Final Exam Review Guide

CLASS SET-- Biotechnology - Final Exam Review Guide (Subterm II)
Directions: Answer the following questions ON YOUR OWN PAPER and in COMPLETE
Protein Structure
(use your chapter 2 lecture notes on proteins to answer these questions or pages 135-154-Chapter 5)
1. What are the 9 different groups of proteins? (Pg. 57 Table 2.1)
2. Name at least 5 functions of proteins.
3. What elements make up proteins?
4. What is the difference between a protein and a polypeptide?
5. What is the monomer of a protein?
6. Draw and label the parts of this monomer?
7. Name some of the different types of R-groups that can be found in this part of the monomer? (pg.
137 Table 5.1)
8. Name the bond found in proteins._____________
9. Draw and explain dehydration synthesis as it pertains to proteins.
10. What are the four 3-D shapes a protein can have? Explain each.
11. What does it mean to denature a protein?
12. Name 4 things that can denature a protein.
II. Protein Synthesis: Transcription/Translation (use the powerpoints on website under NOTES)
13. What is the name of the enzyme that is responsible for unwinding/unzipping the DNA strand and
adding the correct RNA nucleotides to the growing mRNA strand?___________
14. Draw a “generic” amino acid (be sure to label: the “central” or alpha carbon, R-group, amino group,
and the carboxyl group)
15. What the name of the bond that holds the amino acids together in a polypeptide chain? How is this
bond formed?________________________________________________________________
16. mRNA is synthesized (made) in the _______________direction.
17. List 3 ways in which RNA differs from DNA.
18. How do the processes of transcription and translation differ in prokaryotes and eukaryotes?
19. What is the function of a Promotor region on the newly opened DNA strand in eukaryotic cells
during transcription? What is the sequence?____________________
20. How is elongation different than termination during transcription?
21. Using your “genetic map” (use page 145 Table 5.2 or your “universal” mRNA wheel chart used in
CMB) chart, fill in the following table (remember that the anticodon and the mRNA codon are
DNA triplet
mRNA codon
tRNA Anticodon
Amino Acid
22. Draw a “generic” transfer RNA (tRNA) label the anticodon and site of
Amino acid attachment.
23. Sketch and label a typical ribosome.
24. Complete the chart below summarizing the changes made to a pre-mRNA molecule in eukaryotes.
mRNA end
Description of
Function #1
Function #2
5’ end
3’ end
25. Complete the following table for the functions of the various types of RNA molecules in a eukaryotic
Type of RNA
Messenger RNA (mRNA)
Transfer RNA (tRNA)
Ribosomal RNA (rRNA)
26. Describe the “initiation” step in translation.
27. What is the difference between the elongation step and the translocation step in translation?
28. In DETAIL, describe the “termination” step of translation.
29. What is the difference between introns and exons?
30. What is meant by antisense strand of DNA and the sense strand of DNA?
a) What is the purpose of the mRNA “start” codon? What is the start codon? ___________
b) What is the purpose of the 3 mRNA “stop” codons?
c). List these stop codons. _________________________________
32. What is the difference between transcription and translation?
Use pages
142-146 in
33. What is the role of RNA polymerase?
34. Where is mRNA produced?
35. What 3 RNA molecules are needed for translation?
36 . Explain the statement: “There is redundancy in the genetic code, but no ambiguity.” Provide an
example to illustrate your explanation. (remember this from CMB—look at the mRNA codon wheel)
Amgen Lab 6: Purification of mFP (use your lab manual – pdf file of manual on website: pg. E-3 to E-13)
37. Why did we have to grow an overnight culture of our protein expressing bacteria? (pg. E-9)
38. The bacterial colony that was picked from our LB/Amp/Ara plates were grown overnight in nutrient
broth. Define the following phases of bacterial growth.
Lag phase
Log phase
Stationary phase
Death phase
39. What phase of growth was arabinose introduced to the cells? (what was the purpose of adding the
arabinose to the culture? (think of why we put it in our agar plates) EXPLAIN IN DETAIL
40. Why was the overnight culture pink?
41. Explain how we LYSED the bacterial cells.
42. What is in the tube when we broke open the bacterial cells? Why did we centrifuge the sample?
43. Define column chromatography.
44. What physical characteristics of proteins enable them to be separated by column chromatography?
(critical thinking)
45. Define hydrophobicity. What is it important in this lab?
46. Where are the hydrophobic and hydrophilic portions of our protein located? ( pg. E-6 in manual)?
47. Define conformation.
48. How might the conformation of a protein be important for its function? (critical thinking)
49. What group interacts in the protein to provide this conformation? (circle your answer)
(Amino group
carboxyl group
50. Draw a picture of the column that we used in the lab. LABEL the “resin bed”.
51. What types of beads were used in the resin bed of our columns?
52. How did we get the mFP to “stick” to the column? (explain in detail)
53. What was the purpose of the wash buffer (low salt concentration)?
54. What was the purpose of the elution buffer (very low salt concentration)?
55. Explain HOW the mFP is released from the resin bed.
56. Does our tube of mFP contain ONLY mFP protein? Explain.
57. What does it mean when our tube of mFP fluoresces very brightly under UV light?
58. How might the column chromatography procedure be adjusted or modified to increase the purity of
the red fluorescent protein sample? (critical thinking)
Protein Gels (pg. 151-153 in textbook)
59. Are gels used for protein analysis run in a vertical or horizontal gel box?
59. What does PAGE stand for?
60. What is the name of the polymer that protein gels are made from?
61. Why didn’t we pour our own PAGE gels when Dr. Gillespie visited?
62. Explain the 2 purposes of the SDS that was added to our gel running buffer? EXPLAIN in detail.
63. What is the purpose of running a “molecular weight” marker with our samples? (2 reasons)
64. Look at the 2 gels on page 154 (figure 5.28 and 5.29). Which stain was used in order to analyze our
65. What step is next after the gel is stained? What does the analyst do?
66. What is a chromophore?
67. Describe the shape of the fluorescent proteins. (Dr. Gillespie had a name for them based on their