Question 1

In the microarray shown in the textbook, the cDNAs were labeled with red and green fluorescent tags. Why do some spots on the microarray emit yellow light?

Accepted Answer

A) Red and green are two of the primary colors, and if both cDNAs hybridize to the spot, the combination of the two will produce yellow light. 
B) The yellow light comes from the laser, and a yellow spot indicates that neither cDNA hybridized to that spot on the microarray. 
C) The over expression of one cDNA relative to the other will skew the color pattern of the spot on the microarray, resulting in the yellow color. 
D) The color choice was an arbitrary decision by the artist and doesn't reflect how the process actually works. 
E) Yellow spots are those that contain no DNA probes on the chip. 
A) Red and green are two of the primary colors, and if both cDNAs hybridize to the spot, the combination of the two will produce yellow light. 
B) The yellow light comes from the laser, and a yellow spot indicates that neither cDNA hybridized to that spot on the microarray. 
C) The over expression of one cDNA relative to the other will skew the color pattern of the spot on the microarray, resulting in the yellow color. 
D) The color choice was an arbitrary decision by the artist and doesn't reflect how the process actually works. 
E) Yellow spots are those that contain no DNA probes on the chip.

Question 2

A researcher obtains a sequence of a gene of interest including the ORF, 5 ¢ untranslated region, and 3 ¢ untranslated region. Which portion of the gene sequence encodes the protein? ​

Accepted Answer

A) the 5 ¢ untranslated region and the ORF only ​ 
B) the ORF only 
C) the ORF and 3 ¢ untranslated region only 
D) the 5 ¢ and 3 ¢ untranslated regions only 
E) the ORF, 5 ¢ untranslated region, and 3 ¢ untranslated region 
A) the 5 ¢ untranslated region and the ORF only ​ 
B) the ORF only 
C) the ORF and 3 ¢ untranslated region only 
D) the 5 ¢ and 3 ¢ untranslated regions only 
E) the ORF, 5 ¢ untranslated region, and 3 ¢ untranslated region

Question 3

Match between columns
                        Premises: bioinformatics

Accepted Answer

The Answer of The study of all transcripts produced from is...

Question 4

A researcher obtains the results of his RNA-seq analysis. Several transcripts are listed as being derived from the same gene. How is this possible? ​

Accepted Answer

A) Alternative splicing allows for different transcripts to be created by the same gene sequence. 
B) The researcher's sample was contaminated. 
C) Exon shuffling allows for different transcripts to be created by the same gene sequence. 
D) Intron shuffling allows for different transcripts to be created by the same gene sequence. 
E) It is not possible; there was an error in the alignment process. 
A) Alternative splicing allows for different transcripts to be created by the same gene sequence. 
B) The researcher's sample was contaminated. 
C) Exon shuffling allows for different transcripts to be created by the same gene sequence. 
D) Intron shuffling allows for different transcripts to be created by the same gene sequence. 
E) It is not possible; there was an error in the alignment process.

Question 5

Proteomics _____. ​

Accepted Answer

A) refers to the analysis of the entire protein content of a cell ​ 
B) refers to the analysis of all the DNA of a species 
C) looks only at plasmids 
D) studies mRNA levels 
E) uses DNA chips 
A) refers to the analysis of the entire protein content of a cell ​ 
B) refers to the analysis of all the DNA of a species 
C) looks only at plasmids 
D) studies mRNA levels 
E) uses DNA chips

Question 6

Match between columns
                        Premises: Proteomics

Accepted Answer

The Answer of DNA and protein and mRNA/cDNA is...

Question 7

Which pre-mRNA processing mechanism allows different proteins to be produced from the same DNA sequence? ​

Accepted Answer

A) transposition 
B) alternative splicing 
C) intron shuffling 
D) intron splicing 
E) open reading frame shuffling 
A) transposition 
B) alternative splicing 
C) intron shuffling 
D) intron splicing 
E) open reading frame shuffling

Question 8

To experimentally determine the function of an annotated gene, a researcher may _____. ​

Accepted Answer

A) look for similar gene sequences of known function 
B) examine the putative protein structure 
C) perform a gene knockout 
D) find a pseudogene for the gene 
E) determine the amino acid sequence 
A) look for similar gene sequences of known function 
B) examine the putative protein structure 
C) perform a gene knockout 
D) find a pseudogene for the gene 
E) determine the amino acid sequence

Question 9

The percentage of the human genome that is protein-coding is less than _____. ​

Accepted Answer

A) 2% 
B) 20% 
C) 30% 
D) 50% 
E) 85% 
A) 2% 
B) 20% 
C) 30% 
D) 50% 
E) 85%

Question 10

What is a difference between human male and female genomes? ​

Accepted Answer

A) Males have 46 chromosomes; females have 45. 
B) Males have 22 pairs of autosomal chromosomes; females have 21 pairs of autosomal chromosomes. 
C) Males have 23 pairs of chromosomes plus 1 Y chromosome; females have 23 pairs of chromosomes. 
D) Males have 24 different chromosomes; females have 23 different chromosomes 
E) Males have an X chromosome; females do not. 
A) Males have 46 chromosomes; females have 45. 
B) Males have 22 pairs of autosomal chromosomes; females have 21 pairs of autosomal chromosomes. 
C) Males have 23 pairs of chromosomes plus 1 Y chromosome; females have 23 pairs of chromosomes. 
D) Males have 24 different chromosomes; females have 23 different chromosomes 
E) Males have an X chromosome; females do not.

Question 11

How can microarrays help us understand cellular functions?

Accepted Answer

A) Microarrays let us study different cellular structures under different conditions. 
B) Microarrays let us directly measure protein expression in individual cells. 
C) Microarrayslet us identify which portions of a genome were being expressed in a cell at a particular time. 
D) Microarrays let us identify which DNA sequences are present in a particular cell type under certain conditions. 
E) Microarrays let us identify which portions of a genome serve as regulatory sequences. 
A) Microarrays let us study different cellular structures under different conditions. 
B) Microarrays let us directly measure protein expression in individual cells. 
C) Microarrayslet us identify which portions of a genome were being expressed in a cell at a particular time. 
D) Microarrays let us identify which DNA sequences are present in a particular cell type under certain conditions. 
E) Microarrays let us identify which portions of a genome serve as regulatory sequences.

Question 12

Match between columns
                        Premises: Shotgun library

Accepted Answer

The Answer of DNA and mRNA/cDNA and protein is...

Question 13

Which domain(s)have densely packed genomes with little noncoding space? ​

Accepted Answer

A) Archaea only 
B) Bacteria only 
C) Eukarya only 
D) Archaea and Eukarya 
E) Bacteria and Archaea 
A) Archaea only 
B) Bacteria only 
C) Eukarya only 
D) Archaea and Eukarya 
E) Bacteria and Archaea

Question 14

Which ethical dilemma may arise from the application of pharmagogenomics? ​

Accepted Answer

A) The use of embryonic stem cells for gene therapy. ​ 
B) The discovery of a gene that predicts an unfavorable drug response in an individual, for whom there are no alternative treatments available. 
C) The use of vaccination to prevent diseases. 
D) The use of blood transfusions to treat diseases. 
E) The introduction of foreign genes to restore loss of vital gene function in a patient with an infectious disease. 
A) The use of embryonic stem cells for gene therapy. ​ 
B) The discovery of a gene that predicts an unfavorable drug response in an individual, for whom there are no alternative treatments available. 
C) The use of vaccination to prevent diseases. 
D) The use of blood transfusions to treat diseases. 
E) The introduction of foreign genes to restore loss of vital gene function in a patient with an infectious disease.

Question 15

Which event can introduce a protein domain into a pre-existing protein? ​

Accepted Answer

A) gene alignment 
B) intron shuffling 
C) exon shuffling 
D) peptide shuffling 
E) exon splicing 
A) gene alignment 
B) intron shuffling 
C) exon shuffling 
D) peptide shuffling 
E) exon splicing

Question 16

In whole-genome shotgun sequencing, ____.

Accepted Answer

A) DNA is broken into many random, overlapping fragments that are sequenced and then assembled using computer algorithms 
B) whole chromosomes are sequencedintact from the 3'end to the 5' end 
C) whole chromosomes are sequenced intactfrom the 5'end to the 3' end 
D) DNA is broken into a few, non-overlapping fragments that can be read directly by computer algorithms 
E) DNA is broken into individual nucleotides that are sequenced and then assembled using computer algorithms 
A) DNA is broken into many random, overlapping fragments that are sequenced and then assembled using computer algorithms 
B) whole chromosomes are sequencedintact from the 3'end to the 5' end 
C) whole chromosomes are sequenced intactfrom the 5'end to the 3' end 
D) DNA is broken into a few, non-overlapping fragments that can be read directly by computer algorithms 
E) DNA is broken into individual nucleotides that are sequenced and then assembled using computer algorithms

Question 17

What is an open reading frame (ORF)? ​

Accepted Answer

A) a protein coding sequence plus associated regulatory sequences 
B) the sequence between and including a start codon and an stop codon 
C) the sequence between and including a start codon and an stop codon, minus the introns 
D) the sequence between and including a start codon and an stop codon, minus the exons 
E) the sequence between a start codon and stop codon in prokaryotes only 
A) a protein coding sequence plus associated regulatory sequences 
B) the sequence between and including a start codon and an stop codon 
C) the sequence between and including a start codon and an stop codon, minus the introns 
D) the sequence between and including a start codon and an stop codon, minus the exons 
E) the sequence between a start codon and stop codon in prokaryotes only

Question 18

When the human genome was sequenced, we learned that there are fewer than expected protein coding genes (approximately 20,000). Yet, the total number of proteins produced in humans approaches 100,000. What accounts for this discrepancy in numbers?

Accepted Answer

A) We have not yet identified all of the open reading frames in the human genome. 
B) We have not yet fully sequenced the human genome. 
C) mRNA processing mechanisms allowmultiple proteins to be produced from a single DNA sequence. 
D) Some noncoding DNA sequences encode proteins. 
E) There has been a gross over-estimation of the number of proteins produced in humans. 
A) We have not yet identified all of the open reading frames in the human genome. 
B) We have not yet fully sequenced the human genome. 
C) mRNA processing mechanisms allowmultiple proteins to be produced from a single DNA sequence. 
D) Some noncoding DNA sequences encode proteins. 
E) There has been a gross over-estimation of the number of proteins produced in humans.

Question 19

A gene encoding a subunit of hemoglobin in humans is found to be homologous to a gene in chimpanzees. The homologous gene in chimpanzees likely _____. ​

Accepted Answer

A) is a pseudogene 
B) encodes the same hemoglobin subunit 
C) is inactive because it is in a different species 
D) is a regulatory sequence 
E) encodes a respiratory enzyme 
A) is a pseudogene 
B) encodes the same hemoglobin subunit 
C) is inactive because it is in a different species 
D) is a regulatory sequence 
E) encodes a respiratory enzyme

Question 20

An application of pharmacogenomics is the study of ____ for determining the appropriate dosages of certain drugs in specific patients. ​

Accepted Answer

A) drug metabolism genes ​ 
B) body size 
C) blood volume 
D) trial and error methods 
E) drug interactions 
A) drug metabolism genes ​ 
B) body size 
C) blood volume 
D) trial and error methods 
E) drug interactions

Exam 19: Genomes and Proteomes

In the microarray shown in the textbook, the cDNAs were labeled with red and green fluorescent tags. Why do some spots on the microarray emit yellow light?

A researcher obtains a sequence of a gene of interest including the ORF, 5 ¢ untranslated region, and 3 ¢ untranslated region. Which portion of the gene sequence encodes the protein? ​

A researcher obtains the results of his RNA-seq analysis. Several transcripts are listed as being derived from the same gene. How is this possible? ​

Proteomics _____. ​

Which pre-mRNA processing mechanism allows different proteins to be produced from the same DNA sequence? ​

To experimentally determine the function of an annotated gene, a researcher may _____. ​

The percentage of the human genome that is protein-coding is less than _____. ​

What is a difference between human male and female genomes? ​

How can microarrays help us understand cellular functions?

Which domain(s)have densely packed genomes with little noncoding space? ​

Which ethical dilemma may arise from the application of pharmagogenomics? ​

Which event can introduce a protein domain into a pre-existing protein? ​

In whole-genome shotgun sequencing, ____.

What is an open reading frame (ORF)? ​

When the human genome was sequenced, we learned that there are fewer than expected protein coding genes (approximately 20,000). Yet, the total number of proteins produced in humans approaches 100,000. What accounts for this discrepancy in numbers?

A gene encoding a subunit of hemoglobin in humans is found to be homologous to a gene in chimpanzees. The homologous gene in chimpanzees likely _____. ​

An application of pharmacogenomics is the study of ____ for determining the appropriate dosages of certain drugs in specific patients. ​

Introduction to Biological Concepts and Research

Life, Chemistry, and Water

Biological Molecules: the Carbon Compounds of Life

Cells

Membranes and Transport

Energy, Enzymes, and Biological Reactions

Cellular Respiration: Harvesting Chemical Energy

Photosynthesis

Cell Communication

Cell Division and Mitosis

Meiosis: the Cellular Basis of Sexual Reproduction

Mendel, Genes, and Inheritance

Genes, Chromosomes, and Human Genetics

DNA Structure, Replication, and Organization

From DNA to Protein

Regulation of Gene Expression

Bacterial and Viral Genetics

Dna Technologies: Making and Using Genetically Altered Organisms, and Other Applications

The Development of Evolutionary Thought

Microevolution: Genetic Changes Within Populations

Speciation

Paleobiology and Macroevolution

Systematic Biology: Phylogeny and Classification

The Origin of Life

Prokaryotes and Viruses

Protists

Seedless Plants

Seed Plants

Fungi

Animal Phylogeny, Acoelomates, and Protostomes

Deuterostomes: Vertebrates and Their Closest Relatives

The Plant Body

Transport in Plants

Plant Nutrition

Reproduction and Development in Flowering Plants

Plant Signals and Responses to the Environment

Introduction to Animal Organization and Physiology

Information Flow and the Neuron

Nervous Systems

Sensory Systems

The Endocrine System

Muscles, Bones, and Body Movements

The Circulatory System

Defenses Against Disease

Gas Exchange: the Respiratory System

Animal Nutrition

Regulating the Internal Environment

Animal Reproduction

Animal Development

Ecology and the Biosphere

Population Ecology

Population Interactions and Community Ecology

Ecosystems

Biodiversity and Conservation Biology

Animal Behavior

Filters

A researcher obtains a sequence of a gene of interest including the ORF, 5 ¢ untranslated region, and 3 ¢ untranslated region. Which portion of the gene sequence encodes the protein?

A researcher obtains the results of his RNA-seq analysis. Several transcripts are listed as being derived from the same gene. How is this possible?

Proteomics _____.

Which pre-mRNA processing mechanism allows different proteins to be produced from the same DNA sequence?

To experimentally determine the function of an annotated gene, a researcher may _____.

The percentage of the human genome that is protein-coding is less than _____.

What is a difference between human male and female genomes?

Which domain(s)have densely packed genomes with little noncoding space?

Which ethical dilemma may arise from the application of pharmagogenomics?

Which event can introduce a protein domain into a pre-existing protein?

What is an open reading frame (ORF)?

A gene encoding a subunit of hemoglobin in humans is found to be homologous to a gene in chimpanzees. The homologous gene in chimpanzees likely _____.

An application of pharmacogenomics is the study of ____ for determining the appropriate dosages of certain drugs in specific patients.