1. Chapter 3: Amino Acids, Peptides, Proteins
HLY-JU-JS-CD

2. Amino Acids (AA) are the building blocks of peptides and proteins
Peptides generally contain 2-10 AA
Polypeptides contain AA
Proteins contain >100 AA
General structure of AA:
at pH ~7.4:

3. L-Amino Acids are the biologically relevant enantiomer

4. Of the 20 common AA, 10 of them are considered essential
see page 67 of your book

6. Of the 20 common AA, 10 of them are considered essential
see page 67 of your book
Mnemonics: MILK FTW RHV
“ESSENTIAL” = cannot be produced de novo by the body
Some AA are conditionally essential
Note though that there are now more than 20 AA! (but we will only focus on the 20)

7. Selenocysteine is a derivative of Cys used to derive protein structures

8. The 20 AA can be grouped according to functional classes
Aliphatic (GAVLIMP)
Aromatic (WYF)
Polar, uncharged (CHNQST)
Polar, charged – acidic (DE)
Polar, charged – basic (RK)
*Histidine is basic but uncharged
See structures on page 70 of your book.

9. There are 7 AA With Aliphatic Side Chains

11. Pro is an aliphatic AA with the amino and the acid group in one 5-membered ring

12. There are 3 AA with Aromatic Side Chains

13. Of the 6 polar uncharged AA, 2 have Hydroxyl Side Chains (except Tyr)

14. One AA has a Sulfhydryl (-SH) Side Chain

15. There are 3 AA With Basic Side Chains, 2 of them ccharged (RK)

16. Two AA have acidic side chains (DE)
Two AA have acidic side chains (DE). Their amide counterparts (NQ) are polar, uncharged

17. Chemical reactivity of AA are dependent on their “R group”
AA structures and reactivity will be important in understanding protein structures and functions
AA electric charges also affects protein structure and function

18. Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0

20. Isoelectric point (pI) of an AA (or peptide/protein) is equal to the pH when net charge = 0
pK1: -COOH  -COO- + H+
pK2: -NH3+  -NH2 + H+
pKR: -RH  -R- + H+

21. AA net charge is (-) if pH > pI, and (+) if pH < pI
pI is estimated to be the AVERAGE of the two pK values representing neutral species.

22. AA net charge is (-) if pH > pI, and (+) if pH < pI
CASE I: ONLY TWO IONIZABLE GROUPS:
Ex. Alanine:

24. AA net charge is (-) if pH > pI, and (+) if pH < pI
Case II: MORE THAN TWO IONIZABLE GROUPS. Ex. Aspartic Acid

26. Activity, open book/notes BUT no talking (20 points)
Determine the pI of Lysine. Show ALL conformations and the net charges at different pH’s.
Draw the titration curve for Lysine.
Determine the inflection points, and draw the structure/s of Lysine at each interval (i.e., before pK1, at pK1, after pK1 but before pK2, etc.)

27. AA can link together via AMIDE BOND to form peptides
Two ends are form: amino or N terminus and carboxyl or C terminus
Peptide formation is a condensation reaction (loss of H2O)

28. AA can link together via AMIDE BOND to form peptides
VIDEO!

29. Peptides are cleaved via hydrolysis
Acids, bases or enzymes can be used to facilitate the hydrolysis
In our stomach or intestine, peptidases or proteases are present
Enzymes specific to some AA are used for protein analysis (more of this later )

30. Proteins in our body play different important roles
Biological functions of proteins depend on the AA sequence (central dogma!)
Six major classes of protein functions:
Enzyme
Transport and Storage Proteins
Structural Proteins
Muscle Contraction and Mobility Proteins
Regulatory and Receptor Proteins
Immune or Defense Proteins

31. There are six major classes of functions of proteins
Catalysts (Enzymes)
Transport & Storage
The largest class of proteins, accelerate rates of reactions
DNA Polymerase
Catalase
CK2 Kinase
Ovalbumin
Ion channels
Hemoglobin
Serum albumin

32. There are six major classes of functions of proteins
Structural
Generate Movement
Collagen
Keratin
Silk Fibroin
Actin
Myosin

33. There are six major classes of functions of proteins
Regulation of Metabolism and Gene Expression
Protection
Insulin
Lac repressor
Thrombin and Fibrinogen
Immunoglobulin
Venom Proteins

34. Proteins have four levels of structure