PSwk9 - 
 Problem
Set
Week
9
 
...

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Unformatted text preview: 
 Problem
Set
Week
9
 
 MCB110,
Spring‘11
 
 1. True
or
False
 
 ________
The
Mediator
complex
contacts
RNAP
II,
general
transcription
factors,
and
 specific
transcription
factors
 
 ________

Specific
transcription
factors
bind
only
within
proximal
promoter
elements
 
 ________
Glucocorticoid
receptor
GR
can
enter
the
nucleus
without
its
LBD
(ligand
 binding
domain)
 
 ________

mature
eukaryotic
mRNAs
can
be
exported
out
of
the
nucleus
without
a
 5’Cap
 
 ________

The
5’cap
of
eukaryotic
mRNA
contains
only
1
phosphate
 
 ________

Splicing
reaction
occurs
through
2
transesterification
reactions
 
 ______

During
5’cap
addition,
Guanylyltransferase
is
recruited
and
activated
through
 binding
to
the
Ser5‐
phosphorylated
Pol
II
CTD
 
 ________

During,
addition
of
the
poly
A
tail,

PAP
(PolyA
polymerase)
binds
to
the
 complex
prior
to
cleavage
of
the
Poly
signal
sequence
 
 ________

The
CTD
of
RNA
Pol
II
serves
as
a
scaffold
for
coupling
transcription
to
 mRNA
capping,
polyadenylation,
and
splicing
 
 ________
Splicing
factors
can
also
act
like
elongation
factors
by
facilitating
elongation
 
 ________
All
of
the
steps
in
E.
coli
protein
synthesis
utilize
GTP
as
an
energy
source
 
 ________
Aminoacyl‐tRNA
synthetase
recognizes
their
specific
tRNA
by
a
single
 interaction
at
the
anti‐codon
loop.
 
 ________
Mistakes
in
decoding
mRNA
into
amino
acid
sequences
usually
occur
and
are
 fixed
during
matching
of
an
amino
acid
to
the
appropriate
tRNA.
 
 ________
Eukaryotic
and
prokaryotic
translation
are
both
directed
by
the
Shine‐ Dalgarno
sequence.
 
 
 
 2.

Why
are
insulator/boundary
elements
important
in
transcriptional
regulation?

 
 
 
 
 
 
 3.

How
is
the
5’
G7‐methyl
cap
added
to
nascent
mRNAs?

 
 
 
 
 
 
 
 
 
 4.
In
class
we
discussed
the
importance
of
the
Poly
A
Signal
sequence
during
Poly
A
 tail
addition.

Describe
an
experiment
that
you
could
do
to
verify
whether
the
entire
 PolyA
signal
sequence
is
necessary
for
cleavage.
 
 
 
 
 
 
 
 
 
 5.

You
are
given
the
DNA
sequence
for
a
gene.

How
can
you
identify
the
introns
of
 this
sequence?

 
 
 
 
 
 
 
 
 6.
Why
is
a
gene
so
much
bigger
than
an
mRNA?
 
 
 
 
7.
What
are
two
benefits
of
splicing?
 
 
 
 8.
Name
two
RNA
modifications,
where
they
occur
on
the
RNA,
where
in
the
cell
the
 RNA
is
modified
and
what
role
the
modifications
serve
in
protein
synthesis.
 
 
 
 9.

Describe
the
2
steps
of
the
Spliceosome‐mediated
splicing
reaction?
 
 
 
 10.

How
are
the
5’Splice
Site
and
the
BPS
(Branch
point
site)
recognized
by
the
 spliceosome?
 
 
 
 11.
You
are
studying
a
gene
called
TREE.

You
discover
a
mutation
within
TREE
 residing
within
the
5’Splice
site
of
exon
1.

This
mutation
results
in
failure
to
 undergo
splicing.

You
observe
that
the
mutation
is
not
within
the
GU
sequence
of
 the
5’SS.
 a.
What
would
you
hypothesize
is
the
reason
this
mutation
result
in
a
failure
to
do
 splicing?
 b.
What
experiment
would
you
do
to
support
your
hypothesis?

 
 
 
 12.

You
are
workingwith
a
gene
called
PANDA
containing
6
Exons.

Heart
cells
 express
a
version
of
PANDA
which
includes
all
exons
whereas
muscle
cells
express
a
 version
of
PANDA
that
doesn’t
contain
Exon
4.


 Describe
an
experiment
which
would
allow
you
to
determine
whether
mRNA
 transcripts
made
from
either
heart
or
muscle
cells
contain
Exon
4.
 
 
 
 
 13.

What
role
do
SR
proteins
play
in
splicing?
Explain
in
both
general
and
specific
 terms.
 
 
 
 
 14.
Describe
the
four
sequence
components
of
the
tRNA
that
all
of
them
share.
 
 
 
 
 15.
How
can
an
aminoacyl
tRNA
synthetase
fix
a
mistake
in
attachment
of
the
wrong
 amino
acid
to
a
tRNA?
 
 
 
 

 16.
Consider
prokaryotic
translation
and
answer
the
following
questions:
 a.
Which
subunit
contains
the
E,
P,
A
sites?
 
 
 b.
What’s
special
about
the
first
amino
acid
to
a
polypeptide?
What
does
the
 modification
prevent?
 
 
 c.
Since
formylmethione
and
methione
are
both
conjugated
to
the
same
tRNA,
how
is
 it
possible
for
cells
to
ensure
an
fMet
is
placed
at
the
AUG
start
codon
and
that
Met
is
 placed
elsewhere?
 
 
 

 d.

At
the
initiation
of
translation,
what
are
the
roles
of
IF‐1
and
IF‐3?
 
 
 
 17.
How
does
the
ribosome
know
where
to
start
in
prokaryotes
and
eukaryotes?
 Which
part
of
the
ribosome
is
involved
in
recognition?
 
 ...
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