BMB170 2017 Lecture1 - California Institute of...

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Transcript of BMB170 2017 Lecture1 - California Institute of...

Page 1: BMB170 2017 Lecture1 - California Institute of Technologysaf.bio.caltech.edu/bi170/BMB170_2017_LECTURE1.pdf · Cf,+0Q3./5 •g+;.?

!"!#!$#%&'()!*+,-./+0'102/3-+$45106+7-809:-&

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9)'(0;/<=.<-+0>+??3@5&$70=+<=?$4+5• A6B00

– C,-3D+/09E/=00F?$>+05,$+4,+5G0

– C,-3D+/09H-&0F%3I7.-+/0<4=0$4>3/I<J3406,$+4,+0<4=0K4;$4++/$4;G0

– C,-3D+/09(-&00F,&+I$5-/LM7&L5$,5G0

– &N7O##@@@845>8;3P#;/>70

• Q+/-R0 0 0

– C,-3D+/09(-&0FS.<4-80D$3?3;L0<4=0D$3T+4;G0

– @@@8&+/-R>3.4=<J3483/;

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!"!0%3./5+5• !"!#!$#%&0

– !$3,&+I$5-/L0<4=0!$37&L5$,503>0"<,/3I3?+,.?+50<4=0"3?+,.?</0U55+ID?$+580V0.4$-50FET'TWGX0Y/5-105+,34=10-&$/=0-+/I500

– B$/5-0-+/I0F%?+I345G0'()0• <4<?L5$503>0-&+05-/.,-./+503>0-&+0H0,?<55+503>0D$3?3;$,<?0I3?+,.?+50<4=0-&+0>3/,+50-&<-05&<7+0-&+I0

– 6+,34=0-+/I0FZ+45+4G0'(E0• D<5$,07/$4,$7?+503>0I3=+/40D$37&L5$,<?0<4=05-/.,-./<?0I+-&3=50>/3I0-&+0<-3I$,0-30,+??.?</0?+P+?50

– [&$/=0-+/I0F6&<4G'(H0• =+-<$?+=0<4<?L5$503>057+,$Y,0I<,/3I3?+,.?</0I<,&$4+50<4=05L5-+I50

• !"!#%&0'(\0F6&<4G0– K4RLI+0]$4+J,50<4=0"+,&<4$5I580V0.4$-50FET)T:GX0Y/5-0-+/I0

• ^$5,.55$3403>0-&+0+4+/;+J,07/$4,$7?+50<4=0I3?+,.?</03>0+4RLI+50• 2/<,J,<?0_$4+J,505+,J3450=$5,.550&3@0-30$4>+/0I3?+,.?</0I+,&<4$5I50>/3I0/<-+#+S.$?$D/$.I0

I+<5./+I+4-50• !"!#%&09)90<D,80!$3,&+I$5-/L06+I$4</0%3./5+0

– '0.4$-X0Y/5-105+,34=10-&$/=0-+/I50– ^$5,.55$3405+,J340I<-,&+=0-30D$3,&+I$5-/L05+I$4</05+/$+5

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!"!'()

• `45-/.,-3/50– !$?0%?+I3450

• [+<,&$4;0U55$5-<4-50– `4&<0%&30• aH9)W10$,&3b,<?-+,&8+=.10'9V067<?=$4;00

– %?<.=$<0Z+N+0• acccc10,<d+N+b,<?-+,&8+=.10!/<.400

– Z$4;R&3.0e<4;0• acccc10d$4;R&3.b,<?-+,&8+=.10!/3<=0%+4-0

H

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Cf,+0Q3./5

• g+;.?</034+50=34h-0@3/_0530@+h??0&<P+034+0<0@++_0

• K<,&0@++_0– [&+/+0@$??0D+034+03403i0@++_500– C4+07/$3/0-307/3D?+I05+-0=.+0=<-+

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e+D5$-+• "<$4-<$4+=0DL0^<P$=0"<-&3;0• &N7O##5<>8D$38,<?-+,&8+=.#@@@#D$'()8&-I?0• U??0,3./5+0/+?<-+=0I<-+/$<?0@$??0D+034?$4+0• 6L??<D.510,3./5+043-+5107/3D?+I05+-510<45@+/0_+L5

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[+a-5

• *$?d<510*$?d<5102$5_./10*$4=D?3I10A$55+40j0]d+?=;<</=0k[+a-D33_03>05-/.,-./<?0D$3?3;Ll0

• C40g+5+/P+0– !/<4=340j0[33R+0k`4-/3=.,J340-302/3-+$406-/.,-./+l0– %/+$;&-340k2/3-+$45O06-/.,-./+10>.4,J340<4=0I3?+,.?</07/37+/J+5l0– 2+-5_30<4=0g$4;+0k2/3-+$406-/.,-./+0<4=0B.4,J34l0– m3+-0j0m3+-0k!$3,&+I$5-/Ll0– 6-/L+/0k!$3,&+I$5-/Ll0– 6&.?R0j06,&$/I+/0k2/$4,$7?+503>02/3-+$406-/.,-./+l0– n+44$50k!$3I+ID/<4+5l

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"+,&<4$,5• *+,-./+50</+037+410!"#$%&'()*+(0• Q<4=3.-5034?$4+0<4=07/3P$=+=0$40,?<550• n/<=+50

– 2/3D?+I05+-50• ^+5$;4+=0-30;$P+0<0=++7+/0.4=+/5-<4=$4;03>07/$4,$7?+50=$5,.55+=0$40

,?<5500• B$P+05+-50@3/-&0'Wo0+<,&0F(WoG0• g+S.$/+50.5+03>0,3I7.-+/0F2LI3?G0• ^.+0-@30@++_50<p+/0&<4=+=03.-0q0*<-+5043-0<,,+7-+=0@$-&3.-0

=3,-3/h5043-+rrrrrr0s3.0I.5-043J>L0.50D+>3/+0-&+0<55$;4I+4-0$50=.+rrr0

• ^3043-0,37L10=$5,.550-&+07/$4,$7?+50D.-043-0-&+0+a<,-0<45@+/5r0– B$4<?0Ka<I0F9Wo03>0;/<=+G0

• `0@$??0-/L0-307/3P$=+02^!0`^50<4=0/+>+/+4,+50-307/$I</L0?$-+/<-./+8

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6L??<D.5

BMB/BI/CH 170 SYLLABUS Fall 2017 http://saf.bio.caltech.edu/bi170.html

TUES/THUR 10:30 A.M. - 12 NOON 151 Crellin

Instructors Bil Clemons 157 Broad, x1796 [email protected]

Teaching Assistants Inha Cho, x4205, [email protected], 129 Spalding Claudia Jette, x , [email protected], ? Braun Jingzhou Wang, x , [email protected], ? Broad

Suggested Text: “Textbook of Structural Biology” Liljas, Liljas, Piskur et al PROTEINS 09/26 01) Introduction, history and basic chemistry #1CJ 09/28 02) Peptide bonds and secondary structure 10/03 03) Tertiary structure 10/05 04) Hydrophobic effect and stabilizing forces 10/10 05) Stability, folding and chaperones #2IC 10/12 06) Chaperones (cont.) and aggregates; motifs, oligomers, assemblies 10/17 07) Cytoskeleton and symmetrical assemblies 10/19 08) Viruses 10/24 09) Metals, enzymes and nucleotide binding proteins #3IC NUCLEIC ACIDS 10/26 10) Basic Chemistry, DNA/RNA structure 10/31 11) Protein interactions, transcription factors 11/02 12) Transcription factors (cont) and ribosomes 11/07 13) Ribosomes and translation #4CJ

MEMBRANES & LIPIDS 11/09 14) Lipids and biological membranes 11/14 15) Membrane protein synthesis and stability 11/16 16) Membrane proteins continued CARBOHYDRATES 11/21 17) Basic chemistry and CAZy #5JZ 11/23 Thanksgiving Holiday 11/28 18) More glycozymes and biological roles 11/30 19) Lectins and glycobiology 12/01 Last problem set due 5PM. 12/08 Finals due by 5PM. (Bil’s office or ????)

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*+-h50$4-/3=.,+03./5+?P+5

• e&<-0</+0-&+0;3<?503>0!"!'()0• e&30</+0L3.0–A<I+0–s+</#"<d3/0• n/<=50I+4J3407/+P$3.50$45J-.-+0

–g+5+</,&0`4-+/+5-50–Q37+50>3/0-&+0,3./5+

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,'-./0+'$1/*2'3+$$.3*(4+25'(3(

t [<$?T<4,&3/+=0-</;+J4;0

t "+ID/<4+07/3-+$40+a7/+55$34

Clemons lab @ Caltech

'(

6748*85'-3(2/4$3+$.3*7*93807$-'-./0+'(

t AT?$4_+=0n?L,35L?<J340t 2+7J=3;?L,<400D$35L4-&+5$5

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*+-h50$4-/3=.,+03./5+?P+5

• e&<-0</+0-&+0;3<?503>0!"!'()0• e&30</+0L3.0–A<I+0–s+</#"<d3/0• n/<=50I+4J3407/+P$3.50$45J-.-+0

–g+5+</,&0`4-+/+5-50–Q37+50>3/0-&+0,3./5+

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6P+=D+/;0!"#$%&'#(%&)#$%0!:;<10H)T(V0F'VEVG

[&+3=3/+0u[&+h06P+=D+/;• A3D+?0%&+I$5-/L0'V9:0

– >3/0,3??3$=50– ,34Y/I+=0K$45-+$40j0

6I3?.,&3@5_$h50D/3@4$<40I3J340&L73-&+5$50

– ,/+<-+=0-&+0.?-/<,+4-/$>.;+0

• A3-+=0-&<-0I+<5./+=0"e503>07/3-+$450,3.?=0D+0D/3_+40=3@40$4-30$4-+;+/503>0v'(8:0_^

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A.I+/3?3;Lw0F,3I735$J34<?0,345$=+/<J345G

• 6P+=D+/;0.4$-0EW0_^0x09\\0<I$430<,$=50x09W0tE90• B<,-3/<D?+07/3-+$450@+/+07/3735+=0-30,34-<$409IE40• k+<,&0<I$430<,$=0/+5$=.+0$50=$5-/$D.-+=0-&/3.;&0-&+0+4J/+07+7J=+0,&<$40<-0

,345-<4-0$4-+/P<?5X0$+10+<,&0<I$430<,$=0/+5$=.+0/+,./50@$-&0<0,&</<,-+/$5J,0@&3?+04.ID+/0>/+S.+4,Ll800

• Q+I3;?3D$40@<50-&3.;&-0-30&<P+0,3I735$J340– W(:0<I$430<,$=509:0a0E90– ]FE:G10QFE9G10^FE9G10KF':G10sF'9G102F'9G10gF'9G10%FEG0– B3/0?L5$4+0E:0x0F99E9G0q05+7</<-+=0'W0/+5$=.+50FE:a':xW(:x9a9\\G0

• 04.I+/3?3;$,<?0,345$=+/<J345O0&+7-<=0/+7+<-510,3??<;+40-/$7?+-5

!+/;I<440j0A$+I<440*+,0::=0F'VE(G0E)'T'H

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[&+0k7/3-+$405-/.,-./+07/3D?+Il0!!/$+>0&$5-3/L0

• Q+I3;?3D$40,/L5-<?50=+5,/$D+=0DL0v'\E)0• Z8!806.I4+/0,/L5-<??$R+=0./+<5+0$40'V9:0• %/3@>33-0FQ3=;_$4G0j0!+/4<?0=+I345-/<-+=07/3-+$40,/L5-<?50

=$i/<,-+=0aT/<L50@+??0@&+40&L=/<-+=0F'VEHG0• K</?L0+i3/-50-3053?P+0-&+0k7/3-+$405-/.,-./+07/3D?+Il0.5$4;0aT/<L0

=$i/<,J340– K4;?<4=0T0U5-D./L10!+/4<?10!/<;;0T053?P+07/3-+$405-/.,-./+50=$/+,-?L0>/3I0

=$i/<,J3407<N+/4503>0,/L5-<?50<4=0YD+/50– 2<5<=+4<0T02<.?$4;0T0=+=.,+0D<5$,03/;<4$R<J34<?07/$4,$7?+50>/3I0

5-/.,-./+503>0<I$430<,$=50<4=07+7J=+5

[<4>3/=0<4=0g+L43?=510>02&/'?($@*.*2(10Ca>3/=109))'0

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Z3&40]+4=/+@10'VW\O0k2+/&<750-&+0I35-0/+I</_<D?+0>+<-./+503>0-&+0I3?+,.?+0</+0$-50,3I7?+a$-L0<4=0$-50?<,_03>05LII+-/L80[&+0<//<4;+I+4-05++I50<?I35-0-3-<??L0?<,_$4;0$40-&+0_$4=503>0/+;.?</$J+50@&$,&034+0$45J4,JP+?L0<4J,$7<-+58l

"<a02+/.-R10'V:HO0k%3.?=0-&+05+</,&0>3/0.?JI<-+0-/.-&0/+<??L0&<P+0/+P+<?+=0530&$=+3.50<4=0P$5,+/<?T?33_$4;0<403Dd+,-wl

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*T<I$430<,$=5

• *0$50-&+0<D53?.-+0,34Y;./<J340–e&L0430gw0

• 63I+0$40D<,-+/$<0

• 6$=+0,&<$4043I+4,?<-./+0– !, ", #, $, %, &, '

!!

"!

#!$!

%! &!

+H3N

C!

CO2-

HR

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UI$430<,$=5

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e8g80[<L?3/0*%&-./#"%&+0#1%0::A109)W0F'V\:G

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M

TQ9C M

TQ9C

2+7J=+0D34=0>3/I<J34

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%</?5D+/;0*<D3/<-3/$+5

B/34-03>0-&+0?<D5

[&+0D/+@+/L

B3.4=+=0DL0Z8%80Z<,3D5+40'\H(0*<D0>3.4=+=0$40'\(W0)2$$.2"#3($/4&$2"145/"6/74040682806{/+45+40F7QG02/3-+$40,&+I$5-/L0F'VH)50j0W)5G

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]<d0*$4=+/5-/{IT*<4;

• QL=/3;+4#=+.-+/$.I0+a,&<4;+0

• Q3@0@+0=+5,/$D+07/3-+$450

– 2/$I</L0T0<I$430<,$=05+S.+4,+0

– 6+,34=</LT0/+;.?</073?L7+7J=+0,34>3/I<J340

– [+/J</LT07<,_$4;0-3;+-&+/03>05+,34=</L05-/.,-./+0+?+I+4-50

– *$4;.$5J,0<4<?3;$+50T0?+N+/5#@3/=5#5+4-+4,+50

– ky.<-+/4</Ll

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B$D+/0=$i/<,J3405-.=$+5

• B$D/3.507/3-+$450@+/+0.5+=0Y/5-0– e$??$<I0U5-D./L0F*++=5G0

• [&/++07/+=3I$4<4-0>3/I50– |0q0@33?0F_+/<J4G10I.5,?+0– }0q05$?_105-/+-,&+=0@33?0– %3??<;+40F-+4=345G

|0FIL35$4G

}0F5$?_G %3??<;+4

6.7+/0,34-/<,-+=U5-D./L0U440g+P0!$3,&+I0F'VEVG0\O''E

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ZU%60F'VEVG0:'O'\:)

%/3@>33-02/3,0g3L063,0F'VE\G0U':HOW\)

0^/$+=0$45.?$40,/L5-<?5

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!"#$&'#(21&)#$&80F'VW)G09)EOE9'TEW:

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*$4.502<.?$4;0<4=0-&+07?<4</07+7J=+0D34=0F%U*[K%QrG

• %/L5-<?05-/.,-./+500– =+Y4+=0/+>+/+4,+0D34=0?+4;-&50– 5$4;?+0D34=0%TA0'8H(~00

• "+-&L?<I$4+0T0e8A80*$75,3ID0<4=0K8e80Q.;&+50F'VWEG0U,-<0%/L5-0

– =3.D?+0D34=0%xC00'89)0~0F_+-34+G0– =+I345-/<-+=0v07?<4</$-L0

• 63I+0z+a$D$?$-L0$40-&+07+7J=+0D34=0– +P$=+4,+=0DL0-&+0=$5-/$D.J3403>0(0– D<//$+/0$509)TE)0_,<?#I3?0F<502<.?$4;0

<4J,$7<-+=G

K=$5340A<-06-/0!$30F9))'G0\O9)'

!"#$%&%'"(#)&*+,+-&.$%(/0120(

C! NH

C!

O

C! NH

C!

O

+

-

C!C

NH

C!

O

1.32Å1.24Å

!"

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A34T7/3?$4+0,$50v0)8)Ho

2/3?$4+10,$50v0:o

e+$550/9&2110A<-./+06-/.,-0!$3?3;L0F'VV\G0WO:(:

2+7J=+0D34=0,$5T-/<450$53I+/$R<J34

C! NH

C!

O

C!

NH

C!

O

3.2Å3.8Å

C! N

C"

C!

C! N

C!

O O

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2+7J=+50<4=0&L=/3;+40D34=$4;• QL=/3;+40D34=503,,./0D+-@++40<0

B343/0<4=0!,,+7-3/0– ^TQ�����U0@&+/+0^0j0U0</+0-L7$,<??L0

A10C0F6G0– !<,_D34+0$405+,34=</L05-/.,-./+0

ATQ��������Cx%0• ^$5-<4,+098WTE8W~0UT^0• %34-/$D.-+50vE_,<?#I3?+0Fv'))a0

5I<??+/0-&<40<0,3P<?+4-0D34=G0• U??0&L=/3;+40D34=50I.5-0D+0

5<J5Y+=0F+$-&+/0$4-/<I3?+,.?</03/0DL053?P+4-G

2.8Å

C!

HN

CO

C!NH

OC

C!NH

OC

C!

HN

CO