Amino Acids, Peptides, and Proteins: A Comprehensive Guide PDF

Amino Acids can be Classified by R Group Standard amino acids are divided into five groups based on the properties of R-groups, particularly their polarity, or tendency to interact with water at biological pH (near 7.0). 1. Non-polar, aliphatic R groups: R-...

Amino Acids can be Classified by R Group Standard amino acids are divided into five groups based on the properties of R-groups, particularly their polarity, or tendency to interact with water at biological pH (near 7.0). 1. Non-polar, aliphatic R groups: R-groups in this class of amino acids are Neutral, non-polar, and hydrophobic (water fearing or insoluble in water) When present in proteins, they are located in the interior of protein where there is no polarity. 2. Non-polar, aromatic R groups: aromatic side chains are neutral and non-polar and participates in hydrophobic interactions. 3. Polar amino acids: R-groups are polar, hydrophilic (water loving) Three types: 3a. Polar-neutral: contains polar but neutral side chains and more soluble in H2O 3b. Polar acidic: contain carboxyl group as part of the side chains 3c. Polar basic: contain amino group as part of the side chain  Nomenclature and Forms Common names assigned to the amino acids are currently used. Shorthand notations are used to indicate the composition and amino acid sequence. Three letter abbreviations - widely used for naming:  First letter of amino acid name is compulsory and capitalized followed by next two letters not capitalized except in the case of Asparagine (Asn), Glutamine (Gln) and tryptophan (Trp). One-letter symbols - commonly used for comparing amino acid sequences of proteins:  Usually the first letter of the name  When more than one amino acid has the same letter the most abundant amino acid gets the first letter. Although α-amino acids are commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt) form. Copyright © Cengage Learning. All rights reserved Practice Exercise Classify the following amino acids based on the polarity of their R-groups. O O a. H 2N CH C OH d. H 2N CH C OH Non-polar Non-polar CH2 CH3 O H 2N CH C OH CH2 Polar Neutral b. O H 2N CH C OH e. CH2 OH Polar Basic CH2 CH2 O CH2 Polar Acidic c. H 2N CH C OH NH2 CH2 C O OH Copyright © Cengage Learning. All rights reserved Acid-Base Properties of Amino Acids (Lehninger 6th Ed.) Exists as Zwitterion: A dipolar ion with both + (positive) and – (negative) charge on the same molecule with a net zero charge. Carboxyl groups give-up a proton (H+) to get negative charge Amino groups accept a proton (H+) to become positive Amino acids in solution exist in three different species (zwitterions, positive ion, and negative ion) - Equilibrium shifts with change in pH  Ionization vs. pH The net charge on an amino acid depends on the pH of the solution in which it is dissolved.  If we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion. They act as amphiprotic substance, and aqueous solution of them is called buffers. Proteins act as buffers, especially in the blood. (Seager et al. 10th Ed.)  Ionization vs. pH Isoelectric point (pI) or also called as Isoelectric pH – the characteristic solution pH at which an amino acid has a net charge of zero. Different amino acids have different isoelectric points. At isoelectric point - amino acids are not attracted towards an applied electric field because they have net zero charge. (Stryer 8th Ed.)  Guidelines for Amino Acid Forms at Different pH: Low pH: All acid groups are protonated. All amino groups are protonated High pH: All acid groups are deprotonated. All amino groups are deprotonated. Neutral pH: All acid groups are deprotonated. All amino groups are protonated. COOH COO- COO- + + H3N C H H3N C H H2N C H CH3 CH3 CH3 Low pH High pH Zwitter Ion (net + charge) (net neutral charge) (net - charge) Copyright © Cengage Learning. All rights reserved Isoelectric Point (pI) Nonpolar & Acidic polar side chains pI Side Chains pI Isoelectric point, pI: The pH alanine 6.01 aspartic acid 2.77 at which the majority of asparagine 5.41 glutamic acid 3.22 molecules of a compound in cysteine 5.07 solution have no net charge. glutamine 5.65 glycine 5.97 isoleucine 6.02 Basic leucine 5.98 Side Chains pI methionine 5.74 arginine 10.76 phenylalanine 5.48 histidine 7.59 proline 6.48 lysine 9.74 serine 5.68 threonine 5.87 tyrosine 5.66 tryptophan 5.88 valine 5.97 (Mathews 4th Ed.)  The side chains of several of the amino acids also contain dissociable groups. (Garrett & Grisham 6th Ed.) (Garrett & Grisham 6th Ed.) Most amino acids contain two ionizable groups (COOH- COO- and NH3+ - NH2) have typical titration curves as shown for glycine. Amino acids with ionizable side chains, such as for amino acids containing –COOH in their side chains have titration curves with three leveling- offs. 16 Peptides and Proteins Proteins behave as zwitterions. Proteins have an isoelectric point, pI. At its isoelectric point, the protein has no net charge. At any pH above (more basic than) its pI, it has a net negative charge. At any pH below (more acidic than) its pI, it has a net positive charge. Peptides and Proteins Hemoglobin, for example, has an almost equal number of acidic and basic side chains; its pI is 6.8. Serum albumin has more acidic side chains; its pI is 4.9. Serum albumin is the most abundant plasma protein and is produced in the liver. Peptides and Proteins Proteins are least soluble in water at their isoelectric points and can be precipitated from solution when pH = pI.  Determining Amino Acid Form in Solutions of Various pH A. Draw the structural form of the amino acid alanine that predominates in solution at each of the following pH values: a. pH=1.0 b. pH=7.0 c. pH=13.0 9.7 2.3 9.7 2.3 + 9.7 +1 0 −1 pI = =𝟔 2.3 pH = 1 pH = 7 pH = 13 2 Isoelectric point of alanine pKa of a-COO- group = 2.3 pKa of a-NH3+ group = 9.7 pH = 1 pH = 7 pH = 13 NOTE: At acidic pH less than 2.3, the carboxyl and amino group of alanine are protonated and the net charge is +1. At isoelectric point, between 2.3 – 9.7, alanine is in its zwitterionic form where the net charge is zero. At alkaline pH greater than 9.7, the carboxyl and amino group of alanine are deprotonated and the net charge is -1.  Determining Amino Acid Form in Solutions of Various pH B. Draw the structural form of lysine at each of the following pH values: a. pH=1.0 b. pH=7.0 c. pH=10.0 d. pH=13.0 2.2 9.0 10.0 Isoelectric 9.0 2.2 +2 +1 0 −1 10.0 + 9.0 pI = = 𝟗. 𝟓 point of lysine pH = 1 pH = 7 pH = 10 pH = 13 2 10.0 pKa of a-COO- group = 2.2 pKa of a-NH3+ group = 9.0 pKa of NH3+ side chain = 10.0 pH = 1 pH = 7 pH = 10 pH = 13 22  Determining Amino Acid Form in Solutions of Various pH B. Draw the structural form of arginine at each of the following pH values: a. pH=1.0 b. pH=7.0 c. pH=10.0 d. pH=13.0 9.0 2.2 2.2 9.0 12.5 +2 +1 0 −1 Isoelectric point of pH = 1 pH = 7 pH = 10 pH = 13 12.5 + 9.0 alanine pI = = 𝟏𝟎. 𝟕𝟓 2 12.5 pKa of a-COO- group = 2.2 pKa of a-NH3+ group = 9.0 pKa of NH2+ side chain = 12.5 pH = 1 pH = 7 pH = 10 pH = 13  Determining Amino Acid Form in Solutions of Various pH C. Draw the structural form of glutamate or glutamic acid at each of the following pH values: a. pH=1.0 b. pH=7.0 c. pH=10.0 d. pH=13.0 2.2 4.2 9.7 2.2+4.2 Isoelectric +1 0 −1 − 2 pI = = 𝟑. 𝟐 point of alanine 9.7 2.2 pH = 1 pH = 7 pH = 10 pH = 13 2 4.2 pKa of a-COO- group = 2.2 pKa of a-NH3+ group = 9.7 pKa of COO- side chain = 4.2 pH = 1 pH = 7 pH = 10 pH = 13 25 Formation of Peptides Proteins are unbranched polymers of amino acids linked head-to-tail, from carboxyl group to amino group, through formation of covalent peptide bonds, a type of amide linkage. The length of the amino acid chain can vary from a few amino acids to many amino acids. Peptide bond formation results in the release of H2O. The peptide “backbone” of a protein consists of the repeated sequence —N—Cα—Co— (Garrett & Grisham 4th Ed.) Copyright © Cengage Learning. All rights reserved Formation of Peptides In 1902, Emil Fischer proposed that proteins are long chains of amino acids joined by amide bonds. Peptide bond (peptide linkage): The special name given to the amide bond between the α-carboxyl group of one amino acid and the α -amino group of another. (Bettelheim et al. 12th Ed.)  Writing Peptides By convention, peptides are written from the left to right, beginning with the free -NH3+ group and ending with the free -COO- group. C-terminal amino acid: The amino acid at the end of the chain having the free -COO- group. N-terminal amino acid: The amino acid at the end of the chain having the free -NH3+ group. Alternatively they are referred to as the C-terminus and the N-terminus. (Stryer 8th Ed.)  Peptide Nomenclature: IUPAC The amino acid naming sequence begins at the N-terminal amino acid residue. Name the amino acid in the exact order, replacing the name ending to –yl for every amino acid. The -yl suffix replaces the -ine or -ic acid ending of the amino acid name, except for tryptophan, for which -yl is added to the name to become tryptophanyl. The C-terminal amino acid residue keeps its orginal full amino acid name. OH N-terminal end O O CH2 O +H 3N CH C H N CH C H N CH C O- Example: CH 3 CH2 C-terminal end Ala-Phe-Ser AFS IUPAC name: Alanylphenylalanylserine Alanine Phenylalanine Serine Copyright © Cengage Learning. All rights reserved Other Examples Sample Exercise Identify the number of peptide bonds and classify the type of peptide. Then write the IUPAC name, three-letter abbreviation and one letter abbreviation of the chain. (Lehninger 6th Ed.) 4 peptide bonds Pentapeptide IUPAC name: Serylglycyltyrosylalanylleucine Ser–Gly–Tyr–Ala–Leu/ SGYAL. Sample Exercise 1. What is the name of the peptide? 2. Classify the type of peptide. 3. What is the 3-letter and 1-letter abbreviation? 2 peptide bonds Tripeptide IUPAC name: Alanylaspartylphenylalanine Ala-Asp-Phe/ ADF. Proteins and Amino Acids End