16.3 Rx of Amino Acids

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 Net charge 0 Fill the IEP into your AA sheet….

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-

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

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

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

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

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.)

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.)

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

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!

Glycine + Alanine: Alanine + Glycine:

Naming Short Peptides N-terminal AA and center AA: Replace –ine with –yl C-terminal AA name stays same Example: GlycylValylAlanine 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….

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

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

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

Protein Synthesis- a two step process A. Transcription

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

B. Translation

simple 2 min from AP bio shows speed realistic