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 propertyThat 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 respirationGlucose 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 storedBehind 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 H2Owhen 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

instability- it’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 (G change in free energy) predicts whether a reaction will occur spontaneously or not. G = 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 G.

• Ex. Glucose + O2 CO2 + H20 + 38 ATP energy

More free energy LESS STABLE Stretched slinkyGirl at top of slide Glucose molecule

Less free energy MORE STABLECompact slinkyGirl 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

Exergonic Rxns have a - G. Endergonic Rxns have a + G.

you may have learned the terms Exo and Endothermic

1.EXERGONIC “energy outward”

• G is negative • Why? Because the chemical mixture loses free

energy.• Energy is released.• The reaction is spontaneous.

Ex. C6H12O6 + 6 02 --> 6 CO2 + 6 H20G = -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”

• G is positive • Why? Because this reaction stores free

energy in larger molecules.• Energy is absorbed from its surroundings.• The reaction is non-spontaneous.• G 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) Heat2) 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 substratesHow do enzymes recognize specific

substrates?• Specificity is a result of it’s shape-Protein… 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

TEMPERATUREcold- little movement ofSubstrate to enzymeIncreased temperature Increases # collisionsToo HIGH denatures enzymes. No RXN.

pHDeviations from optimal pH denaturethe enzymes & makethem 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 ACTIVITY1. 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 INHIBITIONSwitching 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 form2) 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) COOPERATIVITYOne 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).