Chapter 3 - Chapter 3 : Amino Acids, Peptides, and Proteins...

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Chapter 3 : Amino Acids, Peptides, and Proteins *** A. Amino Acids a. Residue —reflects loss of elements of water when one amino acid is joined to another a.i. “Proteins are polymers of amino acids, with each amino acid residue joined to its neighbor by a specific type of covalent bond.” b. Amino Acids Share Common Structural Features b.i. Carboxyl group and an amino group bonded to the same carbon atom** b.ii. Differ from each other in R groups —side chains b.ii.1. Vary in structure, size, and electric charge b.ii.2. Influence solubility in water b.iii. “a” Carbon bonded to four different groups: carboxyl, amino, R, and a hydrogen atom b.iii.1. Except for glycine: a hydrogen atom replaces the R group b.iii.2. “a” Carbon is a chiral center b.iv. AAs have two possible stereoisomers b.iv.1. Since the four different groups can occupy two unique spatial arrangements b.v. **All molecules with a chiral center are also optically active —rotate plane-polarized light c. Amino Acid residues in Proteins Are “L” Stereoisomers c.i. Most biological compounds occur naturally in either D or L stereoisomeric form c.ii. In proteins: exclusively L c.iii. D and L are difficult to distinguish in the lab but in the body are very different c.iv. * “Cells are able to specifically synthesize the L isomers of amino acids because the active sites of enzymes are asymmetric, causing the reactions they catalyze to be stereo-specific.” d. Amino Acids Can Be Classified by R Group d.i. Based on polarity —tendency to interact with water biological pH d.ii. Nonpolar, Aliphatic, Hydrophobic R Groups d.ii.1. Alanine , valine , leucine , isoleucine —cluster together within proteins, stabilizing their structure by means of hydrophobic interactions d.ii.2. Glycine —simplest structure, very small side chain makes no contribution to hydrophobic interactions d.ii.3. Methionine —one of 2 S-containing AAs, d.ii.4. Proline —aliphatic side chain with distinctive cyclic structure d.iii. Aromatic R Groups d.iii.1. Phenylalanine , tyrosine , tryptophan —mostly nonpolar (hydrophobic) d.iii.2. Participate in hydrophobic interactions d.iii.3. Tyrosine’s hydroxyl group forms H bonds
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d.iii.4. T & T much more polar than P and absorb more UV light than P d.iii.4.a. *This accounts for characteristic strong absorbance of light by most proteins and wavelength 280 nm d.iv. Polar, Uncharged R Groups d.iv.1. Contain f-groups that H-bond with water d.iv.2. Serine , threonine —polarity contributed by hydroxyl groups d.iv.3. Cysteine —contributed by sulfhydryl group (weak acid that makes H-bonds with oxygen or nitrogen) d.iv.3.a. Readily oxidized to form a c-linked dimeric AA,
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Chapter 3 - Chapter 3 : Amino Acids, Peptides, and Proteins...

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