Chemical reactions involve the rearrangement of the atoms within and between molecules that results in the formation of new molecules.

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.
• 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

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
• 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
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

2C8H18 25 O2 --gt 16 CO2 18 H2O
4
Oxidation and Reduction

• In Unit 1 we discussed some of the strategies
  that atoms use to obtain 8 valence electrons.
• See Unit IElaboration - The Octet Rule
• See Unit 1Elaboration - Compounds

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.
• Chlorine, Cl2 (g), is toxic green gas.
• Sodium chloride, NaCl (s), is a crystalline white
  solid comprising sodium ions, Na, and chloride
  ions, Cl.

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.
• In the previous example, the sodium is oxidized
• The atom gaining the electrons is reduced.
• In the previous example, the chlorine is reduced
• While the two processes can be separated, one
  cannot occur without the other.

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.
• 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.
• In the previous example, the sodium is the
  reducing agent.
• The sodium gave the electrons to the chlorine.

8
Oxidation and Reduction

• In oxidation and reduction, metals can also
  transfer electrons between themselves
• 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, NO3-.
• copper(II) nitrate, Cu(NO3)2 (aq), a green
  aqueous solution containing copper(II) ions,
  Cu2, ions and nitrate ions, NO3-.
• Silver, Ag (s), a silvery metal

9
Oxidation and Reduction

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

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,
• And
• Polar covalent bonds are produced or eliminated
• Or
• Double or triple bonds are produced or eliminated
  
• See Unit 1Elaboration - Polarity

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 carbon atom in CO2
• The hydrogen atoms in H2O
• The carbons and the hydrogens are being oxidized.
• The oxygen is being reduced.

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

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 also being oxidized because it is
  losing bonds to hydrogen.
• The hydrogens are being oxidized because they
  gain bonds to oxygen.

14
Oxidation and Reduction
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 O2, O3, P4, S8, 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 CH4, NH3, H2O, 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, CaH2, and
LiAlH4. The metals in Group IA form
compounds (such as Li3N and Na2S) in which the
metal atom is in the 1 oxidation state.
The elements in Group IIA form compounds (such as
Mg3N2 and CaCO3) 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 O2, O3, H2O2, and the O22- ion.
The nonmetals in Group VIIA often form
compounds (such as AlF3, HCl, and ZnBr2) 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.
http//chemed.chem.purdue.edu/genchem/topicreview/
bp/ch19/oxred_1.phpassign
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

16
Oxidation and Reduction

• Hydrogenation
• Another type of oxidation/reduction reaction is
  the hydrogenation reaction
• 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.

saturated
unsaturated
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
• One of the reactants, H2, 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
• In this case it is the alkene.

18
Oxidation and Reduction

• Saturated vs Unsaturated Fats

19
Oxidation and Reduction

• Saturated vs Unsaturated Fats

20
Oxidation and Reduction

• Saturated vs Unsaturated Fats

21
Oxidation and Reduction

• Saturated vs Unsaturated Fats

22
Oxidation and Reduction

• Saturated vs Unsaturated Fats

Fat (Triacylglyceride)
23
Oxidation and Reduction

• 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
• 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.

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

25
Oxidation and Reduction

• Dehydration example
• The oxidation of ethanol to form acetaldehyde
• This reaction occurs in liver after consuming
  alcohol.
• The NAD is an abbreviation for a large organic
  molecule named Nicotinamide Adenine Dinucleotide.

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
• Acid-catalzyed hydrolysis
• Base-catalyzed hydrolysis
• Hydration
• Dehydration

27
Nobel prize in chemistry-2008

• Chalfie, Chimomura and Tsien-Green Fluorescent
  Protein-GFP

GFP mouse
Now red fluorescent protein cat
28
Nobel prize in chemistry-2008

• Chalfie, Chimomura and Tsien-Green Fluorescent
  Protein-GFP

A whole bunch of new fluorescent proteins-Roger
Tsien
Brainbows!
29
Nobel prize in physiology or medicine-2009
The 2009 Nobel Prize in medicine Telomeres
30
Nobel prize in chemistry-2009
The 2009 Nobel Prize in chemistry-Ribosome
Structure
31
Reactions Involving Water

• Hydrolysis
• 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.

32
Reactions Involving Water

• Hydrolysis example
• The hydrolysis of the ester bond in the
  neurotransmitter acetylcholine.
• Again, shorthand notation is being used
• The H2O reactant is placed above the reaction
  arrow,
• The H below the arrow indicates an acid catalyst
  is used.

33
Reactions Involving Water

• Hydrolysis
• 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.
• The base catalyzed hydrolysis of esters is also
  called saponification
• We will be discussing acids and bases in Unit 6

34
Reactions With Water

• Hydrolysis example
• The base catalyzed hydrolysis of fats produces
  soap and glycerol

Fat
35
Reactions With Water

• Hydrolysis example
• The base catalyzed hydrolysis of fats produces
  soap and glycerol

Soap
Glycerol
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.
• 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.

1
1
-2
-2
-2
-1
1
1
-3
1
1
1
1
1
1
37
Reactions Involving Water

• Hydration
• 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 shorthand is used to emphasize what happens
  to the key reactant.

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.
• The sequent reaction in the Citric Acid Cycle is
  an example of a hydration reaction

39
Reactions Involving Water

• Dehydration
• In the dehydration reaction is the reverse of the
  hydration reaction.
• The water it is removed from an alcohol
• The dehydration of an alcohol produces an alkene.

40
Reactions Involving Water

• Dehydration example
• 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

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)

?G lt 0 spontaneous
?G gt 0 nonspontaneous
42
Free Energy and Reaction Rates

• The same principles can be applied to chemical
  reactions to predict whether they are favorable
  or not

? ? B
? ? B
?G gt 0 nonspontaneous
?G lt 0 spontaneous
A
?
?
A
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
• This does not make diamonds a bad investment for
  fear that they will turn into pencil lead.
• Why?

Diamond ? Graphite
?G lt 0 spontaneous
Diamond
Free Energy (G)
Graphite
Progress ofreaction
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.

? ? B
A
?
45
Free Energy and Reaction Rates

• The height of this hill is called the activation
  energy, Eact.
• The activation energy has no effect on the
  overall change in the free energy for the
  reaction.

? ? B
Eact gt 0
A
?G lt 0 spontaneous
?
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.

Diamond ? Graphite
Eact gt 0
Diamond
?G lt 0 spontaneous
Graphite
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.

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.
• 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.
• This increases the number of reactant molecules.
  This also increases the frequency with which they
  will collide with other reactant molecules.

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.

? ? B
Eact gt 0 without catalyst - with catalyst
A
?G lt 0 spontaneous
?
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.
• They have not effect on the change in free energy
  for the reaction, ?G.
• They cannot be used to make an unfavorable
  reaction favorable.

51
Free Energy and Reaction Rates

• In biological systems, catalysts are called
  enzymes.
• Most enzymes are proteins.
• 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.

52
Free Energy and Reaction Rates

• Example
• Hexokinase

See Jmol Model of Hexokinase
53
The End