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Medical Cell Biology & Genetics > Mutations & Diagnostic Tools > Flashcards

Mutations & Diagnostic Tools Flashcards

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1
Q

What is a mutation?

A

A mutation is a heritable alteration in a gene or a chromosome, caused by a change in the sequence of amino acids

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2
Q

Name a major source of ionising radiation.

A

Radon

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3
Q

Describe what a transposable element is, and define some of their characteristics.

A

A transposable element is a specific DNA sequence (usually containing more than 1 gene) that move (as a discrete unit) to a random site - they’re always contained within DNA and are never in a free form, and can insertion ally inactivate target genes

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4
Q

Are larger or smaller genes more susceptible to transposable elements?

A

Larger genes, as they have a greater area and usually are composed of a greater number of genes

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5
Q

What is the difference between a ‘micro’ and a ‘macro’ mutation?

A

A ‘micro’ mutation is a mutation of a single nucleotide base (insertion, deletion, substitution etc) while a ‘macro’ mutation is a mutation that describes changes on a chromosomal level

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6
Q

What is the difference between a transition and a transversion?

A

A transition is a nucleotide change to the same type of base (e.g. purine-purine or pyrimidine-pyrimidine), while a transversion is a nucleotide change to a different type of base (e.g. purine-pyrimidine or vice versa)

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7
Q

What mutation produces sickle cell anaemia?

A

A substitution mutation (missense) in the 6th amino acid on codon 7 from a glutamic acid to a valine

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8
Q

What is a mis-sense mutation?

A

A mutation that leads to a change in the amino acid in a polypeptide sequence

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9
Q

What is a silent/silence mutation?

A

A mutation that causes no change in the amino acid sequence coded for

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10
Q

What is a nonsense mutation?

A

A mutation that causes a (premature) stop codon

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11
Q

What is a frameshift?

A

A change in the nucleotide reading frame, by either a deletion (-1) or an addition (+1)

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12
Q

What is an inversion?

A

The rearrangement of a chromosome where a segment of it is reversed

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13
Q

Does an insertion of 3 nucleotides cause a frameshift?

A

No, as the frame will be read the same across the whole DNA sequence, only now there is a new codon inserted

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14
Q

What is the difference between a missense and a nonsense mutation?

A
  • a nonsense mutation is a change in the nucleotide sequence where a stop codon is formed
  • a missense mutation is a change in the nucleotide sequence where a different a amino acid is coded for
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15
Q

What is the difference between an oncogene and a proto-oncogene?

A

A proto-oncogene is a wild-type gene that regulates cell division, while an oncogene is a mutated form that is often unable to adequately regulate cell division (and as such is highly implicated in many cancers)

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16
Q

Why is a ‘gain of function’ mutation more likely to infer a dominant trait than a recessive trait?

A

If a ‘gain of function’ mutation was recessive there would be no gain in function as it would still be secondary to the dominant allele - a ‘gain of function’ mutation must therefore be dominant as to gain the function, the protein it codes for must still work, only in an enhanced way - if it wasn’t enhanced, either the other allele would attribute to ensuring the old proteins function, or the cell wouldn’t be viable and die (meaning there would be no gain of anything)

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17
Q

Are all mutations harmful?

A

No, as some may infer evolutionary advantages (the whole principle of evolution is based on genetic mutations)

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18
Q

How is nitrous acid formed? How does this cause genetic mutations?

A

It is formed from the nitrates and secondary amines formed in the stomach under acidic conditions -

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19
Q

What is cytogenetics?

A

The study of the genetic constitution of cells through the visualisation and analysis of chromosomes

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20
Q

Concerning leukaemia, why might cytogenetics be a useful diagnostic tool?

A

Various chromosomal translocations can infer the specific type of leukaemia an individual is suffering

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21
Q

What is aneuploidy? Give 4 specific examples.

A

Aneuploidy is an abnormal number of chromosomes, due to errors in cell division at meiosis:

  • Down syndrome - a trisomy, an extra chromosome 21
  • patau syndrome - a trisomy, an extra chromosome 13
  • Edwards syndrome - a trisomy, an extra chromosome 18
  • Turner syndrome - a monosomy, female missing an X chromosome
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22
Q

How would you write the Karyotype of a standard female in a chromosome report? What about a standard male?

A
  • 46,XX

- 46,XY

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23
Q

How would you write the Karyotype of a male with Down syndrome in a chromosome report?

A

47,XY+21

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24
Q

What is unique about Turner syndrome?

A

It is the only monosomy that is still viable

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25
Q

What is amniocentesis? When should it be carried out? Is there a risk of miscarriage?

A

Amniocentesis is a test a female can undergo during pregnancy to check whether the embryo has a genetic disorder - it involves removing and testing a small sample of cells from the amniotic fluid, which surrounds the foetus in the womb - this is carried out after around 15 weeks, and gives a 0.8% chance of a miscarriage

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26
Q

What is chorionic villus sampling? When should it be carried out? Is there a risk of miscarriage?

A

Chorionic villus sampling is a test a female may be offered during pregnancy to check if the embryo has a genetic order - this involves removing and testing a small sample of cells from the placenta - this is carried out around 11-12 weeks after gestation, and gives a 1.2% of miscarriage

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27
Q

What is polyploidy? How would you write this in a chromosomal report?

A

Polyploidy is the gain of a whole haploid set of chromosomes, producing triploidy
- 69,XXX

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28
Q

What is the most common cause of polyploidy?

A

Polyspermy - fertilisation of an egg by more than one sperm (usually 2 sperm)

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29
Q

What percentage of pregnancies result in triploidy? What about tetraploidy?

A

Triploidy occurs in around 2-3% of all pregnancies (most of these embryos are not viable) - tetraploidy occurs in 1-2% of all pregnancies

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30
Q

How is the viability of an individual with aneuploidy determined?

A

By which chromosomes are involved in the non-disjunction event

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31
Q

What is the cause of aneuploidy?

A

A non-disjunction at meiosis, leading to an abnormal number of chromosomes in a gamete - one gamete will have an extra chromosome, while one will be missing a chromosome

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32
Q

What is anaphase lag?

A

Anaphase lag describe a delayed movement during anaphase, where a chromatid/chromosome fails to attach to the mitotic spindle, or its migration towards the pole is delayed, and overall fails to be included in the reforming nucleus

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33
Q

What does X activation ensure?

A

That across both males and female species, only one X chromosomes complement is active

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34
Q

In spite of their differences, what allows the X and Y chromosomes to join as a pair during cell division?

A

Homologous PAR1 and PAR2 regions

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35
Q

In Turner syndrome, what gene has been linked to the stunted growth seen in affected individuals?

A

The SHOX gene

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36
Q

List 2 observable features of a newborn baby with Turner syndrome.

A
  • puffy/swollen feet

- excess skin at the back of the neck

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37
Q

What is mosaicism? How is it caused?

A

Mosaicism is the presence of 2 or more cell lines in an individual - it results from a non-disjunction event in mitosis at an early stage of development, forming a new converging cell line

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38
Q

What is a reciprocal translocation?

A

The transfer of genetic material between 2 non-homologous chromosomes

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39
Q

What is the difference between a balanced and an unbalanced gamete?

A

A balanced gamete has undergone a reciprocal translocation, but overall no genomic data has been lost from the genome - an unbalanced gamete has undergone reciprocal translocation, and has lost/gained part of the genome it, and so is missing DNA

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40
Q

What is a Robertsonian translocation?

A

A robertsonian translocation involves the fusion of 2 acrocentric centromeres, resulting in the loss of a chromosome (the genetic material will still remain however)

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41
Q

What 5 chromosomes are most susceptible to robertsonian translocations? Why?

A

Chromosomes 13, 14, 15, 21, & 22 - all these chromosomes are acrocentric, and have very short p arms

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42
Q

List 4 types of FISH probe. What stage(s) of cell division are they

A

Locus/gene specific probes, telomere probes, centromere probes, whole chromosome paints - the probes are usually used in metaphase (and sometimes interphase)

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43
Q

How many days may prenatal aneuploidy screening take? What chromosomes are FISH probes normally used for?

A

Up to 14 days - probes are usually designed for chromosomes 13, 18, 21, and the X & Y chromosomes, are these are more likely to result in aneuploidy

44
Q

What is the difference between a germline mutation and a somatic mutation?

A

A germline mutation is one that occurs in gametes, can be passed on and effect all cells within the body - a somatic mutation occurs in a body cell and is not passed on to any offspring

45
Q

Why are errors in RNA far more common than errors in DNA? Why is this not a huge problem?

A

RNA polymerases do not have a built-in proof-reading mechanism that DNA polymerases do - this isn’t a problem as many RNA copies will be produced, most of which will be correct - therefore, the majority of the protein produced will be correct an should have no major consequence to the cell - RNAs are also quickly degraded, so the mutated copy should be removed relatively quickly

46
Q

Why is a mistake on DNA much more deadly than a mistake in RNA?

A

RNA is not inherited, and is not passed on to the next generation - therefore, making an incorrect copy of RNA will have less consequences than an incorrect copy of DNA, which is universal, coding for mutated RNA and a mutated protein that is lasting and permanent

47
Q

Where do symptoms of mitochondrial disease mainly occur?

A

In organs that require large amounts of energy (and so have a high abundance of mitochondria) such as the heart, brain, and skeletal muscle

48
Q

How may somatic mutations in mitochondria lead to a disease phenotype?

A

Mitochondrial DNA has a limited ability to repair itself, so somatic mutations tend to build up over time - a build up of these mutations has been linked with Alzheimer’s, Parkinson’s, and heart disease

49
Q

Are the majority of germline cell mutations inherited or spontaneous?

A

Inherited

50
Q

What event do insertion and deletion mutations lead to?

A

A frameshift

51
Q

What stage of nuclear division are chromosomes usually in upon analysis?

A

Metaphase

52
Q

What is the systematic sorting of chromosomes called?

A

Karyotyping

53
Q

What type of phenotype will a carrier of unbalanced gametes display?

A

They will always display an abnormal phenotype

54
Q

How would you write the karyotype of an individual who has had a reciprocal translocation in chromosomes 5 & 12 in a chromosome report? What about a reciprocal location in chromosomes 1 & 18?

A
  • 46,XX,t(5,12)

- 46,XX,t(1,18)

55
Q

Do deletions and duplications on a chromosomal level give rise to balanced or imbalanced gametes?

A

Imbalanced (as there is either more genetic information that usual or less genetic information as usual)

56
Q

What would you write in a report describing abnormal Karyotype results?

A
  • give the correct ISCN (46,XX)
  • describe the abnormality in words
    • balanced/unbalanced?
    • monosomy/trisomy?
  • relate the abnormality to clinical problems
57
Q

What is uniparental disomy?

A

The presence of homologous chromosomes from a single parent lineage (ie an offspring as both chromosomes from either their mother or father)

58
Q

What is the difference between isodisomy and heterodisomy?

A

An isodisomy is a uniparental disomy where an individual inherits an identical homologous chromosome pair from one parent - a heterodisomy is where an individual inherits 2 homologous chromosomes from one parent

59
Q

In what stages of meiosis would a isodisomy and a heterodisomy occur?

A

An isodisomy would occur in meiosis II, while a heterodisomy would occur in meiosis I

60
Q

What are the 4 mechanisms that generate uniparental disomy? What do they all require?

A
  • trisomy rescue
  • monosomy rescue
  • gamete complementation
  • mitotic error
  • all require 2 separate abnormal events
61
Q

Can a microarray detect balanced chromosomal rearrangements?

A

No - it can only check for imbalanced rearrangements

62
Q

Can microarrays look for changes in DNA at a single nucleotide level?

A

No, as the signal they would give off would be too small

63
Q

What amplification step is seen in most genetic analysis?

A

PCR

64
Q

List 2 pro’s and 2 con’s of next generation sequencing.

A

Pros

  • increased read length
  • high throughput

Cons

  • insufficient IT capacity
  • lack of knowledge to fully interpret findings - lot of information, however don’t always understand what all this information means
65
Q

What is non-invasive prenatal testing? List a pro and con of this technique.

A

Non-invasive prenatal testing involves analysing the maternal plasma, which contains around 5% foetal DNA (to 95% maternal DNA) - foetal DNA is isolated and analysed

  • a pro includes the removal of any risk of miscarriage
  • a con however includes that the process is technically challenging
66
Q

How may no -invasive techniques be applicable to some cancers?

A

90% of metastatic cancers have circulating cancer cells and cell free DNA - the levels of circulating tumor DNA in plasma may be used as a diagnostic tool

67
Q

What is the difference between the exome and genome?

A

The genome comprises all the genetic information of an organism, while the exome comprises all the coding portion (exons) of an organisms genome

68
Q

What does whole exome sequencing analyse?

A

The coding portion of an organisms genome (it’s exome)

69
Q

At birth, what is the approximate number of primordial germ cells in males and in females?

A

In males there are around 4 million primordial germ cells, while in females there are around 1 million primordial germ cells at birth

70
Q

Why do primordial germ cells only begin to differentiate into spermatozoa in males at puberty?

A

They are only needed when oocytes are available to fertilise (in females of the same age)

71
Q

How does the mutation rate of male gametes compare to female gametes?

A

The mutation rate in male gametes is 5x higher

72
Q

What percentage of pregnancies result from chromosomal abnormalities (structural or numerical)?

A

75%

73
Q

Why do male gametocyte mutations increase with age? What about female gametocyte?

A
  • in males, spermatozoa is continually made - the gametocytes have been exposed to mutagens for a much lone time than in younger males
  • although a similar explanation may be true, the real answer for mutations in female gametocytes is actually unknown
74
Q

What are 3 possible outcomes if a very early embryo was exposed to mutagens?

A
  • abortion (death)
  • teratogenesis (developmental abnormalities in embryo)
  • born with a cancer
75
Q

In general, what do recessive mutations do?

A

Recessive mutations cause loss of function and usually effect biochemical pathways

76
Q

In general, what do dominant mutations do?

A

Dominant mutations cause gain of function and generally cause structural abnormalities

77
Q

What disorder does a mutation in type I collagen often result in?

A

Osteogenesis Imperfecta

78
Q

What are cystine residues commonly associated with?

A

The formation of disulphide bonds (bridges)

79
Q

Why may a patient display both abnormal and normal types of a protein?

A

They may be heterozygotes

80
Q

What is the difference between an endogenous and an exogenous mutagen? Give an example of each.

A

An endogenous mutagen is one produced by the body (DNA replication errors) - an exogenous mutation is a mutagen that is an external agent from the environment (UV light)

81
Q

What is the most toxic form of DNA damage?

A

A double stranded break

82
Q

What is an apurinic/apyrimidinic site?

A

A site on the DNA helix that contains neither a purine or pyrimidine - this can act as a mutagen and propagate cancer

83
Q

What are the 4 main DNA damage response steps?

A
  • signal
  • sensor
  • transducer
  • effector
84
Q

In regards to DNA damage, what can the checkpoints after G1 and G2 provide?

A

Time for the cell to check and repair any abnormal DNA

85
Q

What is senescence?

A

Permanent arrest of the cell cycle

86
Q

Define DNA replication stress.

A

DNA replication stress is defined as inefficient replication that leads to replication fork slowing, stalling, and/or breakage

87
Q

What 3 factors may contribute to replication stress?

A
  • defect in the replication machinery
  • factors may hinder the replication fork progression
  • defects in the response pathways
88
Q

What is slippage? Where does it normally occur?

A

A for, of mutation where DNA polymerase inserts or deletes less/extra nucleotides into a sequence - this often happens at microsatellites where there are tandem repeats of DNA

89
Q

What is nucleotide misincorporation? What is the most common cause of this type of mutation persisting?

A

Simply where DNA polymerase inserts the wrong base - an abnormal endonuclease activity will allow these mutations to persist

90
Q

What are 2 widely considered consequences of DNA double strand breaks?

A
  • genomic mutations - cancer

- cell growth inhibition - ageing

91
Q

Name a disorder associated with trinucleotide tandem repeats? What is the tandem repeat?

A

Huntington’s disease - due to CAG repeats (35-121 repeats)

92
Q

What does an excessive accumulation of mutations in a cell lead to?

A

Cancer

93
Q

What adverse effect may single strand annealing lead to?

A

Deletion of part of the DNA sequence

94
Q

What is a key regulator that is mutated in many cancers?

A

p53

95
Q

What does the evolution of therapy resistance suggest? What is clonal expansion?

A

The heterogeneity of cancers means that continually mutating cells produces a certain cell line which develops resistance to cancer treatment - this leads to clonal expansion, selecting for this particular clone (by killing of other cancer cells), and propagating its existence

96
Q

How may the DNA damage response shape the evolution of a cancer?

A

The DNA damage will kill off certain cell lineages in a cancer and leave others, shaping the cells who thin the cancer which will shape how it acts and grows

97
Q

How may a lot of current cancer treatment seem highly paradoxical? How may this be an issue?

A

They themselves induce DNA damage in an effort to kill cancer cells - this may be a problem if the radiation begins to damage excessive amounts of healthy DNA in healthy cells, who’ll may produce more cancer and/or propagate them further

98
Q

What is a holiday junction?

A

A cross-shaped structure that forms during genetic recombination, where 2 DNA double-strands become separated into 4 strands during homologous recombination (crossing over) in meiosis

99
Q

At birth, how many primordial germ cells in males compared to females?

A

At birth there are around 4 million primordial germ cells in males, while in females there are around 1 million primordial germ cells

100
Q

In females, when do primary oocytes undergo prophase Impf meiosis?

A

At birth

101
Q

What is spermatogenesis? When does it occur?

A

Spermatogenesis involves the differentiation of primordial germ cells in which spermatagonia are transformed into spermatozoa - this occurs around the time of puberty

102
Q

Why do progenitor germ cells only begin to differentiate into spermatozoa at puberty?

A

They are only needed when oocytes are available to fertilise

103
Q

What features would allow a germ cell mutation to be heritable?

A
  • it would not be lethal to the gamete
  • it would not impair gamete function
  • it would not be lethal at fertilisation
  • it would allow the production of a viable adult with normal reproductive capacity
104
Q

What is the Philadelphia chromosome? Where does it arise, and what specifically does it cause?

A

The Philadelphia chromosome develops due to a reciprocal translocation of genetic material between chromosome 22 and 9, causing fusion of the BCR-ABL1 genes - this codes for a tyrosine kinase that is permanently on, causing the cell do divide uncontrollably - this abnormality leads to leukaemia

105
Q

What is the Philadelphia chromosome? Where does it arise, and what specifically does it cause?

A

The Philadelphia chromosome develops due to a reciprocal translocation of genetic material between chromosome 22 and 9, causing fusion of the BCR-ABL1 genes - this codes for a tyrosine kinase that is permanently on, causing the cell do divide uncontrollably - this abnormality leads to leukaemia

Medical Cell Biology & Genetics (11 decks)

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