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Transcript of Figure 5-1 Table 5-1 Figure 5-4 Page 97 Figure 5-5.
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Figure 5-1
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Table 5-1
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Figure 5-4
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Page 97
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Figure 5-5
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Table 5-2
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Figure 5-6
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Figure 5-7
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Figure 5-8
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VVP Fug, 5-8 Purification of Stapylococcal Nuclease
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Stryer Fig. 4.7 PAGE
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Stryer Fig. 4.8
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Page 106
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Animation http://bcs.whfreeman.com/biochem5/cat_040/ch04/ch04xd02.htm
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Stryer Fig. 4.9 Coomassie blue stained SDS gel.
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Figure 5-9
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Figure 5-10
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Figure 5-11
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Figure 5-12
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Box 5-1
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Figure 5-13
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Page 107
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Table 5-3
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Figure 5-14
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Figure 5-14 part 3
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Figure 5-15
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Figure 5-16a
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Figure 5-16b
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Figure 5-18
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Figure 5-19
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Amino acid Models from Cal Lutheran
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See VVP Fig 4-3
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VVP Fig 6-3 p 126
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Example of a protein sequence
MANSKINKQL DKLPENLRLN GRTPSGKLRS FVCEVCTRAF ARQEHLKRHYRSHTNEKPYP CGLCNRCFTR RDLLIRHAQK IDSGNLGETI SHTKKVSRTITKARKNSASS VKFQTPTYGT PDNGGSGGTV LSEGEWQLVL HVWAKVEADVAGHGQDILIR LFKSHPETLE KFDRFKHLKT EAEMKASEDL KKHGVTVLTALGAILKKKGH HEAELKPLAQ SHATKHKIPI KYLEFISEAI IHVLHSRHPGDFGADAQGAM NKALELFRKD IAAKYKELGY G
N-terminus
C-terminus
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N-termini
C-termini
VVP Fig 5-1 p 94
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Other Properties of Amino Acids
• Stereochemistry (all biosynthetic proteins made up of L-isomer)
• Hydropathy (partitioning between polar and nonpolar solvents as indicator of polarity) (see Table 6-2 in VVP p 150)
these two properties are major determinants of peptide conformation
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VVP page 150
“nonpolar”
“polar”
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Figure 6-1 part 4
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Protein Data Bank Workshop
pdb Rasmol
Do the protein explorer tour!!!!!
http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/qtour.htm
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Chapter 6 Opener
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Figure 6-4
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Figure 6-5
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Figure 6-6
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Figure 6-7
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Figure 6-8
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Figure 6-9
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Figure 6-9a
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Figure 6-9b
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Figure 6-10
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Table 6-1
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Figure 6-12
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Figure 6-15 Keratin: a coiled coil
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Figure 6-16 Higher order keratin structure
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Globular Protein 3o Structure
2o structural elements (helices, sheets, turns…) pack together to give a folded protein or subunit. This so-called “tertiary” structure is stabilized by non-covalent interactions, the hydrophobic effect and disulfides. Within the 3o structure are “motifs” and “domains”.
The 3o structure can be derived from one or more domains.
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Figure 6-20b Protein crystals: flavodoxin
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Figure 6-20e Protein crystals: lamprey hemoglobin
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Figure 6-21
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Figure 6-27 cytochrome c: hydrophillic residues and hydrophobic residues
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Figure 6-33 Hemoglobin
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Table 6-3
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Figure 6-35 Bovine chymotrypsin
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Figure 6-38 Molecular dynamics of Mb
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Page 159
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Figure 6-39
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Figure 6-40
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Figure 6-41
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Many conformational states
Fewerconformational states
A “single”conformational state Low energy
High energy
(Fig 6-38)
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Many conformational states
Fewerconformational states
A “single”conformational state
See VVPFig 6-37 p153
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“Ideal”“Real” ?See VVP
Fig 6-38 p154
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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.” (mainchain amides, polar sidechains)
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Table 6-4
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Figure 5-3