BIOL 355 WINTER QUARTER 2014 PG

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BIOL 355 HW#3 AND STUDY GUIDE FOR EXAM 1

1) Complete your entries for HW1 Table 1 for the Ribosome, Nucleolus, Nuclear Pore, and Endoplasmic Reticulum.
a) Know the size, function, chemical composition and cellular location of each structure. Test your knowledge by
describing comparisons and connections between any two structures. Suggest ways that would allow you to see
each structure.
b) Cells regulate the number of ribosomes and nuclear pores and the size of the nucleolus and ER. What do you think
might be required for cellular regulation of quantity, size, or integrity of these particular structures?

2) Explain each of the big ideas below in a single sentence. Then explain how each idea helps us understand the
complex nature of the eukaryotic cell. Limit your answer to 3 or 4 sentences.
a) Endosymbiont hypothesis
b) Catalytic potential of rRNA
c) Topological relationships among cellular compartments (See MBoC, pgs 695-701)

3) Draw a diagram that shows at least five essential steps required for eukaryotic ribosome biogenesis. Start with gene
expression of ribosomal components and end with the small and large ribosomal subunits in the cytoplasm. Write a
figure legend for your diagram. Which steps in your diagram were assayed in the HW2 experiments? Be sure you
incorporate the findings from HW2 into your diagram.

4) Be sure to complete the BQMOC analyses for HW2 Fig. 5-7. Then, describe the main findings of all three
experiments in a single cohesive paragraph. Your paragraph should cite the most important evidence and end with a
sentence that proposes a specific role for Rps15 in ribosome biogenesis. Limit your paragraph to 3 or 4 sentences.

5) Read the abstract below from a recent research paper.
Abstract: Our knowledge of the functions of metazoan ribosomal proteins in ribosome synthesis remains fragmentary
(#1). Using siRNAs, we show that knockdown of 31 of the 32 ribosomal proteins of the human 40S subunit (ribosomal
protein of the small subunit [RPS]) strongly affects pre-ribosomal RNA (rRNA) processing, which often correlates with
nucleolar chromatin disorganization (#2). 16 RPSs are strictly required for initiating processing of the sequences
flanking the 18S rRNA in the pre-rRNA except at the metazoan-specific early cleavage site (#3). The remaining 16
proteins are necessary for progression of the nuclear and cytoplasmic maturation steps and for nuclear export (#4).
Distribution of these two subsets of RPSs in the 40S subunit structure argues for a tight dependence of pre-rRNA
processing initiation on the folding of both the body and the head of the forming subunit (#5). Interestingly, the
functional dichotomy of RPS proteins reported in this study is correlated with the mutation frequency of RPS genes in
Diamond-Blackfan anemia (#6).

a) Use the table below to designate the sentences (#1-6) that correspond to our B, Q, M, O, or C components. If you
think a component is missing from the abstract write NONE in that box. If appropriate, you may also list a sentence
under more than one component.
Component Sentence(s) #
B
Q
M
O
C

b) Select a single result described in the abstract. Suggest a logical experimental approach that you might have used to
get this result. Limit your answer to three sentences, one each for the M (experimental treatment and the control), the
expected O, and the C for your selected result. Your M, O, C should be consistent with the statements in the abstract.

c) How do the findings reported in this abstract expand on what you learned about ribosome biogenesis from lecture
and HW2 findings? Limit your answer to a few sentences.

BIOL 355 WINTER QUARTER 2014 PG
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Questions 6 and 7 are challenge questions that ask that you read the assigned MBoC pages and stretch your thinking
about membrane compartments and protein trafficking this week to prepare for next weeks in-depth coverage.

6) Study MBoC Fig.10.19 which shows the different ways that membrane proteins associate with a membrane.
Imagine that this membrane is the plasma membrane of a cell. Describe experiments that would allow you to confirm
the topology or orientation of each protein. Start with Protein 1, then continue rightward to distinguish Proteins 7 and
8. You may designate the N and C terminus for those proteins that do not already have the ends designated in the
Figure. For this exercise, your molecular biology toolkit includes: 3 antibodies (Ab) for each protein that allow you to
specifically recognize the N terminus (Ab-N), the middle (Ab-M), and the C terminus (Ab-C), a protease that does not
cross a membrane, a mild detergent that disrupts the membrane, and methods for protein immunolocalization in cells
and Western blotting.

7) Study MBoC Fig. 12-6 which shows a roadmap of protein trafficking. Which steps in the roadmap involve post-
translational protein translocation across a membrane? Which involve co-translational translocation? Use your
textbook and the figures in Ch 12 to select an example of each type of translocation, then compare and contrast the
cellular machinery required for import.