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Chapter 4

BIO206H5 Chapter Notes - Chapter 4: Nuclear Magnetic Resonance, X-Ray Crystallography, Antifreeze Protein


Department
Biology
Course Code
BIO206H5
Professor
George S Espie
Chapter
4

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Enzymes
Protein - referred to as polypeptides/ polypeptide chains (arranged in amino acid sequence)
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Shape of protein is specified by its amino acid sequence
Free energy (G) is minimized
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Denatured proteins can renature if denaturing solvent is removed
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H bonds within a protein molecule help stabilize its folded shape
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Molecular chaperones - assist in protein folding in living cells
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Average of 50 to 2000 amino acids long
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Either the use of x-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy can
we predict the precise folding pattern of a protein
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polypeptide backbone model - shows overall organization of polypeptide in a
clean way to compare structures of related proteins
ribbon model - easy way to visualize secondary structures such as αHelices and β
Sheets
wire model that includes amino acid side chains - useful for predicting which AA's
might be involved in a protein's activity (especially enzyme)
Shows how the protein might look to a small molecule (ex. Water) or to
another protein
space-filling model - provides contour map, gives a feel for the shape of protein
and shows which AA side chains are exposed on its surface
Displayed as:
Protein domain - part of a protein, 100-250 amino acids
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Proteins come in a wide variety of complicated shapes
1st one - Found in α-keratin (skin)
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2nd one - Found in fibroin (silk)
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Common b/c they result in H bond between N-H and C=O groups
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SH2 has both
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αHelix and βSheet are common folding patterns
Can be right-handed or left-handed (depending on the twist)
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H bond between N-H and C=O groups in every fourth AA
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Regular helix = complete turn every 3.6 AA
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Hydrophilic backbone, hydrophobic nonpolar side chains
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Coiled-coil - when helices wrap around one another or intertwine (most side chains are on one
side, minimizing contact with cytosol-aqueous environment)
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Helices form readily in biological structures
H bond between segments of polypeptide chains lying side by side
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parallel βsheet - neighbouring polypeptide chain run in the same orientation
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Antiparallel βsheet - opposite (ex. SH2)
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Antifreeze protein - help insects from freezing during winter
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βSheet form rigid structures at the core of many proteins
Primary structure - AA sequence
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Secondary structure -αHelix and βSheet
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Tertiary structure -αHelix and βSheet, ransom coils, any other loops
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Quaternary structure
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Protein domain - any segment of polypeptide chain that can fold independently into a
compact stable structure. Has different functions.
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2 domains: small one binds to DNA, large one binds cyclic AMP
Catabolite activator protein (CAP)
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Proteins have several levels of organization
Few of the many possible polypeptide chains will be useful - others will be eliminated by natural
selection
Chapter 4
September-19-13
4:36 PM
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