BCH 5413 Exam 1 with Actual Complete Questions and
Correct Detailed Answer with Rationales Already
Graded A+ | 2026/2027 Updated
The number of bases per turn of DNA is___________
~10.5
What does the Meselson and Stahl experiment confirm?
DNA replication is semi-conservative
Heavy and light strands with nitrogen isotopes prove
True or False
a. Most biological DNA is positively supercoiled.
b. Triplex DNA is pyrimidine rich
c. Chargaff's rule: A=G & T=C
d. A single zinc finger can recognize 10bp of DNA
A. False, negatively = Left-handed. Some is right handed = positive
B. True
C. False A=T C=G
D. False, 3 bp, use multiple zinc fingers in a row for more sequence specificity/bp
DNA is not a uniform structure, many localized variants
can substitute protein domains, alpha helix/beta hairpin, in zinc fingers to make hybrids with
different binding specificities (designated by alpha helix) for major grooves of DNA
x-ray crystallography allows us to view and design custom designer DNA-binding proteins = alter
gene fxn in intact cells
In A & Z DNA:
a. Which is right-handed helix?
,b. Which one has 12bp per helical turn?
c. Which is the dehydrated form?
a. A
b. Z
c. A
primary DNA is B
Gel electrophoresis
molecular separation technique
can separate nucleic acids or proteins
make AGAROSE gel with slots
hot liquid poured with "teeth"
put DNA in slot, run electric current at neutral pH
DNA = negatively charged (phosphates) = migrates towards positive end
key is friction
DNA stained with fluorescent dye, looked at under UV
unknown DNA electrophoresed parallel with known to determine size
distance migrated = can plot on graph with log of molecular weights or number of bp
ex: 20mm = 910bp
PFGE = Pulsed Field Gel Electrophoresis
for longer sequences
as large as some chromosomes in yeast
What is PAGE?
Polyacrylamide Gel Electrophoresis
, used for PROTEINS
have to denature the protein = treat with detergent, SDS, sodium dodecyl sulfate
SDS-PAGE
SDS advantages:
1) coats polypeptides with (-) charge
2) masks natural charge so results are purely based on molecular weight
What is 2-D gel electrophoresis?
LESS POWER: use two different pH values to compare, pH affects net charge so different rates of
mobility
2-D = 1) proteins electrophoresed through narrow tube gel with pH gradients by ampholytes.
Once protein becomes neutral, no longer moves = isoelectric point
2) gel removed from tube, placed at top of regular gel for SDS-PAGE
What is Ion-Exchange Chromatography?
uses a resin to separate substances according to charge
(+) charged DEAE-Sephadex for anion-exchange
(-) charged phosphocellulose for cation-exchange
even though most proteins negative, center is positive so can still bind cation-exchange resin
What is Gel Filtration Chromatography?
after both anion and cation-exchange chromatography, can target different property of proteins
= protein size
pass a solution through a "whiffle ball" with varying size holes
small proteins get stuck, large pass around and go further
What is Affinity Chromatography?
Takes advantage of the affinity of different proteins to certain ligands.
A ligand or other molecule that binds to a protein of interest is covalently attached to the beads
Correct Detailed Answer with Rationales Already
Graded A+ | 2026/2027 Updated
The number of bases per turn of DNA is___________
~10.5
What does the Meselson and Stahl experiment confirm?
DNA replication is semi-conservative
Heavy and light strands with nitrogen isotopes prove
True or False
a. Most biological DNA is positively supercoiled.
b. Triplex DNA is pyrimidine rich
c. Chargaff's rule: A=G & T=C
d. A single zinc finger can recognize 10bp of DNA
A. False, negatively = Left-handed. Some is right handed = positive
B. True
C. False A=T C=G
D. False, 3 bp, use multiple zinc fingers in a row for more sequence specificity/bp
DNA is not a uniform structure, many localized variants
can substitute protein domains, alpha helix/beta hairpin, in zinc fingers to make hybrids with
different binding specificities (designated by alpha helix) for major grooves of DNA
x-ray crystallography allows us to view and design custom designer DNA-binding proteins = alter
gene fxn in intact cells
In A & Z DNA:
a. Which is right-handed helix?
,b. Which one has 12bp per helical turn?
c. Which is the dehydrated form?
a. A
b. Z
c. A
primary DNA is B
Gel electrophoresis
molecular separation technique
can separate nucleic acids or proteins
make AGAROSE gel with slots
hot liquid poured with "teeth"
put DNA in slot, run electric current at neutral pH
DNA = negatively charged (phosphates) = migrates towards positive end
key is friction
DNA stained with fluorescent dye, looked at under UV
unknown DNA electrophoresed parallel with known to determine size
distance migrated = can plot on graph with log of molecular weights or number of bp
ex: 20mm = 910bp
PFGE = Pulsed Field Gel Electrophoresis
for longer sequences
as large as some chromosomes in yeast
What is PAGE?
Polyacrylamide Gel Electrophoresis
, used for PROTEINS
have to denature the protein = treat with detergent, SDS, sodium dodecyl sulfate
SDS-PAGE
SDS advantages:
1) coats polypeptides with (-) charge
2) masks natural charge so results are purely based on molecular weight
What is 2-D gel electrophoresis?
LESS POWER: use two different pH values to compare, pH affects net charge so different rates of
mobility
2-D = 1) proteins electrophoresed through narrow tube gel with pH gradients by ampholytes.
Once protein becomes neutral, no longer moves = isoelectric point
2) gel removed from tube, placed at top of regular gel for SDS-PAGE
What is Ion-Exchange Chromatography?
uses a resin to separate substances according to charge
(+) charged DEAE-Sephadex for anion-exchange
(-) charged phosphocellulose for cation-exchange
even though most proteins negative, center is positive so can still bind cation-exchange resin
What is Gel Filtration Chromatography?
after both anion and cation-exchange chromatography, can target different property of proteins
= protein size
pass a solution through a "whiffle ball" with varying size holes
small proteins get stuck, large pass around and go further
What is Affinity Chromatography?
Takes advantage of the affinity of different proteins to certain ligands.
A ligand or other molecule that binds to a protein of interest is covalently attached to the beads
