Chapter 7 : Metabolic Regulation Flashcards
What is gene expression?
Transcription of a gene followed by the translation of the resulting mRNA into proteins. Once proteins are made additional mechanisms can regulate their activity.
Cells use 2 major approaches to regulate protein function, in which one regulates the activity of a preformed enzyme or other protein , and the second controls the amount of the enzyme or other protein. (T/F)
True
After translation what are the other regulatory processes can occur?
feedback inhibition, covalent modification, degradation, and interactions with other proteins can further regulate the activity of some proteins.
what is a green florescent protein (GFP)?
A type of reporter protein that fluoresces green and is widely used in genetic analysis. By allowing us to determine the the cellular location of each sigma factor.
what occurs for a gene to be transcribed?
the RNA polymerase must recognize a specific promoter on the DNA and begin its activity; small molecules often influence the binding sites of regulatory proteins to specific sites on DNA and turning off/on transcription.
Because of its size, the minor groove of DNA is the main site of protein binding and identified atoms of these bases in the minor groove that are known to interact with proteins. (T/F)
False- They bind in the major groove
Where do binding proteins acquire their high specificity and binding locations?
Specificity is acquired by the interactions between specific amino acid side chains of the proteins and sugar-phosphate backbone of DNA; to achieve high specificity , the binding protein must interact simultaneously with several nucleotides; usually the inverted repeats are where the regulatory proteins bind.
What is a domain on a protein?
A region of a protein having a defined structure and function.
What is the helix-turn-helix structure?
A structure that consist of 2 segments of polypeptide chain that have an alpha-helix secondary structure connected by by a short sequence forming a turn that is connected by 3 amino acid residues, and is critical to for proper binding to DNA.
What is a zinc finger and a leucine zipper ?
they are protein domains; zinc finger, binds a zinc ion, and leucine zipper contain leucine resides that hold DNA in the correct orientation to bind to.
What is negative control?
A mechanism for regulating gene expression in which a repressor protein prevents transcription genes.
What is enzyme repression?
Prevention of the synthesis of an enzyme in response to a signal. And is widespread in bacteria as a means of controlling the synthesis of enzymes required for the production of amino acids nucleobases.
What is enzyme induction?
Production of an enzyme in response to a signal (often the presence of the substrate for the enzyme)
What is the difference between an inducer and a corepressor?
Both are called effectors, though an inducer induces enzyme synthesis while a corepressor represses enzyme synthesis during transcription.
What is a repressor protein?
A regulatory protein that binds to specific sites on DNA and blocks transcription, involved in negative control.
What does it mean for the repressor protein to be allosteric?
An enzyme that contains 2 combining sites, an active site for binding substrate and an allosteric site for binding an effector molecule such as the end product of a biochemical pathway.
What is an operon?
One or more genes transcribed into a single RNA and under the control of a single operator (regulatory site). located downstream of the promoter where mRNA is initiated.
How is repressor active in repression?
By binding its effector (the inducer) repressor protein is activated and can then bind to a specific area on the DNA near the promoter, physically blocking transcription.
How is a repressor active in induction?
The repressor protein is active in the absence of the inducer, completely blocking transcription, when an inducer is added it combines with the repressor protein and transcription can proceed.
What is Positive Control?
A mechanism for regulating gene expression in which an activator protein functions to promote transcription of genes.
What is an activator protein?
A regulatory protein that binds to specific sites on DNA and stimulates transcription; involved in positive control.
Where do activator proteins bind?
The binding site of the activator is called the activator-binding site which acts as the operator in negative control. but both are still called an operon.
Because the promoters of positively controlled operons have nucleotide sequences that bind RNA polymerase weakly and are poor matches for consensus sequence, thus even the correct sigma factor RNA polymerase has difficulty binding to these promoters thus the role of the activator protein is to help RNA polymerase to recognize the the promoter and begin transcription. (T/F)
True
What is a Regulon?
A regulon is a set of operons that are all controlled by the same regulatory protein (repressor or activator). In regular control a specific DNA-binding protein binds only at the operons it controls regardless of whether it is an activator or repressor, other operons not affected.
What are global control systems?
Regulatory mechanisms that respond to environmental signals by regulating the expression of many different genes.
What is Catabolite repression?
The suppression of alternative catabolic pathways by a preferred source of carbon and energy. The key point is that the favored substrate is a better carbon and energy source than other available sources.
What happens during diauxic growth?
Occurs when 2 available energy sources are present, the better energy source is used up first followed by a lag period when depleted and again followed by growth using the second energy source.
Catabolite repression relies on (CRP) cyclic AMP receptor protein a repressor protein in negative control. (T/F)
False- does rely on CRP but it is an activator protein in positive control.
What is Cyclic AMP?
A regulatory nucleotide that participates in catabolite repression.
Fun FACTS#1 Cyclic AMP is synthesized from ATP from an enzyme called adenylate cyclase, however glucose inhibits the synthesis of cyclic AMP and also stimulates cyclic AMP transport out of the cell.
Fun FACTS#2 When glucose enters the cell, the cyclic AMP level is lowered, CRP cannot bind to DNA, and RNA polymerase fails to bind to the promoters of operons subject to catabolite repression.
In order for the Lac genes to be transcribed what are the 2 requirements necessary?
1) the level of the cyclic AMP must be high enough for the CRP protein to bind to the CRP-binding site and 2)lactose or another suitable inducer must be present so that the lactose repressor do not block the transcription by binding to the promoter. signals that glucose is absent and lac operon can begin.
What are the 2 alternative approaches to regulating the activity of RNA polymerase?
Common in Bacteria- use DNA-binding proteins that either block RNA polymerase activity or stimulate its activity. In Eukaryotes coordinate numerous DNA-binding proteins known as transcription factors to interact with RNA polymerase. Archea have both types of regulatory proteins by blocking the RNA polymerase itself or by blocking the TBP and TFP proteins necessary for the binding of the promoter.
