Chapter 13: Enzymes!!

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Chapter 13 Enzymes!!
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What are enzymes?

• Usually proteins (exception ribozymes)
• Biological Catalysts
• Facilitate reactions under physiological
  conditions that would require very harsh
  conditions in the laboratory

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Enzymes biological catalysts responsible for
supporting almost all of the chemical reactions
that maintain organismall homeostasis. The
macromolecular components of almost all enzymes
are composed of protein, except for a class of
RNA modifying catalysts known as ribozymes.
Ribozymes are molecules of ribonucleic acid that
catalyze reactions on the phosphodiester bond of
other RNAs. Almost every significant life
process is dependent on enzyme activity.
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Stryer Fig. 8.3
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Functions of Catalysts

• Lower the Ea for a reaction
• Are regenerated
• Do not affect equilibrium position

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Table 13-3 Enzyme Classification According to
Reaction Type.
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Figure 13-1 An enzymesubstrate complex
illustrating both the geometric and the physical
complementarity between enzymes and substrates.
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Number Classification Biochemical Properties
1. Oxidoreductases Act on many
chemical groupings to add or remove hydrogen
atoms. 2. Transferases Transfer functional
groups between donor and acceptor
molecules. Kinases are specialized transferases
that regulate metabolism by transferring
phosphate from ATP to other molecules. 3. Hydr
olases Add water across a bond, hydrolyzing
it. 4. Lyases Add water, ammonia or carbon
dioxide across double bonds, or remove these
elements to produce double bonds.
5. Isomerases Carry out many kinds of
isomerization L to D isomerizations, mutase
reactions (shifts of chemical groups) and
others. 6. Ligases Catalyze reactions in which
two chemical groups are joined (or ligated)
using ATP.
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1.Addition or removal of water
a.Hydrolases - these include esterases,
carbohydrases, nucleases, deaminases, amidases,
and proteases b.Hydrases such as
fumarase, enolase, aconitase and carbonic
anhydrase 2.Transfer of electrons
a.Oxidases b.Dehydrogenases
3.Transfer of a radical
a.Transglycosidases - of monosaccharides
b.Transphosphorylases and phosphomutases - of a
phosphate group c.Transaminases - of
amino group d.Transmethylases - of a
methyl group e.Transacetylases - of an
acetyl group 4.Splitting or forming a C-C bond
a.Desmolases 5.Changing geometry or
structure of a molecule a.Isomerases
6.Joining two molecules through hydrolysis of
pyrophosphate bond in ATP or other triphosphate
a.Ligases
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Oxidoreductases--catalyze redox reactions
Usually require a coenzyme
Ethanol NAD ? Acetaldehyde NADH H
Enzymes receive common names reflecting their
function, either in the forward or reverse
direction.
The enzyme for this reaction is called
Alcohol Dehydrogenase
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Transferases-transfer functional groups
Kinases transfer phosphates from ATP (or GTP)
E.g Hexokinase Glucose ATP ?glc-6-P ADP
Hydrolases catalyze hydrolytic cleavages
Proteases are hydrolases
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Lyases catalyze group elimination to form double
bonds
e.g. Enolase (glycolysis)
2-Phosphoglycerate ? H2O phosphoenolpyruvate
Isomerases--duh, interconvert isomers
e.g. phosphoglucose isomerase
Glucose-6-phosphate ? Fructose-6-phosphate
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Ligases--join to substrates together at the
expense of ATP
e.g. DNA Ligase
Joins Okazaki fragments during DNA replication
Some bacterial ligases substitute NAD as the
energy source.
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Coenzymes

• Enzymes often require the participation of other
  small molecules to carry out a particular
  reaction.
• These small molecules, called coenzymes, are
  metabolic derivatives of vitamins.
• Vitamins are nutrients required in small amounts
  by organisms. Vitamin deficiencies usually
  present as metabolic disorders, e.g. scurvy

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Table 13-1 The Common Coenzymes.
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Table 13-2 Vitamins That Are Coenzyme Precursors.
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Figure 13-2 The structures and reaction of
nicotinamide-adenine dinucleotide (NAD) and
nicotinamide adenine dinucleotide phosphate
(NADP).
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Figure 13-4 Structures of nicotinamide and
nicotinic acid.
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Enzyme Activities Are Regulated at Various Levels

• Transcription
• Processing
• Translation
• Post-translational modification
• Transient modification (e.g. phosphorylation)
• Allosteric Effectors

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Figure 13-5 The rate of the reaction catalyzed by
ATCase as a function of aspartate concentration.
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Figure 13-6 Schematic representation of the
pyrimidine biosynthesis pathway.
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Figure 13-7a X-Ray structure of ATCase. (a)
(left) T-state ATCase along the proteins
molecular threefold axis of symmetry (right)
R-state ATCase along the proteins molecular
threefold axis of symmetry.
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Figure 13-7b X-Ray structure of ATCase. (b)
(left) T-state ATCase along the proteins
molecular twofold axis of symmetry (right)
R-state ATCase along the proteins molecular
twofold axis of symmetry.
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Figure 13-8 Comparison of the polypeptide
backbones of the ATCase catalytic subunit in the
T state (orange) and the R state (blue).
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Figure 13-9 Schematic diagram indicating the
tertiary and quaternary conformational changes in
two vertically interacting catalytic ATCase
subunits.
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Styer p.277
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Stryer p. 278
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