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Holiday Concerts: Whatcom Chorale Sunday, Dec. 12 3pm and 7:30 pm First Congregational Church Handel's Messiah. Bellingham Chamber Chorus Friday, December 10 8 pm PAC Concert Hall Bach Magnificat and a bunch of modern stuff. Upcoming Biochemistry Seminars. M November 29 4 pm SL 130.

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Holiday Concerts:

Whatcom Chorale

Sunday, Dec. 12

3pm and 7:30 pm

First Congregational Church

Handel's Messiah


Bellingham Chamber Chorus

Friday, December 10

8 pm PAC Concert Hall

Bach Magnificat

and a bunch of modern stuff.


Upcoming Biochemistry Seminars

M November 29 4 pm SL 130

F December 3 4 pm SL 130

Structure, Function and Engineering of the Homing Endonuclease I-CreI

Extra Credit!!!!


Figure 15-20cX-Ray structure of bovine trypsin. (c) A drawing showing the surface of trypsin (blue) superimposed on its polypeptide backbone (purple).

Page 519


Table 15 4 a selection of serine proteases
Table 15-4 A Selection of Serine Proteases.

Page 516


Example of

“convergent”

evolution.


Figure 15-22 Relative positions of the active site residues in subtilisin, chymotrypsin, serine carboxypeptidase II, and ClpP protease.

Page 521


Figure 15 21 the active site residues of chymotrypsin
Figure 15-21 The active site residues of chymotrypsin.

Page 520


Figure 15 23 catalytic mechanism of the serine proteases
Figure 15-23 Catalytic mechanism ofthe serine proteases.

Page 522


General base

Electrostatic

stabilization

Rate determining step

(Michaelis

complex)

Scissile bond


General base catalysis

decomposition


Water replaces new

N terminal

Now the whole process operates in reverse:


Stable acyl-enzyme intermediate

Attacking nucleophile?

Leaving group?


Figure 15 25a transition state stabilization in the serine proteases a the michaelis complex
Figure 15-25a Transition state stabilization in the serine proteases. (a) The Michaelis complex.

Page 524


Figure 15 25b transition state stabilization in the serine proteases b the tetrahedral intermediate
Figure 15-25b Transition state stabilization in the serine proteases. (b) The tetrahedral intermediate.

Page 524


Figure 15-26a X-Ray structures of porcine pancreatic elastase in complex with the heptapeptide BCM7 (YPFVEPI). (a) The complex at pH 5.

Page 525


Figure 15-26b X-Ray structures of porcine pancreatic elastase in complex with the heptapeptide BCM7 (YPFVEPI). (b) The complex at pH 9.

Page 525


Stryer Fig. 9.16 Site directed mutagenesis of

subtilisin. Note the log scale. Mutations in the

catalytic triad lead to a dramatic loss of activity


Figure 15 27 activation of trypsinogen to form trypsin
Figure 15-27 Activation of trypsinogen to form trypsin.

Page 527


Figure 15 28 activation of chymotrypsinogen by proteolytic cleavage
Figure 15-28 Activation of chymotrypsinogen by proteolytic cleavage.

Page 528


Substrate

activation

schemes

Stryer Fig. 9.17 an 18


Figure 15 8 the alternating nag nam polysaccharide component of bacterial cell walls
Figure 15-8 The alternating NAG–NAM polysaccharide component of bacterial cell walls.

Page 507



C16 and C18 most common

*

*usually. Bacteria have some odd number chains


Rarely

conjugated

rare





Glycerolphospholipids

See Table 12-2



Figures 12-4, 12-6

and 12-7

ganglioside


GM2:sphingosine linked to 4 sugars

Tay-Sachs Disease: GM2 degradation enzyme missing




membrane fluidity is affected by temperature

above transition temp.

below transition temp.

See Table 12-1





Fluid mosaic model of membranes
Fluid Mosaic model of membranes

  • membrane is 2-D fluid lipid matrix in which proteins are imbedded

  • proteins (and lipids) are free to diffuse laterally but not transversely (i.e. they can’t “flip” from one side of bilayer to the other)

  • proteins that don’t migrate freely are bound to an anchoring “skeleton”






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