Amino Acids and their Properties PDF

MODULE 1 1. Amino Acids as the Building Block of Proteins 1S2021 C40 AKQR  Course Outcome/s: At the end of this module, you should be able to: § List the names and abbreviations of amino acids § Describe the structure of amino a...

MODULE 1 1. Amino Acids as the Building Block of Proteins 1S2021 C40 AKQR  Course Outcome/s: At the end of this module, you should be able to: § List the names and abbreviations of amino acids § Describe the structure of amino acid including isomeric forms and structural pattern § Describe the chemical properties of amino acids associated with their structure § Classify amino acids based on the properties of the side chains such as polarity, acidity, and basicity § Relate the dominant charged forms of amino acids with different pH conditions § Draw charged forms including zwitterionic forms of the amino acid § Calculate the isoelectric point for amino acids § Sketch titration curves for amino acids § Define peptide bond § Explain how peptide bonds are formed § Describe the structural properties of peptide bonds 1S2021 C40 AKQR  References In the preparation of this module, the main reference used was Biochemistry by Campbell and Farrell. However, you can use any other reference materials like those listed in the syllabus. Biochemistry by Garrett and Grisham Biochemistry by Mathews and Van Holde Principles of Biochemistry by Lehninger Biochemistry by Horton Principles of Biochemistry by Voet, Voet and Pratt Other reference materials and videos used in this module were obtained from the internet. 1S2021 C40 AKQR  References This module is for the exclusive use for the remote teaching/learning of Chemistry 40, Institute of Chemistry, College of Science, University of the Philippines Diliman during the 1st semester, AY 2020-2021. It is not for sale and can not be reproduced without permission from the Institute. 1S2021 C40 AKQR  What are amino acids? Organic molecule with at least one carboxyl group and at least one amino group side chain (unique per amino acid) carboxyl group amino group carbon center 1S2021 C40 AKQR  There are 20 “standard” amino acids All proteins are composed of 20 “standard” amino acids The common amino acids are known as α – amino acids because they have a primary amino group (─NH2) as a substituent of the carbon atom, the carbon next to the carboxylic acid group The sole exception is proline, which has a secondary amino group (─NH─). 1S2021 C40 AKQR  Essential and Non Essential Acids The 20 amino acids can be divided into essential and non essential amino acids. Essential amino acids – derived from exogenous sources (like diet or supplements) Non essential amino acids – can be synthesized by the body 1S2021 C40 AKQR  How do we name amino acids? 1S2021 C40 AKQR  Amino acids are represented by letters The names of amino acids are abbreviated using the 3 – letter notation or 1 – letter notation. Each amino acids will have a unique abbreviation for them. 3 – letter abbreviation 1 – letter abbreviation 1S2021 C40 AKQR 1S2021 C40 AKQR  Amino acids are chiral molecules All amino acids derived from proteins have the L stereochemical configuration; that is, they all have the same relative configuration around their α – atoms. 1S2021 C40 AKQR  CLASSIFICATION OF AMINO ACIDS 1S2021 C40 AKQR  Classification of Amino Acids There are three major types of amino acids: (1) those with nonpolar R groups, (2) those with uncharged polar R groups, and (3) those with charged polar R groups 1S2021 C40 AKQR 1S2021 C40 AKQR  Classification of Amino Acids A. NON POLAR, HYDROPHOBIC SIDE CHAINS Side-chains have carbon-hydrogen containing aliphatic or aromatic groups and have nonpolar character 1S2021 C40 AKQR  Classification of Amino Acids NON POLAR, HYDROPHOBIC SIDE CHAINS 1S2021 C40 AKQR  Classification of Amino Acids NON POLAR, HYDROPHOBIC SIDE CHAINS 1S2021 C40 AKQR  Classification of Amino Acids NON POLAR, HYDROPHOBIC SIDE CHAINS 2° carbon 1S2021 C40 AKQR  Classification of Amino Acids NON POLAR, HYDROPHOBIC SIDE CHAINS 1S2021 C40 AKQR  Classification of Amino Acids B) POLAR, UNCHARGED CHAINS All have at least one heteroatom (O or S) with electron pairs available for H-bonding 1S2021 C40 AKQR  Classification of Amino Acids POLAR, UNCHARGED SIDE CHAINS 1S2021 C40 AKQR  Classification of Amino Acids POLAR, UNCHARGED SIDE CHAINS 1S2021 C40 AKQR  Classification of Amino Acids POLAR, UNCHARGED SIDE CHAINS Cysteine is unique among the 20 amino acids. It has a thiol group that can form a disulfide bond with another cysteine through the oxidation of the two thiol groups 1S2021 C40 AKQR 1S2021 C40 AKQR  Classification of Amino Acids C) CHARGED, POLAR CHAINS Five amino acids have charged side chains. They can be classified as either basic or acidic amino acids. 1S2021 C40 AKQR  Classification of Amino Acids POLAR, CHARGED SIDE CHAINS BASIC AA 1S2021 C40 AKQR  Classification of Amino Acids POLAR, CHARGED SIDE CHAINS ACIDIC AA 1S2021 C40 AKQR Aliphatic- Glaciers in Alaska Valiantly Located Isolated Prowlers Aromatic- The Aroma of Fine Pine and Yellow Timber are Worth the Tryp OH containing- Alcohol is a Serious Threat Basic- Basically His Lost Kid Always Return Sulfur containing- Methodically Check the path for sulfur 1S2021 C40 AKQR  Are we limited to only 20 amino acids for all organisms? 1S2021 C40 AKQR  Some Uncommon Amino Acids The 20 common amino acids are by no means the only amino acids that occur in biological systems. “Nonstandard” amino acid residues are often important constituents of proteins and biologically active peptides In almost all cases, these unusual amino acids result from the specific modification of an amino acid residue after the polypeptide chain has been synthesized. 1S2021 C40 AKQR  Some Uncommon Amino Acids This amino acid derivatives are both found in structural proteins such as collagen. Modifications include simple addition of small chemical groups to certain amino acid side chains: hydroxylation, methylation, acetylation, carboxylation, and phosphorylation. 1S2021 C40 AKQR  Amino Acids Are Dipolar Ions At physiological pH, amino acids exist as dipolar ionic species. The amino and carboxylic acid groups of amino acids readily ionize. Molecules such as amino acids, which bear charged groups of opposite polarity, are known as dipolar ions or zwitterions Both positive and negative charges occur 1S2021 C40 AKQR  Amino Acids Are Dipolar Ions Note: The pK values of the carboxylic acid group is represented by pK1. The pK values of the α – amino group is represented by pK2. In addition, pK values for amino acids which have ionizable R groups are designated as pKR. The table on the next page shows the pK values for the different amino acids. 1S2021 C40 AKQR 1S2021 C40 AKQR  Amino Acids Are Dipolar Ions Amino acids can be titrated with equivalent amounts of base (ex. NaOH) to give a titration curve. Consider the titration curve for alanine using a strong base (NaOH) 1S2021 C40 AKQR  Amino Acids Are Dipolar Ions At a very low pH (pH ~ 0), all of the ionizable groups of alanine are protonated. All of the available alanine in solution have the form 1S2021 C40 AKQR  Amino Acids Are Dipolar Ions When the pH is increased until pK1 (pH = 2.3), the proton of the –COOH group ionizes. The protonated and deprotonated form are in equilibrium 1S2021 C40 AKQR  Amino Acids Are Dipolar Ions As we further increase the pH to pK2 (9.7), we start to deprotonate the – NH2 group. The protonated and deprotonated form will be in equilibrium 1S2021 C40 AKQR  Increasing the pH (greater than 9.7) of the solution will therefore change the charged of the amino acid until all ionizable groups are deprotonated 1S2021 C40 AKQR  Buffered regions 1S2021 C40 AKQR  Isoelectric Point Defined as the pH at which a molecule carries no net electrical charge or is electrically neutral. It is often designated by pI. For a diprotic acid, pK1 + pK 2 pI = 2 For alanine: 2.3 + 9.7 pI = 2 pI = 6 1S2021 C40 AKQR 1S2021 C40 AKQR  How do we calculate for pI? 1. Draw out the complete ionization of amino acid 2. Determine net charge on each ionized form 3. Find the structure that has no net charge 4. Take the average of the pKa’s that are around the structure with NO NET CHARGE pK1 + pK 2 pI = 2 5. Note do NOT just take the average of all pKa’s. 1S2021 C40 AKQR  Remember! Note: pK1 + pK 2 pI = 2 pI values can be calculated using pKa1 as the highest pKa before pI and pKa2 as the lowest pKa after pI. 1S2021 C40 AKQR  Test Yourself 1. Consider histidine with pK values given below. pKa of α – COOH group = 1.8 pKa of α – NH2 group = 9.2 pKa of side chain = 6.0 Determine the pI of this amino acid. Answer: 7.6 1S2021 C40 AKQR  Solution Step 1: Draw the amino acid and assign the pKa values 1.80 + 3 6.0 9.20 1S2021 C40 AKQR  Solution Step 2: Starting at a low pH (and subsequently increasing the pH), we determine the charge of the amino acid 1S2021 C40 AKQR  Solution Step 3: Calculate pI from the pKa values above and below the charge where amino acid (or peptide) is zero. 1S2021 C40 AKQR  Solution Step 4: Calculate pI using the formula pK1 + pK 2 pI = 2 6.0 + 9.2 pI = 2 pI = 7.6 1S2021 C40 AKQR  PEPTIDE BOND FORMATION 1S2021 C40 AKQR  Peptide Bonds Link Amino Acids Amino acids can be polymerized to form chains via a condensation reaction. The resulting CO – NH linkage is known as a peptide bond 1S2021 C40 AKQR  Peptide Bonds Link Amino Acids The residues at the two ends of the polypeptide each participate in just one peptide bond. The residue with a free amino group (by convention, the leftmost residue) is called the amino terminus or N- terminus. The residue with a free carboxylate group (at the right) is called the carboxyl terminus or C-terminus. N - terminal C - terminal Peptides are always written in the N → C direction Each peptide has ONLY ONE free amino group and ONE free carboxyl group; others are neutralized by formation of the peptide bond 1S2021 C40 AKQR  Important Feature of the Peptide Bond Peptide bonds have double bond character resulting from resonance stabilization (C – N bond has 40% double bond character) C – N and C – O have partial double bond character Resonance Results in Partial Double Bond Character of the Peptide Bond (Amide Bond): Rotation Restricted 1S2021 C40 AKQR  Important Feature of the Peptide Bond PEPTIDE BACKBONE IS RIGID AND PLANAR C, N, H, O are all in the same plane (Cα’s are also in plane) p orbitals can overlap to form partial double bonds between the nitrogen and carbon and the carbon and oxygen 1S2021 C40 AKQR  Important Feature of the Peptide Bond PEPTIDE BACKBONE IS RIGID AND PLANAR Peptide bonds link the peptide groups in the peptide chain: Crucial for protein structure Rotation can occur at the α − carbons However, rotation is limited due to steric hindrance (R groups) These limitations limit the shapes that can be assumed by protein chains 1S2021 C40 AKQR  These limitations force Cα carbons on either side of the peptide bond to be, with few exceptions, trans to each other (opposite sides of the peptide bond) a. Cis configuration is rare; steric hindrance is greater b. Trans is much more stable (sterically favored) c. R – groups (on the Cα carbons) also end up on opposite sides of the peptide bond (R – groups away from each other – favored) 1S2021 C40 AKQR  Summary 1. Cα, O, C, N and H atoms are planar 2. No rotation around the peptide bond 3. Cα (with R groups) groups are in trans configuration (i.e. H on the amide nitrogen is opposite to the oxygen of the carbonyl) 4. Peptide backbone is rigid 1S2021 C40 AKQR  How do we draw the pentapeptide GEVSK? 1S2021 C40 AKQR Gly – Glu – Val – Ser – Lys (pentapeptide) GEVSK 1S2021 C40 AKQR  Test Yourself 1. Consider the pentapeptide GEVSK. What is the pI of this peptide? Recall the steps we discuss earlier for histidine? Now, you can apply it to pentapeptide GEVSK J. 1S2021 C40 AKQR  Additional Video/s Khan Academy. Introduction to amino acids | Macromolecules | Biology. (Accessed on 15 Aug 2020) Khan Academy. Classification of amino acids | Chemical processes | MCAT. (Accessed on 15 Aug 2020) 1S2021 C40 AKQR