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Chapter 3 Notes

by: Megan Cunningham

Chapter 3 Notes Chem150

Megan Cunningham
Fresno State

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About this Document

These notes include information on amino acids and peptide bonds, as well as titration curves and isoelectric points.
Intro to Biochemistry
Class Notes
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This 8 page Class Notes was uploaded by Megan Cunningham on Monday September 12, 2016. The Class Notes belongs to Chem150 at California State University Fresno taught by DeJean in Fall 2016. Since its upload, it has received 3 views. For similar materials see Intro to Biochemistry in Chemistry at California State University Fresno.


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Date Created: 09/12/16
Chapter 3 Amino Acids and Peptides GENERAL STRUCTURE ● ​ α‐carbon = the first carbon of an organic molecule that is attached to a functional (R) group ● All 20 amino acids found in proteins share the same general structure: ○ The​ identity of an amino acid is determined by its side‐chain​ functional group ​(aka R‐group) ● As you’ll recall from the examp​le of ​ irectionality in Chapter 1: ○ Amino group = N‐terminus (‘N’ because nitrogen…) ○ Carboxyl group = C‐terminus STEREOCHEMISTRY ● Most important property of amino acids is 3‐D shape ● The α‐carbon of all* amino acids is ​chiral ○ ​Remember that c ​ hirality refers to substances that are not superimposable over their mirror image ​ ○ A c​ hiral center is a carbon atom with four different groups bonded to it ○ *Glycine is the only amino acid that exhibits symmetry do to being bonded to two hydrogen atoms, and so it is ​achiral ● Chirality gives rise to​ the possibility of two different mirror‐image forms ​ ○ Aka ​stereoisomers ​ (two molecules only differing in spatial arrangement) ○ In amino acids these two forms are: ■ L‐ form = hydroxyl group on left side of molecule (L=levo=left) ■ D‐ form = hydroxyl group on right (D=dextro=right) ○ All amino acids in proteins are L‐form because this is the form preferred by metabolic processes AMINO ACID PROPERTIES ● General formulas for amino acids reference the most predominant ionic form at a neutral pH ○ pH levels will affect the charges of groups​ attached to each α‐carbon ● Individual amino acids are classified and organized into groups according to their side chains (R‐group) ○ Polar ○ Nonpolar ○ Acidic ○ Basic ● Remember the basic structure of all 20 amino acids: NONPOLAR Group A: ​hydrophobic Alanine​ (Ala) | Glycine​ (Gly) | CH₃ H ‐achiral Isoleucine​ (Ile) Leucine​ (Leu) ‐​two stereocenters Methionine​ (Met) Phenylalanine (Phe) ‐sulfur ‐aromatic ‐Alanine+benzene ring Proline​ (Pro) Tryptophan​ (Trp) ***α‐amino group is secondary (attached ‐aromatic directly to R‐group) ‐cyclic side chain Valine​ (Val) **Nonpolar R‐groups will never be protonated because they resist contact with water** (Read: side chain will never be charged) POLAR Group B: Neutral side‐chain Asparagine​ (Asn) Cysteine​ (Cys) ‐sulfur ‐able to form disulfide bonds Glutamine​ (Gln) Serine​ (Ser) Threonine​ (Thr) Tyrosine​ (Tyr) ‐two stereocenters ● Asparagine and Glutamine have amido groups (H2NC=O) ● Cysteine can form disulfide bridges when the sulfhydryl group (SH) oxidizes ACIDIC Group C: ​Negative charge at neutral pH Aspartic acid Glutamic Acid aka aka ​AspartateCOO⁻) ​Glutamate​ (COO⁻) ● Carboxyl group has a low pKₐ making it ​very likely to lose a proton at neutral pH ○ Carboxylate anion (COO⁻) is left BASIC Group D: ​Positive charge at neutral pH Arginine​ (Arg) Histidine​ (His) Lysine​ (Lys) ● R‐groups have high pKₐ ● Nitrogen present in all, ​ rotonated at neutral pH ​ ​ ​ ​ ​ ​


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