1. 16.3 Rx of Amino Acids

2. Isoelectric Point pH where AA is a Zwitterion and overall neutral: positive and negative charges equal each other out. Carboxyl is COO - -1 Amino group is NH 3 + +1 Net charge 0 Fill the IEP into your AA sheet….

3. Protonation Carboxyl and amino groups are sensitive to pH. pH determines if they take up a H+ -protonation Or lose a H+ - deprotonation ProtonatedDeprotonated picked up H+lost H+ -NH2 + H+ = -NH 3+ -NH 3+ - H+ = -NH2 COO- + H+ = -COOH COOH - H+ = -COO-

4. Charge off AA at specific pH’s below IEP at IEP above IEP Lots somelittle [H+] [H+] [H+] positive neutral negative Fully protonated partially protonateddeprotonated

5. IEP pH ranges Polar neutral and non-polar AA: IEP 5 - 6 Acidic AA: IEP ≈ 3 (higher [H+] keeps sidechain protonated as COOH Basic AA: IEP ≈ 7.0-11.0 (lower [H+] prevents sidechain from protonation, stays NH2)

6. Practice Draw the protonated/deprotonated forms of the Amino acid Valine at the following three pH’s a. pH= 3.5 b. pH= 6.0 c. pH= 8.6

7. Charge of an AA at specific pH’s What is the charge of Isoleucine (Ile)at a. pH 4.0 b. pH 6.0 c. pH 10 IEP (Ile) = 6.0 (non-polar AA) Means it’s neutral at exactly pH=6! a.pH 4: Positive +1 b.pH 6.0: Neutral 0 c. pH10: Negative -1

8. Acidic AA at different pH’s What is the charge of Aspartic Acid (Asp) at a. pH 2 b. pH 2.8 IEP c. pH 4 deprotonation of central Carboxyl d. pH 6 deprotonation of R-side chain Carboxyl Answer: a.pH 2: positive +1 (Carbox prot, Aminogrp prot) b.pH 2.8: neutral (Carbox deprot, Aminogrp prot.) c. pH 4: negative -1 (Carbox deprot, Amino grp deprot.) d. pH6: negative -2 (Carbox deprot, R-side chain deprot, Aminogrp. Deprot.)

9. Basic AA at specific pH’s What is the charge of Arginine (Arg)at a. pH 4 protonation of R-side chain Amino group b. pH6 protonation of central Amino group c. pH 10.8 IEP d. pH 14 Answer: Means it’s neutral at exactly pH=10.8! a.pH 4: Positive +2 (both amino groups are protonated!) b. pH 6: Positive +1 (central amino grp protonated) b.pH 10.8: Neutral (amino group protonated/carboxyl deprot.) c. pH14: Negative -1 (amino group and carboxyl both deprot.)

11. Peptide bonds Carboxyl and Amino- groups react in a Dehydration Rx

12. Peptide Bond Formation of an Amide called a Peptide bond Formation of a Dipeptide Order of AA is important!!! Example: Gly–Ala not the same as Ala-Gly!

13. Glycine + Alanine: Alanine + Glycine:

14. Naming Short Peptides N-terminal AA and center AA: Replace –ine with –yl C-terminal AA name stays same Example: GlycylValylAlanine 1. 2. 3. Name reflects number and order of AA Defines structure and function Name all the other possible versions of how Gly, Val, Ala can be linked together….

15. 1 o Structure of Peptides Beginning and end: N- and C-Terminus Peptide backbone: central core of peptide bonds: NCCNCCN…..

16. Peptide Drawing Guide Draw glycylalanylserine 1. # of AA? 3 2. Draw Peptide backbone: 3 x N-C-C N-C-C-N-C-C-N-C-C 3. Attach R-side chains to respective central carbon OH H CH3 CH2 N-C-C-N-C-C-N-C-C

17. Finish by adding H/O to Peptide Backbone OH H CH3 CH2 H 3 N-C-C-N-C- C-N-C-COOH H O H H O H H a. Finish N/C terminus b. Add H to central carbon c. Add Carbonyl to Carboxyl carbon d. Add H to Nitrogen

18. Protein Synthesis- a two step process A. Transcription

19. Reading the code Protein code is on the DNA (nucleus eukaryotes) DNA Polymerase unwinds DNA and copies only one strand (Template strand)

20. B. Translation

21. simple 2 min from AP bio shows speed realistic