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BIO240 Lecture 1

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Jennifer Harris

Lecture 1: DNA & Chromosomes - That DNA in the background of doing its job as template to make RNA is actually being replicated & associated with that replication is going to be some sort of organization with the DNA – how the genome is organized (all the genes in your body). - Associated with that & the process that is going to be necessary in order to get that DNA to actually make that RNA, there is going to have to be some regulation there. When we arrive at that regulation, going to generate not just all RNA molecules but a subset of them & that’s known as the transciptome. The process of translation itself is going to be regulated to give rise again to subset of molecules/proteins known as proteome. - Proteins don’t exist in isolation – bunch of different proteins interacting with each other – this is known as the interactome & working together, going to generate the diversity of metabolic processes that take place in your cells – the metabolome. - There is going to be cross-talk & inter-regulation b/w all of these – central dogma looks very complex now – better reflection of the amazing things that are going on in our cells. Together they give rise to the people we are right now – what geneticists call the phenotype or in grand terms what we call the phenome. - Not only do we make all these things, but we also have to get rid of them as well. st Genome - 1 part of central dogma: DNA. Genome: full complement of genes in an organism. **Don’t need to know the specifics of dates – Want us to know the generality of when things occur though** - 1st eukaryotic genome: yeast Saccharomyces cerivisiae – getting larger (12 Mbp) – started to see then building up an idea what made an organism – what was the set of instructions that DNA that was found in each organism, that entire complement of genes that are there. st - 1stnimal genome: nematode worm. - 1 plant genome: model plant Arabidopsis thaliana – model plant is an organism that one uses to better understand the biology overall of a particular group of organisms. - Getting feeling now for how many genes are necessary to give rise to the organismal diversity that we see in front of us every day. - 1 mammalian genome was the mouse. - Gives you impression of the timeline of what we know about genome – about the info being collected, growing at an ever increasing rate. - Diversity of genome sequences start to give us a better feeling for what is going on in terms of the genes that are necessary to give rise to organismal complexity. - This gives us the feeling of the rate of which genome sequencing is increasing since ’95 when 1 genome was published (Haemophilus influenzae genome) until last year 2007 you can see a logarithmic increase in the amount of genome sequencing that’s been done such that now greater than 600 genomes since 1995. - Where it used to take weeks to sequence things, now it takes days to sequence whole genomes. As a consequence of that, we’re able to enter the so-called the personal genome era. - Personal genome era is a time frame where we’re actually able st acquire genome sequences for individuals on demand. The 1 of those was published last year – the 1 complete genome sequence of a given individual/known individual was J. Craig Venter – his genome sequence was published last year. - Another individual whose genome was sequenced last year – looking at diversity of genes that he has in his genome & what they tell or what they might predict about what kind of individual someone like James Watson is – what sort of maladies/illnesses he may be susceptible for. - There are companies predicting in the course of the next 5 years sequencing individual genomes for b/w 1 & 10 thousand dollars. - This has provided us with an incredible depth of info about the basic building blocks for organisms – set of programs of algorithms that one needs to use to build the individuals. - The personal genome era is going to be to relate all of this info to biology – how do we relate what we know about whole genomes to what goes on so you get the phenomes that you see around you? Nucleoid **Don’t need to know the names of the small proteins** Supercoiling of DNA by (class of enzymes) topoisomerases – proteins that, in energy-dependent fashion, twist the DNA, sometimes actually inducing single-stranded breaks & then rejoins, depending on the class of proteins involved, so that you allow the twisting to occur (to scrunch that up 1000 fold). - In order to get a bacterial genome inside a bacterial cell, you just need to condense it a thousand times – need to take something long & linear (in this case, something circular) & scrunch it up so it’s 1000 times smaller than it would be than if it was its full size – visage doing this by taking an elastic band & twisting it – elastic band will get scrunched up – imagine that occurring at molecular level & that is precisely what bacteria are doing. The way they accomplish this is by using specific proteins to do this scrunching – there are proteins that fulfill an analogous role so together, the DNA & protein form the nucleoid. - The proteins are positively charged b/c DNA is negatively charged so if you have positively charged proteins, they’re going to neutralize the charges & allow you to pack things in close together b/c you won’t have like charges repelling each other. There are numerous small proteins then that fulfill this role of neutralizing the charges but also beginning to do the twisting of the elastic band. - If DNA was the size of yarn, each cell would have 20 return trips worth of DNA from Con Hall to City Hall & back. - Bottom line is: there is an awful lot of DNA in your body that you are handling moment to moment, minute to minute, every day. Each chromosome contains a single, long linear DNA molecule & associated proteins. Together what these DNA + proteins are is something known as chromatin. Way that we fulfill that is that it’s dynamic. - All of that DNA is packaged into chromosomes – there are 23 pairs of chromosomes in the human genome. - Diagram: Each chromosome has been fluorescently labeled – fluorescently “painted” by using hybridization of DNA molecules that recognize individual chromosomes & each of them have been labeled with a differe
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