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BIOSCI 2223: Genetics > Test 4 > Flashcards

Test 4 Flashcards

1
Q

What are plasmids?

A

Small circular DNA molecules that hold bacterial extrachromosomal genes.

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2
Q

What are the three things that plasmids used in genetic engineering contain?

A

Antibiotic resistant gene (to select against bacteria that have not taken up the plasmid), an origin of replication, and Polylinkers

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3
Q

What is a polylinker? What is its purpose?

A

A cluster of unique restriction endonuclease sites. That way there is only one area that plasmid can be cut so that the plasmid is linearized but not cut up into pieces (each one of the restrictions endonuclease sites is unique to this area, and the presence of multiple endonuclease sites means multiple endonuclease can be used.)

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4
Q

What are inserts? What are their purpose?

A

An insert is a specific DNA sequence (can be gene, ribosome binding site, etc) that is placed into a polylinker to be inserted into bacteria.

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5
Q

Describe the concept of insertional mutagenesis

A

The creation of mutations in DNA by the addition of one or more base pairs

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6
Q

What type of gene typically makes up a polylinker and allows for selection of bacteria that have a plasmid with the insert in it?

A

A chromogenic gene, if an insert is placed in a chromogenic gene the gene will not function and the bacteria will no display color

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7
Q

What type of gene is the LacZ gene?

A

Chromogenic. (Also serves as part of the lac operon)

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8
Q

What are restriction endonucleases?

A

Naturally occurring enzymes that bacteria use to cut the DNA of invading viruses

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9
Q

Differentiate between endonuclease and exonucleases.

A

Endonuclease breaks an internal phosphodiester linkage causing fragmentation of the DNA molecule

Exonuclease breaks a terminal phosphodiester linkage in DNA replication (DNA polymerase removing incorrect bases from the strand it is creating)

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10
Q

What are sticky ends? How are they created?

A

A DNA molecule where each strand ends at a different nucleotide, called sticky because they have a high affinity to hydrogen bond with their complementary pair.

Created by restriction endonucleases.

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11
Q

What kind of symmetry does the recognition sites of sticky ends have? (The recognition site is where they are split apart by the restriction endonuclease)

A

Dyad symmetry (same 5* -> 3* on both strands)

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12
Q

What creates the linkages between two sticky ends?

A

DNA ligase forms hydrogen bonds between the sticky ends of two different DNA molecules (hybridization), creating a recombinant DNA molecule

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13
Q

What was the first restriction endonuclease isolated from?

A

E coli (EcoRI)

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14
Q

What is the issue with using a different species (not the host) promoter in recombinant DNA?

A

RNA polymerase only recognizes and initiates transcription for promoters of its own species.

Recombinant plasmids must contain the host species promoter before the gene of interest

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15
Q

What major issue can arise from recombining eukaryotic DNA in a prokaryotic host?

A

The gene of interest from the eukaryote must have it’s introns removed from its coding region

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16
Q

What is the name of the plant pathogen used to genetically engineer plants?

A

Agrobacterium tumefaciens

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17
Q

How can you insert a piece of DNA into a plant?

A

A Ti plasmid containing transfer functions (that move T-DNA to the plant from recipient), and T-DNA composed of a plant promoter and coding region are inserted into a plant cell.

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18
Q

What is the issue with producing clotting factor VII?

A

Codon bias (predisposition to use one codon over another) means that mammalian cells were required instead of E coli

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19
Q

What are the components of CRISPR-Cas9?

A

dCas9 (similar to a restriction endonuclease), sg RNA 1 and 2 (that tell dCas9 where to cut at each end) and the donor DNA (plant promoter and coding region).

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20
Q

How is CRISPR-Cas9 genetic engineering an improvement upon using a pathogen?

A

It will cut only in a specific spot that is indicated by the RNA, and it has a higher frequency of inserting DNA.

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21
Q

What is a callus?

A

the mass of plant cells called after they have been transformed (have DNA inserted) and are growing on agar

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22
Q

What are the next steps to create an adult genetically engineered plant after the plant cells have been transformed?

A

the cells are grown in two sets of media that have different hormone ratios to promote the growth of both roots and shoots

the plant can then be placed in soil

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23
Q

After the transformed plant has grown up, how do researchers make sure that all of the cells of the plant have the DNA inside?

A

after the plant is treated with the agrobacterium or crispr and grown into an adult, some of the cells may have not taken up the DNA (mosaic plant), so fully transformed pollen/eggs are obtained so a plant can be made that has DNA in all its cells

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24
Q

Describe the early use of genetic engineering in corn/soybean

A

Bacillus thuringiensis (BT) toxin was inserted into corn/soybean to protect against lepidopteran larvae (hornworm/cutworm).

BT toxin works by crystallizing in the gut. It is extremely species specific and is used in a powder form as Thuricide

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25
Q

What was the pre-emergent chemical that “RoundUpReady” crops were resistant to?

A

glyphosate

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26
Q

What type of stem cells are used to create a genetically engineered animal?

A

embryonic stem cells from a blastocyst

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27
Q

How were blastocyst embryonic cells used to create a genetically engineered animal?

A

Re-introduce cells into blastocyst → chimeric/mosaic animal → breeding → Embryonic Stem cell derived animal

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28
Q

What is a chimera?

A

an animal whose cells have been partially genetically engineered

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29
Q

What is SCIDS?

A

SCIDS (severe combined immunodeficiency syndrome) has defective ADA (adenosine deaminase) that is a part of T-lymphocytes and allows immune response

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30
Q

Why was SCIDS chosen to be the first disease cured by genetic engineering?

A

Single gene, simple regulation (always on), gene was isolated and cloned, white blood cells could be removed → modified → returned

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31
Q

What was the first method used to treat people with SCIDS?

A

disarmed retrovirus (RNA as genetic material, host reverse transcriptase converts to DNA integrated into host chromosome)

Disarmed = can’t produce new viruses

Procedure → remove T-lymphocytes → transform with retrovirus → select and amplify transformed cells (selectable marker + induce mitosis with cytokines) → inject into patient

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32
Q

What was the second phase for the treatment of SCIDS?

A

T-cells do not normally undergo mitosis, so patients had to undergo continuous treatment → need to transform bone marrow stem cells

Same procedure with CRISPR-Cas9 → insert gene into safe harbor (open chromatin = good expression = no genes)

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33
Q

What were the problems with the first method used to treat SCIDS?

A

2003 2 SCIDS patients got leukemia (retrovirus inserts at random location, may accidentally turn on oncogenes)

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34
Q

How do get from the frequency of alleles to the genotypic frequencies? (#A1, #A2 → A1A2)

A

2 * (frequency of A1) * (frequency of A2) = frequency of A1A2

Don’t need 2* for homo

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35
Q

How do you get from the genotypic frequencies to the allele frequencies?

A

Frequency of homozygotes + ½ Frequency of heterozygotes = Allele Frequencies

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36
Q

How do you go from partial genotypic frequencies to allele frequencies? (ex: missing hetero)

A

If the frequency of one or more is not given, must assume population follows HWE

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37
Q

What is Hardy-Weinberg Equilibrium?

A

If there are only two alleles for a gene, such that p + q = 1, then the genotypic frequencies will be p2 + 2pq + q2 = 1 and the allele frequencies will stay the same generation after generation

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38
Q

What (5) factors are needed to make alleles into HWE?

A

(1) random mating, (2) no migration, (3) no mutation, (4) infinite population size, and (5) no selection

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39
Q

If a population is out of HWE, what can/will return it to HWE?

A

One generation of random mating will put things into HWE (if other factors as well)

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40
Q

What would the HWE equation be for a gene with three alleles?

A

(a + b + c)2 = a2 + b2 + c2 + 2ab + 2bc + 2ca

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41
Q

What is a polymorphism?

A

Many forms of a trait/gene in the population

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42
Q

What is DNA fingerprinting?

A

a way to match DNA samples based on polymorphisms so extreme that every human on the planet has a unique DNA fingerprint

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43
Q

What is a restriction fragment length polymorphism (RFLP)?

A

The resulting length of a piece of DNA cut with two restriction enzymes

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44
Q

How are different restriction fragment length polymorphisms created (2 main)?

A

Missing or extra RE site
- a single nucleotide polymorphism (SNP) → one nucleotide changes that creates/destroys a site (3 genotypes for each SNP with 2 alleles)

More or less DNA between RE recognition sites

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45
Q

What is a variable number tandem repeat (VNTP)? Why were they used in DNA fingerprinting?

A

Sections of DNA with repeating ~15 nu sequences

test for more than one at a time, 100s of VNTRs each with 10-50 alleles

**Example of more or less DNA between RE recognition sites

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46
Q

What were some of the early criticisms of DNA fingerprinting and how were they addressed?

A

Not all alleles are of equal frequency (may have 30 alleles, but 2 account for 99%)
More sampling to more accurately describe allele frequencies

Assume independence among alleles at different VNTRs
More sampling to determine linkage equilibrium (alleles turned out to be independent)

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47
Q

What are short tandem repeats (STRs)?

A

like VNTRs, but with fewer bases in each repeated section → many more alleles and more sites (called satellites)

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48
Q

How did the invention of polymerase chain reactions (PCRs) change DNA forensics?

A

More reliable results with less DNA and fewer steps

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49
Q

What is a target sequence in PCR?

A

Known sequence of DNA that contains the short tandum repeat or other region that you want amplified

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50
Q

What components are needed for PCR?

A

2 primers (one for each strand of DNA), template DNA, taq polymerase (a temp-resistant DNA polymerase), and free nucleotides

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51
Q

How does PCR work?

A

Cycle 1: Raise temp to break apart strands of DNA → two primers (one for each strand) that bind to the ends of the target sequence → synthesis temperature + taq polymerase + free nucleotides → synthesize two pieces of DNA that include the target sequence and extend beyond it to one side (taq polymerase does not know where to stop
Cycle 2: Raise temp to break apart strands of DNA → excess primer → synthesis temp and taq polymerase → 2 template strands, 4 with excess DNA on both sides, 2 with excess DNA on only one side
Cycle 3: Produces 6 larger molecules and 2 molecules that are the length of the target sequence
Cycle 4: Produces 8 larger molecules and 8 that are the right length
Repeat for 30 cycles to get 60 long molecules and 1,073,741,766 the length of the target sequence

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52
Q

How are more alleles created for STRs and VNTRs?

A

Unequal crossover at meiosis

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53
Q

What are quantitative traits?

A

Continuous variation between extremes in phenotype, 2+ genes

54
Q

Describe the alleles for quantitative traits? What is assumed?

A

Contributing alleles add to a baseline value for the trait
Non-contributing alleles do not add to the baseline value
Assume that contributing allele effects are equal and additive

55
Q

How can you figure out the number of genes (n) for a quantitative trait based on the percentage of offspring with each phenotype from two pure-breeding adults from either extreme in phenotype?

A

(¼)^N = fraction of F2 as extreme in phenotype as one of the parents (all contributing or all non-contributing)

Can average with fraction at other maximum and go with the closest fraction (1/250 ~ 1/256)

56
Q

How can you figure out the number of genes for a quantitative trait based number of phenotypic classes observed in offspring from two pure-breeding adults from either extreme in phenotype?

A

Number of F2 phenotypic classes = 2n + 1, where n = number of genes

57
Q

In a research setting, which generations will have environmental variation (s^2)? Which will have genotypic variation (s^2)?

A

Parental Generation and F1 Generation have only environmental variation (genetically identical parents (1 max, 1 min) produce genetically identical F1)

F2 and beyond have environmental and genotypic variation

58
Q

How can deduce genotypic variation given the variation (s^2) from each generation of an experimental population?

A

To find genotypic, take the variation from F2 - P/F1

59
Q

Given the mean and variation (s^2) of the parental generation in an experimental population, what will be the mean and variation (s^2) of the F1?

A

Parental → F1 = average the mean, same variation

60
Q

Quantitative Traits: Formula for mean

A

Sum of each value divided by the number of values in the sample

61
Q

Quantitative Traits: Formula for variance (s^2) (definitional formula, for only a few data points)

A

Sum of the squared difference between each value and the mean, divided by n-1

(For each value, subtract by the mean and square the result. Add those results together and divide by the number of values minus 1)

62
Q

Quantitative Traits: Formula for variance (s^2) (computational formula, for many data points)

A

(1/n * (sum of all the squared values)) - (mean^2)

For the HW problem, it would be the sum of (number of each value)*(value^2) over number of values, minus mean^2

63
Q

What is the meaning of variance (s^2) in regards to quantitative traits?

A

the average of (the difference between all the values and the mean)SQUARED

64
Q

Quantitative Traits: Formula for standard deviation (s)

A

Square root of the variance

65
Q

What is the meaning of standard deviation in regards to quantitative traits?

A

Describes bell curve, 67% of the values fall within 1 SD, 96% of the values fall within 2 SD, 99% of the values fall within 3 SD

66
Q

What is heritability?

A

Fraction of the total variation that is genetic

67
Q

How do you find heritability from an experimental population?

A

s^2 for F2 minus s^2 for F1 all over s^2 for F2

Genotypic variation over total

68
Q

How do you find heritability from a natural population?

A

Plot the midparent value (x-axis) by the midoffspring value (y-axis) and take the slope of the line

69
Q

Define evolution

A

a process of change over time

70
Q

Define biological evolution

A

a process of change in populations over time

71
Q

Define microevolution

A

allele frequency changes in populations

72
Q

Define macroevolution

A

large differences as a result of accumulated microevolutionary changes over time, also called speciation

73
Q

What are the three subtypes of non-random mating?

A

Positive/Negative
Phenotypic/Genotypic
Complete/Partial

74
Q

What is positive vs negative assortative mating?

A

Positive is like with like or inbreeding

Negative is unlike with unlike or outbreeding

75
Q

What is phenotypic vs genotypic assortative mating?

A

Based on look/behavior or genetic factors

Feather/coat color vs plant self-incompatibility

76
Q

What are the effects of assortative mating? (+/-)

A

Inbreeding: decreases heterozygosity and increases homozygosity

Outbreeding: increases heterozygosity and decreases homozygosity

77
Q

What does the inbreeding coefficient (F) measure?

A

the amount of assortative mating in a population

78
Q

How can you calculate the inbreeding coefficient (F) for a population and what does it mean?

A

1 minus (observed freq. of heterozygotes)/(expected freq. of heterozygotes by HWE)

Positive for inbreeding, 0 for HWE/random mating, negative for outbreeding

79
Q

Assortative mating changes ____ frequencies but not ____ frequencies

A

genotypic

allele

80
Q

What is migration?

A

Gene flow from one population to another

81
Q

What is the equation for migration?

A

p(new) = mp(migrant) + (1-m)p(native)

M is migration rate / fraction of new population composed of migrants
P is allele frequency
**Assumes admixture

82
Q

What are the (general) effects of migration?

A

Changes allele frequencies but does not lead to adaptations (traits that are better for that environment), which can affect the direction of allele frequency change = direction of evolution

83
Q

What is mutation?

A

Change one allele into another

84
Q

What is the equation for mutation?

A

p(n) = p(0) * e ^ (-n*u)

pn is the frequency of the allele after n generations
p0 is the current frequency
μ (u) is the mutation rate in alleles/gametes per generation

85
Q

What are the (general) effects of mutation?

A

Mutation alone does not have a significant effect on allele frequencies but it is the source of new alleles

86
Q

What is genetic drift?

A

An allele’s frequency is free to drift over many generations, and the amount of drift is a function of population size
Chance leads to offspring with slightly different allele frequencies than the adults

87
Q

What are the effects of genetic drift?

A

Can change allele frequencies (alleles can even be lost or fixed purely due to drift) but does not lead to adaptations (traits that are better for that environment)

88
Q

What is the founder effect?

A

Small sample of larger population establishes a new population → small sample may not reflect the same allele frequencies as larger populations

89
Q

What will be the impact of a population bottleneck?

A

Loss of genetic diversity

90
Q

Define selection

A

Differential reproductive success → not all phenotypes (genotypes) have the same number of offspring → selection is a function of the environment

91
Q

Define fitness (w)? What does it mean?

A

Selection’s relationship to the environment → how well a phenotype fits the environment

Probability of survival and rate of reproduction relative to other phenotypes in a particular environment

92
Q

What are the four types of selection?

A

zygotic, sexual, fecundity, gametic

93
Q

What is zygotic selection? Give some examples

A

survival from a zygote to maturity

run fast, hide from predators, efficient food gathering

94
Q

What is sexual selection? Give some examples

A

finding a mate

coloration of feathers or fur, mating behaviors, antler or horn size

95
Q

What is fecundity selection? Give some examples

A

gamete production

sperm count, frequency of ovulation

96
Q

What is gametic selection? Give some examples

A

gamete quality

deformed sperm or sperm with short tails

97
Q

What is the selection coefficient (S)?

A

the fraction by which fitness is reduced relative to the phenotype with maximum probability of survival and maximum rate of reproduction

98
Q

What is the equation relating fitness to the selection coefficient?

A

w (fitness) = 1 - s (selection coefficient)

99
Q

Does the selection coefficient change? If so, what factors would cause it to change?

A

Selection coefficient is not always constant for a genotype, may be dependent on population density and/or allele frequency
Selection depends on the environment (sickle cell)

100
Q

Describe directional selection and its effects

A

One homozygote has the highest fitness and the other homozygote has the lowest fitness
Deleterious allele frequency moves towards 0 while the beneficial allele frequency moves towards 1

101
Q

Describe heterozygote advantage selection and its effects

A

Heterozygote has the highest fitness

Alleles are maintained around a certain medium frequency dependant on their effects on each homozygote

102
Q

Define homozygote advantage selection and its effects

A

Heterozygote has lowest fitness
One allele frequency will move towards 1 and the other will move towards 0 dependent on the starting allele frequencies and the relative fitness of the homozygotes

103
Q

What are some examples of homozygote advantage?

A

Inversion heterozygotes, translocation heterozygotes

104
Q

What is the effect of selection on a population?

A

Extremely powerful force in changing allele frequencies, when combined with mutation a newly created beneficial allele will sweep through a population and become fixed

105
Q

What are Darwin’s (4) postulates?

A

Individuals are variable
Some of these variations are passed on
More offspring are produced than can survive
Survival and reproduction are not random, they favor the “fittest” variations

106
Q

What are the (3) concepts behind Darwin’s postulates of natural selection?

A

variation, heredity, selection

107
Q

What are the (3) major steps of speciation?

A

Elimination or reduction in gene flow, divergence, speciation

108
Q

What is allopatric speciation? What are the two types?

A

different range (geographic barrier)

Can be dispersal (leave to island) or vicariance (split by creation of mountain, river)

109
Q

What is sympatric speciation?

A

same range

Mating cycles (hawthorn and apple maggot flies)

110
Q

What is parapatric speciation?

A

nearby/overlapping range

Populations on edges do not have much gene flow with each other

111
Q

How can separated populations diverge through mutation?

A

creation of new alleles

112
Q

How can separated populations diverge through selection?

A

can have a different environment is different selection pressures or same environment/pressures but different starting alleles

113
Q

How can separated populations diverge through drift?

A

different alleles fixed/lost due to random chance

114
Q

How can separated populations diverge through migration?

A

different populations migrate to different areas, are affected by migration different

115
Q

How can separated populations diverge through nonrandom mating?

A

Nonrandom mating reinforces isolation and decreases gene flow

116
Q

What will be the eventual effect of microevolutionary changes in separated populations?

A

over time, changes in allele frequencies will cause populations to accumulate changes in the actual alleles

117
Q

What is genetic distance?

A

the accumulation of allele differences (dif in allele, not diff in freq) between populations

118
Q

How can inversions lead to divergence between populations?

A

inversion heterozygotes have reduced fertility, but pass on inversion to half of offspring
Inversion homozygotes will have no reduced fertility, unless mating with non-inversion homozygotes

-same as translocations

119
Q

How can translocations lead to divergence between populations?

A

translocation heterozygotes have reduced fertility, but pass on translocation to half of offspring
Translocation homozygotes will have no reduced fertility, unless mating with non-inversion homozygotes

-same as inversions

120
Q

How can polyploidy lead to divergence between populations?

A

instant specialization due to inability to interbreed

121
Q

What is the strictest concept of what makes two populations separate species?

A

Biological Species Concept: The ability to mate and produce fertile offspring

122
Q

What are the issues with the harshest concept of species?

A

Issues → cannot use with asexually reproducing organisms, extinct organisms, mating in nature will be different than mating in lab (in vitro fertilization does not count)

123
Q

Define sociobiology

A

the evolution of social behavior

124
Q

What is r in regards to kin selection? What does it mean?

A

coefficient of relatedness

Fraction of alleles shared by a relative or probability of finding the same allele at any given gene in a relative

125
Q

What would be the r value for offspring-parents? Siblings? Cousins?

A

Parents and siblings → ½

Cousins → ⅛

126
Q

What is Hamilton’s Rule

A

If Br - C > 0 (B = benefit, C = cost), then those behavior alleles will increase in frequency

127
Q

What is the principle behind reciprocal altruism?

A

Natural selection will favor alleles that cause altruistic acts to non-kin if equally valuable acts are returned

128
Q

What is used as a model to study reciprocal altrusism?

A

Prisoner’s Dilemma
Incriminate partner → lighter sentence, each thief has 2 choices

T > R > P > S (T = you defect, partner quiet, R = both cooperate, S = opp T, P = opp R)

R > (S+T)/2 → cooperation > than randomly defecting and cooperating

T + P = 2R → still temptation to defect

129
Q

What was the best strategy to use for reciprocal altruism?

A

Tit For Tat

Start by cooperating, then repeat opponents last decision

130
Q

What is an ESS or evolutionary stable strategy?

A

A behavior strategy is evolutionarily stable if the population practicing it cannot be exploited by a rare form practicing another strategy

BIOSCI 2223: Genetics (4 decks)

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