Biochemistry : Enzyme Kinetics and Models

Study concepts, example questions & explanations for Biochemistry

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Example Questions

Example Question #3 : Vmax And Km

Which of these are representations of ?

I. 

II. 

III. Y-intercept on a Lineweaver-Burk plot

Possible Answers:

II and III

I and II

I and III

I, II, III

I only

Correct answer:

I and II

Explanation:

 can be defined as  or as .

However, on a Lineweaver-Burk plot, the Y-intercept actually represents . It is the X-intercept that  can be derived from. The X-intercept is equivalent to .

Example Question #1 : Vmax And Km

When an enzyme is in the presence of a competitive inhibitor, which of the following will happen to the enzyme?

Possible Answers:

 will increase.

 will decrease.

 will increase.

 will decrease.

Correct answer:

 will increase.

Explanation:

Competitive inhibitors will block the active site of the enzyme. The presence of the competitive inhibitor increases the amount of substrate required to get the enzyme to half of its maximum velocity. As a result, the  of the enzyme will increase. Note that a competitive inhibitor will not affect the maximum velocity of the enzyme.

Example Question #1 : Rate Limiting Step

According to Michaelis-Menton kinetics, what is a characteristic of the rate limiting step in enzyme kinetics?

Possible Answers:

It dissociates the enzyme-substrate complex into enzyme + substrate

Enzyme is not present

It is dependent on activation energy from catalysis

The enzyme-substrate complex is formed

Does not involve a catalyst

Correct answer:

It is dependent on activation energy from catalysis

Explanation:

The enzyme-substrate complex dissociates into enzyme + product. The rate limiting step is providing the activation energy to get to the transition state, which is greatly decreased by an enzyme.

Example Question #1 : Rate Limiting Step

Which of the following best describes the rate-limiting step in a chemical reaction?

Possible Answers:

It is always an anabolic reaction

It is the step that liberates the most amount of energy in the overall reaction

It is the slowest step of the overall reaction

It is the fastest step in the overall reaction

It is the step that consumes the most amount of energy in the overall reaction

Correct answer:

It is the slowest step of the overall reaction

Explanation:

Although chemical reactions are typically displayed in the form of an equation, with reactants on the left and products on the right, these reactions are not a simple one step conversion. Often, there are several individual steps that the reactants go through on their way to becoming products. This is shown by the mechanism for that particular reaction.

Furthermore, when talking about chemical reactions, it is very important to distinguish between two concepts that are sometimes confused with one another. The first concerns the kinetics of the reaction, while the second concerns the thermodynamics.

Chemical kinetics is concerned with time. If a chemical reaction is occurring, kinetics answers the question of how fast the reaction is going. Thermodynamics, on the other hand, is not concerned with time. It doesn't care how fast or how slow a reaction goes. All it cares about is whether a chemical reaction is spontaneous or nonspontaneous. To answer this, thermodynamics considers the energetics of a reaction.

When looking at the answer choices, we can immediately eliminate three of them based on this information. The rate-limiting step of a chemical reaction is not concerned with how much energy is liberated or consumed. Instead, the rate-limiting step is defined as the slowest step out of all the steps that occur for a given chemical reaction. In other words, a reaction can only proceed as fast as its slowest step, just like a chain is only as strong as its weakest link. Further, the rate-limiting step in a reaction may be anabolic or catabolic.

It is important to note, however, that there is one component of energy that does affect the rate of a reaction. This energy is called the activation energy, and it represents how much energy needs to be invested into a reaction in order for that reaction to proceed. The reason why this is distinct from thermodynamics, however, is because thermodynamics cares only about initial and final energy states; it doesn't care about how a reaction goes from initial to final, whereas kinetics does. Even though the activation energy for a reaction can change (via enzymes, for instance), this will not affect the initial and final energy levels.

Example Question #1 : Rate Limiting Step

Which of the following is true regarding the rate-limiting reaction?

Possible Answers:

It has the lowest activation energy

It is always endothermic

More than one of these are true

It has the highest activation energy

Correct answer:

It has the highest activation energy

Explanation:

Rate-limiting reaction is the slowest reaction in a series of reactions. It is used to calculate the rate law of the overall reaction. Recall from thermochemistry that slow reactions tend to have higher activation energy (energy “hill’). Slower reactions have to climb a higher energy hill to produce transition states and, subsequently, products; therefore, rate-limiting reaction will have the highest activation energy of all reactions in the series. Enthalpy (exothermic or endothermic) does not determine the speed of a reaction; therefore, a rate-limiting reaction could be exothermic or endothermic.

Example Question #1 : Rate Limiting Step

Consider the following series of reactions.

Reaction 1:  (fast)

Reaction 2:  (slow)

Reaction 3:  (fast)

What is the rate law for the overall reaction? ( and  are arbitrary reaction orders)

Possible Answers:

None of these are correct

Correct answer:

Explanation:

The overall reaction is as follows.

          

The rest of the molecules are intermediates (meaning they are produced and consumed in the reaction). The overall reaction rate always depends on the slowest step, which is also called the rate-determining step. Reaction 2 is the rate-determining step in this series of reactions; therefore, the rate law for the overall reaction is:

where  is the reaction order. Since it is an intermediate, molecule C is not part of the final reaction and, therefore, not part of the rate law. We cannot determine the reaction order from the given information.

Example Question #1 : Other Kinetics Principles

Suppose that an enzyme has a critical functional group in its active site that is heavily involved in carrying out the catalytic mechanism. To perform its role in catalyzing its target reaction, this particular functional group must be able to accept a proton from the intermediate during the process. If the pKa of this functional group is equal to 7.0, then what percentage of the total enzyme active sites for this enzyme would be in the active form in a solution in which the pH is equal to 6.4?

Possible Answers:

Correct answer:

Explanation:

In order to solve this problem, we'll need to make use of the Henderson-Hasselbalch equation.

Therefore, for every 0.25mol of base (deprotonated functional group), there is 1mol of acid (protonated functional group). Furthermore, we're told in the question stem that the functional group must be able to accept a proton from the intermediate during the catalytic mechanism. To accept a proton, the functional group would need to be in its deprotonated form to be active. Hence, we're trying to find the percentage of the deprotonated form. To find this value, we'll use the following expression:

Example Question #2 : Other Kinetics Principles

Which of the following does not increase reaction rate?

Possible Answers:

Increasing the concentration of substrates

Optimizing pH

Increasing temperature

Introducing cofactors

Decrease amount of catalysts

Correct answer:

Decrease amount of catalysts

Explanation:

Catalysts lower activation energy. Lowering activation energy causes the reaction rate to increase. Removing catalysts will cause the reaction to slow down because the activation energy will be higher. Cofactors assist in the function of enzymes and can increase reaction rate.

Example Question #3 : Other Kinetics Principles

There are at least four types of glucose transporter in the body. GLUT1 and GLUT3 are located in most tissues including the brain and the red blood cells. These glucose transporters rapidly take up glucose from the blood but have the lowest  value. GLUT2 is commonly found in the liver and the pancreas. GLUT2 has a lower affinity for glucose but has the highest  value. GLUT4 is common in skeletal tissues and in adipose tissues. This transporter is normally not active for uptake unless stimulated by insulin or during exercise.  

What is the mechanism by which the GLUT proteins in the transport glucose into the cell from the blood?

Possible Answers:

Facilitated diffusion

Antiport

Active transport 

Voltage-gated channel

Symport

Correct answer:

Facilitated diffusion

Explanation:

Since there will be more glucose surrounding the cell, the GLUT proteins utilize a chemical gradient to transport glucose into the cell.  

Example Question #2 : Other Kinetics Principles

If the level of ATP suddenly increases in a cell, facilitated diffusion in the cell will __________.

Possible Answers:

increase instantly

remain unchanged

increase slowly

decrease slowly

decrease instantly

Correct answer:

remain unchanged

Explanation:

Facilitated diffusion acts independently of the level of intracellular ATP. Therefore, a change in ATP concentration will not affect the rate of facilitated diffusion.

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