Study new BMB 400 Chap 17 Flash Cards

 
Pile Management Card
new BMB 400 Chap 17

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primary marker of regions of the genome that are silenced
DNA methylation
epigenetic regulation
-inheritance of gene expression patterns
-in the absence of either mutation or the initiating signal
-Nucleosome and DNA modifications can provide the basis
imprinting
In the diploid cell, in most cases, the two alleles (one from father, the other from mother) are expressed at comparable levels
Sometime, one copy of a gene is expressed while the other is silent.
methylation is permanent
maintained across cellular generations. The hemimethylated DNA following DNA replication are restored by adding methyl groups to the newly synthesized DNA.
5-Met-cytosines
methylated DNA
MeCP2
-protein binds to methylated DNA
-recruit histone modifiers that completely turn off expression
DNA methylation in mammalian cells
Want to complete turn off gene
Methylated DNA (5-Met-cytosines) disrupts binding of the transcription machinery and activators
Methylated DNA can be bound by diff proteins (ex: MeCP2)
MeCP2 recruit histone modifiers that completely turn off expression
Silencing in yeast
SIR genes (Silent Information Regulator)
SIR genes (Silent Information Regulator)
Rap1 recruits Sir to the telemere
Sir2 (a part of Sir1) deacetylates the nearby nucleosomes
Unacetylated tails bind to Sir3 and Sir4
Binds many more Sir proteins
Spreading of silencing effect
most common form of gene silencing
heterochromatin
telomeres and centromeres
Gene silencing
-position effect
-not in response to a specific signal
-can switch off multiple genes
-most common form: heterochromatin
-telomeres and centromeres (typically composed of repetitive sequences and contain few protein coding genes)
If a gene is experimentally moved into these regions (e.g., by homologous recombination), that gene is typically switched off
Euk transcription is regulated
1) unmasking an activating region (23)
2) transport into and out of the nucleus (22)
Signal cascade
-cell surface receptor gets signal
-transfers to intermediate protein (e.g., kinase)
-transfer to other intermediate proteins to reach to the transcription factor for gene regulation
most common way to repress the transcription in eukaryotes
recruitment of histone modifier (remove acetyl group -> forming higher order chromatin structure)
Euk repressors
competition: Hides DNA sequence for activator binding

inhibition: Hides activating region

direct repression: Inhibit transcription initiation
combinatorial control
2 genes; each controlled by mult signals (4 in A, 3 in B)
Regulatory protein 3 acts at both genes
Human b-Interferon Gene
3 activators: (NFkB, IRF, Jun/ATF)
1 architechural DNA binding protein: (HMG)
-all bind to enhancer
HO gene
-SWI5 can bind to chromatin unaided
-SBF cannot
-SWI5recruits histone remodelling complexes
-alter nucelosome for SBF binding site
Synergy
-2 activators working together is much greater than 1 working alone
-critical for signal integration by activators
-ex: HO gene expression by SWI5 and SBF (mediator)
Nucleosome Modifiers
histone acetylase: modifies histone tails to alter packing of nucleosomes

chromatin remodeling complex: allows the transcription machinery accessing to the promoter
Activator recruits Pol II indirectly
1) Recruits trx machinery (TFIID complex/Mediator); usually recruited by >1 activator upstream
2) Recruits nucleosome modification factors; alter chromatin
Pro-rich
in mammalian
-weaker and work less universally than member of the acidic class
Glu-rich
in mammalian SP1
-weaker and work less universally than member of the acidic class
acidic region in activating region
preponderance acidic amino acids (Glu & Asp), yeast Gal4
-strong and work in any eukaryotic organism
Activating regions
-no well-defined structures
-some form A helices
-sticky surfaces
-small weak units; the more, the more, the stronger the resulting activating region.
-grouped by amino acid content:
1. Acidic region
2. Gln-rich
3. Pro-rich
sticky surfaces
-surfaces capable of interacting w/ several protein surface
Basic zipper/HLH
region of the a helix that binds DNA contains basic amino acids.
Helix-Loop-Helix Proteins
Dimer
2 helical regions: recognition A helix, flexible loop, shorter A helix
Leucine Zipper Motif
-2 long a helices grip DNA
-each a helix inserts into the major groove half a turn apart.
-Dimerization via coiled coil: 2 helices are held together by hydrophobic interactions between Leu
-homodimers and heterodimers
Gal4
zinc cluster domain v
TFIIIA
Zinc finger protein
Zinc Containing DNA-Binding Domains
-Zinc finger protein (TFIIIA) and zinc cluster domain (Gal4)
-Zn atom interacts w/ Cys and His
-Zn serves a structural role in DNA-binding domain
-Recognition a helix inserted into the major groove.
>2 zinc finger linked: increases length DNA recognized
homeodomain proteins
-Helix-turn-helix DNA binding domain
-recognition helix for DNA
-discovered in Drosophila
-in all eukaryotes
-bind DNA as heterodimer
recognition helix
-mainly recognizes DNA sequences
-Discovered in Drosophila
-Found in all eukaryotes
euk transcription factors
-dimers
-recognize specific DNA using an a helix inserted into the major groove
-Some heterodimers
-Some are monomers
bacterial transcription regulators
-homordimers
-Each monomer inserts an a helix into DNA major groove
-Most use helix-turn-helix motif
2 Hybrid Assay
-ID’s proteins that interact w/ each other in vivo
-Activation of gene depends protein A interacting w/ Protein B
-yeast
-finds B proteins that interact w/ a known starting protein (A: bait, B: prey)
Domain swap experiment
-Hybrid protein: (Gal4 activating region fused to the LexA DNA-binding domain)
-activated LexA DNA
-common
-Can be carried on separate polypeptides; form complex on DNA
transcription factor binding sites differences in euk and pros
-Euk transcription factors have multiple-binding sites
-only single-binding site in bacteria
Gal 4 in yeast
-binds to 4 sites upstream of Gal 1
-activates GAL1 1,000x in galactose
-Euk transcription factors have multiple-binding sites
Euk activator
-2 separate domains (DNA and activating) connected by flexible linker
-ex: Gal4 in yeast
-Euk transcription factors have multiple-binding sites
Regulator binding sites
individual regulatory protein binding site
euk core promoter
-transcriptional machinery(RNAP & GTF) binding site
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