chapter 6 dynamic study module #2

why is it is more difficult to make a noncompetitive inhibitor?

because it is less obvious what the noncompetitive inhibitor's shape and structure should be.

A decrease in concentration of a reactant will cause

the reactant molecules to collide less frequently; reaction rate would decrease

When the noncompetitive inhibitor is bonded to the enzyme

the shape of the enzyme is distorted.

Some bacteria are metabolically active in hot springs because __________.

their enzymes have high optimal temperatures

A plot of reaction rate (velocity) against temperature for an enzyme indicates little activity at 10°C and 45°C, with peak activity at 35°C. The most reasonable explanation for the low velocity at 10°C is that __________.

there is too little activation energy available

Allosteric proteins

(regulatory molecules?) proteins that undergo reversible changes in conformation when bound to another molecule; sensitive to environmental conditions (pH and temperature), acted on by inhibitors, and exist in active and inactive conformations; regulate enzyme activity in a cell behave like reversible noncompetitive inhibitors: change an enzyme's shape and the functioning of its active site by binding to a site elsewhere on the molecule, via noncovalent interactions.

Enzymes use a variety of mechanisms that lower activation energy and speed up a reaction.

1) in reactions involving two or more reactants, the active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. 2) the active site of an enzyme holds bound substrates, the enzyme may stretch the substrate molecules toward their transition-state form, stressing and bending critical chemical bonds that must be broken during the reaction. Because EA is proportional to 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. 3) the active site may also provide a microenvironment that is more conducive to a particular type of reaction than the solution itself would be without the enzyme. 4) 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. Subsequent steps of the reaction restore the side chains to their original states, so that the active site is the same after the reaction as it was before. into its active site.

Photosynthesis equation

6CO2 + 6H2O --> light energy --> C6H12O6 + 6O2 Photosynthesis takes CO2 and H2O (quite low energy molecules), and then assembles them into glucose; ANABOLIC

Which of the following statements about the combustion of glucose with oxygen to form water and carbon dioxide (C6H12O6 + 6 O2 → 6 CO2 + 6 H2O) is correct?

A large molecule (glucose) has been converted into several smaller molecules (water and carbon dioxide); thus, the products have more disorder (greater entropy) than the reactants.

competitive inhibitor

A substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics. can be overcome by adding more substrate to outcompete the inhibitor. ex: Many drugs used to treat different medical condition; easy to make molecule that is similar in structure to a particular substrate because the known enzyme's shape can be used as a model of what the molecule needs to look like.

Above a certain substrate concentration, the rate of an enzyme-catalyzed reaction drops as the enzymes become saturated. Which of the following would lead to a faster conversion of substrate into product under these saturated conditions?

An increase in concentration of enzyme AND increasing the temperature by a few degrees

How do enzymes lower activation energy?

By locally concentrating the reactants. One of the ways enzymes work is to increase the concentrations of reactants at a single place.

Which of the following metabolic processes can occur without a net influx of energy from some other process

C6H12O6 + 6 O2 → 6 CO2 + 6 H2O

Which of the following statements about enzyme function is correct?

Enzymes can lower the activation energy of reactions, but they cannot change the equilibrium point because they cannot change the net energy output.

Which of the following statements correctly describe(s) the role(s) of heat in biological reactions?

Heat from the environment is necessary for substrates to get over the activation energy barrier AND The kinetic energy of the substrates is increased as the amount of heat in the system is increased.

Under most conditions, the supply of energy by catabolic pathways is regulated by the demand for energy by anabolic pathways. Considering the role of ATP formation and hydrolysis in energy coupling of anabolic and catabolic pathways, which of the following statements is most likely to be true?

High levels of ADP act as an allosteric activator of catabolic pathways Fluctuating concentrations of regulators can cause a sophisticated pattern of response in the activity of cellular enzymes. The products of ATP hydrolysis (ADP and a phosphate ion), for example, play a complex role in balancing the flow of traffic between anabolic and catabolic pathways by their effects on key enzymes. ATP binds to several catabolic enzymes allosterically, lowering their affinity for substrate and thus inhibiting their activity. ADP, however, functions as an activator of the same enzymes. This is logical because catabolism functions in regenerating ATP. If ATP production lags behind its use, ADP accumulates and activates the enzymes that speed up catabolism, producing more ATP. If the supply of ATP exceeds demand, then catabolism slows down as ATP molecules accumulate and bind to the same enzymes, inhibiting them. ATP, ADP, and other related molecules also affect key enzymes in anabolic pathways. In this way, allosteric enzymes control the rates of important reactions in both sorts of metabolic pathways.

If an enzyme is added to a solution where its substrate and product are in equilibrium, what will occur?

Nothing; the reaction will stay at equilibrium

Succinylcholine is structurally almost identical to acetylcholine. If succinylcholine is added to a mixture that contains acetylcholine and the enzyme that hydrolyzes acetylcholine (but not succinylcholine), the rate of acetylcholine hydrolysis is decreased. Subsequent addition of more acetylcholine restores the original rate of acetylcholine hydrolysis. Which of the following correctly explains this observation?

Succinylcholine must be a competitive inhibitor with acetylcholine.

Which of these statements about enzyme inhibitors is true?

The action of competitive inhibitors may be reversible or irreversible. If the inhibitor attaches to the enzyme by covalent bonds, inhibition is usually irreversible. Many enzyme inhibitors, however, bind to the enzyme by weak interactions, in which case inhibition is reversible.

Which of the following statements about the active site of an enzyme is correct?

The active site may resemble a groove or pocket in the surface of a protein into which the substrate fits.

The binding of an allosteric inhibitor to an enzyme causes the rate of product formation by the enzyme to decrease. Which of the following best explains why this decrease occurs?

The allosteric inhibitor causes a structural change in the enzyme that prevents the substrate from binding at the active site.

What is meant by the "induced fit" of an enzyme?

The enzyme changes its shape slightly as the substrate binds to it.

substrate concentration affecting rate of enzyme reaction

The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules (higher concentration = faster reaction) limit: concentration of substrate will be high enough that all enzyme molecules have their active sites engaged; As soon as the product exits an active site, another substrate molecule enters; the enzyme is saturated; rate of the reaction is determined by the speed at which the active site converts substrate to product; the way to increase the rate of product formation is to add more enzyme

Which of the following statements about allosteric proteins is/are true?

They exist in active and inactive conformations. They are acted on by inhibitors.They are sensitive to environmental conditions.

saturated enzyme

When the concentration of substrate is high enough that all enzyme molecules have their active sites engaged; As soon as the product exits an active site, another substrate molecule enters; rate of the reaction is determined by the speed at which the active site converts substrate to product; the way to increase the rate of product formation is to add more enzymes Some enzymes can be activated further by allosteric activators, in which case one might add some activator to the reaction

The specificity of an enzyme is attributed to

a compatible fit between the shape of its active site and the shape of the substrate. The shape that best fits the substrate isn't necessarily the one with the lowest energy, but during the very short time the enzyme takes on this shape, its active site can bind to the substrate. It has been known for more than 50 years that the active site itself is also not a rigid receptacle for the substrate. An enzyme is not a stiff structure locked into a given shape. In fact, recent work by biochemists has shown clearly that enzymes (and other proteins as well) seem to "dance" between subtly different shapes in a dynamic equilibrium, with slight differences in free energy for each "pose."

If an enzyme in solution is saturated with substrate, the most effective way to obtain a faster yield of products is to __________.

add more of the enzyme

The process of stabilizing the structure of an enzyme in its active form by the binding of a molecule is an example of __________.

allosteric regulation

allosteric inhibitor

bind to an allosteric site and keep the enzyme in its inactive form; reducing enzymatic activity

allosteric activator

binds to allosteric site and increases enzyme activity by inducing its active form; causes a structural change in the enzyme that prevents the substrate from binding at the active site.

What will happen to the rates of the forward and reverse reactions when a catalyst is added?

both forward and reverse reaction rates increase

organisms use __ to speed up reactions

catalysts

example of catabolic reaction

cellular respiration (C6H12O6 + 6 O2 → 6 CO2 + 6 H2O); hydrolysis; digestion

rate of reaction

change in concentration/ change in time affected by: temperature, concentration, and catalysts. increase in temperature, an increase in reactant concentration, or the presence of a catalyst will all increase the rate of the reaction.

coenzyme

cofactor that is an organic molecule; ex: vitamins (act as coenzymes or raw materials from which coenzymes are made)

examples of anabolic reactions

combining amino acids to form proteins (protein synthesis); combining simple sugars to form disaccharides; photosynthesis (6CO2+6H20→C6H12O6 + 6 O2

allosterically regulated enzymes

constructed from two or more subunits, each composed of a polypeptide chain with its own active site. The entire complex oscillates between two different shapes, one catalytically active and the other

Allosterically regulated enzymes

constructed from two or more subunits, each composed of a polypeptide chain with its own active site; oscillates between two different shapes: one catalytically active and the other inactive

cell's ability to tightly regulate its metabolic pathways

controls when and where its various enzymes are active by switching on and off the genes that encode specific enzymes or by regulating the activity of enzymes once they are made. In many cases, the molecules that naturally regulate enzyme activity in a cell behave something like reversible noncompetitive inhibitors: These regulatory molecules change an enzyme's shape and the functioning of its active site by binding to a site elsewhere on the molecule, via noncovalent interactions.

noncompetitive inhibitors

do not directly compete with the substrate to bind to the enzyme at the active site; they impede enzymatic reactions by binding to another part of the enzyme, causing the enzyme molecule to change its shape in such a way that the active site becomes less effective at catalyzing the conversion of substrate to product.

ph affecting enzyme reaction rate

each enzyme has a pH at which it is most active; optimal pH 6-8; acidic environment denatures most enzymes; ex: trypsin (optimal ph 8), a digestive enzyme residing in the alkaline environment of the human intestine exceptions: pepsin (optimal ph 2), a digestive enzyme in the human stomach; is adapted to maintain its functional three-dimensional structure in the acidic environment of the stomach.

Most medications are

enzyme inhibitors

cellular respiration

exergonic and catabolic process that releases energy by breaking down glucose and other food molecules in the presence of oxygen; converts food energy to energy stored in ATP. by products that are produced: heat, carbon dioxide, and water

irreversible inhibitor

forms a covalent bond with an amino acid side group within the active site, which prevents the substrate from entering the active site or prevents catalytic activity; bind directly to the active site by covalent bonds; permanently render an enzyme inactive ex: drugs; antibiotic penicillin (which inhibits an enzyme involved in bacterial cell-wall synthesis); aspirin (which inhibits cyclooxygenase-2, the enzyme involved in the inflammatory reaction). if, when added, the reaction has stopped completely, then the enzyme is inactive at this point and new enzyme must be added to regain enzyme activity

Enzyme activity is affected by pH because __________.

high or low pH may disrupt hydrogen bonding or ionic interactions and thus change the shape of the active site

why can't heat be used in biological reactions?

high temperature denatures proteins and kills cells; heat would speed up all reactions, not just those that are needed

Allosteric regulation

involves stabilizing the structure of an enzyme in its active form by the binding of a molecule; any case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site; may result in either inhibition or stimulation of an enzyme's activity. - simplest kind: an activating or inhibiting regulatory molecule binds to a regulatory site (allosteric site), often located where subunits join. The binding of an activator to a regulatory site stabilizes the shape that has functional active sites, whereas the binding of an inhibitor stabilizes the inactive form of the enzyme. The subunits of an allosteric enzyme 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.

denatured enzyme

lost its native conformation and its biological activity; can no longer carry out its function

catalyzed reaction

more likely to proceed than an uncatalyzed reaction; forms products more rapidly than an uncatalyzed reaction.

heat in reactions

necessary for substrates to get over the activation energy (EA) barrier; leads to increase in the kinetic energy of the substrates; The activation energy provides a barrier that determines the rate of the reaction. The reactants must absorb enough energy to reach the top of the activation energy barrier before the reaction can occur. For some reactions, EA is modest enough that even at room temperature there is sufficient thermal energy for many of the reactant molecules to reach the transition state in a short time. In most cases, however, EA is so high and 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. Proteins, DNA, and other complex molecules of the cell are rich in free energy and have the potential to decompose spontaneously; that is, the laws of thermodynamics favor their breakdown. These molecules persist only because at temperatures typical for cells, few molecules can make it over the hump of activation energy. However, the barriers for selected reactions must occasionally be surmounted for cells to carry out the processes needed for life. Heat speeds a reaction by allowing reactants to attain the transition state more often

cofactors

non protein helpers that enzymes require for catalytic activity; may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate; some are inorganic (ex: metal atoms zinc, iron, and copper in ionic form)

Chemical energy is a form of __ energy.

potential (stored)

Allosteric regulation

protein's function at one site is affected by the binding of a regulatory molecule to a separate site; results in either inhibition or stimulation of an enzyme's activity

temperature affecting enzyme reaction rate

rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly; at optimal temperature: reaction rate is greatest; allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules; human enzymes: 35-40°C. Above the optimal temperature: the speed of the enzymatic reaction drops sharply; The thermal agitation of the enzyme molecule disrupts the hydrogen bonds, ionic bonds, and other weak interactions that stabilize the active shape of the enzyme, and the protein molecule eventually denatures.

The rate of a reaction is affected by the concentration of

reactants only.

active site

restricted region of the enzyme molecule that binds to the substrate; typically a pocket or groove on the surface of the enzyme where catalysis occurs; usually formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the configuration of the active site.

competitive inhibitors

reversible inhibitors that resemble the normal substrate molecule and compete for admission into the active site; reduce the productivity of enzymes by blocking substrates from entering active sites; can 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 sites.

what affects the rate of an enzyme reaction?

substrate concentration pH cooling the enzyme heating the enzyme

Most cells cannot harness heat to perform work because __________.

temperature is usually uniform throughout a cell