Fill in the blanks with the cellular compartment or compartments that correctly complete the statements. Use only words from the list. Words may be used more than once. Your answer sheet should contain only the word(s) used to complete each statement.
Chloroplast, Cytosol, Endoplasmic Reticulum, Nucleus, Plasma Membrane
1. Degradation of proteins occurs in the _______.
2. The _______ is/are the primary site(s) of hnRNA processing in eukaryotic
cells.
3. Protein transport within the ________ can require two signal peptides.
4. New lipids are synthesized and inserted into the outer leaflet of
the _______ membrane.
5. Mature red blood cells are like bacterial cells in that they contain
_______.
6. In prokaryotic cells, transcription takes place in the _______.
7. DNA is found in the _______.
Section II Questions 1-7 (19pt total)
Short answers. Answer each of the following question with one or two
complete sentences. Calculations need not be in sentence form.
1. What are the three steps in transcription? (3pt)
2. What is the name of the organism we are studying in lab? (1pt for common name, 2pt for latin name OR 2.5pt for both)
3. Which nucleotides form 2 hydrogen bonds when base-pairing. (3pt)
4. Proteins are chains of amino acids. What is the name of the bond that links the amino acids together and where does that linking occur? (3pt)
5. You are given a stock solution that is 0.3ug Chemical Y/ul. You need to make 5ml of growth media that has a final concentration of 1.5ug Y/ml. How much of the Chemical Y stock solution do you need? (3pt)
6. To what does the term carboxyl terminus refer? (3pt)
7. What is the name of the end of the mRNA that is transcribed first? (2pt)
Section III Question 1-3 (27pt total)
Answer each of the following questions in complete sentences. Brevity
is encouraged but be sure to answer the question asked. (9pt each)
1. Briefly compare and contrast the characteristics of a 'normal' mRNA with the mRNA studied in the Chapman and Walter paper. (You may assume the mRNAs share characteristics not specifically mentioned in the paper.)
2. When placed in water why do fatty acids form micelles while phospholipids form bilayers? Include a discussion of each molecule's general structure in your answer. (Hand-drawn diagrams may be included.)
3. Biological membranes exhibit asymmetric organization. What
does the preceding statement mean? Briefly explain how a biological membrane
becomes asymmetric.
Section IV Questions A-H (38pt total)
The following 8 questions all refer to the scenario and data presented
below. Answer the questions in complete sentences.
You are a cancer researcher trying to determine why some cells undergo unregulated growth and become a tumor. Through diligence and hard work you have discovered a new protein that appears to be a receptor involved in cell-to-cell contact. You know that the protein is synthesized on ribosomes that are bound to the ER and that it is inserted into the ER but its targeting signal sequence isn't following predicted rules. You are trying to determine the minimal protein region needed for this protein's ER insertion.
A) What is the process of inserting a protein through a membrane called?
(2pt)
B) Name 2 general characteristics of a 'normal' ER signal peptide.
(6pt)
To determine the minimal region you prepare a series of ER insertion assays. Each insertion assay contains all of the cellular elements needed for translation with radioactive amino acids and all of the cellular elements necessary for insertion. The variable in each assay is the mRNA construct added to the assay (these constructs are listed below). After each assay was complete it was centrifuged and the contents of the supernatant (S) and pellet (P) were run on SDS-PAGE and the radioactive products detected by X-ray film.
The full length mRNA is diagrammed below. Each letter represents a section
of RNA. Translation start and stop (**) are indicated.
| Assay # | Insertion Assay mix |
|
| 1 | yes | ABCDEF |
| 2 | yes | ACDEF |
| 3 | yes | ABCEF |
| 4 | yes | ABCDF |
| 5 | yes | ABCDE |
| 6 | yes | AEF |
Data as seen on X-ray film:
C) Why was 'region A' included in all constructs? What role does this
region play in the synthesis and/or insertion of this protein? (3pt)
D) Which assay(s) are positive controls for insertion of the encoded protein? Why, in general, are controls important to any experiment? (7pt)
E) Why were radioactive amino acids and X-ray film needed? (2pt)
F) From the data given, what is the minimal region of the protein necessary for insertion? Explain using data to support your answer. (5pt)
G) The objective of these experiments was to determine the minimal region necessary for this protein's insertion into the ER. How could you determine whether the region was both necessary and sufficient for insertion? (5pt)
H) Insertion into the ER is known to follow either the Sec pathway or SRP pathway. Given the information above, which pathway is this protein following? (Explain your answer) (4pt)
I) Design an experiment that would test your answer in part H. Be sure
to explain how the data would support or refute your choice of pathway.
(4pt)