfunctional

56
Q

What is the process of how an RNA interference (RNAi) works?

A
  1. You introduce double strand RNA into the body as your “drug”
  2. A protein called dicer cuts the dsRNA into short double stranded RNA segments called small interfering RNA (siRNA)
  3. these siRNA bind to the RNA-induced silencing complex (RISC)
  4. RISC then binds to complementary mRNA strands and cuts them into pieces

Pharm 411: fundamentals of molecular bio (9 decks)

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