Chapter 14_Gene Regulation In Bacteria And Bacteriophages Flashcards
Constitutive Genes
Unregulated genes
Repressor
A regulatory protein that binds to the DNA and inhibits transcription
Activator
A regulatory protein that increases the rate of transcription.
Negative vs. Positive Control
- Negative: Transcriptional regulation by a repressor protein.
- Positive: Regulation by an activator protein.
Do effector molecules bind directly to the DNA?
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.
Genetic regulatory proteins that respond to small effector molecules have two functional domains:
One is a site where the protein binds to the DNA; the other is the binding site for the effector molecule.
Inducer
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.
Inducible Genes
Genes regulated with an inducer molecule.
Corepressor
A small molecule that binds to a repressor protein, thereby causing the protein to bind to the DNA.
Inhibitor
Binds to an activator protein and prevents it from binding to the DNA.
Repressible genes
Genes regulated by corepressors and inhibitors, because they both reduce the rate of transcription.
Enzyme Adaptation
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.
Operon
A group of two or more genes under the transcriptional control of a single promoter.
Why do operons occur in bacteria?
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.
Promoter vs. Terminator
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.
What does the lac operon contain?
- CAP site
- Promoter (lacP)
- Operator Site (lacO)
- Three structural genes, lacZ, lacY, and lacA
- Terminator
CAP site
A DNA sequence recognized by an activator protein called the catabolite activator protein (CAP).
Operator Site
A sequence of bases that provides a binding site for a repressor protein.
Lac Repressor
A protein that is important for the regulation of the lac operon.
Allosteric Regulation
The action of a small effector molecule.
trans-acting factor
A regulatory protein, such as the lac repressor.
cis-acting element
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.
Catabolite Repression
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.
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?
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.
Is glucose the small effector molecule?
No, it is cAMP that does this.
cAMP
Cyclic AMP, which is produced form ATP via an enzyme known as adenylyl cyclase.
When a bacterium is exposed to glucose…
…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.
The effect of cAMP on the lac operon…
…is mediated by an activator protein called the catabolite activator protein (CAP).
Trp Repressor
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.
Attenuation
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.
Possible stem loop structures formed from trpL mRNA under different conditions of translation
- No translation: 1-2 stem loop, 3-4 stem loop
- Low tryptophan levels: 2-3 stem loop
- High tryptophan levels: 3-4 stem loop
Posttranslational Regulation
The functional control of proteins that are already present in the cell rather than regulation of transcription or translation.
Translational regulatory protein
Recognizes sequences within the mRNA, much as transcription factors recognize DNA sequences.
Translational repressors
Translational regulatory proteins that act to inhibit translation.
When a translational repressor protein binds to the mRNA, it can inhibit translational initiation in one of two ways:
- 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.
Antisense RNA
An RNA strand that is complementary to a strand of mRNA
Allosteric Enzyme
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.
Posttranslational covalent modification
The covalent modification of a protein.
Riboswitch
An RNA molecule can exist in two different secondary conformations. It can regulate transcription, translation, RNA stability, and splicing.
Riboswitch regulating transcription
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.
Riboswitch regulating translation
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.
Lytic Cycle
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.
Lysogenic Cycle
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.
Prophage
Can exist in a dormant state for a long time, during which no new bacteriophages are made.
Antitermination
To prevent transcriptional termination
