Class Note for CHEM 490 at UMass(22)
Class Note for CHEM 490 at UMass(22)
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This 23 page Class Notes was uploaded by an elite notetaker on Friday February 6, 2015. The Class Notes belongs to a course at University of Massachusetts taught by a professor in Fall. Since its upload, it has received 26 views.
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Date Created: 02/06/15
Protein Structure Ch 2 Mon 22Wed 2409 Amino acids defined Sidechain proper ries range of size shape reac rivi ry nonpolarpolar Hydrophobici ry H bonding charged pK acidbase chemis rry buffer pI 06W geome rry of Gly amp Pro s reric cons rrain rs aroma ric UV absorbance 39 Pep ride backbone Pep ride bond planar gt 1111 conforma rional space Ramachandran plo r l Alpha Helix 36 residuesTurn COi to NHi4H bonds 15Aresidue compac r Helical wheels sidechains OUT 9 Be ra Shee r Parallel or an riparallel 35A residue nearly ex rended Sidechains al rerna re abovebelow shee r Ter riary s rruc rure Hydrophobic core Qua rernary s rruc rure Hmwk Ch1 13458310 Pro rein FOldll lg Coopera rive Ch21 3 5 6 7 9 10 W7 Ma r mvo bllmo 180 120 Ill 60 7 120 v l l Al I 180 180 120 60 o 60 120 180 4 90 ll 90 4 a Disfavored Figure 228 Biochemistry Sixth Edition 2007 W H Freeman and Company 180 l 120 120 v 180 120 60 o 60 120 180 90 lll3990 Disfavored Figure 228 Biochemistry Sixth Edition 2007 W H Freeman and Company H H H R 0 1 85 180 by sfn e at W twovJquot wwds 4 0 Stef39 xn Vt 6 erlt Mde Ta 1 s 39st a M A4 bowls 39 P less bhgcm 180 180 bac cb observed for a typical protein 4 alpha helix beta strand other A c1wlcr3 gigglfmzi rismudimn O NHi4 H bonding 2007 w H Freeman and Company Ends have unsatis ed H bonds at protein surface polar Figure 230 Biochemistry Sixth Edition 2007 W HFreeman and Company Alpha helix Predicted by Linus Pauling amp Robert Corey 195i Veri ed by Xray diffraction of myoglobin 1958 C01 to NH H bonding 14 180 120 180 180 120 60 0 Lefthanded helix very rare Righthanded helix common H I III I 60 120 184 gt Protein Structure Ch 2 Mon 22Wed 2409 Amino acids defined Sidechain proper ries range of size shape reac rivi ry nonpolarpolar Hydrophobici ry H bonding charged pK acidbase chemis rry buffer pI geome rry of Gly amp Pro s reric cons rrain rs aroma ric UV absorbance Pep ride backbone Pep ride bond planar 1111 conforma rional space Ramachandran plo r Alpha Helix 36 residuesTurn COi to NH4H bonds 1 15Aresidue compac r Helical wheels sidechains ou r Be ra Shee r Parallel or an riparallel 35A residue nearly ex rended Sidechains al rerna re abovebelow shee r Ter riary s rruc rure Hydrophobic core Qua rernary s rruc rure Hmwk Ch1 13458310 Pro rein FOldll lg Coopera rive Ch21 3 5 6 7 9 10 Beta strand represent by N to C arrow plum GWLAME PUBLISHWG IC mmmm 1 M 1111 e Fumr mum Both pleated Sidechains alternate sides 8 Almost all 12 Beta Strands twisted strands so 0 RH twist 030quot I o 60 120 180 l I A1 I 180 120 60 0 60 120 180 12 Human insulin Primary Secondary Tertiary Quarternary structure structure structure structure 322de v4 T LFrEeman and Company B 3951 rquot 2 Abwak Globular proteins are compact B Conformation 2000 X 5 A or Helix Native globular form 900x11A 1oogtlt60A 585 residues 1 AD 3 x 35 Aresidue z 2000 A Qb i g vgl 0L x15 Alresidue z 900 A globular human serum albumin 100A longest dimension Visualizing protein structures lysozyme W rigmm rigmm HumanStu sum Emma Piotremit m1wwmmw SQ A Visualizing protein structures lysozyme Disulfide bonds Activesite aspartate residue Even better RNAse A in Proteopedia httpwwwproteopediaorqwikiindexpho1rta Explore Jmol menu Select gt All Style gt Scheme gt try each one What s inside proteins momma M s 9 kvlalvvy roh c rare all Hszytwstd39j d What s on the surface POD as 0903 39S hmj E A 3939c 0L Dump 39 B A B Heme group Heme group Fig ure 248 Biarhemistry Sixth Editian 2007 w H Freeman and Company Figure 249 Biazhemistry Sixth Edilian c 2007 w H Freeman and Company 7 il pe39k Hydrophobic blue Charged red a Hydrophobic blue 7 Charged red Figure 4 1 3 Printiples of Biochemistry Ale 2006 Pearson Prentice Hall Inn 360 1000 Helical wheels 36 residues per turn Repeats after 5 turns 18 residues blue offset to see repeat coiled coils 35 residues per turn LH supercoil heptad repeat 2 abcdef g Hydrophobic groups at interface 2 a amp d Bordered by charged groups gt salt bridges e amp g U W E r 4 parallel antiparallel interactions ad hydrophobic aa amp dd quot m eg ionic ee amp gg it How could you predict anti or parallel based on sequence L39 I Which of the following sequences is likely to be found in a beta strand at the surface of a protein 00e c009 al m 3lt7 3 mN c H e I mN c H b nz TH c L I n f l I T at 39 TH NH3 Histidine H Lysine K His Lys cooe cooe c009 c009 ea I lt9 I e ea H3N IZ H H3N f H H3N IZ H H3N T H CH2 CH2 IIHZ IIHZ 9 COO CH C CH I 2 H N o I 2 cooe 2 c MN 0 Aspartate D Glutamate E Aspargine N Glutamine Q Asp Glu Unnumbered fiqure nu 60b Princinles of Biohemistrv4e Asn Gln cooe e l mN f H quot2 cm cm NH C HZN NH2 Arginine R Arg
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