Question 1

What is gene annotation in bioinformatics?

Accepted Answer

A) identifying protein coding regions within a sequence 
B) describing the functions of protein-coding genes 
C) describing the functions of noncoding regions of the genome 
D) matching the corresponding phenotypes of different species 
E) comparing the protein sequences within a single phylum 
A) identifying protein coding regions within a sequence 
B) describing the functions of protein-coding genes 
C) describing the functions of noncoding regions of the genome 
D) matching the corresponding phenotypes of different species 
E) comparing the protein sequences within a single phylum

Question 2

In comparing the genomes of humans and those of other higher primates, it is seen that humans have a large metacentric pair we call chromosome 2 among our 46 chromosomes, whereas the other primates of this group have 48 chromosomes and any pair like the human chromosome 2 pair is not present; instead, the primate groups each have two pairs of midsize acrocentric chromosomes. What is the most likely explanation?

Accepted Answer

A) The ancestral organism had 48 chromosomes and at some point a centric fusion event occurred and provided some selective advantage. 
B) The ancestral organism had 46 chromosomes, but primates evolved when one of the pairs broke in half. 
C) At some point in evolution, human ancestors and primate ancestors were able to mate and produce fertile offspring, making a new species. 
D) Chromosome breakage results in additional centromeres being made in order for meiosis to proceed successfully. 
E) Transposable elements transferred significantly large segments of the chromosomes to new locations. 
A) The ancestral organism had 48 chromosomes and at some point a centric fusion event occurred and provided some selective advantage. 
B) The ancestral organism had 46 chromosomes, but primates evolved when one of the pairs broke in half. 
C) At some point in evolution, human ancestors and primate ancestors were able to mate and produce fertile offspring, making a new species. 
D) Chromosome breakage results in additional centromeres being made in order for meiosis to proceed successfully. 
E) Transposable elements transferred significantly large segments of the chromosomes to new locations.

Question 3

Fragments of DNA have been extracted from the remnants of extinct woolly mammoths, amplified, and sequenced. These can now be used to

Accepted Answer

A) introduce into relatives, such as elephants, certain mammoth traits. 
B) clone live woolly mammoths. 
C) study the relationships among woolly mammoths and other wool-producers. 
D) understand the evolutionary relationships among members of related taxa. 
E) appreciate the reasons why mammoths went extinct. 
A) introduce into relatives, such as elephants, certain mammoth traits. 
B) clone live woolly mammoths. 
C) study the relationships among woolly mammoths and other wool-producers. 
D) understand the evolutionary relationships among members of related taxa. 
E) appreciate the reasons why mammoths went extinct.

Question 4

The biggest problem with the shotgun technique is its tendency to underestimate the size of the genome. Which of the following might best account for this?

Accepted Answer

A) skipping some of the clones to be sequenced 
B) missing some of the overlapping regions of the clones 
C) counting some of the overlapping regions of the clones twice 
D) having some of the clones die during the experiment and therefore not be represented 
E) short repetitive sequences hinder reassembly 
A) skipping some of the clones to be sequenced 
B) missing some of the overlapping regions of the clones 
C) counting some of the overlapping regions of the clones twice 
D) having some of the clones die during the experiment and therefore not be represented 
E) short repetitive sequences hinder reassembly

Question 5

Homeotic genes contain a homeobox sequence that is highly conserved among very diverse species. The homeobox is the code for that domain of a protein that binds to DNA in a regulatory developmental process. Which of the following would you then expect?

Accepted Answer

A) that homeotic genes are selectively expressed over developmental time 
B) that a homeobox-containing gene has to be a developmental regulator 
C) that homeoboxes cannot be expressed in nonhomeotic genes 
D) that all organisms must have homeotic genes 
E) that all organisms must have homeobox-containing genes 
A) that homeotic genes are selectively expressed over developmental time 
B) that a homeobox-containing gene has to be a developmental regulator 
C) that homeoboxes cannot be expressed in nonhomeotic genes 
D) that all organisms must have homeotic genes 
E) that all organisms must have homeobox-containing genes

Question 6

A multigene family is composed of

Accepted Answer

A) multiple genes whose products must be coordinately expressed. 
B) genes whose sequences are very similar and that probably arose by duplication. 
C) the many tandem repeats such as those found in centromeres and telomeres. 
D) a gene whose exons can be spliced in a number of different ways. 
E) a highly conserved gene found in a number of different species. 
A) multiple genes whose products must be coordinately expressed. 
B) genes whose sequences are very similar and that probably arose by duplication. 
C) the many tandem repeats such as those found in centromeres and telomeres. 
D) a gene whose exons can be spliced in a number of different ways. 
E) a highly conserved gene found in a number of different species.

Question 7

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database. Your sequence hit several EST sequences that were identified as transcription factors. These sequences were found in E.coli, Chlamydomonas (a green algae), yeast, mice, and humans and only had a few base pair differences.
-What can be surmised about your transcription factor?

Accepted Answer

A) It is likely involved in a universal metabolic function. 
B) There is not enough information to conclude anything. 
C) It is unique to Arabidopsis. 
D) It is part of a large gene family. 
E) It is a transgene. 
A) It is likely involved in a universal metabolic function. 
B) There is not enough information to conclude anything. 
C) It is unique to Arabidopsis. 
D) It is part of a large gene family. 
E) It is a transgene.

Question 8

The large common repository for genetic sequences hosted by NCBI is called

Accepted Answer

A) GenBank. 
B) BLAST. 
C) GenesRus. 
D) Prodata. 
E) TreeNoMix. 
A) GenBank. 
B) BLAST. 
C) GenesRus. 
D) Prodata. 
E) TreeNoMix.

Question 9

A project initiated at the University of Guelph is attempting to catalogue the differences of a short sequence within the mitochondrial DNA in all animal species. This ________ should allow the quick identification of a species.

Accepted Answer

A) shotgun approach 
B) DNA barcoding 
C) microarray 
D) genechip 
E) STR DNA 
A) shotgun approach 
B) DNA barcoding 
C) microarray 
D) genechip 
E) STR DNA

Question 10

Use the following figure to answer the next few questions.
   
This figure shows a diagram of blocks of genes on human chromosome 16 and the locations of blocks of similar genes on four chromosomes of the mouse.
-Which of the following represents another example of the same phenomenon as that shown in the above figure?

Accepted Answer

A) the apparent centric fusion between two chromosome pairs of primates such as chimps to form the ancestor of human chromosome 2 
B) the difference in the numbers of chromosomes in five species of one genus of birds 
C) the formation of several pseudogenes in the globin gene family subsequent to human divergence from other primates 
D) the high frequency of polyploidy in many species of angiosperms 
A) the apparent centric fusion between two chromosome pairs of primates such as chimps to form the ancestor of human chromosome 2 
B) the difference in the numbers of chromosomes in five species of one genus of birds 
C) the formation of several pseudogenes in the globin gene family subsequent to human divergence from other primates 
D) the high frequency of polyploidy in many species of angiosperms

Question 11

Which of the following most correctly describes a shotgun technique for sequencing a genome?

Accepted Answer

A) genetic mapping followed immediately by sequencing 
B) physical mapping followed immediately by sequencing 
C) cloning large genome fragments into very large vectors, followed by sequencing 
D) cloning several sizes of fragments into various size vectors, sequencing the clone and then ordering them 
E) cloning the whole genome directly, from one end to the other 
A) genetic mapping followed immediately by sequencing 
B) physical mapping followed immediately by sequencing 
C) cloning large genome fragments into very large vectors, followed by sequencing 
D) cloning several sizes of fragments into various size vectors, sequencing the clone and then ordering them 
E) cloning the whole genome directly, from one end to the other

Question 12

If humans have 2900 Mb, a specific member of the lily family has 120 000 Mb, and a yeast has ~13 Mb, why can't this data allow us to order their evolutionary significance?

Accepted Answer

A) Size matters less than gene density. 
B) Size does not compare to gene density. 
C) Size does not vary with gene complexity. 
D) Size is mostly due to "junk" DNA. 
E) Size is comparable only within phyla. 
A) Size matters less than gene density. 
B) Size does not compare to gene density. 
C) Size does not vary with gene complexity. 
D) Size is mostly due to "junk" DNA. 
E) Size is comparable only within phyla.

Question 13

What characteristic of short tandem repeat DNA makes it useful for studying evolution?

Accepted Answer

A) The number of repeats varies widely from person to person or animal to animal. 
B) The sequence of DNA that is repeated varies significantly from individual to individual. 
C) The sequence variation is acted upon differently by natural selection in different environments. 
D) Every racial and ethnic group has inherited different short tandem repeats. 
A) The number of repeats varies widely from person to person or animal to animal. 
B) The sequence of DNA that is repeated varies significantly from individual to individual. 
C) The sequence variation is acted upon differently by natural selection in different environments. 
D) Every racial and ethnic group has inherited different short tandem repeats.

Question 14

Alu elements account for about 10% of the human genome. What are Alu elements?

Accepted Answer

A) noncoding regions 
B) viral remnants 
C) transposable elements 
D) short sequences that code for RNA 
E) transposons that code for RNA 
A) noncoding regions 
B) viral remnants 
C) transposable elements 
D) short sequences that code for RNA 
E) transposons that code for RNA

Question 15

Homeotic genes

Accepted Answer

A) encode transcription factors that control the expression of genes responsible for specific anatomical structures. 
B) are found only in Drosophila and other arthropods. 
C) are the only genes that contain the homeobox domain. 
D) encode proteins that form anatomical structures in the fly. 
E) are responsible for patterning during plant development. 
A) encode transcription factors that control the expression of genes responsible for specific anatomical structures. 
B) are found only in Drosophila and other arthropods. 
C) are the only genes that contain the homeobox domain. 
D) encode proteins that form anatomical structures in the fly. 
E) are responsible for patterning during plant development.

Question 16

Bioinformatics can be used to scan sequences for probable genes looking for start and stop sites for transcription and for translation, for probable splice sites, and for sequences that specify known mRNAs. Such sequences containing these elements are called

Accepted Answer

A) expressed sequence tags. 
B) cDNA. 
C) multigene families. 
D) proteomes. 
E) short tandem repeats. 
A) expressed sequence tags. 
B) cDNA. 
C) multigene families. 
D) proteomes. 
E) short tandem repeats.

Question 17

Researchers at the University of British Columbia are working on a way to analyze gene expression within a single cell as it differentiates. This is significant because

Accepted Answer

A) cDNA libraries could be made. 
B) tissue identification would be easier. 
C) RNA is needed to understand expression and probing a cell as it undergoes differentiation is impossible at this point. 
D) DNA within a single cell is difficult to extract. 
E) generation of totipotent adult stem cells would be possible. 
A) cDNA libraries could be made. 
B) tissue identification would be easier. 
C) RNA is needed to understand expression and probing a cell as it undergoes differentiation is impossible at this point. 
D) DNA within a single cell is difficult to extract. 
E) generation of totipotent adult stem cells would be possible.

Question 18

By the year 2012, ________ genomes had been completely sequenced.

Accepted Answer

A) 1000 
B) 2500 
C) 2800 
D) 3800 
E) 5300 
A) 1000 
B) 2500 
C) 2800 
D) 3800 
E) 5300

Question 19

When does exon shuffling occur?

Accepted Answer

A) during splicing of DNA 
B) during mitotic recombination 
C) as an alternative splicing pattern in post-transcriptional processing 
D) as an alternative cleavage or modification post-translationally 
E) as the result of faulty DNA repair 
A) during splicing of DNA 
B) during mitotic recombination 
C) as an alternative splicing pattern in post-transcriptional processing 
D) as an alternative cleavage or modification post-translationally 
E) as the result of faulty DNA repair

Question 20

Use the following information to answer the questions below.
You have isolated a gene sequence from the mustard plant Arabidopsis and have BLAST searched the NCBI database. Your sequence hit several EST sequences that were identified as transcription factors. These sequences were found in E.coli, Chlamydomonas (a green algae), yeast, mice, and humans and only had a few base pair differences.
-What can be said about this sequence?

Accepted Answer

A) It appears to be highly conserved. 
B) It has had many duplication events. 
C) It is an ancient gene. 
D) This sequence has been transposed to other species. 
E) It must be junk DNA. 
A) It appears to be highly conserved. 
B) It has had many duplication events. 
C) It is an ancient gene. 
D) This sequence has been transposed to other species. 
E) It must be junk DNA.

Exam 21: Genomes and Their Evolution

What is gene annotation in bioinformatics?

Fragments of DNA have been extracted from the remnants of extinct woolly mammoths, amplified, and sequenced. These can now be used to

The biggest problem with the shotgun technique is its tendency to underestimate the size of the genome. Which of the following might best account for this?

Homeotic genes contain a homeobox sequence that is highly conserved among very diverse species. The homeobox is the code for that domain of a protein that binds to DNA in a regulatory developmental process. Which of the following would you then expect?

A multigene family is composed of

The large common repository for genetic sequences hosted by NCBI is called

A project initiated at the University of Guelph is attempting to catalogue the differences of a short sequence within the mitochondrial DNA in all animal species. This ________ should allow the quick identification of a species.

Which of the following most correctly describes a shotgun technique for sequencing a genome?

If humans have 2900 Mb, a specific member of the lily family has 120 000 Mb, and a yeast has ~13 Mb, why can't this data allow us to order their evolutionary significance?

What characteristic of short tandem repeat DNA makes it useful for studying evolution?

Alu elements account for about 10% of the human genome. What are Alu elements?

Homeotic genes

Bioinformatics can be used to scan sequences for probable genes looking for start and stop sites for transcription and for translation, for probable splice sites, and for sequences that specify known mRNAs. Such sequences containing these elements are called

Researchers at the University of British Columbia are working on a way to analyze gene expression within a single cell as it differentiates. This is significant because

By the year 2012, ________ genomes had been completely sequenced.

When does exon shuffling occur?

Introduction: Evolution and Themes of Biology

The Chemical Context of Life

Water and Life

Carbon and the Molecular Diversity of Life

The Structure and Function of Large Biological Molecules

A Tour of the Cell

Membrane Structure and Function

An Introduction to Metabolism

Cellular Respiration and Fermentation

Photosynthesis

Cell Communication

The Cell Cycle

Meiosis and Sexual Life Cycles

Mendel and the Gene Idea

The Chromosomal Basis of Inheritance

The Molecular Basis of Inheritance

From Gene to Protein

Regulation of Gene Expression

Viruses

Dna Tools and Biotechnology

Descent With Modification: a Darwinian View of Life

The Evolution of Populations

The Origin of Species

The History of Life on Earth

Phylogeny and the Tree of Life

Bacteria and Archaea

Protists

Plant Diversity I: How Plants Colonized Land

Plant Diversity Ii: the Evolution of Seed Plants

Fungi

An Overview of Animal Diversity

An Introduction to Invertebrates

The Origin and Evolution of Vertebrates

Plant Structure, Growth, and Development

Resource Acquisition and Transport in Vascular Plants

Soil and Plant Nutrition

Angiosperm Reproduction and Biotechnology

Plant Responses to Internal and External Signals

Basic Principles of Animal Form and Function

Animal Nutrition

Circulation and Gas Exchange

The Immune System

Osmoregulation and Excretion

Hormones and the Endocrine System

Animal Reproduction

Animal Development

Neurons, Synapses, and Signalling

Nervous Systems

Sensory and Motor Mechanisms

Animal Behaviour

An Introduction to Ecology and the Biosphere

Population Ecology

Community Ecology

Ecosystems and Restoration Ecology

Conservation Biology and Global Change

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