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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
is the alteration of gene expression due to epigenetic inheritance permanent?
No, it is reversible
26
What is DNA Methylation and what does it result in?
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
27
What is the purpose of dosage compensation?
to offset differences in the number of active sex chromosomes (reduces active X chromosomes to 1)
28
what are the mechanisms of dosage compensation and what taxa would you expect to exhibit each mechanism?
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%
29
what is genomic imprinting and what does it result in?
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.
30
what is mono-allelic expression?
Only one allele is expressed (paternal or maternal, not both)
31
explain the mechanism of imprinting
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
32
What are some similarities between epigenetics in dosage compensation and genomic imprinting?
in both, a portion of genomic info is silenced for the life of the individual
33
Explain the mechanism of mammalian X-chromosome inactivation
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.
34
What happens if an inactivated X is replicated during cell division? (in Mammalian X-chrom inactivation)
Both copies will remain highly compacted and inactive. X-chrom inactivation is passed along to all future somatic cells
35
what is the Xic and what is its function during X-chrom inactivation?
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
What is a Barr body?
A condensed, inactivated X chromosome
37
What is extranuclear inheritance?
inheritance patterns involving genetic material outside the nucleus (i.e. mitochondria and chloroplasts)
38
What is heteroplasmy (w/ respect to organelles)?
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
Describe how Morgan's experiments led him to propose that recombinants result from crossing over
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
When should you use association mapping? (when should you not?) When is it most successful?
Good for common disease, not as strong for rare disease. Most successful when the causal variant is widespread in the population.
41
When should you use Linkage in 3-factor mapping? When should you not use it?
Good for both common and rare diseases. Bad for diseases where the affected are unlikely to have children.
42
what is a complex trait?
traits determined by several genes and are significantly influenced by environmental factors
43
what is a quantitative trait?
a trait you can assign a number to (i.e. height)
44
what is a categorical trait?
this OR that (i.e. yellow or green, tumor or no tumor)
45
what is a continuous quantitative trait?
quantitative traits with a continuous range (i.e. height, skin color)
46
what is heritability?
the extent to which genetic causes lead to phenotype of interest
47
How do you calculate the variance of trait phenotypes? What does each variable stand for?
``` Vp = Vg + Ve Vp = phenotype variance Vg = genetic variance Ve = environmental variance ```
48
How do you design an experiment where Vg = 0?
use highly inbred strains or identical twins
49
what is the equation for broad sense heritability?
hB2 = Vg/Vp
50
what is the equation for narrow sense heritability?
``` hN2 = Va/Vp Va= variance due to additive effects of alleles ```
51
What is a QTL (Quantitative trait locus)
the location on a chromosome that harbors one or more genes that affect the outcome of a quantitative trait
52
What are the approaches to measuring broad sense heritability?
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
What type of individuals do you need to identify QTLs?
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
define variance
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
define standard deviation
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
What type of inheritance is seen for the transmission of Human Mitochondrial diseases?
Maternal inheritance
57
define linkage
The tendency for genes or segments of DNA closely positioned along a chromosome to segregate together at meiosis, and therefore be inherited together.
58
what is the result of segregation
separation of allele pairs
59
What methods did Creighton and McClintock used to confirm Morgan’s hypothesis that genetic recombination is the result of physical crossing over?
Observed physical crossing over via microscopy AND genetic crossing over via trait inheritance in cross of maize (corn) strains.
60
What are recombination hotspots?
regions in a genome that exhibit elevated rates of recombination relative to a neutral expectation
61
What is a haplotype?
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
What are haplotype blocks?
regions of chromosomes between the recombination hotspots. recombination is extremely rare in haplotype blocks.
63
What is Linkage disequilibrium?
the nonrandom association of alleles at 2 loci - i.e. the alleles "stick together" (ex. haplotype blocks)
64
Recombination hotspots, haplotypes, haplotype blocks, and linkage disequilibrium are all products of what?
the product of many generations of crossing over in a population
65
How do you calculate the odds ratio for association?
odds (SNP = X, disease) / odds (SNP = Y, disease) | i.e. (disease/not disease for SNP X) / (disease/ not disease for SNP Y)
66
when is your SNP (association) odds ratio considered significant?
if p < 10^-8
67
What is the primary difference between association mapping and linkage mapping?
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
what is association mapping?
finding the tendency of a molecular marker to co-occur with a disease phenotype within a population. Does not rely on heritability.
69
explain epistasis
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
if parentals are more common than recombinants, are the genes linked?
Yes
71
what are lethal alleles? how are they inherited (usually)?
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
What is the result of a lethal allele?
an allele that is lethal to the organism will skew expected phenotypic ratios (i.e. expected 3:1, actual 2:1)
73
What are additive interactions (for alleles)?
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
what is pathway epistasis?
alleles at one gene block phenotypic effects of alleles of a different gene
75
What is the gene modifier effect?
A genetic modifier, when expressed, is able to alter the expression of another gene. (this is a weaker version of epistasis)
76
what is gene redundancy?
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
explain complementation
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
This method requires the experimenter to make crosses between two different strains to produce a mapping population. Linkage/Pedigree, GWAS, or both?
Linkage/Pedigree
79
This method can scan the entire genome to find QTL for a trait. Linkage/Pedigree, GWAS, or both?
both
80
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?
GWAS
81
This method sometimes has sufficiently high resolution to identify the specific genes that represent the QTL Linkage/Pedigree, GWAS, or both?
GWAS
82
Results of this method must be replicated to confirm the QTL Linkage/Pedigree, GWAS, or both?
both
83
When are Log odds considered significant?
log odds > 3
84
what is broad heritability?
the genotype fraction of phenotype
85
what is narrow heritability?
the additive genetic fraction of phenotype

GENETICS (3 decks)

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