Download Protein Review Worksheet

Biotechnology: Protein Review Worksheet
1. How many different kinds of amino acids are found in proteins? What distinguishes one amino acid
from another?
2. What causes polypeptide chains to fold into functional proteins?
3. What are the four levels of protein structure? For each level, list what types of bonds and where in the
structure each bond is found?
4. What does the structure have to do with the function of the protein?
5. What makes proteins so important? What do they do in your body? What happens if there is a mistake
in the structure?
6. Explain the impact of each of the following on protein structure. Distinguish between
 Ionic and hydrogen bonds
 Polar and nonpolar covalent bonds
 Hydrophilic and hydrophobic interactions
7. In proteins, most of the bonds are either hydrogen, ionic, covalent or Van der Walls (hydrophobic).
Explain:
 Where in the structure these are usually found
 Which are considered to be strong vs weak.
 Which types are most likely to be affected by environmental changes around the protein.
8. Label the atoms in each water molecule in the sketch below (left). Based on the pictures below explain
why certain types of molecules dissolve in water and others do not.
9. Many reactions occur in open spaces of enzymes and other proteins. In order for the reaction to occur
that open space/active site must be accessible. Using the picture above and to the right:
 Identify one possible active site- label it. Then explain your reasoning.
 What could happen to the protein structure if the number of + around the protein was to change?
i. Explain why the pH of the environment affects protein function.
 Explain what types of amino acids are most likely on the surface of this protein? How would
that be different if the protein was one that was inside of a hydrophobic cell membrane?
10. What is the difference between a polar covalent & nonpolar covalent bond? Which types of elements
are most likely to be found in each?
11. Cysteine is an amino acid that can form covalent bonds called disulfide bridges in the amino acid
tertiary and quaternary structure. Explain why this would be an important amino acid found in proteins?
(Hint: why are more cysteines found in the proteins of organisms that live in hot springs).
12. What is an enzyme?
13. What happens if an enzyme:
 is at its optimal temperature
 is at a temperature significantly above or below its optimum level?
 is at a pH significantly above or below its optimum level?
 Is at a pH slightly above or below its optimum level?
14. What causes the difference between normal and sickled cells in sickle cell disease?
 Sickle hemoglobin and normal hemoglobin are structurally different, how come on the gel that
we ran, individuals with both types of hemoglobin (sickle trait) didn’t show 2 bands, but one inbetween band.
15. Enzyme solutions are always prepared using a buffer at a specific pH as the solvent. Why is a buffered
solvent important for enzymes and other protein solutions?
16. Protein is an important food nutrient. A technician working at a food company is interested in the
nutritional content of seeds/nuts. She runs a protein gel with samples from two different seed extracts
and stains it with Coomassie Blue.
 What is the purpose of using Coomassie Blue?
 Seed extract #1 has three faint bands at 25, 30, and 35 kDa.
 Seed extract #2 has two very dark bands at 25 and 35 kDa.
 What might she conclude from her results about the nutritional value of the seed extracts?
17. When working with enzymes, one has to be aware of the optimal range. What three things does this
typically refer to?
 If you are using an enzyme with an optimal range of 55C -65C and a pH of 9, explain two
ways in which to stop the enzyme from working.
18. You discover that a disease is caused by a mutated protein. After some analysis, you determine that the
normal protein has isoelectric point of 8.6 and the mutated version of the protein has an isoelectric point
of 7.9. If you were to run a protein gel with a buffer of pH 9,
 Predict the outcome for each protein. (Draw)
 Draw and explain how you could use the gel to determine if a person is at risk for developing the
disease.
 Explain how you could use protein electrophoresis to determine if a couple was at risk for having
a child with the disease. Draw a labeled gel of a couple that would be at risk.
19. Use the figures above for the following questions: The figures show the results of a protein denaturing
gel (meaning that they are treated to separate based on size of the polypeptide chains not shape or charge
of the protein- runs like a DNA gel).
 Measure and compare the distance protein 1 traveled in each of the two gels above. Explain why
they are different if both ran for the same amount of time and voltage.
 Look at the standards, why did the smallest proteins move the farthest in the gel?
 For proteins 1, 2, and 3, determine how many polypeptide chains can be found in each and how
you can tell.
 Build a standard curve from the standards and determine the size of each of the polypeptide
strands in proteins 1, 2, and 3. (Keep sig figs). HINT: you only need to use the data from 1 gel
(be able to explain why).