Chapter 8
An Introduction to Metabolism
Major Topics
Energy
Regulation of cellular chemistry
Free energy change
Coupled reactions
Activation energy
Enzymes
Metabolism
All the chemical changes that occur in an organism
Metabolic pathways begin with a specific molecule, which is
then altered in a series of defined steps.
A biochemical pathway.
What controls what molecules are produced? Are others
possible, eg., compound “E” instead of “B,” etc. Quantities? All
the time or just some times? In all cells?
Enzymes - serve as catalysts (chemical agents that change
the rate of a reaction without being consumed by the
reaction)
Metabolism
2 types of pathways metabolism can follow
1. Catabolic - breaks down complex molecules to
simpler compounds (from proteins to amino acids)
2. Anabolic - consume energy to build complex
molecules from simpler ones (synthesis of proteins
from amino acids)
Energy coupling - interaction between catabolic
and anabolic pathways
From an interactive chart at [Link]
Energy
Energy = capacity to do work
Energy is the ability to rearrange a collection of
matter (eg.: your cells expend energy moving
substances across membranes)
Forms of energy
• Types of energy
• chemical energy:
energy stored in
chemical bonds and
other chemical
processes
• kinetic energy:
energy of movement
• heat energy: kinetic
energy applied to
atoms/molecules
• potential energy:
energy possessed by
matter due to location
or position
How does energy work
in a cell?
The study of energy transformations that
occur in a collection of matter is called
thermodynamics
2 important laws of thermodynamics apply to
biological systems
◦ 1st law of thermodynamics
◦ 2nd law of thermodynamics
1 st law of thermodynamics
Energy can be transferred and transformed
but it can not be created or destroyed
AKA conservation of energy
◦ eg.: an electric company does not make energy but it
converts it to a form we can use
◦ eg.: a green plant does not produce energy, it converts
light to chemical energy (photosynthesis)
◦ eg: student eats a candy bar and runs laps at the Rec
Center (chemical energy converted to kinetic energy
and heat).
Energy in a system will change only when heat or
work is added or removed.
2 nd law of thermodynamics
Every energy transfer or transformation increases
the entropy of the universe or system
◦ Entropy, a measure of disorder @ randomness, is a
mathematical formulation, difficult to express in words.
◦ Entropy is less apparent in biological systems b/c it
takes the form of heat
◦ Biological systems are not very efficient b/c a great
deal of energy is lost through heat
Heat is energy in a random state, we have not created or
destroyed energy
◦ System @ an isolated reaction, no matter or energy
transfer in or out.
◦ The purpose of this law is to determine whether or
not a process is spontaneous!
Example of Entropy ****
Ice cube… order and structure
Ice cube melts. . . gains entropy and
energy but loses order and structure
Ice cube becomes water…more energy
(moving around) but increased disorder
Water becomes water vapor…lot of
energy and lot of disorder.. little to no
structure
Two sets of examples of the laws of thermodynamics
Only ~25% of the chemical energy of a car makes it go, the
remaining 75% is lost as heat
Applying thermodynamics to
biological reactions
Thermodynamics apply to the whole universe
Biologists want to understand metabolic
reactions
One way of determining whether metabolic
reactions are spontaneous is by measuring free
energy
Free energy (G) is the portion of a system’s
energy that is available for conversion to some
other form. All molecules have an inherent free
energy. Willard Gibbs!
Applying thermodynamics to
biological reactions
• Why these two sugars? Why
a C1 to C2 bond?
• Why these two amino acids?
Why joined in this way?
• Related issues: Why do
antibiotics kill bacteria? Why
are bacteria becoming
resistant to antibiotics? How
do pesticides kill insects?
How do statins lower
cholesterol?
Free energy
Example: chemical energy in glucose can be
converted into chemical energy of other
molecules, or kinetic energy (movement), heat
energy, etc.
The change in free energy (G) can be
calculated using the formula:
G = H - TS
H = total energy
S = system’s entropy
T = absolute temperature in Kelvin units
G
When we know G for a process, we can predict whether
the reaction will be spontaneous (without outside energy)
Spontaneous does not necessarily mean fast, simply that it
can occur eventually without energy
◦ Spontaneous reactions have a negative G value (G < 0)
◦ Processes that have a positive or zero G are never spontaneous!
For a chemical reaction
A+B→C+D
G = (free energy of C + D) – (free energy of A + B)
More generally:
G = G(final state) – G(initial state)
Why do biologists care about G?
Gives us the power to predict which kinds of
changes can happen without assistance
Important for metabolism b/c we need to know
which reactions can supply energy to do work
for other reactions in a cell
Free energy change
Using G (free energy change of A +B C +D)
= (free energy of C and D) – (free energy of A and B)
◦ Example: glucose + fructose sucrose and H2O
◦ G = (free energy of sucrose + H2O) – (free energy of
glucose + fructose) = +7 kcal/mol *
◦ That is, sucrose and H2O have more free energy than
glucose and fructose.
*kcal = kilocalories, a measure of energy. mol = mole, a
quantity of molecules/atoms/etc.
Maximum stability
Max stability = equilibrium
Most chemical reactions are reversible (and
proceed forward and backward at the same
rate)
As a reaction proceeds toward equilibrium the
mixture of reactants and products decreases
and G approaches 0.
Classification of free energy
changes and metabolism
If G < 0, or negative,
chemical reaction it is
exergonic.
◦ AKA “spontaneous.” Releases
energy.
If G > 0, chemical reaction
or positive it is endergonic.
◦ Requires input of energy.
Cannot occur unless energy
from some other source is
added.
Free energy change
If S has more free energy than R, how can the
reaction R → S occur?
How does sucrose get made if
glucose + fructose sucrose + H2O has a G of
+7 kcal/mol?
Energy must be added from an outside source to
make possible R → S, or synthesis of sucrose.
Cellular respiration
C6H12O6 + O2 6CO2 +6H2O
For every 180 grams of glucose broken
down by cellular respiration, 686 kcal/mol of
energy are made available for work
G = -686 kcal/mol
This is exergonic
*kcal = kilocalories, a measure of energy. mol = mole, a
quantity of molecules/atoms/etc.
Synthesizing glucose via
photosynthesis
How do plants make sugars?
The reverse process - conversion of CO2
and H2O into sugar
Strongly endergonic
G = +686 kcal/mol
Need an energy source - Sunlight
Energy coupling
Cells carry out endergonic reactions (G > 0), by
coupling them to a more strongly exergonic
reaction.
The most common exergonic reaction is ATP
hydrolysis.
ATP
The source of energy that drives cellular work is
ATP (adenosine triphosphate)
Structurally similar to one type of nucleotide found
in nucleic acid (A in RNA or DNA)
◦ Adenine nitrogenous
base
◦ Ribose sugar
◦ 3 phosphate groups
(instead of 1 as in
the base A in RNA)
ATP
The energy of ATP is stored in the bonds between the 3
phosphates
When these bonds are broken by ATP hydrolysis
a large amount of energy is released
◦ Terminal phosphate is removed, producing ADP and Pi
(inorganic phosphate), eg: ATP + H2O ADP + PO4
G = -7.3 kcal/mol.
How ATP performs work
The triphosphate tail is highly unstable
When water hydrolyzes the terminal phosphate
bond a molecule of inorganic phosphate (Pi) is
removed
What happens to the phosphate?
The phosphate group generated is transferred to some
other molecule with the help of an enzyme
The molecule that receives the phosphate is
phosphorylated
◦ This molecule is energized and perform work
E.g.: ATP powers the movement of muscles by
transferring phosphate to contractile proteins
How ATP hydrolysis of ATP performs
work
With the help of specific enzymes, the cell is able
to use the energy released by ATP hydrolysis
directly to drive chemical reactions that, by
themselves, are endergonic
This is called energy coupling
ATP can be regenerated
ATP is regenerated by the addition of phosphate to ADP
The ATP cycle can work at an incredible pace
eg.: a working muscle cell recycles its entire pool of ATP
about once each minute. That turnover represents 10
million molecules of ATP consumed and regenerated per
second per cell!
Energy is needed in
chemical reactions!!!!!
Enzymes
Catalyst: a substance that accelerates a chemical
reaction without being changed by it.
Lower the activation energy, so that it is not a barrier
under cellular conditions.
Biological catalysts = enzyme.
Speed up the rate of reactions
Although a reaction my be
spontaneous, it may take years
for the hydrolysis to take place
◦ The ending -ASE indicates an enzyme
Enzyme example
The hydrolysis of sucrose into glucose and
fructose could take years sitting in sterile water
at room temp. Adding the enzyme sucrase will
allow the hydrolysis to take place within
seconds
Characteristics of enzymes
Lower the activation energy
Increase the rates of
reactions
A chemical reaction involves
breaking and making
bonds. The bonds on
existing reactants must be
broken and new bonds
formed, creating the
products
Activation Energy:Video
Activation Energy
Most molecules are stable, even if they contain a lot of
free energy.
Sucrose glucose + fructose (ΔG = -7 kcal/mol).
But sucrose is stable; does not readily break down.
Complete oxidation of glucose:
C6H12O6 + 6O2 6CO2 + 6H2O (ΔG = -686
kcal/mol)
Paper (cellulose = glucose polymer) does not break
down into CO2 and H2O.
Starting an exergonic reaction requires overcoming a
barrier, the activation energy.
Activation Energy
Energy must be added to
break bonds before others
are formed.
Reactants Products,
G < 0
◦ But some energy must be
added before the
reaction can proceed.
A common non-catalytic way to overcome
activation energy (EA) is heat (eg., burning paper).
Enzymes
Enzymes lower the activation energy by:
◦ acting as a template to bring reactive groups into
proximity
◦ straining bonds & stabilizing transition state
◦ providing microenvironment to chemical reaction
◦ participating directly in chemical reaction
Substrates
The substance on which an enzyme will work
Enzymes are picky and will only react with certain
molecules
◦ Lock and key type relationship (in most cases)
Enzymes & Substrates
There are many different enzymes and many
different substrates
Enzymes actually bind to substrates
An enzyme increases the rate of a reaction
without becoming consumed in the process
A single enzyme molecule can act on
average1,000 substrate molecules per second
◦ Some enzymes are even faster
◦ Some are slower
Active site of an enzyme
Enzymes are usually proteins (plus a few RNAs)
Usually globular proteins.
◦ Only one part of the molecule is used in the
reaction (the active site)
The active site is usually a pocket or groove
on the surface of the protein composed of only
a few of the enzyme’s amino acids
◦ The remainder of the protein provides “structure”
or a framework that keeps the active site in an
appropriate configuration
◦ Regulates enzyme activity
Steps in catalysis:
◦ substrate(s) bind in active site
◦ Change in protein folding tightens fit around substrate after
binding (= induced fit).
◦ chemical reaction takes place
◦ product(s) released
Enzyme Function and Inhibition:
Video
Enzyme Regulation
Given the bewildering
array of chemistry in the
cell (v. small part shown
here), how is cellular
metabolism regulated?
Answer: Enzymes.
◦ Enzymes can be regulated:
can be turned on or off,
or their rate of action
adjusted.
Enzyme Regulation
All biochemical reactions are exergonic.
◦ Some are inherently exergonic.
◦ Others are endergonic reactions coupled to an
exergonic reaction (eg., ATP hydrolysis).
Most exergonic reactions require catalysis to
overcome the activation energy.
Enzyme activity is regulated to provide cellular
requirements. Types of enzyme regulation:
◦ competitive
◦ non–competitive (common, examples to come).
◦ compartmentalization of enzymes and substrates
(common, later).
Environmental factors
Just as there is an optimal
environment for our cells,
enzymes have optimal
conditions in which they
perform at their best
3 groups of factors affect
enzyme activity
◦ Environmental conditions
Temperature, pH, salt conc.
◦ Cofactors
◦ Enzyme inhibitors
Cofactors
Non-protein molecule required for catalytic
activity
◦ eg.: Cofactor (metal ions)
Zinc
Iron
Copper
◦ eg.: Coenzyme: organic molecules that act as cofactor
Vitamins
Enzyme Inhibitors
Competitive inhibitors
◦ Resemble the substrate and compete for the active site
◦ One way to get around this problem is to increase the
amount of substrate so that there is more substrate than
the competitive inhibitor
Enzyme Inhibitors
Noncompetitive inhibitors
◦ Binds to the enzyme at a location away from the active
site but alters the conformation of the enzyme so that
the active site is no longer functional
◦ Synonym: allosteric regulation.
◦ Allosteric site: site to which regulator binds. Not
the active site.
Enzyme Inhibitors
Proteins exist in 2 or more alternative, slightly
different 3D shapes or conformations.
Binding of a molecule induces a change in
conformation. Change in conformation changes
shape of active site.
◦ Binding of regulator may
be inhibitory (as in figure) or
stimulatory (not shown).
◦ Major mechanism of biological
regulation.
Allosteric and Cooperativity
Cooperativity: binding of one substrate molecule
induces a conformational change that increases the
possibility of binding a second substrate molecule.
Enzyme Inhibitors
Important in pharmacology (drug discovery and
design)
Toxins and poisons are often irreversible enzyme
inhibitors
◦ Sarin (nerve gas)
◦ Other examples
penicillin (inhibits enzyme that produces cell wall)
protease inhibitors (HIV)
glyphosate (herbicide Roundup; inhibits amino acid
biosynthesis)
insecticide (neural poison; inhibits enzyme req’d for nerve
transmission)
Feedback Inhibition
Feedback inhibition: a
“downstream” product
inhibits an earlier step in a
biochemical pathway.
◦ Usually allosteric; almost never
competitive. Why?
Feedback Inhibition Video
Learning objectives
Types of energy
Free energy and free energy change; endergonic and
exergonic reactions
ATP structure and hydrolysis
Coupled reactions
Activation energy
Enzyme structure
Mechanism of enzyme catalysis
Enzyme regulation
◦ Competitive, non-competitive (allosteric), feedback
inhibition, cooperativity.