denser DNA 30 nm fiber less accessible for transcription hypoacetylation

less dense DNA beads on a string more available for RNA transcription hyperacetlyation

2 types of DNA remoldeling

chromatin remodeling nucleosome modification

adding an acetyl group on DNA, less positive charge, less attraction, loosens DNA, more transcription methylation can block this

removing a histone sliding a histone

detect if chromatin remodeling is taking place

exposure to new restriction enzymes radioactive probe to bind to free floating histones

patterns in gene expression controlled by heritable changes in chromatin structure (histones also replicate in DNA)

see which proteins interact with other proteins put a protein in vector with a DBD (DNA binding domain) put other protein in a vector with a TAD (transcription activator domain) if cells grow, it means DBD and TAD came together - proteins interact

addition of 5' cap poly A tail splicing out introns

why mRNA processing? (only in eukaryotes)

stability of mRNA nuclear export promote translation

5' end of a mature mRNA

guanosine nucleotide added to 5' end 5i to 5' linkage some 2' methyl groups triphosphate present

occurs at the same time as transcription termination RNAPII transcribes poly A addition site polyadeylation factors bind to the poly A signal, initiating cleavage PAP synthesizes the poly A tail PABP protects tail from degradtion

alternative splicing options

exon is skipped or included only one exon is included an intron is retained or included exon may have alternative splice sites at 3' end exon may have alternative splice sites at 5' end

advantages to alternative splicing?

more proteins with only one gene

takes place via a branchpoint in the middle of the intron to form a lariat structure

splicing consensus sequence

GU (5' splice site) AG (3' splice site)

part circular, part linear 2' OH group on A attacks the 5' P on G

splisosome assembly and splicing steps

U1 locates GU 5' site U2 recognizes A branchpoint U4 comes in wtih U5 adn U6, takes U1 away with it U5 and U6 assit the 2' OH group attack the 5' end of intron

splisosome assembly and splicing steps (continued)

U5 and U6 help the exon ends find each other the exons are covalently linked the lariat is now separated

do not use splisosome, cleaves itself out

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MMBIO Quiz 10

Question	Answer
heterochromatin	denser DNA 30 nm fiber less accessible for transcription hypoacetylation
euchromatin	less dense DNA beads on a string more available for RNA transcription hyperacetlyation
2 types of DNA remoldeling	chromatin remodeling nucleosome modification
acetylation	adding an acetyl group on DNA, less positive charge, less attraction, loosens DNA, more transcription methylation can block this
chromatin remodeling	removing a histone sliding a histone
detect if chromatin remodeling is taking place	exposure to new restriction enzymes radioactive probe to bind to free floating histones
epigenetics	patterns in gene expression controlled by heritable changes in chromatin structure (histones also replicate in DNA)
yeast-2 hybrid assay	see which proteins interact with other proteins put a protein in vector with a DBD (DNA binding domain) put other protein in a vector with a TAD (transcription activator domain) if cells grow, it means DBD and TAD came together - proteins interact
mRNA processing	addition of 5' cap poly A tail splicing out introns
why mRNA processing? (only in eukaryotes)	stability of mRNA nuclear export promote translation
5' end of a mature mRNA	guanosine nucleotide added to 5' end 5i to 5' linkage some 2' methyl groups triphosphate present
poly A tails	occurs at the same time as transcription termination RNAPII transcribes poly A addition site polyadeylation factors bind to the poly A signal, initiating cleavage PAP synthesizes the poly A tail PABP protects tail from degradtion
alternative splicing options	exon is skipped or included only one exon is included an intron is retained or included exon may have alternative splice sites at 3' end exon may have alternative splice sites at 5' end
advantages to alternative splicing?	more proteins with only one gene
splicing	takes place via a branchpoint in the middle of the intron to form a lariat structure
splicing consensus sequence	GU (5' splice site) AG (3' splice site)
lariat structure	part circular, part linear 2' OH group on A attacks the 5' P on G
splisosome assembly and splicing steps	U1 locates GU 5' site U2 recognizes A branchpoint U4 comes in wtih U5 adn U6, takes U1 away with it U5 and U6 assit the 2' OH group attack the 5' end of intron
splisosome assembly and splicing steps (continued)	U5 and U6 help the exon ends find each other the exons are covalently linked the lariat is now separated
self-splicing	do not use splisosome, cleaves itself out

Created by: anyasalmon

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