Genetics chp.12

negative repressible operon with product U present-

1. After levels of U product build up, the the product U binds to the regulator protein, 2. making it active and able to bind to the operator, 3. and thus prevents transcription.

How does the acetylation of histones control flowering in arabidopsis?

1. acetyl groups on histone proteins destabilize chromatin structure. 2. flowering locus C (FLC) encodes a regulator protein that represses flowering. 3. no flowering takes place. flowering does take place when: 4. Flowering locus D (FLD) encodes a deacetylase enzyme.... 5. that removes acetyl groups and restores chromatin structure. 6. no transcription takes place. 7. flowering is not suppressed, and so flowering takes place.

levels of gene control 1-5

1. genes may be regulated through the alternation of DNA or chromatin structure; usually takes place in Eukaryotes. Modifications to DNA or its packaging may help to determine which sequences are available for transcription or the rate at which sequences are transcribed.

Operon structure

1. structural genes are transcribed into a single mRNA 2. which is translated to produce enzymes A, B, and C. 3. These enzymes carry out a series of biochemical reactions that convert precursor molecule X into product Y. 4. The transcription of structural genes a, b, and c is under the control of a promoter, which lies upstream of the first structural gene. 5. RNA polymerase binds to the promoter and then moves downstream, transcribing the structural genes.

regulation of the lac operon - what are the three structural genes and how do they act?

1. the proteins B-galactosidase, perm ease, and transacetylase are encoded by adjacent structural genes in the lac operon and have a common promoter (lac P). 2. three structural genes act as follows: a) B-galactosidase is encoded by the lacZ gene b) perm ease is encoded by the lacY gene c) transacetylase is encoded by the lacA gene.

negative repressible operon with NO product U present -

1.the regulator protein is an inactive repressor, unable to bind to the operator. 2.transcription of the structural genes therefore take place. 3. levels of product U build up.

constitutive

A gene that is transcribed at a relatively constant level regardless of the cell environmental conditions. Supplement. Unlike facultative genes that are transcribed only when needed, constitutive genes are expressed continuously.

polypeptide chain

A polypeptide is a single linear chain of many amino acids, held together by amide bonds. A protein consists of one or more polypeptides (more than about 50 amino acids long). An oligopeptide consists of only a few amino acids (between two and twenty).

regulatory gene

A regulator gene, regulator, or regulatory gene is a gene involved in controlling the expression of one or more other genes. ... A regulator gene may encode a protein, or it may work at the level of RNA, as in the case of genes encoding microRNAs.

What are enhancers and insulators?

An insulator is a genetic boundary element that blocks the interaction between enhancers and promoters. It is thought that an insulator must reside between the enhancer and promoter to inhibit their subsequent interactions. Insulators therefore determine the set of genes an enhancer can influence.see figure 17.8 in notes or 12.18 in textbook.

What are some similarities and differences in gene regulation between prokaryotes and eukaryotes?

Both: in both types of cells, DNA binding proteins influence the ability of RNA polymerase to initiate transcription. Differences: 1. many prokaryotic genes are organized into operons and are transcribed into a single RNA molecule. 2. chromatin structure affects gene expression in eukaryotic cells:DNA must partly unwind from the histone proteins before transcription can take place. 3. the presence of the nuclear membrane in eukaryotic cells separates transcription and translation in time and space. Thus, the regulation of gene expression in eukaryotic cells is characterized by greater diversity of mechanisms that act at different points in the transfer of information from DNA to protein.

How is the expression of the lac operon influenced by glucose? What brings about catabolite repression?

Catabolite repression results from positive control in response to glucose. PC is accomplished through the binding of a protein called catabolite activator protein (CAP) to a site about 22 nucleotides long that is located within or slightly upstream of the promoter of the lac genes.

How is the transcription of eukaryotic genes coordinated if they are not organized into an operon?

Genes that are coordinately expressed in eukaryotic cells are able to respond to the same stimulus because they share short regulatory sequences in their promoters or enhancers (ex. heat shock genes genes possess a common regulatory element upstream of their start sites - response elements- which contain the same short consensus sequences at varying distances from the gene being regulated).

What is the role of cyclic AMP or cAMP?

RNA polymerase does not bind efficiently to some promoters unless CAP can bind to DNA, however it must form a complex with a modified nucleotide called adenosine 3', 5' -cyclic monophosphate (cyclic AMP or cAMP). In E.coli the concentration of this is regulated so that it is inversely proportional to the level of available glucose. Low concentrations of glucose stimulate high levels of cAMP, resulting in increased cAMP-CAP binding to DNA. see figure 12.12 for condensed processes.

How doe the binding of regulatory proteins to enhancers affect transcription at genes that are thousands of base pairs away?

The DNA between the enhancer and the promoter loops out, so that transcription activators bound to the enhancer are able to interact directly with the basal transcription apparatus.

regulator protein

The regulator gene has its own promoter and is transcribed into a short mRNA, which is translated into a small ___________ protein, which can bind to a region of the operon called the OPERATOR and affect whether transcription can take place.

What is an example of a negative repressible operon in E. coli and how does it work?

The trp operon is a negative repressible operon that controls the biosynthesis of tryptophan. In a repressible operon, transcription is normally turned on and must be repressed: this is accomplished through the binding of tryptophan to the repressor, which renders the repressor active. The active repressor binds to the operator and prevents RNA polymerase from transcribing the structural genes. see figure 12.13.

What did Francois Jacob and Jacques Monod's work accomplish?

Their work was the first to describe the genetic control of lactose metabolism in E. coli. It and subsequent research on the genetics of lactose metabolism established the operon as the basic unit of transcriptional control in bacteria. They deduced the structure of the operon genetically by analyzing the interactions of mutations that interfered with the normal regulation of lactose metabolism.

partial diploid

a cell carrying two copies of some, but not all, of its GENES. In BACTERIA where one copy of the genes of interest is carried on the chromosome, a second copy may be introduced on a PLASMID. The cells therefore carry one complete set of genes and a duplicated copy of part of the GENOME. Partial diploids have been constructed in order, for example, to perform the CIS-TRANS TEST.

nucleotide

a compound consisting of a nucleoside linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA.

point 2 levels of gene regulation

a gene can be regulated at the level of transcription. For the sake of cellular economy, limiting the production of protein early in the process makes sense- important in bacteria and eukaryotes.

how is the lac operon a negative inducible operon?

a regulator gene produces a repressor that binds to the operator and prevents the transcription of the structural genes. The presence of allolactose inactivates the repressor and allows the transcription of the lac operon.

How does the lac operon act differently in the absence of lactose vs. the presence of lactose?

absence: 1. In the absence of lactose, the regulator protein (a repressor) binds to the operator and inhibits transcription. presence: 2. when lactose is present, some of it is converted into allolactose,.... 3. which then binds to the regulator protein, making the protein inactive. 4. then the regulator protein cannot bind to the operator,... 5. and the structural genes are transcribed and translated.

What is the inducer for the lac operon in E.coli ?

allolactose (in the presence of this, the lac operon repressor cannot bind to the operator).

acetylation of histones

alters accessibility of chromatin and allows DNA binding proteins to interact with exposed sites to activate gene transcription and downstream cellular functions.

in a negative repressible operon, the regulator protein is synthesized as what?

an inactive repressor

regulatory elements

are DNA sequences that are not transcribed, but affect the expression of genes. They affect the expression of DNA sequences to which they are physically linked.

repressible operons

are those in which transcription is normal on (taking place); something must happen to repress transcription, or turn it off.

inducible operons

are those in which transcription is normally off (not taking place); so something must happen to induce transcription, or turn it on.

What kind of control does the lac operon act as and how does it do this?

as a positive control, in the lac operon an activator protein binds to the promoter and increases the efficiency with which RNA polymerase binds to the promoter and transcribes the structural genes.

Why do E.Coli and other bacteria metabolize glucose preferentially in the presence of lactose and other sugars?

because glucose enters glycolysis without further modification and therefore requires less energy to metabolize than do other sugars.

How can chromatin structure be altered?

by chromatin-remodeling complexes that reposition nucleosomes, by modifications of histone proteins, and by the methylation of DNA.

What happens when lactose is absent from the medium with E.coli?

few molecules of each protein are produced

point 6

finally, many proteins are modified after translation, and these modifications affect whether the proteins become active; therefore, genes can be regulated through processes that affect post translational modification. Gene expression can be affected by regulatory activities at any or all of these points.

histone modification

is a covalent post-translational modification (PTM) to histone proteins which includes methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation. The PTMs made to histones can impact gene expression by altering chromatin structure or recruiting histone modifiers.

structural genes

is a gene that codes for any RNA or protein product other than a regulatory factor (i.e. regulatory protein). It may code for a structural protein, an enzyme, or an RNA molecule not involved in regulation.

methylation of histones

is a process by which methyl groups are transferred to amino acids of histone proteins that make up nucleosomes, which the DNA double helix wraps around to form chromosomes.

negative repressible operon

is a process where the active regulator protein binds to the operator which prevents RNA polymerase from transcribing. ... In the presence of lactose, the repressor binds to the protein altering its shape so that it doesn't bind to the lac operator, and transcription occurs.

Negative inducible operons

is a process where the active regulator protein binds to the operator which prevents RNA polymerase from transcribing. If precursor five is present, it acts as and inducer altering the shape of the regulator protein disabling it to bind to DNA, and transcription can occur.

transcriptional activator

is a protein (transcription factor) that increases gene transcription of a gene or set of genes. Most activators are DNA-binding proteins that bind to enhancers or promoter-proximal elements.

coactivators

is a protein that increases gene expression by binding to an activator (transcription factor) which contains a DNA binding domain.

DNA methylation

is an epigenetic mechanism used by cells to control gene expression. A number of mechanisms exist to control gene expression in eukaryotes, but DNA methylation is a commonly used epigenetic signaling tool that can fix genes in the "off" position.

point 5

is at the level of translation, a complex process requiring a large number of enzymes, protein factors, and RNA molecules. All these factors, as well as the availability of amino acids, affect the rate at which proteins are produced and therefore provide points at which gene expression can be controlled. Translation can also be affected by sequences in mRNA.

point 3

is mRNA processing. Eukaryotic mRNA is extensively modified before it is translated: a 5' cap is added, the 3' end is cleaved and polyadenylated, and introns are removed. These modifications determine the stability of the mRNA, the movement of the mRNA into the cytoplasm, whether mRNA can be translated, the rate of translation, and the amino acid sequence of protein produced.

Chromatin remodeling

is the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.

what happens in a negative inducible operon if an inducer is present vs. not present

no inducer present - the regulator protein is a repressor that binds to the operator and prevents transcription of the structural genes - no transcription. inducer present - when the inducer is present, it binds to the regulator, thereby making the regulator unable to bind to the operator - transcription takes place.

point 4

of gene regulation is at the regulation of mRNA stability. The amount of protein produced depends not only on the amount of mRNA synthesized, but also on the rate at which the mRNA is degraded.

positive and negative control mechanisms

positive - stimulate gene expression (ex. drinking too much increasing liver function) negative - inhibit gene expression (ex. bone development)

gene expression in bacteria and eukaryotes

see page 330-331 in textbook for full review and comparison.

transcriptional repressor

some regulatory proteins in eukaryotic cells act as repressors, inhibiting transcription. These repressors bind to sequences in the regulatory promoter or to SILENCERS.

operon

the ________ regulates the expression of the structural genes by controlling transcription, which, in bacteria, is usually the most important level of gene regulation.

what happens if lactose is added to the medium and glucose is absent? What is the result of this?

the rate of synthesis of all three proteins simultaneously increases about a thousandfold within 2 to 3 minutes. - this boost in protein synthesis, which results from the simultaneous transcription of lacZ, lacY, and lacA, exemplifies COORDINATE INDUCTION, stimulation of the simultaneous synthesis of several proteins by a specific molecule, the inducer.

how do transcriptional regulator proteins act in eukaryotic cells?

they can influence the initiation of transcription by affecting the stability or assembly of the basal transcription apparatus. Some transcriptional regulator proteins are activators that stimulate transcription; others are repressors that inhibit the initiation of transcription.

how were lac mutations discovered?

through partial diploid studies

lactose metabolism

to use lactose as energy it must be broken down to glucose and galactose, a reaction catalyzed by the enzyme B-glactosidase.

negative control

when a regulatory protein is a repressor, binding to DNA and inhibiting transcription.

positive control

when a regulatory protein is an activator, stimulating transcription: it binds to DNA (usually at a site other than the operator) and stimulates transcription.