ENZYMES

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ENZYMES

• IB TOPICS
• SL 2.3.1 - 2.3.5
• HL 6.6.1 - 6.6.5

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OBJECTIVES

• Define enzyme, substrate, active site, and
  allosteric site.
• Explain how enzymes affect the rate of metabolic
  reactions in an organism
• Explain enzyme substrate specificity (Lock and
  Key Model, Induced-Fit Model)
• Define denaturing
• Describe the effects of temperature, pH, and
  substrate concentration on enzyme activity
• Describe, compare and contrast competitive and
  non- competitive inhibition of enzymes.
• Define metabolic pathway and how allosteric
  enzymes regulate these pathways by
  non-competitive inhibition by an end product of
  the specific pathway.
• Explain the industrial uses and biotechnological
  uses of enzymes.
• Define co-enzymes and co-factors, give examples
  and describe their role in enzymatic activity.

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Enzymes

• Enzymes are organic catalysts. Catalyst are
  molecules which speed up the rate of a chemical
  reaction (catabolic or anabolic) by lowering the
  energy of activation (the energy needed to bring
  reactants into close enough proximity for contact
  and often enough for the reaction to occur).
• All enzymes are composed of proteins.
• Because enzymes are composed of proteins, their
  shape is important to their function. If you
  change the shape of the protein that composes
  the enzyme you alter or destroy the enzyme.
• Enzymes are specific to which molecules they act
  upon. The substances they act upon are called
  substrates.
• Most enzymes end with the suffix ase. Typically
  it is a portion of the substrates name -ase.
  For example the enzyme found in saliva which
  begins the chemical hydrolysis of amylose is
  called amylase.
• Enzymes are not used up or destroyed in the
  reaction process and at the end of their reaction
  will bind with more substrate molecules and
  repeat the same chemical process. Therefore,
  small numbers of these molecules can have a great
  effect.

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Reaction Forms
Energy of Activation
products
E
E
reactants
E
Free energy
Free energy
E
E
E
E
E
reactants
products
Rate of reaction
Rate of reaction
The reaction above is an endergonic reaction.
Energy is being put in to drive the reaction.
Ex. Photosynthesis
The reaction above is an exergonic reaction.
After the reaction begins energy is released.
Ex. Cellular Respiration
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How Enzymes Affect Reaction Rates

• Enzymes affect the rates of reactions by lowering
  the amount of energy of activation required for
  the reactions to begin. Therefore processes can
  occur in living systems at lower temperatures or
  energy levels than it would require for these
  same reactions to occur without the enzymes
  present.

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How Enzymes Affect Reaction Rates

• C6H1206 602 ? 6CO2 6H20
• Above is the formula for the complete combustion
  of glucose. This reaction can be carried out in
  a laboratory at several hundred degrees Celsius.
• The same reaction occurs during the process of
  cellular respiration in living cells. In humans
  at a temperature of 37o Celsius. What makes the
  difference?

Energy
ENZYMES!
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Enzyme Structure

• All enzymes have an active site where the
  substrate binds. The active site and the
  substrate have complimentary shapes.
• Some enzymes have a second site called an
  allosteric site to which molecules other than
  substrate bind to activate the enzyme or
  deactivate the enzyme. Enzymes with this
  structure are called allosteric enzymes. If the
  molecule activates the enzyme it is called an
  allosteric activator. If the molecule binds to
  the site and deactivates the enzyme it is called
  an allosteric inhibitor. When they bind they
  cause a change in the shape of the active site of
  the enzyme. These molecules are important in the
  regulation of enzyme activity.

Allosteric sites can be thought of as on and
off switches, depending on the effect they have
on the active site.
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How Enzymes Bind to Substrates

• There are two proposed methods by which enzymes
  bind to their substrate molecules
• a. Lock and Key Model
• b. Induced-Fit Model

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Lock and Key Model

• The lock and key model states that the enzymes
  active site shape is specific and complimentary
  in shape to a specific substrate. If the
  substrate does not fit the active site, no
  enzymatic reaction can occur. Just as a specific
  key fits a specific lock, each substrate has a
  specific enzyme with a complimentary active site.

Products
P
Active site
P
S2
S1
S2
S1
ENZYME SUBSTRATE COMPLEX
SUBSTRATE MOLECULES
Enzyme returns from the reaction unchanged and
can now react with more substrate.
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Induced-Fit Model

• The induced model states that the substrate binds
  to the active site and induces or causes a change
  in shape of the active site so that it is a
  complimentary fit. This model explains why some
  enzymes can act on more than one substrate.

Substrate induces a change in active site so that
it is complimentary
Products
Active site in inactive state
P1
P1
SUBSTRATE MOLECULES
S3

S2
S1
S1
ENZYME
ENZYME SUBSTRATE COMPLEX
The active site of the enzyme returns to the
inactive state after the products are released
and now can react with more substrate.
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Induced-Fit Model
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Enzyme Cooperativity

• Some enzymes have multiple active site. It has
  been observed that when one substrate molecule
  binds to a single active site in the inactive
  form or tense state of the enzyme, a
  configurational change occurs in the other active
  sites making them more receptive to other
  substrate molecules.

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Regulation of Enzyme Activity

• To regulate enzyme activity, there must be some
  form of prevention of binding of substrate with
  active site. This is called enzymatic
  inhibition. There are two forms of inhibition
• 1. Competitive inhibition
• 2. Noncompetitive inhibition

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Competitive Inhibition

• This type of inhibition occurs when another
  molecule is structurally similar to the substrate
  and can bind to the active site of the substrate.
  However, since it is not the actual substrate,
  there is no reaction and the substance remains in
  the active site, disabling the enzyme. This is a
  non-reversible process and the enzyme is no
  longer functional. The mimic molecule competes
  with the substrate for the active site.
• These mimic molecules are commonly called
  poisons! The pesticide DDT works in this manner.
  The miracle antibiotic penicillin works in the
  same manner. It inhibits the enzyme certain
  types of pathogenic bacteria use to build their
  cell walls. Without the functional enzyme the
  bacterial cell walls are defective and weak or
  rupture. If the bacteria survive, this makes
  them weak and easy targets for antibodies and our
  white blood cells. Penicillin has little or no
  effect on human cells because we dont have cell
  walls, therefore no enzyme that produces cell
  walls!

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Noncompetitive Inhibition

• This type of inhibition is common in metabolic
  pathways. A metabolic pathway is a series of
  interconnected enzymatic steps where the products
  of one reaction becomes the substrates for
  subsequent enzymatic reactions in the pathway.
  This process is reversible and the enzymes are
  undamaged by the inhibitor molecules. This
  process is best observed in allosteric enzymes,
  where the inhibitor molecules bind to the
  allosteric site to deactivate the enzyme. This
  is called negative-feedback inhibition. This
  form of inhibition prevents the build up of
  excess products and the use of energy to produce
  them.

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Negative-Feedback Inhibition

• This example demonstrates how an end product can
  inhibit the first step in its production.
  Isoleucine binds to the allosteric site of
  threonine deaminase and prevents threonine from
  binding to the active site because the shape of
  the active site is altered. When the level of
  isoleucine drops in the cells cytoplasm, the
  isoleucine is removed from the allosteric site on
  the enzyme, the active site resumes the activated
  shape and the pathway is cut back on and
  isoleucine begins to be produced.

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Environmental Factors Which Affect Enzyme Activity

• Since enzymes are protein any environmental
  change that can affect their structure affects
  their activity. All protein shape determine
  their function. Their structure is due
  primarily to hydrogen bonding at the various
  levels. If any thing disrupts or interferes with
  the hydrogen bonding the proteins level of
  structure begins to breakdown and the protein
  unravels or unfolds and becomes
  non-functional. Denaturing is the destruction of
  a proteins function due to the breakdown or loss
  of its structure. Denaturing is an irreversible
  process (ex. egg albumin before and after
  cooking) Any environmental factor that has an
  effect of hydrogen bonding can denature proteins.
  Temperature and pH both effect hydrogen bonding
  and can denature proteins. Therefore they would
  have a definite effect on enzyme activity.

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Environmental Factors Which Affect Enzyme
Activity Temperature

• All enzymes have an optimum temperature at which
  they work best. If you observe the enzymes
  activity below the specific temperature it will
  steadily increase until it reaches the optimum.
  After the optimum temperature is reached the
  enzymes activity drops dramatically due to
  denaturing.

Depending on the species, the range of optimum
activity is very broad. Above is a comparison
of human enzyme activity with that of bacteria
found in hot springs and oceanic vents.
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Environmental Factors Which Affect Enzyme
Activity pH
In the human bodys digestive tract there are
variations in pH from area to area. The
stomachs juices pH is around 2 (acidic), the
enzyme pepsin found in the gastric juices has
optimum activity at a pH of 2. The
small intestines juices pH is around 8
(basic). The enzyme trypsin found in the small
intestines juices has optimum activity at a pH
of 8.

• All enzymes have an optimum pH at which they work
  best. If the pH falls below or rises above the
  optimum value, enzymatic activity decreases
• as a result of denaturing.

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Environmental Factors Which Affect Enzyme
Activity Substrate Concentration

• The concentration of substrate also has an affect
  on the rate of enzyme activity. If the
  concentration of substrate is increased while the
  concentration of enzyme is constant, the level of
  enzyme activity will increase until a point of
  saturation is reached. At this point there are
  no enzymes available to react with excess
  substrate and the rate of the reaction
  stabilizes. No matter if you continue to add
  substrate, the reaction rate will not increase!

Point of Saturation, all active sites are filled
with substrate.
Rate of Reaction
Increasing Substrate Concentration
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Co-Enzymes and Co-Factors

• Some enzymes require another organic molecule or
  substance to be present before they can function.
  These organic molecules or substances are called
  Co-enzymes or Co-factors. Co-enzymes are organic
  molecules (usually vitamins) and co-factors are
  inorganic substance (minerals). This is one of
  the reasons it is so important to eat a well
  balanced diet. For example, Vitamin K is
  necessary for the enzyme responsible for blood
  clot formation. A lack of vitamin K leads to
  easy bruising and prolonged bleeding when
  injuries occur. Calcium is a co-factor which is
  required by several enzymes for their activation.