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GENETICS > Exam 2 Units 4-5 > Flashcards

Exam 2 Units 4-5 Flashcards

1
Q

What is a screen?

A

Screens help distinguish mutant and wildtype organisms from each other

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2
Q

What is forward genetics?

A

identify the gene responsible for a mutation or specific phenotype using mapping
(phenotype to genotype)

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3
Q

What is mapping?

A

The idea that genes are in certain areas of a chromosome and if we can identify landmarks on the chromosomes then we can determine where that genes resides on the chromosome

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4
Q

Which common mutagen(s) cause random mutations?

A

Ethyl methanesulfanate (EMS) and trans lesion synthesis

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5
Q

Which common mutagen(s) cause specific mutations?

A

Transposon hopping

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6
Q

What is a phase?

A

The configuration of alleles on a single chromosome

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7
Q

Explain a test cross

A

one parent homozygous recessive at all three loci (unless human disease mapping- then only need homozgy. recessive for gene in question), the other heterozygous (WT at all three loci- must be XX parent if x-linked)

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8
Q

How do you calculate the recombination fraction?

A

(total recombinant offspring) / (total observed offspring) * 100

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9
Q

What is the recombination fraction used for?

A

to calculate distance between middle and flanking genes

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10
Q

What is interference (of crossing over)?

A

the occurrence of one crossover reduces the likelihood that another will occur in adjacent parts of the chromosome

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11
Q

When do you use phenotypic markers?

A

in 3-factor mapping

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12
Q

When do you use molecular markers?

A

3-factor mapping for human disease

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13
Q

How do you determine which gene is in the middle in 3-factor mapping?

A

compare the parentals to the DC-Rs - find a pair that involves only one phenotypic difference. That one difference is the middle gene

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14
Q

which classes in a 3-factor mapping are the DC-Rs?

A

the 2 least frequent classes

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15
Q

which classes in a 3-factor mapping are the parentals (or NRs)

A

the 2 most frequent classes

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16
Q

what is reverse genetics?

A

select a specific gene and purposefully alter it, then identify the phenotype resulting from alteration

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17
Q

will you expect to see rigid inheritance of genes as a unit?

A

No

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18
Q

can you infer the order of genes in a 2-factor mapping cross?

A

No- only genetic distance between them

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19
Q

What is the cause of less than expected observed double cross overs?

A

interference

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20
Q

what is the maternal effect? when does it usually occur?

A

an inheritance pattern in which the genotype of the mother directly determines the phenotype of her offspring (usually occurs early in development)

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21
Q

what is gametogenesis?

A

the process by which gametes, or germ cells, are produced in an organism

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22
Q

what causes the maternal effect?

A

the accumulation of gene products that the mother provides to her developing eggs

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23
Q

What do maternal effect genes do?

A

encode RNA and proteins that play important roles in the early steps of embryogenesis (can include cell division, cleavage pattern, and body axis orientation)

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24
Q

what is Epigenetic Inheritance?

A

a pattern in which modification occurs to a nuclear gene or chromosome that alters gene expression (i.e. dosage compensation, genomic imprinting)

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25
Q

is the alteration of gene expression due to epigenetic inheritance permanent?

A

No, it is reversible

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26
Q

What is DNA Methylation and what does it result in?

A

Addition of a CH3 methyl group to a cytosine, typically in CG dinucleotide. Usually results in condensed (heterochromatin) chromatin and decreased transcription of nearby genes

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27
Q

What is the purpose of dosage compensation?

A

to offset differences in the number of active sex chromosomes (reduces active X chromosomes to 1)

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28
Q

what are the mechanisms of dosage compensation and what taxa would you expect to exhibit each mechanism?

A

placental mammals and marsupial mammals- one of the X chromosomes in the somatic cells of the female is inactivated
Drosophila - level of expression of genes in the X chromosome of the males is doubled
C. elegans - level of expression on each X in hermaphrodites is decreased to 50%

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29
Q

what is genomic imprinting and what does it result in?

A

a phenomenon in which a segment of DNA is marked and silenced and the effect is maintained throughout the life of the organism inheriting the marked DNA. The offspring expresses either the maternally-inherited OR the paternally inherited allele, never both.

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30
Q

what is mono-allelic expression?

A

Only one allele is expressed (paternal or maternal, not both)

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31
Q

explain the mechanism of imprinting

A
  1. establishment of the imprint during gametogenesis
  2. maintenance of the imprint during embryogenesis and in the adult somatic cells
  3. ensure reestablishment of the imprint in the germ cells
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32
Q

What are some similarities between epigenetics in dosage compensation and genomic imprinting?

A

in both, a portion of genomic info is silenced for the life of the individual

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33
Q

Explain the mechanism of mammalian X-chromosome inactivation

A

Random X-chrom inactivation occurs in early development.

During X-chrom inactivation, the DNA becomes highly compacted and most genes on the inactivated X cannot be expressed.

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34
Q

What happens if an inactivated X is replicated during cell division? (in Mammalian X-chrom inactivation)

A

Both copies will remain highly compacted and inactive. X-chrom inactivation is passed along to all future somatic cells

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35
Q

what is the Xic and what is its function during X-chrom inactivation?

A

the X-inactivation center - required for inactivation to occur.
Functions: Nucleation (# of Xics counted and chrom remains active while the other is targeted for inactivation), Spreading (begins at Xic and progresses toward both ends until the entire chromosome is inactivated and becomes a Barr body), and Maintenance (inactivated X chrom maintained as such during subsequent cell divisions)

36
Q

What is a Barr body?

A

A condensed, inactivated X chromosome

37
Q

What is extranuclear inheritance?

A

inheritance patterns involving genetic material outside the nucleus (i.e. mitochondria and chloroplasts)

38
Q

What is heteroplasmy (w/ respect to organelles)?

A

Having multiple versions of a chloroplast or mitochondrial
genome in a cell.

important factor in mitochondrial disease-
Cells contain a mixed population of mitochondria. Some may carry disease causing mutation while others do not- so as cells divide, some may receive a high ratio of mutant to normal mitochondria.

39
Q

Describe how Morgan’s experiments led him to propose that recombinants result from crossing over

A

If crossing over didn’t occur, you would expect to see only nonrecombinants, Morgan discovered that while the nonrecombinants (parentals) were most abundant, he also found a range of recombinants, some which were more likely to be observed than others.

40
Q

When should you use association mapping? (when should you not?) When is it most successful?

A

Good for common disease, not as strong for rare disease. Most successful when the causal variant is widespread in the population.

41
Q

When should you use Linkage in 3-factor mapping? When should you not use it?

A

Good for both common and rare diseases. Bad for diseases where the affected are unlikely to have children.

42
Q

what is a complex trait?

A

traits determined by several genes and are significantly influenced by environmental factors

43
Q

what is a quantitative trait?

A

a trait you can assign a number to (i.e. height)

44
Q

what is a categorical trait?

A

this OR that (i.e. yellow or green, tumor or no tumor)

45
Q

what is a continuous quantitative trait?

A

quantitative traits with a continuous range (i.e. height, skin color)

46
Q

what is heritability?

A

the extent to which genetic causes lead to phenotype of interest

47
Q

How do you calculate the variance of trait phenotypes? What does each variable stand for?

A 
Vp = Vg + Ve 
Vp = phenotype variance
Vg = genetic variance 
Ve = environmental variance
48
Q

How do you design an experiment where Vg = 0?

A

use highly inbred strains or identical twins

49
Q

what is the equation for broad sense heritability?

A

hB2 = Vg/Vp

50
Q

what is the equation for narrow sense heritability?

A 
hN2 = Va/Vp
Va= variance due to additive effects of alleles
51
Q

What is a QTL (Quantitative trait locus)

A

the location on a chromosome that harbors one or more genes that affect the outcome of a quantitative trait

52
Q

What are the approaches to measuring broad sense heritability?

A
  1. Correlation - see if the phenotype of the offspring correlates with the phenotype of the parents in the same environment
  2. Experiment - select extreme outliers and breed them. If the avg curve shifts in response to selection, they are additives
  3. Monozygotic/Dizygotic twin studies
53
Q

What type of individuals do you need to identify QTLs?

A

You need 2 different highly inbred strains of a diploid species. They must be different in regard to quantitative trait of interest and also in regard to MANY molecular markers.

54
Q

define variance

A

Variance is a measure of dispersion, meaning it is a measure of how far a set of numbers is spread out from their average value

55
Q

define standard deviation

A

the standard deviation is a measure of the amount of variation or dispersion of a set of values.
A low standard deviation indicates that the values tend to be close to the mean of the set, while a high standard deviation indicates that the values are spread out over a wider range

56
Q

What type of inheritance is seen for the transmission of Human Mitochondrial diseases?

A

Maternal inheritance

57
Q

define linkage

A

The tendency for genes or segments of DNA closely positioned along a chromosome to segregate together at meiosis, and therefore be inherited together.

58
Q

what is the result of segregation

A

separation of allele pairs

59
Q

What methods did Creighton and McClintock used to confirm Morgan’s hypothesis that genetic recombination is the result of physical crossing over?

A

Observed physical crossing over via microscopy AND genetic crossing over via trait inheritance in cross of maize (corn) strains.

60
Q

What are recombination hotspots?

A

regions in a genome that exhibit elevated rates of recombination relative to a neutral expectation

61
Q

What is a haplotype?

A

a set of DNA variations, or polymorphisms, that tend to be inherited together.
A haplotype can refer to a combination of alleles or to a set of single nucleotide polymorphisms (SNPs) found on the same chromosome

62
Q

What are haplotype blocks?

A

regions of chromosomes between the recombination hotspots. recombination is extremely rare in haplotype blocks.

63
Q

What is Linkage disequilibrium?

A

the nonrandom association of alleles at 2 loci - i.e. the alleles “stick together” (ex. haplotype blocks)

64
Q

Recombination hotspots, haplotypes, haplotype blocks, and linkage disequilibrium are all products of what?

A

the product of many generations of crossing over in a population

65
Q

How do you calculate the odds ratio for association?

A

odds (SNP = X, disease) / odds (SNP = Y, disease)

i.e. (disease/not disease for SNP X) / (disease/ not disease for SNP Y)

66
Q

when is your SNP (association) odds ratio considered significant?

A

if p < 10^-8

67
Q

What is the primary difference between association mapping and linkage mapping?

A

linkage analysis looks at the relation between the transmission of a locus and the disease/trait within families, and association analysis focuses on the relation between a specific allele and the disease/trait within a population

68
Q

what is association mapping?

A

finding the tendency of a molecular marker to co-occur with a disease phenotype within a population. Does not rely on heritability.

69
Q

explain epistasis

A

An inheritance pattern in which the alleles of one gene affect the phenotypic effects of the alleles of a different gene (i.e. gene interaction)

70
Q

if parentals are more common than recombinants, are the genes linked?

A

Yes

71
Q

what are lethal alleles? how are they inherited (usually)?

A

A lethal allele is one that has the potential to cause the death of an organism. They typically the result of mutations in essential genes and are usually inherited recessively.

72
Q

What is the result of a lethal allele?

A

an allele that is lethal to the organism will skew expected phenotypic ratios (i.e. expected 3:1, actual 2:1)

73
Q

What are additive interactions (for alleles)?

A

the more dominant alleles you have, the greater the effect of the dominant phenotype
- ex. no dominant alleles = white, 2 dominant alleles = intermediate red, 4 dominant alleles = dark red

74
Q

what is pathway epistasis?

A

alleles at one gene block phenotypic effects of alleles of a different gene

75
Q

What is the gene modifier effect?

A

A genetic modifier, when expressed, is able to alter the expression of another gene. (this is a weaker version of epistasis)

76
Q

what is gene redundancy?

A

two or more genes are performing the same function and inactivation of one of these genes has little or no impact on the phenotype

77
Q

explain complementation

A

parents are homozygous recessive at one locus and WT at the other locus (ie. PPcc x ppCC). Their offspring (mutants) will be heterozygous at both loci. When the F1 offspring are crossed with one another, you will see a restoration of the WT phenotype in the F2 generation

78
Q

This method requires the experimenter to make crosses between two different strains to produce a mapping population.

Linkage/Pedigree, GWAS, or both?

A

Linkage/Pedigree

79
Q

This method can scan the entire genome to find QTL for a trait.

Linkage/Pedigree, GWAS, or both?

A

both

80
Q

This method may sample a large number of individuals from a random-mating population that has variation for the trait being studied.

Linkage/Pedigree, GWAS, or both?

A

GWAS

81
Q

This method sometimes has sufficiently high resolution to identify the specific genes that represent the QTL

Linkage/Pedigree, GWAS, or both?

A

GWAS

82
Q

Results of this method must be replicated to confirm the QTL

Linkage/Pedigree, GWAS, or both?

A

both

83
Q

When are Log odds considered significant?

A

log odds > 3

84
Q

what is broad heritability?

A

the genotype fraction of phenotype

85
Q

what is narrow heritability?

A

the additive genetic fraction of phenotype

GENETICS (3 decks)

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