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by: Shira Clements


Shira Clements

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Chapter 18 textbook notes
Principles of Biology I
Norma Allewell
Class Notes
Biology, bsci105
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This 7 page Class Notes was uploaded by Shira Clements on Wednesday March 30, 2016. The Class Notes belongs to BSCI105 at University of Maryland taught by Norma Allewell in Fall 2015. Since its upload, it has received 26 views. For similar materials see Principles of Biology I in Biology at University of Maryland.

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Date Created: 03/30/16
Shira Clements BSCI105 Chapter 18- Regulation of Gene Expression - Everyone must change pattern of gene expression in response to environment - Each cell contains same genome but expresses different genes - Usually regulated during transcription, but still need control at different stages Bacteria Often Respond to Environmental Change by Regulating Transcription - Cells don’t want to work so much, so natural selection favors bacteria that express only the genes whose products are needed by cell (save energy) - Ex- E coli lives in human, but needs amino acid tryptophan to survive, so cell responds by activating metabolic pathway to make tryptophan, but once the human eat something with tryptophan, the metabolic pathway will stop. (change based on enviro) - Two levels of metabolic control- o Cells can adjust activity of enzymes present- which is fast  Feedback inhibition- end product said that there is too much, so it stops the anabolic pathway (creation) of that product from the first enzyme- makes cell adapt- make quick changes based on cells’ needs o Cells can adjust production of certain enzymes- regulate expression of genes coding for the enzyme  If too much of something, the cell will repress expression of the genes encoding for the enzyme that creates the product  Occurs in transcription- synthesis of mRNA coding for enzyme Operons - The cell can translate one mRNA into five peparate polypeptides, which make up the different enzymes because of the start and stop codons that signal different polypeptides. - A transcription unit groups genes of related functions together, and therefore only have one “on-off” switch that can control the whole cluster - The switch is the operator (DNA segment)- o Positioned with promoter or between enzyme coding genes o Controls access of RNA-polymerase to genes (allows transcription) - Promoter, operator, and genes they control= operon o Trp operon is one of many in E coli genome - Operator is operon’s switch for controlling transcription- o By itself, trp operon is turned on- RNA polymerase can bind to promoter and transcribe genes of operon o Can be turned off by a protein called trp repressor- binds to operator and blocks attachment of RNA polymerase to promoter (can’t transcribe)  Specific for operator of particular operon  Trp repressor is protein product of regulatory gene called trpR, located near trp operon and has own promoter.  Expressed continuously at a low rate, but not switched off permanently because o Binding of repressors to operators is reversible- operators waver between a state of without repressor bound and a state of being repressor bound, and the time of each state depends on the amount of repressors there are around. Also regulatory proteins are allosteric, with an inactive shape and an active shape. Trp repressor is made in an inactive form with little affinity for trp operator- only if trp binds to trp repressor at an allosteric site, then the repressor protein changes to active site and attaches to the operator, turning the operon off. o Corepressor- a small molecule that cooperates with a repressor protein to switch operon off.  Trp functions as one- as trp accumulates, trp molecules associate with trp repressor molecules, which then bind to trp operator and shuts the trp pathway enzymes off. If trp levels drop, then transcription of operon’s genes resume.  Trp repressor is inactive by itself and need tryptophan as a corepressor in order to bind to operator Repressible and Inducible Operons- - Repressible Operon- inhibits transcription when small molecule binds allosterically to regulatory protein (trp operon) - Inducible Operon- usually off but can be stimulated when specific small molecule interacts with a regulatory protein (lac operon) o Lactose is available to E coli in human colon if human drinks milk  Metabolism begins with hydrolysis of the disaccharide into glucose and galactose, which is catalyzed by an enzyme, and only a few molecules of that enzyme are present in an E coli cell growing in absence of lactose. But if lactose is added, then the number of that enzyme increases majorly.  Active by itself, and binding to operator and switching the lac operon off  This is an example of inducer (inactivates repressor), and for lac it is allolactose (inducible enzymes)  In absence of lactose (and allolactose), lac repressor is in active configuration, and gene of lac operon are silenced.  If lactose is there, then allolactose binds to lac repressor and changes conformation, nullifying repressor’s ability to attach to operator. Without bound repressor, the lac operon is transcribed into mRNA for the lactose- utilizing enzyme.  Repressible enzymes function in anabolic pathways- suspend end product, and use energy for other uses  Inducible enzymes- catabolic pathways, producing enzymes when nutrient is available  Both negative control of genes because it is turned off by active form of repressor protein Positive Gene Regulation - E coli prefers glucose over any other sugar. When glucose is not present, it will use lactose as energy source - It can tell that glucose is not there and relays it to gene by- o Allosteric protein interacts with cAMP, small protein that accumulates when glucose is scarce. o The regulatory protein CAP (catabolite activator protein) is an activator, which is a protein that binds to DNA and stimulates transcription of a gene.  When cAMP binds, CAP assumes active shape and can attach to specific site upstream end of lac promoter This increases the affinity of RNA polymerase for promoter, which is low when no repressor is bound to operator. Attachment of CAP, directly stimulates gene expression- binding of RNA polymerase to promoter which increase transcription o If amount of glucose increases, cAMP concentration falls; without cAMP, CAP detaches from operon, and is inactive, so RNA polymerase attaches less efficiently to promoter, and transcription of lac operon proceeds at low level even in presence of lactose.  Lac operon is under negative control by lac repressor and positive control by CAP State of lac repressor (w/ or w/o allolactose) determines if transcription will occur State of CAP (w/ or w/o cAMP) control rate of transcription if operon is repressor free o CAP helps regulate other operons that encode enzymes used in catabolic pathways o When glucose is plenty, and CAP is inactive, synthesis of enzymes that catabolize compounds other than glucose generally slows down  Compounds present in the cell at the moment determine which operons are switched on Eukaryotic Gene Expression is Regulated at Many Stages Differential Gene Expression - Human cells only show 20% of their genes- all cells have same genome, except show it differently and different ones are expressed, allowing the different functions - Differential gene expression- expression of different genes by cells with same genome - Transcription factors of cell must locate right genes at right time o Regulation of Chromatin Structure  DNA of eukaryotic cells is packaged proteins= chromatin  It helps regulate gene expression- location of gene’s promoter relative to nucleotsomes and to site where DNA attaches to the chromosome scaffold can effect if gene is transcribed and chemical modifications to histone proteins and to DNA of chromatin can influence the chromatin structure and gene expression  Histone Modification- histone= protein in which DNA is wrapped in nucleosomes  N terminus faces outwards of the nucleosome and are accessible to various modifying enzymes that catalyze addition/removal of specific chemical groups o Histone Acetylation- acetyl groups (COCH ) 3 are attached to lysine in histone tails; when they are acetylated, the lysine positive charge are neutralized and histone tails no longer bind to neighboring nucleosome, which promotes folding of chromatin into more compact structure, so transcription proteins have easier access to genes in acetylated region  Associated with components of transcription factors that bind to promoter- may promote initiation of transcription o Methyl can promote condensation of chromatin, while addition of phosphate group near methylated group can have opposite effect o DNA Methylation- different set of enzymes can methylate certain bases in DNA itself (don’t change DNA sequence)  long stretches of inactive DNA are usually more methylated than active DNA, but on a smaller scale, single genes are more methylated in cells that they aren’t expressed now- removal of methyl groups will turn on some genes  essential for long term inactivation during normal cell differentiation in embryo  genetic imprinting- methylation permanently regulates expression of allele of genes  methylation patterns are passed on to next generation o Epigenetic Inheritance- inheritance of genes not directly involving nucleotide sequence  Modifications in chromatin can be reversed (can silence a specific gene)  DNA methylation and histone deacetylation can repress transcription  Trying to figure out why with identical twins, one has something but other does not, and seem in some cancers  Enzymes that modify chromatin structure are integral for regulating eukaryotic transcription Regulation of Transcription Initiation - Chromatin modifying enzymes provide initial control of gene expression by making a region of DNA more or less able to bind to transcription machinery - Once chromatin is modified for expression, transcription initiation regulation can occur Typical Eukaryotic Gene - Transcription initiation complex comes on promoter sequence upstream end of gene - RNA polymerase II (one of the proteins) transcribes the gene, making pre-mRNA - 5’ Cap is added and poly-A tail, splicing out introns= mature mRNA - control elements- segments of noncoding DNA that serve as binding sites for transcription factors (regulate transcription) - Roles of Transcription Factors o RNA polymerase needs it to start initiation process o A few independently bind a DNA sequence (TATA box with promoter), usually bind proteins, which is crucial- allows RNA polymerase to go o Some are general and some are specific o Proximal control elements- located close to promoter o Distal control elements= enhancers- many nucleotides away (upstream or downstream)  Gene can have many, activated at diff times and locations, but specific for gene o Rate of transcription is increased/decreased by binding of transcription factors (activators or repressors) to control elements of enhancers o Two common structural elements in activator proteins- a DNA binding domain and one or more activation domains (which bind other regulatory proteins or components of transcription Same gene is machinery that result in transcription of gene) expressed in o Binding activators to distal enhancers can effect transcription- certain tissue but  Activator proteins bind to distal control elements grouped not others as enhancer in DNA, which has three binding sites, each The DNA of both liver and called distal control elements lens cells contain the  DNA bending protein brings bound activators closer to genes for both the protein promoter. General transcription factors, mediator proteins, albumin and the protein crystallin and RNA polymerase II are close However, the albumin gene Activators bind t certain mediator proteins and general is expressed only in liver transcription factors, helping them form an active while the crystallin gene is transcription initiation complex on promoter expressed only in the eye In other words, the proteinription factors that act as repressors inhibit gene albumin is synthesized onlyssion by binding directly to control element DNA in the liver (although(enhancers sometimes), blocking activator binding, or turning off then transported to thtranscription. blood) while the protein  Some effect indirectly- affect chromatin structure- crystallin is synthesized in acetylate histones near promoters of genes, which promotes transcription  Repressors recruit proteins that deacetylate histones, which reduces transcription= silencing o Combinatorial Control of Gene Activation- control of transcription depends on binding of activators to DNA control elements. Each enhancer is composed of 10 control elements, which can bind 1- 2 specific transcription factors. Particular combination of control elements in an enhancer association with gene, rather presence of a single unique control element  Specific factors made in cell determine which genes are expressed  Although enhancers for two genes share one element, each enhancer has unique combination of elements o Coordinately Controlled Genes- co-expressed eukaryotic genes (genes coding for the enzymes of metabolic pathway) are usually scattered over diff chromosomes  Expression depends on association of specific combination of control elements with every gene of a dispersed group (compared to flags on mailbox- signaling to mail carrier to check those boxes)- copies of activators that recognize the control elements bind to them, promoting simultaneous transcription of genes  Occurs in response to chemical signals from outside cell  Cellular hormone enters cell and binds to intracellular receptor protein complex that serves as transcription activator- every gene whose transcription is stimulated by hormone has a control element recognized by that hormone-receptor complex (estrogen activates group of genes that stimulate cell division in uterine cells)  Signaling molecules bind to receptors on cell’s surface, never enter cell o Triggering signal transduction pathways that lead to activation of particular transcription activators/repressors  Gene with same control elements are activated by same chemical signals Techniques to cross-link and identify regions of chromosomes  Remember that eukaryotic genes are not grouped into operons  Instead: Groups of gene involved in the same function and need to be expressed together may be scattered throughout the genome or located on different chromosomes  Strategy 1: Genes with similar functions will use the same or similar sets of control elements. When the right set of transcription factors is present, all the genes will be turned on  Strategy 2: The loops of chromosome(s) that contain these genes may be co-located in the nucleus in transcription factories


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