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Flashcards in Control of Gene Expression Deck (27)

Parts of the lac operon

Regulatory Gene: binds repressor
Promoter- has the operator and CRP gene
z gene: beta galactosidase --> lactose --> glucose + galactose
y gene: galactoside permease --> lactose --> into cell
a gene: thiogalactoside transacetylase --> ?

^genes right next to eachother: polycistronic message


lac operon- glucose only

1) regulatory gene creates mRNA for repressor protein
2) repressor binds to operator
3) RNA polymerase cannot bind promoter
4) transcription blocked


lac operon- little lactose present
what does beta galactosidase make?

beta galactosidase
lactose --> glucose + galactose


lactose --> allolactose (isomer)


What happens when little lactose present in the lac operon?

1) regulatory gene creates mRNA for repressor protein
2)allolactose binds to repressor
3) repressor cannot bind operator
4) RNA polymerase binds to promoter
5) transcription...but at a LOW level


How are cAMP and glucose levels related?

increase glucose, decrease cAMP
decrease glucose, increase cAMP


lac operon: lots of lactose and glucose

1) high CRP levels --> but doesn't do anything
2) RNA pol binds to promoter
3) low transcription


lac operon: lots of lactose and little glucose

1) CRP and cAMP bind leading to a conformational change in CRP
2) bind onto the promoter
3) Stimulates binding of RNA polymerase to the promoter
4) Transcription level is high


Helix-turn-Helix motif (transcription motif)

Recognition binds major groove
dimer alpha helices are bound to the major groove of DNA

H bonding between bases on DNA and the protein end up becoming really strong since there are so many bonds made --> this makes this process very specific
ie: CRP (cAMP receptor protein)


Function of CRP

acts as a dimer on the major groove to give a wide array of protein possibilities for interactions


Pitt Hopkins Syndrome

Creates mutation in the basic region of a transcription factor...affects DNA binding of the transcription factor

*Arg 576 highly conserved and essential for DNA recognition*


Zn (transcription motif)

alpha helices bind major groove
not a dimer

Use of 1 or more molecules of Zn
Repetitive motif of 2 cystine and 2 histidine (or cystine) residues in the sequence

Repetitive so can maker different fingers
Also has specific and strong interactions with DNA


Leucine Zipper/bZip (transcription motif)

dimer alpha helices are bound to the major groove of DNA

Has 2 parts:
1) Zipper alpha helix: coil formed so that leucines stick out on one side --> hydrophobic interactions

2)Basic region DNA binding alpha helix: this is the part that interacts with DNA


Basic helix-loop-helix (transcription motif)

dimer alpha helices are bound to the major groove of DNA
has alpha helix non helical loop alpha helix on the top

Bottom is a basic region- DNA binding and an alpha-helix


How do you make different zipper motifs?

Different amino acids can replace the leucines on the zipper alpha helix

ie: arginine, histidine


Ways to regulate transcription factors

1- protein synthesis
2- ligand binding
3- protein phosphorylation
4- Addition of subunit
5- unmasking
6- Stimulation of nuclear entry
7- release from membrane


How do estrogen receptors work?

Estrogen receptor and ligand estrogen bind to estrogen response element (ERE)

this binding unmasks the receptor and allows for transfer into the nucleus --> bind to coactivaters in nucleus --> transcription


DNA methylation and cancer

DNA methylation suppresses the expression of tumor suppressor genes in cancer


How does methylation block gene expression?

1) Methylated CpG islands inhibits transcription by physically precluding transcription factor recruitment

2) Methylated CpG binding protein 2 (MeCP2) binds to methyl groups and prevents transcription by recruiting chromatin recruiting factors


Rett Syndrome

mutation in MeCP2 gene --> over transcription


Methylation can also lead to gene activation

ie: Igf2

Insulin-like growth factor- imprinted gene


Why in Igf2 are the paternal genes expressed even if they are methylated?

Methylation is at a DMR (differentiated methylated region) and promoter is open. Methylation at this regulatory region of the paternal chromosome prevents binding of a repressor to the region and transcription can occur


Cutaneous T-cell lymphoma

Treated with HDAC inhibitor so that tumor surpressor gene expression increases

HDAC inhibitor --> more acetylation of histones


Nucleosomes and gene expression

Positive superhelical tension

ATP-driven chromatin remodeling
-remodeling factors interact with C terminal of large subunit of RNA polymerase II and use ATP to open up nucleosome

Covalent Modification of histone tails
-Methylation of lysine or arginine (HMT


3 ways of modifying histone tails

1) Acetylation of lysines

2) Phosphorylation of serines

3) Methylation of lysines and arginines


Acetylation of histone tails

acetylation thru HAT reduces amount of + charge --> becomes loosely associated with DNA backbone --> can do transcription!

HDAC deacetylates and pushes reaction opposite way


Thyroid Hormone Receptor- HAT and HDAC

Thyroid receptor and Reitinoid X receptor when attached to DNA both are attached to one another --> attratcs a co-repressor --> deacetylates histones --> tightly wrapped DNA --> transcription not initiated

Thyroid Hormone (T3) changes conformation of TR/RXR --> corepressor doesn't bind --> coactivator with HAT can attach --> transcription!


Methylation on lysine

can activate and repress!