Enzyme Function
Complete online Biology Place Enzyme Catalysis and then answer the following
questions.
1 How do enzymes lower the energy of activation?
A. Enzymes catalyze reactions by lower the energy of activation. This occurs when the
enzyme acts on a substrate. In this type of reaction (enzyme-mediated) substrate
molecules change and form a product. The enzyme stays unchanged and can
continue catalyzing other molecules.
2 How does the active site of an enzyme change when it binds a substrate molecule?
A. When an enzyme binds to a substrate, what is called an induced fit – an alteration of
the active site, which enhances catalysis – occurs. The enzyme then converts the
substrate to a product.
3 Is the change to the active site of an enzyme permanent? How do you know?
A. Enzymes return to their original form after the release of products; Because if they
weren’t restored to their original form it couldn’t perform this catalysis over and
over.
4 What types of molecular interactions occur between the active site and the substrate?
(Hint: You might need to read additional resources such as Wikipedia's Active
Site)
A. The active site is the location on an enzyme where substrate molecules undergo
chemical reactions after they bind. The active site has binding sites – residues
that form temp. bonds with the substrate- and catalytic sites – residues that speed
up reactions of the substrate. Active sites catalyze reactions because their
residues are unchanged at the end of the chemical reactions.
5 How does pH affect the ability of an enzyme to bind a substrate? Explain the
mechanism.
A. pH levels are specific to different enzymes. When the pH changes the active site
changes shape and affects the function of the enzyme. This is because of the
presence of either H+ (acidic) or OH- (basic) ions. Enzymes in your stomach,
like lipase, function best in acidic environments and enzymes found in your small
intestine work best in basic environments.
6 How does temperature affect the ability of an enzyme to bind a substrate? Sketch a
graph depicting the relationship between temperature and enzyme activity. Be
certain to label both axes.
A. Catalysis increases at higher temperatures because chemical reactions speed up as
temperature increases. However, each enzyme has a specific heat optimum,
beyond which point an enzymes shape is lost. Also, boiling water denatures most
enzymes.
7 What specific changes occur to the structure of an enzyme when it is boiled?
A. Boiling water denatures most enzymes’ functional shape, so it would not be able to
make any more catalytic reactions.
Enzyme structure
Use FirstGlance to answer the following questions about enzymes bound to substrates.
1 Enter 1V4S into the PDB identification code box.
a
What is the name of the enzyme?
glucokinase.
b
What is the name of the organism (scientific and common) from which the
enzyme was isolated?
Isolated from humans
c
Where in the organism is the enzyme located?
Pancreas and liver
d
What is the function of the enzyme?
Glucokinase acts as a “glucose sensor”, which means it recognizes the blood
glucose level in the body. When blood glucose rises, the amount of
insulin in the pancreas also increases.
e
How many chains are present in this enzyme?
One chain: A
f
Capture an image of the molecule which displays a view that depicts the
function of the enzyme?
g
How many substrate molecules are bound to this enzyme? (Please note that not
all ligands are substrates!)
h
One substrate (glucose) is bound to this enzyme
Predict how the enzyme likely binds to the substrate (e.g., hydrogen bonds,
hydrophobic/hydrophilic interactions, weak covalent bonds) and explain
your reasoning.
The picture probably depicts this enzyme bonds to the substrate through
hydrophilic interactions. You can tell because the substrate is surrounded
by hydrophilic molecules. Hydroxyl groups result from the enzyme being
polar and hydrophilic.
2 Enter 3MMT into the PDB identification code box.
a
What is the name of the enzyme?
Fructose Bisphosphate Adolase
b
What is the name of the organism (scientific and common) from which the
enzyme was isolated?
Found in eukaryotic and prokaryotic organisms. This specific enzyme was
isolated from a form of probacteria known as bartonella henselae.
c
Where in the organism is the enzyme located?
A bacterium.
d
What is the function of the enzyme?
To break down fructose, biphosphate and adol.
e
How many chains are present in this enzyme?
Four chains: A=B=C=D
f
Capture an image of the molecule which displays a view that depicts the
function of the enzyme?
g
How many substrate molecules are bound to this enzyme? (Please note that not
all ligands are substrates!)
Three: fructose, biphosphate & adol
h
Predict how the enzyme likely binds to the substrate (e.g., hydrogen bonds,
hydrophobic/hydrophilic interactions, weak covalent bonds) and explain
your reasoning.
I think the enzyme binds to the substrate through hydrophilic reactions because
of the amount of polar ions surrounding the substrates.
3 Enter 2YLJ into the PDB identification code box.
a
What is the name of the enzyme?
Horseradish Peroxidase
b
What is the name of the organism (scientific and common) from which the
enzyme was isolated?
Horseradish plants
c
Where in the organism is the enzyme located?
Roots of horseradish plants.
d
What is the function of the enzyme?
Uses hydrogen peroxide to oxidize organic and inorganic compound molecules.
Horseradish peroxidase speeds up the conversion of chromogenic
substrates, and produces light when acting on specific substrates.
e
How many chains are present in this enzyme?
One chain: A
f
Capture an image of the molecule which displays a view that depicts the
function of the enzyme?
g
How many substrate molecules are bound to this enzyme? (Please note that not
all ligands are substrates!)
There are chromogenix and chemiluminescent substrates
Predict how the enzyme likely binds to the substrate (e.g., hydrogen bonds,
hydrophobic/hydrophilic interactions, weak covalent bonds) and explain your reasoning.
Because of the various types of substrates found in the enzyme I think it binds to
the substrate through weak covalent bonds, and those are the most broad for binding.