NFS 3083 Biology Enzyme Kinetics Questions
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• Do NOT delete the “Instructions” and the “Rubric”,
• Type your answers after each question (or question part), and save your work.
Make sure to provide thorough and specific answers to each question. Try to be concise, making sure to address all the KEY POINTS. However, if you feel the need to explain, feel free to do so (don’t assume things are implied), because you would rather get more points for explaining than losing out the key points in trying to be concise (don’t ramble).
While you may discuss the questions with your classmates, you each should write the answers down in your own words. Plagiarism (including copying and pasting outside sources or previous submissions) will not be accepted and can result in an automatic zero!
All the answers to this assignment should be found in your notes and/or textbook, however you may use outside sources as well (make sure to cite in APA format!)
One points will be given for writing what your favorite thing about winter after your name at the top of this assignment
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• This assignment is 50 points total (5% of grade):
5 points for correct grammar/spelling and FOLLOWING INSTRUCTIONS.
The rest of the points are indicated next to each question below.
1. You recently were hired at a pharmaceutical company and are responsible for developing a new medication that targets the enzyme PAI-1. One of the main functions of PAI-1 is to inhibit the activation of plasmin from plasminogen (involved in breakdown of blood clots). Therefore, elevated PAI-1 is a risk factor for thrombosis and atherosclerosis. To design your novel medication, you first need to answer the following questions: (13pt)
a) What is enzyme kinetics? Why should we measure it? (2pt)
b) What are Km and Vmax? What do they tell us? (3pt)
c) How would pH and temperature affect enzyme kinetics? (2pt)
d) You want to make sure your drug is specific, which model of specificity should your follow, the lock and key model or induced fit model? Why? Make sure to describe both models (3pt)
e) Your coworker, mentions something about basing your design on a transition state analog, what is this? What is a transition state? Why would the analog be a good basis for your drug design? (3pt)
2. You presented your drug design for the PAI-1 medication to your boss, Dr. LeMieux. However, she would like a little bit more information regarding its method of inhibition. Specifically, she would like to know the answers to the following questions: (10pt)
a) What four factors influence enzymatic activity? (2pt)
b) What are the three types of reversible inhibition? Describe each of them (3pt)
c) What is allosteric inhibition? Provide an example of it. This example does not have to be a real-life one, you can use letters and numbers to prove your point. (2pts)
d) What is the difference between zymogens and isozymes? How are isozymes similar to each other and how are they different? (3pt)
3. It is commonly held that “a calorie is a calorie”, (i.e. that diets of equal caloric content will result in identical weight change independent of macronutrient composition). However, there is controversy among scientists if this belief violates the laws of thermodynamics (Ex: “metabolic advantage” of low-carbohydrate diets compared to isocaloric diets of different compositions). (9pt)
a) What are the first two laws of thermodynamics? Make sure to describe each of them (2pt)
b) What do the terms entropy, enthalpy and free energy mean? What do positive and negative changes in free energy indicate in terms of exergonic and endergonic reactions? (4pt)
c) Based on your answers above, do you agree that the phrase “a calorie is a calorie” breaks the laws of thermodynamics? Why or why not? You may use outside sources to support your answer, just make sure to cite them. (3pt)
4. Your classmate, Patty Pioneer, comes to you in a panic and tells you that she is so confused about protein folding, and asks you to help her. You agree and answer her questions below: (8pt)
a) What determines the 3D structure of a protein? (1pt)
b) What is the hydrophobic effect and why is it important for protein folding? (2pts)
c) Can you explain each of the different levels of protein structure? Patty is a visual learner, so make sure to include pictures with each description. (5pts) (You can hand draw this and post a picture here or use shapes in Powerpoint).
5. Complete the crossword (5pts). (You can put the answers right next to hints or in a numbered list if you like)
2. amino acid Q
5. A _____ – ____ binds more tightly to the active site than the does the substrate molecule
6. level of protein structure that is three-dimensional structure of folding
8. amino acid E
11. amino acid W
12. amino acid D
14. interactions that drive folding
17. level of protein structure that is a-helix and b-sheets
18. complete enzyme including all of the protein subunits and prosthetic groups
20. an enzyme without its prosthetic groups
1. loss of structure and function
3. describes a reaction for which the free-energy change (delta G) is negative
4. level of protein structure that is single chain of amino acids
7. the randomness of the components of a chemical system S
9. level of protein structure that is the assembly of individual polypeptides into a larger functional cluster
10. inhibitor that binds only to the ES complex, and therefore cannot bind to the substrate-binding site
13. The pH at which the numbers of positive and negative charges on an amino acid are equal is referred to as the ______
15. gives each amino acid their “identity”
16. trypsin is to trypsinogen as active enzyme is to
19. the energy of heat content of a system H