Exam 3

Question 1

What is a null hypothesis?

Answer 1

A null hypothesis assumes data will fit a given ratio or model, and that any variation is purely by chance.

Question 2

True or False:
A null hypothesis can be proven.

Answer 2

False:
A null hypothesis cannot be proven, but it can be either supported (failed to reject) or rejected.

Question 3

What does the Chi-square statistical test accomplish?

Answer 3

Known as the ‘goodness of fit’ test, it evaluates the influence of chance on data and assesses whether the data is consistent with the model (expected outcome) and determines if the null hypothesis should be rejected or not.

Question 4

What is p-value (Chi-square test calculation)?

Answer 4

P-value is a statistical measure of significant differences between datasets calculated using a Chi-square statistical test and has a cut-off (a) frequently set to 0.05.

Question 5

What does the value (i.e. 0.5) of p-value mean?

Answer 5

The value (0.5) obtained from calculating p-value is the percent (5%) that if this experiment is repeated, there is a 5 percent chance that the same or greater variation in data would be observed again.

Question 6

When should one reject or accept the null hypothesis based on the p-value?

Answer 6

If the p-value of the data is greater than the cut-off (a) then the null hypothesis is supported. However, if the p-value of the data is less than the (a) then the null hypothesis is rejected due to too much variation.

Question 7

How do you determine how many degrees of freedom?

Answer 7

Degrees of freedom are determined by taking the sum of how many variants are being analysed and subtracted by one.

Question 8

Example: Vestigial wings are completely recessive to wild-type wings in Drosophila melanogaster.
Monohybrid cross data:
315 F2 flies with wild-type wings
97 F2 flies with vestigial wings
Model?
Null Hypothesis?

(X^2)?

Degrees of Freedom?

p-value?

Fail to reject or reject?

Answer 8

Model? 3:1

Null Hypothesis? There is no difference between the monohybrid cross results and the model; the monohybrid results follow a 3:1 ratio.

(X^2)?
X^2 = sum of ((Observed - Expected)^2) / Expected
wild-type: 315 309 0.117
vestigial: 97 103 0.350
412
Sum (wild-type + vestigial X2) = 0.467 = X2

Degrees of freedom? 1

p-value? 0.50

Fail to reject or reject? Fail to reject

Question 9

Gene mapping

What is linkage?

Answer 9

Genes (alleles) on the same chromosome are likely to be inherited together known as linked genes.

Question 10

Gene mapping

What is a linkage group and provide an example?

Answer 10

A linkage group is a set of linked genes.
(i.e. Genes located on chromosome 4 are in linkage group IV; Genes located on the X chromosome are X-linked)

Question 11

Gene mapping

What is a genetic map?

Answer 11

A genetic map shows the order of linked genes and distances between genes on chromosomes.

Question 12

Gene mapping

What is an example of linkage?

Answer 12

Two genes on a single pair of homologs; exchange occurs between two nonsister chromatids.

Question 13

Gene mapping

What determines the likelihood of recombination?

Answer 13

The distance between genes determines the likelihood of recombination.
Two genes that are far apart have many chances of crossing over while two genes that are extremely close together do not have the possibility of crossing over due to strong linkage.

Question 14

Gene mapping

What are genetic and physical markers?

Answer 14

A genetic marker is a DNA sequence, such as an SNP or repeat.
A physical marker is a phenotype associated with a gene locus.

Question 15

Gene mapping

What is a test cross and what are they used to determine?

Answer 15

A test cross crosses an F1 heterozygote with a homozygous recessive tester. If we are interested in two genes, a two-point test cross is used.

Question 16

Gene mapping

How do we know which progeny (offspring) are recombinant and which are parental?

Answer 16

Recombinant progeny have a different combination of markers from the parent, indicating a crossover has occurred.
Parental progeny have the same combination of markers as the parent.

Question 17

Gene mapping

What do the results of a test cross indicate if:

50% recombination between e and vg genes

F2 phenotypic classes:
e vg : 25% parental
e vg+ : 25% recombinant
e+ vg : 25% recombinant
e+ vg+ : 25% parental

Answer 17

The genes are very far apart on the same chromosome, OR on different chromosomes indicating independent assortment.

Question 18

Gene mapping

What do the results of a test cross indicate if:

No recombination between e and vg genes.

F2 phenotypic classes:
e vg : 50% parental
e vg+ : 0% recombinant
e+ vg : 0% recombinant
e+ vg+ : 50% parental

Answer 18

Genes are very close on the same chromosome and have complete linkage.

Question 19

Gene mapping

What do the results of this experiment indicate? And how do we determine the distance between the e and vg genes?

F2 phenotypic classes:
e vg : 1418 flies : 43.8% parental
e vg+ : 241 flies : 7.4% recombinant
e+ vg : 283 flies : 8.7% recombinant
e+ vg+ : 1294 flies : 40.0% parental

Answer 19

The e and vg genes are linked.
We determine the distance between genes by dividing the number of recombinants by the total number of progeny and then multiplying by 100 to get the number of map units (mu) the genes are apart.

((241 + 283) / 3236) * 100 = 16.2 mu

Genes e and vg are 16.2 map units apart.

Question 20

Gene mapping

What happens during a double-crossover (DCO)?

Answer 20

A double crossover occurs when two chiasmata form and there is a double exchange between two nonsister chromatids.

Question 21

Gene mapping

True or False:
Double-crossovers occur far less than single-crossovers.

Answer 21

True

Question 22

Gene mapping

How do we know which progeny are parental, single-crossover, or double-crossover in a three-point cross?

Answer 22

Progeny in the lowest abundance are double-crossover recombinants.
Progeny in the highest abundance are parental.
Progeny in the intermediate range of abundance are single-crossover recombinants.

Question 23

Gene mapping

What four steps will help in the determination of a three-test cross?

Answer 23

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

Question 24

Gene mapping

Identify parental, region 1 SCO recombinants, region 2 SCO recombinants, DCO recombinants, gene order, recombination frequency, and map unit distance from the following data:

p+ j+ r+ 179
p j r 173
p+ j r 52
p j+ r+ 46
p+ j+ r 22
p j r+ 22
p+ j r+ 4
p j+ r 2

Total: 500

Answer 24

Parental:
p+ j+ r+ 179
p j r 173

SCO region 1:
p+ j r 52
p j+ r+ 46

SCO region 2:
p+ j+ r 22
p j r+ 22

DCO:
p+ j r+ 4
p j+ r 2

Gene order: pjr or rjp

DIstance p to j (region 1)
(SCO region 1 + DCO) / Total Progeny * 100
=20.8 mu

Distance j to r (region 2)
(SCO region 2 + DCO) / Total Progeny * 100
=10 mu

Distance p to r (region 1 + region 2)
20.8 mu + 10 mu = 30.8 mu

Question 25

# Gene mapping In the progeny of a two-point test cross, what percentage of recombinant phenotypes is expected if the genes under study are independently assorting?

Answer 25

50%

Question 26

# Gene mapping 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 generation is two-point testcrossed back to an ab tester (aabb). What percent of the progeny is expected to be Ab? ## Footnote number of mu = % recombinants

Answer 26

40 mu = 40 % recombinants **20 % Ab** and 20 % aB

Question 27

# Gene mapping Three genes on the Drosophila X chromosome are examined pairwise. It is determined that they have the following recombination rates: yellow, white 0.5% white, miniature 34.5% yellow, miniature 35.4% Which two genes are physically closest together?

Answer 27

Yellow and white are physically closest together because 0.5% recombination translates to 0.5 map units between the genes compared to the other genes being 34.5 mu and 35.4 mu apart from each other.

Question 28

# Gene mapping True or False: Crossing over occurs at random.

Answer 28

False: Chromosomes have recombination hot spots and cold spots.

Question 29

# Gene mapping What causes a DCO recombinant to look like the parental phenotype?

Answer 29

The farther apart two genes are, the greater the probability that undetected DCOs will occur.

Question 30

# Gene mapping What are some limits of mapping human genomes?

Answer 30

1) Unrealistic to use the same methods as model organisms ^Ethical considerations ^Long wait times (across generations) ^Low offspring number (low sample size) 2) Analyze multiple pedigrees using special algorithms 3) Analyze DNA markers (SNPs, microsatellites, etc.) from saliva samples using DNA arrays and genome sequencing ^Direct-to-consumer genotyping services like 23andMe are producing in population genetics data

Question 31

# Sex linkage What are the two sex determination systems?

Answer 31

1) Genotypic sex determination -due to specific DNA sequences 2) Environmental sex determination -signals from environment

Question 32

# Sex linkage What is genotypic sex determination and what are the three subcategories? ## Footnote Remember GeChMa

Answer 32

Genotypic sex determination is due to specific DNA sequences. The three subcategories are: 1) Genic balance 2) Chromosome determination 3) Mating-type determination

Question 33

# Sex linkage What is Genic balance?

Answer 33

The ratio of sex chromosomes to autosomes controls the amount of sex-determining gene products

Question 34

# Sex linkage What is Chromosome determination?

Answer 34

Chromosome determination is the presence or absence of gene product(s) encoded by sex chromosomes; or the presence or absence of a sex chromosome.

Question 35

# Sex linkage What is Mating-type determination?

Answer 35

Mating-type determination is the expression of gene variants called idiomorphs, control mating type (in some haploid microbes). (i.e. yeast can have MAYa and MAY(alpha) alleles.

Question 36

# Sex linkage What is environmental sex determination? List examples.

Answer 36

Environmental sex determination is the signals from the environment. (i.e. day length, temperature, social cues)

Question 37

# Sex linkage List two examples of genic balance in organisms.

Answer 37

C. elegans : hermaphrodite-XX male-XO Drosophila melanogaster: female-XX male-XY

Question 38

# Sex linkage List two examples of chromosome determination in organisms.

Answer 38

Mus musculus (mice): female-XX male-XY Xenopus laevis (frogs): female-ZW male-ZZ

Question 39

# Sex linkage List an example of environmental sex determination in organisms.

Answer 39

Danio rerio (fish): female-None male-None

Question 40

# Sex linkage What type of chromosomes determine biological sex?

Answer 40

A combination of heteromorphic sex chromosomes determine biological sex.

Question 41

# Sex linkage The XX sex chromosome combination causes what biological features to develop?

Answer 41

The XX sec chromosomes cause the development of gonads into ovaries and produce eggs (a wild-type biological female).

Question 42

# Sex linkage The XY sex chromosome combination causes what biological features to develop?

Answer 42

The XY chromosomes cause the gonads to develop into testes and produce sperm (a wild-type biological male).

Question 43

# Sex linkage What are the different regions of a Y chromosome? ## Footnote There are two main regions, one region includes SRY, euchromatin, centromere, and heterochromatin.

Answer 43

Pseudoautosomal region (PAR), Male-specific region of the Y (MSY)

Question 44

# Sex linkage What is the function of the PAR?

Answer 44

PAR synapses with the X chromosomes during meiosis.

Question 45

# Sex linkage What is the function and sub parts of MSY?

Answer 45

MSY contains euchromatin which includes **SRY, the sex-determining region of the Y chromosome**.

Question 46

# Sex linkage When is SRY expressed in development and what is its function?

Answer 46

SRY is expressed approximately 6-8 weeks after fertilization. SRY activates the SOX9 gene (testes development which secretes testosterone-shapes male sexual development). SRY represses WNT4 gene expression (controls expression of ovary development, which secrete estrogen-shapes female sexual development).

Question 47

# Sex linkage Who and how was sex linkage discovered?

Answer 47

Sex linkage was discovered by Thomas Hunt Morgan through observing fruit flies.

Question 48

# Sex linkage True or False Many linked genes do not influence sex development

Answer 48

True

Question 49

# Sex linkage True or False Most sex-linked genes are Y-linked and not X-linked.

Answer 49

False: Most sex-linked genes are X-linked because Y does not contain many genes.

Question 50

# Sex linkage What are some examples of X-linked genes?

Answer 50

In humans: color perception, dystrophin (structure protein in muscles), blood clotting factors. In cats: fur color pattern In fruit flies: eye color

Question 51

# Sex linkage Why are X-linked recessive inheritance traits more frequently observed in males in a family?

Answer 51

Males are hemizygous for genes on the X chromosome and have no second allele (i.e. XX in females) to compensate for the recessive allele.

Question 52

# Sex linkage When do females with X-linked recessive inheritance alleles express the trait?

Answer 52

Females only express X-linked recessive inheritance traits when they are homozygous for the recessive allele. *Females with only one recessive allele are carriers

Question 53

# Sex linkage What are Barr bodies and what is their function?

Answer 53

Barr bodies are inactive X chromosomes that were deactivated during the blastocyst stage in XX mammals.

Question 54

# Sex linkage What are two forms of imprinting regarding Barr bodies?

Answer 54

1) Monoalleleic expression allows for gene dosage compensation 2) Equal amounts of X-linked gene expression between males and females

Question 55

# Sex linkage True or False A Barr body is formed through lyonization

Answer 55

True

Question 56

# Sex linkage What gene is involved with Barr bodies?

Answer 56

Involves XIST gene on the X chromosome and is weakly expressed from both X chromosomes.

Question 57

# Sex linkage What occurs to the XIST gene and what does it do?

Answer 57

During early development, one XIST gene copy is silenced and becomes the active X chromosome while the other active XIST gene causes that X chromosome to become a Barr body. XIST encodes a long non-coding RNA (lncRNA) using DNA methyltransferases and HDAC to pack up the chromosome.

Question 58

# Sex linkage What is mosaicism?

Answer 58

Mosaicism is a mixed phenotype resulting from different genotypes or gene expression levels in the cells of a multicellular organism.

Question 59

# Sex linkage Can random Barr body lyonization cause monoallelic expression?

Answer 59

Yes, Barr bodies can cause monoallelic expression in different cells of the body as well as some cells either having the paternally or maternally derived X chromosome silenced and only express maternally or paternally derived X chromosome genes, respectively.

Question 60

# Sex linkage True or False All mitotic descendants of a cell inherit the parent cell's inactivation pattern.

Answer 60

True

Question 61

# Sex linkage What is an example of Mosaicism?

Answer 61

In cats, mosaicism is observed as multiple coat colors. Coat color locus on the X chromosome codes for orange and black alleles. Some cells with X chromosome express the black fur pigment allele, while others express orange fur pigment allele.

Question 62

# Sex linkage What are some cytogenetic observations that supported a Y chromosome sex determination mechanism in humans?

Answer 62

Aneuploid conditions: 1) 45, XO (Turner syndrome) are phenotypically female w/ ovaries 2) 47, XXY (Klinefelter syndrome) are phenotypically male w/ testes Sex reversal conditions: 1) 46, XY females with deletion of the Y chromosome 2) 46, XX males had a small piece of Y attached to X (most likely the SRY region)

Question 63

# Sex linkage What are three types of sex-linked disorders in humans?

Answer 63

1) X-linked recessive: Human color blindness -Loss of function mutations in genes encoding photoreceptor proteins in the eye located on the X chromosome cause color blindness 2) X-linked dominant: Rett syndrome -Type of autism caused by the missence or nonsense mutations in gene encoding methyl-CpG-binding protein 2. -This gene must function properly in order for maturation of neurons. 3) Y-linked (holandric traits) -Very few identified

Question 64

# Sex linkage Questions about X-linked recessive inheritance: 1) What proportion of the sons of an affected XX mother would show the trait? 2) What proportion of the sons of a carrier XX mother would show the trait? 3) What proportion of XX daughters would show the trait from an unaffected XX mother and affected XY father? 4) What proportion of XX daughters would show the trait from an affected XX mother and unaffected XY father? ## Footnote 3) Assume "unaffected XX mother" could be heterozygous for the trait or homozygous unaffected. Solve for both.

Answer 64

1) 100% of sons would show the trait 2) 50% of sons would show the trait 3) 0% if homozygous, 25% of daughters affected if heterozygous for the trait. 4) 0% of daughters affected

Question 65

# Sex linkage What does hemizygous mean and how is it related to XY humans?

Answer 65

Hemizygous means an individual who has one member of a homologous pair of chromosomes rather than two. Males are hemizygous for the gene on the X chromosome.

Question 66

# Sex linkage Questions about X-linked dominant inheritance: 1) If the XX mother is heterozygous and XY father is unaffected, what proportion of their XY sons will be affected? XX daughters? 2) If the XX mother is unaffected but the XY father is affected, what proportion of their XX daughters will be affected? XY sons?

Answer 66

1) 50% XY sons affected, 50% XX daughters affected 2) 100% XX daughters affected, 0% XY sons affected

Question 67

# Sex linkage How does the determination of the sex of the fly (*D. melanogaster*) differ from human sex determination?

Answer 67

The ratio of the number of X chromosomes to sets of autosomes determine the sex of the fly.

Question 68

# Extensions of Mendel How many alleles can a single diploid have for a given genes?

Answer 68

A single diploid can only have up to 2 alleles for a given gene. Mutations can lead to more than 2 alleles.

Question 69

# Extensions of Mendel How is the number of possible genotypes in a population calculated?

Answer 69

Possible genotypes = n(n+1)/2 n= number of alleles (i.e. If there are 4 possible alleles, the number of genotypes in the population is 4(4+1)/2 = 10)

Question 70

# Extensions of Mendel What is codominance?

Answer 70

Codominance is when heterozygotes simultaneously show the phenotypes that would be seen in the homozygotes. (i.e. a cow heterozygous for white and red hair = white and red hair both shown in the cow, no blending of colors) (i.e. Blood type, AB, both alleles are expressed)

Question 71

# Extensions of Mendel Explain codominance on a molecular level? ## Footnote Three answers

Answer 71

1) Equal amounts of gene product from both alleles 2) Both alleles are expressed and have equal activities 3) Gene products do not interfere with each other

Question 72

# Extensions of Mendel What is incomplete dominance?

Answer 72

Incomplete dominance is when one allele is not completely dominant to the other allele. A third, blended phenotype is presnt in the population. (i.e. palomino horses: Chesnut (dark brown), Palomino (medium brown), Cremello (light brown))

Question 73

# Extensions of Mendel What is the molecular explanation of incomplete dominance? ## Footnote 2 answers, one has 3 subfields

Answer 73

1) Varies from trait to trait 2) Can be dependent on gene dosage -Homozygosity for functional allele causes two doses of the gene product i.e. red snap dragon -Heterozygosity causes one dose i.e. pink snap dragon -Homozygosity for the null allele no dose i.e. white snap dragon

Question 74

# Extensions of Mendel What is pleiotrophy?

Answer 74

Pleiotrophy is when one gene is responsible for multiple traits. (i.e. phenylketonuria (PKU): PAH gene product involved in metabolizing phenylalanine; PKU caused by homozygosity or compound heterozygosity (having 2 different mutant alleles) for loss-of-function pah alleles, so that phenylalanine accumulates in cells; lower IQ, seizures, light skin pigmentation result)

Question 75

# Extensions of Mendel What is pleiotrophy on a molecular level? ## Footnote 2 answers

Answer 75

1) Promiscuous protein has more than one function 2) Cell-specific effects of protein variants -(i.e. neurons are more sensitive to loss of PAH function than other cells types)

Question 76

# Extensions of Mendel What is an essential gene?

Answer 76

An essential gene is a gene product required for life of a cell or organism. -No compensating gene or gene with redundant function to take its place -When the function of the gene product is mutated, a lethal allele results

Question 77

# Extensions of Mendel What is a lethal allele?

Answer 77

A lethal allele causes the death of the organism. -aka. deleterious allele -Different than a null allele, although a lethal allele can also be a null allele

Question 78

# Extensions of Mendel What are polygenic traits?

Answer 78

Polygenic traits are multiple genes that contribute to a trait.

Question 79

# Extensions of Mendel What is epistasis?

Answer 79

Epistasis refers to when two genes are involved, and one gene interferes with the expression of the other gene. The epistatic gene suppresses the phenotype from the hypostatic gene.

Question 80

# Extensions of Mendel What are complete recessive alleles?

Answer 80

Complete recessive alleles are often null alleles due to loss-of-function mutation. (i.e. wrinkled pea vs round pea)

Question 81

# Extensions of Mendel What are complete dominant alleles?

Answer 81

1) Gain of function: amount of gene product activity is wild type or increased 2) Loss of function: null allele -Dominant negative mutant -Haploinsufficiency

Question 82

# Extensions of Mendel What is a dominant negative mutant?

Answer 82

A dominant negative mutant is a mutant gene product that interferes with the wild-type gene product.

Question 83

# Extensions of Mendel What is haploinsufficiency?

Answer 83

In haploinsufficiency, heterozygosity reduces the amount of gene product so that the wild-type phenotype cannot occur.

Question 84

# Extensions of Mendel Traits like familial hypercholesterolemia follow incomplete dominance are actually considered dominant. Why?

Answer 84

Phenotype is still visible in heterozygotes, even though it is to a lesser extent.