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Unformatted text preview: CEE
266
Environmental
Biotechnology
 Homework
#
3
 
 
 1. [5
points]

The
enzyme
that
covalently
links
both
strands
of
a
vector
and
inserted
DNA
in
 molecular
cloning
is



 a. ligase


 b. helicase


 c. endonuclease


 d. polymerase
 
 2. [5
points]

Genes
for
heavy
metal
resistance
in
bacteria
tend
to
be
found


 a. in
the
chromosome.


 b. free
in
the
cytoplasm.


 c. on
a
plasmid.


 d. attached
to
the
cell
wall.


 
 3. What
are
the
anaerobic
organisms
that
carry
out
biological
methanogenesis?


 a. algae


 b. Archaea
 c. protozoans


 d. cyanobacteria


 
 4. 
[5
points]

Sulfate
reducing
bacteria
use
sulfate
as

 a. electron
donor
under
aerobic
conditions
 b. electron
donor
under
anaerobic
conditions
 c. electron
acceptor
under
aerobic
conditions
 d. electron
acceptor
under
anaerobic
conditions
 
 5. [5
points]

In
the
oxidation
pond
during
microbial
leaching
of
pyrite
ores,
the
redox
state
of
iron
 changes
from

 a. ferric
to
ferrous
 b. ferrous
to
ferric
 c. sulfide
to
oxide
 d. sulfide
to
sulfate
 
 6. [5
points]

In
the
precipitation
pond
during
microbial
leaching
of
pyrite
ores,
the
redox
state
of
 iron
changes
from

 a. zerovalent
iron
to
ferrous
 b. ferrous
to
ferric
 c. zerovalent
iron
to
zerovalent
copper

 d. zerovalent
iron
to
cupric
 
 7. [40
points]

A
recent
paper
describing
“A
Bacterium
That
Can
Grow
by
Using
Arsenic
Instead
of
 Phosphorus”
published
by
Wolfe‐Simon
and
colleagues
is
posted
on
courseweb.

Please
read
the
 paper
before
answering
the
following
questions:

 
 a. How
are
arsenic
species
toxic
to
living
cells?

 Answer:

As
(III)
is
more
toxic
than
As
(V);
Substitutes
P
during
ATP
formation
through
 arsenolysis
@
substrate
&
mitochondrial
levels;
Reacts
with
enzymatic
functional
 groups,
decreases
ATP
formation

 b. What
is
the
morphological
classification
of
strain
GFAJ‐1?

 Answer:

(Gram
negative)
cells
are
oblong
and
approximately
two
by
one
microns.

 c. On
what
basis
was
strain
GFAJ‐1
classified
as
belonging
to
Halomonadaceae
family?

 Answer:

16SrRNA
sequence
phylogeny
 d. What
is
the
trophic
classification?
 Answer:

chemoorganoheterotroph
 e. Which
two
microbial
growth
estimation
methods
were
used?


 Answer:

Optical
density
and
direct
counts
 f. Which
macromolecule
class
contained
the
largest
fraction
of
arsenate?
 Answer:

protein
 g. What
was
the
oxidation
state
of
arsenic
in
macromolecules?
 Answer:
+5
 h. Which
techniques
were
used
to
confirm
arsenate
in
genomic
DNA?
 Answer:


NanoSIMS

 
 8. [30
points]

Partial
sequence
of
16SrDNA
gene
of
strain
GFAJ‐1
is
given
below:


 5’
CAC
ATG
CAA
GTC
GAG
CGG
TAA
CAG
ATC
3’

 a. Predict
the
complementary
DNA
sequence
(3’

5’)

 Answer:

3’
GTG
TAC
GTT
CAG
CTC
GCC
ATT
GTC
TAG
5’
 b. Predict
the
mRNA
sequence
(5’

3’)
for
the
given
strand
as
coding
strand
 Answer:

5’
CAC
AUG
CAA
GUC
GAG
CGG
UAA
CAG
AUC
3’

 c. What
is
the
length
of
the
gene
(write
units)?
 Answer:

18
bp
 d. Identify
the
region
recognized
by
Taq1
restriction
enzyme.
 Answer:

TCGA
 e. Predict
the
amino
acid
sequence
of
the
gene
(NH4+
to
COO‐)
 Answer:

NH4+
methionine‐glutamine‐valine‐glutamic
acid‐arginine‐(stop)
COO‐
 f. By
introducing
a
point
mutation,
you
need
to
change
glutamic
acid
to
aspartic
acid.

 Write
the
new
codon?
 Answer:

GAC
or
GAU
 
 ...
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