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Bioorganic Chemistry

by: Schuyler Nikolaus

Bioorganic Chemistry CHEM 468

Marketplace > George Mason University > Chemistry > CHEM 468 > Bioorganic Chemistry
Schuyler Nikolaus
GPA 3.72

Barney Bishop

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Barney Bishop
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This 32 page Class Notes was uploaded by Schuyler Nikolaus on Monday September 28, 2015. The Class Notes belongs to CHEM 468 at George Mason University taught by Barney Bishop in Fall. Since its upload, it has received 61 views. For similar materials see /class/215235/chem-468-george-mason-university in Chemistry at George Mason University.


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Date Created: 09/28/15
Bioorganic Chemistry Chem 468 January 21 2009 Bioorganic Chemistry Developmenls in medicinal Chemislry biotechnology and biolheropeulics hove blurred lhe lrodilionol boundaries belween Chemislry 0nd Granuloeyte colony stimulating factor G GSF A protein hormone stimulating the production and activation of neutrophils a type of white blood cell The natural protein was developed by AMGEN into a therapeutic Neupogen gt used to reduce the risks of infection in cancer patients undergoing chemotherapy i Amgen now produces a O i chemicallymodified GCSF 39 Neulasta with improved Lijwfammus therapeutic properties ciorerminus Amino Acids Amino Acids Pep rides and Pro reins Pro reins and pep rides have a covalen rly linked linear sequence Amino acids are rhe basic building blocks of pep rides and pro reins All pro reins are assembled From rhe 20 s randard amino acids oc amino acids Amino acid side chains confer R lil O Rquot lil O N N H O R39 H O R39quot dis rinc r chemical proper ries Ff Fl The observed physical and H2NCa frOH gt H2N fa002H chemical proper ries of pro reins o H are direc r resul rs of rhe sequence of rhese amino acid General Proper ries pK 0F fhe occarboxylic acids are in fhe range near 22 pK 0F fhe ocamino groups are near 94 M physiological pH bofh HNCOH fhe carboxylic acid and 2 14 2 fhe amino groups are ionized zwiHerions Amino acids can serve in acid or base capacities fhey are amphoferic T gt H3N CuCOQ39 H Pep ride Bonds Pepfides and profeins are Fl H Fl39 linear polymers oF amino H3NcuCO HNCuc02 acids linked by pepfide g o H H bondsquot Pepfide bonds are amide bonds between amino acids H O Formafion oF pepfide bond produces a wafer molecule 77777 Dipepfides fripepfides H N ENI CO oligopepfides and 3 A 2 polypepfides profeins peptide bond Classi cation of Amino Acids o Classi ca rion based on proper ries and charac reris rics oF ihe amino acid side I30239 chains HCR Nonpolar NH3 Uncharged Polar Charged polar Nonpolar Side Chains Nine amino acids wi rh hydrophobic side chains Alipha ric side chains Aroma ric side chains i0 H ID H NH3 Glycine GlyG 0239 H ID CH3 NH3 Alanine Ala A 020 C 3902 0H3 H CCH ng CH3 Valine Val V 00 39 I 2 CH3 H C CHQ39CQ H3 CH3 00239 H C CHQCl lgSCH3 NH Metihonine Met M 5 2 sTCH2 02 h l cHg Hg Proline Pro P 00239 H ID CH2 NH3 Phenylalanine Phe F Leucine Leu L 02 00239 CHg H C CH2 3 H C Cl l Cl l20H3 l 2 NH 1 NH N lsoleucine lle l H Tryptophan Trp W 9 Uncharged Polar Side Chains Six amino acids wi rh uncharged polar side chains Side chain hydroxyl Side chain amide Side chain phenol Side chain rhiol 00239 O H C CHgC I NH NH3 2 Asparagine Asn N 00 39 I 2 0 H ID Cl lgcl lgC NH3 NH2 Glutamine Gln Q 00239 H ID CH2 OH N H3 Tyrosine Tyr Y i0 H IZ CHgOH NH Serine Ser S 05 H ID IDH CH3 NH OH Threonine Thr T 02 H ID CHgSH NH Cysteine Cys C 10 Charged Polar Side Chains 00239 o 0 FIV amino acnds have H CH2CO 027 charged polar side my H p CHchchchz Nw Chains Aspartlc ACld Asp D NH3 Lysine Lys K 0 Side chain carboxyllc 02 C CH2CH2C 002 NH and groups lms 039 I 2 H C CH2 CH2CH2NH C 0 Side chain amines and GlutamicAcid glu E ilng NH2 guanidino group ArginineArg a 0 Sidechain imidazole 027 NH group H jCH2ltNJ NH8 H Histidine His H 11 Amino Acid Hydrogathx Ile 45 Hydropa rhy of Val 42 Leu 38 Ammo ACId Side Phe 28 Cys 25 Chains Met 19 Ala 18 Gly o4 Thr o7 Ser 08 Trp 09 Tyr 13 Pro 16 His 32 Glu 35 Gln 35 Asp 35 Asn 35 Lys 39 Arg 45 Disul de Bonds Cysfeine Cys C residues CO H N are unlque39 H gu Crb SH HS CH2m H They can Form disul de ii H 0 bonds between two Cys Cysteine Cysteine residue residue residues Disul de bonds can link separafe polypepfide chains or fhey can link cysfeine residues wifhin fhe same polypepfide chain H20 disulfide bond General Proper ries pK oF fhe occarboxylic acids are in fhe range near 22 pK oF fhe ocamino groups are near 94 M physiological pH bofh HNCOH fhe carboxylic acid and 2 14 2 fhe amino groups are ionized zwiHerions Amino acids can serve in acid or base capacifies fhey are amphoferic T gt H3N CuCOQ39 H AcidBase Proper ries oc amino acids have 2 or 3 ionizable groups H I K1 H3N caCOQH H3N cacog H I K2 I H N C CO pK oF oc carboxylic acid is A 2 A 2 in uenced by x NH3 pK of Gy Gly0 Gly39 ace nc acnd 476 pK of oc NH3 is in uence by oc carboxyla re pK of Gly me rhyl 9393 H20 G39Vquot H30 es rer 775 K lGy IlH30I Side chain Func nonal groups see 1 W PKI 203924 similar bu r weaker in uence Ti rra rion curves of pro reins and Gly0 H20 Gly39 H30 pep rides rend ro be complica red and rarely re ec r K2 Gly39lleO pK2 9o 9s individual pK values G39yol pH pK logAHA Pl12PK1 PK2 Amino Acid Nomencla rure In pep rides amino acid residues are are named by replacing ine wi rh yl Pep rides are wri r ren From amine rerminus N lerminus and carboxyl rerminus C rerminus Glx re ec rs uncer rain ry be rwen Glu or Gln Asx re ec rs uncer rain ry be rween Asp or Asn Posi rion of nonhydrogen side chain a roms indica red by greek alphabe r 0L 5 y 6 a 7 H o H N Ca C H20 H20 coo N Ca C N Hy Amino Acids Op rical Ac rivi ry All amino acids ofher fhan glycine are opfically ac ve They demonsfrafe an asymmefry such 1 ha1L fheir mirror images are n01L superimposable Asymmefric cenfers ltgt H chiral cem ers Enan omers are molecules ha1L are nonsuperimposable mirror images oF each ofher Fischer Conven rion Con guration oF groups around a chiral cenfer can be related lo glyceraldehyde Designafe isomer gt D glyceraldehyde isomer gt L glyceraldehyde All ocamino acids From profeins have fhe L sfereochemical con gura on glycine being achiral is an excep on CI F F Br Br H 17 gm a oHo Ho H H OH CIDHQOH CIDHQOH CHO CHO HO H i H OH CH20H CH20H LGlyceraldehyde DGlyceraldehyde 9H0 90239 Ho E H H3N H CIDHQOH F39i LGlyceraldehyde LcxAm ino acid 18 Dias rereomers Molecules wi rh mul riple 2 or more chiralasymme rric cen rers have 2 isomers Dias rereomers are s rereoisomers rha r differ by a r leas r one bu r no r all asymme rric cen rers Dias rereomers of L amino acids are referred ro as rhe allo Forms The D allo and L allo dias rereomers are enan riomers of each o rher Dias rereomers are physically and chemically dis rinc r Meso reFers ro molecules wi rh asymme rric cen rers rha r have an in rernal plane of re ec rion such molecules are op rically inac rive LalloThreonine cog cog H3NH H3NH ch s S cHg LQsline cog H3NH ch s cog H NHa HO H cHa DThreonine cog DalloThreonine cog cog HNH3 HNH3 ch s s cHg DQsline mesoQsline CahnIngoldPrelog Sys rem The Fischer nomencla rure sys rem can be ambiguous and awkward The Cahn Ingold Prelog sys rem provides a nomen rla rure rha r unambiguously indica res rhe absolu re con gura rion of rhe asymme rric cen rer Subs ri ruen rs on rhe chiral carbon a rom are ranked in order of priori ryHe View chiral cen rer wi rh lowes r priori ry group direc red back in ro rhe page IF priori ry of subsi ren r groups decreases going clockwise around rhe asymme rric cen rer rhen designa re if R IF coun rerclockwise designa red S Hogt H E LGlyceraldehyde cHo CHgOH 902 CO moo z w N CfH E c E 5 HaC a NH3 y w H30 CH3 LAlanine Order of prioirity functional grouips wgtxgtygtz XCHO CHO z x HOH2 OH y w HOH2 84 y SGlyceraldehyde NH3 W SAlanine SH gt OH gt NH2 gt COOH gt CHO onln gtCHgOHgt05H5gtCHggt2HgtiH biomolecules Prochiral Cen rers Tetrahedral centers Two chemically Iden rical 90239 subs ri ruen rs on a H 6 H a a b re rrahedral carbon may be 6H 8 geome rrically dis rinc r Two such a roms are referred ro as being prochiral Designa red as proR or pro5 based on same cri reria as R and S Proper ry of prochirali ry also applicable ro planar carbon cen rers H Faces are designa red as re 0 V H30 face or 5 face re face Chirali ry and Biochemis rry Chemical syn rhesis of chiral molecules usually resul rs in racemic mix rures In order ro chemically or physically differen ria re be rween enan riomers rhe process mus r involve an I asymme rric elemen r or Fl in uence ie chiral reagen rs or chiral chroma rography columns The biosynfhesis of compounds con raining asymme rric cen rers almos r always yields enan riopure produc rs 90239 H3Ngt QltH LAmino acid Triganol planar centers Covalent Slruc rures of Proteins Pro reins Pro reins serve in a broad range oF capaci ries They are oF ren reFerred ro as he building blocks oF liFe They can vary enormously in size and composi rion They demons rra re unbelievable Func rional diversi ry Their biological Func rion is a direc r resul r oF heir unique and complex s rruc rures 24 Protein Functions 0 Enzymes 0 Spider Webs o Hormones o Rhinoceros Horn 0 Antibodies o Poisons o Transporters o Antibiotics 0 Muscle 0 Structural o Feathers Levels oF Organization Primary structure 1 structure the amino acid sequence of polypeptide chain Secondary structure 2 structure local spatial organization and arrangement of the peptide backbone Generally refers to easily localized structural elements ie helices and sheets Tertiary structure 3 structure the comprehensive threedimensional structure of a protein Quaternary structure 4 structure assembly through noncovalent interactions of a larger protein structure From 2 or more polypeptide chains subunits and the organization of these subunits Sanger Method 0 The basic chemical method For protein sequence determination was developed by Sanger and involves three basic steps 1 Prepare the protein For sequencing Determine the number oF subunits Cleave disul de bonds 0 PuriFy individual subunits Determine the amino acid compositions 2 Sequence the polypeptide chains Fragment the subunits 0 Separate and puriFy the Fragments Determine the amino acid sequence oF each Fragment Repeat the above steps with a different Fragmentation process 3 Organize the completed structure 0 Use overlapping peptides to align the Fragments o Elucidate the positions oF disul de bonds End Group Analysis 0 Nterminus identi cation 1 Dimethyl amino naphthalene S sulFonyl chloride dansyl chloride reacts with primary amines Requires acid hydrolysis oF peptide Adducts detectable by Fluorescence Phenylisothiocyanate PITC Edman s reagent reacts with N terminal amine to Form phenylthiocarbamyl PTC adducts PTC adduct can be cleaved From peptide by Forming the thiazolinine using anhydrous strong acid 0 Cterminus identi cation No chemical method comparable to Edman degradation Exopeptidases gtcarboxypeptpidases can be used Generally demonstrate amino acid speci cty Usually only useFull For identiFying the rst Few amino acid residues Hydrazinolysis the peptide is treated with hydrazine and heated at 90 C Treatment with mildly acidic ion exchange resin results in cleavage oF peptide bonds producing aminoacyl hydrazides oF all the amino acid residues except the C terminal amino acid 28 NCH12 Dawsyl chlonde Fl 0 R2 0 l H L l o o a OH N ChS New HO Phenyllsolhlocyawale Fl 0 Fl 0 Hydvazme H H2 I H H l2 ll w7H Cl HiiNial 7 HzN NHZ o3o s ll Hl z Hih HFlK HN W C N Cl Fci iNiCl HiiNial39 Anhwvcus Amman 002 m 15m H O Thlazollnone denvallve mam 2 Fl Hz 0 H 04 Mg WM 0 H30 Fl 0 H2 0 i HHampHLHHHH2 Haw MLHHM O R O Mnnacyl 0 FM 0 H2 0 94 hy mzlnes 4le W44le H20 0 Dawsylmno am 6 39 quot PM I u u HaN wO NHM HzN OlO NHNHZ HMO Fl 0 HlN S LLOH H3NbLOH PTHamlnoaad lquot l HKHHCHVCHOH Reduc rion 0F ELM Disul de Bonds CH20 I Required For separahon 0F ELM IL H2OH Dlmomelol 2 x HSCHQCHQOH H CHZSH or disul de linked polypephde Dlmoerymol sfrands H JO H JO PrevemL disul de sfabilized H wile sfrucfures From inferFering SH 232223 SH 53 wifh eF cienf profeolysis 320 2 2 320 HO Disul des usually cleaved fMHJL H fhrough reduc on 3973 2 mercap roe rhanol Y gt Di rhioery rhri rolDi rhio rhrei rol Em CHE Cap Free fhiols wifh lHQ o s CH2 U alkylahng agemL O searboxymemylcysleme Iodoace ric acid s CHQH o CHQO H l N CH 30 Amino Acid Composi lion Amino acid composilion is delermined lhrough lhe complele hydrolysis oF lhe peplide and quanililalive analysis oF lhe liberaled amino acids Usually achieved lhrough acid hydrolysis using 6M HCl healed al ICC120 C Involves long hydrolysis limes 10 100h Ser Thr and Tyr are parlially degraded and lhe side chain amides of Gln and Asn are hydrolyzed in lhe process The process deslroys Trp residues Basecalalyzed hydrolysis involves lhe use oF 24M NaOH and healing lo 100 C Cys Ser Thr and Arg residues decompose under lhese condi lions Resulls in parlial deaminalion and reacemizalion of amino acids Complele enzymalic proleolysis requires lhe use oF combinalions oF proleasespeplidases Usually employed lo quanliFy Trp Asn and Gln 31 Amino Acid Composilion II Leu Ala Gly Ser Val and Glu are lhe mosl abundanl in proleins gt6 His Mel Cys and Trp are lhe leasl abundanl lt3 Ralio oF amino acids wilh polar lo nonpolar side chains is gt1 This lends lo decrease wilh prolein size Re ecls increases in volume relalive lo surFace area Folded proleins generally have a hydrophobic core and a hydrophilic exlerior Con rrolled Pep ride Fragmen ra rion 0 Endopepfidases p2 Trypsin basic residues ii LYSI Arg O rher endopep ridases show broader speci ci ries 0 Chemical hydrolysis Cyanogen bromide Me r 0 Peptide Fragmem s can usually be resolved by reversedphase chromafography gt HPLC I O HC N CHC N CH 0 H 0 Fl 0 H20 Fl 0 H H H H H H N CHC N CHC N CHC N CHO g 2 20 R 0 H20 II H I II H Fl 0 I II N CHC H20 R 0 H20 H2 Fl 0 l H H I I ll N CHC N CHC N CH C HJN CHC O 33 Sequence De rermina rion Sequencing of pep des usually done fhrough repealed cycles of Edman degrada on Peptide is usually adsorbed lo solid suppor1L PVDF or glass ller paper impregnafed wifh polybrene CNBr Limifed lo 4060 Nferminal amino acid residues Sequences of larger polypepfides can be defermined using overlapping pep de Fragmem s CNBr Trypsin 34 Characterization by Mass Spec rrome rry 0 Mass speclromelry MS is used lo accuralely measure lhe mass lo charge mz rafio For ions in lhe gas phase Elec rrospray ioniza rion ESI Yields macromolecular ions 05 ro 2 per kD Pro rona rion of basic groups MnHn ions Ma rrixassis red laser desorpfionioniza on MALDI u rilizes in rense shor r laser pulses a r A absorbed by ma rrix ma rerial In rac r macromolecules ejec red in ro gas phase usually wi rh charge of 1 2 or 3 no r uncommon Can charac rerize pro reins zSOOkD Fasf afom bombardmenl39 FAB Macromolecules are ejec red From low vola rili ry solven r using a low energy beam of Ar or Xe a roms or Cs ions Macromolecules are ejec red wi rh charge of 1 Prac rical limi r of 7kD 0 Can measure mz wilh accuracy of gt00l Pep ride Sequencing by MS MS can be used lo sequence shorf peplides lt25 residues 0 Uses a fandem mass speclromefer MSMS Chemically iner1L afoms are used lo FragmemL selecfed pepfide ions Masses of Fragmem s can lhen be delermined Analysis of lhe mass speclra of Families of Fragmem s make if possible lo assign amino acid sequence of Fragmem s and lhe Full lengfh polypepfide Canno r differen ria re be rween Ile and Leu Similarly Gin and Lys can be diF cul r ro diFFeren ria re 35 Pep ride Mapping Used fo Facilifafe fhe defermina on oF profeins similarrelafed fo profeins wifh known sequence Begins wifh confrolled Fragmem a on oF fhe known and unknown profeins Comparison oF Fragmem s by PAGE or HPLC should indicafed Fragmem s in fhe unknown profein fhaf diFFer From fhaf oF fhe known profein The varianf Fragmem s can be isolafed and sequenced Three Dimensional S rruc rures of Pro reins Bio ogica activity and therapeutic uti ity is inextricab y inked fo ded conformation of the protein Granuloeyte colony stimulating factor G GSF A protein hormone Igt stimulating the production and activation of neutrophils a type of white blood cell tothe 3dimenslona Protein fo ded conformation is margina y stab e and is impacted by environmenta conditions i N tar39minus Cetermlnus Protein 3 D Structure The 3D structure of 0 protein is determined by the amino acid sequence A protein has 0 unique or nearly unique structure Protein function depends on structure Although multiple structures are theoretically possible proteins qdopt unique structures Noncovolent interqctions stqbilize protein structure Protein structure is dynamic in nature Structures of proteins can be elucidated by means of crystallography or by NMR 40 Levels of Organization Primary structure 1 structure the amino acid sequence of polypeptide chain Secondary structure 2 structure local spatial organization and arrangement of the peptide backbone Generally refers to easily localized structural elements ie helices and sheets Tertiary structure 3 structure the comprehensive threedimensional structure of a protein Quaternary structure 4 structure assembly through noncovalent interactions of a larger protein structure from 2 or more polypeptide chains subunits and the organization of these subunits 41 Secondary Structure and the Peptide Backbone Secondary structure 2 structure the local conformation of the peptide R backbone ZC39KVM Z Regular backbone folding patterns R R Helices Ola Pleated sheets 339 Ca Turns Peptide group has rigid planar structure Peptide bond has 40 double bond character due to resonance Peptide bonds are usually in trans conformation H II o T 31 TNkcat O39 R 0 5 42 Peptide Conformation and Torsion Angles Peptide backbone is a linked sequence of nearly planar peptide groups 4 Cu N W Cu39ccarbonyl Steric constraints associated with 4 and 1p angles Staggered vs eclipsed conformations in ethane Eclipsed conformation is leJ mol39l less stable than is the staggered conformation an energy barrier Substituents other than H result in even greater steric interference to free rotation Some conformations ma become sterically forbidden Secondary Structure 0 There are three common secondary structural elements Helices or helix Sheets B sheet Turns isturn Loops Q loop Helical Structures Helices result Wheh a polypeptide chaih lS TWisTed The same exTehT about each ofiTs Co s q aha 1p A helix cah be characterized by The humber of residues n required To make a complete Turh aha by iTs pitch which is The distahce a helix rises with each Turh Helices have ah ihhereht chirality cah be either righT or left hahded BackbOhe HbOhdihg COhTribuTes To stability of The helices aha other 2 structure elemehTs Figum 810 Examples of helices The x helix Right handed helix combining allowed conformational angles and favorable backbone Hbonding 57 w 47 7 h 36 residuesTum 7 pitch 54 A Hbonds between NH group donor of nth residue and the CO group acceptor of the n4th residue Core of the helix is tightly packedvan der Waals contacts The side chains are directed outward and backward Present in both fibrous and globular 1 proteins 39 g Sequence and Helix Stability The stability of the oc hellX is affected by the amino acid sequence A stretch or clusters of charged residues can be destabilizing Amino acid residues with bulky side chains can be destabilizing Appropriately placed charged residues can form stabilizing ion pairs Appropriately placed aromatic residues can have favorable hydrophobic interactions Proline and Glycine are not common in 0L helices 47 Other Helical Conformtions 0 Less prevalent than the ahelix Described using nm notation n number of residues per turn m number of atoms including H in the ring formed by the backbone Hbond An ochelix would be a 3613 helix 0 The 310 helix right handed helix with pitch 60 A torsion angles slightly in forbidden range Usually observed only for short segments 0 The nhelix 4416 helix the wideflat conformation results in the an axial hole A mildly forbidden conformation Only found in short segments a few residues within larger helices Polyprolinehelices left handed helix with 3 residues per turn and a pitch of 94 A 48 3 Structures The Bsheet is characterized by peptide chains in extended conformdtions with d repeating pattern of q and 1p dngles Hbonding between adjacent peptide strdnds 5 strdnds Two varieties of 3sheet Antiporollel 5 pleoted sheet gt H bonded peptide stronds run in opposite directions Porollel 5 pleoted sheet gt H bonded peptide stronds run in the some direction term pleoted refers to the foct thot sheets hove o rippled or pleoted oppeoronce when viewed from edge Mixed poroIIeI ontiporollel sheets ore common In 5sheets the side chains of successive amino acids are extend to opposite sides of the sheet 49 B sheet Configurotions AM a 0 0 o c o v v39v v t v v o o o 39 o o o K 13ij 393 391 339 z 0 C 0 39 m a o o a 5 W v v o vtv r v r o o c Iquot C a C W W c r t b a o B sheei Topology The 5 pledled sheels in globuldr proleins exhibil d pronounced righl hdnded lvvisl dnd oflen form The cenlrdl cores of proleins The conneclions belween slrdnds mdy be or simple hdirpin lurn or mdy be or more complex crossover eilher dbove or below The pldne of lhe sheel Conneclivily of slrdnds comprising 0 sheel cdn be very complex Anlipdrdllel slrdnds mdy be linked by or simple hdirpin lurn Pdrdllel slrdnds usUdlly linked by or longer crossover conneclion lhdl does nol lie in The pldne of lhe sheel S rruc rurol Propensi ries a b e Ix Sheet Ammo Ac39d P Classification PF ClaSSificatiOquot Ala 142 H 083 i Arg 098 i 093 i Asn 067 b 089 iv Asp 101 I 054 BF Cys 070 i 119 hi Gln 111 h 110 hi Glu 151 H 037 3 Gly 057 B 075 bn His 100 I 087 hi Ile 108 h 160 H Leu 121 H 130 hi Lys 116 h 074 bn Mei 145 H 105 hi Phe 113 h 138 hi Pro 057 B 055 BF Ser 077 i 075 bu Thr 083 i 119 hi Trp 108 h 137 h Tyr 069 b 147 H Val 106 h 170 H 52 Turns and Loops These are nonrepetitive structures rm Yypa u n mm 0 Reverse turns is bends l O S turns ll 0 e g Usually involve 4 7 c1 a 1 successive amino acids Two classes Type land quot 0 3 Type II V W The Q loops C Usually 6 1 6 residues O a O l39 Enduto end distance of Link successive helix or sheet structures Tertiary Structures 0 The tertiary structure describes the long range interactions of amino acids 0 There are two major protein classes Fibrous Globular Proteins can be subdivided into four classes All oc l tellX All S sheet Mixed ocS proteins Mixed or 5 proteins 6 Superseconddry Structure 0 Secondary structures ore often grouped together into superseconddry structures or motifs thdt ore used by mdny globuldr proteins 0 Groups of structurdl motifs combine to form the fold 3 structure of Cl protein 0 There ore Cl finite number of unique folds The number of unique folds is estimdted to be iOOO To ddte only 6OO hove been observed in ndture 55 Superseconddry Structurdl Motifs Greek key motif l i 1 5045 motif 5 hairpin cm motif l d N Hit N C motif Greek key 0 The 3043 motif is the most common motif in proteins An x hellCCll crossover connects two consecutive pdrdllel strdnds of d 3 sheet The 3 hairpin is dnother common motif Here two sequentidl ontipdrdllel strdnds of d 3 sheet ore connected by or tight reverse turn The do motif involves two successive 0L helices pocking dgdinst edch other with their oxes incline so OS to allow efficient hydrophobic pecking The helices ore oligned ontipdrdllel to edch other In the Greek key motif 1 3 hdirpin folds in upon itself so OS to form 1 4 strdnded ontipdrdllel 3 sheet Most common motif used to achieve this 56 Fibrous vs Globular Proteins Fibrous Proteins Highly elongated molecules Secondary structure is dominant structural motif Relatively simple Generally serve in structural capacities protective connective supportive Structures not known in great detail Globular Proteins Large and highly diverse grouping of proteins The 3 structure of globular proteins arises from the folding and organization of 2 structural elements Serve in a variety of capacities Despite vast structural diversity globular proteins share some common structural features Globular Proteins Spa rial Dis rribu rion of Amino Acids Amino acid residues wi rh nonpolar side chains Val Leu lle Mel and Phe usually lie in The in rerior of a pro rein Amino acid residues wi rh charged polar side chains Arg His Lys Asp and Glu usually lie al The pro rein surface Amino acid residues wi rh noncharged polar side chains Ser Thr Asn Gln Tyr and Trp usually lie on The surface of pro reins bu r frequen rly are in The in rerior When in The in rerior They are usually involved in hydrogen bonding Nearly all buried hydrogen bond donors form H bonds wi rh buried hydrogen bond accep rors Globular Pro rein Inleriors Globular proleins are relalively compacl The inlerior region is lighlly packed wilh a packing densily of O75 This packing densily is comparable To lhal associaled wilh molecular cryslals of small organic molecules Despile The lighl packing inlerior side chains adopl exlendedlow energy relaxed conformalions Hierarchal Organization 0 Proteins are hierarchically organized Domains large protein subunits consisting of contiguous compact and physically separable segments Subdomains and sub subdomains smaller discreet structural subunits combine to form domains and subdomains respectively Hierarchal Organization Consistent with the observation that most hydrogen bonding in proteins occurs locally 0 They are structurally independent and have characteristics of small globular proteins 0 Domains often have specific functions such as binding of small molecules These binding sites are often located near the domain clefts QuaTernary STrucTure Many proTeins consisT of more Than one pepTide chain They consisT of mulTiple subuniTs A proTein s auaTernary sTrucTure consisTs of The spaTial arrangemenT of These subuniTs The subuniT consTrucTion of many enzymes provides The sTrucTural basis for The regulaTion of Their acTiviTies ProTomers in The majoriTy of oligomeric proTeins are arranged symmeTrically ProTein STabiliTy NaTive proTeins are only marginally sTable under physiological condiTions The free energy of denaTuraTion is only O4 lltJmol of amino acid meaning a lOO residue proTein is sTable by 40 lltJmol The energy required To break a hydrogen bond is 20 ltJ mol 0 ProTein sTrucTure and sTabiliTy arises Through a delicaTe balance of sTabilizing and desTabilizing forces


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