C785 Protein Folding

7. Diabetic ketoacidosis can lower blood pH, which affects the structure of important proteins like hemoglobin. Which of the following bonds are most likely affected by the change in pH? Check all that apply.

(A) Ionic Bonds (B) Hydrogen Bonds

25.) Pick the correct definition for activation energy

Activation energy is the energy required to convert the substrate to the products

14.) A substrate binds to an enzyme at a specific site, which is referred to as a(n)_________________.

Active site Imagine that the enzyme can be activated when the substrate binds in the active site.

26.) Induced fit describes which of the following?

An enzyme slightly changes its shape to accommodate specific substrates Enzymes have a high degree of specificity. They will bind to one specific class of molecules and usually catalyze only one type of reaction. The enzyme has the right amino acids in the right locations to be able to recognize a particular type of substrate. Imagine a baseball glove. The glove is designed to catch a baseball. It doesn't work as well for other types of balls. An enzyme recognizes the right kind of substrate (like the baseball glove recognizes the right type of ball), and it helps convert that special substrate into product. The baseball glove is open when the ball approaches the glove, and its shape changes in just the right way as it wraps itself around the ball after it enters so that the ball stays in the glove. In a similar way, an enzyme changes its shape in just the right way when a substrate enters its active site. A baseball glove can catch new baseballs, old baseballs, or ones that are made of higher- or lower-quality materials. These baseballs are very similar to each other, but they are not identical. This is similar to how an enzyme can recognize a certain type of molecule, or a class of very similar molecules that have very similar structures, but are not identical to each other.

11. Which of the following amino acids would you expect to find in the interior of a protein rather than on its exterior?

B nonpolar amino acid, with a side-chain comprised of only nonpolar C-C and C-H bonds that is hydrophobic. This hydrophobic nature leads this amino acid to be in the interior of the protein, hidden away from the water surrounding the protein.

9. In order to fulfill their function, proteins must fold in proper, three-dimensional conformations. Which one of the following molecules, available in a cell, is likely to help a protein fold properly?

Chaperone

12.) A researcher develops a drug that binds tightly to an enzyme. Unfortunately, the efficacy of this drug decreases when there is an abundance of substrate present. This is an example of _____ inhibition.

Competitive In competitive inhibition, the substrate and the inhibitor compete for the active site. When more substrate is present, more of the enzyme will be bound to substrate. When less substrate is present, more of the enzyme will be bound to the inhibitor.

9.) Enzymes increase the rate of reaction by doing which of the following:

Decreasing the activation energy of a reaction.

18.) The rate of an enzyme reaction can be increased by which of the following:

Decreasing the activation energy of the reaction. The enzyme brings the right amino acids into the right locations so that the enzyme can bind the substrate and allow the substrate to change into product. Since the groups are in the right places, less energy needs to be added to get the reaction over the energy hill. This results in a decrease in the activation energy and a faster reaction.

1. A toddler mistakenly swallows a bathroom cleaning solution, containing a strong reducing agent. Which interaction is most likely to be disrupted within a glycoprotein in the lining of the toddlerʼs esophagus?

Disulfide Bond

20.) True of False: An enzyme that normally functions well at 25 degrees C will perform much better if you increase the temperature to 40 degrees C?

False

21.) True or False: An enzyme that performs well at a pH range of 7.4 will perform much better by drastically increasing the hydrogen ion concentration.

False The enzyme has an optimum pH range in which it performs best. If the pH is changed drastically, the change in pH will disrupt ionic bonds and hydrogen bonds in the protein's tertiary structure, and the enzyme will no longer function properly. Increasing the hydrogen ion concentration means that the H+ concentration has gone up, and the pH has gone down.

19.) True or False: An enzyme increases the activation energy for a chemical reaction.

False An enzyme decreases the activation energy for a chemical reaction. The enzyme brings the right amino acids into the right locations so that the enzyme can bind the substrate and allow the substrate to change into product. Since the groups are in the right places, less energy needs to be added to get the reaction over the energy hill. This results in a decrease in the activation energy and faster reaction.

Learning Objective

Given a scenario where a protein structure changes (e.g., a fried egg, boiling water, etc.) the student identifies how structure impacts function. (4 questions on the assessment)

23.) In Chronic Mylogenous Leukemia (CML), a mutation results in the production of BCR-ABL, an enzyme that speeds up cell division. The drug Gleevec impairs the activity of the enzyme. Using the illustrations of the enzyme below, what best describes how the drug exerts its effect?

Gleevec is a competitive inhibitor and prevents ATP from binding with the active site of the enzyme. The active site of the enzyme binds ATP as its substrate, as seen in the figure on the left. Gleevec also binds in the active site, so it is no longer available for binding ATP. Since ATP and Gleevec both bind at the active site, Gleevec is a competitive inhibitor of BCR-ABL.

28.) Glucokinase catalyzes the conversion of glucose to glucose-6-phosphate. Which one is the substrate?

Glucose

15.) Which of the following factors can affect the protein folding and activity of an enzyme?

Heat All of the options are correct pH Reducing agents

3. A diabetic patient is suffering from ketoacidosis. Which interaction(s) could be disrupted within the patientʼs hemoglobin due to this condition. (Click all that apply)

Hydrogen Bond Ionic Bonds Diabetic ketoacidosis leads to a lower pH than normal. Changes in pH can disrupt both hydrogen bonds and ionic bonds inside of a protein.

22.) Pick the bonds that stabilize the three dimensional structure of an enzyme. (Select all that apply)

Hydrogen bonds Disulfide bonds Hydrophobic effect

4. Frying an egg in a pan changes the egg white color from translucent to white. Which interaction(s) would be disrupted within the Ovalbumin protein?

Hydrophobic Interactions

2. A patient presents with a fever of 110°F. Which interaction(s) would be disrupted within a neuronal protein if the fever is not resolved quickly.

Hydrophobic Interactions The patient's temperature is much higher than normal. High temperatures disrupt hydrophobic interactions.

6. The two amino acids below are part of the myosin protein. What interaction can these amino acids form, and where are they likely to be located in the protein?

Hydrophobic interaction, the core of the protein

8. The two amino acids below are part of the myosin protein. What interaction can these amino acids form, and where are they likely to be located in the protein?

Hydrophobic interaction, the core of the protein The two amino acids presented have side-chains comprised of only nonpolar C-C and C-H bonds. These amino acids belong to the nonpolar group and can form hydrophobic interactions. Because these amino acids cannot form hydrogen bonds they are hydrophobic in nature. This hydrophobic nature leads these amino acids to be in the interior/core of the protein, hidden away from the water surrounding the protein.

12. As a piece of bacon is heated in a skillet on the stove, you observe that the appearance of the bacon changes. You may even notice that the bacon becomes crispy if left in the skillet. What types of bonds or interactions in proteins are susceptible to temperature changes?

Hydrophobic interactions

9. As a piece of bacon is heated in a skillet on the stove, you observe that the appearance of the bacon changes. You may even notice that the bacon becomes crispy if left in the skillet. What types of bonds or interactions in proteins are susceptible to temperature changes?

Hydrophobic interactions

1.) Which one of the following paths requires less activation energy to convert the reactants into the products? The options include the path indicated by a bold line, and the path indicated by a dotted line.

In presence of an enzyme-Dotted line The dotted line represents the path with the lower activation energy, or the one in which less activation energy is required to get the reaction started. The reactants have a lower energy hill to climb to begin the reaction.

10. Which of the following are true about a misfolded protein? You may select more than one answer.

It will lose its normal function. It can be degraded by the cell. It can be the result of denaturation. It can cause protein aggregation.

7. Which of the following are true about a misfolded protein? You may select more than one answer.

It will lose its normal function. It can be the result of denaturation. It can cause protein aggregation.

24.) The diagram below illustrates the pathway that synthesizes isoleucine. When isoleucine levels drop, how would you describe the activity of threonine deaminase?

Its activity is high since feedback inhibition is relieved.

16.) What type of enzyme adds a phosphate to another molecule?

Kinase kinases are kind and giving" and give phosphates to another structure. Proteases disrupt protein primary structure. Phosphatases remove a phosphate group from a structure. Dehydrogenases change the oxidation state of a substrate.

27.) The enzyme's active binding site is _______________ to the substrate.

Specific None of the options

10.) Which level of protein structure provides enzymes with their substrate specificity?

Tertiary structure

6.) The action of which inhibitor can be influenced by the amount of the substrate present, competitive or noncompetitive?

The competitive inhibitor

4.) How do enzymes eliminate the need for high temperatures to complete a reaction?

The need for high temperatures is eliminated by lowering the activation energy needed for the reaction

13. If lysine is required at position #150 in the peptide chain in order for a protein to properly fold and function, what happens if amino acid #150 is mutated from lysine to alanine? (The structures of lysine and alanine are provided below.)

The protein will not fold properly

10. If lysine is required at position #150 in the peptide chain in order for a protein to properly fold and function, what happens if amino acid #150 is mutated from lysine to alanine? (The structures of lysine and alanine are provided below.)

The protein will not fold properly.

13.) Which of the following are characteristics of enzymes? (select all that apply)

They are reusable They speed up a reaction They catalyze a specific type of reaction

3.) Select True or False: Enzymes have a high degree of specificity. Specificity means that they will bind to one specific molecule or class of molecules and usually catalyze only one type of reaction.

True Enzymes have a high degree of specificity. They will bind to one specific class of molecules and usually catalyze only one type of reaction. The enzyme has the right amino acids in the right locations to be able to recognize a particular type of substrate.

2.) Select True or False: the lower the activation energy for a reaction, the faster the reaction rate.

True If less energy is needed to get the reaction over the energy hill, it goes faster. Enzymes help bring all of the items needed for a reaction together in the best way, so less energy is needed for the reaction to get started. This lowers the activation energy for the reaction and speeds up the reaction so that it can go much faster than if the enzyme were not present.

17.) Which of the following are possible effect(s) that phosphorylation/dephosphorylation can have on the activity of an enzyme? Select all that apply.

Turn the enzyme "on". Turn the enzyme "off".

5.) A competitive inhibitor binds to the____________ site of the enzyme, whereas the noncompetitive inhibitor binds to the ___________ site of the enzyme.

active, allosteric

11.) The product of a 4-step pathway accumulates and inhibits the first enzyme in the pathway. This is an example of ________ inhibition.

feedback

4. Which of the following forces can lead to aggregation as a result of protein misfolding?

hydrophobic interactions

5. Which of the following forces can lead to aggregation as a result of protein misfolding?

hydrophobic interactions

8.) An enzyme that adds a phosphate group is a __________. An enzyme that removes a phosphate group is known as a

kinase, phosphatase Just to help remember the difference between the two terms, think "kinases are kind and giving" and phosphatases take away phosphates.

5. Which of the following interactions involve a covalent bond? (check all that apply)

peptide bond disulfide bond

6. Which of the following interactions involve a covalent bond? (check all that apply)

peptide bond disulfide bond