1. Chapter 24-2: Introduction to Polymers and Biopolymers
General Definitions
Drawing Polymers (short-hand method)
Examples of manufactured and natural polymers
Unintended consequences of polymers from non- renewable feedstocks
Biopolymers: Proteins from Amino Acid Monomer Units
Amino acid structure, chirality, R-groups
Amino acid pKa values of acidic groups
Peptide structure based on pKa and pH

2. The Common Amino Acids
20 amino acids are all -amino acids. The -amino and - carboxyl are connected to the same -carbon.
They differ by the substituent attached to the -carbon, called the side chain (R group), with H as the fourth substituent (except for proline).
The -carbons of 19 of the 20 amino acids are chiral centers (for glycine the R group is H, so the a-C is achiral).

3. Biopolymers from Amino Acids
Individual amino acid monomers (called residues) are linked together by the a-amino group and a-carboxyl group to form the amide bond (peptide bond) in peptides and proteins.
Peptides are written left-right (N-C), with the N-terminal amino acid (free a-NH2 group) on the left and the C-terminal amino acid (free a-CO2H group) on the right.
The amino acid sequence of peptides and proteins is referred to as the 1o structure.
The field of Biochemistry studies the structural, physiological, and catalytic chemistry of proteins.

4. Types of Amino Acid Side Chains (R-groups)
Depending on the R group, an amino acid can be Neutral, Acidic, Basic, or Nucleophilic.
Neutral: Fifteen of the twenty have neutral side chains
Asp and Glu have a second COOH and are acidic
Lys, Arg, His have additional basic amino groups side chains (the N in tryptophan is a very weak base)
Cys, Ser, Tyr (OH and SH) are good nucleophiles
The next slides provide information on amino acid structure, 3-letter abbreviations, R-group classification, and pKa values of acidic groups.

5. Amino Acids - Neutral R Groups

6. Amino Acids - Acidic R Groups

7. Amino Acids – Basic R Groups

8. Amino Acids - Unusual R Groups

9. Amino Acids - Non-Polar R Groups: Alkyl Groups

10. Amino Acids - Non-Polar R Groups: Aromatic Groups

11. pH, pKa & Amino Acid Acid/Base Structure
The aqueous pH will determine the structure of an amino acid which can effect biological activity.
What is the acid/base structure of the amino acid Lysine at physiological pH? (~pH 7.4)

12. Acid/Base Structure of Lysine at pH 7.4
If the pH > pKa for a specific acidic functional group, this group is said to be in a basic environment, and will exist in its basic form (Conjugate Base).
If the pH < pKa for a specific acidic functional group, this group is said to be in an acidic environment, and will remain in its acid form.
pKa 2.2
pKa 10.7
pKa 9.2
Structure of Lysine at pH 7.4:

13. Example: What is the acid/base structure of the tripeptide ala-cys-glu at pH 9?
1) Draw the tripeptide of the amino acids alanine, cysteine and glutamic acid. Ala is N-terminal and Glu is C-terminal.
2) Verify the peptide structure above. You should label all three amino acids, the N and C terminal groups, chiral a-C’s, the peptide bonds, and R groups.

14. Example: What is the acid/base structure of the tripeptide ala-cys-glu at pH 9?
3) Label the acid groups with the proper pKa values. You need to label the N-terminal a-amino group, the C-terminal a-carboxyl group, and all acidic R groups.
pKa 4.2
pKa 9.7
pKa 2.2
pKa 8.1

15. Example: What is the acid/base structure of the tripeptide ala-cys-glu at pH 9?
Structure of Functional Groups depends on pH:
pH>pKa…functional group is in its base form
pH<pka…functional group is in its acid form.

16. Summary 24-2 Based on this video you should be able to:
Identify specific amino acids based on name, three-letter code, and R-group (using provided tables).
Take a peptide and identify the amino acid residues, the N and C terminal groups, chiral a-C’s, the peptide bonds, and R groups.
Given the 1o sequence of a peptide, be able to draw the 3D peptide structure with the correct N and C terminal groups.
Given a peptide structure, be able to label all acidic groups with their correct pKa values (N-terminal a-amino group, the C-terminal a-carboxyl group, and all acidic R groups).
Be able to draw the correct acid/base structure of a peptide given the aqueous pH environment.