Chapter 5c: The Structure and Function of Macromolecules (Proteins)

1. Chapter 5c:The Structure andFunction ofMacromolecules(Proteins)

2. Polymers, Monomers, and Lipids

3. Major constituent of most cells (>50% dry weight) • Highly sophisticated molecules (or multi-molecular complexes) • Extremely large number of unique proteins exist • They are polymers folded into specific conformations (shapes) • Conformation and functional-group chemistry controls function • Made up of 20 different types of amino-acid monomers • Proteins define what an organism is, what it looks like, how it behaves, etc. (responsible for most phenotype) • You are your proteins! Protein Overview

4. Protein Function

5. Globular versus Fibrous Fibrous protein (e.g., collagen) Just know general shapes Globular protein (e.g., hemoglobin)

6. Enzymatic Catalysis Globular protein

7. Monomer (amino acid) Structure “R” group

8. Amino Acid Structure The chemistry of R groups distinguishes amino acids and their properties

9. Amino Acid Ionization

10. Amino Acid Types

11. Non-Polar R groups Know me!

12. Polar R groups

13. Five Categories Note 20 (naturally translated) amino acids

14. No need to know side chain structures The Peptide Backbone = -N-C-C-N-C-C-N- Polypeptide = linear chain of amino acids linked by peptide bonds

15. Making the Peptide Bond

16. Explanation of double-bond character (resonance) Limited Rotation Be able to know which is the peptide bond

17. Backbone Rigidity Because of Resonance the backbone of polypeptides has greater rigidity than otherwise might be expected Polypeptide backbones are more than just wet noodles!

18. Conformation = Shape  Function Protein Depiction (4 ways) The surface chemistry of a protein is determined by the chemistry of exposed amino-acid R groups The interior of proteins is held together by R-group-to-R-group and backbone-to-backbone interactions

19. ATP Synthase This is what you use to make the bulk of your ATP

20. Pseudo 3D Image

21. Conformation = Shape  Function

22. Levels of Protein Structure

23. Protein Primary Structure 1’ structure = ordered sequence of amino acids

24. Protein Primary Structure Note the Polarity of the sequence (amino  carboxy) Note also the disulfide linkages (cys-cys  S-S bonds; actually considered a component of tertiary structure)

25. Protein Secondary Structure Be able to recognize & name these Held together by interactions (H-bonds) between peptide backbones

26. 2’ Structure: H-Bonds

27. 2’ to Tertiary Structure

28. Tertiary structure is controlled by the interactions between non-adjacent amino acid R groups (note bond types) Protein Tertiary Structure

29. Quaternary structure is the interaction between adjacent polypeptides that make up a single protein Protein Quaternary Structure Note that the polypeptides reside in discrete subunits rather than being tangled together like spaghetti

30. “’Polypeptide’ is not quite synonymous with ‘protein.’ The relationship is somewhat analogous to that between a long strand of yarn and a sweater of a particular size and shape that one can knit from the yarn. A functional protein is not just a polypeptide chain, but one or more polypeptides precisely twisted, folded, and coiled into a molecule of unique shape. It is the amino-acid sequence of a polypeptide that determines what three-dimensional conformation the protein will take.” (p. 70, Campbell et al., 1999) (see p. 81 of 2005 edition) Protein Structure Overview

31. Sickle-Cell Disease

32. Protein Denaturation Destruction of Conformation = Loss of Function Some simple proteins can spontaneously renature

33. “A protein’s specific conformation determines how it works. In almost every case, the function of a protein depends on its ability to recognize and bind to some other molecule.” p. 81, Campbell & Reece (2005) Protein Folding

34. Chaparonins They segregate protein folding from “bad influences” in the cell Chaparonins Assist in Protein Folding

35. The End