Deck 20: Variation and Selection in Populations

Question 1

What accounts for the differences between the number of protein coding genes in the genome and the number of different proteins expressed?

A) Not all genes are translated,so the number of expressed proteins is lower than the number of protein coding genes.
B) Not all genes are transcribed,so the number of expressed proteins is lower than the number of protein coding genes.
C) Alternative splicing is very common and increases the diversity of expressed proteins so the number of expressed proteins is higher than the number of protein coding genes.
D) Alternative splicing is very common and decreases the diversity of expressed proteins so the number of expressed proteins is lower than the number of protein coding genes.
E) Protein turnover is rapid and decreases the diversity of expressed proteins so the number of expressed proteins is lower than the number of protein coding genes.

Answer 1

C

Question 2

Approximately how many protein coding genes are encoded in the human genome?

A) 500
B) 5,000
C) 25,000
D) 50,000
E) 500,000

Answer 2

C

Question 3

What is the relevance of a collision cell in mass spectrometry?

A) It increases the precision of the analysis.
B) It is used to break apart large protein complexes prior to mass spectrometry.
C) It is the site of undesirable reactions that can reduce accuracy.
D) It is the primary site of ionization.
E) It rejoins peptide fragments into their original configuration.

Answer 3

A

Question 4

What is the role of Gal4 in yeast two-hybrid experiments?

A) It is a selectable marker.
B) It is a reporter gene.
C) It metabolizes galactose,which is used as an energy source.
D) It is split into two domains that together promote transcription of a target gene.
E) Its ability to interact with other proteins is tested.

Question 5

Why is trypsin normally used in protein mass spectrometry?

A) It is a positive control found in almost all animal cells.
B) It is used as a standard to define the upper and lower boundaries of mass sensitivity.
C) It cuts the protein into smaller peptides,which can be more accurately analyzed than longer fragments.
D) It is a useful general capture molecule for affinity purification.
E) It is an effective antibiotic to suppress contamination from microbes.

Question 6

What is the role of HIS3 in yeast two-hybrid experiments?

A) It is a reporter gene.
B) It is required for growth in media that contain histidine.
C) It activates transcription.
D) It binds DNA.
E) It acts as a bait for other proteins.

Question 7

What is an advantage of affinity purification-based methods over yeast two-hybrid (Y2H)methods,when screening for interacting proteins?

A) Affinity methods isolate molecules from their native context and do not require recombinant protein production.
B) Affinity methods use fusion proteins rather than antibodies,which are more expensive to produce.
C) Affinity methods,but not Y2H,can be used to find proteins that interact with transcription factors.
D) Proteins used in affinity methods do not need to be properly folded.
E) Affinity methods can be applied to proteins from a wider range of eukaryotes than can be used in Y2H.

Question 8

Approximately how many unique proteins are produced by a human cell?

A) 500
B) 5,000
C) 25,000
D) 50,000
E) 500,000

Question 9

In a typical yeast two-hybrid experiment,which of the following is true of a cell that contains an interaction between bait and prey?

A) No growth on media that contains His,and no growth on media that contains Gal
B) No growth on media that lacks His,and no growth on media that lacks Gal
C) Growth on media that lacks His,and no growth on media that contains His
D) Growth on media that contains His,and no growth on media that lacks His
E) Growth on media that lacks His,and growth on media that contains His

Question 10

Which of the following would be required for affinity purification but not for yeast two-hybrid (Y2H)?

A) A fusion protein including the protein of interest.
B) A fluorescent reporter gene.
C) A selectable marker.
D) An antibody.
E) An antibiotic.

Question 11

Which of the following is not an example of posttranslational modification?

A) phosphorylation
B) polyadenylation
C) glycosylation
D) ubiquitination
E) acetylation

Question 12

Which of the following is not an example of a molecular machine that is comprised of many proteins?

A) DNA repair complex
B) proteasome
C) nuclear pore complex
D) proteome
E) spliceosome

Question 13

You are conducting a yeast two-hybrid experiment to discover proteins that interact with a particular protein of interest (protein X).Which of the following would be a useful step in this process?

A) Fuse X to the HIS3 promoter.
B) Fuse X to a DNA binding domain.
C) Fuse X to the complete HIS3 gene.
D) Purify X from recombinant yeast.
E) Fuse X to the complete Gal4 gene.

Question 14

In a typical yeast two-hybrid experiment,which of the following occurs when bait and prey interact?

A) HIS3 binds to the promoter of a reporter gene.
B) Gal4 activator and binding domains form a complex.
C) HIS3 and Gal4 form a complex.
D) HIS3 transcription is blocked.
E) Expression of Gal4 is activated.

Question 15

Which of the following properties of a gene or proteins is not affected by alternative splicing?

A) CpG methylation
B) protein structure
C) subcellular localization
D) enzymatic activity
E) protein stability

Question 16

Which of the following is not a component of a mass spectrometry system used to identify proteins?

A) ionization
B) mass analyzer
C) detector
D) computer
E) gas chromatograph

Question 17

Which of the following is not directly involved in ICAT (isotope coded affinity tag)labelling and purification?

A) cysteine
B) deuterium
C) avidin
D) biotin
E) antibodies

Question 18

Which of the following can be used in mass spectrometry for quantifying differences in protein abundance in a comparison of two samples?

A) relative fluorescent intensity
B) relative gamma emissions
C) relative beta emissions
D) relative height of peaks in the mass spectrum
E) relative increases in molecular mass

Question 19

Which of the following limits the utility of yeast two-hybrid screens in identifying protein interactions?

A) Yeast two-hybrid screens can only be applied to bait proteins that are less than 20kDa.
B) Only two proteins can be tested for their ability to interact,per day.
C) Yeast two-hybrid screens can only find proteins that interact with transcription factors.
D) Fusion proteins must be affinity purified.
E) Bait proteins may not fold properly when fused to other proteins.

Question 20

Which of these moves most quickly through a mass spectrometer?

A) a large,uncharged molecule
B) a small,uncharged molecule
C) a large,charged molecule
D) a small,charged molecule
E) an uncharged protein complex

Question 21

Which of the following tasks is most often performed by robots during yeast two-hybrid screens?

A) prey cloning
B) bait cloning
C) replica pinning
D) yeast electroporation
E) library construction

Question 22

Each cell can be considered to have its own proteome.

Question 23

The intracellular environment of yeast is sufficiently similar to animal cells that any protein interaction that occurs in a yeast cell will also occur in an animal cell.

Question 24

The nuclear pore complex is formed by a single large protein that undergoes extensive alternative splicing prior to translation.

Question 25

Protein arrays are often made using

A) 96 well plates
B) agar medium
C) microscope slides
D) petri dishes
E) 1536 well plates

Question 26

Yeast two-hybrid experiments can only be used to find proteins that interact with transcription factors.

Question 27

Human tears contain approximately 500 different proteins.

Question 28

Affinity purification is often involved in the production of protein microarrays.

Question 29

The structural diversity of proteins in a cell is greatly increased by alternative splicing and posttranslational modifications.

Question 30

Ionization is required in mass spectrometry to allow formation of stable ionic bonds between peptides.

Question 31

The centrality-lethality rule states that

A) lethality of cancer cells is central to their evolutionary persistence.
B) yeast colonies nearest to the center of a petri dish have the lowest viability.
C) the amino acids at the center of a folded protein can cause lethality if unfolding occurs.
D) no two proteins at the center of a protein interaction network can exist in the same cell.
E) hub proteins are likely to be essential for viability.

Question 32

An application of protein arrays is

A) screening thousands of proteins to identify substrates of a particular kinase
B) identifying interacting proteins by parallel sequencing
C) detecting protein interactions through two-hybrid reporter gene activation
D) detecting differential protein expression
E) structural determination through x-ray analysis

Question 33

The Gal4 DNA binding domain will bind to any eukaryotic promoter.

Question 34

Hub proteins are proteins that interact with a large number of other proteins.

Question 35

The nuclear pore complex transports mRNA but not proteins.

Question 36

In mass spectrometry,m/z represents

A) mass/charge.
B) mass/peak height.
C) mass/abundance.
D) mass/size.
E) mass/interactions.

Question 37

In ICAT (isotope coded affinity tag)methods,proteins are labelled with radioactive isotopes.

Question 38

In the yeast two-hybrid system,the Gal4 DNA binding domain is unable to activate transcription when it is bound to a promoter.

Question 39

Yeast two-hybrid screens may produce false-positives.

Question 40

A mass spectrometer can be used to identify a protein only if peptides or proteins with the same sequence are already in a database.

Question 41

In ICAT labelling,heavy and light linkers differ by 8kDa.

Question 42

Design an experiment to identify proteins that are more abundant in malignant tumours,but not in normal tissues.

Question 43

How would the results be impacted if a collision cell was not functioning?

Question 44

In high throughput yeast two-hybrid assays,bait and prey strains are of the same mating type.

Question 45

Given a set of genes that you know to be more abundant in tumour than in normal tissues,design an experiment to identify networks of protein-protein interactions that exist in malignant tumours,but not in normal tissues.How would the network analysis affect your choice of proteins to target with new chemotherapy drugs?

Question 46

A mass analyzer separates ions based on their mass and charge.

Question 47

Mass spectrometers operate under high vacuum.

Question 48

Compare all of the methods of identifying protein interactions in terms of their relative advantages and disadvantages.