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Biology 1002B Final: Cycle 9

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Western University
Biology 1002B
Tom Haffie

1 Cycle 9: Development and Death Different types of mutations in protein coding genes Silent mutation: the codon still codes for the same amino acid o There is a difference in DNA sequence, but not in the protein o Due to the redundancy in genetic code Missense mutation: codon codes for another amino acid o Impact is hard to predict (could have no effect or could be devastating) Nonsense mutation: codon doesn’t code for anything o Causes a premature ending of translation -> much more severe Frameshift mutation: inserted/deleted base in the sequence o Entire sequence is read in the wrong frame which probably produces all the wrong amino acids Consider a single base pair insertion into the DNA coding for the first exon of a gene. o Splicing is not affected b/c splicing is caused by snRNAs o All codons downstream will be in the wrong frame and code for the wrong amino acids o Whether the protein is too long or too short depends (we don’t actually know)  Find a stop codon somewhere along the sequence -> too short  No stop codon -> too long Characteristics that make Drosophila an attractive model system o Genome codes for 2 organisms – larva and fly o Mutations are easily identifiable phenotypically  Can knockout a gene using RNA interference and see its effect on development o Short embryo period o We can follow a gene at different stages and see if its expression changes  Is it on at some times and off at others?  Notice when the gene products are present Main stages in Drosophila embryonic development 1. Fertilization 2. Division of the nucleus through mitosis -> blastoderm  No cytokinesis 3. 10 nuclear division -> nuclei migrate to periphery of embryo 4. 3 more divisions -> ~6000 nuclei are organized into separate cells -> cellular blastoderm 5. 10 hours after fertilization: maternal effect genes create protein gradients -> segmented embryo 6. 24 hours after fertilization: egg hatches into larva 7. 3 moults -> pupa 8. Homeotic genes turn on 9. 10-12 days after fertilization -> metamorphosis -> adult fly o When mothers make eggs, they pack them full of mRNA 2 Main role of maternal-effect, segmentation, and homeotic genes in Drosophila development Maternal-effect genes: transcribed in mothers during oogenesis, mRNAs are deposited in the egg and then translated in babies o Control egg/embryo polarity by forming axis o Bicoid – development of the head and thorax (anterior/posterior)  Forms a gradient throughout the zygote (picture)  High concentration at anterior  BICOID: a transcription factor that activates some genes and represses others throughout the zygote  Mutations: lack thoracic structures and have posterior structures at each end (b/c those develop in areas of no/low BICOID) o Nanos – development of posterior structures  Mutations: lack abdominal segments, but anterior/posterior normal o Gurken – establishes top and bottom (dorsal and ventral)  Also a transcription factor Consider… Drosophila that are heterozygous for a loss of function bicoid. o None of their offspring would have no heads b/c mom can still pack bicoid into baby cells o However, ¼ of the female offspring cannot make bicoid -> their kids won’t have heads  Males don’t make eggs so it doesn’t matter o Genotype of mothers matter, not babies Segmentation genes: subdivides the embryo into regions which determines segments of embryo/adult o Only turned on after protein gradients are in place o Maternal-effect genes regulate expression of segmentation genes o Each segmentation gene is expressed at a particular time and location Homeotic genes: specify what each segment will become after metamorphosis o Controls the development of structures such as eyes, antennae, legs, etc. by producing transcription factors  Certain homeotic genes are activated in specific segments to create segment specific structures o Antennapedia – legs develop instead of antennae o Bithorax – 2 sets of wings (doesn’t have musculature/neurology to work but structures are there) Which of the following classes of genes would be the first to be expressed in nuclei of zygotes? o Segmentation genes! o Maternal effect genes are expressed in mothers (first one expressed in the embryo, but not in the nucleus) 3 o Homeotic genes come after segmentation genes Structure/function of the “homeobox” in homeotic genes Homeobox (Hox) genes: a 180 bp sequence which codes for transcription factors called homeodomains Homeodomains: bind to regions in the promoter of the genes they regulate Significance of evolutionary conservation of Hox genes o If you only have one gene controlling a segment, your segments are all the same o If you have more than one gene, your segments can grow different structures -> you can diverge o Over evolutionary time, there have been whole genome duplications  We have more copies of genes o There are 8 Hox genes in Drosophila and they are organized along a chromosome in the same order they are expressed along the anterior- posterior body axis (head first, tail last)  They are present in all major animal phyla o Highly conserved b/c they have a common function Mechanism of plasmid toxin/antitoxin system as a possible origin for cell death o Bacterial plasmids are mobile -> they can code for their own transfer  Plasmid coded toxin (red)  Plasmid coded antitoxin (blue) o Antitoxin is degraded more quickly by protease (green) but is replenished o Cells that lose the plasmid are killed by the toxin  It will very rapidly run out of antitoxin and die o CED-3 is a toxin protein, CED-4 is like the antitoxin Programmed cell death cascade in C. elegans Division of zygote produces 1090 cells -> 131 die at prescribed times -> adult has 959 cells and we can track every single cell 1. Membrane receptor is inactive -> CED-9 is active  CED-9 inhibits CED-4 which means CED-3 is inactive 2. A death signal molecule binds to the receptor 3. Receptor is activated -> inactivates CED-9 -> activates CED-4 -> activates CED-3 4. CED-3 triggers a cascade of reactions  Activation of proteases and nucleases that degrades cell structures/chromosomes Mutants lack normal ced-3/ced-4 genes -> cell fails to die -> disorganized/nonfunctional embryo Function of caspases “Executioner” caspases: proteases that cleave specific essential proteins o Leads to a controlled and irreversible biochemical cascade causing cell shrinkage, chromatin fragmentation and cell death Caspase-9: equivalent to ced-3, but in humans/other mammals Apaf gene: equivalent to ced-4 -> codes for apoptotic protease-activating factor 4 Bcl gene: equivalent to ced-9 These genes are so closely related they retain their function if exchanged between C. elegans and human cells Possible evolutionary origin of programmed cell death genes o Genes for programmed cell death are found all over the eukaryotic world  The mechanisms are just there waiting to be activated o Through in silico methods, we identified caspase orthologues in bacteria  Possibly we took them in through endosymbiosis? o CED-3 is like toxin protein, CED-4 is like antitoxin Role of programmed cell death in Drosophila development Imaginal discs: bundles of cells in the larvae that don’t function o They’re waiting to become adult structures o Under the influence of hormones, they are activated and expand to become adult tissues Apoptosis: the larvae stuff that the adult doesn’t need goes through programmed cell death Reaper: genes that kill a cell o Starts by activating a pr
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