Lecture 3: 8/24. CHAPTER 3 Amino Acids

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1 Lecture 3: 8/24 CHAPTER 3 Amino Acids 1

2 Chapter 3 Outline 2

3 Amino Acid Are Biomolecules and their Atoms Can Be Visualized by Two Different Ways 1) Fischer projections: Two dimensional representation of a three dimensional organic molecule Every atom is identified, and the bonds to the central atom are depicted as vertical and horizontal lines. The horizontal bonds are taken to project out of the plane toward the viewer, whereas the vertical bonds are assumed to project behind the viewer. 2) Stereochemical rendering or configuration: This configuration is useful for visualizing the shape of the molecule. Wedges are used to depict the direction of bond projection. A solid wedge shows the bond projecting toward the viewer out of the plane. A dashed wedge shows the bond projecting behind the plane, away from the viewer. The remaining bonds are depicted as straight lines. 3

4 Amino Acids Are Building Blocks of Proteins Amino Acid Structure: An amino acid is composed of a central carbon atom called the tetrahedral carbon. The carbon is linked to an amino group, a carboxylic acid, a hydrogen atom, and a distinctive side chain called the R group. Side chain or R group Amino Acid (un ionized form) Amino Acid (ionized form) Amino acids have three letter abbreviations and one letter symbols e.g. Alanine, Ala, A 4

5 Most Amino Acids Exist in Two Mirror Image Forms When four different groups are bonded to the carbon, the amino acids are chiral or asymmetric. This means that they exist as two mirror image forms called the L isomer and the D isomer. This chemical structure is optically active. Only the L isomers are found in proteins. 5

6 All Amino Acids Have at Least Two Charged Groups The amino group (NH 3+ ) and the carboxyl group (COO ). Alanine At neutral ph, free amino acids in solution exist as dipolar ions. This is called zwitterions. This means that; Amino group is protonated (NH 3+ ) and Carboxyl group is deprotonated (COO ) 6

7 Ionization state of amino acid as a function of ph Change in ph alters the ionization state of amino acids. The zwitterionic form predominates near physiological ph (near 7.4). 7

8 All Amino Acids Have Diverse Functions Groups Amino acids have unique side chains that vary in size, shape, charge, hydrogen bonding capacity, hydrophobic character, and chemical reactivity. Amino acids have three letter abbreviations and one letter symbols. 8

9 Classification of Amino Acid Based on the Chemical Characteristics of their R groups 1. Hydrophobic amino acids with nonpolar R group Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Proline, Phenylalanine, and Tryptophan 2. Polar amino acids with neutral R groups that contain electronegative atom Serine, Threonine, Tyrosine, Cysteine, Asparagine, and Glutamine 3. Positively charged amino acids that have positively charged R group at physiological ph (7.4) Lysine, Arginine, and Histidine 4. Negatively charged amino acid that have negatively charged or acid R group at physiological ph (7.4) Aspartic acid (aspartate) an Glutamic acid (glutamate) 9

10 1) Hydrophobic amino acids Hydrophobic Amino Acids Have Mainly Hydrocarbon Side chains 10

11 2. Polar amino acids Polar Amino Acids Have Side Chains That Contain an Electronegative Atom 11

12 3. Positively Charged Amino Acids Are Hydrophilic The R group of lysine is topped with an amino group while that of arginine is topped with a guanidium group. 12

13 3. Positively charged amino acids The R group of lysine is topped with an amino group while that of arginine is topped with a guanidium group 13

14 Histidine ionization Histidine can bind or release protons near physiological ph. 14

15 4. Negatively charged amino acids Negatively Charged Amino Acids Have Acidic Side Chains 15

16 Ionizable groups in proteins and their pka values The Ionizable Side Chains Enhance Reactivity and Bonding 16

17 Essential Amino Acids Must be Obtained from the Diet Kwashiorkor is a form of malnutrition resulting from inadequate consumption of amino acids usually ingested as proteins. 17

18 Basic set of 20 Amino Acids Essential amino acids must be obtained from the diet because human cannot synthesizes. 18

19 Summary of the Lecture 3 There are 20 amino acids and only the L isomer amino acid exist in proteins Each amino acid consists of a central alpha carbon that is bonded by an amino group, a carboxyl group, a hydrogen atom and distinctive side chain or R group Amino acid can be classified based on the chemical properties of the side chains: 1. Hydrophobic amino acids 2. Polar amino acids 3. Positively charged amino acids 4. Negatively charged amino acids Essential amino acids (9 of them) must be obtained through diet and they are required for healthy growth and development 19

20 20

21 Lecture 4: 8/26 CHAPTER 4 Protein Three Dimensional Structure Assignment: Please read the chapter 4 prior to class 21

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