Chapter 15 Enzymes

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Chapter 15 Enzymes
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Enzymes

• Ribbon diagram of cytochrome c oxidase, the
  enzyme that directly uses oxygen during
  respiration.

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Enzyme Catalysis

• Enzyme A biological catalyst.
• With the exception of some RNAs that catalyze
  their own self-cleavage, all enzymes are
  proteins.
• Enzymes can increase the rate of a reaction by a
  factor of 109 to 1020 over an uncatalyzed
  reaction.
• Some catalyze the reaction of only one compound.
• Others are stereoselective for example, enzymes
  that catalyze the reactions of only L-amino
  acids.
• Others catalyze reactions of specific types of
  compounds or bonds for example, trypsin
  catalyzes hydrolysis of peptide bonds formed by
  the carboxyl groups of Lys and Arg.

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Enzyme Catalysis

• Figure 15.1 Trypsin catalyzes the hydrolysis of
  peptide bonds formed by the carboxyl group of
  lysine and arginine.

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Classification of Enzymes

• Enzymes are commonly named after the reaction or
  reactions they catalyze.
• Example lactate dehydrogenase, acid phosphatase.
• Enzymes are classified into six major groups
  according to the type of reaction catalyzed
• Oxidoreductases Oxidation-reduction reactions.
• Transferases Group transfer reactions.
• Hydrolases Hydrolysis reactions.
• Lyases Addition of two groups to a double bond,
  or removal of two groups to create a double bond.
• Isomerases Isomerization reactions.
• Ligases The joining to two molecules.

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Classification of Enzymes

• 1. Oxidoreductase
• 2. Transferase

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Classification of Enzymes
3. Hydrolase
4. Lyase
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Classification of Enzymes

• 5. Isomerase
• 6. Ligase

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Enzyme Terminology

• Apoenzyme The protein part of an enzyme.
• Cofactor A nonprotein portion of an enzyme that
  is necessary for catalytic function examples are
  metallic ions such as Zn2 and Mg2.
• Coenzyme A nonprotein organic molecule,
  frequently a B vitamin, that acts as a cofactor.
• Substrate The compound or compounds whose
  reaction an enzyme catalyzes.
• Active site The specific portion of the enzyme
  to which a substrate binds during reaction.

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Schematic of an Active Site

• Figure 15.2 Schematic diagram of the active site
  of an enzyme and the participating components.

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Terms in Enzyme Chemistry

• Activation Any process that initiates or
  increases the activity of an enzyme.
• Inhibition Any process that makes an active
  enzyme less active or inactive.
• Competitive inhibitor A substance that binds to
  the active site of an enzyme thereby preventing
  binding of substrate.
• Noncompetitive inhibitor Any substance that
  binds to a portion of the enzyme other than the
  active site and thereby inhibits the activity of
  the enzyme.

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Enzyme Activity

• Enzyme activity A measure of how much a
  reaction rate is increased.
• We examine how the rate of an enzyme-catalyzed
  reaction is affected by
• Enzyme concentration.
• Substrate concentration.
• Temperature.
• pH.

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Enzyme Activity

• Figure 15.3 The effect of enzyme concentration
  on the rate of an enzyme-catalyzed reaction.
  Substrate concentration, temperature, and pH are
  constant.

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Enzyme Activity

• Figure 15.4 The effect of substrate
  concentration on the rate of an enzyme-catalyzed
  reaction. Enzyme concentration, temperature, and
  pH are constant.

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Enzyme Activity

• Figure 23.5 The effect of temperature on the
  rate of an enzyme-catalyzed reaction. Substrate
  and enzyme concentrations and pH are constant.

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Enzyme Activity

• Figure 23.6 The effect of pH on the rate of an
  enzyme-catalyzed reaction. Substrate and enzyme
  concentrations and temperature are constant.

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Mechanism of Action

• Figure 15.7 Lock-and-key model of enzyme
  mechanism.
• The enzyme is a rigid three-dimensional body.
• The enzyme surface contains the active site.

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Mechanism of Action

• Figure 15.8 The Induced-fit model of an enzyme
  mechanism.
• The active site becomes modified to accommodate
  the substrate.

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Mechanism of Action

• Figure 23.9 The mechanism of competitive
  inhibition.
• When a competitive inhibitor enters the active
  site, the substrate cannot enter.

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Mechanism of Action

• Figure 15.10 Mechanism of noncompetitive
  inhibition. The inhibitor binds itself to a site
  other than the active site (allosterism), thereby
  changing the conformation of the active site.
  The substrate still binds but there is no
  catalysis.

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Mechanism of Action

• Figure 15.11 Enzyme kinetics in the presence and
  the absence of inhibitors.

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Mechanism of Action

• Both the lock-and-key model and the induced-fit
  model emphasize the shape of the active site.
• However, the chemistry of the active site is the
  most important.
• Just five amino acids participate in the active
  site in more than 65 of the enzymes studied to
  date.
• These five are His gt Cys gt Asp gt Arg gt Glu.
• Four of these amino acids have either acidic or
  basic side chains the fifth has a sulfhydryl
  group (-SH).

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Catalytic Power

• Figure 23.12 Enzymes provide an alternative
  pathway for reaction. (a) The activation energy
  profile for a typical reaction. (b) A comparison
  of the activation energy profiles for a catalyzed
  and uncatalyzed reactions.

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Enzyme Regulation

• Feedback control An enzyme-regulation process
  where the product of a series of
  enzyme-catalyzed reactions inhibits an earlier
  reaction in the sequence.
• The inhibition may be competitive or
  noncompetitive.

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Enzyme Regulation

• Proenzyme (zymogen) An inactive form of an
  enzyme that must have part of its polypeptide
  chain hydrolyzed and removed before it becomes
  active.
• An example is trypsin, a digestive enzyme.
• It is synthesized and stored as trypsinogen,
  which has no enzyme activity.
• It becomes active only after a six-amino acid
  fragment is hydrolyzed and removed from the
  N-terminal end of its chain.
• Removal of this small fragment changes not only
  the primary structure but also the tertiary
  structure, allowing the molecule to achieve its
  active form.

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Enzyme Regulation

• Allosterism Enzyme regulation based on an event
  occurring at a place other than the active site
  but that creates a change in the active site.
• An enzyme regulated by this mechanism is called
  an allosteric enzyme.
• Allosteric enzymes often have multiple
  polypeptide chains.
• Negative modulation Inhibition of an allosteric
  enzyme.
• Positive modulation Stimulation of an allosteric
  enzyme.
• Regulator A substance that binds to an
  allosteric enzyme.

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Enzyme Regulation

• Figure 15.14 The allosteric effect. Binding of
  the regulator to a site other than the active
  site changes the shape of the active site.

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Enzyme Regulation

• Figure 15.15 Effects of binding activators and
  inhibitors to allosteric enzymes. The enzyme has
  an equilibrium between the T form and the R form.

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Enzyme Regulation

• Protein modification The process of affecting
  enzyme activity by covalently modifying it.
• The best known examples of protein modification
  involve phosphorylation/dephosphorylation.
• Example Pyruvate kinase (PK) is the active form
  of the enzyme it is inactivated by
  phosphorylation to pyruvate kinase phosphate
  (PKP).

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Enzyme Regulation

• Isoenzyme (Isozymes) An enzyme that occurs in
  multiple forms each catalyzes the same reaction.
• Example lactate dehydrogenase (LDH) catalyzes
  the oxidation of lactate to pyruvate.
• The enzyme is a tetramer of H and M chains.
• H4 is present predominately in heart muscle.
• M4 is present predominantly in the liver and in
  skeletal muscle.
• H3M, H2M2, and HM3 also exist.
• H4 is allosterically inhibited by high levels of
  pyruvate while M4 is not.
• H4 in serum correlates with the severity of heart
  attack.

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Enzyme Regulation

• Figure 15.16 The isozymes of lactate
  dehydrogenase (LDH). The electrophoresis gel
  depicts the relative isozyme types found in
  different tissues.

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Enzymes Used in Medicine
Table 15.2 Enzyme Assays useful in Medical
Diagnosis
Insert Table 23.2, page 648
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Transition-State Analogs

• Transition state analog A molecule whose shape
  mimics the transition state of a substrate.
• Figure 15.17 The proline racemase reaction.
  Pyrrole-2-carboxylate mimics the planar
  transition state of the reaction (next screen).

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Transition-State Analog
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Transition-State Analogs

• Abzyme An antibody that has catalytic activity
  because it was created using a transition state
  analog as an immunogen. (a) The molecule below is
  a transition analog for the reaction of an amino
  acid with pyridoxal-5-phosphate. (b) The abzyme
  is then used to catalyze the reaction on the next
  screen.

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Transition-State Analogs
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Catalytic Antibodies Against Cocaine
p652
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Catalytic Antibodies Against Cocaine
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