Test 4 chapter 16

what mutation encodes a super-repressor with a mutation in the binding site for allolactose that prevents binding of the inducer?

lacI^S

the lac operon in E.coli encodes genes required to utilize ? as a carbon source

lactose

the two genes required for lactose utilization (encoded by the lac operon) encode a permease and b-galactosidase which cleaves?

lactose

binding to DNA is dynamic. DNA binding proteins come on and off the DNA . they are NEVER?

permanently bound

what will be the expected net charge of the DNA binding domain of a protein?

since DNA is negatively charged, it needs to be positive charged in order to interact with it

what regulator acts as a binding site for trans-regulatory proteins to anchor them close to a gene?

cis-regulatory

For the lac operon contrast negative and positive control of transcription

- Negative control occurs when the repressor binds to the operator in the absence of lactose. The operon is not transcribed. - Positive control occurs in the presence of lactose when CAP-cAMP help RNA polymerase to bind to the promoter and activate transcription.

there are two types of control?

1. positive control 2. negative control

Regulatory gene are?

A gene that encodes a protein or RNA product that controls the expression of other genes - (e.g. a gene that encodes sigma factor in bacteria)

Structural gene is?

A gene that encodes a protein or RNA product that does not control the expression of other genes - Does work in the cells

lacZ encodes?

B-galactosidase

The lac operon is transcribed at high levels when lactose is the only carbon source. However, transcription of the operon is greatly reduced in the presence of lactose and glucose. Why?

Glucose lowers the levels of cAMP. cAMP binds to CAP and together these proteins help RNA polymerase to bind to the promoter. If cAMP levels are low, CAP and RNA polymerase have difficulty binding to the promoter to initiate transcription.

what is an operon?

a gene cluster controlled by a single promoter that transcribes to a single mRNA strand

the super-repressor binds permanently to the operator and the operon cannot be?

activated in the presence of lactose

what inducer induces its own utilization?

allolactose

operons are common in ? and rare in ?

bacteria, eukaryotes

in the presence of lactose the genes of the lac operon are?

coordinately induced

trans-regulatory proteins are? - ex: RNA polymerase and lac repressor

diffusible

Not the whole gene will bind to the protein but only a?

specific region will bind to it - weak or strong binding - weak will break off sooner but long binding will bind and stay for a while and they are on and off

what happens when glucose levels are high in a positive control of the lac operon?

synthesis of cAMP from ATP is inhibite without cAMP, CAP has low affinity for its binding site, and RNA polymerase has difficulty binding to the promoter and initiating transcription (transcription of the lac operon is reduced in the presence of glucose and lactose as compared to a low glucose environment)

in bacteria control is primarily at?

the level of transcription

What is catabolite repression? How does it allow a bacterial cell to use glucose in preference to other sugars?

- In catabolite repression, the presence of glucose inhibits or represses the transcription of genes involved in the metabolism of other sugars. - Because the gene expression necessary for utilizing other sugars is turned off, only enzymes involved in the metabolism of glucose will be synthesized. - Operons that exhibit catabolite repression are under the positive control of catabolic activator protein (CAP). For CAP to be active, it must form a complex with cAMP. - Glucose affects the level of cAMP. The levels of glucose and cAMP are inversely proportional -as glucose levels increase, the level of cAMP decreases. Thus, CAP is not activated.

Explain why mutations in the lacI gene are trans in their effects, but mutations in the lacO gene are cis in their effects

- The lacI gene encodes the lac repressor protein, which can diffuse within the cell and attach to any operator. It can therefore affect the expression of genes on the same or different molecules of DNA. - The lacO gene encodes the operator. The binding of the lac repressor to the operator affects the binding of RNA polymerase to the DNA, and therefore affects only the expression of genes on the same molecule of DNA.

carbohydrate metabolism in E.coli

- bacteria use a variety of carbon sources (e.g. glucose, lactose, fructose, maltose) to generate ATP for metabolic functions.... - bacteria have different sets of genes organized into operons that enable them to take advantage of each kind of carbon source

what are the two classes of lac Operon mutations?

- cis-mutations - trans-mutations

what are some examples of cis-regulators?

- operators - bacterial promoters - eukaryotic core and regulatory promoters and enhancers

the lac repressor covers transcription start and is close enough to ? to interfere with binding of RNA polymerase to the promoter

-10

For a negative control in a inducible operon, indicate whether the protein produced by the regulator gene will be synthesized initially as an active repressor or an inactive repressor.

Active repressor

What is the difference between negative inducible and negative repressible control of gene expression?

In negative control, a repressor protein inhibits or turns off transcription - A negative inducible operon normally is not transcribed. It requires an inducer molecule to stimulate transcription by inactivating a repressor protein. Transcription normally occurs in a repressible operon. - In a repressible operon, transcription is turned off by the repressor becoming active.

For a negative control in a repressible operon, indicate whether the protein produced by the regulator gene will be synthesized initially as an active repressor or an inactive repressor.

Inactive repressor

who came up with the gene regulation work?

Jacob, Monod, and Lwoff - shared a Nobel Prize

Why does E. coli prefer to use glucose as a carbon source even if lactose is also present?

Lactose must be cleaved to generate glucose and galactose. If free glucose is already available, the cell does not need to make -galactosidase and permease to utilize lactose. This would be an inefficient use of cellular energy resources.

Briefly describe the lac operon and how it controls the metabolism of lactose.

The lac operon consists of three structural genes involved in lactose metabolism, the lacZ gene, the lacY gene, and the lacA gene. Each of these three genes has a different role in the metabolism of lactose. The lacZ gene codes for the enzyme β-galactosidase, which breaks the disaccharide lactose into galactose and glucose, and converts lactose into allolactose. The lacY gene, located downstream of the lacZ gene, codes for lactose permease. Permease is necessary for the passage of lactose through the E. coli cell membrane. The lacA gene, located downstream of lacY, encodes the enzyme thiogalactoside transacetylase whose function in lactose metabolism has not yet been determined. All of these genes share a common overlapping promoter and operator region. Upstream from the lactose operon is the lacI gene that encodes the lac operon repressor. The repressor binds at the operator region and inhibits transcription of the lac operon by preventing RNA polymerase from successfully initiating transcription. When lactose is present in the cell, the enzyme β-galactosidase converts some of it into allolactose. Allolactose binds to the lac repressor, altering its shape and reducing the repressor's affinity for the operator. Since this allolactose-bound repressor does not occupy the operator, RNA polymerase can initiate transcription of the lac structural genes from the lac promoter.

How does the term allosteric transition apply to the regulation of the lac operon?

When lactose binds to the repressor, the repressor undergoes a conformational change (allosteric transition). The altered repressor is unable to bind to the operator and inhibit transcription by RNA polymerase.

cis-regulator?

a DNA sequence physically connected to and adjacent to a gene: controls transcription of the gene (e.g. promoter and operator) ... is considered to be part of the gene

trans-regulator?

a gene product (e.g. lac repressor or RNA polymerase) that controls transcription of other genes by binding to cis-regulators; in eukaryotes a trans regulatory gene is often not physically linked to the genes it controls (i.e. may be on another chromosome)

constitutive gene is?

a gene whose expression is not regulated - (i.e. it is always on) - not all genes are regulated, sometimes a gene is always transcribed (does not control what it makes or when) - this type of gene is essential for us to live and is active on every cell

What is an operon?

a group of structural genes with related functions that are expressed under the control of a common promoter; the genes are transcribed into a single polycistronic mRNA that is then translated into individual proteins

what are cis-mutations?

a mutation that must be physically linked to the operon to affect expression - ex: on the same double helix of DNA

what is negative control?

a process that inhibits gene expression - bacteria tend to favor this control

what is positive control?

a process that stimulates gene expression - eukayotes tend to favor this control

regulatory element is?

a sequence of DNA that is not transcribed and controls the expression of genes it is directly linked to by binding the products of regulatory genes - (e.g. bacterial promoter, eukaryotic core or regulatory promoter)

an inducer binding to the repressor changes its shape preventing it from binding to the operator, this is called?

allosteric transcription

if the lac I- repressor scans along the DNA strand on which it was made and in the absence of lactose the bottom operon will be on and ?

b-galactosidase will be produced

why are operons with promoters mutation never transcribed?

because RNA polymerase cannot bind to the promoter - only structural genes physically linked to the promoter are affected

in the absence of lactose wild-type B-galactosidase is made because the repressor cannot?

bind to the lacO^c mutant opoerator

allolactose binds to the repressor and induces an allosteric transition in the repressor so it can no longer?

bind to the operator

the lac I- repressor produces a repressor protein that cannot?

bind to the operator

what is cooperative binding?

binding of the CAP-cAMP complex facilitates binding of RNA polymerase to the promoter

the lacO^c mutation prevents the repressor from?

binding to the operator

what lac operon mutations are regulatory mutations in the promoter and operator

both cis-mutations and transmutations

the super repressor can diffuse and?

can go to any other piece of DNA and bind to an operator

what lac operon mutation in structural genes affect only one gene

cis-mutations

glucose and galactose are both used to?

generate ATP

DNA binding proteins control the expression of?

genes

eukaryotes control the expression of their?

genes at many levels

With respect to the lac operon, define the term induction

he relief of repression of transcription caused by the repressor protein. This occurs after allolactose binds to the repressor causing an allosteric change in its shape.

what are the two types of negative control?

inducible or repressible

a is-regulator cannot?

influence the transcription of a gene that it is not physically linked to

what happens if glucose and lactose are available at the same time?

it is energetically wasteful to induce the lac operon because lactose is cleaved into glucose and galactose by B-galactosidase

how does the repressor work in the regulation of the lac operon?

it might diffuse to the promoter site or it might scan along the DNA

The lac operon encodes two genes required for?

lactose utilization

what are trans-mutations?

mutations in the gene encoding the repressor that can affect expression of the lac operon even if the lacl gene is not on the same double helix of DNA

the amount of individual protein in, or secreted by cells, varies depending on?

need

inducible operons are?

normally not trasncribed (repressor) and repression must be relieved to allow transcribed

repressible operons are?

normally transcribed and must be repressed to inhibit transcription

inducible operons are normally ? and something must happen to ?

not transcribed, activate transcription

in eukaryotes there is 5 genes with its own promoter but in bacteria there are 5 genes linked to?

only one promoter

lacY encodes?

permease

inducible operon need to be able to?

relieve repression

the regulatory protein is a ? that binds to DNA and inhibits transcription

repressor

activating the genes in bacteria requires to utilize a particular carbon source only when?

the carbon source is available prevents waste of energy for unnecessary transcription and translation

what does P- means ?

the promoter is damaged so transcription is not possible because RNA polymerase cannot bind to the promoter

how does cis-regulation works?

they are not diffusible and can only control the expression of genes they are physically linked to

what happens to the genes used to metabolize other sugars when glucose is available?

they are repressed even if the other sugars are present (catabolite repression)

the regulatory gene makes an inactive repressor so the operon is?

transcribed

repressible operoms are normally ? and something must happen to ?

transcribed, turn repress transcription

lacA encodes a transacetylase whose function in lactose utilization is?

unknown

Positive control of the lac Operon?

when glucose levels are low, cAMP forms a complex with catabolite activator protein (CAP) and binds near the promoter of the lac operon