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Genetics > Chapter 15.2: Regulation of Transcription Initiation via DNA-Binding Proteins > Flashcards

Chapter 15.2: Regulation of Transcription Initiation via DNA-Binding Proteins Flashcards

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1
Q

Does DNA act in trans or cis?

A

cis

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2
Q

What is the order of ZYA on the lac operon?

A

 Order on bacterial chromosome is lacZ-lacY-lacA

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3
Q

Describe the helix-turn-helix (HTF) motif

A

• Two α-helical regions are separated by a turn
o One of the α helixes in each HTH-containing transcription factor carries unique amino acids that recognize a specific DNA sequence of nucleotides. As a result, various HTH-containing proteins can bind to unique DNA sequences

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4
Q

What does it mean to act in trans?

A

 Elements that act in trans can diffuse through the cytoplasm and act at target DNA sites on any DNA molecule in the cell

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5
Q

What is induction?

A

 The process by which a specific molecule stimulates synthesis of a given protein

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6
Q

 The process by which a specific molecule stimulates synthesis of a given protein is known as?

A

induction

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7
Q

What are pathways in which complicated molecules are broken down for the use of the cell?

A

catabolic pathways

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8
Q

What are pathways that allow cells to construct end product molecules they need from simple constituents?

A

anabolic pathways

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9
Q

What is the effect of lacI- mutations?

A

 Mutations in a gene called lacI, located near but not within the lac operon, produce constitutive mutants that synthesize β-galactosidase and Lac permease even in the absence of lactose

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10
Q

What is the function of the repressor encoded by the lacI gene?

A

• The repressor protein prevents further transcription of lacY and lacZ by binding to a hypothetical operator site

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11
Q

What is the effect of supperrepressor (lacI^s) mutations?

A

 The lacIS mutants, although they cannot bind inducer, can still bind to DNA and repress transcription of the operon

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12
Q

Define operon theory

A

o The operon theory suggests that a single signal can simultaneously regulate the expression of several genes that are clustered together on a chromosome and are involved in the same process

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13
Q

What is the effect of operator mutants?

A

 When mutations change the nucleotide sequence of the operator, the repressor is unable to recognize and bind to the site; the resulting phenotype is the constitutive synthesis of the lactose-utilization proteins
• They call the constitutive operator DNA alterations oc mutations

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14
Q

What is the relationship between glucose and levels of cAMP?

A

 When glucose is present, the level of cAMP remains low; when glucose is absent, cAMP synthesis increases

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15
Q

What are the 5 gene in order on the E. coli tryptophan operon?

A

o The E.coli tryptophan (trp) operon is composed of a group of five genes—trpE, trpD, trpC, trpB, and trpA—required for biosynthesis of the amino acid tryptophan

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16
Q

What does the lacA gene code for?

A

 lacA encode a transacetylase enzyme that adds an acetyl group to lactose and other sugars
• not required for the breakdown of lactose

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17
Q

Define effector

A

a small molecule that binds to an allosteric protein or an RNA molecule and causes a conformational change

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18
Q

What is the function of the promoter site in the lactose operon in E. coli?

A

 A promoter site, from which RNA polymerase initiates transcription of a polycistronic mRNA. The promoter acts in cis, affecting the expression of only downstream structural lac genes on the same DNA molecule

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19
Q

What is the function of the promoter site in the lactose operon in E. coli?

A

 An inducer (allolactose) that prevents the repressor’s binding to the operator.

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20
Q

Define repressible regulation

A

the pathway should be turned on only when the cell does not have enough of the needed end product. If the end product is present in sufficient quantities, the pathway should be turned off/repressed so the cell does not waste resources trying to make molecules that it already has.

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21
Q

What means the pathway should be turned on/induced only when the complex molecules to be broken down (catabolites) are present in the cell’s environment?

A

inducible regulation

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22
Q

What is the function of B-galactosidase?

A

 There the enzyme β-galactosidase splits the lactose into galactose and glucose (catabolic)

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23
Q

Define lac operon

A

a single DNA unit enabling the simultaneous regulation of the three structural genes in response to environmental changes

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24
Q

What type of regulation do catabolic pathways require?

A

inducible regulation

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25
Q

Define inducible regulation

A

the pathway should be turned on/induced only when the complex molecules to be broken down (catabolites) are present in the cell’s environment

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26
Q

What are catabolic pathways?

A

pathways in which complicated molecules are broken down for the use of the cell

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27
Q

Describe the levels of lac permease and B-galactosidase without lactose present?

A

 The two proteins Lac permease and β-galactosidase are present at very low levels in cells grown without lactose

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28
Q

Where does the inducer bind?

A

to the repressor

29
Q

What makes up the lac operon?

A

o Structural genes (lacZ, lacY, lacA) encoding proteins needed for lactose utilization, together with two regulatory elements—the promoter (P) and the operator (o)—make up the lac operon

30
Q

Describe induction in the lac operon in E. coli

A
  • When lactose is present, allolactose, an inducer derived from the sugar, binds to the repressor. This binding changes the shape of the repressor, making it unable to bind to the operator.
  • With the release of the repressor from the operator, RNA polymerase gains access to the lac operon and initiates transcription of the three lactose-utilization genes into a single polycistronic mRNA
31
Q

What does the lacZ gene code for?

A

 LacZ encodes β-galactosidase

32
Q

What are the two molecules that interact with the operon in prokaryotes?

A

repressor and inducer

33
Q

Where does the repressor bind?

A

binds to the operon’s operator

34
Q

What does the lacY gene code for?

A

 LacY encodes Lac permease

35
Q

Do proteins act in trans or cis?

A

trans

36
Q

When does maximal expression the trp genes occur?

A

o Maximal expression of the trp genes occurs when tryptophan is absent from the growth medium

37
Q

What is the function of lac permease?

A

 A membrane protein, Lac permease, transports lactose in the medium in the E. coli cell

38
Q

What are anabolic pathways?

A

pathways that allow cells to construct end product molecules they need from simple constituents

39
Q

How does an inducer trigger enzyme synthesis?

A

 The binding of inducer to repressor thus causes an allosteric effect that abolishes the repressor’s ability to bind the operator
• The inducer is an effector molecule that releases repression without itself binding to the DNA

40
Q

Describe the dominance pattern of lacI gene mutations

A

lacI^s > lacI+ > lacI- in trans

41
Q

Define operator site

A

a DNA sequence near the promoter of the lactose-utilization genes

42
Q

Describe repression in the lac operon in E. coli

A

• In the absence of lactose, the repressor binds to the DNA of the operator, and this binding prevents transcription. The repressor this serves as a negative regulatory element

43
Q

How is the trp operon controlled?

A

o The trp operon is controlled in part at the level of transcription initiation trough the action of a repressor protein that is the product of the trpR gene
 Tryptophan functions as a corepressor for the TrpR repressor protein

44
Q

What do constitutive mutants do?

A

• Constitutive mutants synthesize certain mutants all the time, irrespective of environmental conditions

45
Q

What does it mean to act in cis?

A

 Elements that act in cis can influence only the expression of adjacent genes on the same DNA molecule

46
Q

What suggests that a single signal can simultaneously regulate the expression of several genes that are clustered together on a chromosome and are involved in the same process?

A

operon theory

47
Q

What is  The molecule responsible for stimulating production of the protein called?

A

inducer

48
Q

What are the 3 domains of the lac repressor protein?

A
  • Inducer-binding domain
  • DNA-binding domain
  • Multimerization domain
49
Q

What is the function of the cAMP-CRP complex?

A

 When bound to DNA, CRP helps recruit RNA polymerase to the promoter by making physical contacts with the polymerase enzyme; in essence, then, the DNA binding of CRP increases the ability of RNA polymerase to transcribe the lac genes
 CRP thus function as a positive regulator that enhances the transcriptional activity of RNA polymerase at the lac promoter, while cAMP is an effector whose binding to CRP enables CRP to bind to DNA near the promoter and carry out its regulatory function

50
Q

What is the function of the operator site in the lactose operon in E. coli?

A

 A cis-acting DNA operator site lying very near the lac operon promoter on the same DNA molecule

51
Q

What type of regulation do anabolic pathways require?

A

repressible regulation

52
Q

What means the pathway should be turned on only when the cell does not have enough of the needed end product. If the end product is present in sufficient quantities, the pathway should be turned off/repressed so the cell does not waste resources trying to make molecules that it already has.?

A

repressible regulation

53
Q

What does the lacI gene code for?

A

 lacI encodes a negative regulator, or repressor

54
Q

What is a protein that undergoes a reversible change in conformation when bound to another molecule?

A

allosteric protein

55
Q

What is a DNA sequence near the promoter of the lactose-utilization genes?

A

operator site

56
Q

How are partial diploid made?

A

 The merodiploids (partial diploids) were made using F’ plasmids that carry a few chromosomal bacterial genes.
• When F’ (lac) plasmids are present in a bacterium, the cell has two copies of the region containing both the lactose-utilization genes and lacI—one on the plasmid and one on the bacterial chromosome

57
Q

What is the function of the inducer?

A

prevents repressor from binding to the operator

58
Q

What is allolactose and what is its purpose?

A

 Lactose modified to a derivative known as allolactose is the inducer of the genes for lactose utilization

59
Q

What is a result of helix-turn-helix motifs (HTF)?

A

 Helix-turn-helix (HTF) motif in the protein fits well into the major groove of the DNA

60
Q

What is a small molecule that binds to an allosteric protein or an RNA molecule and causes a conformational change?

A

effector

61
Q

What is a single DNA unit enabling the simultaneous regulation of the three structural genes in response to environmental changes?

A

lac operon

62
Q

What is the function of the repressor in the lactose operon in E. coli?

A

 A trans-acting repressor that can bind to the operator. The repressor is encoded by the lacI gene, which is separate from the operon and is unregulated. After synthesis, the repressor diffuses through the cytoplasm and binds with its target

63
Q

What sugars is lactose composed of?

A

o Lactose is composed of glucose and galactose

64
Q

Define operons

A

o Clusters of genes regulated through mRNA transcription

65
Q

What are o Clusters of genes regulated through mRNA transcription ?

A

operons

66
Q

Define inducer

A

 The molecule responsible for stimulating production of the protein

67
Q

Define allosteric protein

A

a protein that undergoes a reversible change in conformation when bound to another molecule

68
Q

Why is the overall effect of glucose in preventing lac gene transcription known as catabolite repression?

A

 The overall effect of glucose in preventing lac gene transcription is known as catabolite repression, because the presence of a preferred catabolite (glucose) represses transcription of the operon

69
Q

Describe the cAMP-CRP complex

A

 Inside bacterial cells, the small nucleotide known as cAMP (cyclic adenosine monophosphate) binds to a protein called cAMP receptor protein, or CRP
 The binding of cAMP to CRP enables CRP to bind to DNA in the regulatory region of the lac operon near the promoter

Genetics (62 decks)

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