Biology 1201A Lecture Notes - Lecture 18: Molecular Clock, Systematics, Chloroplast Dna

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4 Jan 2018

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Molecular data include: nucleotide base sequences of dna and rna or the amino acid sequences of the proteins for which they code. Drawbacks: are only 4 alternative character states at each position in a dna or rna sequence and only. 20 alternative character states at each position in a protein. If two species have the same nucleotide base substitution at a given position in a dna segment, their similarity may have evolved independently. Systematics often find it difficult to verify that molecular similarities were inherited from a common ancestor. 18. 7a: molecular clocks estimate times of divergences using shared mutations. Molecular phylogenics is based on the observation that many molecules have been conserved by evolution. Mutations in some types of dna appear to arise at a relatively constant rate. Therefore, differences in the dna sequences of two species can serve as a molecular clock, indexing their time of divergence. Large differences imply divergence in the distant past.

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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

You decide to identify the CFTR mutation by analyzing the genomic DNA of your patients compared to healthy individuals. You specifically are looking to see whether a specific 3' gene truncation has occurred in the patients. You will determine this using hybridization techniques with samples from healthy and CF patients. Which of the following will allow you to accomplish this?

	Using an RNA probe complementary to the region not removed by the truncation.
	Using an RNA probe complementary to the region removed by the truncation.
	Using an DNA probe complementary to the region not removed by the truncation.
	Using an DNA probe complementary to the region removed by the truncation.

To conduct the hybridization experiment, you are trying to decide between using a DNA or RNA probe. Which would be ideal to use and why?

	As both are composed of nucleic acids, using either would result in identical results.
	An RNA probe because RNA has uracil bases.
	An RNA probe because it could also be used in a translation experiment.
	A DNA probe because it is more stable than RNA.
	A DNA probe because RNA cannot bind to DNA.

Imagine Hershey/Chase had used an RNA virus (genome composed of RNA) instead of a DNA virus in their experiment. Would radioactivity still have been found in the pellet?

	No, because only DNA can be labeled with radioactivity.
	No, because the RNA genome would not enter the bacteria upon infection.
	No, because while DNA and RNA nucleotides are similar, they are not identical.
	Yes, because DNA and RNA nucleotides are similar.
	Yes, because genome in any form (DNA, RNA, protein) would be labeled similarly.

The human genome consists mostly of non-coding DNA. Which of the following are benefits of this?

	Random DNA mutations generally won't affect RNA and protein function.
	It is faster to duplicate the genome when these are present.
	The existence of introns can lead to multiple variations of proteins encoded by a single gene.
	It is unlikely transposons would exist in the genome if there was too much protein coding DNA.

You accidentally add a mutant dNTP (which has an H instead of an OH connected to the 3â carbon) to a reaction where DNA is being replicated. Which of the following is true of this mutant dNTP?

	It can be incorporated into DNA strand but cannot form a phosphodiester bond with an incoming wild type dNTP
	It can be incorporated into a DNA strand but cannot base pair with a complementary nucleotide
	It can be incorporated into a DNA strand and can form a phosphodiester bond with an incoming dNTP, but only if it is another mutant dNTP
	It cannot be incorporated into a DNA strand.

Andrew Murray's sister, Andrea, is adding to her brother's work on chromosomes. She is using cells that are unable to synthesize adenine (âade) and histidine (âhis). The plasmid she is currently working with consists of an origin of replication and the Ade gene.

Following her transformation of the plasmid into her yeast, what media will the cells be plated on to select for cells that have picked up the plasmid?

	Media containing histidine
	Media containing adenine
	Media lacking adenine
	Media lacking histidine

She starts by attempting to add the centromere DNA into a plasmid containing the origin of replication. Unfortunately, when adding the centromere sequence, the origin of replication is removed, thus leaving a plasmid with only a centromere and selection marker. Following plasmid transformation, what growth result will she see on her plates?

	No colonies
	Little colonies
	Big colonies

She fixes the mistakes from the previous experiment and now has a complete plasmid (selection marker, origin of replication, centromere). She then inserts telomere sequences into the plasmid. How will this impact her transformation?

	It will not impact her transformation
	Her transformation will no longer work because plasmids donât require telomeres
	She will now see much larger colonies
	She will now see fewer but larger colonies
	She will now see smaller colonies

In the Meselson/Stahl experiment, E. coli were first grown in media containing heavy nitrogen, 15N, and then transferred to light nitrogen, 14N, at the beginning of the experiment.

Imagine that their data showed that replication occurs in a conservative manner instead of semi-conservative. What fraction of the DNA helices will consist of mixed DNA after 4 rounds of replication in this case?

	None
	More than 75%
	25-50%
	51-75%
	Less than 25%

peachmarten804

__________ are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. These chemicals are both generated and broken down in the same location.

Lysosomes

Endosomes

Peroxisomes

Nucleosomes

Biologists cannot possibly study all living species. Instead, they try to understand cell behavior by studying a select subset of them. Which of the following characteristics are useful in an organism chosen for use as a model in laboratory studies?

rapid rate of reproduction

all of the above

ability to grow under controlled conditions

amenability to genetic manipulation

By definition, prokaryotic cells do not possess __________.

ribosomes.

a nucleus.

membrane bilayers.

replication machinery.

Cell biologists employ targeted fluorescent dyes or modified fluorescent proteins in both standard fluorescence microscopy and confocal microscopy to observe specific details in the cell. Even though fluorescence permits better visualization, the resolving power is essentially the same as that of a standard light microscope because the resolving power of a microscope is limited by the __________ of light.

intensity

absorption

wavelength

filtering

Choose the phrase that best completes this sentence: Microtubules ____________ and are required to pull duplicated chromosomes to opposite poles of dividing cells.

generate contractile forces

can rapidly reorganize

are found in especially large numbers in muscle cells

are intermediate in thickness

Despite the differences between eukaryotic and prokaryotic cells, prokaryotes have proteins that are distantly related to eukaryotic actin filaments and microtubules. What is likely to be the most ancient function of the cytoskeleton?

cell division

cell motility

vesicle transport

membrane support

DNA and RNA are different types of nucleic acid polymer. Which of the following is true of DNA but not true of RNA?

It contains thymine.

It has 5'-to-3' directionality.

It is single-stranded.

It contains uracil.

Double covalent bonds are both shorter and stronger than single covalent bonds, but they also limit the geometry of the molecule because they ____________________.

prevent additional bonds from being formed with the bonded atoms.

limit the rotation of the bonded atoms.

create a new arrangement of electron shells.

change the reactivity of the bonded atoms.

Drosophila melanogaster is a/an __________. This type of animal is the most abundant of all animal species, making it an appropriate choice as an experimental model.

mammal

amphibian

bird

insect

10.

If the isotope 32S has 16 protons and 16 neutrons, how many protons, neutrons, and electrons will the isotope 35S have, respectively?

16, 19, 17

16, 19, 15

16, 19, 16

16, 20, 15

11.

Living systems are incredibly diverse in size, shape, environment, and behavior. It is estimated that there are between 10 million and 100 million different species. Despite this wide variety of organisms, it remains difficult to define what it means to say something is alive. Which of the following can be described as the smallest living unit?

cell

organelle

protein

DNA

12.

Macromolecules in the cell can often interact transiently as a result of noncovalent interactions. These weak interactions also produce stable, highly specific interactions between molecules. Which of the factors below is the most significant in determining whether the interaction will be transient or stable?

the concentration of each molecule

the size of each molecule

surface complementarity between molecules

the rate of synthesis

13.

Many of the mechanisms that cells use for maintenance and reproduction were first studied at the molecular level in bacteria. Which bacterial species had a central role in advancing the field of molecular biology?

E. coli

S. pombe

C. elegans

D. melanogaster

14.

Many types of cells have stores of lipids in their cytoplasm, usually seen as fat droplets. What is the lipid most commonly found in these droplets?

cholesterol

isoprene

triacylglycerol

palmitic acid

15.

Mitochondria contain their own genome, are able to duplicate, and actually divide on a different time line from the rest of the cell. Nevertheless, mitochondria cannot function for long when isolated from the cell because they are __________________.

anaerobes.

viruses.

parasites.

endosymbionts.

16.

Mitochondria perform cellular respiration, a process that uses oxygen, generates carbon dioxide, and produces chemical energy for the cell. Which answer below indicates a correct pairing of material âburnedâ and the form of energy produced during cellular respiration?

17.

Polar covalent bonds are formed when the electrons in the bond are not shared equally between the two nuclei. Which one of these molecules contains polar bonds?

Biology 1201A Lecture Notes - Lecture 18: Molecular Clock, Systematics, Chloroplast Dna

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