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24 Apr 2019

You sequence a particular MHC gene in 10 people of Scandinavian descent and 10 people of Japanese descent and identify 20 point mutations that are fixed for one base in the Scandinavian population and a different base in the Japanese population. 15 of these point mutations are nonsynonymous and 5 are synonymous. Does this gene appear to be under negative (aka purifying) selection, positive selection, or no selection? Explain your reasoning (~2 sentences).

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Hubert KochLv2

26 Apr 2019

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13. The arms of a human and the wing of a bat are _________________ structures, composed of the same bones that have been modified for different functions.

analogous

vestigial

c.	homologous

d.	convergent

14. Xeroderma pigmentosum is an autosomal recessive genetic disorder. People who are homozygous for the disease-causing allele have skin that is damaged by exposure to ultraviolet radiation; this can lead to skin cancer at an early age. The mutation that causes this disorder is in a gene that functions:

a.	to repair DNA by excising (removing) nucleotides damaged by UV light.

b.	in lysosomes, to break down lipids that otherwise accumulate in the nervous system.

c.	to produce the UV blocking pigment melanin in the skin cells

d.	in red blood cells to carry oxygen to the skin.

15. The Amish are a religious sect descended from a small group of colonists who came to the United States over 200 years ago. Their religious beliefs have kept them isolated from society. The Amish have a much higher than average incidence of both polydactyly (extra fingers and toes) and dwarfism in their communities. This is most likely explained by:

a.	inheritance of acquired characters.

b.	the founder effect.

c.	disruptive selection.

d.	natural selection.

16. In the structure of DNA that Watson and Crick proposed, the sides of the "ladder" of the DNA molecule are always the same distance apart, making the molecule a constant width. This occurs because when the bases hydrogen bond to form the rungs of the "ladder", a:

a.	purine always pairs with a pyrimidine.

b.	purine always pairs with a purine.

c.	pyrimidine always pairs with a pyrmidine.

d.	The structure of the double helix is not determined by how the bases pair.

17. The RNA transcript of DNA that travels to the cytoplasm, carrying the instructions to make a protein, is called:

rRNA.

tRNA.

mRNA.

d.	RNA polymerase.

18. When DNA is replicated, the error rate is approximately one error for every 10,000 nucleotides copied. However, that error rate is reduced to only 1 error for every 1 billion nucleotides. The DNA sequence is "corrected" by:

a.	repeating S phase to see if the error rate is lower the second time around.

b.	enzymes that proofread the DNA and repair errors.

c.	messenger RNA during the process of transcription.

d.	Any errors made during DNA replication cannot be corrected. If errors are detected after S phase, the cell is destroyed.

19. Mendel's principle of segregation says that:

a.	when gametes are formed, each gamete receives only one allele for a particular gene.

b.	some genes are dominant to others.

c.	a testcross must be used to determine the genotype of an organism with a dominant phenotype.

d.	all of the above

20. Tay-Sachs disease is lethal before reproductive age, but the allele persists in Louisiana French Canadians because:

a.	it is a dominant allele.

b.	new mutations causing this disease are common in that population.

c.	it is not expressed in the phenotype of heterozygous individuals.

d.	the disease is contagious and can be transmitted by nonheritable means.

21. Physical features that are similar in organisms which are not closely related to each other are most likely a result of ____________. A good example of this is the similarities seen between some marsupial and placental mammals.

a.	natural selection.

b.	adaptation to similar environments

c.	convergent evolution

d.	All of the above phrases can be used to correctly fill this blank.

22. In humans, which of the following sex chromosome compliments could be found in males?

23. The proteins that are associated with eukaryotic chromosomes:

a.	help to package the DNA within the nucleus.

b.	are involved in gene expression, through binding with the DNA.

c.	may be replicating or transcribing the DNA.

d.	All of these are true of proteins that are associated with eukaryotic chromosomes.

24. A sequence of DNA nucleotides that contains the information to produce a single protein is a(n):

codon.

gene.

c.	polypeptide.

d.	anticodon.

whitelizard672

Cystic Fibrosis (CF) is an autosomal recessive genetic disease that is characterized by the secretion of thick, abnormal mucous in the lungs. The mutated gene that leads these symptoms is the CF transmembrane conductance regulator (CFTR gene). The encoded protein is a chloride channel that moves chloride ions out of epithelial cells. In a homozygous individual, the lack of this chloride channel function in a mutant slows the flow of water into extracellular spaces. This lack of water export leads to the heavy mucus in the lungs of CF patients. Although children with CF would die in childhood, current treatments provide life expectancies into the 30âs.

CF is the most frequently inherited genetic disorder among American children. It affects 1 of every 2,500 children; 30,000 currently have the disease. Although its frequency is higher in European populations, it affects all human populations. Heterozygous carrier frequencies in the US are estimated to be 1 out of 29 Caucasians, 1 out of 46 Hispanics, 1 out of 61 African Americans and 1 out of 90 Asians. There are genetic screens for carriers of CF but they are not routinely performed despite this high frequency of carriers. At least all states in the US proscribe testing of newborns to identify children with CF early so that treatment can be started. Newborn tests for CF: http://www.cff.org/AboutCF/Testing/NewbornScreening/ScreeningforCF/ . If CF is such a common genetic disease, and such a simple Mendelian trait, why is genetic screening of parents not done more frequently? Is it just economic, a pain to do, or is it more complex such that the results of genetic testing are not just positive or negative?

Answer the following questions:
1. If two parents are heterozygous carriers of CF, show a pedigree with four children showing the incidence of carriers and afflicted children. If each unafflicted child (carrier or not) mates with another person, who has a 1 out of 30 chance of being a carrier of CF, what is the expected incidence CF disease in the third generation (frequency of CF in any one of grandchildren of the original couple)?

2. Pleiotropy of Cystic Fibrosis. Watch the two videos on the left at:

http://www.cftrscience.com/MOD-animation
or, if you can not view these, read the short NIH Genetics Home Reference for Cystic Fibrosis http://ghr.nlm.nih.gov/condition/cystic-fibrosis

Connect the description with one of the following videos, or related ones (there are many) you see:
video (10 minutes) of daily life of a child with Cystic Fibrosis http://www.youtube.com/watch?v=WUsuGKzdDg8
Lauraâs (20 year old) video diary of life with CF http://www.youtube.com/watch?v=Pgrf8qJXhpc&feature=related

In your own words, describe the range of CF phenotypes. List the other organs besides lungs that are affected and how does it affects those organs.

3.The DNA sequence of the CFTR gene is 170,000 base pairs in length and encodes the CFTR protein that is 1480 amino acids long. Open the accompanying text file (in Canvas/Files/Discussion folder) âCFTR gene DNA sequenceâ. You will see an alignment of the NIH human genome sequence of the CFTR gene â called âReferenceâ rather than âwild-typeâ- against a gene sequence containing a common mutation in CFTR. Look at the alignment and determine how the DNA sequence differs between them. What is the position number where they differ? How many and what nucleotides do they differ in? A â-â mark in one sequence in the alignment means that that base sequence is missing the corresponding bases in the other sequence. The sequence is a long one but the differences are in bolded bright red text. Matching sequence is marked with a | linking the two sequences. Look near the sequence AAATATCATC if you use FIND tool in Word.

In another file, you will an alignment of the reference translated into a protein sequence, compared to the mutant allele translated into protein sequence. The differences are again in red whereas the areas where the proteins match are in black. Look at the alignment. How do these two proteins differ? Again, find the position number and describe how they differ at that location. A â-â mark in the alignment means that amino acid is missing when compared to the other sequence.

4. Given that the CFTR gene can be analyzed for a mutation that causes CF, couples interested in being tested as carriers face several choices given the results.
What could be a consequence of a false positive result (couple is identified as carriers but they would not produce any children with symptoms)?

What could be a consequence of a false negative result (a test indicates the couple is not both carriers but they would produce some children with CF)?

5. The sensitivity of the test can vary with ethnic group. The following is a chart from the NCBI Genetic testing site. A sensitivity less than 100% would be likely to produce false negative results from an inability to determine that someone is carrier.

CF Carrier Test Sensitivity by Ethnic Group http://www.ncbi.nlm.nih.gov/projects/GeneTests/static/concepts/primer/ptscarr5.shtml
Ethnic Group ¹	Population Frequency of CF	Sensitivity of Carrier Detection ²
Caucasian	1 in 29	90%
Ashkenazi Jewish	1 in 29	97%
Native American	1 in 32	94%
Latino	1 in 46	57%
African-American	1 in 60	75%
Asian	1 in 90	30%

Why might different ethnic populations differ in the ability of the genetic test to identify carriers of CF?

Some of you will have seen Starship Troopers, a moviebased upon a novel by Robert Heinlein. The film deviates from thebook in some ways, for example the book describes a visit to aplanet to resupply the dropships used in combat operations by theM.I. (mobile infantry). Heinlein describes this visit in the book;a portion of the novel is reproduced on the followingpage.

The followig passage contains two concepts we havediscussed in class in relation to the effects of mutation onpopulations, one positive and one negative. Describe the twomutation related concepts Heinlein discusses. You must describethese concepts as a biologist - you must use the technical terms wehave used in class properly and explain the positive and negativeeffect of mutation on the evolution and health of apopulation.

(a) What is the positive effect of mutation as describedby Heinlein?

(I.E., what does Heinlein describe as a benefit ofhaving more mutations)

(b) What is the negative effect of mutation as describedby Heinlein?

(I.E., what does Heinlein describe as a problem ofhaving more mutations)

I never have learned the co-ordinates of Sanctuary,nor the name or catalogue number of the star it orbits - becausewhat you donât know, you canât spill; the location isultra-top-secret, known only to shipâs captains, piloting officers,and such ... and I understand, with each of them under orders andhypnotic compulsion to suicide if necessary to avoid capture. So Idonât want to know. With the possibility that Luna Base might betaken and Terra herself occupied, the Federation kept as much ofits beef as possible as Sanctuary, so that a disaster back homewould not necessarily mean capitulation.

But I can tell you what sort of a planet itis. Like Earth, but retarded.

Literally retarded, like a kid who takes tenyears to learn to wave bye-bye and never does manage to masterpatty cake. It is a planet as near Earth as two planets can be,same age according to the planetologists and its star is the sameage as the Sun and the same type, so say the astrophysicists. Ithas plenty of flora and fauna, the same atmosphere as Earth, nearenough, and much the same weather; it even has a good-sized moonand Earthâs exceptional tides.

With all these advantages it barely got awayfrom the starting gate. You see, itâs short on mutations; it doesnot enjoy Earths high level of natural radiation.

Its typical and most highly developed plantlife is a very primitive giant fern; its top animal life is aproto-insect which hasnât even developed colonies. I am notspeaking of transplanted Terran flora and fauna - our stuff movesin and brushes the native stuff aside.

With its evolutionary progress held down toalmost to zero by lack of radiation and a consequent mostunhealthily low mutation rate, native life forms of Sanctuary justhavenât had a decent chance to evolve and arenât fit to compete.Their gene patterns remain fixed for a relatively long time; theyarenât adaptable - like being forced to play the same bridge handover and over again, for eons, with no hope of getting a betterone.

As long as they just competed with eachother, this didnât matter too much - morons among morons, so tospeak. But when types that had evolved on a planet enjoying highradiation and fierce competition were introduced, the native stuffwas outclassed.

Now all the above is perfectly obvious fromhigh school biology ... but the high forehead from the researchstation there who was telling me about this brought up a point Iwould have never thought of.

What about the human beings who havecolonized Sanctuary?

Not transients like me, but the colonists wholive there, many of whom were born there, and whose descendantswill live there, even unto the umpteenth generation - what aboutthose descendants? It doesnât do a person any harm not to beradiated; in fact itâs a bit safer - leukemia and some types ofcancer are almost unknown there. Besides that, the economicsituation is at present all in their favor; when they plant a fieldof (Terran) wheat;, they donât even have to clear out the weeds.Terran wheat displaces anything native.

But the descendants of those colonists wonâtevolve. Not much, anyhow. This chap told me that they could improvea little through mutation from other causes, from new blood addedby immigration, and from natural selection among the gene patternsthey already own - but that is all very minor compared with theevolutionary rate on Terra and on any usual planet. So whathappens? Do they stay frozen at their present levels while the restof the human race moves on past them, until they are livingfossils, as out of place as a pithecanthropus in a spaceship?

Or will they worry about the fate of theirdescendants and dose themselves regularly with X-rays or maybe setof lots of dirty-type nuclear explosions each year to build up afallout reservoir in their atmosphere? (Accepting, of course, theimmediate dangers of radiation to themselves in order to provide aproper genetic heritage of mutation for the benefit of theirdescendants.)

This bloke predicted that they would not doanything. He claims that the human is too individualistic, tooself-centered, to worry that much about future generations. He saysthat the genetic impoverishment of distant generations through thelack of radiation is something most people are simply incapable ofworrying about. And of course it is a far-distant threat; evolutionworks so slowly, even on Terra, that the development of a newspecies is a matter of many, many thousands of years.

I donât know. Shucks, I donât know what Imyself will do more than half the time; how can I predict what acolony of strangers will do? But Iâm sure of this: Sanctuary isgoing to be fully settled, either by us or by the bugs. Or bysomebody. It is a potential utopia, and, with desirable real estateso scarce in this end of the Galaxy, it will not be left in thepossession of primitive life forms that failed to make thegrade.