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Y2 EMS > 1. Genetics > Flashcards

1. Genetics Flashcards

1
Q

What is a genotype?

A

The actual information written in your genes

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2
Q

What is a phenotype?

A

The manifestation of the genotype

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3
Q

Give 2 examples of non-genetic tests for genetic disorders.

A
  1. Blood tests

2. X-Rays

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4
Q

What is genetic counselling?

A

Educating individuals at risk/who have a genetic disorder on their condition and the options they have in management and family planning.

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5
Q

What is the total number of nucleotides in the human genome (haploid)?

4 x 10 *8
4 x 10 *9
3 x 10 *8
3 x 10 *9

A

3 x 10*9

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6
Q

Which is more stable, DNA or RNA?

Why?

A

DNA

RNA breaks apart easily due to the presence of an hydroxyl group on C2 which is susceptible to hydrolysis.

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7
Q

DNA stores more information than RNA.

True or False?

A

FALSE

there is no extra info on a double stranded molecule vs single stranded molecule.

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8
Q

Which direction are DNA + RNA synthesised in?

A

5’ –> 3’

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9
Q

During DNA replication, there is a ‘leading’ strand and a ‘lagging’ strand.
How does the synthesis of their complimentary strands differ?

A

The lagging strand requires okazaki fragments to replicate because synthesis can only occur 5’ to 3’ which clashes with the direction in which the parent DNA is unzipped.

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10
Q

What is a karyotype?

A

An arrangement showing an individuals complete number of chromosomes and their appearance.

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11
Q

What is the pinch in the middle of a chromosome called?

A

Centromere

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12
Q

What are the arms on a chromosome called?

A

Short arms = p (petite)
Long arms = q

e.g. chromosome 7 would have 7p + 7q

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13
Q

What are telomeres?

How do they change over time?

A

Repeat sequences (TTAGGG) at the ends of DNA which protect the ends and prevent deterioration.

Telomeres get shorter with each cell division, eventually when they become too short the cell can no longer divide and may die.

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14
Q

What is the role of telomerase?

A

Adds TTAGGG repeat sequences to the ends of DNA; reducing the rate at which cells reach senescence (can no longer divide).
This is an issue in cancer.

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15
Q

Why do X-related recessive conditions mainly occur in men?

A

Men only have one X chromosome.

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16
Q

What percentage of DNA is non-coding?

> 50%
90%
<30%
<70%

A

> 90%

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17
Q

Approximately how many protein-coding genes are in the human genome?

A

20,000

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18
Q

What are genes?

A

Functional units of DNA

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19
Q

What are genes composed of?

A

Introns
Exons
Regulatory sequences (promoters, enhancers, locus control regions)

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20
Q

What is always the first two and last two bases of an intron?

A

GT + AG

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21
Q

What is alternative splicing and why is it important?

A

Alternative splicing is the process by which different combinations of exons are produced from a single gene.
This means multiple proteins can be made from a single gene.
Duplications in exons produce slightly different proteins which can be advantageous in evolutionary terms.

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22
Q

What is satellite DNA?

What are its characteristics?

A

Large blocks of repetitive DNA sequences found at the centromere and heterochromatic (tighly packed, less expression) regions.

Simple tandem repeated sequences e.g. AATGAATGAATG
Size of the blocks may vary - 1,9,16,Y

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23
Q

What is EGFR overexpressed in?

A

Certain human carcinomas e.g. non-small cell lung cancers

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24
Q

What is the drug ‘gefitinib’ used to treat?

A

EGFR (epidermal growth factor receptor) inhibitor.

Certain cancers like breast and lung.

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25
Q

What is ‘Gleevec’ used to treat and how does it do this?

A

Chronic myeloid/myelogenous leukaemia (CML).
It inhibits the signalling protein produced by the mutated fusion gene of the Philadelphia chromosome, to prevent the uncontrolled division of white blood cells.

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26
Q

The Philadelphia chromosome is a characteristic of what disease?

A

Chronic myeloid/myelogenous leukaemia (CML)

translocation between chromosome 9 + 22

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27
Q

Cadasil is a gene associated with a high risk of what?

A

People with the single gene Cadasil have a high risk of stroke.

Rare - stroke is usually multifactorial.

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28
Q 
What class of genetic disorder is a mutation in a gene in a specific group of cells which is not inherited?
Chromosomal
Mitochondrial
Multifactorial/Complex
Single gene
Somatic mutation
A

Somatic mutation

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29
Q 
Which of these is not a single gene mode of inheritance?
Autosomal dominant
Autosomal recessive
Chromosomal
Mitochondrial
X-linked
A

Chromosomal

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30
Q

How many chromosomes do humans have?

A 
46 chromosomes
23 pairs (diploid cells)
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31
Q

How many chromosomes do gametes have?

A

23 chromosomes (1 copy of each gene)

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32
Q

Myotonic dystrophy, Marfan syndrome, Huntington disease

are all examples of what form of inheritance?

A

Autosomal dominant

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33
Q

Huntington disease has 100% penetrance by 80 years.

What does penetrance mean?

A

The frequency with which the specific genotype (mutation) is expressed in the individuals who have it.
i.e. everyone with the genotype for Huntington disease will express the disease by the age of 80.

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34
Q

What term is used to describe the increase in severity of symptoms as a genetic disorder is passed from one generation to the next and their appearance at an earlier age?

A

Anticipation

e.g. myotonic dystrophy, Huntington disease

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35
Q

What is a ‘de novo’ mutation?

A

New mutation that has occurred in gametogenesis (meiosis) or early embryonic development.
Offspring is the first in family to be affected and can pass it on to their kids.

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36
Q

In autosomal recessive inheritance, if 2 carriers have children, what are the chances of the offspring being affected?

A

25%

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37
Q

Give 3 examples of autosomal recessive diseases.

A

Cystic fibrosis
Haemochromatosis
Sickle cell disease
Metabolic disorders (anything ending in -aciduria is likely AR inheritance)

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38
Q

Male to male transmission is not possible in X-linked inheritance.
True or False?

A

TRUE

39
Q

Give 3 examples of X-linked inherited disorders.

A

Haemophilia (difficulty making blood clots)
Fragile X syndrome (learning disability)
Duchenne muscle dystrophy
Red/green colour blindness (see red + green as identical colours)

40
Q

What are the two main factors which influence the expression of X-linked phenotypes in females?

A

X-inactivation
XL dominant vs XL recessive

often cannot accurately predict a female phenotype in prenatal testing.

41
Q

What is Lyonisation?

A

X-inactivation
the process by which a random X chromosome is switched off in every cell in the female body.
This occurs in the first few weeks of pregnancy to compensate for the double X gene dose in females.

42
Q

What is a Barr body and where is it found?

A

The inactivated and condensed X chromosome which is seen on the rim of the female cell nucleus.

(Some women have 3 X chromosomes so switch off 2, leaving 2 Barr bodies)

43
Q

How can skewed X-inactivation lead to a significant phenotype of a genetic disorder?

A

If there is a random preference for more of the ‘normal’ X chromosomes to be switched off in cells, there will be much more of the mutated gene left; leading to a more significant phenotype.

However it is usually 50/50 so the body can deal with it alright.

44
Q

Duchenne muscular dystrophy is a result of tissue variability in X-inactivation.
Explain what is meant by this.

A

Tissue variability = random preference for the X chromosome with the mutation to be active in a crucial tissue group.

Muscles in DMD.

45
Q

Give 2 examples of XL dominant disorders.

A

Rett Syndrome (neurological disorder - lethal in males, mainly females live with it)

Fragile X syndrome (learning disability, boys more severely affected since they cant deactivate X genes like in females)

46
Q

Give 3 examples of XL recessive disorders.

A

Red/green colour blindness
Haemophilia
Duchenne muscular dystrophy

47
Q

Mitochondrial inheritance is from the father.

True or False?

A

FALSE
all our mitochondria are inherited from our mother including their DNA.
An affected mother will give ALL her children the mutation.

48
Q

How many genes are there in mitochondrial DNA?

A

27 genes

49
Q

What chemical group is responsible for making DNA more stable than RNA?

A

Hydroxyl group on C2

50
Q

All information is contained within the nucleotide sequence.

True or False?

A

FALSE

there is also epigenetic information

51
Q

How many hydrogen bonds are there between Adenine + Thymine?

A

2

52
Q

How many hydrogen bonds are there between Cytosine + Guanine?

A

3

53
Q

Okazaki fragments are synthesised by which enzyme?

A

DNA polymerase I

54
Q

What does a mutation of the BRCA1 gene make you more susceptible to?

A

Breast + Ovarian cancer

55
Q

What are pseudogenes?

A

Genes that were once functional, but have accumulated so many mutations through evolution that they are now no-functional.

56
Q

What are processed pseudogenes?

A

Non-functional mRNA that has been reintegrated into DNA (reverse transcription)

57
Q

Give an example of satellite DNA.

A

Alphoid DNA

found at centromeres

58
Q

Alu repeats are an example of what?

A

Interspersed repeats.

Alu is a SINE which makes up 5% of the genome

59
Q

What are interspersed repeats?

A

Repeats of DNA that are scattered around the genome in different locations

60
Q

Which organelle has circular DNA that is inherited via the oocyte?

A

Mitochondria

61
Q

What is the most common interspersed repeat?

A

LINE1 (long interspersed nuclear element)

62
Q

What is the genetic cause of Haemophilia A?

A

Faulty F8C gene (factor 8 clotting gene) in X chromosome.

A result of intra-chromosomal recombination due to the presence of repeat sequences within and outside the gene which cause crossing-over within the chromosome and invert that part of the chromosome.
All the sequence is still there, but the gene is not in tact. So you can’t make factor 8 protein.

63
Q

Which part of meiosis can interspersed repeats cause problems?

A

Recombination

they can cause the misalignment of chromosomes which results in unequal crossing over e.g. one small + one extra big chromosome.

64
Q

What is the point of contact between chromosomes in recombination called?

A

Chiasma

65
Q

What is a common chromosome 22 deletion syndrome?

A

DiGeorge syndrome

66
Q

What is a common chromosome 7 deletion syndrome?

A

Williams syndrome

67
Q

Would someone with Duchenne muscular dystrophy suffer a more severe phenotype if they had a deletion of a 68bp exon or a 69bp exon?

A

68bp exon

this would cause a frameshift because it is not a multiple of 3, so would mess up the rest of the sequence after this exon.

68
Q

A mutation where a nucleotide changes, but the amino acid produced is unaltered.

A

Silent point mutation

69
Q

A mutation where a change in nucleotide results in a codon which codes for a different amino acid.

A

Missense mutation

70
Q

What is a non-conservative mutation?

A 
A mutation where the class of amino acid produced is changed.
e.g. acidic > basic   /   aromatic > polar   /  Arg > Trp

more likely to cause structural problems in protein than a conservative mutation.

71
Q

What is a nonsense mutation?

A

A point mutation where a change in nucleotide results in a stop codon, this produces a truncated (short) protein.

72
Q

Why does CG -> TG make up a third of pathogenic mutations (why are they so common)?

A

Methylation of cytosine produces thymine (only one step away).

73
Q

Splice junction mutations are when the nucleotides which mark the splicing site mutate, resulting in some of the intron being included which shouldn’t be.
What nucleotides mark the start and end of an intron?

A

GT = start AG = end

74
Q 
What do these mean:
c.8C>T
p.Ala3Val
c.114+1G>A
c.233_234delCT
[44C>T] ; [826G>A]
p.Trp144*
A

the 8th nucleotide on the cDNA has changed from a C > T

the 3rd amino acid on the protein has changed from Ala > Val

the 1st nucleotide on the intron after nucleotide 114 has changed from G > A

deletion of an adjacent C + T at positions 233 and 234

two seperate mutations at positions 44 and 826

the chain terminates at Trp at position 144

75
Q

What type of inheritance pattern do mutations which cause a loss of function usually follow?

A

Recessive (usually, not always)

1 copy of the functional gene is enough to compensate

76
Q

What type of inheritance pattern do mutations which result in a gain / alteration of function usually follow?

A

Dominant (usually, not always)

cannot be compensated for by a normal copy of the gene

77
Q

Compound heterozygosity is when you have a different mutation on each allele (recessive disorder).
Give an example of a disease with compound heterozygous inheritance.

A
  1. Cystic fibrosis

2. Beta thalassemia

78
Q

CAG triplet repeat expansion is seen in which condition?

A

Huntington’s disease

the larger the repeat, more severe phenotype and earlier onset.

79
Q

CGG triplet repeat expansion is seen in which condition?

A

Fragile X syndrome

80
Q

Can an oligonucleotide ligation assay be used to identify the identity of an unknown disease causing mutation?

A

NO

need to sequence DNA

81
Q

What term is used to refer to the normal variation in genome between individuals?

A

Polymorphism

82
Q

What crucial element does Sanger sequencing require?

A

ddNTP Chain terminators

i.e. ddATP, ddTTP, ddCTP, ddGTP

83
Q

What are the limitations of PCR + Sanger sequencing?

A 
Size limit (max 500bp at a time) therefore genes are sequenced an exon at a time.
Very time consuming + expensive.
84
Q

What is the main advantage of modern ‘next gen’ sequencing techniques?

What isn’t so great?

A

Much cheaper
Quicker

There is a lot of data, which is difficult to interpret and find the important information you are after

85
Q

Why are live cells required in cytogenetics (e.g. karyotyping) rather than just DNA?

A

Chromosomes are only visible when they condense during metaphase.
(cell division is inhibited at this stage for study)

86
Q

How is FISH superior to G-banding?

A

G-banding has limited optical resolution
(can’t see anything smaller than 5Mbp under a microscope).

FISH has much better resolution (uses a fluorescent tag which can be detected easily e.g. detecting microdeletions).
Can also look at chromosomes in interphase as well as metaphase.

87
Q

A cheap and easy first-line sequencing method.

A

aCGH (Array comparative genomic hybridization)

88
Q

DNA based sequencing methods are cheaper, easier, and give a higher resolution.
Why is cytogenetic analysis still used?

A

DNA sequencing methods cannot detect genome rearrangements e.g. translocations (chromosomes exchange material between each other, but the total amount of DNA remains the same).
DNA sequencing just measures the amount of DNA in a locus, so this is invisible to it.

Cytogenetic techniques and FISH allow you to see the change in shape/structure of a chromosome to detect these changes.

89
Q

What are genetic bottlenecks?

A

Reduction in genetic variation

can be caused by speciation, migration, environment, disease.

90
Q 
Which of these are endogenous factors which can cause genetic variation?
Segregation
Chemicals
Recombination
Radiation
DNA replication errors
Inadequate DNA repair mechanisms
A
  1. Segregation (aneuploidies, downs syndrome, edwards syndrome)
  2. Recombinations (translocations)
  3. DNA replication errors (mis-paired bases, slippage)
  4. Inadequate DNA repair mechanisms (mismatch repair, base excision repair)

Chemicals + radiation = EXOgenous

91
Q

What percentage of a population does a single nucleotide variant need to affect for it to be classed as a single nucleotide polymorphism?

A

> /= 1%

less than 1% = rare variant

92
Q

What is an indel?

A

Insertion or deletion of one or more nucleotides.

93
Q

SNPs
Indel (1-10 nucleotides)
Indel (11-100 nucleotides)
CNVs

Which of these variation types impact the greatest number of nucleotides?

A

CNVs (copy number variants)

they only represent 0.1% of all variation compared to SNPs with 90% (most abundant type of variation), but because they are so much larger they have a greater impact.

Y2 EMS (4 decks)

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