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Topic 8: Regulation - Fall 2013

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BIOL 240
Josh Neufeld

BIOL 240 Fall 2013 Topic 8: Regulation Review of the Basics 1. Replication begins at the origin of replication and is a semi-conservative process • 2. Transcription sigma factors bound to RNA polymerase core enzyme direct it to a promoter • • different sigma factors can direct core RNA polymerase enzyme to different genes as needed • transcription proceeds 3. Translation rho- dependent - rho protein follows RNA polymerase and removes it from the DNA when it reaches a termination sequence rho-independent - RNA hairpin loop forms, causing RNA polymerase to dissociate from the DNA • the small ribosome subunit and the Shine-Dalgarno sequence help align all the machinery to the correct starting location • multiple shine-Dalgarno sequences allow bacteria mRNA to be polycistronic (multiple translations can occur simultaneously on the same strand) 4. DNA repair • systems must have the ability to deal with damage ____________________________________________________________________________________ Differential Gene Expression - How are gene expression and enzyme activity controlled? • constitutive expression: genes encoding a certain molecule are always on inducible expression: expression of genes encoding a certain molecule is turned on or off as needed • • allosteric inhibition: substrate becomes unable to bind to the active site • covalent modification: regulation of enzyme activity; ex. phosphorylation or methylation Phosphorylation: PO 4 Methylation: CH 3 Acetylation: CH 3O Glycosylation: carbohydrate groups ____________________________________________________________________________________ The Operon - How do Feature Definition regulatory proteins control transcription? Promoter directs initiation of transcription - bound by RNA polymerase Operon: a transcriptional Activator protein that assists with the binding of the RNA polymerase to the promoter - unit consisting of: increased transcription initation a. a series of structural genes that code for Activator binding site on DNA bound by the activator polypeptides site b. regulatory elements Repressor binds to operator site on DNA, inhibits transcription that affect their transcription Operator site on DNA bound by the repressor • operons are common in Effector small molecule - binds to activator or repressor proteins - modifies their gene bacteria, where mRNA regulation activity can be polycistronic and Inducer effector - increases transcription by enabling an activator or disabling a not generally present in repressor eukarya Corepressor effector - decreases transcription by enabling repressor i Regulating Transcription Negative Control Positive Control allosteric protein acts to prevent mRNA synthesis - blocks allosteric protein acts to activate mRNA synthesis - increased transcription transcription Repression: inhibit transcription in response to a signal •• alosterrc eguuatorrprotenssacctvate binding ofRNNA pooymmerasse • affects anabolic (biosynthetic) enzymes o DNNAA •• E..collimaaloseeacctvatorrproein only binds DNAA in heh Induction: depression of enzyme production in response presencce ofmaalosse to a signal • affects catabolic enzymes no wasted energy • • enzymes synthesized only when substrates available The lac operon - Escherichia coli • is not expressed until all glucose is consumed • consists: • three structural genes: • lacZ - product: ß-galactosidase - facilitates lactose’s enzymatic breakdown (to glucose and galactose) • lacY - product: permease - facilitates the uptake of lactose by the cell lacA - encodes ß-galactoside transacetylase - role remains unclear • • operator: a DNA sequence to which regulatory proteins can bind • diauxic growth curve - when glucose becomes depleted, ß-galactosidase and permease must be produced before the cells can begin to use lactose - results in a lag in growth • Negative control: • repressor protein (Lacl) - binds to operator, blocks RNA polymerase and inhibits transcription effector molecule (allolactose) - inhibits binding of repressor to the operator - induces transcription • • can also inhibit transcription by binding to the repressor protein and enhancing its ability to bind to the operator • Positive control: • activator protein (cyclic AMP receptor - CRP) - binds and increases transcription rates when cAMP present (low glucose) • cAMP - induces conformational change in activator protein - increases affinity for binding site - increasing RNA polymerase affinity for the Lac operon promoter Table 11.8 Glucose Lactose cAMP Operon Status Level of lacZ, lacY, Lactose Concentration Concentration concentration and lacA Metabolized? low high high CRP and cAMP bind to activation site high yes allolactose inhibits binding of Lacl to operator low low high CRP and cAMP bind to activation site low no Lacl repressor binds to operator high low low Lacl repressor binds to operator low no high high low nothing is bound to the operon low no The trp Operon - Escherichia Coli • structural genes: trpE, trpD, trpC, trpB, trpA • model for attenuation - operons that use attenuation are often amino acid biosynthetic operons ii BIOL 240 Fall 2013 • attenuation: interruption of transcription after initiation but before termination - does not influence rate of transcription initiation • control of transcription by mRNA secondary structure • attenuation of the tryptophan biosynthetic operon involves a translated leader sequence immediately following the operator. The leader sequence contains two tandem tryptophan codons: • high levels of tryptophan: • incorporated into the leader peptide chain from the corresponding aminoacyl-tRNA • terminator loop forms and stops transcription of structural genes - tryptophan not made • low levels of tryptophan: • tryptophan aminoacyl-tRNA is rare - leader peptide will not be completely synthesized • terminator loop does not form - transcription of structural genes continuous - tryptophan is made • if leader is fully translated (leader encoded by trpL), then transcription of the downstream genes in the operon will be terminated • in prokaryotes, transcription and translation are coupled - so the 5’ end of a transcript can be translated before synthesis of that transcript is complete • the tryptophan operon transcript is subject to strong intramolecular base-pairing • if the translation of the leader peptide does occur, then the translating ribosome is able to continue along the transcript - blocks formation of the antitermination stem-loop structure • the termination stem-loop structure can then form - this causes the transcript to be released by the RNA polymerase • if the translation of the leader peptide does not occur (because of tryptophan starvation) - ribosome pauses, and blocks the formation of the termination stem-loop structure - transcription can then continue • the tryptophan operon is also subject to regulation by repression at the promoter - the attenuator control acts to fine-tune the level of expression given by repression control _____
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