Class Note for ECOL 320 at UA
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Date Created: 02/06/15
Gene Expression Translation Reminder DNA alieatien transcription reverse transcription RNA Glieatien translation protein Genes that encode proteins are transcribed and the transcript is processed to make mRNA 0Next the base sequence in the mRNA must be translated into amino acid sequences in a polypeptide Once polypeptides are formed they fold up and combine with other molecules but this is the realm of biochemistry not genetics Review structure of polypeptides a protein consists of one or more polypeptides The Code Problem E iii5 George G mow Crick Leslie Orgel Sidney AleX Rich Jim Watson and RNA Tie Club ties DNA and RNA sequences are written in an alphabet of 4 different bases G A T U C Protein sequences are written in an alphabet of 20 different amino acids Therefore there must be a code that relates a base sequence to an amino acid sequence J Heinrich Matthei Marshall Nirenberg alanine agsteine aspantie aaid glatamie acid phenglalanine glgaine histidine isaleaeine lgsine leaeine methianine asparagine pnaline glatamine anginine senine threanine ualine tngptaphan unknown tgnasine iHl iWID39UZIIEIm39 l39 l Severo Ochoa ala egs asp gla phe all his ile gs lea met asn pea gin arg sen the val twp akw tgn Important The Amino ACidS features D1ffer only 1n T 0 II 0 II 0 III 0 I III 0 Slde chalns quot1quot T OH 2 T OH quot2quot T COH quotzquot T E H MIN T cOH HzN T c H 0Each has three quot quot quot CH CHz c CH1 CH2 c 1 d I I II an I I Ho 0 etter an one H fa If quotkm Vex FM HzN C N H IIzN xm2 o Arginine Lyslne Hislidine Glulamic acid Gh amina Aspanic acid MILE Lys K HisH Glu E GlnIQ Asp D abbrev1atlons H H H H H H 0 o 0 I o o I o Y h HzN T Cfo HzN lIZ CSDH HIM IE O quot Mai oft HiN T C H HN lt cDH 011 s 011 CH CH2 CH2 cH2 CH OH I I n c NH cc on W CH understand that g 4quot Hac cns Mac the sequence of OH 555 l amlno ac1ds 1n a V quotwequot Asgaras ne Tyrosme PhiEKIaIaFrJIme Try1pmpwhan lfeucmi lst fu re 39 Tyr v e rp Len L e polypeptlde 5quot I H H H H H H Preteln can be H2N KIZ C o HZN lP D u HQN c D HZN tlz c o NN c HIM c OH on ou OH oH I OH wrltten two 5 1in II cI cu w fa 0H3 6 CH on on an 5H wa s 1 y g nn Al g Set Set Valine MeIhIonine Threonine Sarina CysIaIne AIanIne R T s 8 Val V MelMJ ThrT Sens oys C AIaA H H H I I I o Hiw cc N c c I 0quot 39 Polypeptldes H HER CH1 You don t have to memorlze these but you 0 2 do have to know there are 20 and recognlze have an N and a wine Wine me my ammo ac1d sequences Cterminal AA The Genetic Code The code is 0 Written in RNA because it is the mRNA sequence that is read 0 Universal almost Exceptions small Vertebrate mitochondria Invertebrate mitochondria Chloroplasts Ciliate nuclear Mycoplasma nuclear Candida nuclear etc 0 Triplet 0 Nonoverlapping 0 Commaless 0 Degenerate First Third position Second position position 1539 end 339 end U C A G UUU PheF UCU Ser UAU TyrY UGU CysC U U UUCPhe UCCSer S UAC Tvr UGCCys C UUA LeuL UCA Ser UAA St m A UUGLeu UCGSer UAG St UGG TrpW G CUULeu CCU Pro CAU HisH CGUArg U C CUCLeu L CCCPro P CAC His CGCArg R C CUA Leu CCA Pro CAA GinQ CGAArg A CUGLeu ECG Pro CAB Gin EGG Am G AUU lie AEU Thr AAU AsnN AGU SerS U A AUClIe 1 AEEThr T AAC Asn AGCSer C AUA lie AEA Thr AAA LysK AGA ArgR A MM AEGThr AAG Lys AGGArg G GUU Val GCU Ala GAU AspD GGU Gly U G GUC Val V GEEAIa A GAC Asp GGCGIV G C GUA Val GCA Ala GAA GluE GSA Gly A BUG Val GEG Ala GAG Glu GGGGIV G Nam Each amino acid is giVE its conventionai abbreviation in both the singieeietter and the threeeietter Fovmat The codon AUG which codes for methionine boxed is generally used For Initiation The codons are conventionally written With the 5 base on the Ian and the 3 base on the right First Third position Second position position T I 1539 end 3 end UUU PheF UCU Ser UAU TyrY UGU Cys U U UUC Phe UCCSer S UAC Tyr UGCCys C o UUA LeuL UCA Ser m A IS UUE Leu UCGSer UGGTrpW G o CUULeu CCU Pro CAU HisH CGUArg U CUCLeu CCCPro CAC His CGCArg C 0 Unlversal almost c L P R A CUE Leu CCGPro CAB Gln CGGArg G o I AUU lie ACU Thr AAU AsnN ABU SerS U A AUClie 1 ACCThr T AAC Asn AGCSer C AUA lie ACA Thr AAA LysK ABA ArgR A ACG Thr AAG Lys ABE Arg G GUU Val GCU Ala GAU AspD GGUGIy U GUC Val GEE Ala GAC Asp GGCGIy C oNonoverlapplng 6 sum V W A Mink may 6 A BUG Val GCG Ala GAG Glu GGG Gly G C S Note Each amino acid is given its unventionai abbreviation in both the singisrietter and the threerieiter Format The codon AUG which codes or methionine boxed is generally used For Initiation The codons are conventionaliy written with the 5 base on we left and the 3 base om the right CACCAUGGUGCACCUGACUCCUGAGmCACUAAGCU Qua9let AUGGUGCACCUGA Overlaping AUG CACCUGACUC Co v g ccgg ccg pc G First Third I position Second position position The Ge netlc Code U c A G UUUPhe UCUSer UAU Tvr UGUCys U UAA UAG and UGA are U UUC PheF ucc Ser 3 UAC TyrY use Cysc c U UA L U CA s A nonsense codons they do not we Sh not 8 m Filipw G code for any amino acid and CUULeu ECU Pro CAU H5H CGUArg U CUCLeu EEC Pro CAC Hi5 CGCArg C hence are Stop or C CUA LeuL EBA P4P CAA Glu CGA ArgR A termination codons cue Leu E CE Pro CAB Gln 0 cm Avg G AUU He ACUThr AAU AsnN AGUSerS U A AUCHe1 ACCThrT AACAsn AGCSer c All the rest are sense codons AUA He ACA Thr AAA LysK ABA ArgR A WM ACGThr AAG Lys AssArg G suu Val GCU Ala GAU Asp GGUGIy U AUG 15 the Start COdon and G GUC Valv GCC AlaA GAC AspD GGC GIyG C GUA Val GEA Ala GAA Glu SBA Gly A COdeS for methlonlne Met GUG Val GEG Ala GAE GIUE EGG Gly G Nmz Each amino acid is gwsn its conventiona abbreviation in both the sing erletter dmcmrm fmtThe d AUG hh dsf mth 39eb d only one to memorlze ggnemely use 0i1iunThe Egdggs are ctyw ecmxfnaiy irrwtte W EThe s39obxaese the le and he 3 base on the right CACCAUGGUGCACCUGACUCCUGAGCACUAAGCU Met Val His Leu Thr Pro Glu His Stop Start Open Reading Frames An open reading frame ORF is a string of sense codons starting With the start codon ATG and anked at the 3 end by a stop codon All genes that code for proteins must have an ORF CACCAUGGUGCACCUGAC UCCUGAGCACUAAGCU Met Val His Leu Thr Pro Glu His Stop Start Using Open Reading Frames to Find Genes A computer program can search a sequence of bases for open reading frames These are candidates for genes encoding proteins Problems CACCAUGGUGCACCUGAC UCCUGAGCACUAAGCU Met Val His Leu Thr Pro Glu His Stop Start Using Open Reading Frames to Find Genes A computer program can search a sequence of bases for open reading frames These are candidates for genes encoding proteins Problems 0A gene can be on either strand but the sequence is only written for one strand Solution search both complementary sequences 0A random sequence of bases can have an ORF Partial solutions look for long ORFs starting with ATG 0 Introns can interrupt ORFs The introns are spliced out of the mRNA leaving only the exons which form a continuous ORF but DNA sequences will still have the introns Partial solution look for sequences that often ank introns Designing computer programs to seach complete genome sequences is a major problem in bioinformatics The Mechanics of Translation 1 Translation requires Small ribosomal subunit SSUrRNA ribosomal proteins Large ribosomal subunit LSUrRNA ribosomal proteins SSrRNA eukaryotes Small and large subunits also have S names 168 188 238 etc S is for Svedberg units describing how fast something moves in a centrifugal field Aminoacyl tRNAs transfer RNAs amino acids Accessory proteins that promote various steps 2 mRNA is translated 5 to 3 3 Polypeptide is made Nterminal to Cterminal aminnacid H L tRNA folding DUlLIDE39IJUEIB completed palgpeptide DUlHDBDtlE MK J C mRfr m 539 quot I C i 32 f a39 quot J xx HtIIZISDmES free ribosome Bubumts 39 Cellular Sites of Transcription amp Translation After eukaryotic nuclear genes are transcribed and processed the mRNA must be moved to the cytoplasm for translation Prokaryotic genes and those in the chloroplasts and mitochondria are not separated from the sites of protein synthesis Transcription and translation proceed simultaneously protein O chloroplast Making Aminoacyl tRNAs A 339 OlHAmino acid attachment site Each tRNA has a specific base sequence including an anticodon that can base pair with a codon 39Q Anticodon Anticodon looip An aminoacyl tRNA synthase recognizes a tRNA and its corresponding amino acid and joins them The anticodon on the aminoacyl tRNA base pairs With its codon on the mRNA A new peptide bond is formed to join the amino acids E UUA Y IE UUA Ill A s U AAAAAU s s llllll A A AAAU llllll El l a AAAAAU W Wobble There are 61 sense codons However organisms may not have 61 different tRNAs 1st 5 base in anticodon can sometimes pair with 2 or 3 bases pairs with 3rd 3 base in codon 5 anticodon base E coli S cerevisiae A U C G G U A or G A G C or U C or U Inosine A C or U C or U Don t need to memorize these just know basic principle Translation in More Detail than You Wanted or Need to Know see text Figure 1017 for a better diagram Aminoacyl site ribosome small elF proteins subunit 0 elF4B u Peptld l elF4A qbQ site y 9F4F Ribosome Ex39t s39te EF1u7GDP large subunit 603 C Translation begins mllllllllllllllll39 bbhk blIIIIIIIIIIIIIIIIIII 5 Next tRNA in line Ribosome Binding Translation Initiation and Termination Signals on mRNAs ribosume binding site H Mala stop H 39 39I Prokaryotes a special sequence the llShineDelgarno sequence is the ribosome binding site quot39 STEP AUG 311qu pawA tail H39lRNei39l Eukaryotes the 5 end of the mRNA is modified to form the 5 cap that initiates ribosome binding Prokaryotes and eukaryotes the AUG start codon is the signal to initiate translation the nonsense stop codon binds no tRNA and this stops translation ribusume binding site H A148 stop H 39 39I 5 UTR 3 UTR 539 3933P REG SEQpuma tail Ti H e5 I C B am Unique Features of Translation in Prokaryotes One mRNA can encode more than one polypeptide With prokaryotic ribosomeshree 2 2 polypeptides are made because the ribosomes can initiate translation within an mRNA Polypeptides g E mRNA 539 I I 339 Stopi Stop Stop Polypeptide w With eukaryotic ribosomes only one polypeptide is made because the ribosomes can initiate translation only at the 539 end Unique Features of Translation in Prokaryotes Translation of an mRNA can begin before transcription is complete because these processes are not separated by a nuclear membrane g r I hi 1m nail1 Where the Machinery Comes From The machinery for DNA replication and repair transcription and translation includes various enzymes and other proteins as well as rRNAs and tRNAs Each of these is encoded by genes which in turn are transcribed to make RNAs and these are processed in various ways The enzymes and proteins are themselves translated from mRNAs using the machinery of which they are components Like all genes they are subject to mutations that can change the rate or manner in which they act Like all genes they are the product of evolution
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