Protein Structure. Primary. Secondary. Tertiary. Quaternary
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1 Protein Structure Primary Secondary Tertiary Quaternary
2 Fibrous vs Globular
3 Fibrous - Collagen
4 Globular - myoglobin
5 Protein Folding Rules 1. Hydrophobic in buried in core 2. B-conformation and a-helix found in different layers 3. Segments close to each other in sequence are usually close together in folded 4. Connections of elements do not typically form knots or crossover 5. B-conformation most stable with a slight right twist
6 Domains
7 Motifs Recognizable folding pattern of 2 or more secondary structural elements and connections between
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9 Motifs used to classify proteins
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13 Protein Folding and Denaturation
14 Protein Folding and Denaturation
15 Protein Folding and Renaturation
16 Protein Folding
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18 Protein Folding Molecular Chaperones 1. Hsp Chaperonins 3. Enzymes
19 Protein Diseases
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21 Prion Disease
22 Purifying Proteins Page 77 Identify source Natural sources Recombinant Stablizing Many conditions affect the stablity ph, temperature, degradative enzymes Assay enzymatic, immunological, absorbance Separation solubility, affinity, size, charge, polarity
23 Purifying Proteins Page 77 Identify source Natural sources Recombinant Stablizing Many conditions affect the stablity ph, temperature, degradative enzymes Assay enzymatic, immunological, absorbance Separation solubility, affinity, size, charge, polarity
24 Assaying Proteins Page 77 Enzymatic reactions Amount of product proportional to amount of enzyme Coupled enzymatic reaction Immunological reactions Radioimmunoassay ELISA Absorbance UV Bradford
25 Page 77 Assaying Proteins
26 Purifying Proteins Solubilty Page 77
27 Purifying Proteins Chromatography
28 Ion Exchange Chromatography
29 Gel Filtration or Size Exclusion Chromatography
30 Page 77 Affinity Chromatography
31 Epitope Tagged Recombinant Protein
32 Are you purification steps working?
33 Electrophoresis
34 Determining Molecular Weight
35 Purifying Proteins Affinity Chromatography Page 77 Graphic from NEB 96/97 Catalog who owns copyright
36 Isoelectric Focusing
37 2 D Gel Electrophoresis
38
39 Western Blotting V Page 77
40 Protein Sequencing 1. Determine the number of different types of subunits 2. Disrupt any disulfide bonds 3. Optional - Determine AA composition 4. Cleave into small polypeptides 5. Sequence 6. Repeat steps 4 and 5 with different cleavage to generate overlapping polypeptides 7. Reconstruct
41 Protein Sequencing 1. Determine the number of different types of subunits
42 Protein Sequencing Disrupt Disulfide Bonds V Page 77
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44 Protein Sequencing AA Composition Page 77
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46 Protein Sequencing Edman Degradation Page 77
47 Protein Sequencing Cleavage into smaller fragments
48 Protein Sequencing V Page 77
49 Protein Sequencing V Page 77 CNBr Fragments - Phe - Trp - Met Gly - Ala - Lys - Leu - Pro - Met Asp - Gly - Arg - Cys - Ala - Gln Trypsin Fragments - Phe - Trp - Met - Gly - Ala - Lys Leu - Pro - Met - Asp - Gly - Arg Cys - Ala - Gln
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51 Protein Sequencing V Page 77
52 Protein Sequencing Mass Spectroscopy V Page 77
53 Protein Sequencing V Page 77
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56 Protein Sequencing V Page 77
57 Protein Evolution V Page 77
58 Protein Function Hemoglobin Enzymes
59 Reversible Binding of Protein Geometric complementarity - Electronic complemenatarity - to Ligand ligand protein Binding site Two Models: Lock and Key model of enzyme - Induced fit -
60 Substrate Specificity Geometric complementarity - shape Electronic complemenatarity - charge Two Models: Lock and Key model of enzyme - substrate specificity Induced fit - can have conformational changes on substrate binding
61 Heme Groups Oxygen can bind Heme Prosthetic Group
62 Hemoglobin Function
63 Myoglobin Function
64 Myoglobin Function
65 Myoglobin vs Hemoglobin
66 Myoglobin vs Hemoglobin
67 Structure of Hemoglobin
68 Interaction between subunits
69 Interaction between subunits
70 Two states of Hemoglobin
71
72 Cooperative Binding
73 Cooperative Binding
74 Effect of ph on Oxygen Binding
75 Effect of CO 2 on Oxygen Binding
76 Effect of BPG on Oxygen Binding
77 Effect of BPG on Oxygen Binding
78 Sickle Cell Anemia
79 Sickle Cell Anemia
80 General Properties of Enzymes 1. Higher reaction rates 2. Milder reaction conditions 3. Greater reaction specificity 4. Capacity for regulation
81 Enzyme Nomenclature Commonly add - ase to the name of the enzymes substrate or to a phrase describing its action urease - hydrolysis of urea alcohol dehydrogenase - oxidation of primary and secondary alcohols Alternative name - commonly used everyday name (usually the trivial name from before the system) Systematic name - name of the substrate followed by the type of chemical reaction ending in - ase along with a classification number carboxypeptidase A vs peptidyl-l-amino acid hydrolase EC
82 Cofactors and Coenzymes Cofactor - a small organic molecule (coenzyme) or metal ion that is required for enzymatic activity Metal Ions - Copper, Iron, Zinc Heavy metal toxicity (mercury can replace zinc and render enzymes inactive) Coenzyme - cosubstrate (transiently associated) - NAD+, NADP+
83 Cofactors and Coenzymes Cofactor - a small organic molecule (coenzyme) or metal ion that is required for enzymatic activity Coenzyme - cosubstrate (transiently associated) - NAD+, NADP+
84 Cofactors and Coenzymes Cofactor - a small organic molecule (coenzyme) or metal ion that is required for enzymatic activity Metal Ions - Copper, Iron, Zinc Heavy metal toxicity (mercury can replace zinc and render enzymes inactive) Coenzyme - cosubstrate (transiently associated) - NAD+, NADP+ prosthetic group (permanently associated) - heme groups found in cytochromes Holoenzyme - active enzyme-cofactor complex Apoenzyme (inactive) + cofactor holoenzyme (active)
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86 Enzymes reduce the activation energy Or enzymes act by providing a reaction pathway with a transition state whose free energy is lower than that of the uncatalyzed reaction Note - the ΔG of the reaction is not changed
87
88 Transition State Theory Transition state is an unstable transitory combination of reactant molecules which occurs at the potential energy maximum (free energy maximum). Website with nice details
89 Catalytic Mechanisms 1. Acid-Base Catalysis 2. Covalent Catalysis 3. Metal Ion Catalysis 4. Proximity and Orientation Effects 5. Preferential binding of the transition state
A. A peptide with 12 amino acids has the following amino acid composition: 2 Met, 1 Tyr, 1 Trp, 2 Glu, 1 Lys, 1 Arg, 1 Thr, 1 Asn, 1 Ile, 1 Cys
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Catalysis by Enzymes Enzyme A protein that acts as a catalyst for a biochemical reaction. Enzymatic Reaction Specificity Enzyme Cofactors Many enzymes are conjugated proteins that require nonprotein portions