Bioinformatics

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Bioinformatics Chapter 7 Special lecture by Dr.
Jeff Young on Friday.
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Yipee!!! Protein Structure!!!
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Stryer Fig. 4.49
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Stryer Fig. 4.50
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Stryer Fig. 4.52 Electron Density Map of Mb vs.
USGS map (Fig. 4.53)
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Photo of Parthenon
Diffraction pattern of Parthenon
Refined image from more data points.
Reconstructed image
Stryer Fig. 4.54
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Figure 7-1 The structural hierarchy in proteins.
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Figure 8-62 Melting temperature of RNase A as a
function of the concentration of various salts.
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Figure 8-1 The trans-peptide group.
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Figure 8-2 The cis-peptide group.
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Figure 8-3 A polypeptide chain in its fully
extended conformation showing the planarity of
each of its peptide groups.
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Figure 8-6 Steric interference between adjacent
residues.
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Figure 8-4 The torsional degrees of freedom in a
peptide unit.
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Figure 8-7 The Ramachandran diagram.
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Poly ala
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Ideal Phi and Psi Values for Types of Secondary
Structure Conformation Phi Psi a-helix (right
handed) -57 -47 a-helix (left
handed) 57 47 310 helix (right
handed) -49 -26 collagen helix -51 153 b
sheet (antiparallel) -139 135 b sheet
(parallel) -119 113 Type II turn (2nd
aa) -60 120 Type II turn (3rd
aa) 90 0 Fully extended chain -180 -180
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Figure 8-8 Conformation angles in proteins.
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Figure 8-9 The Ramachandran diagram of Gly
residues in a polypeptide chain.
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Figure 8-10 Examples of helices.
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Figure 8-11 The right-handed a helix.
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Figure 8-12 Stereo, space-filling representation
of an a helical segment of sperm whale myoglobin
(its E. helix) as determined by X-ray crystal
structure analysis.
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Figure 8-13 The hydrogen bonding pattern of
several polypeptide helices.
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Figure 8-16a b pleated sheets. (a) The
antiparallel b pleated sheets.
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Figure 8-16b b pleated sheets. (b) The parallel b
pleated sheets.
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Figure 8-17 A two-stranded b antiparallel pleated
sheet drawn to emphasize its pleated appearance.
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Figure 8-18 Stereo, space-filling representation
of the 6-stranded antiparallel b pleated sheet in
jack bean concanavalin A as determined by crystal
X-ray analysis.
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Figure 8-20 Connections between adjacent
polypeptide strands in b pleated sheets.
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Figure 8-22 Reverse turns in polypeptide chains.
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Figure 8-23 Space-filling representation of an ?
loop comprising residues 40 to 54 of cytochrome c.
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Figure 8-25 The microscopic organization of hair.
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Figure 8-26 The structure of a keratin.
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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.
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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.
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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.
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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.
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Figure 8-29 The triple helix of collagen.
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Figure 8-46abc Schematic diagrams of
supersecondary structures
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Figure 8-46d Schematic diagrams of supersecondary
structures.
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Figure 8-47a X-Ray structures of 4-helix bundle
proteins.(a) E. coli cytochrome b562.
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Figure 8-63 The quaternary structure of
hemoglobin.
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