Control of gene expression in eukaryotes part 2 Flashcards Preview

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Define the Helix-turn- Helix motif

1. Present in RDBPs of both euk and prok.
2. Contains C-terminal DNA binding domain (alpha helix) rick in R and K amino acids
3. Interacts primarily with the major groove


Define the "Homeodomain" motif

1. improvement of the Helix-turn-Helix
2. Instead of two alpha helices, it has three.
3. Helix 3 interacts with major groove, flexible portion of Helix 1 interacts with minor groove


Define the Zinc Finger

1. Consists of a loop containing zinc, 2 B sheets, and one alpha helix
2. Contacts mainly through guanine-R interactions
3. Major groove generally requires 3 zinc fingers for proper binding


What is an example of a B-sheet RDBP?

TATA binding protein


What is an example of a protruding loop RDBP?



Define the leucine zipper dimerization motif

- consists of 8-10 regularly spaced leucines in an amphipathic helix.
- dimerizes with another to form RDBP
- example is the c1 protein


Define the Helix-Loop-Helix motif

- performs dimerization
- made of two alpha helices, and one loop


Three important consequences of dimerization for eukaryotes

- It allows the simultaneous recognition of two regulatory motifs on the DNA. The two
motifs will be identical in the case of homodimers and will be different in the case
of heterodimers.
- It increases the variety of regulatory sites in the genome.
- It allows the regulation of a large number of genes while requiring only a limited
number of RDBPs through a combinatorial control.


What is the role of truncated HLH proteins?

Participate in sequestering other HLH proteins, since they themsleves dont possess a DNA-interaction protein


Give an example of a truncated HLH protein

Id protein


Define the modular nature of RDBPs

The DNA binding piece and the activation domain piece can be switched in and out


Name four ways that RDBPs can be regulated?

Unmasking, Release from membrane, synthesis, phosphorylation


Can a single RDBP influence the expression of multiple genes?



Define synergy

Great output than sum of the parts


What are six ways that RDBPs can reduce transcriptional activity

1. competitive DNA binding between repressor and activator
2. Masking activation surface
3. Competitive direct interaction with the general transcription factors
4. Recruitment of histone deacetylases
5. Recruitment of CRCs
6. Recruitment of methyl transferases


cytosine methylation is carried out by what protein?



Define de novo methyl-transfereases

Put initial methylation pattern at specific sequences


Define maintainance methyltransferases

Responsible for methylating a newly synthesized strand that is connected to a previously methylated strand


What is thought to be an important step in demethylation?

transformtion of 5-mC into 5-hmC


Where is cytosine methylation often found?

in CpG islands


How can methylation of CpG islands really inhibt expression of the gene?

Methylation of CpGs can bring over 5meC-binding proteins, that then recruit CRCs and histone deacetylases


What is imprinting?

Soon after egg and sperm meet, most of the epigenetic tags that activate and silence genes are stripped from the DNA. However, in mammals, imprinted genes keep their epigenetic tags. Imprinted genes begin the process of development with epigenetic tags in place.


Remember, there is this weird example where methyloation can actually activate a gene because the insulator element is methylated