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by: Kavon Huel


Kavon Huel
GPA 3.59


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Class Notes
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Popular in Biochemistry and Molecular Biology

This 42 page Class Notes was uploaded by Kavon Huel on Friday September 18, 2015. The Class Notes belongs to BCH 6746 at University of Florida taught by Staff in Fall. Since its upload, it has received 10 views. For similar materials see /class/206966/bch-6746-university-of-florida in Biochemistry and Molecular Biology at University of Florida.

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Date Created: 09/18/15
RNA structure Uracil replaces thymine RNA does not adopt the classic BDNA helix conformation when it forms a selfcomplementarV double helix Reason RNA has ribose sugar ring with a hydroxyl group OH If RNA in Bfrom conformation there would be unfavorable steric contact between the hydroxyl group base and phosphate backbone At least 50 double stranded in solution of any random RNA molecule incl mRNA 5560 in tRNA Most bases are stacked shortrange pairings gthai1pins loops bulges junctions Compacted globular fold longrange pairing gtintramolecular structural roles stabilizing 3D folding l l loop U T Lu l l A xyu a c 0quot bulge uA l w ya u g u Internal U 39 loop cls c AU ul l l 1 l 43 W uni 66 c L Internal loop a l l ut x 5 z SecondaIy sttuctural elements 3 539 a three nuclamide bugs 3 5 sing e nucleolide bulge a s symmemc nwmal loop mismatch pair on symmelno Internal loop a 2 nuclw des E hairpin Jump 3 5 3 5 asymmelnc imemal lacy RNA tertiary structure Mainly based on transfer RNA structures Yeast phenylalanine transfer RNA tRNA Phe Findings universal L shape solution elongation experiments Two segments of double Helix ADNA like 10 base pairs in length Non helical regions participate in unusual hydrogen bonding interactio Primary structure sequence Secondary structure Watson Crick base pairs tertiary structure tertiary interactions unusual base pairs base triples looploop interactions cross strand stacking THREE commonly found RNAbinding domains Ribonucleoprotein RNP domain Double stranded RNA binding domain dsRSB K homology KH domain ALL shown to have ocB domain similar to ribosomal proteins Speci c RNAprotein interactions play crucial roles in gene regulation through transcription control RNA processing transport and translational control Ribonucleoprotein RN39P domain Very common Contains two short conserved sequences within a weakly conserved motif 7090 aa RNPl RNP octamer RNP2 RNP hexamer 4 antiparallel 3 stands anked by 2 on helices Biai i iw topology RNPl and RNP2 located on central strands Loop 3 crucial role in RNA binding Loop 1 Aromatic aa exposed on Bsheet sheet provides a large surface area Double stranded RNA binding domain Short motif 65 aa oc B B B oc topology 3 antiparallel B stands anked by 2 or helices Conserved positive charged residues hydrogen donoracceptors in loops 2 and 4 dsRBD and N terminal domain of ribosomal protein s5 share sequence and structure similarities Fold speci c The KH domain Short conserved sequence found in heterogeneous nuclear RNP hnRNP K associated with mRNA precursors Domain B oc oc B B oc topology 3 antiparallel B stands and 3 or helices AminoacyltRNA synthetases complexed with cognate tRNAs h 1 Transfer RNA tRNA is the 39adaptor39 molecule that enables the Genetic Code contained in the nucleotide sequence of a messenger RNA mRNA molecule to be translated into the amino acid sequence of a polypeptide chain The key to this process lies in the specific recognition of the correct tRNA molecule by an aminoacyltRNA synthetase enzyme Which attaches the correct amino acid for the tRNA to the acceptor stem at the 339 end of the molecule AminoacyltRNA synthetases from all organisms belong to one of two classes depending on the amino acid they are responsible for Class I enzymes are generally though not always monomeric and attach the carboxyl of their target amino acid to the 239 OH of adenosine 76 in the tRNA molecule Class II enzymes are generally dimeric or tetrameric and attach their amino acid to the 339 OH of their tRNA except for phenylalaninyltRNA synthetase which uses the 239 OH Class I Glu Gln Arg Gys Met Val Ile Leu Tyr Trp 1 l a 02 12 a a 1 1391 1quot Class II Gly Ala Pru Ear Thr His Asp Asn Lys Phe HELL3239 mi 2 sci3 12 or 22 121 Two distinct domains connected by hinge module 20 oftRNA surface is buried 2500 A When function as dimers each bind one tRNA Acceptor stern Hinge region Anti codon reccogniti on Structure of GlutaminyltRNA swthetase Cterminal domain 241557 6 antiparallel Bstrands enclosed by loops and ochelices Interact with acceptor stern of tRNA and perform catalysis The structure also contains a classic 39Rossman Fold39 Hinge connection 207240 Consists of 4 short ochelices Interact with ribose and phosphate groups N terrninal domain 1206 Recognition of anticodon Speci c interaction Consist of 5 stranded Bbarrel Lies on the side of the major groove Strands S1 S4 S5 S3 S2 S1 antiparallel except between S5 and S3 1 ocheliX between S3 and S4 ProteinRNA and RNARNA interactions GlutaminyltRNA synthetase D 100p T PC loop 39 fE quot5 I l I 6 G G C Interactlons 200 A A 2 0 Speci c El conformational Nonspeci c Anticodon Stern with 0c he1ices 5 antiparallel Bstrands anked ssRNA genome M82 bacteriophage M82 capsid protein binds to sequence speci c RNA stemloop structure controls assembly of Virus 0 us T L 3 A61 o quotA85 y HOSewn Asn A87 0 39 I lt IN Nquot 3939OCIgt ThrA59 H N gtS Va1A29 o r ThrA45 Val 829 N N 39 OH39 ThrB45 SerB47 Lysem 5 RNA bases A4C5 U6 and A10 A10 shown to ip out from unbound state RNA binding proteins N Wu Mm AW 0ng Fula39m 1 lwirp m RNA 0f asp zl Hum RNA seems to bind to surface of Bsheet RNA bases in ss loop regions seem to be able to conformationally move to base stack with adjacent bases or aromatic side chains Not possible in dsDNA unless heliX distorted bent as seen in TATA boxbinding protein ssDNA proteins may function the same way as RNA binding com um 14 m many ToMn39l39if Svde clams ruler5 frm 0L Slw l prote1ns Proteins and symmetry Protein Ncuvamwnidase bunil pemamer of AB5 toxins Senum amyloid P component Anrolysw n GroEL 205 proleasame Bacterial LH 1m RNAbinding attenlualion protein Puna protein from bacteriophage SPPI Baclcnal LH1 Tobacco mosaic virus disk Rotational s elry Composition ml 7 757 57017 a By IBBIE 0 17 17 Buried surface1 00 A2 14 1953 39 2941 15 1547 15 3702 38 45 38336 49 2383 30 4541 Viruses symmetry Viruses come in many shapes sizes and compositions All carry genomic nucleic acid RNA or DNA 21 a Sdlvllilf Tobmm Nr mlsls Virus 1 Tmn Bum39rv39npmgu39 In Tuburm Mnsuk Virus 1001quotquot Structurally and genetically the simplest are the spherical viruses Purpose of protein Viral capsid Assembly Subunits must recognize each other to form a stable capsid noncovalent interactions gtgt self assemble Infection Must be able to transfer nucleic acid from one host to another gtgt stable and recognize receptor Small genome Genetic economy few structural proteins symmetry identical building blocks Simple Spherical Viruses Watch 30 nm From geometry considerations Two 3D solid objects use a single point symmetry operator to produce the theoretical maximum possible identical units to build a solid object Icosahedron and Dodecahedron Identical symmetry point group 532 Enclose maximum volume Icosahedron Dodecahedron Spherical Virus Shells have Icosahedral Symmetry Built from 20 identical equilateral triangles 5fOld aXlS at each corner Triangles are arranged to enclose the volume inside 1 If If NM 3fold at each facewm 5 triangles 10 triangles 5 triangles Icosahedr al Symmetry Axes 339f01d 2fold Icosahedral Symmetry Each triangle is divided into 3 asymmetric units gt A related by 3fold aXis Tl 60 proteins Minimum number of protein subunits that can form a Virus shell with icosahedral symmetry is therefore equal to 60 gtgt Since there are 20 faces and each face has three subunits the total number of subunits is 3 X 20 60 Triangulation numbers T There are constraints preserving speci city of interactions within an icosahedron Caspar and Klug 1962 Showed that only certain multiples l347 of 60 subunits are likely to occur The more subunits used to build the Virus the larger the volume it encloses T h2hkk2 Where h and k are any integers Satellite Viruses STNV are Tl Bromo Viruses T3 Icosahedral Symmetry Slightly More Complicated arrangements entamer 180 proteins p 240 PrOtelnS 60 X T of subunits in a capsid Can get up to T217 Iridoviridae Coat protein capsid Capsid Proteins Bacterial Plant insect and animal Viruses have a similar motif an eightstranded antiparallel Bbarrel loops Wedgeshaped arrangement seen in Virus structures Inside is hydrophobic Examples of Viral Bbarrels Satellite tobacoo necrosis virus Polio Virus VPl quotrarerc All proteins in a given virus Human rhinovirus 14 VP2 have very similar motifs even N42 when there are no amino acid similarities Virus life cycle structurefunction Attachment to host cell gtgt Host cell receptor recognition Proteinligand interaction Transfer of genetic material gtgt transport to nucleus Nucleic acid and protein syntheses Assembly Release from host cell Avoid immune system Picornaviruses Examples common cold polio hepatitis Small RNA virus 300A diameter Contains 4 structural proteins VPl4 VPl 3 MW 30000 different aa sequences P3 VP4 7000 interior 15 A vm A vvz Surface of Virus gtgt function canyon 25A deep and 1230A wide a if mountain antibody binding sites 5fold axis Receptor the adhesion molecule ICAM I Antibody binding sites decoys Antiviral drug design Base of WI hydrophobic pocket WIN compounds bind deep in the Bbarrel motif Prevent uncoating gtgt spin off vaccine stability Virus Structure Exceptions to the Bbarrel motif Bacteriophage M82 ssRNA genome 5stranded antiparallel sheet small hairpin and two ochelices Dimer is the basic building block of the capsid lO Bstrands with interchanged ochelices Virus Structure Exceptions to the B barrel motif Alphaviruses Example Sinbis Virus enveloped RNA genome cause encephalitis T4 eapsid Virus Structure Other arrangements eg Retroviruses Type B Lentiviruses Type C CryoElectron Micrograph HIV 1 AAV 2f01d 3 fold 5 fold Future Gene therapy


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