1. Chapter Twenty Proteins

2. Roles of Proteins TypeExamples • Structural tendons, cartilage, hair, nails • Contractile muscles • Transport hemoglobin • Storage milk • Hormonal insulin, growth hormone • Enzyme catalyzes reactions in cells • Protection immune response

3. Roles of Proteins

4. Amino Acids • Proteins are polymers of amino acids • Contain a carboxylic acid group and an amino group on the alpha carbon • Side group R gives unique characteristics R side chain I H2N— C — COOH I H

5. Classifying Amino Acids • Nonpolar • An amino acid that contains a nonpolar side chain • R = H, CH3, alkyl groups, aromatic • Polar • An amino acid with a side chain that is polar but neutral • O ll R = –CH2OH, –CH2SH, –CH2C–NH2, (polar groups with –O-, -SH, -N-)

6. The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity.

7. The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity. (cont’d)

8. Classifying Amino Acids • Polar/Acidic • An amino acid that contains a second carboxyl group in its side chain • R = –CH2COOH, or -COOH • Polar/ Basic • An amino acid that contains a second amino group in its side chain • R = –CH2CH2NH2

9. The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity. (cont’d)

10. Essential Amino Acids • 10 amino acids not synthesized by the body • Arg, His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val • Must obtain from the diet • All in diary products • 1 or more missing in grains and vegetables

11. Fischer Projections of Amino Acids • All amino acids except glycine are chiral. • Amino acids have stereoisomers • In biological systems, only L amino acids are used in proteins D-Alanine L-Alanine L-Cysteine D-Cysteine

12. Designation of handedness in standard amino acid structures involves aligning the carbon chain vertically and looking at the position of the horizontally aligned NH2 group.

13. Zwitterions • Ionization of the –NH2 and the –COOH group • -COOH loses a proton (acid) • -NH2 gains a proton (base) • Zwitterion has both a + and – charge • Zwitterion is neutral overall NH2–CH2–COOHH3N–CH2–COO– glycine Zwitterion of glycine +

14. pH and Ionization H+ OH– + + H3N–CH2–COOHH3N–CH2–COO–H2N–CH2–COO– Positive ion zwitterion Negative ion Low pHneutral pHHigh pH In solution, at least three different forms of amino acids can exist: positive ion, zwitterion, and negative ion

15. pH and Ionization • Acidic amino acids such as aspartic acid have a second carboxyl group that can donate and accept protons • Amino acids with ionizable side chains have 4 forms in solution • -Cys, Tyr, Lys, Arg, His, Asp, Glu • Whether a group is ionized or not depends on its pKa • If pH > pKa, the group has been deprotonated • If pH < pKa, the group is protonated

17. Step-wise Ionization of Amino Acids • 1. Draw the amino acid in the fully protonated form • Low pH • All acid groups are protonated (-COOH) • All amino groups are protonated (-NH3+) • 2. Identify the protons that will come off (and the order in which they will come off) • 3. Take the protons off 1 by 1 • Example: Glutamic Acid

18. Ionization of Glutamic Acid • Draw the step-wise ionization of glutamic acid

19. HomeWork Assignment • What overall charge will the following amino acids have at pH 5.5? • Lysine • Phenylalanine • Glutamic Acid

20. Electrophoresis • Electrophoresis separates amino acids according to their charges • Positively charged amino acids move towards the negative electrode • Negatively charged amino acids move toward the positive electrode • Neutral amino acids will not move in either direction • Amino acids are visualized as separate bands on filter paper or thin layer plate

21. Electrophoresis

22. Peptide Bonds Amide bond formed by the carboxylate group of an amino acid and the –amino group of the next amino acid O CH3 + || + | NH3–CH2–COH + H3N–CH–COO– O CH3 + ||| NH3–CH2–C – N–CH–COO– | peptide bond H

23. Peptides • Peptide • A sequence of amino acids in which the amino acids are joined together through amide (peptide) bonds • Dipeptide • A peptide consisting of 2 amino acids • Tripeptide • A peptide consisting of 3 amino acids • Polypeptide • A peptide consisting of many amino acids

24. Peptides • Amino acids linked by amide (peptide) bonds GlyLysPheArgSer H2N- -COOH end Peptide bonds end Name: Glycyllysylphenylarginylserine C-terminus N-terminus

25. Protein Structure • A polypeptide containing 50 or more amino acids is called a protein • There are different ways to describe the structure of a protein: • Primary Structure • Secondary Structure • Tertiary Structure • Quaternary Structure

26. Secondary Structure: Alpha Helices • Three-dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape • Held by H bonds between the H of –N-H group and the –O of C=O of the fourth amino acid along the chain • Looks like a coiled “telephone cord”

27. Tertiary Structure • Specific overall shape of a protein • Results from cross-links between R groups of amino acids in chain disulfide –S–S– + ionic –COO– H3N– H bonds C=O HO– hydrophobic –CH3 H3C–

28. Levels of Protein Structure

29. Levels of Protein Structure A telephone cord has three levels of structure.

30. Primary Structure Human Myoglobin

31. Secondary Structure • Geometrical orientation of polypeptide chains • Two main kinds of secondary structure: • Alpha helices • Beta pleated sheets

32. Secondary Structure The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage.

33. Secondary Structure Two pleated sheet protein structure.

34. Secondary Structure Four representations of the helix secondary structure.

35. Secondary Structure The secondary structure of a single protein.

36. Tertiary Structure Four types of interactions between amino acid R groups produce the tertiary structure of a protein.

37. Tertiary Structure The tertiary structure of the single-chain protein myoglobin.

38. Disulfide Bonding Disulfide bonds involving cysteine residues can form in two different ways.

39. Human Insulin Human insulin, a small two-chain protein, has both intrachain and interchain disulfide linkages as part of its tertiary structure.

40. Substitutions in Insulin

41. Disulfides and Hair

42. A schematic diagram showing the tertiary structure of the single-chain protein myoglobin.

43. Quaternary Structure • Proteins with two or more chains • Quaternary structure is the relative organization of multiple chains to each other • Example is hemoglobin Carries oxygen in blood Four polypeptide chains Each chain has a heme group to bind oxygen A conjugated protein (has a prosthetic group)

44. Quaternary Structure Tertiary and quaternary structure of the oxygen-carrying protein hemoglobin.

45. Globular and Fibrous Proteins Globular proteins Fibrous proteins “spherical” shape long, thin fibers Water soluble Not water soluble Multiple Types of 2o structure 1 Type of 2o Structure Transport, Metabolism, etc. Strength, Protection More numerous Few in the body Insulin Hair Hemoglobin Wool Enzymes Skin Antibodies Nails

46. Fibrous Proteins The tail feathers of a peacock. Fibrous Protein is α-keratin PhotoDisc

47. Fibrous Proteins The coiled-coil structure of the fibrous protein alpha keratin.

48. Fibrous Proteins

49. Collagen Three helical peptide chains.

50. Collagen • Electron Micrograph Collagen fibers Prof. P.M. Motta & E. Vizza / Photo Researchers