Nuclear Domains FISH an extension of FISH is chromosomal painting Foci are made of 200 300 ori note DNA replication pattern correlates with euchromatin heterochromatin Gene Density vs Packing Density Lower gene density increases the likeliness of it being heterochromatin A is likely to be euchromatin B is likely to be heterochromatin Also heterochromatin B is likely to replicated later in S phase Chromosomal Territories vs Interchromosomal Domains and hey A is a domain The zoomed in figure is euchromatin that has been unwound to be accessible to transcription The red is transcriptionally active genes B demonstrates the chromosome arms do not overlap Green is one arm red is another arm and the orange is the centromere C shows euchromatin vs heterochromatin Yellow is euchromatin on the periphery of the territory Red is heterochromatin on the periphery of the nucleus D shows early vs later replication Green is early replication red is late replication yellow is scaffolding proteins E is transcriptionally active vs not white is active black is silent genes makes sense because white is on periphery of territory and black is packed away green is an interchromosomal territory where DNA genes aren t yellow is speckles the machinery for transcription speckles are like motherships vs little battleships big speckles mother ships and little speckles are the indv ships to complete work F is interchromosomal domain vs machinery proteins N is the nucleolus the dark center Nucleolus the nucleolus the genes in the nucleolus are the tandem arrays coding for 45S rRNA CHRISTMAS TREE of RNA poly I transcribing rRNA in the nucleolus Fibrillar Center ribosomal genes so yes it is DNA specifically euchromatin Dense Fibrillar Region where ribosomal genes are being transcribed into pre rRNA beginning the assembly of ribosomal SUBunits Granular Zone just putting together ribosomal subunits even more don t forget 5S rRNA genes are NOT in the nucleolus and ribosomes never fully assembled until the cytoplasm this is another picture of what s going on in the nucleolus Mutations E Coli methyl directed mismatch repair system Mut L distinguishes parental from newly synthesized DNA MutH recognizes mismatched base pairs MutS brings together other members of the MMR system types of mutations these are types of base substitutions also types of base substitutions these are types of chromosomal level mutations Nuclear Transport NLS NES Dalton Da is a unit of molecular weight size things between 20 60 kDa will not be asked about on the exam they will get through somehow though them NLS basic as hell yo this bitch bipartite some NLS form through folding too note GAP is what causes the Ran GTP to form Ran GDP NES bitches love leucine Exportins love that leucine rich NES too btw Ran GTP has a high affinity for both importin and exportin Hella different effects though mRNA does not have an NLS Its friendly neighborhood protein does The exporter complex does have both NES and NLS Mitochondria you cannot build an entire ETC with just a mitochondrial genome but all proteins encoded by the mitochondrial genome are involved in the ETC noncoding DNA D loop where ori located any gene many necessary genes not found in mitochondria are in the host cell s genes some plants yeast have mitochondria with a larger genome though the electrochemical gradient is a source of energy Targeting signal for Mitochondria presequence transit sequence this is positively charged TOM and TIM are a one way street in the negative matrix attracts the positively charged presequence thanks electrochemical gradient transit peptidase mitochondrial presequence peptidase MPP the pulling through TOM and cutting off of signal happens according to whatever protein reaches the cargo protein first opening the door uses ATP even though it uses a lot of energy it s impt to let the Mitochondria focus on respiration RER Golgi Palade s Pulse Chase experiment RER protein secretion synthesis of membrane proteins protein processing SER lipid bilayer synthesis detoxification screencasts about signal peptides the protein has a n terminus signal and one stop transfer sequence single pass TMP stop transfer sequence IS NOT a stop codon this protein has an ISS only single pass TMP but the c terminus is in the lumen ISS is not cut off ISS is not recognized by signal peptidase The translocon closes because the ribosome dissociates When the translocon closes it squeezes out whatever is left inside of it This protein has an ISS stop transfer and ISS 3 time multipass TMP If last signal is stop transfer then C terminus in cytoplasm If last signal is ISS then C terminus in lumen Stop transfer and ISS signals must alternate but not necessarily have a subsequent signal Each ISS and stop transfer a TMP pass in the membrane Disulfide bond formation can only occur in the lumen of the RER no other cellular environment is suitable virtually every protein going through RER experiences N linked glycosylation the 3 amino signal has asparagine Asn or N must be presented to be N linked dolichol is the platform to which the 14mer oligosaccharide tree is attached dolichol is in the membrane of the ER the 14mer is trimmed to a 11mer example of 11mer is mannose an enzyme recognizes the signal trims the tree and attaches the tree to the Asn in the signal A DIFFERENT type of modification is GPI Anchors Glycosyl Phosphatidyl Inositol creates lipid linked proteins aka a lipid linked glycoprotein GPIs also go thru N link very few proteins receive GPI GPIs begin same as TMP had a N terminus signal and a stop tansfer N terminus has been cut off already phosphatidyl sugar GPI done in RER lumen Then an enzyme cuts the protein and covalently links to GPI GPI proteins produce integral membrane proteins bc in lumen will be extracellular at SER not in SER Golgi Lysosome Plasma Membrane Actin Actin and Myosin Myosin II is walking towards barbed the actin is being pulled into each other movement of myosin along actin filament DOES NOT ACCOUNT FOR TRANSLOCATION Translocation is accomplished by myosin contracting actin filaments to move the entire cell body Cell crawling consists of 4 steps occurs during M phase the contractile ring is INSIDE of the cell the hanging part of the belt is depolymerized meaning diameter of actin is the same but the length of the filament changes note vesicle transport can be done with microtubules Myosin I is unconventional bc it doesn t form thick myosin filaments The letters correspond