Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

McG > Quiz 5 > Flashcards

Quiz 5 Flashcards

1
Q

SNV

A

single nucleotide variant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

SNP

A

single nucleotide polymorphism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

VUS

A

variation of unknown significance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

pathogenic variation

A

mutation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

microsatellites

A

di and trinucleotide repeats important in gene mapping and pathogenesis - sometimes can result in disruption of txn, tln, or protein function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

somatic vs germline variant

A

SOMATIC: mutation occured AFTER fertilization so not in all cells in the body, can be tissue or organ specific
GERMLINE: mutation occurred before fertilization so generally in every cell in body incl. spermatocytes and ooctyes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

recessive inheritance usually leads to

A

loss of function when get an inherited copy from BOTH parents. half normal abundance is adequate in carrier state

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

gaucher’s disease is an example of

A

autosomal recessive inheritance (anemia, growth retardation, moderate to sever hepatomegaly, moderate to severe splenomegaly)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

what causes gaucher’s

A

glucocerobroside usually broken down by glucocerebrosidase into glucose and ceramide. in gaucher’s get a build up.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

how can you do an enzyme activity assay

A

4MU+substrate catalyzed by a specific enzyme to seperate these - concentration of protein alone is proportional to enzyme activity

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

dominant inheritance results in

A

gain of function or loss of function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

what are subtypes of loss of function

A

haploinsufficiency: one copy of the gene is enough (this is opposite of dominant)
dominant negative: one copy of gene messes up all the others (collagen)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

when do you get male to male transmission

A

dominant inheritance

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

x linked inheritance results in

A

gain of function, loss of function (dominant negative)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

who is affected in x linked inheritance

A

females less affected, no male to male transmission

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

allelic heterogeneity

A

different variations in one gene can have different effects on phenotype

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what happens in bone if FGFR3 is constitutively activated

A

get molecular signaling at growth plate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

achondroplasia (inheritance and mutation)

A

AD inheritance

Mutation causes constitutive activation of FGFR3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

hypochondroplasia (inheritance and mutation)

A

AD inheritance, mutation also causes activation of FGFR3 but to a lesser extent so phenotype is less affected

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

thanatophoric dysplasia (inheritance and mutation)

A

AD inheritance, mutation also causes activation of FGFR3 but usually not compatible with life

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

genetic or locus heterogeneity

A

mutations in different genes can cause a similar phenotype (EX: many genes affect primary cilia!)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

bardet biedl syndrom inheritance and mutation

A

Autosomal recessive and associated with multiple genes involved in the primary cilia

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

bardet biedl syndrome clinical features

A

obesity, retinal rod/cone disease, renal disease, plydactyly and brachydactyly, abnormal genitalia, low fertility

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

why is the primary cilia important

A

required for the cell to receive signal and stimuli (hormones, chemokines, growth factors). Important in Wnt and SHH pathways

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

triplet repeat expansions

A

expansion of a simple sequence repeat

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

disease caused by simple sequence repeats

A

huntingtons (polyQ) - expansion predominantly in males

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

clinical features huntingtons

A

progressive movement disorder, dementia, seizures, atrophy of caudate nucleus

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

penetrance options

A 
complete (mutation = disease) 
incomplete (skips generations)
age related (symptom onset with age)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

anticipation

A

increased severity in later generations (ex huntingtons where expansion will continue)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

what is neurofibromatosis caused by

A

mutation of NF1 gene

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

neurofibromatsosis inheritance

A

AD, 100 % penetrant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

clinical features neurofibromatosis

A

neurofibromas, cafe au lait spots, freckles, bony lesions, optic glioma

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

what does NF1 regulate

A

RAS signaling. In neurofibromatosis, lose NF1 signaling with increases RAS signaling

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

pleiotropy

A

gene affects many different tissues

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

how do you get somatic mosaicisms

A

fertilized zygote doesn’t carry mutation, happens spontaneously in one spot and remains clustered

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

proteus syndrome

A

AKT1 mutation. segmented - only affects specific parts of the body

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

germline mosaicism

A

germ cell progenitor cells carry mutation, cause risk of recurrence in family

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

what happens with mutations in conserved intron splice donor/acceptor sites

A

misspliced transcripts

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

ESE

A

exonic splice enhancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

what do mutations in ESE cause

A

missplicing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

anticipation

A

increased disease severity manifesting as earlier age of onset in succeeding generations

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

pleiotropy

A

one gene influences multiple, seemingly unrelated phenotypic traits.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

how many newborns have major anomalies

A

2-3%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

how many newborns have minor anomalies

A

15%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

death percentages attributed to anomalies

A

20-30% infant deaths

30-50% deaths of neonatal period

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

deformation

A

developmental process is normal but mechanical force alters structure
ex: external forces: oligohydramnios (not enough amniotic fluid) can be secondary to renal hypoplasia

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

ex of deformations

A

Potter’s Facies

Clubbed Feet

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

disruption

A

developmental process is NORMAL but interrupted

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

examples and causes of disruption

A

vascular accident - amniotic band sequence or fetal cocaine exposure, porencephaly

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

malformation

A

morphological, macroscopic defect from an INTRINSICALLY abnormal developmental process

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

ex of malformation

A

holoprosencephaly, congenital heart disease, neural tube defect, unilateral cleft lip and palate

52
Q

dysplasia

A

abnormal microscopic tissue organization and development

53
Q

ex of dysplasia

A

skeletal or connective tissue dysplasia, ectodermal dysplasias

54
Q

sequence

A

a series of congenital anomalies derived from a single anomaly - can be part of a syndrome or an isolated event

55
Q

ex of sequence

A

pierre robin sequence

56
Q

sydnrome

A

a recognizable pattern of anomalies presumed to be causally related, and NOT a sequence

57
Q

associations

A

a group of congenital anomalies that co-occur more frequently than expected by chance. these are of unknown etiology.

58
Q

FAS

A

fetal alcohol syndrome caused by the fetus being exposed to alcohol

59
Q

teratogen

A

exposure during pregnancy that has a harmful effect on the developing fetus

60
Q

ex of teratogens

A

maternal phenylketonuria (PKU), maternal diabetes, TORCH infections, anticonvulsants, retinoic acid embryopathy

61
Q

what is more common, cleft lip and palate or cleft lip alone

A

CLP more common, more frequent in mailes

62
Q

what causes Van Der Woude

A

AD dominant mutations in interferon regulatory factor IRF6 - lip pits and cleft lip, palate

63
Q

IRF6 mutation

A

Van der Woude (lip pits, CLP CLA)

64
Q

what typically causes developmental disorders

A

txn factors (25-35%)
enzymes (19%)
structural proteins (18%)
receptors (9%)

65
Q

what is homeobox (HOX) involved in

A

patterining (anterior, posterior, head, tail)

66
Q

unmethylated genes are usually (active vs inactive)

A

active

67
Q

methylated genes are usually

A

repressed

68
Q

MOST CpG dinucleotides are

A

methylated (repressed)

69
Q

anhidrotic ectodermal dysplasia in heterozygous woman caused by

A

mutation in EDA gene

70
Q

praeder willi and angelman syndrome are caused by

A

mutation in proximal chr15 - same mutation with different outcomes depending on maternal/paternal because imprinted

71
Q

agouti encodes for

A

yellow pigment hair color gene

72
Q

what does normal agouti expression give

A

brown coat (yellow coat is when agouti is turned ON and you also get tumors)

73
Q

insulin like growth factor affected by

A

reduced methylation at promoter in individuals who conceived during the famine

74
Q

x chromosome modification is a mechanism of

A

dosage compensation

75
Q

pharmacogenetics

A

study of drug response in relation to genetic variation in specific candidate genes

76
Q

pharmacogenomics

A

study of drug response in relation to genetic variation in the entire genome

77
Q

pharmocokinetics implications (PK)

A 
ADME 
A: Absorption
D: Distribution
M: Metabolism
E: Elimination
78
Q

pharmacodynamics (PD) implications

A 
receptor interactions
ion channel interactions
enzyme interactions
signaling pathway interactions
immune system interactions
79
Q

what genes are responsible for metabolism of a lot of medications

A

P450 (CYP2C9, CYP2C19, CYP2D6)

80
Q

what are CYP450s

A

a large diverse superfamily of hemoproteins that catalyze hydroxylation and other metabolic reactions. MAJOR ENZYMES involved in drug metabolism and bioactivation

81
Q

what gene metabolies 20-25% of all medications

A

CYP2D6

82
Q

what is VKORC1 associated with

A

warfarin dose requirements

83
Q

what is warfarin used for

A

widely used anticoagulant for prevention of thrombosis and embolism

84
Q

what is the mechanism of warfarin

A

impairs synthesis of vitamin K dependent clotting factors

85
Q

why is use of warfarin complicated clinically

A

wide individual differences in drug response, narrow therapeutic range, high risk of bleeding or stroke

86
Q

LOOK AT WARFARIN PATHWAY

A

?

87
Q

what is warfarin’s target

A

VKORC1 which is important in vitamin K reduction cycle and is necessary for clotting factors to become carboxylated so they can continue in clotting cascade

88
Q

what is a common tx for patients with acute coronary syndromes or undergoing percutaneous interventions

A

clopidogrel (plavix) and aspirin

89
Q

variable response in plavix (clopidogrel) due to PK and PD

A

PK: metabolites
PD: ex vivo platelet aggregation

90
Q

LOOK AT CLOPIDOGREL (PLAVIX PATHWAY

A

?

91
Q

where are plavix and warfarin absorbed and metabolized

A

absorbed in intestine, metabolized in the liver

92
Q

what kind of drug is plavix

A

pro drug because P450 activation steps are what generates the metabolite. THEN it can travel to platelets and bind irreversibly

93
Q

what gene is involved in active AND inactive pathway in plavix

A

CYP2C19

94
Q

what is the issue with *2 carriers in plavix tx

A

they do not get anticoagulation effects - these individuals have increased risk of death from cardiovascular causes, MI, or stroke compared to non carriers

95
Q

karyotype

A

arranging chromosomes into pairs

96
Q

protein coding genes comprise what percentage of DNA

A

1.5%

97
Q

conserved region of DNA through evolution

A

2-5%, suggests functionality. Many probably regulatory elements

98
Q

why would there be a specific area of the genome where there aren’t many mutations

A

because some areas end up in very unregulated development if mutated so wouldnt get passed down (ex: HOX)

99
Q

microarray

A

fluorescently labeled DNA is hybridized to an array of probes on a glass slide that bind either normal or variant DNA

100
Q

microarray comparative genomic hybridization

A

use control and test DNA - two different fluorescent dyes but hybridize them together on same slide

101
Q

why can DNA polymerase get confused at tandem repeat areas

A

because these dinucleotide repeats can form a strong secondary structure

102
Q

fragile X

A

get over 200 repeats (50 is max normal) of CGG near FMR1 gene on ChrX. DNA polymerase has trouble replicating here so get pinched off area where genes aren’t being transcibed

103
Q

salivary amylase

A

large tandem repeat area that contains entire gene

104
Q

CCL3L1

A

copy number inversely correlates with susceptibility to HIV infection

105
Q

allele frequence

A

proportion of CHROMOSOMES in a population carrying a particular allele at some locus

106
Q

genotype frequency

A

proportion of individuals in a population with a particular genotype at some locus

107
Q

in HW equilibirum
A,a
P
Q

A

A,a: alleles at a single locus

p: relative frequency of A
q: relative frequency of a

P+Q=1

108
Q

things to consider for HW equilibirum

A

It takes into consideration that population is indefinitely large or large enough to neglect errors, mating in population occurs at random, there is no advantage for any genotype, no migration and new mutations.

109
Q

HW law

A

p^2 + 2pq + q^2=1
P+Q = 1

All allelic frequencies will remain constant over time if certain conditions are met

110
Q

what causes derivation from HWE expected frequencies

A 
Genotyping Errors 
Selection
Genetic Drift
Non-random Mating
Population Structure
111
Q

deleterious mutations

A

mutations that increase
mortality or reduce fertility [dominant ones – cannot
escape selection upon first appearance; recessive ones –
can accumulate in a population].

112
Q

does genetic drift produce adaptations

A

NO - completely random. Some individuals will just by chance leave behind a few more descendents.

113
Q

founder effect

A

population descended from a few colonists - can have higher proportion of disease in these populations

114
Q

non random mating due to

A

mate selection and inbreeding (mates selected from within own communities which results in positive assortative effects on their gene pool)

115
Q

non random mating (inbreeding) can cause evolution of

A

subpopulations

116
Q

HWE issues

A

assumes sample came from single population, actually may be from 2+ with different allele frequencies. Usually has higher than expected homozygosity and sometimes has false positive associations.

117
Q

what can happen if cases and controls are not well matched ancestrally

A

any allele more common in population with increased risk of disease may appear to be associated with that disease, even if it isnt

118
Q

AIM

A

ancestry informative markers. set of polymorphisms which exhibit substantially difference frequencies between populations from different geographical regions.

119
Q

linkage disequilibrium (LD) description

A

non random association of alleles at two or more loci

120
Q

D and r^2 in LD

A

D’ varies from 0 (complete equilibrium) to 1 (complete disequilibrium) *DOES NOT ADEQUATELY ACCOUNT FOR ALLELE FREQUENCIES.

r^2 is correlation between SNPs, preferred measure.

121
Q

D and r^2 = 0

A

typing one SNP provides no info on other

122
Q

D or r^2 >0.8

A

two SNPs are in LD - typing one provides information on others

123
Q

what will have more linkage equilibriums, new or old populations>

A

new, isolated populations

124
Q

what does array CGH provide

A

genome wide view of copy number variations

125
Q

what can array CGH not tell us

A

cannot detect chromosomal abnormalities that maintain normal copy numbers (balanced translocation, inversion) OR data on repeat rich regions such as centromeres and heterochromatin

126
Q

what is FISH useful for

A

deletion or duplication of genomic regions too small to be detected by karyotype analysis

McG (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions