Enzyme Structure and
Function
Protein catalysts
Enzymes are Catalysts
• This means that enzymes help speed up
chemical reactions.
• How?
– Enzymes lower the activation energy of a
reaction.
– If the Ea is lower, more reactant molecules
will make it over the “energy hill”, so more
products are produced per second.
Analogy: Plasma HD TVs
• What has happened to the rate of purchase of
plasma HD TVs over the last 10 years?
– The rate has increased (i.e.: Best Buy might have
sold an average of 2 per month in 1997 but sell an
average of 25 per month in 2007)
– Just like, with enzymes, the rate of the reaction
increases.
• Why has the number changed?
– The price has decreased, allowing more people to
overcome the “cost barrier”.
– Enzymes lower the “energy barrier” so more reactants
can overcome it.
Lock and Key Model
• Enzymes are specific
– each one helps only one type of reaction to occur.
• Each enzyme has a unique “active site”.
– An enzyme binds a substrate molecule in its active
site.
• When the substrate is bound to the enzyme, the
bonds are easier to break, so less energy is
required for the reaction to occur.
“Lock and Key” Model
Enzymes are Organic Catalysts
• Organic compound = made by living things,
carbon based.
– Lipids, carbohydrates, proteins, nucleic acids
• Enzymes are proteins.
– Proteins are polypeptides. They are long chains
of amino acids.
– The number, type, and sequence of amino acids
determines a protein’s shape.
– So, what makes each enzyme different (i.e.: the
active sites different) are the amino acids that make
up each enzyme.
Enzyme (and protein) structure
“Magnified” section of
protein (unfolded)
This is the enzyme
“catalase”, the
enzyme found in liver
Amino Acids
• “Building Blocks” of proteins.
• 20 different ones
• Each one has an amino group, a carboxyl
group, and an “R-group”.
• The R-group of each amino acid is
unique.
General
Structure
Specific Examples
DNA and Proteins
• The N-base sequence (ATCG) of a gene is the
“recipe” for making a protein.
– The N-base sequence dictates the correct sequence of
amino acids.
More on Protein Structure
• An enzyme (and any other protein) is made by
linking amino acids together in the correct order
(sequence).
• Reaction = dehydration synthesis (condensation)
reaction.
– Many of these reactions occur until the protein consists of
100+ amino acids linked together.
–http://trc.ucdavis.edu/biosci10v/bis10v/media/ch02/peptide_bonding.html
Your Turn!
• Draw a dipeptide that consists of serine
and threonine.
The amino acid chain (polypeptide) twists
and folds to form a functional protein
• The sequence of
amino acids making
up an enzyme
determines how that
enzyme folds into the
correct 3-D shape,
allowing it to bind with
its substrate.
– So a “real” enzyme looks
something like this.
An enzyme cannot function if it has
an improper shape
• Environmental factors:
– May temporarily change the shape of the
enzyme = denaturation
– May “block” the active site, rather than
change the shape
• Genetic disorder:
– Enzyme never folds into the correct shape
because the “recipe” is wrong.
– Adding the wrong amino acid(s) is like adding
the wrong ingredient(s) = incorrect product.
The Story so far…
• Substrate Concentration:
– Decreases over time
– Less collisions between substrate & enzyme =
decreased reaction rate
• Bubbling slows due to less hydrogen peroxide
molecules colliding with liver enzymes.
(Remember the toothpicks)
– When all of the substrate has been used, the
reaction stops.
• Heavy Metal Concentration:
– As heavy metal concentration increases,
reaction rate decreases.
• The copper sulfate soaked liver had a reaction rate of 1 vs.
the water soaked liver had a reaction rate of 3.
– A heavy metal can bind to an enzyme’s active
site.
• Think of the straws mixed with toothpicks.
– Enzyme can’t bind to substrate as often so the
reaction is slower.
Metal Ions and Enzyme Inhibition
Hydrogen peroxide
(substrate) binds to
enzyme and is broken
down (reaction occursbubbling observed.)
Metal ion gets in the way
and hydrogen peroxide
cannot bind to the
enzyme. Reaction either
doesn’t occur or occurs
at a slower rate. (Not all
enzymes are blocked.)
• pH
– For catalase (liver enzyme) a neutral pH (7) is
ideal. Lowering or raising pH decreases
reaction rate.
• Acid (pH of 2): reaction rate of 1
• Base (pH of 12): reaction rate of 2
– H+ and OH- ions do NOT block the enzyme’s
active site. They DO change the 3-D shape of
an enzyme, thereby changing its active site.
– “Lock and Key” no longer match; enzyme
can’t bind to substrate when they collide.
pH and denaturation
Not all enzymes have the same “optimal” pH. Catalase
(liver enzyme) is more like chymotrypsin. However,
pepsin (a stomach enzyme) functions best at a low
(acidic) pH. At pH 1, pepsin is in it’s functional shape; it
would be able to bind to its substate. At pH 5, the
enzyme’s shape is different and it no longer has an active
site able to bind the substrate. The change in enzyme
activity is observed as a difference in reaction rate.
• Temperature
– The ideal temperature for the functioning of
catalase is around 40°C (human body temp.)
– At lower temperatures enzyme and substrate
molecules move less, so fewer collisions
occur and the reaction is slower
– At higher temperatures the 3-D shape of the
enzyme changes and the active site takes on
a different shape (denaturation)
• Substrate can’t fit into active site
Temperature and Reaction Rate
Shape of active
site changes
(substrate can’t
bind)
Slower reaction due
to fewer collisions