HBio Enzyme test

What is the specificity of an enzyme attributed to? (It's kind of the same answer as question 27)

A complementary fit between the shape of its active site and the shape of the substrate.

Cooperativity

A kind of allosteric regulation whereby a shape change in one subunit of a protein caused by substrate binding is transmitted to all the other subunits, facilitating binding of additional substrate molecules to those subunits. One substrate molecule primes an enzyme to act on additional substrate molecules more readily.

Enzyme

A macromolecule that acts as a catalyst by lowering the energy barrier of the reactant molecules.

Feedback inhibition

A method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway. A metabolic pathway is switched off by the inhibitory binding of its end product to an enzyme that acts early in the pathway. They prevent cells from wasting chemical resources by making more isoleucine than is necessary.

From what are enzymes known to be allosterically regulated constructed?

A polypeptide chain with its own active site.

Many spontaneous reactions occur very slowly. Why don't all spontaneous reactions occur instantly?

A spontaneous reaction is exergonic; however, if it has a high activation energy that is rarely attained, the rate of the reaction may be low.

Noncompetitive inhibitor

A substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzyme's shape so that the active site no longer effectively catalyzes the conversion of substrate to product.

Competitive inhibitors

A substance that reduces the activity of an enzyme by entering the active site in place of the substrate, whose structure it mimics. They resemble the normal substrate molecule and compete for admission into the active site.

Entropy can drive a chemical reaction; for example,

A+B+C-----D

Coenzyme

An organic molecule serving as a cofactor. Most vitamins function as coenzymes in metabolic reactions.

Cofactor

Any nonprotein molecule or ion that is required for the proper functioning of an enzyme. Cofactors can be permanently bound to the active site or many bind loosely and reversibly, along with the substrate, during catalysis. Can be organic or inorganic.

In order to carry out the processes needed for life, what has to happen?

Barriers for selected reactions must occaisionally be surmounted.

Why is cooperativity considered allosteric regulation?

Because binding of the substrate to one active site affects catalysis in another active site.

How can competitive inhibition be overcome?

By increasing the concentration of substrate so that as active sites become available, more substrate molecules than inhibitor molecules are around to gain entry to the active sites.

How does an enzyme catalyze a reaction?

By lowering the energy barrier, which enables the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.

How do enzymes speed up metabolic reactions?

By lowering the energy barriers.

How does a cell do the above?

By switching on and off the genes that encode specific enzymes or by regulating the activity of enzymes once they are made.

Instead of heat, what do organisms use to speed up reactions?

Catalysis.

Induced fit

Caused by the entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate. It brings chemical groups of the active site into positions that enhance their ability to catalyze the chemical reaction.

How can molecules reach the contorted state where bonds can change? What is the contorted state exactly?

Changing one molecule into another generally involves contorting the starting molecule into a highly unstable state so that a reaction or bond breaking can occur. To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings.

Why does the shape of the active site change slightly when the substrate binds?

Due to interactions between the substrate's chemical groups and chemical groups on the side chains of the amino acids that form the active site. It changes so that the active site fits even more snugly around the substrate. This in INDUCED FIT (next card, starting thinking).

Remember exergonic/endergonic? Define them. Now.

Endergonic: a nonspontaneous chemical reaction, in which free energy is absorbed from the surroundings. Exergonic: a spontaneous chemical reaction, in which there is a net release of free energy.

True or False At temperatures typical for cells, MOST molecules make it over the hump of activation energy.

FALSE!!!!!! FEW MOLECULES MAKE IT OVER THE HUMP OF ACTIVATION ENERGY...WHICH IS WHY MOLECULES PERSIST!!!

True or False Most metabolic reactions are irreversible.

False! Most are reversible.

True or False An enzyme can change the change in G for a reaction.

False. It cannot make an endergonic reaction exergonic...enzymes can only hasten reactions that would eventually occur anyway, but this function makes it possible for a cell to have a dynamic metabolism, routing chemical smoothly through the cell's metabolic pathways.

The oxidation of glucose to CO2 and H2O is highly exergonic: change G=-636 kcal/mol. This is spontaneous, but why is it very slow?

Few glucose molecules have the activation energy at room temperature.

In what form is energy release once new bonds of the product molecules form?

Heat

Name four meachanisms that enzymes use to lower activation energy and speed up reaction.

I. In reactions in involving two or more reactants, the active site provides a template on whicht he substrates can come together in the proper orientation for a reaction to occur between them. II. As the active site of an enzyme clutches the bound substrates, the enzymes may stretch the substrate molecules toward their transition state form, stressing and bending critical chemical bonds that must be broken during the reaction (to elaborate, review the card above). III. The active site may also provide a microenvironment that is more conductive to a particular type of reaction than the solution itself would be without the enzyme. For example, if the active site has amino acids with acidic R groups, the active site may be a pocket of low pH in an otherwise neutral cell. In such cases, am acidic amino acid may facilitate H+ transfer to the substrate as a key step in catalyzing the reaction. IV. The direct participation of the active site in the chemical reaction. Sometimes this process even involves brief covalent bonding between the substrate and the side chain of an amino acid of the enzyme.

In what way do the subunits of the allosteric site fit together?

In such a way that a shape change in one subunit is transmitted to all others. Through this interaction of subunits, a single activator or inhibitor molecule that binds to one regulatory site will affect the active sites of all subunits.

Malonate is an inhibitor of the enzyme succinate dehydrogenase. How would you determine whether malonate is a competitive or noncompetitive inhibitor?

In the presenceof malonate, increase the concentration of the normal substrate (succinate) and see whether the rate of reaction increases. If it does, malonate is a competitive inhibitor.

A cell's ability to tightly regulate its metabolic pathways by controlling when and where its various enzymes are active is __________ __ ______ _________.

Intrinsic to life's processes.

What supplies E(sub)A

It is often supplied by heat in some form of thermal energy that the reactant molecules absorb from their surroundings.

From what does the specificity of an enzyme result?

Its shape...which is a consequence of its amino acid sequence.

How do living organisms create macromolecules, organelles, cells, tissues, and complex higher-order structures?

Living organisms create order locally, but the energy transformations generate waste heat that increases the entropy of the universe.

What does regulation of enzyme activity help control?

Metabolism.

What accounts for this molecular recognition?

Most enzymes are proteins, and proteins are macromolecules with unique three-dimensional configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence.

Are most chemical reactions at equilibrium in living cells?

NOOO!

Are enzymes stiff structures?

NOPE. Enzymes seem to "dance" between subtly different shapes in a dynamic equilibrium, with slight differences in free energy for each "pose."

Are toxins and poisons reversible inhibitors?

No, not really. They're mostly irreversible.

Why do enzymes act only on very specific substrates?

Only the specific substrate(s) will fit properly into the active site of an enzyme, the part of the enzyme that carries out catalysis.

What are most enzymes?

Proteins

What does the binding of an inhibitor do?

Stabilizes the inactive form of the enzyme.

What does the binding of an activiator to a regulatory site do?

Stabilizes the shape that has functional active site.

True or False The solution of heat is inappropriate for biological systems because heat denatures proteins and kills cells and heat would speed up all reactions, not just those that are needed.

TRUE

True or False The breakdown of food molecules in the gut does not require coupling of ATP hydrolysis, but enzymes are required to speed up the spontaneous reaction.

TRUE.

True or False Molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors.

TRUE. Inhibition is not abnormal.

What affects the activity of an enzyme?

Temperature and pH, and also chemicals that specifically influence that enzyme.

How do an activator and an inhibitor have different effects on an allosterically regulated enzyme?

The activator binds in such a way that is stabilizes the active form of an enzyme, whereas the inhibitor stabilizes the inactive form.

Allosteric regulation

The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site. They can either inhibit or stimulate the enzyme's activity.

What happens while enzyme and substrate(s) are joined?

The catalytic action of the enzyme converts the substrate to the product (or products) of the reaction. Enzyme+Substrate(s)----Enzyme-Substrate Complex----Enzyme+Product(s)

Optimal condition

The condition under which an enzyme works best/most efficiently.

To what is activation energy proportional?

The difficulty of breaking the bonds...distorting the substrate helps it approach the transition state and thus reduces the amount of free energy that must be absorbed to achieve that state.

Of what is the rate at which a particular amount of enzyme converts substrate to product a function?

The initial concentration of the substrate. The more substrate molecules available, the more frequently they access the active sites of the enzyme molecules.

What is activation energy or free energy of activation?

The initial investment of energy for starting a reaction--the energy required to contort the reactant molecules so the bonds can break. Abbreviated as E(sub)A. The amount of energy needed to push the reactants to the top of an energy barrier, or uphill, so that the "downhill" part of the reaction can begin.

Whata determines the speed of the reaction?

The rate at which the active site converts substrate to product.

Substrate #thisisIMPORTANT

The reactant on which an enzyme works.

A reaction has a change G of -5.6 kcal/mol. What would most likely be true?

The reaction would proceed by itself but might be very slow.

Active site

The restricted region of the enzyme molecule that binds to the substrate and that forms the pocket in which catalysis occurs.

Enzyme-Substrate Complex (clue: it's basically what is sounds like)

The structure when an enzyme binds to its substrate (or substrates, when there are more than two reactants).

Why does the rate of reaction drop rapidly when the temperature goes above the optimal condition?

The thermal agitation of the enzyme molecules disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures.

What happens when the E(sub)A barrier is too high?

The transition state is reached so rarely that the reaction will hardly proceed at all. In these cases, the reaction will occur at a noticeable rate only if the reactants are heated.

Key characteristics of enzymes

They are specific. They are not used up by a reaction. They will catalyze a reaction that would not normally occur. They're typically proteins. They work by lowering the activation energy of a reaction. A reaction that is exert/endergonic is still the same even w/the use of an enzyme.

What does the absorbtion of this thermal energy do to the reactant molecules and atoms?

They speed up/accelerate and collide with each other more forcefully. Agitates the atoms within the molecules, making the breakage of bonds more likely.

True or False If the inhibitor attaches to the enzyme by weak interactions, inhibition is usually reversible, but if the inhibitor attaches to the enzyme by covalent bonds, inhibition is usually irreversible...like pooooiiiiissssooooonnnn!

True.

True or False The entire allosteric complex oscillates between two different shapes, one catalytically active and the other inactive.

True.

T or F As the atoms then settle into their new, more stable bonding arrangements, energy is released to the surroundings.

Truuuue.

Is the substrate held with weak or strong bonds?

Weak interactions/bonds

Transition state

When the molecules have absorbed enough energy for the bonds to break.

Allosteric site

Where an activating or inhibiting regulatory molecule binds to a regulatory site (allosteric site).

Do the molecules return to stable shapes with lower energy than the contorted state after the reaction?

YES

Does low pH/high acidity denature most enzymes?

YES. Obviously.

Do enzymes emerge from reactions in their original state/form?

Yes.

Can an enzyme recognize its substrate among similar/closely related compounds?

Yes...It's super specific and whatnot.

Because enzymes are very specific for the reactions that catalyze....

they determine which chemical processes will be going on in the cell at any particular time.