Protein Structure

Protein Structure - C H A P T E R 2 PROTEIN STRUCTURE Amino...

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6 C H A P T E R 2 PROTEIN STRUCTURE Amino Acid Structure Interactions Water Hydrophobic Interaction Van der Waals Interactions and London Dispersion Forces Hydrogen Bonds Secondary Structure Protein Stability Favorable (Good) Interactions Unfavorable (Bad) Interactions Temperature-Sensitive Mutations Ligand-Binding Specificity Global Conclusion Proteins start out life as a bunch of amino acids linked together in a head- to-tail fashion—the primary sequence. The one-dimensional information contained in the primary amino acid sequence of cellular proteins is enough to guide a protein into its three-dimensional structure, to deter- mine its specificity for interaction with other molecules, to determine its ability to function as an enzyme, and to set its stability and lifetime. AMINO ACID STRUCTURE Remember a few of the amino acids by functional groups. The rest are hydrophobic.
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Remembering something about the structures of the amino acids is just one to those basic language things that must be dealt with since it crops up over and over again—not only in protein structure but later in metabolism. You need to get to the point that when you see Asp you don’t think snake but see a negative charge. Don’t memorize the amino acids down to the last atom, and don’t spend too much time worrying about whether glycine is polar or nonpolar. Methylene groups (–CH 2 –) may be important, but keeping track of them on an individual basis is just too much to ask. Organize the amino acids based on the functional group of the side chain. Having an idea about functional groups of amino acids will also help when you get to the biosynthesis and catabolism of amino acids. Might as well bite the bullet early. HYDROPHILIC (POLAR) • CHARGED POLAR Acidic (–COO 2 ) and basic (–NH 1 3 ) amino acid side chains have a charge at neutral pH and strongly “prefer” to be on the exterior, exposed to water, rather than in the interior of the protein. The terms acidic and basic for residues may seem a little strange. Asp and Glu are called acidic amino acids, although at neutral pH in most proteins, Asp and Glu are not present in the acidic form (–COOH) but are present in the basic form (–COO 2 ). So the acidic amino acids, Asp and Glu, are really bases (proton acceptors). The reason that Asp and Glu are called acidic residues is that they are such strong acids (proton donors) they have already lost their protons. Lys, Arg, and His are con- sidered basic amino acids, even though they have a proton at neutral pH. The same argument applies: Lys, Arg, and His are such good bases (pro- ton acceptors) that they have already picked up a proton at neutral pH. FUNCTIONAL GROUP AMINO ACID Hydrophilic, Polar Acidic Carboxylates —COO 2 Asp, Glu Basic Amines —NH 1 3 Lys, Arg, His Neutral Amides —CONH 2 Asn, Gln Alcohols —OH Ser, Thr, Tyr Thiol —SH Cys Hydrophobic, Apolar Aliphatic —CH 2 Ala, Val, Leu, Ile, Met Aromatic C Rings Phe, Trp, Tyr Whatever Pro, Gly 2 Protein Structure 7
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Charged groups are usually found on the surface of proteins. It is
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This note was uploaded on 04/09/2008 for the course BIO SCI 98 taught by Professor Goulding during the Spring '08 term at UC Irvine.

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Protein Structure - C H A P T E R 2 PROTEIN STRUCTURE Amino...

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