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Regulatory transcription factors

serve to regulate the transcription of nearby genes. Found in eukaryotes.


helix-turn-helix motif

Structural domain for transcription factor protein. Two alpha helices are connected by a turn. The alpha helices lie in the major groove of the DNA.


Helix-loop-helix motif

structural domain for transcription factor protein. A short alpha helix is connected to a longer alpha helix by a loop.


Zinc finger motif

Structural domain for transcription factor protein. Each zinc finger is composed of one alpha helix and two antiparallel beta sheets. A zinc atom holds the zinc finger together.


Leucine zipper motif

Structural domain for transcription factor protein. Promotes the dimerization of two transcription factors. Two alpha helices (a coiled coil) are intertwined due to the leucine residues.



Response element that increases level of transcription when transcription factor binds to it



Response element that inhibits transcription.


How do regulatory transcription factors affect transcription? Three ways.

1. They may interact with TFIID and influence whether or not RNA polymerase can bind to the core promoter and/or initiate transcription.
2. They can interact with a multiprotein complex called mediator. When they interact with mediator, regulatory transcription factors influence whether or not RNA polymerase can proceed to the elongation phase of transcription.
3. Regulatory transcription factors can influence the degree of chromatic packing.


cAMP response element-binding protein (CREB)

Transcription factor. Recognizes a response element with consensus sequence 5'-TGACGTCA-3'. cAMP follows MAP A kinase pathway. Forms diner with receptor, binds response element. The CREB protein ins Protein kinase A.


Can unphosphorylated CREB protein still bind to CREs?

Yes, but it does not activate transcription.


Gene amplifiation

Copy number of a gene increases


Gene rearrangement

DNA can become rearranged to affect gene expression.


Mechanisms for altering chromatic structure

1. Posttranslational modification of proteins that are bound to the DNA
2. A variety of proteins may play an important role in altering chromatic structure during gene activation or expression


Experiment 15A: Chromatic Structure
What technique is used to monitor DNA conformation?

DNase I, which is more likely to cleave DNA if it has an open conformation


Experiment 15A: Chromatic Structure

A loosening of chromatic structure occurs when beta-globin genes are transcriptionally active.


Experiment 15A: Chromatic Structure
Starting material

Nuclei were isolated from three different cell types in chicken: reticulocytes (immature red blood cells), brain cells and fibroblasts. The globin genes are expressed in red blood cells but not in the others.


Experiment 15A: Chromatic Structure
Interpreting the Data

A much smaller percentage of the radiolabeled DNA probe hybridized to the chromosomal DNA in reticulocytes than brain cells or fibroblasts. This indicates that DNase I had digested the globin gene in the chromatic of reticulocytes into small fragments that were too small to hybridized to the radiolabeled DNA probe. The globin genes in reticulocytes were more sensitive to DNase I digestion. These results are consistent with the hypothesis that the globin gene is less tightly packed when it is being expressed.


Three ways in which RNA function can be controlled

1. pre-mRNA processing
2. The regulation of RNA levels
3. The regulation of RNA translation


What factors affect mRNA stability?

A long poly (A) tail promotes stability.
Certain mRNAs may contain sequences that act as destabilizing elements.


AU-rich element (ARE)

Found in many short-lived mRNAs. Recognized by cellular proteins that bind to the ARE and thereby influence whether or not the mRNA is rapidly degraded.


Steps of RNA interference

A. when double-stranded RNA is present in the cell, it is recognized by an endonuclease called dicer, which cleaves the RNA into fragments that are 21 to 23 nucleotides long.
2. Some of these fragments associate with proteins to form an RNA-induced silencing complex (RISC)
3. If the RISC contains an RNA that is complementary to a cellular mRNA, it will bind to that mRNA and cut it into small pieces. In this way, the cellular mRNA is silenced.


How does phosphorylation of eIFs affection translation?

When the alpha-subunit of eIF-2 (eIF-2alpha) is phosphorylates, translation is inhibited.
when eIF 4 is phosphorylates, the rate of translation increases.


How does phosphorylation of iEF-2alpha inhibit translation?

1. Conditions like viral infection, nutrient deprivation, heat shock or toxic heavy metals will activate eIF2alpha protein kinase.
2. eIF2alpha protein kinase phosphorylates eIF2alpha
3. Phosphorylates eIF2alpha binds to eIF2B
4. eIF2B becomes inactive
5. eIF2B usually promotes the binding of initiation tRNAmet to 40S subunit, but when it is inactive, it does not function, so translation is inhibited


Iron regulatory factor

RNA-binding protein that influences the two mRNAs that encode ferreting and the transferring receptor


What does iron regulatory factor bind to?

A regulatory element within the mRNA known as the iron regulatory element or IRE.


What happens when IRF bind to IRE?

It inhibits translation of the ferritin mRNA.


What happens when iron concentration is high?

The iron binds directly to the IRF protein and prevents it from binding to the IRE. Then the ferritin mRNA is translated to make more ferritin protein.


What does synthesis of ferritin mRNA accomplish?

It prevents the toxic buildup of iron within the cytosol.


Where are the IREs in the transferring receptor mRNA?



What happens when IRF proteins bind to the receptor IREs?

The stability of the mRNA is increased, which leads to increase in the amount of transferrin receptor mRNA within the cell when cytosolic levels of iron are very low. More transferrin receptors are made and more iron is taken up when it is in short supply.