 I did want to, I've been asked to let you know that I will share the slides so you can have those. But also, most of the genetics and genomics images and diagrams and so forth are on the NHGRI website. And who's going to talk about where those are? He's going to talk about that Wednesday morning where you can get those. So they're really great diagrams and they're very useful for teaching, I think. So those will be available to you. It's a very basic question I'm asking from the student perspective. You know, when you show us the replication animation, we have tons of animation on YouTube. Yeah. And we know that when you see something on an electron microscope, you need to kill the specimen to dry it and to process it and to get the image and everything. Right. How did the scientists come up with the process going on? How did you see the process? That's okay. You are showing us the animation. Yeah. How did you know that this is a DNA polymerase and this is helicase cutting it or like joining all those enzymes? Yeah. That's a great question. And I would say that it was basically the experimental process of taking, you know, a cell extract and saying, you know, here's what we can do with this extract and then starting to take mutations that don't do that. Okay. So variations that inactivate the helicase which then prevents the DNA from unwinding. And then you can look if you can, there are ways to differentiate twisted DNA from untwisted DNA. Okay. And to be able to tell whether it's twisting or untwisting or let's say it just slowed it down. Okay. That process. And then you can identify that there's a protein which when mutated will slow down that unwinding process but the replication will go on. Okay. Or, and then in terms of the sort of leading and lagging strand bits. So you can tell that there are these short pieces that are generated. So there's a long piece that generated off the leading strand and then the lagging strand is called lagging because the length of the DNA that you've replicated so far is shorter than the other one by roughly one of those segments. And then you can actually detect those little segments as well. So you say, well, we have, you know, a long segment, a slightly shorter segment. And then we have these little tiny segments that are exactly the difference between those two. And then they sort of start putting the pieces together and make a hypothesis about what's going on. You figure out a way to test that hypothesis and you generate that model. Okay. So in, in, in, in, in essence it is a model that's been generated through experimental testing, experimental hypothesis and testing. And then the animation that was done is a synthesis of that model into an animation, right? It may not be perfectly correct, but it's pretty correct. Yeah. Okay. So this is a gene. It's, it's a funny gene. It's Gene Wilder who's a comedian. He's been around for a long time. He's done some very funny stuff. So there are many different kinds of genes. That's not the one we're going to talk about. I want to go back and talk a little bit about basics of information containing molecules just so we make sure we're on the same page before we move through this, what does a gene do? How does it do it? Segment. So there's the DNA. We've talked about that a lot. It's double-stranded, et cetera, et cetera. There's the RNA ribonucleic acid. And the DNA is this kind of summary. I mean, this is a repeat of what we've talked about already. And RNA and protein. So RNA is nucleotide units. It's usually single-stranded. It can be double-stranded. You can make RNA complementary the same as you can DNA. It has four possible bases, A, C, G, and U. U is the complementary base in RNA for T in DNA. You're a cell, okay? It has lots of different uses in the cell. The one that we're most familiar with is the one that plays a role in the central dogma in messenger RNA, all right? And its template, its RNA is the template for complementary DNA or cDNA, all right? So you'll see that in talking about cDNA. And cDNA is basically the DNA that's replicated from the RNA message after it's been spliced. After the exons have been spliced down. We'll talk about that, too. Okay. So this little thing here is just to show that thymine goes to uracil from when you're talking about the difference between DNA and RNA. The other difference is that the ribose portion of the backbone is missing an oxygen, deoxy, in DNA, whereas in RNA it's not. Okay? Slight difference. Protein is a strand of amino acids. There are 20 possible amino acids in the sequences encoded by the triplet codons in DNA and messenger RNA, okay? So we're going in the DNA, the instruction set from four letter code to 20 different things in proteins. And how do we do that? I'll get to that in the next slide. Genes are things. I mean, before we had a concept of DNA, RNA, the genetic code, we had a concept of gene, but it was an abstract concept. And it was a thing. It was a thing which, when inherited, corresponded to a trait, a phenotype. Okay? So that's just kind of this really vague, abstract kind of thing that scientists started to think about when you couldn't see what was really going on. Now we know that a gene is encodes a functional transcriptional, I mean a functional unit from a single transcription unit. Okay? We're going to talk about transcription in a minute. So the concept of gene has really varied over time and is still somewhat controversial. So here's a series. This is a series you can get off genome.gov. A bunch of famous scientists talking about what is a gene. Okay? What's a gene these days? I think a gene is like R, right? It's up to your interpretation. I know it when I see it. I think we have a much more nuanced view. The genome is dynamic. The idea that most of it is junk DNA I think has now been tempered. We know gene regulation is far more important and far more complex. But we remain with the view that in and of itself DNA is an incredibly inert molecule. It is the blueprint for cellular machines. Okay. So that moves on to the next guide. But I think Carl has just said it well. We have a basic agreement of what a gene is, but there are lots of variations on that. And as we learn more, somebody asked me in the breaks, talk about the things we don't know. So we don't know a lot of stuff. And this is one of the things we don't know. We don't know all the things sort of this concept of gene can apply to. So we can continue to talk about that as we go on. But from a simple standpoint, a gene encodes a functional unit, a protein, an RNA that does something, and it's from a single transcription meaning that it's one strand of RNA that's transcribed. Okay. What do genes do? They code for things. A blueprint or a deep-tailed plan for how to run and build an organism. It's kind of like an orchestra. They regulate each other. Okay. So one gene may produce a product which regulates other genes. Okay. It turns them on and off, makes differentiation happen, makes species, makes organ-specific genes be expressed, et cetera. They genes make through transcription RNA, through translation, eventually through RNA. They make protein. And genes can also make proteins that are modified and have other complex stuff happen to them even after translation. All right. Basic gene structure. So this is an important point, which I'm not really showing well on the slides, but there's a difference between prokaryotic genes and eukaryotic genes. Prokaryotes are things like bacteria. Eukaryotes are things like yeast, plants, humans, other big complicated things. What's the main difference in the genes that we think about when we think about those two groups of organisms? Yeah. So that's one thing. So the structure of the compacted DNA is different. Okay. And in terms of the gene structure itself, the prokaryotes, the bacteria and so forth are not broken up into these segments called exons and introns. Okay? It's one continuous stream of protein-coding DNA in a gene. In us, however, the chromosome, if you spread it out, you get to the DNA level. And then there are segments of the DNA which are marketed as genes, partly because they do something that we just talked about. But they have these sort of recognizable hunks called exons. And the exons are actually the coding parts of the gene. And it's like taking a prokaryotic gene and it's slicing into pieces and sticking junk DNA in between. Okay? Why do we do that? Lots of reasons, but that's the way it is. So exons are the coding parts, introns. The intervening sequences inside, in between are the pieces that separate the exons. And how do we put these back together? I'll show you in a second. So exons are segments of genes that contain code for proteins. Just a couple of minor exceptions to that. Introns are spacers that get cut out after transcription. And gene coding regions are about 1% of the genome. Okay? So there's 99%. We don't know a whole lot about it. All right. Transcription. How do we take that gene DNA-encoded stuff and turn it into RNA? The word transcribe. You think about ascribe as somebody copying a copy from one thing to another thing. They're copying it. It's the same thing. They're just copying it. Transcription. And in this case, in genomics, we're talking about transcribing from DNA to RNA. It's the same information. It's a three-letter code. It's the same code, same basis, et cetera. And it's done by a molecule like DNA polymerase, but it's RNA polymerase. Instead of getting deoxynucleotides, it uses nucleotides and it makes RNA instead. Okay? There's also the concept of a synth strand, the strand that contains the protein information in the direction that it will be sequ- will be synthesized, and the anti-synth strand, just because you have to have two strands. Okay? Can I make a comment? Yeah. Because I think it helps with the intron exon thing, something that I've struggled with the last couple of years, trying to figure stuff out. So I work on a project that does whole exome sequencing versus whole genome sequencing. So when I first signed on to the project, they said, well, what is the difference between those two things? And what they said to me was, think of like a necklace with beads on it. If you cut the necklace and you keep the bead and maybe a little bit around each bead, there's in between those sections are your introns. Yeah. And you might miss some, like there's stuff in the junk DNA that you might miss, but the whole exon sequencing is really getting at the heart of those beads and what's maybe right around the beads, but we could miss this other stuff. You miss a lot of stuff. So you miss many? That kind of helped me. I just thought it might be a good teaching point for other people to think about because that's, I still think people get confused about the difference between a whole genome and whole exome. Yeah. Right. So when we talk about sequencing the whole genome, we're talking about sequencing every last base that the technology will allow us to, at this point in time, which is not every last base. Okay. When we talk about sequencing for medical purposes, most of what we know right now for medical purposes has to do with what the coding regions of the genes, those parts of the genes that encode proteins, because the proteins do stuff. Okay. And we understand that a lot better than the parts of the genome that don't. Okay. But that's only 1% of the genome. Right. So when we're sequencing the whole genome, we sequence everything, we get the genes, we get the coding regions, we get the non-coding regions, we get the intermediate regions, we get the junk DNA, we get lots of stuff. Okay. Lots more data, 100 times more data to analyze when we're trying to really focus in where the information is going to be most useful. We do a step at the beginning of the whole genome sequencing, where we select just for these segments, these exons. Okay. And that's called a whole exome. Right. So we're selecting for that. We're selecting out of all that DNA just the segments that are important for encoding proteins. And that's all that we sequence. Okay. It's a lot less sequencing and we know more about it. So that's our current approach to doing things. I hope that's helpful. Okay. So transcription. When we, after the RNA is transcribed, it's got this genetic code in it. And it's genetic code is universal, which is also really cool. Okay. Bacteria have the same genetic code as we do. Right. Viruses have the same genetic code as we do or they wouldn't be able to infect us. Okay. The code is three bases long, one amino acid out of three bases, or a signal to say, stop transcribing. It is degenerate. Some bases don't, some base changes don't result in amino acid changes. They're synonymous. Okay. There's synonyms. So for example, serine here, amino acid, can be encoded by a triplet of U, C, U, or UCC, or UCA, or UCG. And in fact, down here, it's also encoded by A, G, U, or A, G, C. Okay. Any of those triplets encodes for the amino acid protein, amino acid serine, and once it's in the protein, who cares what the codon was that generated it? You can't tell the difference. Okay. Translation is a reading frame dependent. So if you insert or delete any number of bases other than three, you have shifted the reading frame instead of something being in the first position, second position, then you'll get a different amino acid, or maybe even a stock out of it. Okay. That's called a frame shift. Here's a nice diagram of translation. We'll start with the DNA, and we transcribe the RNA. The RNA is pushed through a pore out of the nucleus into the cytoplasm. It goes to endoplasm. We're ticking them where these big machines called ribosomes that are very fast and very efficient, and the ribosome takes up the RNA, and it recruits these transfer RNAs, which basically have three single codon, complementary codon here, and also attach the specific amino acid that's for that complementary codon, and it brings them down and then attaches that new amino acid to the growing chain of amino acids in the polypeptide. So here's codon 1, the start codon, which is always AUG, methionine, and then the sequence of the protein with all these amino acids encoded by it. You can see if you delete the C, you're going to get a different set of triplets going further. That's the frame shift, okay? And then one UAA for stop. So whenever the ribosome reaches that particular codon, it says, oh, I don't have an amino acid to add there. That's my signal to stop making this chain longer and longer. Okay. Proteins, what do they do? I'm sorry. How are they organized? So it's a chain, and the chain has a secondary protein structure, which is it tends to sort of get itself into things called pleated sheets or alpha helix, okay? So there are segments that will go in one direction, so it will go in the other direction, segments that are still amorphous, okay? So it's kind of loose out there. Then once those are formed, then it starts to fold itself onto itself and into a structure which has a good energy and bonding between the different segments. And that's the tertiary protein structure. And I'm not a protein structure guy, so give me a little break here. So then the final level, which I think is really very important, is that quaternary protein structure where proteins fit together. Two proteins, more than two proteins fit together, okay? So this tertiary protein structure is actually also really important, because if you have an amino acid in here, that's really important for forming the right bend or the right cross-link there. And it's changed. It's variant. You may not get the same shape, and the protein may not get its whatever function it is that it's supposed to do. Okay, so what do proteins do? They hold. They digest. They cut. Those are enzymes. They build. They convert one chemical into another chemical. They take up space, okay? They send messages. They can send signals. They can glue or attach two cells together. They can glue or attach molecules together. They can specify. They can identify. Think of antibodies, okay? Those are things. Antibodies are the things in the immune system that say, this is me. This is part of me. It's not, you know, that thing that just got injected into the bloodstream isn't me. Go kill it. Logic. There are ways that proteins can encode logic. They can respond and regulate. Think of hormones. Some hormones are proteins, polypeptides. And they can contract and expand. Think of muscles, all right? This is sort of getting back to the idea of the protein function and the variation and its interaction with environment. And you can have the variation reduce in less function or loss of function. These are terms you'll hear or read if you read the medical literature. More function, gain of function. New functions, also gain of function or neomorphism. Or no change. Let's call it benign, okay? Why is all of this important? It's all integral to life. It affects aspects of health and illness. And I guess I put this here in part for those of you who have students who are interested not in science but in other things, okay? That they may be interested in health and illness because of something going on in their family. They may be interested in chemistry or the effect of things in the environment. They may be interested in IT, information science. There's a lot of information science in genomics. Behavior, genes affect behavior. Reproduction, also known as sex in high school. History, there's a very rich history in genomics. Sociology, how do we deal with all this information that is important for a lot of reasons. But one of the things is it tells us who we are. It tells us about identity. Geography, so when populations grow and their resources are limited, they migrate, right? So we have an idea about geography and populations. Economics, increasingly important. Environment, crime, right? Everybody watches CSI. And also because it's still very mysterious. There are lots of things about genomics that I think are very mysterious, okay? And I'm gonna have to speed up a little bit. So inheritance, I'm gonna go through inheritance here. These are inheritance of phenotypic traits here. And it's kind of about looking at yourself. Gregor Mendel, I just have one slide, I promise. I'm Gregor Mendel. He's this guy who really is a great story, really great story about how he inferred genes from playing with peace over time when he had time. Like everybody has that much time. Okay, so what I think is really cool is that he really did use some version of the scientific process, right? And that's really what this slide is about, scientific process. So he's a good example of that. I did talk earlier about balance and unbalance in balance in the genome. So balance means in humans, you have two copies of every gene, when you hear from mom, when you hear from dad, with the exception of a few on the X chromosome, which when you're a guy, you only have one copy of. And so balance is really important. If you take a recipe for a cake, think of the genome as a recipe for a cake, and you change the recipe, you modify the recipe. My sister does this all the time. And you give her a good recipe and whatever happens. So she says, well, I'm going to add half as much sugar because I don't want to be as filling, right? It's still cake, right? It's not the same cake, right? Some things, if you don't add as much of it, it will come out completely wrong. It won't be a cake anymore, right? So the same thing applies in genetic phenotypes and genetic diseases. It's like a recipe. If you change the recipe, sometimes it matters, and sometimes it doesn't, right? Sometimes it's just as good, a little different, but it's still a good cake. All right. I'm going to skip this slide because it's really complicated, but it basically goes through all the details that are dominant and recessive that I think most of you are probably familiar with, but it takes too much time to go through at the moment. Examples given of Domino's Huntington's disease, Huntington's Korea, so a disease where you have uncontrolled movements and eventually some dementia, okay? And sickle cell anemia, which is a recessive disorder in which it has highest incidence in African populations or African derived populations, including African-Americans and cystic fibrosis, which has highest incidence in Caucasian populations. Two examples of the founder effect we talked about earlier. So meiosis is not mitosis. It's a different kind of thing. Meiosis is about taking a regular diploid cell, the same one we started with when we started with mitosis, but turning it into four cells that only have half the genetic material, one full copy of a genome instead of two full copies of a genome. And meiosis starts with DNA replication, same as mitosis. And then it goes through phases, which I won't really have time to go through, that break it into multiple parts. So then the outcome of this is four haploid daughter cells, each with 23 chromosomes. Those are the germ cells, those are the sperms or eggs, okay? Questions about meiosis? And I purposefully separated mitosis and meiosis but I think of them as kind of different, even though they have some of the same things. And when you put them on the same pages in the book, they look very similar. Recessive is a concept that is often described as having two bad genes, all right? And I want to flip that on its head and say recessive means that you don't have any good ones, all right? So for a lot of genes, having one copy that works just fine is perfectly fine. There's no difference that you can detect from having two copies versus one copy. You just have a backup, right? And when one of the backups is gone, you're still fine, okay? When both copies are gone, you have a problem because whatever instructions that was important for, it's missing. So my very generic example is, I only need one hammer to hammer nails, okay? I can hammer nails, but I have two hammers, okay? Who doesn't? If I take away one hammer, I can still hammer nails. Same thing with the needle and thread, I can still sew. I do sew. But if you take away both, you've got nothing. You close it and fall apart. Your house falls apart. You can't do it, all right? That's my concept of recessive. All right, how do you tell recessive inheritance there's no normal copy? In a recessive inheritance pedigree, an unaffected person has at least one normal copy. That's just the converse of what I was saying. So long as you have one normal copy, you're okay. A carrier is a person who has one normal copy who's unaffected and transmits 50% of the time. They transmit the normal copy half the time and the messed up copy the other half of the time. When I say transmit, I mean pass it on on your germline to your offspring. And both parents of an affected person are always a carrier. Okay, that's the rule. Ex-linked recessive inheritance is pretty much the same, except that there's no normal copy. But it affects predominantly males because males only have one X chromosome to start with. They only have one copy to start with. If they're missing that copy, it's the same as having no hammers. Okay? And I'm running out of time, so I'm going to go through this pretty quickly. Carriers are females and males with an extra X chromosome. That's Gleinfilter syndrome for anybody who cares. And the carriers are females because they have an extra copy, right? They have two X chromosomes. Males can't be carriers unless they have an extra X chromosome, which is an unusual but not infrequent occurrence. All right. White-linked inheritance. Why don't we hear about much about this? Because the white doesn't have much on it. It has a few sex-determining genes that say, yes, make some testes, make this a male, and a few other things, but it doesn't have a lot more. Okay, so you can pretty much ignore that. Mitochondrial inheritance. We touched on it at the very beginning. Both sexes are affected. It has a variable expression because there are lots of mitochondria passed on. Some of them may have a problem in them and others don't. It's vertical transmission, meaning in a pedigree. Like in a pedigree like this, it's passed down through the generations. But it's only passed down through the maternal lineage because everybody's mitochondria, my mitochondria, came from my mother's egg. My father's sperm has mitochondria, but only in the tail to make the tail spin around. It's an energy source to make the tail spin around, but those don't get ordinarily dropped into the egg that becomes the zygote that becomes the human. And the disorders affected by mitochondrial inheritance are those that are in energy-intensive organs, brain, muscle, liver, et cetera, because it's an energy factory. New mutations, I'll skip over that. Beth, what do you think I should keep talking about? Okay. Okay. I wanted to talk about chance and risk because these are concepts that come up in genetics a lot, and in particular in medical genetics, which is my expertise. And I wanted to differentiate between two sort of concepts of chance and risk. One is it happened by chance. It was unplanned, it wasn't orchestrated, and it was apparently completely random. So not terribly predictable in terms of what would happen. And my metaphor for that is a dartboard. You throw it at the dartboard, and it may be predicted roughly how close it is, but you're not going to predict exactly which side it's going to go on, okay? Whereas then there's a chance that's like likelihood. You can figure out what the likelihood is empirically, but it's a predictable process with random step, okay? And the thing to slide is dice. So you can, you know how likely it is that you're going to come up with a six, right, when you roll the dice. So that's a little bit more like knowing how something is inherited in a family and being able to predict how likely that's going to happen with the next child, okay? If you don't know how it's inherited in the family, you can't give them information. So chance and genetics, a new genetic change, like a mutation, is kind of one of those unpredictable things. You can have a rough idea of what the frequency is, but you can't predict where it's going to happen or what basis is going to change. Whereas inheritance of a genetic trait or disorder is something that is predictable if you understand the phenomenology. Yeah. So your patient can maybe know that most of the time they're bad or sometimes they cannot detect that at all, but can they be good? Yeah. So that's why I try to stay away from the idea of the word of mutation, but I've probably failed you in that. So the variation happens and then depending on whether, so it can change the protein even, but if that's a positive change for the organism in its environment, if it allows that organism to withstand warmer temperatures in the ocean, for example, that may be a good thing, okay? And then if that advantage allows the organism to reproduce more efficiently than the one that didn't have the change or one that had a bad change, then over time that single mutation or single variation will expand in the population and become predominant, okay? All right. Lots of applications. I think you're going to hear about some of these in the next few days, so I'll skip over that. And I just mentioned, because I think you're going to hear about cancer as well, that these concepts of cell division are crying DNA replication. Normal growth, this is a growth chart that we use from the pediatric office for kids growing, make sure they're growing at the right rate. Overgrowth in disorders where certain parts of the body may overgrow as in Proteus Syndrome. And cancer is also a disorder of overgrowth. So you take the same concept of growth, which is good in certain circumstances. You dysregulate it, and you have disease. There's a whole segment on precision medicine, which I don't have time to talk about. Somebody else may talk about it, I don't know. Okay. All right, let's zoom through here. The basic concept is that you have people that are defined as having a medical condition in the yellow, and you try treatment, and if the majority of people respond to that treatment, then you say, okay, that's a treatment for that condition, even though there's a segment of people who don't respond to that condition. That's the way we do medicine now, okay? We try something, if it doesn't work, then we try something else, okay? There's a lot of trial and error, and that costs money, and people get sicker in the meantime, all right? What we can understand using genome science is that people actually are not all the same, and they may have variations which may affect their responsiveness to a particular drug or to a particular therapeutic approach, or in fact, they may have different conditions that on the outside look exactly the same. So diabetes is not one disease. It's many, many diseases, okay? If we understand what causes it, we can target therapies to those individuals. So if we understand what's going on behind the disease and what's going on behind susceptibility to treatments, we can target therapy and treat a lot more people effectively. And I think all of this is going over the plan, resources, and thank you. I do want to say that I'm here because I had teachers in middle school and in high school who cared about science and who cared about me understanding it and teaching. So if that wasn't the case, then I wouldn't be here. So it's really important that you guys are here and you have the commitment to take your summer away from the beach and come in here in a dark room and listen to me talk. So it really does have an impact and I want to emphasize that very much. And for the nurses in the room, you are teachers too, and you are an important part of the team and increasingly a segment of what you do, lots of what you do, is teaching the patient about their condition, helping them understand what they're doing so they can know how to help themselves through the process of medical care. So it's really, really important. And I'll end there.