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Bio 240 Chapter 17 Notes!

by: Izabella Nill Gomez

Bio 240 Chapter 17 Notes! Bio 240

Izabella Nill Gomez
GPA 3.81
General Genetics (Bio 240)
Dr. Hughes

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Hey guys! With the end of the semester approaching, I've begun to gather everything in preparation for our concepts exam! However, this set of notes is just chapter 17! Very extensive, it has infor...
General Genetics (Bio 240)
Dr. Hughes
Class Notes
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This 0 page Class Notes was uploaded by Izabella Nill Gomez on Thursday November 26, 2015. The Class Notes belongs to Bio 240 at University of Tennessee - Knoxville taught by Dr. Hughes in Summer 2015. Since its upload, it has received 25 views. For similar materials see General Genetics (Bio 240) in Biology at University of Tennessee - Knoxville.


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Date Created: 11/26/15
Biology 240 Chapter 17 Notes Regulation of eukaryotic gene expression can occur at many different levels alteration of DNA template initiation of transcription mRNA modi cations and stability synthesis modi cation and stability of protein product Difference between eukarya and prokarya More DNA also associated with histones These modify structure to in uence gene expression mRNA needs to be spliced capped and polyadenylated before transportation out of the nucleus Genes are located on many chromosomes within double membrane walls mRNAs live variable lives Translation is mediated proton are modi ed RNAP ll transcribes genes that encode all mRNAs and some snRNAs RNA pol l and Ill transcribe genes for rRNA tRNA Genes by these are regulated differently than those that are transcribed by RNAP II In the interphase nucleus each chromosome occupies chromosome territory and stays separate from other chromosomes Channels between contain little to no DNA and are called interchromosomal domains Transcriptionally active genes are located at the edges of chromosomes close 0 interchromosomal domains brings genes close to transcription factors or other active genes Transcription factory also contributes to regulation Tfactories are nuclear sites that contain most of the active RNA pol and transcription regulatory molecules These are dynamic structures that assembledisassemble rapidly quotClosedquot chromatin does not allow access for transcription Must open transcriptionally activeinactive genes are both associated with nucleosomes but the nucleosomes associated with active genes are altered in formation Nucleosomes can be modi ed by variant histones affects mobility and positioning Depending on the position genes can be activated or repressed Histone modi cation involves Nterminal tails of histone proteins with addition of acetyl methyl or phosphate groups to tails Histone acetylation which opens chromatin is catalyzed by histone acetyltransferase enzymes HATs Can be recruited to genes by the presence of certain transcription activators that bind to transcriptional regulatory regions Sometimes activators are the HATs Histone deacetylases HDACs remove acetate groups from the histone tails recruited by repressor proteins Chromatin remodeling involves repositioning or removal of nucleosomes on DNA from chromatin remodeling complexes large multisubunit complexes that use ATP to move and rearrange nucleosomes on DNASWSNF Can loosen attachment between histones and DNA resulting in nucleosome sliding along DNA and exposing regulatory regions Alternatively it may loosen a DNA strand from nucleosome core or reorganization of internal nucleosome components The DNA that is left exposed to association with transcription factors and RNA pol can be recruited by activator proteins DNA regulation occurs and position 5 of cytosine in the cytosine CG doublets in DNA on both strands CpG sequences in rich regions CpG islands are located on 539 ends of genes in promoter regions 5 is usually methylated Inert regions of the genome are heavily methylated also tissue speci c and once established heritable for all cells of that tissue Critical for normal mammalian development 539alacytidine base analog can be incorporated into DNA instead of cytosine for DNA replication Cannot be methylated and stimulates gene expression Methylated DNA can inhibit transcription factors and recruit repressive chromatin remodeling complexes and HDACs to regulatory regions The Cisacting sequence is located on the same chromosome as the gene it regulates transacting factors DNA binding proteins of small RNA molecules that can in uence gene expression on any chromosome Promoter region of DNA that recognizes transcription machinery and binds 1 or more proteins that regulate transcription initiation Adjacent to the genes they regulate Promoter elements short nucleotide sequences bind speci c regulatory factors The core promoter determines the accurate initiation of transcription by RNAP ll Proximal promoter elements modulate the ef ciency of basal levels of transcription Focused promoters specify transcription initiation at a single speci c nucleotide transcription start site Dispersed promoters direct initiation from a number of weak transcription start sites over 50100 nucleotide region Focused is the major type of initiation for lower eukaryotes but only for 30 of vertebrate genes Focused promoters are associated with highly regulated genes Constitutive genes use dispersed promoters Dispersed promoters are usually found within CpG islands suggesting chromatin modi cations may in uence initiation Focused promoters are made up of one or more DNA sequence elements Initiator TATA TFIIB downstream promoter element DPE motif ten element MTE DPRE and MTE are found only in some promoters lnr element encompasses the transcription start site 2 and 4 TATA box is located 30 relative to transcription start BRE is found in core promoters at positions immediately up and downstream of TATA MTE and DPE are motifs located downstream of start 18 to 27 and 28 to 33 Proximal promoter elements like CAAT box have consensus sequences CAATCCAAT usually located 7080 base pairs upstream from start CAAT boxes when present are critical to a promoter39s ability to initiate transcription mutation lowers the transcription rate GC box is also found in promoter regions GGGCGG at the 110 position Enhancers are DNA sequences that can be located on either side of gene at some distance of the gene or even within the gene cis regulators These are necessary to achieve the maximum level of transcription Responsible also for time and tissue speci c gene expression The position of the enhancer need not be xed relative to the gene it regulates Orientation can be inverted without signi cant effect If the enhancer is cloned next to a cloned gene that it does not normally regulate transcription is enhanced Silencer acts to regulate by repressing transcription initiation levels Cisacting DNA sequences act in tissuetemporalspeci c ways Transcription factors can increase levels of transcription activators initiation or reduce repressors Can interact with each other in a gene regulatory region to nely tune transcription levels Targets cis acting sites of genes hMTllA is an example of how transcription of one gene can be regulated by multiple promoter and enhancer elements and the transcription factors that bind to them The product of hMTllA protects the cell from high levels of heavy metals Cis acting elements controlling include promoter enhancer and silencer elements Has TATA and lnr which specify start ProximalPromoter element GC binds to the SP1 factor present always and stimulates transcription at low levels BLE and ARE are enhancer elements Bind activators AP1 2 and 4 present at various levels in different cell types High levels of transcription are stimulated by enhancer MRE GRE MTF1 a transcription factor binds to MRE in the presence of heavy metals The presence of excess heavy metals displaces zinc from metallothionein proteins present at low levels in all cells Free zinc ions bind to zinc nger motifs within DNA binding domains of MTFI transcription factors altering the conformation After binding MTFI moves from the cytoplasm to the nucleus and binds to MREs upstream of the gene activating metallothionein gene transcription The glucocorticoid receptor protein binds to GRE but only when the receptor is in a complex with the hormone The receptor is normally in the cytoplasm but when the hormone is in the cytoplasm it binds to the receptor and causes it to allow entry into the nucleus bind to GRE and stimulate hMTllA transcription Can be repressed by PZl20 DNA binding domain transcription factor transcription initiation activationrepression is achieved through the presence of this binds to speci c DNA sequences present in cis acting regulatory site Transactivatingrepression domain activatesrepresses transcription Ex helixturnhelix HTH motif present in prokaryotes and eukaryotes TFs are characterized by certain geometric conformation rather than a distinctive amino acid sequence The presence of 2 alpha helices separated by a quotturnquot of amino acids enable the protein to bind to DNA Zinc nger motifs found in a wider range of TFs that regulate gene expression The typical zinc nger has clusters of 2 cystines and 2 histidines These bind zinc atoms fold into loops and interact with speci c DNA sequences The Basic leucine zipper bZlB motif contains a region of the leucine zipper that binds to phosphate residues and speci c bases in DNA binding site results TFs also have transactivatingrepressing 30900 amino acids domains different from DNA binding domains These vary General transcription factors proteins needed at a promoter in order to initiate basal level or enhanced levels of transcription These form in an order for the pre initiation complex PIC that provides the platform for RNAPII to recognize transcription start sites and initiate General TFs are called TFIID TFIIBTFIIATFIIETFIIH and the Mediator TFIID binds to TATA of the core promoter TFIID contains TBP TATA binding protein and TAFs TBP associated Subsets bind to lnr elements and DREsMTEs TFIIA helps TFIID by binding TFIID to core promoter TFIIB then binds to BREs on one or both sides of the TATA Other general TFs then interact with RNAPII to recruit to the promoter The full form of PIC mediates unwinding of promoter DNA and the transition of RNAPII from initiation to elongation In higher eukaryotes RNAPII immediately leaves the promoter region and proceeds down DNA template in an elongation complex Formation of loops for transcription activatorssuppressors are supported by formaldehyde and direct visualization assays The recruitment model suggests DNA looping delivers activators repressors and general transcription factors to the vicinity of promotors Enhancer and silencer elements act as donors that increase concentrations of important regulatory proteins and gene promoters By enhancing the rate of PIC assemblystability or accelerate the release of RNAP II from the promoter transcription activators stimulate initiation Activators interact with coactivators that form an enhanceosome complex May directly contact PIC through mediator and TFIID Same way repressors can decrease the rate of transcription initiation In the second model DNA looping results in chromatin alterations that stimulate or repress transcription of target genes Once chromatin remodelinx complexes are delivered to the vicinity of the promoter may openclose the promoter to general TF interactions or RNAPII or inhibit the release of RNAPII The third model is a nuclear relocation model where enhancerrepressor looping may relocate the target gene to a nuclear region favorableinhibitory to transcription The GAL gene system is comprised of 4 structural genes GAL 11027 and 3 regulatory genes GAL 14 80 3 The products of structural genes transport galactose into the cell and metabolize sugar Products of regulation positivelynegatively control transcription of structural genes Transcription of GAL structural genes is inducible regulated by the presence or absence of galactose In the absence it is not transcribed The gene system exerts positive control activator protein turns on transcription UASg upstream activating sequence of GAL genes controls transcription of 2 genes GAL 1 and GAL 10simiar to enhancers The chromatin structure of UASg is constitutively open DNAse is hypersensitiveloosey associated with nucleosomes There are 4 binding sites for the GAL 4 protein Gal4pencoded by the GAL 4 gene These are permanently occupied by Gal4p whether or not GAL 4 and 10 are transcribed Ga4p is negatively regulated by Gal80p In the absence of galactose Gal80p is always bound to Gal4p Transcription activation occurs when galactose interacts with Gal3p When bound Gal3p changes its conformation to interact with Gal4p80p complex exposes Gal4p activation domain Gal4p is a transactivating domain The coactivator SAGA interacts with Gal4p the Mediator with Gal4p and enters the complex general TFs and RNAPll are recruited to the PIC on GAL promoters Nucleosome remodeling occurs to open the genes Posttranscriptional regulation plays an important role in gene regulation mRNA can be processed to remove introns splice exons molding caps and tails RNA molecules can be edited and bases modi ed Alternate splicing generates different forms of mRNA from identical premRNA molecules so expression of one gene can give rise to different but similar proteins Cacitonincalcitonin genereated peptide gene CTCGRD gene Primary transcript in thyroid cells spliced so mature mRNA has only exons 14 In the brain it expresses exons 5 and 6 but not 4 Through splicing different versions of the same protein are made Proteome the number of proteins an organism can makenot the same as the number of genes in the genome Protein diversity can exceed in gene number RNA editing involves base substitutions made after transcriptions and splicing With both alternative splicing and editing a gene can produce many more different transcripts Mutations that affect regulation of splicing contribute to several genetic disorders Ex myotonic dystrophymost common form of adult muscular dystrophy Autosomal dominant with forms of DM1 and DM2 Sex in Drosophila is determined by the ratio of Xchromosomes to autosomes 5males 1femaes betweenintersex 3 major genes sex lethal le transformer tra double sex dsx Sex lethal le is a regulatory gene that encodes an RNA binding protein In females transcription factors are encoded by genes on the X chromosome activate transcription of le gene Lower concentration of these transcription factors is not suf cient to activate le The le protein is only expressed in females Causes a cascade of premRNA splicing events speci c for females or males Transformer tra is a target of the le protein Tra encodes pre mRNA which is transcribed in both sexes When the le protein is present tra pre mRNAs are spliced to produce mature mRNAs translated into a functional TRA protein lf absent tra premRNAs are spliced to the translation stop codon in mature mRNA nonfunctional protein The doublesex dsx is a critical control point in the development of the sex phenotype Produces functional mRNA and protein in both sexes speci c In females DSXf protein represses male development DSXm for males activates Steadystate level of mRNA determines how many are available for translation There are 3 pathways to degradation Poly A binding proteins help stabilize mRNA by poy A tai If shortened by enzymes becomes unstable and becomes substrate to exonucleases that degrade RNA in either direction Decapping enzymes can remove 7Mg cap to make the RNA unstable mRNA can also be degraded naturally by endonuclease Ex can occur during nonsensemediated decaywhen translation stops at the premature stop codon Posttransationa modi cation controls stabilityquantity of protein produced RNAi interference sequence speci c posttranscriptional regulation These repress and trigger degradation of mRNAs RNA induced genesilencing short RNAs acting to alter chromatin structure to repress transcription SiRNAs small interfering RNAs and microRNAs are both short double stranded molecules Double stranded RNAs are cleaved by the enzyme Dicer into siRNAs microRNAs are derived from one stranded RNAs that have a stem oop structureaso cleaved by Dicer The RNA induced silencing complex RISC is associated with simicroRNAs Short double stranded RNAS are denatured and degraded The complex becomes functional with a speci c agent of RNAi looking for a complimentary strand to the antisense RNA strand that is incorporated in RISC Once paired it can silence via mRNA stabilitytranslation RNA induced silencing complex RITS also represses transcriptiontargets speci c gene promoterslarger regions of chromatin DNA is methylated and siencedmight be related to epigenetic phenomena Possible Exam questions 1 One of the earliest steps in the RNAi pathway involves the association of siRNA molecules with an enzyme complex composed mainly of reverse transcriptase False 2 The GAL4 protein has which of the following functional domain A DNA binding domain and an activation domain


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