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Biology 1A03 > Theme 4: DNA Replication and Mitosis - Module 3: Applications of DNA Replication > Flashcards

Theme 4: DNA Replication and Mitosis - Module 3: Applications of DNA Replication Flashcards

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1
Q

what technique did Kary Mullis develop?

A

the ability to amplify DNA in a rube vie polymerase chain reaction (PCR) technique

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2
Q

what did this technique allow scientists to do?

A

to be able to copy (amplify) millions of copies of DNA from very small starting samples

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3
Q

DNA in a tube has revolutionized the world of cellular and molecular biology in what ways?

A
  • has shed light on diagnosis of genetic defeats
  • detection of viral DNA in cells
  • producing large amounts of DNA from fossils containing trace amounts of DNA
  • being able to link specific individuals to DNA samples during forensic investigations
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4
Q

how is a PCR set up?

A

a sample of DNA is placed into a tube containing a buffered solution with essential ions and salts, along with a pair of short single-stranded DNA primers (usually 15-30 nucleotides in length)

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5
Q

what do the primers do?

A

bind in a complementary manner to specific regions of the template DNA and serve as starting points for DNA copying

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6
Q

since this is a cell-free system what else is also added within the tube?

A

free deoxyribonucleotides (dNTPs)

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7
Q

when are the dNTPs utilized?

A

during the replication process

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8
Q

what does PCR not require?

A

the multiple enzymes that cells utilize to unwind and stabilize the DNA double helix

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9
Q

where are the tubes placed instead?

A

in a thermocycler machine

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10
Q

what happens with the thermocycler machine?

A

it goes through various phases of heating and cooling in automatic programmed steps to facilitate the DNA replication process over various repeated cycles

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11
Q

how many key DNA replication enzymes are still required?

A

one

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12
Q

what is it?

A

a special DNA polymerase

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13
Q

what is special about this DNA polymerase?

A

it is tolerant to high temperatures

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14
Q

why is it added to the tube?

A

to catalyze the polymerization of each daughter strand within the tube with each replication cycle

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15
Q

what is an example of this type of heat-tolerant DNA polymerase?

A

Taq polymerase

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16
Q

where was this first isolated from?

A

the bacterial species Thermus aquaticus - adapted to live in hot springs with temperatures as high as 95 degrees celsius

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17
Q

how many key stages are involved in a PCR reaction

A

three

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18
Q

what are they

A

denaturation, annealing, and extension

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19
Q

what does this three step cycle bring?

A

a chain reaction that produces an exponentially growing population of identical DNA molecules

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20
Q

the types of DNA molecules were referring to depends on what?

A

the types of primers that are designed

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21
Q

most researchers have a sequence of a gene or DNA segment that they wish to replicate or cone, thus how will researchers design primers?

A

design primers to bind to or anneal to their complementary sequence on either side of the DNA sequence of interest on the DNA template strands

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22
Q

how must the DNA double helix be at the start of a PCR?

A

unwound

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23
Q

how is this facilitated?

A

by a high temperature stage of the reaction

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24
Q

what happens during the denaturation stage?

A

the reaction mixture is heated to separate the strands of the double-stranded DNA

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25
Q

what will then happen with the thermocycler?

A

it will cool the solution

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26
Q

what does this allow?

A

allows the two primers to anneal to their complementary sequences on the DNA template strands on either side of the DNA sequence of interest during the annealing phase

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27
Q

where will the primers bind?

A

on opposite strands at each end of the target sequence

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28
Q

when does the heat-stable DNA polymerase extend and polymerize the daughter strands?

A

during the extension phase

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29
Q

what is used?

A

four dNTPs, starting from the primers and extending the daughter strand in a 5’ to 3’ direction

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30
Q

what does each complete cycle result in?

A

two double stranded helices containing the desired target sequence portion of the original template DNA

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31
Q

summarize the denaturation step:

A

a solution containing double-stranded DNA (the template duplex) is heated to separate the DNA into two individual strands

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32
Q

summarize the annealing step:

A

when the solution is cooled, the two primers anneal to their complementary sequence on the DNA template strands

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33
Q

summarize Extension:

A

DNA polymerase synthesizes new DNA strands (complementary to the template) by extending primers in a 5’ to 3’ direction

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34
Q

are PCR reactions fast and specific for the DNA sequence that is replicated

A

yes

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35
Q

with each successive cycle the number of replicated DNA molecules with the same sequence as the parent template duplex is what?

A

double

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36
Q

what is present after the first cycle of PCR?

A

two copies of the template duplex - each consisting of one new and one old DNA strand

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37
Q

with each cycle what do the newly synthesized DNA segments serve as?

A

templates in later cycles

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38
Q

after the second PCR cycle how many copies would be present?

A

4

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39
Q

what equation can be used to represent the number of copies of the template DNA target sequence

A

2^n (n=cycles)

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40
Q

what is essential for many of the applications of PCR?

A

the huge amplification

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41
Q

do the tubes look different after removing them from the thermocycler?

A

no

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42
Q

what will be in the tube if the PCR was successful?

A

millions of molecules of amplified segments of DNA

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43
Q

what do researchers use in order to visualize DNA molecules?

A

gel electrophoresis

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44
Q

what does gel electrophoresis do?

A

general technique used to separate DNA fragments from other sources, not just from PCR

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45
Q

what else can gel electrophoresis be used to separate?

A

other macromolecules including RNA and proteins, all on the basis of their rate of movement through an agarose gel in an electric field

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46
Q

where are molecules loaded during DNA gel electrophoresis?

A

into wells of a porous gel

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47
Q

where do the molecules travel? how?

A
  • along the length of the gel

- because of an electrical field that is applied along the length of the gel

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48
Q

what are the different charges established and where are they located?

A

positive at one end of the gel and negative at the other end of the gel

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49
Q

what is the charge on DNA and RNA? Why?

A
  • negatively charged

- due to ionized phosphate groups along the phosphodiester backbone

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50
Q

where will they be attracted towards?

A

attracted towards the positively charged (anode) end of the gel

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51
Q

what also affects how far through the gel the molecules will travel?

A

size of the molecule

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52
Q

the molecules that travel through the gel at the highest speed tend to be what size?

A

the smallest molecules

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53
Q

what is the travelling speed and distance of larger molecules?

A
  • slower speed

- smaller distanced along the gel compared to smaller molecules

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54
Q

what is the range of nucleotides that gel electrophoresis can separate?

A

several hundreds of nucleotides to over 10, 000 nucleotides

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55
Q

what are the PCR results typically?

A

the amplification of just a single size of DNA molecule

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56
Q

what is it also possible to utilize gel electrophoresis for?

A

to separate and visualize a DNA sample containing a mixture of DNA fragments of different sizes

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57
Q

what is also loaded onto the gel electrophoresis along with the DNA samples?

A

a standardized ladder

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58
Q

what is a standardized ladder?

A

contains DNA fragments of known sizes

59
Q

what is possible after the actual electrophoresis process?

A

can visualize the separated DNA fragments

60
Q

what is used to visualize the separated DNA fragments?

A

special dyes that intercalate with and stain the DNA fragments

61
Q

what do these dyes do when exposed to ultraviolet light?

A

fluoresce

62
Q

how can the different bands containing the DNA fragments of different sizes be visualized ?

A

visualization can be detected on the gel using UV light

63
Q

how is it possible to learn a lot about the function of a gene?

A

by identifying its nucleotide sequence

64
Q

along with identifying the nucleotide sequences of important regions that code for functional proteins in our DNA, what can we also identify?

A

the nucleotide sequences of non-coding regions

65
Q

why was DNA sequencing developed by Frederick Sanger?

A

to be able to determine the sequence of a DNA molecule

66
Q

how was he able to develop this technique?

A

based largely on his knowledge of DNA replication

67
Q

what was a limitation to Sanger’s DNA sequencing technique?

A

it could only determine the sequence of small fragments of DNA

68
Q

what did Gene Myers and Jim Weber do?

A

came up with an approach that would revolutionize large-scale sequencing projects and would facilitate the identification of the DNA sequence of the entire genome of any organism

69
Q

what was this technique refereed to as?

A

shotgun sequencing

70
Q

what was this technique based on?

A

being able to break the entire genome into different sized pieces and then proceed with 3 specific phases

71
Q

what was the first phase?

A

Random sequencing of the DNA in each fragment

72
Q

what was the second phase?

A

Identifying the regions of overlap between the generated fragments and inferring or assembling the long, continuous sequence of nucleotides in the DNA molecule that makes up each chromosome

73
Q

what was the third phase?

A

annotating the sequences to best identify the regions of genomic DNA that encode genes, regulatory regions and even non-coding regions of the DNA

74
Q

what was critical to the process of whole-genome sequencing?

A

the development of computational software capable of facilitating the assembly of fragments

75
Q

when was the whole human genome sequenced?

A

2000

76
Q

summarize the three phases

A

1) sequence DNA
2) assemble sequences
3) annotate the sequences

77
Q

how is DNA sequencing carried out today?

A

by sequencing machines

78
Q

what did early approaches to DNA sequencing use?

A

the Sanger sequencing technique

79
Q

what is this technique also known as?

A

dideoxy chain-termniation method or dideoxy sequencing

80
Q

since DNA sequencing is based upon our knowledge of DNA replication, during Sanger sequencing, the DNA to be sequenced serves as what?

A

a template for DNA synthesis

81
Q

what are the key components required for dideoxy sequencing?

A

include all the components required for DNA replication

82
Q

what do these components include?

A
  • denatured, single-stranded template DNA
  • short single-stranded DNA primers
  • sufficient free deoxyribonucleotides(dNTPs)
  • DNA polymerase
83
Q

what do short single-stranded DNA primers do?

A

will bind in a complementary manner to specific regions of the template DNA and serve as starting points for DNA copying

84
Q

how does DNA polymerase link adjacent deoxynucleotides?

A

catalyzing a covalent bond between the 5’ -phosphate on one nucleotide and the 3’ - OH group on the previous nucleotide

85
Q

because of this how this occurs the basis of the dideoxy chain-termination method requires what?

A

the use of modified deoxyribonucleotides

86
Q

which didexoynucleotides (ddNTPs) will not allow for further elongation of a growing DNA strand?

A

dideoxynucleotides that are missing the -OH group at the 3’ position

87
Q

why is this?

A

the -OH group is required for the attachment of the next nucleotide

88
Q

as a result of this what did Sanger add into the sequencing reaction tubes in addition to all other components required for DNA replication?

A

labelled ddNTPs

89
Q

what will the dideoxynucleotides within the tubes will lead to what?

A

to a series of interrupted daughter strands

90
Q

where is each terminating DNA replication located during this?

A

at the site where dideoxynucleotide is incorporated

91
Q

during dideoxy sequencing, the sequencing of each daughter strand begins where? and continues until when?

A
  • begins at the 3’ end of the primer

- continues until a dideoxynucleotide is inserted

92
Q

what happens once a ddNTP is inserted in a daughter strand?

A

prevents further elongation of the strand

93
Q

how many molecules of the template DNA does the sequencing reaction contain?

A

millions of molecules of template DNA

94
Q

what kind of process is the insertion of the ddNTPs or dNTPs?

A

random process

95
Q

between ddNTPs and dNTPs which is added in a smaller amount?

A

smaller amount of ddNTPs are added relative to the amount of dNTPs

96
Q

what does this allow for?

A

the generation of many fragments of many different sizes potentially terminating at every possible nucleotide within a given region

97
Q

for DNA sequencing to be of us what is it essential to be able to identify?

A

the molecules in which chain termination has occurred

98
Q

what must be done to achieve this?

A

each of the four dideoxynucleotides can be labelled with a fluorescent dye

99
Q

is the fluorescent dye labelling each of the four ddNTPs the same or different?

A

different

100
Q

in this manner what is it possible to do?

A

distinguish all the chain terminators that are present in all the replicated DNA fragments within a DNA sequencing reaction

101
Q

after DNA synthesis and chain termination where are the labelled strands in the mixture loaded?

A

onto a gel and the fragments are separated by gel electrophoresis

102
Q

how long does electrophoresis continue for?

A

until each DNA band emerges from the bottom of a gel and a laser excites the fluorescent dye attached to each dideoxynucleotide

103
Q

what can record the amount of fluorescence that is emitted?

A

a fluorescent detector

104
Q

what does the fluorescent detector do after recording the amount of fluorescence emitted?

A

match this to one of four wavelengths that corresponds to the four fluorescent tags that are attached to each of the ddNTPs

105
Q

what does the fluorescence detector then do?

A

distinguishes strands differing in length by as little as one nucleotide

106
Q

what can then be generated by the laser and detector with every peak corresponding to the nucleotides that make up the DNA sequence that is complementary to the template strand, and always begins after the primer?

A

a spectrogram trace

107
Q

what is a limitation of the Sanger method?

A

it can only determine the sequence of fragments of DNA up to several hundred nucleotides in length

108
Q

thus what is this technique convenient for?

A

sequencing short sequences of DNA

109
Q

what should be used for large stretches of DNA?

A

shot gun sequencing

110
Q

what does this technique allow?

A

the information from multiple DNA sequences to be assembled by examining the regions of overlap between sequenced random DNA fragments

111
Q

when assembling the sequence of a series of sequenced DNA fragments what occurs?

A
  • the short sequences are examined
  • regions of overlap are identified
  • short sequences are put together to generate long continuous sequences of nucleotides
112
Q

therefore what is possible?

A

it is possible to attain long sequences of large portions of chromosomes on the order of millions of nucleotides in length

113
Q

what is the assembly of these fragments into one continuous sequence accomplished by?

A

complex algorithms in an automated fashion through various computer programs

114
Q

what are contigs?

A

refers to overlapping DNA segments that are assembled into a consensus region of DNA

115
Q

what is the assembly of he final DNA sequence based on?

A

the overlap of sequence similarities between various DNA fragments

116
Q

consider the sequences of DNA fragments to be represented by sentence fragments of this/a statement. Based on the information in the fragments and identifying the regions of overlap (contigs) between fragments, the full sentence can be assembled in the correct order, generating the complete statement

A

.

117
Q

therefore how can the sequences of entire genomes be determined?

A

based on the sequence similarities within overlapping sequenced DNA fragments

118
Q

what are researchers able to do once the sequences are assembled?

A

able to annotate the sequence and identify specific regions of interest along the sequenced DNA

119
Q

what does annotation of DNA sequences allow?

A

allows us to obtain a better understudying of the series of A, C, G and T nucleotides that encode all our genetic information in our DNA

120
Q

is all our DNA in our genome transcribed into RNA? is all our RNA translated into a functional protein product?

A

no and no

121
Q

how many possible reading frame are there for any double-stranded DNA sequence?

A

6

122
Q

what is one of the first steps following sequence assembly?

A

to establish the correct reading frame

123
Q

what are computer programs able to do?

A

scan the sequence of a genome in both directions and identify each reading frame that is possible on both DNA strands

124
Q

what is a long stretch of codons that lacks a stop codon identified as?

A

a good reading frame and indication that that may be the coding sequence

125
Q

in the example of the human beta glob in gene, only one reading frame will give the full length protein, why is this?

A

because other reading frame will terminate translation after only a few amino acids

126
Q

what are annotation softwares able to do as a result?

A

can identify any gene-sized protein coding stretches of DNA sequences (one reading frames) that lack internal stop codons, but that are flanked on either side by a start and stop codon

127
Q

what will the computer programs also look for?

A

typical sequences that code for promoters, or other regulatory sites

128
Q

are prokaryotic or eukaryotic genomes easily scanned to identify regions of interest?

A

prokaryotic

129
Q

why are there different techniques used for eukaryotic genomes?

A

to identify intron and exon regions amid other regions of the genome

130
Q

along with identifying the reading farm of a specific DNA sequence, genome annotation requires the identification of?

A

various patterns (sequence motifs) in the sequenced DNA molecule

131
Q

protein-coding regions of DNA can be inferred based on?

A

the identifcaiont of open-reading frames in the DNA or RNA sequence and it consist of triplets of nucleotides that can specify amino acids that will make up the protein and contain no interrupting stop codons

132
Q

what other sequence motifs can be identified in sequenced DNA?

A

binding sites for the transcription factors that regulate gene expression

133
Q

where are these transcription factors located?

A

upstream, downstream or within introns of a gene

134
Q

how can some sequence motifs be identified?

A

from the hypothetical RNA molecule that is inferred from the sequenced DNA molecule

135
Q

RNA sequences that makes up a transfer RNA (tRNA) molecules forms what?

A

characteristic hairpin structures - molecule folds back on itself and undergoes complementary base pairing within the molecule itself

136
Q

how can these sequences be inferred from a DNA molecule?

A

by looking for nearby complementary sequences within the sequence

137
Q

do exons and regulatory elements that code for proteins make up a large or small portion of the genome?

A

small

138
Q

what do most of the prokaryotic genomes consist of?

A

genes

139
Q

what does 50% of the average eukaryotic genome consist of?

A

repeated sequences that do not code for functional gene products

140
Q

what were these non-coding repeated sequences originally believed to be?

A

unimportant/”junk DNA” although may have been found to have their own functions

141
Q

are there regions in the eukaryotic genome that encodes noncoding RNA as well as many types of repeated, noncoding sequences?

A

yes

142
Q

how do these sequences compare in different individuals?

A

vary from individual to individual and especially across species

143
Q

what does this contribute to?

A

the diversity that we can observe across different organisms

Biology 1A03 (5 decks)

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