Amino Acids and Proteins PDF

Chapter 1-2: Amino Acids and Proteins Dr. James Martin II Assistant Professor, Rowan-Virtua SOM Email: [email protected]  Learning Objectives 1. Amino Acid Basics a) Describe the basic structure of amino acids and categoriz...

Chapter 1-2: Amino Acids and Proteins Dr. James Martin II Assistant Professor, Rowan-Virtua SOM Email: [email protected]  Learning Objectives 1. Amino Acid Basics a) Describe the basic structure of amino acids and categorize them based on their R group properties. 2. Protein Structure a) Explain the four levels of protein structure: primary, secondary, tertiary, and quaternary. b) Identify common secondary structure elements (alpha helices and beta sheets). 3. Protein Stability and Folding a) Discuss the main forces that stabilize protein structure. b) Explain the basic concept of protein folding and factors that can lead to denaturation. 4. Structure-Function Relationships a) Describe how protein structure relates to function, using examples like enzymes or structural proteins. 5. Protein Modifications a) Explain the concept of post-translational modifications and their significance. 6. Protein Misfolding and Disease a) Discuss the relationship between protein misfolding and certain diseases. Part 1 - Amino Acids Structure and Chemistry Building Blocks of Proteins Essential Amino Acids Basic Structure Stereochemistry Side Chain Chemistry Properties Ionization Bonding Amino Acids & Proteins Workhorses of cell – Catalysis – Signaling – Structure – Energy/Gradient Generation Proteins comprised of 20-21 amino acids Amino Acids Essential Amino Acids  Alpha Carbon Basics of Structure Elements Alpha Carboxyl Alpha Amino Acids Differences in R Groups Alpha Amine  Alpha Carbon Basics of Structure Elements Alpha Carboxyl Alpha Amino Acids Differences in R Groups Alpha Amine Examples Asymmetric Center Alpha Carbon Alpha Carboxyl R Alpha Amine  Alpha Carbon Basics of Structure Elements Alpha Carboxyl Alpha Amino Acids Differences in R Groups Alpha Amine Examples Asymmetric Center Alpha Carbon Alpha Carboxyl R 18 Alpha Amine  o n rb Amino Acids C a Stereochemistry ri c et m D and L Isomers y m A s Almost all biological amino acids are in the L-configuration Categorizing Amino Acids Non-Polar Carboxyl Amine Aromatic Hydroxyl Other Alanine Aspartic Acid Arginine Phenylalanine Serine Asparagine Glycine Glutamic Acid Histidine Tryptophan Threonine Cysteine Isoleucine Lysine Tyrosine Tyrosine Glutamine Leucine Selenocysteine Methionine Pyrrolysine Proline Valine Ionizable R-groups Name Charged R-group Approximate R-group pKa - Aspartic Acid -COO 4.1 - Glutamic Acid -COO 4.1 + Lysine -NH3 10.5 + Arginine =NH2 12.5 + Histidine =-NH 6.0 - Cysteine -S 8.2 - Tyrosine -O 10.5 Amino Acids Aromatic R-Groups Alpha Carbon Tryptophan Alpha Amine Alpha Carboxyl Tyrosine Phenylalanine Amino Acids R Aromatic R-Groups Tryptophan R R Tyrosine Phenylalanine Amino Acids R Aromatic R-Groups Charges at Physiological pH Tryptophan R R Ionizes at high pH Tyrosine Phenylalanine Amino Acids Aliphatic R-Groups H Alanine Glycine Proline Isoleucine Leucine Valine Methionine Amino Acids Aliphatic R-Groups H Alanine Glycine Proline Isoleucine Leucine Valine Methionine Amino Acids Aliphatic R-Groups Charges at Physiological pH Amino Acids R-Group Carboxyls Aspartic Acid Glutamic Acid Amino Acids R-Group Carboxyls R R Aspartic Acid Glutamic Acid Amino Acids R-Group Carboxyls Charges at physiological pH R R Aspartic Acid Glutamic Acid Amino Acids Hydroxyl R-Groups Serine Threonine Tyrosine Amino Acids Hydroxyl R-Groups Serine Threonine Tyrosine Amino Acids Hydroxyl R-Groups Charges at Physiological pH Serine Threonine Ionizes at high pH Tyrosine Amino Acids Sulfhydryl R-Group Cysteine Amino Acids Sulfhydryl R-Group Ionizes at about pH = 8 + Cysteine Amino Acids Carboxamide R-Groups Asparagine Glutamine Amino Acids Carboxamide R-Groups Asparagine Glutamine Amino Acids Carboxamide R-Groups Asparagine Glutamine Amino Acids Ionizable Amine R-Groups Arginine Lysine Histidine Amino Acids Ionizable Amine R-Groups Arginine Lysine Histidine Amino Acids Ionizable Amine R-Groups Charges at Physiological pH Arginine Lysine Histidine Rare Amino Acids Non-Protein Amino Acids Carnitine Also - Citrulline, Ornithine, others Amino Acids Ionization Amino Acids Ionization -by pKa Values Amino Acids Ionization -by pKa Values Amino Acids Ionization -by pKa Values Amino Acids Ion Locations in Titration Charge = -1 Amino Acids Ionization -by pKa Values Charge = 0 Amino Acids Ionization -by pKa Values Charge = -1 Amino Acids Ionization -by pKa Values Charge = -2 Ionization Changes Charges Within Proteins Changes in Charge Change Activities Post-translational Modifications Phosphorylated Amino Acids Breakdown of Amino Acids From Amino Acids to Proteins Peptide Bonds In Ribosomes Alpha Carboxyl Alpha Amine Primary Protein Structure Linear sequence of amino acids Joined by Peptide Bonds Translated from mRNA using Genetic Code Synthesis begins at amino end and terminates at carboxyl end Ultimately determines all properties of a protein Polypeptides Alternating Orientations of R-groups A simple view Peptide Bond Peptide Bond Free Carboxyl Group Amino Terminus Peptide Bond Carboxyl Terminus Peptide Bond Peptide Bond Free Alpha Amine Alternating Orientations of R-groups Peptide Bonds Chemical Character Double Bond Behavior Alpha Carbons Usually Trans-oriented  Separated bulky groups Proteins Alpha Carbons Trans Steric Hindrance Separated bulky groups Interacting Bulky Groups Alpha Carbons Cis Polypeptides Multiple Peptide Bond Planes Free Rotation Phi and Psi Angles Peptide Bond Omega Angle Psi Angle Phi Angle Peptide Bond Ramachandran Plot Bond Angles Primary Angles of Stability Secondary Structure Alpha Helix Secondary Structure Alpha Helix Hydrogen bonds stabilize structure Hydrogen bonds stabilize structure  Hydrogen Bonds Secondary Structure Beta Strands / Beta Sheets Anti-Parallel Parallel Beta-Sheet Interactions Secondary / Supersecondary Structures Ramachandran Plot Labeled Secondary Structure Fibrous Proteins Collagen Connective tissue Keratin Hair / nails Fibroin Silk  Collagen Partial Sequence Primary Structure Hydroxyproline Proline in Helix Abundant Glycine Occasional Lysine Structural Proteins Keratins Fibrous 50 in Humans Intermediate Filaments of Cytoskeleton Hair, nails, horns Fibroin Silk Beta sheets Repeating glycines Secondary Structure Types Alpha Helix Beta Strands / Beta Helix Reverse turns (5 types) 310 Helix Secondary Structure Tendencies of Amino Acids High Propensity for Alpha Helices High Propensity for Reverse Turns High Propensity for Beta Strands Amino Acid Hydropathy Soluble vs. Membrane Bound Proteins Hydrophobic Amino Acid Bias Inside Hydrophilic Amino Acid Bias Outside Hydrophobic Amino Acid Bias In Bilayer Hydrophilic Amino Acid Bias Outside of Bilayer Reverse Turns Tertiary Structure Folding and Turns Beta Strands Alpha Helices Random Coil Turns Folding of a Globular Protein Unfolding of a Globular Protein Forces Stabilizing Tertiary Structure Hydrogen Bonds Forces Stabilizing Tertiary Structure Disulfide Bonds (Covalent) Forces Stabilizing Tertiary Structure Denaturing/Unfolding Proteins Break forces stabilizing them Mercaptoethanol/dithiothreitol - break disulfide bonds Detergent - disrupt hydrophobic interactions Heat - break hydrogen bonds pH - change charge/alter ionic interactions Chelators - bind metal ions Denaturing/Unfolding Proteins Folding of a Globular Protein Energetics of Folding Protein Structural Domains Leucine Zipper - Prot.-Prot. and Prot.-DNA Helix Turn Helix - Protein-DNA Leucine Zipper Zinc Fingers SH2 Domains - Protein-Protein Pleckstrin Homology Domains - Signaling (Membrane) Leucine Zipper Zinc Finger SH2 Domain Helix-Turn-Helix Pleckstrin Domains Folding Errors Prion Replication Model Amyloids and Disease Amyloids - a collection of improperly folded protein aggregates found in the human body. When misfolded, they are insoluble and contribute to some twenty human diseases including important neurological ones involving prions. Amyloid diseases include (affected protein in parentheses) - Alzheimer’s disease (Amyloid β) Parkinson’s disease (α-synuclein) Huntington’s disease (huntingtin), Rheumatoid arthritis (serum amyloid A), Sc Fatal familial insomnia (PrP ) Protein Processing Chaperonins - Proper folding - environment for hydrophobic sequences GroEL / GroEL-GroES Proteasomes - Degradation to oligopeptides of about 8 amino acids each Role of Ubiquitin Flag for protein destruction by proteasome Intrinsically Disordered Proteins Not all proteins folded into stable structures Intrinsically Disordered Proteins (IDPs) have regions favoring disorder IDP regions tend to lack hydrophobic residues Rich in polar amino acids and proline IDPs may favor adaptation to binding another protein IDPs may favor being modified IDPs may be more involved in signaling and regulation Non-IDPs more involved in catalysis and transport Metamorphic Proteins May adopt more than one stable structure Lymphotactin - monomeric receptor. Binds heparin as dimer Protein Structure Primary – Amino Acid Sequence Secondary / Supersecondary – Repeating Structures – short range forces Tertiary – Folded structures – longer range interactions