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Introductionto Biochemistry

by: Mrs. Francis Runolfsson

Introductionto Biochemistry CHEM 501

Mrs. Francis Runolfsson
GPA 3.93

Guilherme Indig

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Guilherme Indig
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This 184 page Class Notes was uploaded by Mrs. Francis Runolfsson on Tuesday October 27, 2015. The Class Notes belongs to CHEM 501 at University of Wisconsin - Milwaukee taught by Guilherme Indig in Fall. Since its upload, it has received 18 views. For similar materials see /class/230294/chem-501-university-of-wisconsin-milwaukee in Chemistry at University of Wisconsin - Milwaukee.


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Date Created: 10/27/15
f t a UNIVERSITYofWISCONSIN MILWAUKEE a Dep of Chemistry amp Biochemistry Prof Ihdig Chemistry 501 Handout3 Amino Acids Peptides and Proteins Chapter 3 Lehninger Principles of Biochemistry by Nelson and Cox 5 Edition WH Freeman and Company 39200 Amino ACIds H3NC H R 1C1HO gHO HO H H ltOH 3ZH20H HZOH I I I I COO coo 39 of L and D glyceraldehyde H3N clt H cltfm3 EH3 EH3 LAlanine DAlanine The amino acid residues in proteins are the L isomers Amino acids can be classified by R groups Nonpolaraliphal39ic R groups coo H3N CI H c0039 H3N Cl H H CH3 Glycine Alanine COO H3N ltII H 1 2 CH CH3 CH3 Leucine c0039 l H HZN cle l HZC CH2 Proline C00 4 H 3N C H H CI CH3 CH2 CH3 lsoleucine COO39 Il l N f H CH CH3 CH3 VaHne CO 039 39l mN c H Methionine Polar uncharged R groups C00 C00quot H3N C H H3KI c H CHZOH H CI OH CH3 Serine Threonine COO39 H3N C H 2 c H2N o Asparagine COOquot H3N CI H 1 2 SH Cysteine COO39 H3N H Clquot 139 c H2N o Glutamine Reversible formation ofdisul de bond by the oxidation of two molecules of cysteine C00 C0039 Cysteine I I CH2 CH2 l 2H 2e Vt Cystine I 2H 2equot CH2 CH2 Cystelne CH NH3 CH NH3 C00 C0039 eg two polypeptide chains of insuline Aromatic R groups c0039 c0039 coo l H3N C H H3N C H H3N C H CH2 CH2 I C CH Indoe NH ring OH Phenylalanine Tyrosine Tryptophan Absorbance 0 230 240 Absorption of ultra violet light by aromatic amino acids Tryptophan Tyrosine 250 260 270 280 290 300 310 Wavelength nm Intensity of Intensity of incident transmitted light light Monochromator V A10012 I Detector Sample uvette with c molesliter of absorbing species LambertBeer Law log IoI 8 C L Positively charged R groups C00quot C00quot C00 I H3N CI H H3N CI H H3N CI H CH cl Cl CH2 CH2 C NH CIH imidazole 2 2 I C N CH2 NH H NH3 CI KIH2 guanidino NH2 Lysine Arginine Histidine Negatively charged R groups c0039 c0039 l f H l f H EH2 EH2 c0039 EH2 c0039 Aspartate Glutamate Uncommon amino acids also have important functions prothrombim coo at a of Ca binding proteins OOC CH CH2 CH COO39 I 4 3 NH3 plant cell wall HO C CH2 collagen 5 2 1 yCarboxyglutamate HZC CH COO quot H H elastln 4Hydroxyproline H3ltl CH2 CIH CH2 CH2 IJH C00 1 Ema aC5 V 1 collagen OH NH3 TEE23 5Hydroxylysine I Militia git Ti Lysine CH3 NH CH2 CH2 CH2 CH2 CH COO residues can NH3 Hg Rm 6 N Methyllysine Desmosine myosin Residues created by modi cation of common residues already incorporated into a polypeptide HSe CH2 CH COO39 rare introduced during protein 300 additiona amino acids NH3 synthesis rather than created have been found in cells selenocysteine through a postsynthetic modi cation Reversible amino acid modifications involved in regulation of protein activity 1 0 P O CHz CH COO o NH3 Phosphoserine u 1 Cquot HEC o c CH 2 CH 2 CIH COO39 O F39 O CH CH COO NH3 0 NH Glutamate methyl ester Phosphothreonine o N II o OP O CHz CH COO39 H I I o H2C 0 I3 0 CH a cu coo39 o 390 1le3 HZN Phosphotyrosine 39 NH 3 c NH CH CH2 CHz CH COOquot 395 Adenylyltyrosine I NH CH 3 aN Methylarginine HN CH2 CH2 CH2 CH2 CH COO co NH3 6N Acetyllysine Amino acids can act as acids and bases Nonionic and zwitterionic forms of amino acids Titration of glycine T quotrz R C co R C c 0 CIHz L CIHz 3 clquot Hsz OH H3 1ICOOH 0039 C00 Glycine Nonlonlc form ZWItterIonIc form PK 950 39i T 39 R C COO 2 R C COO H 7 NH l IIH PH 39 Fl 5 3 2 Zwitterion 39 PKI 234 as acid 4 H H n 015 15 2 R c coo H R c COOH quot eqmva39emquot NH 411m Titration curves predict the zWittzrion 3 electric charge of amino acids as base lsoelectric point or isoelectric pH amphoteric amphoytes amphoteric electrolytes pl 12 mm mm 12 23934 93960 53997 Effect of chemical environment on pKa pKu 2 4 6 8 10 12 Methylsubstituted W H carboxyl and amino groups CH3 coon CH3 coo CH3 N3 CH3 NH2 H H Acetic acid Methylamine The normal pKa for a The normal pKa for an carboxyl group is about 48 amino group is about 106 H NH2 Carboxyl and EH3 H EH3 Z l H C 39 COO VT H C C00 amino groups l in glycine H c coo T I H H H H H uAmino acid glycine aAmino acid glycine K 234 O Electronegative oxygen atoms in the carboxyl group pull electrons away from the amino group lowering its pKa a Repulsion between the amino group and the departing proton lowers the pKa for the carboxyl group and oppositely charged groups lower the pKa by stabi lizing the zwitterion Amino acids differ in their acidbase properties Amino acids with pka of the COOH group 18 24 R groups that do not ionize pka of the NH3 group as 110 Amino acids with ionizable R groups eg 00 C0 20039 3900 CIOOH CIUO III C OUquot H3N lt 2H Hg EH Zita 31 quotZn 3931 HN H HN H H3N CIH HIM EH CH CH1 CH2 CH2 CH CH CH i PKI PKR PKz I ci39 fquot 139 CIHZ H cu K n cu K H CH K H cH COOH CODH NT 00 ci P L ci p L cgr P 2 c 1 H H e H e H e K Glul amule P 2 1 93957 1o Histidine PKz 917 a 8 pKR 5 60 pH pk pH 6 535 PK1 E pK1 519 i 132 i i 5 u i 0 1o 20 30 0 10 20 30 OH equivalents OHquot equivalents three stages three ionization steps gt three pka values TABLE 3 1 Properties and Conventions Associated with the Common Amino Acids Found in Proteins pKa values Abbreviation pK1 pK2 pKR Hydropathy Occurrence in Amino acid symbol M COOH NHg R group pl index proteins T Nonpolar aliphatic R groups Glycine Gly G 75 234 960 597 04 72 Alanine Ala A 89 234 969 601 18 78 Proline Pro P 115 199 1096 648 16 52 Valine Val V 117 232 962 597 42 66 Leucine Leu L 131 236 960 598 38 91 Isoleucine Ha I 131 236 968 602 45 53 Methionine Met M 149 228 921 574 19 23 Aromatic R groups Phenylalanine Phe F 165 183 913 548 28 39 Tyrosine Tyr Y 181 220 911 1007 566 713 32 Tryptophan Trp W 204 238 939 589 09 14 A scale combining hydrophobiclty and hydroohiiiolty of R groups it can be used to measure the tendency of an amino acid to seek an aqueous environment 7 vaiues or a hy drophobic environment values See Chapter 11 From Kyte1 amp Doolittle RF 1982 A simple method for displaying the hydropathic character oi a protein J Mol Biol 157 7 32 39Average occurrence in more than 1150 proteins From Doolittle RE 1989 Redundancies in protein sequences In Prediction olPruteln Structure and the Principles ometein Conr formation Fasman 60 ed pp 599623 Plenum Press New York TABLE 3 1 Properties and Conventions Associated with the Common Amino Acids Found in Proteins pKa values Abbreviation pK1 pK2 pKR Hydropathy Occurrence in Amino acid symbol Mr COOH NH R group pl index proteins T Polar uncharged R groups Serine Ser S 105 221 915 568 708 68 Threonine Thr T 119 211 962 587 07 59 Cysteine Cys C 121 196 1028 818 507 25 19 Asparagine Asn N 132 202 880 541 35 43 Glutamine Gin Q 146 217 913 565 735 42 Positively charged R groups Lysine Lys K 146 218 895 1053 974 739 59 Histidine His H 155 182 917 600 759 32 23 Arginine Arg R 174 217 904 1248 1076 45 51 Negatively charged R groups Aspartate Asp D 133 188 960 365 277 735 53 Glutamate Glu E 147 219 967 425 322 35 63 A scale combining hydrophobiclty and hydrophiliclty of R groups it can he used to measure the tendency oi an amino acid to seek an aqueous environment 7 values or a hy drophobic environment values See Chapter 11 From Kyle J amp Doolittle RF 1982 A simple method for displaying the hydropathic character of a protein J Mol Biol 157 32 Average occurrence in more than 1150 proteins From Doolittle RF 1989 Redundancies in protein sequences In Prediction ofProtein Structure and the Principles ofProtein Conr formation Fasman 60 ed pp 5997623 Plenum Press New Vork Peptides are Chains of amino acids T1 39l T2 Hs CH fl OH H N CH COO39 o hydrolysis H20 H20 condensation R1 R1 I H3 CH CH COO39 W Two amino acid molecules can be covalently joined through a substituted amide linkage termed a peptide bond to yield a dipeptide Pentapeptide 0H Amino Carboxyl terminal end terminal en Serylgchiltyrosylalanylleucine or SerGIyTyrAIaLeu or SGYAL Peptides are named beginning with the aminoterminal residue which by convention is placed at the left just a few residues a oligopeptide many residues a polypeptide Biologically active peptides and polypeptides occur in a vast range of sizes 39 c lt quotntltltm I n n cln N L Asyanylrvphenylalanlne methyl em ispi lme wall If at least two chains are identical a the protein is said to be oligomeric and the identical units consisting of one or more chains are referred to as protomers Multisubunit proteins have two or more polypeptide chains associated noncovalently 3 2 hi1 Molecular Number of Number of weight residues polypeptide chains Cytochrome c human 13000 104 1 Ribonuclease A bovine pancreas 13700 124 1 Lysozyme chicken egg white 13930 129 1 Myoglobin equine heart 16890 153 1 Chymotrypsin bovine pancreas 21600 241 3 Chymotrypsinogen bovine 22000 245 1 Hemoglobin human 64500 574 4 Serum albumin human 68500 609 1 Hexokinase yeast 102000 972 2 RNA polymerase E coli 450000 4158 5 Apolipoprotein B human 513000 4536 1 Glutamine synthetase E coli 619000 5628 1 2 Titin human 2993000 26926 1 The vast majority of naturally occurring proteins contain fewer than 2000 amino acid residues Polypeptides have characteristic amino acid compositions TABLE 3 3 Amino Acid Composition of Two Proteins Number of residues per molecule of prurein Some proteins contain chemical groups other than amino acids conjugated proteins TABLE 3 4 Conjugated Proteins Class Prosthetic group Example Ammo Bowquote Bowquote Lipoproteins Lipids BlLipoprotein acid cytochrome c chymotrypsirlugerl of bood Ala e 22 Glycoproteins Carbohydrates Immunoglobulin G g I Phosphoproteins Phosphate groups Casein of milk Asp 3 s Hemoproteins Heme iron porphyrin Hemoglobin glls g 18 Flavoproteins Flavin nucleotides Succinate I1 any 9 5 dehydrogenase Ely 1 31 2 Metalloproteins Iron Ferritin His e 6 10 Zlnc Alcohol Leu 6 19 dehydrogenase by 1 1 21 Calcium Calmodulin File 4 s Molybdenum Dinitrogenase Pro 4 9 SII I 28 Copper Plastocyanln Thr 8 23 Try 1 8 Tyr 4 4 I I I I I Val 3 23 The nonammo aCId part of the conjugated protein IS Total 104 245 usually called its prosthetic group ln some common analyses such as acld nymalyga Asp and Asn are not readily aislmgulslled lmnl aaan mum and are logem a 5i naer Asx lm a Slmllarly ylnan Gin and Gin cannul be disll gmshem llley ale tog lher designated Glx or Z In aadluonrm ls oeslmyed dluunai placedwes must he Employed in man an aaaumle amssmem ul mnlplela ammo acld content Protein Separation and Purification Column Chromatography Reservoir Protein sample mobile phase Solid porous matrix stationary phase Porous support Crude extract gt gt gt fractionation 0 Large net positive charge IonEXChange Net positive charge C h romatOg rap Net negative charge 0 Large net negative charge Example Cationexchange chromatography Polymer beads with negatively charged functional groups Protein mixture is added to column containing cation exchangers Proteins move through the column at rates determined by their net charge at the pH being used With cation exchangers proteins with a more negative net charge move faster and elute earlier Exclusion Chromatography gel filtration to column containing cross linked polymer Protein molecules separate by size larger molecules pass more freely appearing in the earlier fractions lt ii Affinity Chromatography 0 Protein of interest 0 Ligand Mixture of proteins Solution of ligand Protein mixture is added to column containing a polymerbound ligand specific for protein of interest Unwanted proteins ii I 5 Protein of interest are washed through E j i is eluted by ligand column 3 4 5 6 7 8 solutlon Refers to the total number of units of enzyme in a solution TABLE 3 5 A Purification Table for a Hypothetical Enzyme Fraction volume Total protein Activity Speci c activity Procedure or step ml mg units unitsmg 1 Crude cellular extract 1400 10000 100000 10 2 Precipitation with ammonium sulfate 280 3000 96000 32 3 Ion exchange chromatography 90 400 80000 200 4 Sizeexclusion chromatography 80 100 60000 600 5 Affinity chromatography 6 3 45000 15000 Note All data represent the status of the sample after the designated procedure has been carried out Activity and specific activity are de fined on page 94 A measure of enzyme purity it increases during purification of an enzyme and becomes maximal and constant when the enzyme is pure Number of enzyme units per milligram of total protein 10 unit of enzyme activity amount of enzyme causing the transformation of 10 pmol of substrate per minute at 25 C under optimal conditions of measurement Electrophoresis gel stained with a proteinspeci c dye eg coomasie blue SDSpolyacrylamide gel 1 2 s O m Myosin 200000 Well sGalactosidase 116250 A Glycogen phosphorylase b 97400 jlf Dlregtlon Bovine serum albumin 66200 migration Ovalbumin 45000 Carbonic anhydrase 31000 i L Soybean trypsin inhibitor 21500 Lysozyme 14400 Crosslinked polymer Pm m im quotfRNA UnkMWquot I palymerizefrum E mzi Protein M Unknown pOIyacrylamlde S standards protein a as 2 acts as a molecular sieve slowing the migration of proteins approximately in proportion to their chargetomass ratio CH3CH211SO Na Relative migration soeectrio focusing Twodimensional electrophoresis d 1 3 t i An Imphnlyte 7 Firs 39 saluxinn is 9N9 G i De easlng Ivuorparaled O dlmensmn t P into 9a Isoelemi i focusing i it 2 m i 39 5 er A g p i v N a is l is r M J mi n z i o i r F r0 0 A419 lsoeletmdows ng A slnble pH gladlonl minin xalulinn is Mm staining Woleins gall 395 Fla 5quot sols Is asubllxhed In nu Idded and eledvk areshown m be Pquot 3 3quot 9 9 gll a u uppnuuo eld ls reapplied dlstribuled llong pquot anquot elenric uid gradiennccordingm mm pl values TABLE 3 6 The lsoelectric Points of Some Proteins Protein pl gt Pepsin lt10 quot 1 L i v Egg albumin palyltryImldeael Serum albumin 49 Urease 5 0 BLacroglobulin 52 Hemoglobin 68 Sound Myogiohin 70 Chymotrypsinogen 95 galelenwvhuruls Cytochrome c 107 maxim Lysozyme 110 There are several levels of protein structure Primary Secondary Tertiary Quaternary structure structure structure structure iffy y 0 9hr u i 1 e ml v 27 g 53 k t u gilt s 2quot r I 7 I I a 1quot x Amino acid a Helix Polypeptide chain Assembled subunits residues Multisubunit roteins Particularly stable arrangements of ArrangementIS Spec 0f amino acid residues giving rise to POIYPePt de SUbun tS recurring structural paterns All aspects of the 3D folding Includes disul de bonds of a polypeptide Determination of amino acid sequence A chain IQHS 81 B chain Amino acid sequence if 1 of bovine insulin 5 12 5 23 10 years of work by Sanger i LIE The amino acid sequences of millions of proteins have been determined Identical in human pig too quot9 rabbit and sperm whale 25 I a 1 Identical in cow dog Thr goat and horse Short polypeptides are sequenced using automated procedures r 33 Polypeptide N02 N02 N02 FZNB N02 N 2 NE NH39 A R1IH w VRV1 I H 25quot Identify amino terminal Sanger s met70d a Clad C o acids residue of polypeptide for the zfDirl tro ml 24Dinitrophenyl aminoterminal P any 2 derivative derivative R H of aminoterminal reSIdue of polypeptide E 0 residue N Phenylisothio TH TH H cyanate 5C C l V C N Identify aminoterminal Isl H 5 l l39 Sc residue purify and recycle CF3COOH H bl 0 1 CIH HN LIZH remaining peptidefragment I I 1 throu hEdman rocess co o R R1 9 p all n I R2CH derivative of amino derivative of amino The Edman degradation d 39d 39d 39d o acu res ue acl res ue procedure carned out R2 R3 H ampCICNCCM Shortened on a sequenator PTC adduct 3 H lcl H H lg Peptide d I reveals the entire sequence of a peptide Large proteins must be sequenced in smaller fragments Breaking disulfide bonds Disulfide bond cystlne cf szSH irer o HOH Cl CHI Clquot IZHOH C quotquot JJ 1 CHZSH Dithiothreitol DTT NH 0CI I IIH OC Hcecuzilslio 390 CH2 ltIZH HCI CH2 SH HS CHz CIH 20 0 O H N CO HN J J Cysteic acid 11 Fr aetylation R YESIdIlES I by d tat LL IO BREE 9 JJ Nquot r HZCH2SCH27COO39 ooccnzisicr11clu 0 HN r1quot Acetylated 39H cysteine residues Ceaving the polypeptide chain TABLE 37 The Speci city of Some Common Methods for Fragmenting Polypeptide Chains Reagent biological source Trypsin bovine pancreas Submaxillarus protease mouse submaxillary gland Chymotrypsin bovine pancreas Staphylococcus aureus V8 protease bacterium S aureus Aspvarotease bacterium Pseudomonas fragi epsin porcine stomach Endoproteinase Lys C bacterium Lysobacter enzymogenes Cyanogen bromide Cleavage pointsi Lys Arg C AYE C Phe Trp Tyr C Asp Glu C Asp Glu N Phe Trp Tyr N Lys C Met C All reagents except cyanogen bromide are proteases All are available lrom commercial sources Residues furnishing the primary recognition point for the protease or reagent peptide bond cleavage occurs on either the carbonyl C or the amino N Slde of the indicated amino acid resrdues Some proteases cleave only the peptide bond adjacent to particular amino acid residues Result H 2 55 Procedure hydrolyze separate amino aci 5 Ordering the pep de fragments ltltIm N adN mnrrlongt waNhNur Polypeptide react with FDNB hydrolyze separate amino acids 24 DInltrophenylglutamate reduce Conclusion Polypeptide has 38 amino acid residues Tryp sin will cleave three times at one R Arg and two K Lys to give four frag ments Cyanogen bromide will cleave at two M Met to give three fragments E Glu is amino detected terminal residue dlsulfide bonds if present H5 SH cleave with trypsin GASMALIK placed at amino terminus separate fragments sequence by Edman degrada on EGAAYHDFEPIDPR because It begins With E Glu DCVHSD placed at carboxyl terminus because it does not end with TABLE 3 7 lhe Speci city of Some Common YLIACGPMTK R Arg or K Lys Methods for Fragmenting Polypeptide Chains Reagent Dialogcal source Cleavage nulnls leave with Cyanogen I Trypsln LysrAmC bromide separate fragments EGAAYHDFEPIDPRGASM overlaps Wlth S Abovlrlr39e nancwlasl A g C sequence by Edman degradation TKDCVHSD and allowin U max am pm ease I I mouse submaxlllary gland Met C g Chymol in PheTrpTyrC ALIKYLIACGPM them to be ordered bovme pancreas Staphylococcus aureus V8 protease Aspr Glu C 39 reus Asp Nplolease Aspr Glu N establish baclenum Pseudomunas frag sequence r Amino l l l Carbox mm stomach Phe39T39p39T N EGAAYHDFEPIDPREASMALIQlLIACGPMTHbCVHSD y terminus I u I n I I terminus EndOprutemase Lys C Lys C bacterium LysDbaclEr enzymagenes Cyanogen bromide Mel C Amino acid sequences can also be deduced by other methods Amino acid sequence protein I II II II DNA sequence gene CAGTATCCTACGATTTGG codon Correspondence of DNA and amino acid sequences Gln Tyr Pro Thr lle Trp Investigating proteins with mass spectrometry Mass Glass Sample spectrometer capillary so ution lt E 39G i a u 5 High 3 voltage 39 T Vacuum 9 interface 0 Callisiun 800 1000 1200 1400 1600 MSl V ell MSZ Detedov 21 Li i mz ii pltlt T i i I Eiemaspray Separation BJang ionizaron 100 A V2quot 9quot b gt 75 t39 R o R3 n5 v n i H H H i H H u i 0 5 ya HIM C C N C C N C N C C N C C 50 H H i Ii H H 1 II N u39 g R1 0 a o y4u y u H y g ysrr 6 y7 25 u R o n3 o 5 Y1 n y ii HHIii HHl 0 7 llllhl H2NCcuf N 39fENCCO x l H ii ml i 4 Huh ll l I quot R 200 400 soo 800 1000 mz Insoluble II 39 d Cl CH1 polystyrene ma peptl es AA m h R o a mi quotmm a w 1 Attachment of arboxyHerminal t eaclive it and proteins can 1T 22quot39 Fm TCH J gifesf be Chemically R a I II Fm E cquot C Cquot2 J quot39 i o i Fm NCIH02 Protecting group is removed I bv ushingwilh solution i H onlaininga mild organic base Amino add 2mm i ON Cgt protected 1 raminn group is 39f 7 Dicyclahexylcarbodiimide amva equot a HzNCHCO C z O I carboxyl group 7 i DCC by DCCt i I u Aminn mupolamino i and 1 a GCks amvated I I E quotfquot arbnxylgmup alaminu acid Fmoc hl CH C O 2 tolarm peptide and g I H N o i II quotrtquoti H H TABLE 3 8 Effect of Stepwise Yield on Overall Dicvchhexv39ma WM 5 Yield in Pa tide S nthesis Reactions to l R2 o n1 o I I I H I repeated as neressary Overall yield of nal peptide Fm l u I rrx gt when the yleld of each step ls H H Number of restdues In Completed peptide is the nal polypeptide 960 998 HF dEPVO EK EdBS in reaction HF cleaves ester linkage between 1 ii 3 pepiiae and 1 i l l fl 7 31 29 94 Ha cH c N CH c tr F CH 51 13 90 39 39 H o R1 0 CHZ o c Ir CH c o H 00 Amino acid Fmo residue 9fuorenyImethoxycarbonyl Nonpolaraiphatic R groups coo coo 60039 l l H HaN CH H3N C H l 1 RIM H H H l l HZC CH2 Glycine Alanine Proline coo39 coo39 HaN lI H HgN CI H le H CH3 cH clH CH CH3 CH3 Leucine lsoleucine Aromatic R groups coo 00 0039 A e Hsuecl H H3N ltZ H 3Nc 7H CH1 CH2 cl it CCH NH OH Phenylalanine Tyrosine Tryptophan Polar uncharged R groups cooquot coo 0039 o coo H H I H c H HgN C H 3 f quot3quotf 3 f H 01on H Cl OH In CH3 CH3 a 5 Vanna Serine Threonine Cysteine Cleo coo cloa H3NCIH H3N f H H3N cl H EH2 cle le CH2 EH2 HIN o C s HZN o 3 As ara Ine Glutamlne Methlonlne p g Positively charged R groups Lysine Negatively charged R groups CI M CI 7 00 0039 H3Nv Ci H3NC H I clquot clui HSN ltIZ H HsN lZ H C NH n cu 2 Cl 2 H quot c0039 le ltiH maquot quot5quot Aspartate Glutamate Arglnlne HHO WM o CH2 o CH2 0 0 OH UNIYERSITY WFSCQNSIN MIlWAIIKEE Dep of Chemistry amp Biochemistry f Indig OHH Chemistry 501 Handout 14 Glycolysis Gluconeogenesis and the Pentose Phosphate Pathway Chapter 14 Lehninger Printiple uf Biathemistry by Nelsun and Cu 5 quot Edi un WH Freeman and Cumpany Major pathways of glucose utilization Extracellular matrix and cell wall Glycogen polysaccharides starch sucrose synthesis of structural storage polymers OXidation Via oxidation via pentose phosphate pathway glycolySIs Ribose 5phosphate Pyruvate The first phase of glycolysis the preparatory phase a Glucose Preparatory phase m Phosphorylation of glucose priming and its conversion to reaction ADP 0 glyceraldehyde 3phosphate Glucose 6 phosphate Hexokinase Phosphohexose H OH isomerase Fructose 6phosphate 9 0 012 o HZ 0H second H HO Phospho priming H 0 fructokinase1 reaction ADP OH H Fructose16 bisphosphate O CH2 o CH2 0 Aldolase cleavage H H0 of 6carbon H OH Triose sugar phosphate phosphate 2 Sucarbon OH H isomerase phosphates f0 Glyceraldehyde 3phosphate O CH2 fHCH 39I OH Dihydroxyacetone phosphate e eHz EH26H O The second phase of glycolysis the payoff phase 0 GI ceraldeh de 3 hos hate V V P P o CHz IZH cH 0 Triose Dlhydroxyacetone phosphate OCH2CCH20H Phosphate E isomerase b Payoff phase 0 Oxidative conversion of Glyceraldehyde 3phosphate 2 o CH2 ClH C gy eradehyde 3phosphate 2P3 on H to pyruvate and the coupled oxidation and ZNAD formation of ATP and NADH phosphorylation 2 H o Glyceraldehyde 13Bisphosphoglycerate 2 0 CH2 CH Clt 3p as hate first ATP 2 ADP cl O dehydrogenase forming reaction substratelevel 2 Phosphm phosphorylatian 0 glycerate 3Phosphoglycerate 2 0 CH2 H Co kinase OH o Phospho I cerate 2 Ph h I t 2 CH CH C 9y osp og ycera e I 2 I O mutase OH 0 2H 0 2 d 0 Enolase Phosphoenolpyruvate 2 CH2C C second ATP ZADP J o yruvate Inase forming reaction substratelevel 2 phosphorylation CH3CC Pyruvate 2 g o The two phases of glycolysis lza Fructose 6phosphate semnd prlmlng readion Fructose 16 bisphasphate vagz nf Ealhnn x phnspham sug w me 313mm sugar phosphms Glyceraldehyde 3phosphate Dihydmxyacemne phosphate H on isomerase o clIz o Hz 0H Phosphor fructakinase1 H Ho H OH OH H o cH2 Caro G Aldolase H H0 H on Tviase OH H phusphate isomerase IO w cHz fn c 0H vO CHz CH20H o o 137Eisphosphoglyceram2 o ch fN c 4 I 2RD on Imbslmelzvel 1 Dhasnhurvlixianl 3Phosphoglyzemle 2 2Phosphuulycemte 2 aw o inzAcKH c ON 0 0 2 uc and m fun 0 39 mug unlov mmm x2 phnsphnryla nn Pyruvate l2 u Wary R DH D 5 a Glucose quot05quot Prepurulory phase WINNEHWE quot05th o cuz fn c O H 0N T m 4 H 141 Phosphorylauon ofgluwse WWVW quotEphespm nm1w Pzzizhm priming G OH H and Its comers n to I HO OH I L a vsamerase reac um ADP 3 2 y r H on 0 Pay Phase Glucose 6phosphale o cH2 0 Oxidadve canvevsion o H 393 H Hexokinase Glyceraldehyde wvhasnhule 2 o o x TIH glytzralde ydESVphnsphake H 2 on N m pymvme and the oupled on n d i a 2mm gunman umer mm HO 0H Phusphuhexase 32F n39lw392 m C 2 H Glyceraldehyde 31 n dehydvoganusa Phospha glywaxa kinase Phospha QIytelate mmase Enohse Pyvuvne kinase Three possible cataboic fates of the pyruvate I col sis formed in gyCOySiS agschessive reactions hypoxic or V V conditiy I 2 Pyruvatel wens aerobic 2 Ethanol 2C02 nditi ns 2 Lactate 2C0 Fermentation to ethanol V 2 reamfnfat39P to ac a e In Vigor in yeast 2 AcetyICoA ously contracting muscle in erythro METABOUC citric cytes in some acid other cells and cycle in some micro organisms W 4C02 4H20 Animal plant and many microbial cells under aerobic conditions 1 Phosphorylation of glucose 6 CH2 0P0339 CHz OH 0 ATP ADP H H H Mg 4H OH H 39 Ho OH hexoklnase Ho 3 H OH H OH Glucose Glucose 6phosphate A6 167 kJmol 2 Conversion of glucose 6phosphate to fructose 6phosphate 6 2 CH20P03 1 H H Mg CHZOH 4 1 5 2 Ho OH phosphohexose H OH 2 isomerase 3 H OH Glucose 6phosphate Fructose 6phosphate AG 0 17 kJmol The phosphohexose isomerase reaction Glucose 6phosphate 4 HO 1 Phosphohexose isomerase HSCOH CHZOPOS 39 Fructose 6phosphate 5 I H pm I rl BH 3 a H c o il g oln W 0 HOCIH L HOCIH Holzon HIZOH HCOH H OH CHZOP03239 CH20P032 cisEnediol intermediate 3 Phosphorylation of fructose 6phosphate to fructose 16bisphosphate 6 CH20P0339 o EH24 ATP ADP M 2 5 H HO 2 9 H OH phosphofructokinase1 4 3 PFK1 OH H 6 Fructose6 phosphate CHZOPO 1 O CH2 0P03 5 H H0 H H 4 3 OH H AGquotD 142 kJmol Fructose 16bisphosphate 4 Cleavage of fructose 16bisphosphate 6 1 CH20P03 CH20P0339 O 5 H HO 2 OH aldolase 4 3 OH H Fructose16bis hos hate H P P 0 mezOPO3 4C 2C0 5CHOH 3CH 20H 6CH20PO339 Dihydroxyacetone Glyceraldehyde phosphate 3phosphate AG 238 kJmol The class adoase reaction CH 0P0 2 1 0 I CHZOPDJ H H6 H H Ho H Fructose 16bisphosphate Binding and opening Pmmnated f 2 ring Schiff base l 10mg CH opol 39 39 H fH20Pog I H H l H quotIo H I 2 s zmme Lysn 2co HA Ij cl om A 4 Lys 427quot M l lt quot03 quot H HocH f quot0quotquot 4 l H cI o H ActiV39eAsite Lys Rearrangement Mira H y l 5 attacks substrate leads 0 math 0 anquot HCOH l l H f0 carbonyl leading I m mat s quot l 2 1 CH0PO 39 to formation of 39 0120 base zyme CH2 P s I quot39 tetrahedral electron delocaliza ra quot Aldolase intermediatg tion facilitates subsequent steps C C bond D39hvdmxvacmne Glyceraldehyde rst cleavage phosphate 3Ph spham product reverse of cquot 0102 CIO released aldnl conden Proton I 2 3 l sation leads to exchange C0r HEDH 69 release of rst wi d ct CH OH 1 Pquot solution a mlom restores 521 i P enzyme released H lcnopo 39 H ICH20P0 391 L s Nx H20 Lys Hc Lys N c m y H I I l 17g I 0 CI H 0 H H W 5 3 Schiff base is g H B Isomenzatwn BH quot H 3 hydralyzed in l 1 quot l reverse of Schiff j l 7 base formation In Protonated Covalent enzyme Sch iff base enamine intermediate Derived from glucose carbon 1 2 3 Fructose 16bisphosphate 5 Interconversion of the triose phosphates phosphate triose phosphate isornera se 0 CH2 o Dihydroxyacetone Glyceraldehyde 3phosphate 1CH2 0 cho Ho Jc H H c OH H 5C 0H 6tLH2 o aldolase CH2 0 H co c o 4 0 CHZOH I Derived from glucose carbons Derived from glucose carbon 4 5 6 1 4 or 3 HCo DGlyceraldehyde 5 or 2 ii 0H 3phosphate 6 or 1 3CH20 Subsequent reactions of glycolysis b Fate of the glucose carbons in theformation 0f glyceraldehyde 3 ph0sphate AG 75 kJmol 6 Oxidation of glyceraldehyde 3phosphate to 13bisphosphoglycerate o H NAD NADH H C O HCIOH HO IIl O39 393 92f39 Glyceraldehyde Inorganic dehydrogenase 3phosphate phosphate 0 II OC I O HOH CHZOPog39 AG 63 kJmol 13Bisphosphoglycerate The glyceraldehyde 3phosphate dehydrogenase reaction I V szomg WADquot Glyceraldehyde NAB HltZOH quot 3 hos hate is P P cv l l Glyceraldehyde r 7 7 3Ph05Phate 395 Formation of enzyme Is 39 dehydrogenase Cys substrate complex The Cys gng39git fzzgas a reduced 1 covalent thiohemiacetal a 39 s lnnkage forms between the of 8 when NAD r IS bound and is in the more reactive SUbSIratfetzndclhe d thiolate form mm o e39 ys res39 ue39 mu szoPo HCOH CH20P0 The covalent thioester p HCOH linkage between the quot C 0 substrate and enzyme s A 3 co I undergoes phosphorolySIs Cys 0P0 attack by Pi releasing the 13Bisphosphoglycerate satond product 13 bisphosphoglycerate The enzymesubstrate intermediate is oxidized by the NAD39l39 bound to the CH20P0 39 I actlve Site r iNAD C0 O P OH NADH lleoPog l Pi NAD 0 0 HltltH NADH lx C o l The NADH product leaves the active site and is replaced by another molecule of NAD n E 7 Phosphoryl transfer from 13bisphosphoglycerate u 0 to ADP quotquot 3 C 039 I o HCOH 20 m 13Bisphosphoglycerate ADP 2 phosphoglycerate Mg kinase 0 o o o r o c o HCIZOH 0 CH20P0 39 0 IE 3Phosphoglycerate ATP AG o 185 kJmol 8 Conversion of 3phosphoglycerate to 2 phosphoglycerate 0 039 o 039 M92 HC OH phosphoglycerate C op03 mutase I CH2OP03 CHz OH 339Ph05Phoglycerate 2Phosphoglycerate AG 1 44 kJmol Th e p h p h Phosphoglycerate mutase 39 7 7 His mutase reaction ml H c 0 H lt H N Hzc o Po HN 3 Phosphoglycerate I His Phosphoryl transfer occurs between an activesite His and 2 CH of the substrate A second activesite His acts as general base catalyst ooci His I 2 N H c 0 P03 vquot H1C o Po H H UN 23Bisphosphoglycerate 23BPG N HIS Phosphoryl transfer from 23 of the substrate to the rst active site His The second activesite His acts as general acid catalyst 39 39 His 2 V 00C 03F My H IJ o Po 39 N HZC 0 H 2Phosphoglycerate quotN H 7 Is 9 Dehydration of 2 phosphoglycerate to phosphoenolpyruvate O O O 0 C H20 C H C OPO3 A C 0P03 enolase HO CHZ CH 2 2Phosphoglycerate Phosphoenolpyruvate AG 0 75 kJmol 10 Transfer of the o o 9 phosphoryl group from Cquot phosphoenolpyruvate quotZ O P O39 9 to ADP CH2 039 0 IE Phosphoenolpyruvate ADP Mg K pyruvate kinase 0 039 0 f oo c co 2H2 taummerization EH3 9 Pyruvate Pyruvate C H 3 enol form keto form Pyruvate 9 o m Adenine AG 314 kJmol ATP Entry of glycogen starch disaccharides and hexoses into the preparatory stage of glycolysis CHon O Trehalose Lactose Ho H lactase trehalase OH H H H 0 CHZOH z o 1 4 Glycogen starch H I OH H H H amylase DGa actose I OH H P39 phosphorylase sucrose HO OH UDPgalactose sucrase H OH Glucose UDPglucose oGlucose ATP 1phosphate CHZOH hexokinase O phosphogluco H H HOCH CH CH mutase 2 2 OH Ho H Ho Glucose H on 6phosphate DMannose DFruct se A1lllexokinase Fru ctose ATP lfructokinase 6phosphate Fructose 1phosphate frucm phosphate aldolase Fructose 16 bisphosphate Glyceraldehyde Dihydroxyacetone osphate triose phosphate 1 isomevase Glyceraldehyde 3 phosphate Mannose 6phosphate phosphomannose isomerase Feeder pathways for glycol ysis H OH Feeder pathways for glycolysis EHzOH O Trehalose Lanose Ho H H u h I Iadase e a 352 H H OH Hzou 2 0 L Glycogen starch H oquot H H H uimylase DGa anose OH H Pi phosphmylase 1 sucrose HO OH UDPgalactase sucrase H OH Glucose UDPglucose DGlucose ATP 1phosphate CHZOH hexukinase h 0 p osphogluco H H MUCH cmou mutase H Ho OH HO OH H Ho Glucose H OH 6phosphate H OH H DMannuse nFructose ATP Aexaklnase m llruclokinase Fructose M quotquot e E39Ph phaquot 6phosphate Fructose 1phosphate phosphomannose fructose l isnmerase phasphim aldolase Fructose 16 bisphosphate Glyceraldehyde Dihydroxvacetone phcsp a e triase phosphate isomerase Glyceraldehyde 3phosphale ATP M m m no fw mme ppm w an Fmplunylnhm u gmquot A Me An quotmum u clump mam 4512 x 3 mm a U 1 9mmquot mm W LHquot A O u nu gymng mm a n n munquoter a AD u qunmI hphnwhu MN MW 53 any 4quot n 5 mg a 1151quot 5 quot WET 11me a ammmmyaqpnmm ma ag v an 39 mnmmnmdnummn 4 m imun n Win 141 g m pmpm mu m Wu n Ia N In 391 Na i5quot39 mw umquot um 13 pump Dietary polysaccharides and disaccharides undergo hydrolysis to monosaccharides Dextrin nHZO n Dglucose Maltose H20 2 D glucose Lactose H20 Dgalactose Dglucose Sucrose H20 D fructose D glucose Trehalose H20 2 D glucose Glycogen breakdown by glycogen phosphorylase Nonreducing end CHZOH CHZOH o o H H H H H H H OH H OH H Ho 0 o H OH H OH Glycogen starch n glucose units I 0FLo glycogen starch 0H phosphorylase CHZOH CHZOH H o H H o H H H H OH H I OH H quot0 O P O quot0 o H OH I H OH Glucose Glycogen starch 1 phosphate n1 glucose units Other monosaccharides enter the glycolytic pathway at several points CIHZOPO C0 1 CH20P0339 CHZOH 2CO Dihydroxyacetone 3 phosphate HOCH 4 H HCOH fructose 1phosphate I HSCOH aldolase Io 6CHZOH HEOH Fructose 1phosphate CHZOH Glyceraldehyde Conversion of galactose to glucose 1phosphate Defects in any of the three enzymes in this phatway Cause galactosemia in humans CHon H vlz OH Ho nlz H HO Ii H H OH nzon DGalactitcl Galactose methabolite involved in galactokinase de ciency galactosemia Galactose Mg galanukinase ADP CH20H O HO H H OH H o Galactose1phasphate H OH UDP UDPglucose galactose I 4 91mm phosphate uridylyluansferase Glucose 1phosphate HIGH 0 UDPgalactose H0 H H 4 OH H O UDP H OH NAD UDPglucose NADH H 4 epimerase CHZOH O H H O 4 OH H o H OH NAD UDP quose NADH H1 4epimerase CH2OH o UDPglucase H H H OH H H OH Fates of pyruvate under anaerobic conditions Fermentation O O O O C NADH Hquot39 C NAD O HO IZ H lactate CH3 dehydrogenase CH3 Pyruvate LLactate Pyruvate is the terminal electron acceptor in lactic acid fermentation O 2 5 1 kJ lmo39 no net change in G39W m NAD or NADH acidification in muscle and blood limits the period of vigorous activity ZNAD 2NADH 2 Pyruvate 2 Lactate Ethanol is the reduced product in ethanol fermentation tightly bound coenzyme thiamine pymphosphate C0 NADH H quot39 O O 2 c TPP O H NAD OH I M9 2 I CO C CH 2 I pyruvate alcohol I CH 3 decarboxylase CH 3 dehydrogenase CH 3 Pyruvate Acetaldehyde Ethanol Industn39alscae fermentations yield a variety of common foods and industrial chemicals The alcohol dehydrogenase reaction Acetaldehyde H P4 7 7 7 coz 2 7 n CH3 0 H H 05 d 0 Alcohol dehydrogenase 0 T q I Iquot I I o I I Z I C 2 I N on m NADH Nicotinamide adenine dinucleotide NAN OP70 quotquot2 l ltN fquot o cn2 o N quot2 lt M H 7 H H OH OH Zn2 at the active site polarizes the carbonyl oxygen of acetaldehyde allowing transfer of a hydride ion pink from NADHThe reduced intermediate acquires a proton from the medium blue to form ethanol I I 4 LZ Z c If an CH3 c OH r L NAD Fl Ethanol Thiamine pyrophosphate TPP and its role in pyruvate decarboxylation CH3 thiazolium ring l I H NH2 c s CHZ N g2 1 I Cquot k JCH2 CHz o P o P 039 N CHI l 0 O Thiamine pyrophosphate TPP N CH3 I NH2 c s CHz N I 39139 x CHz CH2 o ili o ii N CH3 0 0 H acti CHZHC 0 acetaldehyde Hydroxyethyl thiamine pyrophosphate 02 in the H thiazolium cl ring of TPP R I S ionizes rapidly R r H 0 CH 3 H 0i c TPP C H cs CH Elimination of R N I Pyruvate the thiazolium I o R CH c cation yields CH3 3 Il amta39dehyde TPP carbanion Ace a39dEthe The TPP carbanion H H n attacks the carbonyl CH3 c o H group of pyruvate Cb I S OH R N 0 R39 Ha fvl C H 3 Hydroxyethyl c o TPP R 5 5 R Protonatlon CH3 generates Decarboxylation is hydroxyethyl H facilitated by electron co2 delocalization into the thiazolium ring of TPP CH H E on zcOH 3 A i3 R IJV s N S S resonance R 39 stabilization gt R 39 CH3 C H 3 Thiamine pyrophosphate Enzyme Pathways Bond cleaved Bond formed 0 1 0 I 0 Pyruvate decarboxylase Ethanol fermentation R C39C R 39C 039 H 0 o Pyruvate dehydrogenase Synthesis of acetyl CoA R gc R2c aKetoglutarate dehydrogenase Citric acid cycle sc A u n Transkemlase Carbonassumllatlon reactions R3 c CR R3 ccR5 Pentose phosphate pathway I I H H Blood Other glucose Glycoproteins monosaccharides Sucrose Gluconeogenesis Glycogen Disaccha rides Starch L Glucose 6 ohosphate A Animals KEnergy Plants Carbohydrate synthesis from simple precursors Phosphoenol pyruvate Citric acid cycle Pyruvate Glucogenic Glycerol 3Phospho amino glycerate acids Lactate Triacyl C02 glycerols xation Glycolysis Gluconeogenesis ATP lums I hexokinase glucose srphosphalase Glucose ADP 6phosphate H20 ATP Fructose pi phospho 5 Ph s ha e fruuose fructokinase1 Dihydroszzzetone yeacetone glycoysis and phate 2 Glyceraldehyde 3phosphate 2P 2P 2 NADquot 2 NAD gluconeogeneSIs WWW WW I 39 213Bisphosphoglycevate In r IV r at e 2ADP ZMDP 2ATP 2ATP 2 3Phosphoglycerate 2 2 Phosphoglycerate 2 an 2 ADP 2 Ph sph quot PEP arboxykinase pyruvate kinase 2 GTP 2 Oxaoacetate 2 ATP 2 ADP 2 Pyruvale pyruvate carboxylase 2 ATP Glycolytic reaction step AG klmo AG Idmol 1 Glucose ATP 4 glucose 6phosphate ADP 167 334 2 r39 3 FL 39 r 17 0t025 3 Fructose 6phusphate ATP gt fructose 16bisphosphate ADP 142 222 4 Fructose 1 39 39 39 39 quot39 39 phmpknh 238 6 to D glyceraldehyde 3phosphate quot 39 rquot F39 39 39 quot 39 39 3phosphate 75 0to4 Glyceraldehyde 3phosphate Pi NAD 13bisphosphoglycerate NADH H 63 2 to 2 5 6 7 13Bisphosphoglycerate ADP 3phosphoglycerate ATP 188 0 to 2 8 39 39 39 quot 39 39 39 44 0 to 08 9 2 Iquot 39 39 ti 39 39 39 H20 75 Oto 33 Phosphoenolpyruvate ADP gt pyruvate ATP 314 1 67 O m J Ar L Note Au r u um 191 4mm L a n 7 J 39 L 39 L r501 MIN H a cm x 39u Pmpnmtoryphnsn m W Enm meymmaNuwNm 4m mm m K N umwmnuamuxm 3 7 mm mm a I on glymmldnhydaiphmphme Pnyn p manhunmlnamr mm mm mm N N D Nmmm 2n N mmntmmrd Q N my oN N N N 3 Phusphchnxoso Io N J mum N W Barman N m mmquot Frudon vnuxvhau HN New D m a u a Mamrun mm N Na 99quot th W N N 2 i a VIIuh MINquot Aup aN N Menm o MNN iN R gmquot NWLENNWWN QM KN mm W N quot5quot quot N No x 5 I n gm quotquot quot quotW m n u N quot4 gumu awry quotmm m an M m 15 N quotI mquot quot lawman 1N2 W a numammdtmmk ltgth gtlt lt m m L 6 5933 39 7 2 o ninydmymmnphnspm Mari m Immmhmm quot44 5 mm 5 r Bicarbonate Pyruvate 0 HO c CH J c o 3 ATP Synthesis 3f phosphoefopyruvate pyruvate rom I uva e carboxylase blotm ADP Pi o o C CH 2 c c Oxaloacetate o 39o g o rugtc CH2 c c 390 Oxaloacetate U c 0 ll O Ir O Ir I O 0 0 0 GTP PEP GDP carboxykinase C02 0 Po Ph h t CH2cl coo SP Denolpyruva e Role of biotin in the pyruvate carboxyase reaction Pyruvate carboxyluse HC0339 ATP Site1 ADP cHgt 0 0 0 r Long biotinylLyslquot tether moves o 39 COZfrom site1 39I 57 3945 to site 2 M o I Y 36 e oc I 7 o o o I Site 2 c c cunoz o Pyruvate l o o I c CH2 C Oxaloacetate Alternative paths from pyruvate to phosphoenopyruvate AmrylnA D 17 mm m c srm m mm mm quotFm Wm f oE co Pram Dehydlogml m 35322 mineW new Citric acid mm quot0 j cycle o TN im m Milm gt1 DV iI39A lilHlE In u m Mvdmlnn 1mquot 3 a quotIquot Nydnlmn 7o quotrm mm m x l J NFL Isedtnle gammy d 32mm nxyl m a Dahydmgznllinn PC n gm EA5N 4SM 0 v39 mmwmi PEP cytosolic PEP arboxykinase co Oxaloacetate cytosolic H ma te 0 dehydrogenase NAD Ma ate Malate PEP mitochondrim NAD mitochondrial PEP co ma arboxykinase 2 dehydrogenase w H Oxaloacetate Oxaloacetate pyruvale pyruvate carboxylase C02 carboxylase CO2 Pyruvate ruvate Mitochondrlon Cytosol Pyruvate Pyruvate lactate w H dehydrogenase NAD Lactate Fhowhomuiun Pyruvate HCO 3 ATP gt oxaloacetate ADP Pi X2 Oxaloacetate GTP phosphoenolpyruvate CO2 GDP X2 Phosphoenolpyruvate H20 2phosphoglycerate X2 2Phosphoglycerate 3phosphoglycerate X2 3Phosphoglycerate ATP 13bisphosphoglycerate ADP X2 13Bisphosphoglycerate NADH H r glyceraldehyde 3phosphate NAD r Pi X2 Glyceraldehyde 3phosphate dihydroxyacetone phosphate Glyceraldehyde 3phosphate dihydroxyacetone phosphate fructose 16bisphosphate Fructose 16bisphosphate gt fructose 6phosphate Pi Fructose 6phosphate glucose 6phosphate Glucose 6phosphate H20 gt glucose Pi Sum 2 Pyruvate 4ATP ZGTP 2NADH 2H r 4H20 gt glucose 4ADP ZGDP 6Pi 2NAD Note The bypass reactions are in red all other reactions are reversible steps of glycolysisTl1e gures at the rig ht indicate that the reaction is to be counted twice because two threecarbon precursors are required to make a molecule of glucoseThe reactions required to replace the cytosolic NADH consumed in the glyceraldehyde 3phosphate dehydrogenase reaction the conversion of lactate to pyruvate in the cytosol or the transport of reducing equivalents from mitochondria to the cytosol in the form of malate are not considered in this summary Biochemical equations are not necessarily bal anced for H and charge p 501 Citric acid intermediates and many amino acids are glucogenic Citrate Pyruvate Isocitrate ocketoglutarate T SuccinyICoA QA9 gt oxaloacetate Succinate Ammo aCId Fumarate catabollsm Malate CAC Intermediates TABLE 14 4 Pyruvate Succinyl CoA Alanine lsoleucine Cysteine Methionine Glycine Threonine Serine Valine Threonine Fumarate Tryptophan Phenylalanine aKetoglutarate TYTDSlne Arginine Oxaloacatate Glutamate Asparagine Glutamine Aspartate Histi ine Proline mm L a u r nI A 39 liver glycogen 39 quot I I 39 n the an quotm 39 39 leucine and lysine 39A are unable to furnish arbon for net glucose synthesis AmyKoA um Jam 91 a cuo ua i ceo39 x OO39 N Wgt DI lIlhu buntingmm mum luau m malaln I m Mug 1 quot0 n mm in Cilric acid mu 39 cycle 4 c can 1 1Amnlma on cau39 D m Hymunn 1mm am M Hydntlan I I Fumnrale l H ou u Ko u lsudlmu l mumLI liorlllnie cor dullymagnnam mum mmquot dnlbulylIlun WWHB M YNz C 39 My 00 mle tall ymhlun IWV im ma Suninile hemqluu lu inraw 0 M dihydmyMu my 39 wKelnglullnle 1w 5 i s an any P39os inylu p ox an ImlbulyIIlm phnlplnryll an METABOLIC PATHWAYS hypoxic or ana r b39 o Ic conditions 2 Ethanol 2C02 Fermentation to ethanol in yeast 2 Acet glycolysis 10 successive reactions anaerobic 2 Pyruvate ndifons aerobic conditions 2co2 Fermentation to lactate in vigor OA ously contracting muscle in erythro citric cytes in some acid other cells and cycle in some micro organlsms Animal plant and many microbial cells under aerobic conditions AcetylCDA O H Condensation Hg E SACDA H20 IDASH mm r m oc coo39 Ho c coo39 quot2 C CH2 c Dehydration Dehydrogenatmn oxaloaceraw mare mam Citric and 0mm quot2 deh dro enase 3900 y 9 cycle H0CIH CH coo39 Malate clil2 mo cisAconitale COO II 20039 H H Hydration umarase acunitase H20 Hydration oo39 0 Fumarate quot Hcl Ho CH lsocitrate coo quotmime isocitrate 10039 dehydragenase dehydmgenase Oxidatlve decarboxylation Dehydrogenation C 2 C uketaglutarale H2coo col C39H su ylCnA dehydrogenase I Clo W cl rcov complex H2 0 Succinate CIH2 lac aKetoglutarate CoA SH CS C A GDP C02 ADP Succln lCoA P y Oxidalive Substratelevel decarboxyla lon phosphorylation Extracellular matrix and cell wall Glycogen polysaccharides starch sucrose symhasis ol ural storage mars am Vi axidalian via pamose phosphate I c I 5 pathway 9 y 7 yquot Ribose Sphosphate Pyruvate Blood her glucose Glycoproxeins monosaccharides Sucrose Starch Disacc Iarldes A Glultose 6 phosphate AL Animals KEnergy Plums Phosph ol pyruvate Pyruvate Glucogenic Glycerol 3Phospho amino glycerale acids Lactate Tviac co2 glycerols xation Glycolysis Gluconeogenesis ATP lucos pl hexokinase glutose 5phosphatase 058 ADP 6 phosphate 10 ATP Fructose phospho G39Pl pha e fructose lmctokinase1 F to e 16 bisphosphatase ADP 16 bisphusphate H20 Dihydroxyacetone Dihydroxyacetone p ospha e phosphate 2 Glyceraldehyde 3phosphate 2 PI 2 Pi 2 NAD 2 NAD39 1 NADH 2 H4 1 NADH H 2 13Bisphosphoglycerate l2 ADP 2 ADP 2 ATP 1 ATP 2 3Phosphoglycerate 2 2Phosphoglycerate 2 GDP 2 Phosphoenol 2 ADP pyruvale PEP carboxykmase pyruvata kinase 2 GTP 2 Oxaloacelate 2 ATP 2 ADP 2 Pyruvale pyruvale arboxylase 2 ATP Dihydmxyacuono phosphnle 0 M i NM 0 a quot1 Glucose bio Sc a Preparavory phase m u u Phnsphnryhllon olglucose plimlng D on n I and its unvenlan m vuuiun W 0quot glyceraldehyde3phosphale ADP 1 I H OH Glultose6phosphlle o o n H n D Hexokinnse on n H H C2 thphnhexase quot W lsomemsa Fructose phnsphlle o N o Mr cm mud n No hawker mame quot 0quot 39runukinasel ruuion aquot Fructosel6 lsphosphnle M cw o Aldolase d w M quot0 n has wguglluivhlll has halc V M I1 9 P 2330 6 immense uhosyiulu a I Glyceuldehyde rphosphale 0ckzNH on Feeder path ways for glycolysis preparatory phase CHZOH O Trehalose Lactose Ho H H trehalase lactase OH H H OH CH20H 2 0 L Glycogen starch H I OH H H H amylase DGa actose OH H Pi phosphorylase Sucrose HO OH UDPgalactose SUCI BSE H OH Glucose 4 UDPglucose DGlucose ATP 1phosphate aon hexokinase Phosphoglum H 0 H HOCHz CHZOH mutase H 0 OH HO H Ho Glucose H OH 6phosphate OH H DMannose p D39chmse Aexokinase ATP liructokinase Frucmse mannose aphosphate 6 phosphate Fructose 1phosphate phosphomannose fructose 1 isomerase phosphate aldolase Fructose 16 bisphosphate Glyceraldehyde Dihydroxyacetone phos ha te 39 se phosphate somerase Glyceraldehyde 3phosphate General scheme of the pentose phosphate pathway of glucose oxidation Nonoxiclative Oxidative phase phase I I I Glucose 6 phosphate l NADP 2 GSH glutathione reductase NADPH GSSG Fatty acids sterols etc reductive biosynthesis transketolase transaldolase 6Phosphogluconate NADP C02 NADPH ibulose 5ph sphate Precursors l Ribose 5phosphate Nucleotides coenzymes DNA RNA Extracellular matrix and cell wall Glycogen palysactharldes starch sucrose synthesis or siruuuml storage polymers quotmmquot 3 oxldatlon via pentose phosphate l I I pathway 9 yquot VS 5 Ribose 5phosphate Pyruvate z glucuse 6pnospnaxe dehydrngenzse x Inclonase Oxidative reactions of the pentose phosphate pathway rphnsphnglucanam dehydmgenasa H H NADP H phosphupenmse isamerase HD a 2 OH OH O Gluzose Erphnsphate H 2090 OH O 5Phusphn 0quot gluconoMaclone H H Zomg39 DP E NADPH q H 1L 6Phospho gluconate uRibulose 5phnsphate uRibose 5 phospha e Nonoxidative reactions of the pentose phosphate pathway oxidative reactions of pentose phosphate pathway 7C 6C I c c z 6C Ribose Sedoheptulose Fructose Glucose 5C 3C 4C 5phosphate 7phosphate 6phosphate 6 phosphate 6C epimerase I ggggggexm 5c 3c 239 transketolase transaidulase 5C BC Xylulose Glyceraldehyde Erythrose Fructose 5phosphate 3phosphate 4phosphate 6phosphate fructose 16 bispllosphatase transketolase aldolase triose phosphate isomerase 5C 7C 5 CH20H CH20H co 0 Xylulose HCOH H H 5phosphate Glyceraldehyde n use Hebeou Srphnsphaxe He eo 3 Ph05Phate Damage I cuppa CHZOP0 a Xylulose 5phosphate Siphosphate The nonoxidative phase recycles pentose phosphates to glucose 6phosphate The first reaction H CHZOH oc II 0 H C OH HO Cl H H C OH H CI 0H H C OH IZH20P03 CH20P03 Xylulose Ribose 5phosphate 5phosphate catalyzed by transketolase EHZOH f HO C H thiamine pyrophosphate I H C OH H 1 TPP C H C OH I I transketolase Hc H H IZ OH CH2 P 3 CHZOPO Glyceraldehyde Sedoheptulose 3phosphate 7phosphate CH20H CHZOH 4 0 CLO General reaction I oHiaoHl CHOH c mnskmhse c CH0quot Transfer of a twocarbon 41 R2 41 A group from a ketose donor to Ketose Aldose an aldose acceptor donor acceptor The reaction catalyzed by transaldolase CIHon Co HO C H H C OH O H H C OH c I H C OH H C0H CHZOPOE39 Sedoheptulose Glyceraldehyde 3phosphate 7phosphate CHZOPog CIHZOH CO 0 H I CI HO I H H C OH H C OH I I H C OH H C OH transaldolase I CH20P0 CH20PO Erythrose Fructose 4phosphate 6phosphate The second reaction catalyzed CH OH by transketolase 2 H f 1 HO C H H C OH I I H C OH H C OH CH20P0339 CH20P0339 Xylulose Erythrose 5phosphate 4phosphate EHZOH f H0 C H H TPP c Hc0H transketolase HCOH H IZ OH CH20P0339 CH20P0339 Glyceraldehyde Fructose 3phosphate 6phosphate Role of NADPH in regulating the partitioning of glucose 6phosphate between glycolysis and the pentose phosphate pathway Glucose glycolysis Glucose gt ATP 6phosphate pentose 6 phosphate NADPH pathway 6Phospho gluconolactone b NADPH Pentose phosphates Role of NADPH and glutathione GSH in protecting cells against highly reactive oxygen derivatives 02 Mitochondrial respiration ionizing radiation sulfa drugs herbicides antimalarials divicine Superoxide 02 radical 2H 239 H d glutathioneperoxidase y rogen H202 szo perOXIde H e H20 255 GSSG I l Hydroxyl OH free radical 1 4 glutathione reductase NADPH H Oxidative damage to Amy lipids proteins DNA Glucose 6phosphate glumse 6phosphate dehydrogenase G PD 6 Phospho glucono lactone a CD UNIVERSITYMWISCONSIN MILWAUKEE Dep of Chemistry amp Biochemistry Prof Ihdig Chemistry 501 Handout 11 Biological Membranes and Transport Chapter 11 Lehninger Principles of Biochemistry by Nelson and Cox 5 Edition WH Freeman and Company Membrane b ayer Fluid mosaic model for membrane structure Oligosaccha ride chains of glycoprotein Lipid bilayer 0 Phosphollpid K L polar he ds 2 V 1 V K 39 Integral protein Peripheral Integralprotein Peripheral single trans protein multiple Harm protein membrane helix covalently membrane helices linked to lipid Rat hepatocyte membrane type Lipid composition of the plasma membrane and organelle membranes of a rat hepatocyte Plasma r Cholesterol Inner I Cardiolipin mitochondrial r IEI Minor lipids I Sphingolipids D Phosphatidylcholine I Phosphatidylethanolamine Percent membrane lipid Glycerophospholipids 1cuzon OH 2clt H c 3CH2 o r o o LGlycerol 3phosphate snglycerol 3phosphate Saturated fatty acid eg palmitic acid V Unsaturated fatty acid eg oleic acid Glycerophospholipid general structure 0 1CH2 O no 2CH o 0 3c Hz O P O x 0 Headgroup a J s u bstituent The backbone of hOS me 0 Net charge p p p glycerophospholipid Name of X Formula of X at pH 7 Phosphatidic acid H 1 4 Phosphatldylethanolamine Ethanolamlne Hz CHZ N H3 0 35quot Cholesterol Phosphatldylchollne Choline C Hz CHz NCH33 o 3 Inner I Cardiolipin 3 mitochondrial quot El Minorlipids Phosphatidylserine Serine CHz CH NH3 1 g h 0d 561 Sphingolipids coo39 mltoc on ma c 2 V Phosphaudykho39me Phosphatidylglyterol Glycerol CH2 TH CH2 0H 1 u Lysosomal I Phosphatidylethanolamine 0 E 1 Nuclear 39 8 3 Rough ER Phosphatidylinosltol myolnosltol 45 4 3 45blsphosphate blsphosphate 2 739 Smooth ER if I Golgi Cardiollpln Fhosphatidyl CIHZ 2 Percent membrane lipid glycerol CIHOH 0 cnz o ilv o cnz O 0 ll 391 H O C Ru o i II b 239 cnz o c g Sphingolipids are derivatives of Sphingosine Sphingosine HO 3CH CH CH CH212 CH3 Fatty acid 1CH2 O X 1mm Ceramide Sphingollpld 1 general NA Ion n H mm Sphingnmyelin Phosphothnllne ilocnm3m caty neuvamnuc ac asialicadd 0 structure 0 Neutralglycolipids H H alumsylmebmside 61mm N H I Choles eml I Cardiolipin a an Minar ids Lanasykeramide Dixrior a a globaside teirasaltdlaride Gangllaside 6M2 MPIEX nlignsatdlaride a a w Sphingoliplds Phosphatidylcholine Rat hepatocyte mam bra ne ype Percent membrane lipid Rat hepalocy e membrane type Sterols have four fused carbon rings Cholesterol Percent membrane lipid Steroid nucleus Asymmetric distribution of phospholipids between the inner and outer monolayers of the erythrocyte plasma membrane Percent of total Membrane membrane Distribution in phospholipid phosphonpid membrane Inner Outer monolayer monolayer 0 0 100 Phosphatidyl 30 ethanolamine Phosphatidylcholine 27 Sphingomyelin 23 Phosphatidylserine 15 Phosphatidylinositol Phosphatidylinositol 4phosphate Phosphatidylinositol 45 bisphosphate Phosphatidic acid Peripheral and Integral Proteins Peripheral protein change in pH chelating agent urea CO I detergent Integral protein hydrophobic y domain coated GPllinked with detergent protein Proteinglycan GPI glycosyl phosphatidylinositol The speci cities of phosphoipases Phospholipase A 1 kl hospholipase A2 Phospholipase C H o H H Phospholipase D 5V Palmitoylgroup on internal Cys or Ser Cys CH1 5 0039 L ipid n ked NMyristoyl group on aminoterminal Gly membrane proteins I 00quot CH30 cf CH CH2 NH 39NH 0 ox39gt oo m 1393 mm clquot m Zo c39Hz mm mm o CIHz 0 39NH O 0 CHZ CHZ NH C 1 139 GPI anchor on carboxyl terminus Glycoproteins have covalently attached oligosaccharides W aOIinked blNlinked I CH KOCH lco 0 I H H M i0 H N H H ICH quot OH H o Hz ICH 0 on H M H rlm NH H 5104 f f CH CH GalNAc Ser GltNAc Asn Examples39 Examples w Y m39 Carboxyl terminus 131 Integral membrane proteins II 2 NH3 quotooc Type I i coo Haui Typequot i Type III Type IV Inside categories Bacteriorhodopsin a membranespanning protein Amino terminus Oul39icle Halobacten39um salinarum 3D structure of the photosynthetic reaction center of Rhodopseudomonas viridis 6 a 6 39 s 3 5 I A 395 I 1 3394 rv 5 E 5 v I quot l quot 39 l a quot t r r 39 t 39 V l u 39 a 39 395 39 J 39 Protein Architecture Secondary Structure ElkIN E A few types of secondary structures are particularly stable and occur widely in proteins Most prominent on helix and B conformations 0 Carbon Amino terminus 0 Hydrogen Oxygen Nitrogen I Rgroup NOtG The a heIX Spalgiggling u IS not hollow Balland stick 5 4 A model b Ballandstick model of a The 0 helX as Viewed The atoms in the center from one end lo kng I of the a helix are in the intrachain H bonds dOWn the longtUdna aXS very close contact V Formation of a lighthanded a helix righthanded 0r helix showing TABLE 3 1 Properties and Conventions Associated with the Common Amino Acids Found in Proteins pKa values Abbreviation pK1 pK2 pKR Hydropathy Occurrence in Amino acid symbol M COOH NHg R group pl index proteins T Nonpolar aliphatic R groups Glycine Gly G 75 234 960 597 04 72 Alanine Ala A 89 234 969 601 18 78 Proline Pro P 115 199 1096 648 16 52 Valine Val V 117 232 962 597 42 66 Leucine Leu L 131 236 960 598 38 91 Isoleucine Ha I 131 236 968 602 45 53 Methionine Met M 149 228 921 574 19 23 Aromatic R groups Phenylalanine Phe F 165 183 913 548 28 39 Tyrosine Tyr Y 181 220 911 1007 566 713 32 Tryptophan Trp W 204 238 939 589 09 14 A scale combining hydrophobiclty and hydroohiiiolty of R groups it can be used to measure the tendency of an amino acid to seek an aqueous environment 7 vaiues or a hy drophobic environment values See Chapter 11 From Kyte1 amp Doolittle RF 1982 A simple method for displaying the hydropathic character oi a protein J Mol Biol 157 7 32 39Average occurrence in more than 1150 proteins From Doolittle RE 1989 Redundancies in protein sequences In Prediction olPruteln Structure and the Principles ometein Conr formation Fasman 60 ed pp 599623 Plenum Press New York TABLE 3 1 Properties and Conventions Associated with the Common Amino Acids Found in Proteins pKa values Abbreviation pK1 pK2 pKR Hydropathy Occurrence in Amino acid symbol Mr COOH NH R group pl index proteins T Polar uncharged R groups Serine Ser S 105 221 915 568 708 68 Threonine Thr T 119 211 962 587 07 59 Cysteine Cys C 121 196 1028 818 507 25 19 Asparagine Asn N 132 202 880 541 35 43 Glutamine Gin Q 146 217 913 565 735 42 Positively charged R groups Lysine Lys K 146 218 895 1053 974 739 59 Histidine His H 155 182 917 600 759 32 23 Arginine Arg R 174 217 904 1248 1076 45 51 Negatively charged R groups Aspartate Asp D 133 188 960 365 277 735 53 Glutamate Glu E 147 219 967 425 322 35 63 A scale combining hydrophobiclty and hydrophiliclty of R groups it can he used to measure the tendency oi an amino acid to seek an aqueous environment 7 values or a hy drophobic environment values See Chapter 11 From Kyle J amp Doolittle RF 1982 A simple method for displaying the hydropathic character of a protein J Mol Biol 157 32 Average occurrence in more than 1150 proteins From Doolittle RF 1989 Redundancies in protein sequences In Prediction ofProtein Structure and the Principles ofProtein Conr formation Fasman 60 ed pp 5997623 Plenum Press New Vork Hydrophobic Hydropathy index 9 Hydrophilic c 50 100 130 Residue number Hydropathy a Glycophorln Plots 10 50 100 150 200 6 250 7 Hydrophobic Hydrophilic Hydropathy index 0 3 10 50 100 150 200 250 Residue number b Bacteriorhoclopsin Membrane proteins with Bbarrel structure quot w Maltoporin I 3 Top View Solute transport across membranes m Facilitated diffusion down electrochemical gradient Simple diffusion nonpolar compounds only down concentration gradient Primary active transport against electrochemical gradient Sout ion transport own electrochemical gradient 9 Ion Ion channel down electrochemical gbradlenti 39 Secondary active transport b 39l39f39ay d9 93 e 0 against electrochemical ya 3993 gradientdriven by ion moving down its gradient Movement of solutes across a permeable membrane Before equilibrium At equilibrium Net flux No net flux gt Movement of solutes across a permeable membrane Vm gt 0 Vm 0 Before equilibrium At equilibrium Energy changes accompanying passage of a hydrophilic solute through the lipid bilayer of a biological membrane a 4 Free energy 6 b Hydrated solute Simple diffusion without transporter T Diffusion AGsimple with transporter diffusmn AG transport Transporter Facilitated diffusion or passive transport E G UNIVE RSITYofWISCONSIN MILWAUKEE Dep of Chemistry amp Biochemistry Prof Ihdig Chemistry 501 Handout 10 Lipids Chapter 10 Spermaceti organ Lehninger Principles of Biochemistry by Nelson and Cox 5 Edition WH Freeman and Company Two conventions for naming fatty acids 0 1 a c2W18 3 910 O a 181 A9 cis9Octadecenoic acid a 012345 678 91011121314151617181920 C 7 654 321 0 co b 205A5398391139143917 Eicosapentaenoic acid EPA an omega3 fatty acid TABLE 1 Solubility at 30 C Carbon Common name Melting lmgg New skeleton Structure Systemaiir name deiivdiiun point 0 Wdiev Benlene 120 CH3CH21DCOOH nDodecanoic acid Lauric acid 442 M163 2600 lLaiin Iaurus quotlaurel plantquot 140 CH3CH1uCOOH nTecradecanoic acid Myrisli acid 539 0024 574 Latin Myrisl im nutmeg genus 160 CH3CHZ COOH nHexadecanoic acid Palmitic acid 531 00083 348 Latin pulmu quotpal Kleequot 180 cHcH5cooH nOdadecanoi acid Siearic acid 696 00034 124 Greek near quothard fM 200 CH3CH1COOH n Eicosannic acid Aracnidic acid 755 Latin Arachis u e genus 240 CH3CHHCOOH nTetracosanoic acid 161 A9 CH3CH25CH cis9Hexadecenoic CHCH17C00H acid 131119 CHCH2CH tisS Odadecenak CHCH1DDH acid 181A9v391 CH3EH1CH isds 9I1 Linoleic acid 1 5 CHCHICH Ocladecadienui Greek linen CHCHcomi acid flax 183A S41391quot HZCHZCHZCHCHICH cisci 9 u linoleni d 1 1 CHCHZCH 0ciadecatrienoic cmcnlhcoon acid 204A W 1quot CH3CH1CH ladsdsxisS 811 Araciiidonic acid 495 Huich 14 Icosateiraenoic CHCHZCHCHCHZCH id CHCH23CODH a u he cavboxyl carbon m V indicncd in binlogicll any acids the can gnmian is nnasc leys cis Fatty Acids a Carboxyl o o h group c Hydrocarbon chain Slearic acid Oleic acid u camoxyl o a b armIv c ltI The packing of fatty acids into stable aggregates Hymn quot d Saturated Mixture of saturated and fatty acids unsaturated fatty acids Glycerol andatrlacylglycerol H0 cIH 0H 0H Glycerol 0 1CH2 jcuI2 o c o gtcllI o c 0 o cl 1 Stearoyl 2linoleoyl 3 palmitoyl glycerol a mixed triacylglycerol Triacylglycerols provide stored energy and insulation Fatty stores in cells 95 Ea 93999 J 43930 39 vl i I 39q 0 3 myig g 61995 3 w 39 n 1 3 39 was mean w I 3 1 VA gg l 13 1 a 555 quotP a 3 nast zg39fagg k1 51 l 2 Q 0 39quotv 39 39 Guinea pig adipocytes Arabidopsis 233 f 0 gr Cotyedon cell from a seed of Fatty acids of total 80 60 40 20 Many foods contain triacylglycerols C16 and C18 C16 and C18 CLI to C14 saturated unsaturated saturated Olive oil Butter Beef fat liquid soft solid hard solid Natural fats at 25 C Fatty acid composition of three food fats Trans fatty acid content In a typical As of serving 9 total fatty acids French fries 47 61 28 36 Breaded fish burger 56 28 Breaded chicken nuggets 50 25 Pizza 11 9 Corn tortilla chips 16 22 Doughnut 27 25 Muffin 07 14 Chocolate bar 02 2 Source Adapted from Table 1 in Mozaffarian D Katan MB Ascherio PH Stampfer MJ amp WilletWC 2006 Trans fatty acids and cardiovas cular disease N Engl J M21354 1 604 1 605 llote All data for foods prepared with partially hydrogenated vegetable oil in the United States in 2002 Waxes serve as energy stores and water repellents Triacontanoypamitate CH3CH214 C 0 CH2 CH228 CH3 L k 1 The major component of beeswax Palmitic acid 1T riacontanol Some common types of storage and membrane lipids Membrane lipids polar Phospholipids Glycolipids Archaebacterial ether lipids Triatylglyzerols Glycerophospholipids Sphingolipids Sphingolipids Galacmlipids sulfolipids E g g 1 a To E 39g 39 To 5 G E E E G Mono or oligosaccharide ether linkage Glycerophospholipid Saturated fatty acid general structure l eg palmitic acid 1CH2 c o Glycerophospholipids kin aim o 3CH2OF1O x Unsaturated fatty acid 0 Headgroup egolelc acud s u bstltue nt Net charge glycerophospholipid Name of X Formula of X at pH 7 Phosphatidic acid H 1 1ltH20H i Phosphatidylelhanolamine Ethanolamine Hz CHz H3 0 H 2g OH o Phosphatldylchollne Choline C Hz CHz NCH33 0 3CH2 o P o I Phosphatidylserine Serine CHz Cl l N a 1 O coo39 Phasphatidylglyceml Glycerul CH2 TH CH2 0H 1 snglycerol 3phosphate H o 6 5 f J Phosphatldylinosltol myolnosltal 45 H 4 45blsphosphate blsphasphate 1 4 The backbone of H o 2 3 phosphollplds H H Cardiollpln Phasphalidyl CIHZ 2 glycerol CH0quot 0 cuz o slv o cnz O 0 u 1 H O C R 0 2 CHz O C R Some phospholipids have etherlinked fatty acids etherlinked alkene herlinked alkane H H 39 CIHz o cc 39fH2 392 CH1 2 2CIH O IiW CI 0 fl CH3 3012 o SCHZ o I acetyl ester 39 I 0P 0 CH1 CH2 NCH33 OF 0 CH2 CH2 NCH33 choline 0 choline Plateletactivating factor Plasmalogen Galactolipids 0 and clquot2 ogF II SUIfO39ipidS CW c39 o CH H OH H H Monogalactosyldiacylglycerol Three glycolipids of quot chloroplast membranes a sulfolipid Archaebacteria contain unique membrane lipids Glycerol phosphate ll 390 P O CH2 Diphytanyl groups Glycerol quot 3 1 HzC I aGlcB1 gt2Gal1 Sphingolipids are derivatives of sphingosine Sphingosine HO 3CH CH CH CH212 CH3 2 CH lil H 1CH2 O X Sphingolipid general structure CH3 0 2 H o co n I o I Hquot quot n c ou H H H 0quot H C OH OH H 20quot NAcetylneuraminic acid a sialic acid Sphingomyelin Neutral glycolipids Glucosylcerebroside Lactosylceramide a glabosidel Ganglioside 6M2 Fatty acid Glucose Dil tri or tetrasaccharlde Com ex aligosaccharide 3 Sphingolipids at cell surfaces are sites of biological recognition Glycosphingolipids as determinants of blood groups Phospholipids and sphingolipids are degraded in lysosomes The specificities of phospholipases lt Phospholipase A1 1 u Cquot2 C Phospholipase A2 0 Phospholipase C o Phospholipase D Inherited human diseases resulting from abnormal accumulations of membrane lipids Ceramide O GM2 hexosaminidaseA gt TaySachsdisease GalNAc ganglioside neuraminidase NeuSAc agalactosidase A Globoside O O C hexojamgngdase gt Sandhoff sdisease an DGaINAc D Q39Q gt Fabry s disease Gaquot 3 galactosidase glucocerebrosidase gt Gaucher39sdisease Glc Gal sph ingomyelinase Sphingomyelin Phosphachollne gt NiemannPick disease Phosphocholine 1 um Abnormal ganglioside deposits in lysosomes brain cell TaySachs Sterols have fourfused carbon rings Cholesterol 26CH 3 ZSCH 27CH 3 CH2 Alkyl 23C 2 Side I chah1 SterOId Pohr H0 nudeus head Arachidonic acid and some eicosanoid derivatives 0 a 5 1 Arachidonic acid o 0 quot rquot 39 0 Lo NSAIDs 1 CH 0 CH3 12 3 3K ll 0H 0H 0 039 Leukotriene A4 CH3 Prostaglandln E1 0 12 PGE1 0H Thromboxane A2 Eicosanoids Steroids derived from cholesterol OH H3C H3C H 3c 0 HO Testosterone Estradiol CHZOH IZH 20H H co 0 c 0 H 3c OH c H O H O H 3c H 3c 0 0 Cortisol Aldosterone Brassinolide a brassinosteroid Prednisolone Prednisone Vitamin D3 production and metabolism uv light H03 5 7 gt gt 1 step in the liver 1 step in the kidney gt gt 2 t 39 k39 7Dehydrocholesterol s Epshns m Rickets 125Dihyd roxycholecalciferol 125dihydroxyvitamin D3 a hormone that regulates Ca uptake in the intestines and calcium levels in kidney and bones 354 MEETINGBRIEFSgtgt AMERICANASSOCIATION 0F FHYSiCALANTHROPOLOGISTS 25 31 MARCH i PHILADELPHIAFENN5VLVANIA European Skin Turned Pale Only rm nrcnsiii39skins humus d I WW pnlcmlnihnvpuiugbi xuu Jiibiimih ni39l SU m Siam Cuii Such u mi cliimucs In Skill color mm Recently Gene Suggests mmmpuiugm HEW I39l rpt udll g quotmm UmV A A I my i iivki 39V MamaIii did he nm maulquot himmm wim m m simvlui up 454mm vcnrs aga and have no gun um Eimvpunns lightened up quilt V mum ycurs I V i39i m Medium u licniicy ibund mo mn umum mu lt IIIIAI sum Jilcicv imm um ui39lhc II 7 nth mu Nu um iirii i 39 Iinmmum um Unim y ui Armmu sim wquunced won hm mus 0139 DNA n ihc 39 HF vcnc In cnslncmu mm Amcrium iudmns mg unzuiim m Im gun um um um mus ming minim mincdlihl Ii sim 3 L Amquot 4 mi ud ihc hicigmmnu L d are mu 339 in Ii3iiiiliycnr mm magnum niicl w 1 va m Eumpmm u milsani mm liming IiI quotch vIIlIIhc 39 39 39m crrmrma mqu on mmnmi m I c ruunu mu 1 mums m a suggcsl um ii width 5300 i0 lvDDDyenr IL is cisiolIafIlIcllindl I luck 1 1000wa In minim mid Sin mica nu m m I um guns prubnhiy also calls puiing in Eumpcnn Either quot a II Iinmmi miicr m Iur 31 in Gene SLC24A5 Two variants Difference just one amino acid I slap In um um I my in m nuny no 1 chaiamlciferol vitamin Dal ms hydroxydluleu ml I ZSdihydvoxyvltamin n3 r m in mm mialwoly rerenlly u i pmdu I I It mun riulllill D For Imii WIII an ca icium Ihsni39plluil I I cvniuimn In iigiii S Eumpcnn nnccslms wen bruii nskinml rm Ions ui ilinusmnds oi enrsgn sugge 5i gmmcmL i L argued mm Hi My imm immm m Eumpc nmimiaranmmpuiugm 1m 39Nunun ui me Uliwcrsiry qunmna Imam IiIIIIni Iaik mules ui39bIIlwgy Ruseurchcn mzidu n msunIvcd oi mid nudesourm o 39 1m D In in din Bu Mien running siimnd m m pm Iuilii yi argued aim w m nmducc m mmm in their gene my mm Appamni mines pal V nin mm H g miqu 113 hm i39murcil ncmmd many I zoAPRILzoLW VOLJU SCIENCE wwwscisncemagmg Vitamin A1 and its precursor and derivatives CH3 CH3 I t t I t oxidation soprene 5 rue ura um ofaldehyde Retinoic acid 39gt H rmonal CH3 to acid signal to epithelial CH3 I cells gt I I CH3 CH3 l CH3 CH3 CH3 CH3 Yisible CH3 light CH Neuronal CH3 3 si nal point of oxidation of 9 cleavage alcohol to I 1 11 to brain CH3 aldehyde 12 12 CH3 CH3 CHon C c 15 H o CH3 I I H o Vitamm A1 1139Cis39Ret39nal all trans Retinal CH3 retinol visual pigment CH3 CH3 CH3 I BCarotene CH2 c CH CH2 lsoprene Some other biologically active isoprenoid compounds CH3 Ho CH3 CH3 CH3 I I I CH2CHz CHz CH CH2CH2 CH2 CH CH2CH2 CH2 CH CH3 CH3 0 CH3 39 39 39 CH3 0 Vitamin E an antioxidant 0 CH3 CH3 CH3 CH3 I l CHz CH c CH2 CH2 CH2 CH CH22CH2 CH2 CH CH3 I I involved in theformation of Vitamin K1 a bloodclotting CtiVerthmmbi cofactor phylloquinone brinogen gt fibrin c Wa a inhibits theformalion ofacliveprolhrombin O Wisconsm Alumni OH I CHz III CH3 Research Foundation arm 0 o CH30 CH3 I c 3 CH3 CH3 I I CH30 ICHz CH CH2HCH2 CHI CH2nCH2 CHg CH3 o I I d Ubiquinone a mitochondrial electron carrier coenzyme Q n 4 to 8 CH3 I CH3 CH3 CH3 I I CH3 ICHz CHC CH2CH2 CHC CH2CH 2 CHC CH3 o I I e Plastoquinone a chloroplast electron carrier n 4 to 8 CH3 CH3 CH3 I I I H0CH2 CH2 CH CH2CH2 CH c CH2CH2 CH C CH3 l l l f Dolichol a sugar carrier n 9 to 22 Lipids as pigments in plants and bird feathers Canthaxanthin bright red OH HO Zeaxanthin bright yellow Working with Lipids Tissue 7 7 homogenized in chloroformmethanolwater a Water Methanolwater Chloroform MethanoUWater ChlorofOrm 3i m Adsorption chromatOgraphy Thin39layer Chr ma 9raphy 45 Neutral Polar Charged lipids lipids lipids Adsorption chromatography Thinlayer chromatography g 5 1 2 3 4 5 6 7 s 9 Neutral Polar Charged lipids lipids lipids NaOHmethanol Fatty acyl methyl esters Fatty acyl methyl esters e Gasliquid chromatography f High performance liquid chromatography 140 1 80 161 160 Concentration Elution time Abundance 90 80 70 60 50 40 30 20 Determination of the structure of a fatty acid by mass spectrometry 371 m quot O 2To 92 0H1 1 I I I I I I I I I I I I I I N 108 178 220 260 300328l356 I I I I I I I 92 164 206 234 274 314 342 108 164 67 314 E 3 s 55 151 274 220 300 178 206 123 J J l 234 I l L 356 11 L II 1II 111511 I It I I a J111 I IlLLI I 1 I lu I1 60 so 100 120 140 160 180 200 220 240 260 230 300 320 340 360 380 mz a CD UNIVERSITYMWISCONSIN MILWAUKEE Dep of Chemistry amp Biochemistry Prof Ihdig Chemistry 501 Handout 4 The ThreeDimensional Structure of Proteins Chapter 4 Lehninger Principles of Biochemistry by Nelson and Cox 5 Edition WH Freeman and Company A protein s conformation is stabilized largely by weak interactions Glycine Structure of the enzyme Quaternary structure of deoxyhemoglobin chymotrypsin a globular protein a A ribbon representation PDB le 6GCH b A space lling model The known 3D structures of proteins are archived in the Protein Data Bank PDB Each structure is assigned a fourcharacter identifier or PDB ID Protein Architecture Primarv Structure CO The planar peptide bond cNCa C5ca c a a y C N W I Each peptide bond has some double H H H bond character due to resonance and The carb quotV39 quot3 99quot has a partia39 negative cannot rotate charge and the amide nitrogen a partial positive charge setting up a small electric dipole rSen39es of rigid planes sharing a common point of rotation at Ca Carboxyl terminus Three bonds separate the or carbons in a polypeptide chain w 180 when the peptide is in its fully extended conformation and all peptide groups are in the same plane 1 degrees 18039 qb degrees 180 v V Convention In this conformation u 0 In a protein this conformation is prohibited by steric overlap between an a carbonyl oxygen and an a amino hydrogen atom Ramachandran plot for LAla residues Conformations deemed possible are those that involve little or no steric interference based on calculations using known van der Walls Radii and bond angles Protein Architecture Secondary Structure A few types of secondary structures are particularly stable and occur widely in proteins Most prominent or helix and B conformations Amino terminus Lefthanded Righthanded helix 0 Carbon 0 Hydrogen 0 Oxygen o Nitrogen R group Note The a helix Space lling model a Carboxyl terminus b c d Balland stickr model of a The a heligs viewed The atoms hithe center Helicalwheel righthanded a helix showing from one end looking of the a helix are in representation of an the intrachain H bonds down the longitudinal axis very close contact a helix Not all polypeptides can form a stable a helix Interactions between side chains can stabilize of destabilize this structure Arg103 ASP100 Interaction between R groups of amino acids three residues apart in an a helix Troponin C shown a helix segment 13 residues long The identity of the amino acid residues near the ends of the a helical segment also affects the stability of the helix Amino terminus Carboxyl terminus The four amino acid residues at each end of the helix do not participate fully in the helix hydrogen bonds The conformation organizes turns are Common in pmtems polypeptide chains into sheets a 3 Turns 1800 turn involving four amino acid residues Gy and Pro residues often occur in 3 turns Gy small and flexible Pro the cis con guration is particularly amenable to a tight turn Proline isomers R H c 1 H cN R c H I c o H 10 c quot I 0 B sheets trans cls Common secondary structures have characteristic bond angles and amino acid content Ramachandran plots for a variety of structures Antiparallel Collagen triple BSheEtS Parallel helix R39 ht t 39 t d 399 Wquot e Common secondary structures can be assessed asheets 5 sheets by circular dichroism CD spectroscopy Lefthanded 01 helix 25 I I I 76 20 1 a g g Right handed 15 0 He39lx g or helix 10 mm b 2 5 Conformation 80 0 80 Random coil o degrees 0 1O 7 15 2 I I I I I 5 190 200 210 220 230 240 250 3 Wavelength nm 180 r TY V 0 180 Pyruvate klnase all amino aCId res1dues except Gy o degrees Protein tertiary and quaternary structures a helix loop deoxyhemoglobin 3 conformation Lysozyme Tertiary structure includes longrange aspects of amino acid sequence Quaternary structure includes the threedimensional arrangement of polypeptide chains in multisubunit proteins Example of Fibrous Proteins quaternary structure structure support shape protection mwmwm Polypeptide chains arranged in long strands of sheets Keratin X helix handed Tw I 7 ha ailflffm supertwrsted m39 e m39 coiled coil TABLE 4 Ww h wmml 20 30 A P otof lament 39 Snumm halamrisiits Examplunmmmm r I quotdamquot quot I R W aisumde hands varying hardness and exihi ty a Cunlunna nn 5u uihe lilimems silk hmin Disulfide SS bonds stabilize the quarternary structure kzmaemeue mueunquzw Protofibril WNW 222 714 mWszuzzzu 21222213 maezeyzrwzg kzzezzzzzezau mmaz mnmimmzzza mmmw reduce 39 curl gt gt a II Bl Twuchain oiledcoil Permanent wavmg n Helix Cross section of a hair a Keraz in Collagen connective tissue tendons cartilage organic matrix of bone cornea Structure of collagen brils 250 nm Heads of collagen Crossstriations molecules 640 A 64 nm The threestranded collagen superheliX shown sel it39on 0f from one end ballandstick representation 0 agequot molecule Three helix wraQ around one 4 H another With a righthanded twist c quot 39quot quot quot quot quot 5 quot quotquot ca Oquot Polypeptide Lysresidue HyLys Polypeptide tilill minusezmino resldu chain group norleucinel oc chain repeating tripeptide sequence generally Gly XY Where X is often Dehydrohydmxylyslnonmendn 0c Pro and Y is often 4Hypadopts a lefthanded helical structure With three residues Qer turn Structure of silk Permits close packing and interlocking of R groups Ala and Gy residues Fibroin 39 layers of antiparalle 3 sheets rich in Sheets held together by n rous wee interactions rather than covalent bonds such as disulfide bonds in a keratin Strands of broin blue emerge from the spinnerets of a spider colorized electron micrograph Globular Proteins Structures compact and varied eg human serum albumin 585 residues in a single chain Mr 64500 Approximate dimensions its single polypeptide chain would have if it occurred entirely in l3 Conformation 2000 X 5 A oz HEIIX Native globular form 900x11A 100gtlt60A O 0 a K C C In gtCH2 CINz Iquot H C Cltquot C C CH w t IL rII c 3 N l quot C c quot7amp3 cCH N I I cH c c c 01 a clr c y CII H H 31 CHI I 02 The heme group Tertiary structure of a small globular protein sperm whale myoglobin a Polypeptide backbone shown in a ribbon representation b Surface contour image useful for visualizing pockets in the protein c Ribbon representation including side chains for the hydrophobic residues Leu le Val and Phe d Space lling model with all amino acid side chains Su erseconda structures motifs or simply folds T Particulary stabe arrangements of several elements of secondary structure and the connections between them a Loop J V 9 Barrel Motifs TA B LE 4 3 Residues Protein total residues or Helix B Conformation Chymotrypsin 247 1 4 45 Ribonuclease 124 26 35 Carboxypeptidase 307 38 17 Cytochrome c 1 04 39 0 Lysozyme 129 40 12 Myoglobin 153 78 0 Source Data from Cantor CR amp Schimmel RR 1980 Biophysical Chem istry Part I The Conformation of Biological Macromolecules p 100 W H Freeman and Company NewYork Portions of the polypeptide chains not accounted for by or helix or B conformation consist of bends and irregularly coiled or extended stretches Segments of or helix and B conformation sometimes deviate slightly from their normal dimensions and geometry Stable folding patterns in proteins m a Typical connections Crossover connection in an allB motif not observed b Righthanded connection Lefthanded connection between B strands between B strands very rare C Twisted B sheet Protein motifs are the basis for protein structural classification Constructing large motifs from smaller ones The Structural Classification of Proteins SCOP database Protein structures divided into four classes all or all 3 0c3 0c and 3 segments interspersed or alternate oc3 0c and 3 regions are somewhat segregated aB Loop alBBarrel V thin each class tens to hundreds ofdifferent folding arrangements built up form increasingly identi able structures a I3 I Pilin Neisserin gnuanhaeae I ICE 1an i Amylasa inhibitor Singlbslmnded lefthanded p helix I 05 I quot5 H ltAmylas inhibitor TrimerichlAIike en mes 59mm albumquot Ferrftznlfke H Amyla 39 i or unr Nacetylglucosamlne azyllranslerase Serum albumin Ferthnllke HOE46 unv NaKelylglumsamlne azyimnsimse Serum albumin 2 rltin smmomyus tendne4158 Esrhrrkhlu ml r Serum albumin Baneriolerrilincytodiwmeb Human Hamn sapiens Esdlerizhi39a nli Cr ulse Iik Enoylvtoll hydnuxa a Almholdehydmgmnse I Raqnumu null291m Human Mom sapierul Protein quaternary structures range from simple dimers to large complexes Viral capsids RNA Protein subunit Quaternary structure of deoxyhemogobin b a The coat protein of poliovirus assemble into an icosahedron 300 Angstrons in diameter b Tabaco mosaic virus rodshaped virus 3000 Angstrons long and 180 Angstrons in diameter with helical symmetry Protein denaturation and folding Loss of protein structure results in loss of function 100 m E RibonucleaseA I 3 80 26 Native state I E catalytlcally active 3 E 60 Tm Tm addition of urea and IE 40 mercaptoethanol 2 Apomy 9 bm 5 20 g a D 20 40 60 80 39l 0 iJnfolIded scatei a Temperature 0C Inactive DIsulfIde crosslinks reduced to 10 yield Cys residues 5 80 43 removal of urea and E 60 R39bonUdease A mercapto ethanol g a Tm 5 40 U Native 3 J catalytically 20 active state Disulfide crosslinks I I I correctly reformed 1 2 3 4 g b GdnHCl M The thermodynamics of protein folding depicted as a freeenergy funnel Beginning of helix formation and collapse Polypeptides fold rapidly by a stepwise process l 7 Tl iEquotquot quotTW l O Energy in native conformation Percentage of residues of protein Discrete folding intermediates J L 100 Natlve structure Folding for many proteins is facilitated by the action of specialized proteins chaperones DnaJ binds to the DnaJ stimulates ATP unfolded or partially 2 Pi hydrolysis by DnaK folded protein and DnaK ADP binds tightly then to DnaK to the unfolded protein E37 my Unfolded protein 3 e To GroEL tO Partially 777 7 system 1 folded Ex protein 1 A l or i G E Folded rp Protein i native r conformatlon Q l ATP binds to i In bacteria the DnaK and the l nucleotideexchange factor GrpE stimulates release of ADP ADP GrpE DnaJ 2 Ci protein dissociates E Coli chaperone proteins DnaK and DnaJ Chaperonins in protein folding D Unfolded U fOIded PquotOtein N 6 The released protein binds fl 39 protein is full to the GroEL GrOEL Foldefi a folded or in ay pocket not promquot partially folded blocked by f 39 39 39 39 39 39 39 39 39 39 39 39 39 39 state that is GroES 7 Pi committed to 7 adopt the native Q GroEs conformation I 0 ATP binds to D Proteins not 39 lds each subunit folded when gt 7AA enclosure of the GroEL released are heptamer rapidly bound again a l ATP hydrolysis 7 Pi39 7 leads to release 7N1 of 14 ADP and GroES I I I 7 GroESQ 39 7 ATP and GroES L L bind to GroEL with a filled pocket Proposed pathway for the action of the E coi Chaperonins GroEL and GroES GroELGroES complex an Defects in protein folding may be the molecular basis for a wide range of genetic disorders 46 I Phe w Natlve Molten globule Denatured l N c1129 Selfassociation N cf Amyloid bril core structure Further assembly of pro o laments Formation of diseasecausing amyloid brils Prion Diseases Stained section of cerebral cortex from autopsy of a patient with Structure of the globular domain of human PrP CreutzfeldtJakob disease shows spongiform vacuolar in monomeric left and dimeric right forms degeneration the most characteristic neurohistological feature Proteinaceous infectious only protein PrP Nonpolaraiphatic R groups coo coo 60039 l l H HaN CH H3N C H l 1 RIM H H H l l HZC CH2 Glycine Alanine Proline coo39 coo39 HaN lI H HgN CI H le H CH3 cH clH CH CH3 CH3 Leucine lsoleucine Aromatic R groups coo 00 0039 A e Hsuecl H H3N ltZ H 3Nc 7H CH1 CH2 cl it CCH NH OH Phenylalanine Tyrosine Tryptophan Polar uncharged R groups cooquot coo 0039 o coo H H I H c H HgN C H 3 f quot3quotf 3 f H 01on H Cl OH In CH3 CH3 a 5 Vanna Serine Threonine Cysteine Cleo coo cloa H3NCIH H3N f H H3N cl H EH2 cle le CH2 EH2 HIN o C s HZN o 3 As ara Ine Glutamlne Methlonlne p g Positively charged R groups Lysine Negatively charged R groups CI M CI 7 00 0039 H3Nv Ci H3NC H I clquot clui HSN ltIZ H HsN lZ H C NH n cu 2 Cl 2 H quot c0039 le ltiH maquot quot5quot Aspartate Glutamate Arglnlne E E UNIVERSITYMWISCONSIN MILWAUKEE Dep of Chemistry amp Biochemistry Prof Ihdig Chemistry 501 Handout2 Water Chapter 2 Lehninger Principles of Biochemistry by Nelson and Cox 5 Edition WH Freeman and Company Hydrogen bonding gives water its unusual properties TABLE 21 Melting Point Boiling Point and Heat of Vaporization of Some Common Solvents Melting point C Boiling point C Heat of vaporization Jgrk Water 0 100 2260 Methanol CH30H 798 65 1100 Ethanol CHSCHZOH 7117 78 854 Propanol CH3CHZCH20H 7127 97 687 Butanol CH3CH2ZCH20H 90 117 590 Acetone CHSCOCHS 795 56 523 Hexane CH3CH2ACH3 798 69 423 Benzene CSHS 6 80 394 Butane CH3CH2ZCH3 7135 705 381 Chloroform CHCIS 763 61 247 The heat energy required to convert 10 g of a liquid at its boiling point at atmospheric pressure into its gaseous state at the same temperature It is a direct measure oi the energy required to overcome attractive forces between molecules In the liquid phase 5 Hydrogen bond Covalent band 965 nm 0 Hydrogen bonding in ice Common hydrogen bonds in biological systems I I Vdmgen C c acceptor 9 39139 9 9 9 39139 Hydrogen Fl Fl Fl lTI Fl Fl A J A l l l Ice 4 Hbonds per molecule of water Liquid at RT 34 Hbonds per water FIiCKe ing cluster molecule on average Some biologically important hydrogen bonds Between the hydroxyl group of an alcohol and water R I III O oriented to maximize electrostatic interaction l 39U OIIII O l Between peptide groups in Between the carbonyl group of a ketone polypeptides and water l2 R W H C C H Rll N C g 9 H I 39 39i39 x0 H N H c c II R R i Strong Weaker hydrogen 0 hydrogen bond ep bond Directionality of the hydrogen bond Between complementary bases of DNA Thym ine Adenine z can hold two Hbonded molecules or groups in a speci c geometric arrangement TABLE 22 Polar Glucose Glycine Aspa rtate La ctate Glycerol Some Examples of Polar Nonpolar and Amphipathic Biomolecules Shown as Ionic Forms at pH 7 CHZOH H O OH H HO OH H H H OH NH3 CH2 COO NH3 39OOC CHz CH COO CH3 CH COO 6H IDH HOCHg CH CH20H Nonpolar H Typ39cal wax CHECH2CHGHLCHQ6CH2 C 0 l GH3CH2397 QHQH QH27CH2 Amphipathic Phenylalanine NH I 3 CH2 CH 000 Phosphatidylcholine O l ll CH3CH21ECH C O CH2 QH3ltCH 1sCH2 O CIIH I IIICH33 O CHg O P O CHz CHQ 0 l Polar groups Nonpolargroups Water interacts electrostatically with charged solutes Hydrated CI39 ion Note the nonrandom orientation of the water moleculies quot I 5 I i O 1 i a 5 7 I Hydrated Na quot ion Entropy increases as crystalline substances dissolve Nonpolar compounds force energetically unfavorable changes in the structure of water Hydrophilic quot 1 quothead groupquot Hydrophobic l alkyl group g 0 quotFlickering clustersquot of H20 0 molecules in bulk phase Highly ordered H20 molecules form quotcagesquot around the hydrophobic alkyl chains Amphipatic compounds in aqueous solution Dispersion of lipids in H20 Each lipid molecule forces surrounding H20 molecules to become highly ordered Clusters of lipid molecules Only lipid portions at the edge of the cluster force the ordering of water Fewer H20 molecules are ordered and entropy is increased Micelles All hydrophobic groups are sequestered from water ordered shell of H20 molecules is minimized and entropy Release of ordered water favors formation of an enzymesubstrate compex Ordered water interacting with 0 substrate and enzyme 5 a f amp7 C Disordered water 39 displaced by 0 gt lt enzymesubstrate interaction 7 L if k ed Enzyme 7 Va Enzymesubstrate interaction stabilized by hydrogen honding ionic and hydrophobic interac ons van der Walls interactions are weak interatomic attractions Element van der Waals Covalent radius for radius nm single bond nm H 01 1 0030 O 015 0066 N 015 0070 C 01 7 0077 S 018 0104 P 01 9 01 10 I 021 0133 Sources For van der Waals radii Chauvin R 1992 Explicit periodic trend of van der Waals radiiJ Phys Chem 96 9194 9197 For covalent radii Pauling L 1960 Nature ofthe Chemical Bond 3rd edn Cornell University Press Ithaca NY Note van der 39 1 he s quotquot atomsWhen two atoms are joined covalently the atomic ra ii at the point of bonding are less than the van der Waals radii because thejoined atoms are pulled together by the shared electron pairl39he distance between nuclei in a van der Waals interaction or a covalent bond is about equal to the sum of the van der Waals or covalent radii respectively for the quot 39L L 39 a 4 L 39 l J about 0077 nm 0077 nm 0154 nm 1 Weak interactions are crucial to macromolecular structure and function Hydrogen bonds Between neutra mu 5 c g P omH o c Between peptide bonds ol I HN Ionic interactions Attraction Repulsion Hydrophobic interactions Van der Waals interactions Any two atoms in close proximity Water binding in hemoglobin Val 31 I 59 Pro G n I 0 H 39 39 N Ho Ash Water chain in cytochromef Amway xquot 0 gt 0 Solutes affect the Colligative Properties of aqueous solutions vapor pressure boiling pointfreezing point and osmotic pressure Pure Nonpermeant Extrxellular water solute dissolved Piston S Irmw39lular lutes in water 39 39 5 0 H20 Forming 77 39 3quot 39 I r I 39 a cell In ISO39OIIK 39jl 39 39 5 j l 39 39 I 1 SOIUte quot9 ry al 39 so unon no net water i r z r r movement h l J i a a H a 0 cl 39 In pure water every In this solution the b I M L Semlpermeable solutionwater moves out solutionzwatermovesin H20 and all ontrlbute H20 Is reduced only 3 of membrane H and cell shrinks creating ourward Piessurg to the vapor pressure every 4 molecules at the all swells may eventually Every molewle in the bulk surface and in the bulk burst solution Is H201 an can phase are H10 The vapor ize crystals tendency of liquid water to enter a rystal are reduced proportionate y Venus flytrap Mimosa pudica H20 lt gt H OH Ionization of water Keq HOH391 H20 2 1398 X 1046 M Keq H20 H OH39 KW ion product of water H20 555 M gt KW H OH39 10 X1O3914 M2 Hydronium ion gives up a proton H H HOH1OX1O7M o Proton hop 0 H ZB 39l pH og H pOH Iog OH gt pH pOH 14 III 0 V m v H 0 11 m 111 or u now 1o 1 o 10quot 14 Q5quot 1r1 1 111quot3 13 0 1013 2 101 2 12 102 3 10 11 d 10 4 10 quot 10 105 5 1n9 9 H 1015 6 10quot 107 7 107 7 10a a 10396 6 i 10quot9 9 105 s 1010 10 10 4 0 Wateraccepts proton and 10 1 10 3 H becomes a hydronium ion 1 12 1 2 10quot3 13 1Dquot 1 10quot 14 1o l1 o 1112 upmsinn pOH is mmuimes used m desuib mp hasicily or alr wniemndan M a suluunn pDH ls de ngd by he Axprzssian pan ng lolrl whkh ls analogous to the expresslon lar nu Man that In all uses pH poll 14 HM pH or m p0H 10 1 o 1014 14 10 1 1 10 13 13 10 2 2 10 12 12 1o3 3 1o11 11 1o 4 4 1010 1o 105 5 109 9 106 6 108 s 107 7 10 7 7 1o 8 8 1o 6 6 109 9 1o 5 5 1o1 1o 104 4 10quot 11 103 3 1o 12 12 1o 2 2 10 13 13 10 1 1 1014 14 10 1 o The expression pOH is sometimes used to describe the basicity or 0H Ma 0 log OH which OH r I r P is analogous to the expression for pH Note that in all cases pH p 14 pH of some aqueous fluids 1 M NaOH h Neutral Household bleach Household ammonia Solution of baking soda NaHCO3 Seawater egg white Human blood tears Milk saliva Black coffee Increasingly eer Tomatp Julce Red Wine Cola vinegar Lemonjuice Gastricjuice 1MHC Weak acids and bases have HA ltgt H A characteristic dissociation constants Keq H A HA Ka Monoprotic acids Acetic acid CH3C CH3C Hquot39 Ka 174 X 10395 M O 39l O pKa 476 Ammonium ion NH NH3 Hquot Ka562 gtlt1o1 M Mfg Diprofic acids Carbonic acid 2 FUD X 104M H2C03 Hco3 H Hco3 v co3 H Bicarbonate pKa 377 K3 102 Ka631 gtlt1o11 m Glycine carboxyl NH3 3 I H3 0 0 I Ka457 X1 393 M CH2C CH2C M HZC CH2C 1 Glyclne amlno 3H 0 o Ka 251 gtlt1o10 m pKa 234 pKa 960 NHZ n Z Triprotic acids Phosphoric acid K3 725 x 103 m aghyci rggse gigofprate H3P 4 F H2P H H2Po HPO 39 4quot HPo P02 H a 39Mi pK 214 K124 Monohydrogen phosphate 3 pKa 63986 p a quotFm x 1 43 Conjugated acidbase pairs consist of a proton donor and a proton acceptor H20 ltgt H OH Titration curves reveal the pKa of weak acids HAC ltgt H Ac 14 14 2 Midpoint KW HOH 10X1O M 13 of 2 titration lE 39 5 1 39 Ka H AC HAC 174 x 10 M K 3925 Buffering 11 P a regIons 9 10 T1025 NH 8 CII3coo 9 a I 8 H P021 HPOZ39 325 7 CH3COOHCH3coo 2 a 4 786 7 Phosphate 6 pH 576 pH 6 pKa 686 CH3C00 is 86 5 I 39 Buffering PKa 43976 576 PH region 5 Acetate 4 H 376 4 3 P PKa 475 P CH3COOH CH3C0039 375 3 2 CH COOH 2 3 I I I I I I I I o l I I I I I I I 00 01 02 03 04 05 06 07 08 09 10 0 01 02 03 04 05 06 07 08 09 10 OH added equivalents I OH added eqUiva39ents I I o 50 100 50 100 Percent titrated Percent tItrated Buffers are mixtures of weak acids and their conjugate bases The HendersonHassebach Equation pH pKa log lgroton acoegtorl proton donor The pH optima of some enzymes KW HOH39 OH H20 Acetic acid H Ac Ac Acetate CH3COOH CH3COO HI HAC Ka 39 HAc Percent maximum activity O 0 U1 0 Pepsm Trypsin Alkaline phosphatase Weak acids or bases buffer cells and tissues against pH changes Contribution from proteins eg CH CH 2 H 2 H N CHH C N C C l H II HC N HC N H histidine pKa60 Two particularly important biological buffers Phosphate H2PO4 H HPO42 Bicarbonate HZCO3 H HCO339 H Hco reaction 1 Aqueous phase H2c 3 blood in capillaries reaction 2 H20 H20 C02d reaction 3 Gas phase lung air space c029 Water as a reactant Phosphoanhydride ll R O P Oquot H20 0 Phosphate ester R1 C 0R2 H20 Carboxylate ester 1 IT R C O IT O H20 0 Acyl phosphate A d o ADP I I R OH HO P O o o 2 R1 C H0 R OH 0 N R C HO P O 0H 0


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