5- Chapter 6 Flashcards
What are the two major approaches cells use to regulate protein function?
One controls the amount of an enzyme or other protein
The other controls the activity of a performed enzyme or other protein
What is gene expression?
The processes that regulate the amount of protein synthesized at the level of transcription, or by varying the amount of mRNA made, or at the level of translation
What is the main site of protein binding on DNA?
What is a protein domain?
The major groove of DNA
To achieve high specificity, the binding protein must interact simultaneously with several nucleotides
Protein domain is regions of the protein with a specific structure and function
What is the most common protein domain structure critical for proper binding to DNA?
Helix-turn-helix structure that consists of 2 segments of polypeptide that have alpha helix connected by a short sequence forming a turn
First helix is recognition helix, interacts with DNA
Second helix is stabilizing helix that stabilizes the first helix by using hydrophobic interactions
Page 175 diagram
What is negative control of transcription?
What is repression and induction?
It is a control that prevents transcription
Repression is where the enzymes that catalyze a product are not made if the product is already in the medium (shuts off pathways)
Induction is the opposite where an enzyme is only made when the product is present (turns on pathways)
Genes that are negatively controlled haveba default of ON
Look at graphs of induction and repression on page 176
What are inducers and corepressors?
Inducers- substance that induces enzyme synthesis (loss of repression)
Corepressors- substance that represses enzyme synthesis
These are both effectors and are normal cell metabolites
They affect transcription by binding to specific DNA binding molecules
Diagram on page 177
What is a repressor protein?
What arginine (corepressor or inducer) binds to
It is allosteric which means it’s confirmation is altered when the effector molecule binds to it
Repressor protein is activated when effector binds to it
Picture on 177
What is the operator and operon?
What is a regulon?
Operator is the specific region of the DNA near the promoter of the gene where the repressor protein binds
Operon is a cluster of consecutive genes who’s expression is under the control of a single operator
When more than one operon is under the control of a single regulatory protein, these operons are called a regulon
Pictures on 177
What is positive control of transcription?
The regulatory protein activates the binding of rna polymerase to dna
Binds activator protein to DNA which allows RNA polymerase to begin transcription
Genes that are positively controlled have a default OFF
If proteins that regulate the expression of the gene are removed, the gene would not be expressed
What is catabolite repression?
What is a downside if this
Is an extreme example of global control (regulate expression of many different genes simultaneously)
That control the use of carbon sources of more than one is present (best carbon is used first)
Lac operon is under control of this (uses positive and negative control)
Downside is it might lead to two exponential growth phases called diauxic growth
Graph on page 180
What is cyclic AMP and Cyclic AMP receptor protein?
Cyclic AMP receptor protein is the positively controlled activator protein that catabolite repression depends on
Cyclic AMP is a key molecule in many metabolic control systems (only made when cell is low on glucose) and is a regulatory nucleotide
How is transcription controlled in archaea?
Archaea use DNA binding proteins to control transcription and have both types of regulatory proteins
Example of repressor protein is NrpR protein
Diagram on page 181
Some arachael regulators can work as both a repressor and an activator (dusk functionality)
What are two component regulatory systems?
Single transduction systems with two parts
2 proteins: sensor kinase (detects environmental signal
Response regulator (DNA binding protein regulates transcription)
Contains a feedback loop
Almost 50 different ones in E. coli
Some signal transduction systems have multiple regulatory elements
What are phosphatases and what is their role?
The feedback loop employs a phosphatase which is an enzyme that removes the phosphate from the response regulator at a constant rate in two component regulator systems
Picture on page 183
How does chemotaxis use two component systems?
It uses modified two component systems to sense temporal changes in attractants or repellents and process this information to regulate the direction of flagellate rotation
Several sensory proteins sit in membrane and sense attractants or repellents
What is adaptation?
Once an organism has successfully responded to a stimulus, it must stop responding and reset the sensory system to await further signals
Adaptation of the chemotaxis involves a feedback loop resetting the system
What is quorum sensing?
Bacteria use this phenomenon to respond to the presence in their surroundings of other cells of their own species (some species regulatory pathways are controlled by the density of cells of their own kind)
Bacteria use this approach to ensure that sufficient cell numbers are present before initiating activities that require a certain cell density to work correctly
What is an autoinducer?
A specific signal molecule that quorum sensing employs that diffuses freely across the cell envelope in either direction
It binds to a specific activator protein that triggers transcription of specific genes
What is the stringent response?
Widely distributed regulatory mechanism used by bacteria to survive nutrient deprivation, environmental stresses, and antibiotic exposure
Triggering the stringent response shuts down of macromolecule synthesis and activated stress survival pathways
What two regulatory nucleotides mix to trigger the stringent response?
Guanosine tetraphosphate (ppGpp) Guanosine pentaphosphate (pppGpp)
What is the heat shock response?
Controlled by alternate σ factors in all 3 domains of life
Responds to
Heat shock proteins sense to heat shock and inactivates rpoH
How quickly the cell can synthesize heat shock proteins determines how it survives
What are noncoding RNA’s?
What are small RNA’s?
ncRNA are RNA molecules that are not translated to give proteins
Includes rRNA and tRNA
sRNA regulate gene expression and are widely distributed in in both prokaryotic and eukaryotic cells
How do sRNA’s alter the translation of target mRNA’s?
sRNA’s base pair directly to mRNA which modulates the rate of target mRNA translation because a ribosome can not translate double stranded RNA
So SRNA can be a mechanism for regulating the synthesis of a protein
What are riboswitches?
RNA molecules that resemble depressors and activators in binding small metabolites and regulating gene expression
Riboswitches control translation of the mRNA rather than transcription
Picture on page 194
