Deck 15: Genomes

Question 1

Which of these techniques would a company that analyzes personal genomes most likely use?

A) DNA cloning
B) gene cloning
C) PCR
D) fingerprinting

Answer 1

C

Question 2

Which of the following is a difference between prokaryotic and eukaryotic genomes?

A) Eukaryotic protein-coding genes typically lack introns, so more sophisticated algorithms must be used to identify such genes.
B) Eukaryotic protein-coding genes typically have introns, so more sophisticated algorithms must be used to identify such genes.
C) Because many genes have introns in prokaryotic genomes, searching for protein-coding ORFs is straightforward.
D) Because many genes have introns in prokaryotic genomes, searching for protein-coding ORFs is very difficult.

Answer 2

B

Question 3

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

Answer 3

A

Question 4

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 5

Which of the following is included in functional analysis of protein-coding genes?

A) determining the base-by-base sequence of an entire genome
B) scanning of genomes for potential protein-producing sequences
C) scanning of genomes for potential RNA-producing sequences
D) determining what proteins they encode and how those proteins function in the organism's metabolic processes

Question 6

How can microarrays help us understand cellular functions?

A) Microarrays let us study different cells under different conditions.
B) Microarrays let us directly measure protein expression in individual cells.
C) Microarrays, by hybridizing cDNAs to DNA sequences already present on a chip, let us identify which portions of a genome are 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.

Question 7

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 8

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

Question 9

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 10

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 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

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.

Question 13

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 14

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 15

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 16

Which of these statements 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 17

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.

Question 18

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 19

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 20

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 21

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 22

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

Question 23

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 24

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 25

Which of these statements best describes the human genome?

A) There are about 12 000 genes that do not encode proteins.
B) Each gene averages 30 regulatory sequences for expression.
C) There are no pseudogenes.
D) There are, on average, 10 exons per gene.

Question 26

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

Question 27

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 28

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

Question 29

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

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

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

Question 32

Over half of your DNA sequence is comprised of transposable elements that were once mobile. Which of these statements best identifies such sequences?

A) They contain genes that encompass about 15% to 25% of your genome.
B) They contain genes that are not coding for human proteins, and are called "junk DNA."
C) They contain genes that are coding for human proteins, but they are not expressed.
D) They do not contain genes, and are called "junk DNA."

Question 33

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 34

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

Question 35

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 36

Which of the following values is your genome size?

A) S-value
B) G-value
C) C-value
D) D-value

Question 37

What are the main differences among the studies of genomics, transcriptomics, and proteomics?

Question 38

Which of the following is your "C-value"?

A) RNA size
B) genome size
C) chromosome size
D) DNA size

Question 39

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 40

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 41

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 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
genomics

Question 43

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 44

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 45

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 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
sequencing

Question 47

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 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
Sanger method

Question 49

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 50

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 51

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 52

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 53

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