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MS1 Fall > Genetics 1- 10 > Flashcards

Genetics 1- 10 Flashcards

1
Q

Sildenafil (Viagara) works by

A

blocking the enzyme PDE5, which relaxes arteries & results in increased blood flow

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2
Q

Transformation

A

ability to deliver foreign DNA to cells, both prokaryotic and eukaryotic

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3
Q

Plasmid

A

Autonomously replicating DNA molecule; single origin of replication & can replicate itself in bacterial cells

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4
Q

Restriction endonucleases (enzymes)

A

molecular scissors to selectively cut DNA

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5
Q

Selection

A

methods to rapidly select those host cells that contain recombinant DNA

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6
Q

Personal genomics

A

branch of genomics where the genotyping stage employs single-nucleotide polymorphsm (SNP) analysis (0.2%of genome) or partial/full genome sequencing

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7
Q

Kinetochore

A

repeated sequence known as alpha satellite DNA

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8
Q

Telomere length is controlled by

A

erosion and addition

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9
Q

Chronic myeloid leukemia (CML)

A

malignant transformation of hematopoietic stem cells; accounts for 20% of all adult leukemias

caused by translocation between chromosomes 9 and 22 (BCR-ABL oncogene creation). Philadelphia chromosome!

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10
Q

CML is classified into three phases

A

chronic phase (less than 10% blasts), accelerated phase (10-20% blasts), and blastic phase (20% or more). These phases are based mainly on the number of immature white blood cells, myeoblasts, seen in the blood or bone marrow

Chronic is the most treatable phase

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11
Q

Philadelphia Chromosome

A

a reciprocal translocation between chromosomes 9 and 22

The ABL1 proto-oncogene encodes a cytoplasmic and nuclear protein tyrosine kinase; it is moved adjacent to BCR (breakpoint cluster region protein) on chromosome 22

BCR-ABL is a mutant tyrosine kinase that stimulates uncontrolled cell division of abnormal blood cells by the bone marrow

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12
Q

Epigenetics

A

heritable alternations in gene expression, which are not due to structural changes in the DNA; induced spontaneously

Methylation (turns gene off)
Acetylation (turns gene on)
Phosphorylation (positive and negative consequences)
Ubiquination (targets histones for degradation)
Sumolaytion (promotes gene silencing by affecting histones)

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13
Q

Functions of DNA methylation in mammals

A

Transcription gene silencing
genome stability
chromatin compaction
X chromosome inactivation (females)

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14
Q

Etopside (VP-16)

A

derivative of podophyllotoxin from the mandrake plant
etopside inhibits the re-ligation of the strands resulting in the accumulation or irreversible double strand breaks lethal to cells

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15
Q

snRNA

A

small nuclear RNAs, complexed with protein in the nucleus, invovled in RNA splicing

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16
Q

snoRNAs

A

small nucleolar RNAs, used to process and chemically modify rRNAS

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17
Q

Spinal Muscular Atrophy (SMA)

A

Second most-common recessive human disorder and the most common inherited cause of infant mortality

Mutations in the SMN1 encoding the survival motor neuron (SMN) protein cause SMA

SMN is needed in pre-RNA splicing

SMN2 is already damaged in us so it can’t make up for a errors in SMN1

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18
Q

Cryptic splice site

A

a randomly occurring site in the genome that contains a consensus sequence for 5’ or 3’ intron splicing but is not normally used for that purpose, until mutated

ex: progeria

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19
Q

Hutchinson-Gilford progeria syndrome (HGPS)

A

a point mutation activates a cryptic splice site and thus leads to the production of a mutant prelamin A protein, progerin. An internal cleavage site is removed, and the progerin protein is never properly cleaved (leaving it permanently farnesylated and carboxymethylated)

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20
Q

ncRNA (non-coding RNA)

A

a functional RNA molecule that is not translated into a protein

ex: rRNA, tRNA, snoRNA, microRNA, siRNA, piRNA, and long ncRNAs

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21
Q

Xist

A

non-coding RNA gene on the X chromosome that participates in X chromosome inactivation

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22
Q

miRNA

A

post-transcriptional regulators that bind to complementary sequences in multiple target mRNAS, usually resulting in translation repression or target degradation and gene silencing

(Dicer chops it up and then miRNA complexes with the RISC complex to attack mRNA)

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23
Q

siRNA

A

Small Interfering RNA - double-stranded RNA molecules that can be chemically synthesized and are used in therapeutic gene silencing (similar function to miRNA)

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24
Q

Gene drive

A

genetic systems that circumvent the traditional rules (50% chance of inheriting genes from either parent); they greatly increase the odds that the drive will be passed onto offspring

“Cas9 to the nth degree,” “eliminating Mendellian genetics”

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25
Q

circular RNA

A

ciRNAs might modulate RNA polymerase II in cis and thereby alter the expression of their gene.

ciRNAs also accumulate in the nucleus and can be localized to their sites of transcription

function as an miRNA sponge?

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26
Q

centimorgan (cM)

A

the genetic distance between two loci that yields recombination in 1% of gametes

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27
Q

LOD score

A

statistical measure of the likelihood of odds that the observed marker is indeed linked and not inherited with disease by chance

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28
Q

SNVs

A

single nucleotide variation seen in a single family or individual

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29
Q

CNVs

A

copy number variations - duplications or deletions, often 1000 to several million bp

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30
Q

Genome-Wide Association Study (GWAS)

A

how we map for polygenic traits

compare 100,000s of polymorphisms between cases and controls and identifies SNPs frequently associated with case

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31
Q

Levels of gene expression control in eukaryotes

A
  1. Chromatin structure
  2. Epigenetics control
  3. Transcriptional initiation
  4. Transcript processing and modification
  5. RNA transport
  6. Transcript stability
  7. Control of transcript mRNA levels by non-coding RNAs
  8. Post-translational modification
  9. Protein transport
  10. Control of protein stability
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32
Q

Regulation of transcriptional activators

A
  1. Phosphorylation stimulates cytoplasmic proteins to move to the nucleus
  2. Ligand binding increases or decreases affinity for DNA
  3. Some are already bound to their target site but remain inactive until they are stimualted
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33
Q

3 parts of a nuclear hormone receptor

A
  1. AD - activation domain
  2. DBD - DNA binding domain
  3. LBD - ligand binding domain
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34
Q

Burkitt Lymphoma

A

A very fast growing version of non-Hodgkin’s lymphoma. Caused by reciprocal translocation of the c-Myc locus on chromosome 8 with iG enhancer on chromosome 14.

35
Q

Three clinical variants of Burkitt lymphoma

A
  1. Endemic - equatorial Africa along with Epstein-Barr virus
  2. Sporadic - outside Africa
  3. Immunodeficiency - usually associated with HIV or in post-transplant patients
36
Q

Penetrance

A

the percentage of individuals of a specific genotype showing the expected phenotype

can be fully penetrant (always expressed) or incompletely penetrant (only shown sometimes)

37
Q

Expressivity

A

measures the extent to which a given genotype is expressed in the phenotype (variability of a trait based upon a specific genotype)

38
Q

Roberts syndrome (RBS)

A

caused by a mutation in ESCO2, a human homolog of yeast ECO1, that is essential for the establishment of sister chromatid cohesion

RBS cells have too few or too many chromosomes that ultimately lead to aborted cell divisions

Present with hands and feet attached to abbreviated arms and legs (phocomelia)

39
Q

Phocomelia

A

congenital malformation in which hands and feet are attached to abbreviated arms and legs

Seen in Roberts Syndrome (RBS)

40
Q

Harlequin ichthyosis (HI)

A

severe, often fatal congenital ichthyosis with an autosomal recessive inheritance pattern caused by a defect in the ATP-binding cassette transporter ABCA12

presents with hyperkeratosis, ectropion, and eclabium

41
Q

hyperkeratosis

A

thickening of the stratum corneum, the outermost layer of the epidermis (fissures all over the body)

42
Q

ectropion

A

lower eyelid turns outward

43
Q

eclabium

A

the lips turn outward

44
Q

“Second hits” in retinoblastoma

A

non-disjunction, non-disjunction reduplication, mitotic recombination, gene conversion, deletion, and point mutation

45
Q

genetic imprinting

A

differential expression of a gene or chromosome region, according to the parent-of-origin of the allele

one parent’s allele is selectively silenced

“functional hemizygosity”

46
Q

hydatiform mole

A

two sets of paternal chromosomes only

47
Q

ovarian teratoma

A

two sets of maternal chromosomes only

48
Q

Prader-Willi Syndrome (PWS)

A

Paternal-only genes on chromosome 15 fail to be expressed

49
Q

Angelman Syndrome

A

Maternal-only gene UBE3A on chromosome 15 fails to be expressed

50
Q

Four genetic mechanisms to PWS & Angelman

A
  1. Deletion (usually in a long-copy repeat area)
  2. Uniparental disomy (two copies of the chromosome from one parent)
  3. Mutation (more common in Angelman than PWS)
  4. Imprinting defect
51
Q

Epigenotype

A

epigenetic parent of origin information

typically reprogrammed between generations

52
Q

Myotonic Dystrophy Type 1 is caused by

A

Expanded CTG repeats in the 3’ UTR. Mild affect is 50-80 repeats. Severe is over 2000 repeats. CTG repeat length correlates with age of onset (more repeats, earlier age)

These CTG repeats are transcribed into CUG repeats. The CUG RNA sequesters RNA binding proteins like MBNL.

MBNL can now no longer perform its alternative splicing function, and muscle cells revert to fetal-like muscle cells which causes rigidity and myotonia

53
Q

cytogenetics

A

brand of genetics focused on the structure and function of chromosomes

54
Q

G-banding detects the following cytogenetic anomalies:

A
  1. Deletions > 5Mb
  2. Some translocations
  3. Aneuploidy
  4. Mosaicism
  5. Ring, marker, and isochromosomes (fragments)
55
Q

Acrocentric chromosomes

A

13, 14, 15, 21, and 22

56
Q

Aneuploidy

A

abnormal number of chromosomes

57
Q

Edward’s Syndrome

A

Trisomy 18

rare to survive until 6 months, often stillborn. Low birth weight, cleft palate, heart & kidney defects, irregularly shaped head

58
Q

Triploidy

A

three sets of chromosomes

85% are diandric (2 paternal). These fetuses are near normal size.

15% are digynic (2 maternal). These fetuses have intrauterine growth retardation.

59
Q

Unbalanced translocations

A

Arise from fertilization of a gamete with a balanced translocation

Result may be 46 chromosomes but monosomy and trisomy for some segments

80-90% are usually normal, whereas theoretical outcome would be 25%

60
Q

Robertsonian translocations

A

Between acrocentric chromosomes

Breakpoints at or near centromere and yield a metacentric or submetacentric chromosome (often dicentic)

Creates one giant chromosome and then a fragment piece thats usually lost

61
Q

Paracentric inversion

A

within one arm of chromosome

risk for liveborn children is low (but 50% are often not viable due to acentricity or dicentricity)

62
Q

Pericentric

A

inversion involving the centromere

risk for offspring is similar to balanced translocation

often less severe than paracentric because all chromosomes end up with a centromere

63
Q

Primary mechanism of duplications and deletions

A

nonallelic recombination between low copy repeats

64
Q

Marker chromosome

A

structurally abnormal chromosome often of unknown origin

ex: Cat Eye Syndrome

65
Q

Isochromosome

A

Separation along the wrong axis in anaphase creates a chromosome that is p/p or q/q

ex: Pallister-Killian Syndrome is a isochromosome tetrasomy of 12p

66
Q

Ring chromosome

A

Breaks on both p and q arms, ends fuse

Mitotically unstable

Yields a “dynamic mosaicism”

Heritable

ex: 6% of Turner syndrome cases are due to a ring X chromosome [ 46,X, r(X) ]

67
Q

Mosaicism

A

individual with 2 or more genetically different cell varieties; cell types differ due to mutation or nondisjunction

68
Q

Cytogenetic technologies

A

FISH
Microarray
SNP microarray
MS-MLPA

69
Q

FISH

A

Fluorescence in situ hybridization

Clinical applications: aneuploidy, microdeletions and duplications, marker chromosome, and to refine breakpoints of insertions, deletions, translocations, etc

Benefits: rapid analysis for high risk pregnancies

Limitations: may not detect low-level mosaicism or structural chromosome anomalies (only sees region complementary to probe)

70
Q

Charcot-Marie Tooth Type 1A

A

LCR-mediated duplication on chromosome 17

Demyelinating peripheral neuropathy, progressive distal muscle weakness and atrophy, sensory loss and slow nerve conduction

71
Q

Comparative Genome Hybridization (CGH)

A

Chromosome microarray where subject DNA is hybridized with reference DNA and applied to an array. You compare and can tell if there is an extra copy or missing copy.

Great for high resolution of location/breakpoints of deletions or duplications

Will NOT detect balanced translocations

72
Q

Chromosome microarray - SNP array

A

Detects variants (consanguinity) and copy number. The resolution is determined by the density of SNPs

73
Q

Benefits of microarrays

A

high resolution, objectivity, nondividing tissue, detect several disorders at one time

74
Q

Limitations of microarrays

A

Does not detect balanced rearrangements or point mutations; detects copy number variation of uncertain signifigance

75
Q

isodisomy

A

two copies of the same homolog from one parent

76
Q

Heterodisomy

A

two different homologs from one parent

77
Q

Factors affecting pathogenicity of anomalies

A

Extent of genome affected, location in genome, inherited vs. de novo

78
Q

DNA primase does what?

A

Makes RNA primer that initiates DNA replication

79
Q

Components of a human gene

A

Exons, Introns, a transcription start site, a promoter (base or core promoter AND an “upstream” promoter), TATA Box (positions RNAPII) and enhancers

80
Q

Factors influencing penetrance

A
  1. modifier genes
  2. Response to DNA damage
  3. Epigenetic factors: DNA methylation
  4. Age-related penetrance
81
Q

Types of nonmendelian inheritance

A

triplet repeats, genomic imprinting, mosaicism, mitochondrial inheritance

82
Q

Chromosomes are always named after what?

A

The source of the centromere

83
Q

Unbalanced translocations arise from what?

A

The fertilization of a gamete with a balanced translocation

84
Q

Limitations of microarrays?

A

Do not detect balanced rearrangements or point mutations

Detects copy number variations of uncertain significance

MS1 Fall (23 decks)

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