Bio 122 Chapter 8 Study Guide: An introduction to Metabolism

What are the four characteristics of enzymes?

1) An enzyme is a protein catalyst 2) Enzymes are specific for a particular chemical reaction 3) Enzymes are not changed after the reaction 4) Enzymes can only catalyze a spontaneous or net exergonic reaction

What is the active site and catalytic cycle of an enzyme?

1) Substrates enter the active site; the enzyme changes shape such that its active site enfolds the substrates (induced fit) 2) Substrates are held in the active site by weak interactions, such as hydrogen bonds and ionic bonds 3) The active site lowers the activation energy and speeds up the reaction 4) Substrates are converted to products 5) Products are released 6) Active site is available for two new substrate molecules

An enzyme-catalyzed reaction has a ΔG of -20 kcal/mol under standard conditions. What will be the ΔG for the reaction if the amount of enzyme is doubled? A) -20 kcal/mol B) -40 kcal/mol C) +20 kcal/mol D) -10 kcal/mol

A

The ΔG of ATP hydrolysis in a test tube under standard conditions is -7.3 kcal/mol. The ΔG for the reaction A + B = C under the same conditions is +4.0 kcal/mol. What is the overall free-energy change for the coupled reactions under these conditions? A) -3.3 kcal/mol. B) -7.3 kcal/mol. C) -11.3 kcal/mol. D) +3.3 kcal/mol.

A

Which of the following metabolic processes can occur without a net influx of energy from some other process? A) C6H12O6+6O2→6CO2+6H2O B) ADP+Pi→ATP+H2O C) Amino acids →→Protein D) 6CO2+6H2O→C6H12O6+6O2

A

Phosphorylated intermediate

A molecule that is often a reactant with a phosphate group covalently bound to it, making it more reactive and less stable than the unphosphorylated. The key to coupling exergonic and endergonic ​reactions is the formation of this phosphorylated intermediate, which is more reactive (less stable, with more free energy) than the original unphosphorylated molecule

Metabolic pathway

A series of chemical reactions that either builds a complex molecule (anabolic pathway) or breaks down a complex molecule into simpler compounds (catabolic pathway). In a metabolic pathway, a specific molecule is altered in a series of defined steps, resulting in a certain product. Each step is catalyzed by a specific enzyme, a macromolecule that speeds up a chemical reaction. Each step or reaction has a stating molecule called a substrate and an ending molecule called a product.

Exergonic reaction

A spontaneous chemical reaction in which there is a net release of free energy. Because the chemical mixture loses free energy (G decreases), delta G is a negative for an exergonic reaction.

What is meant by a "spontaneous chemical reaction?"

A spontaneous chemical reaction or physical change is one that, once started, will continue without any outside help. A nonspontaneous chemical reaction or physical change is one that requires assistance to keep going.

Noncompetive 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 can no longer effectively catalyze the conversion of a substrate to product.

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. This kind of inhibition 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.

ATP structure

ATP is a nucleotide that consists of three main structures: the nitrogenous base, adenine; the sugar, ribose; and a chain of three phosphate groups bound to ribose. The phosphate tail of ATP is the actual power source in which the cell taps.

How does ATP typically transfer energy from an exergonic to an endergonic reaction in the cell?

ATP usually transfers energy to an endergonic process by phosphorylating (adding a phosphate group to) another molecule. (Exergonic processes, in turn, phosphorylate ADP to regenerate ATP.)

Chemical equailibrium is reached when A) concentrations of reactants and products remain the same B) the forward and reverse reactions occur at the same rate C) concentrations of products are higher than the concentrations of reactants D) there are equal concentrations of reactants and products

B. Chemical equilibrium is the point at which the forward and reverse reactions of a chemical reaction offset one another exactly. Equilibrium does not mean that the reactants and products are equal in concentration, but only that their concentrations have stabilized at a particular ratio. Reactions are still going on it both directions, but with no net effect on the concentrations of reactants and products.

The ΔG of ATP hydrolysis in a test tube under standard conditions is -7.3 kcal/mol. The ΔG for the reaction A+B C under the same conditions is +4.0 kcal/mol. How would the addition of an enzyme that catalyzes A+B C most likely alter the coupled reactions? A) It would increase the rate of production of C and increase the overall ΔG for the coupled reactions. B) It would result in no change in the rate of production of C and decrease the overall ΔG for the coupled reactions. C) It would result in no change in the overall ΔG for the coupled reactions. D) It would increase the rate of production of C and decrease the overall ΔG for the coupled reactions.

C

Which of the following terms best describes a chemical reaction for which ΔG is positive? A) spontaneous B) enthalpic C) endergonic D) exergonic

C

Induced Fit

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

Mechanical work

Cell motility and movement of structures within cells such as the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction.

Cellular respiration uses glucose and oxygen, which have high levels of free energy, and releases carbon dioxide and water, which have low levels of free energy. Is cellular respiration spontaneous or not? Is it exergonic or endergonic? What happens to the energy released from glucose?

Cellular respiration is a spontaneous and exergonic process. The energy released from glucose is used to do work in the cell or is lost as heat.

What does it mean to say that enzymes are specific?

Changing even one atom on the substrates will prevent them from being recognized by the enzyme.

What are the three main kinds of work cells do?

Chemical work, transport work, and mechanical work.

The relationship between the breakdown of macromolecules and the biosynthesis of macromolecules is most similar to the relationship between which of the following pairs of terms? A) exergonic and spontaneous B) work and free energy C) free energy and entropy D) exergonic and endergonic

D

Which of the following statements best describes how addition of a catalyst will affect a chemical reaction? A) The catalyzed reaction will consume all of the catalyst. B) The catalyzed reaction will have a lower ΔG than the uncatalyzed reaction. C) The catalyzed reaction will have a higher ΔG than the uncatalyzed reaction. D) The catalyzed reaction will have the same ΔG as the uncatalyzed reaction.

D

Which of the following is a chemical reaction? A) the melting of ice B) making a hydrogen bond between a water molecule and a sugar molecule C) changing a carbon atom to a nitrogen atom by radioactive decay D) the formation of a covalent bond between two amino acids

D. Chemical reactions involve the making and breaking of chemical bonds, leading to changes in the composition of matter.

Which type releases energy and which type absorbs energy (endergonic and exergonic)?

Exergonic is energy releasing and endergonic is energy consuming.

ATP is a subunit for what kind of polymer?

It is a subunit for nucleotides.

What is the difference between a pathway and a reaction?

Metabolic pathways are the chemical reactions that take place to create and use energy. Chemical reaction, a process in which one or more substances, the reactants, are converted to one or more different substances, the products. Substances are either chemical elements or compounds.

Catabolism

Metabolic pathways that break down molecules, releasing energy.

Anabolism

Metabolic pathways that construct molecules, requiring energy.

What name is given to the reactants in an enzymatically catalyzed reaction?

Substrate.

Enthalpy

The heat content of a system at constant pressure. Or TdeltaS must be positive (the system gives of order and S increases).

Bioenergetics

The overall flow and transformation of energy in an organism. The study of how energy flows through organisms.

Free energy

The portion of a biological system's energy that can perform work when temperature and pressure are uniform throughout the system. The change in free energy of a system (delta G) is calculated by the equation delta G = delta H - TdeltaS, when delta H is the change in enthalpy (total energy), delta T is the absolute temperature in Kelvin, and delta S is the change in entropy.

First law of thermodynamics

The principle of conservation of energy: Energy can be transferred and transformed, but it cannot be created or destroyed.

Second law of thermodynamics

The principle stating that every energy transfer or transformation increases the entropy of the universe. Unusable forms of energy are at least partly converted to heat.

Transport work

The pumping of substances across membranes against the direction of spontaneous movement.

Is the purpose of a coupled reaction to make an endergonic or exergonic reaction happen?

The purpose is to make an exergonic reaction. When the two reactions are coupled they release more energy than is used, so the net reaction is exergonic.

Chemical work

The pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers.

Metabolism

The totality of an organism's chemical reactions.

What is meant by "coupled reactions?"

Two (or more) reactions may be combined such that a spontaneous reaction may 'drive' an nonspontaneous one. An example is the formation of ATP, which is an endergonic process and is coupled to the dissipation of a proton gradient.

Which phosphate is released when ATP generates energy?

When the cell needs energy to do work, ATP loses its 3rd phosphate group, releasing energy stored in the bond that the cell can use to do work.

The process of cellular respiration, which converts simple sugars such as glucose into CO2 and water, is an example of __________.

a catabolic pathway.

The rate at which a particular amount of enzyme converts substrate to product is partly a function of the initial concentration of the substrate: The more substrate molecules that are available, the more frequently they

access the active sites of the enzyme molecules.

An enzyme catalyzes a reaction by lowering the

activation energy barrier, enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures.

Only a restricted region of the enzyme molecule actually binds to the substrate. This region, called the

active site is typically a pocket or a groove on the surface of the enzyme where catalysis occurs. Usually, the active site is formed by only a few of the enzyme's amino acids, with the rest of the protein molecule providing a framework that determines the shape of the active site. The specificity of an enzyme is attributed to a complementary fit between the shape of its active site and the shape of the substrate.

When an enzyme population is saturated with substrates, the only way to increase the rate of product formation is to

add more enzyme. Cells often increase the rate of a reaction by producing more enzyme molecules.

Catabolic pathways release energy by

breaking down molecules into simpler compounds. Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a catabolic pathway.

One major catabolic pathway is cellular respiration, which

breaks down glucose and other organic fuels in the presence of oxygen to carbon dioxide and water.

Instead of heat, organisms carry out

catalysis, the process by which a catalyst selectively speeds up a reaction without itself being consumed.

If the cofactor is an organic molecule, it is referred to, more specifically, as a

coenzyme. Most vitamins are important in nutrition because they act as coenzymes or raw materials from which coenzymes are made.

Many enzymes require nonprotein helpers for catalytic activity, often for chemical processes like electron transfers that cannot easily be carried out by the amino acids in proteins. These adjuncts, called

cofactors, may be bound tightly to the enzyme as permanent residents, or they may bind loosely and reversibly along with the substrate. The cofactors of some enzymes are inorganic, such as the metal atoms zinc, iron, and copper in ionic form.

Anabolic pathways consume energy to build

complex molecules from simpler ones. The synthesis of proteins from amino acids is an example of an example of an anabolic pathway.

When a process occurs spontaneously in a system, we can be sure that

delta G is negative. Another way to think of delta G is to realize that it represents the difference between the free energy of the final state and the free energy of the initial state. Delta G = G final state - G initial state.

A non-spontaneous reaction is called an

endergonic reaction because the reaction needs to have energy added.

A key feature in the way cells manage their energy resources to do work is

energy coupling, the use of energy released from an exergonic process to drive an endergonic one.

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

enzyme-substrate complex. While enzyme and substrate are joined, the catalytic action of the enzyme converts the substrate to the product (or products) of the reaction.

Based on their free-energy changes, chemical reactions can be classified as either

exergonic ("energy outward") or endergonic ("energy inward").

An organism at work uses ATP continuously, but ATP is a renewable resource that can be regenerated by the addition of phosphate to ADP. The free energy required to phosphorylate ADP comes from

exergonic breakdown reactions (catabolism) in the cell. This shuttling of inorganic phosphate and energy is called the ATP cycle, and it couples the cell's energy-yielding (exergonic) processes to the energy-consuming (endergonic) ones.

A spontaneous reaction is called an

exergonic reaction because there is a release of energy.

The magnitude of delta G

for an exergonic reaction represents the maximum amount of work the reaction can perform.​ The greater the decrease in free energy, the greater the amount of work that can be done.

A thermodynamic unit called

free energy (G) indicates whether a reaction will be spontaneous or not.

Proteins, DNA, and other complex cellular molecules are rich in

free energy and have the potential to decompose spontaneously; that is, the laws of thermodynamics favor their breakdown. These molecules only persist because at temperatures typical for cells, few molecules can make it over the hump of activation energy. The barriers for selected reactions must occasionally be surmounted, however, for cells to carry out the processes needed for life.

It is crucial to note that an enzyme cannot change the

free energy for a reaction; it cannot make an endergonic reaction exergonic. Enzymes can only hasten reactions that would eventually occur anyway, but this enables the cell to have a dynamic metabolism, routing chemicals smoothly through metabolic pathways. Also, enzymes are very specific for the reactions they catalyze, so they determine which chemical processes will be going on in the cell at any given time.

An endergonic reaction is one that absorbs

free energy from its surroundings (Figure 8.6b). Because this kind of reaction essentially stores free energy in molecules (G increases), delta G is positive. Such reactions are non-spontaneous, and the magnitude of delta G is the quantity of energy required to drive the reaction. If a chemical process is exergonic (downhill), releasing energy in one direction, then the reverse process must be endergonic (uphill), using energy. A reversible process cannot be downhill in both directions.

The initial investment of energy for starting a reaction—the energy required to contort the reactant molecules so the bonds can break—is known as the

free energy of activation, or activation energy. We can think of activation energy as 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.

Changing one molecule into another generally involves contorting the starting molecule into a

highly unstable state before the reaction can proceed. This contortion can be compared to the bending of a metal key ring when you pry it open to add a new key. The key ring is highly unstable in its opened form but returns to a stable state once the key is threaded all the way onto the ring. To reach the contorted state where bonds can change, reactant molecules must absorb energy from their surroundings. When the new bonds of the product molecules form, energy is released as heat, and the molecules return to stable shapes with lower energy than the contorted state.

In most enzymatic reactions, the substrate is held in the active site by so-called weak interactions, such as

hydrogen bonds and ionic bonds. The R groups of a few of the amino acids that make up the active site catalyze the conversion of substrate to product, and the product departs from the active site. The enzyme is then free to take another substrate molecule into its active site.

Enzymes are described as catalysts, which means that they __________.

increase the rate of a reaction without being consumed by the reaction. This permits enzyme molecules to be used repeatedly.

We can think of free energy as a measure of a system's

instability. Its tendency to change to a more stable state. Unstable systems (higher G) tend to change in such a way that they become more stable (lower G). For example, a diver on top of a platform is less stable (more likely to fall) than when floating in the water; a drop of concentrated dye is less stable (more likely to disperse) than when the dye is spread randomly through the liquid; and a glucose molecule is less stable (more likely to break down) than the simpler molecules into which it can be split. Unless something prevents it, each of these systems will move toward greater stability: The diver falls, the solution becomes uniformly colored, and the glucose molecule is broken down into smaller molecules.

The active site itself is also not a rigid receptacle for the substrate. When the substrate enters the active site, the enzyme changes shape slightly 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. This shape change makes the active site fit even more snugly around the substrate.

Certain chemicals selectively inhibit the action of specific enzymes. Sometimes the inhibitor attaches to the enzyme by covalent bonds, in which case the inhibition is usually

irreversible. Many enzyme inhibitors, however, bind to the enzyme by weak interactions, and when this occurs the inhibition is reversible. Some reversible inhibitors resemble the normal substrate molecule and compete for admission into the active site.

An enzyme

is an organic catalyst.

As a result of its involvement in a reaction, an enzyme _____.

is unchanged.

For a reaction to have a negative delta G, the system must

lose free energy during the change from initial state to final state. Because it has less free energy, the system in its final state is less likely to change and is therefore more stable than it was previously.

For a system at equilibrium,​ G is at its

lowest possible value in that system. Free energy increases when a reaction is somehow pushed away from equilibrium, perhaps by removing some of the products (and thus changing their concentration relative to that of the reactants). We can think of the equilibrium state as a free-energy valley. Any change from the equilibrium position will have a positive delta G and will not be spontaneous. For this reason, systems never spontaneously move away from equilibrium. Because a system at equilibrium cannot spontaneously change, it can do no work. A process is spontaneous and can perform work only when it is moving toward equilibrium.

An enzyme is a

macromolecule that acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction. Without regulation by enzymes, chemical traffic through the pathways of metabolism would become terribly congested because many chemical reactions would take such a long time.

Metabolism as a whole manages the

material and energy resources of the cell.

Citing enzyme inhibitors that are metabolic poisons may give the impression that enzyme inhibition is generally abnormal and harmful. In fact,

molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors. Such regulation—selective inhibition—is essential to the control of cellular metabolism

An increase in free energy means a reaction will

not be spontaneous.

Metabolism is an emergent property of life that arises from

orderly interactions between molecules.

Enzymes work by

reducing the energy of activation.

The reaction catalyzed by each enzyme is very

specific; an enzyme can recognize its specific substrate even among closely related compounds. What accounts for this molecular recognition? Recall that most enzymes are proteins, and that proteins are macromolecules with unique 3-D configurations. The specificity of an enzyme results from its shape, which is a consequence of its amino acid sequence.

A decrease in free energy means a reaction will be

spontaneous.

Only processes with a negative delta G are

spontaneous. For delta G to be negative, delta H must be negative (the system gives up enthalpy and H decreases). When delta H and TdeltaS are tallied, delta G has a negative value for all spontaneous processes. In other words, every spontaneous process decreases the system's free energy, and processes that have a positive or zero delta G are never spontaneous.

The reactant an enzyme acts on is referred to as the enzyme's

substrate.

The activity of an enzyme—how efficiently the enzyme functions—is affected by general environmental factors, such as

temperature and pH. It can also be affected by chemicals that specifically influence that enzyme.

The word spontaneous implies that it is energetically favorable, not

that it will occur rapidly.

Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for

the endergonic process of making ATP.

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.

Up to a point, the rate of an enzymatic reaction increases with increasing temperature, partly because substrates collide with active sites more frequently when the molecules move rapidly. Above that temperature, however,

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. Each enzyme has an optimal temperature at which its reaction rate is greatest. Without denaturing the enzyme, this temperature allows the greatest number of molecular collisions and the fastest conversion of the reactants to product molecules.

The proteins in a cell harness energy released during ATP hydrolysis in several ways to perform

the three types of cellular work.

Activation energy is often supplied by heat in the form of

thermal energy that the reactant molecules absorb from the surroundings. The absorption of thermal energy accelerates the reactant molecules, so they collide more often and more forcefully. It also agitates the atoms within the molecules, making the breakage of bonds more likely. When the molecules have absorbed enough energy for the bonds to break, the reactants are in an unstable condition known as the transition state. They are activated, and their bonds can be broken. As the atoms then settle into their new, more stable bonding arrangements, energy is released to the surroundings.

Thermodynamics can tell us

when a chemical reaction will occur automatically or will be spontaneous.

A spontaneous chemical reaction occurs

without any requirement for outside energy.

Spontaneous reactions occur

without energy input. They can happen quickly or slowly.