C132 Spring 2016 Final Exam Questions
The final exam will include a series of questions chosen from the list below and
from the list of midterm questions. The points for each question are indicated to
the left. The total points on the exam will be 100, wi
C132 Spring 2016 Final Exam Questions
The final exam will include a series of questions chosen from the list below and from the
list of midterm questions. The points for each question are indicated to the left. The
total points on the exam will be 100, wi
Nearly all molecules passing in and
out of the nucleus go through a
The nuclear pore is a highly
specialized structure that allows
diffusion of small molecules into the
nucleus, but is a barrier to most
proteins and RNAs. (Some proteins
Once in the cytoplasm, sequences in the 5 UTR, 3
UTR, and coding region of the mRNA, along with the
proteins that bind to these regions, will determine the
localization, translation, and decay of the mRNA.
Gebauer F, Hentze MW. Nat Rev Mol Cell Biol. 2004
Genetic regulatory processes act on RNA as well as DNA.
The protein output of
genes is regulated at
every step in the life
of an mRNA from the
initiation of synthesis
The three major processing reactions that generate a mature
The most complex RNA processing reaction is pre-mRNA splicing. Most genes
in metazoan (multicellular) organisms contain multiple introns that must be
precisely excised from the mRNA precursor and the exons ligated together to
produce a mature translatable
Each intron in a premRNA is excised by the
same two step pathway
requiring recognition of
the 5 and 3 splice sites.
Each intron must
assemble its own
from snRNPs and
Arrangement of Eukaryotic Genes, Fig. 9-33
Yeast genes ha
1. LTR retrotransposons are thought to have arisen from viruses. What features
and gene products found in a typical retrovirus are missing from an LTR
retrotransposon? What roles in the transposition cycle are played by the LTRs?
How are the two complete
Polynucleotide synthesis in all cells
proceeds in the 53 direction for both
RNA and DNA.
This is because the precursors are
5-nucloeside triphosphates and the
polynucleotide chain grows by a
nucleophilic attack by the 3-OH group
of the growing polynucleot
26. Why do inactivating mutations in the RB (retinoblastoma) gene contribute to the
generation of cancer cells? Why do mutations in INK4 genes contribute to the
generation of cancer cells?
- Rb protein is responsible for binding E2F transcription factors
10. Prior to its charging with an amino acid, how is the 3 end of a transfer RNA modified
from its original structure as a RNA Pol III transcript? Why is this modification so
important in the function of the tRNA? Describe three other RNA processing
28. How were approximately 200 protein substrates of S. cerevisiae Cdc28 (also know
as Cdk1) identified? What was the molecular strategy used to identify these
proteins? What further strategy confirmed that many of these proteins are
phosphorylated by Cdc
1. Alternative cleavage and polyadenylation can be coupled to a change in splicing to
allow the use of two alternative 3 terminal exons and the creation of two possible
C-termini on the encoded protein. This is seen in the regulation of membrane
20. What kind of mutation in a mitotic cyclin can lead to entry into mitosis but failure to
exit mitosis, i.e. failure to decondense the chromosomes and reassemble the
Mutation of the destruction box, which is a series of protein residue
7. Compare the nuclear export of cellular mRNAs in yeast with the export of the HIV
mRNAs. For each case describe the proteins that mediate transit through the
nuclear pore and the processes that ensure the directionality of the movement.
Yeast: [Npl3, Gl
4. There are many human disease mutations that alter splice sites to reduce their match
to the splice site consensus sequences. The most common result of such a
mutation is to cause exon skipping, where the entire exon fails to be spliced rather
17. What are the names of the steps of mitosis? What happens during each of these
phases that distinguishes them from the other phases?
- Kinetochores appear, chromosomes condense, nuclear envelope retracts
- Chromosomes align at metaph
23. How is the dismantling of the nuclear lamina during prophase and its reassembly
during telophase accomplished? Where does the nuclear envelope go during
Dismantling: MPFs cause phosphorylation during prophase of 1) Lamins A, B, and C; 2)
14. The nonsense mediated mRNA decay pathway (NMD) allows the cell to recognize
mutant and incorrectly spliced mRNAs containing premature translation termination
codons. This recognition leads to the degradation of the aberrant mRNAs
preventing the transl
Chromatin decondensation requires two types of protein
complexes each made of several polypeptide subunits:
1. Lysine acetyl transferase complexes.
These are often referred to as HATS for histone
acetylases. or nuclear KATs, for lysine (K) acetyl
chromatin is added to
an egg extract, a
forms around the
sperm chromatin and
decondense (30 min),
These results indicate that cyclin B is the only protein that must be
synthesized in the egg extract in order for cycling mitotic events to
The APC/C (anaphase promoting complex)/cyclosome is the E3 ubiquitin protein
ligase that polyubiqu
Meiosis: Generation of haploid
germ cells (egg and sperm).
Figure 19.38 Meiosis.
Figure 19.37 Comparison of the main features of mitosis and meiosis.
During meiosis, expression of G1 cyclins is repressed, blocking the
normal progression of G1 in cells as
Figure 19.1 The fate of a single parental chromosome throughout the eukaryotic cell cycle.
Phases of the eukaryotic cell cycle
Figure 18.36 The stages of mitosis.
Centrosomes duplicate by G2
Johnson RT and Rao PN (1970) Biol. Rev. 46:97.
There must be a Mitosis Promoting Factor in the cytoplasm of
mitotic cells that will act on the nucleus of an interphase cell in G1
and induce many of the events of prophase.
The next breakthrough in the stor