AP Lesson 3 Genomics, Proteomics, and Related Approaches to Phys

AP Lesson 3 Genomics, Proteomics, and Related Approaches to Physiology

By Joerick Paderogao

Multiple Choice

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

• are sluggish and therefore prone to predation

• are restricted to very cold water

• have bluish blood

• are very small in size

Multiple Choice

The coldest water that icefish typically inhabit is ______.

• 1.9°C

• 0°C

• –1.9°C

• –4.9°C

Multiple Choice

Today, there are _______ species of icefish.

• 2

• about 16

• about 50

• about 100

Multiple Choice

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

• 1

• 2

• 4

• 8

Multiple Choice

Which statement regarding the vertebrate hemoglobin molecule is false?

• Vertebrates have multiple copies of the genes that code for globins

• The genes that code for globin diverged only recently

• In birds and mammals, genes that code for α-globin are located on a different chromosome from those that code for β-globin

• In fish, genes that code for globins are found on a single chromosome

Multiple Choice

The genes on the figure are aligned based on ______.

• homologous sequences

• a matching of intron sequences

• gene function

• the beginning sequence on the chromosome

Multiple Choice

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

• Redundant gene sequences have been selected against and removed over time

• The α-globin gene is nonfunctional; the β-globin gene has been moved to another chromosome but is functional

• The α-globin gene is nonfunctional; the β-globin gene has been moved to another chromosome and is nonfunctional

• Deletions have rendered the α-globin gene nonfunctional and the β-globin gene has been removed

Multiple Choice

Which statement about the figure is true?

• It shows when icefish diverged from red-blooded fish

• It shows the phylogeny of teleost fish outgroups and their relatedness to icefish

• It shows an evolutionary tree of 22 species of related Antarctic fish

• It shows the relatedness of Antarctic fish that use antifreeze proteins

Multiple Choice

This phylogenetic tree is based on ____.

• bone morphology

• similarities of mitochondrial DNA

• sequences of the hemoglobin genes

• sequences of antifreeze genes

Multiple Choice

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

• I

• II

• III

• Both I and II

Multiple Choice

Which statement about the numbered points on the figure is true?

• All of the species beyond point B share the same missing portions of DNA.

• Species beyond points A and B share the same missing portions of DNA

• Only species beyond point C share the missing sequences that render hemoglobin nonfunctional

• Species beyond points C and D have nonfunctional hemoglobin but the missing sequences are different

Multiple Choice

At which location on the figure did antifreeze proteins evolve?

• I

• II

• III

• Before point I and II

Multiple Choice

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

• Presence of antifreeze proteins → presence of hemoglobin → loss of functional hemoglobin → loss of functional myoglobin

• Presence of antifreeze proteins → presence of hemoglobin → loss of functional myoglobin → loss of functional hemoglobin

• No functional hemoglobin → presence of antifreeze proteins → loss of functional myoglobin → presence of functional hemoglobin

• Presence of hemoglobin → presence of antifreeze proteins → loss of functional hemoglobin → loss of functional myoglobin

Multiple Choice

Which statement about the figure is true?

• It shows when icefish diverged from red-blooded fish.

• It shows the lineages of icefish that have lost functional myoglobin

• It shows the lineages of icefish that have regained functional hemoglobin

• It shows the lineages of Antarctic fish that use antifreeze proteins

Multiple Choice

This phylogenetic was tree constructed on the basis of _______.

• bone morphology

• similarities of mitochondrial DNA

• sequences of the hemoglobin genes

• sequences of antifreeze genes

Multiple Choice

What is the strongest evidence supporting the four independent events occurring in the figure?

• The sequence changes occurring at the four independent points are very different from one another

• The sequence changes occurring at the four independent points are exactly the same

• The loss of function resulting from the sequence changes is exactly the same

• The morphology of the species at the four independent points is exactly the same

Multiple Choice

Which statement regarding myoglobin in Antarctic fish is true?

• All icefish have nonfunctional myoglobin

• Mutations that eliminated myoglobin function occurred independently in four lines of icefish

• Mutations that eliminated myoglobin function occurred once in early icefish evolution and have affected six species in different lineages

• Identical mutations that eliminated myoglobin function occurred in four separate lineages of icefish

Multiple Choice

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

• An increase in fitness was shown following the appearance of nonfunctional hemoglobin

• The appearance of nonfunctional hemoglobin was accompanied by a decrease in fitness

• Icefish have enlarged hearts and faster blood circulation compared to red-blooded fish

• Icefish have a very small body size to compensate for the loss of functional hemoglobin

Multiple Choice

Which protein is common in all species of icefish?

• Ventricular myoglobin

• Antifreeze glycoproteins

• Hemoglobin

• Myoglobin

Multiple Choice

Which statement about glycoproteins is false?

• The genes responsible for producing the suite of glycoproteins in Antarctic fish evolved after the appearance of icefish

• Glycoproteins reduce the freezing point of blood plasma

• Genes coding for glycoproteins are similar in all species of Antarctic fish

• When hemoglobin became deleted in icefish, they already had the genes coding for glycoproteins

Multiple Choice

A species’ full set of genetic material is termed its _______.

• genome

• sequence

• transcriptome

• proteome

Multiple Choice

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

• via manual transcription by a team of genetic scientists

• using experimental processes

• by computers using high-throughput methods

• by hand with a team of information scientists

Multiple Choice

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

• high-throughput processing

• information processing

• annotation

• bioinformatics

Multiple Choice

Which process is not an overarching goal of genomics?

• Elucidating the evolution of genomes

• Elucidating the current function of genes

• Elucidating the current function of genomes

• Elucidating the evolution of species through genomes

Multiple Choice

The genes coding for antifreeze proteins in Antarctic fish evolved from ______.

• genes coding for plasma albumin

• genes coding for pancreatic proteins such as trypsin

• spontaneous mutations in intron sequences

• insertion events from ancient bacteria

Multiple Choice

All genes in a gene family share ________.

• distinctive DNA sequences

• distinctive RNA sequences

• distinctive gene expression patterns

• identical exon sequences

Multiple Choice

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 _______.

• there are no gap junctions in sea urchins

• there is no cellular communication system in sea urchins

• sea urchins are not related to vertebrates

• the cellular communication system of sea urchins is unusual

Multiple Choice

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

• are not susceptible to diseases

• have a long lifespan

• are bombarded by pathogens and must react constantly

• have unusually elaborate immune and detoxification systems

Multiple Choice

Which statement regarding sea urchins is false?

• No genes are present that code for gap-junction proteins

• No genes are present that code for the enzymatic synthesis of adrenaline

• Genes that code for cytochrome P450 detoxification enzymes are extraordinarily numerous

• Genes that code for skeleton mineralization are very similar to those found in vertebrates

Multiple Choice

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?

• The function predicted by extrapolation from already known genes always matches the current function

• Even if the function is known, the expression pattern may differ

• The function predicted by extrapolation may vary extensively within individuals of the species

• Often, the introns within species vary too much between individuals

Multiple Choice

After the genome of a species has been sequenced, ________.

• it is said to enter the postgenomic era

• bioinformatics takes over

• annotation is all that can take place

• functional genomics is all that is left for that species

Multiple Choice

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

• Animal function → tissue-specific proteins → tissue function → genes

• Genes → tissue function → tissue-specific proteins → animal function

• Animal function → tissue function → tissue-specific proteins → genes

• Genes → tissue-specific proteins → tissue function → animal function

Multiple Choice

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

• It is specific in searching for proteins and metabolites instead of genes.

• It can proceed without preexisting biases regarding which genes are involved in a particular function.

• It can focus on a defined phenomenon of known importance to the whole organism.

• It is specific in searching for gene expression instead of profiling proteins or metabolites

Multiple Choice

In terms of the labels in the figure, the classic experimental approach begins with _____.

• a survey of substances at II.

• the sequencing of I.

• an a priori hypothesis regarding III.

• an a priori hypothesis regarding IV

Multiple Choice

The study of the process of catalysis would take place between levels _____.

• II and I.

• II and III.

• I and III.

• I and II.

Multiple Choice

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

• screening

• sequencing

• transcriptomics

• expression profiling

Multiple Choice

The hypotheses from bottom-up research _________.

• are all statistically significant, given the number of tests involved

• typically are not formed ba priori

• produce false positives most of the time

• cannot be validated statistically

Multiple Choice

Transcriptomics is the study of __________.

• mRNA

• genes

• DNA

• tRNA

Multiple Choice

The figure shows a classic data set in the field of ______.

• genomics

• transcriptomics

• proteomics

• metabolomics

Multiple Choice

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

• These genes are not as important as the other two categories in response to exercise

• These mRNAs cannot be detected as easily as those of the other two categories

• There are fewer genes producing this set of mRNAs compared to those producing the other two categories

• Although the mRNAs are produced in small quantities, their half-lives are long

Multiple Choice

Which statement about the figure is true?

• It represents the output of a genomic analysis

• It shows a two-species genomic analysis

• It is a proteomic output

• It is the output of a microarray

Multiple Choice

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

• hybridize with

• bind to

• transcribe

• reverse transcribe

Multiple Choice

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

• RNA interference

• forced overexpression

• gene knockout

• expression profiling

Multiple Choice

The figure is based on the measurement of _______.

• proteins.

• metabolites.

• mRNA.

• DNA.

Multiple Choice

This figure depicts ______.

• proteins.the response of a selection of mRNAs to malarial parasites

• the daily patterns of enzymes that are responsible for combating the malarial parasite

• the daily patterns of mRNAs that code for detoxification enzymes

• three enzymatic responses to a daily light cycle in the malarial parasite

Multiple Choice

Which statement about the figure is true?

• It shows a two-species genomic analysis

• It shows a two-species environmental response at the protein level

• It shows the separation of proteins by a gel

• It is the output of a microarray

Multiple Choice

The circles in the figure represent ___.

• genes.

• mRNA.

• DNA.

• proteins.

Multiple Choice

Which statement about the figure is true?

• It represents the output of an NMR spectrum

• It shows a two-species environmental response at the protein level

• It shows the separation of proteins by a gel

• It is the output of a microarray

Multiple Choice

Which statement about the figure is true?

• The amplitudes of the peaks are used to sequence the metabolite.

• The amplitudes of the peaks are irrelevant and only provide information on the presence or absence of metabolites

• The amplitudes of the peaks are used to calculate metabolite concentrations.

• The order of the metabolites on the spectrum is related to their concentration.