Configuration vs. Conformation. Configuration: Covalent bonds must be broken. Two kinds of isomers to consider

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1 Stereochemistry onfiguration vs. onformation onfiguration: ovalent bonds must be broken onformation: hanges do NT require breaking of covalent bonds onfiguration Two kinds of isomers to consider is/trans: substituents in different positions in relation to double bond Maleic acid (cis) Fumaric acid (trans) 1

2 onfiguration Two kinds of isomers to consider Stereoisomers: substituents differ in placement around a chiral center onformation?? onformation: hanges do NT require breaking of covalent bonds - only rotation about a single bond! EX. Would Lysine act the same way in a protein binding site in different conformations? 2

3 Amino Acid Stereochemistry D-glyceraldehyde L-glyceraldehyde D-amino acid L-amino acid May 7 th, 2008 Recitation MBioS 303 Summer

4 Today s Brief Review Topics ydrophobic effect The ydrophobic Effect ΔG = Δ -TΔS Berg, Tymoczko and Stryer: Biochemistry, 5 th Ed. 2002, W Freeman and o. 4

5 Today s Main Topics Amino acids Acid/base calculations Effect of chemical environment on substituents reminder ydropathy index Amino Acid charge, movement in electric field, pi Naming a peptide, calculating charge Protein Structures: 1⁰, 2⁰, 3⁰, 4⁰ Bond rotation in a peptide α-helices, β-strands Amino Acids 5

6 Acid/Base and Net harge Info Understand conceptually what the approximate percentage of acid or base form is at p = pk a +/- 1 and +/- 2 Know how to calculate net charge at these pk a values Each ionizable group on an amino acid will require separate calculations!! EXAMPLE: Worked on whiteboard ydrophobic Amino Acids (7) ydropathy index: Would you predict it to be negative or positive?

7 harged Amino Acids (4) ydropathy index: Would you predict it to be negative or positive? Polar Amino Acids (8) ydropathy index: Would you predict it to be negative or positive? (Any exceptions?)

8 Effect of hemical Environment Is solvent p important? ow might a change from p 2 to p 12 affect an amino acid? an cause protonation or deprotonation of carboxyl, amine and dissociable R groups 8

9 ow can you predict this? Each substituent has a known pka value, which tells you about the tendency of a proton to dissociate Below the known pka, the substituent will be protonated Above the known pka, the substituent will be de-protonated EXAMPLE: pka - ~2.3, pka N 3+ ~9.6 p 1.5 ~ p 2.3 p 7 ~ p 9.6 p 11 Berg, Tymoczko and Stryer: Biochemistry, 5 th Ed. 2002, W Freeman and o. Example Problem A ❶ B ❹ ❷ ❺ ❻ ❸ What is the name of amino acid A? Amino Acid B? Would groups 1-6 be protonated or depronated at p 7? What would be the charge on each group at p 7? n the entire amino acid? 9

10 Example Problem A ❶ B ❹ ❷ ❺ ❻ ❸ Which direction would amino acid A move in an electric field (towards the positive or negative pole)? Amino acid B? Given: pi A = 9.74, pi B = If the p of the gel was 9.74, which way would A move? If the p was 3.22, which way would B move? Peptides an you name the peptide below? Which direction do you write the name? Which resides have ionizable side chains? 2 N N N N N N N 2 10

11 Peptides What would be the total charge on the peptide at p = 7? 2 N N N N N N N 2 harge = NET ARGE = 0 + (-1) (-1) = -1 Peptides ow many peptide bonds are in this peptide? Which bonds in the backbone would allow free rotation? 2 N N N N N N N 2 11

12 Questions??? 12