Lec 26: Prokaryote regulation Flashcards
Gene Regulation
the mechanisms and systems that control the expression of genes
structural genes
encode proteins that are used in metabolism or play a role structural in the cell
Regulatory Genes
are genes that encode products (RNA or Proteins),
-interact with other DNA sequence and affect the transcription and or translation of those sequences
Regulatory Elements
DNA sequences that are not transcribed, but play a role in regulating other nucleotide sequences (that they are linked to)
Helix-turn-Helix
DNA binding Protein MOtif
- consists of two alpha helices connected by a turn
- location: bacterial regulatory proteins, related motifs in eukaryotic proteins
- binding site in DNA: major groove
Zink Fingers
DNA binding protein motif
- -consists of a loop of amino acids containing a zinc ion
- location: eukaryotic regulatory and other proteins
- binding site in DNA: major groove
Leucine Zipper
DNA binding protein Motif
- Helix of leucine residues and a basic arm, two leucine residue interdigitate
- location: eukaryotic transcription factors
- binding site in DNA-two adjacent major groves
Operon
a group of bacterial structural genes that are transcribed together (along with their promoter and additional sequences that control transcription)
- regulates the expression of the structural genes by controlling transcription
- usually mot important level of gene regulation
Regulator Proteins:
can bind to a region of the operon called the operator and affect whether transcription will take place
Characteristic os the regulation mechs. for transcirption
Rapid turn ON and rapid turn OFF
- provides the ability to respond rapidly to sudden changes
Sequential Gene Expression
-cascades of gene expression that turn on in order-these are cyclical
Constitutive Expression/Housekeeping Genes
-continuously expressed under normal conditions always ON such as tRNA and rRNA
Negative control
regulatory molecule is a repressor that binds to DNA and inhibits transcription
Positive Control
regulator molecule is a activator, binds to the DNA to stimulate Transcription
Inducible operon
transcription is normally off and is turned on when an inducer interacts with the repressor
Repressible Operon
transcription is normally on and is turned off when a corepressor interacts with repressor
Negative inducible
- the regulator gene encodes an active repressor that readily binds to the operator, which blocks the RNA polymerase from binding to the promoter and prevents transcription
- For transcription to take place, something must happen to prevent the binding of the repressor to the operator
- SAID to be inducible because transcription is normally turned off and needs to be turned on/induced
- Inducer binds to repressor and alters shape preventing it from bind to DNA-CALLED ALLOSTERIC PROTEIN
Negative Repressible
- transcription normally takes place and must be turned off or repressed
- the regulator protein is a repressor but is synthesized in a inactive form that cannot by itself bind to the operator
- since there is no repressor bound to the operator RNA polymerase readily binds to the promoter and transcription of the structural genes take place
- To turn off transcription, a COREPRESSOR binds to the repressor and makes it capable of binding to the operator
Positive inducible
- Regulatory Protein=activator- it binds to the DNA (usually at a site other than the operator) and stimulates transcription
- transcription takes place when an inducer has become attached to the regulator protein-making the regulator active
Positive Repressible
- The regulatory protein is produced in a form that readily binds to DNA- meaning that transcription normally takes place and has to be repressed
- Transcription is turned off when a substance becomes attachéd to the activator and makes unable to bind to the DNA
Lac Operon
- basic unit for transcriptional control in bacteria
- Lactose is broken down into galactose and glucose with the enzyme B-galactdisoe
- Example of a negative inducible operon
Operon
As a segment of DNA containing Control regions and structural genes, the structural regions are controlled by the controlling region
- when lactose is absent from the medium few molecules of each protein is produced
- if lactose is present and glucose is absent the rate of production increases
structural gene
Z, Y, and A
-transcribed and translated into proteins
LacZ
B-galactidose
LacY
Permease
LacA
transacetylase
Inducer
Allolactose
I
- regulator gene-codes for the repressor, has two binding sites either binds to the allolactose or DNA
- in the absence of lactose the repressor binds to the operator, thus RNA polymerase is blocked and NO TRANSCRIPTION
- when lactose is present the repressor is inactivated by allolactose- RNA polymerase isn’t blocked and transcription is turned on
P
promoter- binds RNA polymerase to allow transcription
O
operator-interacts with repressor
What is product during transcription?
polycistronic mRNA- which is translated into 3 different gene products
Cis acting mutations of the lac operon
action of an element affects only the genes adjacent to it
EX: operator and promoter
Trans acting mutations of the lac operon
Diffusible product is produced. The mutant gene does not have to be adjacent to the other genes to affect them
EX: repressor
Structural gene mutations
Z-, Y-, A-
-results in defective enzymes
Regulatory Gene mutations
mutations in LacI gene affect the production of both Z and Y because genes from both proteins are in the same operon and are regulated coordinately
I-
mutation was constitutive, causing the lac proteins to be produced all the time whether lactose is present or not
- repressor cannot bind to operator due to the repressors bad bind site
- Lac I+ dominates over I- which brings normal regulation of protein production
I+
trans acting
-dominates of I- which brings normal regulation of protein production
I^s
prevents transcription form taking place even in the presence of lactose
- produce defective repressors that could not be inactivated by an inducer (cannot bind to allolactose)
- it dominates over I+
- S=super repressor since it stays stuck to operator
I^(-d)
had subunit of repressor are produced so that repressor cannot bind to operator
-Transdominant to I+
Operator Mutation: O^c
constitutive operator- alters the sequence of DNA at the operator so that the repressor was no longer able to bind
- Lac O^c is dominant over O+
- cis acting
EX: I+O+Z+/I+OcZ-
-produced B-galactidose only in presence of lactose
Promoter mutations: P-
- promoter cannot bind to RNA Polymerase
- dont produce the protein in either the presence or absence of lactose
- cis acting
cAMP
the presence of glucose inhibits
- binding of cAMP-CAP complex is required for proper binding of RNA polymerase
- NO glucose=cAMP present=active transcription
- Positive control- activator (cAMP-CAP) binds to DNA to allow transcription at max level
Tryptophan operon
- makes tryptophan
- negative control- regulating molecules bind to the DNA to turn genes off
- Repressible system- repressor must interact with a corepressor (trp) and then the repressor-corepressor can bind to the DNA to turn off the operon
- Alosteric aciton: a change occurs in the conformation of the repressor when it binds to TRP
Constitutive mutants in TRP operon
R-= inactive repressor- operon always on Oc= operator cannot bind to repressor,always on
TRP low levels present
- repressor isn’t activated so doesn’t bind to the operator-transcription is ON
- Regions 2 pairs with region 3, doesn’t terminate transcription (ANTITERMINATION)
MECH:
- 2 trp codons in a row stall ribosome
- Transcription gets ahead of ribosome
- Allows regions 2 and 3 to pair which isn’t a termination signal
High levels of TRP present
- -decreases the production of the enzymes used to make TRP
- repressor can bind to operator so NO Transcripton
- Regions 3 pairs with region 4 which terminates transcription (ATTNENUATION)
MECH:
- ribosome is just behind transcription
- Ribosome blocks region 2
- Regions 3 and 4 pair which is termination signal
Yanofsky
Attenuation
- premature termination of transcription
- noticed that a deletion around 140-160 BP allowed an increase in transcription even when TRP is present
- ATTENUATOR- located in the leader sequence and responsible for decreasing transcription when TRP is present
- normally if TRP is present, some RNA polymerase escapes repressor complex and starts transcribing, but transcription ends after about 140 its. (in attenuator region)
Antisense RNA
prokaryotic regulation at the translation level
-small RNA molecules complementary to parts of the mRNA base pair to mRNA and inhibit translation
Riboswitches
Prokaryotic regulation at the translation level
- are RNA sequence in the mRNA that affect the translation of that mRNA
- REgulatory protein can be a end product from a biochemical reaction and can be regulating its ow production
- REgulatory protein binds to the riboswitch area
- Riboswitch forms a secondary structure that blocks the ribosome binding site thus preventing TRANSLATION
