Deck 23: Gene Regulation

Question 1

The phrase trans-acting factors is short for __________ factor protein.

A) translation
B) transcription
C) transunion
D) transform

Answer 1

transcription

Question 2

$\alpha$ -Helices are usually found in DNA binding proteins because they

A) are the only secondary feature found in proteins.
B) are the only stable secondary feature in proteins.
C) have the appropriate diameter to fit into the major groove of DNA.
D) have the appropriate diameter to fit into the minor groove of DNA.

Answer 2

have the appropriate diameter to fit into the major groove of DNA.

Question 3

What kind of control mechanism is ligand-induced binding of an activator protein?

A) positive
B) negative
C) neutral
D) covalent

Answer 3

positive

Question 4

Which of the following best describes how trans- and cis-acting factors operate?

A) Cis-acting factors can bind to specific DNA sequences whereas trans-acting sites are DNA sequences.
B) Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites are DNA sequences.
C) Trans- and cis-acting factors can both bind to specific DNA sequences.
D) Trans- and cis-acting factors can both only bind to DNA elements to which they are physically linked.

Question 5

In a leucine zipper, the leucine resides are found every seventh amino residue. This forces the supersecondary structure to be a(n)

A) " $\alpha$ -helix."
B) " $\beta$ -sheet."
C) "coiled-coil."
D) "hairpin turn."

Question 6

A protein that has a weak affinity for a DNA site and is at concentrations of protein will bind to DNA _.

A) low; strongly
B) high; strongly
C) low; indiscriminately
D) high; indiscriminately

Question 7

What by-product can be measured for in a cell if lacZ is being used as a reporter gene?

A) "luciferase"
B) "chloramphenicol acetyltransferase"
C) " $\beta$ -galactosidase"
D) "GFP"

Question 8

IPTG causes the lac promoter to

A) bind irreversibly to the DNA.
B) dissociate from the DNA.
C) perform ligand-regulated repression.
D) perform ligand-activated deregulation.

Question 9

Which of the following is NOT a common mechanism for modifying transcription factor activity?

A) allosteric activation
B) covalent modification
C) ionic modification
D) positive modulation

Question 10

The figure below shows autoregulation and will .

A) positive; reach a steady state
B) positive; be zero in the absence of an activator
C) negative; reach a steady state
D) negative; be zero in the absence of an activator

Question 11

The best description of how allosteric regulation works is that a ligand the transcriptional regulatory protein, which __________ the protein's affinity for DNA.

A) covalently modifies; increases
B) covalently modifies; decreases
C) binds to; causes conformational changes that affect
D) binds to; causes conformational changes that can only decrease

Question 12

The control point for most gene regulation occurs at the initiation of

A) transcription.
B) RNA processing.
C) protein synthesis.
D) protein modifications.

Question 13

In negative autoregulation,

A) proteins activate their own expression.
B) proteins repress their own expression.
C) a regulatory protein controls DNA expression.
D) a regulatory protein turns off DNA expression.

Question 14

In cooperative DNA binding, the binding of

A) both proteins must occur at the same time.
B) one protein molecule is more favored when another one is bound to a nearby site on the DNA.
C) one protein molecule is less favored when another one is bound to a nearby site on the DNA.
D) one protein molecule is only possible if two other molecules are bound to a nearby site on the DNA.

Question 15

When IPTG is added to a cell, what is the predicted outcome?

A) Protein synthesis stops.
B) Protein overproduction occurs.
C) The DNA sequence coding for a given protein is altered.
D) An epigenetic state occurs.

Question 16

When running an assay for luciferase, what reporter gene has been inserted into the plasmid?

A) lacZ
B) luc
C) cat
D) gfp

Question 17

One of the most common binding interactions between proteins and DNA are __________ bonds.

A) ionic
B) covalent
C) hydrogen
D) polar

Question 18

Which of the following best describes when a pattern of gene expression is altered without change in the DNA sequence?

A) epigenetic states
B) negative autoregulation
C) positive autoregulation
D) meiosis

Question 19

A reporter gene can be defined as a gene that

A) has a product that is easy to detect.
B) prevents protein synthesis.
C) overproduces proteins.
D) causes an epigenetic sate.

Question 20

A helix-turn-helix motif can best be described as a(n) followed by a(n) .

A) " $\alpha$ -helix; $\beta$ -helix"
B) " $\alpha$ -helix; $\alpha$ -helix"
C) " $\beta$ -helix; $\beta$ -helix"
D) " $\beta$ -helix; $\alpha$ -helix"

Question 21

When there is no lactose in a cell, production of lac operon

A) increases.
B) decreases.
C) turns off completely.
D) production of lac operon does not depend on lactose concentration.

Question 22

The role of the CI protein in the lysogenic pathway is that the

A) lysogenic pathway is favored when CI binds.
B) lytic pathway is favored when CI binds.
C) CI protein activates the P_R promoter.
D) CI protein inhibits the P_RM promoter.

Question 23

Operons can be defined as units of DNA containing gene(s) under control of __________ promotor(s).

A) one; one
B) multiple; one
C) multiple; multiple
D) one; multiple

Question 24

The function of RecA* is to

A) inhibit expression of its own gene.
B) repress SOS genes.
C) stimulate LexA autocleavage.
D) allow LexA to accumulate.

Question 25

A result of the DNA bend induced by the lac repressor binding is that the groove of the DNA is widened to allow binding of the lac repressor _.

A) minor; $\alpha$ -helix
B) major; $\alpha$ -helix
C) minor; $\beta$ -helix
D) major; $\beta$ -helix

Question 26

What is the function of the SOS regulatory system in the cell?

A) DNA repair
B) DNA translation
C) lactose degradation
D) glucose inhibition

Question 27

The function of CRP in lac operon expression is to the promoter by causing RNA polymerase to _.

A) stimulate; dissociate
B) stimulate; bind tighter
C) inhibit; dissociate
D) inhibit; bind tighter

Question 28

If P_RM is autoactivated and P_R is inhibited, then is/are bound.

A) CI
B) Cro
C) both CI and Cro
D) neither CI and Cro

Question 29

When bacteriophage $\lambda$ integrates into the E. coli genome, what is that lifestyle called?

A) lysis
B) lysogeny
C) lyophilize
D) lysine

Question 30

When Cro is bound to O_R3, the

A) lysogenic pathway is favored.
B) lytic pathway is favored.
C) Cro protein inhibits the P_R promoter.
D) CI protein activates the P_RM promoter.

Question 31

Allolactose acts as a(n)

A) repressor by causing the lac repressor to bind.
B) inducer by binding to the lac repressor and causing it to dissociate.
C) repressor by increasing the binding affinity of the lac repressor.
D) inducer by binding to CRP.

Question 32

An unusual structural feature of the lac repressor is that it is a

A) homodimer.
B) homotetramer.
C) heterodimer.
D) heterotetramer.

Question 33

A regulon can best be described as units of DNA containing gene(s) under control of promotor(s).

A) one; one
B) multiple; one
C) multiple; multiple
D) one; multiple

Question 34

When LexA is autocleaved by RecA*, the SOS genes

A) are repressed.
B) are activated.
C) are unaffected.
D) produce operons.

Question 35

When DNA is damaged, what protein is activated?

A) LexA repressor
B) RecA
C) SOS operon
D) lac operon

Question 36

When bacteriophage $\lambda$ generates progeny viruses that kill the bacterial host E. coli genome, what is that lifestyle called?

A) lytic
B) lysogeny
C) lyophilize
D) lysine

Question 37

The function of the lac operon is to provide

A) the enzymes needed to utilize the disaccharide lactose.
B) the enzymes needed to produce lactose.
C) lactose.
D) glucose and galactose to make lactose.

Question 38

High concentration of CI protein in the cell __________ expression of the _.

A) prevents; lytic promoter
B) allows; lytic promoter
C) prevents; trp operon
D) allows; attenuator sequence

Question 39

Once RecA is no longer activated, what happens to the SOS regulon?

A) LexA builds up and represses the SOS regulon.
B) LexA autocleaves and SOS regulon is activated.
C) LexA binds to the RecA.
D) LexA binds to the SOS regulon.

Question 40

What will happen to the lac operon when there are elevated levels of glucose in a cell?

A) CRP binds strongly.
B) Transcription occurs at a very high rate of expression.
C) Transcription occurs at a very low rate of expression.
D) The lac repressor is bound.

Question 41

By wrapping DNA around the histone octamer, how much smaller can DNA be?

A) tenfold
B) eightfold
C) sevenfold
D) twofold

Question 42

Histone acetylation leads to transcriptional activation by

A) increasing the interaction between the histone tail and DNA.
B) decreasing the interaction between the histone tail and DNA.
C) strengthening the interactions between nucleosomes.
D) removing binding sites for additional transcriptional factors.

Question 43

A nucleosome can best be described as a protein core containing molecules each of __________ histones and a segment of DNA.

A) four; four
B) two; four
C) two; two
D) four; two

Question 44

Together, the eight histone molecules are called the histone

A) octane.
B) octamer.
C) dimer.
D) tetramer.

Question 45

Lysine methylation has what effect on the histone?

A) leaves a positive charge on the amino acid
B) leaves a neutral charge on the amino acid
C) binds more strongly to the histone
D) removes chromatin docking sites

Question 46

The portion of the histone that can be acetylated is the

A) head.
B) body.
C) tail.
D) arm.

Question 47

When trp operon is attenuated, what does that mean for the trp operon?

A) inhibition of transcriptional initiation by RNA polymerase
B) disruption of transcriptional elongation by RNA polymerase
C) initiation by RNA polymerase
D) enhancement of transcriptional elongation by RNA polymerase

Question 48

Bromodomain-containing complexes bind to __________ lysines in histones.

A) methylated
B) acetylated
C) brominated
D) chlorinated

Question 49

Why are long tracts of A residues not found in regions of stable nucleosome positioning?

A) They are too flexible.
B) They are too stiff.
C) DNA cannot have long tracts of A residues.
D) DNA cannot have A residues.

Question 50

When histones are acetylated, the nucleosome-histone interaction

A) is weakened.
B) is strengthened.
C) dissociates the nucleosome from the histone.
D) covalently binds the nucleosome to the histone.

Question 51

When the lysine side chain in a histone is acetylated, the amino group is now

A) positively charged.
B) neutral.
C) negatively charged.
D) removed.

Question 52

What is a result of histone acetylation?

A) repression of transcription
B) increased transcriptional activity
C) no effect
D) remodeling of histone

Question 53

Which amino acid residues on histones are acetylated?

A) histidine
B) lysine
C) arginine
D) serine

Question 54

Transcriptional elongation is favored by the trp operon when tryptophan levels are

A) high.
B) low.
C) constant.
D) The trp operon is not affected by tryptophan levels.

Question 55

When there is a large presence of tryptophan, what effect that does that have on the Trp repressor?

A) Trp repressor is bound.
B) Trp repressor is not bound.
C) There is initiation of RNA polymerase.
D) Transcriptional elongation by RNA polymerase is enhanced.

Question 56

The correct mRNA secondary structure of transcriptional termination is __________ stem-loop structure.

A) 2-3
B) 3-4
C) 1-3
D) 2-4

Question 57

The pioneer factor can be defined as the

A) last transcription factor protein complex to bind.
B) first transcription factor protein complex to bind.
C) last cis-acting site in a chain.
D) first cis-acting site in a chain.

Question 58

The Swi-Snf complex affects chromatin by

A) creating extra nucleosomes near the promoter.
B) being a promoter.
C) creating a nucleosome-free region near the promoter.
D) transcribing the chromatin.

Question 59

When the Trp repressor is bound to the trp operon, it results in the by RNA polymerase.

A) inhibition of transcriptional initiation
B) disruption of transcriptional elongation
C) initiation
D) enhancement of transcriptional elongation

Question 60

What function do HAT and HDAC perform in the chromatin-modifying process?

A) Both HAT and HDAC activate the gene.
B) Both HAT and HDAC repress the gene.
C) HAT represses the gene and HDAC activates the gene.
D) HAT activates the gene and HDAC represses the gene.

Question 61

Stem cells can undergo two different pathways: cell and cell .

A) proliferation; dedifferentiation
B) proliferation; differentiation
C) differentiation; dedifferentiation
D) differentiation; integration

Question 62

The function of an insulator sequence in DNA is to

A) amplify the action of enhancers.
B) counteract the action of enhancers.
C) inhibit promoters.
D) activate RNA synthesis.

Question 63

Using the figure below, explain how cooperativity works.

Question 64

Predict the state of yeast when GAL 80 is bound to GAL 4 activation domain.

A) high glucose concentration
B) low glucose concentration
C) high galactose concentration
D) low galactose concentration

Question 65

The proteins encoded by GAL1, GAL2, GAL7, and GAL10 are all needed for converting __________ to glucose-6-phosphate.

A) glucose
B) fructose
C) galiactose
D) galactose

Question 66

Why are Arg, Lys, Gln, and Asn commonly found to make specific contact with nucleotide bases?

Question 67

iPS cells can be defined as cells.

A) differentiated
B) dedifferentiated
C) embryonic stem
D) somatic stem

Question 68

Draw the four combinations of nucleotides and label the major groove in each as either an H-bond donor, an H-bond acceptor, or hydrophobic.

Question 69

In yeast, the sugar galactose is converted to what molecule to enter glycolysis?

A) glucose
B) fructose
C) glucose-6-phosphate
D) fructose-6-phosphate

Question 70

What are the two key protein complexes recruited to the preinitiation complex by activator proteins?

A) mediator complex and DNA polymerase
B) mediator complex and TFIID
C) TFIID and RNA polymerase
D) TFIID and DNA polymerase

Question 71

What are two medical applications that iPS could be used for?

A) type 1 diabetes and Parkinson's
B) type 2 diabetes and Parkinson's
C) Alzheimer's and Parkinson's
D) Alzheimer's and type 2 diabetes

Question 72

Pluripotent state can be defined as a cell.

A) differentiated
B) predifferentiated
C) G1 state of the
D) S state of the

Question 73

A function of transcriptional activator proteins is to

A) recruit gene promotors.
B) initiate RNA synthesis.
C) recruit chromatin modifiers.
D) initiate DNA synthesis.

Question 74

Introducing Oct4, Sox2, c-Myc, or Klf4 into a differentiated cell causes

A) cell death.
B) a pluripotent state.
C) no change.
D) cell meiosis.

Question 75

The eve stripe 2 enhancer can be defined as multiple sites for at least four .

A) trans-binding; transcription factor proteins
B) cis-binding; transcription factor proteins
C) cis-binding; insulator genes
D) cis-binding; gene promoters

Question 76

Producing an iPS cell is remarkable because the pathway

A) for conversion is general, not specific.
B) is a highly irreversible reaction.
C) for conversion is very specific and limited.
D) produces a very unstable cell.

Question 77

Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

Question 78

Bicoid, Hunchback, Giant, and Kruppel are all transcription factor proteins involved in pattern.

A) even-skipped expression
B) odd-skipped expression
C) even-skipped transcription
D) odd-skipped transcription

Question 79

How does entropy drive protein-DNA complex formations?

Question 80

What are the two main types of stem cells?

A) somatic and embryonic
B) somatic and epithelial
C) stromal and somatic
D) stromal and embryonic