14.1 - 14.5

Question 1

constitutive transcription

Answer 1

a term identifying genes as being continuously translated with no transcriptional control

-make products that are needed continuously to perform routine tasks

Question 2

regulated transcription

Answer 2

satisfies the need for agile and calibrated responses to changing environmental behavior

Question 3

levels of regulated transcription

Answer 3

-result from interactions between DNA binding proteins and specific regulatory sequences of DNA

First level: Initiation of transcription

second level: amount of transcription

Question 4

first level of control of transcription

Answer 4

Initiation of Transcription

determines if the gene in question is even being transcribed at all

Question 5

second level of control of transcritpion

Answer 5

Amount of transcription

regulates either the duration of transcription or the amount of mRNA transcript produced from gene

Question 6

Negative transcriptional control

Answer 6

binding of a REPRESSOR PROTEIN to a regulatory DNA sequence, with the consequence of preventing transcription of a gene or a cluster of genes

Question 7

Positive Transcriptional control

Answer 7

involves binding of an activator protein to a regulatory DNA sequence with the result of initiating DNA transcription

Question 8

Repressor proteins

Answer 8

a broad category of regulatory proteins that exert negative control of transcription.

• in active form, they bind to regulatory DNA sequences, including “operators”/
• blocks transcription initiation by RNA polymerase
• acts by occupying the space on regulatory DNA where the polymerase would otherwise bind or by preventing formation of the open promoter complex necessary for transcription initiation.

can be activated or inactivated by interactions with other compounds

Question 9

DNA binding domain

Answer 9

one of two repressor protein commonly active sites

responsible for locating and binding operator DNA sequences or other target regulatory sequences

Question 10

allosteric domain

Answer 10

one of two repressor protein commonly active sites

binds a molecule or protein and, in so doing, causes a change in the conformation of the DNA-binding site

Question 11

allostery

Answer 11

the property belonging to some enzymes of changing conformation at the active site as a result of binding a substance at a different site

Question 12

inducer

Answer 12

one of two modes of operation in allosteric domains

inactivate DNA binding domains because of allosteric changes brought about by an INDUCER compound binding to an allosteric site

Question 13

corepressor

Answer 13

a molecule that binds at the allosteric site of some repressor proteins

activates a DNA binding site. transcriptional repression is reversed when the corepressor is removed from the allosteric site.

Question 14

activator proteins

Answer 14

bind to regulatory DNA sequences called activator binding sites.

binding facilitates RNA polymerase binding at promotors and helps initiate transcription.

have a DNA binding domain and an allosteric domain

Question 15

activator binding site

Answer 15

activator proteins bind to them

Question 16

allosteric effector compound

Answer 16

DNA binding domain remains inactive in some activator proteins until the allosteric domain is bound by an allosteric effector compound

then the DNA binding domain becomes active

Question 17

inhibitor

Answer 17

certain activator proteins have functional DNA binding domains that are turned inactive by binding of an INHIBITOR compound to the allosteric binding domain

Question 18

how do DNA binding proteins interact with DNA

Answer 18

amino acid side chains of the proteins with specific nucleotide bases and the sugar phosphate backbone of DNA

make contact with specific base pairs located in the major and minor groove of the DNA helix using a unique pattern of hydrogen, nitrogen, and oxygen atoms that characterize each base pair

common motif in structures is formation of protein secondary structures, most commonly alpha helices, that contain the amino acids that contact regulatory nucleotides.

Question 19

helix-turn-helix (HTH) motif

Answer 19

the most common structural motif seen in homodimeric DNA binding proteins

two alpha helical regions in each of the two polypeptides in a homodimer interact with inverted repeat regulatory sequences in DNA.

in each of the polypeptides, one alpha helical region forms the recognition helix. this is connected to a short string of amino acids forming the “turn” that is connnected to a second alpha helical region known as the stabilizing helix that functions to hold the two polypeptides together

Question 20

operons

Answer 20

clusters of genes undergoing coordinated transcriptional regulation by a shared regulatory region

common in bacterial genomes, and the genes that are part of a given operon almost always participate in the same metabolic or biosynthesis pathway

Question 21

lactose operon

Answer 21

responsible for the production of three polypeptides that permit E. coli to utilize the sugar lactose as a carbon source for growth and metabolic energy

Question 22

glycolysis

Answer 22

a biochemical pathway for the metabolization of the monosaccharide sugar glucose.

a sequence of biochemical reactions that oxidizes glucose to produce pyruvate and ATP (adenosine triphosphate)

occurs in virtually all cells as part of fermentation and cellular repiration.

Ecoli consumes all available glucose before a genetic swith siflipped that changes their metabolic pathway to one that uses an alternative sugar.

Question 23

inducible operon

Answer 23

under a specific set of circumstances, transcription of the operon genes is activated, or induced

Question 24

lac+ phenoptype

Answer 24

bacteria with this phenotype are able to grow on a medium with lactose as the only sugar

produces a gated channel allowing lactose to enter the cell and the enzyme beta-galactosidase that breaks the beta-galactoside linkage to release glucose and galactose

Question 25

allolactose

Answer 25

a modified form of lactose. a small amount is produced in the breakdown of lactose made by beta galactosidase plays a critical role in the transcription of lac operon genes by acting as the inducer compound.

Question 26

lac- phenotype

Answer 26

bacteria with this phenotype are unable to grow on a lactose-containing medium either unable to import lactose to the cell, break it down once in the cell, or both

Question 27

what are the three structural genes of the lac operon?

Answer 27

lacZ lacY lacA transcribed as polycystronic mRNA

Question 28

lacZ

Answer 28

a gene encoding the enzyme beta-galactosidase

Question 29

lacY

Answer 29

a gene encoding the enzyme permease

Question 30

lacA

Answer 30

a gene encoding the enzyme transacetylase

Question 31

polycistronic mRNA

Answer 31

an mRNA molecule that is the trnscript of all the genes in the operon each gene transcript part of a polycistronic mRNA contains a start and a stop codon sequence. translation generates a distinct polypeptide for each gene

Question 32

permease

Answer 32

functions at the cell membrane to facilitate the entry of lactose into the cell.

Question 33

lacI

Answer 33

adjacent to, but not part of the lac operon codes for the lac repressor protein has its own promoter and undergoes constitutive transcription

Question 34

inducer-repressor complex

Answer 34

the formation of this complex induces an allosteric change that alters the conformation of the DNA-binding domain of the repressor protein to a form that does not recognize or bind the operator. ex: lactose formed when allolactose binds to the allosteric domain of the repressor protein.

Question 35

CAP binding site

Answer 35

site part of lac operon promoter positive control of the lac operon transcription lies in a DNA-protein interaction that occurs at the site located at approximately -60 P

Question 36

CAP-cAMP complex

Answer 36

a small molecular complex composed of a protein known as the catabolite activator protein (CAP) and the nucleotide cyclic adenosine monophosphate (cAMP). DNA binding causes DNA to bend around the complex, and it increases the ability of RNA polymerase to transcribe lac operon genes

Question 37

how is the positive regulatory process for the lac operon regulated

Answer 37

indirectly by the level of glucose, which modulates the availability of cAMP. this is because adenylate cyclase is used for glycolysis and cAMP production and glucose means more glycolysis means more competition for enzyme binding means less cAMP production

Question 38

catabolite repression

Answer 38

the presence of the preferred catabolite (glucose for the regulation of the positive regulatory process for the lac operon) represses the transcription of genes for an alternative catabolite (lactose, in this case)

Question 39

constitutive mutants

Answer 39

in the case of constitutive mutants of bacteria, they are unresponsive to the presence or absence of lactose in a growth medium They continuously transcribe the operon genes, rather than transcribing the genes in an inducible manner.

Question 40

cis-acting

Answer 40

an operator mutation mutations that only influence transcription of genes on the same chromosome

Question 41

cis-dominant

Answer 41

reflects the ability of an operator to only influence the transcription of downstream genes

Question 42

trans-acting

Answer 42

describes a protein capable of diffusing through the cell and binding to a cis-acting target sequence lacI dominance of I+ over I- despite them being on different chromosomes indicates it is trans-acting

Question 43

constitutive repressor protein mutations

Answer 43

a mutation of a repressor protein producing gene that leads to constitutive transcription of a gene that would normally be transcribed in a regulatory fashion This is caused by a mutation altering the DNA-binding domain of the protein, rendering it incapable of binding the operator seuence ex: lacI-

Question 44

Super-repressor protein mutations

Answer 44

these mutations intensify repression from repression proteins by altering the allosteric domain of the repressor protein, rendering it ineffective the DNA-binding domain is unaffected, but because the allosteric domain of the protein is ineffective, the repressor protein stays bound to the operator sequence genes with this are given the superscript s they are dominant over genes with working allosteric domains because responsiveness to inducers becomes less and less pronounced as super-repressors bind to more operators

Question 45

noninducible

Answer 45

operon gene transcription cannot be induced Ex: Haploids and partial diploids with mutations of the allosteric domain of repressor proteins are noninducible

Question 46

Promotor Mutations

Answer 46

significantly reduce transcription or may eliminate it entirely

Question 47

what genes are dominant over what?

Answer 47

to be updated at end of chapter

Question 48

superscripts describing mutations

Answer 48

to be updated at end of chapter

Question 49

what are the most basic conditions for lac operon gene transcription?

Answer 49

depletion of glucose and presence of lactose in the cell

Question 50

what events occur to initiate lac operon gene transcription?

Answer 50

1) Cyclic AMP level rises as a result of the availability of adenyl cyclase 2) CAP-cAMP complex forms and binds to the CAP site of the lac promotor 3) Allolactose is produced by a side reaction of the metabolism of lactose by beta galactosidase 4) Repressor protein conformation is modified by interaction with allolactose, causing the protein to release from the operator, thus allowing operon gene transcription

Question 51

what are the three distinct segments of operator DNA (which interacts with repressor proteins)

Answer 51

O1 O2 O3 the combination of interactions of these three operator segments with the repressor protein provides a mechanism by which repressor protein binding can block RNA polymerase access to the promoter.

Question 52

repressor DNA-binding mechanism

Answer 52

to be updated at end of chapter

Question 53

DNA-loop

Answer 53

a loop of DNA with repressor protein DNA binding in regards to the lac Operon: the tetrameric repressor protein binds to O1 and O3 and the DNA loop formation draws the O1 and O3 regions closer together the loop structure contains part of the lac promoter and prevents transcription by blocking access of RNA polymerase.

Question 54

Arabinose (ara) operon

Answer 54

Arabinose is another of the alternative sugars that bacteria use as a source of carbon when glucose is depleted and the ara operon contains the genes responsible for arabinose metabolism. The transcription of these genes is under inducible control, and the ara operon is an inducible operon system. A single regulatory protein carries out both positive and negative transcriptional regulation.

Question 55

what are the three ara operon genes?

Answer 55

araB, araA, and araD | they produce a polycistronic mRNA that has a unique mechanism of transcriptional control

Question 56

what is the promotor and three operator sites for the ara operon gene?

Answer 56

promoter: Para operator sites: araI araO1 ara O2 the ara O2 operator is located in the araC gene, which produces the regulatory protein for the ara operon.

Question 57

araC

Answer 57

produces regulatory protein for the ara operator has its own promotor (Pc), which overlaps the operator sequence araO1. its adjacent to the ara operon, with a CAP binding site seperating Pc from araI and the rest of the ara operon

Question 58

ara operon regulation mechanism

Answer 58

to be updated at end of chapter

Question 59

repressible operons

Answer 59

operons that are regulated by negative feedback mechanisms that operate through the activity of the end product of the pathway to block operon gene transcription. operons involved in anaboloic pathways (pathways that synthesize compounds needed by the cell) often fall into this category

Question 60

attenuation

Answer 60

an additional regulatory capability held by repressible operons has the ability to fine tune transcripition to match the momentary requirements of the cell, achieving a more-or-less steady state of compound availability attenuation maintains levels while feedback inhibition simply turns off operon gene transcription when the end product is readily available

Question 61

tryptophan (trp) operon

Answer 61

contains five structural genes that share a regulatory region containing a promoter (trpP), an operator (trpO), and a leader region (trpL) that contains the attenuator region. the gene encoding the repressor protein (trpR) lies outside the the operon and is not activated until it pairs with tryptophan

Question 62

what are the five structural genes transcribed in the trp operon

Answer 62

trpE, trpD, trpC, trpB, and trpA. | Together, the protein products of these genes are responsible for the synthesis of the mino acid tryptophan.

Question 63

3-4 stem loop | in relation to the trpL operon

Answer 63

a structure formed from trpL mRNA this structure signals transcription termination for the trp operon This is the same thing as intrinsic termination may be proceeded by a 1-2 stem loop

Question 64

1-2 stem loop | in relation to the trpL operon

Answer 64

A structure formed from trpL mRNA may precede the 3-4 stem loop structure causes a pause in the attenuation process

Question 65

2-3 stem loop | in relation to the trpL operon

Answer 65

a structure formed from trpL mRNA it is the antitermination stem loop forms when region 1 is unavailable for immediate pairing with region 2 it precludes the formation of a 3-4 stem loop

Question 66

antitermmination stem loop | in relation to the trpL operon

Answer 66

describes the 2-3 stem loop allows RNA polymerase to continue transcription through the leader region and into the structural genes of the trp operon, beginning with the transcription of trpE if transcription progresses past region 4, a polycistronic mRNA spanning the five trp genes is produced. translation of the five enzymes required for synthesis follows

Question 67

alternative sigma factor

Answer 67

expressed in rare situations in bacteria for rare necessities of gene regulation for bacteria heat shock alternative sigma factor: know sigma 32, expressed by the rpoH gene

Question 68

translation repressor proteins

Answer 68

regulate translation by binding mRNA to the Shine-Dalgarno sequence

Question 69

antisense RNA

Answer 69

an RNA molecule that is complementary to a portion of a specific mRNA. the binding of an mRNA by an antisense RNA prevents ribosome attachment to the mRNA and blocks translation.