Lecture 2-2008

Lecture 2-2008 - Hierarchy of structures Primary structure...

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Hierarchy of structures 1. Primary structure Linear sequence of residues from N to C 1. Secondary structure Arrangement of adjacent residues in characteristic patterns 1. Tertiary structure Three-dimensional arrangement of all atoms 1. Quarternary structure Arrangement of different subunits in an oligomeric protein
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Pauling and Corey 1951 Secondary Structure Elements
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Coiled-Coil Keratin in hair
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Extended Conformation
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Antiparallel β -sheet
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Parallel β -sheet
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Mixed β -sheet
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β -turn or reverse turn
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Structure of Myoglobin (tertiary structure) O 2 storage protein in muscle / Binds O 2 reversibly
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Cross-section Surface Hydrophobic: yellow; Charged: blue; Others: white Residue distribution in myoglobin
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Four-domain structure Domain: Independently folding unit (Ig fold shown) 30 - 400 residues (100 reasonable average) Shown here: extracellular part of CD4
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Quarternary Structure - Dimer Homodimer ( α 2 -dimer): two identical chains Two subunits
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Tetramer Heterotetramer ( α 2 β 2 ) Hemoglobin
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Primary sequence of bovine ribonuclease A 124 residues 4 disulfide bonds Protein Folding
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Action of β -mercaptoethanol
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Chaotropic Agents Unfold proteins
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Anfinsen’s classical experiment Denatured ribonuclease has no catalytic activity. Catalytic activity is dependent on the native 3D structure Random coil
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Information required for proper folding is contained in the primary sequence!!!
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Secondary structure prediction α helix is the default β -branched and aromatic residues prefer β sheets Turns: Gly, Pro unusual main chain features; Asx, Ser can H-bond to main chain Accuracy: Up to 80% Structure Prediction
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The same hexapeptide can have two completely different structures Importance of long-range interactions (tertiary interactions) Limitations of Secondary Structure Prediction
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Partly correct structures are retained during protein folding Levinthal paradox: 100 residue protein, 3 conformations/residue -> 3 100 = 5x10 47 conformations 10 -13 s to interconvert conformers -> 1.6x10 27 years (longer than the age of the universe 13-14x10 9 years) Protein folding cannot proceed by random sampling of conformations Partly correct intermediates are retained Proteins are only marginally stable: For 100 residue protein G for unfolding is ~40 kJ/mol (or 0.4 kJ/mol on a per-residue basis). This corresponds to two H-bonds. Thermal energy is 2.5kJ/ mol at room temp! Thus even correct intermediates can be lost.
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Experimental Techniques in Biochemistry
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Proteome comprises the complete set of proteins inside cell. Proteome vs. genome Genome: List of all parts of a car Proteome: Manual describing how parts fit together and how they operate Proteome varies with cell type / cell cycle / developmental status / environmental conditions Humans: 40,000 proteins, but additional factors increase complexity of human proteome. Alternative splicing/Modifications/Protein-protein
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This note was uploaded on 09/09/2008 for the course BIO 361 taught by Professor Lake during the Spring '08 term at SUNY Stony Brook.

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Lecture 2-2008 - Hierarchy of structures Primary structure...

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