Chapter 06 - Energy - Enzymes - and Biological Reactions: Flashcards

A comprehensive set of practice flashcards covering thermodynamics, energy, reaction spontaneity, enzymology, and ribozymes from the chapter notes.

The first law of thermodynamics states that the total disorder of a system always increases.

False - second law of thermodynamics

The potential energy in a chemical bond is defined as chemical energy.

True

At equilibrium, the concentrations of the reactants equals that of the products.

False - rate of formation

Reactions that reach an equilibrium point are reversible.

True

ATP synthesis is exergonic.

False - endergonic

Enzymes alter the equilibrium point of a reaction.

False - activation energy

Enzymes don't change the DG of a reaction.

True

The rate of catalysis is proportional to the concentration of the enzyme.

True

If an enzyme is bound by an allosteric activator, the enzyme will convert from a low-affinity state to a high-affinity state.

True

Ribozymes are enzymes.

False - biological catalysts

The term that best describes all of the chemical reactions of a cell, including acquisition and use of molecules and energy, is ____.

metabolism

The removal of a phosphate group during an enzyme-catalyzed reaction takes ____.

about 10 milliseconds

A child swinging on a swing utilizes which type(s) of energy?

kinetic and potential energy: changing ratios; at the bottom kinetic, at the ends potential

The ultimate fate of the energy used by organisms is ____.

conversion into heat

In molecules, the constant motion of the atoms is an example of ____ energy, while the arrangement of atoms and bonds is an example of ____ energy.

kinetic; potential

Which system is considered a closed system?

the Earth

Which system is considered an open system?

a human

According to the first law of thermodynamics, ____.

Energy can be neither created nor destroyed; energy can only be transformed

Which statement is a part of the first law of thermodynamics?

Energy cannot be created nor destroyed.

Which is the ultimate source of energy for almost all organisms?

the sun

We can calculate whether a reaction is spontaneous by calculating the change in free energy and accounting for entropy. Your paycheck always lists your gross pay, net (take home) pay, and tax withholdings. Which of the following best correlates your paycheck to the changes in free energy?

net salary = gross salary - tax; free energy = total energy - entropy

During every energy transformation, it can be said that ____.

the entropy of the universe increases

Which example would have a negative change in entropy?

water freezing

Which equation is used to calculate the free energy associated with a reaction?

ΔG = ΔH - TΔS

In an exothermic reaction, ____.

the products have less potential energy than the reactants

Which system is most likely to have a negative change in entropy?

water freezing

Which statement is true for exergonic reactions?

The products have less free energy than the reactants.

Which reaction DG value is most likely to produce more products than reactants at equilibrium?

DG = -100 kcal/mol

An exergonic reaction will have a ____.

negative change in free energy

Eating and digesting a candy bar for energy during a sports event is an example of ____.

catabolism

The breakdown of glucose into carbon dioxide, water, and ATP is an example of a(n) ____ pathway.

catabolic

Energy from ATP is transferred to the reactant of an endergonic reaction by addition of a(n) _ group to that molecule.

phosphate

The overall free energy for the coupled reaction ATP hydrolysis (-31.0 kJ/mol) and glucose phosphorylation (+14.3 kJ/mol) is ____.

-16.7 kJ/mol

How does energy coupling allow chemical reactions that are not spontaneous to proceed?

The energy from the exergonic reaction is transferred to the substrate to destabilize it (as per the provided key).

How do cells overcome the energy requirement of endergonic reactions?

by coupling endergonic and exergonic reactions.

Where does the energy for ATP synthesis come from?

catabolism of complex molecules into simpler molecules

Approximately how many ATP molecules are hydrolyzed and resynthesized each second in a typical cell?

10,000,000

Figure 6.2: Which portion of the graph shows the activation energy in the absence of enzyme?

A

Figure 6.2: Which portion shows the activation energy in the presence of enzyme?

B

Figure 6.2: Which portion shows the free energy of the reaction?

C

Why are most diamond rings preferred over graphite rings from a spontaneous perspective?

The energy of activation is very high (activation energy barrier) for the diamond-to-graphite transformation.

Enzymes aid in metabolism by ____.

stabilizing the transition state

Enzymes change the rate of a reaction by ___.

changing the rate, not the DG or direction

What is the primary determinant of the function and specificity of an enzyme?

the enzyme's conformation

Enzymes function primarily by ___.

increasing the probability that reactants come into close proximity in the proper orientation for forming the transition state

Enzymes are ____ catalysts.

protein

You modify the active site of an enzyme; predicted outcome?

The enzyme will not bind to the substrate properly.

What is the difference between cofactors and coenzymes?

Cofactors can be inorganic or organic; coenzymes are organic cofactors.

What is the name of the specific region of an enzyme responsible for catalysis?

active site

Coenzymes that bind tightly to enzymes are called ____.

prosthetic groups

What happens to an enzyme after it has catalyzed a reaction?

it returns to its original state

What is the purpose of ionic groups in the active sites of enzymes?

to alter the substrate in a way that favors catalysis

Illustrate the three mechanisms by which enzymes stabilize the transition state of molecules.

Acid/base catalysis, covalent catalysis, and proximity/orientation to stabilize transition state

If an enzyme is saturated, ____.

the reaction is being catalyzed at the maximum rate

You add increasing amounts of substrate to an enzyme at optimal temperature; the rate of reaction will ___ over time.

increase rapidly, then plateau

In competitive inhibition, the ____.

inhibitor binds to the active site of the enzyme

How would you classify the inhibition described as the DHT hair-loss treatment?

competitive inhibition

Allosteric inhibitors are often ____.

products of the reactions that they regulate

What happens when an allosteric activator binds to an enzyme?

The enzyme transitions from a low affinity state to a high affinity state

In Figure 6.3, why does the curve sharply drop after ~45°C?

The enzyme denatures at higher temperatures, eliminating catalytic activity

If an enzyme's optimal temperature is 37°C, then the enzyme will ___ at temperatures above 37°C.

activity will drop and likely be eliminated by 60°C

What is the optimal pH for enzyme 1 according to Figure 6.4?

pH 3

What is the optimal pH for enzyme 2 according to Figure 6.4?

pH 7

If all three enzymes catalyze the same reaction and you require pH 8, which enzyme would you choose?

enzyme 3

Why do Siamese cats have brown ears, noses, tails, and paws?

They have temperature-sensitive enzymes that are more active in the extremities.

What is the optimum pH of most enzymes?

pH 7

Is a ribozyme a true enzyme?

No, because it is not a protein.

Zhang and Cech’s experiments confirmed which feature of ribozyme activity?

Ribozymes can link nucleic acids together even if their proteins are removed.

Ribozymes are ____.

RNA catalysts

What was the major flaw in Harry Noller’s ribosome experiment?

The extraction process may have altered the RNA molecules (undetectable protein may have remained).

How did Zhang and Cech purify the RNA molecules that catalyze the linkage between amino acids?

Passing the reaction mixture through a column that binds RNA (biotin column)

The discovery of ____ suggested that nucleic acids likely existed prior to proteins.

ribozymes

Because of problems with explaining the origin of RNA-based life, an alternative possibility proposed that ____ existed before the RNA world.

a different form of life existed before the RNA world

Match the term to its correct definition: coupled reaction

The coupling of an exergonic reaction with an endergonic reaction that allows a cell to drive a nonspontaneous reaction to completion

Match the term to its correct definition: equilibrium point

The rate of forward reaction equals the rate of reverse reaction

Match the term to its correct definition: metabolic pathway

A series of chemical reactions where the products of one reaction are the reactants for a subsequent reaction

Match the term to its correct definition: catalyst

A substance that facilitates a chemical reaction without itself being consumed by the reaction

Match the term to its correct definition: activation energy

The energy needed to start a reaction, be it endergonic or exergonic

Match the term to its correct definition: active site

The portion of the enzyme that binds to a reactant or reactants

Match the term to its correct definition: substrate

The reactant molecule that binds to an enzyme

Match the term to its correct definition: transition state

An intermediate arrangement of unstable bonds between atoms that can proceed towards either the reactants or products of a reaction

Match the term to its correct definition: allosteric regulation

The product of the reaction interacts with an enzyme in a noncompetitive way to inhibit or enhance enzyme activity

Identify the exergonic reaction in the list below

burning wood for a campfire

Which statement is true for exergonic reactions?

The products have less free energy than the reactants.

Which DG value is most likely to result in more products than reactants at equilibrium?

DG = -100 kcal/mol

An exergonic reaction will have a ____.

negative change in free energy

Eating and digesting a candy bar for energy during a sports event is a good example of ____.

catabolism

The breakdown of glucose into carbon dioxide, water, and ATP is an example of a catabolic pathway.

catabolic

Energy from ATP is transferred to the reactant of an endergonic reaction by addition of a(n) ____ group to that molecule.

phosphate

The overall free energy for the coupled reaction ATP hydrolysis and glucose phosphorylation is ____.

-16.7 kJ/mol

How does energy coupling allow non-spontaneous reactions to proceed?

The energy from the exergonic reaction is transferred to the substrate to destabilize it (as per the provided key).

Where does the energy for ATP synthesis come from?

catabolism of complex molecules into simpler molecules

Approximately how many ATP molecules are hydrolyzed and resynthesized each second in a typical cell?

10,000,000

Figure 6.2: Which portion shows the activation energy in the absence of enzyme?

A

Figure 6.2: Which portion shows the activation energy in the presence of enzyme?

B

Figure 6.2: Which portion shows the free energy of the reaction?

C

Diamond-to-graphite conversion is spontaneous. Why do people wear diamond rings rather than graphite rings?

The energy of activation is very high for the conversion; diamonds are kinetically stable.

Enzymes aid in metabolism by ___.

stabilizing the transition state

Enzymes change the rate of a reaction by ____.

changing the rate (not DG)

What is the primary determinant of the function and specificity of an enzyme?

the enzyme's conformation