Deck 9: Genome Annotation

Question 1

Initiation of transcription by RNA polymerase involves the binding of which of the following subunits to the core enzyme?

A) delta
B) sigma
C) gamma
D) alpha
E) zeta

Answer 1

B

Question 2

Proteins that undergo reversible changes in conformation when bound to another molecule are called ________________.

A) reverse proteins
B) allosteric proteins
C) regulatory proteins
D) activator proteins
E) allostatic proteins

Answer 2

B

Question 3

How are complex processes such as sporulation,synthesis of flagella,and nitrogen fixation that require the transcription of multiple sets of genes regulated in bacteria?

A) Multiple operons are simultaneously induced.
B) A hormone activates transcription of each gene simultaneously.
C) The end product of one operon is used as an inducer of the next operon in sequence.
D) There are single operons consisting of many genes for each of these processes.
E) Cascades of sigma factors synthesized in a temporal order,allow the turning on of successive sets of genes.

Answer 3

E

Question 4

Which of the following choices is NOT a correct description of a reporter gene?

A) a protein-encoding gene whose expression is easily quantifiable.
B) always co-translated as a fusion with another protein.
C) often fused to another gene's regulatory region to determine control.
D) may encode an enzyme.
E) a protein used to study gene expression.

Question 5

The critical step in the regulation of most bacterial genes occurs _____________.

A) during transcription
B) at the release of mRNA
C) during translation
D) posttranslationally
E) during replication

Question 6

How do positive regulators stimulate initiation of transcription by RNA polymerase?

A) by allowing passage of the polymerase through the operator
B) by binding to the polymerase and increasing its ability to initiate transcription
C) by causing the helix to unwind in the operator allowing easier initiation
D) by making the transcription start site more exposed to the polymerase
E) by accelerating alpha helix formation

Question 7

Anabolic pathways involved in the synthesis of essential molecules are usually regulated by

A) end product of the pathway.
B) substrate of the pathway.
C) other metabolites that are limiting.
D) upstream intermediates of the pathway.
E) ATP.

Question 8

How is glucose involved in the catabolite repression of the lactose operon?

A) It has nothing to do with regulation of the lactose operon.
B) It results in decreased cAMP levels,which in turn leads to decreased CRP binding;thus the lac operon is repressed even if lactose is present along with the glucose.
C) It is also a substrate for β-galactosidase and thus competes with lactose for this enzyme.
D) Its presence in the cell increases the amount of lac repressor in the cell.
E) It provides energy to the operon.

Question 9

Catabolic pathways that break down complex substances into more usable units are usually regulated by the

A) end products of the pathway.
B) substrate of an enzyme in the pathway.
C) other metabolites that are limiting.
D) upstream intermediates of the pathway.
E) ATP.

Question 10

A common amino acid motif found in many of the polypeptides that function as repressors is

A) Leucine zipper motif.
B) Zinc finger motif.
C) Helix-turn-helix motif.
D) Helix-loop-helix motif.
E) Alpha-beta-alpha motif.

Question 11

As a general principle of gene regulation through operons,regulatory genes encode

A) trans-acting proteins that interact with cis-acting DNA elements.
B) cis-acting proteins that interact with cis-acting DNA elements.
C) cis-acting proteins that interact with trans-acting DNA elements.
D) trans-acting proteins that interact with trans-acting DNA elements.
E) trans-acting proteins that act autonomously.

Question 12

You have isolated 15 mutant bacteria unable to use maltose.All 15 mutations map in the same region.You have tested the mutant for two enzymes in maltose metabolism and find at least one of the mutants lacks one of the enzymes,other mutants lack the other.What does this suggest?

A) There are lots of enzymes in maltose metabolism.
B) All the genes for maltose metabolism are in a cluster and could be one operon.
C) There are genes scattered all over,we've simply found one set of mutants.
D) Maltose transport is very complex,these are transport mutants.
E) None of the choices are correct.

Question 13

What term describes a second level of regulation of the trp operon that occurs in TrpR^- mutants suggesting that it is repressor independent?

A) modulation
B) derepression
C) attenuation
D) amplification
E) desensitization

Question 14

How does tryptophan,the end product of the trp operon,function in the regulation of the operon?

A) It binds to the repressor preventing it from binding to DNA thus allowing transcription of the operon.
B) It binds to the repressor and only then can the repressor bind to DNA allowing transcription of the operon.
C) It binds directly to RNA and inhibits translation of the operon.
D) It binds to the repressor and only then can this complex bind to DNA preventing transcription of the operon.
E) It binds directly to DNA and inhibits transcription of the operon.

Question 15

A common DNA structural feature involved in gene regulatory systems is

A) supercoiling of DNA.
B) looping of the DNA.
C) unwinding of the double helix.
D) coiling into Z-DNA.
E) plasmid formation.

Question 16

A single DNA unit that enables the simultaneous regulation of more than one gene in response to environmental changes is called

A) promoter.
B) operator.
C) regulator.
D) inducer.
E) operon.

Question 17

What would be the phenotype of a mutation that altered lac repressor function?

A) constitutive
B) inducible
C) permanently repressed
D) auxotrophic
E) allotrophic

Question 18

The transition from transcriptional initiation to elongation involves

A) binding of sigma factor.
B) release of sigma factor.
C) release of RNA polymerase from DNA.
D) binding of RNA polymerase to DNA.
E) binding of rho factor.

Question 19

How do negative regulators such as the lac repressor prevent RNA polymerase from initiating transcription?

A) by blocking passage of the polymerase through the operator
B) by forming a loop in the operator that restricts the passage of the polymerase
C) by physically blocking the DNA binding site of RNA polymerase
D) by binding to the polymerase,thus preventing its binding
E) by degrading metabolic activators

Question 20

The scientists who proposed the operon theory are

A) Monod and Jacob.
B) Watson and Crick.
C) Hardy and Weinberg.
D) Darwin and Mendel.
E) Hershey and Chase.

Question 21

Negative regulation of gene expression usually takes place through enhancement of RNA polymerase activity.

Question 22

Medium #1 contains lactose.Medium #2 contains no lactose.Which of the following strains will produce a different level of β-galactosidase activity on medium #1 as on medium #2?

A) lacI^s,lacO^c
B) lacI^s,lacZ⁺
C) lacI⁺,lacZ^-
D) lacI^s,lacZ^-
E) lacI⁺,lacZ⁺

Question 23

Which of the following is not a property of cis-elements?

A) bind to proteins
B) comprised of nucleic acids
C) often exhibit multiple binding sites
D) often have rotational symmetry
E) not found in eukaryotes

Question 24

The concept that proteins bind to DNA and regulate transcription holds true for both positive as well as negative regulation of gene expression.

Question 25

Positive regulators actually physically bind to RNA polymerase and enhance the enzyme's ability to initiate transcription.

Question 26

Which of the following strains will be useful in demonstrating trans- regulation? In the genotypes listed below,the genes on the chromosome are on the left of the slash (/)symbol and the genes F' episome are on the right.

A) lacI⁺ lacO⁺ lacZ⁺/lacI⁺ lacO⁺ lacZ⁺
B) lacI⁺ lacO^c lacZ⁺/lacI⁺ lacO⁺ lacZ^-
C) lacI⁺ lacO⁺ lacZ⁺/lacI⁺ lacO^c lacZ^-
D) lacI⁺ lacO⁺ lacZ⁺/lacI^s lacO⁺ lacZ^-
E) lacI^s lacO^c lacZ⁺/lacI⁺ lacO⁺ lacZ^-

Question 27

Posttranscriptional controls of gene expression in bacteria often serve to fine-tune the amount of protein needed.

Question 28

In bacteria,alterations to DNA sites such as promoters and operators can act either in cis or in trans.

Question 29

Attenuation of gene expression is unique to prokaryotes,because it requires translation of a leader sequence at the same time transcription is taking place.

Question 30

Which of the following combinations will produce the highest expression of β-galactosidase?

A) lacI ⁺on medium with lactose
B) lacI^s on medium with lactose
C) lacI⁺ on medium with no lactose
D) lacI^s on medium with no lactose
E) lacZ^- on medium with no lactose

Question 31

In the regulation of the trp operon,tryptophan acts as a(n)

A) repressor.
B) attenuator.
C) activator.
D) corepressor.
E) operator.

Question 32

Because there is no nuclear membrane in prokaryotes,transcription and translation from a single gene can be taking place at the same.

Question 33

Which of the following does not act in cis?

A) lacO
B) attenuation
C) lacO^c
D) trpR
E) araI

Question 34

Which of the following statements about araC^- and lacI^- mutants are true,with reference their respective operons? Assume both of these are loss of function mutations.

A) araC^- mutants do not allow transcription,but lacI^- mutants do
B) araC^- mutants do allow transcription,but lacI^- mutants do not
C) both araC^- mutants and lacI^- mutants allow transcription
D) neither araC^- mutants nor lacI^- mutants allow transcription
E) araC^- mutants do allow transcription,but lacI^- mutants do not,except if lacI^s is also present

Question 35

DNase is most useful in characterization of which of the following?

A) cis- regulatory sites
B) trans- regulators
C) dimeric proteins
D) operons
E) reporter genes

Question 36

Which of the following combinations will produce the highest expression of ?-galactosidase? Assume crp^- is a complete deletion of CRP (cAMP receptor protein).

A) crp^- on medium with glucose but no lactose
B) crp^- on medium with lactose but no glucose
C) crp^- on medium with both glucose and lactose
D) crp⁺ on medium with lactose but no glucose
E) crp⁺ on medium with both glucose and lactose

Question 37

A chaperone protein is used to aid in the transport of other proteins across cellular membranes.

Question 38

Which of the following combinations will produce the highest expression of ?-galactosidase? Assume crp^- is a complete deletion of CRP (cAMP receptor protein).

A) lacO^c,crp^- on medium with glucose but no lactose
B) lacO^c,crp^- on medium with lactose but no glucose
C) lacO^c,crp^- on medium with both glucose and lactose
D) lacO^c,crp⁺ on medium with both glucose and lactose
E) lacO^c,crp⁺,on medium with no lactose and no glucose

Question 39

Which of the following strains will be useful in demonstrating cis- regulation? In the genotypes listed below,the genes on the chromosome are on the left of the slash (/)symbol and the genes F' episome are on the right.

A) lacI⁺ lacO⁺ lacZ⁺/lacI⁺ lacO⁺ lacZ⁺
B) lacI⁺ lacO^c lacZ⁺/lacI⁺ lacO⁺ lacZ^-
C) lacI⁺ lacO⁺ lacZ⁺/lacI⁺ lacO^c lacZ^-
D) lacI⁺ lacO⁺ lacZ⁺/lacI^s lacO⁺ lacZ^-
E) lacI^s lacO⁺ lacZ⁺/lacI⁺ lacO⁺ lacZ^-

Question 40

Which of the following combinations will produce the highest expression of ?-galactosidase? Assume crp^- is a complete deletion of CRP (cAMP receptor protein).

A) lacI⁺,crp^- on medium with glucose but no lactose
B) lacI^s,crp^- on medium with lactose but no glucose
C) lacI⁺,crp^- on medium with both glucose and lactose
D) lacO^c,crp⁺ on medium with glucose but no lactose
E) lacO^c,crp⁺,on medium with both glucose and lactose

Question 41

Describe the unique feature of the base sequence of the lac operator to which the lac repressor binds?

Question 42

An underlying principle of prokaryotic gene regulation is that it occurs through the binding of regulatory proteins to specific DNA sequences.

Question 43

In prokaryotes,the gene regulation primarily occurs by either blocking or enhancing transcription.

Question 44

In the operon model of gene regulation,transcription is shut off by the binding of the repressor to the promoter.

Question 45

In the trp operon,the protein repressor alone cannot bind to the operator to be a negative regulator.

Question 46

Why is the lactose operon not fully induced in the presence of both lactose and glucose?

Question 47

In the example of the lac operon,and most operons,what is the significance of a polycistronic message?

Question 48

The presence of a diffusible gene product (e.g.protein)is a requirement for regulatory genes to act in trans.

Question 49

Describe the molecular subunit structure of the lac repressor and explain what enables it to bind to the operator.

Question 50

Both inducers and corepressors lead to allosteric alterations in the repressor molecule.

Question 51

Describe the conditions for maximum induction of the lactose operon.

Question 52

Global regulatory control of the heat-shock response in bacteria is achieved by the binding of σ⁷⁰ to RNA polymerase.

Question 53

Describe the two binding domains on the lac repressor protein.

Question 54

Attenuation of the trp operon requires the presence of tryptophanyl-tRNA^Trp.

Question 55

There is only one site on the operator to which the lac repressor binds.

Question 56

The occurrence of constitutive mutations of all three of the lactose utilizing enzymes indicates that their synthesis is regulated together,probably by another gene.

Question 57

The mechanisms of gene regulation discovered in E.coli are not found in most other prokaryotes.

Question 58

Global regulatory control of gene expression in bacteria can be achieved by the binding of alternate sigma (σ)factors to RNA polymerase.

Question 59

In a repressible operon,the repressor alone can bind to the operator and shut down transcription.

Question 60

A distinguishing feature of control of gene expression in prokaryotes is that transcription and translation occur completely independently of each other.

Question 61

In the trp operon,attenuation occurs through the recognition of two trp codons in the leader sequence.What would happen if these two codons were mutated to stop codons?

Question 62

More than 20 different DNA-binding proteins in bacteria are similar to the LacI repressor,creating the LacI repressor family of proteins.Why do they all not bind at the lac operator and repress the lac operon?

Question 63

Explain how the presence or absence of the amino acid tryptophan attenuates the transcription of the genes in the trp operon.

Question 64

Compare and contrast AraC with trans-factors that regulate the lac operon.

Question 65

Explain what is meant by trans-acting and cis-acting elements.

Question 66

Explain how the CRP protein functions as a positive regulator of the lac operon.

Question 67

What are the three enzymes in the lactose operon and what are their enzymatic functions? E.coli cell;and transacetylase (lacA)adds an acetyl group to lactose and other β galactosides.

Question 68

Compare and contrast the trans-factors that regulate the lac and trp operons.

Question 69

How does the operator function in the regulation of an operon?

Question 70

Explain how three enzymes appear simultaneously when lactose is introduced into a bacterial culture medium as the sole carbon source.

Question 71

What is the role of the σ subunit of RNA polymerase in transcription?

Question 72

Distinguish between positive and negative regulation of transcription.