1. PROTEIN NOTES: You are proteins and the result of protein action! Warm-Up: Match the function to the examples Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings FunctionExample a.support b.enzymes c.transport d.cell communications (hormones) e.defense against foreign substances i.antibodies ii.insulin iii.ATP synthase, sucrase, lactase iv.proton pumps v.keratin and collagen

2. Dehydration: two monomers bond together; loss of a water molecule Polymers are disassembled to monomers by hydrolysis The Synthesis and Breakdown of Polymers Animation: Polymers Animation: Polymers Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Short polymer HO 123H H Unlinked monomer Dehydration removes a water molecule, forming a new bond HO H2OH2O H 1 2 3 4 Longer polymer (a) Dehydration reaction in the synthesis of a polymer HO 1 2 3 4 H H2OH2O Hydrolysis adds a water molecule, breaking a bond HO H H 1 2 3 (b) Hydrolysis of a polymer

3. Fig. 5-UN1

4. Fig. 5-17 Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Trypotphan (Trp or W) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Electrically charged AcidicBasic Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

5. Quiz Make-Up: DUE Tomorrow – 1 page on each of the following: A summary of the light reactions. Compare the potential energy in sugar, fat, and carbon dioxide. The role proton pumps and ATP synthase in photosynthesis.

6. Proteins: aka: polypeptide a polymer of amino acids linked by peptide bonds range in length – a few amino acids – more than a thousand amino acids each has a unique linear sequence of amino acids Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Peptide bond Amino end (N-terminus) Peptide bond Side chains Backbone Carboxyl end (C-terminus) (a) (b)

7. Building Proteins Build and DRAW an amino acid (skip the R group for now): In your team: 1 glycine, 1 serine, 1 threonine, 1 alanine Polymerize! and DRAW

8. Fig. 5-21 Primary Structure Secondary Structure Tertiary Structure  pleated sheet Examples of amino acid subunits + H 3 N Amino end  helix Quaternary Structure sequence of amino acids folding due to interactions among various side chains (R groups)

9. Protein Structure and Function: FORM FOLLOWs FUNCTION A protein consists of one or more polypeptides twisted, folded, and coiled into a unique shape Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings A ribbon model of lysozyme (a)(b) A space-filling model of lysozyme Active Site

10. Tertiary Structure folding due to interactions among various side chains (R groups)

11. Fig. 5-20 Antibody protein Protein from flu virus

12. Fig. 5-21g Polypeptide chain  Chains Heme Iron  Chains Collagen Hemoglobin

13. Practice Polypeptide with amino acid sequence (glycine, alanine, serine)  p. 72-73

14. Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a protein’s structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

15. Warm-Up: 1.Draw the dipeptide 2.What would cause it to fold? not fold? 3.What kinds of factors might change a protein? Brainstorm factors other than genetic changes.

16. Fig. 5.19 Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

17. Fig. 5-22 Primary structure Secondary and tertiary structures Quaternary structure Normal hemoglobin (top view) Primary structure Secondary and tertiary structures Quaternary structure Function  subunit Molecules do not associate with one another; each carries oxygen. Red blood cell shape Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. 10 µm Normal hemoglobin     1234567 Val His Leu ThrPro Glu Red blood cell shape  subunit Exposed hydrophobic region Sickle-cell hemoglobin   Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.   Fibers of abnormal hemoglobin deform red blood cell into sickle shape. 10 µm Sickle-cell hemoglobin GluPro Thr Leu His Val 1234567 http://www.nslc.wustl.edu/sicklecell/sicklecell.html

18. Changes in the Tertiary Structure (Shape) of Proteins Caused by: Mutations in DNA: changes primary structure, which changes folding (i.e. the shape) Denaturation: i.e. unfolding pH: adding protons to the environment changes the hydrogen bonding between R groups Heat: breaks R groups (weakest) bonds first – ionic bonds – hydrogen bonds – hydrophobic interactions Normal protein Denatured protein Denaturation

19. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Water is not all H 2 O. 99.99% H 2 0. 0.01% OH- 0.01% H 3 0+ Rarely, the hydrogen bond overcomes the polar covalent bond (i.e. the proton from 1 water leaves and joins another water) Water is not all H 2 O. 99.99% H 2 0. 0.01% OH- 0.01% H 3 0+ Rarely, the hydrogen bond overcomes the polar covalent bond (i.e. the proton from 1 water leaves and joins another water) Review of pH

20. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Review of pH Simplified: Water is not all H 2 O. 99.99% H 2 0. 0.01% OH- 0.01% H 3 0+ Rarely, the hydrogen bond overcomes the polar covalent bond (i.e. the proton from 1 water leaves and joins another water) pH: A meause of the [H+] vs [OH-] Water is not all H 2 O. 99.99% H 2 0. 0.01% OH- 0.01% H 3 0+ Rarely, the hydrogen bond overcomes the polar covalent bond (i.e. the proton from 1 water leaves and joins another water) pH: A meause of the [H+] vs [OH-]

21. Water (neutral): [H+] = [OH-] [H + ] = 10 -7 pH=7 Acidic solution [H+] > [OH-] [H + ] > 10 -7 i.e. is 10 -4 pH< 7 Basic solution: H+ < OH- [H + ] < 10 -7 i.e. is 10 -9 pH> 7 Water (neutral): [H+] = [OH-] [H + ] = 10 -7 pH=7 Acidic solution [H+] > [OH-] [H + ] > 10 -7 i.e. is 10 -4 pH< 7 Basic solution: H+ < OH- [H + ] < 10 -7 i.e. is 10 -9 pH> 7

22. acid: a molecule that increases the H+ in a solution. – Example: DRAW IT! hydrochloric acid is added to water hydrogen ions dissociate from chloride ions: – HCl  H + + Cl - base: a molecule that reduces the H+ in a solution – Example: Some bases reduce H + directly by accepting H+ Ammonia (NH 3 ): nitrogen’s unshared electron pair attracts a hydrogen ion from the solution creating an ammonium in (NH 4 + ). – NH 3 + H +  NH 4 + – Example: Other bases reduce H + indirectly by dissociating to OH - – NaOH  Na + + OH - The OH- then decreases H+ by combining with H + to form water. – OH - + H +  H 2 O Acids vs Bases

23. acid: a molecule that increases the H+ in a solution. – Example: DRAW IT! – hydrochloric acid is added to water – hydrogen ions dissociate from chloride ions: base: a molecule that reduces the H+ in a solution – Example: Some bases reduce H + directly by accepting H+ DRAW IT! – Ammonia (NH 3 ): nitrogen’s unshared electron pair attracts a hydrogen ion from the solution – creating an ammonium in (NH 4 + ). – Example: Other bases reduce H + indirectly by dissociating to OH - – NaOH  Na + + OH - The OH- then decreases H+ by combining with H + to form water. – OH - + H +  H 2 O Acids vs Bases

24. Tertiary Structure folding due to interactions among various side chains (R groups) Why does pH affect proteins?

26. If hydrogen bonding is disrupted, the shape of the molecule will change. If the shape changes, the function changes. If hydrogen bonding is disrupted, the shape of the molecule will change. If the shape changes, the function changes.

27. Fig. 6.15

28. Enzymes Drawings DrawExplain Begin1 enzyme 2 substrates "free" 1 substrate "active" Middle1 enzyme 1 substrate "free" 1 substrate "active" 1 of each product End1 enzyme 0 substrate ? product

29. Enzymes Drawings: Analysis 1.What happens to the amount of substrate during the reaction? 2.the amount of enzyme? 3.Why would the reaction stop? 4.What could make the reaction speed up?

30. Enzymes Model 1.What happens to the amount of substrate during the reaction? 2.the amount of enzyme? 3.Why would the reaction stop? 4.What could make the reaction speed up?

31. DrawingGraphExplanation Notes: Enzymes and Activation Energy: WHY DO ENZYMES SPEED UP REACTIONS? Warm-UP: 1.Match the drawings to the graphs. 2.Sketch the drawings and graphs in a table. 3.Explain what is happening.

32. 1.Explain what is happening. Remember entropy (the 2 nd law of thermodynamics)? 2.Explain why the graph matches the drawing 3.What would the graph look like if the arrow pointed the other direction? Explain. 1.Explain what is happening. Remember entropy (the 2 nd law of thermodynamics)? 2.Explain why the graph matches the drawing 3.What would the graph look like if the arrow pointed the other direction? Explain. Enzymes and Activation Energy

33. ∆G < 0 Gibbs Free Energy G = H - T S S: entropy G: free energy As entropy increases, energy in the system decreases ∆G > 0 Enzymes and Activation Energy

34. ∆G < 0 Enzymes and Activation Energy Exergonic Reactions: “Spontaneous” ∆G < 0 Energy is released from the system Example: glucose –> CO 2 Energy transferred to ATP Amount of energy of products is less than it was with the reactants

35. Activation energy: An energy “hump” All reaction (even exergonic) reactions have a barrier to starting Examples: 1.Wood doesn’t just spontaneously combust. 2.Sugar isn’t digested on its own. Activation energy: An energy “hump” All reaction (even exergonic) reactions have a barrier to starting Examples: 1.Wood doesn’t just spontaneously combust. 2.Sugar isn’t digested on its own. Enzymes and Activation Energy

36. Enzymes speed up the rate of reactions by lowering activation energy.

37. ∆G > 0 Enzymes and Activation Energy Enzymes speed up the rate of reactions by lowering activation energy. Endergonic Reactions ∆G > 0 Energy is added to the system Example: CO 2  glucose Energy transferred in: from light to glucose Amount of energy of products is more than it was with the reactants

38. What is the role of enzymes in the reaction?

39. Gibbs Free Energy exergonic: spontaneous reactions: release of energy endergonic: energy is stored (a) Gravitational motion (b) Diffusion(c) Chemical reaction More free energy (higher G) Less stable Greater work capacity In a spontaneous change The free energy of the system decreases (∆G < 0) The system becomes more stable The released free energy can be harnessed to do work Less free energy (lower G) More stable Less work capacity