Proteins Function and Structure

1. Proteins Function and Structure

2. Proteins • more than 50% of dry mass of most cells • functions include • structural support • storage, transport • cellular communication • movement • defense against foreign substances (immunity) - enzymatic reactions

3. Cell communication

4. Think of conditions or diseases where malfunctioning proteins are responsible?

5. Structure of Proteins • Monomer: amino acid • 20 different a.a. used in cells • Polymer of amino acids-->polypeptide Complex of >1 polypeptides-->protein (a protein often refers to the functional entity)

6. Amino Acid Structure • Organic molecules with • Amino end ? • Carboxyl end ? • Central -carbon • Distinct side chain (or R group) bonded to -carbon

7. a carbon LE 5-UN78 H+ What happens to the end groups in a cellular environment? Carboxyl group Amino group

8. How are 20 amino acids be different from each other? R groups are unique Note: R groups- aka side chains

9. Glycine (Gly) Amino acids Memorize structure LE 5-17a Alanine (Ala) Valine (Val) Isoleucine (Ile) Leucine (Leu) Nonpolar Methionine (Met) Phenylalanine (Phe) Proline (Pro) Tryptophan (Trp)

10. LE 5-17b Polar Tyrosine (Tyr) Serine (Ser) Asparagine (Asn) Threonine (Thr) Cysteine (Cys) Glutamine (Gln)

11. LE 5-17c Acidic Basic Electrically charged Aspartic acid (Asp) Lysine (Lys) Arginine (Arg) Glutamic acid (Glu) Histidine (His)

12. Amino acids • linked together through peptide bonds • Draw dipeptide bond showing bond • Polypeptides range in length • a few a.a. to > thousand • Each polypeptide has unique linear sequence of amino acids

13. Protein Conformation • Helices, coils, pleats • Sequence of amino acids determines 3-D conformation--> function • Depicted in ribbon and space-filling models

14. LE 5-19 Groove A ribbon model Groove A space-filling model

15. Four Levels of Protein Structure • Primary structure (1o) • unique sequence of amino acids, like letters in a word • Secondary structure (2o) • -helices and -pleated sheets • Stabilized by H-bonds • Tertiary structure (3o) • determined by interactions among various side chains (R groups) • Quaternary structure (4o) • Multiple polypeptide chains forming a functional protein

16. Amino end Amino acid subunits 1o structure LE 5-20a Gly Ser Tyr Phe…. Carboxyl end

17. Four Levels of Protein Structure • Primary structure (1o) • unique sequence of amino acids, like letters in a word • Secondary structure (2o) • -helices and -pleated sheets • Stabilized by H-bonds between amino and carbonyl groups - Creates 3-D conformation • Tertiary structure (3o) • determined by interactions among various side chains (R groups) • Quaternary structure (4o) • Multiple polypeptide chains forming a functional protein

18. 2o structure LE 5-20b b pleated sheet Amino acid subunits  helix

19. Four Levels of Protein Structure • Primary structure (1o) • unique sequence of amino acids, like letters in a word • Secondary structure (2o) • -helices and -pleated sheets • Stabilized by H-bonds • Tertiary structure (3o) - determined by bonds between side chains (R groups) often between linearly distant amino acids -ionic bonds, disulfide bonds, van der Waals forces, H-bonds - creates to 3-D conformation • Quaternary structure (4o) • Multiple polypeptide chains forming a functional protein

20. LE 5-20d Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Cysteines form disulfide bonds. Look at R group of cysteine to see why. Disulfide bridge Ionic bond

21. Four Levels of Protein Structure • Primary structure (1o) • unique sequence of amino acids, like letters in a word • Secondary structure (2o) • -helices and -pleated sheets • Stabilized by H-bonds • Tertiary structure (3o) - determined by bonds between side chains (R groups) often between linearly distant amino acids -ionic bonds, disulfide bonds, van der Waals forces, H-bonds - contributes to 3-D conformation • Quaternary structure (4o) • Multiple polypeptide chains forming a functional protein

22. How many of you have or are singing in a choir? How many in the group? Play on a team? How many on the team? Worked in theater? With how many others? Could you have accomplished the group’s goal alone?

23. Polypeptide chain LE 5-20e b Chains Iron Heme Complex of polypeptide subunits a Chains Hemoglobin Collagen

24. LE 5-20 b pleated sheet +H3N Amino end Amino acid subunits  helix

25. Significance of Protein Conformation • Small change in 1o structure • can change protein’s conformation and function • Example • Sickle-cell disease • an inherited blood disorder-->anemia Caused by single amino acid substitution in hemoglobin

26. Sickled RBC Normal RBC 10 µm 10 µm Fibers of abnormal hemoglobin deform cell into sickle shape. Normal cells are full of individual hemoglobin molecules, each carrying oxygen. LE 5-21a

27. One Amino Acid Substitution: Huge Effect! Sickle-cell hemoglobin Normal hemoglobin Primary structure Primary structure Val Val His His Thr Pro Glu Glu Thr Pro Val Glu Leu Leu LE 5-21b 1 1 2 4 6 2 4 6 7 7 3 5 3 5 Exposed hydrophobic region Secondary and tertiary structures Secondary and tertiary structures b subunit b subunit a  a  Quaternary structure Sickle-cell hemoglobin Normal hemoglobin (top view) Quaternary structure a   a Function Molecules do not associate with one another; each carries oxygen. Molecules interact with one another to crystallize into a fiber; capacity to carry oxygen is greatly reduced. Function

28. Environment Affects Protein Structure & Function ? pH salt concentration temperature other environmental factors Extreme conditions cause unraveling of protein structure:denaturation

29. Caused by, for example, high temperature (100oC) Denaturation LE 5-22 Normal protein Denatured protein Renaturation Lowered Temp (37oC)

30. Proper Protein-Folding • Chaperonins • protein complexes that assist in the proper folding of other proteins

31. Cap LE 5-23a Hollow cylinder Chaperonin (fully assembled)

32. Model Correctly folded protein LE 5-23b Polypeptide Steps of Chaperonin Action: The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comes off, and the properly folded protein is released. An unfolded poly- peptide enters the cylinder from one end.

33. Techniques to Determine Protein Structure • X-ray crystallography (need to make protein crystals) • Nuclear magnetic resonance (NMR) spectroscopy (not dependent on making protein crystals)

34. How is the sequence of proteins determined? -encoded in DNA - two step process to decode DNA is transcribed into mRNA 2. mRNA is translated into polypetide More later