1. Proteins
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
Amino group is NH
Net charge
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 Protonated Deprotonated picked up H+ lost H+ -NH2 + H+ = -NH3+ -NH3+ - H+ = -NH2 COO- + H+ = -COOH COOH - H+ = -COO-

4. 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

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 ≈ (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
pH= 3.5
pH= 6.0
pH= 8.6

7. 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

8. 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.)

9. 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.)

10. 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

11. 16.4 Formation of Peptides

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

13. 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!

14. Glycine + Alanine:
Alanine + Glycine:

15. 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….

16. 1o Structure of Peptides
Beginning and end: N- and C-Terminus
Peptide backbone: central core of peptide bonds:
NCCNCCN…..

17. 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

18. Finish by adding H/O to Peptide BackboneOH
H CH 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

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

20. Protein Synthesis- a two step process: Transcription

21. 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

22. B. Translation

23. simple 2 min from AP bio shows speed realistic