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Exam 3 Week 1 Notes (2/24/16-2/29/16)

by: Luke Holden

Exam 3 Week 1 Notes (2/24/16-2/29/16) 3050

Marketplace > Clemson University > Biochemistry > 3050 > Exam 3 Week 1 Notes 2 24 16 2 29 16
Luke Holden

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This is the first week of notes created following Dr. Sri's lecture and using some pictures from her lecture as well. Hope this helps!
Essential Elements of Biochemistry
Dr. Srikripa Chandrasekaran
Class Notes
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This 6 page Class Notes was uploaded by Luke Holden on Friday March 4, 2016. The Class Notes belongs to 3050 at Clemson University taught by Dr. Srikripa Chandrasekaran in Winter 2016. Since its upload, it has received 101 views. For similar materials see Essential Elements of Biochemistry in Biochemistry at Clemson University.

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Date Created: 03/04/16
Exam 3­ Week 1 Notes Transcription (CH 18)  Transcription­ use of DNA to synthesize an RNA strand  A small portion of the genes are expressed at any given moment  Expressed: o 3­30% in prokaryotes o 1­10% in Euk  RNA only molecules – Retrovirus o Know what reverse transcription is  One gene one enzyme hypothesis: o Gene: cluster of nucleotides in a defined spot that express o True in most cases o Exceptions:  Albinism­ 1 gene Multiple enzymes  Skin Color Enzyme Grow? Add More  Add  Add  Add Arginine Precursor Ornithine  Citrulline Wild Type Yes Yes Yes Yes Yes Enzyme 1 Δ No No Yes Yes Yes Enzyme 2 Δ No No No Yes Yes Enzyme 3 Δ No No No No Yes Δ­ Means mutated enzyme (nonfunctional) Sample Question: If you have a chain like this: A BC ….. And you have a mutation on the enzyme between the  B and C…  Adding back all the three products will mean the chain will carry on like normal….. True or  False? False: this because if you add back compound B or A, the reaction still would be unable to form  C You can’t add back enzymes (practically), you have to add back the substrates.  Transcription: o RNA polymerase choose a template strand (can pick either one) o Terms  Non template strand (sense)  RNA polymerase goes 5’3’! o Background information  Promoter­ region of nucleotides 20­200 bases upstream of the open  reading frame  Open reading Frame (ORF)­ This is the gene of interest that will be  transcribed  Promoter 10 bp before ORF in prokaryotes  Promoter 35 bp before ORF in eukaryotes  o When she gives us a DNA strand or mRNA strand she will always tell us which is which o Cheat code: THE NONTEMPLATE STRAND IS THE SAME THING AS THE  mRNA STRAND (EXCEPT “T” IS EXCCHANGED WITH“U”) 2/26/16 RNA Polymerase­ The enzyme that reads DNA to synthesize RNA  Gene specific  Subunit Structure o Five poly peptides o Core enzyme: ααββ’(i) o o Sigma factor binds to the promoter and prevents DNA from going back into  heterochromatin  Promoter recognition  Binds to the core enzyme o Function of the subunits:  α­ promoter binding and assembly and regulation  β’­ DNA Binding  β­ Catalytic site (polymerization part) (The part that RNA is no for  (i)­ structural role , restores activity Sample Question: I will compare polymerases (DNA + RNA)  Prokaryotic Transcription o 3 Stages   Initiation and Elongation  RNA Poly binds to initiation  After 10bps = Elongation  Elongation is the process of transcribing mRNA.  Termination  Rho (ρ) factor­ ATP dependent helicase that stops transcription in  prokaryotes o ρ­ Attaches to mRNA and follows behind the RNA poly  o When RNA poly 3 stalls, the ρ factor can catch up and  essentially knock of the mRNA strand o This is kind of like you are swimming a way from a shark  and then catch a cramp…. You die  Eukaryotic Transcription RNA Polymerase Location Function I Nucleolus Transcribes large rRNA’s II  Nucleus Transcribes mRNA and  snRNA’s III Nucleus Transcribes tRNA 5s rRNAs  EUKARYOTIC POLYMERASE CANT INITIATE TRANSCRIPTION LIKE  PROKAROYTES!!!!! o Initiation  DON’T HAVE TO KNOW SPECIFIC TRNASCRIPTION FACTORS  Several transcription factors  TF’s bind to TATA box  Polymerase binds to the promoter  TFIH­ gets polymerase going via phosphorylation  Promoters: Promoter Consensus  Position Function Sequence TATA TATAAAA ­25 Indicates  transcription  Start Site CAAT GGCCAATCT ­50 Indicates Strong  promoter (High  Rate) GC Box GGGCGG ­80 Indicates House  Keeping gene  (All the Time  Enhancers­ Assist in the formation of the transcription complex  1000­2000 bp away  DNA will bend back on itself and attach IF to promoter   Gives the polymerase a sort of shove Compare and Contrast Prokaryotic and Eukaryotic Characteristic Prokaryotes Eukaryotic Polymerase RNA Poly: Can do it all! RNA poly I: large RNA rRNA RNA poly II: mRNA mRNA RNA poly III: tRNA small  tRNA tRNA Initiation Factors σ factor further binds to theTF IIs bind to the promoter promoter o Termination   RNA poly reaches the end of the terminator regions of DNA  Terminator: Poly A consensus sequences that code for hairpin structures  The hair pin forms kind of like Velcro where in latches on to itself and then it  falls off. RNA processing in Eukaryotes ONLY  3 Types of Processing o ­5’ Cap­ addition of 7­ methyl­guanosine  Need to know chemically what is a cap or a tail  5’5’ addition (not and error there) with a triphosphate   Fig. 18.24 (McKee & McKee)  3 nucleotides before are methylated at the 2’ OH group  This cap serves as the recognition site for attachment and prevents  degradation by exonucleases  o 3’ polyaddenation­ ADDs 100­250 AA   Helps direct mRNA’s out of the cell  Protection from degradation   RNA Poly A Polymerase Polymerase  Increase the length of the tail increases the longevity of the mRNA 2/29/16 o Splicing of mRNA  snRNP’s and splicesomes (exonuclease)  premRNAs have nucleotide sequences that serve as the splicing  signals   snRNPS’s recognize the sites  Multiple snRNP’s join together to form a splicesome  (RNA ligase and Exonuclease)  Know this  Cuts out introns and stiches together Exons  Occurs in the nucleus o Functions of introns  Exon shuffling­ Exons correspond to different functional regions of a  polypeptide  Provide cross over recombination sites  Help with recombination to promote function  Help signal when mRNA is ready o Active Genes  Transcribestmany times nd  After the 1  wave of ribosomes go through, the 2  and third wave  comes in which increase the amount of the gene that can be expressed  Need to know about lamp brush chromosomes  Constantly transcribed  Only in eukaryotic Regulation of transcription  Operons­ group of genes together that are controlled by a single promoter o Only in prokaryotes  4 types of DNA binding regulatory proteins (motifs) o Helix­turn – helix o Zinc Fingers o Leucine Zippers o Helix­ Loop­ Helix  Each of these different motifs above all bind a different way to the major groove of the  DNA and thus express DNA differently. This increase the variability of the expression. o DNA Binding Domain  Rich in α­ helices  Interact with the major groove with h bonds  Salt bridges and hydrophobic  interactions  Can bind to promoters and enhances o Active domain  Mainly acidic amino acids  Bind to other factors, RNA poly II and activators  Positive control­ genes have to have activator o Activation­on o Deactivation­off  Negative Control­ constant being transcribed unless you add a repressor o Repressed­off o Derepression­on  Lac operon o Inducible Operon­ stimulated with reactant (lactose) o Jacob and Monod o Lactose V Glucose Don’t have to know these structures


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