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so um good morning everyone that was a

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great introduction by dr. waters so we

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think my job much easier okay so my name

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is Nicola watch I am a bioinformatics

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PhD student at the Georgia Institute of

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Technology biome format assist is

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someone who looked at biology using

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computers in statistics so my advisor is

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dr. lauren williams and my presentation

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today is on evolution of protein folding

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so to begin with like dr. waters is

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saying the ribosome takes nucleic acid

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which encodes information and turns it

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into protein which is function so yep

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that's the ribosome right there and it's

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taking deal well the RNA that comes from

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DNA and it turns it into protein and the

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ribosome itself is a large back row

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molecular structure of RNA and protein

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and it does its function so when you

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look at these phylogenetic trees that

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relate bacteria to archaea and

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eukaryotes and you look at like all

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animals are distantly related to fungi

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and plants that's by looking at the

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sequence of the ribosome on the DNA so

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the ribosome encodes species

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relationship and which is why we kind of

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say that the world started with the RNA

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RNA world hypothesis when you take the

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ribosome and you look at the size of it

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and you look at the size of it within

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the organisms on the tree of life you

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can see that prokaryotes have really

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small ribosomes that i have here

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represented by released small little

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circles and that simple york eukaryotes

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have larger ribosomes metazoans animals

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have even larger and then mammalian

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ribosomes are the largest found in

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nature and which very interesting is

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that these mammalian ribosomes contain

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the ribosomes of these animals and the

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ribosomes these animals contain within

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them the ribosomes of these yeast or

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simple eukaryotes and these simple

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eukaryotes the ribosomes of those

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contain the ribosomes

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prokaryotes and so when you look at that

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of the ribosomes of extent life and look

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at the way that they've evolved since

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the last Universal common ancestor 3.53

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point Oh 3.5 or 3.8 billion years ago

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and we just use the same mechanisms that

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we hypothesize that they've been growing

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since since then well yeah so okay Lucas

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here extend Webster here sorry about

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that we can see you can see exact same

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mechanisms that the ribosome that

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relates ribosome of all species in

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extant life today we'll just reuse that

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we can just deconstruct the ribosome and

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go back in time and see where life

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started with just the very first piece

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of RNA and these very first pieces of

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RNA are the catalytic centers I the

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ribosome and so that's where proteins

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are formed right at these little pieces

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of RNA and so but we hypothesize is that

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the ribosome very early on in the

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beginning of life was making small

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little pieces of proteins and as it as

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more pieces of RNA kind of stuck onto

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the ribosome its ability to synthesize

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proteins of increasing complexity just

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started happening and so we eventually

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ended up with a very functional ribosome

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back in code that can make very nice and

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complex proteins needed for life today

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so I've been talking about the RNA of

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the ribosome so far and I want to talk

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about the proteins of the ribosome so

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when you look at the prokaryotic

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ribosomes wheat there are 29 ribosomal

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proteins in just the large subunit i'll

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be talking about just a large subunit

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today there's off this also applies to

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the small subunit so there's 29 are

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those little proteins of the e.coli

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ribosome and what's very interesting

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about these proteins is that a lot of

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them have these globular like spherical

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domains that sit on the exterior of the

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ribosome and those look like proteins

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that we find in life today but they have

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these really weird segments that we just

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don't really find anywhere else these

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tail segments and they penetrate deep

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down into the

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core the ribosome close to where peptide

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bonds are actually made where proteins

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are actually synthesized by the ribosome

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and so looking at these proteins in what

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they contact of the ribosomal RNA so a

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very beginning you saw that I had one

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piece of RNA and then as was growing

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throughout the evolution of life we can

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see that more RNA was conglomerating

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onto it and if we look at the proteins

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of the ribosome and which pieces of RNA

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they contact we can cut we can see a

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timeline of ribosomal evolution or in

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just run resume approaching evolution

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and just protein evolution for that

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matter so at the very beginning we only

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had small little peptides that we're

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sticking on there but as ribosome grew

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the proteins that could stick on to it

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we're growing as well and I'm going to

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look at the structure of these proteins

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and see how it's changed since the

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origin play okay so a lot of these

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proteins are very positively charged

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because RNA is very negatively charged

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so we see a lot of arginine and lysine

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and hypothesize that well we know that

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they kind just hold the RNA together

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they kind of just act as a glue so

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they're needed for the ribosome okay and

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then so my background is in biochemistry

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so I want to give you a brief background

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on what a popular plot that biochemistry

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is called the ramachandran plot and so

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biochemists really like proteins and

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light protein structure and so in

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proteins that we find today we see a lot

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of approach like looking at the angles

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that the amino acids in the protein form

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with each other they typically just the

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way they just fold into the protein we

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typically find them in these centers

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right here in the red and so we see this

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alpha helix which is very common in

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proteins today and that's usually just

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looking at the angles of those buns

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usually find them right in this red

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region and we also see a lot of beta

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sheets that's another common secondary

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structure of proteins and that usually

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falls within this red region and then

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all these like white area over here we

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don't find too many

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um amino acids in there but that's kind

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of unstructured they usually don't like

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hydrogen bond with each other you can't

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it's just don't really form any like

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functional catalytic parts typically

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okay so looking at the secondary

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structure of ribosomal proteins so in

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the very beginning you could see that I

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had this little peptide earlier on two

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slides ago that was like composed of I

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think 12 amino acids and approximately

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one third of them fell within these red

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regions then we look at when the next

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little phase of evolution a few more of

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the amino acids are starting to fall

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into these red regions and as we keep on

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going through we can see that more and

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more of these amino acids the bonds

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between them we're falling into these

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red regions so when the ribosomes

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started producing proteins they weren't

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really structured but as drivers ohm

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evolved so did its ability to synthesize

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proteins of increasing complexity and

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now they have these structures that we

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find in life and many of them not within

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the ribosome but these structures are

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often catalytic okay so what about like

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hydrogen bonds within the ribosomal

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proteins so I brought up earlier beta

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sheets and alpha helix ease and they

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have a lot of hydrogen bonds and so when

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I look at the the phases of ribosomal

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evolution from the origin of life until

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last Universal common as sensitive right

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over here we can see that the hydrogen

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bonds per residue are increasing so

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these proteins are just folding more and

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more compact and they're just looking

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more and more like proteins that we find

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an extent like today and then when we

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look at the surface area of them by just

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a computational method of just pretty

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much just rolling a ball around the

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ribosomal proteins we can see that their

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their surface area is going down and we

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just see that they're just folding more

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compactly and that they're just looking

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more in

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more like proteins we find today so I

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believe that is what I have for today so

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my name is watch my name is Nicholas

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kawatche and I'd like I working dr.

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Warren Williams lab and I really like to

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thank dr. Anton Petrov and dr. chadbourn

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yer who are having my mentors and I

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would just like to thank a grad calm in

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Georgia Tech and the IBB at Georgia Tech

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for providing my funding hi I was

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wondering what like you know what the

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minimum number of residues like a

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polypeptide or I guess a short protein

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if you define it that way would have to

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have to like start exhibiting some type

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of defined structure um there is

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recently a paper we're just through like

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just directed evolution i think it was i

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think was like 12 amino acids they could

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make a functional protein when there are

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about 20 amino acids found today in all

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of life and those 12 a lot of them i

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think almost all of them were actually

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the same amino acids found the

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miller-urey experiment which we

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hypothesize owe their very first amino

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acids of life I think you might have

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just answered my question but I was

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gonna ask how did you determine the

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sequence of proteins for your early

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proteins um well I was just looking at

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the crystal structures of available of

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the ribosome today so we have crystal

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structures of the e.coli ribosome yeast

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drosophila human in a few other species

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and I was just taking the sequences

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found within those proteins of those

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yeah thanks a great talk I find it

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interesting this idea that species

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complexity is related to the size of the

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ribosome is that possibly because we

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have a lack of data on ribosomes that

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are out there yet or is this not been

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shown across the board so far I mean for

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i'm looking at crystal structures and I

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mean there's just not that many of them

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available just yet I mean the very first

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one was like we crystallized or of his

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own like in the early 2000s so there's

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not that many of them but we can look at

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the genes of that encode for these

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ribosomes in species you know really

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easily we've been doing it for quite a

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while and so I that's the mile out

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knowledge i think these mammalian ones

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are the largest we've seen interesting

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here's the end up for a long time we

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thought that genome why's that we humans

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would be the best we'd have the most

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genes of anything and that's not the

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case and we've now found out that

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complexity in our little viewpoint of

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complexity isn't really related to

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genome size and so i was just wondering

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if that would be the case with ribosomes

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once we get more data as well yeah well

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what's interesting is that fly that

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ribosome work was based on a paper we

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had and we put it on someone pick it up

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on reddit and people were kind of

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getting like really like up in arms

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about like a big like discussions

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because we are just the biggest rivals

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own we've seen today is the human

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ribosome and then people we're just

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going off on like tangents about like

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why we're the most like the highest most

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dominant species because of that and

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just people were you know biologists are

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getting in there and getting mad and

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well so I've heard this idea before that

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you can see sort of the ribosomes of

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less complex species embedded in the

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ribosomes of more complex ones but

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obviously like you know if you take

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humans and like a fly for example those

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diverged in their evolution a really

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really long time ago so why would you

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necessarily find like a fly's ribosome

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embedded in there do you think that

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there's intrinsic sort of evolutionary

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bottlenecks that only the ribozyme can

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sort of get past and it has to evolve

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particular features

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or is it just oh you have to actually

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strip away some of these a lot evolved

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features to find like you know there's

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something on top of the fly ribosome

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that's not in the human one well I was

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looking at the structure and so like a

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lot of times like you can have like an

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80 base pair or you can have like or

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sorry ribosome au base pair or a GC base

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pair and like there's like differences

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in that but like we look at the

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structure of it it looks the same

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approximately but like those sequences

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might be different and there's like some

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parts that like are unique to different

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species so and plus I just like the RNA

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without like the protein like the

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proteins are very different between a a

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lot of organisms some homology

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okay well uh have people don't gather a

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metric measurements of ribozymes like

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measuring heat capacities and volumes

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hmm yeah yeah of course I think some all

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right IDC experiments that everything

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like that cool thanks i'm done with nam