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Figure 5-1
Table 5-1
Figure 5-4
Page 97
Figure 5-5
Table 5-2
Figure 5-6
Figure 5-7
Figure 5-8
VVP Fug, 5-8 Purification of Stapylococcal Nuclease
Stryer Fig. 4.7 PAGE
Stryer Fig. 4.8
Page 106
Animation http://bcs.whfreeman.com/biochem5/cat_040/ch04/ch04xd02.htm
Stryer Fig. 4.9 Coomassie blue stained SDS gel.
Figure 5-9
Figure 5-10
Figure 5-11
Figure 5-12
Box 5-1
Figure 5-13
Page 107
Table 5-3
Figure 5-14
Figure 5-14 part 3
Figure 5-15
Figure 5-16a
Figure 5-16b
Figure 5-18
Figure 5-19
Amino acid Models from Cal Lutheran
See VVP Fig 4-3
VVP Fig 6-3 p 126
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
N-termini
C-termini
VVP Fig 5-1 p 94
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
VVP page 150
“nonpolar”
“polar”
Figure 6-1 part 4
Protein Data Bank Workshop
pdb Rasmol
Do the protein explorer tour!!!!!
http://www.umass.edu/microbio/chime/pe_beta/pe/protexpl/qtour.htm
Chapter 6 Opener
Figure 6-4
Figure 6-5
Figure 6-6
Figure 6-7
Figure 6-8
Figure 6-9
Figure 6-9a
Figure 6-9b
Figure 6-10
Table 6-1
Figure 6-12
Figure 6-15 Keratin: a coiled coil
Figure 6-16 Higher order keratin structure
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.
Figure 6-20b Protein crystals: flavodoxin
Figure 6-20e Protein crystals: lamprey hemoglobin
Figure 6-21
Figure 6-27 cytochrome c: hydrophillic residues and hydrophobic residues
Figure 6-33 Hemoglobin
Table 6-3
Figure 6-35 Bovine chymotrypsin
Figure 6-38 Molecular dynamics of Mb
Page 159
Figure 6-39
Figure 6-40
Figure 6-41
Many conformational states
Fewerconformational states
A “single”conformational state Low energy
High energy
(Fig 6-38)
Many conformational states
Fewerconformational states
A “single”conformational state
See VVPFig 6-37 p153
“Ideal”“Real” ?See VVP
Fig 6-38 p154
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)
Table 6-4
Figure 5-3
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