Lecture 16- RNA structureso Loop stemo Hairpino Bulgeo Can have series of all three in the molecule and there are many possibilities What is the most stable preferred tructureo 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- Conceptso Circuits = analogy of electrical circuit – want to power something Various components added to circuitso Switches – basic controllers of electrical circuits and come in rich variety On/off controllerso Feedback loops – control strategies Negative, positive- RNAs with catalytic activitieso Ribosome: peptide bond formation catalyzed by 23S rRNAo Ribozyme: RNA with catalytic activity One of the first cut mRNA and cleaved the RNA messages- E. coli has about 4200 protein coding geneso It lives in a dynamic environmento Lots of different nutrientso 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 Expressiono “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 cello Constitutive – encode essential cellular functions and are expressed continually Not regulated- Regulatory genes – genes whose products, either RNA or proteins, interact with other DNA sequences and affect the transcription of translation of those sequenceso Ex of products: DNA-binding proteinso Used to control expression of structural genes- Regulatory elements – affect the expression of sequences to which they are physically linkedo DNA sequences that are not transcribed but play a role in regulating genes- Controlo Positive control – stimulate gene expression More common for eukaryoteso Negative control – inhibit gene expression More common for prokaryote- Gene expression can be regulated at many levelsoo 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 chromatino 2. At the level of transcription limiting the production of a proteino 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 sequenceo 4. Regulation of RNA stability rate mRNA is degradedo 5. Level of translation requires lots of enzymes, protein factors, and RNA molecules – affect rateo 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 mRNAo Bacterial structural genes that was transcribed together = operono Operon regulated expression of structural genes by controlling transcriptiono Polycistronic mRNA in prokaryotes One promoter, one mRNA, multiple genes/proteins! Ribosome attaches to Shine-Delgarno sequences and reinitiates translationfor each gene- Structure of an operon:oo Genes on one end (a,b,c) transcribed into single mRNA and translated to produce enzymes A, B, C Enzymes carry out biochemical reactions that convert precursor molecule X into product Y 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 operono Not part of the operono Has its own promoter and transcriber into short mRNA which is translated into a small proteino Regulator protein – bind to region of operon called operator and affects whether transcription can take place Operator overlaps the 3’ end of the promoter and sometimes the 5’ end of the first gene- Negative and Positive control: inducible and repressible operonso 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 transcriptiono 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 operonso The repressor that readily binds to the operatoro Operator sites overlap promoter site so binding of this protein to operator physically blocks binding of RNA polymerase to promoter and prevents transcriptiono 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 moleculeo When inducer absent – repressor binds to operator and genes not transcribedo 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 producto Enzymes synthesized only when their substrate is availableo Inducible operons usually control proteins that carry out degradative processes - Negative repressible operonso Regulator protein is also a repressor but is synthesized in an inactive form that cannot by itself bind to the operatoro No repressor bound to the operator RNA polymerase binds to promoter and transcription takes placeo To turn off a small molecule –