BCH5413 A Graded Exam with Questions and 100% Correct Answers
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Course
BCH 5413
Institution
BCH 5413
DNA is negatively charged and will move to the positive side
the smaller travel more quickly
*rate inversely proportional to their length
What is used to view DNA in gel - Answer ethydium bromide
Sournces of dsDNA - Answer - eukaryotic genome
bacterial genome
plasmid
viral genome
BCH5413 A Graded Exam with
Questions and 100% Correct Answers
Differences between types of blots - Answer Southern: DNA
Nothern: RNA
Western: Protein
gel elecrophoresis
matrix
gel
buffers - Answer separation of charged molecules in an electric field
matrix can be made from agarose or polyacrylamide
apparatus can be horizontal or vertical
buffers can be low or high salt, neutral or denaturing
Principal of gel electrophoresis - Answer separation based on
size - DNA restriction fragments are placed in well of gel
, DNA is negatively charged and will move to the positive side
the smaller travel more quickly
*rate inversely proportional to their length
What is used to view DNA in gel - Answer ethydium bromide
What is used for digestion of dsRNA.. - Answer use restriction endonuclease(s)
Eg. EcoR1
What is a gel ladder - Answer has bands of a known size
southern blot analysis does what - Answer identify DNA fragments based on their
actual sequence
Steps of southern blot - Answer - starts with electrophoresis of DNA sample
denature DNA and blot using transfer apparatus (eg. capillary action) onto membrane
southern blot with invisible DNA bands now on filter
block membrane with nonspecific DNA or protein
incubate with labeled probe
, photographic detection
positive band "lights up"
DNA structure - Answer - nucleic acid bases (purine (A,G) and pyrimidine (C,U,T))
sugars (ribose, deoxyribose)
sugars linked by phosphate groups (sugar-phosphate backbone)
*form antiparallel strands
In mammilian DNA, which base has various forms - Answer cytosine
Chargaff's rule - Answer A=T and C=G
Is DNA conservative or semi-conservative? - Answer semi-conservative
- parental sequence and daughter strand bind together
Alternative Double stranded DNA conformation
A and Z DNA - Answer A DNA
dehydrated form
right handed helix
11 bp per helical
bp tilted 19 degrees
major groove narrow and deep
found with dsRNA and RNA-DNA duplex
z-DNA
- >1% of cellular DNA
, favored by G-C repeats and alternating purines-pyrimidines
left handed helix
12 bp per turn
bp tilted 9 degrees
major groove flattened, nearly gone
bound by poxvirus E3L virulence factor and down regulates apoptosis genes
Non-duplex DNA structures
cruciform DNA - Answer - inverted repeat sequence
favored by excessive negative supercoiling
AT-rich cruciforms associated with 'fragile' DNA
Alternative modes of base pairing - Answer Watson Crick:
A--T and C---G
- adenine is at anti-conformation
Hoogsteen:
- adenine or guanine can be flipped to sin-conformation (different H-bonding)
Hoogsteen base pairing
- when can it occur - Answer - in triplex and quadruplex DNA structures
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