Term
| gene expression is said to occur when _____ |
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Definition
| a protein or other gene product is synthesized and is active in the cell |
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Term
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Definition
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Term
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Definition
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Term
| protein -> activated protein |
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Definition
| post-translational modifications |
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Term
| three mechanisms of flow of info from DNA to protein |
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Definition
| transcriptional, translational, and post-translational control |
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Term
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Definition
| cell cold avoid making mRNAs for particular enzymes; DNA *->* mRNA -> protein -> activated protein; very efficient/saves most energy for cell/stops process at earliest possible point; slow |
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Term
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Definition
| prevents mRNA from being translated into protein; DNA -> mRNA *->* protein -> activated protein; allows cell to make rapid changes in its array of proteins |
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Term
| post-translational control |
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Definition
| proteins are manufactured in inactive form and have to be activated by chemical modification, such as phosphorylation; DNA -> mRNA -> protein *->* activated protein; provides most rapid response; energetically expensive |
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Term
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Definition
| some genes that are transcribed all the time, such as those that code for enzymes needed for glycolysis |
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Term
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Definition
| molecule that stimulates expression of a specific gene or genes; binds to bacterial regulatory protein and changes its shape so it cannot bind to an operator, thus switching an operon on |
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Term
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Definition
| produce a product at all times |
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Term
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Definition
| block of sterilized velvet used to transfer |
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Term
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Definition
| where mutants are observed directly |
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Term
| gene expression isn't just all the way on or off - allows cells to _____ |
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Definition
| respond to environment changes |
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Term
| transcription and translation of individual genes in bacteria are triggered by ______ |
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Definition
| specific signals from the environment, such as presence of specific sugars |
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Term
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Definition
| regulatory protein binds to DNA and shuts down transcription |
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Term
| positive control/induction |
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Definition
| regulatory protein binds to DNA and triggers transcription |
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Term
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Definition
| inhibitor that exerts negative control over genes; thought to bind directly to DNA near or on the promoter for that gene |
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Term
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Definition
| stretch of DNA consisting of an operator, a promoter, and genes for a related set of proteins, usually making up an entire metabolic pathway; genes of an operon arranged sequentially after the promoter; set of coordinately regulated bacterial genes that are transcribed together into one mRNA |
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Term
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Definition
| small molecule binds directly to a protein and causes it to change its shape and activity |
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Term
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Definition
| message that contains more than one protein-encoding segment; • usually code for products devoted to a common end – increase efficiency of gene expression; common in bacteria but rare in most eukaryotes |
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Term
| lacY and lacZ controlled by _____ |
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Definition
| both positive and negative control |
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Term
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Definition
| showed repressor physically binds to DNA sequences of operator; confirmed operator is not a protein or RNA product, but part of DNA sequence of lac operon |
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Term
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Definition
| a type of positive transcriptional control in which the end product of a catabolic pathway inhibits further transcription of the gene encoding an enzyme early in the pathway; form of end-product inhibition |
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Term
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Definition
| DNA sequence located just upstream of lac promoter |
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Term
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Definition
| regulatory molecule that binds to CAP |
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Term
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Definition
| enzyme that produces cAMP from ATP; is inhibited by extracellular glucose |
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Term
| catabolite activator protein (CAP) |
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Definition
| binds to DNA sequence (CAP binding site) and triggers transcription of lac operon; allosterically regulated (changes shape when cAMP binds to it; only when cAMP is attached to CAP can it bind to DNA; same type of allosteric regulation in negative control with repressor and lactose during negative control except repressor binds to DNA only in absence of inducer) |
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Term
| what is required for DNA-binding protein to control transcription |
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Definition
| (1) protein must bind to a specific DNA sequence associated with a specific gene or operon (2) protein’s structure must allow it to bind to DNA, interact with a regulatory molecule such as cAMP and lactose, and affect RNA polymerase |
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Term
| twofold rotational symmetry/dyad symmetry |
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Definition
| object can be superimposed on itself if rotated 180; many DNA-binding proteins have this |
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Term
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Definition
| regions with distinctive three-dimensional structure and function |
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Term
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Definition
| a domain observed in many different proteins |
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Term
| vast majority of bacteria able to switch among several different sources of carbon and energy |
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Definition
| each type of nutrient requires a different membrane transport protein to bring nutrient into cell and different suite of enzymes to process it |
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Term
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Definition
| specific nucleotide sequence in DNA that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place |
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Term
| regulatory gene (bacteria) |
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Definition
| codes for a protein, such as a repressor, that controls the transcription of another gene or group of genes |
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Term
| regulatory proteins bind to ____ |
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Definition
| operator to control expression of operon |
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Term
| repressor in prokaryotes binds ______ |
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Definition
| to DNA in or near promoter to inhibit gene transcription |
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Term
| The operon model of the regulation of gene expression in bacteria was proposed by ______ |
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Definition
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Term
| In the presence of a regulatory protein the lac operon is _____ |
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Definition
| not transcribed (the regulatory protein of the lac operon is a repressor) |
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Term
| example of genes you would predict to be constitutively expressed |
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Definition
| genes that that code for ribosomal RNAs |
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Term
| Full induction of the lac operon occurs when ______ |
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Definition
| lactose levels are high and glucose levels are low |
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Term
| An E. coli cell without a functional lacI gene is expected to _______ |
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Definition
| always produce beta-galactosidase |
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Term
| According to the lac operon model proposed by Jacob and Monod, what is predicted to occur if the operator is removed from the operon? |
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Definition
| The lac operon would be transcribed constitutively. |
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Term
| CAP is said to be responsible for positive regulation of the lac operon because ______ |
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Definition
| CAP bound to the CAP binding site increases the frequency of transcription initiation. |
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Term
| E. coli adenylyl cyclase is most active when _______ |
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Definition
| extracellular glucose levels are low |
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Term
| _______ allows more than one type of protein to be produced from one gene |
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Definition
| alternative forms of RNA splicing |
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Term
| RNA polymerase attaches to _____ |
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Definition
| decondensed DNA double helix |
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Term
| DNase ___________, which makes it useful for assessing whether chromatin is in a closed (tightly condensed) or open (loosely packed) configuration |
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Definition
| preferentially digests DNA not associated with protein |
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Term
| If the DNA sequences of a particular gene in a skin cell and a liver cell were compared there would be _______ |
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Definition
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Term
| E. coli prefers to use ______ and uses ______ only when ______ is unavailable |
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Definition
| glucose; lactose; glucose |
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Term
| lactose is made of ______ & ______ |
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Definition
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Term
| to use lactose, it is ______ |
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Definition
| taken inside cell, then enzyme β-galactosidase catalyzes reaction that breaks it into glucose and galactose |
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Term
| β-galactosidase only produced when ______ present |
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Definition
| lactose; thought lactose might regulate gene for β-galactosidase (example of inducer) |
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Term
| Monod discovered β-galactosidase wasn’t produced when ______ present, but when _____ present |
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Definition
| both lactose & glucose; only lactose |
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Term
| Monod & Jacob studied mutants that couldn't ______, meaning they were missing either ______ or _____ |
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Definition
| metabolize lactose; β-galactosidase; lactose-transporter protein |
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Term
| three types of mutants Monod & Jacob got |
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Definition
| (1) mutant cells unable to cleave indicator molecule even if lactose was present; must lack functioning β-galactosidase, meaning gene for it is defective (gene called lacZ and mutant allele called lacZ-) (2) cell failed to accumulate lactose inside cell; defective copies of membrane protein that brings lactose into cell (protein called galactoside permease; gene that encodes it is lacY) (3) indicator molecule is cleaved even if lactose is absent (no inducer); constitutive expression of lacZ and lacY; have defect in gene regulation (remains on when should be off) (gene called lacI) |
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Term
| when lactose absent, lacI ______ |
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Definition
| shuts down expression of lacZ and lacY |
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Term
| when lactose present, _______ |
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Definition
| transcription of lacZ and lacY induced |
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Term
| lac I, lacZ and lacY are all _____, which suggests lacZ and lacY might be controlled by lacI |
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Definition
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Term
| lacZ and lacY code for _______ and lacI has a ______ function |
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Definition
| proteins involved in metabolism and import of lactose; regulatory |
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Term
| transcription of lac operon greatly _______ when glucose is present, even if _______ |
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Definition
| reduced; there is lactose |
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Term
| can have strong and weak promoters; lac promoter is ______ |
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Definition
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Term
| lacI codes for a product that __________ |
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Definition
| represses transcription of lacZ and lacY |
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Term
| regulation fails in a lacI- mutant when ________ |
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Definition
| the lacI+ protein, which normally prevents protein synthesis, is inactive |
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Term
| lactose makes the repressor _______; lactose induces transcription by _______ |
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Definition
| release from its binding site; removing negative control |
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Term
| genes for β-galactosidase and galactoside permease are controlled ________ |
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Definition
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Term
| lacA codes for enzyme transacetylase, which is ________ in nature - it catalyzes reactions that _________ |
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Definition
| protective; allow certain types of sugars to be exported when there are too many of them |
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Term
| lacZ, lacY and lacA genes adjacent and transcribed into one mRNA initiated from single promoter of lac operon. expression of three genes is therefore _________ |
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Definition
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Term
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Definition
| protein encoded by lacI that binds to DNA and prevents transcription of lacZ, lacY and lacA; binds to operator; lacI expressed constitutively |
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Term
| inducer (_______) interacts directly with repressor by ______. causes repressor to ________ (allosteric regulation). negative control ends and transcription can proceed |
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Definition
| lactose; binding to it; change shape and drop off DNA strand |
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Term
| lac operon model introduced idea that ________ |
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Definition
| gene expression is regulated by physical contact between specific regions in regulatory proteins and specific regulatory sites in DNA |
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Term
| trp operon produces a ______, like lac operon |
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Definition
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Term
| trp operon under _______ control, but codes for enzymes that perform _________, but __________ |
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Definition
| negative; anabolism; catabolism; should favor cells where gene expression starts when molecule is absent and needed by the cell, and where transcription is reduced when molecule is present |
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Term
| tryptophan binds to repressor to regulate transcription, just as _______ binds to lac operon’s repressor to regulate transcription |
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Definition
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Term
| trp repressor binds operator DNA and exerts negative control only when ________; when tryptophan is ______, repressor doesn’t bind to operator and operon is expressed constitutively - exact opposite of how lactose affects lac repressor |
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Definition
| it is complexed with tryptophan; absent |
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Term
| in both lac and trp operons, operator sequence overlaps promoter and repressor protein that binds to operator to ______ transcription |
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Definition
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Term
| activity of key regulatory proteins controlled by _________ |
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Definition
| post-translational modifications |
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Term
| why glucose inhibits transcription when lactose is there too |
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Definition
| glucose is produced when β-galactosidase cleaves lactose; when glucose already present, not necessary to cleave lactose and produce more glucose |
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Term
| hydrolysis of lactose into glucose and galactose is an example of _______ |
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Definition
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Term
| operons that encode catabolic enzymes are inhibited when end product (catabolite) is ______ |
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Definition
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Term
| in lac operon, catabolite is ________; when it is abundant, transcription is decreased by catabolite repression |
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Definition
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Term
| when CAP regulatory protein is bound to CAP site, ________ |
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Definition
| protein interacts with RNA polymerase to allow transcription to begin more frequently |
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Term
| CAP binding ______ the lac promoter, exerting positive control of lac operon |
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Definition
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Term
| when CAP is active, transcription _______ |
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Definition
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Term
| during positive control, the CAP-cAMP complex binds to ______ |
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Definition
| CAP binding site; as long as a repressor isn’t bound to operator, complex increases efficiency of transcription |
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Term
| if no cAMP bound to CAP, _______ |
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Definition
| CAP doesn’t allow binding at CAP |
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Term
| cAMP is ______ light that tells CAP to ______ |
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Definition
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Term
| glucose levels outside cell and cAMP levels inside cell are _______ related; when extracellular glucose _____, intracellular cAMP ____; relationship driven by _________; when low levels of cAMP, can't bind to CAP site and stimulate transcription of lac operon |
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Definition
| inversely; high; low; adenylyl cyclase |
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Term
| as long as _________, transcription of lac operon initiated frequently & lactose can be employed as an alternative energy source |
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Definition
| repressor not bound to operator |
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Term
| E. coli fully activates genes for lactose metabolism only when _________ |
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Definition
| lactose is available and glucose scarce or absent |
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Term
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Definition
| consists of two α-helices connected by a short stretch of amino acids that form a turn; many bacteria have this; section of the repressor that binds to DNA; DNA doesn’t have to be single stranded for helix-turn-helix domain of repressor to bind to operator |
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Term
| why a protein with helix-turn-helix motif can bind to DNA |
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Definition
| b/c one of the helices interacts with sugar-phosphate backbone of DNA strand while other helix binds to base pairs in major groove |
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Term
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Definition
| section of helix-turn-helix motif that binds inside major groove; each type of regulatory protein with a helix-turn-helix motif has a unique sequence of amino acids in its recognition sequence - as a result, each of the regulatory proteins binds to a unique regulatory sequence in DNA |
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Term
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Definition
| lac operon contains three sites where repressor protein can bind: O1, O2, and O3; when repressor protein bound to DNA, protein simultaneously binds to O1 and either O2 or O3; all three operators have a similar DNA sequence with dyad symmetry |
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Term
| negative control is based on repressor proteins, such as lacI product |
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Definition
| repressor proteins, such as lacI product |
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Term
| positive control is based on ______ |
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Definition
| transcription activator proteins, such as CAP |
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