biochem exam sample

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Name: _____________________________
TU ID: _____________________________
PRACTICE EXAM: SAMPLE Midterm #3 PROBLEMS
Biochemistry I (CHEM 4401)
Instructor: Vincent Voelz
Instructions
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•
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This is a closed-book, closed-note exam. Aside from calculators no other resources (e.g.
notes, books, individuals, and papers) may be consulted during the exam.
o DO use a basic calculator for numerical calculations.
o DO NOT use cell phones or graphing calculators.
Write your NAME and TUID on the front of the exam!
Attempt ALL questions and SHOW YOUR WORK when applicable for a correct
answer (and partial credit for an incorrect answer). Use backs of pages for extra work
space if needed. Circle final answers.
When applicable, show UNITS in calculations to two significant figures
Amino Acid pKa Information
Amino acid
Alanine
Arginine
Asparagine
Aspartic Acid
Cysteine
Glutamic Acid
Glutamine
Glycine
Histidine
Isoleucine
pK1
2.34
2.17
2.02
1.88
1.96
2.19
2.17
2.34
1.82
2.36
pK2
9.69
9.04
8.80
9.60
10.28
9.67
9.13
9.60
9.17
9.68
pKR
12.48
3.65
8.18
4.25
6.00
Amino acid
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
pK1
2.36
2.18
2.28
1.83
1.99
2.21
2.11
2.38
2.20
2.32
Points
Enzymes
Carbohydrates
Nucleotides and Nucleic Acids
______ / xx
______ / xx
______ / xx
TOTAL
______ / 100
1
pK2
pKR
9.60
8.95 10.53
9.21
9.13
10.96
9.15
9.62
9.39
9.11 10.07
9.62
Enzymes
1. For serine to work effectively as a nucleophile in covalent catalysis in chymotrypsin a
nearby amino acid, histidine, must serve as general base catalyst. Briefly describe, in
words, how these two amino acids work together.
2. Draw the acyl-enzyme intermediate of chymotrypsin for the following peptide substrate:
O
+H
3N
CH
CH3
C
O
H
N
CH
CH2
C
O
N
H
CH
C
O-
H
OH
3. Which enzyme uses general acid-base catalysis and/or covalent catalysis mechanisms to
hydrolyze peptidoglycan? (circle one)
a. Enolase
b. Lysozyme
c. Chymotrypsin
d. Pepsin
e. β lactamase
4. Allosteric enzymes (circle one)
a. always have both inhibitory and activating modulators
b. always exhibit Michaelis-Menten kinetics
c. exhibit conformational changes with the reversible binding of a modulator
d. are never regulated by substrate binding
e. have modulators that bind at the active site of the protein
Carbohydrates
5. Draw 2-deoxy-D-ribose in linear (Fisher projection) and cyclic (Haworth) forms. In the
cyclic form draw the α anomer. What specific long-from name does the cyclic form
have?
6. Draw the complete structure of Glc(α1→4)Glc. Assume both monosaccharides have Dstereochemistry. What is the complete long form name of this disaccharide?
7. When two carbohydrates are epimers:
a. one is a pyranose, the other a furanose.
b. one is an aldose, the other a ketose.
2
c. they differ in length by one carbon.
d. they differ only in the configuration around one carbon atom.
e. they rotate plane-polarized light in the same direction.
8. Starch and glycogen are both polymers of:
a. fructose.
b. glucose1-phosphate.
c. sucrose.
d. α-D-glucose
e. β-D-glucose.
9. Which monosaccharide is NOT a six-carbon monosaccharide?
a. fructose
b. ribose
c. mannose
d. glucose
e. galactose
10. Based on the form of the cyclic sugar shown below in a Haworth projection, which
Fischer projection formula could have formed this structure?
3
11. What is the CORRECT name for the linkage between these monosaccharide derivatives?
a.
b.
c.
d.
e.
(α1→4)
(β1→4)
(1 4)
(α1→β4)
(α1→α4)
12. Which type of protein interaction is NOT one with the NS domains of heparan sulfate?
a. Conformational activation
b. cell-surface localization/concentration
c. enhanced protein-protein interaction
d. binding extra cellular signaling molecules
e. All of the answer choices are types of protein interaction with heparan sulfate.
13. Name a sugar constituent of chitin. Is chitin a homopolysaccharide or
heteropolysaccharide?
Nucleotides and Nucleic Acids
14. Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change
DNA molecules by:
a. breakage of phosphodiesterbonds.
b. deamination of bases.
c. depurination.
d. formation of thymine dimers.
e. transformation of A → T.
15. What is the difference between a nucleoside and a nucleotide?
16. Draw the structure of your favorite purine-pyrimidine base pair as found in the WatsonCrick double-helical structure of DNA. Include all hydrogen bonds.
17. Shown below is the structure of _______________. Draw the structure of its canonical
base pair and mark which atoms participate in hydrogen bonds. Draw and name the
(deoxy) nucleoside corresponding to this base.
4
NH2
N
N
H
N
N
18. Compounds that contain a nitrogenous base, a sugar, and a phosphate group are called
__________ . (fill in the blank)
19. Two purines found in DNA are __________and __________ . (fill in the blanks)
20. A pyrimidine found in all DNA but in only some RNA is __________ . (fill in the blank)
21. In DNA, the base pair __________–__________ is held together by three hydrogen
bonds; the base pair __________–__________ has only two such bonds. (fill in the
blanks)
22. Explain the likely reason why DNA utilized the base thymine to store information rather
than uracil.
23. What is the average diameter of double-stranded B-form DNA?
24. What sugar “pucker” conformation is most common in B-form DNA?
25. Explain the similarities and differences between monocistronic and polycistronic
mRNAs. State the domains (Bacteria, Archaea, Eukaryota) in which these types of
mRNAs may be found.
26. Name and briefly describe one specific example of DNA damage that occurs through UV
radiation.
27. In the chemical synthesis of DNA:
a. the dimethoxytrityl (DMT) group catalyzes formation of the phosphodiester bond.
b. direction of synthesis is 5' to 3'.
c. The maximum length of oligonucleotide that can be synthesized is 8–10
nucleotides.
d. The nucleotide initially attached to the silica gel support will become the 3' end of
the finished product.
e. protecting cyanoethyl groups are removed after each step.
28. Describe one method to sequence DNA.
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