Tips for Your Preparation of the 1st Mid term Exam 1 How to make a buffer and adjust the buffer pH 2 How to making a buffer with an amino acid with a known side chain pKR How to draw a titration curve to determine pKa 3 How to draw the steric structure of each of the four ribonucleotides and four deoxynucleotides short double stranded DNA oligomers and short double stranded RNA oligomers 4 How to draw the steric structure of each of the 20 common amino acids L and D conformers and short peptides 5 How to calculate the charge of a peptide under a buffer pH What stabilizes protein secondary and tertiary structure Know how to draw the steric structure of a parallel or anti parallel beta sheet 7 Understand protein folding and unfolding O2 binding proteins and structural proteins 6 Read and understand my slides and the textbook Study recitations and quizzes answer keys Study sample exams Water as a Molecule Two Alternative Views An electron from hydrogen is shared with one from oxygen Oxygen has lone pairs Space Filling Tetrahedral sp3 orbitals Donors and Acceptors A molecule can be both a hydrogen bond donor and acceptor Acceptor provides lone pair Donor donates proton Acceptor provides lone pair Hydrogen bonds to other groups N O are good acceptors in biomolecules Nucleic Acids DNA RNA Nucleotide Monomers bases in DNA or RNA Phosphodiester linkage But plentiful Proteins Water as solvent Nonpolar Solutes No hydrogen bonds available with solute Water maximizes H bonds to itself forming a highly ordered water cage Water cage has a huge entropic cost and is extremely important for proper protein folding and the formation of cellular membranes Hydrophobic effect pH and Buffers Biochem 4511 Figures Essentials of Biochemistry 3rd Ed OSU Custom Edition Lehninger Principles of Biochemistry 5th Ed Nelson Cox Fundamentals of Biochemistry 2nd Ed Voet Voet Pratt The Henderson Hasselbalch Equation Ka HA H A and Ka H A HA H Ka HA A log H logKa log HA A pH pKa log A HA The Henderson Hasselbalch Buffer equation The Henderson Hasselbalch Equation The Henderson Hasselbalch Equation is true only for weak acids and bases in an aqueous environment pH pKa log A HA Use when you know pKa and A HA but not pH Rearrange A HA 10pH pKa Use when you know pH and pKa but not A and HA Determining pH Weak Acids What is the pH of a 2 L aqueous solution which contains 10 mL of 5 M acetic acid 10 mL of 1 M sodium acetate For a weak acid like acetic acid we can use the Henderson Hasselbalch equation 1 Determine concentrations A and HA 2 Substitute these concentrations into the equation pH pKa log A HA See also sample calculations 2 2 2 3 Determining pH Weak Acids What is the pH of a 2 L aqueous solution which contains 10 mL of 5 M acetic acid 10 mL of 1 M sodium acetate 1 A 5 mM and HA 25 mM 2 Substitute these concentrations into the equation pH pKa log pH 4 76 log A HA 5 25 pH 4 76 7 pH 4 06 Polyprotic Acids Phosphate Some important biological buffers have multiple ionization states Buffers Problem 1 Determine the initial amount of HA and A in the solution HA A 5 x 10 3 moles 2 Determine how the addition of strong acid and base will change these concentrations If we add 10 L of 1 M HCl it will dissociate completely H will react with A to generate HA HA HA 0 H A A 0 H H generated by 10 L of 1 M HCl 1 x 10 5 mol New HA 5 x 10 3 mol 1 x 10 5 mol 5 01 x 10 3 mol New A 5 x 10 3 mol 1 x 10 5 mol 4 99 x 10 3 mol Buffers Problem 1 Determine the initial amount of HA and A in the solution HA A 5 x 10 3 moles 2 Determine how the addition of strong acid and base will change these concentrations HA 5 01 x 10 3 moles A 4 99 x 10 3 moles 3 Use Henderson Hasselbalch equation to figure out the pH change pH pKa log A HA log A HA log 4 99 x 10 3 5 01 x 10 3 0 0017 pH units Why spend so much time on pKa 1 Buffers are essential in life see section 2 10 2 Buffers are essential in the biochemical laboratory 3 You need an intuitive understanding of how pKa relates to ionization state of an acid base to understand concepts Electrostatic interactions in protein structure Protein nucleic interactions Role of amino acid side chains in enzymatic reactions pKa 6 0 Ionization of Histidine Simple Stock Solutions NaCl Extra How would you prepare 1 L of a 5 M NaCl solution The molecular weight of NaCl is 58 44 g mol Molarity M mol L Molecular Weight MW g mol We need to calculate how much NaCl to add to reach the desired concentration and volume 58 44 g mol x 5 mol L x 1 L 292 2 g Nucleic Acids Biochem 4511 Chapter 3 Figures from Essentials of Biochemistry 3rd Ed OSU Custom Edition Lehninger Principles of Biochemistry 4th 5th Ed Voet Voet Biochemistry 3E Voet Voet Pratt Fundamentals of Biochemistry 2E PURINES Bases Adenine Guanine Same bases rotate 180 PYRIMIDINES DNA Bases PYRIMIDINES RNA Cytosine Uracil Nucleotides Most often 5 phosphate Nucleic Acids Default 5 3 Individual nucleotide formally called a residue Phosphodiester bond Dinucleotide 2 nucleotides Trinucleotide 3 nucleotides Oligonucleotide many Watson Crick Pairings Major Groove Minor Groove Forces in DNA base stacking Bases in double helix are stacked Distance between bases is 3 4 same size as predicted by van der Waals interactions stacking DNA double helix can be denatured Monitoring DNA structure UV detection Hyperchromic effect Environment of the base affects UV absorbance Implications of Hydrogen Bonding Don t memorize numbers but be able to predict pattern Ring pucker don t memorize this DNA RNA Ribose is puckered 2 hydroxyl changes conformational preferences DNA vs RNA Other nucleic acid double strand helices Don t need to memorize this What does it mean to go from genes to proteins Central dogma simple view Genes are sequences of DNA Replication copying DNA Transcription converting DNA into RNA Reverse transcription converting RNA into DNA Translation making proteins from an RNA template Transcription Translation Translation tRNA Aminoacylation covalently link amino acid Anticodon which amino acid Translation Genetic Code Codon Chart Pyrrolysine encoded by UAG Do not memorize Amino Acids Biochem 4511 Figures Essentials of Biochemistry 3rd Ed OSU Custom Edition Principles of Biochemistry 5th Ed Moran et al Lehninger Principles of Biochemistry 5th Ed Nelson Cox Fundamentals of Biochemistry 2nd Ed Voet Voet Pratt 20 Common or Natural AAs A Ala Alanine F Phe Phenylalanine K Lys Lysine P Pro Proline T Thr Threonine C Cys Cysteine G Gly Glycine L Leu Leucine Q Gln Glutamine V Val Valine
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