Sections in Voet to Study or Read

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Sections in Voet to Study or Read Study Read
Ch 8 pp. 219-233 Collagen pp. 233-240 Mb pp.
240-248 pp. 248-256 Bioinfo pp.
256-258 Stability pp. 258-262 Hydropathy pp.
263-266 Symmetry pp. 266-end Ch 9 pp.
276-278 pp. 278-283 Folding pp.
283-290 Chaperones pp. 290-306 Prions pp.
306-312 Evolution pp. 312-end
Suggested Problems Ch 9 3, 4, 6, 12, 14
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Protein Explorer http//molvis.sdsc.edu/protexpl/
frntdoor.htm Do the 1 hour tour at this site.
http//molvis.sdsc.edu/protexpl/qtour.htm It may
take longer than 1 h.
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Table 8-6 Hydropathy Scale for Amino Acid Side
Chains.
Values below line are NEGATIVE!!
Page 263
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Figure 8-60 Hydropathic index plot for bovine
chymotrypsinogen.
Page 263
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Figure 8-46abc Schematic diagrams of
supersecondary structures
Page 249
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Figure 8-46d Schematic diagrams of supersecondary
structures.
Page 249
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Figure 8-47a X-Ray structures of 4-helix bundle
proteins.(a) E. coli cytochrome b562.
Page 250
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Fibrous Proteins
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Figure 8-25 The microscopic organization of hair.
Page 232
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Figure 8-26 The structure of a keratin.
Page 232
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Figure 8-27a The two-stranded coiled coil. (a)
View down the coil axis showing the interactions
between the nonpolar edges of the a helices.
Page 233
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Figure 8-27b The two-stranded coiled coil. (b)
Side view in which the polypeptide back bone is
represented by skeletal (left) and space-filling
(right) forms.
Page 233
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Exploring collagen
http//www.rcsb.org/pdb/molecules/pdb4_1.html
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Figure 8-28 The amino acid sequence at the
C-terminal end of the triple helical region of
the bovine a1(I) collagen chain.
Page 234
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Figure 8-29 The triple helix of collagen.
Page 235
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Figure 8-30a X-Ray structure of the triple
helical collagen model peptide (Pro-Hyp-Gly)10 in
which the fifth Gly is replaced by Ala. (a) Ball
and stick representation.
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Figure 8-30b X-Ray structure of the triple
helical collagen model peptide (Pro-Hyp-Gly)10 in
which the fifth Gly is replaced by Ala. (b) View
along helix axis.
Page 235
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Figure 8-30c X-Ray structure of the triple
helical collagen model peptide (Pro-Hyp-Gly)10 in
which the fifth Gly is replaced by Ala. (c) A
schematic diagram.
Page 236
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Figure 8-31 Electron micrograph of collagen
fibrils from skin.
Page 237
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Figure 8-32 Banded appearance of collagen fibrils.
Page 237
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Figure 8-33 A biosynthetic pathway for
cross-linking Lys, Hyl, and His side chains in
collagen.
Page 238
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Figure 8-34 Distorted structure in abnormal
collagen.
Page 239
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Globular Proteins
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Figure 8-35 X-Ray diffraction photograph of a
single crystal of sperm whale myoglobin.
Page 240
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Figure 8-39a Representations of the X-ray
structure of sperm whale myoglobin. (a) The
protein and its bound heme are drawn in stick
form.
Page 244
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Figure 8-39b Representations of the X-ray
structure of sperm whale myoglobin. (b) A diagram
in which the protein is represented by its
computer-generated Ca backbone.
Page 244
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Figure 8-39c Representations of the X-ray
structure of sperm whale myoglobin. (c) A
computer-generated cartoon drawing in an
orientation similar to that of Part b.
Page 244
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Figure 8-43a The H helix of sperm whale
myoglobin. (a) A helical wheel representation in
which the side chain positions about the a helix
are projected down the helix axis onto a plane.
Page 247
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Mb
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Cut-away view
surface
Stryer Fig. 3.45 Mb yellow hydrophobic,
bluecharged, whiteothers
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Stryer Fig. 3.46 Porin
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Porin
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Structural features of most globular proteins
1. Very compact e.g. Mb has room for only4
water molecules in its interior.
2. Most polar/charged R groups are on the
surface and are hydrated.
3. Nearly all the hydrophobic R groups are on
the interior.
4. Pro occurs at bends/loops/random structures
and in sheets
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Figure 9-1
Chapter 9!!!
Page 277
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Figure 9-2 Reductive denaturation and oxidative
renaturation of RNase A.
Page 277
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Figure 9-3 Plausible mechanism for the thiol- or
enzyme-catalyzed disulfide interchange reaction
in a protein.
Page 278
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Figure 9-14b Reactions catalyzed by protein
disulfide isomerase (PDI). (b) The oxidized
PDI-dependent synthesis of disulfide bonds in
proteins.
Page 288
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Figure 9-4 Primary structure of porcine
proinsulin.
Page 278
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H-bond Fun Fact

• 1984 survey of protein crystal data shows that
  almost all groups capable of forming H-bonds do
  so. (main chain amides, polar side chains)

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Many conformational states
Fewer conformational states
A single conformational state
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High energy
Many conformational states
Fewer conformational states
A single conformational state
Low energy
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Figure 9-11c Folding funnels. (c) Classic
folding landscape.
Page 285
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Figure 9-11d Folding funnels. (d) Rugged energy
surface.
Page 285
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Ideal
Real ?
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Figure 9-12 Polypeptide backbone and disulfide
bonds of native BPTI.
Page 286
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Figure 9-13 Renaturation of BPTI.
Page 287
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Figure 9-26 Secondary structure prediction.
Page 301
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Figure 9-28 Conformational fluctuations in
myoglobin.
Page 303
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Figure 9-30a The internal motions of myoglobin as
determined by a molecular dynamics simulation.
(a) The Ca backbone and the heme group.
Page 305
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Figure 9-30b The internal motions of myoglobin as
determined by a molecular dynamics simulation.
(b) An a helix.
Page 305
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Figure 9-32a Amyloid fibrils. (a) An electron
micrograph of amyloid fibrils of the protein PrP
27-30.
Page 307
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Figure 9-32bc Amyloid fibrils. (b) and (c) Model
and isolated b sheet.
Page 307
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Figure 9-34a Evidence that the scrapie agent is a
protein.(a) Scrapie agent is inactivated by
treatment with diethylpyrocarbonate, which reacts
with His side chains.
Page 310
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Figure 9-34b Evidence that the scrapie agent is a
protein.(b) Scrapie agent is unaffected by
treatment with hydroxylamine, which reacts with
cystosine residues.
Page 310
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Figure 9-34c Evidence that the scrapie agent is a
protein.(c) Hydroxylamine rescues
diethylpyrocarbonate-inactivated scrapie reagent.
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Figure 9-35a Prion protein conformations. (a) The
NMR structure of human prion protein (PrPC).
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Figure 9-35b Prion protein conformations. (b) A
plausible model for the structure of PrPSc.
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Figure 9-36 Molecular formula for
iron-protoporphyrin IX (heme).
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Figure 9-37 Primary structures of some
representative c-type cytochromes.
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Figure 9-38 Three-dimensional structures of the
c-type cytochromes whose primary structures are
displayed in Fig. 9-37.
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