CH 395G Lecture 5 Fall 2009
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1 CH 395G Lecture 5 Fall 2009 Voet Biochemistry 3e Chapter 6 : Separation of Proteins We will discuss a liitle more re protein purification and proteomics and the Protein Center facilities at UT before moving on to Chapter 7,which covers the primary and secondary structures of proteins.
2 Gel Filtration Voet Biochemistry 3e
3 Figure 6-9 Gel filtration chromatography. Voet Biochemistry 3e Page 137
4 Gel Filtration Voet Biochemistry 3e
5 Figure 6-10 Molecular mass determination by gel filtration chromatography. Voet Biochemistry 3e Page 138
6 Table 6-3 Some Commonly Used Gel Filtration Materials. Voet Biochemistry 3e Page 138
7 Figure 6-12 Affinity chromatography. His tags & NiChromatography (elute imidazole or EDTA) Voet Biochemistry 3e Page 139
8 Voet Biochemistry 3e Page 141 Figure 6-15 Purification of staphylococcal nuclease by affinity chromatography on bisphosphothymidine-linked agarose.
9 Figure 6-20 Apparatus for slab gel electrophoresis. Voet Biochemistry 3e Page 146
10 Figure 6-23 Detection of proteins by immunoblotting. Voet Biochemistry 3e Page 148
11 Figure 6-24 SDS-PAGE. Voet Biochemistry 3e Page 149
12 Voet Biochemistry 3e Page 149 Figure 6-25 Logarithmic relationship between the molecular mass of a protein and its relative electrophoretic mobility in SDS-PAGE.
13 Figure 6-26 General formula of the ampholytes used in isoelectric focusing. Voet Biochemistry 3e Page 150
14 Figure 6-27 Two-dimensional (2D) gel electrophoresis. Voet Biochemistry 3e Page 150
15 Voet Biochemistry 3e
16 Table 6-4 Purification of Rat Liver Glucokinase. Voet Biochemistry 3e Page 142
17 ICMB Facilities Voet Biochemistry 3e
18 Proteomics Voet Biochemistry 3e
19 Analytical Ultracentrifugation Voet Biochemistry 3e Protein Characterization
20 Analytical Ultracentrifugation Voet Biochemistry 3e
21 Isoelectric Focussing Figure 6-26 General formula of the ampholytes used in isoelectric focusing. Voet Biochemistry 3e Page 150
22 Figure 6-27 Two-dimensional (2D) gel electrophoresis. Voet Biochemistry 3e Page 150
23 Enzyme Purification Table Voet Biochemistry 3e
24 Table 6-4 Purification of Rat Liver Glucokinase. Voet Biochemistry 3e Page 142
25 ICMB Facilities Voet Biochemistry 3e
26 Proteomics Voet Biochemistry 3e
27 Equilibrium Centrifugation Can provide an accurate measure of the molecular weight of globular proteins. Generally need very purified protein samples. Voet Biochemistry 3e
28 Analytical Ultracentrifugation Voet Biochemistry 3e Protein Characterization
29 Voet Biochemistry 3e
30 Lecture 4: Primary Structure of Proteins (Chapter 7) Outline A few important peptides Voet Biochemistry 3e The primary structure of proteins Number of chains Chain separation (maybe disulfide bond cleaveage) Amino acid composition N-terminal residues C-terminal residues N-terminal sequencing Peptide cleavage Peptide fractionation and sequencing Ordering of peptides Assignment of disulfide bridges
31 What function does this molecule serve? Voet Biochemistry 3e
32 Voet Biochemistry 3e
33 Note: Action of glutathione reductase Voet Biochemistry 3e
34 Cyclic Antibiotic Peptides Voet Biochemistry 3e
35 Aspartame Voet Biochemistry 3e
36 Figure 7-1 The structural hierarchy in proteins. Voet Biochemistry 3e Page 162
37 Biological Functions of Proteins Enzymes Structural Regulatory Voet Biochemistry 3e Transport Storage Contractile Protective Sensory
38 Chapter 7 Covalent Structures of Proteins Overview Voet Biochemistry 3e Number of chains Chain separation (maybe disulfide bond cleaveage) Amino acid composition N-terminal residues C-terminal residues N-terminal sequencing Peptide cleavage Peptide fractionation and sequencing Ordering of peptides Assignment of disulfide bridges
39 Voet Biochemistry 3e
40 Voet Biochemistry 3e
41 Figure 7-2 Primary structure of bovine insulin. Voet Biochemistry 3e Page 163
42 Voet Biochemistry 3e
43 Figure 7-3 The reaction of dansyl chloride in end group analysis. Voet Biochemistry 3e Page 164
44 Voet Biochemistry 3e
45 Figure 7-4 The Edman degradation. Voet Biochemistry 3e Page 165
46 Figure 7-4 The Edman degradation. When does the Edman degradation not work? Voet Biochemistry 3e Page 165
47 Figure 7-6 Amino acid analysis. Voet Biochemistry 3e
48 How can the amino acids destroyed by acid be measured? Voet Biochemistry 3e
49 Voet Biochemistry 3e
50 Voet Biochemistry 3e
51 Voet Biochemistry 3e
52 Voet Biochemistry 3e
53 C-Terminal Analysis Voet Biochemistry 3e Page 165 Figure 7-5a The hypothetical rate of the carboxypeptidasecatalyzed release of amino acids. (a) All bonds cleaved at the same rate.
54 Voet Biochemistry 3e Page 165 Figure 7-5b The hypothetical rate of the carboxypeptidasecatalyzed release of amino acids. (b) Ser slow, Tyr fast, and Leu intermediate.
55 Table 7-1 Specificities of Various Exopeptidases. Voet Biochemistry 3e Page 166
56 Figure 7-7 The amino acid sequence of a polypeptide chain. Voet Biochemistry 3e Page 171
57 Table 7-2 Specificities of Various Endopeptidases. Voet Biochemistry 3e Page 168
58 MS Analysis of Proteins Voet Biochemistry 3e Page 172 Figure 7-8a The generation of the gas phase ions required for the mass spectrometric analysis of proteins. (a) By electrospray ionization (ESI).
59 Voet Biochemistry 3e Page 172 Figure 7-8b The generation of the gas phase ions required for the mass spectrometric analysis of proteins. (b) By matrix-assisted laser desorption/ionization (MALDI).
60 Voet Biochemistry 3e Page 172 Figure 7-8c The generation of the gas phase ions required for the mass spectrometric analysis of proteins. (c) By fast atom bombardment (FAB).
61 Figure 7-9 The ESI (electrospray ionization) -MS spectrum of the 16,951-D horse heart protein apomyoglobin. Voet Biochemistry 3e Page 173
62 Figure 7-10 The use of a tandem mass spectrometer (MS/MS) in amino acid sequencing. Voet Biochemistry 3e Page 174
63 Voet Biochemistry 3e Page 174 Figure 7-11 The tandem mass spectrum of the doubly charged ion of the 14-residue human [Glu 1 ]fibrinopeptide B (m/z = 786).
64 Figure 7-12a Peptide mapping. Voet Biochemistry 3e Page 175
65 Figure 7-12b Peptide mapping. Voet Biochemistry 3e Page 175
66 Genetic Defect in Sickle Cell Anemia Voet Biochemistry 3e Change is in beta chain of hemoglobin Protein sequence changed from Glu to Val at position 6 ie from charged to hydrophobic side chain. Homozygous patients have sickle cell anemia. Heterozygous individuals show few effects except under stress.
67 Voet Biochemistry 3e Page 183 Figure 7-18a Scanning electron microscope of human erythrocytes. (a) Normal human erythrocytes revealing their biconcave disklike shape.
68 Voet Biochemistry 3e Page 183 Figure 7-18b Scanning electron microscope of human erythrocytes. (b) Sickled erythrocytes from an individual with sickle-cell anemia.
69 Voet Biochemistry 3e Page 184 Figure 7-20 A map indicating the regions of the world where malaria caused by P. falciparum was prevalent before 1930.
70 Figure 7-21 Phylogenic tree of cytochrome c, based on protein sequences. Voet Biochemistry 3e Page 187
71 Figure 7-22 Rates of evolution of four unrelated proteins. Voet Biochemistry 3e Page 188
72 Figure 7-23 A phylogenetic tree for cytochrome c. Voet Biochemistry 3e Page 189
73 Figure 7-24 Phylogenetic tree of the globin family. Voet Biochemistry 3e Page 191
74 Figure 7-34 Flow diagram for polypeptide synthesis by the solid phase method. Voet Biochemistry 3e Page 204
75 Figure 7-35 A selection of amino acids with benzylprotected side chains and a Boc-protected α-amino acid group. Voet Biochemistry 3e Page 206
76 Figure 7-36 The native chemical ligation reaction. Voet Biochemistry 3e Page 207
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