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bms2062 > From Genotype to Phenotype > Flashcards

From Genotype to Phenotype Flashcards

1
Q

Define

Single nucleotide polymorphism (SNP)

A

a DNA sequence variation occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (G]) in the genome (or other shared sequence) differs between members of a species or paired chromosomes in an individual

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2
Q

Definition

a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity

A

CRISPR/Cas

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3
Q

How do SNP arrays work?

A
  • A “gene chip” contains thousands of spots, each containing single-stranded 25 base reference DNA molecules (oligonucleotides)
  • Each reference DNA is complementary to an SNP allele
  • Oligonucleotides are printed onto the chip, or synthesised directly on it
  • Genomic DNA to be tested is fragmented, amplified as a single strand, labelled, then put on the chip
  • Binding conditinos favour perfet matching between probe DNA and chip DNA
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4
Q

What three major classes of RNAs make up the eukaryotic transcriptome?

A
  • Ribosomal RNAs (rRNA)
  • Protein-encoding RNAs (mRNA)
  • Small RNAs (including tRNA)
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5
Q

Define

Polymorphism

A

a DNA variation present in more than 1% of people

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6
Q

Definition

a molecular biology term for an insertion or deletion of bases in the genome of an organism

A

INDELs

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7
Q

Define

Haplotype

A

the unique combination of alleles that makes up an individual

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8
Q

Define

Orthologues

A

Any of two or more homologous gene sequences found in different species related by linear descent

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9
Q

Define

Complementary DNA (cDNA)

A

DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA) template in a reaction catalyzed by the enzyme reverse transcriptase

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10
Q

How does silencing gene expression through RNAi work?

A
  • dsRNA is formed in the cytoplasm
  • dsRNA is cleaved into 21-23 nt short interfering (si)RNA duplexes by Dicer enzyme
  • siRNAs are incorporated into multiprotein RNA-inducing silencing complex (RISC)
  • siRNA is unwound - antisense strand remains associated with RISC and base-pairs with target mRNA
  • RISC cleaves and inactivates target mRNA. Expression is reduced but not completely abolished
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11
Q

Define

Allele

A

an alternative form of a genetic locus

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12
Q

Why is gene identification in eukaryotic genomes more difficult than gene identification in prokaryotes?

A
  • Density of genes varies
    • Genes are concentrated in G/C rich areas of the genome
    • < 2% of human genome encodes protein or ncRNA
    • ~25% of human genome is regulatory/introns
    • Rest of the genome is scaffolding or “junk DNA”
  • Promotor sequences are not easily recognisable
    • Regulatory factors bind enhancers far form the transcription initiation site
  • Most genes are interrupted (introns)
    • Exons (ORFs) can be very small (< 600 codons)
    • Particular exons do not always appear in mRNA (alternative splicing)
  • Some genes encode microRNAs (small and not translated)
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13
Q

True or False:

Each EST only contains exons

A

True

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14
Q

Define

Isoforms

A

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed

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15
Q
A
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16
Q

Most RNA is highly susceptible to _____________, so it is very difficult to purify and maintain an RNA molecule in an intact state

A

Most RNA is highly susceptible to nucleases, so it is very difficult to purify and maintain an RNA molecule in an intact state

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17
Q

Definition

Any of two or more homologous gene sequences found in different species related by linear descent

A

Orthologues

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18
Q

What do we need to know about each gene? How do we obtain this information?

A

For each gene we need to know:

  • Where and when it is transcribed into RNA
  • How it is spliced, and how many spliceoforms there are
  • Whether particular spliceoforms are restricted to particular cells or growth stage

This information cannot be directly deduced from genomic sequence with confidence. We rely on analysis of complementary DNA (cDNA) and Expression Sequence Tages (ESTs), derived from RNA.

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19
Q

Definition

an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism

A

Forward genetics

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20
Q

Definition

the polymerase that only transcribes ribosomal RNA (but not 5S rRNA), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell

A

RNA polymerase I

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21
Q

________ genetic analysis can be applied to specifically mutate the gene in question

A

Reverse genetic analysis can be applied to specifically mutate the gene in question

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22
Q

Definition

the complete collection of RNA produced from a genome

A

Transcriptome

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23
Q

True or False:

Each EST is a small segment of mRNA generated by reverse transcriptase

A

False

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24
Q

What can be concluded if a DNA sequence from a genome matches exactly to a specific EST?

A

It can be concluded that the genomic DNA is transcribed and that it represents a gene (or gene fragment)

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25
Q

What is the first step to understanding gene function?

A

Determine where and when the gene is expressed

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26
Q

Definition

short sub-sequence of a cDNA sequence. They may be used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination

A

Expression sequence tags (ESTs)

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27
Q

True or False:

Each EST has a 5’ end matching the transciptional start point of its gene

A

False

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28
Q

Definition

the study of thousands of RNAs, simultaneously

A

Transcriptomics

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29
Q

Definition

the general concept of aiming for high number of unique reads of each region of a sequence

A

Deep sequencing

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30
Q

Definition

the occurrence in members of a population of combinations of linked genes in non-random proportions

A

Linkage disequilibrium

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31
Q

90% of human genome variation is in the form of _____

A

90% of human genome variation is in the form of SNPs

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32
Q

_________ are cDNAs made from mRNAs originating from a specific cell or tissue

A

ESTs are cDNAs made from mRNAs originating from a specific cell or tissue

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33
Q

What RNA polymerase transcribes rRNA?

A

RNA polymerase I

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34
Q

Definition

a multiprotein complex. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA

A

RNA polymerase II

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35
Q

Inter-species comparisons reveal segment boundaries, and _________ regions where orthologous genes are likely to be located

A

Inter-species comparisons reveal segment boundaries, and syntenic regions where orthologous genes are likely to be located

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36
Q

How is protein expression detected?

A
  • Antibodies or other binding reagent (cell/tissue structure can be maintained)
  • Enzyme activity (usually in cell or fluid extracts)
  • Mass spectrometry/proteomics (usually in cll or fluid extracts)
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37
Q

What do all mRNAs have at their 3’ ends?

A

A stretch of adenines

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38
Q

Define

RNA polymerase II

A

a multiprotein complex. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. It catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA

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39
Q

Define

Forward genetics

A

an approach used to identify genes (or set of genes) responsible for a particular phenotype of an organism

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40
Q

What are the advantages or CRISPR/Cas editing?

A
  • Can be used in any organism where IVF technology exists
  • CRISPR knockout mice can be generated in ~ 3-6 months, compared to 18 months for conventional mouse knockout
  • Both alleles can be mutated simultaneously to make homozygous deficient animals
  • Precise changes can be made
  • Up to five genes have been edited at once in mice
  • Can be adapted to global functioning genomic/network studies
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41
Q

Definition

transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs

A

RNA polymerase III

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42
Q

How is rRNA modified after transcription?

A

rRNAs are cut out from a longer precursor (pre-rRNA)

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43
Q

Definition

a DNA variation present in more than 1% of people

A

Polymorphism

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44
Q

Define

Expression sequence tags (ESTs)

A

short sub-sequence of a cDNA sequence. They may be used to identify gene transcripts, and are instrumental in gene discovery and in gene-sequence determination

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45
Q

Genomes from different species can be compared to identify _______ genes that lie in _________chromosomal regions

A

Genomes from different species can be compared to identify orthologous genes that lie in syntenic chromosomal regions

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46
Q

How many different mRNAs can be produced from this precursor if any splice donor can interact with any splice acceptor?

A

4

A-B-C-D

A-C-D

A-B-D

A-D

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47
Q

Predicting susceptibility profiles for broad range of disease or treatments for a particular individual requires what?

A
  1. A reference map of SNPs
  2. Developing rapid (and cheap) screening methods to map at least 10,000 of these SNPs in a patint
48
Q

What genetic information does SNP analysis not provide about an individual?

A

Variations not represented in SNP arrays, like INDELs and mobile elements

49
Q

Theoretically, a SNP could have ___ possible alleles, but most SNPs have only __ alleles

A

Theoretically, a SNP could have 4 possible alleles, but most SNPs have only 2 alleles

50
Q

What RNA polymerase transcribes mRNA?

A

RNA polymerase II

51
Q

How are false positives reduced in SNP arrays?

A

Each SNP position is represented by up to forty different but overlapping DNA sequences

52
Q

Define

RNA interference (RNAi)

A

a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules

53
Q

The number of clones containing the same EST in one library is proportional to what?

A

The transcriptional activity of the gene

54
Q

True or False:

The order of orthologous genes is conserved in syntenic blocks

A
55
Q

Definition

the branch of pharmacology concerned with the effect of genetic factors on reactions to drugs

A

Pharmacogenetics

56
Q

True or False:

ESTs will only match exons

A

True

57
Q

Definition

a laboratory mouse in which researchers have inactivated, or “knocked out,” an existing gene by replacing it or disrupting it with an artificial piece of DNA.

A

Knockout mice

58
Q

Define

RNA polymerase I

A

the polymerase that only transcribes ribosomal RNA (but not 5S rRNA), a type of RNA that accounts for over 50% of the total RNA synthesized in a cell

59
Q

Definition

a genomic technique for sequencing all of the protein-coding region of genes in a genome (known as the exome)

A

Whole exome sequencing (WES)

60
Q

The point at which an EST to genomic DNA match ends can indicate what?

A

An intro/exon boundary or transcriptional start/end point

61
Q

Define

Mutation

A

a sequence present in less than 0.1% of people

62
Q

True or False:

Each EST represents genes active in every cell

A

False

63
Q

Define

Whole exome sequencing (WES)

A

a genomic technique for sequencing all of the protein-coding region of genes in a genome (known as the exome)

64
Q

How does in situ hybridsation work?

A

Labelled DNA or RNA complementary to target mRNA is soaked into cell or tissue, treated to minimise disruption to structure.

Probe will bind specifically to the target mRNA and identify where it is being produced

65
Q

What enzyme allows DNA to be produced from RNA?

A
66
Q

Definition

the unique combination of alleles that makes up an individual

A

Haplotype

67
Q

Define

SNP microarrays

A

a type of DNA microarray which is used to detect polymorphisms within a population

68
Q

Definition

analyzes the phenotype of an organism following the disruption of a known gene

A

Reverse genetics

69
Q

Definition

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed

A

Isoforms

70
Q

How can transcripts from a single gene be assessed?

A

in situ hybridisation on intact cells or tissue

Reverse transcriptase PCR, and real time quantitative PCR

71
Q

Why are there different numbers of read for different parts of mRNA?

A

Alternative splicing removes exon 4 from some RNAS

72
Q

What accounts for the majority of human sequence variation?

A

SNPs

73
Q

Chromosomes recombine segments called ________ blocks

A

Chromosomes recombine segments called haplotype blocks

74
Q

Define

Reverse genetics

A

analyzes the phenotype of an organism following the disruption of a known gene

75
Q

Define

RNA polymerase III

A

transcribes DNA to synthesize ribosomal 5S rRNA, tRNA and other small RNAs

76
Q

Definition

a biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules

A

RNA interference (RNAi)

77
Q

Definition

either of a pair of genes that derives from the same ancestral gene. (genomics) a pair of genes that derives from the same ancestral gene and now reside at different locations within the same genome

A

Paralogues

78
Q

Definition

a sequence present in less than 0.1% of people

A

Mutation

79
Q

How does reverse transcriptase PCR work?

A
80
Q

What RNA polymerase transcribes small RNAs?

A

RNA polymerase III

81
Q

________ of the gene can be assessed in specific cells, most recently via deep sequencing analyisis

A

Transcription of the gene can be assessed in specific cells, most recently via deep sequencing analyisis

82
Q

Definition

a DNA sequence variation occurring when a single nucleotide adenine (A), thymine (T), cytosine (C), or guanine (G]) in the genome (or other shared sequence) differs between members of a species or paired chromosomes in an individual

A

Single nucleotide polymorphism (SNP)

83
Q

Definition

DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA) template in a reaction catalyzed by the enzyme reverse transcriptase

A

Complementary DNA (cDNA)

84
Q

Define

Paralogues

A

either of a pair of genes that derives from the same ancestral gene. (genomics) a pair of genes that derives from the same ancestral gene and now reside at different locations within the same genome

85
Q

Define

CRISPR/Cas

A

a prokaryotic immune system that confers resistance to foreign genetic elements such as those present within plasmids and phages that provides a form of acquired immunity

86
Q

In the older knockout mouse technology ________ are manipulated in the laboratory to mutate one ____ of the gene of interest, then the mutant cell are injected into a blastocyst, which is transferred into a foster mother. Resulting chimeric mice that can transmit the mutation to offspring become the founders of a knockout line, which can be examined for changes to ________

A

In the older knockout mouse technology embryonic stem cells are manipulated in the laboratory to mutate one allele of the gene of interest, then the mutant cell are injected into a blastocyst, which is transferred into a foster mother. Resulting chimeric mice that can transmit the mutation to offspring become the founders of a knockout line, which can be examined for changes to phenotype

87
Q
A
88
Q

Define

Alternative splicing

A

A mechanism by which different forms of mature mRNAs (messengers RNAs) are generated from the same gene

89
Q

Why can relatively few genes in the genome give rise to a vastly greater number of proteins?

A

Alternative splicing

90
Q

Define

Pharmacogenetics

A

the branch of pharmacology concerned with the effect of genetic factors on reactions to drugs

91
Q

Definition

DNA sequences that can move around the genome, changing their number of copies or simply changing their location, often affecting the activity of nearby genes

A

Mobile genetic elements

92
Q

How can transcripts from a many genes be assessed?

A

Microarray analysis

RNA deep sequencing

93
Q

Define

Transcriptomics

A

the study of thousands of RNAs, simultaneously

94
Q

Definition

an alternative form of a genetic locus

A

Allele

95
Q

Related but different polypetides can be generated from the same primary transcript through which process?

A

Alternative splicing

96
Q

Define

INDELs

A

a molecular biology term for an insertion or deletion of bases in the genome of an organism

97
Q

Define

Linkage disequilibrium

A

the occurrence in members of a population of combinations of linked genes in non-random proportions

98
Q

Define

Mobile genetic elements

A

DNA sequences that can move around the genome, changing their number of copies or simply changing their location, often affecting the activity of nearby genes

99
Q

What can you conclude about the abundance of this mRNA in the liver?

A

About 50% is alternatively spliced

100
Q

Define

Transcriptome

A

the complete collection of RNA produced from a genome

101
Q

What can make identifying orthologs difficult?

A
  • Orthologous genes may be on different chromosomes in different species
  • There may be a number of similar (paralogues) in the genome
102
Q

Definition

A mechanism by which different forms of mature mRNAs (messengers RNAs) are generated from the same gene

A

Alternative splicing

103
Q

Any two people picked at random show > 97% nucleotide identity in their genomes. How do variations arise?

A
  1. Large-scale or small-scale INDELs
  2. Differing numbers or positions of mobile genetic elements
  3. Single nucleotide polymorphisms (SNPs)
104
Q

Define

Knockout mice

A

a laboratory mouse in which researchers have inactivated, or “knocked out,” an existing gene by replacing it or disrupting it with an artificial piece of DNA.

105
Q

Splicing errors are a common result of mutation. How can they cause disease?

A
  • Mutations can occur in splice donor or acceptor sequences, or can generate new (cryptic) splice sequences
  • Exons can be ommited, deleting a section of protein, severly affecting structure
  • Use of false (cryptic) acceptor or donor sites can truncate or lengthen exons, severly affecting protein structure
106
Q

Define

Deep sequencing

A

the general concept of aiming for high number of unique reads of each region of a sequence

107
Q

Recently the CRISPR/Cas gene _______ system developed from bacteria has revolutionized _______ genetic analysis. This involved short _________ sequences that bind both the target DNA and ________ which makes a double strand break in the DNA. Repair of the break by the cell’s machinery often introduces a short __________ that mutates the gene

A

Recently the CRISPR/Cas gene editing system developed from bacteria has revolutionized reverse genetic analysis. This involved short RNA sequences that bind both the target DNA and endonuclease which makes a double strand break in the DNA. Repair of the break by the cell’s machinery often introduces a short deletion that mutates the gene

108
Q

Definition

a type of DNA microarray which is used to detect polymorphisms within a population

A

SNP microarrays

109
Q

Which of the following SNPs is most likely to alter gene expression?

Select one:

Synonymous SNPs

Nonsense SNPs

Missense SNPs

Non-coding region SNPs

A

Which of the following SNPs is most likely to alter gene expression?

Select one:

Synonymous SNPs

Nonsense SNPs

Missense SNPs

Non-coding region SNPs

110
Q

Forward genetics describes a process of discovery of the relationship between gene and phenotype…

Select one:

by comparing the function of corresponding genes in two species

by identifying the gene responsible for a particular phenotype

by specifically mutating a gene and analysing the resulting phenotype

by introducing a gene into cultured cells and analysing the resulting phenotype

A

Forward genetics describes a process of discovery of the relationship between gene and phenotype…

Select one:

by comparing the function of corresponding genes in two species

by identifying the gene responsible for a particular phenotype

by specifically mutating a gene and analysing the resulting phenotype

by introducing a gene into cultured cells and analysing the resulting phenotype

111
Q

Whole exome sequencing differs from whole genome sequencing in that…

Select one:

Whole exon sequencing focuses mostly on the protein coding regions of the genome

Whole exon sequencing focuses mostly on the non-coding regions of the genome

Whole exon sequencing focuses specifically on identifying indels and SNPs in individuals

Whole exon sequencing focuses specifically on identifying indels and SNPs in populations

A

Whole exome sequencing differs from whole genome sequencing in that…

Select one:

Whole exon sequencing focuses mostly on the protein coding regions of the genome

Whole exon sequencing focuses mostly on the non-coding regions of the genome

Whole exon sequencing focuses specifically on identifying indels and SNPs in individuals

Whole exon sequencing focuses specifically on identifying indels and SNPs in populations

112
Q

The transcriptome of a cell…

Select one:

represents the total nuclear and mitochondrial DNA content of the cell

represents all genes ever expressed in that cell

represents only the genes transcribed at the time of sampling

represents only mRNA

A

The transcriptome of a cell…

Select one:

represents the total nuclear and mitochondrial DNA content of the cell

represents all genes ever expressed in that cell

represents only the genes transcribed at the time of sampling

represents only mRNA

113
Q

One of the greatest advantages of RNA-sequencing over microarrays is that…

Select one:

RNA sequencing can identify SNPs

RNA sequencing can measure expression across every known gene

RNA sequencing is much faster

RNA sequencing can measure when genes are expressed

A

One of the greatest advantages of RNA-sequencing over microarrays is that…

Select one:

RNA sequencing can identify SNPs

RNA sequencing can measure expression across every known gene

RNA sequencing is much faster

RNA sequencing can measure when genes are expressed

114
Q

CpG islands usually mark regions of the genome where…

Select one:

transcription is occurring

transcription is silenced

replication is initiated

replication is terminated

A

CpG islands usually mark regions of the genome where…

Select one:

transcription is occurring

transcription is silenced

replication is initiated

replication is terminated

115
Q

Which of the following statements about single nucleotide polymorphisms (SNPs) is FALSE?

Select one:

SNPs are found in all sequenced mammalian genomes

SNPs are concentrated in CpG islands

SNPs are the greatest source of variation between individual genomes

SNPs may contribute to disease

A

Which of the following statements about single nucleotide polymorphisms (SNPs) is FALSE?

Select one:

SNPs are found in all sequenced mammalian genomes

SNPs are concentrated in CpG islands

SNPs are the greatest source of variation between individual genomes

SNPs may contribute to disease

116
Q

Sickle cell anaemia is an inherited blood disorder associated with a single nucleotide polymorphism (SNP) designated rs334 in the human beta globin (HBB) gene. Individuals with sickle cell anaemia are about the 10-fold more resistant to life-threatening forms of malaria. The most common allele is rs334(A), encoding the normal form of haemoglobin. Individuals homozygous for the rs334(T) allele exhibit the sickling form of hemoglobin, Hb-S.

Shown below are the maternal and paternal HBB gene sequences from 4 individuals being assessed for sickle cell anaemia with the SNP indicated in bold. The coding sequence commences at nucleotide position 25.

In terms of its effect on the HBB coding sequence the rs334(T) allele can be best described as…

Select one:

sense

nonsense

missense

antisense

A

In terms of its effect on the HBB coding sequence the rs334(T) allele can be best described as…

Select one:

sense

nonsense

missense

antisense

117
Q

Sickle cell anaemia is an inherited blood disorder associated with a single nucleotide polymorphism (SNP) designated rs334 in the human beta globin (HBB) gene. Individuals with sickle cell anaemia are about the 10-fold more resistant to life-threatening forms of malaria. The most common allele is rs334(A), encoding the normal form of haemoglobin. Individuals homozygous for the rs334(T) allele exhibit the sickling form of hemoglobin, Hb-S.

Shown below are the maternal and paternal HBB gene sequences from 4 individuals being assessed for sickle cell anaemia with the SNP indicated in bold. The coding sequence commences at nucleotide position 25.

A new rs334 (G) allele was recently discovered, which would vary the codon to…

Select one:

glutamic acid

glycine

valine

glutamine

A

A new rs334 (G) allele was recently discovered, which would vary the codon to…

Select one:

glutamic acid

glycine

valine

glutamine

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