CHM ENG 170A Midterm: cheme170-fa2002-mt1-Clark-soln
8 Jan 2019
School
Department
Course
Professor
1
Chemical Engineering 170 October 7, 2002
Midterm Exam
Closed Book and Closed Notes
One 8.5 x 11 in. page of notes allowed
Section 1. Short Answers
1. (3 pts.) The serine protease subtilisin is the active enzyme in many household laundry
detergents. This enzyme is inactivated readily by oxidation of Met 222, a residue that is
conserved in all known subtilisin sequences and occupies a partially buried position next to the
catalytic Ser 221. It should thus be possible to produce a more stable and useful enzyme by
mutating this residue to one that is not susceptible to oxidation. Which amino acid do you believe
would be best to use as a replacement for the Met residue, and why?
Valine and Leucine would be the best amino acids based on size and hydrophobicity. Cysteine is
not a good answer because it has sulfur which is site of oxidation (if mention that cysteine would
be a good substitute because of sulfur we gave partial credits)
2. (3 pts.) Name three interactions involved in maintaining the tertiary structure of proteins.
Any 3 of 5:
Hydrogen bond; Hydrophobic Interactions; Ionic Interactions (electrostatic); Van der Waals;
Disulfide bonds
3. a. (4 pts.) What are the definitions of the Dämkohler number (Da) and the Thiele Modulus (φ)
for Michaelis-Menten kinetics?
RateTransport Maximum
RateReaction Maximum
Da =;
oS SK
Vmax
Da =
rateTransport
rateReaction
2=
φ
effm DK
V
Rmax
3
=
φ
b. (1 pt.) Which of the two deals with external mass transfer?
Damkohler number
2
c. (1 pt.) What does Da >>1 imply about the limiting rate of the process?
Da>>1 implies that the reaction rate is much greater than the transport rate, therefore the
mass transfer rate is the limiting step of the process.
d. (1 pt.) What does φ << 1 imply about the limiting rate of the process?
φ>>1 implies that the transport rate is much greater than the reaction rate, therefore the
reaction rate is the limiting step of the process.
4. (3 pts.) Define the following terms:
a. DNA ligase
Covalently link strands of nucleic acid on a template, the oligonucleotide may have a blunt
end or sticky end
b. Plasmid
Closed circular (supercoiled) piece of DNA, found in bacteria, usually a few thousand base
pairs long; Plasmids are normally double-stranded
c. Restriction endonucleases
Recognize a particular sequence of nucleotides in a polynucleotide or nucleic acid, and cleave
at a specific site.
5. (4 pts.) What are the two steps of protein synthesis? Give a brief description of each step.
1) Transcription: Synthesis of mRNA from DNA. RNA polymerase is directed to start site
of transcription by one of its subunits affinity to a particular DNA sequence (promoter)
that appears at the beginning of genes. The promoter is a unidirectional sequence on one
strand of the DNA and it tells RNA polymerase where to start and in which direction to
continue synthesis
2) Translation: Synthesis of polypeptide chain from mRNA. The mRNA has codons (triplets
of bases) that specify the specific amino acid to be added to the protein. The amino acids
are brought to the ribosome by tRNA, in the ribosome the amino acid is added to the
growing protein chain. mRNA (messenger RNA); tRNA (transfer RNA)
3
6. (6 pts.) Describe a PCR cycle?
A PCR cycle consists of three steps:
1) Denaturation: Heat double stranded DNA (dsDNA) to cause separation of both strands of
DNA. Use temperatures around 94oC for 1 minute.
2) Annealing: Forward and reverse primers (oligonucleutide) anneal to a single strand DNA
(ssDNA). This is achieved by using setting the temperature around 54oC for
approximately 45 seconds
3) Extension: dNTP’s are added to the growing DNA strand. The addition is done by a
thermostable DNA polymerase. Use temperatures around 72oC for 2 minutes.
PCR cycle allows an exponential amplification of part of DNA. The use of a thermostable
polymerase is essential as it avoids the need to add a DNA polymerase in each cycle, hence there
is no addition of impurities in each cycle.
7. (1 pt.) What type of enzyme do you need to carry a PCR?
DNA polymerase
8. (2 pts.) What are two advantages for the cell to have an intermediate (mRNA) in protein
synthesis?
Any two of three:
1) The DNA can stay pristine and protected, away from the caustic chemistry of the
cytoplasm
2) Gene information can be amplified by having many copies of an RNA made from one
copy of DNA
3) Regulation of gene expression can be effected by having specific controls at each element
of the pathway between DNA and proteins. The more elements there are in the pathway,
the more opportunities there are to control it in different circumstances.
Document Summary
One 8. 5 x 11 in. page of notes allowed. The serine protease subtilisin is the active enzyme in many household laundry detergents. This enzyme is inactivated readily by oxidation of met 222, a residue that is conserved in all known subtilisin sequences and occupies a partially buried position next to the catalytic ser 221. It should thus be possible to produce a more stable and useful enzyme by mutating this residue to one that is not susceptible to oxidation. Valine and leucine would be the best amino acids based on size and hydrophobicity. Cysteine is not a good answer because it has sulfur which is site of oxidation (if mention that cysteine would be a good substitute because of sulfur we gave partial credits: (3 pts. ) Name three interactions involved in maintaining the tertiary structure of proteins. Hydrogen bond; hydrophobic interactions; ionic interactions (electrostatic); van der waals;
