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Exam 1 Concepts Flashcards

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1
Q

t or f: chronic diseases may consist of acute episodes

A

True

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2
Q

what disease is epstein barr virus linked to

A

mononucleosis

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3
Q

in chronic latent infection of EBV, how is it controlled?

A

it is controlled by the host immune system

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4
Q

what are post transplant lymphoproliferative disorders results of?

A

reactivation of latent ebv

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5
Q

what are the genetic programs realized by ebv?

A

Latency 1,2,3

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6
Q

t or f: ebv is found in all burkitt lymphomas and many ebv infected people have lymphomas

A

false: ebv is found in all burkitt lymphomas but many ebv infected people remain lymphoma free

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7
Q

what are ways to classify human disease according to genetics?

A
  1. chromosomal diseases
  2. single gene disorders
  3. polygenic (complex or multifactorial)
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8
Q

what are ways to find whether a certain disease has genetic components?

A
  1. use classical family study
  2. use twin studies
  3. use adoption studies
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9
Q

how does one conduct a classical family study?

A
  1. identify the family
  2. determine the proportion of the relatives affected
  3. calculate the lifetime risk
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10
Q

what is the relationship when describing the calculation of the lifetime expectation?

A

somewhat linear

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11
Q

what studies show greater risk to relatives of affected individuals than that of the population incidence?

A

family, twin, and adoption studies. This is due to genes being shared more with your relatives than a random stranger

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12
Q

what problem does using twin studies solve?

A

the problem of assigning the shares for genetic and environmental components

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13
Q

what is the rate of concordance in identical twins an important indicator of?

A

heritability

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14
Q

what is the concordance in genetic and environmental conditions for twins?

A

genetic conditios concordance is near 100% and environmental conditions it is never 0%

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15
Q

for multifactorial conditions, which has a greater concordance MZ or DZ?

A

MZ concordance is greater than DZ concordance in multifactorial conditions

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16
Q

what are the difficulties with twin studies?

A
  1. rarity of twins
  2. more concordant pairs of twins being enrolled in studies than discordant
  3. MZ twins often sharing environment more than DZ
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17
Q

how are difficulties of twin studies solved?

A

with the study of separated twins

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18
Q

how are adoption studies done?

A
  1. evaluating incidence of the disease in the biological relatives and adoptive relatives
  2. figure out relative importance of the genetic and environmental contributor
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19
Q

concerning human weight, genetic influences have an important role in determining what? what role does the family environment play?

A

genetics influences fatness in adults and family environment has no apparent effect

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20
Q

what human characteristics are inherited as normally continuously distributed?

A

weight, height , and skin color

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21
Q

T or F: heritability is the mode of inheritance

A

False: heritability is not the mode of inheritance, mode of inheritance is a fixed property of a trait but heritability is not

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22
Q

Pure environmental disease also could be viewed as what?

A

as determined by genes, such as having a pseudo lethal mutation causing trauma seeking behavior

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23
Q

what is the formula for total phenotypic variance?

A

Ve + Vg=Vp where Ve is the variance within identical genotypes, Vg is variance within identical environments and Vp is the total phenotypic variance

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24
Q

Liability to the condition is described as what?

A

as polygenic and normally distributed, if liability is above a threshold then they are affected

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25
Q

even in cases of dichotomous characters (diseases) inheritance could be what?

A

true polygenic

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26
Q

siblings of affected individuals cause the curve to shift in which direction?

A

to the right and have a higher average liability to the population mean and a greater proportion of them have liability exceeding the threshold so condition tends to run in families

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27
Q

what are the practical conclusions from the liability threshold model?

A
  1. as we get closer to the sick relative, greater the risk
  2. for someone who has more than one affected relative the risk are even greater
  3. for some characteristics, more severe the disease is in proband the stronger the risk is for the relative
  4. there is a difference in incidence of the disease between genders
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28
Q

t or f: we do not know what drives liability threshold model at the genetic level

A

True

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29
Q

t or f: cancers and common human disease have very few candidate genes

A

False, cancers and common human diseases have many candidate genes

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30
Q

how many gene players do monogenic disease typically have?

A

typically have more than one gene player

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31
Q

how much are rare and common diseases effected by genes?

A

rare disease are affected by genes alot, common disease are affected very little

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32
Q

what are the three ways to find CDCV genes?

A
  1. linkage analysis
  2. association studies
  3. linkage disequilibrium analysis
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33
Q

what are families linkage studies?

A

simple inheritance, single gene with major effect, and variant rate in the population

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34
Q

what is linkage analysis used for?

A

used for multi factorial disease

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35
Q

how is a linkage analysis done?

A
  1. get at least 200 affected sibling pairs and parents
  2. analyze with at least 300 polymorphic markers
  3. use gene hunter or mapmaker software to detect positional linkage
  4. identified areas are IBD or shared segments
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36
Q

how is linkage analysis done in many non related families?

A

done by using LOD score

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37
Q

what is the formula for LOD score?

A

LOD Score= (probability of obtaining the results assuming the two loci are linked)/ ( probability of obtaining the results assuming the two loci are not linked)

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38
Q

what is the odds ratio formula?

A

OR= (odds for minor allele carrier)/ (odds for non carriers) it can also be done as cross product as well

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39
Q

what are the reasons that an association between polymorphism and a complex disease may exist?

A
  1. the polymorphism is causative for the disease
  2. association is a false positive due to random chance
  3. polymorphism is associated because of some systematic biased in the biology, study, samples analysis
  4. polymorphism is in disequilibrium with the true causative allele
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40
Q

what are the methods for proving that the variant is causative for the disease?

A
  1. using indirect clues such as SNP in the promoter changing gene expression
  2. sherlock holmes method
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41
Q

how are genome wide association assays done?

A
  1. scanning the entire genome with a dense collection of genetic markers
  2. calculating association at each polymorphic marker along the genome
  3. identify regions which show significant associations
  4. study possible disease contributing genes from the linked region in functional assays
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42
Q

what is the evidence that alzheimers is genetic?

A
  1. if the a first relative has alzheimers then it is a 30% greater risk
  2. twin concordance rates are 30-80% MZ and 10-40 DZ
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43
Q

how is alzheimers inherited more than 99% of the time?

A

as a multifactorial disease

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44
Q

what are the genetic and environmental factors that contribute to alzheimers?

A 
genetic factors are the genes like apo e4
environmental factors are: 
1. head injuries
2. high BP
3. high cholesterol
4. heart disease
5. stroke 
6. diabetes
7. smoking
8. engaging in active learning
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45
Q

patients with mutations in what genes will develop alzheimers earlier than those with PSEN1 and E3/E2 alleles?

A

PSEN1 and apo e4 allele

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46
Q

risk for AD after what is much greater in individuals with one or more apo e4 alleles?

A

severe head injury with loss of consciousness

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47
Q

what is normal plasma glucose?

A

3.9-8.3 mM

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48
Q

what is high plasma glucose bad?

A
  1. activates the protein kinase C beta
  2. glycation
  3. oxidative stress
  4. depletes NAD+ (metabolic pseudohypoxia)
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49
Q

hyperglycaemia induced activation of DAG PKC pathway leads to what?

A

vascular dysfunction in kidneys

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50
Q

what are some complications with a diabetic kidney?

A
  1. leaks proteins

2. high BP whcih always develops of worsens in diabetic neuropathy and can be the first abnormality to develop

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51
Q

what is diabetes 1 abbreviation?

A

IDDM for insulin dependent diabetes mellitus and is juvenile onset

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52
Q

what is the abbreviation for diabetes type 2?

A

NIDDM for non insulin dependent diabetes mellitus and is adult onset

53
Q

diabetes type 1 consists of hypoinsulinemia that requires what?

A

insulin injections

54
Q

diabetes type 1 that consists of an autoimmune disease part that does what?

A

beta cells are destroyed by T cells and several antibodies against beta cells are circulating

55
Q

what are the diabetes type 1 risk factors from the environment?

A
  1. cow milk that leads to antibodies against cow insulin that resembles human insulin
  2. viral infection of mumps, rubella, and coxsackie
56
Q

hyperinsulinemia and obesity is associated with which type of diabetes?

A

type 2

57
Q

how would one describe the mode of inheritance of IDDM type 2?

A

very complex

58
Q

what kind of disease is hirschprung disease?

A

oligogenic disease

59
Q

what are the three kids of neural tube defects?

A
  1. spina bifida occulta
  2. meningocele
  3. myelomeningocele
60
Q

what are the risks associated with elevated homocysteine levels?

A
  1. CAD
  2. peripheral arterial disease
  3. dementia
  4. having a child with neural tube defect
61
Q

what is the hierarchy of risk when it comes to schizophrenia?

A

with the highest risk are identical twins > fraternal twins > children > siblings > parents

62
Q

genes that make women more vulnerable to breast cancer appear to be protected against what?

A

bipolar disorder and schizophrenia

63
Q

what is the relationship between schizophrenia, bipolar, and autism?

A

there is a strong positive correlation because they are caused by a common group of genes

64
Q

predisposition to migraines has a strong correlation to what?

A

autism

65
Q

Hep B and meningococcus overlap with what kinds of diseases?

A

neurological diseases like migraines, autism, and schizophrenia

66
Q

your ancestry and your traits can be found typically how?

A

with the help of a DTC report

67
Q

why are risk predictions from DTC so different?

A

because companies use differing sets of markers with moderate to high odds ratios

68
Q

what are the types of mutations?

A
  1. point mutations
  2. regulatory point mutations
  3. alternative splicing point mutations
  4. deletions/insertions
  5. retrotransposition
  6. unstable repeat expansion
69
Q

what happens in a nonsense mutation

A

a stop codon appears

70
Q

what are the ways of damage control?

A
  1. mRNA with premature stop codons getting degraded

2. truncated proteins that are synthesized getting degraded in the ER

71
Q

what are people with duffy negative phenotype resistant to?

A

p. vivax (malaria) invasion

72
Q

what do human genes contain?

A

INTRONS

73
Q

slippage of DNA replication leads to what?

A

deletions or insertions causing misalignment making a loop in the nascent strand and increase the repeat length. Same happens on template strand causing decrease of repeat length

74
Q

what are the two possible outcomes for in frame deletions?

A
  1. is that protein is too short and doesnt fold and gets degraded
  2. protein comes out too short but still folds ok
75
Q

what does unequal crossing over cause?

A
  1. disruption of the entire genome
  2. change gene structure
  3. produce fusion of genes
76
Q

what does slippage probably cause?

A

an increase in the size of the triplet repeat

77
Q

unstable repeat expansion causes what?

A

suppression of FMR1 gene and results in fragile X syndrome

78
Q

what are the ways expanded repeats cause disease?

A
  1. repeats in the protein coding sequences make toxic proteins
  2. repeats in the RNA coding regions causes altered RNA function
  3. repeats in non coding regions cause reduced transcription or translation
79
Q

what are the two kinds of functional classes of mutations?

A

loss and gain of function mutations

80
Q

what kind of traits do loss of function mutations cause?

A

recessive

81
Q

what is haploinsufficiency such as osteogenesis imperfecta aka brittle bone disease an example of?

A

loss of function causing a dominant trait

82
Q

what are some dominant loss of function mutations called?

A

dominant negative or antimorphic mutations

83
Q

by how much do mutagens increase mistakes?

A

increase mistakes by 100,000 or 1000 per replicated gene. mutations overload natural repair systems of the human genome

84
Q

what are the different classes of mutagens?

A
  1. chemical
  2. physical
  3. biological
85
Q

what are examples of of chemical mutagens?

A
  1. alkylating agents
  2. aromatic hydrocarbons
  3. intercalating agents (fluorescent dyes)
  4. artificial derivatives of DNA bases
86
Q

what are physical examples of mutagens?

A
  1. ionizing radiation

2. UV radiation

87
Q

what are biological examples of mutagens?

A
  1. viruses

2. transposable elements

88
Q

what is point mutation in the biochemical view point?

A

deamination

89
Q

what do many mutagens intercalate into?

A

DNA

90
Q

UV exposure causes what?

A

thymine dimers, a specific damage

91
Q

what are the steps to fix a thymine dimer?

A
  1. DNA glycosylase removes base
  2. AP endonuclease makes cut
  3. excision exonuclease removes stretch of DNA
  4. Polymerase synthesizes new DNA
  5. DNA ligase seals nick
92
Q

what does lots of sun exposure do to our repair systems?

A

overloads it

93
Q

what are the outcomes when the repair job introduces a wrong nucleotide leading to a point mutation?

A
  1. mutation in germline may be passed to an offspring (worst case scenario)
  2. mutation in somatic cell might lead to cancer (not good scenario)
  3. most cases mutations in somatic cells dont produce effect (best case scenario)
94
Q

de novo mutations in germplasm leads to what?

A
  1. spontaneous abortion, 2. baby with genetic syndromes

3. nothing, baby inherits mutations towards evolution

95
Q

de novo mutations in somatic cells leads to what?

A
  1. cell death
  2. improperly functioning cell
  3. cancer
  4. nothing happens, it never gets inherited and its lost in evolution
96
Q

how often do mutations happen in the egg or sperm

A

rarely

97
Q

mutations usually happen where?

A

in the germline cells which are the precursors of sperm and eggs

98
Q

mutation rates for base substitutions is much higher in who?

A

males than in females and increases with paternal age

99
Q

what is the rate of mutation in humans?

A

very high spontaneous mutation rate

100
Q

how many new mutations does a new born have?

A

50-100 new mutations in their genome

101
Q

what explains high frequency of conditions that causes reduced fecundity?

A

high frequency of de novo mutations

102
Q

what is paternal age a strong contributor to?

A

to a number of de novo mutations per genome

103
Q

PAE mutations provide selective advantage for who?

A

mutated cells through dysregulation of spermatological cell behavior by growth factor receptor RAS signal transduction pathway

104
Q

what are the three scenarios for spermatological mutations?

A
  1. functionally neutral mutations
  2. typical PAE mutations
  3. intermediate scenario
105
Q

what are the steps for identifying a causative de novo mutation?

A
  1. sequence the genome
  2. select only coding mutations
  3. exclude known variants seen in healthy people
  4. sequence parents and exclude their private variants
  5. look at affected gene function and mutational impact
106
Q

what helped show the mutation rate in humans?

A

pseudogene resequencing (no selection)

107
Q

what are the ways that point mutations occur?

A
  1. oxidation
  2. methylation
  3. hydrolysis
108
Q

what are transitions?

A

when a purine is paired to another purine and pyrimidine is paired with another pyrimidine. Most common and due to tautomeric shifts or ionizing mispairs can happen

109
Q

what are transversions?

A

when purine pairs with pyrimidine and vice versa. Pairing is energetically favorable but are possible

110
Q

what other kind of mutation is in the same class as point mutation?

A

carcinogenic mutation

111
Q

what kind of mutation is unlikely to awaken apoptosis and is more tolerable for cell reparation?

A

point mutation

112
Q

what are the different rate of mutations in human genes?

A
  1. random gain
  2. forced gain
  3. very high rate
113
Q

human lymphocytes can survive treatment with 6 thioguanine a poison if only what happens?

A

if only the HPRT gene is mutated

114
Q

how are HPRT assays done?

A
  1. treating cells with 6 thioguanine
  2. counting colonies that survived
  3. if colonies remain then HPRT mutations, if no colonies then no mutation
115
Q

classical HPRT assays in lymphocytes do not support any hypothesis explaining what?

A

explaining population variance of the mutational load

116
Q

T or F: somatic mutation rates are the same as germline mutation rates

A

False, somatic mutation rates are different from germline mutation rates?

117
Q

between somatc, germline and mitochondria, who has the highest rates of mutation?

A

mito mutation rates > somatic cells > germline

118
Q

how is the extent of DNA damage measured in comet assays?

A

measured by the size and intensity of the tail produced from a single nucleus following electrophoresis

119
Q

what happens in airways cell following exposure to whole smoke?

A

oxidative DNA damage

120
Q

PAH’s polycyclic aromatic hydrocarbon derivatives do what?

A

bind and damage DNA

121
Q

most syndromes caused by mutations in DNA repair genes cause what?

A
  1. progeria
  2. short life span
  3. cancer
122
Q

syndromes connected to mutations in reparation related genes are associated with what?

A

an increase in cancer incidence

123
Q

what is the modern concept of checkpoints?

A

several checkpoint genes such as ATR and Chk1 are essential for cell and organism survival

124
Q

what are checkpoint pathways?

A

surveyors of occasional damage and integrated components of cell physiology

125
Q

what do damage checkpoint pathways do?

A
  1. controlling cell cycel arrest
  2. activate DNA repair pathways
  3. activate different transcriptional programs
  4. induce apoptosis
  5. control telomere length
126
Q

what are examples of repair requiring events being apart of the normal life of our body?

A
  1. stalled replication forks need to be removed during regular cell divisions
  2. DSBs in normal VDJ recombination
  3. repair in meiosis
  4. cells under high oxidative stress and long living cells need repair
127
Q

ATM carriers develop breast cancer in response to what?

A

radiation since they have higher radiosensitivity and TB screens and mammograms are harmful as well

128
Q

what kind of gene is ATM?

A

a true suppressor gene

genetics concepts (13 decks)

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