Chem 150 Unit 10 - Biological Molecules III Peptides, Proteins and Enzymes

1. Chem 150Unit 10 - Biological Molecules IIIPeptides, Proteins and Enzymes • Proteins are the workhorses in living systems. Their many roles include providing structure, catalyzing nearly all the reactions that take place in a living cell, transporting and storing materials, and controlling and defending living systems. Like carbohydrates, proteins are polymers, but unlike the polysaccharides, proteins are able to assume a much wider range of 3-dimensional structures and a functions. In this unit we will focus on one the of the most important functions of proteins; that of biological catalysts (enzymes).

2. Amino Acids • α-Amino acids are the building blocks (monomers) for polypeptides and proteins. • Every amino acid contains, • A carboxylic acid group • An amino group • A side chain (R)

3. Amino Acids • Back in Unit 7 we saw that carboxylic acids behave as acids when dissolved in water.

4. Question (Clickers) (Unit 7) • At pH 7, which will be the predominant species? • Carboxylic acid • Carboxylate ion pKa ≈ 5 carboxylic acid carboxylate ion

5. Carboxylic Acids & Phenols as Weak Acids (Unit 7) • At pH 7, the carboxylate ion of carboxylic acids predominate • At pH = pKa • At pH < pKa • At pH > pKa pH = 7 pKa ≈ 5

6. Amino Acids • Back in Unit 7 we also saw that amines behave as bases when dissolved in water.

7. Amines as Weak Bases (Unit 7) • Like ammonia, 1°, 2° and 3°, act as Brønsted-Lowry bases.

8. Amines as Weak Bases (Unit 7) • The conjugate acids are called ammonium ions • When placed in water, these ammonium ions will behave like acids.

9. Amino Acids Net charge • At pH 7, amino acids are in their zwitterionic form. • There is no pH value at which there are no charges on an amino acids. • However, there is a pH value at which the net charge is zero. • This pH value is called the isoelectric point. +1 0 -1

10. Amino Acids • There are 20 different sidechains for the amino acids that are used to build proteins. • These are classified according to their physical properties as • Non-polar • Polar acidic (negatively charged at pH 7) • Polar basic (positively charged at pH 7) • Polar neutral (polar, but not charged at pH 7)

11. Amino Acids • Non polar sidechains • Most of these sidechains are hydrocarbons

12. Amino Acids • Polar acidic sidechains • Sidechains contain carboxylic acids • Negatively charged at pH 7

13. Amino Acids • Polar basic sidechains • Sidechains contain amines • Positively charged at pH 7

14. Amino Acids • Polar neutral sidechains • Sidechains contain polar groups that are capable of hydrogen bonding • alcohols • phenols • amides • Uncharged at pH 7

15. Amino Acids • For all of the amino acids, except one (glycine), the α-carbon is chiral. • Fisher projection of the amino acids alanine: • With few exceptions, only the L-amino acids are used to make proteins.

16. Peptides, Proteins, and pH • Amino acids are joined together to form polymers of amino acids called oligopeptides (2-10 amino acids) and polypeptides (more than 10 amino acids). • Collectively, oligopeptides and polypeptides are called peptides. • The amino acids are joind together by an amide bond called a peptide bond, which is analogous to the glycosidic bond found in oligosaccharides and polysaccharides. • Back in Unit 7 we saw how carboxylic acids can react with ammonia and amines to form amides.

17. Amides (Unit 7) • When a carboxylic acid reacts with an amine it also produces and ammonium salt • If the ammonium salt is then heated, an amide is produced.

18. Amides (Unit 7) • Amides are important in biochemistry. • For example, amino acids are connected together to form proteins using amide groups. amino acid

19. Peptides, Proteins, and pH • Peptide bond formation Peptide Bond Dipeptide

20. Peptides, Proteins, and pH • The amide bond that connects the amino acids together in a peptide is called a peptide bond. • Proteins are long polypeptide chains, usually with 50 or more amino acids, which fold into a well defined structure. The proteinubiquitin

21. Peptides, Proteins, and pH • Proteins are sensitive to the pH because they contain numberous acid and base groups • The pH affects the charge on a proteins, which in turn, can have a marked effect on a protein’s structure and function.

22. Peptides, Proteins, and pH • Example • The charges on the tripeptideLys-Ser-Asnas a function of pH. Net Charge +2 0 -2

23. Peptides, Proteins, and pH • Example • The charges on the tripeptideLys-Lys-Alaas a function of pH. Net Charge +3 +2 -1

24. Peptides, Proteins, and pH • Amino acids with acid or base side chains have additional charge groups: • e.g. Glutamic acid is an acid amino acid • At pH’s below the isoionic point (pI) the charge is positive • At pH’s above the isoionic point (pI), the charge is negative pI = 3.2

25. Peptides, Proteins, and pH • Amino acids with acid or base side chains have additional charge groups: • e.g. Lysine is a basic amino acid • At pH’s below the isoionic point (pI) the charge is positive • At pH’s above the isoionic point (pI), the charge is negative pI = 9.7

26. Charges at different pH values pH 1 pH 7 pH 14 Acids A Include: α-COOH Asp sidechain Glu sidechain 0 -1 -1 Bases B Includes: α-NH2 His sidechain Lys sidechain Arg sidechain +1 +1 0 Peptides, Proteins, and pH • We are going to simplify the determination of charge as a function of pH by looking only at pH 1, pH 7, and pH 14:

27. Question • At pH 7, which of the following amino acids have a net positive charge, which have a net negative charge, and which are neutral? • Lysine • Phenylalanine • Leucine

28. Charges at different pH values pH 1 pH 7 pH 14 A α-COOH 0 -1 -1 B α-NH2 +1 +1 0 B Lys sidechain +1 +1 0 Net +2 +1 -1 Question • Lysine B A B

29. Question • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14.

30. Question • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14. Draw the backbone

31. Question • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14. Add the sidechains and identify the acids (A) and bases (B) A B A A

32. A B A A Question • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14. At pH 1, Acids (A) are 0 and Bases (B) are +1 Net Charge = +1 at pH 1

33. A B A A Question • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14. At pH 14, Acids (A) are -1 and Bases (B) are 0 Net Charge = -3 at pH 14

34. Protein Structure • Proteins are polypeptides that fold to adopt a well-defined, three-dimensional structure. • There two general classifications of proteins • Fibrous proteins exist as long fibers that are usually tough and insoluble in water; examples include • collagen (skin and bones) • Keratin (hair) • Globular proteins are spherical, highly folded, and usually soluble in water; examples include • enzymes • antibodies • transport proteins like hemoglobin and myoglobin

35. Protein Structure • Fibrous versus globular

36. Protein Structure • Proteins display up to four levels of structure • Primary structure • This is the amino acid sequence, which is unique for each protein • This defines the covalent structure of a protein • Secondary structure • Regular, periodic structures, that involve hydrogen bonding between the backbone amides

37. Protein Structure • Proteins display up to four levels of structure • Tertiary structure • The 3-dimensional fold of the the polypeptide in which the backbone twists and turns its way through the folded structure of the protein. • It involves interactions between the sidechains of the the amino acids and is highly influenced by the amino acid sequence. The proteinubiquitin

38. Protein Structure • Primary Structure • A protein’s amino acid sequence is referred to as its primary structure. • Every protein has a unique primary structure that is determined by the gene for that protein. • The primary structure defines the covalent structure of a protein.

39. Protein Structure • Primary Structure Glycine Gly Alanine Ala Serine Ser Aspartic Acid Asp C-Terminus N-Terminus Phenylalanine Phe Leucine Leu Lysine Lys Gluctamine Gln

40. Protein Structure • Primary Structure C-Terminus N-Terminus Glycylphenylalanylalanylleucylseryllysylaspartylglutamine H2H-Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln-COOH Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln GFALSKDQ

41. Protein Structure • Primary structure • The Central Dogma • DNA → mRNA → Polypeptide • The genetic code is used to match up the DNA/mRNA sequence to the sequence of amino acids in a protein • All living organisms use the same code

42. Protein Structure • The functional diversity of proteins results from the large number of possible proteins that can be built using the 20 different amino acids • Question: How much mass would it take to construct one molecule each of all of the possible polypeptides containing 100 amino acids residues? • View the polypeptides as beads on a string, with one of 20 possible types of beads at each position. o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o

43. Protein Structure • The Earth weighs 6.0 x 1027 g, how many Earths would it take?

44. Protein Structure • The Sun weighs 2.0 x 1033 g, how many Suns would it take?

45. Protein Structure • The Milky Way galaxy weighs 1.2 x 1045 times the mass of the sun • (1.2 x 1045suns)(2.0 x 1033 g/sun) = 2.4 x 1078 g • How may galaxies would it take?

46. Protein Structure • The Coma galaxy cluster contains several thousand galaxies, how many ...?

47. Number of polypeptides (20100) 1.26 x 10130 Avg. Mass of each polypeptide 1.83 x 10-22g Total mass needed 2.32 x 10108g Number of Earths 3.9 x 1080 Number of Suns 1.2 x 1075 Number of Galaxies 9.7 x 1029 Protein Structure

48. Protein Structure • Secondary structure • The polypeptide backbone can take on regular shapes that allow the backbone amides to hydrogen bond to one another. • The primary forms of secondary structure include • α-helix • β-sheet

49. Protein Structure • Secondary structure α-Helix

50. Protein Structure • Secondary Structure β-Sheet