VIP molecules

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Enzymes

• ----VIP molecules

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Lecture Outline

• What do enzymes do?
• Why study enzymes?
• How do enzymes work?

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What is the difference between an enzyme and a
protein?
Proteins
Enzymes
Nearly all enzymes are proteins, but not all
proteins are enzymes
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What do enzymes do?

• Enzymes are protein catalysts that accelerate
  the rates of chemical reactions.

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Substrates, products, and enzymes

• Enzymes catalyze the rate at which substrates are
  converted to product

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Enzymes convert substrates into products

• What is a substrate?
• A substrate is the compound that is converted
  into the product in an enzyme catalyzed reaction.
• For the reaction catalyzed by aldolase, fructose
  1,6-phosphate is the substrate.

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Enzymes convert substrates into products
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What is the difference between enzyme catalyzed
reactions and uncatalyzed chemical reactions?

• Enzyme catalyzed reactions are much faster than
  uncatalyzed reactions.
• Enzyme catalyzed reactions display saturation
  kinetics with respect to substrate concentration.
• Enzyme catalyzed reactions are optimized for
  specific temperature and pH values.

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Enzyme catalyzed reactions are much faster than
uncatalyzed reactions
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Enzyme catalyzed reactions display saturation
kinetics with respect to reactant concentration
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Enzymes catalyze a wide variety of chemical
reactions

• Oxidoreductases catalyze the transfer of hydrogen
  atoms and electrons
• Transferases catalyze the transfer of functional
  groups from donors to acceptors
• Hydrolases catalyze the cleavage of bonds by the
  addition of water (hydrolysis)
• Lyases catalyze the cleavage of C-C, C-O, or C-N
  bonds
• Isomerases catalyze the transfer of functional
  groups within the same molecule
• Ligases use ATP to catalyze the formation of new
  covalent bonds

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Characteristics

• High efficiency
• Each enzyme has its specific substrate
• (target molecule).
• Regulated activity
• Enzymes are not changed by reactions

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Oxidoreductases catalyze the transfer of hydrogen
atoms and electrons

• Example - Lactate Dehydrogenase

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Transferases catalyze the transfer of functional
groups from donors to acceptors

• Example - Alanine aminotransferase

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Hydrolases catalyze the cleavage of bonds by the
addition of water (hydrolysis)

• Example - Trypsin

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Lyases catalyze the cleavage of C-C, C-O, or C-N
bonds(addition of groups to double bonds or
formation of double bonds by removal of groups)

• Example - ATP-citrate lyase

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Isomerases catalyze the transfer of functional
groups within the same molecule

• Example - Phosphoglucose isomerase

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Ligases use ATP to catalyze the formation of new
covalent bonds

• Example - DNA ligase

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Summary Enzyme classes and major subclasses

• Oxidoreductases
• Dehydrogenases
• Oxidases
• Reductases
• Peroxidases
• Catalase
• Oxygenases
• Hydroxylases

Hydrolases Esterases Glycosidases Peptidases Phosp
hatases Thiolases Phospholipases Amidases Deaminas
es Ribonucleases
Transferases Transaldolase Transketolase Acyltrans
ferase Methyltransferase Glucosyltransferase Phosp
horyltransferase Kinases Phosphomutases
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Summary Enzyme classes and major subclasses

• Lyases
• Decarboxylases
• Aldolases
• Hydratases
• Dehydratases
• Synthases
• Lyases

Ligases Synthetases Carboxylases
Isomerases Racemases Epimerases Isomerases Some
mutases
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Nomenclature

• LDH EC.1.1.1.27 lactate dehydrogenase

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Enzymes do more than just increase the rate of a
chemical reaction

• Control when and where reactions occur
• Regulate the rate of a reaction
• (controlled combustion)
• Optimize reaction for specific conditions
• (e.g. pH, temperature)

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Enzymes control when reactions occur
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The phosphofructokinase/fructose
1,6-bisphosphatase switch prevents glycolysis
(glucose breakdown) and gluconeogenesis (glucose
formation) from occurring at the same time.
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Enzymes are responsible for the controlled
combustion (oxidation) of foodstuffs

• 5 O2 C3H8 4 H2O 3 CO2
  
• propane ?Go-2264 kJ/mol
• 6 O2 C6H12 O6 6 H2O 6 CO2
• glucose ?Go-2876 kJ/mol

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Enzyme catalyzed reactions are optimized for
specific values of temperature and pH
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Important things to remember about enzymes

• 1. Enzymes are not consumed or altered by the
  reaction they catalyze.

Just as a construction worker can take a pile
of lumber and build a home without being
physically changed by the process.
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• 2. Enzymes catalyze both the forward and the
  reverse reaction.

This is an important point. An enzyme does
not determine which direction the reaction goes,
it only increases the rate at which the reaction
approaches equilibrium.
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Enzymes catalyze both the reactions in both the
forward and reverse direction
LDH
LDH
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• 3. Enzymes do not alter the equilibrium (or
  equilibrium constant) between substrates and
  products.

At equilibrium, the ratio of substrates to
products is the same regardless of whether an
enzyme catalyst is present. The rate at
equilibrium is achieved is increased.
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Thermodynamics vs. Kinetics

• Thermodynamics tells us whether a reaction can
  occur.
• Kinetics tells us whether the reaction will occur
  in our lifetimes.

diamond into graphite
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• Consider a bowl of sugar

Decomposition of the sugar C12H22O11 12O2
12CO2 11 H2O
(sucrose) ?Gorxn -5,693 kJ/mol Why doesnt
the bowl of sugar combust when we set it on the
table? Because ?Grxn tells us only whether a
reaction will occur without the addition of
energy, it says nothing about the probability of
the reaction occurring.
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Why study enzymes?

• Understanding how enzymes work is crucial for
  understanding both the physiological basis of
  most diseases and the mechanism of action of
  drugs used to treat these diseases

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Medical Relevance

• Many diseases are caused by the absence,
  malfunction, or inappropriate expression of a
  particular enzyme---SOD
• Enzymes serve as targets for a variety of drugs
• Enzymes are sometimes administered in the
  treatment of disease
• The presence or absence of specific enzymes can
  be used to diagnose specific diseases

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Serum enzymes are commonly used in diagnostic
tests for a variety of diseases

• Myocardial Infarction Lactate dehydrogenase (H4
  isozyme), Aspartate aminotransferase, Creatine
  kinase
• Viral hepatitis Alanine aminotransferase
• Acute pancreatitis Amylase, Lipase
• Liver disease Alkaline phosphatase, Lactate
  dehydrogenase (M4 isozyme)

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Real Life - Tissue Specificity of Lactate
Dehydrogenase
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Lactate Dehydrogenase is composed of four monomers
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What is an isozyme?(1) Isozymes are
physically distinct forms of the same enzyme.
(2) Isozymes may differ from each other by
differences in their amino acid sequences or by
the presence of different posttranslational
modifications in each isozyme. (3) The
relative abundance of different isozymes varies
for different tissues.
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Isozymes An automotive analogy
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Each isozyme of LDH can be separated by
electrophoresis
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Coenzymes and Cofactors Some enzyme proteins
stay in an inactive form until binding with a
coenzyme or a cofactor Apoenzyme Coenzyme
(vitamins) ? Holoenzyme Cofactor
(minerals)   Cofactors Ca, Mg, Mn, Cu, Zn
Coenzymes organic molecules associated with
Vitamins (Vitamin B)
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Some definitions

• Apoenzyme the protein part of an enzyme without
  coenzymes or prosthetic groups that are required
  for the enzyme to have activity.
• Coenzyme small organic or inorganic molecules
  which are bound to the apoenzyme and are required
  for the enzyme to catalyze the chemical reaction.
• Prosthetic group similar to a coenzyme, but is
  tightly bound to the apoenzyme. Heme is a
  prosthetic group in cytochrome c and hemoglobin.
• Holoenzyme the apoenzyme with the coenzyme or
  prosthetic group bound to it (i.e. the active
  form of the enzyme).