Week One Lecture Notes
Week One Lecture Notes BI404
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This page Class Notes was uploaded by Jessica Niswonger on Saturday February 6, 2016. The Class Notes belongs to BI404 at Southeast Missouri State University taught by Dr.Lilly in Spring 2015. Since its upload, it has received 17 views. For similar materials see cell biology in Biology at Southeast Missouri State University.
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Date Created: 02/06/16
Bl404 Week 1 Protein Structure 12516 mtida bands 180 Peptide Bond Undergoes resonance delocalization of e Acts as a plane effects structure End up with 2 planes connected with two bonds with free rotation around them only certain angles favored Regions of stability Regular structures not random 0 Repeated Alpha Helix m iinn tgrm nlus 39 r u or I Amino Carbonyl terminus Iemminus B39Cta Turn lb Side View 36 residues 39utrn Flgili L5 Mommaquot hbjy ii39ulh Edam 3912mwHl39num1Multanpans Cariboxyl terminus Eur 3H MaliaIII 6c Bilth Six r Edition EDGE WH heeman and Company Secondarv Structures Helix o Formed because bond angles 0 Stabilized by H bonding on peptide backbone 0 Extended alpha helix is B sheet Align in antiparallel strands lntramolecular H bonding Connected by loop or turn BI404 Week 1 Protein Structure 12516 B sheets can have different characteristics on either plane Can have different characteristics 0 Different geometric shapes can have different properties Structures have to get connected 0 Turn B turn shortest H bonding along peptide backbone Sharp turn Wont typically form a box 0 Usually will have longer stretches loops connecting protein structures 0 Not de ned structures 0 No regularity in loops unlike a sheets and a helix 0 No hydrogen bond to produce regularity Core IQ Folding if e Water Unfoldln g 7 Surface U nfollded protein lNative protein Protein Folding All structures end up under in uence of solvent water 0 Will drvie folding o Hydrophobic core hydrophilic edge usually Maximize interaction of polar R groups and water 0 Energy releasing process Forms stable folded proteins BI404 Week 1 Protein Structure 12516 all Ca baclklbnne trace b Ball and stick 7 1 Mmlerulnr f2 Eiallogy Sun39th Edition a 20031 HvFreeman and Company Visualizing Protein Structure Look at trace of peptide backbone Ribbons are most common If it s important to know where atoms are use ball and stick Space lling shows characteristics and which will interact with which parts Structure Depiction RAS How do we know 3D structure of protein Xray crystallography 0 Have to have crystalized pure proteins 0 Cloning genes allows this to be done more Biochemistry BI404 Week 1 Protein Structure 12516 a Coiledcoil motif b iEFhandl39helixlloopheliix motif 1 Zinc nger motif Figure 39 Molecular Cell iolngy Sixth Edition 6 2008 W HlnFreweman and Company Motifs and Functional Domains Certain types of tertiary structures that are found in proteins A a motif that cos proteins B held together by R groups and divalent cations 0 Calcium ion ionic bond a helix with parallel B sheet 0 Zinc ion stabilizes it In complex organisms there are a lot of modi cations 0 About 10000 unique kinds of proteins I msmb lnhulimr domain PnoxiMAIL i Fi hmus dummirl Ellie fwl l lllli Wm manilaulna Internal i quot39 IIIh lt Iquotquot ha 1 Figure 34 rquot r F u i I J I ii MafmlfmCa iulqg smh Edition 53935 f r 2 quot39F i i E 1003 W H1Freeman and Cutmoan Hemagglutinin Some proteins form dimers by bonding to other proteins Bl404 Week 1 Protein Structure 12516 Illl rri u leg r er in l n General transcription factors L if c J xi K C o 0 RNA polymerase Q DNA Promoter Mediator complex 39l39ira nscription pitainitiation corn plex Macromolecular Machines Protein binds to other molecules and proteins 0 Bind to each other to drive function Promoter binds to form transcription initiation Few examples of proteins that work by themselves the surfaces of molecules A and B and A and C are a poor metoh and are capable of torming only a low weak hoods thermal motion rapidly lbreelre them apart molecule A randomly encounters other molecules 8 C and Ell the surfaces of molecules A and D imatoh well and therefore can form enotlgh weak bonds to withstand thermal jiolting their theretore cs stair bound to each other inure H3 Dart l of 2 Molecular iBioloeIr ollhe Cell 4th Edition Figure 3 43 Fall 2 ml 2 lMO IE Clllal BlDlDQW 03917 the CF 4th Edition Shape and Fit ProteinProtein interactions An equilibrium process 0 Cells are manifestations of equilibrium binding processes 0 Look at how long proteins stay associated Equiibrium constant Drives cellular processing Bl404 Week 1 Protein Structure 12516 f l L l 7 L 3 l 5 I i I mquot A Mini HN iiIHN Us 939 s 4cm H c a ii EH3 H13 39 cw e o i l i 5 T n 39y I l j Li cio H3C 4 Protein A Protein E Protein in Protein C Stable complex less stable temple ProteinProtein interactions driven by complementary surfaces Interactions driven by shape and electrostatic qualities If interactions make multiple ionic bonds they are stronger Vanderwals is weaker o Enough vw bonds can make it strong Multiligand binding macromolecmlle leg protein Ligand lB ieg small Ligand A maiecm39ei leg small protein All binding interactions are equilibrium driven Equilibrium binding constant by one proteins can change binding constant of other binding proteins Has to be experimentally determined Have to biochemically solve binding constant BI404 Week 1 Protein Structure 12516 1i 39 l Unfolded Mohair globule Native Protein Folding delta g Series of inermediates o Semistable initial forms 0 Single stable energy conformation is native form of protein Pathway to native form is very complicated A Hieterieal GASP Performanee 1 or a S H ll ict icin EDITJ ED 4 l Quality of Best Pre Tia rig D iffi c u Ity From Science 23 Nov 2012 Fro1n et a1 Unexpeeted features of the dark Proteume Frau IMTmff Dark Proteins Don t know anything about structure and function of proteins Dark regions 0 Know park of sequence folding but not others 0 About 50 in eukaryotes that we know nothing about BI404 Week 1 Protein Structure 12516 Folding Energv Funnel Protein folding energetically is a big funnel 0 As it turns different shapes it will ultimately end up in native shape at bottom of the funnel Peaks catch things that catch high energy folding Some are semistable and they can39t get out of it Energy needs to be added to get over energy peak All semistable shapes that can occur 0 It can signi cantly slow down folding process Go in to semi stable shapes collapse and vibrate o Successive vibrations that occur as it foes down in energy levels 0 If a region doesn39t come apart during vibration it will keep it 12716 BI404 Week 1 Protein Structure 12516 protein aggregate ine wly synthesized protein cerrect iy correctly incompletely folded folded folded forms without help with hei digested in of a prdteasome molecular increasing time Gl pe rone Figure 6 85 Molecular Eielegv of the Cell 4th Edition Protein Folding Some proteins require assistance to get folded 0 Protein chaperone Unfold it destabilize it a little bit raise energy to cause it to change shape so it can get closer to its native state Misfolded proteins aggregate together in cell Smller protein the easier the folding process 12716 Week 1 Protein Regulation Protein regulation mechanisms 1 It is there being made 0 Synthesize or destroy proteins 0 synthesis take a while signals transcription ect o Often regulation by synthesis 0 Synthesis is major development or bid responses to changes in environment 0 Relatively slow Destruction 0 Slow o Selectively tag protein Deiver to apparatus to chew them up 2 Switch on and off 0 Change in conformation Modify slightly 0 Covalent modify by attaching o Allosteric event 0 Proteinprotein interaction 0 All happen fast thistheaters These ipteteins tiinijl te genes at sites kneein as enhancers pm mm Astiveters heip dete nli39ie prawns him which ge nes Iitiill be switched m sawtng Sam at gamg m1 3quot Wattle the am at sites seem es si39ii eneers 9quot WWWi They interl39ere with the I Emmi7W functi enirig DI estimate rs l F gt and tiltiusslew transcription I TATA limit esstiustuts v A W Tltsss quotseemsquot mslesules Ema pmmu ar Lintegteite signals from estivalers arid pathspe LI39EFPFESSQFE and asset titanzsmiiprti ni tasters relay the results ts beset fEEEIDEE In magmas t9 injunetionis rem eclith rs these tasters pesilicin RNA pslymsrss at the start DI the protein ceding tegleri sf e gene and send the enzyme en its was Regulation of Svnthesis It requires building promoter initiation complex and transcription factors 0 Takes time
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