Term
| Two mechanisms cells need for gene regulation |
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Definition
Ability to recognize environmental conditions in which they should activate or repress the transcription of a relevant gene.
Ability to toggle on and off transcription of each specific gene(s) |
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Term
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Definition
| the DNA segment that participates in DNA-protein interactions |
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Term
| Protein that binds to DNA-protein promoter site |
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Definition
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Term
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Definition
| a protein when bound to a cis-acting regulatory DNA element such as an operator or enhancer activates transcription from an adjacent promoter |
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Term
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Definition
| A protein that binds to a cis-acting element such as an operator or silencer, thereby preventing transcription from an adjacent promoter |
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Term
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Definition
| A DNA region at one end of an operon that acts as a binding site for a repressor protein. Influences only expression of gene linked to it, and makes no gene product. |
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Term
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Definition
| presence of the bound protein is required for transcription. |
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Term
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Definition
| absense of the bound repressor allows transcription to begin. |
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Term
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Definition
| regulatory proteins and their binding sites that control changes in gene expression that occur in response to environmental conditions. |
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Term
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Definition
| sensor that sets the DNA-binding domain to functional or nonfunctional, and interacts with allosteric effectors |
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Term
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Definition
| small molecules that bind to the allosteric site of the regulatory protein that changes its activity. control ability of activator or repressor proteins to bind to their DNA target sites |
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Term
| Two enzymes required for metabolism of lactose |
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Definition
Permease- transports lactose into the cell
B-galactosidase- cleaves the lactose molecule to yield glucose and galatose. |
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Term
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Definition
| Y,Z,A- (segments encoding proteins) ALL transcribed into a single mRNA molecule. This mRNA coordinates the Synthesis of all three enzymes, all or nothing. |
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Term
| Regulatory components of the lac system |
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Definition
1. Gene for Lac repressor- (I) encodes Lax protein, can block expression of Z,Y, and A.
2. Lac promoter site (P)- P is the site on DNA which RNA Pol binds 2 start transcription of the lac Structural genes.
3. Lac Operator Site(O)- O is the site on DNA where lac repressor binds, it's located between promoter and Z gene near point where transcription of the multigeneic mRNA begins. |
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Term
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Definition
| P,O,Y,Z,and A segments, a segment of DNA that encodes a multigenic mRNA , adjacent common promoter and regulatory region. |
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Term
| Induction of lac system-OFF |
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Definition
| An repressor binding to the operator, the repressor prevents transcription by RNA Pol that has bound to the adjacent promoter site, switches operon to "off" |
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Term
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Definition
| When lactose or its analogs bind to the repressor protein changes shape. |
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Term
| Induction of Lac System- ON |
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Definition
| The allosteric transition alters the DNA-binding site, the repressor loses it's affinity for the operator, lactose binds and the repressor falls off, switching the operon "ON" |
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Term
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Definition
| The relief of repression for operon systems. |
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Term
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Definition
| Lactose and analogs that allosterically inactivate the repressor and lead to expression of the lac genes |
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Term
| Induction of lac system Summary |
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Definition
| In the absence of an inducer( lactose or analogs) the Lac repressor binds to the operator site and prevents transcription by blocking movement of RNA Pol. The structural genes are repressed and no, B-gal, permease, or transacetylase are present. When an inducer is present, it binds to the allosteric site of each lac repressor subunit, inactiviating the site that binds to the operator. The repressor falls off the DNA, allowing transcription of the Structural genes. now, B-gal, permease and transacetylase are present. |
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Term
| Lac System- Negative Control |
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Definition
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Term
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Definition
| Haploid with F' factors, hetereozygous for selected lac mutations. Allowed Jacob and Monod to distingish mutations in the lac operator from mutations in the lac repressor (encoded by I) |
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Term
| Z+ Y+ are recessive to their Z- Y- |
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Definition
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Term
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Definition
| O^c and I^-, they caused the lac operon structural genes to be expressed regardless inducer presence. |
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Term
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Definition
| Makes the operator incapable of binding to repressor, they damage the switch so the operon is always "on". These effects are restricted to structural genes on the SAME chromosome. |
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Term
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Definition
| O^c mutations restricted to structural genes on the SAME chromosome. Ex. B-gal(Z+) is cis to the O^c mutant operator, b-gal is expressed constitutively. |
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Term
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Definition
| I^+ gene product can regulate ALL structural lac operon genes resides on the same DNA molecule or different ones. |
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Term
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Definition
| encodes the lac repressor, able to diffuse throughtout a cell and act on both the operators in a partial diploid. |
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Term
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Definition
| I^s mutations cause repression even in the presence of an inducer. They alter he allosteric site so that it can no longer bind to an inducer. They are dominant over I+ unlike I^- |
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Term
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Definition
| affect the transcription of all adjacent structural genes in the operon. They are sites on the DNA molecule bound by proteins and produce NO protein product. |
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Term
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Definition
| Mutations to the Z and Y genes, affecting them "downstream" to the operon. result from stop codons that cause ribosomes to fall off the transcript |
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Term
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Definition
| The repression of the transcription of the lactose-metabolizing genes in the presence of glucose |
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Term
| Cyclic adenosine Monophosphate (cAMP) |
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Definition
| An important cellular constituent in regulation. Glucose high=cAMP low, glucose low= cAMP high. High cAMP is needed for activation of lac operon. |
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Term
| Catabolite activator protein (CAP) |
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Definition
| encoded by the crp gene. Binds to the specific DNA sequence of the lac operon(CAP-binding site), this makes DNA able to physically interact with RNA Pol and increases that enzymes affinity for hte lac promoter. If CAP binds to cAMP (it's allosteric effecors) it is able to bind to the CAP-binding site and activate transcription by RNA Pol. |
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Term
| Structure of target DNA sites |
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Definition
| DNA as occupied by regulatory proteins binding to the operator sites that they control. THe exact pattern of binding will depend on which genes are turned on or off and whether activators or repressors regulate particular operons. |
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Term
| CAP-cAMO and RNA-Pol binding sites in summary of the lac operon |
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Definition
| The presence of glucose prevents lactose metabolism b/c a glucose breakdown product inhibits maintenance of high cAMP levels needed for formation of the CAP-cAMP complex, which is required for the RNA polymerase to attach to the promoter site. A shortage of glucose catabolites and CAP-cAMP forms, the mechanism for lactose metabolism will be implemented only if lactose is present. It's accomplished b/c lactose must bind to the repressor protein to remove it from the operator site and permit transcription. |
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Term
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Definition
| Inducer-repressor control of lac operon is an example of repression, which expression is blocked. |
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Term
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Definition
| CAP-cAMP system is example of activation because it acts as a signal that activates expression. The activating signal is the interaction of the CAP-cAMP complex with the CAP-binding site on DNA. |
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Term
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Definition
| Special tRNA that inserts the first AA of a polypeptide chain into the ribosomal P site at the start of translation. |
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Term
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Definition
| When trp is absent from the growth medium, trp gene expression is high, when levels of trp are high, the trp operon is repressed. |
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Term
| simple mechanism for trp regulation |
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Definition
| trp repressor binds trp and switches OFF transcription when adequate levels of the AA are present. |
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Term
| Attenuation mechanism of trp regulation |
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Definition
| NEG control, happens after transcription initiation. Proposed 2ndry structures in conformation of trp leader strand mRNA that facors termination of transcription. Four regioins can base-pair to form 3 stem and loop structures. |
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Term
| trp operon- High TRP levels |
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Definition
| segment 1 of the trp mRNA is translated. Segment 2 enters the ribosome which enables segments 3 and 4 to base-pair. This b-pair causes RNA Pol to terminate transcription. |
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Term
| Attenuation of TRP Operon- Low TRP levels |
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Definition
| ribosome stalls at codons of segment 1, seg 2 interacts w/ segment 3 instead of being drawn into ribosome, so segments 3 and 4 cannot b-pair, transcription continues. |
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Term
| Differences between gene regulation in prokaryotes and Eukaryotes |
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Definition
Most genes are not found in operons.
Protein and DNA sequences participating in regulation are more numerous
Many DNA-binding protenis act on a single switch, with many seperate switches per gene and regulatory sequences of these genes are located far from the promoter
Access to eukaryotic gene promoters is restricted by chromatin.
Regulation requires activity of large protein complexes that promote or restrict access to promoters by RNA Pol. |
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Term
| Transcriptional regulation in Eukaryotes |
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Definition
| Packaging of DNA with nucleosomes prevents transcription unless other regulatory protein are present. These regulatory proteins expose promoter sequences by altering nucleosome density or position. They may also recruit RNA Pol II more directly through binding. |
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Term
| Transcriptional regulation in Eukaryotes Part II |
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Definition
Gene regulation takes place at many levels, including mRNA level through alterations in splicing or the stability of the mRNA, and AFTER translation by modifications of proteins.
Molecular signals from outside or inside of cell lead to the binding of regulatory proteins to specific DNA sites outide of protein-encoding regions and these bindings modulate rate of transcription. |
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Term
| Transcription regulation of Eukaryotes |
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Definition
Eukaryotic genomes are bigger and their range of properties is larger than those of bacteria.
DNA is packaged ino nucleosomes forming CHROMATIN. |
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Term
| Ground state of Eukaryotes |
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Definition
| Ground state in eukaryotes is "off", the transcriptional machinery ( including RNA pol II and GTFs) cannot bind to the promoter in the absence of other regulatory proteins. |
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Term
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Definition
| Chromatin structures usually have to be changed to activate eukaryotic transcription. The structure of chromatin around activated or repressed genes within cells can be quiet stable and inherited by daughter cells. |
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Term
| Differences between Eukaryotic and Prokaryotic transcriptional regulation |
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Definition
1. In bacteria, all genes are transcribed into RNA by the same RNA Pol, whereas three RNA polymerases function in Eukaryotes.
2. RNA transcripts are extensively processed during transcription in eukaryotes, the 5' and 3' ends are modified and introns are spliced out.
3. RNA Pol II is much larger and more complex than its bacterial counterpart. RNA Pol II must synthesize RNA AND coordinate the special processing events unique to eukaryotes. |
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Term
| abilities eukaryotic gene regulation must be able to do |
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Definition
1. Ensure that expression of most genes in the genome is off at any one time while activating a subset of genes.
2.Generate thousands of patterns of gene expression. |
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Term
| Promoter-proximal elements |
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Definition
| DNA sequences near the promoter of a gene that interact with a set of proteins comprised of RNA Pol II and general transcription factors. |
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Term
| Enhancers or Upstream Activation Sequences (UASs) |
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Definition
| Cis-acting regulatory sequences in DNA that the second ground of protein components that consists of specific transcription factors bind too. |
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Term
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Definition
| Promoter-proximal elements are bound by transcription factors that affect expression of many genes while enhancers targets more specific transcription factors that control regulation of smaller subsets of genes. |
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Term
| RNA II to transcribe DNA into RNA- Eukaryotes |
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Definition
promoters, promoter-promixal elements and enhancers are all targets for binding by different TRANS-acting DNA binding proteins. RNA Pol III binding to promoter isn't efficient for transcription itself. It requires the binding of GTF to additional promoter-proximal elements found w/in 100bp of transcription initiation sites.
CCAAT box and GC-rich segments upstream are two of these elements.
GTF that bind to the P-PE are expressed in most cells, so transcription initation is availaible. |
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Term
| Functional domains to modulate transcription |
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Definition
1. Domain that recognizes a DNA regulatory sequence ( the protein's DNA-binding site)
2. Domain that interacts w/ 1 or more proteins of the transcriptional apparatus( RNA Pol or assoc protein)
3. Domain that interacts w/ proteins bound to nearby regulatory sequences on DNA that they can act cooperatively to regulate transcription.
4. Domain that influences chromatin condensation either directly or indirectly.
5. Domain that acts as sensor of physiological conditions w/in the cell. |
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Term
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Definition
GAL1, GAL2, GAL7, GAL10 genes encode enzymes that catalyze steps in the biochemical pathway that converts galactose into glucose.
In the presence of galatcose(and absence of glucose), the GAL genes are induced. Vis Versa. |
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Term
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Definition
| Encode proteins that regulate the expression of the enzyme genes. |
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Term
| Regulator of GAL gene expression |
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Definition
| GAL4, a sequence specific DNA-binding protein. |
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Term
| In the presence of galatcose, GAL1,GAL2, Gal7,and GAL80 genes are induced, unless in GAL4 mutants, where they are silent. |
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Definition
| GAL1,GAL2, Gal7,and GAL80 has two or more GAL4-binding sites located 5' (upstream) of it's promoter |
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Term
| The GAL4 binding sites are required for gene activation in VIVO, if they are deleted, the genes are silent, even in the presence of galactose. |
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Definition
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Term
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Definition
| A distinct domain of the GAL4 protein that is required for regulatory activity. GAL4 has two domains: 1 for DNA-binding and another for activating transcription. |
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Term
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Definition
A gene whose phenotypic expression is easy to monitor. These are used to monitor expression of GAL genes and other targets of transcription factors.
The coding region of these reporter genes and promoter are placed downstream of UAS element from a GAL gene. Reporter Expression is then read out of GAL4 Activity in cells. |
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Term
| When a form of the GAL4 protein lacking the activation domain is expressed in yeast, the binding sites of the UAS element are occupied by no transcription is stimulated. |
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Definition
When other regulatory protein lacking the activation domain is expressed in yeast, the binding sites of the UAS element are occupied by not transcription is stimulated such as LexA protein.
When a Gal4 protein lacking the DNA-binding domain is grafted to the LexA DNA-binding domain, the hybrid protein activates transcription form the LexA binding sites. |
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Term
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Definition
| transcriptional activation function of GAL4 proteins reside in two small domains about 50-100 AA long. These domains are seperable from those used in the dimerization of the protein, DNA binding |
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