CHAPTER 19

1. CHAPTER 19 AMINO ACIDS AND PROTEINS

2. The Importance of Proteins… • Many functions in the body! (supportive, enzymes, hormones, antibodies…) • Can be small or very large (hemoglobin: molar mass 64,000) • Composed of individual amino acids

3. A. Proteins and Amino Acids • Amino acid: the building block of a protein • Contain two functional groups: amino (-NH2) and carboxylic acid (-COOH) • At physiological pH, the carboxyl group and the amino group are usually ionized • There are 20 naturally occurring amino acids. The R group gives each its unique characteristics. • Based on R group, amino acids can be classified as nonpolar, polar, acidic, or basic.

4. 20 Amino Acids…

5. Now, let’s think. • The pI of cysteine is 5.1. Draw the predominant form of this amino acid at pH 1, and at pH 12. (you will have two different drawings!)

6. Proteins and Amino Acids • Except for glycine, all amino acids are chiral. • We can also write Fischer projections for amino acids -- just place the carboxyl group (the most highly oxidized carbon) at the top. • L isomer: amino group on the left • D isomer: amino group on the right • In biological systems, only L amino acids are incorporated into proteins.

7. B. Amino Acids as Acids and Bases • The form of the amino acid at physiological pH (with amino and carboxyl groups ionized) is called a zwitterion • For a given amino acid, there is a pH where the positive and negative charges are equal. This is called the pI -- isoelectric point. Here, the amino acid has a net charge = 0. • When the solution pH < pI, the -COO- group accepts a proton. • When the solution pH > pI, the -NH3+ group donates a proton.

8. Zwitterions and pI • For polar and nonpolar amino acids, the pI is typically in the pH 5.0-6.0 range. • For acidic amino acids, the pI is around pH 3 due to the presence of a carboxyl group in the side chain • For basic amino acids, the pI is in the pH 7.6-10.8 range due to amino groups in the side chain

9. Electrophoresis • A method to separate a mixture of amino acids (also used to separate mixtures of proteins and nucleic acids) • Place a mixture of amino acids in the center of a chamber between a positive and negative electrode. Start an electric current. • Amino acids with zero net charge will not move; those with a positive charge will migrate toward the negative electrode; those with a negative charge will migrate toward the positive electrode.

10. An Electrophoresis Setup

11. C. Formation of Peptides • Peptide: two or more amino acids linked together • Peptide bond: amide bond between the -COO- of one amino acid and the -NH3+ of another amino acid • In a long peptide chain, one end is called the N terminal, and the other end is called the C terminal

12. Peptide Bond Between Gly and Ala

13. Naming Peptides • Starting with the N terminus… name each amino acid in sequence with a -yl ending. • Until you get to the amino acid at the C terminus, and you use the full name of that amino acid. • Example: alanylglycylserine However… we typically use 3 letter abbreviations out of convenience (Ala-Gly-Ser)

14. D. Protein Structure: Primary and Secondary Levels • Larger peptides are called proteins (usually >50 amino acids) • Primary structure refers to the sequence of amino acids in a protein. • The secondary structure refers to the first level of folding. The primary structure curls back in upon itself, initially in a few very regular patterns. The most common types of secondary structure = alpha helix, beta-pleated sheet, and triple helix. • Secondary: hydrogen bonds between backbone

15. Alpha helix

16. Beta pleated sheet

17. E. Protein Structure: Tertiary and Quaternary Levels • Tertiary structure: additional folding above and beyond that of secondary structure. May involve: • Hydrophobic interactions between nonpolar R groups • Hydrophilic interactions between polar/ionized R groups and aqueous environment • Salt bridges between ionized basic/acidic R groups How might a change in pH affect this? • Hydrogen bonds between polar amino acid R groups • Disulfide bonds between R groups that contain sulfur (cysteine)

18. Tertiary Structure in a Protein

19. Protein Structure • Quaternary structure: protein consisting of two or more peptide subunits • Example: hemoglobin -- two alpha chains, two beta chains. Four chains all together. • Quaternary structure is held together by the same forces that hold tertiary forces together.

20. An Example of Quaternary Structure

21. Overview: Levels of Protein Structure

22. Thought question… What kind of interaction would you expect between a glutamic acid and a lysine, in the tertiary structure of a peptide?

23. F. Protein Hydrolysis and Denaturation • A protein or peptide can be hydrolyzed into individual amino acids. (This is what happens in the stomach…) • Denaturation occurs when secondary, tertiary, or quaternary structure is disrupted. Primary structure is not affected. The protein unfolds “like a loose piece of spaghetti”.

24. Denaturation • How do various denaturing agents work? • Heat breaks hydrogen bonds • Acids/bases protonate/deprotonate key areas, affecting hydrogen bonding and disrupting any ionic bonding • Organic compounds destroy hydrophobic interactions by forming their own hydrophobic interactions with the protein • Heavy metals disrupt ionic bonding and disrupt disulfide bonds • Agitation stretches polypeptide chains

25. Denaturation

26. One more time… let’s think What structural level of a protein is affected by denaturation? How is this different from the structural level of a protein affected by hydrolysis?