Samantha s Week 2 SI Sheet Amino Acids and Peptides Structures to know Amino acids nitrogenous bases Numbers to know 110 Daltons 50 20 000 aa 330 daltons 1 Draw an L alanine in a fischer projection CH3 l NH3 COO l H Remember proteins go from N C If you read it C N it is a completely different protein 2 Draw an L isoleucine in wedge dash form see your picture 3 One of these things is not like the other amino acid version a Valine Alanine Methionine Isoleucine a Answer Methionine because it has a sulphur The other three Valine Alanine and Isoleucine side chains are just alkyl groups and are nonpolar b Tyrosine Tryptophan Serine Histidine a Answer Serine Serine is the smallest The other three Tyrosine Tryptophan Histidine are large and have rings c Aspartic Acid Cysteine Histidine Lysine a Cysteine is the only amino acid with sulphur It is not charged and can be ionized but not at physiological pH The other 3 aspartic acid histidine and lysine act as acids bases d Tryptophan Glutamine Proline Arginine a Proline Proline does not belong since the alpha helix breaks its side chain can bind back to the alpha carbon Other three Tryptophan Glutamine Arginine all have nitrogen in their side chains Fill in the Chart things to know o polar vs nonpolar o reactivity special properties o pKa Y Tyr Tyrosine nonpolar OR polar R Arg Arginine positive physiological pH Basic pKa 12 5 W Trp Tryptophan nonpolar G Gly Glycine achiral R side chain H N Asn Asparagine polar D Asp Aspartic Acid acidic Pka 4 I Ile Isoleucine nonpolar E Glu Glutamic Acid Carboxylate group Acidic pKa 4 K Lys Lysine polar charged Basic pKa 11 Q Gln Glutamine polar How is a peptide bond formed How is it broken a peptide bond is an amide bond carbonyl amino groups It is broken via hydrolysis generally favorable process Why is it stable o Gibbs free energy is negative so bond formation is spontaneous It is kinetically unfavorable but hydrolysis is very slow for a peptide bond so the bond remains stable What are some physical features of a peptide bond Planar partial double bond character due to resonance Cis trans trans are more stable except for proline where both are equally favorable You cannot switch proline bonds because it is not energetically favorable to switch and break resonance bonds What happens when you change the primary structure of a protein You change the identity of the protein Changing structure changing folding changing function What kinds of bonds can you theoretically see between the side chains on a peptide Which do we actually see NH3 COO amide bond But this doesn t happen A peptide is mostly completely straight no branching Disulfide bonds S S cys cys SH HS redox reaction under oxidizing conditions Provides intra inter connections Mostly see these bonds outside the cell since the inside of the cell is a reductive environment It increases stability and the life of a protein Assess oxidation and reductive environment different structures functions in different environments How does protein rigidity or flexibility affect protein function Proteins often flexible change structure and function Good way of regulating proteins o Allosteric interactions Lactoferrose protein iron Iron must bind to protein to activate o Some proteins only on once they find a substrate