Deck 3: Genomics, Proteomics, and Related Approaches to Physiology

Question 1

The coldest water that icefish typically inhabit is

A) 1.9°C.
B) 0°C.
C) -1.9°C.
D) -4.9°C.

Answer 1

C

Question 2

Today, there are _______ species of icefish.

A) two
B) about 16
C) about 50
D) about 100

Answer 2

B

Question 3

How many genes code for the protein portion of the hemoglobin molecule?

A) 1
B) 2
C) 4
D) 8

Answer 3

B

Question 4

Which statement regarding the vertebrate hemoglobin molecule is false?

A) Vertebrates have multiple copies of the genes that code for globins.
B) The genes that code for globin diverged only recently.
C) In birds and mammals, genes that code for α-globin are located on a different chromosome from those that code for β-globin.
D) In fish, genes that code for globins are found on a single chromosome.

Question 5

Refer to the figure shown.
The genes on the figure are aligned based on

A) homologous sequences.
B) a matching of intron sequences.
C) gene function.
D) the beginning sequence on the chromosome.

Question 6

Refer to the figure shown.
What is the best explanation for the differences, as shown in the figure, in the icefish globin genes?

A) Redundant gene sequences have been selected against and removed over time.
B) The α-globin gene is nonfunctional; the β-globin gene has been moved to another chromosome but is functional.
C) The α-globin gene is nonfunctional; the β-globin gene has been moved to another chromosome and is nonfunctional.
D) Deletions have rendered the α-globin gene nonfunctional and the β-globin gene has been removed.

Question 7

Refer to the figure shown.
Which statement about the figure is true?

A) It shows when icefish diverged from red-blooded fish.
B) It shows the phylogeny of teleost fish outgroups and their relatedness to icefish.
C) It shows an evolutionary tree of 22 species of related Antarctic fish.
D) It shows the relatedness of Antarctic fish that use antifreeze proteins.

Question 8

Refer to the figure shown.
This phylogenetic tree is based on

A) bone morphology.
B) similarities of mitochondrial DNA.
C) sequences of the hemoglobin genes.
D) sequences of antifreeze genes.

Question 9

Refer to the figure shown.
Which point(s) refer(s) to the most likely divergence(s) of the hemoglobin-free icefish?

A) I
B) II
C) III
D) Both I and II

Question 10

Refer to the figure shown.
Which statement about the numbered points on the figure is true?

A) All of the species beyond point II share the same missing portions of DNA.
B) Species beyond points I and II share the same missing portions of DNA.
C) Only species beyond point III share the missing sequences that render hemoglobin nonfunctional.
D) Species beyond points III and IV have nonfunctional hemoglobin but the missing sequences are different.

Question 11

Refer to the figure shown.
At which location on the figure did antifreeze proteins evolve?

A) I
B) II
C) III
D) Before point I-II

Question 12

Which sequence represents the correct evolutionary order of events in some species of Antarctic fish?

A) Presence of antifreeze proteins → presence of hemoglobin → loss of functional hemoglobin → loss of functional myoglobin
B) Presence of antifreeze proteins → presence of hemoglobin → loss of functional myoglobin → loss of functional hemoglobin
C) No functional hemoglobin → presence of antifreeze proteins → loss of functional myoglobin → presence of functional hemoglobin
D) Presence of hemoglobin → presence of antifreeze proteins → loss of functional hemoglobin → loss of functional myoglobin

Question 13

Refer to the figure shown.
Which statement about the figure is true?

A) It shows when icefish diverged from red-blooded fish.
B) It shows the lineages of icefish that have lost functional myoglobin.
C) It shows the lineages of icefish that have regained functional hemoglobin.
D) It shows the lineages of Antarctic fish that use antifreeze proteins.

Question 14

Refer to the figure shown.
This phylogenetic was tree constructed on the basis of

A) bone morphology.
B) similarities of mitochondrial DNA.
C) sequences of the hemoglobin genes.
D) sequences of antifreeze genes.

Question 15

Refer to the figure shown.
What is the strongest evidence supporting the four independent events occurring in the figure?

A) The sequence changes occurring at the four independent points are very different from one another.
B) The sequence changes occurring at the four independent points are exactly the same.
C) The loss of function resulting from the sequence changes is exactly the same.
D) The morphology of the species at the four independent points is exactly the same.

Question 16

Which statement regarding myoglobin in Antarctic fish is true?

A) All icefish have nonfunctional myoglobin.
B) Mutations that eliminated myoglobin function occurred independently in four lines of icefish.
C) Mutations that eliminated myoglobin function occurred once in early icefish evolution and have affected six species in different lineages.
D) Identical mutations that eliminated myoglobin function occurred in four separate lineages of icefish.

Question 17

Which protein is common in all species of Antarctic fish?

A) Ventricular myoglobin
B) Antifreeze glycoproteins
C) Hemoglobin
D) Myoglobin

Question 18

Which protein is common in all species of icefish?

A) Ventricular myoglobin
B) Antifreeze glycoproteins
C) Hemoglobin
D) Myoglobin

Question 19

Which statement about glycoproteins is false?

A) The genes responsible for producing the suite of glycoproteins in Antarctic fish evolved after the appearance of icefish.
B) Glycoproteins reduce the freezing point of blood plasma.
C) Genes coding for glycoproteins are similar in all species of Antarctic fish.
D) When hemoglobin became deleted in icefish, they already had the genes coding for glycoproteins.

Question 20

In what way is the loss of functional hemoglobin in icefish a disadvantage?

A) An increase in fitness was shown following the appearance of nonfunctional hemoglobin.
B) The appearance of nonfunctional hemoglobin was accompanied by a decrease in fitness.
C) Icefish have enlarged hearts and faster blood circulation compared to red-blooded fish.
D) Icefish have a very small body size to compensate for the loss of functional hemoglobin.

Question 21

For the Antarctic icefish, a consequence of their lack of hemoglobin is that they

A) are sluggish and therefore prone to predation.
B) are restricted to very cold water.
C) have bluish blood.
D) are very small in size.

Question 22

A species' full set of genetic material is termed its

A) genome.
B) sequence.
C) transcriptome.
D) proteome.

Question 23

Sequencing a genome and identifying individual genes are processes typically carried out

A) via manual transcription by a team of genetic scientists.
B) using experimental processes.
C) by computers using high-throughput methods.
D) by hand with a team of information scientists.

Question 24

The process of adding direct human interpretation to genetic sequencing data is called

A) high-throughput processing.
B) information processing.
C) annotation.
D) bioinformatics.

Question 25

Which process is not an overarching goal of genomics?

A) Elucidating the evolution of genomes
B) Elucidating the current function of genes
C) Elucidating the current function of genomes
D) Elucidating the evolution of species through genomes

Question 26

The genes coding for antifreeze proteins in Antarctic fish evolved from

A) genes coding for plasma albumin.
B) genes coding for pancreatic proteins such as trypsin.
C) spontaneous mutations in intron sequences.
D) insertion events from ancient bacteria.

Question 27

All genes in a gene family share

A) distinctive DNA sequences.
B) distinctive RNA sequences.
C) distinctive gene expression patterns.
D) identical exon sequences.

Question 28

Genomic analysis of the sea urchin led to the discovery that there are no genes coding for gap-junction proteins or for adrenaline. Functionally, this suggests that

A) there are no gap junctions in sea urchins.
B) there is no cellular communication system in sea urchins.
C) sea urchins are not related to vertebrates.
D) the cellular communication system of sea urchins is unusual.

Question 29

Genomic analysis of the sea urchin led to the discovery of an exceptional number of genes that code for immune and detoxification proteins. Functionally, this suggests that sea urchins

A) are not susceptible to diseases.
B) have a long lifespan.
C) are bombarded by pathogens and must react constantly.
D) have unusually elaborate immune and detoxification systems.

Question 30

Which statement regarding sea urchins is false?

A) No genes are present that code for gap-junction proteins.
B) No genes are present that code for the enzymatic synthesis of adrenaline.
C) Genes that code for cytochrome P450 detoxification enzymes are extraordinarily numerous.
D) Genes that code for skeleton mineralization are very similar to those found in vertebrates.

Question 31

When predictions are made from the genome of a species alone, they may prove to be wrong for several reasons. What is one of those reasons?

A) The function predicted by extrapolation from already known genes always matches the current function.
B) Even if the function is known, the expression pattern may differ.
C) The function predicted by extrapolation may vary extensively within individuals of the species.
D) Often, the introns within species vary too much between individuals.

Question 32

After the genome of a species has been sequenced,

A) it is said to enter the postgenomic era.
B) bioinformatics takes over.
C) annotation is all that can take place.
D) functional genomics is all that is left for that species.

Question 33

Which sequence represents the order of investigation of the traditional, top-down approach to the study of animal physiology?

A) Animal function → tissue-specific proteins → tissue function → genes
B) Genes → tissue function → tissue-specific proteins → animal function
C) Animal function → tissue function → tissue-specific proteins → genes
D) Genes → tissue-specific proteins → tissue function → animal function

Question 34

In the study of animal physiology, which statement expresses an advantage of the bottom-up approach pursued with high-throughput methods?

A) It is specific in searching for proteins and metabolites instead of genes.
B) It can proceed without preexisting biases regarding which genes are involved in a particular function.
C) It can focus on a defined phenomenon of known importance to the whole organism.
D) It is specific in searching for gene expression instead of profiling proteins or metabolites.

Question 35

Refer to the figure shown.
In terms of the labels in the figure, the classic experimental approach begins with

A) a survey of substances at II.
B) the sequencing of I.
C) an a priori hypothesis regarding III.
D) an a priori hypothesis regarding IV.

Question 36

Refer to the figure shown.
The study of the process of catalysis would take place between levels

A) II and I.
B) II and III.
C) I and III.
D) I and II.

Question 37

At each stage of the bottom-up approach in the study of animal physiology, the most common strategy is the use of

A) screening.
B) sequencing.
C) transcriptomics.
D) expression profiling.

Question 38

The hypotheses from bottom-up research

A) are all statistically significant, given the number of tests involved.
B) typically are not formed a priori.
C) produce false positives most of the time.
D) cannot be validated statistically.

Question 39

You are examining 1000 genes to investigate a stress response and it seems that in 335 genes, there was some increased transcription. Why do standard statistical programs yield invalid results when analyzing the data from this study?

A) All tests will be statistically significant, given the number of tests involved.
B) Most statistical programs cannot handle this much raw data, so calculation errors are made.
C) The high number of statistical analyses will produce false positives.
D) The results will not be repeatable.

Question 40

Transcriptomics is the study of

A) mRNA.
B) genes.
C) DNA.
D) tRNA.

Question 41

Refer to the figure shown.
The figure shows a classic data set in the field of

A) genomics.
B) transcriptomics.
C) proteomics.
D) metabolomics.

Question 42

Refer to the figure shown.
Which explanation is the most valid for the low levels of mRNAs of the metabolic/mitochondrial enzyme genes shown in the figure?

A) These genes are not as important as the other two categories in response to exercise.
B) These mRNAs cannot be detected as easily as those of the other two categories.
C) There are fewer genes producing this set of mRNAs compared to those producing the other two categories.
D) Although the mRNAs are produced in small quantities, their half-lives are long.

Question 43

Refer to the figure shown.
Which statement about the figure is true?

A) It represents the output of a genomic analysis.
B) It shows a two-species genomic analysis.
C) It is a proteomic output.
D) It is the output of a microarray.

Question 44

In a microarray technique, an mRNA will _______ the DNA spot representing its specific gene.

A) hybridize with
B) bind to
C) transcribe
D) reverse transcribe

Question 45

In the _______ technique, tissues are subjected to experimentally increased synthesis of mRNA associated with the gene of interest.

A) RNA interference
B) forced overexpression
C) gene knockout
D) expression profiling

Question 46

Refer to the figure shown.
The figure is based on the measurement of

A) proteins.
B) metabolites.
C) mRNA.
D) DNA.

Question 47

Refer to the figure shown.
This figure depicts

A) the response of a selection of mRNAs to malarial parasites.
B) the daily patterns of enzymes that are responsible for combating the malarial parasite.
C) the daily patterns of mRNAs that code for detoxification enzymes.
D) three enzymatic responses to a daily light cycle in the malarial parasite.

Question 48

Refer to the figure shown.
Which statement about the figure is true?

A) It shows a two-species genomic analysis.
B) It shows a two-species environmental response at the protein level.
C) It shows the separation of proteins by a gel.
D) It is the output of a microarray.

Question 49

Refer to the figure shown.
The circles in the figure represent

A) genes.
B) mRNA.
C) DNA.
D) proteins.

Question 50

Even though a transcriptomic study has been performed, why perform a proteomic study on the same tissue?

A) It allows a more statistically accurate investigation of gene expression.
B) It matches the proteins formed with the mRNAs synthesized.
C) The proteins coded by many genes are unknown and are part of the phenotype.
D) There is no reason to perform a proteomic study on the tissue if the transcriptomic study was performed correctly.

Question 51

Which observation proves the best evidence that a parasite could be causing a behavioral change in the host?

A) The protein profile of the parasitized animal is different from the unparasitized animal.
B) Many proteins increase or decrease in the brain of a parasitized animal.
C) The parasitized animal behaves in a manner never observed in unparasitized animals.
D) The parasitized animal dies from the parasite.

Question 52

Which definition of metabolomics is the most accurate?

A) The study of all organic compounds in cells and tissues other than macromolecules.
B) The study of proteins being synthesized by cells and tissues.
C) The study of which genes are being transcribed in cells and tissues.
D) The study of energy-containing sugars in cells and tissues coded by the genome.

Question 53

In studying animal hibernation, why might a metabolomic approach be helpful in studying this phenomenon?

A) Metabolomics would categorize which macromolecules are involved in hibernation.
B) Metabolomics would isolate which metabolites cause hibernation.
C) Hibernation would likely show large shifts in protein responses.
D) Hibernation is defined by a change in metabolism.

Question 54

Why are metabolomic studies useful?

A) Metabolomic studies often reveal metabolites that may not have even been considered as part of a particular hypothesis.
B) Metabolomics isolate which metabolites are used in a particular biochemical pathway.
C) Metabolomics catalogues the protein synthesis changes in particular cells.
D) Metabolomics are typically not as useful as proteomic studies.

Question 55

Discuss in detail how hemoglobin evolved in the vertebrates.

Question 56

What is the leading hypothesis for why icefish lost their hemoglobin?

Question 57

Was the loss of hemoglobin in icefish an advantage or a disadvantage? Discuss.

Question 58

Discuss the evidence suggesting that antifreeze proteins evolved after the loss of hemoglobin.

Question 59

What are the two overarching goals of genomics, and why is each of these goals important?

Question 60

Compare and contrast top-down and bottom-up methods of study in physiology.

Question 61

Why are screening studies at odds with a priori hypotheses?

Question 62

Explain how a DNA microarray works.

Question 63

Describe how RNA interference promises to provide important insights into gene function.

Question 64

Compare and contrast proteomics and metabolomics.