Chapter 14_Gene Regulation In Bacteria And Bacteriophages

Question 1

Constitutive Genes

Answer 1

Unregulated genes

Question 2

Repressor

Answer 2

A regulatory protein that binds to the DNA and inhibits transcription

Question 3

Activator

Answer 3

A regulatory protein that increases the rate of transcription.

Question 4

Negative vs. Positive Control

Answer 4

• Negative: Transcriptional regulation by a repressor protein.
• Positive: Regulation by an activator protein.

Question 5

Do effector molecules bind directly to the DNA?

Answer 5

No, it exerts its effects by binding to an activator or repressor. The binding of the effector molecule causes a conformational change in the regulatory protein and thereby influences whether or not the protein can bind to the DNA.

Question 6

Genetic regulatory proteins that respond to small effector molecules have two functional domains:

Answer 6

One is a site where the protein binds to the DNA; the other is the binding site for the effector molecule.

Question 7

Inducer

Answer 7

A small effector molecule that causes transcription to increase. An inducer can accomplish this in two ways: It could bind to a repressor protein and prevent it from binding to the DNA, or it could bind to an activator protein and cause it to bind to the DNA.

Question 8

Inducible Genes

Answer 8

Genes regulated with an inducer molecule.

Question 9

Corepressor

Answer 9

A small molecule that binds to a repressor protein, thereby causing the protein to bind to the DNA.

Question 10

Inhibitor

Answer 10

Binds to an activator protein and prevents it from binding to the DNA.

Question 11

Repressible genes

Answer 11

Genes regulated by corepressors and inhibitors, because they both reduce the rate of transcription.

Question 12

Enzyme Adaptation

Answer 12

Refers to the observation that a particular enzyme appears within a living cell only after the cell has been exposed to the substrate for that enzyme.

Question 13

Operon

Answer 13

A group of two or more genes under the transcriptional control of a single promoter.

Question 14

Why do operons occur in bacteria?

Answer 14

One biological advantage of an operon organization is that it allows a bacterium to coordinately regulate a group of two or more genes that are involved with a common functional goal; the expression of the genes occurs as a single unit.

Question 15

Promoter vs. Terminator

Answer 15

For transcription to take place, an operon is flanked by a promoter that signals the beginning of transcription and a terminator that specifies the end of transcription.

Question 16

What does the lac operon contain?

Answer 16

• CAP site
• Promoter (lacP)
• Operator Site (lacO)
• Three structural genes, lacZ, lacY, and lacA
• Terminator

Question 17

CAP site

Answer 17

A DNA sequence recognized by an activator protein called the catabolite activator protein (CAP).

Question 18

Operator Site

Answer 18

A sequence of bases that provides a binding site for a repressor protein.

Question 19

Lac Repressor

Answer 19

A protein that is important for the regulation of the lac operon.

Question 20

Allosteric Regulation

Answer 20

The action of a small effector molecule.

Question 21

trans-acting factor

Answer 21

A regulatory protein, such as the lac repressor.

Question 22

cis-acting element

Answer 22

A DNA segment that must be adjacent to the gene(s) that it regulates, and it is said to have a “cis-effect” on gene expression.

Question 23

Catabolite Repression

Answer 23

This form of transcriptional regulation is influenced by the presence of glucose, which is a catabolite (a substance that is broken down inside the cell). The presence of glucose ultimately leads to repression of the lac operon.

Question 24

When exposed to both glucose and lactose, E. coli cells first use glucose, and catabolite repression prevents the use of lactose. Why is this an advantage?

Answer 24

The explanation is efficiency. The bacterium does not have to express all of the genes necessary for both glucose and lactose metabolism. If the glucose is used up, catabolite repression prevents the use of lactose.

Question 25

Is glucose the small effector molecule?

Answer 25

No, it is cAMP that does this.

Question 26

cAMP

Answer 26

Cyclic AMP, which is produced form ATP via an enzyme known as adenylyl cyclase.

Question 27

When a bacterium is exposed to glucose…

Answer 27

…the transport of glucose into the cell stimulates a signaling pathway that causes the intracellular concentration of cAMP to decrease because the pathway inhibits adenylyl cyclase, the enzyme needed for cAMP synthesis.

Question 28

The effect of cAMP on the lac operon…

Answer 28

…is mediated by an activator protein called the catabolite activator protein (CAP).

Question 29

Trp Repressor

Answer 29

Encoded by the trpR gene. When tryptophan levels within hte cell are low, the trp repressor cannot bind to the operator site. RNA polymerase then transdribes the trp operon, which makes tryptophan, which acts as a corepressor that binds to the trp repressor protein, which will then bind to the trp operator site inhibiting the ability of RNA polymerase to transribe the operon. NEGATIVE FEEDBACK.

Question 30

Attenuation

Answer 30

It is a second regulatory mechanism in the trp operon mediated by the region that includes the trpL gene. During attenuation, transcription actually begins, but it is terminated before the entire mRNA is made. A segment of DNA, termed the attenuator sequence, is important in facilitating this termination.

Question 31

Possible stem loop structures formed from trpL mRNA under different conditions of translation

Answer 31

• No translation: 1-2 stem loop, 3-4 stem loop
• Low tryptophan levels: 2-3 stem loop
• High tryptophan levels: 3-4 stem loop

Question 32

Posttranslational Regulation

Answer 32

The functional control of proteins that are already present in the cell rather than regulation of transcription or translation.

Question 33

Translational regulatory protein

Answer 33

Recognizes sequences within the mRNA, much as transcription factors recognize DNA sequences.

Question 34

Translational repressors

Answer 34

Translational regulatory proteins that act to inhibit translation.

Question 35

When a translational repressor protein binds to the mRNA, it can inhibit translational initiation in one of two ways:

Answer 35

• It can bind in the vicinity of the Shine Dalgarno sequence and or the start codon and thereby sterically block the ribosome’s ability to initiate translation in this region.
• The repressor protein may bind outside the Shine Dalgarno/start codon region but stabilize the mRNA secondary structure that prevents initiation.

Question 36

Antisense RNA

Answer 36

An RNA strand that is complementary to a strand of mRNA

Question 37

Allosteric Enzyme

Answer 37

An enzyme that contains two different binding sites. Often the second binding site inhibits the enzyme from producing the first intermediate that enzyme 2 needs.

Question 38

Posttranslational covalent modification

Answer 38

The covalent modification of a protein.

Question 39

Riboswitch

Answer 39

An RNA molecule can exist in two different secondary conformations. It can regulate transcription, translation, RNA stability, and splicing.

Question 40

Riboswitch regulating transcription

Answer 40

The 5’ region of an mRNA may exist in one conformation that forms a rho independent terminator, which causes attenuation of transcription. The other conformation does not form a terminator and is completely transcribed.

Question 41

Riboswitch regulating translation

Answer 41

The 5’ region of an mRNA may in exist in one conformation in which the Shine-Dalgarno sequence cannot be recognized by the ribosome, whereas the other conformation has an accessible Shine-Dalgarno sequence that allows the mRNA to be translated.

Question 42

Lytic Cycle

Answer 42

The genetic instructions of the bacteriophage direct the synthesis of many copies of the phage genetic material and coat proteins that are then assembled to make new phages. When synthesis and assembly are completed, the bacterial host cell is lysed, and the newly made phages are released into the environment.

Question 43

Lysogenic Cycle

Answer 43

The phage can act as a temperate phage (does not produce new phages and does not kill the bacterial cell that acts as its host). During the lysogenic cycle, phage lambda integrates its genetic material into the chromosome of the bacterium. This integrated phage DNA is known as a prophage.

Question 44

Prophage

Answer 44

Can exist in a dormant state for a long time, during which no new bacteriophages are made.

Question 45

Antitermination

Answer 45

To prevent transcriptional termination