Sections in Voet to Study or Read
Download
1 / 65

Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233Collagen pp. 233-240 - PowerPoint PPT Presentation


  • 80 Views
  • Uploaded on
  • Presentation posted in: General

Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233Collagen pp. 233-240 Mb pp. 240-248pp. 248-256 Bioinfo pp. 256-258Stability pp. 258-262 Hydropathy pp. 263-266Symmetry pp. 266-end Ch 9: pp. 276-278pp. 278-283 Folding pp. 283-290Chaperones pp. 290-306

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha

Download Presentation

Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233Collagen pp. 233-240

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -

Presentation Transcript


Sections in Voet to Study or Read

StudyRead

Ch 8: pp. 219-233Collagen pp. 233-240

Mb pp. 240-248pp. 248-256

Bioinfo pp. 256-258Stability pp. 258-262

Hydropathy pp. 263-266Symmetry pp. 266-end

Ch 9: pp. 276-278pp. 278-283

Folding pp. 283-290Chaperones pp. 290-306

Prions pp. 306-312Evolution pp. 312-end

Suggested Problems Ch 9: 3, 4, 6, 12, 14


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.


Table 8-6Hydropathy Scale for Amino Acid Side Chains.

Values below line

are NEGATIVE!!

Page 263


Figure 8-60Hydropathic index plot for bovine chymotrypsinogen.

Page 263


Figure 8-46abcSchematic diagrams of supersecondary structures

Page 249


Figure 8-46dSchematic diagrams of supersecondary structures.

Page 249


Figure 8-47aX-Ray structures of 4-helix bundle proteins.(a) E. coli cytochrome b562.

Page 250


Fibrous Proteins


Figure 8-25The microscopic organization of hair.

Page 232


Figure 8-26The structure of a keratin.

Page 232


Figure 8-27aThe two-stranded coiled coil. (a) View down the coil axis showing the interactions between the nonpolar edges of the a helices.

Page 233


Figure 8-27bThe 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


Exploring collagen

http://www.rcsb.org/pdb/molecules/pdb4_1.html


Figure 8-28The amino acid sequence at the C-terminal end of the triple helical region of the bovine a1(I) collagen chain.

Page 234


Figure 8-29The triple helix of collagen.

Page 235


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.


Figure 8-30bX-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


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


Figure 8-31Electron micrograph of collagen fibrils from skin.

Page 237


Figure 8-32Banded appearance of collagen fibrils.

Page 237


Figure 8-33A biosynthetic pathway for cross-linking Lys, Hyl, and His side chains in collagen.

Page 238


Figure 8-34Distorted structure in abnormal collagen.

Page 239


Globular Proteins


Figure 8-35X-Ray diffraction photograph of a single crystal of sperm whale myoglobin.

Page 240


Figure 8-39aRepresentations of the X-ray structure of sperm whale myoglobin. (a) The protein and its bound heme are drawn in stick form.

Page 244


Figure 8-39bRepresentations 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


Figure 8-39cRepresentations 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


Figure 8-43aThe 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


Mb


Cut-away view

surface

Stryer Fig. 3.45 Mb yellow = hydrophobic, blue=charged,

white=others


Stryer Fig. 3.46 Porin


Porin


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


Chapter 9!!!

Figure 9-1

Page 277


Figure 9-2Reductive denaturation and oxidative renaturation of RNase A.

Page 277


Figure 9-3Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein.

Page 278


Figure 9-14bReactions catalyzed by protein disulfide isomerase (PDI). (b) The oxidized PDI-dependent synthesis of disulfide bonds in proteins.

Page 288


Figure 9-4Primary structure of porcine proinsulin.

Page 278


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)


Many

conformational

states

Fewer

conformational

states

A “single”

conformational state


High energy

Many

conformational

states

Fewer

conformational

states

A “single”

conformational state

Low energy


Figure 9-11c Folding funnels. (c) Classic folding landscape.

Page 285


Figure 9-11d Folding funnels. (d) Rugged energy surface.

Page 285


“Ideal”

“Real” ?


Figure 9-12Polypeptide backbone and disulfide bonds of native BPTI.

Page 286


Figure 9-13Renaturation of BPTI.

Page 287


Figure 9-26Secondary structure prediction.

Page 301


Figure 9-28Conformational fluctuations in myoglobin.

Page 303


Figure 9-30aThe internal motions of myoglobin as determined by a molecular dynamics simulation. (a) The Ca backbone and the heme group.

Page 305


Figure 9-30bThe internal motions of myoglobin as determined by a molecular dynamics simulation. (b) An a helix.

Page 305


Figure 9-32aAmyloid fibrils. (a) An electron micrograph of amyloid fibrils of the protein PrP 27-30.

Page 307


Figure 9-32bcAmyloid fibrils. (b) and (c) Model and isolated b sheet.

Page 307


Figure 9-34aEvidence that the scrapie agent is a protein.(a) Scrapie agent is inactivated by treatment with diethylpyrocarbonate, which reacts with His side chains.

Page 310


Figure 9-34bEvidence that the scrapie agent is a protein.(b) Scrapie agent is unaffected by treatment with hydroxylamine, which reacts with cystosine residues.

Page 310


Figure 9-34cEvidence that the scrapie agent is a protein.(c) Hydroxylamine rescues diethylpyrocarbonate-inactivated scrapie reagent.

Page 310


Figure 9-35aPrion protein conformations. (a) The NMR structure of human prion protein (PrPC).

Page 311


Figure 9-35bPrion protein conformations. (b) A plausible model for the structure of PrPSc.


Figure 9-36Molecular formula for iron-protoporphyrin IX (heme).

Page 313


Figure 9-37Primary structures of some representative c-type cytochromes.

Page 313


Figure 9-38Three-dimensional structures of the c-type cytochromes whose primary structures are displayed in Fig. 9-37.

Page 314


ad
  • Login