CHAPTER 6
AN INTRODUCTION TO
METABOLISM
Figure 6.1 The complexity of metabolism
Metabolism
is the sum total
of all of an
organism’s
chemical reactions.
It is an emergent property
That arises from interactions
between molecules within
the cell.
• Enzymes (biological catalysts) direct matter
through the metabolic pathways by selectively
accelerating each step. We’ll learn all about
enzymes in a minute…
• In the next class we will perform a lab dealing
with enzymes… LAB #2: enzyme catalysis.
You must let me know if your lab manual
hasn’t arrived yet so I can photocopy the first
lab for you. Pick it up from me tomorrow so
you can do your HW.
• HW: pre-read the lab and do the lab bench
exercise for lab #2. PopQUIZ next class on
the procedure!!!
METABOLISM all the rxns…
• Catabolic pathways (catabolism) =
degradative processes that release energy by breaking down
complex molecules into simpler ones.
Ex. Cellular respiration
Glucose or Amino Acids -> CO2 + H20 + ATP (energy)
• Anabolic Pathways (anabolism) =
processes that consume energy to build complicated molecules
from simpler ones.
Ex. Synthesis of Protein from amino acids or glucose by PhotoS
Forming peptide bonds requires energy
• Energy released from “downhill” reactions of catabolism (ATP
ADP) is used to drive the “uphill” reactions of anabolism
(polymerization) = “coupled reaction”
THIS IS CALLED COUPLING!!!!
(ewwww. How cute.)
BIOENERGETICS & ENERGY
• Energy- the capacity to do work… to
move matter against the forces of
gravity and friction.
• What are the three forms of energy?
BIOENERGETICS & ENERGY
• What are the three forms of energy?
Potential, Kinetic, Chemical
Water stored
Behind a dam.
(potential energy)
Water rushing out
Of the dam.
(kinetic energy)
Cheetah… also,
potential & kinetic energy.
How is the cheetah storing it’s
potential energy???
CHEMICAL ENERGY
• A form of potential energy
• Stored in molecules as a result of the
arrangement of the atoms in the molecules.
• Big molecules like glucose and proteins have
a lot of stored chemical energy.
• Small molecules like carbon dioxide, oxygen
and water have little stored energy.
• Enormous molecules like glycogen, starch
(amylose & amylopectin) and lipids have
even more chemical energy.
THERMODYNAMICS
•
The study of energy transformations
that occur in a collection of matter.
1. 1st law = energy can be transferred
and transformed but not created nor
destroyed.
2. 2nd law = every energy transfer
increases the entropy (randomness)
of the universe.
Ex. messy room, random molecular motion,
macromolecules to small ones.
How do these pictures
exemplify the 2 laws of
thermodynamics?
How do these pictures
exemplify the 2 laws???
Octane, a hydrocarbon, is reduced to CO2 and H2O
when burned, transferring energy from chemical to kinetic…
increasing the entropy of the environment
THE QUANTITY OF ENERGY IN THE
UNIVERSE IS CONSTANT…
BUT THE QUALITY ISN’T.
Considering the laws of thermodynamics…
how do we explain the orderliness of life?
Considering the laws of thermodynamics…
how do we explain the orderliness of life?
Organisms are open
systems!
Matter & energy are
transferred
between the
system & it’s
surroundings.
There is a constant
source of
energy.
Ex. Cells take in starch, protein, lipids &
release energy (ATP) CO2 and water.
Figure 6.7 Disequilibrium and work in closed and open systems
A. FREE ENERGY (G)
• Free energy is a measure of a system’s instabilityit’s tendency to change to a more stable state.
– FYI- big molecules w/ lots of covalent bonds are
unstable. Small molecules like CO2 are stable.
• Thus, free energy is the portion of a system’s
energy that is available to perform work.
Equation: Free energy (G) = total energy - entropy (temp
K)
• What about heat?
• Temperature amplifies the entropy of a system so
the higher the temperature, the less free energy
there is left available (because you have to
subtract this from the total energy.)
• The amount of free energy at the beginning and end of
a reaction (sG change in free energy) predicts whether
a reaction will occur spontaneously or not.
sG = free energyfinal - free energyinitial
• TO OCCUR SPONTANEOUSLY The system must
give up order, energy, or both. It will have a negative
value.
• Ex. Cellular Respiration has a negative sG.
• Ex. Glucose + O2  CO2 + H20 + 38 ATP energy
More free energy
LESS STABLE
Stretched slinky
Girl at top of slide
Glucose molecule
Less free energy
MORE STABLE
Compact slinky
Girl at bottom of slide
CO2 & H20
Biochemical reactions can be
1) exergonic or 2) endergonic
Figure 6.6 Energy changes in exergonic and endergonic reactions
you may have learned the terms Exo and Endothermic
Exergonic Rxns have a - sG. Endergonic Rxns have a + sG.
1. EXERGONIC “energy outward”
•
•
•
•
sG is negative
Why? Because the chemical mixture loses free
energy.
Energy is released.
The reaction is spontaneous.
Ex. C6H12O6 + 6 02 --> 6 CO2 + 6 H20
sG = -686 kcal/mol
The products have 686 kcal less free energy than
the reactants. We’ll learn that the energy is
converted to ATP molecules (and lost as heat).
Figure 6.12 Energy profile of an exergonic reaction
2. ENDERGONIC = “energy inward”
•
•
•
•
•
•
sG is positive
Why? Because this reaction stores free energy
in larger molecules.
Energy is absorbed from its surroundings.
The reaction is non-spontaneous.
sG is the amount of energy required to drive the
reaction.
Ex. Photons + 6CO2 + 6H20 --> C6H12O6 + 6O2
Many biological pathways rely on energy
coupling, using the free energy released
from an exergonic process to drive an
endergonic one.
ALL reactions are coupled with the
degradation OR synthesis of ATP
ATP adenosine-tri-phosphate
• Made of: adenine + ribose
+ 3 phosphates
(basically, an Adenine RNA
nucleotide w/ 3 not 1 P)
• When the terminal
phosphate bond is broken,
a molecule of inorganic
phosphate leaves the ATP
and ADP is left
• Phosphorylation =
transferring a phosphate
group from ATP to some
other molecule.
• This makes the molecule
more reactive (less stable)
than the original molecule.
Figure 6.9 Energy coupling by phosphate transfer
B. ACTIVATION ENERGY
(Ea)• the initial investment of
energy “energy hump”
needed for starting a
reaction (energy
needed to break the
bonds of the reactant
molecules)
• Activation energy
prevents spontaneous
reactions from going
forward (occurring)
What would happen to biochemical
reactions and high-energy molecules
without activation energy? What would
happen to you???? (discuss)
What would happen to biochemical
reactions and high-energy molecules
without activation energy? What would
happen to you????
• Complex molecules of the cell
(ie. proteins, DNA, carbs) would decompose
spontaneously because they are rich in free
energy.
• The laws of thermodynamics favor their
breakdown.
How can cellular reactions
overcome activation energy?
1) Heat
2) Enzyme (biological catalyst)
Figure 6.11 Example of an enzyme-catalyzed reaction: Hydrolysis of sucrose
C. CATALYSTS
• What do they do?
• Speed up chemical reactions.
• How do they do it?
• by lowering the amount of activation
energy needed.
ENZYMES
• Are globular proteins
• Names ending in -ase
• Enzymes act on substrates
How do enzymes recognize specific
substrates?
• Specificity is a result of it’s shapeProtein… structure/function
The “lock and key” model
- substrate is the key
- enzyme is the lock
• the active site is a
restricted region of the
enzyme molecule that
actually binds to the
substrate. (the key
hole)
THE INDUCED FIT MODEL
Like the clasping of a handshake, brings
chemical groups of the active site into
positions that enhance their ability to
catalyze the reaction.
Figure 6.15 The catalytic cycle of an enzyme
Figure 6.16 Environmental factors affecting enzyme activity
TEMPERATURE
cold- little movement of
Substrate to enzyme
Increased temperature
Increases # collisions
Too HIGH denatures
enzymes. No RXN.
pH
Deviations from
optimal pH denature
the enzymes & make
them inactive
Some enzymes are assisted
by prosthetic groups called:
• Cofactors are non-protein helpers for
catalytic activity that may be inorganic
(like: zinc, iron, and copper).
• Coenzymes are cofactors that ARE
organic molecules. (vitamins)
Figure 6.21 Organelles and structural order in metabolism
D. CONTROLLING ENZYME
ACTIVITY
1. COMPETITIVE INHIBITION
molecular mimics bind to the active site, thus
reducing productivity of enzymes by blocking
substrates from binding the active sites.
Ex) Penicillin blocks the active site of an enzyme
bacteria use to make their cell walls.
2. NONCOMPETITIVE INHIBITION
Molecules bind to a part of the enzyme that is
not the active site (allosteric site) causing the
enzyme to change its shape, making the
active site useless.
Ex) DDT, parathion are inhibitors of main
enzymes of the nervous system.
Figure 6.17 Inhibition of enzyme activity
3. FEEDBACK
INHIBITION
Switching off of a
metabolic pathway by
its end-product,
which acts as an
inhibitor of an
enzyme within the
pathway.
Negative feedback.
•
4. ALLOSTERIC
REGULATION
Allosteric enzymes are typically made of 2 or more
polypeptide subunits, each having its own active
site. (ex. Of quaternary structure)
• Allosteric enzymes have 2 conformations (shapes):
1) Active form
2) Inactive form
Figure 6.18 Allosteric regulation of enzyme activity
•ACTIVATOR MOLECULES stabilize
the “active form” of the allosteric enzyme.
•INHIBITOR MOLECULES stabilize
the “inactive form”.
5) COOPERATIVITY
One substrate molecule primes the
enzyme to accept additional substrate
molecules more readily.
DESIGN AN EXPERIMENT
TESTING THE RATE OF
ENZYME ACTIVITY and ONE
TO TEST THE EFFECT OF
ENVIRONMENT ON
ENZYMES
• What materials will you need?
• What will the control group be?
• What will your independent and dependent variables
be?
• What variables will you control?
• What will the resulting graph look like?
• Extra credit opportunity Monday 7th period.
• I need help setting up the lab after school
during 7th period so it is ready for our next
class.
• Lab set up extra credit is limited so if you
can’t do it this time you can do it next time.
• I need 12 helpers (4 from each period).