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Main ideas for BIO 1002B - 2.docx

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Department
Biology
Course
Biology 1002B
Professor
Denis Maxwell
Semester
Winter

Description
Main ideas for BIO 1002B – Term Test 2 Evolution of Eukaryotes  Endomembrane: unique series of intracellular membrane compartments found in eukaryotic cells  Ancestral anaerobic bacteria  infolding of plasma membrane  nuclear envelope, ER  phagocytosis of aerobic bacteria (ATP advantage) into mitochondria  cyanobacteria into chloroplast (plants have both M & C)  Endosymbiosis: mitochondria and chloroplasts derive from symbiotic relationships with prokaryotic cells o Bacteria can go through oxygenic phosphorylation/ETC to support themselves by making own ATP o Same morphology between mitochondria and bacteria o No genes that code for chloroplast and mitochondria since they have their own genome  Giardia o Eukaryotic, anaerobic, symbiotic (get ATP from others since it has no mitochondria) o Cpn60 – chaperone essential for mitochondria to work relocated to nucleus through lateral gene transfer o Descended from bacteria with mitochondria and not intermediates of prokaryotes and eukaryotes o Lost mitochondria because protein synthesis to maintain it uses up a lot of resources Lateral Gene Transfer  Genes from mitochondria and chloroplast relocate to nucleus over millions of years so single cell can cooperate o Only relocation of gene is changed and not what the function of the gene o Began 2 bya beginning of eukaryotic cells and still happening today o Elysia puts chloroplast from vaucheria’s coenocyic cells (no cell wall) into own cells to be autotrophic  Why is the modern mitochondria genome smaller? o Lateral gene transfer to nucleus for control  Safely store and edit RNA in nucleus unlike ROS in mitochondria  Variation through sexual recombination o Redundant (hexokinase in nucleus) or no purpose (flagella) genes  Why have some genes not moved yet? o Haven’t had the chance o More convenient and easier if genes are used and made locally  Crazy coding system e.g. chloroplast makes large rubisco subunit but nucleus makes small subunit o Prokaryotic genes cannot move because it is too big or it doesn’t work in the eukaryotic nucleus  Detection through Southern Blot o Isolate single stranded DNA and hybridize probe o If present in mitochondria only, it has not moved o If present in nucleus only, it has moved o If present in both, it is caught transferring to the nucleus before original is degraded  Relationship between genes and proteins o About 1kb/gene = 1000 nucleotides/gene = 333 amino acids in protein (3 nucleotides in codon) o Genes > proteins – backup genes and a lot of non-protein coding genes (e.g. rRNA, tRNA, mRNA) o Genes < proteins – genes transcribed on top and bottom strand and end at the same terminator or overlapping genes due to a different reading frame overlap Transcription and Translation Relationship Nuclear Membrane Traffic  Non template DNA = mRNA  mRNA – made inside, translate outside  Template DNA = tRNA  rRNA – made inside, function outside  poly-A polymerase – made out, function inside DNA Non Template (Codon) 5' > T G G> 3'  tRNA – made inside but function outside  snRNA – made inside and function inside Template (Anti-codons) 3' < A C C < 5'  Nuclear proteins – made outside, function in mRNA Message (Codons) 5' > U G G > 3' tRNA Transfer (Anti-codons) 3' < A C C < 5'  miRNA – made inside but function outside Protein Amino Acid Amino > trp > Carboxyl  All proteins made outside but nuclear protein function inside e.g. snRNP Eukaryotes Prokaryotes  ↑ size = ↑ SA of cristae = ↑ ox phos = ↑↑  SA of plasma membrane controlling size = ↓ volume = ↑ ATP = ↑ genome = ↓ PS ATP = ↓genome = ↑ protein synthesis Advantages and Disadvantages  Vary genome size since it uses 2% of ATP  Small genome range (smaller is better)  Multicellularity and complex traits  None (evolution is stepwise, not gradual)  Nucleus control transcription, translation  No nucleus = not separated  premRNA  No premRNA  Not simultaneous transcription and translation  Simultaneous transcription and translation Gene Expression due to nuclear membrane  Translated longest: mRNA translated first  5’ enhancer –/– promoter proximal region –  5’ – promoter – 5’ UTR, SD BOX – start codon – promoter – 5’ UTR – introns, exons – 3’ UTR gene – stop – terminator – 3' UTR  All proteins under same transcript factor  Polycistronic: more than one protein/gene  Universal – proof that universal ancestor uses this or lateral gene transfer not possible Genetic Code  Redundant codons – different organisms have different preferences Transcription  5’ end (upstream); 3’ end (downstream/after) Regulation  Chromatin remodelling in eukaryotes, regulate initiation  Position and direction independent – attractive  Enhancer (silencers are bend and twist attach coactivator to PPR  none opposite)  Too enhance can overexpress gene  Promoter proximal region -35 of promoter  -35 TTGACA, - 10 TATA upstream of start  Position dependent: far = not transcribed  Attract RNA polymerase to begin transcription  RNA  Direction dependent: cannot invert at +1 start point promoter  TATA binding protein make promoter more  Efficiency of promoter due to attraction attractive to polymerase II strength (TATA box in  DNA binding protein/transcription factor often  Give direction since no universal template eukaryotes vs AT rich region in are dimers (work in pairs): strand prokaryotes)  Helix-turn-helix electrostatic attraction  Whichever side promoter is on, promoter  Zinc finger associate with zinc cofactors attach to 5’ end and that will become the  Leucine zipper hold 2 proteins in shape template strand  RNA  Protein understands promoters polymerase  Binds and create bubble to start transcription from 3’ to 5’ on template strand Polyadenylation signal in 3’ UTR Terminator Loop in 3’ UTR of mRNA  Transcribed and signal RNAse to stop  Downstream of stop codon  Ending  Poly – A polymerase adds poly tail (A’s) at 3’  Self-pairing hair pin loop to stop transcription (not base pairing)  ↑ GC hydrogen bond or ↑ base pairs = ↑  No signal for 5’ G cap stability = ↑ efficient  preMRNA  Intron attract snRNP (snRNA + protein)  none  Spliceosome (several snRNP) loop and pair remove introns, snRNA – mRNA to alternatively splice different masking, alternative combinations of introns, exons splicing, miRNA  Masking bind to make unavailable  mRNA  5’cap–UTR–start–coding–stop–UTR–poly-A-tail  5’ UTR SD box – start codon – coding – stop  Peptide or nuclear tag (begin of coding) to codon – terminator loop – 3’ UTR (tags for post organelles via channels or to nucleus via pores translation)  Endomembrane tag: rough ER translation  Small ribosome subunit recognize 5’ cap  5’ UTR SD box mRNA/ rRNA ribosome binding Translation  Slide down to find start codon to stabilize translation since not tRNA pairing  Ribosomes (rRNA + large + small subunit with E, P, A site) bind to 5’ UTR  Travel 5’ to 3’ on mRNA and interact with tRNA (understands mRNA) to make amino acids and proteins  Universal signal to start translation mRNA 5’AUG3’; template 3’TAC5’ (understood in RNA)  Start codon  Mutation would cause it to not start translating  Not necessarily the first three bases due to upstream UTR (untranslated regions)  Stop translation: mRNA 5’ UAA, UAG, UGA 3’; template 3’ ATT, ATC, ACT 5’  Stop codon  Mutation would cause it to not stop or no effect if silent substitution into another stop  No tRNA match stop codon but protein release factor bind in A site (not base pairing) stops translation  Each gene has one stop codon e.g. lac operon has 4 stop codons  Post trans  Modify chemically, breakdown, activate/inhibit  Breakdown regulation, activate/inhibit E. Coli Metabolism of Lactose: Inducible Lac Operon  Constitutive (always expressed) gene lacI separate from lac operon make regulatory protein, lactose repressor o Mutation: no repressors – operon always on o Mutation: repressor cannot be unbind – operon always off  lacZ – lactose > glucose + galactose (energy for glycolysis and Kreb’s) o Mutation: no glucose or energy and built up of lactose but transcription of lacY and A still occur  lacY – make permease enzyme that transports lactose actively into the cell o Mutation: lactose cannot enter cell and operon remains turned off  lacA – make transacetylase enzyme to metabolize acetyl-CoA’s acetyl transfer to β-galactosidase  No lactose (normal)  When lactose is present, lac operon is turned on o Lac repressor electrostatically (+ and – o Lactose + very little ß-galactosidase  charges on double helix) bind to operator allolactose inducer (isomer of lactose) o Bind to DNA as dimer to stabilize loop that o Bind and alter lac repressor conformation block RNA polymerase promoter binding and released, RNA polymerase replaces  Due to short life of enzymes, there is a quick turnover of lactose and no allolactose to inactivate repressor  Mutation in promoter: no transcription of gene (always off)
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