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Exam 3 Flashcards

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1
Q

How do you know linkage has occurred?

A

recombination frequency - crossing over happens more frequently when genes are on different chromosomes
so if low recombination frequency, genes are linked/on same chromosome

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2
Q

How do you calculate recombination frequencies?

A

recombinant progeny/total progeny x 100%

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3
Q

coupling (cis) v.s. repulsion (trans)?

A

coupling: wild-type alleles on one chromosome
mutant alleles on other
repulsion: each chromosome has one wild one mutant

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4
Q

how do double crossovers affect gene mapping?

A

double crossovers basically reverse effects of first crossover (restoring original parental combination)
produce only nonrecombinant gametes (although some parts of chromosome have recombined)

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5
Q

Why are testcrosses used for mapping?

A

recombination frequencies can be calculated which tells you how far apart the genes are

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6
Q

recombination

A

when F1 reproduces, combination of alleles in gametes may differ from combination of alleles in parents

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7
Q

linked genes

A

genes that are close together on same chromosome
travel together during meiosis –> not expected to sort independently

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8
Q

How can you use a pedigree to see if genes are linked?

A

If two genes are located close together on the same chromosome, they are more likely to be inherited together as a unit, rather than separately

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9
Q

What is a SNP and how are they used in mapping studies?

A

variant at single point in base pairs
at a particular point in DNA you can have a different base
can treat as a locus (location on a chromosome)

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10
Q

linkage disequilibrium

A

SNPs that ARE linked to trait
physically close on genome, reduced by recombination

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11
Q

GWAS

A

used to look for correlation between SNPs and particular trait (looking for gene that is responsible for trait)
- eliminate SNPs with independent assortment (NOT linked to trait)

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12
Q

What ratio will unlinked genes have?

A

1:1:1:1

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13
Q

describe the strategy of a 3 point testcross

A
  • determine nonrecombinants (highest number of progeny)
  • determine double recombinants (lowest number of recombinants)
  • determine middle gene
  • calculate map distances between st and ss
    - recombinants/total progeny x 100%
    - include double recombinants
  • do same for ss and e
  • add to get distance btwn st and e
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14
Q

linked genes segregate through ___, unlinked genes segregate ___

A

recombination
independently

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15
Q

Why are SNPs with highest LD closest to gene?

A

increasing distance leads to recombination, which reduces LD

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16
Q

Why are particular SNPs linked to a trait?

A

when trait causing mutation occurs, person has a particular haplotype (SNP genotypes in immediate vicinity)
haplotype inherited as unit through generations
association with SNPs lost over time (because recombination)

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17
Q

Why can GWAS pick up most traits?

A

many genes will be in LD because most traits have multigene causes

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18
Q

What are the consequences of these rearrangements (nondisjunction) on the products of meiosis?

A

genetic info gained or lost
gene dosage altered

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19
Q

What are the different types of chromosome structures?

A

telocentric - centromere at end
acrocentric - centromere close to end
submetacentric - off center
metacentric - centered
short arm p
long arm q

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20
Q

What is a satellite chromosome?

A

contains satellite (region of highly condensed DNA; repetitive sequences of DNA near centromere)

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21
Q

What is karyotyping and what information can it provide?

A

cells frozen in mitosis when chromosomes are most condensed
stained and arranged into pairs
provides info on:
- individual’s sex chromosome composition
- number of autosomes
- presence of any chromosome abnormalities (deletions, duplications, inversions, or translocations)
used for prenatal testing and finding genetic disorders

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22
Q

What are the physical/health effects of deletions and duplications within chromosomes? how severe are these changes?

A

structural change so developmental delays, intellectual disability, birth defects, or other health problems
severity depends on genes involved and how they’re affected by change

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23
Q

What are the consequences of inversions on the products of meiosis?

A

part of chromosome is flipped around
crossing over may be inhibited or the resulting recombinant chromosomes may contain duplicated or deleted genetic material (and you could get 2 centromeres)
any crossover within inverted region won’t survive (anything outside might)

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24
Q

What are the consequences of translocations on the products of meiosis?

A

segment of one chromosome is exchanged with a segment of another chromosome
crossing over may be inhibited or the resulting recombinant chromosomes may contain duplicated or deleted genetic material (bcus homologous chromosomes won’t pair up properly during meiosis I)

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25
What is a Robertsonian translocation?
segment exchange btwn 2 acrocentric chromosomes short and long arms switched = one long metacentric chromosome + 1 short chromosome fragment (usually fails to segregate and is lost, loses 1 chromosome)
26
What is the apparent origin of human chromosome 2?
fusion of two ancestral chromosomes - has telomere sequences at the center of the chromosome and two centromere-like regions occured after divergence from chimps, since chimps have 2 chromosomes that are homologous to human chromosome
27
Large chromosomal changes can be:
rearrangements within chromosomes rearrangements between chromosomes changes in number of chromosomes
28
how are duplications or deletions caused?
errors in lining up during meisosis
29
somatic v.s. germline mutations
Somatic - non-reproductive cells; are not passed on to offspring germline - reproductive cells; passed on to offspring. Somatic contributes to cancer; germline leads to genetic disorders and other inherited conditions
30
What products could form in meiosis between duplicated regions?
homologous chromosomes paired during meiosis, duplication can form chiasmata = crossover events (genetic info is exchanged) = recombinant chromosomes (genetic info from each parent)
31
fragile sites
weird sequences in DNA can cause weird structure susceptible to breakage common v.s. rare: depends on how prevelant in population common: cancer rare: genetic diseases
32
What are CNVs?
copy number variation- sections of genomes are repeated (number of repeats varies between individuals)
33
What is aneuploidy and how is it caused?
one chromosome present at different copy number than others (either extra or missing chromosomes) down syndrome, trisomy 21 caused by nondisjunction in meiosis
34
How is polyploidy different from aneuploidy?
ALL chromosomes present at different copy numbers gene balance not affected (more than 2 sets of chromosomes)
35
Distinguish autopolyploidy from allopolyploidy and show the consequences on reproduction
mistake in mitosis or meiosis that creates extra chromosomes auto - sets from same species (because chromosomes are homologous, they attempt to line up --> sterility) allo - sets from different (but still related) species (do not pair/segregate properly in meiosis --> unbalanced, nonviable gametes
36
why is down syndrome more of a risk the older the mother gets? why does the father not have an effect in this?
oocyte is stuck in prophase, the longer its stuck there, higher chance of abnormalities males have continual production/process of meiosis
37
when can autopolyploidy occur?
in mitosis (if cell division doesn't occur)
38
polyploidy in plants v.s humans?
plants- larger genomes, nuclei, cells, plants humans- lethal, usually cause miscarriages (but some tissues, like liver, are polyploid [binucleated] and can regenerate)
39
mosaicism
patches of aneuploid cells
40
What are HeLa cells?
taken from Henrietta Lacks without permission, cervical cancer cells don't have normal number of chromosomes
41
How can autopolyploidy be chemically induced?
colchicine - disrupts mitotic spindle formation (so chromosomes can't segregate during meiosis)
42
Bananas are sterile, so how do we grow bananas? Why is this an issue?
cloning or making cuttings all are going to be genetically identical, no variation that can save from genetic diseases (currently a banana fungus happening rn)
43
What regions of a gene are more sensitive to mutations, and why?
coding sequences - changes what protein is being encoded promoter sequences - changes how much a gene is expressed
44
transition v.s. transversion mutations
transitions - doesn't change whether its pyrimidine or purine (A--->T) transversions - changes from pyrimidine to purine or vis versa (T--->G)
45
What are indels and what are their effects?
insertion or deletion of bases can change the reading frame (which can have drastic effects) may not have drastic effect if deletes more than 3 bases pairs (entire codon)
46
Why are nucleotide repeats a frequent location of mutations?
repeats --> folding/hairpin thing (kind of like a slippage thing)
47
missense mutations
change one amino acid --> another amino acid
48
nonsense mutations
changes amino acid --> stop codon
49
silent mutations
encodes same amino acid (UCC-->UCU, both encode same protein)
50
neutral mutations
amino acid that's encoded is simiar to OG (Leu to Ile --> similar proteins)
51
loss-of-function v.s. gain-of-function mutations
loss of function: inactive protein gain of function: more active protein or new function less common, associated with cancers dominant phenotype protein may be "permanently" on or gene may be turned on inappropriately by mutated promoter
52
nonsense suppressor
reverses phenotype of any mutation caused by nonsense mutation
53
How does generation time correlate with mutation rate?
organisms with shorter generation time evolve faster because they accumulate more DNA replication errors in a shorter amount of time
54
mispairing during replication
bases don't pair correctly (i.e. A with G instead of T) so coding sequence is changed
55
strand slippage
common in runs of a single letter slippage in replication adds or deletes a base causes change in reading frame
56
unequal crossover
homologous chromosomes missalign and crossover at wrong spot
57
depurination
loss of A or G gene more common than loss of pyrimidine every cell loses thousands per day (usually repaired) main cause in difficulty in replicating ancient DNA
58
why is depurination problematic?
when a G goes missing, A usually replaces it this changes CPG islands (G ---> A)
59
deamination
amino group spontaneously gets lost, amino group --> ketone (cytosine has an amino group, uracil has ketone so C --> U and then DNA transcription changes U --> T)
60
chemical mutagens
base analogs - resemble base nucleotides chemically, get integrated into DNA but don't base pair well alkylating agents - chemically modify base, alters base pairing (chemotherapy: drugs integrated into reproducing cells until cells reproduce mutation and die) intercalating agents - insert between base pairs, cause frameshift
61
radiation
ionizaton (high energy) - breaks bonds, forms free radicals UV (low energy) - forms pyrimidine dimers (bond between Ts, replication gets stuck there, if not repaired, cells die)
62
How does the cell know which strand to repair?
bacterial (and eukaryotic) DNA is methylated, so old strand will be methylated, new will be unmethylated
63
hypomorph
mutation causes protein to have reduced (partial) function (person may still be able to live, but protein doesn't work super well)
64
what are gain of function mutations and why are they less common?
protein is regulated to turn on and off, mutation keeps it permanently on RAS mutations common in cancer
65
causes of mutations?
incorporation - incorrect base inserted at replication replication - mutation carries on to next gen because mutation wasn't corrected
66
what do these represent? p + q = 1 p2+ 2pq + q2 = 1
frequency of allele A frequency of allele a basically different frequencies of alleles should add up to 1
67
Under what conditions can we use allele frequency to predict genotype frequency, and vice versa?
large population random mating no mutation, migration, or selection
68
What is the effect of allele frequency on genotype frequency, under these conditions?
when allelic frequencies are equal, heterozygous frequency is greater if one allele predominates, most individuals homozygous
69
How would you find the allelic frequencies of these values? R2R2: 135 R2R3: 44 R3R3: 11
- add them and multiply by 2 (because everyone in population has 2 alleles) - split up values (i.e. for first one R2 will have 135 x 2, R3 will have 0; for second, R2 and R3 will both have 44) - add new values - divide by 380 (total population x 2) to get p and q values
70
What does it mean that selection acts on the phenotype, not the genotype? What can you do with this info?
if we have a dominant recessive situation, dominant and recessive have same fitness (reproductive success of genotype) you can calculate frequencies of next generation based off how fit genotype is
71
What is W and why can we not quantify it generally?
fitness (relative reproductive success of genotype) fitness can vary depending on environment/situation
72
How can we use selection coefficients to predict genotype frequencies, assuming other factors are not at play?
can just multiply so if AA has fitness 0, next gen won't have any AA if Aa has fitness .5, next gen will have half whatever frequency Aa was to find specific fitness, how many survive/total --> x g frequency / biggest w
73
What are underdominance and overdominance, and how do they affect allele and genotype frequencies?
overdominance: heterozygote more fit than homozygote underdominance: homozygote more fit than heterozygote obviously overdominance would see a decrease in homozygote frequency and an increase in heterozygote frequency (and vis versa for under)
74
why doesn't eliminating defective alleles by selection work?
defective alleles are usually recessive (i.e. aa), if the q (recessive) value decreases and eventually vanishes, little a alleles show up in heterozygous form only, and are not exposed to selection (basically allele won't show up, kinda protected from natural selection because of dominant allelle)
75
How does mutation relate to speciation?
provide new alleles good (works) for evolution in long run
76
How does overdominance relate to speciation?
(heterozygote advantage) stabilizes a population works against evolution
77
How does underdominance relate to speciation?
separates population into 2 over change in population
78
How does migration relate to speciation?
restores alleles stabilizes allele frequencies works against evolution
79
How does drift relate to speciation?
eliminates alleles makes population less fit over time
80
How does positive assortative mating/inbreeding relate to speciation?
basically same as underdominance
81
What are the two types of nonrandom mating and how do they affect genotype frequency?
positive assortative: prefers like individuals (inbreeding; fewer heterozygotes) negative assortative: prefers unlike individuals (more heterozygotes)
82
What is the effect of inbreeding on the appearance of recessive and defective phenotypes (aka why shouldn't you marry your cousin)? How is inbreeding useful?
recessive genes exposed --> causes inbreeding depression (increased homozygous, decreased fitness) deliberate inbreeding can expose defective alleles, which can then be eliminated
83
How can we calculate inbreeding coefficients from genotype frequencies, assuming no other factors are in play?
if F is 0 (no inbreeding), equations all stay the same if 1 (complete inbreeding), heterozygotes would be 0 F(AA) = P^2 + Fpq --> either p^2 (normal, like HWE) or 2pq - 2Fpq (complete inbreeding) basically, value between 0 and 1 decreases heterozygotes
84
How do gene mutations affect allele frequencies?
mutations introduce new alleles (A could turn to a, changing proportions/frequency)
85
How does migration affect allele and genotype frequencies?
also introduces new alleles, changes p and q values
86
What is the role of population size on the effects of these changes (gene mutations; migration)?
small populations more susceptible to change (migration from mainland to island would have bigger impact than island --> mainland)
87
How do the effects of drift and migration affect each other?
work against each other new individuals help stabilize drift
88
what is genetic drift? what effect does population size have on it?
basically, alleles lost because of chance, not selection how likely is it that allele gets passed on to next generation? (flip a coin once, you'll chalk it landing on heads to chance, flip it 500 times and it always lands on heads, something else is at play) smaller population = allele inheritance more up to chance
89
selfing
extreme of inbreeding same genotype mates with same genotype genotypic frequency of homozygotes are going to increase; frequency of heterozygotes decreases by 1/2 each generation
90
why is underdominance more rare than overdominance? (what usually causes underdominance?)
usually only occurs if there's a large chromosomal inversion, making heterozygotes less fit bcus you'd get crossovers within inverted region --> lethal
91
paracentric v.s. pericentric inversions?
para - do not include centromere peri - includes centromere
92
what are the two types of double strand DNA repair?
homologous recombination: requires single strand tails - use homologous sequence on other chromosome or chromatid -uses some of the same enzymes used in meiosis (like BRCA1 and BRCA2) nonhomologous end joining: simply joins broken ends together - error prone, leads to gaps, insertions
93
intragenic translocations
translocations inside gene may produce fusion proteins --> new function may fuse different promoter to gene
94
what effect do intragenic translocations have if it occurs in mitosis v.s. meiosis?
mitosis - cancer cells meiosis - new genes
95
what are 3 possible causes of aneuploidy?
nondisjunction centromere lost (happens in paracentric inversions) robertsonian translocation

Genetics (5 decks)

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