NOTES FOR BIOLOGY 1001

SECTION 005

Spring 2005

DR. STEVEN POMARICO

CHAPTER 6

GROUND RULES FOR METABOLISM

>>>DEFINING ENERGY

---Energy is the ability to do work.

                     There are two major categories of energy

                                           1) potential energy

                                           2) kinetic energy

---Potential energy is energy stored in matter because of its position or location.

---Kinetic energy is the energy of motion.

                                 Rubber band analogy

Potential energy in biological systems can be stored in chemical bonds as chemical energy.

Kinetic energy can result in the release of heat, or thermal energy.

>>>The Laws of Thermodynamics Describe the Properties of Energy

Energy transfer by organisms is subject to two laws of thermodynamics

---First Law of Thermodynamics which states that energy can be transferred and transformed, but it cannot be created or destroyed (i.e., the energy of the universe is constant).

---Second Law of Thermodynamics which states that every energy transfer or transformation makes the universe more disordered (i.e., every process increases entropy at the cost of useful energy)

---Entropy is the measure of disorder, randomness

If every energy transfer loses energy, why doesn’t life on the planet simply run out of energy?

          The planet isn’t a closed system. Energy is constantly flowing in from the sun.

The universe is a closed system and the solar system is almost a closed system. All other closed systems are created in the lab.

A closed system is a system which is completely isolated from its surroundings. In an open system energy can be transferred between the system and it’s surroundings.

>>>ENERGY FLOW IN CHEMICAL REACTIONS

Thermodynamics determines whether or not a chemical reaction will occur in the cell, and how much energy it will consume or release

Chemical reactions are either exergonic or endergonic

---Exergonic reactions are reactions that release energy.

---Endergonic reactions are energy-requiring reactions.

>>>>>ATP powers cellular work by coupling exergonic reactions to endergonic reactions

The Structure and Hydrolysis of ATP (See fig. 6.6)

>>>>>How does ATP drive work?

-Phosphorylated or activated intermediates (See fig 6.7)

>>>>>ATP is continually regenerated

>>>>>Redox reactions release energy when electrons move closer to electronegative atoms.

---Redox reactions (a.k.a. Oxidation-reduction reactions)

---Oxidation is the loss (or partial loss) of electrons from an atom or molecule.

---Reduction is the gain (or partial gain) of electrons by an atom or molecule.

>>>>>Chemical reactions make-up metabolism

In all chemical reactions you begin with one set of substances, reactants, and end with a different set of substances, products.

>>>CONTROLLING THE METABOLISM OF LIVING CELLS

---Metabolism is the totality of an organism’s chemical processes

          -Uptake of matter and energy

          -Conversion to usable form

          -Synthesis of cellular materials

          -Elimination of waste products

>>>The chemistry of life is organized into metabolic pathways

Two types of metabolic pathways:

          Catabolic pathways and anabolic pathways

---Catabolic pathways are metabolic pathways which release energy by breaking down complex molecules to simpler compounds.

-degradation, releases energy

---Anabolic pathways are metabolic pathways which consume energy to build complicated molecules from simpler ones.

                                           -synthesis, energy requiring

>>>Chemical reactions are reversible and will reach a chemical equilibrium.

---Chemical equilibrium is the equilibrium reached when the rate of the forward reaction is equal to the rate of the reverse reaction.

This does not mean that the concentration of reactants and products are equal.

                                Example of tennis balls across a net;

                                                                | 

                                                                |

                     PERSON “A”                   |          PERSON “B”

                                                                |

                     Hits balls as             |         Hits balls very

                     quick as possible               |         leisurely

                                                                |

Even if “A” starts with all the balls, when equilibrium is reached,

“B” will have most but not all of the balls

Now imagine a change conditions: “A” still hits as quick but only

                                                     gets half over the net.

The equilibrium shifts so that “B” has fewer balls than before and “A” has more.

>>>>>Enzymes speed up metabolic reactions by lowering energy barriers (See fig. 6.12)

---Catalysts are chemical agents that accelerate a reaction without being permanently changed in the process (i.e., a catalyst is reusable and is not destroyed by the reaction)

---Enzymes are biological catalysts which are usually proteins.

Although exergonic reactions release energy overall, they may require some energy to get them started. This “starter energy” is called activation energy. (See fig. 6.12)

--- Activation energy is the amount of energy that reactant molecules must absorb to start a reaction

>>>>>Enzymes are substrate-specific

---Substrates are the substances which enzymes act on. In the presence of the appropriate enzyme the substrates become more reactive.

          An enzyme binds to its substrate and catalyzes the conversion of the substrate(reactants) to the product. The enzyme is unchanged by the process.

          The substrate binds to the active site of an enzyme.

---Active site is the restricted region of an enzyme molecule where the substrate is bound (See fig 6.13)

          The active site is usually a pocket or groove on the surface of the protein.

          The active site is usually formed by only a few amino acid R-groups.

          The shape, size, and binding ability of the active site confer specificity                for the substrate (i.e., the substrate has to fit the active site)

>>>>>How enzymes work

The activation energy can be thought of as the energy needed to put the substrates into the transition state.

---Transition state is an energy rich state where the reaction can proceed easily in either a forward or reverse direction.

One model for how enzymes work says the enzyme can help the substrates achieve the transition state by changing shape. This shape change is “induced” by the binding of the substrate and is known as the induced-fit model.

---Induced fit (See fig 6.13) is a shape change of the enzyme (and the active site) that is triggered by the binding of the substrate.

>>>>>Some enzymes require cofactors or coenzymes to function.

—Cofactors are inorganic atoms, ions, or molecules that are required for proper enzyme catalysis.

---Coenzymes are small nonprotein organic molecules that are required for proper enzyme catalysis (e.g., vitamins).

>>>Regulating Metabolic Reactions

Metabolic pathways are regulated by controlling enzyme activity.

---Feedback inhibition (See fig 6.15) is the regulation of a metabolic pathway by its end product, which inhibits an enzyme within the pathway.

          -This usually occurs at a branch-point or at a committed step.

          -Prevents the cell from making something it has enough of already.

>>>>>Allosteric regulation (See fig. 6.15)

---Allosteric sites are specific receptor sites on some part of the enzyme molecules other than the active site.

          -Allosteric enzymes have two conformations, one is catalytically active and the                      other is inactive.

          -Binding of an inhibitor (or an activator) to an allosteric site stabilizes the inactive conformation.

          -Allosteric enzymes are often found at key, regulatory positions in metabolic                      pathways.

>>>>>A cell’s chemical and physical environment affects enzyme activity

---Effect of temperature and pH (See fig. 6.17) can change the shape and activity of an enzyme.