Biology 1002B Lecture 12: Lecture 20

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greenduck439

20 Apr 2016

School

Western University

Department

Biology

Course

Biology 1002B

Professor

Beth Mac Dougall- Shackleton

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Document Summary

This is a volvox and chlamydomonas sequence. Nucleotide alignment at the top, and amino acid alignment at the bottom. High levels of sequence conservation: sequences are the same, then they are conserved. It is high in the nucleotide, and it is absolute if you look at the amino acid sequence. It matches perfectly with the 30 amino acids we see on the amino acid sequence. Amino acids sequences are entirely conserved: nucleic acid is highly conserved, but it is not absolute. Explain the difference between synonymous and nonsynonymous mutations (substitutions) Synonymous mutations: changing the nucleotide sequence and having no effect on the amino acid sequence: due to redundancy of genetic code, you get the same amino acid, can see many variations in nucleotide sequences. Indicates that over time sequences have diverged: many mutations seem to be neutral, for example: in chlamydomonas, it"s aag and in volvox aaa. There is no consequence here; still coding for amino acid lysine.

Related Questions

I'm having trouble simplifying this 6 question paper. Pleaserewrite this then post in comments. thanks! just 1-5 senstences perquestion please. please!

1.Among systems for study of macro evolutionary change (e.g.,major change in anatomy, moving from water to land or vice versa,acquisition of flight, etc.), the cetaceans have become the 'posterchild'. Explain why cetaceans are a better system in which to studyevolutionary transitions than each of the following vertebrategroups:

Cetaceans have primitive taxa thatrecords sequences of change at three critical phases:

-Initial aquatic specialization

-Evolution of filter feeding withbaleen

-Derivation of echolaction.

Divergence times in cetaceans areconducive to detection of positive selection and inactive loci.Evolutionary splits in cetacea are deep enough to provide adequatechange for statistically robust analyses of molecular evolution butare not so deep that substitution patterns are saturated andrecognition of pseudogenes is hindered.

They have an impressive fossilrecord.

Whole genomes for both cetaceans andterrestrial cetartiodactyles can illuminate transitions andcandidate loci associated with aquatic features and degenerativeevolution have been characterized by several research groups.

turtles: highly derived taxa but areancient clades and more difficult to study from a molecularperspective.

manatees: The extant diversity ofaquatic manatees is limited.

bats: have a poor fossil record.

pterosaurs (ancient winged reptiles):Lack genetic Data.

2. What is myoglobin?

A myoglobin is a small 153-amino acidprotein that is the primary carrier and storage center of oxygen inmuscle.

Explain why increased diving ability should be correlated withspecific types of replacement mutations of the gene encoding theprotein myoglobin.

Amino acid replacement that increasedcharge occurred overwhelmingly in lineages of extreme divers withsemiaquatic or aquatic lifestyles. The greatest increase in chargeoccurred independently in cetaceans, pinnipeds, and the bever, allof which share at least two convergent amino acid replacementswithin each lineage.

What specific kinds of amino acid replacements are favored bypositive selection when increased diving ability is favored?

High net surface charge enableselectrostatic repulsion that might reduce deleterious selfassociation of myoglobin molecules; protein folding stability couldhave a similar impact by limiting the percentage of misfoldedmolecules at high expression levels.

Explain how the maximum dive capability of an extinct whalespecies can be estimated.

By combining body mass with inferredconcentration of myoglobin based on net surface charge they wereable to estimate the maximum dive times of extinct cetaceans.

3. What is the general function of the protein prestin?

Is involved in conferringelectromotility to the outer hair cells of the cochlea, enablingsensitive to sound by driving the cochlear amplifier.

Explain why a phylogenetic treereconstructed using the characters of prestin amino acid sequencesshowed at first that the whales form a subgroup within thebats!

A phylogenetic analysis of prestinamino acid sequences supported a tree in which some odontocetecetaceans were nested within bats with high support, despitephylogenetic analsysts of nucleotides sequences favoring a moredistant relations.

This pattern was driven by convergentamino acid changes in that were shared between toothed whales andecholocating bats.

4. Relative to terrestrial mammals, what changes occurred togive deep diving cetaceans 'rod monochromacy'?

Rod monochromancy is unique amongmammals due to extreme adaptation to low light levels.

What is the advantage of rod monochromacy?

Allows you to see in low lightlevels.

Why does it make sense that rhodopsins of cetaceans are shiftedfrom red (low energy) to blue (high energy) sensitivity?

The mechanisms underlying the spectraltuning of two of these blue-shifted pigments have recently beenelucidated and depend on three amino acid substitutions(⁸³Asn, ²⁹²Ser, and ²⁹⁹Ser) indolphin rhodopsin, but only one amino acid substitution(³⁰⁸Ser) in the dolphin long-wavelength-sensitivepigment. The objective of this study was to investigate themolecular basis for changes in the spectral sensitivity of rodvisual pigments from seven distantly related marine mammals. Theresults show a relationship between blue-shifted rhodopsins([lambda]_max [less-than-or-equal] 490 nm), deep-divingforaging behavior, and the substitutions ⁸³Asn and²⁹²Ser. Species that forage primarily near the surfacein coastal habitats have a rhodopsin with a [lambda]_maxsimilar to that of terrestrial mammals (500 nm) and possess thesubstitutions ⁸³Asp and ²⁹²Ala, identical torhodopsins from terrestrial mammals.

5. What is the function of the protein ameloblastin?

Is an enamel matrix protein. Theprotein that encodes AMBN gene. Allows growth activity andstructure of the tooth enamel.

Characterize the specific nucleotide sequence and functionaldifferences in ameloblastin genes between baleen whales versusother mammals.

Baleen whale a toothed whale and moredistantly related mammals with single base pair frameshiftinsertion in the baleen whale AMBN pseudogene. Clear cut molecularsignature of a shared signature of shared aquatic ancestry forhippos and whales is currently lacking. Loci related to underwatercision, deep diving and lung surfactant do not show evidence ofmolecular adapation in the common ancestor of these taxa.

6. What are the two main general categories of convergentevolution described in cetaceans and other vertebrates?

Auditory genes. Bats and odontecetshave many similar capabilities with regards to high frequency soundperception.

Selection has driven the independentloss of both OPNI1SQ and OPN1LW in deep diving cetaceans tooptimize visual acuity at depth and at night.

Loss of functional TAS1R genes alsooccurred independently in Otariidae (sea lions) and many carnivorsmammals convergently lack the fuctional sugar taste perception geneTAS1R2

Based on these studies why is it important to use neutral ornearly neutral characters in phylogenetic analyses wheneverpossible?

Comparison amobg a broader taxonomicsample of geneoms can reveal learge suits of genes that haveundergone convergent recruitment and subsittuions among multipleclades of aquatic tetrapods.

orangebear508

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?

For this assignment, we will consider a protein expressed in theliver of an African cheetah (Acinonyx jubatus). Biochemistsdetermined that this protein is involved in the production ofglycogen.

In a stunning announcement, a snowboarder in Antarctica claimsto have found a new species of cheetah that is able to survivefreezing temperatures and a long, dark winter. The snowboarderdescribed a slow, fat, white-furred cheetah that may be related tothe African cheetah. Scientists isolated a fragment of DNA from theobese feline creature which codes for the liver protein:

(3' end) ...CTACGTTCAGCTTGTCACGACTGGTTA... (5' end)

(5' end) ...GATGCAAGTCGAACAGTGCTGACCAAT... (3' end)

At almost the same time, a sleek, fast, white-coated cheetah wasfound in the Andes in South America where cheetahs were not knownto exist. With some difficulty, a geneticist convinced the cheetahto allow her to swab the inside of the big cat's cheek to get asample of DNA. Soon after, the geneticist was able to isolate thefollowing DNA fragment believed to be involved with glycogenproduction in the liver:

(3' end) ...TCACCTACGTTCAATAGGTCACGACTGG... (5' end)

(5' end) ...AGTGGATGCAAGTTATCCAGTGCTGACC... (3' end)

The original African cheetah DNA fragment describing the liverprotein in question is this:

(3' end) ...CACCTACGTTCAGGAGGTCAGGACTGGTTA... (5' end)

(5' end) ...GTGGATGCAAGTCCTCCAGTCCTGACCAAT... (3' end)

You are part of a team of geneticists, evolutionary biologists,and bioinformatics experts. You will attempt to describe thedifferences between the three species of cheetah in both geneticand evolutionary terms.

1)For each DNA sequence, transcribe to mRNA and then find thechain of amino acids that it produces. Remember that a gene mustbegin with the "Start" codon.

2)Describe the differences in the basic genetic code between thethree species. How many DNA point mutations would be required tochange from one species to the others? How do the amino acidsequences of the proteins differ? Are there any silent mutationsthat may not effect the function of the protein?

3)Looking at the amino acid substitutions that exist between thespecies, would you expect there to be large functional differencesbetween the two slightly different proteins based on the propertiesof the substituted amino acids? Explain why you think this might bethe case.

4)Quantitatively assess the evolutionary distance between eachpair of the three species using the substitution matrix and PAMscores. (This involves three pairs: African/Andes,African/Antarctic, and Antarctic/Andes.)

5)Propose a scenario describing how the two new cheetah speciesmight have evolved from the African cheetah. Were the two newcheetahs once a single species which then branched to form twoseparate species? Or did they evolve independently from the Africancheetah? Be sure to include in your scenario how the new cheetahsmanaged to move from Africa to their present locations. Estimate arelative time line for each separate speciation event. (Aspeciation event is the genetic or environmental event that resultsin the creation of a new species.) How might the three proteinsexplain the survivability of the three species in their nativehabitat? (A little speculation is OK here. You are presenting ahypothesis based on the available evidence. Further research wouldbe required to prove your hypothesis.)

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Biology 1002B Lecture 12: Lecture 20

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