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Biology 2581B Lecture Notes - Lecture 13: Collinearity, Gene Mapping, Synteny

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ivoryjackal749
19 Feb 2018
School
Western University
Department
Biology
Course
Biology 2581B
Professor
Susanne Kohalmi David Smith

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Document Summary

At the sequence level many similarities: same types of genes, genes with similar sequences. Same types of genes often have very similar sequences. There may also be gene families represent in both organisms. Isolate chromosomes from the cell and arrange them: 20 mouse vs 23 human chromosomes different number, both sets of chromosomes are comprised of somatic chromosomes and x/y chromosomes. Collinearity mapping alignment genomes of different species. Each mouse chromosome could be pieced together from different human chromosomes: left figure: the mouse chromosome is the red line, the human genome and its similar genes are aligned to the mouse chromosome. The different colours represent different human chromosomes containing the homologous mouse gene. The similar genes are present in both genomes, but on different chromosomes. Mouse genome can be broken and aligned with the human genome: right figure: human chromosomes colour coded with mouse genes. These mutations were maintained there must have been tolerance of chromosomal rearrangements.

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Related Questions

1). Thyroid hormone (TH) has been identified as one of the factors promoting phenotype development in the Mexican axolotl salamander. Which of the following statements regarding the impact of TH is FALSE?

A). Axolotls maturing in water with high concentration of TH (thyroxine; T4) metamorphose into a terrestrial form.

B). A genome-wide scan of both the axolotl and its sister species found a large reduction in the number of mRNA transcripts that regulate the production of TH.

C). Adding TH (thyroxine; T4) to the water in which axolotl individuals are reared causes them to remain in a larval stage.

D). Most salamander species produce a burst of TH when they move from water to land.

2).What would be an appropriate evolutionary explanation of the fact that the ordering of some homeotic genes (such as Hox genes) on vertebrate chromosomes parallels the ordering of homeotic genes on fruit fly chromosomes?

A). The similarity is a coincidence, not documented in other invertebrates and largely a result of random mutations.

B). Homeotic genes show that insects and vertebrates are closer relatives than the traditional classification system indicates.

C). Homeotic genes of different animal lineages might be ordered in a similar fashion, yet their sequences are completely different.

D). The similar ordering of homeotic genes in animals, both vertebrate and insect, is due to ancient homology.

3). Which of the following correctly defines "homeotic genes"?

A). Homeotic genes encode proteins that control the cellular environment in a differentiated cell tissue.

B). Homeotic genes are DNA sequences that turn off, but not on, the expression of other genes and are controlled by "master-switch" genes.

C). Homeotic genes are "master-switch" genes that control other genes in a set sequence and thereby affect cell size, shape, division, and the positioning of the cells within the organism.

D). Homeotic genes are DNA sequences that turn on, but not off, the expression of other genes and are controlled by "master-switch" genes.

4). Which of the following is NOT considered a type of heterochrony (change in the rate and timing of development)?

A). hypermorphosis

B). acceleration

C). neoteny

D). ontogeny

5). How does the dominance theory explain why the heterogametic sex is at a disadvantage in Haldane's rule?

A). Beneficial dominant alleles will never be fully expressed in hybrids as they only carry one copy of the sex chromosome that carries the allele.

B). If a dominant allele has a negative effect on the fitness of hybrids, it will always be expressed in the heterogametic hybrids that possess that allele because they only need one copy of the respective sex chromosome.

C). If a recessive allele linked to a sex chromosome has a negative effect on the fitness of hybrids, that allele will always be expressed in the heterogametic hybrids that possess that allele because they only have one copy of the sex chromosome that carries the allele.

D). If a recessive allele linked to a sex chromosome has a positive effect on the fitness of hybrids, that allele will never be expressed in the heterogametic hybrids that possess that allele because they only have one copy of the sex chromosome that carries the allele.

6). In a hypothetical flowering plant species, one population evolves a different response to environmental stimuli and begins to bloom significantly later in the season than nearby populations. What type of reproductive isolating mechanism would this be?

A). hybrid sterility

B). postzygotic

C). prezygotic

D). gametic incompatibility

7). In a study of red spruce trees and black spruce trees, scientists found that the red spruce was living in a smaller geographic area and had much less genetic variation than the black spruce. They proposed that the red spruce might have arisen from a southern population of black spruce, which became geographically isolated from other black spruce populations at some point during the Pleistocene glaciations. What is this an example of?

A). allopatric speciation with the vicariance model

B). sympatric speciation

C). allopatric speciation with the peripheral isolate model

D). sympatric speciation with the ring species model

8). Which of the following defines Haldane's rule and its predictions?

A). If among hybrid offspring one sex is absent, rare, or sterile, that sex is always male.

B). If among hybrid offspring one sex is absent, rare, or sterile, that sex is always female.

C). If among hybrid offspring one sex is absent, rare, or sterile, that sex is heterogametic (has two different sex chromosomes).

D). If among hybrid offspring one sex is absent, rare, or sterile, that sex is homogametic (has two of the same sex chromosomes).

8.) Which of the following statements best explains secondary reinforcement?

A). If the reproductive isolating mechanisms that developed during the geographic isolation are strong but the hybrids have higher fitness than the parent species, then the speciation process will cease.

B). If the reproductive isolating mechanisms that developed during the geographic isolation are somewhat weak but the hybrids between two populations have lower fitness, then the speciation process may continue.

C). If the reproductive isolating mechanisms that developed during the geographic isolation are sufficiently weak as to allow free interbreeding across reunited populations, then the speciation process will halt and a single species will remain.

D). When geographic isolation comes to an end, two populations always complete the divergence process and become separate species.

What is a genome? What is a genome made of? Describe the bacterial genome. How do bacteria reproduce? What is binary fission? Distinguish between a chromosome and chromatin. Where are chromosomes located in eukaryotic cells? What is the chromosome made of? What is a centromere? What is the centromere's role? What are sister chromatids and how do they arise? Distinguish between somatic cells and germ (gametes) cells. Describe the cell cycle. What are the different phases? What occurs during S phase? What is interphase? How is the cell cycle controlled?

Describe mitosis. What are the phases of mitosis? What occurs in each of the phases of mitosis? What is cytokinesis? How does this differ between plant and animal cells? What is a kinetochore? Where does it form? What is its role? What is the role of microtubules in mitosis? What is a centriole and what is it composed of? What is a centrosome and what is its role in mitosis? What is the metaphase plate and why is this important? What is the mitotic spindle, its role and its makeup? What defines a diploid cell? How many copies of each chromosome is in a diploid cell? What about a haploid cell? Why do the daughter cells of mitosis always have the same complement of chromosomes?

Describe meiosis. What are the phases of meiosis? What occurs in each of the phases of meiosis? Distinguish between meiosis I and meiosis II and describe how each of these processes compare to mitosis. Why do animal cells undergo meiosis? What is a gamete? What is a zygote? What are recombination, crossing-over, and chiasma? When and why does this occur? What is meant by 'homologous pair of chromosomes'? Why don't the daughter cells of meiosis have the same genetic makeup? What controls the segregation of chromosomes into the gametes?

What are genetic characters? What are genetic traits? What is an allele? What is a locus? How many alleles at each locus would a human cell have and why? Distinguish between genotype and phenotype. What is meant by a dominant gene? What is meant by a recessive gene? How do these differ? What is the genotype of a homozygous dominant organism? What is its phenotype? What is the genotype of a homozygous recessive organism? What is its phenotype? What is the genotype of a heterozygous organism? What is its phenotype? What is a genetic cross? Distinguish between the P, F1, and F2 generations. What is a true-breeding line? What is the genotype and phenotype of a cross between homozygous dominant and homozygous recessive parents? If the F1 progeny are crossed, what would be the genotype and phenotype of the F2 generation? What would be the phenotypic ratio? What would be the genotypic ratio? Be ready to generate Punnet square tests or probability analyses of crosses involving more than one genetic locus. Describe a dihybrid cross where two alleles are homozygous dominant in one parent and homozygous recessive in the other. What would be the phenotypic ratio of the F2 generation from this dihybrid cross? What is meant by independent assortment? Be prepared to calculate probabilities resulting from different crosses.

Distinguish between complete and incomplete dominance. How would incomplete dominance alter the results of a hybrid cross? What would the resulting F2 generation phenotype and genotype ratios be? What is codominance? How does this affect the results of crosses? Be prepared to determine likely blood types of parents based on the blood types of their offspring. What is a polygenic trait? What is a carrier state for a genetic disease? What is meant by linked genes? How does this affect expected outcomes of genetic crosses? How is gene linkage used for chromosomal mapping? Distinguish between autosomes and sex chromosomes. What sex chromosomes are found in women? What sex chromosomes are found in men? What are sex-linked traits? Be prepared to give the results of crosses that involve sex-linked recessive traits. What is the process of nondisjunction? What are the likely results? Why is this important? What is a Barr body? Recognize the genetic abnormality of Downs Syndrome, Turner's Syndrome, and Klinefelter's Syndrome.

Expression vectors inprokaryotes do not make functional eukaryotic gene products inbacteria very well because

Answer Not sure which one ?!

· the codon sequence for prokaryotes is differentthan the codon sequence in eukaryotes

· there are no disulfide bridges formed in proteinsnormally made in prokaryotes

· prokaryotic expression vectors cannot translateeukarytic sequences

· eukaryotic genes have introns, and prokaryotesdon't

· eukaryotic genes have exons and prokaryotesdon't


I create a knockout mouseusing the agouti/black fur system \. When I cross the agoutioffspring of the originally engineered mouse, I find a ratio of 2agouti mice to 1 black furred mouse. What is the bestexplanation?

Answer not sure which one?!

· The gene knocked out was recessive.

· The gene knocked out was dominant.

· The gene knocked out was a lethalgene.

· The knockput was integrated into a random spot,and did not knockput the original gene.

A restriction enzyme cuts DNAand leaves the following end

xxCTGCA
xxG

Which of the following could be the sequence of the correspondingend of the other end of the cut DNA?

Answer

· xxG
xxCTGCA

· xxC
xxGTGCA

· xxCCGAT
xxG

· xxGGCTA
xxC


An SNP always occurs dueto

Answer

· a one base-pair change.

· a three base-pair change.

· a single restriction site change.

· a single amino acid change.

· None of these.


I PCR out a mutated gene in apatient with Lisenbee chorea (the inability to dance in acoordinated fashion) and I compare it to another patient with thatsame disease phenotype. One subject had a mutation on chromosome 4,and the other subject couldn't rock it because of a mutation onchromosome 5. This is an exampe of

Answer

· pleitropy

· locus heterogeneity

· allelic heterogeneity

· dominant negative mutation

· penetrance

In his experiments, Mendelnoted that when two traits are involved in a genetic cross, theyare inherited independently of each other. Though Mendel didn'tknow about chromosomes, this still holds true (mostly)because

Answer

· genes on the same chromosome are often mixedthrough meiotic crossover during the formation ofgametes.

· variant alleles of the same gene do not interferewith the phenotypic expression of the gentoype in different geneticloci.

· most higher organisms are diploid, making only twoalleles available for every genetic locus, and there is a 50/50chance of geting either allele from a single parent.

· expression of phenotypes can vary from thegenotypes because of encironmantal influences.

· chromosomes often recombine

Anticipation is caused by amutation that increases in expressivity over subsequentgenerations.

Answer

· True

· False

Question 44

I have a genotype that shouldproduce a specific phenotype, but some of the individuals with thegenotype do not demonstrate any evidence of the phenotype. I wouldconsider this an example of

Answer

· allelic heterogeneity.

· locus heterogeneity.

· penetrance.

· expressitivity.

· sheer luck.

Question

Which of the following doesnot occur during the PCR reactions?

Answer

· Changes in the reaction temperature by athermocycler

· Denaturation at high temperatures

· Synthesis of oligonucleotide primers

· Extension of primers by DNA polymerase

· Annealing of oligonucleotide primers

Question

DNA markers, or variantnon-coding regions of DNA, are DNA polymorphisms that are usefulfor genetic mapping.

Answer

· True

· False

A mosaic is an organismwith

Answer

· multiple genotypes within one organism

· multiple alleles within one genotype

· more than one color of fur

· transgenes added to the zygote beforedevelopement

· a wt phenotype but a mutated genotype

Question

Genotype causesphenotype.

Answer

· No, gentoype just influences phenotype.

· Yes, genotype is the DNA sequence that createsphenotype.

Question

A true genetic chimera can becreated by

Answer

· mutating a gene early on in the development of anorganism resulting in different alleles being present in theadult

· multiple fertilized eggs or zygotes fusing to formone embryo

· adding a transgene to the genome of an organismduring fetal development only

· adding cells of a different species to an adultorganism

· adding a transgene to the genome of an animal atany stage in development

Question

The ABO blood group can bestbe explained by the concept of _______.

Answer

· dominant traits

· recessive traits

· allelic heterogeneity

· locus heterogeneity

· vampirism

If a loss of functionmutation creates a dominant phenotype, it may be becauseof

Answer

· haploinsufficiency

· penetrance

· expressivity

· allelic heterogeneity

· locus heterogeneity

Please select the best matchfor each.

Answer

· PCR: Technique used to generatecopies of a DNA fragment

· Southern blot : Screeningprocedure used to assay DNA fragments

· RFLPs : DNA fragments generatedby restriction enzymes that vary in length betweenindividuals

· Northern blot : Screeningprocedure used to assay mRNA fragments

· Electrophoresis Movement ofmacromolecules in an electrical field

Answer

A.

Screening procedure used toassay DNA fragments

B.

Movement ofmacromolecules in an electrical field

C.

Screening procedure used toassay mRNA fragments

D.

DNA fragments generated byrestriction enzymes that vary in length betweenindividuals

E.

Technique used to generatecopies of a DNA fragment

A gene mutates, and theprotein produced has a novel way of interacting with the cell, andcreates a new phenotype because of this new functionality. This iscalled

Answer

· pleitropy

· locus heterogeneity

· allelic heterogeneity

· dominant negative mutation

· gain of function dominant mutation

Question 62

Mutations in the somaticchromosomes may be inherited by the next generation.

Answer

· True

· False


A degenerate PCR primer withmany variant sequences must be used to make multiple copies of agene

Answer

· if only the protein sequence of the gene productis known to construct the primers

· if the DNA you are using is cDNA to constructthe primers

· if the DNA you are using is genomic DNA to becopied

· if the DNA you are trying to copy iscDNA

· if the vector is prokaryotic and the transformedcell is eukarytotic

Question

Please select the best matchfor each term.

Answer

· Restriction enzyme


· PCR C

· Plasmid

· YAC A

· Dideoxynucleotide

Answer

A.

Endonuclease isolated frombacteria

B.

Eukaryotic cloningvector

C.

Method for amplification ofDNA sequences

D.

Small circular fragment ofDNA

E.

Molecule used in DNAsequencing

Question

A couple goes on MauryPovitch, and the results are in: you are not the father. But noother man impregnated the female (granted, unlikely for a MauryPovitch guest, but work with me here) and he must be the father.DNA analysis claims otherwise, though the child definitely wasmom's (poor thing). What may be going on here?

Answer

· the child is parthenogenic because the motheractually impregnated herself like a shark, and the child's DNA isall mom's

· the child had a mutation that changed the genethat is used to trace paternity

· the child is a mosaic because he is actually a setof twins fused early during fetal development, and therefore camefrom 2 eggs and 2 sperm

· the dad may have germ-line mosaicism, meaning thatthe genotype of his sperm is different from his somaticgenotype

· mitochondrial DNA only comes from mom, so there isno way to tell whobthe baby's father is