AP Biology Chapter 6:An Introduction to Energy and Enzymes

Metabolism Totality of an organism’s reactions

(from Greek metabole, to change)

An emergent property from interactions between chemicals within the environment of the cell

Concerned with managing the material and energy resources of the cell

Metabolism Two types of reactions:

Catabolic Pathways: release energy by breaking down complex molecules into simpler compounds (e.g. cellular respiration)

“downhill” reactions

Anabolic Pathways: consume energy to build complicated molecules from simpler ones (e.g. synthesis of proteins from amino acids)

“uphill” reactions

These reactions are coupled together

BioenergeticsThe study of how organisms manage their energy resources

Energy: the capacity to do work—ability to rearrange a collection of matterKinetic: energy of motion

Potential: stored energy

Chemical: form of potential energy stored in molecules as the result of the arrangement of atoms

ThermodynamicsStudy of the energy transformations that occur in a collection of matter

First Law of Thermodynamics: energy is constant—energy can be transferred and transformed, but it cannot be created nor destroyed

Second Law of Thermodynamics: every energy transfer makes the universe more disordered or random, a.k.a. increases the entropy (measure of disorder)

EntropyIn most energy transformations, some of the energy stored is converted to heat (the most random - entropic - form of energy)

Organisms are open systems and exchange energy and materials with the surroundings—taking in both organized and unorganized forms of matter and energy and releasing both into the environment

Depletions of energy in organisms is due to the loss as heat.Put more simply…

Entropy“Living organisms preserve their internal order by taking from their surroundings free energy, in the form of nutrients or sunlight, and returning to their surroundings an equal amount of energy as heat and entropy.” - Albert Lehninger

Cells maintain their orderliness by taking in highly ordered things like light photons or polymers, and discharging disorderly things.

Life makes its environment more disorderly, in order to be orderly.

Free Energy Free energy: The portions of a system’s energy that is available to perform work when temperature is uniform throughout the system

Not all of the energy in a system is available for work

G= H – T S

G = Free EnergyH = Total Energy (of the system)T = Temperature (in Kelvin)S = Entropy

Discussion∆G= ∆H - T ∆S

∆G= change in free energy, ∆H = change in total energy, T = temperature, ∆S = change in entropy

What happens to the amount of free energy available if we…

Increase the total amount of energy in the system?

Increase the temperature of the system?

Increase the entropy of the system?

So, how can organisms use free energy to reduce their entropy?

Energy Changes∆G= ∆H - T ∆S

For spontaneous, “downhill” reactions, ∆G must be negative (∆G < 0). In other words, a loss of free energy.

Free Energy and MetabolismExergonic Reactions:

(“energy outward”) proceeds with a net release of free energy. ∆G is negative. Reactions are spontaneous.

Endergonic Reactions: (“energy inward”) absorbs free energy from its surroundings, stores free energy in molecules. ∆G is positive. Reactions are nonspontaneous. Require energy to drive the reaction.

Energy Changes

Metabolic DisequilibriumEquilibrium: ∆G = 0. There is no

net change in the system. No work is being performed

Reactions in closed systems will eventually reach equilibriumLiving organisms are open systems, and maintain disequilibrium by constantly flowing materials into and out of the cell

DiscussionTogether with a partner, draw a picture or pictures summarizing metabolism, energy, and entropy

CatalystsCatalyst = chemical agent that changes the rate of a reaction without being consumed by the reaction

Enzymes are biological catalysts, most often made of protein (there are a few ribozymes made of RNA)Without enzymes, most bio reactions (even spontaneous, exothermic reactions) proceed VERY slowly.

Example: Leave a cracker out on the counter. How long will it take for all the starch to turn to sugar?

Activation Energy Barrier Chemical reactions involve forming and

breaking of bonds. Existing bonds in reactants must be broken and new bonds of products formed.

Breaking bonds requires an input of energy

The initial investment of energy for starting a reaction—energy required to break bonds– is called the activation energy or free energy of activation (EA)

Enzymes and Activation EnergyEnzymes speed up reactions by

lowering the activation energy, i.e. the EA barrier, so the transition state is within reach at moderate temperatures.

They do not change the ΔG of the reactionAnalogy: They don’t help the high jumper up, they lower the bar

Enzymes are Substrate SpecificThe reactant a specific enzyme works

on is called a substrate

Enzymes bind to their substrate(s) allowing the catalytic action of the enzyme to create the products

Substrate Enzyme Product

Enzymes can distinguish their substrate by shape. The substrate must “fit” into the active site of the enzyme, a groove or pocket in the protein

http://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.html

Enzyme-Substrate Cycle

Induced FitActive sites are not rigid like a “lock-and-key” but instead change shape slightly to fit snugly around the substrate—like a handshake

Induced fit brings chemicals together into positions that enhance their ability to catalyze

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter25/animation__enzyme_action_and_the_hydrolysis_of_sucrose.htm

Discussion

• When making jello with fruit in it, you must be careful as it will not “gel” if fresh pineapple is used, but it will gel with canned pineapple. Fresh pineapple contains the enzyme bromelain which prevents proteins from arranging into tertiary and quaternary structures.

• Explain!

Discussion

• Papain is a hydrolytic enzyme that is present in papaya. It is sold as a component in powdered meat tenderizer available in most supermarkets.

• How might such powders make meat more tender?

Environmental Effects on Enzymes

Enzymes have optimal conditions where they work “best.” These tend to match the environment (think evolution)

http://www.kscience.co.uk/animations/model.swf

Environmental Effects on Enzymes

Temperature: thermal agitation can disrupt conformation. Optimal temp allows greatest

number of molecular collisions without denaturing

pH: H+ concentration can also disrupt conformation.

Denaturation

Denaturation = The loss of a protein’s secondary (tertiary, quaternary) structure by the application of an external stressStrong acids, strong bases, and high temperatures cause denaturation

Warped protein shape -> Substrate cannot bind to active site -> Function reduced or eliminated

http://highered.mcgraw-hill.com/sites/0072507470/student_view0/chapter2/animation__protein_denaturation.html

Discussion

• Pepsin is a digestive enzyme that functions in the stomach to break down proteins, while salivary amylase is an enzyme that functions in the mouth to break down carbohydrates. Using the following information, discuss the answers to these questions…

Discussion• What is the optimal pH for pepsin? How does this relate to its environment?

• What is the optimal pH for amylase? How does this relate to its environment?

• (Note: amylase breaks down starch starting in the mouth, continuing with the food bolus through the esophagus, stomach, and small intestine.)

Discussion

• Would you expect carbohydrate breakdown to be ongoing in the stomach? Why/why not?

• Would you expect pepsin to work in the intestine? Why/why not?

Discussion

• When fruits & veggies are frozen, the water in the vacuoles tends to expand and cause it to burst. This releases a number of hydrolytic enzymes and can cause the fruit to become mushy.

• Fruits & veggies are often blanched (placed in boiling water for a short time) before being frozen to prevent this.

• Why does blanching help at all?

Discussion

• When slicing fruit, an enzyme called catecholase causes a reaction between catechol and oxygen. The products formed by this reaction are benzoquinone and water; since benzoquinone has a brown color, this results in the fruit browning.

• Browning can be prevented by adding lemon juice to cut fruit. Why?

CofactorsMany enzymes require non-protein helpers for catalytic activity, called cofactors which are bound to the active siteThey can be permanent or bind reversibly with the substrate

Cofactors are inorganic such as iron, zinc, or copper

Coenzymes are organic cofactors

http://highered.mcgraw-hill.com/sites/0070960526/student_view0/chapter6/

animations.html

Enzyme Inhibitors Certain chemicals selectively inhibit the action of an enzyme by covalently bonding to the active site. Usually irreversibly.

Competitive Inhibition: bind with the active site, competing with the substrate for access to the active site Can be overcome by increase the concentration of the substrate

Noncompetitive Inhibition: bind with the enzyme outside of the active site, changing the enzyme’s conformation and impeding the substrate binding

Examples: poisons, antibiotics

Allosteric RegulationReversible noncompetitive inhibitors are in charge of most of the control of metabolism

Regulatory molecules (activators or inhibitors) bind at an allosteric site away from the active site to turn on/off an enzyme’s activity

Allosteric enzymes have multiple subunits (polypeptide chains)

Feedback InhibitionProducts of a pathway can act as the allosteric inhibitors and switch off an enzyme in the catabolic process

Example: ATP is the allosteric inhibitor for the ATP-generating catabolic pathway

http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/

animation__feedback_inhibition_of_biochemical_pathways.html

CooperativitySubstrate molecules can stimulate an enzyme. Binding a substrate can induce the enzyme to change into a shape which is more favorable for binding at other sites

Amplifies the response of enzymes to substrates

Localization of EnzymesOrganisms are more efficient because they can keep all the enzymes required for a pathway in one place, organ or organelle.

Metabolic pathways can be assembled together into a multienzyme complex to keep everything organized and efficient

DiscussionWork together with a partner to invent an enzyme.Determine what species it’s in

Determine its optimum environment

Determine what reaction it catalyzes, substrates and products

Determine how it’s regulated. How does the organism ensure that it’s only carrying out the reaction when needed, and that it does so efficiently?