Chapter 6
An Introduction To Metabolism
Metabolism/Bioenergetics
• Metabolism: The totality of an organism’s
chemical processes; managing the material and
energy resources of the cell
• Catabolic pathways: degradative process such
as cellular respiration; releases energy
• Anabolic pathways: building process such as
protein synthesis; photosynthesis; consumes
energy
Complexity of Metabolism
Thermodynamics
•
•
•
•
•
Energy (E)~ capacity to do work;
Kinetic energy~ energy of motion;
Potential energy~ stored energy
Thermodynamics~ study of E transformations
1st Law: conservation of energy;
E transferred/transformed, not created/destroyed
• 2nd Law: transformations increase entropy (disorder,
randomness)
• quantity of E is constant, quality is not
Stability, Spontaneous Change,
Equilibrium and Work
Free Energy
• Free energy: portion of system’s E that can perform work (at a
constant T)
• Exergonic reaction: net release of free E to surroundings
• Endergonic reaction: absorbs free E from surroundings
Free Energy Equation
Organisms live at the expense of free energy.
The amount of energy available to do work.
G = H - TS
G = free energy
H = enthalpy or total energy
T = temperature in 0K
S = entropy (disorder/randomness)
Significance of Free Energy
Indicates whether a reaction will occur spontaneously
or not.
In a spontaneous reaction, G decreases, DG<0 (negative)
EXERGONIC REACTION
Products have less G
Reaction is ‘downhill’
Spontaneous
DG is negative
ENDERGONIC REACTION
Products have more G
Reaction is ‘uphill’
Require energy input
DG is positive
Metabolic Disequilibrium
Many metabolic reactions are reversible and reach
equilibriuim.
At equilibrium a cell is dead!
Disequilibrium is maintained by the continual use/removal
of products e.g. respiration
Free Energy Gradient Keeps Metabolism
away from Equilibrium
Energy Coupling & ATP
• E coupling: use of exergonic process to drive an
endergonic one (ATP)
• Adenosine triphosphate
• ATP tail: high negative charge
• ATP hydrolysis: release of free E
• Phosphorylation (phosphorylated intermediate)~
enzymes
Energy
Coupling
by
Phosphate
Transfer
The ATP Cycle
Chemical Reactions
Animation 6.1.1
An Energy Profile of a Reaction
Enzymes
• Catalytic proteins: change the rate of reactions
w/o being consumed
• Free E of activation (activation E): the E
required to break bonds
• Substrate: enzyme reactant
• Active site: pocket or groove on enzyme that
binds to substrate
• Induced fit model binding of substrate changes
shape of the active site so that the substrate can
bind
Enzyme Properties
•Are proteins
•Lower the activation energy of a reaction –
transition state can be reached at cellular temperatures.
•Do not change the nature of the reaction –
only speed up a reaction that would have occurred anyway.
•Are very selective for which reaction they will catalyze
Substrate + enzyme
enzyme-substrate complex
product + enzyme
The Catalytic Cycle of an Enzyme
How an Enzyme Lowers
Activation Energy
• Active site holds 2 or more reactants.
• Induced fit distorts bonds-less E required to break them.
• Active site may produce a micro-environment.
• Side chains of amino acids may participate.
How Enzymes Work
Animation 6.1.6
http://www.chem.ufl.edu/~itl/2045/lectures/lec_m.html
Initial Substrate Conc. Determines
Rate of an Enzyme-Controlled
Reaction
• The higher the substrate conc. the faster the reaction
• If the substrate concentration is high enough –
the enzyme may become saturated, reaction will slow
• Reaction rate may be increased by adding more enzyme.
Effects on Enzyme Activity
• Temperature
• pH
• Cofactors:
inorganic, nonprotein
helpers;
e.g. zinc, iron, copper
• Coenzymes:
organic helpers;
e.g. vitamins
Enzyme Inhibitors
• Irreversible (covalent);
Reversible (weak bonds)
• Competitive: competes for
active site (reversible);
mimics the substrate
• Noncompetitive: bind to
another part of enzyme
(allosteric site) altering its
conformation (shape);
poisons, antibiotics
Allosteric Regulation
Allosteric enzymes have two conformations, one
catalytically active, the other inactive.
Binding of an activator to the allosteric site stabilizes
the active conformation of the enzyme
Binding of an inhibitor to the allosteric site stabilizes
the inactive form of the enzyme (non-competitive)
Allosteric Inhibition
Feedback
Inhibition
Cooperativity
Binding at one site enhances binding at other sites
Enzyme Catalysis Lab
Each enzyme is specific for the reaction it will catalyze. In this laboratory,
Enzyme = catalase
Substrate = hydrogen peroxide (H2O2)
Products = water and oxygen
H 2 O2
H 2O + O2
If a small amount of catalase is added to hydrogen peroxide,
you will be able to observe bubbles of oxygen forming.
To determine the amount of hydrogen peroxide that remains after
the reaction, you will do a titration with KMnO4.
In such a titration, you slowly add a chemical (KMnO4) that
will cause a color change until a target is achieved.
To determine how much hydrogen peroxide (substrate) has
been broken down by catalase at varying times, you measure
the amount of peroxide remaining in each flask.
Reading the Burette
Analysis of Results Enzyme Action Over Time
We can calculate the rate of a reaction by measuring, over
time, either the disappearance of substrate or the
appearance of product.
For example, on the graph above, what is the rate, in
moles/second, over the interval from 0 to 10 seconds?
Rate =
Dx
Dy
= 7-0 moles
10-0 seconds
=
7 = 0.7 mols/sec
10
Calculate the rate in moles/second
between 40 and 50 seconds.
After 40 seconds there were no more
substrate molecules. The curve becomes flat
at this point, and the rate is zero.
During what time interval is the enzyme working at its
maximum velocity?
a.
b.
c.
d.
0–30 seconds
60–120 seconds
120–180 seconds
Over the entire time course
In order to keep the rate constant over the entire time course,
which of the following should be done?
a.
b.
c.
d.
e.
Add more enzyme.
Gradually increase the temperature after 60 seconds.
Add more substrate
Add H2SO4 after 60 seconds.
Remove the accumulating product.
Which of the following graphs represents the rate of the
reaction shown above? Notice that in the graphs below,
the y-axis is number of molecules/sec.
What is the role of sulfuric acid (H2SO4) in this
experiment?
a. It is the substrate on which catalase acts
b. It binds with the remaining hydrogen peroxide during titration
c. It accelerates the reaction between enzyme and substrate
d. It blocks the active site of the enzyme
e. It denatures the enzyme by altering the active site
A student was performing a titration for this laboratory,
and accidentally exceeded the endpoint. What would be
the best step to obtain good data for this point?
a. Estimate the amount of KMnO4 that was in excess, and subtract this
from the result
b. Repeat the titration using the reserved remaining sample.
c. Obtain data for this point from another lab group
d. Prepare a graph of the data without this point, and then read the
estimated value from the graph.