Regulation of Eukaryotic Gene Expression (Biochem Ch 5) Flashcards Preview

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Flashcards in Regulation of Eukaryotic Gene Expression (Biochem Ch 5) Deck (37)
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Result of acetylating lysyl residues in histones

- acetylating certain lysyl residues in the histones decreases the positive charge and weakens the interaction with DNA, which affects chromatin remodeling and ultimately gene expression
- a chromatin remodeling engine binds to acetylated lysyl residues and reconfigures the DNA to expose the promoter region.
- additional transcription factors (i.e. TBP, TFIID, etc) then bind in the promotor region and recruit RNA Polymerase


General Transcription Factor

binds to promotors and is necessary for every gene to be expressed


Specific Transcription Factors

- increase expression of specific genes
- bind to enhancers (enhancers can be upstream or downstream of a gene)
- hold general transcription factors in place at promotor so genes are expressed at a higher rate
- in a few cases bind to silencers


Examples of enhancers (found in Eukaryotes)

Enhancers are binding sites for activator proteins. Ex:
- Glucocorticoid response element (GRE)
- cAMP Response Element (CRE)
- Estrogen Response Element (ERE)

- remember: specific transcription factors bind to enhancers to increase expression of specific genes


Do Histone acetylases favor gene expression or inactive chromatin?

- Histone acetylases favor gene expression (acetylate certain lysyl residues --> decreases + charge--> weakens interaction with DNA)
- histone deacetylases favor inactive chromatin


Upstream promotor elements and location

- a CCAAT box (around -75) that binds a transcription factor NF-1
- a GC-rich sequence that binds a general transcription factor SP-1


Characteristics of enhancers (5)

1. they may be up to 1000bp away from the gene
2. may be upstream, downstream or within an intron of the gene they control
3. orientation of the enhancer sequence w.r.t the gene is not important
4. enhancers can appear to act in tissue-specific manner if the DNA-binding proteins that interact with them are present only in certain tissues
5. enhancers may be brought close to the basal promoter region in space by bending the DNA molecule



sequences that bind repressor proteins in eukaryotes


cis regulators

- cis regulators are DNA sequences on the same chromosome as the genes they regulate
- the DNA regulatory base sequences (i.e. promotors, enhancers, silencers, response elements, etc) in the vicinity of genes that serve as binding sites for proteins


trans regulators

- transcription factors and the genes that code for them are called trans regulators
- trans regulatory proteins can diffuse through the cell to their point of action
- these are on other chromosomes than the genes they regulate


Transcription factors

- transcription factors: the activator proteins that bind response elements
- contain at least 2 recognizable domains: a DNA-binding domain and an activation domain


Examples of DNA-binding domains in transcription factors

the DNA-binding domain binds to a specific nucleotide sequence in the promotor or response element. Ex:
- zinc fingers (steroid hormone receptors)
- leucine zippers (cAMP-dependent transcription factor)
- helix-loop-helix
- helix-turn-helix (homeodomain proteins encoded by homeotic/homeobox genes)



- polypeptide with zinc
- translocates to nucleus when activated
- can bend in major and minor grooves because of the + charge in the zinc ion
- most common protein binding to DNA
- ex) found in steroid hormone receptors (all steroid receptors bind to DNA with zinc fingers)


the function of the activation domain on the transcription factor

the activation domain of transcription factors allows the transcription factor to:
- bind to other transcription factors
- interact w RNA polynmerase II to stabilize the formation of the initiation complex
- recruit chromatin-modifying proteins like histone acetylases or deacetylases


Steroid Receptors
- response element (binding site)
- function
- protein class

- response element (binding site): HRE/GRE
- function: steroid response
- protein class: zinc finger


cAMP response element binding (CREB) protein
- response element (binding site)
- function
- protein class

- response element (binding site): CRE (cAMP response element)
- function: response to cAMP; active when phosphorylated
- protein class: leucine zipper


Peroxisome proliferator-activated receptors (PPARs)
- response element (binding site)
- function
- protein class

- response element (binding site): PPREs (DNA response elements)
- function: decrease serum TG; regulate multiple aspects of lipid metabolism. Activated by fibrates (increase PPAR alpha) and thiazolidinediones (increase PPAR gamma)
- protein class: zinc fingers

- members of this family of zinc-fingers are activated by a variety of natural or xenobiotic ligands including:
- fatty acids, prostaglandin derivatives, vibrates, thiazolidinediones.


NFkB (nuclear factor kappa-B)
- response element (binding site)
- function
- protein class

- response element (binding site): kB elements
- function: regulates expression of many genes in immune system.
ex) glucocorticoids decrease signaling, therefore decrease immune system of patients
- protein class: Rel domains


Homeodomain proteins
- response element (binding site)
- function
- protein class

- response element (binding site): none. embryologically regulated factor
- function: regulate gene expression during development
- protein class: helix-turn-helix

- homeobox/Pax gene produces homeodomain protein which affects a number of enhancers, turning on many genes at one time


- what, who

- hypolipidemic drug prescribed to patients with elevated blood TG but normal cholesterol and LDL
- acts by stimulating proliferation of peroxisomes and increasing gene expression of lipoprotein lipase, resulting in the induction of the FA oxidation pathway
- more peroxisomes = more burning FA = decrease TG in blood


Zellweger Syndrome

- genetic disease caused by a mutation in any one of several genes (locus heterogeneity) involved in peroxisome biogenesis
- characterized by deficiency of peroxisomes that causes an accumulation of very long chain FA and several unusual FA, such as hydroxylated and branched FA.
- a defect in FA efflux from peroxisomes


MC features of Zellweger Syndrome

- enlarged liver
- high blood levels of copper and iron
- vision problems
- in affected infants there is failure to grow, mental retardation, abnormal muscle tone, and multiple developmental abnormalities
- infants usually die within the first year.


Klein-Waardenburg Syndrome

- defective PAX gene
- all of the tissues involved in KWS are derived from embryonic tissue in which PAX-3 is expressed
- symptoms:
- dystopia canthorum (lateral displacement of the inner corner of the eye)
- pigmentary abnormalities (frontal white blaze of hair, patchy HYPOpigmentation of skin, heterochromia irides)
- congenital deafness
- limb abnormalities

(summary: limb abnormalities, congenital deafness, facial anomalies, HYPOpigmentation of skin, white frontal hair)


methylation of ____ bases in DNA silences genes

- methylation of CYTOSINE bases in DNA silences genes
- involved in down-regulation of gene expression


Prader-Willi syndrome
- cause
- genetic inheritance

- chromosome 15
- result of genetic imprinting
- methylation of DNA silences genes in genetic imprinting
- imprinted so that it is normally expressed only from the PATERNAL chromosome
- if one inherits a paternal chromosome in which this region has been deleted, will get Prade-WIlli syndrome
- can also result from uniparental (maternal) disomy of chromosome 15 (when person receives 2 copies from mom and none from dad)


Symptoms of Prader-Willi

- childhood obesity and hyperphagia
- hypogonadotrophic hypogonadism (hypogonadism due to an impaired secretion of gonadotropins due to problem with pituitary gland or hypothalamus)
- small hands and feet
- mental retardation
- hypotonia


what is the half life of ALA synthase in the hepatocyte?

1 hour


heme increases the initiation of ??

heme increases the initiation of beta-globing translation


Homeotic gene or homeobox gene (HOX)

- regulate the development of anatomical structures
- mutations of these genes can result in multiple developmental abnormalities due to mutation of a SINGLE GENE
- encode for homeodomain proteins
- similar set of gene = PAX genes (paired-box)
- mutations in HOX or PAX might be expected to produce developmental errors
- ie in Klein-Waardenburg Syndrome


Enhancers are transcriptional regulatory sequences that function by enhancing the activity of

- specific transcription factors (i.e. any steroid receptor) bind to specific DNA sequences (enhancers) and to RNA polymerase at a SINGLE promotor sequence and enable the RNA polymerase to transcribe the gene more efficiently