AP Bio

Chapt e r 18 Notes : Regulation of Gene Expres sio n

Part 1 Prokaryotes I. Bacterial Genomes Genophore - bacterial double stranded DNA found in a single circular chromosome, much smaller than eukaryotic DNA, found in small nucleoid region, less elaborately structured and folded than eukaryotic DNA, associated with only a few protein molecules, DNA-protein fiber forms loops that are anchored to the plasma membrane Plasmid - a small double-stranded ring of DNA that carries extra- chromosomal genes in some bacteria Binary fission - replication of bacterial chromosome from a single point in both directions! and an e"ual di#ision of the cell contents producing two daughter cells that are genetically identical II. Genetic Recombination and Gene Transfer in Bacteria A$ %ransformation - process of gene transfer during which a bacterial cell assimilates genetic material naked, foreign DNA! from the surroundings B$ %ransduction - gene transfer from one bacterium to another by a bacteriophage General %ransduction - transduction that occurs when random pieces of host cell DNA are packaged within a phage capsid during the lytic cycle of a phage &peciali'ed transduction restricted transduction! - transduction that occurs when a prophage excises from the bacterial chromosome and carries with it some host genes ad(acent to the excision site also called restricted transduction! )$ )on(ugation - the direct transfer of genes between two cells that are temporarily (oined D$ Plasmids* General )haracteristics Plasmid - a small double-stranded ring of DNA that carries extra- chromosomal genes in some bacteria +eplication of Plasmids a$ replicate in synchrony with bacterial chromosome b$ replicate on own schedule ,pisomes - genetic elements that can replicate either independently as free molecules in the cytoplasm or as integrated parts of the main bacterial chromosome Differences between Plasmids and -iruses a$ plasmids lack an extracellular stage, #iruses ha#e an extracellular stage b$ plasmids are generally beneficial to cell, #iruses are parasites that usually harm their host III. The Control of Gene Expression in Prokaryotes Genes switch on and off as conditions in the intracellular en#ironment change$ .eedback inhibition - egulation of en'yme acti#ity/ end product of anabolic pathway may turn off it0s own production by inhibiting the acti#ity of en'yme at the beginning of the pathway/ useful for immediate, shortterm responses +egulation A$ perons* %he Basic )oncept +egulated genes can be switched on or off depending on the cell0s metabolic needs$ &tructural genes - genes that code for polypeptides with related functions 1peron - a regulated cluster of ad(acent structural genes and the operator and the promotor Polycistronic m+NA - a large m+NA molecule that is a transcript of se#eral genes, translated into separate polypeptides and contains the codons for start and stop of each polypeptide
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 Grouping genes into operons is ad#antageous because the expression of these genes can be coordinated and the entire operon can be controlled by a single operator$ 1perator - a DNA segment part of an operon0s promoter or between an operon0s promoter and structural genes which controls access of +NA polymerase to the structural genes by itself, operator is in the 2on3 mode and is switched 2off3 by the repressor +epressor - specific protein that binds to an operator and blocks transcription of the operon similar to an en'yme* 4$ has an acti#e site with a specific conformation, which discriminates among operators$ 5$ binds re#ersibly to DNA 6$ may ha#e an allosteric site in addition to its DNA-binding site +egulatory genes - located some distance upstream from the operon they control, genes that code for repressors or regulators of other genes +egulatory genes process in switching on or off of the transcription of structural genes* transcription of the regulatory gene produces m+NA translated into regulatory protein repressor) binds to operator represses or acti#ates transcription of operon0s structural genes +egulatory genes repressor! are continually transcribed, so their acti#ity depends upon how efficient their promoters are in binding +NA polymerase/ alternate between acti#e and inacti#e forms +epressor0s acti#ity depends upon the presence of key metabolites in the cell$ B$ +epressible -ersus 7nducible ,n'ymes* %wo %ypes of Negati#e Gene +egulation +epressible en'ymes - en'ymes which ha#e their synthesis inhibited by a metabolite 7nducible en'ymes - en'ymes which ha#e their synthesis stimulated or induced by specific metabolites Re!"lation of trp operon in E. coli 4$ +epressible en'ymes cataly'e the anabolic pathway that produces tryptophan$ 5$ %ryptophan accumulation represses synthesis of the en'ymes that cataly'e its production$ absent present 8888888-88888%ryptophan88888888888888 repressor protein is in repressor protein is in inacti#e conformation acti#e conformation trp operon is turned on binds to operator trp operon is switched off how tryptophan acti#ates the repressor protein 4$ repressor protein, which usually has a low affinity for the operator, has a DNA binding site plus an allosteric site specific for tryptophan
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5$ when tryptophan binds to the repressor0s allosteric site, it acti#ates the repressor causing it to change its conformation 6$ the acti#ated repressor binds to the operator, which switches the trp operon off 9$ tryptophan functions in this regulatory system as a corepressor )orepressor - a molecule, usually a metabolite, that binds to a repressor protein in its inacti#e conformation and causes the repressor protein to change into its acti#e conformation 4$ 1nly the repressor-corepressor complex can attach to the operator and turn off the operon$ 5$ :hen tryptophan concentrations drop, it is less likely to be bound to repressor protein$ %he trp operon, once free from repression, begins transcription$ 6$ As concentrations of tryptophan rise, it turns off its own production by acti#ating the repressor$ 9$ ,n'ymes of the tryptophan pathway are said to be repressible$ Ind"ction of lac operon in E. coli ,$ coli can metaboli'e the disaccharide lactose$ 1nce lactose is transported into the cell, ;galactosidase splits lactose into glucose and galactose$ :hen lactose is absent from the medium, E. coli contain only a few ;-galactosidase molecules$ :hen lactose is present in the medium, E. coli increase the number of m+NA molecules coding for ;-galactosidase$ <actose metabolism in ,$ coli is programmed by the lac operon which has three structural genes* 4$ lac Z - codes for ;-galactosidase which hydroly'es lactose 5$ lac Y - codes for a permease, a membrane protein that transports lactose into the cell 6$ lac A - codes for transacetylase, an en'yme that has no known role in lactose metabolism %he lac operon has a single promoter and operator$ %he lac repressor is innately acti#e, so it attaches to the operon without a corepressor$ Allolactose, an isomer of lactose, acts as an inducer to turn on the lac operon* allolactose binds to repressor inacti#ated repressor loses affinity for lac operon operon is transcribed en'ymes for lactose metabolism are produced +epressible and inducible operons share similar features of gene regulation* specific repressor proteins control gene expression repressors can assume an acti#e conformation that blocks transcription and an inacti#e conformation that allows transcription which form the repressor assumes depends upon cues from a metabolite both systems are examples of negati#e control Difference between repressible and inducible operons reflect differences in the pathways they control* Repressible En#ymes Ind"cible En#ymes
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%heir genes are switched on until a specific %heir genes are switched off until a specific metabolite acti#ates the repressor$ metabolite inacti#ates the repressor$ Generally function in anabolic pathways$ .unction in catabolic pathways$ Pathway end product switches off its own ,n'yme synthesis is switched on by production by repressing en'yme synthesis$ the nutrient the pathway uses$ Negati#e control of a regulatory system negati#e regulator! - binding of acti#e repressor to an operator always turns off structural gene expression Positi#e control of a regulatory system positi#e regulator! - occurs only if an acti#ator molecule interacts directly with the genome to turn on transcription )$ )AP* An ,xample of Positi#e Gene +egulation %he lac operon is under dual regulation which includes negati#e control by repressor protein and positi#e control by catabolite acti#ator protein$ )AP catabolic acti#ator protein! - a protein that binds within an operon0s promoter region and enhances the promoter0s affinity for +NA polymerase/ it is a positi#e regulator )onstituti#e genes - unregulated genes that are continually transcribed, genes that produce proteins that are A<:A=& needed eg. en'ymes for glycolysis how )AP is affected by the absence or presence of glucose glucose missing, cell accumulates cyclic A>P cA>P! cA>P acti#ates )AP so that is binds to the lac promoter, increases the rate of transcription if repressor free glucose concentration rises, glucose catabolism decreases the intracellular concentration of cA>P low high 888888888888Glucose concentration8888888888888 cA>P concentration rises cA>P becomes scarce cA>P binds to )AP )AP loses its cA>P cA>P-)AP complex binds to lac promoter )AP disengages from the lac promoter efficient transcription of lac operon slowed transcription of lac operon 7n this dual regulation of the lac operon negati#e control by the repressor determines whether or not the operon will transcribe the structural genes and the positi#e control by )AP determines the rate of transcription$ E. coli economi'e on +NA and protein synthesis with the help of these negati#e and positi#e controls$ :hen glucose is absent, the cell metaboli'es alternate energy sources$

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Part $ % E"karyotes )ellular differentiation - di#ergence in structure and function of different cell types as they become speciali'ed during an organism0s de#elopment$ ,ukaryotes ha#e greater genome si'e and greater cell speciali'ation than prokaryotes$ I. Chromatin &tr"ct"re complexed with a large amount of protein to form chromatin highly extended and tangled during interphase/ during mitosis, condensed into short, thick, discrete chromosomes ?istones - small proteins rich in basic amino acids positi#ely charged! that bind to DNA negati#ely charged! forming chromatin, histone amount is approximately e"ual to the amount of DNA A$ <e#els of DNA packing 4$ Nucleosomes, or 2Beads on a &tring3 - basic unit of DNA packing/ formed from DNA wound around a protein core that consists of two copies each of four types of histone/ fifth histone ? 4! may be present on DNA next to nucleosome 5$ 6@-nm )hromatin .iber* tightly wound coil with six nucleosomes per turn, cylinder 6$ <ooped Domains* chromatin fiber forms loops each containing 5@,@@@ to 4@@,@@@ base pairs 9$ >etaphase )hromosome* looped domains coil and fold B$ 7nterphase )hromatin* usually less condensed than mitotic chromatin with higher-order packing ?eterochromatin - chromatin that remains highly condensed during interphase and is not acti#ely transcribed eg. Barr bodies ,uchromatin - chromatin that is less condensed during interphase and is acti#ely transcribed, becomes highly condensed during mitosis and meiosis! II. Genome r!ani#ation at the '() *e+el Prokaryotic DNA codes mostly for proteins andAor +NA but most eukaryotic DNA does not code for protein andAor +NA$ A$ +epetiti#e &e"uences &%+! in eukaryotes, 4@-5BC of total DNA consists of short se"uences that are tandemly repeated thousands of times called satellite DNA/ most is located at the tips telomeres! and the centromere B$ >ultigene .amilies )$ 1rgani'ation of a %ypical ,ukaryotic Gene* A +e#iew 4$ eukaryotic genes contain introns and a promoter se"uence B0 upstream end! 5$ control elements a$ transcription factors b$ enhancer - DNA control se"uence that influences a gene0s transcription and is located thousands of bases away from the gene0s promoter/ acti#ators or repressors bind to enhancers 5$ hn+NA is processed into mature m+NA by the remo#al of introns, the addition of modified G%P at B0 end, and the addition of poly-A tail at 60 end D$ Arrangement of coordinately controlled genes - eukaryotic genes coding for en'ymes of a metabolic pathway are often scattered o#er different chromosomes, but are often coordinately expressed$ &ignal transduction pathways can lead to the acti#ation of transcription acti#ators or repressors promoting the simultaneous transcription, or not, of genes$ III. Genome Plasticity 8 regulation of chromatin structure* conditions that may make a genome in one cell type more a#ailable than in another cell type and may affect the accessibility of specific genes for expression/ mo#ement of DNA within the genome and chemical modification of DNA may influence gene expression$ A$ Gene Amplification and &electi#e Gene <oss
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 Gene amplification - temporary, selecti#e synthesis of DNA resulting in multiple copies of a single gene )hromosome diminution - elimination of whole chromosomes or parts of chromosomes from certain cells early in embryonic de#elopment B$ )hemical modifications 4$ ?istone acetylation - loosens chromatin and makes it more a#ailable for transcription 5$ DNA methylation - addition of methyl groups -)?6! to bases of DNA after DNA synthesis a$ hea#ily methylated genes are usually not expressed b$ drugs that inhibit methylation can induce gene reacti#ation c$ may affect gene expression by causing structural changes in DNA double helix 6$ epigenetic inheritance )$ +earrangements in the Genome 4$ %ransposons - stretches of DNA prone to mo#ing from one location to another within the genome 5$ 7mmunoglobulins - a class of proteins antibodies! produced by ; lymphocytes that specifically recogni'e and help combat #iruses, bacteria, etc$ consists of four polypeptides chains held together by disulfide bridges each chain has a constant region and a #ariable region 7-$ %he )ontrol of Gene ,xpression )hromatin Pre-transcriptional )ontrol DNA packingAunpacking DNA methylationAhistone acetylation Gene rearrangement Gene amplification and loss Gene a#ailable for expression %ranscriptional )ontrol %ranscription* promotor, enhancer, factors 7nitial +NA transcript Post-transcriptional )ontrol +NA processing* cap, tail, intronsAexons m+NA in nucleus, ready for export %ransport 8 export to cytoplasm m+NA in cytoplasm Degradation life span! >askingAunmasking storage! >odification %ranslational )ontrol %ranslation* initiation factors Polypeptide product Post-translational )ontrol Protein processing* clea#age, modification, acti#ation .unctional protein Degradation - proteasomes %ransport Protein in use

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AP Biology Part , (oncodin! R() -$ %he +ole of &mall >olecules in +egulating ,ukaryotic Gene ,xpression A$ )hromosome Puffs* ,#idence for the +egulatory +ole of &teroid ?ormones in 7nsects B$ %he Action of &teroid ?ormones in -ertebrates -7$ Gene ,xpression and )ancer )arcinogens - physical agents that cause cancer by mutating DNA 1ncogene - gene responsible for becoming cancer Proto-oncogene - normal cellular genes which code for proteins which control growth, cell di#ision, cell adhesion change in proto-oncogene to oncogene* gene amplification, transposition, translocation, and point mutation

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