1. 1 Introduction Chemical reactions involve the rearrangement of the atoms within and between molecules that results in the formation of new molecules. This process involves the making and breaking of covalent bonds. This process involves the making and breaking of covalent bonds. An important concept in these processes is that all of the atoms present before a reaction are also present after the reaction An important concept in these processes is that all of the atoms present before a reaction are also present after the reaction This a concept allows us to describe chemical reactions using chemical equations This a concept allows us to describe chemical reactions using chemical equations

2. 2 Introduction If you need to review how to create and balance chemical equation, take a look at Section 6.1 in Raymond. We will focus on some reactions that are important in biological chemistry, including: Oxidation/Reduction reactions Oxidation/Reduction reactions Reactions involving water Reactions involving water We will also look at the different forms of free energy that can be used to predict the directions and rates of chemical reactions.

3. 3 Question When you are driving along in your automobile, octane in the gasoline is reacting with oxygen from the air to produce carbon dioxide and water. Write a balanced chemical equation that can be used to describe this reaction 2C 8 H 18 +25 O 2 --> 16 CO 2 + 18 H 2 O

4. 4 Oxidation and Reduction In Unit 1 we discussed some of the strategies that atoms use to obtain 8 valence electrons. See Unit I Elaboration - The Octet Rule Elaboration - The Octet Rule Elaboration - The Octet Rule See Unit 1 Elaboration - Compounds Elaboration - Compounds Elaboration - Compounds

5. 5 Oxidation and Reduction When metal atoms combine with non-metal atoms, they transfer electrons from the metal to the non-metal to form ionic compounds: Sodium, Na (s), is a soft grey metal. Sodium, Na (s), is a soft grey metal. Chlorine, Cl 2 (g), is toxic green gas. Chlorine, Cl 2 (g), is toxic green gas. Sodium chloride, NaCl (s), is a crystalline white solid comprising sodium ions, Na +, and chloride ions, Cl –. Sodium chloride, NaCl (s), is a crystalline white solid comprising sodium ions, Na +, and chloride ions, Cl –.

6. 6 Oxidation and Reduction Reactions that involve the transfer of electrons from one atom to another are called oxidation/reduction reactions. The atom losing the electrons is oxidized. The atom losing the electrons is oxidized. In the previous example, the sodium is oxidized: In the previous example, the sodium is oxidized: The atom gaining the electrons is reduced. The atom gaining the electrons is reduced. In the previous example, the chlorine is reduced: In the previous example, the chlorine is reduced: While the two processes can be separated, one cannot occur without the other. While the two processes can be separated, one cannot occur without the other.

7. 7 Oxidation and Reduction Reactions that involve the transfer of electrons from one atom to another are called oxidation/reduction reactions. The reactant that takes away the electrons is the oxidizing agent. The reactant that takes away the electrons is the oxidizing agent. In the previous example, the chlorine is the oxidizing agent. In the previous example, the chlorine is the oxidizing agent. ‣ The chlorine took the electrons away from the sodium. The reactant that donates the electrons is the reducing agent. The reactant that donates the electrons is the reducing agent. In the previous example, the sodium is the reducing agent. In the previous example, the sodium is the reducing agent. ‣ The sodium gave the electrons to the chlorine.

8. 8 Oxidation and Reduction In oxidation and reduction, metals can also transfer electrons between themselves: Copper, Cu ( s ), is a reddish metal. Copper, Cu ( s ), is a reddish metal. Silver(I) nitrate, AgNO3 (aq), a colorless aqueous solution containing silver(I) ions, Ag + ions and nitrate ions, NO 3-. Silver(I) nitrate, AgNO3 (aq), a colorless aqueous solution containing silver(I) ions, Ag + ions and nitrate ions, NO 3-. copper(II) nitrate, Cu(NO 3 ) 2 ( aq ), a green aqueous solution containing copper(II) ions, Cu 2+, ions and nitrate ions, NO 3-. copper(II) nitrate, Cu(NO 3 ) 2 ( aq ), a green aqueous solution containing copper(II) ions, Cu 2+, ions and nitrate ions, NO 3-. Silver, Ag ( s ), a silvery metal Silver, Ag ( s ), a silvery metal

9. 9 Oxidation and Reduction The atom losing the electrons is oxidized. The atom losing the electrons is oxidized. In the previous example, the copper is oxidized: In the previous example, the copper is oxidized: The atom gaining the electrons is reduced. The atom gaining the electrons is reduced. In the previous example, the silver(I) ion is reduced: In the previous example, the silver(I) ion is reduced:

10. 10 Oxidation and Reduction Oxidation/reduction reactions can also occur when no ions or metals are involved. This can occur when molecular compounds composed of nonmetals react with one another to form other molecular compounds, This can occur when molecular compounds composed of nonmetals react with one another to form other molecular compounds, And: And: Polar covalent bonds are produced or eliminated Polar covalent bonds are produced or eliminated ‣ Or Double or triple bonds are produced or eliminated Double or triple bonds are produced or eliminated See Unit 1 Elaboration - Polarity Elaboration - Polarity Elaboration - Polarity

11. 11 Oxidation and Reduction The combustion of an organic molecule to produce carbon dioxide and water is an example: The products of this reaction contain polar covalent bonds in which the electrons are being drawn away from The products of this reaction contain polar covalent bonds in which the electrons are being drawn away from The carbon atom in CO 2 The carbon atom in CO 2 The hydrogen atoms in H 2 O The hydrogen atoms in H 2 O The carbons and the hydrogens are being oxidized. The carbons and the hydrogens are being oxidized. The oxygen is being reduced. The oxygen is being reduced.

12. 12 Oxidation and Reduction An easier way to assess whether a reaction is an oxidation/reduction reaction or not is to look for the following: OxidationReduction An atom loses electrons An atom gains electrons An atom gains a bond to oxygen An atom loses a bond to oxygen An atom loses a bond to hydrogen An atom gains a bond to hydrogen

13. 13 Oxidation and Reduction Applying these rules to the combustion of methane: The carbon is being oxidized because it gains bonds to oxygen. The carbon is being oxidized because it gains bonds to oxygen. The carbon is also being oxidized because it is losing bonds to hydrogen. The carbon is also being oxidized because it is losing bonds to hydrogen. The hydrogens are being oxidized because they gain bonds to oxygen. The hydrogens are being oxidized because they gain bonds to oxygen.

14. 14 Oxidation and Reduction http://chemed.chem.purdue.edu/genchem/topicreview/bp/ch19/oxred_1.php#assign Rules for Assigning Oxidation Numbers * The oxidation number of an atom is zero in a neutral substance that contains atoms of only one element. Thus, the atoms in O 2, O 3, P 4, S 8, and aluminum metal all have an oxidation number of 0. * The oxidation number of monatomic ions is equal to the charge on the ion. The oxidation number of sodium in the Na+ ion is +1, for example, and the oxidation number of chlorine in the Cl- ion is -1. * The oxidation number of hydrogen is +1 when it is combined with a nonmetal. Hydrogen is therefore in the +1 oxidation state in CH 4, NH 3, H 2 O, and HCl. * The oxidation number of hydrogen is -1 when it is combined with a metal. Hydrogen is therefore in the -1 oxidation state in LiH, NaH, CaH 2, and LiAlH 4. * The metals in Group IA form compounds (such as Li 3 N and Na 2 S) in which the metal atom is in the +1 oxidation state. * The elements in Group IIA form compounds (such as Mg 3 N 2 and CaCO 3 ) in which the metal atom is in the +2 oxidation state. * Oxygen usually has an oxidation number of -2. Exceptions include molecules and polyatomic ions that contain O-O bonds, such as O 2, O 3, H 2 O 2, and the O 2 2- ion. * The nonmetals in Group VIIA often form compounds (such as AlF 3, HCl, and ZnBr 2 ) in which the nonmetal is in the -1 oxidation state. * The sum of the oxidation numbers of the atoms in a molecule is equal to the charge on the molecule. * The most electronegative element in a compound has a negative oxidation number.

15. 15 Oxidation and Reduction An easier way to assess whether a reaction is an oxidation/reduction reaction or not is to look for the following: OxidationReduction An atom loses electrons An atom gains electrons An atom gains a bond to oxygen An atom loses a bond to oxygen An atom loses a bond to hydrogen An atom gains a bond to hydrogen

16. 16 Oxidation and Reduction Hydrogenation Another type of oxidation/reduction reaction is the hydrogenation reaction: Another type of oxidation/reduction reaction is the hydrogenation reaction: In this example, an alkene is reduced to an alkane. In this example, an alkene is reduced to an alkane. ‣ This is considered reduction, because the hydrogen is bringing in additional electrons to the molecule. The alkane that is produced in this reaction is considered “saturated” because it can no longer absorb any more hydrogen atoms. The alkane that is produced in this reaction is considered “saturated” because it can no longer absorb any more hydrogen atoms. saturatedsaturated unsaturatedunsaturated

17. 17 Oxidation and Reduction Often chemist use a shorthand method of writing equations like these: The equation shown on the previous slide can be written as follows: The equation shown on the previous slide can be written as follows: One of the reactants, H 2, is placed above the reaction arrow One of the reactants, H 2, is placed above the reaction arrow ‣ Technically, this equation is no longer balanced The shorthand method of writing a chemical equation is used to emphasize what happens to a key component of the reaction The shorthand method of writing a chemical equation is used to emphasize what happens to a key component of the reaction ‣ In this case it is the alkene.

18. 18 Oxidation and Reduction Saturated vs Unsaturated Fats

19. 19 Oxidation and Reduction Saturated vs Unsaturated Fats

20. 20 Oxidation and Reduction Saturated vs Unsaturated Fats

21. 21 Oxidation and Reduction Saturated vs Unsaturated Fats

22. 22 Oxidation and Reduction Saturated vs Unsaturated Fats Fat (Triacylglyceride)

23. 23 Oxidation and Reduction Dehydrogenation Oxidation/reduction also occurs when hydrogens are taken away from a molecule. This is called dehydrogenation. Oxidation/reduction also occurs when hydrogens are taken away from a molecule. This is called dehydrogenation. The oxidation of succinic acid to fumaric acid: The oxidation of succinic acid to fumaric acid: This reaction takes place in the Citric Acid Cycle. This reaction takes place in the Citric Acid Cycle. ‣ We will discuss the Citric Acid Cycle in Unit 12. The FAD is an abbreviation for a large organic molecule called Flavin Adenine Dinucleotide. The FAD is an abbreviation for a large organic molecule called Flavin Adenine Dinucleotide.Flavin Adenine DinucleotideFlavin Adenine Dinucleotide

24. 24 Oxidation and Reduction The reaction equation on the previous slide also illustrates another shorthand method of writing equations, which used multiple reaction arrows. The longhand form of this reaction equation is The longhand form of this reaction equation is

25. 25 Oxidation and Reduction Dehydration example The oxidation of ethanol to form acetaldehyde: The oxidation of ethanol to form acetaldehyde: This reaction occurs in liver after consuming alcohol. This reaction occurs in liver after consuming alcohol. The NAD + is an abbreviation for a large organic molecule named Nicotinamide Adenine Dinucleotide. The NAD + is an abbreviation for a large organic molecule named Nicotinamide Adenine Dinucleotide.Nicotinamide Adenine DinucleotideNicotinamide Adenine Dinucleotide

26. 26 Reactions Involving Water While the major role for water in biology is a physical one as the primary solvent in living cell, it also plays a chemical role as a reactant or product in some chemical reactions. Reactions involving water as a reactant or product Reactions involving water as a reactant or product Acid-catalzyed hydrolysis Acid-catalzyed hydrolysis Base-catalyzed hydrolysis Base-catalyzed hydrolysis Hydration Hydration Dehydration Dehydration

27. 27 Nobel prize in chemistry-2008 Chalfie, Chimomura and Tsien-Green Fluorescent Protein-GFP Tsien-Green Fluorescent Protein-GFPTsien-Green Fluorescent Protein-GFP Now: red fluorescent protein cat GFP mouse

28. 28 Nobel prize in chemistry-2008 Chalfie, Chimomura and Tsien-Green Fluorescent Protein-GFP Brainbows! A whole bunch of new fluorescent proteins-Roger Tsien

29. 29 Nobel prize in physiology or medicine-20Nobel prize in physiology or medicine-2009 Nobel prize in physiology or medicine-20Nobel prize in physiology or medicine-2009 The 2009 Nobel Prize in medicine Telomeres The 2009 Nobel Prize in medicine Telomeres

30. 30 Nobel prize in chemistry-20Nobel prize in chemistry-2009 Nobel prize in chemistry-20Nobel prize in chemistry-2009 The 2009 Nobel Prize in chemistry- Ribosome Structure The 2009 Nobel Prize in chemistry- Ribosome Structure

31. 31 Reactions Involving Water Hydrolysis In the hydrolysis reaction, water (hydro) is used to split (lyse) another molelcule. In the hydrolysis reaction, water (hydro) is used to split (lyse) another molelcule. In this case, water is being used to split an ester into a carboxylic acid plus and alcohol. In this case, water is being used to split an ester into a carboxylic acid plus and alcohol.

32. 32 Reactions Involving Water Hydrolysis example The hydrolysis of the ester bond in the neurotransmitter acetylcholine. The hydrolysis of the ester bond in the neurotransmitter acetylcholine. Again, shorthand notation is being used: Again, shorthand notation is being used: The H 2 O reactant is placed above the reaction arrow, The H 2 O reactant is placed above the reaction arrow, The H + below the arrow indicates an acid catalyst is used. The H + below the arrow indicates an acid catalyst is used.

33. 33 Reactions Involving Water Hydrolysis Hydrolysis can also be catalyzed using a base (OH - ):. Hydrolysis can also be catalyzed using a base (OH - ):. Because one of the products of the hydrolysis is a carboxylic acid, in base catalyzed hydrolysis the base undergoes a second acid/base reaction with the carboxylic acid to produce a carboxylate ion. Because one of the products of the hydrolysis is a carboxylic acid, in base catalyzed hydrolysis the base undergoes a second acid/base reaction with the carboxylic acid to produce a carboxylate ion. The base catalyzed hydrolysis of esters is also called saponification The base catalyzed hydrolysis of esters is also called saponification We will be discussing acids and bases in Unit 6 We will be discussing acids and bases in Unit 6

34. 34 Reactions With Water Hydrolysis example: The base catalyzed hydrolysis of fats produces soap and glycerol The base catalyzed hydrolysis of fats produces soap and glycerol FatFat

35. 35 Reactions With Water Hydrolysis example: The base catalyzed hydrolysis of fats produces soap and glycerol The base catalyzed hydrolysis of fats produces soap and glycerol SoapSoapGlycerolGlycerol

36. 36 Reactions Involving Water Hydration In the hydration reaction water is also split, but instead of being used to split another molecule, it is added to another molecule to produce a single product. In the hydration reaction water is also split, but instead of being used to split another molecule, it is added to another molecule to produce a single product. The water it is added to either an alkene or alkyne: The water it is added to either an alkene or alkyne: The hydration of an alkene produces an alcohol. Not a net oxidation or reduction overall. The hydration of an alkene produces an alcohol. Not a net oxidation or reduction overall. +1 -2-2 -3 +1 +1 +1+1 +1 +1 +1 +1 +1-2

37. 37 Reactions Involving Water Hydration This can also be written in shorthand as: This can also be written in shorthand as: The H + below the reaction arrow is used to indicate that this is an acid-catalyzed reaction. The H + below the reaction arrow is used to indicate that this is an acid-catalyzed reaction. The shorthand is used to emphasize what happens to the key reactant. The shorthand is used to emphasize what happens to the key reactant.

38. 38 Reactions Involving Water Hydration example On an earlier slide a reaction from the Citric Acid Cycle was shown, which involved the dehydrogenation of succinic acid to produce fumaric acid. On an earlier slide a reaction from the Citric Acid Cycle was shown, which involved the dehydrogenation of succinic acid to produce fumaric acid. The sequent reaction in the Citric Acid Cycle is an example of a hydration reaction: The sequent reaction in the Citric Acid Cycle is an example of a hydration reaction:

39. 39 Reactions Involving Water Dehydration In the dehydration reaction is the reverse of the hydration reaction. In the dehydration reaction is the reverse of the hydration reaction. The water it is removed from an alcohol: The water it is removed from an alcohol: The dehydration of an alcohol produces an alkene. The dehydration of an alcohol produces an alkene.

40. 40 Reactions Involving Water Dehydration example The Citric Acid Cycle also provides a good example of a dehydration reaction. The Citric Acid Cycle also provides a good example of a dehydration reaction. A dehydration reaction followed by a hydration reaction is used to move a hydroxyl group from one carbon to an adjacent carbon in citric acid: A dehydration reaction followed by a hydration reaction is used to move a hydroxyl group from one carbon to an adjacent carbon in citric acid:

41. 41 Free Energy and Reaction Rates In Unit 3 we discussed how changes in the free energy can be used to predict whether a process is spontaneous (favorable) or nonspontaneous (not favorable) ΔG < 0 spontaneous spontaneous ΔG > 0 nonspontaneous nonspontaneous

42. 42 Free Energy and Reaction Rates The same principles can be applied to chemical reactions to predict whether they are favorable or not: FreeEnergy(G)FreeEnergy(G) Progress of reaction Α → B AA ΒΒ ΔG < 0 spontaneous spontaneous FreeEnergy(G)FreeEnergy(G) Progress of reaction Α → B AA ΒΒ ΔG > 0 nonspontaneous nonspontaneous

43. 43 Free Energy and Reaction Rates Just because a reaction is spontaneous, does not mean that it will occur at an observable rate. For example, diamond and graphite are two different forms of pure carbon. The reaction that converts diamond to graphite is actually a favorable one For example, diamond and graphite are two different forms of pure carbon. The reaction that converts diamond to graphite is actually a favorable one This does not make diamonds a bad investment for fear that they will turn into pencil lead. This does not make diamonds a bad investment for fear that they will turn into pencil lead. Why? Why? FreeEnergy(G)FreeEnergy(G) Progress of reaction Diamond → Graphite DiamondDiamond GraphiteGraphite ΔG < 0 spontaneous spontaneous

44. 44 Free Energy and Reaction Rates There is is a hill that for most reactions the reactants must climb and go over to before they can go on to become product. FreeEnergy(G)FreeEnergy(G) Progress of reaction Α → B AA ΒΒ

45. 45 Free Energy and Reaction Rates The height of this hill is called the activation energy, E act. The activation energy has no effect on the overall change in the free energy for the reaction. The activation energy has no effect on the overall change in the free energy for the reaction. FreeEnergy(G)FreeEnergy(G) Progress of reaction Α → B AA ΒΒ ΔG < 0 spontaneous spontaneous E act > 0

46. 46 Free Energy and Reaction Rates Diamonds are still good investment because the activation energy for the conversion of diamond to graphite is very high. FreeEnergy(G)FreeEnergy(G) Progress of reaction ΔG < 0 spontaneous spontaneous E act > 0 Diamond → Graphite DiamondDiamond GraphiteGraphite

47. 47 Free Energy and Reaction Rates The reaction rate (speed) of a reaction is determined by the height of the hill. The higher the activation energy, the slower the reaction rate. The higher the activation energy, the slower the reaction rate.

48. 48 Free Energy and Reaction Rates There are several ways that reactants can be pushed over the hill to speed up the reaction rate. Two of these include: Increase the temperature of the reactant molecules. Increase the temperature of the reactant molecules. This increases the kinetic energy, which increases the motion of the reactant molecules. This increases the frequency with which they will collide with one another to react. This increases the kinetic energy, which increases the motion of the reactant molecules. This increases the frequency with which they will collide with one another to react. Increase the concentration of the reactant molecules. Increase the concentration of the reactant molecules. This increases the number of reactant molecules. This also increases the frequency with which they will collide with other reactant molecules. This increases the number of reactant molecules. This also increases the frequency with which they will collide with other reactant molecules.

49. 49 Free Energy and Reaction Rates There is a third way to speed up the reaction rate and that is to lower the height of the hill. This is done using catalysts, which provide an alternative pathway over the hill for the reactants. This is done using catalysts, which provide an alternative pathway over the hill for the reactants. FreeEnergy(G)FreeEnergy(G) Progress of reaction Α → B AA ΒΒ ΔG < 0 spontaneous spontaneous E act > 0 without catalyst - with catalyst E act > 0 without catalyst - with catalyst

50. 50 Free Energy and Reaction Rates Catalysts speed up a reaction, but are not produced or consumed in a reaction. In the reaction equation, their presence in indicated above or below the reaction arrow. In the reaction equation, their presence in indicated above or below the reaction arrow. They have not effect on the change in free energy for the reaction, ΔG. They have not effect on the change in free energy for the reaction, ΔG. They cannot be used to make an unfavorable reaction favorable. They cannot be used to make an unfavorable reaction favorable.

51. 51 Free Energy and Reaction Rates In biological systems, catalysts are called enzymes. Most enzymes are proteins. Most enzymes are proteins. Nearly every reaction that takes place in a living cell has an enzyme associated with. Nearly every reaction that takes place in a living cell has an enzyme associated with. Enzymes bind the reactants, facilitate the reaction, and then release the products. Enzymes bind the reactants, facilitate the reaction, and then release the products.

52. 52 Free Energy and Reaction Rates Example Hexokinase Hexokinase See Jmol Model l Modell Model of Hexokinase See Jmol Model l Modell Model of Hexokinase

53. The End