Chapter 14

Cis acting element

A DNA segment that must be adjacent to the gene(s) it regulates.

Lactose

A disaccharide consisting of glucose and galactose.

Trans effect

A form of genetic regulation that can occur even though two DNA segments are not physically adjacent.

Allolactose

A form of lactose that formally acts as an inducer of the lac operon by binding to the repressor and affecting its ability to bind to the operator.

Riboswitch

A form of regulation in which an RNA molecule can exist in two different secondary conformations which differ due to the binding of a small molecule; can regulate transcription, translation, RNA stability, and splicing.

Operon

A group of two or more genes under transcriptional control of a single promoter.

Permease

A membrane protein required for the active transport of lactose into the cytoplasm

Diauxic

A phenomenon in which a bacterial strain will preferentially use on nutrient source (e.g. glucose) before using a secondary nutrient source (e.g. lactose).

Operator Site

A region of DNA between the lac promoter (lacP) and the structural genes of the lac operon; a sequence of bases that provides a binding site for a repressor protein called the lac repressor

Promoter

A region of DNA that RNA polymerase binds to in order to initiate transcription

Terminator

A region of DNA that specifies the end of transcription

Trans acting factor

A regulatory protein that causes the trans effect

Catabolite Repression

A second way the lac operon is regulated in which the regulation is influenced by a substance broken down inside of the cell (e.g. cAMP with respect to the lac operon).

Thiamin pyrophosphate (TPP)

Active form of vitamin B1; involved in regulation of some riboswitches

Polycistronic RNA

An RNA that contains the sequences for two or more genes.

Beta-galactosidase

An enzyme that cleaves/hydrolyzes lactose into glucose and galactose.

CAP site

DNA sequence recognized by an activator protein for the lac operon; binding site for the catabolite activator protein

Most advantageous point of regulation of gene expression

During transcription

covalent modification

Phrase used to describe certain types of changes to the assembly and construction of a functional protein (e.g. disulfide bonds, attachment of sugar or lipids).

Regulatory Proteins

Proteins that can bind to the DNA and affect the rate of transcription of one or more nearby genes.

Lac I gene (repressor)

The gene for the lac repressor; Has its own promoter independent of the lac Z and Y genes.

Cis effect

The impact of a cis-acting element on gene regulation.

Gene Regulation

The phenomenon in which the level of gene expression (i.e. transcription and translation) can vary under different conditions.

Allosteric site

The region on a regulatory protein (other than its active site) that effector molecules can bind to.

LacZ

The structural gene of the lac operon that codes for beta-galactosidase.

Constitutive Genes

Unregulated genes that are continually expressed regardless of conditions.

F' factor

a fertility factor found in certain strains of bacteria in addition to their circular chromosome and also carries genes derived from the bacterial chromosome

Super repressor

a repressor that is more resistant to small effector molecules

Methods of gene expression regulation during transcription

genetic regulatory proteins bind to the DNA and control the rate of transcription; in attenuation, transcription terminates soon after it has begun due to the formation of a transcriptional terminator

Translational regulation proteins

recognizes sequences within the mRNA, similar to the way that transcription factors recognize DNA sequences

I Promoter

responsible for the transcription of the lacI gene

lac promoter

responsible for the transcription of the lacZ, lacY, and lacA genes as a single unit, which ends at the lac terminator

Translational repression

the act of inhibiting translation by translational repressors

Adenylylcyclase

the enzyme that converts ATP to cAMP

lac operon regulation in the presence of lactose

the operon is maximally turned on. The repressor protein is removed from the operator site, and the cAMP-CAP complex is bound to the CAP site

lac operon regulation in the presence of glucose

the operon is turned off due to the dominating effect of the lac repressor protein

lac operon regulation when no glucose or lactose is present

the operon is turned off due to the dominating effect of the lac repressor protein

Methods of gene expression regulation during translation

translational repressor proteins can bind to the mRNA and prevent translation from starting, rigoswitches can produce an mRNA conformation that prevents translation from starting, or antisense RNA can bind to the mRNA and prevent translation from starting

Translation Regulation

A point of regulation of gene expression in which repressor proteins can bind to the mRNA and prevent the start of translation or antisense (i.e. complementary) RNA can bind to the mRNA and prevent translation from starting.

allosteric regulation

A type of regulation in which small effector molecules can bind to a site on a regulatory protein and influence its ability to bind to the DNA.

Activator

A type of regulatory protein that binds to the DNA and increases transcription.

Repressor

A type of regulatory protein that binds to the DNA and inhibits transcription.

Repressible genes

Genes that are regulated by repressors and corepressors.

Effector Molecules

Molecules that don't directly bind to the DNA but exerts its effects by binding to an activator or repressor to cause a conformational change and influence whether or not it can bind to the DNA.

Negative Control

Transcriptional regulation by a repressor protein

Positive Control

Transcriptional regulation by an activator protein.

Feedback inhibition

A common mechanism to regulate the activity of metabolic enzymes; The final product in a metabolic pathway inhibits an enzyme that acts earlier in the pathway.

Enzyme adaptation

A phenomenon in which a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme.

Transcriptional regulation

A point of regulation of gene expression in which regulatory proteins bind to the DNA and control the rate of encoding of information from DNA into RNA

Transcription Regulation

A point of regulation of gene expression in which regulatory proteins bind to the DNA and control the rate of encoding of information from DNA into RNA.

Translational regulation

A point of regulation of gene expression in which repressor proteins can bind to the mRNA and prevent the start of translation or antisense (i.e. complementary) RNA can bind to the mRNA and prevent translation from starting.

Post Translation Regulation

A point of regulation of gene expression which occurs after the protein is produced. Can include mechanisms such as negative feedback control (feedback inhibition) in which the product of a metabolic pathway can inhibit the first enzyme in a pathway.

Antiterminator

A secondary structural feature of riboswitches; results in the formation of a stem-loop which prevents formation of the terminator stem loop.

Inducer

A small effector molecule that causes transcription to increase by either 1) binding to a repressor protein and prevent it from binding to the DNA or 2) bind to an activator protein and cause it to bind to the DNA.

Cyclic AMP (cAMP)

A small effector molecule which is produced by the action of adenylyl cyclase that impacts regulation of the lac operon.

Inducible genes

Genes that are regulated by an inducer.

Interaction between an activator protein, an inducer molecule, and an inducible gene

The activator protein can't bind to the DNA unless an inducer is present. When the inducer is bound to the activator protein, it enables the activator protein to bind to the DNA and activate transcription

LacY

The structural gene of the lac operon that codes for lactose permease.

Transcription factor modulation

a module where an inhibitor molecule and activator protein are involved. The binding of the inhibitor molecule to the activator protein would prevent it from binding to the DNA and thereby inhibit its ability to activate transcription

Merozygote

a strain of bacteria containing F' factor genes; their production was instrumental in allowing Jacob, Monod, and Pardee to elucidate the function of the LacI gene

relationship between adenylylcyclase, glucose, and cAMP

adenylylcyclase has a binding site for glucose. When glucose is bound to adenylylcyclase, the enzyme will undergo a conformational change that prevents it from recognizing ATP and turning it into cAMP

Antisense RNA

an RNA strand that is complementary to a strand of mRNA

Allosteric enzyme

an enzyme that contains two different binding sites

CAP

catabolite activating protein; binds to the CAP site to enhance transcription

Induced

condition of an operon that makes it free to be transcribed by RNA polymerase

Methods of gene expression regulation during posttranslation

in feedback inhibition the product of a metabolic pathway inhibits the first enzyme in the pathway or covalent modifications to the structure of a protein can alter its function

Interaction between a repressor protein, inducer molecule, and inducible gene

in the absence of the inducer, this repressor protein blocks transcription. The presence of the inducer causes a conformational change that inhibits the ability of the repressor protein to bind to the DNA. Transcription proceeds.

lac operon regulation in the presence of lactose and glucose

the expression of the lac operon is greatly decreased. the lac repressor is removed from the operator site, and CAP is not bound to the CAP site which makes it difficult for RNA polymerase to begin transcription. However, a little more transcription occurs under these conditions than in the absence of lactose, when the repressor is bound.

Post translational regulation

the functional control of proteins that are already present in the cell rather than regulation of transcription or translation