BIO 414 - Evolution

Dr. Knight (sorry for spelling errors, a lot of this is copy-pasted from his quizzes which contain a lot of spelling errors!)

What is the HoxBox made of?

DNA

What is the homeodomain made of?

Protein

Where can the Hoxbox be found?

In an exon of a hox gene

A hox gene that controls the placement of the tail bone would most likely be found where on the genome?

Downstream (physically down frame) from Hox genes controlling upper thoracic segments

Life has been evolving on earth x number of years which happens to be the same as the the number of base pairs in the human genome.

3.5 billion

A Hox protein can only bind to one signature sequence.

false

Who said "the search for homologous genes is futile except in very closely related organisms"

Ernst Mayr

Is it true that "the search for homologous genes is futile except in very closely related organisms"

no

Homologous genes found in closely related species are known as:

Orthologous genes

Antennapedia is a homeotic mutant

true

How long is a signature sequence? Approximate range on average.

5-10 basepairs

In the wiring diagram of gene regulatory logic, what denotes a repressor?

A line with a horizontal bar at the tip/end.

Many switches make up the signature sequence.

false

The switch is part of the Hox gene

It's debatable

What is the difference between an analogy and a homology?

A homology is an analogy due to common ancestry

Are homeotic monsters hopeful, helpless, or helpful to geneticists?

Helpful

Are homeotic monsters themselves hopeful, hopeless, or helpful? (in terms of their survival and probability for forming a new species)

Hopeless

What is the enzyme that degrades lactose in E.coli?

B-galactosidase

eyeless is a ortholog to Pax-6 in what organism (what organism is eyeless in?)?

Flies

Who said, "Embryos are fond of Stripes"

Francis Crick

Who discovered Batesian mimicry?

Henry Walter Bates

How many parologous hox genes would you expect flies to have (on average)

10

How many parologous hox genes would you expect humans to have (on average)?

40

Of the hox genes that flies and humans have, how many of them are orthologs to one another?

All of them

What does the Homeodomain do?

Binds to DNA

Helps assemble a transcriptional appratus on the promotor of another gene.

Regulates other proteins

Williston's law states that:

During evolutionary time, organisms with searial homology tend towards a reduction in number of serial homologs with an increased specialization of those that remain

Lobopodians have hox genes?

True

What fauna predated the cambriam radiation?

The ediacarin

Who discovered the burgess shale?

Charles Wolcott

Do switches (promotors like the ones Carroll describes) help solve the 99% paradox?

Yes, but my grandparents would still have a hard time understanding it

How many signature sequences does a typical switch have?

More than one, the upper limit is unknown, but probably 20 or so

If you saw W writing in the genetic code for a signature sequence, what might that mean?

This base pair in the signature sequence could be a couple of different amino acids

Which is greater, the number of antibody genes or the number of antibodies that are formed in human immune systems?

Antibodies

What gene makes hind wings small in Drosophila?

Ubx

What gene controls the placement and formation of appendages?

Distaless

Why is a "more modern synthesis" of evolutionary biology necessary?

Because the modern synthesis did not really incorporate developmental biology

Who Motivated Darwin to go to the tropics

Alexander Von Humbolt

Punctuated equilibria is:

Evolution marked by long periods of stasis (equilibria) interrupted by brief intervals of rapid change (punctuation)

What happens if you divide a two celled newt embryo in two

It depends on where you divide it

Where would you find a hox gene in a drosophila embryo?

In the nucleus

Where would you find a hox protein in a drosophila embryo?

In the nucleus

and

On the ribosome(s)

What genes controls the earliest steps of the formation of the body plan and the ZPA?

Sonic Hedgehog

If you see HOXA written, what is that most likely referring to?

A hox protein

If you see hoxa written, what is that most likely referring to?

A gene

The homeodomain encodes the hoxbox.

False

Are Pax-6, small eye, and eyeless paralogs or orthologs?

Orthologs

Where do transcription factors bind?

DNA in the nuleus

Which molecule has a uracil?

RNA

Carroll refers to concentration gradients of morphogens. What molecules would most logically make up this "concentration graient" and what effect would they have on the cell?

Hormones, transcription

When did the Cambrian begin (approximately)?

550 mya

A duplicate fetua gene in a western diamond back snake can be both a homolog, paraglog, and ortholog at the same time.

True

Fetua genes are a type of SVMP

False

fetua3 refers to the gene for FETUA3

True

Where would you most likely find the Snake Venom Metaloprotenases (SVMPs) in Western Diamondback Rattlesnakes?

The venom

Which is most likely to have the greatest resistance to SVMPs from Western Diamond Back Rattle Snakes?

Western Diamond Back Rattle Snakes

Where would you most likely find the FETUA proteins in Western Diamondback Rattlesnakes?

The serum

How many different SVMPs did FETUA3 bind to in Western Diamondback Rattlesnakes?

20

While it is unknown, and not precisely identified in this paper, based on what we talked about in class, how did the fetua gene family duplicate? Multiple correct answers.

Parsimony suggests unequal crossing over

Transposon copy and pasting because there are LINE and GYPSY transposable elements nearby

Has the fetua3 paralog undergone neofunctionalization?

Yes

Has the fetua3 paralog undergone subfunctionalization?

Unknown based on what we talked about in class

A * below a residue in the amino acid sequence alignment of FETUA proteins presented in Figure 3 represents what?

Complete conservation across all of the sequences aligned

What is meant by residues with the same color but different letter in the amino acid sequence alignment of FETUA proteins presented in Figure 3?

Different amino acids of the same functional group of amino acids

The solid line above parts of the sequence alignment indicated what (Dr. Knight belatedly discovered with your help!)

An exon. The parts without a solid line are a different exon

Some FETUA paralogs increased protease activity of one of the three classes of SVMPs tested

True

FETUA3 decimated all three classes of SVMP activity

True

In Figure 7, some tips have the same color (same greyscale if you are color blind). This most likely represents a \____. There are multiple correct answers to this question.

Synapomorphy

Homologous genes

Fetua orthologs from different species

Synapomorphy

shared derived character

Homologous gene

Genes with DNA sequence derived from a common origin that may or may not have the same function

Orthologous gene

Homologous genes where a gene diverges after a speciation event, but the gene and its main function are conserved

Paralogous gene

Homologous genes present in a particular organism that are related to each other through a gene duplication event

What does EDTA do to proteases?

Inhibits them

Which chemical is FETUA3 similar to?

EDTA

FETUA proteins (and therefore the genes for them) represent a symplesiomorphy in fish, mammals, birds, and reptiles

True

The concept of parallel evolution is most similar to:

Homoplasy

Epistasis refers to how genes interact. Mutations interact too. Mutations have context dependent effects. The context they studied, using artificially re-engineered and produced ancestral proteins (with and without specific mutations), was referred to as the \_____ in this paper

Genetic background

Low p50 equates to...

Higher Hb-O2 binding affinity

Ability to survive at high altitudes

Are there "many ways to get to Rome" when it comes to the molecular basis of Hb-O2 binding affinity?

True

Convergent increases in hemoglobin-oxygen affinity were pervasive among high-altitude taxa. These changes were \_______ associated with parallel amino acid substitutions at key residues

Rarely

The predictable changes in biochemical phenotype uncovered in this paper \___________ a predictable molecular basis.

Do not have

Parallel amino acid substitutions at the same residue are also known as "homoplasy". Homoplasy was \______ in the data set examined in this study. Perhaps because the mutation rate was low.

Infrequent

Why was the mutation rate low in the orthologous Hb molecules/sequences examined in this study?

Hb is highly conserved and does not tolerate many non-synonymous changes in its sequence.

A conspecific population comparison would compare....

Individuals of the same species from two different populations

Hb is a tetramere. Mutations that affect how the monomers interact with one another therefore affect its \_____ structure

Quaternary

How many phylogenetically independent contrasts did this study compare?

28

Which Hb has a greater Oxygen binding affinity?

HbD

Birds that inhabit high altitudes are more likely to upregulate HbD than mutatate HbA or HbD at key residues

False

In the Amino Acid alignment in this paper, if the residue was blank (no letter) that meant that...

The residue was the same at that position as all of the other species

Historical contingency in evolution refers to the idea that if.....

If you replayed the tape of time, life is unlikely to turn out the same way as it is today

What is a cartesian coordinate system?

Where there continuous x and y variables shown in a two dimensional graphic.

Why is it not OK to calculate a regression or correlation between x and y variables representing 20 different species (each point is a species) on a cartesian coordinate system?

The data points are not independent

What is a "contrast" in independent contrasts?

Differences between x and y variables of sister taxa

The ultimate test in independent contrasts of 20 species is...

A correlation through the origin of the x and y contrast values across these 20 species

If you have a hypothesis of causality between x and y (x causes y for example), is it OK to do a regression test

True

Has the Felsenstein paper been cited frequently?

Very frequently

Has Watson and Crick's original paper in Nature titled "A Structure of Deoxyribose Nucleic Acid" been cited frequently?

Very frequently

How did Felsenstein circumvent the non-independence of species in cross species analyses of two traits?

Contrasting the mean values. of tip taxa (sister species)

Reconstructing ancestral trait values of x and y is important for a dataset of 20 species. How are these ancestral values reconstructed?

Taking the arithmetic average of the tip taxa (or sister species)

How many contrasts are there for a completely bifurcating phylogenetic tree of 20 species?

19

Which is a more accurate depiction of evolution: A) "New body structures are created from scratch" or, B) "New body structures are created by remodeling existing body structures".

B

When did Animals move on land?

in the Devonian