Molecular Biology Final Exam (Set A)
(Spring 2009)
Instructors: Profs. JY Yang and Y. Tao
(Note : 4 points/each)
1. Which of the following types of RNAs is thought to play a catalytic role in protein
synthesis?
a.
rRNA
b.
mRNA
c.
tRNA
d.
snRNA
Answer: A
2. Which of the following statements about macromolecular assemblies is NOT true?
a.
They contain one very large polypeptide.
b.
They can exceed one MDa in mass.
c.
They can be 30-300 nm in size.
d.
They can contain nucleic acids in addition to amino acids.
Answer: A
3. Which of the following methods can separate particles on the basis of density?
a.
centrifugation
b.
ion-exchange chromatography
c.
SDS polyacrylamide gel electrophoresis
d.
affinity chromatography
Answer: A
4. Which of the following is NOT true about each of the 20 different aminoacyl-tRNA
synthetases
a.
links an amino acid to the 3’ terminus of a tRNA molecule.
b.
recognizes multiple amino acids.
c.
requires ATP to catalyze reactions.
d.
sometimes make mistakes.
Answer: B
5. DNA replication
a.
requires a DNA template, deoxynucleotides, primers, and DNA
polymerase.
b.
requires the addition of deoxynucleotides to the 5’ free hydroxl group.
c.
occurs on only 1 strand of DNA.
d.
utilizes Okazaki fragments on the leading strand.
Answer: A
6. Alternative splicing can NOT result in which of the following?
a.
production of different mRNA molecules from the same gene
b.
production of different proteins from the same gene
c.
production of two or more proteins that differ in their function
d.
production of novel peptide domains
e.
None of above
Answer: E
7. Using the genetic code found in the following table, determine which of the
following sequences have the potential to encode this peptide sequence:
Val-Leu-Leu-Gln-Asp. i) GTGCTCTTGCAAGACA ii) AGTATTGTTGCAGGATT iii)
TAGTTCTTTTACAGGAC
iv)ATAGTTCTTTTACAGGA. Please note that the
same peptide sequence can be encoded for by multiple nucleotide sequences.
a.
i, ii, iii
b.
i, ii, iv
c.
ii, iii, iv
d.
i, iii, iv
Answer: A
8. Which of the following does NOT happen in protein synthesis in prokaryotes.
a.
Binding of tRNA to a 30S particle
b.
Binding of tRNA to a 70S particle
c.
Seperation of the 70S ribosome to form 30S and 50S particles
d.
Coupling of an amino acid to ribosome by an aminoacyl synthetase
Answer: D
9. Which of the following is NOT true. The active site of an enzyme
a.
contains a substrate binding region.
b.
contains a catalytic region.
c.
is typically located at the amino terminus of the protein.
d.
can be formed from amino acids located throughout the protein.
Answer: C
10. The consensus sequence for poly(A) addition is
a.
the site of poly(A) tail addition.
b.
AAUAAA.
c.
downstream of the cleavage site.
d.
none of the above
Answer: B
11. Explain why RNA is much more variable in its 3-dimensional shape than is DNA.
What are the implications of this difference? Support your statement of the
implications with specific, detailed examples.
DNA is almost always double-stranded, so that each strand of DNA is paired with a
complementary, anti-parallel strand. This means that DNA has a very regular structure,
typically a Watson-Crick double helix, regardless of its sequence.
In contrast, RNA is almost always single-stranded. As an elongated single strand, its
nitrogenous bases would be exposed to the water solvent. This is unfavorable, since
the bases are largely hydrophobic. Instead, RNA folds up on itself, forming internal
basepairs wherever its sequence allows. Since this internal basepairing relies on
self-complementary sequence, the way in which an RNA molecule folds is dependent
on its nucleotide base sequence, and thus is different for every RNA.
The implications of this are that RNA has a much wider range of three-dimensional
shapes than DNA, which allows it to fill a much wider range of functions. RNA
molecules can use their unique shapes to allow them to serve specific cellular roles.
For example, transfer RNA molecules assume an elongated L shape with an anticodon
at one end and an amino acid acceptance site at the other. This shape allows them to
fit into the binding pockets of aminoacyl tRNA synthetases, which attach the
appropriate amino acid. The L shape also allows tRNAs to fit into the binding sites of
translating ribosomes, with their anticodons on the inside, basepaired to the mRNA,
and their attached amino acids extending into the site of protein synthesis. Other types
of RNAs use their three-dimensional shapes to allow them to serve catalytic roles in
cells. Ribosomal RNAs are one example of this. The structure of the ribosomal RNAs
forms much of the structure of the ribosome, including the active site, where peptide
bonds are formed.
12. Describe the four hierarchical levels of protein structure.
The four hierarchical levels of protein structure are the primary, secondary, tertiary,
and quaternary structures. The primary structure is the sequence of amino acid
residues. The secondary structure is the localized organization of parts of a
polypeptide chain. The tertiary structure is the overall conformation of a polypeptide
chain, and the quaternary structure describes the number and relative positions of the
subunits of a multimeric protein.
13. You are asked to design PCR primers (18 nucleotides) to amplify the coding region
(without the stop codon) of the following gene. Please write down the
sequences of the primers. (Indicate the 5’ and 3’ end of the primers)
5’-atgaagaccaatagagagcaggaaatttacgttgaaagaagcttcaaaccaaacaattcaacaattcagaattt
gatggacattgaaaggttcattttgcctcacacttctacatcaggtgtcgcaaggctcaaaatgagggtcatatcatg
ggtcgggcttcagttctacaactactga-3’
forward
reverse
5’-atgaagaccaatagagag-3’
5’-GTAGTTGTAGAACTGAAG-3’
14. Name the four types of noncovalent interactions. What types of noncovalent
interactions were involved in interactions 1-4 (highlighted) in the following
figure:
Hydrogen bonds; The hydrophobic interactions among nonpolar groups; Ionic
interactions between charged groups; Van der Waals interaction
1., 3: hydrophobic interaction, 2: ionic interactions, 4. hydrogen bonds
15. A Tyrosine aminotransferase activity was detected in Arabidopsis total protein
extract from young seedlings. The reaction it can catalyze is: Tyr +
α-ketoglutarate-> p-hydroxylphenylpyruvate + L-glutamate. You’ve got a kit to
do an easy assay to measure L-glutamate production, what approach can you
take to isolate the putative tyrosine aminotransferase?
a) Traditional biochemistry approach: Separate proteins through various
protein separation approaches and monitor the enzyme activity using the
kit. For example, you can extract total proteins from seedlings, using
ammonium sulfate precipitation, gel filtration, various ion-exchange
columns, hydrophobic interaction columns etc. to concentrate the fraction
with the highest enzyme activity. In the end, using mass spec to identify
the candidate enzyme.
b) Genetic approach: mutagenized the wild type plants and measure the
enzyme activity in each mutant. After identifying the mutant, map the
mutation.
c) Generate an expression cDNA library using mRNAs from seedling and
assay for enzyme activity in each clone.
d) Bio-informatics approach: search for tyrosine aminotransferase in other
close species. Search for homologues in Arabidopsis database or design
probes against conserved region and isolate cDNA clones.
Any one of the approaches is OK.
16. List the main stages of a phage life cycle and explain the major differences between
the lytic and lysogenic cycles.
Absorption, entry of nucleic acid, transcription, production of phage proteins,
productions of phage nucleic acid, assembly of particles (including encapsidation of
nucleic acid), release of progeny particles.
A phage in a lytic cycle converts an infected cell into a phage factory , and many
phage progeny are produced.
Under lysogeny, phage DNA becomes integrated into the host genome but the
replication is silenced without induction by certain factors.
17. A hyperthetical transposon has inserted at the target sequence 5’TTAGCA-3’.
Its
left inverted repeat sequence is 5’-GCAATGGCA-3’. This now serves as the
donor molecule for a transposition event to the new target sequence
5’GATCCA-3’, in a recipient molecule. Show the structure of the DNA (both
strands) of the following molecules after all steps of transposition. (Assume that
the inverted repeats on the transposon are perfect).
i.The recipient molecule.
transposon
5’---GATCCAGCAATGGCA-------------------TGCCATTGCGAATCCA---3’
3’---CTAGGTCGTTACCGT--------------------ACGGTAACGCTTAGGT---5’
ii.The donor molecule if transposition occurred by conservative pathway
5’---TTAGCA-3’
5’---TTAGCA-3’
3’---AATCGT-5’
3’---AATCGT-5’
iii.The donor molecule if transposition occurred by the replicative pathway.
transposon
5’---TTAGCAGCAATGGCA-------------------TGCCATTGCTTAGCA-3’
3’---AATCGTCGTTACCGT--------------------ACGGTAACGAATCGT-5’
18. List several mechanisms a cell (eukaryotic) uses to increase the concentration of a
particular mRNA molecule to a very high level.
Increase in the stability of mRNA
Activation of strong promoter by a transcriptional factor
Activation of transcription through binding of a hormone to its receptor
Etc.
19. Give the two types of splicing that can occur in the processing of eukaryotic mRNA,
and state the difference
Both cis and trans-splicing can occur in the processing of eukaryotic mRNA. With
cis-splicing, exons from the same transcript are joined. In trans-splicing, an exon from one
transcript is spliced to an exon located on a different mRNA.
20. In the E. coli lac operon, how would gene expression be affected if one of the
following segments was missing?
a. lac operon promoter
No transcription would take place
b. operator site
No regulation would take place
c. lacA gene
The rest of the operon would function normally, but none of the
transacetylase would be made
21. What distinguishes negative regulation from positive regulation? How would you
distinguish negative and positive autoregulation?
In negative regulation an inhibitor bound to the DNA must be removed before
transcription can occur. In positive regulation an activator molecule must bind to the
DNA. Negative and positive autoregulation is the same, except the gene product is its
own inhibitor or activator.
22. List several epigenetic mechanisms that affect gene expression
ATP-dependent chromatin remodeling
DNA Modification
Histone modification
23. What is a CpG island and what role it plays in gene regulation?
DNA 甲基化是指 CpG 二核昔酸中胞嘧啶的 5 位碳原子加上一个甲基基团,形成 5 甲基
胞嘧啶.在哺乳动物,DNA 甲基化的作用包括调控基因表达、维持基因组和染色体结构的
稳定性、基因印记以及 X 一染色体、转座子和外源 DNA 失活
(CpG 岛位于基因的启动子和第一个外显子区,富含 CpG 二核苷酸,故称为 CpG 岛,一般作
为启动子和基因复制的起始区.在哺乳动物中,几乎所有的甲基化位点均在 CpG 二核苷
酸,并通过对 CpG 的甲基化来调节基因的表达,因为 DNA 的甲基化可改变染色质的结构,
从而引起不同 DNA 结合蛋白的结合。)
24. Explain insertional inactivation.
Insertional inactivation is the process of cloning a DNA fragment into a site within a vector
gene such that the gene is no longer active. Usually the gene encodes an antibiotic
resistance such that colonies transformed with recombinant plasmid will be sensitive
to antibiotic.
25. Once a series of recombinant plasmids or phages have been produced, describe
several ways in which plasmids or phages containing a particular insert many
be identified.
-complementation
Insertional inactivation of a plasmid gene (e.g. antibiotic resistance)
PCR analysis
Analysis of plasmid by restriction digestion
Colony hybridization with a nucleic acid probe having a sequence
complementary to the gene
f) Northern blots to detect mRNA
g) Western blots to detect expressed proteins
a)
b)
c)
d)
e)
(只要答对四个以上正确答案就给满分)