BSCI223 Exam 2 1 Methanogens a Generate methane 2 Cellulolytic bacteria 3 Transcription a RNA polymerase i Denatures DNA at promoter ii DNA closes behind iii 5 to 3 iv at 1 sight starts laying down RNA v new bases are added to the 3 end vi vii Keeps going until gets the he termination site where the transcription bubble moves down and adding bases transcription will be over viii Rho interacts with sites on DNA which stops transcription will form stem loops which will stop RNA polymerase from continuing on b Sigma factor c Promoter i Minus 10 minus 35 ii Stars at 1 d Coding strand i sequence of DNA that when lined up to mRNA have a similar sequence but T is replaced with U ii useful for analyzing DNA make judgments about where genes start and stop based on DNA sequence e template strand i template for RNA synthesis f question when reading the bases of the completed mRNA strand 5 to 3 the sequence is that the U replaces T in the RNA i ANWSER the same as the coding strand 5 to 3 g Transcription strands i Coding strand sequence of mRNA at the bottom of slide 10 is the same as the template strand yet replaces T with U ii ONLY SHOWING 1 STRAND CODIGN STRAND iii Genes do run in both directions coding stands can be on bottom and the top h RNA polymerase interacts at the promoter moves down the strand adds bases to 3 end and synthesizes a new strand costs the cell ATP every base added 1 ATP used i Termination i Rho protein ii Rho independent protein j RNA codon Table U i Read 5 to 3 ii There are start and stop codon iii 3 bases on mRNA 1 amino acid on a peptide iv any change in any codon which will change the protein stricter v AUG is ALWAYS START k Start i Small ribosomal subunit binds to mRNA ii Upstream to the ribosomal binding site iii RNA polymerases know to start transcription at sites iv First codon is AUG v Cells have tRNA which are charged with amino acids Methanynine AUG forms base pairs with mRNA vi Charging of tRNA costs cell ATP vii Large subunit comes in and binds to make the ignition transcription complex l Peptide bond forms between codons m Slides down to the mRNA n o tRNA is injected and amino acid chain forms if the mRNA translation is 3 mRNA bases ones acid must be divisible by 3 a Ribosome binding sites b Start and stop codon c Ribosome ribosome binding site 3 at a time d Stop codon is not tRNA that has an anticodon for it e Once it hits the stop codon protein is release f N terminal end g C terminal end h Can be folded into its appropriate shape i WHERE THE 3 LETTER BLOCKS OCCUR MAKES A DIFFERENCE WHERE EACH PROTEIN IS MADE i In order to be a functional protein starts with AUG cuts off at an appropriate time Average gene is 1000 genes long average amino acids is 330 sequences long 4 Translation 5 Transcription and translation coupled a Chromosomes are not in membrane bound organelles in cytobacteria RNA polymerase makes the mRNA and can start translating it b DNA on an electormicorgraph big blobs RNA polymerase i Each blob has small pieces of RNA coming off of them 1 Tinier blobs off of those the ribosomes synthesizing the peptide as it comes off the mRNA strand Christmas tree AS SOON AS MRNA IS MADE THE PROTEIN IS MADE ii Basic structure of a gene 1 Promoter 2 Transcription start tsite 6 Operon time 3 Translation start site 4 Transcription stop site 5 Translation stop site iii Bacteria don t always put one gene on one RNA transcript a All genes on one mRNA and all proteins are synthesized at the same b Protein that works as a multimero complex Makes A B and C because its more efficient they work together the catalyze therefore they should be synthesized together c One promoter synthesizing many genes on a transcript d mRNA has one ribosome binding site for each gene e one start codon for each gene f one stop codon for each gene g Translation polypeptide 1 2 3 and so on h They might all combine to help the cell in a particular way i IF YOU DRAW THREE LINES TOP DNA MIDDLE RNA LAST PROTEIN i 5 to 3 DNA AND RNA ii and N and C iii start and stop Can align them to specific spots in mRNA iv every protein starts with ribosome binding site and stop codon align with the N and C terminal ends of proteins v KNOW HOW TO DRAW AND LABEL THREE LINES LECTURE 10 SLIDE 27 1 UGA does not actually overlap the C terminal 2 AUG does not overlap the N terminal introns spliced out a Machines RNA polymerase sees a promoter and starts transcribing b mRNA is made with introns and exons c d Exons spliced together e Cancer is unregulated cell divisions f mRNA is exported out of the cell g prokaryotes no compartmentalization 7 Coding vs noncoding regions Lecture 3 1 Regulation of gene expression a Allows an organism to adapt to its changing environment b Cells respond and turn on genes when needed to be turned on c Conserve energy d Switch to developmental growth processes 2 How a Transcription i Constitutive promoters come in two flavors ON ALL THE TIME Inducible mRNA IS TURNED ON MY SIGNALS ii iii Repressible express mRNA until shut of by environment 3 Central dogma diagram a In slides 4 Cells can inhibit enzyme activity a Allosteric Site substrate binds and is converted into products i Cause changes in the confirmation of the protein ii Structure relates to function iii No reaction can proceed b Enzymes i Substrates to products ii Transition state iii Produce enzyme is recycled iv INHIBITOR can bind the active site of the enzyme and can compete and competitor v Can slow down the reaction vi Allosteric inhibition inhibitor bind the enzyme and changes the active site where substrate cant bind vii How much inhibition creates the inhibition viii Allosteric activators help enzymes form to proper shape c Translational control i No enzymes ii RNAi interference another RNA and base pairs with mRNA If mRNA is based paired with another RNA then it is unavailable to the ribosomes thus translation cant occur d Transcriptional control no mRNA synthesis i Model for bacterial moderation ii Don t synthesize mRNA for the enzymes they don t need iii Why is why is transcriptional control an efficient form of regulation iv ANWSER it limits the investment of ATP in making mRNA and proteins bacteria can have post transcriptional control v Every time you add an RNA to a chain it costs ATP cell must be selsctive and responsive to the environment to see what enzymes are synthesized Not making mRNA saves the cell 1000 ATP 5 LAC OPERON a Polycitronic mRNA of three genes 3 protiens CRIRICLES REPRESENT PROTEINS i LacZ