Regulation:

Theory

Practice

&

Enzymatic function can be stimulated or inhibited by factors in the cell.

Competitive Interactions

Non-Competitive Interactions

vs.

"-ase"

A molecule other than the substrate binds to the active site.

Regulation is accomplished without occupying the active site.

2 Relevant Laws:

Enzymes!

A common nomenclature suffix for enzymes.

prefix: usually refers to enzyme's substrate

Second:

First:

* there are a few exceptions (e.g. stellar fusion), which don't matter for us

Gibbs Free Energy:

Exergonic Reactions:

A Measurement of the amount of "useful" energy that a system (like a cell)

can use for performing work.

At the cellular level, the major biological source of energy is from the
rearranging of atoms to from higher energy compounds to lower energy
compounds.

 Release energy (matter is converted from higher energy arrangements

to lower energy arrangements) .

 Will happen spontaneously, once they are initiated.

  Change in free energy is NEGATIVE.

Life is Highly Ordered

Open & Closed Systems

Organisms are energy processing systems.

Energy from the Sun, or from Chemical Bonds is used to undertake

cellular/organismal work

Work: Anything that requires atoms to be moved around through cellular

actions (aka: "everything you do")

TS

Endergonic Reactions:

Closed

Inevitably Dull

 Require energy input to occur (matter is converted from lower energy

arrangements to higher energy arrangements) .

 Can not occur spontaneously.

 Change in free energy is POSITIVE.

Biological catalysts.

Proteins and some RNA molecules (examples?)

Kinetic & Potential Energy

Closed systems inexorably tend toward an absence of free energy.

They reach at a state of equilibrium between inputs and outputs.

 G = Free Energy

 H = Enthalpy (energy stored in a substance)

 T = Temperature
  S = Entropy

More PE, Less KE

Less PE, More KE

Biological Systems use Exergonic Reactions to provide the free energy

necessary for endergonic reactions.

Both are useful to organisms for different purposes.

Both contribute to phenomena at all levels of organization in the Universe.

Living systems are not the only systems in the universe that require energy
conversion to function.

Organisms use the energy they convert to power cellular/organismal

processes that decrease their overall entropy (or at least delay its increase).
This process increases the entropy of their surroundings.

Open

Life Requires Energy Input

Usually Interesting

Open systems will not reach equilibrium as long as the processes of the
system recieve inputs and produce outputs.

There is no inherent limit to the complexity of an open system, provided

there is enough input to allow for that complexity

Allosteric Interactions

Binding of a substrate molecule to on active subunit of an enzyme can also

trigger stabilization of the active conformation in all subunits
("cooperativity")

Equilibrium = Death

Life is an open system!

Activation:

A highly ordered living system uses energy input to maintain/increase order

Binding of an activator molecule can stabilize the enzyme in an active

conformation.

How do they do it?

"Other-site"

Cellular Energy Theory:

Ex. Caspase

Activator

Active

Reactants

Induced Fit

Stimulate or inhibit enzyme activity by causing a conformational change in

the enzyme.

Important enzymes for cell death (apoptosis and necrosis).

Data from an experiment to determine if caspase enzymes can have an

allosteric site.

The active and inactive forms of caspase 1 were already known.

Hypothesis: Allosteric inhibition of caspase 1 will lock the enzyme in an

inactive conformation.

Constant Oscillation

Enzyme-Substrate

Complex

Inhibition:

Adenosine Tri-Phosphate

Binding of an inhibitor molecule can stabilize the enzyme in an inactive

conformation.

ATP!

The Return of Kinetics

Enzymes interact with reactants ("substrate")

Cause breaking/formation of particular atomic bonds to be more

energetically favorable.

This work is localized to an area of the enzyme called the "active site".
The short term energy storage/release molecule of choice in cells

tens of millions made and used per second per cell

Inhibitor

Inactive

The shape of the active site of an enzyme is shape-specific for a particular

substrate.

The binding of a substrate to the active site induces the necessary

conformational change of the enzyme to catalyze the reaction.

The Reaction Profile

Metabolism

Enzyme

The bonds between phosphate groups in nucleoside tri-phosphates (like ATP)

are relatively unstable.

The active site is localized to a small area of the enzyme

Organization:

Much more free energy is released when the bonds between them are broken
than is required by the cell to initiate their cleavage.

All reactions require an input of energy (the "activation energy") to make the
breaking of current chemical bonds energetically favorable (the "transition
state").

The relationship between the energy of the products and the energy of the
reactants is what determines if a reaction is exergonic or endergonic.

Products

Examples:

Topoisomerase:

ATP

Evolutionary Considerations:

Refers to the sum total of all chemical reactions that take place in an
organism.
Energy from catabolic reactions (ex: respiration) is used to power the
synthesis of ATP from ADP and Phosphate groups.

ATP (and other NTP's) is used to power the anabolic Reactions that require
chemical energy.

Compartmentalization

Environmental Infuence:

Feedback:

Involved in minimizing mechanical stress on DNA during replication.

Makes a temporary cut in the helix.

Energy!

Many metabolites have regulatory effects on enzymes that catalyze the

metabolic pathways that result in the production of those metabolites.

ADP

Reaction Coupling

Localization of specific enzymes (and the reactions they mediate) within

compartments of the cell allow for more control over when and where
particular metabolic reactions occur in eukaryotes

 Blue: 2 polypeptide chains.

 Orange: DNA Double-Helix

 Purple: Active site.

Evolution plays a central role in enzyme structure and function.

Various studies have been conducted to investigate the effect of evolution on

enzymes.

These include:

 analysis of enzyme genes (sequence comparison).

 Artificial selection of enzyme activity in laboratory settings.

 Ethnographic/Demographic studies of enzyme genotypes and

enzymatically determined phenotypes.

Catalysts!
Rubisco!

Attaches carbon dioxide to sugar precursor molecules in photosynthesis.

50% of all protein found in a chloroplast.

Refers to linking an exergonic process with a cellular process.

If an endergonic process requires less free energy than an exergonic process

produces, coupling those two reactions allows for maximum efficiency, and
an overall negative delta G.

Much of the work done by cellular proteins is mediated by the addition and
removal of

Phosphate groups from ATP by proteins to other proteins (kinases and

phosphatases).

Like all proteins, enzyme structure (and therefore function) can be effected
by the conditions of the enzyme's enviornment.

There are three major environmental conditions that effect enzyme structure
and function

Co-factors

Any substance that increases the rate of a chemical reaction while not
participating in the reaction.

Lowers the activation energy of a reaction.

Reusable (since they don't participate).

Most enzymes require accessory compounds many of which you are familiar
with as ("vitamins") or metal ions (aka "minerals") in order to be functional.

effect of catalyst

Variation + Natural Selection = Adaptation

1. Temperature 2. pH

3. Concentration (enzyme, substrate, cofactors)

Magnesium ion (green) associated with rubisco's active site.

A manganese ion (dark green) is visible in the topoisomerase active site.

Make Sure You Can:

Explain how enzymes function as catalysts.

Explain the induced fit model of enzyme function.

Provide examples of enzyme-catalyzed reactions in biological systems.

Explain the relationship between enzyme structure and function.

Explain the major modes of regulation of enzyme activity.

Explain how living systems adhere to the first and second laws of
thermodynamics.

Explain how living systems can increase in order even though the Universe is
moving toward a state of maximum entropy.

Compare endergonic and exergonic reactions.

Compare open and closed systems.

Explain how ATP allows for cellular work.

Explain the effect of a catalyst on a reaction profile.