Proteins

1. Proteins

2. Concept 5.4: Proteins have many structures, resulting in a wide range of functions • Proteins account for more than 50% of the dry mass of most cells • Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances [Animations are listed on slides that follow the figure]

4. Animation: Structural Proteins Animation: Storage Proteins Animation: Transport Proteins Animation: Receptor Proteins Animation: Contractile Proteins Animation: Defensive Proteins Animation: Enzymes

5. Animation: Hormonal Proteins Animation: Sensory Proteins Animation: Gene Regulatory Proteins

6. Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions • Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

7. LE 5-16 Substrate (sucrose) Glucose Enzyme (sucrose) Fructose

8. Polypeptides • Polypeptides are polymers of amino acids • A protein consists of one or more polypeptides

9. Amino Acid Monomers • Amino acids are organic molecules with carboxyl and amino groups • Amino acids differ in their properties due to differing side chains, called R groups • Cells use 20 amino acids to make thousands of proteins

10. LE 5-UN78 a carbon Carboxyl group Amino group

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

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

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

14. Amino Acid Polymers • Amino acids are linked by peptide bonds • A polypeptide is a polymer of amino acids • Polypeptides range in length from a few monomers to more than a thousand • Each polypeptide has a unique linear sequence of amino acids

15. Determining the Amino Acid Sequence of a Polypeptide • The amino acid sequences of polypeptides were first determined by chemical methods • Most of the steps involved in sequencing a polypeptide are now automated

16. Protein Conformation and Function • A functional protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape • The sequence of amino acids determines a protein’s three-dimensional conformation • A protein’s conformation determines its function • Ribbon models and space-filling models can depict a protein’s conformation

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

18. Four Levels of Protein Structure • The primary structure of a protein is its unique sequence of amino acids • Secondary structure, found in most proteins, consists of coils and folds in the polypeptide chain • Tertiary structure is determined by interactions among various side chains (R groups) • Quaternary structure results when a protein consists of multiple polypeptide chains Animation: Protein Structure Introduction

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

20. Primary structure, the sequence of amino acids in a protein, is like the order of letters in a long word • Primary structure is determined by inherited genetic information Animation: Primary Protein Structure

21. LE 5-20a Amino end Amino acid subunits Carboxyl end

22. The coils and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone • Typical secondary structures are a coil called an alpha helix and a folded structure called a beta pleated sheet Animation: Secondary Protein Structure

23. LE 5-20b b pleated sheet Amino acid subunits  helix

24. Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents • These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions • Strong covalent bonds called disulfide bridges may reinforce the protein’s conformation Animation: Tertiary Protein Structure

25. LE 5-20d Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Ionic bond

26. Quaternary structure results when two or more polypeptide chains form one macromolecule • Collagen is a fibrous protein consisting of three polypeptides coiled like a rope • Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains Animation: Quaternary Protein Structure

27. LE 5-20e Polypeptide chain b Chains Iron Heme a Chains Hemoglobin Polypeptide chain Collagen

28. Sickle-Cell Disease: A Simple Change in Primary Structure • A slight change in primary structure can affect a protein’s conformation and ability to function • Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin

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

30. LE 5-21b Sickle-cell hemoglobin Normal hemoglobin Primary structure Primary structure Val Val His His Thr Pro Glu Glu Thr Pro Val Glu Leu Leu 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

31. What Determines Protein Conformation? • In addition to primary structure, physical and chemical conditions can affect conformation • Alternations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel • This loss of a protein’s native conformation is called denaturation • A denatured protein is biologically inactive

32. LE 5-22 Denaturation Normal protein Denatured protein Renaturation

33. The Protein-Folding Problem • It is hard to predict a protein’s conformation from its primary structure • Most proteins probably go through several states on their way to a stable conformation • Chaperonins are protein molecules that assist the proper folding of other proteins

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

35. LE 5-23b Correctly folded protein 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.

36. Scientists use X-ray crystallography to determine a protein’s conformation • Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization

37. LE 5-24a X-ray diffraction pattern Photographic film Diffracted X-rays X-ray source X-ray beam Crystal

38. LE 5-24b Nucleic acid Protein X-ray diffraction pattern 3D computer model