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week%209-9 - Amino acid and protein structures Outline...

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Amino acid and protein structures Reading assignments: Molecular Biology of the Gene (Watson, 6th ed) chapter 5, chapter 21 p764-771 Outline • amino acid structures • protein structure, conformation, and functions • protein analysis techniques
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Amino Acids are the building blocks of proteins
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Amino Acids Amino acids can be grouped based on their side chains: neutral-nonpolar neutral-polar acidic basic 3
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Neutral Amino Acid Side Chains: I. non-polar
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Neutral Amino Acid Side Chains: I. non-polar
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Neutral Amino Acid Side Chains: II. polar
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Neutral Amino Acid Side Chains: II. polar
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Charged Amino Acid Side Chains: I. acidic Compare to:
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Charged Amino Acid Side Chains: II. basic
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Formation of a Peptide Bond The peptide bond is a planar amide linkage. N C
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The polypeptide (protein) Proteins are linear polymers typically from ~100-1000 amino acid residues in length, but may be a few times larger or smaller. The average amino acid has a molecular weight (MW) of 110 daltons (Da), so most proteins have a mass in the range of ~10-100 kDa. Adjacent amino acids are covalently bonded by peptide bonds.
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Protein Conformation Native conformation -the normal folding structure of a protein. Denaturation -the partial or complete disruption or unfolding of the native protein conformation. Treatment with heat, detergent, or strong salts(ions) cause denaturation. Renaturation-restoration of the native conformation. May be accomplished by heating to completely denature and then slowly cooling to allow proper refolding. Cells have proteins called chaperones that assist in protein folding.
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The side chains (R Groups) determine the folding of the polypeptide Polar amino acids tend to be on the protein surface. Non-polar (hydrophobic) amino acids tend to be internal. Two cysteines can form covalent disulfide bonds. Hydrogen bonding between the C=O group of one peptide bond with the N- H group of a different peptide bond.
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Hierarchies of Protein Structure Primary structure : The linear sequence of amino acids from the N- to C-terminus. Secondary structure: Arrangement of segments of the polypeptide chain into regular structures. Tertiary structure: The overall three-dimensional conformation (shape) of the polypeptide resulting from folding of secondary structures and unstructured regions.
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