L6 - Characterizing The Genome PDF

Summary Why care about characterizing the genome: Methods of quantifying the genome comparison between species insight into evolution, function and complexity of organisms Genome is all of the DNA in once copy of chromosome Chromatids an identical DNA molecules attacked at controversy One chr...

Summary Why care about characterizing the genome: Methods of quantifying the genome comparison between species insight into evolution, function and complexity of organisms Genome is all of the DNA in once copy of chromosome Chromatids an identical DNA molecules attacked at controversy One chromosome = one centromere N-value: number of unique chromosomes in an organism Coefficient of N: ploidy number of unique sets in an organism C-value: amount of DNA in one set of an organism's nuclear chromosomes: genome size Coefficient of C: tells us how many times its entire genome is present in a cell 3.2 billion base pairs one genome set or 6.5 piccigrams Just because n has a certain value a does not have a related value if number of c is high in a small organism may mean lots of infunctional DNA Changes in cell cycle between meiosis and mitosis 2n n 4c G2 M 2C 2n S G1 n 4c c  Cycle 3 Characterizing the Genome (1) DNA as seen with an electron microscope (2) Cell during metaphase Looks very different between organisms Differences in Karyotypes Tetraploid Sunflower Bird 1 set Frog Human Diploid  need to know to understand a cell Why Care? Method of quantifying the genome Anything in cell is coded by genome Humans are the most dominante species Tells a lot of information Changes over time before we can control other species How enzymes behave related here Basis for comparison between species When being studied Make predictions Insight into evolution, function, and “complexity” of an organism Evolving genome Based on sequences Gives idea on how complex an organism is A genome is all of the DNA in one copy of an organism’s chromosomes We have more dna Nuclear than One set from DNA one chromosome mitochondr of a daughter ial DNA cell is thee genome Mitochondrial DNA Chloroplast DNA All things here were free living and therefore have information squandered Chromatids are identical DNA molecules attached at their centromeres Double helix, antiparallèle, polarity - sister of chromatid srutucture has 4 5 prime end 2 3 prime ends chromatid Mitotic G1 S Phase G2 Metaphase Fig. 13.11  Replicated Chromosome Defined by number of centromere - one chromosome ONE chromosome  Quantifying n-value & coefficient of n One unique flavoured chocolates in a box? n-value = number of unique nuclear chromosomes present in an How many unique ones do you have? genes must be unique to be considered different - humans 23 organism. Coefficient of n (ploidy) tells us the number of unique sets that are present in an organism; If you put all unique ones in a box that’s one set, again that’s another set Humans have two Set must have all different chromosomes X2 1 homologous pair 2 sets of 1 unique chromosome 2n = 2 total chromosomes (diploid)  Number of copies of the genome C-value & coefficient of C 3.2 billion base pairs one genome set (one copy not all DNA) 6.5 picigrams Number of base pairs or pgs / C-value represents the amount of DNA in one set of an organism's nuclear chromosomes; genome size C-value of a species is constant!! Genome size ' Quantity of base pairs or mass (picograms) But genome copy number changes Coefficient of C tells us how many times the entire genome is present in a cell Copies of a genome - how many times is the entire genome present in our cell (2) - In humans we have one copy of the genome 1 homologous pair Pervaded other and other repeated twice Each chromosome has been duplicated. Therefore, the entire genome is present 4 times. Genome Genome side does not change  How chromosomes will be shown on an exam Picture during metaphase labeled with numbers = unique chromosomes If another set = diploid Different length chromosomes = unique Example: karyote Identify the ploidy and n-value of this organism Let’s say that 2 sets of homologous triplets make up an organism’s genetic material. 1 unique chromosome copied 3 times A second unique chromosome copied 3 times # of unique chromosomes? 2 Therefore, this is a triploid (3n) organism. # of sets of unique chromosomes? 3 There are 2 unique chromosomes (n = 2 ). This is the set this is the 3n = 6 total chromosomes genome  Copies of genome Example: Identify C-value and coefficient of C This is the genome Let’s say that these homologous triplets make up an organism’s genome C6 organism 23455 Contains 1 part of the whole genome duplicated on each chromosome (x2) copied onto 3 homologous chromosomes (x3) 23456 Contains part 2 of the whole genome duplicated on each chromosome (x2) copied onto 3 homologous chromosomes (x3) Whole genome = part 1 + part 2 Each part is present in the nucleus 6 times. Therefore, 6C, where C is the total mass in pg ( Trick: count the # of sister chromatids in each homologous grouping ) During G1 polity = copy number Box of Chocolate Example One box with six different chocolates - one set of chocolates N = unique flavours - 6 Polity = 1n C-value - weight or length measurement (genome size + based pairs) - 200 g always constant C-value = 1C - one copy of body N=6 C Two boxes N=6 Polity = 2N -C-value is always 200 mg C-value = 2C 2n = 12 - not n=12 still only 6 unique flavours 2C Three boxes N=6 Polity = 3N C-value = 200mg C-value = 3C If in G1 keep ploidy and copy number the same 3n = 18 3c Four boxes N=6 Polity = 4n C-value = 200 mg C-value = 4C 4n = 24 4C  Human Karyotype: Metaphase Homologous pairs 4 sister chromatids  Model the copies of genome in a diploid In humans cell over the cell cycle - 4C Amount of DNA ↑ Goes down just after cytokinesis 2C Photocopier is not on Made double the amount S phase is start button not specifically 4 G1 S G2 M  Model the ploidy in a diploid cell over the In humans cell cycle Number of Chromosomes 4n 2n - All chromosomes are duplicated with sister chromatids but the number of centromeres are still the same so the ploidy is still the same G1 S G2 M Just because n has a nnimplies implies nothing nothing about aboutCC certain value c does not have to have a related value Cucumber Tasmanian devil (Cucumis sativus) (Sarcophilus harrisii) 2n = 14 = 2n = 14 heavier genomes meaning chromosomes could be larger C = 243.5 Mb < C = 3.3 Gb More DNA than humans  n implies nothing about C Tasmanian devil Human (Sarcophilus harrisii) (Homo sapiens) Pack in so many base pairs 2n = 14 < 2n = 46 C = 3.3 Gb = C = 3.2 Gb  n implies nothing about C Human Axolotl (Homo sapiens) (Ambystoma mexicanum) 2n = 46 > 2n = 28 Regions of unfunctional DNA C = 3.2 Gb