Chapter Ten: Digital Analysis of DNA Flashcards

1
Q

___ fragment the genome at specific sites

A

restriction enzymes

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2
Q

each restriction enzyme recognizes a ___

A

specific sequence of bases

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3
Q

restriction enzymes cut ___

A

sugar-phosphate backbones of both strands

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4
Q

___ are generated by digestion of DNA with restriction enzymes

A

restriction fragments

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5
Q

___ is a commonly used restriction enzyme

A

EcoR1 from E. coli

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6
Q

restriction enzyme cuts are straight through both strands of DNA at the line of symmetry

A

blunt ends

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7
Q

restriction enzyme cuts are displaced on either side of the line of symmetry

A

sticky ends

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8
Q

sticky ends have either 5’ or 3’ ___

A

overhangs

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9
Q

sticky ends are good for when you want to make ___

A

recombinant DNA

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10
Q

average restriction fragment size is ___

A

256 base pairs

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11
Q

___ can be used to fragment DNA at random locations

A

mechanical forces

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12
Q

mechanical forces can break ___

A

phosphodiester bonds

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13
Q

two forms of mechanical forces

A

passing DNA through a thin needle at high pressure
sonication (ultrasound energy)

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14
Q

___ distinguishes DNA fragments according to size

A

gel electrophoresis

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15
Q

DNA has a ___ charge

A

negative

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16
Q

___ fragments move further through gel

A

small

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17
Q

a means to purify a specific DNA fragment away from all other fragments and make many copies of the fragment

A

molecular cloning

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18
Q

two basic steps of molecular cloning

A
  1. insert DNA fragments into coning vectors to specialized chromosome-like carriers that ensure transport, replication, and purification of DNA inserts
  2. transport recombinant DNA into living cells to be copied
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19
Q

a group of replicated DNA molecules

A

DNA clone

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20
Q

three main features of a plasmid cloning vector

A
  1. origin of replication
  2. selectable marker gene
  3. synthetic polylinker
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21
Q

DNA sequence containing multiple restriction enzyme sites

A

synthetic polylinker

22
Q

___ and ___ are alternate cloning vectors that can carry large inserts

A

bacterial artificial chromosomes (BAC) and yeast artificial chromosomes (YAC)

23
Q

create ___ using plasmid vectors

A

recombinant DNA

24
Q

digestion of the vector and human genomic DNA with a ___ results in ___

A

restriction enzyme
complementary sticky ends

25
___ is used to deal the phosphodiester backbones between vector and inserted fragment
DNA ligase
26
process by which a cell or organism takes up foreign DNA
transformation
27
only cells that ___ will grow on media specific to the selectable marker gene included in the plasma
took up the plasmid
28
long-lived collection of cellular clones that contains copies of every sequence in the whole genome inserted into a suitable vector
genomic library
29
a perfect genomic library has one copy of ___
every sequence in the entire genome
30
___ to obtain a perfect library
impossible
31
Sanger sequencing uses ___ to make new DNA
DNA polymerase
32
DNA polymerase requires these 4 things
1. template strand to copy 2. deoxyribonucleotide triphosphates 3. primer 4. buffer
33
a ___ is a good template for Sanger sequencing
recombinant plasmid
34
cloned recombinant DNA is ___
denatured
35
strands are mixed with ___
oligonucleotide primer
36
as temperature is lowered, primers and template strand ___
anneal (hybridize)
37
hybridized template and primer are mixed with ___, ___, and ___
DNA polymerase, dNTPs, and small amounts of dideoxyribonucleotide triphosphates (ddNTPs)
38
ddNTPs each have a unique ___
fluorescent tag
39
ddNTPs lack a ___, so once they are added to the new DNA strand ___
3' OH polymerization stops
40
result of this is a set of ___ with different 3' ends
nested fragments
41
nested fragments are separated by size using ___
electrophoresis
42
___ is recorded to identify nucleotide code
color of terminal ddNTP
43
E. coli have ___ chromosome, ___ genes, and a genome size of ___
1, 4400, 4.6 Mb
44
yeast have ___ chromosomes, ___ genes, and a genome size of ___
16, 6000, 12.5 Mb
45
humans have ___ chromosomes, ___ genes, and a genome size of ___
23, 2800, 3300 Mb
46
the human genome project began using the ___
hierarchical strategy
47
steps of hierarchical strategy of sequencing genomes
1. construct BAC genomic library 2. identify sets of overlapping BAC clones 3. shear DNA from each BAC separately to make smaller clones 4. sequence DNA based on overlap
48
steps of whole-genome shotgun strategy for genome sequencing
1. create genomic library of overlapping fragments in plasmid vectors 2. sequence DNA inserts of randomly chosen library plasmids 3. assemble sequences based on overlap of sequences into contigs
49
the whole genome shotgun approach can be highly ___
automated
50
sequencing a BAC clone library rather than smaller inserts of plasma clones
paired-end sequencing
51
trying to figure out what genes code for
annotation