Lecture 2 8/29/2024 Amino Acids - PDF

Amino Acids and Peptides (plus some thermodynamics) CHM 6620/7620 Berg Chapter 2 8/29/2024 Quick announcements If completing honor’s option, please review supplemental syllabus on Canvas If grad student, please review “CHM 7620 Supplemental Sy...

Amino Acids and Peptides (plus some thermodynamics) CHM 6620/7620 Berg Chapter 2 8/29/2024 Quick announcements If completing honor’s option, please review supplemental syllabus on Canvas If grad student, please review “CHM 7620 Supplemental Syllabus” on Canvas Problem Set 1 on Achieve is due Tuesday 9/3 at NOON (typically due Mondays at noon) Course schedule on the Syllabus has been updated to reflect no classes on Election Day, Tuesday 11/5 The threshold concepts of biochemistry Thermodynamics of Physical basis for macromolecular Free Energy interactions structure formation Steady-state Biochemical pathway dynamics and regulation The threshold concepts of biochemistry Thermodynamics of Physical basis for macromolecular Free Energy interactions structure formation Steady-state Biochemical pathway dynamics and regulation  Proteins: Main Agents of Biological Function Catalysis (enzymes) – enolase (in the glycolytic pathway) – DNA polymerase (in DNA replication) Transport (proteins) – hemoglobin (transports O2 in the blood) – lactose permease (transports lactose across the cell membrane) Structure (proteins) – collagen (connective tissue) – keratin (hair, nails, feathers, horns) Motion (enzymes) – myosin (muscle tissue) – actin (muscle tissue, cell motility) http://nnhsbiology.pbworks.com/w/page/109339297/Honors%20Proteins Original author unknown  Amino Acids: Building Blocks of Protein Proteins are linear heteropolymers of -amino acids Amino acids have properties that are well-suited to carry out a variety of biological functions Capacity to polymerize Amino acids differ at Useful acid-base properties the R substituent Varied physical properties Varied chemical functionality L-amino acids are found in proteins  Amino Acids: Atom Naming Organic nomenclature: start from one end and use numbers Biochemical designation: – start from -carbon and go down the R-group, using Greek letters   -amine -carboxylic acid  All amino acids are chiral (except glycine) Proteins only contain L amino acids L-Alanine D-Alanine pH Protonation States of Amino Acids [OH-]  Protonation States of Amino Acids Note that this figure ignores the side chain and its ionization states!  Memorize these structures and pKa ballparks At acidic pH, the carboxyl group is protonated, and the amino acid is in the cationic form. At neutral pH, the carboxyl group is deprotonated, but the amino group is protonated. The net charge is zero; such ions are called Zwitterions. At alkaline pH, the amino group is neutral –NH2 and the amino acid is in the anionic form. Amino Acid Protonation States and pKa values ~2.2 ~9.3 Questions for students in class: 1. What is the net charge on glutamate at pH = 7? 2. What would be the net charge of glutamate be at pH = 2? 3. What would be the net charge of glutamate be at pH = 12? 4. What is the net charge of tyrosine at pH = 7? 5. What would the net charge of tyrosine be at pH = 2? 6. What would the net charge of tyrosine be at pH = 12? Titration of glutamate pH [OH-] Isoelectric point Isoelectric point is the pH at which an amino acid (or peptide, or protein) exhibits ZERO charge Determined as the average between the two pKas that involve the charge neutral species  Formation of Peptides Peptides are small condensation products of amino acids They are “small” compared to proteins (Mw < 10 kDa) Peptide are drawn from the N to C termini Numbering (and naming) starts from the amino (N) terminus Using full amino acid names (what a mess!) – Serylglycyltyrosylalanylleucine Using the three-letter code abbreviation – Ser-Gly-Tyr-Ala-Leu For longer peptides (like proteins) the one-letter code can be used – SGYAL Let’s draw a peptide: HEY (!) 1. Draw the backbone Start with a carbon skeleton Add amides and carbonyl (one per amino acid) from left to right starting with amino terminus Trim your carbon skeleton if too long 2. Draw side chains Enforce stereochem for L-amino acids (wedges up, dashes down) Assume pH = 7.4 unless otherwise specified for protonation of side chains and termini Let’s draw a peptide: HEY (!) 1. Draw the backbone Start with a carbon skeleton Add amides and carbonyl (one per amino acid) from left to right starting with amino terminus Trim your carbon skeleton if too long 2. Draw side chains Enforce stereochem for L-amino acids (wedges up, dashes down) Assume pH = 7.4 unless otherwise specified for protonation of side chains and termini Peptide are drawn from the N to C termini As chemists, we show stereochemistry, and we don’t show hydrogens when attached to carbon. The threshold concepts of biochemistry Thermodynamics of Physical basis for macromolecular Free Energy interactions structure formation Steady-state Biochemical pathway dynamics and regulation The physical basis for interactions …in DNA  The physical basis for interactions Covalent: e.g., Phosphodiester bonds  The physical basis for interactions Covalent: e.g., Phosphodiester bonds G’ºligation = -22.2 kJ/mol Dickson, K.S., et al. J. Biol Chem. 2000, 275 (21). 15828  The physical basis for interactions Covalent: e.g., Phosphodiester bonds Non-covalent: Intermolecular forces electrostatic interactions are the common thread in intermolecular forces  The physical basis for interactions Covalent: e.g., Phosphodiester bonds Non-covalent: Intermolecular forces H-bonds Total H-bond strength: around -80 kJ/mol for G-C around -46 kJ/mol for A-T J. Chem. Inf. Model. 2010, 50, 12, 2151.  The physical basis for interactions Covalent: e.g., Phosphodiester bonds Non-covalent: Intermolecular forces H-bonds Pi-stacking (dispersion/dipole) J. Chem. Inf. Model. 2010, 50, 12, 2151.  The physical basis for interactions Covalent: e.g., Phosphodiester bonds Non-covalent: Intermolecular forces H-bonds Pi-stacking (dispersion/dipole) Total H-bond strength: around -80 kJ/mol for G-C around -46 kJ/mol for A-T How can the energies of weak non-covalent interactions nearly match those of strong interactions?? J. Chem. Inf. Model. 2010, 50, 12, 2151. The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-pairing (-46 to -80 kJ/mol) Base-stacking (-16 to -61 kJ/mol) The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-pairing (-46 to -80 kJ/mol) Base-stacking (-16 to -61 kJ/mol)  The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-pairing (-46 to -80 kJ/mol) Base-stacking (-16 to -61 kJ/mol) In aqueous media, we must also consider the effects of water, in particular solvation energies Free energy STANDARD Gibbs free energy: ΔGº = ΔHº – T ΔSº -All reactants (including H+) at 1.0 M -1 atm pressure -25 ºC Free Energy Free energy STANDARD Gibbs free energy: A B ΔGº = ΔHº – T ΔSº ΔG > 0 → endergonic/unfavorable/ non-spontaneous Free Energy ΔG < 0 → exergonic/favorable/ spontaneous ΔG = 0 → equilibrium Free energy STANDARD Gibbs free energy: A B ΔGº = ΔHº – T ΔSº ΔH is the change in enthalpy in a reaction Free Energy ΔH > 0 → endothermic/requires heat ΔH < 0 →exothermic/releases heat Free energy STANDARD Gibbs free energy: A B ΔGº = ΔHº – T ΔSº ΔS is the change in entropy in a reaction Free Energy ΔS > 0 → order increases ΔS < 0 →order decreases Free energy STANDARD Gibbs free energy: A B ΔGº = ΔHº – T ΔSº In the context of macromolecular assembly: ΔH → electrostatic interactions (i.e. intermolecular forces) Free Energy ΔS → ordering of molecules (the macromolecules and water) The hydrophobic effect The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-pairing (-46 to -80 kJ/mol) Base-stacking (-16 to -61 kJ/mol) The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-pairing (-46 to -80 kJ/mol) ΔG = ΔH – T ΔS The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-stacking (-16 to -61 kJ/mol) ΔG = ΔH – T ΔS The physical basis for interactions How can the energies of weak non-covalent interactions nearly match those of strong interactions?? Base-pairing (-46 to -80 kJ/mol) Base-stacking (-16 to -61 kJ/mol) ΔG = ΔH – T ΔS