Proteins 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 NH3+ +1 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 Protonated Deprotonated picked up H+ lost H+ -NH2 + H+ = -NH3+ -NH3+ - H+ = -NH2 COO- + H+ = -COOH COOH - H+ = -COO-

Charge off AA at specific pH’s below IEP at IEP above IEP Lots some little [H+] [H+] [H+] positive neutral negative Fully protonated partially protonated deprotonated

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)

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

Charge of an AA at specific pH’s What is the charge of Isoleucine (Ile)at pH 4.0 pH 6.0 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 pH 2 pH 2.8 IEP pH 4 deprotonation of central Carboxyl 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 pH 4 protonation of R-side chain Amino group pH6 protonation of central Amino group pH 10.8 IEP 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.)

Warm-up: Draw Glu at pH 1 fully associated pH 3.2 IEP pH 4.0 aminogroup dissociates pH 5.0 R-side chain dissociates

16.4 Formation of Peptides

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 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….

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

Peptide Drawing Guide OH H CH3 CH2 Draw glycylalanylserine # of AA? 3 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

Finish by adding H/O to Peptide Backbone OH H CH3 CH2 H3N-C-C-N-C- C-N-C-COOH H O H H O H H Finish N/C terminus Add H to central carbon Add Carbonyl to Carboxyl carbon Add H to Nitrogen

Protein Synthesis in the body Transcription: copying the genome – nucleus Translation: translating genetic code into AA sequence – ribosomes in the cytoplasm

Protein Synthesis- a two step process: Transcription

Reading the code DNA contains protein code At the promoter of each gene, DNA Polymerase unwinds DNA. One strand ‘Template strand’ is copied (exons + introns) via complementary base pairing A-T, C-G → pre-mRNA Introns (non-coding sequences) are removed (Snurps) → mRNA mRNA

B. Translation

simple 2 min from AP bio shows speed realistic