Deck 5: Genomics, Proteomics, and Systems Biology

Question 1

In 1995, the first complete genome of _______ was sequenced by Dr. Craig Venter.

A) Escherichia coli
B) Saccharomyces cerevisiae
C) Haemophilus influenzae
D) Caenorhabditis elegans

Answer 1

C

Question 2

Analysis of the H. influenza and E. coli genomes revealed that _______% of each genome encodes for protein.

A) 25
B) 50
C) 75
D) 90

Answer 2

D

Question 3

The simplest eukaryotic genome is found in

A) Saccharomyces cerevisiae.
B) Caenorhabditis elegans.
C) Drosophila melanogaster.
D) Arabidopsis thaliana.

Answer 3

A

Question 4

Analysis of the first bacterial genome to be sequenced, H. influenzae, revealed _______ rRNA genes, _______ different tRNA genes, and _______ potential protein-coding genes.

A) 6; 54; 1,743
B) 54; 6; 174
C) 54; 6; 1,743
D) 6; 54; 174

Question 5

The first eukaryotic genome to be completely sequenced was

A) the protist Dictyostelium discoideum.
B) the yeast Saccharomyces cerevisiae.
C) the fruit fly Drosophila melanogaster.
D) the human genome.

Question 6

Which statement below best explains why there are 64 possible codons?

A) There are only four nucleotides and with a triplet code, the total number of possibilities would be 4³.
B) There are 21 amino acids and each amino acid had three codons.
C) There are only four nucleotides and with a triplet code, the total number of possibilities would be 3⁴.
D) There are only four nucleotides, yet in the double-stranded form, there are eight, thus there are 8² possibilities.

Question 7

Stretches of sequenced nucleotides that code for polypeptides are recognized by the

A) presence of a start codon.
B) absence of chain-terminating codons.
C) presence of closed-reading frames.
D) absence of open-reading frames.

Question 8

Potential protein-coding regions of genomic DNA containing long stretches of nucleotide sequences that can encode polypeptides and contain no stop codons are called

A) introns.
B) exons.
C) pseudogenes.
D) open-reading frames.

Question 9

Sequencing the genomes of Caenorhabditis elegans and Drosophila melanogaster led to the discovery of many new genes for

A) enzymes of cell metabolism.
B) proteins regulating the cell cycle.
C) proteins regulating mitosis.
D) proteins regulating animal development.

Question 10

The Arabidopsis genome, like many plant genomes, contains more genes than many animals. This is due largely to

A) fewer stop codons.
B) larger exons.
C) larger introns.
D) gene duplication.

Question 11

Surprisingly, after sequencing many different species, what organism stands out as having the largest number of genes?

A) Arabidopsis
B) Zebrafish
C) Chimpanzee
D) Apple

Question 12

To sequence the human genome, the International Human Genome Sequencing Consortium

A) used the shotgun approach to sequence fragments and assemble them in order using overlaps between the sequences.
B) sequenced cloned DNA and then mapped it by FISH.
C) used BAC clones as substrates for sequencing.
D) used massively parallel sequencing.

Question 13

To sequence the human genome, the Celera Genomics team led by Craig Venter used

A) the shotgun approach to sequence fragments and assemble them in order using overlaps between the sequences.
B) BAC clones as substrates for sequencing.
C) sequence-cloned DNA and then mapped it by FISH.
D) massively parallel sequencing.

Question 14

What percent of genes are similar between mice, rats, and humans?

A) 10%
B) 30%
C) 70%
D) 90%

Question 15

Which method revealed that there were many more RNAs transcribed than are accounted for by the protein-coding genes in human cells?

A) DNA microarray
B) Next-generation sequencing
C) RNA-seq
D) cDNA hybridization

Question 16

There are more distinct proteins in eukaryotic cells than there are number of genes. Which statement best explains this?

A) Many genes can give rise to multiple RNAs through alternate splicing.
B) Pseudogene expression often undergo transcription of truncated mRNAs.
C) Many genes undergo amplification and produce higher levels of mRNA.
D) Some mRNAs cross-hybridize and get translated into fusion proteins.

Question 17

What is a common method for testing blood samples of athletes for the presence of performance enhancing drugs?

A) Next-generation sequencing
B) Mass spectrometry
C) Two-dimensional gel electrophoresis
D) RNA-seq

Question 18

Mass spectrometers are used to

A) transport a molecule against its concentration gradient.
B) couple the energy of ATP hydrolysis to a configurational change.
C) transport H⁺ across a membrane against a pH gradient.
D) identify proteins by mass/ratio peptide analysis as part of proteomic procedures.

Question 19

In tandem mass spectrometry the unique second phase is characterized by

A) the further isolation of the first phase samples by two-dimensional gel electrophoresis.
B) the purification of the first phase samples by column chromatography.
C) the addition of a collision based fragmentation step to the first phase sample to determine amino acid sequence.
D) running simultaneous samples to compare and confirm amino acid identity.

Question 20

Which cellular structure has the largest number of unique proteins?

A) Plasma membrane
B) Endoplasmic reticulum
C) Mitochondria
D) Golgi apparatus

Question 21

Which method uses an antibody that recognizes cellular proteins to investigate protein-protein interactions?

A) Immunoprecipitation
B) The yeast two-hybrid system
C) Protein array
D) Electrophoretic mobility shift assay

Question 22

Which method requires the experimental construction of two fusion proteins to assess protein-protein interactions?

A) Immunoprecipitation
B) The yeast two-hybrid system
C) Protein array
D) Electrophoretic mobility shift assay

Question 23

The new field of science called _______ lies at the interface between biology and computer science. It is focused on developing the computational methods needed to extract useful biological information from the sequence of billions of bases of DNA.

A) systems biology 100
B) genome wide association studies
C) microarray
D) bioinformatics

Question 24

Which phrase best defines systems biology?

A) The use of global experimental data for quantitative modeling of integrated cellular processes
B) The systematic analysis of individual molecules and pathways
C) The comparative analysis of large datasets from multiple cell types, tissues, and/or organs
D) The computational overlay of data from both genomic and proteomic experiments

Question 25

The experimental inactivation of a gene by homologous recombination with an inactive mutant to assess function of the normal genes in intact organisms is often referred to as what type of experiment?

A) Transgenic
B) Hybrid
C) Knockout
D) Gain-of-function

Question 26

In RNA interference experiments, siRNAs homologous to known mRNAs inhibit expression of the proteins by what mechanism?

A) They form double-stranded RNA molecules that get degraded in the cytoplasm.
B) They form double-stranded RNA molecules that block the complete mRNA form traversing through the ribosomal complex.
C) They form double-stranded RNA molecules in pre-spliced primary RNA and prevent passage from the nucleus to the cytoplasm.
D) They form double-stranded RNA molecules in pre-spliced primary RNA and prevent the splicing out of introns.

Question 27

Five percent of the genome is conserved among all mammals, yet only ~1% directly encodes proteins. What is the likely role for the remaining 4%?

A) Pseudogene duplication among species
B) Regulation of expression for the 1% that encodes proteins
C) Redundant open-reading frames
D) Positioning of genes into transcriptional active zones

Question 28

Why is it thought that regulatory elements occur in clusters?

A) Redundancy to ensure stimulation of the gene
B) Allows gene expression to move in both directions on separate strands of the DNA
C) Allows hairpin formation to enhance protein binding
D) Allows the interaction of multiple transcription factors

Question 29

The large-scale project called ENCODE used RNA-seq to characterize all RNAs in 147 human cell types. The surprise result from analysis of the data revealed that even though there is only 1% of the genome that encodes for protein, as much as _______% of the genome is actually transcribed.

A) 30
B) 50
C) 70
D) 90

Question 30

In the upstream promoter of some human genes, a regulatory sequence of eight nucleotides, TGACGTCA, has been shown to regulate a number of cAMP responsive genes. Based on this knowledge, you conduct a genome search and identify 250 of these identical sequences that occur. Could you then conclude that these sequences coincide with genes that are cAMP responsive?

A) Yes, because each of those regulatory regions containing that sequence would only be found near genes.
B) Yes, because this sequence would be unlikely to occur randomly.
C) No, because this sequence, in the context of 3 billion base pairs, would occur fairly regularly and may or may not be associated with a gene.
D) No, because there must be other regulatory sequences present as well.

Question 31

What is the term used in cell biology to describe the transmission of information from the environment, such as the presence of a hormone, to targets within the cell?

A) Crosstalk
B) Networks
C) Hierarchical clustering
D) Signaling pathway

Question 32

Consider a hypothetical signaling pathway where the initiating signal is A, the terminal response is E, and there are three intermediate components, B, C, and D, such that the complete pathway is A-B-C-D-E. Experimentally, you determine that E acts to simulate A. This is an example of

A) negative feedback.
B) positive feedback.
C) feedforward relay.
D) stimulatory crosstalk.

Question 33

Consider two signaling pathways: A-B-C-D-E and 1-2-3-4-5-6-7. Which response would be representative of a feedforward relay?

A) B stimulates E
B) B stimulates 6
C) D stimulates A
D) 2 stimulates E

Question 34

Consider two signaling pathways: A-B-C-D-E and 1-2-3-4-5-6-7.Which response would be representative of stimulatory crosstalk?

A) B stimulates E
B) B stimulates 6
C) D stimulates A
D) 2 stimulates 7

Question 35

Which of the following would not necessarily be part of a cellular signaling network?

A) Crosstalk
B) Feedback loops
C) Synthetic genetic toggle switches
D) Feedforward relays

Question 36

What is best described as an engineering approach to understanding and manipulating biological systems?

A) Synthetic biology
B) Biomedical engineering
C) Systems biology
D) Theranostics

Question 37

In 2010, scientists developed a series of overlapping oligonucleotides that extended a full 1.08 million base pairs and used it to develop the first complete organism using a synthetic genome. The newly created cells had normal growth and morphology. What organism did they generate in these groundbreaking experiments?

A) Escherichia coli
B) Saccharomyces cerevisiae
C) Mycoplasma mycoides
D) Haemophilus influenza

Question 38

In 2010, scientists developed a series of overlapping oligonucleotides that extended a full 1.08 million base pairs and used it to develop the first complete organism using a synthetic genome. The newly created cells had normal growth and morphology. In addition to the synthetic genome, why did the investigators also include a gene that confers resistance to tetracycline?

A) By including an exogenous gene, they could confirm propagation of the genome by PCR.
B) The tetracycline resistance gene increases the genomic stability of genomes in prokaryotes.
C) The tetracycline resistance gene destabilizes the genome of the host DNA allowing the novel synthetic genome to survive.
D) The tetracycline resistance gene allows the selection of only the cells that are resistant to tetracycline and thus cells that survive selection carry the novel synthetic genome.

Question 39

The first complete sequence of a cellular genome was of the bacterium _______.

Question 40

In comparing the genomes of two yeasts, S. pombe and S. cerevisiae, researchers found that S. pombe contains more _______.

Question 41

There are three chain termination or stop codons: UAA, UAG, and _______.

Question 42

In comparing genomes between the plant Arabidopsis thaliana and humans, it was found that _______ had the largest number of protein-coding genes.

Question 43

A long DNA sequence with no stop codons is a(n) _______.

Question 44

The genome of the fruit fly Drosophila contains approximately _______ as many genes as the human genome.

Question 45

Remarkably, approximately _______% of the predicted human proteins are related to proteins in simpler sequenced eukaryotes, including yeast, Drosophila, and C. elegans.

Question 46

The human genome contains approximately _______ base pairs.

Question 47

Remarkably, only _______% of the human genome corresponds to protein-coding sequences.

Question 48

From 2001 to 2014, the cost of sequencing an individual's genome has dropped from several million dollars to several _______ dollars.

Question 49

A more common name for the high-throughput DNA sequencing method of massively parallel sequencing is _______.

Question 50

The source of cDNA used in microarray analyses is _______.

Question 51

A new method that has the ability to assess every RNA expressed in a cell is _______.

Question 52

Mass spectrometry measures the _______ ratio of small peptides that have been proteolytically cleaved.

Question 53

A reasonable method to determine if two proteins differed by only a single amino acid would be to use _______.

Question 54

The use of antibodies to determine protein-protein interactions is known as _______.

Question 55

When an element in one signaling pathway either stimulates or inhibits an element of a second pathway it is referred to as _______.

Question 56

An open-reading frame is a long stretch of nucleotide sequence that contains no chain-terminating (stop) codons.

Question 57

A common characteristic of most bacterial genomes is that ~90% of the genome encodes for proteins.

Question 58

The human genome has more genes than plant genomes have.

Question 59

An open-reading frame of 1,200 base pairs long would contain 300 codons.

Question 60

Surprisingly, the size of genomes among a wide variety of organisms does not correlate with complexity of the organisms.

Question 61

There is only a 1% variance between the genomes of human, Neandertals, and chimpanzees.

Question 62

The 20,000-25,000 human genes may encode more than 100,000 distinct mRNAs and proteins.

Question 63

About half of the human genes identified by sequencing can be assigned a function by homology to previously characterized genes, and the other half represent new genes of unknown function.

Question 64

More than 50% of the human genome is composed of various types of repetitive and duplicated DNA sequences.

Question 65

Hybridization of fluorescent labeled cDNAs to microarrays of thousands of gene sequences allows gene expression to be assayed.

Question 66

Mass spectrometric identification of individual proteins in a complex mixture would be impossible in the absence of large-scale protein sequence databases.

Question 67

Hybridization of fluorescent labeled cDNAs to microarrays of thousands of gene sequences allows gene expression to be assayed.

Question 68

The computational analysis comparing the expression of all mRNAs between two different cells is an example of synthetic biology.

Question 69

If an organism has a 2 million base genome and 90% of it encodes proteins, and the average gene is 300 codons, how many genes does it have?

Question 70

Why would approximately 40% of the predicted human proteins be related to proteins in simpler organisms?

Question 71

Explain the likely effect that the sequencing of the human genome will have on medical science.

Question 72

What is the most significant difference between microarray analyses and RNA-seq analyses?

Question 73

Even though there are only about 20,000 different protein-coding genes in humans, it is estimated that these give rise to more than 100,000 different proteins. What are two mechanisms that can account for this dramatic difference?

Question 74

When carrying out immunoprecipitation experiments to investigate protein-protein interactions, why is it important to isolate the proteins under gentle conditions?

Question 75

You have two proteins you suspect of interacting with each other, but have an antibody to only one of them. Describe an experiment that might allow you to determine if the two proteins do indeed interact with each other.

Question 76

You have identified a unique 8-base sequence in the promoter of a gene that controls growth. Describe an experiment that may address whether this sequence is capable of directing transcription of other genes.

Question 77

You have a cell signaling cascade in which a cell signal initially targets and activates protein 1 which in turn activates protein 2 which then activates protein 3 and finally activates protein 4. You are given a cell line that never expresses protein 2, yet in every experiment in which you give the initiating signal, you get activation of protein 4. How could you explain these results?

Question 78

In the pathway through which epinephrine signals the breakdown of glycogen to glucose in muscle cells, there are at least six different proteins involved before glycogen phosphorylase acts to cleave a glucose off of glycogen. Additional administration of epinephrine will increase the pathway. In a cell line in which phosphorylase kinase is mutated, what will happen if epinephrine is used to treat the cells?

Question 79

In which of the following organisms is the highest percentage of its genome used to encode protein?

A) Haemophilus influenzae
B) Saccharomyces cerevisiae
C) Drosophila melanogaster
D) Caenorhabditis elegans

Question 80

The main difference between the genomes of the bacteria Haemophilus influenzae and E. coli is that

A) the genome of H. influenzae is a circular molecule and that of E. coli is linear.
B) the H. influenzae genome encodes a larger number of genes.
C) the genome of E. coli is much larger than the H. influenzae genome.
D) a higher percentage of the H. influenzae genome contains genes encoding proteins.