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Z MD1 Reproductive Block > genetics > Flashcards

genetics Flashcards

1
Q

what is euchromatin

A

DNA+proteins+RNA

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2
Q

what is the difference between euchromatin and heterochromatin

A

euchromatin - actively transcribed regions of DNA

heterochromatin - few actively transcribed regions of DNA

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3
Q

what bases are euchromatin and heterochromatin rich in

A

euchromatin - rich in GC

heterochromatin - rich in AT

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4
Q

which, euchromatin and heterochromatin look light and dark when chromosomes are stained

A

euchromatin - light

heterochromatin - dark

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5
Q

explain the replication of euchromatin and heterochromatin during S phase

A

euchromatin - replicate early during S phase

heterochromatin - replicate late during S phase

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6
Q

what is the biggest and the smallest proportions of sequence of the human DNA

A

biggest - transposon-based repeats

smallest - protein coding regions

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7
Q

what are the functions of the 5’ cap and the poly A tail to an mRNA transcript

A

5’ - helps position the RNA on the ribosome for translation

polyA tail - confer some stability to the mRNA

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8
Q

how are introns spliced out of the genome

A

by the splicosome (protein complex of snRNA)

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9
Q

how does the splicosome bind exons together

A

recognises the donor and acceptor splice sites

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10
Q

what is the difference between a histone and a nucleosome

A

histone - protein

nucleosome - multiple proteins+DNA coiled

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11
Q

chromatin remodelling is critical to allow

A

access to the transcription machinery

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12
Q

how can histone proteins be modified

A

acetylation of lysine residues

methylation

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13
Q

what are the ways which chromatin can be remodelled

A
  • acetylation of lysine residues of histones
  • methylation of histones
  • methylation of DNA
  • nucleosome moves along the DNA
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14
Q

to go from euchromatin to heterochromatin what must happen

A

chromatin remodelling

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15
Q

in what areas of DNA does methylation occur

A

where we have a C next to a G

C is methylated

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16
Q

what is the role of methylation of DNA

A

silences the gene

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17
Q

CpG regions are associated around which parts of DNA

A

around promoter regions

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18
Q

explain the epigenetics of heterochromatin

A
  • hypermethylation of CpG of DNA
  • low acetylation of histones
  • variable methylation of histones
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19
Q

explain the epigenetics of euchromatin

A
  • hypomethylated CpG of DNA
  • hyperacetylation of histones
  • variable methylation of histones
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20
Q

other than the minimum requirements needed for transcription, what else helps further regulate transcription

A
  • DNA looping around itself causing direct interactions of a promoter with other cis-acting DNA sequences (enhancers, silencers)
  • ncRNA
  • trans-acting proteins
  • alternative promoters in a gene
  • alternative splicing of a transcript
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21
Q

what are the 3 types of non-coding RNA

A 
long non coding RNA (lncRNA)
short interfering RNA (siRNA)
micro RNA (miRNA)
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22
Q

what are the 4 functions of long non coding RNA

A
  • can act as a decoy and take the RNA polymerase away with it to reduce gene expression
  • scaffold to bring in TF (silencing or enhancing gene expression)
  • guide (physically interact with the protein to guide the TF or the polymerase to the right spot)
  • can affect alternative splicing
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23
Q

siRNAs interact with what

A

a protein called RISC (RNA-inducing silencing complex)

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24
Q

function of siRNA

A

RISC complexes with the antisense siRNA –> siRNA binds to mRNA that is fully complementary –> causes cleavage of the region by RISC –> specific mRNA degredation and reducing protein production

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25
Q

function of microRNA

A

binds with RISC –> binds to partly complementary mRNA –> causes repression of translation

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26
Q

what can cause a regulation of translation

A

miRNA

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27
Q

list the mechanisms used in chromatin remodelling

A
  • histone modifications (acetylation and methylation)
  • DNA methylation
  • nucleosome positioning
  • non-coding RNA
  • nuclear location of chromatin
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28
Q

how is it possible that we have 20000 genes but many many more proteins

A

due to:

  • many genes have more than one promoter
  • alternative splicing
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29
Q

the majority of genes have what type of expression

A

biallelelic - giving 100% protein levels

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30
Q

what is the importance of gene dosage

A

it is important in the regulation of levels of protein expression

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31
Q

what is aneuploidy

A

unbalanced sets of chromosomes due to excess or deficiency of individual chromosomes

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32
Q

aneuploidy most often arises due to

A

non-disjunction of 2 homologous chromosomes or sister chromatids during cell division, either in mitosis or meiosis

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33
Q

which trisomy conditions can survive to term

A

13, 18, 21 and sex chromosome trisomy

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34
Q

what causes the abnormal development in trisomy and monosomy conditions

A

trisomy - because there is 50% increased expression of several critical genes
monosomy - because there is 50% decreased expression of several critical genes

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35
Q

which monosomy conditions can survive to term

A

XO (no autosomal monosomies)

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36
Q

trisomy 21 is associated with what

A
  • congenital anomalies of the GIT
  • increased risk of leukaemia
  • IS defects
  • Alzheimer-like disease
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37
Q

what is the colloquial name for trisomy 18

A

Edwards syndrome

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38
Q

what are the physical findings of babies with Edwards syndrome

A
  • overlapping fingers
  • club (rocker-bottom) foot
  • heart defects
  • developmental disability
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39
Q

what is haploinsufficiency

A

where having only one normal copy of a gene is not sufficient to support normal cell function
(autosomal dominant inheritance)

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40
Q

what is monoallelic gene expression

A

certain genes MUST by expressed from ONLY ONE copy for normal cell function and development

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41
Q

which to mechanisms operate to maintain monoallelic gene expression

A 
X chromosome inactivation in females (epigenetic)
genomic imprinting (epigenetic and genetic)
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42
Q

epigenetic regulation encompasses what

A
  • DNA methylation of promoter regions of genes
  • histone modifications - chromatin remodelling
  • gene silencing through non coding RNA
43
Q

how can a female be a mosaic for the X chromosome inactivatedq

A

because the inactivation is random during early foetal development and is passed down along cell lines

44
Q

what is the evidence for some of the genes on the “inactivated” X chromosome still be expressed

A

Turner’s syndrome - if you only have one X chromosome –> syndrome

45
Q

characteristics of Turners syndrome

A
  • short stature
  • infertility due to absent or immature gonadal development
  • absence of secondary sexual development
  • impaired neurocognitive function (visuospatial, perceptual)
46
Q

what is genomic imprinting

A

the process whereby the parental origin of a particular gene is “marked” by a reversible epigenetic mechanism

47
Q

when does imprinting occur

A

when gametes are generated the imprints are erased and then re-established according to the sex of the individual

48
Q

what is parthenogenesis and androgenesis

A

parthenogenesis - whole set of chromosomes from mother

androgenesis - whole set of chromosomes from father

49
Q

what does parthenogenesis result in

A

typically non-viable embryos and can lead to ovarian teratomas

50
Q

what does androgenesis result in

A

typically hydatiform moles which can lead to malignant choriocarcinoma

51
Q

why does parthenogenesis and androgenesis lead to non viable embryos

A

because the gene dosage of imprinted genes is disrupted

52
Q

what is the parental conflict hypothesis

A
  • maternally expressed genes tend to limit foetal growth (involved in resource conservation and less flow to the foetus)
  • paternally expressed genes tend to promote foetal growth (involved in resource extraction to give more energy to the foetus)
53
Q

what are the 4 mechanisms that lead to imprinting disorders (disruption of gene dosage of imprinted genes)

A
  • large deletions or duplications of chromosome regions that contain imprinted genes (LOH)
  • uniparental disomy
  • alteration in epigenetic marks at imprinted loci without alteration in DNA sequence = epimutation
  • DNA mutations in genes that are usually imprinted or in imprinting control centres
54
Q

what is uniparental disomy

A

where instead of one chromosome coming from each mum and dad - one parent provides both
(leads to a deficiency in one parents genes and a duplication of the others)

55
Q

with epimutation, you end up with what type of gene expression

A

biallelic

56
Q

what are the 3 common imprinting disorders

A

Beckwith-Wiedemann syndrome
Prader-Willi syndrome
Angelman syndrome

57
Q

what is associated with a 9x greater risk of a foetus with Beckwith-Wiedemann syndrome

A

reproductive technologies

58
Q

the majority of Beckwith-Wiedemann syndrome is due to which mechanism of disruption of imprinted genes

A

epimutation on maternal allele

59
Q

what is responsible for prader-willi syndrome

A

deficiency of paternally-expressed genes

microdeletions of paternal chromosome –> LOH

60
Q

what is responsible for angelmann syndrome

A

deficiency of maternally expressed genes

microdeletions of maternal chromosome –> LOH

61
Q

explain the inheritance pattern of a mutation in an active paternal gene or inactive maternal gene

A
  • carrier males and affected males can have affected children but not carrier children
  • carrier females and affected females cannot have affected children but can have carrier children
62
Q

explain the inheritance pattern of a mutation in an active maternal gene or inactive paternal gene

A
  • carrier females and affected females can have affected children but not carrier children
  • carrier males and affected males cannot have affected children but can have carrier children
63
Q

How does X inactivation in females occur

A

starts with expression of Xist (lncRNA) –> leads to heterochromatin formation spreading outwards along the chromsome. DNA methylation also plays a role

64
Q

which chromosomes are involved in Beckwith-Weidemann syndrome, Prader Willi syndrome and Angelmann syndrome

A 
BW = 11
PW = 15
AM = 15
65
Q

what percentage of babies have a “birth defect”

A

~4% in Australia

66
Q

what are the two most common chromosomal defects of live births

A

trisomy 21

XXY

67
Q

when taking a family Hx, how many generations should you ideally take

A

3

68
Q

what proportion of pregnancies have a foetus with a neural tube defect

A

1 in 500

69
Q

function of prenatal SCREENING

A

identifies a subset of women from the general population at increased risk of having a child with a birth defect

70
Q

it what stage of pregnancy can you test for neural tube defects

A

second trimester

71
Q

what is the combined screening in the 1st trimester

A
  • blood taken (9-13 weeks)
  • 2 chemical analytes measures (pregnancy associated plasma protein and bhCG)
  • ultrasound performed to measure nuchal transluency
72
Q

what is nuchal translucency

A

thickness of fluid accumulated under the skin at the back of the foetal neck which is measured with ultrasound

73
Q

what is nuchal translucency a marker for

A

thick oedema is a marker for trisomy 21

74
Q

what are the cut offs for further screening from 1st trimester screening for T21 and T18

A 
T21 = 1:300
T18 = 1:175
75
Q

what is the screening in the 2nd trimester

A

blood taken and 4 biochemical analytes measured

76
Q

what are the 4 analytes measured in 2nd trimester screening

A

bHCG
inhibin A
oestriol
alpha foetal protein (AFP)

77
Q

what are the cut offs for further screening from 2nd trimester screening for T21 and T18 and neural tube defects

A

T21 = 1: 250
T18 = 1:200
neural tube defects >2.0MoM

78
Q

which screening (1st or 2nd trimester) is better at detecting T21

A

1st

79
Q

what are the prenatal DIAGNOSTIC tests

A

chorionic villis sampling

amniocentesis

80
Q

when is prenatal diagnostic testing performed

A

offered to women

  • with an increased risk screening result
  • of advanced maternal age
  • who are known carriers
81
Q

at what time of gestation is CVS and amniocentesis performed

A 
CVS = from 11 weeks
amniocentesis = 15-16 weeks
82
Q

what is CVS

A

sampling of placental tissue either transabdominally or transvaginally

83
Q

what is amniocentesis

A

sample of amniotic fluid taken transabdominally

84
Q

what is the risk of miscarriage from CVS and amniocentesis

A

CVS = ~1%
amnio = ~0.5%
(on top of background risk)

85
Q

what are the two different ways of termination and what are their timings

A

less than 16 weeks = dilatation and curettage under GA

more than 16 weeks = prostaglandin induction of labour

86
Q

what tests can you perform on samples taken by CVS or amniocentesis

A

FISH
PCR
karyotype
chromosomal microarray

87
Q

What is FISH

A

fluorescence in situ hybridisation

88
Q

what is the advantage of FISH over karyotype, and karyotype over FISH

A

FISH over karyotype: takes much shorter time period

karyotype over FISH: can show rearrangements and balanced translocations (more information)

89
Q

what are the 2 ways in which trisomy 21 can occur

A
  • extra whole chromosome (95%)

- unbalanced translocation between acrocentric chromosomes (5%)

90
Q

what is a Robertsonian translocation

A

translocation between two acrocentric chromosomes

91
Q

what is an acrocentric chromosome

A

chromosome basically has no short arm (just a little head)

92
Q

what is the difference in phenotype between someone who has a balanced and unbalanced Robertsonian translocation between chromosomes 21 and 14

A 
balanced = carrier
unbalanced = phenotype
93
Q

what is the function of microarrays

A

can look at SNPs and copy number variations (CNVs)

94
Q

what is the first tier test for developmental delay, intellectual disability and autism in Australia

A

Chromosomal microarrays

95
Q

when is a prenatal molecular karotype recommended

A

when:

  • foetal abnormality is identified on US
  • the nuchal translucency measurement is >3.5mm
  • a banded karyotype identifies a complex change
  • a family member has a microdeletion syndrome and a pregnancy is at risk
96
Q

what is pre-implantation genetic diagnosis

A

requires IVF

  • take one or two cells from a 3 day old dividing zygote and do DNA testing or FISH
  • unaffected embryos implanted
97
Q

what is the new alternative to invasive screening tests

A

non-invasive prenatal testing/NIPT - take maternal blood (will have some foetal DNA in it)

98
Q

what things should you ask when gaining a family history for genetic conditions

A
  • inherited conditions
  • Downs syndrome and other chromosomal conditions
  • other birth defects
  • intellectual disability
  • recurrent miscarriage
  • unexplained perinatal deaths
  • consanguinity
  • ethnic background
99
Q

what technology does non-invasive prenatal testing use

A

massive parallel sequencing technology

100
Q

when is nuchal translucency measured and what is the normal value

A

between 11-14 weeks

normal is less than 3mm at this time of gestation

101
Q

what are the results of a first trimester screening test that suggest trisomy 21 and 18

A

21 - increased hCG and PAPP-A

18 - decreased hCG and PAPP-A

102
Q

what other factors are taken into account when calculating a result from combined first trimester screening

A

womans age at EDD
woman’s weight
gestation of pregnancy
(+ blood analytes and nuchal translucency)

103
Q

what is the role of PCR in massively parallel sequencing

A

it creates a large amount of DNA of interest, enough to produce a detectable signal in a sequencing reaction

Z MD1 Reproductive Block (12 decks)

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