BCOR 103 1st Edition Exam 4 Study Guide Lectures 21 27 Lecture 21 April09 Components o Nuclear Envelope Two lipid bilayers In between membranes is perinuclear space o NPC Nuclear Pore Complex Only way in and out of the nucleus with the exception of hydrophobic steroid hormones hydrophobic steroid hormones can diffuse across the membrane o Nucleolus ribosome production o Light Dark areas in transmission electron micrograph heterochromatin euchromatin Light not condensed euchromatin is expressed Dark condensed heterochromatin no expressed Chromatin DNA and associated proteins o 30nm filaments o DNA alone is 2 nm Nucleosomes o Key function package DNA o 147 base pairs wrap around a nucleosome 1 75 times Protamines o Help neutralize charge on DNA so it can be packaged o Spermatids don t express genes so genome can be condensed Histones o Amino terminal tails reversible translation modifications o Flexible o 30 of protein Histone Code o Can be read o Written by writer proteins Outer Membrane of nuclear envelope is contiguous with endoplasmic reticulum Nuclear Lamina o Meshwork of proteins and intermediate filaments that provides structural support for the nucleus Prenylation targets lamins to inner nuclear membrane o Prenyl group is 15 carbons long with a cysteine head o After Lamin A and Lamin C groups are inserted the prenyl group are removed o Doesn t happen with Lamin group B Hutchinson Gilford Progeria Syndrome o Lamins A and C mutations dominant negative deletion removal of prenyl groups doesn t occur o Nuclear morphological abnormalities o Age 8 10X faster o Disorganization of heterochromatin o Defective repair of DNA damage and increased genomic instability o Drug that helps inhibitor of farnesyl transferase initially cancer drug Transport into and out of the nuclear membrane by the NPC o 30 proteins o Requires energy o Is selective o Receptor Proteins In importin Out exportin o RAS Family of small GTP binding proteins bound to GDP off GTP on Lecture 22 April 14 Regulation of Nuclear Transport o Transcription factor import in response to cell signaling o NLS of NF kB is masked by IkB o Phosphorylation of IkB targets for degradation o Import of NF kB Dephosphorylation of Pho4 unmasks an NLS Selective import may be regulated in response to cell signaling Cell Signaling directs the import of transcription factor NF kB through the action of a kinase that phosphorylates the NF kB NLS is accessible to importin Nuclear import of the yeast transcription factor Pho4 is also regulated by phosphorylation Cell signaling activates a phosphatase that dephosphorylates Pho4 thereby allowing importin to access its NLS Bottom Line regulation of access of specific transcription factors to the nucleus acts to regulate the expression of the genes with which those transcription factors interact Androgen signaling regulation of nuclear import in response to a steroid hormone Nucleolus dynamic structure o Not membrane enclosed o Site of RNA Polymerase I RNAPI transcription of ribosomal RNA gene repeats o RNAPI transcription is essential for nucleolus self assembly o Co transcriptional assembly of rRNA with ribosomal proteins o Metabolically active human cells 5 10 million ribosomes cell Humans 200 rRNA gene tandem repeats on 5 chromosomes rRNA gene repeat encodes three different rRNAs 18S 5 8S and 28S o The 4th rRNA 5S rRNA is not encoded within the tandem repeats but rather from 2 000 gene copies located within a single tandem array on human chromosome 1 outside the nucleolus and transcribed by RNAPIII Synthesis of mature 18S 5 8S and 28S rRNA requires both endonucleolytic and exonucleolytic processing of a pre rRNA Cleavage of the primary transcript occurs cotranscriptionally 18S rRNA is incorporated into the 40S ribosomal subunit 28S 5 8S and 5S are incorporated into the 60S ribosomal subunit Key Concept nucleolus is a self organizing structure o Self organization is dependent upon rRNA transcription by RNAPI o Blockage of rRNA transcription by DRB or actinomyosin D results in the disruption of the structure of the nucleolus Key Concept nucleolus is a highly dynamic structure whose activity is tightly coupled to the demand for protein synthesis Initial ribosomal subunit assembly occurs co transcriptionally within the nucleolus Despite the amorphous appearance of the interphase nucleus in the electron microscope the nucleus is highly organized This organization is essential for function of the nucleus especially gene expression Nuclear organization is dynamic FISH fluorescence in situ hybridization Chromosome Territories preferential positions of chromosomal DNA within the nucleusdynamic cell type specific Example Hemoglobin o Hemoglobin is a heterotetramer composed of alpha globin gene encoded on chromosome 6 and beta globin gene encoded on chromosome 11 proteins o The alpha and beta globin genes become spatially juxtaposed within the nucleus of hematopoietic cells upon transcriptional activation Key Concept dynamic changes in the positions of specific chromatin regions within the nucleus in response to cell development differentiation or cell signaling Nuclear sub components o Not membrane bound o Self organizing o Dynamic responsive to cell signaling o Functional significance of many of these compartments has yet to be determined Open mitosis dissolution of the nuclear envelope and consequent mixing of nuclear and cytoplasmic components Key concept sorting of nuclear and cytoplasmic components following cytokinesis is accomplished by nuclear import into the reassembling nucleus Lecture 23 April 16 Key concept complexity of an organism does not correlate directly with genome size or the total number of genes in the genome Genomics the systematic analysis of entire cell genomes First human genome sequence 2000 10 years of work cost 2 7 billiion Key concept Organism complexity does correlate with the percentage of the genome that encodes protein inverse correlation o Example human dystrophin gene encodes a protein that is part of the complex that connects the cytoskeleton to the extracellular matrix dystrophin gene 2 5 million bases 79 exons final mRNA is 14 000 bases 0 61 of the pre mRNA Alternative Splicing Production of Multiple Proteins from single gene o Alternative splicing 90 of human genes Bottom line alternative mRNA processing allows the production of 100 000 distinct human proteins from 20 000 genes DSCAM each neuron expresses a single type of DSCAM mRNA and thus each neuron expresses