Amino Acids
Page 1: Introduction to Amino Acids
Structures of Amino Acids
Chemical representation: R chain, α-Carbon (Cα), Carboxyl (-COO-), Amino (-NH3)
Tetrahedral structures around the α-Carbon
Ball-and-stick models used for visualization
Page 2: General Properties
General formula of amino acids
Unique characteristics:
Titration curves
Optical activity of amino acids
Non-standard amino acids
Reactions involving amino acids
Page 3: α-Amino Acids
Definition: 20 protein amino acids are called α-amino acids
Forms of α-amino acids:
Neutral form
Zwitterionic form
Terminology:
α-Carbon: Carbon next to the carbonyl group (C=O)
Subsequent carbons termed β, γ, etc.
Page 4: Acid-Base Properties
Amino acids can function both as acids and bases due to two ionizable groups:
Carboxyl group (-COOH)
Amino group (-NH2)
Page 5: Amino Acid Classification
Non-Polar Amino Acids
Small side chain: Glycine (Gly), Alanine (Ala), Proline (Pro)
Branched-chain: Valine (Val), Isoleucine (Ile), Leucine (Leu), Methionine (Met)
Aromatic side chains: Phenylalanine (Phe), Tryptophan (Trp), Tyrosine (Tyr)
Polar Amino Acids
Uncharged: Serine (Ser), Threonine (Thr), Tyrosine (Tyr), Glutamine (Gln), Asparagine (Asn), Cysteine (Cys)
Charged:
Positive charge: Lysine (Lys), Arginine (Arg), Histidine (His)
Negative charge: Aspartic acid (Asp), Glutamic acid (Glu)
Page 6: Structure of Specific Amino Acids
Examples of key amino acids:
Glycine (Gly)
Alanine (Ala)
Valine (Val)
Isoleucine (Ile)
Leucine (Leu)
Methionine (Met)
Proline (Pro)
Phenylalanine (Phe)
Tryptophan (Trp)
Page 7: Hydrophobic Properties
Hydrophobic Side Chains:
Aggregate in protein interiors due to hydrophobic effects.
London dispersion forces provide primary interactions in folded proteins.
Page 8: Amino Acid Classification (Repeats)
Review of non-polar and polar amino acids as previously noted.
Page 9: Additional Polar Amino Acids
Specific amino acids:
Asparagine (Asn)
Cysteine (Cys)
Glutamine (Gln)
Page 10: Polar Uncharged and Charged Amino Acids
Polar uncharged side chains can hydrogen bond:
Uniqueness of -SH in Cysteine (Cys) facilitates H bond-forming.
Charged Amino Acids: Each has an ionizable group, providing ionic interactions that stabilize protein structures.
Importance of Histidine (His) due to pKa close to physiological pH (7).
Page 11: Key Charged Amino Acids
Basic Charged Amino Acids:
Arginine (Arg)
Histidine (His)
Lysine (Lys)
Acidic Amino Acids:
Glutamic acid (Glu)
Aspartic acid (Asp)
Page 12: Rare Amino Acids
21st & 22nd Amino Acids:
Selenocysteine and pyrrolysine include special stop codons (UAG) in genetic code.
Presence of specific tRNA and tRNA synthetases.
Page 13: Selenocysteine
Incorporated into ~15 human proteins (e.g., deiodinases, peroxidases).
More reactive than sulfur, amplifying enzymatic activity.
Importance of selenocysteine-specific tRNA (gene deletion causes lethality).
Page 14: Pyrrolysine
Modified lysine with a pyrrole ring attached.
Predominantly found in methanogenic bacteria and archea.
Critical for methyl transferase enzymes.
Page 15: One-Letter and Three-Letter Amino Acid Abbreviations
List of amino acids:
Alanine (Ala, A)
Arginine (Arg, R)
Asparagine (Asn, N)
Aspartic acid (Asp, D)
Cysteine (Cys, C)
Glutamic acid (Glu, E)
Glutamine (Gln, Q)
Glycine (Gly, G)
Histidine (His, H)
Isoleucine (Ile, I)
Leucine (Leu, L)
Lysine (Lys, K)
Methionine (Met, M)
Phenylalanine (Phe, F)
Proline (Pro, P)
Serine (Ser, S)
Threonine (Thr, T)
Tryptophan (Trp, W)
Tyrosine (Tyr, Y)
Valine (Val, V)
Page 16: Cystine Variant
Cystine (disulfide bond of cysteine): C = O structuring, oxidation reaction leading to S-S bond formation.
Page 17: Acid-Base Properties of Amino Acids
Amino acids: polyprotic weak acids with distinct pKa.
Characteristic titration profiles for ionizable groups.
Page 18: Key pKa Values
1st ionization: ~2.2
2nd ionization: ~9.5
Side chain structure impacts alpha amino and carboxylic acid group pKa.
Page 19: Glycine Titration Curve
Overview of glycine's titration curve showcasing charge dynamics at different pH levels.
Page 20: Peptide Titration Curves
One plateau per ionizable group.
Ionizable groups: N-terminal, C-terminal, and side chains.
Page 21: pKa Values Overview
Memorize pKa values for amino acids:
-COOH: ~2.2
-NH3: ~9.5
7 additional pKa values for various amino acids.
Page 22: Calculating Isoelectric Point (pI)
Natc's Net charge = 0 at pI.
Average of two pKa values for two titratable groups (e.g., glycine example provided)
pI = (pKa1 + pKa2) / 2 (For glycine: 6.06).
Page 23: Ionization States
Depicts ionization states at varying pH levels for amino acids.
Cationic form, zwitterion (neutral), anionic form.
Page 24: Protonation States
Detailed overview of amino acid protonation and charge states throughout titration.
Page 25: Glutamic Acid Titration Curve
Visual representation of titration curve for glutamic acid, showcasing pK values.
Page 26: Fractional Charge Calculations
Average of molecular charges in solution and the fraction of charged molecules calculates average fractional charge.
Page 27: Calculating Glutamic Acid at pI
Demonstrates calculation of fractional charge at pI for Glutamic Acid.
Page 28: Charge Calculation for Glutamic Acid
Total charge determination at pI with considerations for functional groups.
Page 29: Fractional Charge at pH 7 for Glutamic Acid
Calculating fractional charges of COOH groups at pH = 7.
Page 30: Total Charge at pH = 7
Summary of total charges of Glutamic Acid at physiological pH (7).
Page 31: Deprotonation Dynamics
Impacts of deprotonation on charges for COOH and NHx groups.
Page 32: Microenvironment Effects on pKa
pKa variation due to microenvironment in folded proteins, impacting stability of charge states.
Page 33: Separation Techniques
Properties for Separation:
Polarity (hydrophobic interactions through silica gel).
Charge (ion exchange chromatography).
Page 34: Hydrophobic Chromatography Technique
Explanation of method for separating amino acids based on hydrophobicity.
Page 35: Elution Profile for Hydrophobic Interaction
Visualization of elution process for amino acids like Ala, Val, and Phe.
Page 36: Cation and Anion Exchange Resins
Cation exchange resins bind to cations with examples of types and their interactions.
Anion exchange resins bind to anions and factors for binding strength.
Page 37: Desorption Techniques
Methods to elute amino acids from columns such as increased salt concentration or pH adjustments.
Page 38: Separation Techniques for Specific Amino Acids
Application of cation and anion exchange to separate specific amino acids like Asp, Leu, and Arg.
Page 39: pI Value Context
Contextualizing pKa values relevant to amino acid charges at pH = 7 for Asp, Leu, Arg.
Page 40: Influence of pI Values
pI values provide insights into charge at physiological pH for each amino acid discussed.
Page 41: Charge Analysis Summary
Determining net charge on amino acids based on pI and pH relation.
Page 42: Charge Analysis Continued
Evaluating amino acid charge conditions at pH = 7 based on pI values.
Page 43: Elution Profile for Ion Exchange
Drawing elution profiles for Glu, Leu, Arg to visualize separation.
Page 44: Summary of Key Points
Free amino acids have charged groups in solution.
pI characterizes charge states: pH effect on net charge.
Page 45: Optical Activity in Amino Acids
Generic structure for L-configuration amino acids as identified by Emil Fischer.
Page 46: Comparisons in Asymmetric Configuration
Alignment of L-glyceraldehyde with L-amino acids, highlighting stereochemistry.
Page 47: Nomenclature in Amino Acids
Three systems: LD (Fischer), RS, and levo/dextrorotatory; with attention to Thr and Ile regarding asymmetric centers.
Page 48: Nonstandard Amino Acids
Identification of other amino acids; post-translational modifications occurring in proteins.
Page 49: Other Amino Acid Derivatives
Listing derivatives and functional roles not encompassed by standard amino acids.
Page 50: Neurotransmitter Conversion
Tryptophan as a precursor for serotonin and melatonin.
Page 51: Additional Functions of Amino Acids
Notable roles of amino acids like leucine and serine in cellular functions and disease management.
Page 52: Reactions of Amino Acids
Overview of interactions (carboxyl/amino groups) and specific reactivities of side chains.
Page 53: Carboxyl Group Reactions
Detailed chemical reactions outlined for carboxyl groups with specific interactions.
Page 54: Amino Group Reactions
Types of reactions involving amino groups and examples thereof.
Page 55: Ninhydrin Analysis
Visualization of amino acid reactions with ninhydrin leading to Ruhemann's Purple formation.
Page 56: Cysteine and Cystine Dynamics
Discussion around cysteine properties and reactions that lead to cystine formation.
Page 57: Fluorescent Proteins
Contextualization of green fluorescent protein's chromophore formation.
Page 58: Mechanistic Pathways
Overview of mechanisms related to chromophore maturation from precursors.
Page 59: Peptide Bonds
Mechanistic overview of peptide bond formation between amino acids indicating N-term and C-term structures.
Page 60: Topic Summary
Overview of amino acid topics:
Structures of 20 protein amino acids
Mechanisms of peptide bonds
Acid-base properties and titration curves
Non-standard amino acids and chemical reactions.