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Sarfaraz K. Niazi and Justin L. Brown
FIRST EDITION
SOLUTIONS MANUAL FOR
FUNDAMENTALS OF MODERN
BIOPROCESSING
SOLUTIONS MANUAL FOR
FUNDAMENTALS OF MODERN
BIOPROCESSING
Sarfaraz K. Niazi and Justin L. Brown
FIRST EDITION
CRC Press
Taylor & Francis Group
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© 2016 by Taylor & Francis Group, LLC
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Version Date: 20150706
International Standard Book Number-13: 978-1-4665-8575-1 (Ancillary)
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Chapter 2:
3. If only around 1% of all DNA in Eukaryotes encodes for proteins but
approximately 80% of DNA is transcribed, is there any function for the remaining
~79% of transcripts?
Answer: Yes, it encodes for regulatory RNA, like miRNA and also
functional RNA such as, tRNA and ribosomal RNA.
are born with) and nurture (the environment they are exposed to). Is there a way
for nurture to alter the nature?
Answer: Yes, many aspects of the environment are capable of inducing
epigenetic modifications in genes – permanently affecting expression
levels of proteins.
stranded RNA weighs approximately 321 Da per nucleotide and the average
amino acid in a protein weighs 110 Da. For a protein that is 20 amino acids long
created from mRNA with no introns, which portion of the genetic message had
the most mass in the cell?
Answer: ssDNA = 304*20*3 = 18.2kDa, however, DNA is double
stranded so the weight is again multiplied by 2 to 36.4kDa. RNA would
be 19.3kDa and the protein only 2.2kDa.
3!−𝐴𝐺𝑈𝑈𝑈𝑈𝐴𝑈𝐶𝐶𝐶𝐶𝐺𝐴𝑈𝐺𝑈𝐺𝐶𝐶𝐺𝐴𝐴𝐺𝑈𝐺𝐺𝐴𝐺𝐴𝐺𝐺𝐴𝐺𝑈𝐴 −5′
Answer: Met-Arg-Arg-Trp-Glu-Ala-Val-Stop
15. Researchers have recently began to use DNA and RNA sequences to generate
functional conformations by relying on complementary sequences to bind and non
complementary sequences to permit bending and folding, like a protein or
ribosomal RNA, as opposed to solely carrying genetic information. For the
following RNA based aptamer sequence identify what shape would be generated:
5!−𝐴𝑈𝑈𝐴𝐶𝐺𝐴𝑈𝐶𝐴𝑈𝐺𝐺𝐴𝐴𝐴𝑈𝐶𝐺𝑈𝐴𝐴𝑈 −3′
Answer: A hairpin with the stem created by pairing 5’-AUUACGAU with
AUCGUAAU-3’
18. In the context of the chromosome, what is the region called that codes for the
production of a protein?
Answer: A gene.
Chapter 3:
3. Double stranded DNA demonstrates a helical structure because of the bonding
between two complementary strands. What type of bond is formed between
complementary strands of DNA and how does the bond vary depending on the
nucleotides present?
a. Answer: Hydrogen bonding. A & T form two hydrogen bonds. C & G for
three hydrogen bonds
6. The deamination of cytosine in DNA results in a separate nucleotide. Is this
challenge would the repair of this mutation present?
a. Answer: Uracil is not normally found in DNA, which allows DNA
glycosylases to easily recognize and repair the mutation. If uracil was
normally found in DNA, this repair mechanism would be complicated
between carbohydrates and lipids?
a. Answer: A few differences would be that carbohydrates have an oxygen
to hydrogen ratio very similar to water, whereas, lipids have considerably
more hydrogen. This results in lipids being very hydrophobic, which
15. The Krebs Cycle relies on the oxidation of multiple components. Oxidation
results in the liberation of an electron, what is the most common electron acceptor
in the Krebs Cycle?
a. Answer: NAD+
18. What is glucose converted to for entry into the Krebs Cycle?
a. Answer: Glucose enters the Krebs Cycle as Acetyl-CoA.
Chapter 4:
3. If you are concerned that eukaryotic cells in culture may have become contaminated by
prokaryotic cells, a typical first step would be to use a Gram stain to identify which cell wall the
bacteria demonstrate and then select an appropriate antibiotic. However, if your culture is
contaminated with mycoplasma, a very small prokaryote that is ubiquitous in cell cultures, it
would not stain either Gram positive or negative due to lacking a cell wall altogether. Propose a
method to identify whether mycoplasma may be present.
A: Answer: There are numerous correct answers. E.g. Staining for DNA will identify small
extracellular particles. Likewise, gene analysis techniques such as PCR can be used to
identify mycoplasma specific genes.
tubes termed myotubules. The formation of these myotubules is associated with an increase in a
particular organelle due to the high energy needs of muscle tissue. Which organelle is upregulated
in myotubules?
A: Answer: Mitochondria increase 2-4 fold in myotubules, which aids in the production of
ATP necessary for actin:myosin contraction and muscle function.
microtubules have?
a. Answer: They serve as both “highways” for transport of intracellular vesicles and are
capable of resisting compressive forces applied to the cell.
benefit the signal propagation?
a. Answer: Yes, it serves to amplify the signal
15. Often in propagating a signal from one cell to the next, the cell membrane resting potential is
dramatically shifted. How does the cell return back to the baseline resting potential?
a. Answer: The cell depolarizes to propagate a signal. The original potential of the cell is
around -40 - -80mV. Depolarization increases this voltage and sodium/potassium pumps
serve to decrease the potential back down to the resting state.
microorganism that uses a prokaryotic cell as a host and what is it?
a. Answer: Yes, a bacteriophage
Chapter 5:
3. The molecular weight of ethanol is 46.07 g/mol, the density of ethanol is 0.789
g/cm3. How many molecules of ethanol are present in 1mL, assuming a 100%
solution of ethanol?
a. Answer: 0.789 g/cm3*1 cm3/mL*1 mL = 0.789g,
0.789g/46.07g/mol=0.01713mol, 0.01713mol*6.022E23 molec/mol =
a. Answer: A simple one dimensional approach indicates the drug would
take 70hrs to reach the peripheral of the tumor, during this same time
period the drug would decay to near zero.
i. Answer: -dA/dt=kA2B, A0-A=2(B0-B), B=B0-A0/2+A/2,
dA/(A2(B0-A0/2+A/2)=-kdt, partial fractions to solve,
C1/A+C2/A2+C3/(A-A0/2+B0/2), cross multiply, C1*A*(A/2-
12. For the following graph:
a. What is the type of reaction occurring? (e.g. parallel, reversible, etc…)
i. Answer: Parallel
b. What can be determined regarding the initial concentrations?
i. Answer: A=10M, B=5M
c. What can be determined regarding the rate constants?
i. Answer: Assume rate constants k1, k2 and k3 for the reactions
producing B, C and D respectively. k2=2k1, k3=3k1
15. For the simple reversible reaction, A<->B, with k1=1/2*k-1, what are the
equilibrium concentrations if:
a. [A]0=10M, [B]0=0M
i. Answer: [A]f=6.667M and [B]f=3.333
b. [A]0=10M, [B]0=5M
(15pts)
t (sec)
C (M)
0
0.000
1
10.000
2
13.333
3
15.000
4
16.000
5
16.667
6
17.143
7
17.500
8
17.778
9
18.000
10
18.182
a. Answer: first determine the concentration of the reactant A, 2(A0-A)=C-
C0, A=A0-C/2, then examine the ln[A] and 1/[A] to determine if the
reaction is 1st or 2nd order:
t (sec)
A (M)
Ln(A)
1/A
0
10.000
2.303
0.1
1
5.000
1.609
0.2
2
3.333
1.204
0.3
3
2.5
0.916
0.4
4
2
0.693
0.5
i. The relationship is linear with 1/A, thus 2nd order
Chapter 6:
3. The enzyme, trypsin has the following kinetic constants at an initial concentration
of 10-6M acting on a substrate at a concentration of 10-3M:
𝐸+𝑆↔𝐸𝑆 →𝐸+𝑃
k1=6*108 M-1*s-1
k-1=5*104 s-1
k2=1*103 s-1
a. What is the value of the Michaelis-Menten constant for this enzyme?
i. Answer, k2/k-1<<1, so assume rapid eq. Km=8.5E-5 M
b. What is the initial rate of product formation?
i. Answer, v=k2[E0][S0]/(Km+[S0])=922µM/s
6. For the following kinetic data:
No Inhibitor
With Inhibitor
v M/min
S M
v M/min
S M
1.43
0.33
1.00
0.33
2.00
0.50
1.43
0.50
3.33
1.00
2.50
1.00
a. What type of inhibition is occurring?
i. Answer: Lineweaver Burk plot of 1/v v 1/S for each yields: For
the uninhibited case, Km=2M and Vm=10 M/min, for the inhibited
case, Km=3M and Vm=10M/min. Thus the inhibition is
for the data given.
9. Using the reaction data in question 8. Apply non-linear regression to find the
linearization strategies.
a. Answer: Using the non-linear regression solver in Excel to minimize the
sum of differences squared between the actual data obtained and a velocity
guessed based on varying Km and Vm values yields:
Km
33.32
11.08%
Vm
80.78
0.97%
Eadie-Hoftsee
Km
33.56
11.86%
Vm
81.18
1.48%
Non-linear Regression
Km
32.08
6.92%
Vm
79.99
0.02%
12. A tethered enzyme demonstrates Vm=10 µM*cm/s and Km=1µM. The substrate
concentration in the bulk liquid is 10µM and the liquid mass transfer coefficient
for the substrate present is 1 cm/s.
a. What is the steady state value of the reaction?
i. Answer: Set the mass transfer equal to enzyme reaction and solve,
results in a velocity of 7.3 µM*cm/s at a substrate concentration of
2.7µM.
i. Answer: Neither, Da=1
15. The conversion of sugars to ethanol by yeast results in the following relationship
for the quantity of substrate (glucose), product (ethanol) and number of yeast
present over time:
a. What is occurring?
i. Answer: Product inhibition by the ethanol slows the growth rate,
ii. then the death rate drives the overall population numbers.
17. A population of cells initially at 2000 is found to have a growth rate of 0.1 hr-1
two cells fuse together, at a rate of 0.05 hr-1; however, they will only undergo
0.00E+00
1.00E+02
2.00E+02
3.00E+02
4.00E+02
5.00E+02
6.00E+02
7.00E+02
8.00E+02
0.00E+00
5.00E+11
1.00E+12
1.50E+12
2.00E+12
2.50E+12
3.00E+12
3.50E+12
4.00E+12
0 2000 4000 6000 8000 10000
Concentration (mM)
Cell Number
Time (min)
N Glucose Ethanol
multinucleation until there are 5 nuclei per cell. The dish holds a maximum of
10,000,000 mononucleated cells.
a. Derive a relationship between the Nmax and the rate of multinucleation,
state all assumptions made.
i. Answer: Assuming that the total cell area increases directly
proportional to the number of nuclei, then Nmax after all cells have
5 nuclei would be 1/5 Nmaxo. The ratio between Nmax and
i. Answer: After a long time all the cells have 5 nuclei,
Nmax=1/5*10,000,000=2,000,000
The balance between the growth and death rates at steady state reduces
on the order of 100,000’s is fine.
i. Answer: This requires a bit of number crunching and taking a
dt=10hr and rounding…
time. This does not need to be exact.
i. Answer:
ii.
*Hint: Assume multinucleation only affects Nmax.
error and relative error. For example, 2.356 ± 0.16 grams shows the reading of mass. The
uncertainty in this reading is 0.16 grams which allows one to judge that this is the actual
measuring range by which the reading is uncertain, it is known as the absolute error. In
the next case mass is represented by the following expression, 2.356 ± 1.50% in which
the relative error is ± 1.50%. For the following calculations, follow engineering
conventions for significant figures.
a.) Given 2.360 ± 0.56 and 1.420 ± 0.25, find the sum of the two numbers.
Solution
(2.360 + 1.420) ± (0.56 + 0.25) = 3.780 ± 0.81 = 3.780 ± 21%
Answer: 3.780 ± 21%
Solution
(147-75) ± (31 + 13) gmol h-1 = 72 ± 44 gmol h-1 = 72 gmol h-1 ± 61%
Answer: 72 gmol h-1 ± 61%
0
1,000,000
2,000,000
3,000,000
4,000,000
5,000,000
6,000,000
-100 100 300 500
Cell Number
Time (hours)
Solution
!.!"
!.!"# ± (0.012 + 0.00756) mol m-3 = 1.4 ± 0.020 mol m-3 = 1.4 mol m-3 ±
Solution
(4.56 x 6.27) ± (0.05 + 0.07) g l-1 = 28.59 ± 0.12 g l-1 = 28.59 g l-1 ± 0.42%
a.) What is the estimated mean pH of this cycle?
Solution
The arithmetic mean is used to find the best estimate of pH,
Solution
The standard deviation is given by,
σ = !!!!!
experiment?
Samples consist of 5.66, 5.97, 6.25, 6.44.
Solution
𝑥 = !.!"!!.!"!!.!"!!.!"!!.!"!!.!"!!.!!!!.!"!!.!"!!.!!
!" = 6.07
𝑥=6.07
a.) During data acquisition a plot of points is generated on linear graph paper
which gives a straight line passing through points (2, 6) and (8, 1.5). Using a
plot of y versus x, determine the equation of the line. Use (x1, y1) and (x2, y2)
as a reference coordinate system.
Solution
The definition of a straight line is represented by the following equation,
The equation of the straight line is given by, y = - !
!x + 7.5
Answer: y = - !
!x + 7.5
b.) A plot of points is generated on linear graph paper which gives a straight line
passing through points (2.8, 15.6) and (9.4, 33.5). Use a plot of y versus x1/3 to
determine the equation of the line.
Solution
Using the definition of a straight line, the equation is given as,
y = Ax1/3 + B
Slope A and y-intercept B are given by,
determine the equation of the line.
Solution
Using the definition of a straight line, the equation on log-log graph paper is
given as,
y = BxA
or
to determine the equation of the line.
Solution
Using the definition of a straight line, the equation on semi-log graph paper is
