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

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

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

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

11. LE 5-17c Electrically charged Aspartic acid (Asp) Acidic Basic Glutamic acid (Glu) Lysine (Lys)Arginine (Arg) 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 A ribbon model Groove A space-filling model

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

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

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

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

19. Four Levels of Protein Structure Primary structure (1 o ) –unique sequence of amino acids, like letters in a word Secondary structure (2 o ) –  -helices and  -pleated sheets –Stabilized by H-bonds Tertiary structure (3 o ) - 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 (4 o ) –Multiple polypeptide chains forming a functional protein

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

21. Four Levels of Protein Structure Primary structure (1 o ) –unique sequence of amino acids, like letters in a word Secondary structure (2 o ) –  -helices and  -pleated sheets –Stabilized by H-bonds Tertiary structure (3 o ) - 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 (4 o ) –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. LE 5-20e  Chains  Chains Hemoglobin Iron Heme Collagen Polypeptide chain Complex of polypeptide subunits

24. LE 5-20 Amino acid subunits  pleated sheet + H 3 N Amino end  helix

25. Significance of Protein Conformation Small change in 1 o 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. LE 5-21a Normal cells are full of individual hemoglobin molecules, each carrying oxygen. 10 µm Fibers of abnormal hemoglobin deform cell into sickle shape. Normal RBC Sickled RBC

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

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

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

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

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

32. LE 5-23b Polypeptide Correctly folded protein An unfolded poly- peptide enters the cylinder from one end. Steps of Chaperonin Action: The cap comes off, and the properly folded protein is released. 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. Model

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

34. How is the sequence of proteins determined? -encoded in DNA - two step process to decode 1.DNA is transcribed into mRNA 2. mRNA is translated into polypetide More later