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Chapter 24-2: Introduction to Polymers and Biopolymers

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

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Chapter 24-2: Introduction to Polymers and Biopolymers

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  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 onamino acid structure, 3-letter abbreviations,R-group classification, and pKa values ofacidic 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.

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