Deck 16: Genomes and Proteomes

Question 1

In the whole-genome shotgun method, the genome is fragmented and individual fragments are sequenced. How do we determine the order of the nucleotides in the intact chromosome?

A)The fragmentation is done in a very systematic way such that the physical arrangement of fragments is readily apparent.
B)The sequences of the ends of the fragments overlap with the ends of other fragments.
C)We supplement our information with data from a different technique to determine the final chromosome arrangement.
D)DNA hybridization assays are conducted to determine the physical arrangement of the genes on the chromosome.

Answer 1

B

Question 2

During a sequencing reaction, the researcher adds all the required components to the reaction, but accidentally adds only one of the four dideoxynucleotides, the ddC. What kinds of products will be observed after this reaction is complete?

A)All fragments will end in A.
B)All fragments will end in C.
C)All fragments will end in G.
D)All fragments will end in T.

Answer 2

B

Question 3

Which of the following is the name of the study of the complete set of transcripts in a cell?

A)genome
B)transcriptome
C)proteome
D)interactome

Answer 3

B

Question 4

In the microarray shown in your textbook, the cDNAs were labelled with red and green fluorescent tags. How then do you end up with spots on the microarray emitting yellow light?

A)In light, red and green are two of the primary colours, and 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 colour pattern of the spot on the microarray. This results in the yellow colour.
D)The colour choice was an arbitrary decision by the artist and doesn't reflect how the process actually works.

Question 5

Which of the following best describes pseudogenes?

A)Most pseudogenes derived from protein-coding genes but are not recognized by their sequence similarities to functional genes.
B)Pseudogenes are short repetitive sequences.
C)Pseudogenes are not similar to functional genes at DNA sequence level.
D)Most pseudogenes are derived from protein-coding genes and are recognized by their sequence similarities to functional genes.

Question 6

Which of the following is NOT added to a single-stranded DNA in order to perform a successful sequencing reaction?

A)a mixture of the four dideoxyribonucleotides, not labelled with a different fluorescent label
B)a DNA primer
C)a mixture of the four deoxyribonucleotides
D)a DNA polymerase

Question 7

Which of the following shows the approximate size of the human genome?

A)1 billion base pairs
B)3 billion base pairs
C)7 billion base pairs
D)10 billion base pairs

Question 8

Which of the following organisms has the largest number of protein-coding genes?

A)E. coli (bacteria)
B)Saccharomyces cerevisiae (yeast)
C)Homo sapiens (human)
D)Oryza sativa (rice)

Question 9

Which of the following is NOT a way to determine the function of annotated genes?

A)looking for similar gene sequences of known function
B)examining the putative protein structure
C)using gene knockout experiments
D)finding a pseudogene for that gene

Question 10

Which of the following best summarizes what proteomics involves?

A)determining protein structure and function
B)determining protein structure and interactions
C)determining protein structure, function, location, and interaction
D)determining protein sequence and interactions

Question 11

Which of the following are NOT identified during annotation?

A)protein-coding genes
B)noncoding RNA genes
C)origins of replication
D)protein interactions

Question 12

Which of the following is NOT a model organism whose genomes were sequenced as part of the original Human Genome Project?

A)Mus musculus (mouse)
B)Escherichia coli (bacteria)
C)Drosophila melanogaster (fruit fly)
D)Danio rerio (zebrafish)

Question 13

Which of the following explains what bioinformatics researchers do?

A)They use small datasets to catalogue the range of human genetic similarities.
B)They use large datasets to catalogue the range of human genetic similarities.
C)They use large datasets to catalogue the range of human genetic variation.
D)They use small datasets to catalogue the range of human genetic variation.

Question 14

Which of the following is NOT considered a source of evolving genes?

A)a gene duplication from unequal crossing-over
B)a gene duplication from replicating transposable elements
C)a gene duplication from crossing-over
D)an exon shuffling

Question 15

Where do multigene families come from?

A)They come from a single gene duplication event.
B)They come from repeated cycles of gene duplication, followed by mutation.
C)They come from single point mutations.
D)They come from exon shuffling.

Question 16

What is an open reading frame?

A)the nucleotides between and including a start codon and an end codon in all chromosomes
B)the nucleotides between and including a start codon and an end codon, minus the introns
C)the nucleotides between and including a start codon and an end codon, minus the exons
D)the nucleotides between a start codon and end codon only in prokaryotes

Question 17

During a microarray analysis, cDNAs made from normal cells are stained with a green fluorescent label and cDNAs from abnormal cells are stained with a red fluorescent label. Which of the following statements best summarizes the results of this experiment?

A)Red spots indicate genes that are underexpressed in abnormal cells.
B)Red spots indicate genes that are not expressed in abnormal cells.
C)Red spots indicate genes that are overexpressed in abnormal cells.
D)Red spots indicate genes that are overexpressed in normal cells.

Question 18

Which of the following is the reason why the genes of living organisms tend to be similar to each other?

A)All genes are old.
B)All genes are new.
C)They have evolved from ancestral genes in ancestral organisms.
D)They have not evolved from ancestral genes in ancestral organisms.

Question 19

Which of the following involves comparing gene expression under a defined experimental condition with expression under a control condition?

A)studies of gene activity using DNA microarrays
B)studies of gene activity using RNA microarrays
C)studies of gene activity using RNA analyses
D)studies of gene activity using DNA analyses

Question 20

Which of the following is NOT an example of a current use of bioinformatics?

A)locating individual genes in a genomic sequence
B)aligning sequences in databases to determine similarities between organisms
C)predicting the structure and function of gene products
D)determining the final protein structure of novel proteins based on just the nucleotide sequence

Question 21

Match the following techniques with the descriptions listed below.
a.whole-genome shotgun sequencing
b.Illumina/Solexa sequencing
c.Sanger sequencing
d.DNA microarray analysis
e.gene knockout
f.gene knockdown
used to determine the entire genome sequence of an organism by sequencing DNA fragments and then assembling them using computer software

Question 22

What is the difference between a gene knockout and a gene knockdown?

Question 23

What are the relationships among the following types of organisms with respect to genome size: viruses, bacteria, archaea, and eukaryotes?

Question 24

How do gene duplication and exon shuffling lead to new genes?

Question 25

Match the following techniques with the descriptions listed below.
a.whole-genome shotgun sequencing
b.Illumina/Solexa sequencing
c.Sanger sequencing
d.DNA microarray analysis
e.gene knockout
f.gene knockdown
used to determine DNA sequence in an automated way

Question 26

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
transcriptome

Question 27

Explain how proteomics is considered by some to be even more important than genome sequencing.

Question 28

What is the main difference among the studies of genomics, transcriptomics, and proteomics?

Question 29

Comparative genomics is done to learn how genes and genomes have evolved. What are three different concepts that we have learned from comparative genomics?

Question 30

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
proteome

Question 31

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
proteomics

Question 32

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
comparative genomics

Question 33

Match the following techniques with the descriptions listed below.
a.whole-genome shotgun sequencing
b.Illumina/Solexa sequencing
c.Sanger sequencing
d.DNA microarray analysis
e.gene knockout
f.gene knockdown
used to determine DNA sequence using dideoxynucleotides

Question 34

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
genomics

Question 35

Match the following techniques with the descriptions listed below.
a.whole-genome shotgun sequencing
b.Illumina/Solexa sequencing
c.Sanger sequencing
d.DNA microarray analysis
e.gene knockout
f.gene knockdown
used to replace a normal gene with a defective one to see the effect

Question 36

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
bioinformatics

Question 37

There are three types of sequencing described in the text: Sanger (dideoxy) sequencing, whole-genome shotgun sequencing, and Illumin/Solexa sequencing. Which one(s) would be best to use for sequencing a single gene versus an entire genome and why?

Question 38

List at least three differences in how the E. coli and human genomes are arranged.

Question 39

Match each of the following terms with its correct definition.
a.all proteins that can be produced by a cell
b.all transcripts that are produced by a cell
c.the study of all of the proteins produced from an organism's genome
d.the study of genome sequences for several organisms
e.the study of the whole genome of an organism
f.the use of computer programs to extract biological information from sequence data
g.the study of all transcripts produced from an organism's genome
transcriptomics

Question 40

Match the following techniques with the descriptions listed below.
a.whole-genome shotgun sequencing
b.Illumina/Solexa sequencing
c.Sanger sequencing
d.DNA microarray analysis
e.gene knockout
f.gene knockdown
used to compare the gene expression patterns of identical cells under different conditions

Question 41

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
cellular proteomics

Question 42

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
Sanger method

Question 43

Match the following techniques with the descriptions listed below.
a.whole-genome shotgun sequencing
b.Illumina/Solexa sequencing
c.Sanger sequencing
d.DNA microarray analysis
e.gene knockout
f.gene knockdown
used to decrease a gene's expression to see the effect

Question 44

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
sequencing

Question 45

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
shotgun sequencing

Question 46

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
proteomics

Question 47

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
microarray

Question 48

For each of the following statements, choose the most appropriate macromolecule being studied or manipulated from the list below.
a.DNA
b.mRNA/cDNA
c.protein
genomics