BIOL 3333 Exam 3 -- Fall 2024 (WORK IN PROGRESS)

In a Chi-square analysis, what general condition causes one to reject the null hypothesis? Always assume alpha is 0.05 unless otherwise stated.

usually when the probability is less than 0.05

The Chi-square test involves a statistical comparison between measured (observed) and predicted (expected) values. One generally determines degrees of freedom as ________.

one less than the number of classes being compared

You have the goal of creating an ideal corn crop that appeals to OU students' appetites. OU students prefer crimson-colored kernels over those awful burnt-orange kernels that Texas students seem to love. In order to expedite your final mass breeding, you decide it is important to understand the inheritance pattern of kernel color. You perform a monohybrid cross and get 910 burnt-orange to 306 crimson kernels. You thus propose a 3:1 model to test using chi-square analysis. Calculate a chi-square value (total deviation). Choose the closest value to the chi square you've calculated.

0.018

You perform a dihybrid cross to test the inheritance of two fruit fly genes: eye color and wing morphology. You propose a 9:3:3:1 model to test using chi-square analysis. You set your alpha to 0.05. Your final p value ends up being 0.09. Which of the following is correct?

There is a 9% chance that if you redid your experiment, you'd get the same or greater amount of observed deviation from the model if your null hypothesis is correct.

If one is testing a goodness of fit to a 9:3:3:1 ratio, how many degrees of freedom would be associated with the Chi-square analysis?

3

In a Chi-square test, as the value of the χ2 increases, the likelihood of rejecting the null hypothesis ________.

increases

G and E are genes in a diploid organism. The cross of genotypes GE/ge × ge/ge produces the following progeny: GE/ge 404; ge/ge 396; gE/ge 97; Ge/ge 103. From these data, one can conclude that ________.

the G and E loci are linked

G and E are genes in a diploid organism. The cross of genotypes GE/ge × ge/ge produces the following progeny: GE/ge 404; ge/ge 396; gE/ge 97; Ge/ge 103. From these data one can conclude that ________. (what is the recombinant progeny?)

gE/ge and Ge/ge

G and E are genes in a diploid organism. The cross of genotypes GE/ge × ge/ge produces the following progeny: GE/ge 404; ge/ge 396; gE/ge 97; Ge/ge 103. From these data, one can conclude that there are ________ map units between the G and E loci.

20

Genes that are linked

do not assort independently during meiosis

The closer together two genes are on a chromosome,

the less likely there will be a recombination event between them.

The genes for purple eyes and curved wings are approximately 21 map units apart on chromosome 2 in Drosophila. A true breeding purple-eyed and wild-type winged female was mated to a true breeding curved wing and wild-type eyed male. The resulting F1 were phenotypically wild-type flies and were mated to purple, curved tester flies. Of 1000 offspring, what would be the expected number of flies with purple eyes and curved wings? (Hint: pay very close attention to the phenotypes of the parents. Each parent is homozygous wild type at one gene and homozygous mutant at the other gene. It may help to draw out a diagram of the cross.)

105

Which of the following is an example of interference in gene mapping?

A crossover in one region inhibits crossovers in nearby regions of a chromosome.

Assume that a testcross is made between AaBb and aabb plants and that the offspring occur in the following numbers: 106 AaBb, 48 Aabb, 52 aaBb, 94 aabb. These results are consistent with which of the following?

linkage with approximately 33 map units between the two gene loci

One form of hemophilia is caused by an X-linked recessive allele of blood clotting factor 8. Assume that an XY man with hemophilia marries a phenotypically wild-type XX woman whose XY father had hemophilia. What is the probability that they will have an XX daughter with hemophilia? (Notice the phrasing of the question. Calculate the probability they will have a daughter with hemophilia considering all their possible sons and daughters.)

1/4

A cross is made between an XX female calico cat and an XY male cat having the allele for black fur on its X chromosome. What fraction of the offspring would one expect to be calico?

1/4

How many Barr bodies would one expect to see in cells of individuals with Turner syndrome (45, XO) and Klinefelter syndrome (47, XXY)?

zero and one

Which of the following is true about human sex chromosomes?

They act like homologous chromosomes during meiosis so each gamete will get one sex chromosome.

What is a chi-square test used for?

Measures how well observed data fit an expected distribution. Used to test hypotheses about observed vs. expected frequencies.

If given an experiment, be able to deduce a model/ratio and state/choose a null hypothesis.

Identify the expected genotypic or phenotypic ratio; null hypothesis typically states no significant difference between observed and expected data.

What is p-value?

Probability of observing results at least as extreme as the data, given that the null hypothesis is true

Be able to work through a chi-square analysis to calculate p-value from a dihybrid cross.

Calculate chi-square using χ^2=∑((O−E)^2/E) for p-value comparison to determine if data deviate from expected Mendelian ratios.

If given alpha, know whether to reject or fail to reject a null hypothesis using the p-value.

If p-value ≤ alpha, reject the null hypothesis; if p-value > alpha, fail to reject.

Gene mapping

Determining the locations of genes on a chromosome

Recombinant progeny/classes

Offspring showing a mix of traits different from parental types

Parental progeny/classes

Offspring with trait combinations identical to parent generation

Map units

Distance measurement on genetic map, 1% recombination = 1 map unit.

What is a two-point test cross?

Involves two genes; assesses linkage and distance between them.

What is a three-point test cross?

Involves three genes; allows mapping of gene order and distances between each.

Fill out the below equation and terminology blanks.

recombinant progeny (numerator)
total progeny (denominantor), called the recombination frequency

How do you calculate recombination frequency?

(recombinant progeny/total progeny) x 100

Complete linkage, test cross expectations

Only parental phenotypes; ~100% parental, ~0% recombinant

Independent assortment, test cross expectations

~50% parental, ~50% recombinant

A true-breeding lavender plant with AB phenotype is two-point test-crossed todetermine the relationship of genes A and B. The following F2 progeny areobserved. Determine if A and B are linked or independently assorting; if they arelinked, how far apart are they in map units?

Phenotypic class: AB, Ab, aB, ab
Number of progeny: 76, 15, 11, 72

The observed F2 progeny numbers indicate non-equal ratios, suggesting linkage.
Determine recombinant progeny: Ab (15) and aB (11), total 26.
Calculate recombination frequency: 26/174 = 0.15 = 15%
Distance between A and B = 15 map units.

In spotted raccoons, the gene for tail length is 21 map units away from the gene for spot size (B). Long tail length (A) is dominant to short tail length (a), and big spots (B) are dominant to small spots (b). What percentage of offspring are expected to have long tails and small spots?

Expected phenotype: Long tail (A) and small spots (b)

Recombination frequency: 21%

Offspring with long tails and small spots: 21%

Double crossover recombinant (DCO)

Offspring with alleles reshuffled by two crossover events between linked genes

Interference

phenomenon where one crossover event reduces the likelihood of another nearby crossover

Recombination hotspot

Genomic regions with a high frequency of crossover events

Recombination coldspot

Genomic regions with few or no crossovers

From a three-point test cross, how does one determine the order of the genes and the distance between each gene?

Gene Order: Identify the most and least frequent offspring phenotypes. The least frequent are double crossovers, revealing the middle gene.

Gene Distance: Calculate distances using recombination frequencies between adjacent gene pairs.

Formula: Distance (map units) = Recombination frequency × 100

Genotypic sex determination

mechanism where sex is determined by specific combinations of sex chromosomes or alleles

Genic balance sex determination

system where sex is determined by the ratio of X chromosomes to autosomes

Chromosomal sex determination

system where sex is determined by specific sex chromosomes

What is environmental sex determination, and what are some examples?

mechanism where the environment influences the sex of an organism rather than genetics
EX: In many reptiles (e.g., turtles, crocodiles), the incubation temp of eggs determines sex; In clownfish, dominant individuals are female -- if the female is removed, a male can become female

Heteromorphic sex chromosomes

Sex chromosomes that differ in size and shape

Label the image of the Y chromosome below. Know the function of each region.

Orange: pseudoautosomal region/telomere (PAR)
Blue: SRY gene
Green: Euchromatin region
Gray: Heterochronatin region

What is the function of the SRY region, and what effect does it have on testosterone levels in a wild-type human?

SRY (Sex-determining Region Y) gene initiates male sex determination by triggering the development of testes, which produce testosterone

The SRY region is activated around 6-8 weeks after fertilization. It activates______ gene expression, which directs testes development. It also represses______ gene expression, which directs ovary development.

SOX9, WNT4

Genes present on the X and Y chromosomes are called ___________ genes. These genes do not necessarily influence sex development. Most are found on the X chromosome because it is a much larger chromosome.

sex-linked

Males are ___________ for genes on the X chromosome, which means they have no second allele to compensate for a recessive allele on their single X chromosome

hemizygous

In humans, the presence or absence of the SRY region is what primarily determines sex. What evidence do we have for this?

- Individuals with an XY genotype lacking a functional SRY gene develop as females
- Males with an XX genotype who possess a translocated SRY gene develop male characteristics

Would a human with a Y chromosome always be male? Describe a situation where a human with XY chromosomes may show female development.

a human with a Y chromosome would not always be male; a person with XY chromosomes can exhibit female development if they have a condition called Androgen Insensitivity Syndrome (AIS) (body doesn't respond to male hormones)

Would a human with two X chromosomes always be female? Describe a situation where a human with XX chromosomes may show male development

a human with two X chromosomes chromosome would not always be female; a person with XX chromosomes can exhibit male development if they have a condition called De la Chapelle syndrome (have two X chromosomes but possess a translocated SRY gene)

What does it mean for an individual to be intersex/have Differences of Sex Development?

An individual who has biological characteristics that do not fit typical definitions of male or female

What do you predict would happen if the SRY region was introduced into XXembryos of mice?

Introducing the SRY region into XX embryos of mice would likely lead to the development of male characteristics

What is a sex-linked gene, and are these genes necessarily involved in sex determination?

A gene located on a sex chromosome (X or Y); Many sex-linked genes influence traits unrelated to sex, such as color vision and hemophilia

Be able to identify an X-linked recessive pedigree and deduce the genotypes of individuals in the pedigree.

Affected Males: Males with the condition (e.g., colored squares) must have the recessive allele on their single X chromosome (X^aY).

Carrier Females: Females with one affected allele are carriers (X^aX) and may appear unaffected.

Unaffected Females: Females without the condition have two normal alleles (XX).

Transmission Pattern: Affected males cannot pass the trait to their sons (Y chromosome) but will pass it to all daughters (who become carriers).

Be able to deduce phenotype, genotype, or probabilities of phenotype/genotype if given a cross involving an X-linked trait.

Use a Punnett square to visualize the genetic combinations and use the ratios to determine probabilities for specific genotypes and phenotypes

What is a Barr body, and how does it cause monoallelic expression and mosaicism?

A condensed, inactivated X chromosome found in females (XX) to equalize gene dosage between sexes
- monoallelic expression: Only one X chromosome is active in each cell, leading to expression of genes from that X while the other is inactivated (Barr body)
- mosaicism: In females, different cells may inactivate different X chromosomes, resulting in a mix (mosaic) of cells expressing genes from either the maternal or paternal X

Describe the role of XIST lncRNA in the lyonization process

XIST (X-inactive specific transcript) is a long non-coding RNA crucial for X chromosome inactivation (lyonization)

Write how many Barr bodies would you expect to find in someone with these chromosomes:
a. XX ->
b. XY ->
c. XXY ->
d. XXX ->

a. 1
b. 0
c. 1
d. 2

# of Barr bodies = # of X chromosomes - 1

Hierarchy of dominance

describes the relationship between alleles, indicating which allele is expressed when both are present

Codominance

both alleles in a heterozygous individual are fully expressed, resulting in a phenotype that displays both traits distinctly

Incomplete dominance

neither allele is completely dominant over the other, resulting in a heterozygous phenotype that is a blend of both traits

Threshold effect

a certain level of a trait or gene expression must be reached before a phenotype is manifested

Embryonic lethal allele

type of allele that, when present in a homozygous state, leads to the death of the embryo

Recessive lethal allele

allele that is lethal when present in a homozygous state, but not lethal when in a heterozygous state, allowing carriers to survive

Dominant lethal allele

allele that causes death when present in just one copy

Dominant negative mutation

allele that produces a mutant protein capable of interfering with the function of the normal protein encoded by the wild-type allele, leading to a loss of function in heterozygous individuals

Genetic anticipation

phenomenon where a genetic disorder appears to worsen or manifest at an earlier age in successive generations

Polygenic traits

traits that are controlled by multiple genes

Recessive epistasis

genetic interaction where one gene's recessive allele masks or modifies the expression of another gene's alleles

Dominant epistasis

genetic interaction where one gene's dominant allele masks or modifies the expression of another gene's alleles

Modifier genes

genes that influence the expression of other genes

Gene interaction

phenomenon where two or more genes influence the same trait

Synthetic lethal

interaction where the simultaneous mutation of two genes leads to death

Negative epistasis

interaction where the presence of a specific allele at one gene locus decreases or inhibits the phenotypic expression of another allele at a different locus

Complementation groups

Groups of mutations that affect the same gene or function and fail to complement each other when present in a heterozygous individual, leading to a mutant phenotype

Norm of reaction

range of phenotypic expressions of a single genotype across different environments

Variable expressivity

range of symptoms or phenotypes that can occur in individuals with the same genotype, indicating that the expression of a trait can vary widely among different individuals

Conditional mutants

organisms with mutations that exhibit a phenotype only under specific environmental conditions or circumstances

Sex-limited traits

traits that are expressed in only one sex

How does pleiotropy cause a dominant allele for a trait to also be a recessive lethal allele? How does this skew progeny ratios?

A dominant allele may cause a specific trait (e.g., color) while also affecting other traits negatively (e.g., viability)
If the lethal allele is expressed in homozygous individuals, they do not survive

At the molecular level, how can one gene cause pleiotropy?

by encoding a protein that has multiple roles in different biological pathways or by affecting various cellular processes

A true-breeding tomato plant with AB phenotype is two-point testcrossed to determine the relationship of genes A and B. The following F2 progeny are observed.
Are A and B linked? Why or why not?
Phenotypic class: AB, Ab, aB, ab
Number of progeny: 207, 210, 209, 211

They may be assorting independently
They may be on opposite ends of the chromosome

In jackalopes, blue eyes are dominant to yellow eyes and having a tail is dominant to being tailless. You cross a true-breeding blue eyed, tailed jackalope parent against a true-breeding yellow eyed, tailless jackalope. As expected, the F1 are all blue eyed and have tails. You perform a test cross with the F1 and score the phenotypes of the F2 as follows:

A. Blue and tailed 521

B. Blue and tailless 432

C. Yellow and tailed 423

D. Yellow and tailless 507

Indicate the parental and recombinant phenotypic classes:

A. Parental
B. Recombinant
C. Recombinant
D. Parental

In jackalopes, blue eyes are dominant to yellow eyes and having a tail is dominant to being tailless. You cross a true-breeding blue eyed, tailed jackalope parent against a true-breeding yellow eyed, tailless jackalope. As expected, the F1 are all blue eyed and have tails. You perform a test cross with the F1 and score the phenotypes of the F2 as follows:

A. Blue and tailed 521

B. Blue and tailless 432

C. Yellow and tailed 423

D. Yellow and tailless 507

Are the eye color and tail genes linked? Why or why not?

There are a lower number of recombinants versus parentals, suggesting the genes are linked

In jackalopes, blue eyes are dominant to yellow eyes and having a tail is dominant to being tailless. You cross a true-breeding blue eyed, tailed jackalope parent against a true-breeding yellow eyed, tailless jackalope. As expected, the F1 are all blue eyed and have tails. You perform a test cross with the F1 and score the phenotypes of the F2 as follows:

A. Blue and tailed 521

B. Blue and tailless 432

C. Yellow and tailed 423

D. Yellow and tailless 507

If they are linked, calculate the map units between them.

45.4

(432+423)/1883*100=45.4mU

Two tomato plant genes A and B are linked and 40 mu apart. A tomato plant homozygous at the A and B loci (AABB) is crossed with an ab plant (aabb). The resulting F1 is two-point testcrossed back to an ab tester. What percent of the progeny is expected to be Ab?

20%

40 mu means 40% of progeny are recombinant

Two recombinant phenotypic classes: Ab or aB

Divide 40 by 2 Therefore Ab = 20%

Two tomato plant genes A and B are 10 mu apart and genes B and C are 30 mu apart. The order of the genes is A-B-C. A tomato plant homozygous at the A B and C loci (AABBCC) is crossed with an abc plant (aabbcc). The resulting F1 is testcrossed back to an abc tester. What percent of the progeny is expected to be Ac?

20%

Double cross over (DCO) does not happen as often as predicted because of ___________.

Interference

Sometimes a DCO recombinant can look like the _____________.

Parental phenotype

Linkage

Genes (alleles) on the same chromosome are likely to be inherited together

Genetic map

Shows the order of linked genes and distances between genes on a chromosome

Linkage group

Set of linked genes

What makes recombinant progeny special?

Progeny with different combination of markers as the parent

Distances on a map are measured in

map units

4 major steps in a three-point test cross

Step 1. Determine the order of the genes
Step 2. Reorganize the data table to reflect the gene order
Step 3. Calculate map units for the first two genes
Step 4: Calculate map units for the second two genes

Which statement best describes wild-type human sex determination?

Individuals with a Y chromosome are male.

A karyotype is done on an individual who has ovaries and no testes, and it is discovered that they are XY. However, the Y chromosome appears to have a deletion. What region is most likely deleted?

SRY