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Flashcards in Chapter 8 Deck (68)

What is gene expression

Gene expression is the production of a gene product, usually transcription (mRNA) and translation (protein)


What are most of the proteins encoded



What are constitutive proteins

They are proteins that are needed at the same level at all times, these genes are continuously expressed (housekeeping gene ex. genes for the ribosomes)


What is gene regulation

Genes can be turned on or off, they coordinate cellular activities and conserves energy and resources


What is a structural gene

It is the open reading frame that codes for the transcript, sequences between the start/stop codon


What is the shine-dalgarno sequence

The sequence that serves as the ribosome-binding site, it is JUST downstream of the start site for transcription and JUST upstream of the translation start codon


What kind of processing does the RNA undergo in bacteria

None, there is no splicing, poly A tail or cappingg


What are the two major levels of regulation in the cell

Control activity of preexisting enzymes and control amount of an enzyme


Describe control activity of preexisting enzymes in regulation

It is very rapid, post translational regulation ex. feedback inhibition and covalent modification


Describe control amount of an enzyme in regulationn

It is very slow, regulates transcription and regulates translation


What are transcription factors

Regulation of transcription typically requires proteins that can bind to DNA known as transcription factors


What regulates transcription factors

They can be regulated by: their own synthesis, allosterically by small molecules (metabolites) and by covalent modification (phosphorylation)


What are the two ways transcription factors can regulate transcription

Negatively (repressors) or positively (activators)


How long is the half-life of mRNA transcripts

They have short half-lifes, only a few minutes. This prevents the production of unneeded proteins


How do DNA-binding proteins interact with DNA

They interact with DNA in a sequence-specific manner, the specificity is provided by amino acid side chains interacting with the DNA bases (on the major groove)


What are homodimeric proteins

Most transcription factors are homodimeric proteins: proteins that are composed of two identical polypeptides, these protein dimers interact with inverted repeats on DNA


How do homodimeric proteins interact with DNA

Each of the polypeptides binds to one side of the inverted repeat on the DNA, this increases specificity of just a single protein


What are inverted repeats

They are sequences on opposite strands and sides of the DNA strands that "move" towards each other


What is one class of protein domain that is critical for binding to DNA



Describe the structure of the Helix-turn-helix protein domain

It has two subunits: one is the stabalizing helix and one is the recognition helix. There is also a strand "turn" that connects the subunits


What are the activities of DNA-binding proteins

They may catalyze a specific reaction on the DNA molecule: transcription by RNA polymerase or transposition by transposase.


What are repressors

DNA binding proteins that block transcription (negative regulation)


What are activators

DNA binding proteins that stimulate transcription (positive regulation)


What regulates the activities of DNA binding proteins

The presence of absence of specific small molecules (metabolites or from environment) and intrecellular regulatory signals resulting in covalent modification, sequestration, o degradation


What are are two methods of negative control of transcription

Repression and Induction


What does negative control of transcription mean

A regulatory mechanism that blocks/stops transcription and involves a repressor DNA-binding protein


What is repression

Preventing the synthesis of an enzyme in response to a signal. Typically affects ANABOLIC enzymes


What are two examples of anabolic enzymes

Arginine and tryptophan BIOSYNTHESIS


How does repression work

Enzymes for arginine biosynthesis are normally turned on. But if arginine is added to the cell culture, the bacterial cell can get arginine from the environment and the enzymes for arginine biosynthesis stop being made because the cell doesn't need too much arginine


Describe the regulatory proteins that are required in repression

The regulatory proteins themselves need to be made. The regulatory gene is a constitutive gene, it constantly produces a small amount of this DNA binding protein, the cell is always ready to turn the operon off but can only turn the operon off if there is a lot of tryptophan available


What is induction

The production of an enzyme in response to a signal. Typically affects CATABOLIC enzymes, these enzymes are only synthesized when they are needed


What is an example of a catabolic enzyme

In the lac operon


How does induction work

It is still considered negative regulation because it involves a repressor protein. First a cell is not making lactase because the genes that encode for it are repressed. If a lot of lactose is suddenly present in the environment, the lactase enzymes will increase. The repressor protein that is sitting on top of the genes that code for lactase will be induced and leave


What are corepressors

Substance that stimulates repressor function to repress enzyme synthesis. The addition of corepressors activate a repressor to turn off transcription


What are inducers

Substance that blocks repressor function and induces enzyme synthesis. The addition of an inducer inactivates the repressor transcription factor to turn on transcription


What are effectors

The collective term for inducer and corepressor molecules. They affect transcription indirectly by binding allosterically to specific transcription factor proteins. Ex. repressor-corepressor blocks transcription


What is an operon

A linear cluster of genes whose expression is under the control of a single OPERATOR sequence


Where it the operator located in relation to the promoter on the DNA

The operator is located downsstream of the promoter


How is transcription blocked

Transcription is physically blocked when repressor binds to operator


What is positive control

A regulator protein that activates the binding of RNA polymerase to DNA


Describe Maltose catabolism in E.coli

The maltose activator protein cannot bind to DNA unless it first binds to maltose, it is going to activate transcription. If maltose is present, its going to make the activator protein bind DNA and stimulate transcription.


Where do activator proteins bind

The activator proteins bind to certain DNA sequences called the activator binding sites, NOT on the operator


How do activators promote transcription

The gene sequence may have a promoter that the RNA polymerase can bind to but it kind of sucks. But near the promoter is an activator binding site. The activator protein coupled with an inducer can bind to the activator binding site and interacts with the RNA polymerase to recognize this promoter region more effectively


What happens with the activator binding site is far away from the promoter

DNA looping is required, this is possible due to the flexibility of the DNA


What is a regulon

Multiple operons that are controlled by the same regulatory protein ex. maltose. In the maltose regulon, all the operons are regulated in the same way


Why and how do prokaryotes regulate cellular metabolism

In response to environmental fluctuations. Can regulate cellular metabolism in response to external signals that are perceived by TF proteins and signal transductrion


Describe how external signals are usually perceived by TF proteins

Signals can be small molecules such as nutrients or they can be physical conditions such as temperature or light


What is signal transduction

External signal is detected by a sensor protein and a signal is then transmitted to regulatory machinery inside the cell (Two-component regulatory system)


What are the two proteins that make up the two-component regulatory system

Sensor kinase and response regulator


Describe the sensor kinase

Is in the cytoplasmic membrane, it detects environment signal and autophosphorylates.


What does the kinase do in the sensor kinase

The kinase adds the phosphate group to itself, usually from ATP


Describe the response regulator

In the cytoplasm, DNA-binding protein that regulates transcription. It is activated by the phophostransfer from the sensor kinase. Without the phosphate it is inactive


How do you stop the signalling in this signalling system

Desphosphorylation termiantes this signal and this can be carried out by phosphatase which removes the phosphate group


What does an activated response regulator do

Once its phosphorylated, it changes shape, and can bind to DNA to repress transcription. These genes can be turned back on again with phosphatase which will remove the phosphate so you can get back to the starting condition


What is Quorum sensing

A mechanism by which bacteria assess their population density


What does quorum sensing ensure

It ensures that a sufficient number of cells are present before initiating a response that requires a large cell density


What are some examples of quorum sensing responses

Light production by symbiotic bacteria, toxin production by pathogenic bacteria, P aeurginose switch from free living single cells to growing as a biofilm in lung, and virulence factors of staphylococcus aureus


What is an autoinducer

Each species of bacteria that does quorum sensing produces a specific autoinducer molecule. Most can diffuse freely out of cell, will reach high concentrations inside cell only if many cells are nearby, and binds to specific activator protein and triggers transcription of specific genes


What was the first autoinducer indentified

AHL - acyl homoserince lactone


What was the first quorum sensing discovered

Quorum sensing first discovered as mechanism regulating light production in bacteria. Establishes symbiosis with various marine animals, such as the squid.


What is the lux operon

The lux operon encodes enzymes for bioluminescence


Describe the mechanism of quorum sensing

All the species of bacteria will produce AHL molecules. When enough AHL molecules enter a cell (when there is high cell density) the AHL will bind to an activator protein and regulate gene expression on the chromosome. It will create quorum-specific proteins and make AHL synthase, which will make more AHLs


Describe endospore formation of Bacillus

There are 2 cell types: vegetative cells and endospores. It is controlled by 4 sigma factors and transcriptional factors. This is triggered by adverse external conditions


Describe the process of endospore formation

External signals for adverse conditions causes a cascade of sigma factors, each directing the expression of a different regulon of genes required for a particular stage of development


What are regulatory RNA molecules

They exert their effects by base pairing with mRNA. Their double-stranded region prevents translation of mRNA


What are antisense RNAs

Small RNAs that are about 100 nucleotides (regulatory RNA molecules). Transcription of the antisense RNA is upregulated when its target genes need to be turned off


What are riboswitches

RNA domains in an mRNA molecule that can bind a small molecule (metabolite) to control translation. Located at the 5' end of the mRNA, binding results from folding of RNA into 3D strucutre, similar to protein recognizing a substrate. Riboswitch is analogous to negative control.


Describe the mechanism of the riboswitch

Normally the RNA will have a secondary structure and a flat shine-dalgarno sequence for ribosome biding and translation will proceed. When a riboswitch binds, it creates a loop secondary structure upstream of the shine-dalgarno sequence and the shine-dalgarno sequence will be moved into another secondary structure loop and translation can't occur