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by: Mrs. Kellen Barrows

StructureandFunctionofBiomolecules BIO404

Marketplace > Drexel University > Biotechnology > BIO404 > StructureandFunctionofBiomolecules
Mrs. Kellen Barrows
GPA 3.53


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This 50 page Class Notes was uploaded by Mrs. Kellen Barrows on Wednesday September 23, 2015. The Class Notes belongs to BIO404 at Drexel University taught by JosephBentz in Fall. Since its upload, it has received 31 views. For similar materials see /class/212315/bio404-drexel-university in Biotechnology at Drexel University.


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Date Created: 09/23/15
David L Nelson and Michael M Cox LEHNINGER PRINCIPLES OF BIOCHEMISTRY Fifth Edition CHAPTERS 1 amp 2 Water Ions amp Weak Interactions 2008 W H Freeman and Company Table l l Composition of the Earth s Crust Seawater and the Human Bodyquot Earth s Crust Seawater Human HoodJr Element Compound mM Element 972 o 7 or lt H20 548 II 63 Si 28 123 4m 0 255 A 79 Mg 54 391 95 Fe 503 28 N 14 Ca 339 10 Ca 031 Na 25 K m P 022 K IICD 23 CI 008 Mg 22 No 001 K 006 Ti 046 11130 lt00m s M15 11 022 Na 003 C 019 Mg Ck l TABLE 11 Strengths if Bands Common in Binmniecules Band dissociation E pe energy of bond Wino Bond dissu ciatiun Type energy quot of band Mfmui Single bands Dalii 470 H H 435 P D 419 C H 414 N H 3 89 87 C 3 48 SEH 339 C N 293 12 3 260 N D 222 5 3 214 Duuble hands CCI 73912 CN 615 CC 6 1 1 PD 53932 Triple hands EEC 81E MEN 930 The greater the energy required for bond dissociation breakage the stronger the bond SiO 45 kJmol Millions of years ago 500 1000 1500 2000 2500 31190 3500 4000 4500 Single celled eukaryotes existed for 1000 million years before multicellular eukaryotes eg sponges evolved from them Diversi cation of multicellular eukaryotes plants fungi animals ppearanze of red and green algae appear1n e of endosymbiants mitochondria plasti dsl prearante of prntists the first eukaryotes Prokaryotes existed for 2000 million years before eukaryotes evolved from them ppearance of aerobic ha denial Development of Ozrich atmosphere Appearante of photosynthetic Diaproduring cyanoba cteria ppearance of photosynthetic sulfur bacteria Appearance of methanoglens 500 million years for prokaryotes to appear after the oceans formed Formation of means and continents Or 5 BYA Formation of Ea rth mifimfoif iiff imStiltl lfli39iliii39 Bilayers formed spontaneously from Produ ion of short FINA molecules rmwommnces amphlphlllc lipids selective rap loatlon of selfduplicating A C u m 0 n O m e rs catalytic RNA segments form polymers Perhaps ribonucleotides to RNA or perhaps some other precursor Membranes were required to segregate the reactions required for life from the outside world fawlu n39 Til njijl vwlv j39slzll l H Im Gellollle size Number 039 Organism milllnnlellldeo de pairs genes Binlnginlinmen Mymplnsma garrlrallum use an Smallesr rrue organlsm Ireparr mapalli 11 1039 causes syp iis Eornll39a burgdarlerl 144 1735 Causes Lyme disease Helrcnbaclerpylan L7 1559 Causes gasmc ulcers at nacoceusjarrrr ehrr 17 1733 Ar 1 arrgraws a a l Meemaplrllus lntluerrxae I a 1735 Causes bacterial lrrlluenz Archaeo lab ful 22 H review we methanngen zhnrysli 5p 36 4003 Cyanohacterrum Butlllus subtlli 42 4779 torrurrorr soil hanenum Escherichia to i 46 4377 Sorrr slrairrs cause roxrc ndr e Sacthammyces cerevisiae 125 5770 Unrcellular eukaryate usmodlum fakipnrum 23 5259 auses human ma arra Caenarhnbdllr39s Iegans loo 19400 Mulrisellular roundworm Arrup elesgarrr irae 273 13700 Malaria venur Ambidapsis rlraliarre 157 15500 Madel pl l Oryta sun39le 390 37500 nice Drosophiln melanogastzr 1 no r amen Laherasury y 39fvuil fly Mus mumalus domes m 24 x In3 25000 La oratory rrr Pan lmgiudyles 24 x m3 25000 chimpanzee Homnsapien 25 x lu3 25noo Human Do humans have the largest genome TABLE 13 Comparison uf Prokaryutlc and Eukarymic Cells Characren39srl c Prakawollc cell Eukaryorl39c cell ize Generally small 1710 lull Generally large 157100 pm Genome DNA Wlth nnnmsmne proteln NA complexed Wllh msmne and nonhlsmlle I in nucleold n m elns in chromosomes chromosomes ln surlounded by membrane nucleus wnh membranous Envelope Cell dlvlSlDll Flssion OI huddlng no mimls MiloSlsv lncluding mimic splndle canlr loles ln an 1 Membranabounded organelles Nulrlllon Enelgy metabvllsm Cymskelemn Inlmcellulal movement Absent Absorption some photosynthesls Nu mlmcl lol l Ddeatlve enzymes hound a plasma me 39 i in metabull c Dallem Nnrle None m MI DEhond al chloroplasts lll plants some algae endoplasmlc leunulum Golgi complexes lysosumes lrl arll mals etc Absorpllon lngestlon pllotosynthesls ln Oxlnallve enzymes packaged In lnllucnondnal more uni ed pattern al nxidatlve mezabollsm Cnmplex wllh micmtubules lnlemlediale lamems aclln laments Cytoplasmlc streamlng endncylnsl s phagocylcsis mumsls veslcle tmnspnn Animal ell nibosomes are protein synthesizing machines Nii Ieus cnnulns the genes hromntin Peroxisame oxldlus 5 Nuclear env I my atid cm kelelon supports cell alds In mavemeni oforganells Lysosame degrades immeuuiar debris m cm w Transport reside shunies lipl s V and prolelns bezween an Goigi Nudenlus is site a Pquot 39 3 oiriiaosomai RNA Golgi ompiex processes synthesis packages and large prouins to other organelles asma membrane s arior an o serif fnquot39f 39glm V r Smoothendoplasmlc m QO a mfwms vetlciilum sen Is site Mo and m and of llpld synuiesi and drug metabolism Mitochondrlon oxidizes Rough endow it f I 2 d 1 e 5 39quot quot e A ielimlum nan IS n quoth pm ein syn 39iesis Why do we have all of these membranes EFunction Structure Metabolism Level 4 Level 3 Level 2 Level 1 The cell and its organelles complexes N crildgs DNA Li I Di h Amino acids M will Plasma membrane Sugars TAB LE 12 E ca Cell Mu ecular Components of an Appmximam num ar M Pamemage at airfare ma weig i mMecu ar a f een39 spe ieg Wamrr TE 1 Framing 15 30610 N ucl si c was DNA 1 1 RNA 6 xSMCI Pa ysa ahamdas 3 Lipids 2 203 anme c Subunits am immermea a te s 2 5m lnmgamc Ems 1 2G superimposed on its mirror What is the chirality of our amino acids and sugars Basic Elements of Biological Macromolecules What is a macromolecule Weak interactions Electrostatic Hydrogen bonding Van der Waals Hydrophobic Effect Water structure Hydrophobic effect Monomers to Polymers Given 20 AA and a peptide length of 100AA Number of possible sequences 20100 10130 1OOAA 14 kD One copy of each sequence requires 14x10131 kD Universe contains 1080 kD Dark Energy Number of different proteins in E coli 3000 Plenty of possibilities and room for errors Chemical Bonds Strong or Covalent Enzymes change covalent bonds Weak or noncovalent Protein folding Membranes Transport Substrate binding LE 5 Four was of Noncwalent Interactions among Einmolecules in Aqneaus Snlvent Hydrogen bunds Between neImaI quIIps Between peptide bonds lunlc interactions Anrac un Repmslun Hydraphuhic intelacmns Van der Waals inlerac nns E f O I H O C Ol I III N W 4 1H Nm R IN Origin of Van der Waals Force FILJCIE US electron cloud 0 1 M 2 Induced dipole attraction En crgy m 1 Sum Df van der Waals radii Table 1 4 Radii of the Common Atoms of Biomulccules Atom Van I121quot 39Waals Covalent represented Atom radius mu radius 11m to scale I l 0 1 gt 0 037 I U l T 0 7 T7 3 39139 1 F 013 TC M Atoms D D 14 0me co 0 rs P D 19 0096 S If 1 S 5 11 1 D4 1 Half Ihickne If an 1 7 ammat ic ring Bonding means getting closer 0 8 1045 8 m 8 Hydrogen bond 01 nm 8 Covalent bond 00965 nm 8 8 I I Hydrogen C C acceptor 9 I 9 9 9 lil Hydrogen l ll Fl ll Fl Fl donor I I I I I I 3 r N N N What about SH What about CH Hbonds have preferred orientations i i I r 39339 Strong H Weaker hydrogen 0 hydrogen Po bond gp bond Why is the Hbond on the right weaker Table 2 l Electrostatics FF0rce e192Dr2 Dielectric Constants of Some Common Solvents at 25 C Solvent Dielectric Constant D W tter 785 Methyl alcohol 326 Ethyl alcohol i39lcetome 20quot Acetic acid 62 Chloroform 50 Benzene 23 Hexane l9 DFormamide where e 1 m charge on 1 or2 r distance between charges no orientation in homogeneous medium but As substrate binds to enzyme how does the D between change How will that affect binding H20 is a dipolar molecule Water as a solvent of polar and nonpolar solutes What weak interactions can it use to quotsolubilizequot solutes AGAHTAS AGltO means what Hydrated Cl39 ion Note the nonrandom orientation of the i 3 water molecules Hydrated Na ion How does the solvent determine the driving force of dissolution What is the structure of waterice 8 8 LEMi 8 8 Hydrogen bond 01 nm 8 Covalent bond 00965 nm 8 8 b Water forms a In ice nearly all the molecules are frozen into the lattice As the temperature increases the fraction of molecules frozen into the lattice decreases When would none of the water molecules be in the tetrahedral lattice structure In liquid water 7080 of Hbonds exist at all times they just change partners on a 5 psec time scale The average size of tetrahedral lattice elements decreases as the temperature increases What is the molarity of water in water 555 M Vaporization leads to 103 fold increase in volume TABLE 2 3 Solubility Gas Structure Polarity in water gL Nitrogen NEN Nonpolar 0018 40 C Oxygen 0 Nonpolar 0035 50 C Carbon dioxide s Nonpolar 097 45 C oc Ammonia H H H Polar 900 10 C N a Hydrogen sulfide H H 1 Polar 1860 40 C 5 s The arrows represent electric dipoles there is a partial negative charge 8 at the head of the arrowa partial posi tive charge 5 not shown here at the tail Note that polar molecules dissolve far better even at low temperatures than do nonpolar molecules at relatively high temperatures TABLE 22 t was a w v 2mmquot U mmquot I H Polar Glucose Glycine Aspartate Lactate Glycerol Nonpolar CH2 Typical wax H H OH H OH Amphipatic NH3CH2COO Phenylalanine an l ooc c1l2 CH coo CHg CfH COO Phosphatidylchollne gygga fakk k 1cr D Ier 0H W o gn 1W3 OH O CHz O lr O CHz CHZ Hocn2 CH CH20H o I Polar groups I Nonpolar groups Molar solubilitymax molecules that can dissolve in water as monomers When Glycinegtmolar sol what happens to the excess When PCgtmoar sol what happens to the excess When Waxgtmoar sol what happens to the excess Shape of an oil droplet in water Spherical Minimum surface area per unit volume Hydrophobic effect minimizes the area of contact between water and nonpolar groups by itself but the other weak interactions add their effects Most of the nonpolar sidechains of proteins and other macromolecules are packed within the folded protein but not all Hydrophilic quothead groupquot Wye Hydrophobic alkyl group quotFlickering clustersquot of H20 molecules in bulk phase A Highly ordered H20 molecules form cages around the hydrophobic alkyl chains Dispersion of lipids in H20 Each lipid molecule forces surrounding H20 molecules to become highly ordered Why must the water molecules be next to the acyl chains if that decreases their entropy 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 is further increased Lipid shape determines aggregate morphology greater than that of side chain Individual units are Individual units are Aqueous wedgeshaped cylindrical cross section cavity s cross section of head of head equals that of 39 side chain a Micelle b Bilayer c Vesicle The bilayer is the permeability barrier for the biological membrane Desired chemicals eg amino acids and glucose have transporters to move them across the bilayer Small molecules can passively cross the bilayer given enough time eg H20 02 Na and CI39 All but 02 have transporters Ordered water interacting with bf substrate and enzyme rig 339 mg 339 E lt V r Enzyme l 33 CV Disordered water displaced by enzymesu bstrate interaction Enzyme substrate interaction stabilized by hydrogen bonding ionic and hydrophobic interactions Table 13 Veak Chemical Forces and Their RelaLiva Strengths and Dislances Strength Distance Fm lgmun inn Desuiptiun Van dci Vani inxcmmmn 04 40 02 Su39cngth dcpsnds on dis rclaLch 39 c ofthc mom or molecules and 1C dismncc betwccn Lhan The size Iactnr rlcmrmmcs Lh area of Contact buncm two moiecnlen The grcater Lhc am Lhc stronger the inmmclion Hydrogen bonds 12 3u 03 Ionic inleracLinns Hydrnphnbit inlcmclinns 21 lt4 U Ralaiji39c sucngm is pmpmiionni In he polaru C band donor and 1 bond icmplm39 More pnlai atoms l39nrm su ongcr 11 hon s SLrenth also depends on me rclaijve polarlq of in mmrat ng charged specie Snmc innit anrariions are also 11 bands N39II 500c Farce i a complex phenomenon determined hv Lbc degree n which the su urtui c ofwzucr IS dimidci39cd alt discmc hydrophobic nmlccnic or molccular rcginm cozlcicn Recitation reprise Water and Protons Review of Protonation pp 6068 Whether or not a group is charged will be very important for its interaction with neighboring groups Protonation state determines whether a group is charged or not The protonation state depends upon the pKa of the group and the pH of the aqueous medium TABLE 2 6 HlM pH 10 1 o 10 14 1 1o 1 1 1 1o 2 2 1 12 12 1o3 3 104 4 10 1o 105 5 1o9 106 6 08 8 1o 7 7 7 7 1o 8 3 1o 6 6 1o9 9 1 5 10 10 1o 1 4 1o11 11 1o 3 1o 12 12 1 1 2 10 13 13 o 1014 14 BronstedLowry Acid Acid is a proton donor Base is a proton acceptor H3PO439 acid H2PO4391 either acid or base HPO4392 either acid or base PO4393 base What determines which of these chemical species is abundant in the test tube 100 5 E Trypsin 4 I E E gtlt 50 M E 39539 3 Alkaline 0 phosphatase 0 l pH pKa of an atom is the pH at which half of the atoms are protonated and half are not What is the pKa of trypsin Histidine as an acid or base 0 His has a protonatable N with pKa6 At pHlt5 the abundant form is NH At pHgt7 the abundant form is N One form interacts as an ion while the other interacts as an Hbond acceptor The energies of interaction with neighbors are very different What neighborhood would be preferred ie lower AG at pH4 39 What about pH8 HIstIdIne W z I I I N n I Inf39 n n n Z I IMPORTANT QUESTION For AA with a side chain which can be protonated what fraction of the side chains will be charged at a given pH The answer has 2 parts The Henderson Hasselbach equation determines whether the sidechain is protonated dentity ofthe protonated atom determines whether it is charged or not If the atom is 0 then no charge If N then 1 charge Determining a pKa HA 69A H 9 s 7 l CH3COOHCH3COO I 6 pH 576 5 Z 39 Buffering pH region 4 3 pH pKa 476 pH 33976 2 CH3C00H 39 1 o l l l l l l l l 0 01 02 03 04 05 06 07 08 09 10 OH added equivalents I l 0 50 1 00 Percent titrated Fraction Protonated 10 and pH LOOJEHJ HoonSHJJ Determining protonation from a pKa Fraction Protonated pKa4 pKa8 Ka fHA HA39HA 0r pKaI0H091o A39JH Fraction protonatedHAHAA 11 1 oltpHpKa Simple HH Numbers Approximate Solution for HendersonHasselbalch Equation pK 4 pK 8 fraction protonated fraction protonated pH exact approx pH pH exact approx 2 990E01 099 pKZ 6 990E01 099 pK Z 3 909E01 09 pK1 7 909E01 09 pK1 4 500E01 05 pK 8 EOE01 05 pK 5 909E02 01 pK1 9 909E02 01 pK1 6 990E03 001 pK2 10 990E03 001 pK2


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