2-Lecture_5

2-Lecture_5 - BCHM 561 Chapter 2 PROTEIN COMPOSITION AND...

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Unformatted text preview: BCHM 561 Chapter 2 PROTEIN COMPOSITION AND STRUCTURE Friday, September 5, 2008 1 Chapter 1 Section 1.4 - Genomics & Biochemistry Read this section but it will not be covered in lecture Read Appendix on the Visualization of Small Molecule Structures Friday, September 5, 2008 3 Previous Lecture Noncovalent interactions involved in the formation of the DNA double helix Acid-Base Equilibria and the Henderson-Hasselbalch Equation Friday, September 5, 2008 4 Acetic acid titration - Friday, September 5, 2008 5 Henderson-Hasselbalch equation pH = pH = pKa + log([ A ] /[HA]) pH " pKa = rearranged pH " pKa = log([ A ] /[HA]) 10 pH " pKa 10 " pKa pH " pKa + log([ A ] /[HA]) " " log([ A ] /[HA]) " = = [ A ] /[HA] " [ A ] /[HA] " Friday, September 5, 2008 6 Tris buf fer tris(hydroxymethyl)aminomethane OH HO NH3 OH HO OH OH NH2 + H+ pKa 8.06 Friday, September 5, 2008 7 pKa 8.06 12 11 HO OH OH NH2 10 9 pH 8 7 6 5 4 0 HO NH3 OH OH 0.2 – OH 0.4 0.6 0.8 1.0 equivalents 8 Friday, September 5, 2008 H3PO4 pKa = 2.15 pKa = 6.82 pKa = 12.38 PO43– HPO42– H2PO4– H3PO4 Friday, September 5, 2008 9 Proteins • • • • • • • • linear polymers (not branched) monomeric units are amino acids amino acids are linked together by peptide bonds 20 dif ferent amino acids peptides (2 to ~10 amino acids) oligopeptides (>3 up to 20-30 amino acids) polypeptides (<100 amino acids) proteins (>100 amino acids) 10 Friday, September 5, 2008 with 20 dif ferent amino acids there can be tremendous diversity among proteins with n residues there can be 20n different protein sequences with 100 residues there can be 100 = 10130 different proteins 20 total mass would be 10134 daltons mass of observable universe is 1080 daltons 300 20 = 390 different 10 proteins 11 Friday, September 5, 2008 General structure of an α-amino acid O R NH3 O Friday, September 5, 2008 12 Peptide Bond Formation Reaction does not occur at pH~7 peptide bond Friday, September 5, 2008 13 random coil fibrous protein globular protein Friday, September 5, 2008 14 Amino acids contain a chiral carbon (asymmetric)-stereoisomers enantiomers-mirror images of each other Friday, September 5, 2008 15 symmetric molecule Friday, September 5, 2008 16 enantiomers Friday, September 5, 2008 17 diastereomers (non-mirror images) Friday, September 5, 2008 18 Biochemists use D,L system for designating stereoisomers Friday, September 5, 2008 19 Numbering convention O Lysine H3N 6 5 ε δ 4 3 γ β 2 1 α O NH3 O β HO α O Serine NH3 Friday, September 5, 2008 20 Amino acids are zwitterions or dipolar 2 charged groups at neutral pH +1 pKa ~ 2 0 pKa ~ 9 -1 Friday, September 5, 2008 21 LEARN THE STRUCTURE OF ALL 20 AMINO ACIDS Friday, September 5, 2008 22 48 Friday, September 5, 2008 3 Å 67 3 Å 23 Aliphatic Amino acids 105 Friday, September 5, 2008 3 Å 124 3 Å 124 3 Å 124 3 Å 24 Cyclic Ring- α-amino group and α-carbon 90 Friday, September 5, 2008 3 Å 25 ...
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