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Exam 18 December 2009, questions
Molecular Biology (McGill University)
Studocu is not sponsored or endorsed by any college or university
Exam 18 December 2009, questions
Molecular Biology (McGill University)
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Student
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Student Number:
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FACULTY
OF
SCIENCE
FINAL
EXAMINATION
2005
BIOL
200
-
MOLECULAR
BIOLOGY
(002)
Examiners:
Profs.
F.
Fagotto
and
P.
Lasko
Date:
December
16,2005
Time:
2:OO
p.m.
Place:
Gym
INSTRUCTIONS:
1.
2.
3.
4.
5.
6.
7.
8.
9.
All
students will
write
the
exam
in
the
room
assigned
and
posted
beforehand.
All
questions
must
be
answered
in
the
examination booklets provided.
Your
name
and
student number
must
be entered
on
your
examination sheet
as
well
as
any
examination
bookIets
that you
have
used.
Both
the
examination
sheet
and
booklets
must
be
submitted at
the
end
of
the
exam.
Calculators
are
not
needed
for
any question
on
this
exam
but
are
permitted in
the
exam room.
A
simple translation dictionary
may
be
used
during
the
exam
by persons in their
first
year
of
studies
in
English.
If
you
find
any
questions
ambiguous,
specify
the
question number
and
explain
your
concerns
at
the
bottom
of
h
s
cover
sheet.
(Important):
It
is
essential
that
your
answers
are
concise. Each question
is
followed
by
our
suggestion
fox
the
maximum
number
of
words
your
answer
should
require.
The
questions
can
all
be
answered
fully
and
correctly
in
fewer
words
than
our
suggestions indicate.
It
is
unnecessary
to
answer
the
questions in
complete sentences. Responses that
exceed
the
suggested
length
limit
may
not
be
read
in
full,
and
may
be
marked
lower if incorrect
information
is included.
This
exam
consists
of
4
pages (1
5
questions) including
the
cover
page.
Am
bigiiities:
Downloaded by Katie Yeung (katieyeung0803@gmail.com)
lOMoARcPSD|31670854
BIOL
200
-
FINAL
EXAMINATION
MOLECULAR
BIOLOGY
(002)
Page
2
Question
I.
(6
points)
Identify the site
at
which
each
of
the
following
molecules interacts with
pre-&A.
(5
words
each).
a.U1
snRNA
b.
U2
snRNA
c.
U2AF
(U2-associated
factor)
Question
2.
(4
points)
What virally
-
encoded protein
is
required
for
transport
of
unspliced
HIV
genomic
RNA
from
the nucleus
to
the cytoplasm?
(5
words).
Question
3.
(4
points)
You
have
identified
a
new protein and
have
found
that
it
contains
two
RRM
domains.
What is its function most likely
to
be?
(5
words).
Question
4.
(8
points)
You
obtain
the
sequence
of
a
gene containing
10
exons,
9
introns,
and
a
3’
UTR
containing
a
polyadenylation consensus sequence. The
fifth
intron
also
contains
a
polyadenylation consensus sequence.
To
test
whether
both
potential polyadenylation
sites
are
used,
you
isolate
mRNA
and
find
a
longer
transcript
from
muscle tissue
and
a
shorter
mRNA
transcript
from
all
other tissues.
a.
What
is
the
most
Iikely mechanism that
accounts
for
these
two
transcripts
b.
What
must
be present in muscle cells
for
them to
express
the longer transcript?
being produced
from
the
same
gene?
(5
words)
(4
points)
(20
words)
(4
points)
Question
5.
(8
points)
A
new microorganism
has
been discovered
on
Mars. Its
genome
is
composed
of
double
-
stranded
DNA,
but it contains only
two
bases,
cytosine and guanine. Nevertheless,
proteins
from
this organism
are
composed
of
the
same
20
amino
acids
as
are found
on
Earth.
a.
Assuming
that protein
synthesis
in
this organism utilizes
mRNA
and
tRNA
intermediates
and
operates
similarly
to
that
on
Earth,
what
is
the
theoretical
minimum size for
a
codon
in
the Martian organism?
Why?
(10
words)
(3
points)
b.
Would genes
from
this Martian organism
be
transcribed efficiently in
cell
extracts
prepared
from
E.
coli?
Why
or
why
not?
(20
words)
(3
points)
c.
If
two
tubes,
one
containing Martian
DNA
and
one
containing
E.
coli
DNA,
were
incubated
at
95
C,
which
would
contain
a
larger proportion
of
double
-
stranded versus single
-
stranded
DNA?
Why?
(I
0
words)
(2
points)
Question
6.
(8
points)
DNA
Replication
a.
Describe
briefly the activity
of
the
primase
and
why
it
is
required
for
replication.
(20
words)
(4
points)
b.
What
is
the role
of
topoisomerase at
the
replication fork?
(20
words)
(I
point)
c.
Describe in
a
few
words
the biochemical
process
performed by
this
topoisomerase.
(20
words)
(2
points)
d.
In
which region
of
the
fork
is
the
topoisomerase active?
(5
words)
(1
point)
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BIOL
200
-
FINAL
EXAMINATTON
2005
MOLECULAR BIOLOGY
(002)
Page
3
Question
7.
(7
points)
Nucleosome:
Describe
the
main
features
of
the
nucleosome:
a.
What
are
the
two
major
components?
(5
words)
(2
points)
b.
What
is
its structure (organization
of
the
components)?
(20
words)
(3
points)
c.
What
is its function?
(20
words)
(2
points)
Question
8.
(4
points)
Hetero/euchrom
atine:
a.
What
is
(in
general)
the
state
of
activity
of
a
gene
in heterochromatic regions?
b.
Which chromatin
component
is
modified
in
euchromatin,
(1
point)
(5
words)
c.
what
is
the
most
frequent type
of
modification,
(5
words)
(1
point)
d. and which
is
the residue modified?
(5
words)
[
1
point)
(5
words)
(1
point)
Question
9.
(8
points)
Telomeredtelomerase
:
a.
b.
c.
d.
e.
f.
What is the modification
brought
to chromosomal
DNA
by
the telomerase?
(5
words)
(2
points)
What
is
the
function
of
this modification?
(20
words)
(2
points)
What
happens
to chromosomes in the
absence
of
telomerase activity?
(20
words)
(1
point)
In
addition
to
proteins,
what
type
of
molecule
is
present
in
the
telomerase?
(5
words)
(1
point)
What
is
the
role
of
this non
-
protein molecule in
the
activity
of
the
telomerase?
(20
words)
(1
point)
What
is
the
state
of
chromatin condensation in the telomere
region?
(1
word)
(1
point)
Question
10.
(4
points)
Genes:
In
higher eukaryotes,
does
the
len&
of
a
gene
and
the
length
of
the
corresponding
cDNA
match?
Explain briefly.
(50
words)
Question
11.
(8
points)
Transgenes
and
gene
disruption:
Imagine
that
a
transgene
X
has
been randomly inserted
in
a
mouse
chromosome,
in
the
reglon
containing
an
essential
gene
A.
a.
Propose three locations
of
the insertion that
could
cause
disruption
of
gene
A,
and
explain
briefly
how
the
insertion would disrupt the gene.
(50
words)
b.
Propose one location
of
the
insertion that
may
have
no
effect
on
gene
A
activity.
(20
words)
(1.5
points)
c.
If
gene
A
is
essential
for
cell
function,
what
phenotype
do
you
expect for the
homozygous progeny
of
two mice
carrying
a
transgene disrupting
gene
A?
(5
words)
(2
points)
(4.5
points)
Downloaded by Katie Yeung (katieyeung0803@gmail.com)
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BIOL
200
-
FINAL
EXAMINATION
2005
MOLECULAR BIOLOGY
(002)
Page
4
Question
12.
(7
points)
DNA
sequencing:
a.
Explain in
a
few
words
the principle
of
DNA
sequencing.
(50
words)
(4
points)
b.
Which
are
the reagents that must
be
present
in
a
sequencing
reaction?
(20
words)
(3
points)
Question
13.
(7
points)
Cloning:
You
want
to
move
a
cDNA
fragment
X
from
vector
A
to
vector
B:
a.
What type
of
enzyme
would
you
use
to take
X
out
of
vector
A?
(5
words)
(2
points)
b.
What
is
special about
the
sites recognized
by
such
enzymes?
(5
words)
(2
points)
c.
What enzyme would
you
use
to
paste the fragment in vector
B?
(5
words)
d.
Is
it
necessary to cut both
the
fragment
and
vector
B
with
exactly
the
same
enzymes?
Explain. (50
words)
(2
points)
(I
point)
Question
14.
(9
points)
Sequence
analysis:
Use
the list
of
amino acids
(3
letter
abbreviation) with
the
main properties
of
their
residues
to
analyzelcompare
the follow
-
ing sequences
from
protein
X.
Note that protein
X
is
a
soluble cytoplasmic protein.
A)
Ser
Glu
Gln
Ala
Cys
Asp
Lys
Lys
Arg
Gln
Gly
B)
Thr
Ala
Gly
Glu Leu Ile
Gly
Asn
Ile
Asp
Tyr
Met Leu
C)
Ala
Tyr
Ala
Leu
Leu
Met
Phe
ne
Val Ala
Gly
Ala
B’)
Thr
Ala
Gly
Glu
Asp
Glu
Gly
Asn
Ile
Asp
Tyr
Met
Leu
B”)
Thr
Ala Gly
Glu
Leu
Ile Gly
Asn
Leu
Glu
Tyr
Met Leu
Amino acid list
:
Hydrophilic basic:
Lys,
A r g ,
His
Hydrophilic acidic
:
Glu,
Asp
Hydrophilic
uncharged:
hydroxyl residue:
Thr,
Ser,
amide residue: Asn,
Gln
Hydrophobic: Ala,
Val,
Leu,
Ile, Met,
Phe,
Trp,
Tyr
Others
:
Gly,
Cys,
Pro
a.
take sequences
A),
B)
and
C): by
loolung
and
the
amino
acid
composition
of
these fragments, infer
the
general properties
of
each
of
these
fragments
and
predict the most likely location within protein
X.
(3
points)
(50
words)
b.
Is
there a least
one
of
these sequences that
would
aIlow
you
to
predict
the
secondary conformation? Explain. (50
words)
(2
points)
c.
B”)
and
B’”)
are
two
mutant alleles
of
B).
For
each
of
these
alleles,
do
you
expect
a
strong
or
weak
effect
on
protein
stmcturelfunction?
Explain
briefly
why?
(50
words)
(2
points)
Question
15.
(8
points)
Protein
separatiodpurification:
a.
Name
two different techniques
to
separate proteins according
to
their
mass.
b.
In
each
case, explain
how
proteins
of
different sizes
are
separated. (50 words)
(20
words)
(2
points)
(6
points)
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