Lecture 16 RNA structures o Loop stem o Hairpin o Bulge o Can have series of all three in the molecule and there are many possibilities What is the most stable preferred tructure o Biologically significant RNA structure 16S Ribosomal RNA makes up most of 30S ribosome small subunit the way is bends and folds specifically makes up the ribosomal subunit Concepts o Circuits analogy of electrical circuit want to power something Various components added to circuits o Switches basic controllers of electrical circuits and come in rich variety On off controllers o Feedback loops control strategies Negative positive RNAs with catalytic activities o Ribosome peptide bond formation catalyzed by 23S rRNA o Ribozyme RNA with catalytic activity One of the first cut mRNA and cleaved the RNA messages E coli has about 4200 protein coding genes o It lives in a dynamic environment o Lots of different nutrients o E coli growth Preferentially metabolizes glucose until that is gone then makes a choice to later metabolize lactose Ability to metabolize lactose preceeded by a lag So it didn t have that ability until it switched Some genes are on all the time Constitutive Gene Expression o housekeeping genes ribosomal proteins elongation factors many others think about basic processes transcription translation etc o Expressing all genes all the time 1 Is expensive ATPs Resources 2 Inefficient making thing you don t need 3 Chaotic some genes have opposite purposes eg synthesis vs degredation o Gene regulation is essential Prokaryotic Gene Expression Structural genes encode proteins that are used in metabolism or biosynthesis or that play a structural role in the cell Not regulated o Constitutive encode essential cellular functions and are expressed continually Regulatory genes genes whose products either RNA or proteins interact with other DNA sequences and affect the transcription of translation of those sequences o Ex of products DNA binding proteins o Used to control expression of structural genes Regulatory elements affect the expression of sequences to which they are physically o DNA sequences that are not transcribed but play a role in regulating genes linked Control o Positive control stimulate gene expression More common for eukaryotes o Negative control inhibit gene expression More common for prokaryote Gene expression can be regulated at many levels o o 1 Regulation through alteration of DNA or chromatin structure eukaryotes modifications to DNA or its packaging determine which sequences are available for transcription or the rate DNA methylation and changes in chromatin o 2 At the level of transcription limiting the production of a protein o 3 mRNA processing Eukaryotic mRNA is modified before translated 5 cap added 3 end cleaved and polyadenelated introns removed determine stability of mRNA where it can be translated rate amino acid sequence o 4 Regulation of RNA stability rate mRNA is degraded o 5 Level of translation requires lots of enzymes protein factors and RNA molecules affect rate o 6 Modification after translation affect whether the protein becomes active Genes in bacteria that have related functions are clustered and under the control of a single promoter co regulated o Transcribed together into a single mRNA o Bacterial structural genes that was transcribed together operon o Operon regulated expression of structural genes by controlling transcription o Polycistronic mRNA in prokaryotes One promoter one mRNA multiple genes proteins Ribosome attaches to Shine Delgarno sequences and reinitiates translation Structure of an operon for each gene o o Genes on one end a b c transcribed into single mRNA and translated to produce enzymes A B C X into product Y Enzymes carry out biochemical reactions that convert precursor molecule Transcription of structural genes a b c is under the control of a promoter which lies upstream of the first structural gene RNA polymerase binds to the promoter and moves downstream transcribing the structural genes Regulator gene helps to control the transcription of structural genes of the operon o Not part of the operon o Has its own promoter and transcriber into short mRNA which is translated into a o Regulator protein bind to region of operon called operator and affects whether Operator overlaps the 3 end of the promoter and sometimes the 5 end of small protein transcription can take place the first gene Negative and Positive control inducible and repressible operons o Two types of transcriptional control Negative control regulatory protein is a repressor binds to DNA and inhibits transcription Positive control regulatory protein is an activator stimulates transcription o Inducible vs repressible Inducible operons transcription is normally off not happening Something must happen to induce transcription Repressible operon transcription is normally on taking place Something must happen to repress transcription Negative inducible operons o The repressor that readily binds to the operator o Operator sites overlap promoter site so binding of this protein to operator physically blocks binding of RNA polymerase to promoter and prevents transcription o For transcription to take place something must happen to precent binding of repressor at operator site Turned on when small molecule inducer binds to repressor Regulatory proteins have 2 binding site 1 for DNA 1 for small molecule Inducer alters shape of repressor preventing it from binding to DNA Allosteric proteins change the shape of another molecule o When inducer absent repressor binds to operator and genes not transcribed o When no precursor for the proteins to metabolize When precursor available some of it binds to repressor changing shape So transcription and translation occur which convert precursor to product o Enzymes synthesized only when their substrate is available o Inducible operons usually control proteins that carry out degradative processes Negative repressible operons o Regulator protein is also a repressor but is synthesized in an inactive form that o No repressor bound to the operator RNA polymerase binds to promoter and o To turn off a small molecule corepressor binds to repressor and makes it cannot by itself bind to the operator transcription takes place capable of binding to the operator o As long as the product is high it can bind to repressor and activate it and block Then no more product created because no proteins o When all product used up repressor not activated cannot bind to operator and