Control of Gene Expression
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| gene regulation | mechanisms and systems that control the expression of genes
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| in bacteria, gene regulation maintains ______ _________ by turing genes on and off in response to environmental changes | internal flexibility
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| in multicellular eukaryotic organisms, gene regulation brings about ______ _________ | cellular differentiation (specialization)
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| genes | DNA sequences that are transcribed into RNA molecules
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| regulatory genes are genes of which the products (RNA or proteins) interact with other DNA sequences and affect the __________ and ___________ of those sequences | transcription and translation
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| a few structure genes, particularly those that encode essential cellular functions, are expressed continually and are called _________ genes. They therefor, are NOT regulated. | constitutive
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| regulatory elements | DNA sequences that are not transcribed but affect the expression of genes
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| the regulation of gene expression can be through processes that STIMULATE gene expression. This is termed ________ control | positive
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| the regulation of gene expression can be through processes that INHIBIT gene expression. This is termed _________ control | negative
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| gene expression can be controlled at any of a number of points along the molecular pathway from DNA to protein including: (6) | DNA or chromatin structure, transcription, mRNA processing, RNA stability, translation, and posttranslational modification
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| concept check: why is transciption a particularly important level of gene regulation in both bacteria and eukaryotes? | it is the first step in the process of information transfer from DNA to protein. (for cellular efficiency, gene expression is often regulated early in the process of protein production)
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| a big difference between bacterial and eukaryotic gene control lies in the organization of functionally ______ genes | functionally related
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| functionally related genes in bacterial cells are clustered together as a single transcriptional unit termed as an _______ | operon
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| operon is a single transcriptional unit that includes what? (3) | a series of structural genes, a promoter for the structural genes, and an operator site (where the product of a regulator gene binds)
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| a regulator gene does what? | helps to control the transcription of the structural genes of the operon
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| although it affects operon function, the regulator gene is not considered part of the operon. It has its own _______ and is transcribed into a short _____, which is translated into a small ______ | promoter, mRNA, protein
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| this regulator protein can bind to a region of DNA called the _______ and affect whether transcription can take place | operator
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| the operator usually overlaps the _' end of the ________ and sometimes the _' end of the first __________ ___ | 5' promoter, 3' structural gene
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| the proteins (enzymes) are the products of mRNA and catalyze what? | reactions in a biochemical pathway
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| what are the two basic types of transcriptional control? | negative and positive
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| negative control | a regulatory protein is a repressor
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| when the regulatory protein is a repressor, binding to DNA will ______ transcription | inhibit
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| positive control | a regulatory protein is an activator
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| when the regulatory protein is an activator, binding to DNA will ______ transcription | stimulate
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| some operons are inducible, which means what? | transcription is normally off and must be turned on
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| some operons are repressible, which means what? | transcription is normally on and must be turned off
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| negative inducible operons: in a negative inducible operon, the regulator gene encodes an ACTIVE ______ | repressor (regulator protein)
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| negative inducible operons: when an inducer is ABSENT the repressor binds to the ________ | operator
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| negative inducible operons: (inducer absent) what does this binding to the operator do? | physically blocks the binding of RNA polymerase to the promoter and prevents transcription of the structural genes
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| negative inducible operons: when an inducer (precursor V) is PRESENT it binds to the ________ | repressor (regulator protein)
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| negative inducible operons: (inducer present) what does this binding to the repressor do? | alters the shape of the repressor, preventing it from binding to the operator (prevents binding to DNA)
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| negative inducible operons: Proteins which change shape on binding to another molecule are called ________ proteins | allosteric
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| negative inducible operons: (inducer present) since the repressor was prevented from binding to the operator, the RNA polymerase is able to bind to the promoter. This allows for what? | transcription of structural genes
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| negative inducible operons: (inducer present) the resulting mRNA is then translated into enzymes (D,E,F) which convert substrate __ into product __ | V to W
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| so, for negative inducible operons, the synthesis of enzymes is _________ | economical (enzymes are synthesized only when their substrate (V) is available)
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| negative repressible operons: the regulator protein in this type of operon also is a repressor but is synthesized in an INACTIVE form. What does this mean? | it cannot itself bind to the operator
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| negative inducible operons: because no repressor is bound to the operator, ____ ________ readily binds to the promoter and transcription of the structural genes takes place | RNA polymerase
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| negative inducible operons: the transcription of structural genes allows for the synthesis of _______ (G,H,I) | enzymes
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| negative inducible operons: the enzymes turn precursor __ into product __ (corepressor) | T into U
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| negative inducible operons: to turn off transcription, the repressor needs to be made ACTIVE. a small molecule called a _________ binds to a repressor and makes it capable of binding to the operator | corepressor (example: product U)
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| negative inducible operons: (product U present) since the operon is repressed, enzymes (G,H,I) are not synthesized. What does this mean? | precursor T is not converted into product U
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| negative inducible operons: (product U present) when all of the available product U is used up, the repressor is no longer _______ by product U and cannot bind to the operator | activated
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| summary: inducible operons usually control proteins that do what? | carry out degradative processes (breakdown of molecules)
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| summary: repressible operons usually control proteins that do what? | carry out the biosynthesis of molecules needed in the cell (amino acids)
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| positive control: with positive control, a regulatory protein is an ________ | activator
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| positive control: because the regulatory protein is an activator, what happens? | it binds to DNA (usually at site other than operator) and STIMULATES transcription
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| positive inducible operon: transcription is normally turned ___ because the regulator protein (an activator) is produced in an inactive form | off
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| positive inducible operon: transcription takes place when an _______ attaches to the regulatory protein, rendering the regulator active | inducer
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| positive repressible operon: it is repressible and the regulatory protein is produced in an ______ form | ACTIVE
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| positive repressible operon: when the regulatory protein is active it is able to do what? | bind to DNA, meaning transcription normally takes place and must be TURNED OFF
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| positive repressible operon: transcription is inhibited when a substance becomes attached to the _______ and render it unable to bind to DNA so that transcription is no longer stimulated | activator
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| positive repressible operon: the product (product P) of the reaction would be the _________ substance because prevention of the transcription of genes that allow the synthesis of P when plenty of P is already available would be economical for the cell | repressing
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| concept check: in a negative repressible operon, the regulator protein is synthesized as an ________ (active/inactive) _________(activator/repressor). | inactive repressor
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| what two people described the "operon model" for the genetic control of lactose metabolism in E. coli? | Jacob and Monod
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| lactose metabolism: lactose is one of the major carbohydrates found in ____; it can be metabolized by E.coli bacteria that reside in the mammalian ___. | milk, gut
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| lactose metabolism: lactose does not easily diffuse across the E. coli cell membrane and must be ______ transported into the cell by the protein ________ | actively, permease
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| lactose metabolism: once the actively transported lactose is in the cell, the enzyme Beta-galactosidase breaks it into __________ and _________ | galactose and glucose
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| lactose metabolism: the enzyme, Beta-galactosidase, can also convert lactose into _________, a compound that plays an important role in regulating lactose metabolism.. | allolactose
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| lactose metabolism: the enzyme, Beta-galactosidase, then converts the allolactose into ________ and _______ | galactose and glucose
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| lactose metabolism: the lac operon is an example of a ________ (positive/negative) ________( repressible/inducible) operon | negative inducible
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| regulation for the lac operon: the lac operon controls the transcription of three genes needed in lactose metabolismL | lacZ, lacY, and lacA
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| regulation for the lac operon: lacZ encodes what enzyme? | Beta-galactosidase
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| regulation for the lac operon: lacY encodes what enzyme? | permease
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| regulation for the lac operon: lacA encodes what enzyme? | thiogalactoside transacetylase
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| regulation for the lac operon: (lactose absent) because the lac operon is negative inducible, a regulator gene produces an active repressor that does what? | binds to the operator site (lacO) and prevents transcription
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| regulation for the lac operon: (lactose present) the presence of allolactose inactivates the repressor, which does what? | allow the transcription of the lac operon
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| concept check: in the presence of allolactose, the lac repressor... | CANNOT bind to the operator
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| Jacob and Monod worked out the structure and function of the lac operon by analyzing ________ that affected lactose metabolism | mutations
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| mutations in lac: to help define the roles of the different components of the operon, they used strains of E. coli that possessed two different DNA molecules. These strains are said to be _______ ________ | partial diploid
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| mutations in lac: What two DNA molecules did these partial diploid strains have? | full bacterial chromosome and an extra piece of DNA
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| mutations in lac: in conjugation, a small circular piece of DNA (F plasmid) is transferred from one bacterium to another. The F plasmid they used had the lac operon; so the recipient became partly diploid, possessing what? | 2 copies of the lac operon
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| mutations in lac: by using different combos of mutations on the bacterial and plasmid DNA, they determined that some parts of the lac operon are ___(control the expression when on SAME DNA) and some ____(control the expression when on 2 diff DNA mol) | cis and trans
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| Jacob and Monod first discovered some mutant strains that had lost the ability to synthesize which enzymes? | Beta-galactosidase or permease
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| structural-gene mutations: the mutations in the mutant strains mapped to the lac_ or lac_ structural genes and altered the amino acid sequences of the proteins encoded by these genes | lacZ or lacY
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| structural-gene mutations: through the use of partial diploids they were able to establish that mutations at the lacZ and lacY genes were ___________ and usually only affected the _______ of the gene in which the mutation occurred | independ, product
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| structural-gene mutations: this means that a single functional gene (lacZ+) is sufficient to produce the enzyme Beta-galactosidase whether the gene is coupled with a functional gene (lacY+) or a defective gene (lacY-) and vice versa. | ;)
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| Jacob and Monod also isolated mutations that affected the ________ of protein production | regulation
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| regulator-gene mutations: the partial diploid lacI+lacZ-/lacI-lacZ+ produces the enzyme beta-galactosidase only in the presence of _______ because the lacI gene is ____ dominant | lactose, trans dominant
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| regulator-gene mutations: the fact the the lacI+ gene could regulate the lacZ+ gene located on a different DNA molecule indicated to them that the lacI+ product was able to operate on either a _______ or the chromosome | plasmid
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| operator mutations: Jacob and Monod mapped a second set of constitutive mutants to a site adjacent to lac_ | lacZ
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| constitutive mutants | mutation that causes structural gene to be continually expressed
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| operator mutations: these mutations occurred at the operator site and were referred to as ____ | lacO^c (O=operator, c=constitutive)
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| operator mutations: what did the lacO^c mutations do? | altered the sequence of DNA at the operator
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| operator mutations: what did this alteration the DNA sequence at the operator cause? | the repressor protein to no longer be able to bind
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| operator mutations: a partial diploid with genotype lacI+ lacO+lacZ- / lacI+ lacOc lacZ+ exhibited constitutive synthesis of beta-galactosidase. What does this indicate about the lacOc? | that lacOc is dominant over lacO+
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| operator mutations: analyses of other partial diploids showed that lacO gene is ___, meaning it affects only genes on the same DNA molecule | cis
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| promoter mutations: mutations affecting lactose metabolism have also been isolated at the promoter site; these mutations are designated lacP-. What do these mutations do? | interfere with the binding of RNA polymerase to the promoter
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| operator mutations: like operator mutations, lacP- mutations are ___ affecting only genes on the same DNAmolecule | cis
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| positive control and catabolite repression: E coli and many other bacteria metabolize _______ preferentially in the presence of lactose and other sugars | glucose
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| positive control and catabolite repression: Why do they prefer glucose? | it requires less energy to metabolize than other sugars
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| positive control and catabolite repression: when glucose is available, genes that participate in the metabolism of other sugars are ________. What is this phenomen known as? | repressed. known as catabolite repression
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| positive control and catabolite repression: what does catabolite repression result from? | positive control in response to glucase
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| positive control and catabolite repression: positive control is accomplished through the binding of a dimeric protein called the _________ _________ _______ to a site near the promoter of the lac genes | catabolite activator protein (CAP)
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| positive control and catabolite repression: before CAP can bind to the DNA what must it do? | form a complex with cAMP (adenosine-3', 5'-cyclic monophosphate)
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| positive control and catabolite repression: the CAP-cAMP complex binds DNA which increases what? | the efficiency of polymerase binding
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| positive control and catabolite repression: The binding of the CAP-cAMP comlex to DNA increases the efficiency of polymerase binding, what is the result? | high rates of transcription and translation of the structural genes and the production of glucose from lactose
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| positive control and catabolite repression: in E. coli, the concentration of cAMP is regulated so that its concentration is __________ proportional to the level of available glucose | inversely
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| positive control and catabolite repression: So what happens when glucose levels are low? | level of cAMP are high so it can form a complex with CAP and bind to DNA causing higher rates of transcription and translation
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| positive control and catabolite repression: what happens when glucose levels are high? | levels of cAMP are low making is less likely to bind to CAP causing a low transcription rate and very little translation
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| the lac operon is an inducible negative operon. Other operons are repressible; transcription in these operons is turned on and must be repressed. What is an example of a negative repressible operon found in E.coli? | tryptophan (trp) operon
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| trp operon: what does the trp operon control? | biosynthesis of the amino acid tryptophan
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| trp operon: the trp repressor is normally inactive, meaning what? | it cannot bind to the operator, which allows RNA polymerase to bind to the promotor and transcription to take place
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| trp operon: How does tryptohan repress transcription? | by binding to the inactive trp repressor, making it active and able to bind to the operator
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| trp operon: When the trp repressor binds to the operator, what does this cause? | it shuts off transcription since the RNA polymerase cannot bind to the promoter
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| trp operon: when cellular levels of tryptophan are ___, transcription of the trp operon takes place and more tryptophan is synthesized | low
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| trp operon: when cellular levels of tryptophan are ____, transcription of the trp operon is inhibited and the synthesis of more tryptophan does not occurr | high
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| concept check: in the trp operon, what happens to the trp repressor in the absence of tryptophan? | it cannot bind to the operator and transcription takes place
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| Gene regulation in ________ cells takes place at multiple levels | eukaryotic
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| eukaryotic and bacteria cells differ in several ways that affect gene regulation: (3) | in eukaryotes: absence of operons, presence of chromatin, and presence of nuclear membrane
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| gene regulation in eukaryotic cells: in the nucleus, histone proteins associate to form octamers, around which helical DNA tightly coils to create chromatin. This chromatin structure __________ gene expression | represses
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| gene regulation in eukaryotic cells: Why does chromatin structure repress gene expression? | RNA polymerase must bind to DNA. This is difficult when DNA is wrapped tightly around histone proteins
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| gene regulation in eukaryotic cells: regulatory proteins alter chromatin structure without altering the chemical structure of the histones directly. What are these proteins called? | chromatin-remodeling complexes
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| gene regulation in eukaryotic cells: how do chromatin-remodeling complexes alter the chromatin structure? | they bind directly to site on DNA and reposition nucelosomes
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| gene regulation in eukaryotic cells: What does this reposition of nucleosomes allow? | allows transcription factors to bind to promoters and initiate transcription
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| gene regulation in eukaryotic cells: histones in the octamer core of the nucleosomes have two domains: | globular domain (associates with other histons and the DNA) and positively charged tail domain (interacts with - charged phosphate groups on the backbone of DNA)
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| gene regulation in eukaryotic cells: how are the tails of histone proteins modified? | by the addition or removal of phosphate groups, methyl groups, or acetyl groups
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| gene regulation in eukaryotic cells: these modifications have sometimes been called the ______ _____, because they encode info that affects how genes are expressed | histone code
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| gene regulation in eukaryotic cells: another change in chromatin structure is associated with the ________ of cytosine in DNA | methylation
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| gene regulation in eukaryotic cells: heavily methylated DNA is associated with the ________ of transcription in vertebrates and plants | repression
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| gene regulation in eukaryotic cells: in summary, what three things can chromatin structure be altered by? | chromatin-remodeling complexes that reposition nucleosomes, modifications of histone proteins, and methylation of DNA
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| the intiation of eukaryotic transcription is controlled by _________ _________ ________ | general transcription factors
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| these general transcription factors assemble into the basal __________ _________ | transcriptional apparatus
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| the initiation of eukaryotic transcription is also controlled by __________ __________ proteins that stimulate normal levels of transcription | transcriptional activator proteins
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| these proteins bind to a regulatory _________, which is located upstream of the core promoter, and to _________, which may be located some distance from the gene | promoter, enhancers
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| some regulatory proteins in eukaryotic cells act as repressors. These repressors bind to sequences in the regulatory promoter or to distant sequences called _______, which, like enhancers, are position and orientation independent | silencers
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| unlike repressors in bacteria, eukaryotic repressors do not directly block ___ _________ | RNA polymerase
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| these repressors may compete with ________ for DNA binding sites | activators
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| explain how these repressors compete with activators | when a site is occupied by an activator, transcription is activated, but if a repressor occupies that site, there is no activiation
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| alternatively, a repressor may bind to a site NEAR an activator site and prevent the avtivator from what? | contacting the basal transcription apparatus
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| a third possible mechanism of repressor action is direct _____________ with the assembly of the basal transcription apparatus, thereby blocking the initiation of transcription | interference
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| summary, transcriptional regulatory proteins in eukaryotic cells can influence the initiation of transcription by affecting the _________or _________ of the basal transcription apparatus | stability or assembly
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| summary, some regulatory proteins are activators and ________ transcription while others are repressors and ______ the initiation of transcriptions | stimulate, inhibit
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| enhancers affect the transcription of ______ genes. Regulatory proteins bind to enhancers and do what? | distant. interact with the basal transcription apparatus by causing the intervening DNA to loop out
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| insulators limit the action of enhancers by doing what? | blocking their action in a position-dependent manner
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| explain how insulators may or may not block an enhancer | if the insulator lies between the enhancer and the promoter, it blocks the action of the enhancer. If it lies outside the region between the two, it has no effect.
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| concept check: how does the binding of regulatory proteins to enhancers affect transcription at genes that are thousands of base pairs apart? | DNA between enhancer and promoter loops out, so transcription activators bound to the enhancer are able to interact directly with the transcription apparatus
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| coordinated gene regulation: although most eukaryotic cells do not possess operons, several eukaryotic genes may be activated by the same _______ | stimulus
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| coordinated gene regulation: many eukaryotic cells respond to extreme hear and other stresses by producing ____-____ _________ that help to prevent damage from such stressing agents | heat-shock proteins
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| coordinated gene regulation: groups of bacterial genes are often coordinately expressed (turned on and off together) because they are physically _______ as an operon and have the same promoter. | clustered
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| coordinated gene regulation: eukaryotic cells are not clustered, so how is the transcription of of eukaryotic genes coordinately controlled? genes that are coordinately expressed are able to respond to the same stimulus because why? | they have short regulatory sequences in common in their promoters or enhancers
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| coordinated gene regulation: coordinately controlled genes in eukaryotic cells respond to the same factors because they have common _______ ________ that are stimulated by the same transcriptional activator | response elements
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| a regulatory protein binds to a response element and stimulates the transcription of a gene. The presence of the SAME response element in SEVERAL promoters or enhancers allows a single factor to _______________ stimulate the transcription of several genes | simultaneously
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| gene regulation: in bacteria, transcription and translation take place simultaneously. In eukaryotes, transcription takes place in the nucleus and the pre-mRNAs are then processed before moving to the cytoplasm for translation. This allows for what? | opportunities for gene control after transcription
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| a common level of gene regulation in eukaryotes is RNA _________ and __________ | processing and degradationg
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| RNA splicing: alternative splicing allows a pre-mRNA to be spliced in multiple ways, generating different _______ in different ______ or at different times in development | proteins, tissues
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| RNA degradation: the amount of a protein that is synthesized depends on the amount of corresponding ______ available for translation | mRNA
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| RNA degradation: the amount of available mRNA depends on both the rate of mRNA ___________ and the rate of mRNA _________ | synthesis, degradation
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| RNA degradation: various factors, including the 5' cap and the poly(A) tail, affect the stability of eukaryotic mRNA. |
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