Proteins: Function & Structure

1. Proteins: Function & Structure

2. Proteins • Cellular Overview • Functions • Key Properties • Core Topics • Amino Acids: properties, classifications, pI • Primary Structure, Secondary Structure, and Motifs • Tertiary Structure • Fibrous vs. Globular • Quaternary Structure

3. Amazing Proteins: Function • The largest class of proteins, accelerate rates of reactions • Catalysts (Enzymes) • Transport & Storage DNA Polymerase CK2 Kinase Catalase Ovalbumin Casein Ion channels Hemoglobin Serum albumin

4. Amazing Proteins: Function • Structural • Generate Movement Collagen Keratin Silk Fibroin Actin Myosin

5. Amazing Proteins: Function • Regulation of Metabolism and Gene Expression • Protection Lac repressor Insulin Thrombin and Fibrinogen Ricin Venom Proteins Immunoglobulins

6. Amazing Proteins: Function • Signaling and response (inter and intracellular) Apoptosis Membrane proteins Signal transduction

7. Amazing Proteins: Properties • Biopolymers of amino acids • Contains a wide range of functional groups • Can interact with other proteins or other biological macromolecules to form complex assemblies • Some are rigid while others display limited flexibility

8. a-Amino Acids: Protein Building Blocks R-group or side-chain a-amino group Carboxyl group a-carbon

9. Amino acids are zwitterionic • “Zwitter” = “hybrid” in German • Fully protonated forms will have specific pKa’s for the different ionizable protons • Amino acids are amphoteric (both acid and base)

10. Stereochemistry of amino acids

11. Stereochemistry of amino acids (AA) • AA’s synthesized in the lab are racemic mixtures. AA’s from nature are “L” isomers • These are all optically-active except for glycine (why?)

12. Synthesis of Proteins + H2O

13. Synthesis of Proteins

14. N-Terminal End C-Terminal End Synthesis of Proteins

15. Synthesis of Proteins = ≠

16. Synthesis of Proteins = ≠

17. Synthesis of Proteins ≠ ≠

18. 20 common amino acids make up the multitude of proteins we know of COMMON AMINO ACIDS

19. Amino Acids With Aliphatic Side Chains

20. Amino Acids With Aliphatic Side Chains

21. Amino Acids With Aliphatic Side Chains

22. Amino Acids With Aromatic Side Chains

23. Amino Acids with Aromatic Side Chains Can Be Analyzed by UV Spectroscopy

24. Amino Acids With Hydroxyl Side Chains

25. Amino Acid with a Sulfhydryl Side Chain

26. Disulfide Bond Formation

27. Amino Acids With Basic Side Chains

28. Amino Acids With Acidic Side Chains and Their Amide Derivatives

30. There are some important uncommon amino acids

31. pH and Amino Acids Net charge: +1 Net charge: -1 Net charge: 0

32. Basic amino acids High pKa Function as bases at physiological pH Side chains with N Acidic amino acids Low pKa Negatively charged at physiological pH Side chains with –COOH Predominantly in unprotonated form Characteristics of Acidic and Basic Amino Acids

34. Isoelectic point (pI) • the pH at which the compound is electrically neutral • Equal number of (+) and (-) charge • At pH < pI amino acid is (+) • At pH > pI amino acid is (-) • CRITICAL FOR: protein analysis, purification, isolation, crystallization

38. Protein Structure We use different “levels” to fully describe the structure of a protein.

39. Primary Structure • Amino acid sequence • Standard: Left to Right means N to C-terminal • Eg. Insulin (AAA40590) • The info needed for further folding is contained in the 1o structure. MAPWMHLLTVLALLALWGPNSVQAYSSQHLCGSNLVEALYMTCGRSGFYRPHDRRELEDLQVEQAELGLEAGGLQPSALEMILQKRGIVDQCCNNICTFNQLQNYCNVP

40. Secondary Structure • The regular local structure based on the hydrogen bonding pattern of the polypeptide backbone • α helices • β strands (β sheets) • Turns and Loops • WHY will there be localized folding and twisting? Are all conformations possible?

41. Consequences of the Amide Plane Two degrees of freedom per residue for the peptide chain • Angle about the C(alpha)-N bond is denoted phi • Angle about the C(alpha)-C bond is denoted psi • The entire path of the peptide backbone is known if all phi and psi angles are specified • Some values of phi and psi are more likely than others.

42. The angles phi and psi are shown here See blackboard for explanation why the peptide bond is planar

43. Unfavorable orbital overlap precludes some combinations of phi and psi • phi = 0, psi = 180 is unfavorable • phi = 180, psi = 0 is unfavorable • phi = 0, psi = 0 is unfavorable

44. Steric Constraints on phi & psi Sasisekharan • G. N. Ramachandran was the first to demonstrate the convenience of plotting phi,psi combinations from known protein structures • The sterically favorable combinations are the basis for preferred secondary structures

45. α Helix • First proposed by Linus Pauling and Robert Corey in 1951. • 3.6 residues per turn, 1.5 Angstroms rise per residue • Residues face outward

46. α Helix • α-helix is stabilized by H-bonding between CO and NH groups • Except for amino acid residues at the end of the α-helix, all main chain CO and NH are H-bonded

47. α Helix representation

49. β strand • Fully extended • β sheets are formed by linking 2 or more strands by H-bonding • Beta-sheet also proposed by Corey and Pauling in 1951.