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Molecular Biology Lecture > 5: Mutation and Detection > Flashcards

5: Mutation and Detection Flashcards

1
Q

Mutation or Polymorphism

A single gene locus causing mutation has a major physiologic impact and considered to be deterministic of a disease

A

Mutation

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2
Q

Mutation or Polymorphism

Seen less commonly in general population.

A

Mutation

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3
Q

Mutation or Polymorphism

Linked to Mendelian disease.

A

Mutation

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4
Q

Mutation or Polymorphism

Correlation on between mutation and disease can be established.

A

Mutation

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5
Q

Mutation or Polymorphism

Single base pair change in nucleotide sequence of genes are called point mutation.

A

Mutation

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6
Q

Mutation or Polymorphism

Genetic alteration that contributes to complex disease has smaller effect.

A

Polymorphism

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7
Q

Mutation or Polymorphism

Present in at least 1% of the population

A

Polymorphism

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8
Q

Mutation or Polymorphism

No correlation between mutation and disease

A

Polymorphism

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9
Q

Mutation or Polymorphism

Single base pair change in nucleotide sequence of genes

A

Polymorphism

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10
Q

In mutation, single base pair change is called?

A

point mutation.

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11
Q

In polymorphism, single base pair change is called?

A

single nucleotide polymorphism (SNP)

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12
Q

What are the types of base pair mutation?

A
  1. Transition
  2. Transversion
  3. Deletion
  4. Insertion
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13
Q

Type of base pair mutation:

T-A to C-G; pyrimidine to pyrimidine or purine to purine

A

Transition

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14
Q

Type of base pair mutation:

CATCCACCTGTACCA
GTAGGTGGACATGGT

[normal sequence:
CATTCACCTGTACCA
GTAAGTGGACATGGT]

A

Transition

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15
Q

Type of base pair mutation:

T – A to G – C; pyrimidine to purine

[normal sequence: CATTCACCTGTACCA GTAAGTGGACATGGT]

A

Transversion

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16
Q

Type of base pair mutation:

can involve more than one base pair

CATGACCTGTGCCA
GTACTGGACACGGT

[normal sequence:
CATTCACCTGTACCA
GTAAGTGGACATGGT]

A

Deletion

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17
Q

Type of base pair mutation:

can involve more than one base pair

CATCACCTGTACCA
GTAGTGGACATGGT

[normal sequence:
CATTCACCTGTACCA
GTAAGTGGACATGGT]

A

Insertion

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18
Q

What are the two types of mutation?

A
  1. Spontaneous mutation
  2. Induced mutation
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19
Q

Type of mutation:

Internal and cannot be controlled

A

Spontaneous mutation

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20
Q

What are the types of SPONTANEOUS MUTATION?

A

Hydrolytic reaction, Replication error

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21
Q

types of SPONTANEOUS MUTATION:

Hydrolysis occurs within part of base pair

A

Hydrolytic reaction

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22
Q

types of SPONTANEOUS MUTATION:

tautomer formation

A

Replication error

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23
Q

Replication error:

C-G→C-G and C-G

A

normal replication of C-G should result to two daughter strands of C-G

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24
Q

Replication error:

C-G→C-A and C-G

A

tautomer formation results in mispairing and insertion of A

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25
Q

Type of mutation:

external and controllable

A

Induced Mutation

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26
Q

What are the 3 examples of INDUCED MUTATION?

A
  1. UVL
  2. Ionizing radiation
  3. Chemical mutagen
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27
Q

Example of Induced mutation:

Formation of thymine dimer by UV light

A

UVL

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28
Q

Example of Induced mutation:

X rays, ɣ rays (gamma rays), and β particles which can significantly damage our DNA.

A

Ionizing radiation

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29
Q

Example of Induced mutation:

deamination of nitrous acid

A

Chemical mutagen

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30
Q

What happens when chemical mutagen occurs in Cytosine?

A
  1. Cytosine is deaminated to uracil
  2. Uracil binds with Adenine
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31
Q

What happens when chemical mutagen occurs in Adenine?

A
  1. Adenine is deaminated to Hypoxanthine
  2. Cytosine binds with Hypoxanthine
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32
Q

→ Also known as SNP.

→ read as “snip”

→ a change in a single nucleotide in the genome
that causes variations in DNA sequences between members of the same species.

→ occurs when two individuals in the population differ by a single base in the DNA sequence.

→ lighter burden

A

Single Nucleotide Polymorphism

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33
Q

Factors to consider in polymorphism?

A

→ Present in more than 1% of the population

→ other wise, Variation is a rare mutation

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34
Q

T or F

Single Nucleotide Polymorphism is not normal and when you have it you should get checked

A

F (its normal bb)

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35
Q

T or F

Single Nucleotide Polymorphism occurs normally throughout a person’s DNA (3 X 10^9 bp).

A

T

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36
Q

T or F

Single Nucleotide Polymorphism commonly found in the DNA between genes.

A

T

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37
Q

How many Single Nucleotide Polymorphism is in a person’s entire genome?

A

4 - 5 M SNPs

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38
Q

T or F

SNP is present almost once in every 5,000 nucleotides

A

F (almost once in every 1,000 NUCLEOTIDES)

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39
Q

T or F

SNP can be caused by induced mutation over time

A

F (caused by SPONTANEOUS MUTATION)

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40
Q

Importance of SNP?

A

→ important in studying human health

→ may predict individuals’ response to drugs, susceptibility to environmental factor, risk to a particular disease, association with complex disease

→ track inheritance of disease (pedigree)

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41
Q

What does not belong?

a. SNP occurs normally throughout a person’s DNA (3 X 10^9 bp)

b. caused by spontaneous mutation over time

c. track inheritance of disease

d. ALL of the aboce

e. NOTA

A

c. track inheritance of disease (c is importance of SNP; other choices answers the question is SNP normal)

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42
Q

Single Nucleotide Polymorphism Facts?

A

→ act as biological markers

→ occurs within a gene that is described as having more than one allele.

→ May lead to variations in amino acid sequence

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43
Q

3 types of genetic disorders

A
  1. Single Gene Disorder
  2. Multifactorial Disorders
  3. Chromosomal Disorder
44
Q

Genetic Disorder:

caused by a single gene, several different mutations can result in the same disease but with varying degrees of severity and phenotype.

A

Single Gene Disorder

45
Q

Genetic Disorder:

main factor is genes, but the cause includes other factors that aren’t genes.

A

Multifactorial Disorders

46
Q

Genetic Disorder:

abnormal chromosome number or constitution

A

Chromosomal Disorder

47
Q

Mutation Detection Techniques? Chromosomal

A
  1. Conventional Karyotyping
  2. Fluorescent in situ Hybridization (FISH)
  3. Spectral Karyotyping (SKY)
48
Q

Identify what mutation detection technique:

→ chromosome abnormality
→ indicative in: sexual disorders, congenital anomalies, developmental retardation, learning disabilities, infertility, multiple miscarriage, stillbirth, malignancy,

A

Conventional Karyotyping

49
Q

Identify what mutation detection technique:

→ provide specific localization of genes on chromosomes

→ indicative in: trisomy and microdeletion using specific probes

A

Fluorescent in situ Hybridization (FISH)

50
Q

Identify what mutation detection technique:

→ homologous pairs of chromosomes are manipulated in such a way that they have distinctive colors.

A

Spectral Karyotyping (SKY)

51
Q

Mutation Detection Techniques under molecular diagnostics?

A
  1. Hybridization Based
  2. Sequencing (Polymerization)
  3. Cleavage Based
52
Q

Under hybridization based molecular diagnostics, what are the methods of molecular diagnostic?

A
  1. Fluorescent in situ Hybridization (FISH)
  2. Allele-specific Oligonucleotide (ASO)
  3. Array-based Comparative Genomic
    Hybridization (aCGH)
  4. Array Technology
53
Q

Hybridization based molecular diagnostics method:

→ hybridization between the ssDNA and target gene with probe.

→ Can be applied in both chromosomal studies and molecular diagnostics.

A

Fluorescent in situ Hybridization (FISH)

54
Q

Hybridization based molecular diagnostics method:

→ “dot blot method”

→ relies on binding effects of nucleotide mismatches

→ stringent conditions are applied so that a single- base mismatch is sufficient to prevent hybridization of the non-matching probe

A

Allele-specific Oligonucleotide (ASO)

55
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

are applied so that a single- base mismatch is sufficient to prevent hybridization of the non-matching probe

A

Stringent conditions

56
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

How many probes does ASO require?

A

2 probes, one specific for each allele

57
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

+ probes is complimentary to what?

A

normal sequence

58
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

m probes is complimentary to what?

A

mutant sequence

59
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

What is the result for individual 1?

60
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

What is the result for individual 2?

[insert image]

A

Normal individual; since +/+ tapos may + probe lang may dot

61
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

What is the result for individual 3?

[insert image]

A

Presence of mutation; since sa may m probe lang may dot

62
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

What is the result for individual 2

[insert image 2]

A

Heterozygous individual; since +/-

63
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

What is the result for individual 2?

[insert image 2]

A

Heterozygous since tapos may dot sa both

64
Q

Hybridization based molecular diagnostics: Allele-specific Oligonucleotide (ASO)

what does m, +, N mean at the end of the photo?

[insert image 2]

A

controls

m - mutant control
+ - normal control
N - negative control

65
Q

Hybridization based molecular diagnostics method:

→ a special FISH technique (dual probes)

→ detecting all genomic imbalances

→ comparison of total genomic DNA of given sample with total genomic DNA of normal cells

A

Array-based Comparative Genomic Hybridization (aCGH)

66
Q

Hybridization based molecular diagnostics: Array-based Comparative Genomic Hybridization (aCGH)

What are the steps?

A
  1. Identical amount of both tumor and normal DNA is labeled with two different fluorescent dyes and mixed (Put fluorophone)
  2. Mixture is added and hybridized to a normal lymphocyte metaphase slide.
  3. A fluorescent microscope is used for evaluation
67
Q

Hybridization based molecular diagnostics: Array-based Comparative Genomic Hybridization (aCGH)

How many fluorescent dyes are used?

A

2, 1 for each sample

68
Q

Hybridization based molecular diagnostics method:

Used to determine copy number alterations (if there are amplification or deletion) of genome in cancer and those cells whose karyotype is hard or impossible to prepare or analyze.

A

Array-based Comparative Genomic Hybridization (aCGH)

69
Q

Hybridization based molecular diagnostics: Array-based Comparative Genomic Hybridization (aCGH)

What color in the result means Tumor & Normal

70
Q

Hybridization based molecular diagnostics: Array-based Comparative Genomic Hybridization (aCGH)

What color in the result means Tumor & Tumor

71
Q

Hybridization based molecular diagnostics: Array-based Comparative Genomic Hybridization (aCGH)

What color in the result means Normal & Normal

72
Q

Hybridization based molecular diagnostics method:

→ reverse dot blot method (based on matching)

→ investigate multiple genomic sites.

→ unlabeled probes are bound to substrate

→ specimen DNA is labeled and hybridized to immobilized probes.

A

Array Technology

73
Q

Which does not belong in Array Technology

a. Detection
b. Method
c. Substrate
d. Enzyme
e. ALL of the above
f. NOTA

74
Q

How many methods are given in Array Technology

75
Q

Hybridization based molecular diagnostics: Array Technology

What are the methods under array tech?

A
  1. Microarray
  2. Macroarray
  3. High Density oligonucleotide arrays
  4. Microelectric arrays
  5. Comparative genomic hybridization
  6. Expression array
  7. SNP detection, mutation analysis, sequencing
76
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of Macroarray method?

A

Substrate: Nitrocellulose

Detection: Radioactive, Chemiluminescent, Chromogenic

77
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of Microarray method?

A

Substrate: Glass, Nitrocellulose on glass

Detection: Fluorescent

78
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of High Density Oligonucleotide array method?

A

Substrate: Glass

Detection: Fluorescent

79
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of Microelectronic arrays

A

Substrate: Electro grid

Detection: Fluorescent

80
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of Comparative Genomic Hybridization

A

Substrate: Micro and Macro array

Detection: Detection of genomic amplifications and deletions

81
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of Expression array

A

Substrate: Micro and Macro array

Detection: Detection of relative changes in gene expression

82
Q

Hybridization based molecular diagnostics: Array Technology

Substrate and Detection of SNP Detection, analysis, sequencing

A

Substrate: High Density Oligonucleotide Array

Detection: Detection of single- base differences in DNA

83
Q

Sequencing (polymerization) comprise of what methods

A
  1. DNA sequencing
  2. Allele specific PCR
84
Q

Sequencing (polymerization) method:

→ allows rapid detection of SNP or mutation.

→ less laborious

→ uses a chromatogram

A

DNA Sequencing

85
Q

Sequencing (polymerization) how many SNP are detected?

A

1 specific SNP

86
Q

Sequencing (polymerization) method: DNA Sequencing

What results are shown?

A

spikes as result

87
Q

Sequencing (polymerization) method:

→ application of PCR that allows the direct detection of any point mutation, single base changes or small deletions in human DNA

→ involves amplification of DNA with single nucleotide polymorphism (SNP)

→ uses SNP-specific primers

→ under stringent conditions PCR is less efficient in the presence of mismatch between the template and primer

→ Successful amplification with an SNP-specific primer signals the presence of the specific SNP in a sequence

A

Allele specific PCR

88
Q

Sequencing (polymerization) method: Allele specific PCR

T or F

The Allele specific PCR uses DNA probes

A

F (SNP-Specific primers)

89
Q

Sequencing (polymerization) method: Allele specific PCR

If a normal primer is used to normal allele, what is the result?

A

Amplification

90
Q

Sequencing (polymerization) method: Allele specific PCR

If a mutant primer is used to mutant allele, what is the result?

A

Amplification

91
Q

Sequencing (polymerization) method: Allele specific PCR

If a mutant primer is used to normal allele, what is the result?

A

No amplification

92
Q

Sequencing (polymerization) method: Allele specific PCR

If a normal primer is used to mutant allele, what is the result?

A

No amplification

93
Q

Sequencing (polymerization) method: Allele specific PCR

T or F

The primers are non-specific to the alleles in Allele specific PCR

A

F (primers are SPECIFIC)

94
Q

Cleavage based type of Mutation Detection Technique comprise of what method?

A

Restriction Fragment Length Polymorphism (RFLP)

95
Q

Cleavage-based:

→ a technique that is used to study genetic variation or polymorphisms among individuals using restriction enzymes.

→ any genomic DNA can be
differentiated according to the presence or absence of restriction enzyme sites.

A

Restriction Fragment Length Polymorphism (RFLP)

96
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

T or F

Restriction enzymes recognize and cut at a random site.

A

F (recognize and cut at PARTICULAR SITE)

97
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

Steps?

A
  1. Restriction Digest
  2. Electrophoresis
  3. Denaturation
  4. Blotting
  5. Baking and Blocking
  6. Probe hybridization and visualization
98
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

What gel is used in electrophoresis?

A

Agarose or Polyacrylamide

99
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

What reagent is used in denaturation?

100
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

What blotting and membrane is used in blotting?

A

Souther blotting, Nitrocellulose paper

101
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

What procedures are done for baking and blocking?

A

Autoclave, Bovine Serum Albumin or Casein

102
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

This is put in baking and blocking step in order to fix DNA

A

Autoclaving

103
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

process that prevents binding of labelled probe non-specifically to charged membrane

104
Q

Cleavage-based: Restriction Fragment Length Polymorphism (RFLP)

What is used in probe hybridization and Visualization

A

labelled RFLP probe, autoradiography

105
Q

Application of Restrction Fragment Length Polymorphism?

A
  1. Crime scene
  2. Paternity
  3. Diseases

Molecular Biology Lecture (17 decks)

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