GENETICS EXAM 3 (USE THIS ONE)

In the lac operon, how would gene expression be affected if each one of the following segments was missing? A. lac operon promoter B. Operator site C. lacA gene

A: The RNA polymerase wouldn't be able to bind and transcription would not occur B: Repressor protein would not be able to bind, so transcription would always occur. C: LacA produces transacetylase, so this would not be produced

Inhibitor Molecule

Activator protein + inhibitor molecule = repressible gene the presence of an inhibitor causes a conformational change that inhibits the ability of the activator protein to bind to the DNA, this inhibits transcription

An operon is repressible—a small effector molecule turns off its transcription. Which combination(s) of small effector molecule and regulatory protein could be involved in this process? A. An inducer plus a repressor B. A corepressor plus a repressor C. An inhibitor plus an activator

B. Repressor and Corepressor C. Inhibitor and activator

Glucose, no lactose (low cAMP)

CAP inactive, transcription is very low due to the lack of CAP binding and by the binding of the repressor

Elements of the lac operon

DNA elements: promoter operator CAP site Structural Genes: LacZ LacY LacA

silencer

DNA sequence binded by a repressor

enhancer

DNA sequence that an activator is bound to

What is diauxic growth? Explain the roles of cAMP and CAP in this process

Diauxic growth is when a bacterium sequentially uses two sugars. The role of cAMP and CAP in this process is that the cells prefer to use glucose because it is a more simple sugar, so in the presence of glucose, the lac operon will function at only very low level and there will be very low levels of cAMP. Whenever glucose is low there will be high levels of cAMP. CAP in the presence of cAMP will bind to the CAP site and further activate transcription.

Catabolite repression of the lac operon

E. coli prefers to use glucose as its carbon source so it represses the lac operon because its is a waster of energy to make product and then use glucose instead. Involves cyclic AMP or cAMP as effector molecule. cAMP binds to an activator protein known as the Catabolite Activator Protein or CAP

histone genes

H1, H2A, H2B, H3, H4

Transcriptional regulation often involves a regulatory protein that binds to a segment of DNA and a small effector molecule that binds to the regulatory protein. Do each of the following terms apply to a regulatory protein, a segment of DNA, or a small effector molecule? A. Repressor B. Inducer C. Operator site D. Corepressor E. Activator F. Attenuator G. Inhibitor

Repressor: regulatory protein inducer: effector molecule operator site: segment of DNA corepressor: effector molecule activator: regulatory protein attenuator: DNA segment inhibitor: effector molecule

If an abnormal repressor protein could still bind allolactose but the binding of allolactose did not alter the conformation of the repressor protein, how would the expression of the lac operon be affected?

The allolactose is an inducer molecule that binds to the repressor protein and changes it conformationally to keep it from binding to the operator site and blocking the RNA polymerase, if this did not alter the conformation of the repressor protein then the protein would still be able to bind to the DNA and therefore transcription could not occur.

merozygote

The recipient cell, with an extra copy of any gene carried by the F' plasmid. two lacI genes in merozygote might be different alleles

Would a mutation that inactivated lac repressor and prevented it from binding to the lac operator site result in the constitutive expression of the lac operon under all conditions? Explain. What is the disadvantage to the bacterium of having a constitutive lac operon?

This would result in the constitutive expression of the lac operon only in the presence of glucose. The disadvantage is loss of energy.

No lactose or glucose (high cAMP)

Transcription is very low due to the binding of the repressor

cis-effect

a DNA sequence that must be adjacent to the genes it regulates. mediated by sequences that bind regulatory proteins. EX: the lac operator

motif

a domain. or portion of a domain, that has a very similar structure in many different proteins.

CpG islands

a group of CG sequences that may be clustered near a promoter region of a gene. The methylation of the cytosine bases usually inhibits transcription.

genomic imprinting

a phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent

CREB protein

a regulatory transcription factor, called cAMP response element binding, becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentration of cAMP. CREB protein recognizes a response element with the consensus sequence 5'-TGACGTCA-3' called the cAMP response element. Phosphorylated CREB binds to DNA and stimulates transcription, unphosphorylated CREB can bind to DNA but can't activate RNA polymerase.

Transcriptional activation via mediator

activator protein interacts with the mediator which results in phosphorylation of the carboxyl termina domain of RNA polymerase. Some general transcription factors are released and RNA pol proceeds to elongation phase of transcription. Transcriptional activator stimulates function of mediator, this enables RNA pol to form preinitiation complex, proceeds to eleongation phase of transcription.

glucose + lactose

allolactose binds to repressor so RNA polymerase can transcribe, but becuase glucose is present there will be low levels of cAMP so the CAP isnt going to bind to the CAP site to further activate transcription, so you'll have slower transcription.

no glucose + lactose

allolactose binds to the repressor and keeps the repressor from binding to the operator, RNA polymerase is able to transcribe. With no glucose the CAP site is involved. CAP in in the presence of cAMP will bind to the CAP site and further activate transcription. If you don't have any glucose then the cell really needs to transcribe its lactose, which is why it needs the extra boost from cAMP

down regulation

binding of a transcription factor to a silencer decreases the rate of transcription

up-regulation

binding of a transcription factor to an enhancer increases the rate of transcription.

promoter

binds RNA polymerase

operator

binds lac repressor protein

CAP site

binds the catabolite activator protein (CAP)

activator protein

binds to DNA and increases transcription

repressor protein

binds to DNA and inhibits transcription

ron regulatory protein (IRP)

binds to a regulatory element within these two mRNAs known as the iron response element (IRE)•IRE in ferritin mRNA is in 5' UTR•IRE in transferrin receptor mRNA is in 3' UTR

high glucose inhibits production of

cAMP because cAMP further activates the transcription of the lac operon, and the cell would rather use glucose first.

DNA methylation

change in chromatin structure that silences gene expression. carried out by enzyme DNA methyltransferase

change in nucleosome position

change in relative position of a few nucleosomes or change in spacing of nucleosomes over long distance

open conformation chromatin structure

chromatin is accessible to transcription factors, transcription can take place

closed conformation chromatin structure

chromatin is very tightly packed, transcription may be difficult or impossible.

What is the difference between a constitutive gene and a regulated gene?

constitutive: unregulated, constantly being transcribed, frequently required for organism survival regulated: genes are only transcribed when the cell needs it

ATP dependent chromatin remodeling

dynamic changes in chromatin structure. Energy of ATP hydrolysis is used to drive change in location or composition of nucleosomes. makes DNA more or less amenable to transcription.

LacZ gene

encodes B-galactosidase, which enzymatically cleaves lactose and lactose analogues. CONVERTS LACTOSE TO ALLOLACTOSE

LacA

encodes galactoside transacetylase, which covalently modifies lactose and analogues. functional necessity remains unclear

LacY

encodes lactose permease, a membrane protein required for the transport of lactose and analogues

the encode project

encyclopedia of DNA elements consortium. 1. isolate and sequence RNA from humans 2. identify transcription factor binding sites 3. map DNA methylation sites 4. identify histone modification sites 5. map DNaseI cleavage sites ongoing. identifying all regulatory elements of human DNA

what is enzyme adaptation? from a genetic view how does it occur?

enzyme adaptation is when an enzyme isn't present in a cell until the enzyme's substrate occurs. When cells are exposed to an enzymes substrate they the genes needed to process it are transcribed and not otherwise.

histone code

enzymes that selectively modify amino terminal tails of histones. These modifications affect the level of transcription and may influence interactions between nucleosomes. They occur in patterns that are recognizable to proteins. The pattern of modification provides binding sites for proteins that specify alterations to be made to chromatin structure. These proteins bind based on code and affect transcription.

Gonadcorticoids

estrogen and testosterone, influence growth and function of gonads

constitutive genes

genes that are unregulated and have essentially constant levels of expression, frequently constitutive genes encode proteins that are continuously necessary for the survival of the organism

trans-effect

genetic regulation that can occur even though DNA segments are not physically adjacent to the genes it regulates. Mediated by sequences that bind regulatory proteins EX: action of the lac repressor on lac operon

LacI gene

has its own promotoer (i promoter) constitutively expressed at fairly low levels Encodes lac repressor (lac repressor protein functions as a tetramer, only a small amount is needed to repress lac operon) allolactase acts as inducer and binds to lac repressor, inactivating it.

histone eviction

histone octamers are removed by a chromatin-remodeling complex, create a gap with no nucleosomes

repressor protein + inducer molecule

in the absence of the inducer a repressor protein blocks transcription, the presence of the inducer causes a confromational change that inhibits the ability of the repressor protein to bind to the DNA so transcription proceeds

glucocorticoids

influence nutrient metabolism in most cells, promote glucose utilization, fat mobilization, and protein breakdown

high iron

iron binds to IRP, which causes IRP to dissociate from transferrin receptor mRNA, exposing sites that are recognized by endonucleases and the mRNA is degraded

ferritin

iron storage protein

In general, why is it important to regulate genes? Discuss examples of situations in which it would be advantageous for a bacterial cell to regulate genes

it's important to regulate genes to control when specific genes are expressed. One reason you might want to do this is to save energy, why use energy to transcribe the genes to metabolize a certain item if you don't currently have access to that item. Another time genes might be regulated is during different periods of life, perhaps there are genes that control a growth hormone that need to be transcribed when an organism is young, but when the organism reaches adulthood it doesn't need to grow anymore so it shouldn't produce that hormone anymore.

overview of lac operon

lac operon goes in the following order: CAP site: promoter: operator: LacZ: LacY: LacA RNA polyermase binds to the promoter and goes down the line of DNA to transcribe it. The lac repressor binds to the operator in front of the promotoer, which blocks the RNA polymerase and keeps transcription form happening. The activator binds behind the promoter and helps push it forward, increasing transcription. If there is no lactose, the lac repressor protein is bound to the operator meaning no transcription. If lactose is present you have an isomer of lactose, allolactose, that is an effector molecule and acts as an inducer. Allolactose binds to the repressor and keeps it from being able to bind to the operator site, it can't block the RNA polymerase, so transcription and lactose metabolism can occur.

Gene Regulation

level of gen expression can vary under different conditions

Low iron

mRNA is translated to make more transferrin receptor protein

What is meant by the term attenuation? Is it an example of gene regulation at the level of transcription or translation? Explain your answer

means to make the gene weak or suppress the effect of the gene. In genetics it is used to refer to describe finishing transcription early, before it is complete. It is an example of transcription regulation.

histone variants

mutations of histone gene that alter amino acid sequence

X chromosome inactivation

process that occurs in female mammals in which one of the X chromosomes is randomly turned off in each cell

transferrin

protein carries iron through the bloodstream transported into the cytosol by endocytosis

transcription factors

proteins that influence the ability of RNA polymerase to transcribe genes

domain

regions in transcriptional factor proteins that have specific functions. EX: a domain for DNA binding, a domain for binding site for effector molecules

If a gene is repressible and under positive control, what kind of effector molecule and regulatory protein are involved in its regulation? Explain how the binding of the effector molecule affects the regulatory protein.

regulatory protein is an activator (positive control) and the effector molecule is an inhibitor (repressible). The inhibitor binds to the activator and keeps it from being able to bind to the DNA.

steroid receptors

regulatory transcription factors that respond to steroid hormones (hormone binds to transcription factor)

replacement with histone variants

replace a histone with a different molecule, region with variant histones affect transcription

lactose and glucose (low cAMP)

repressor inactive, CAP inactive, transcription rate is low due to the lack of CAP binding

Lactose, no glucose (high cAMP)

repressor inactive, high rate of transcription, binding of RNA polymerase to promoter is enhanced by CAP binding

Corepressor molecule

repressor protein + corepressor molecule = repressible gene in the absence of a corepressor some repressor proteins will not bind to the DNA so transcription will occur. When the corepressor is bound to the repressor protein a confromational change occurs which allows the repressor to bind to the DNA and inhibit transcription.

Transcriptional repression via TFIID

repressor protein inhibits binding of TFIID to the core promoter or inhibits its function. Transcription is silenced.

Transcriptional repression via mediator

repressor protein interacts with mediator in a way that prevents the phosphorylation of RNA polymerase. it cant proceed to elongation phase of transcription. Transcriptional repression inhibits function of mediator, transcription is repressed.

general transcription factors

required for binding of the RNA pol to the core promoter and its progression to the elongation stage, necessary for basal transcription

LacI- mutant

resulted in constitutive expression of lac operon, even in absence of lactose. LacI- eliminates function of lac repressor

insulators

segments of DNA that insulate a gene from the regulatory effects of other genes. Some act as barriers to chromatin remodeling, others block the effects of enhancers (may use chromatin looping)

regulatory transcription factors

serve to regulate the rate of transcription of target genes, influence ability of RNA pol to begin transcription of a particular gene.

Activator protein + inducer molecule

some activator proteins cannot bind to the DNA unless an inducer is present. When the inducer is bound to the activator protein this enables the activator protein to bind to the DNA and activate transcription.

Transcriptional Activation via TFIID

the activator/coactivator complex recruits TFIID to the core promoter and/or activates its function. Transcription will be enhanced

TFIID

the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP) and plays a role in activating eukaryotic genes transcribed by RNA polymerase II

diauxic growth

the sequential use of two sugars by a bacterium

Some mutations have a cis-effect, whereas others have a trans-effect. Explain the molecular differences between cis- and trans-mutations. Which type of mutation (cis or trans) can be complemented in a merozygote experiment?

trans means transcription can occur without the genes being immediately adjacent to the DNA segment. Cis must be right next to each other for transcription. A merozygote experiment is done with trans mutations, where you can have two different copies of an allele.

positive control

transcriptional regulation by activator proteins

negative control

transcriptional regulation by repressor proteins