AN INTRODUCTION TO METABOLISM

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CHAPTER 6

• AN INTRODUCTION TO METABOLISM

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Figure 6.1  The complexity of metabolism
Metabolism is the sum total of all of an
organisms chemical reactions.
It is an emergent property That arises from
interactions between molecules within the cell.
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• Enzymes (biological catalysts) direct matter
  through the metabolic pathways by selectively
  accelerating each step. Well 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 hasnt 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!!!

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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 -gt 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

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• THIS IS CALLED COUPLING!!!!
• (ewwww. How cute.)

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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?

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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)
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Cheetah also, potential kinetic energy.How
is the cheetah storing its potential energy???
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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.

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THERMODYNAMICS

• The study of energy transformations that occur in
  a collection of matter.
• 1st law energy can be transferred and
  transformed but not created nor destroyed.
• 2nd law every energy transfer increases the
  entropy (randomness) of the universe.
• Ex. messy room, random molecular motion,
  macromolecules to small ones.

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How do these pictures exemplify the 2 laws of
thermodynamics?
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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
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• THE QUANTITY OF ENERGY IN THE UNIVERSE IS
  CONSTANT
• BUT THE QUALITY ISNT.

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Considering the laws of thermodynamics how do
we explain the orderliness of life?
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Considering the laws of thermodynamics how do
we explain the orderliness of life?
Organisms are open systems! Matter energy
are transferred between the system its
surroundings. There is a constant source of
energy.
Ex. Cells take in starch, protein, lipids
release energy (ATP) CO2 and water.
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Figure 6.7 Disequilibrium and work in closed and
open systems
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A. FREE ENERGY (G)

• Free energy is a measure of a systems
  instability- its 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 systems
  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.)

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• 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

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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
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Biochemical reactions can be 1) exergonic or 2)
endergonic
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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.
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• 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 --gt 6 CO2 6 H20
• sG -686 kcal/mol
• The products have 686 kcal less free energy than
  the reactants. Well learn that the energy is
  converted to ATP molecules (and lost as heat).

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Figure 6.12 Energy profile of an exergonic
reaction
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• 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 --gt C6H12O6 6O2

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• 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

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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.

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Figure 6.9  Energy coupling by phosphate transfer
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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)

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What would happen to biochemical reactions and
high-energy molecules without activation energy?
What would happen to you???? (discuss)
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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.

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How can cellular reactions overcome activation
energy?

1. Heat
2. Enzyme (biological catalyst)

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Figure 6.11 Example of an enzyme-catalyzed
reaction Hydrolysis of sucrose
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C. CATALYSTS

• What do they do?
• Speed up chemical reactions.
• How do they do it?
• by lowering the amount of activation energy
  needed.

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ENZYMES

• Are globular proteins
• Names ending in -ase
• Enzymes act on substrates
• How do enzymes recognize specific substrates?
• Specificity is a result of its shape-
• Protein structure/function

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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)

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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.

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Figure 6.15 The catalytic cycle of an enzyme
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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
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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)

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Figure 6.21 Organelles and structural order in
metabolism
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D. CONTROLLING ENZYME ACTIVITY

• 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.

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• 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.

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Figure 6.17 Inhibition of enzyme activity
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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.

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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)
• Active form
• Inactive form

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Figure 6.18 Allosteric regulation of enzyme
activity

• ACTIVATOR MOLECULES stabilize
• the active form of the allosteric enzyme.
• INHIBITOR MOLECULES stabilize
• the inactive form.

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5) COOPERATIVITY

• One substrate molecule primes the enzyme to
  accept additional substrate molecules more
  readily.

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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?

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• 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
  cant do it this time you can do it next time.
• I need 12 helpers (4 from each period).