Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

[MT 6319] Molecular Biology & Diagnostics Laboratory > [2S] UNIT 5 Characterization of Nucleic Acid > Flashcards

[2S] UNIT 5 Characterization of Nucleic Acid Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

Degrade DNA molecules by breaking the phosphodiester bonds that link one nucleotide to the next in a DNA strand.

A

Nucleases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

NUCLEASES SPECIFICITY

Specific for DNA

A

DNAse

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

NUCLEASES SPECIFICITY

  • Targets RNA
  • Degrades all RNA
A

RNAse

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

NUCLEASES SPECIFICITY

  • Able to cleave DNA and RNA hybrid
  • Subtype of RNase
A

RNAse H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

NUCLEASES SPECIFICITY

Degrades RNA bound covalently to DNA

A

RNAse H

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

When a nuclease hydrolyzes an ester bond in a phosphodiester linkage, it will have a specificity for either of the two ester bonds. This generates what nucleotides?

A

5’ nucleotides or 3’ nucleotides.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

For single strand molecules (RNA), ______ can rapidly degrade RNA molecules into ribonucleotide subunits.

A

ribonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

TWO TYPES OF NUCLEASE

Hydrolyze internal bonds within a polynucleotide chain

A

Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

TWO TYPES OF NUCLEASE

● Cut the length of the DNA sequence
● Break internal phosphodiester bonds

A

Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

TWO TYPES OF NUCLEASE

Cut at any point depending on its target site
○ Usually in the middle portion of the fragment
○ Between the 5’ and 3’ terminus

A

Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

TWO TYPES OF NUCLEASE

Produce several segments of our polynucleotide

A

Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

TWO TYPES OF NUCLEASE

Target and remove the terminal nucleotide

A

Exonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

TWO TYPES OF NUCLEASE

Removes nucleotides one at a time from the end of a DNA molecule

A

Exonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

TWO TYPES OF NUCLEASE

Cuts the terminal nucleotide whether it is on the 5’ or 3’ (only at the end of the fragment)

A

Exonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Removes nucleotides from both strands of a double-stranded molecule

A

Bal31

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Progressive shortening of the dsDNA from both ends after treatment

A

Bal31

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

MECHANISM OF NUCLEASE HYDROLYSIS

● Removes nucleotides from the 3’ terminus
● Can only cut through double strands

A

Exonuclease III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Cleaves only single-stranded DNA, including single-stranded nicks in mainly double-stranded molecules

A

S1 Nuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Can only cut single strands nucleotides
○ Create a nick in our double stranded nucleotide
○ Cannot entirely cut the sequence (double
stranded)

A

S1 Nuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Refers to a specific type of discontinuity

A

Nick

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

MECHANISM OF NUCLEASE HYDROLYSIS

You need another digestion for that exposed single strand to fully cut the segment
○ However, if your DNA is single stranded, it
can entirely create fragments

A

S1 Nuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Cleaves both single and double-stranded DNA

A

DNAse I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Depending on which part it attaches to or targets
○ Can cleave segments or several segments

A

DNAse I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Produce mononucleotide

A

DNAse I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Non-specific nuclease (can cut phosphodiester bond)

A

DNAse I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

MECHANISM OF NUCLEASE HYDROLYSIS

Enables to characterize nucleic acid sequences if it contains the specific sequence

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

MECHANISM OF NUCLEASE HYDROLYSIS

● Very much utilized
● Can recognize and cut specific nucleotide sequence
○ Can cleave DNA molecules internally

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

ENDONUCLEASES FOR CUTTING DNA

It was shown that some strains of bacteria are immune to bacteriophage infection
○ Host defense mechanism

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

ENDONUCLEASES FOR CUTTING DNA

T/F: Initial observation that led to the eventual discovery of restriction endonucleases was made in the early 1960s

A

F; 1950s

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

ENDONUCLEASES FOR CUTTING DNA

Restriction endonuclease are found only in?

A

Microorganisms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

ENDONUCLEASES FOR CUTTING DNA

Occurs because bacterium produces an
enzyme that degrades the phage DNA before it has time to replicate and direct synthesis of new phage particles

A

Restriction

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

ENDONUCLEASES FOR CUTTING DNA

Degradative enzyme is called _______ _________ synthesized by many species of bacteria

A

restriction endonucleases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

ENDONUCLEASES FOR CUTTING DNA

T/F: Bacterium’s DNA carries additional methyl groups that protect and prevent the degradative enzyme action

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

ENDONUCLEASES FOR CUTTING DNA

T/F: Roughly round 2000 distinct restriction enzymes have been identified in the bacteria

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

ENDONUCLEASES FOR CUTTING DNA

Function as homodimer; recognize symmetrical dsDNA (palindromes)

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

ENDONUCLEASES FOR CUTTING DNA

Utilized in the digestion of DNA molecules for hybridization procedures or in the direct identification of mutations

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

ENDONUCLEASES FOR CUTTING DNA

Recognize specific sequences of 4, 5, or 6 nucleotides

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

ENDONUCLEASES FOR CUTTING DNA

Cut by breaking the phosphodiester bond in both strands

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

ENDONUCLEASES FOR CUTTING DNA

T/F: Cutting genomic DNA with a RE results in many fragments of different sizes

A

T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

ENDONUCLEASES FOR CUTTING DNA

The smaller the recognition sequence the larger the number of fragments produced

A

Restriction Endonuclease

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

ENDONUCLEASES FOR CUTTING DNA

T/F: RE recognizes palindromes

A

T

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

ENDONUCLEASES FOR CUTTING DNA

Reads the same in both directions
○ Sequences directly opposite one another on opposite strands of the dsDNA molecule

A

Palindromes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

TYPES OF RESTRICTION ENDONUCLEASES

● Cleaves DNA at random sites far from its recognition sequence
● Non specific

A

Type I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

TYPES OF RESTRICTION ENDONUCLEASES

Cleaves DNA at defined positions close to or within its recognition sequence

A
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

TYPES OF RESTRICTION ENDONUCLEASES

● Most employed: due to where it cleaves unlike types I and III which have different target sites from their recognition sequences
● Most used
● More specific

A

Type II

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

TYPES OF RESTRICTION ENDONUCLEASES

Cleaves outside its recognition sequence with both REase and MTase enzymatic activities in the same protein

A

Type IIG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

TYPES OF RESTRICTION ENDONUCLEASES

Cleaves symmetric targets and cleavage sites

A

Type IIP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

TYPES OF RESTRICTION ENDONUCLEASES

Recognizes asymmetric sequences

A

Type IIS

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

TYPES OF RESTRICTION ENDONUCLEASES

Cleaves outside its recognition sequence and require two sequences in opposite orientations within the same DNA

A

Type III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

TYPES OF RESTRICTION ENDONUCLEASES

Cleaves modified (e.g. methylated) DNA

A

Type IV

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

T/F: RE can’t protect bacterial cell from phage infection

A

F; can protect

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

RESTRICTION ENDONUCLEASE (Type II)

Can recognize the palindromic GAATTC sequence (hexanucleotide)
○ Needs to be palindromic to the complementary or opposite strand

A

E.COLI RESTRICTION ENZYME I (ECORI)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

RESTRICTION ENDONUCLEASE (Type II)

Recognition Site of ECORI

A

Sequence

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

RESTRICTION ENDONUCLEASE (Type II)

Cleavage Site of ECORI

A

between the G and A (both sense and antisense strand)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

RESTRICTION ENDONUCLEASE (Type II)

Produces staggered or cohesive cut (sticky ends)

A

ECORI & PSTI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

RESTRICTION ENDONUCLEASE (Type II)

Overhang of ECORI
○ Left: Overhang at the bottom
○ Right: Overhang at the top

A

5’ Overhang

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

RESTRICTION ENDONUCLEASE (Type II)

Can recognize the palindromic CTGCAG sequence

A

PSTI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

RESTRICTION ENDONUCLEASE (Type II)

Obtained from Providencia stuartii

A

PSTI

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

RESTRICTION ENDONUCLEASE (Type II)

Cleavage Site of PSTI

A

between A and G (and the other
strand)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

RESTRICTION ENDONUCLEASE (Type II)

Overhang of PSTI

A

3’ Overhang

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

RESTRICTION ENDONUCLEASE (Type II)

Obtained from Arthrobacter luteus

A

ALUL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

RESTRICTION ENDONUCLEASE (Type II)

Can recognize the AGCT sequence (four palindromic nucleotide)

A

ALUL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

RESTRICTION ENDONUCLEASE (Type II)

Cleavage Site of ALUL

A

in between C and G (as well as for the
other strand)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

RESTRICTION ENDONUCLEASE (Type II)

Produces a blunt cut

A

ALUL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

RESTRICTION ENDONUCLEASE (Type II)

No cohesive ends and overhang are produced

A

ALUL

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

RESTRICTION ENZYMES

● Uneven cleavage
● 5’Overhaul

A

BamH1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

RESTRICTION ENZYMES

● Recognizes GGATCC
● Cutting in between two G’s
○ Cohesive or Sticky ends

A

BamH1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

RESTRICTION ENZYMES

DpnI, HaeIII

A

METHYLATION-SENSITIVE ENZYMES

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

RESTRICTION ENZYMES

BamHI, BG1II

A

ENZYMES GENERATING COMPATIBLE COHESIVE ENDS

62
Q

RESTRICTION ENZYMES

● Recognizes GGTACC
● Cutting in between two C’s
● 3’ Overhang

A

Kpnl

63
Q

RESTRICTION ENZYMES

● Recognizes GGCC
● Blunt Ends
● No Overhang

A

HaeIII

64
Q

RESTRICTION ENZYMES

produces staggered cut

A

BamHI, BG1II

65
Q

RESTRICTION ENZYMES

■ BamHI: GGATCC
■ BglII: AGATCT

A

ENZYMES GENERATING COMPATIBLE COHESIVE ENDS

66
Q

RESTRICTION ENZYMES

Produce compatible overhangs upon cutting

A

ENZYMES GENERATING COMPATIBLE COHESIVE ENDS

67
Q

RESTRICTION ENZYMES

Produced from Haemophilus spp.

A
67
Q

RESTRICTION ENZYMES

T/F: If a sequence is methylated, it is unable to cut

A

T

67
Q

RESTRICTION ENZYMES

○ ____: requires methylation to function
○ ____: inhibited by methylation

A

DpnI
HaeIII

68
Q

RESTRICTION ENZYMES

principle of bacteria preserving its own
DNA

A

Methylation

69
Q

RESTRICTION ENZYMES

When these nucleases were produced, this may be a response to the ___________
○ (Ex.) GATC (A is methylated)

A

methylation

70
Q

RESTRICTION ENZYMES

T/F: All of the restriction endonucleases requires methylated nucleotides

A

F; some not all

71
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

Recognize and cut DNA at the same site or palindromic sequence but cuts differently

A

Isoschizomers

72
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

○ BspEI from a Bacillus species
○ AccIII: Acinetobacter calcoaceticus

A

Isoschizomers

72
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

SmaI, XmaI
○ (Ex.) CCC|GGG producing blunt ends ( | as blunt end) in Smal
○ (Ex.) XmaI targeting the same recognition site

A

Isoschizomers

73
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

Recognize and bind to the same sequence of DNA but cleave at different position

A

Neoschizomers

74
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

○ NarI: Nocardia argentinensis
○ SfoI: Serratia fonticola

A

Neoschizomers

74
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

Different single stranded extensions

A

Neoschizomers

75
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

Restriction endonucleases that have the same nucleotide extensions (or overhangs) but have different recognition sites

A

Isocaudomers

76
Q

DIFFERENT SOURCES OF TYPE II RESTRICTION ENDONUCLEASES

○ NcoI: Nocardia corallina
○ PagI: Pseudomonas alcaligenes

A

Isocaudomers

77
Q

Governs the sequence of recognition

A

Restriction-Modification System / (R-M) System

78
Q

Each endonuclease has its own pair of methylase

A

Restriction-Modification System / (R-M) System

79
Q

○ Protective mechanism of bacteria for preventing its own DNA from being cut or degraded by its own restriction enzymes
○ Important during replication

A

Restriction-Modification System / (R-M) System

80
Q

RESTRICTION-MODIFICATION SYSTEM

Which strand is methylated?

A

Parent Strand

81
Q

RESTRICTION-MODIFICATION SYSTEM

T/F: Almost all restriction endonucleases are paired with methylases that recognize and methylate the same DNA sites

A

T

82
Q

THE FREQUENCY OF RECOGNITION SEQUENCES IN A DNA MOLECULE

Can be performed in a microcentrifuge tube
in the presence of all necessary components including:
■ Template DNA
■ Restriction enzyme
■ Mg2+ at the right conditions

A

Restriction Digest

82
Q

Both restriction endonucleases and methylases are collectively called a _________

A

Restriction-Modification System / (R-M) System

83
Q

ANALYSIS OF RESTRICTION DIGESTED FRAGMENTS

T/F: RD results in a number of DNA fragments. Sizes depend on the exact positions of the recognition sequences for the endonuclease in the original molecule and can be analyzed by gel electrophoresis

A

T

83
Q

Enzymes synthesizing a new strand of DNA complementary to an existing DNA or RNA template

A

Polymerases

84
Q

Most function only if the template possesses a double-stranded region that acts as a primer for initiation of polymerization.

A

Polymerases

85
Q

POLYMERASES

Prepared from E. coli

A

DNA Pol I

86
Q

POLYMERASES

DNA polymerase activity: attach to a short
single-stranded region (or nick) in a mainly double stranded DNA molecule (synthesizes a completely new strand)

A

DNA Pol I

87
Q

POLYMERASES

Exonuclease activity
○ 3’-5’: proofreading newly synthesized DNA
○ 5’-3’: degrade a strand / remove and replace strand

A

DNA Pol I

88
Q

POLYMERASES

DNA polymerization and DNA degradation

A

DNA Pol I

89
Q

POLYMERASES

● Large fragment
○ 3’- 5’ exonuclease activity and no 5’-3’ exonuclease activity
● Small fragment
○ 5’-3’ exonuclease activity

A

Klenow Fragment

90
Q

POLYMERASES

Synthesize a complementary DNA strand
(nick region)

A

Klenow Fragment

91
Q

POLYMERASES

DNA end-filling or DNA sequencing

A

Klenow Fragment

92
Q

POLYMERASES

Used in the PCR as the DNA polymerase I enzyme of the bacterium Thermus aquaticus

A

Taq DNA Pol

93
Q

POLYMERASES

Thermostable: resistant to denaturation by heat
○ Suitable for PCR: -94° C (denature the DNA)
○ Resistant to denaturation by heat treatment

A

Taq DNA Pol

94
Q

POLYMERASES

Would not be inactivated when the temperature of the reaction was raised to 94° C to denature the DNA

A

Taq DNA Pol

95
Q

POLYMERASES

● Replication of virus
○ Uses RNA as a template not DNA
○ Synthesize complementary DNA (cDNA)

A

Reverse Transcriptase

96
Q

POLYMERASES

● Evaluate the amount of RNA
● Establish the expression profile
● Change in gene expression pattern

A

Reverse Transcriptase

97
Q

NUCLEIC ACID MODIFYING ENZYMES

Numerous enzymes modify DNA molecules by addition or removal of specific chemical groups

A

DNA Modifying Enzymes

98
Q

NUCLEIC ACID MODIFYING ENZYMES

Repair single-stranded breaks (discontinuities)
○ Arise in double-stranded DNA molecules
during DNA replication or during DNA damage repair

A

DNA Ligase

99
Q

NUCLEIC ACID MODIFYING ENZYMES

Can also join together two individual fragments of double-stranded DNA

A

DNA Ligase

100
Q

NUCLEIC ACID MODIFYING ENZYMES

Catalyses formation of bonds between 5’-P and 3’-OH groups on backbone of DNA

A

DNA Ligase

101
Q

NUCLEIC ACID MODIFYING ENZYMES

● Ligate “blunt end” or “sticky ends”
● Repair “nicks” in DNA

A

DNA Ligase

102
Q

NUCLEIC ACID MODIFYING ENZYMES

Require primers to extend and copy DNA

A

DNA Polymerase

103
Q

NUCLEIC ACID MODIFYING ENZYMES

● All extend 5’→3’ by adding on to 3’-OH
● Make a reverse, complimentary copy

A

DNA Polymerase

104
Q

NUCLEIC ACID MODIFYING ENZYMES

T/F: Two Reactions Catalyzed by DNA Ligase

1) DNA ligase repair of discontinuity. A missing phosphodiester bond in one strand of a double-stranded molecule
2) DNA ligase joining molecules

A

T

105
Q

NUCLEIC ACID MODIFYING ENZYMES

Cut DNA in non-sequence specific manner

A

Nucleases - Exonucleases

106
Q

NUCLEIC ACID MODIFYING ENZYMES

Can digest DNA from either 5’-3’ or 3’-5’ direction

A

Nucleases - Exonucleases

106
Q

NUCLEIC ACID MODIFYING ENZYMES

● Prefer ssDNA
● Proofreading function of polymerase Alkaline phosphatase

A

Nucleases - Exonucleases

107
Q

NUCLEIC ACID MODIFYING ENZYMES

Removes 5’ P: prevents recircularization of plasmids

A

Alkaline Phosphate

108
Q

NUCLEIC ACID MODIFYING ENZYMES

Phosphatases (dephosphorylate 5’-terminus of DNA molecule)

A

Alkaline Phosphate

109
Q

NUCLEIC ACID MODIFYING ENZYMES

● Digest DNA molecules: non-specifically digests dsDNA or ss DNA
● Commonly found on most surfaces, including hands

A

DNAse

110
Q

NUCLEIC ACID MODIFYING ENZYMES

digest RNA molecule

A

RNAse: Ribonuclease

111
Q

NUCLEIC ACID MODIFYING ENZYMES

● Many different types, may be specific for ssRNA or RNA/DNA hybrids (RNAse H)
● Extremely common (especially on hands), very stable

A

RNAse

112
Q

THE APPLICATION OF NUCLEIC ACID HYBRIDIZATION

Formation of hydrogen bonds between
two complementary strands of nucleic acids

A

Hybridization

113
Q

THE APPLICATION OF NUCLEIC ACID HYBRIDIZATION

T/F: Binding between separate, complementary nucleic acids is both irreversible and base sequence-specific

A

F; reversible

113
Q

THE APPLICATION OF NUCLEIC ACID HYBRIDIZATION

Direct consequence of the stable
double-stranded structure of nucleic acid
under physiological conditions

A

Hybridization

114
Q

THE APPLICATION OF NUCLEIC ACID HYBRIDIZATION

T/F: During the annealing process, both nucleic acid strands are not labeled with any isotopes or fluorescence

A

T

115
Q

THE APPLICATION OF NUCLEIC ACID HYBRIDIZATION

● Probe: labeled strand
● Process of labeling: hybridization
○ Hybrid molecule: formed between a labeled and unlabeled strand
● Hybridization assay: used to analyze the nucleic acid content of an unknown sample

A

Hybridization

116
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Detection of a given DNA sequence in a complex mixture of DNA sequences

A

Southern Hybridization

117
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Identify homologous sequences in genomic DNA

A

Southern Hybridization

117
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Facilitate gene mapping through restriction mapping of genes

A

Southern Hybridization

118
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Detect of restriction fragment length polymorphisms

A

Southern Hybridization

119
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Northern Blot Denaturing, Staining & Electrophoretic

A

Northern Hybridization

120
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Technique used to study gene expression by detecting specific RNA sequences

A

Northern Hybridization

121
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

The availability of a variety of restriction endonuclease enzymes that cleave DNA at specific sites has made it possible to identify the presence of polymorphic regions in the isolated fragments

A

Restriction Fragment Length Polymorphism (RFLP)

121
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

● In DNA fingerprinting
● In paternity testing

A

Restriction Fragment Length Polymorphism (RFLP)

122
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

T/F: RFLP as a molecular marker is specific to a single clone / restriction enzyme combination

A

T

122
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Results from a variable number of tandem repeats (VNTR) in a short DNA segment

A

Restriction Fragment Length Polymorphism (RFLP)

123
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

  1. Genomic DNA collected
  2. Digested with a specific restriction enzyme
  3. Gel electrophoresis
  4. Southern blot analysis
A

RFLP Analysis

124
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

● Genetic disease marker
● Closeness to the disease gene
● Sufficient DNA

A

Restriction Fragment Length Polymorphism (RFLP)

125
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Cleaved amplified polymorphic sequence (CAPS) assay

A

Restriction Fragment Length Polymorphism (RFLP)

126
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

● Fingerprinting technique
● Permits the simultaneous evaluation of different DNA regions distributed randomly throughout the genome without prior sequence knowledge

A

Amplified Fragment Length Polymorphism (AFLP)

127
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Useful in non-model species which have no complete genome sequences available and where other types of genome-wide markers are difficult to obtain

A

Amplified Fragment Length Polymorphism (AFLP)

128
Q

DETECTION METHODS

Labeled, denatured single-strand
○ Label: radioactive or other type of marker
○ Denatured by heating
○ Applied to the membrane

A

Probe

128
Q

DETECTION METHODS

● Hybridizes to membrane-bound DNA or RNA
● Promote nucleic acid hybridization

A

Probe

128
Q

TYPES OF NUCLEIC ACID HYBRIDIZATION

Is highly reproducible and robust because it combines the specificity of RFLP with the sensitivity of the PCR

A

Amplified Fragment Length Polymorphism (AFLP)

129
Q

DETECTION METHODS

Shows unique blotting pattern characteristic of a specific genotype at a specific locus

A

RFLP Probe

129
Q

DETECTION METHODS

● Labeled DNA sequence
● Hybridizes with fragments of the digested DNA sample after gel electrophoresis

A

RFLP Probe

130
Q

DETECTION METHODS

Typically short, single- or low-copy genomic DNA or cDNA clones

A

RFLP Probe

131
Q

DETECTION METHODS

Used in genome mapping and variation analysis

A

RFLP Probe

132
Q

DETECTION METHODS

DNA molecule is usually labeled by incorporating nucleotides that carry a radioactive isotope of phosphorus, 32P

A

Labeling With a Radioactive Marker

133
Q

DETECTION METHODS

This reaction requires a supply of nucleotides, one of which is radioactively labeled with 32P-modified deoxynucleoside triphosphate

A

Labeling With a Radioactive Marker

133
Q

4 Detection Methods

A
  • Probe
  • RFLP Probe
  • Labeling With a Radioactive Marker
  • Labeling With a Nonradioactive Marker
133
Q

DETECTION METHODS

During the synthesis, the DNA molecule will become labeled as the radiolabeled deoxynucleotides are attached to the newly synthesized strand

A

Labeling With a Radioactive Marker

134
Q

DETECTION METHODS

Probe DNA is complexed with the enzyme horseradish peroxidase

A

Nonradioactive hybridization probing

135
Q

DETECTION METHODS

Deoxyuridine triphosphate (dUTP) nucleotides modified by reaction with biotin

A

Labeling With a Nonradioactive Marker

136
Q

DETECTION METHODS: Labeling With a Nonradioactive Marker

An organic molecule that has a high affinity for a protein called avidin

A

Biotin

137
Q

Reverse dot/slot blot of several thousand targets on nitrocellulose or nylon membranes

A

Macroarrays

137
Q

Sample does not pass through gel electrophoresis, samples are instead directly applied onto your membrane: Arrangements include:
● Dot Blot and Slot Blot Hybridization
● Macroarrays
● Microarrays
● Microarray-Manufacturing Technology
● Sample Processing and Detection

A

Array-Based Hybridization

138
Q

● Visualized without magnification
● Typically use radioactive or chemiluminescent signals

A

Macroarrays

139
Q

Probes deposited onto the membrane by printing or dot blotting, then dried and stored for future use

A

Macroarrays

140
Q

Limitations:
- area of the membrane
- specimen requirement

A

Macroarrays

141
Q

Variation of the dot/slot blot iarranged in a regular gridlike pattern

A

Microarrays

142
Q

● Microarray - delivery
● GeneChips - synthesis

A

Microarrays

143
Q

The most common application of ______ technology is transcript profiling

A

Microarrays

144
Q

Most critical in sample processing & detection

A

Isolation of mRNA from cells or tissues

145
Q

Sample Processing and Detection

Surface plasma resonance

A

Unlabeled Probes

[MT 6319] Molecular Biology & Diagnostics Laboratory (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions