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Chapter 4

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

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George S Espie

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