Chapter 21

1. Chapter 21 Proteins 4/15/09 Spider Silk, a fibrous protein. . .tough on bugs Not on you. . .(soft and smooth)

2. Proteins • Proteins many have functions: • 1.Structure: collagen and keratin are the chief constituents of skin, bone, hair, and nails. • 2. Catalysts: virtually all reactions in living systems are catalyzed by • proteins called enzymes. • 3. Movement: muscles are made up of proteins called myosin and actin. • 4. Transport: hemoglobin transports oxygen from the lungs to cells; other proteins transport molecules across cell membranes. • 5. Hormones: many hormones are proteins, among them insulin, • oxytocin, and human growth hormone.

3. Proteins 6. Protection: blood clotting involves the protein fibrinogen; the body used proteins called antibodies to fight disease. • 7. Storage: casein in milk and ovalbumin in eggs store nutrients for newborn infants and birds; ferritin, a protein in the liver, stores iron. 8. Regulation: certain proteins not only control the expression of genes, but also control when gene expression takes place. • Proteins are divided into two types: • 1. fibrous proteins (e.g. collagen, keratin) • 2. globular proteins (e.g. Hemoglobin)

4. Amino Acids  proteins • A.A.s contains amino group, carboxyl group, R group. R- group polarity Most imp. In Nature 20 alpha Amino acids exist (see table 21.1) : AKA α A.A.s b/c amino group is on the αcarbon

5. Chirality of Amino Acids • Except glycine, all protein-derived amino acids have at least one stereocenter (the α-carbon) and are chiral. • In Nature majority of protein-derived α-amino acids are in the L-form. • How do we know when/where it’s L vs D? NH3 on the “Left” in Fischer proj.

6. Chirality of Amino Acids • A comparison of the stereochemistry of L-alanine and D-glyceraldehyde (as Fischer projections):

7. See table 21.1 R-group polarity  classification: 1.Nonpolar (hydrophobic-repel H2O 2. Polar (hydrophillic) 3. Basic (hydrophillic) 4. Acidic (hydrophillic) Determines structure + function of protein

8. 20 Protein-Derived AA Red = R Groups, AKA Side Chains • Nonpolar side chains (at pH 7.0)

9. 20 Protein-Derived AA • Polar side chains (at pH 7.0) Red = R Groups, AKA Side Chains

10. 20 Protein-Derived AA • Acidic and basic side chains (at pH 7.0) Red = R Groups, AKA Side Chains

11. Zwitterions –molecules that have: • + charge on one atom • - charge on another atom Although amino acids commonly written in the un-ionized form, they are more properly written in the zwitterion (internal salt) form. COOH (Acid) donates H+ to NH2 (base)

12. Zwitterions ADD acid (decrease pH) what happens? ADD base (increase pH) what happens? When A.A.s have equal + & - charges aka: isoelectric point (pI)

13. Ionization vs pH • The net charge on an amino acid depends on the pH of the solution in which it is dissolved. • If we dissolve an amino acid in water, it is present in the aqueous solution as its zwitterion. • to summarize:

14. Isoelectric Point • Isoelectric point, pI: The pH at which the majority of molecules of a compound in solution have no net charge.

15. Cysteine • The -SH (sulfhydryl) group of cysteine is easily oxidized to an -S-S- (disulfide).

16. H2O Peptide named starting @ N-terminus (e.g. Gly-Ala, see Table 21.1) Peptides and Proteins • Formation of an amide The Peptide bond

17. Peptides • 1902, Emil Fischer proposed proteins are long chains of amino acids joined by amide bonds. • peptide bond: amide bond between the -carboxyl group of one amino acid and the -amino group of another. α

18. Writing Peptides • Start at left, beginning with the free -NH3+ group and ending with the free -COO- group on the right. • C-terminal amino acid: the amino acid at the end of the chain having the free -COO- group. • N-terminal amino acid: the amino acid at the end of the • chain having the free -NH3+ group.

19. Peptides and Proteins • What would this tri-peptide be called? Note: short chain A.A.s = peptides Longer chained 10-20 A.A.s = polypeptides > 30 A.A. chains = proteins (residues)

20. Other Amino Acids • Hydroxylation (oxidation) of proline, lysine, and tyrosine, and iodination for tyrosine, give these nonstandard amino acids.

21. Properties of peptides and proteins Note: R groups = AKA Side chains (See table 21.1, previous slides) 1. determine Chem. + phys. Properties acid base behavior = most imp. Know Which A.A.s: polar? Non polar? basic? acidic? ~ by LOOKING @ R-group

22. Tryptophan lysine Glutamic acid Determine the chemical nature of these A.A.s(i.e. R groups as Polar, Non polar, Basic or Acidic) serine Which is the only A.A. that forms di-sulfide bonds?

23. Peptides and Proteins • Proteins behave as zwitterions. • Proteins isoelectric point, pI. • At its pI, the protein has no net charge. • At higher pH (more basic) than its pI, has net (-)charge. • At lower pH (more acidic) than its pI, has net (+)charge. • Hemoglobin, almost equal number of acidic and basic side chains; its pI is 6.8. ~ 7 • Serum albumin has acidic side chains; its pI is 4.9. • Proteins are least soluble in water at their isoelectric points and can be precipitated from solution at this pH. Changing the pH changes “the Nature” of Protein,)

24. Denaturing a Protein Isoelectric point (pI) neutral Acidic solut. pH 2 (protonated) basic solut. pH 10 (deprotonated) NOTE: form/shape changes w/ pH change

25. Levels of Structure • Primary structure:the sequence of amino acids in a polypeptide chain; read from the N-terminal amino acid to the C-terminal amino acid. • Secondary structure:conformations of amino acids in localized regions of a polypeptide chain; examples are a-helix, b-pleated sheet, and random coil. • Tertiary structure:the complete three-dimensional arrangement of atoms of a polypeptide chain. • Quaternary structure:the spatial relationship and interactions between subunits in a protein that has more than one polypeptide chain. • See Hemoglobin next slide. . .

26. Structure(s) of Proteins