BCH 5413 EXAM 1 STUDY GUIDE QUESTIONS AND
CORRECT DETAILED ANSWERS WITH COMPLETE
SOLUTIONS | NEW UPDATE 2025-2026
topoisomerase - ANSWER relieves supercoiling in front of replication fork
Left-handed DNA - ANSWER negative *under wrapped supercoiling
Right-handed DNA - ANSWER positive *over wrapped supercoiling
Gel Electrophoresis: Matrix - ANSWER 1. agarose (polysaccharide)
2. polyacrylamide (neurotoxin)
Gel Electrophoresis: Sample possiblitiies - ANSWER 1. Eukaryotic genome
2. Bacterial genome
3. Viral genome
4. Plasmid
Digest with __ - ANSWER EcoR1
steps of Southern Blotting - ANSWER 1. Agarose gel electrophoresis of DNA
fragments
2. Denature DNA and blot (converts to ssDNA)
3. Southern Blot on filter
, 4. Block nonspecific DNA or protein then incubate with labeled probe
5. Photographic detection
6. Positive band "lights up"
Klenow fragments - ANSWER large fragment of DNA polymerase, used to
extend primers
Stringency - ANSWER Properties of hybridization conditions that dictate the
degree of base mismatch permitted between probe and DNA trage
Low stringency: Increase in number of mismatch (high background noise)
High stringency: Decrease in number of mismatch (low background noise) *high
temp, low salt
Gel filtration - ANSWER Gel filtration chromatography uses
columns fi lled with porous resins that let in smaller
substances, but exclude larger ones. Thus, the
smaller substances are slowed in their journey
through the column, but larger substances travel
relatively rapidly through the column.
autoradiography - ANSWER is a means of detection using radioactively labeled
DNA, when these high-energy electrons strike the screen, they cause
fluorescence, which is detected by the film.
Wash in Southern Blot - ANSWER removes probe that is nonspecifically bound
to solid support (nylon membrane)
CORRECT DETAILED ANSWERS WITH COMPLETE
SOLUTIONS | NEW UPDATE 2025-2026
topoisomerase - ANSWER relieves supercoiling in front of replication fork
Left-handed DNA - ANSWER negative *under wrapped supercoiling
Right-handed DNA - ANSWER positive *over wrapped supercoiling
Gel Electrophoresis: Matrix - ANSWER 1. agarose (polysaccharide)
2. polyacrylamide (neurotoxin)
Gel Electrophoresis: Sample possiblitiies - ANSWER 1. Eukaryotic genome
2. Bacterial genome
3. Viral genome
4. Plasmid
Digest with __ - ANSWER EcoR1
steps of Southern Blotting - ANSWER 1. Agarose gel electrophoresis of DNA
fragments
2. Denature DNA and blot (converts to ssDNA)
3. Southern Blot on filter
, 4. Block nonspecific DNA or protein then incubate with labeled probe
5. Photographic detection
6. Positive band "lights up"
Klenow fragments - ANSWER large fragment of DNA polymerase, used to
extend primers
Stringency - ANSWER Properties of hybridization conditions that dictate the
degree of base mismatch permitted between probe and DNA trage
Low stringency: Increase in number of mismatch (high background noise)
High stringency: Decrease in number of mismatch (low background noise) *high
temp, low salt
Gel filtration - ANSWER Gel filtration chromatography uses
columns fi lled with porous resins that let in smaller
substances, but exclude larger ones. Thus, the
smaller substances are slowed in their journey
through the column, but larger substances travel
relatively rapidly through the column.
autoradiography - ANSWER is a means of detection using radioactively labeled
DNA, when these high-energy electrons strike the screen, they cause
fluorescence, which is detected by the film.
Wash in Southern Blot - ANSWER removes probe that is nonspecifically bound
to solid support (nylon membrane)
