Human Genetics PDF

Translated from Persian to English - www.onlinedoctranslator.com Second session All the traits we have, whether those we know as diseases or those we see as abilities orbenefits We know that it is mainly directly and sometimes indirectly related to the genetic material and ge...

Translated from Persian to English - www.onlinedoctranslator.com Second session All the traits we have, whether those we know as diseases or those we see as abilities orbenefits We know that it is mainly directly and sometimes indirectly related to the genetic material and genetics of individuals. For example, the diseases that a person gets, for example, one's skin color is white and the other's is dark, one's eye color is light and the other's is dark, one is intelligent and the other has a different intelligence, height, weight, size, whether they are interested in music, whether they are interested in a specific job, whether they have a talent for 3D modeling, whether they are more successful in engineering or in the humanities, whether they are a thinker, whether they are good-natured or bad-natured, etc., all of these have their roots in genetics. Now, in order to determine which traits we want to study and examine, whether in terms of disease or generality, as aTo determine whether a person has a genetic origin or not, we must examine these three options: benefit To identify the origin of the adjective, we must examine three options: 1) Recurrence in the family(repeat in a family2) Recurrence in monozygotic twins(concordance3) Possibility of creating animal models)For the gene to which we have attributed the trait (development of animal model) If a trait is genetic, all three of these options must be true for that trait and the gene or genes that predispose to it. 1)The meaning of a trait being repeated in a family is that the trait is repeated vertically in successive generations. In medical genetics, in order to study disease and provide us with a lot of information at once, we use a series of symptoms and characteristics calledOr we use a family tree where men are marked with squares, women with circles, and ragged people have no markings on them, but a pedigree We draw a line over the dead people. Each generation is identified by a series of Latin numbers. We draw the people of each generation in order of age from left to right. We usually show the occurrence of a trait with a specific symbol in the family tree and it has been transmitted in several generations and affects a large number of people. We have family trees where the disease is common in one generation, for example, it does not exist in the first and second generations, but in the third generation it affects a large number of people. We cannot necessarily say that it is genetic. The reason could be that the trait is formed under the influence of environmental factors. For example, consider a family affected by a lack of food and they all suffer from muscular and degenerative diseases of the nervous system and suddenly we see a large number of sick people in a family. When there is no vertical transmission between generations and it is observed in one generation, we tend to think that it is probably not genetic and is due to other factors. So the sufficient and necessary condition for us to consider a trait as genetic is that this trait is passed on in successive generations. pg. 1 It can be transmitted vertically and involve a large number of family members. 2)The next point is the repetition in monozygotic twins. Twins are either monozygotic or fraternal. The two eggs are completely separate and two separate individuals can have different sexes, the genetic background of each is different. Why? Because they are created by two completely separate eggs that are released by the mother and the genetic makeup of each egg is independent of the other. These are not our concerns. Monozygotes are monozygotic. In the first cell division, instead of remaining connected after division and both forming an embryo, they separate and each becomes the origin of the formation of an independent embryo. So, genetically, they are identical. Usually, there are no phenotypic differences, especially in the case of traits that have a genetic origin. Of course, between the two monozygotic twins that we have seen, there are differences throughout their lives, and not everything is necessarily the same. These differences that arise in their lives, in phenotype and behavior, and in a series of characteristics, are usually related to a series of traits that are influenced by the environment in addition to genetics, or that changes have occurred in the genetic material due to growth in different environments. Very minor changes that are, for example, due to successive divisions. For example, monozygotic twins who grow up in separate environments and in two separate families will have a series of differences based on the type of nutrition they have, their type of behavior, and their lifestyle. These differences, which are influenced by the environment, come and go. It creates changes in their genetic material, which we don't call genetic differences. If we see a trait that is repeated in identical twins, we say that this trait isIt has a high concordance coefficient. It has a high compatibility and this is a genetic trait. pg. 2 Application of the monozygotic twin study: - In the study of diseases(Does it have a genetic root or not?) Of course, if it has a genetic root and the individual has inherited it, its rate in monozygotic twins is much higher than in the general population, and this indicates a genetic root. - EndophenotypesCompare (the traits we study about a specific disease and find differences in that disease) We see) usually uses this term in neurological diseases, although now it is also used in some way for other diseases. It is usually to evaluate the environment and genetics, for example, people with schizophrenia whoIt is common in society, double rate We have two types of schizophrenia, one that begins in youth or adolescence and reaches its peak by the age of 25, and the other that occurs in middle age, above 40-45 years. In each of these, we have significant differences. For example, in young people, which is mainly genetic in origin, we see people who carry the same disease name but have different severity of symptoms. They show different phenotypes, for example, one attacks while the other does not listen. This is called an endophenotype, meaning differences in the occurrence of symptoms or traits that lead to attributing a disease or a specific phenotype to an individual. Usually, a series ofStandards criteria We have to label someone as sick, but we can't necessarily say that someone is sick until they have a characteristic. The attributes that a person criteria It should show how many there are and that they are not the same in terms of valuation, they are different from each other, and then it is the job of the specialist to see which one of these the person has.And under what conditions does a person become sick? Endophenotypes within individuals that are labeled as disease criteria "They ate" means not that it has not yet been determined whether or not he has the disease. ExampleAn example of schizophrenia is that when we talk to people, some of them seem logical and some seem illogical. The point is that schizophrenia is usually seen in families with genetic roots, who are intelligent people. That is, many top-level experts have shown symptoms of schizophrenia. Schizophrenia is caused by a lack of proper communication between brain cells. pg. 3 The brain is formed in different parts, and the connection between nerve cells that guides our behavior creates misaligned connections between nerve connections. As a result, in addition to increasing the brain's ability, it causes it to display a series of phenotypes or behaviors. That's why we say that not all people with schizophrenia are necessarily sick, and sometimes they can be intelligent people and can be repeated in families. - Quantitative trait evaluationQuantitative traits are traits that are usually influenced by multiple genes at different points, and the phenotype we see from an individual is due to the accumulation of different genes. Due to their identical genetics, these twins are a great tool for quantitative traits such as intelligence, height, skin, etc. - Heritability rateFor example, people who have a good voice inherit it from their parents and usually pass it on to their children.It is used in humans. It is also very important in the case of race and breed. Heritability is a key factor in countries. They use advanced technology to racialize their populations. :Eugenics It is a science that is used in some countries and is used to breed a society that has the abilities that separate an individual from the general public and more importantly, the genetic makeup of the individual and provides the talent to manifest it. The society uses these individuals more and adds them to its genetic pool (for example, it attracts top candidates in the entrance exam or sports champions of that country) to enable the country to progress more in the long term. (It allows top candidates to participate more in creating the next generation). For example, we do this too. In a flock of sheep, we allow those who give birth to twins to survive more than those who give birth to singletons. Nature allows those who are strong to survive longer and prevents people from doing so. Natural selection that have defects to contribute to the genetic pool of the next generation. For this reason, in many countries, people with defects such as the blind, deaf, etc. are not given the same opportunities to contribute to the next generation. In some countries, these people were even deliberately sterilized.To thisIt is said to be eugenic, meaning the science that allows superior traits to participate more. Gives it to the next generation.Now, to implement this, we need to see how much of that trait is heritable and how much of the genetic pool plays a role in creating and shaping it. So here we need toOr let's examine heritability. Monozygotic rhizomes are very good at helping us with this. - Gene expression level:Study of gene expression levels of mechanismsWe can examine genetic factors in gene regulation. The promoter region of these genes is the same in individuals, and only environmental and epigenetic differences can alter gene expression. - Studying the interaction or the degree of influence of a trait by environmental factors:When the genetic background is the same, the differences we see in the expression of traits or phenotypes will definitely be influenced by environmental factors. pg. 4 3)Possibility of creating an animal model: If we say that one or more genes play a role in causing a disease or trait, and if this gene is really responsible for causing this type of phenotype or disease, if we create a model organism in which all its genes are healthy and only the gene wecandidate We have changed to create a trait, we expect our model organism to show the phenotype or trait we want. To create animal models, the best model is a human, that is, we create a human with a problem with the gene we want and now see if it has that trait or not. That is not possible in humans and we cannot do this on a human embryo, so we have to use animal models and manipulate that genetic background and see if it creates the trait or not. So we need models that are very similar to humans. The closest model that is genetically similar to humans is the orangutan. It has a lifespan similar to humans and is very similar in terms of genetic makeup. But if a scientist with a limited lifespan wants to study a trait and see its phenotypic effects, his life span is not long enough to fully notice the changes until the orangutan grows up and see what that trait is like. So we need to use a model that has both a genetic background close to ours and can complete its life span in short intervals. And the other thing is the conditions of its maintenance. We need toheritability We need to manipulate several model creatures of the same species at the same time. We need to be able to use space optimally, so the size of the model must be small so that we can maintain it. Another issue is nutrition. For example, an elephant is genetically close, but it eats 150 kilograms of food a day and its maintenance conditions are difficult. The next point is that our model must give birth to a large number of babies. So, all these conditions lead us to choose a model that is a little different from humans but has other advantages such as lifespan, number of offspring, maintenance conditions, cost, and availability of appropriate genetic material. As a result, we use mice. Of course, the results obtained from mouse models are not 100% consistent, but more than 90% are successful and have the necessary consistency. To choose a model organism, we need to look at its embryogenesis. For example, we look at the development of a mouse embryo in its mother's womb.E means half a day (3.5 E and the numbers after it are the length of time it has an embryo) 0.5 emberyonic is the abbreviation for E That is, the embryo is three and a half days old. The embryonic period of a mouse is 20 to 21 days. It has a short reproductive period, meaning that we can have a number of generations in a short period of time. The lifespan of a mouse is 2 years, so the mouse is an ideal model. In order to create a model organism, the genetic change of the desired model must occur in each of its cells.Note:When we say that a trait is genetic, it means that the individual can acquire the genetics or genetic change that causes this trait in two ways: 1)It has acquired this change through its parents and sexual gametes, and in this case, this change occurs within the zygote, and of course, this zygote that creates the existing body has this change in all its cells, and this change remains with this change until the end of its life. Genetic variant. Inherited or something inherited from parents. pg. 5 2)But anyone can experience changes throughout their lives. For example, someone with skin cancer. Cancers occur mainly due to changes in genetic material. This change, which occurs in a skin cell on the hand and causes melanoma, is not necessarily inherited from parents. A trait that is passed down from parents comes through the germline. That's why it's called a germline trait, which comes from the zygote and spreads to all cells. This trait is acquired by the tissue itself in the area to which it belongs.They call it somatic variation or changes that occur in cells. It occurs somatically. These changes do not have the ability to be inherited, but in contrast to the first case, these are 100% heritable and pass on to the next generation. So when we want to work on traits or diseases, we must make sure that the trait we are studying and the genetics we attribute to this trait are genetically transmitted (through germline) from parents to the individual or are the result of somatic changes. If the changes that cause the disease have reached the individual through the germline and that change has caused the disease, the change is not only in the diseased tissue but also in all cells of the body, then we can study that change in other tissues as well. For example, if someone has breast cancer, it is not necessary to take a biopsy of the breast; it is enough to take a blood sample or buccal cells from the mouth. If we look at the developmental stages of a mouse, the zygote cell divides and goes through various stages to form the blastula, which is hollow. A group of specialized cells separate, which are calledIt is said that it can form the inner cell mass germ layers. It forms the ectoderm, mesoderm, and endoderm, and these germ layers together form the organs. So, if I want to create a model of an organism that has a genetic change, in the laboratory we take the gene we want and change it, for example, we delete a fragment or change the sequence, we manipulate it, we disrupt its function. This is done in the laboratory. page 6 On the surfaceThen we have to give this change to the cells and get it from the living organism. This is done in vitro, in DNA conditions. For this purpose, cellsWe separate the inner cell mass, the stem cells that have the ability to make all cells. We take these cells from a mouse that we have selected. It has a pure genetic background, it is completely purified, we take the embryo and we put it on the blastocyst cells orWe perform the manipulation and confirm it with the inner cell mass technique. Genetic engineering techniques that have made the changes we wanted in our target gene. After these changes, we need to get a living organism from these and to do this, we transfer the cells whose genetic changes have been confirmed to another blastocyst (to another mouse). Because we killed the mouse from which we got the embryo and we kill another mouse to get the unaltered blastocyst from that, now we transfer these altered cells through a microscope.We do IVF in this space (blastocyst space) and we inject This embryo that we had before has a series of germ layers and is a complete embryo. Now these cells that we introduced mix with the previous cells and participate in the different layers and in their construction. Now when we transfer this to the embryo, another female mouse that has been falsely pregnant (using a series of techniques, we create hormonal changes in her body) while she has no zygote. We introduce these manipulated embryos into the body of a third mother, who is forced to (They are precious mothers and are very kind because in animal embryos, if they have organ defects and are born (mother foster) Let's say one of the people who quickly destroys the fetus is the mother herself and does not let the fetus suffer. Now we have selected a gene and we do not know what trait it causes. It may become sick or have no arms or legs or other problems. Under normal circumstances, the mother kills this fetus. So let's choose an expensive mother, transfer the fetuses into her body. That expensive mother mouse has the property that it will keep this fetus no matter what and feed it, so we can see the creature. page 7 These children who are born with patchy skin are called chimeras. A chimera is someone whose body cells are not from a single source but from two or more sources. These mice are born, and if we are lucky, the manipulated cells in the germline of this mouse have gone to chimera. Note that this chimera creature has two or more cell lines. We want a mouse that has all the genes in its body changed and that this mouse can transmit the manipulated gene through its gamete. We provide the conditions for survival for this mouse, we provide the conditions for the production of the next generation, and now the creatures that it gives birth to have some of the manipulated alleles according to what we want (gray mice), and some of them do not have the manipulated allele (white mice). We call this organism a heterozygote. Now, if we breed two heterozygous mice, we can obtain organisms that can be homozygous, heterozygous, or wild for the trait we want. Based on the phenotype we see, we can now determine whether the gene that we had nominated to create the trait was correct or not, because all of its cells have been manipulated. It is like a person who has acquired a mutation through their germline that will show it throughout their life. (The manipulation we perform is on one allele)And whether this change is in the gamete or somatic, it is a matter of chance, which is why they create multiple embryos to increase the chances of this happening. We know Mendel. He started his work with peas. The work he did created a series of traits and laws that still exist today and that we use and that form the basis of research. Mendel's three laws are very important, especially in medical genetics. page 8 He did not know about genes and alleles and presented these hypotheses based on the phenotype he saw. When we want to do something, we should see and report what happened, not what we want. Mendel also analyzed the data he obtained, not what he wanted. 1)The factors that create traits are not mixable. At that time, genes and alleles were not known, and there was a low level of uniformity. These later have their own nature when they separate, which is shown in the second law 2) the law of segregation, meaning that what creates a trait separates in the next generation and can pass on the ability it carries to the next generation, and third 3) that those factors that create a trait are inherited independently of each other and do not necessarily tend to come together. Today we know that genes that are on separate chromosomes are inherited independently, and those that are on the same chromosome, if they are distant, can separate from each other by recombination and independently participate in creating the next generation.. We have a number of diseases and phenotypes in humans whose origin is important, whetherOnly a single gene in the creation of that single gene Does it matter whether a moleculeWhich is controlled during cell division, takes the form of a chromosome and contains tens and sometimes hundreds of DNA Genes cause diseases or traits. We need to recognize this point when we want to study a trait. The next point is whether the trait we are studying is under genetics or does the environment also play a role in it, and we need to obtain the percentage of how much each of them affects. The next point is that for many traits or diseases that we have, this issue is usually mixed with the above cases, whether it is due to changes that occur in somatic cells or cancer. For example, in the case of cancer, changes occur both due to changes in somatic cells and cancer is caused, and also due to genes that a person inherits from his parents through his genes. He can have a predisposition to cancer. We need to distinguish them from each other, whether we are dealing with a single gene or a chromosome, a germline trait or a somatic trait, which is especially important in medical genetics, for example, a mother who is infected with pg. 9 Is she pregnant with Mongolism? Will her child be Mongoloid? Whether the chromosomal disorder she has is due to the joining of two chromosomes or not, is it a fixed numerical disorder, it is influential. We need to recognize the extent of genetics and the influence of the environment. For example, in the case of schizophrenia, which occurs in women over 35 to 40, it is not necessarily genetic. Usually, the behaviors, lifestyle, family relationships, and social relationships that occur to a woman during pregnancy and childbirth cause her to develop the disease in old age.It is effective to treat depression. Family behavior is extremely effective on depression. There is something called a standard in society, for example, the blood pressure of women in society is 10 over 8, but a person may have a lower pressure, and this is normal for that person because they live a normal life and have no problems. So we have to differentiate between the norm (Society and the natural conditions of the individual's body, that's why we say the individual should come to counseling to see how the individual (norm) We have to look at him from the outside, see his size, see everything. In genetic work, we have to be very careful and not quickly say that there is a problem because it is not according to the standard. And we have to see whether what the person says is according to the society's standard or his own standard. So we have to distinguish between the standard norm and the physiological conditions of the people. But the point that we have when working with genetics is that when we want to study a trait or phenotype and study the role of genes, we want to see what role these genes that we want to study really play, what we should expect from the genetic material and what we should not expect, in the developmental stages of the embryo, when an organism wants to form, like a mouse, a human or anything else, a zygote is formed. The zygote cell is formed by the sperm head entering the egg, and the two nuclei mix together and form one nucleus. These two genetic materials, two haploids that are placed together, are supposed to form an embryo and many other things. In the first stage, when the zygote is formed, it begins to divide at a certain interval, and these divisions are added. The control of whether the cell should divide after formation is under the control of a series of genes. This division that is carried out is of the type of mitosis. It is a division in which a mother cell creates two identical daughter cells. Here, too, a daughter cell is created that is quantitatively similar to the mother cell in terms of genetic material, but qualitatively different from it. Because at this multicellular stage, if we were to separate one of these cells, it would not be able to create this mass like a zygote. That is, with this division that it performs, it is true that it increases the genetic material. It also has energy. It does something with this genetic material. This cell (the first cell) has the ability to create a complete organism, but the cell that is two and a half days old does not have the ability to create a gamete. That is, in this two and a half day interval, something happens that takes this ability away, but the ability of the cell as a It gives it the inner cell mass, and at the same time it divides, so this genetic material that's here has this inner cell mass. It directs when the cells divide and when they settle in a specific area, and now these specific areas form a series of layers of ectoderm, mesoderm, and endoderm, and perform gastrulation. This gastrulation that occurs either alone or with the help of others leads to organogenesis and builds organs, and in addition, it also determines their number and location. So it also provides information on the structure of organs. page 10 It is also controlling the positioning information of the organs, which comes from genetic material that is two meters long (for example, a mouse). Gradually, the organs communicate with each other, blood vessels form, then the digestive system forms, the organs become more complete, the coverings become more complete. What guides it? Those two meters.So we have a control setting, DNA. In the genetic material and information that is in each individual cell, but each of the cells that make up the different parts can no longer be the same as the first, it all proceeds with mitotic division. So this mitotic division that proceeds distributes the amount of genetic material equally among the daughter cells. However, this mitotic division is accompanied by qualitative changes in the genetic material that can allow the genetic material to start forming organs at one stage or another. For example, at the two and a half day stage, it does not form the eyes of the embryo, but according to a precise and detailed planning, it forms the embryo completely. The same thing happens for the human embryo, which takes 9 months for these events. The reason for this difference is due to the size and complexity of the embryo. Now the fetus is born, its birth mechanism, its suckling mechanism, its heart is controlled, it speaks at a certain time, its hearing is working, it reaches sexual maturity at a certain age. Each organ works independently, and at the same time, although they are independent organs, each of which requires genes and functions to build the organ, to maintain the organ and the specialized organ function in which the organ works, from there they are connected to the rest of the organs and the body's homeostasis system without us controlling them, all of this goes back to the same genome. This genetic material must cause the cell to die, for example, in humans, the germ layer between the fingers dies so that the fingers separate. And this genetic material itself knows when, where and how much to express. We who want to solve the problem head on, that is, to get from disease to gene, must know what function the tissue has, how it is related to homeostasis, and how it is disrupted, that is, we must know the infrastructure. pg. 11 pg. 12 In the name of Allah, the Merciful. Third session of human genetics. Zainab needs God. Genetic disorderare affected4 factors can be included: We have a series of patterns that, in terms of traits, can cause disease. First:A series of patterns are created through a gene:Such as phenylketonuria or single gene disorder Hemoglobinopathies, alpha or beta thalassemia, usually have well-known dominant and recessive inheritance patterns, and in some cases are also influenced by gender. Second category:Disorders that have a chromosomal origin, given that a chromosome is a large piece ofand several genes are DNA It involves, usually their symptoms are multiple and simultaneous. It can beEndophenotypeIt means that people who have the same abnormality will show different patterns and usually show chromosome-related disorders.They say syndrome Such as Patau syndrome, Edward's syndrome, trisomy 21. Third category:Disorders that are influenced by multiple factors. These are some of the factors.twoCategory: A trait that is influenced byHow many genes?different. Like height and weight and skin color. Sometimes several genes are combined with another factor, that isEnvironmental factorIt is combined. For example, we either have one gene and an environmental factor or we have several genes and environmental factors. Usually, such traits can change greatly under the influence of environmental factors. It affects how they occur and their severity. For example, diseases caused by the nervous system such asIts prevalence is higher in women. In addition to genetic differences between men and women, environmental factors are also strongly involved. Fourth category:Malignancies and cancer (malignancy) are mainly referred to as somatic genetic disorders. We call them cancers. Of course, not cancers that have hereditary roots and are inherited from parents. Cancers are of two types:FirstThose that have a genetic and hereditary origin, and the person has had this cancer in their family. CategorySecondChanges that occur in somatic cells and have nothing to do with germ cells. Therefore, mutations that occur are called somatic mutations and are usually not inherited. If the mutation occurs in the germline region, 1 It can also be passed on to subsequent generations. Usually, in the inheritance patterns we examine, the parents themselves do not show the trait, but the children do. 4 Genetic terms: Incidence: or incidence rateIt indicates what percentage of individuals in a population with a mutation have that trait. They "show or occur" rather than how many people have the genetic mutation. They usually define it in newborn babies. For example, the incidence of cleft lip in the population is 1 in 1000, meaning that one in every thousand newborns has a cleft lip. A series of mutations are involved in causing cleft lip, but those mutations do not necessarily cause people who have the mutation to exhibit the trait. SoIt only shows the incidence in the population. Or Prevalence: What is the "incidence rate" of a trait in a population or a province? For example, the frequency of the mutation that causes cleft palate is 1 in 1000 (i.e. 1 in 1000 people has a chance of developing it). incidence (but some who "show" the disease,, indicate the incidence of the disease in different cities of Iran. People who have this trait can be the same in the entire population, but the number of people who show the trait together is not the same in all provinces and can vary. For example, in Tehran, out of every thousand people, 5 people show the trait and the frequency of the trait is 5 people. In Isfahan, 4 people and Tabriz, 3 people. [I didn't understand the teacher's explanation. My own explanation:Update:The number of people who have the disease and show signs of it when screened at birth, for example, 10 per thousand.Prevalence:In this society, the number of people who have a disease. For example, maybe two people died at birth. So it's 8 per thousand. And the prevalence is always lower than the incidence. But on the exam, maybe you should write the professor's definition.] The term abundancefrequency: Indicates allele frequency or genotypic frequency in the population. Not used much. But for computational and population genetics work, we use it to know how genetically susceptible a country or population is to a series of traits in the future. In addition, in the research work we do, for example, diabetes and cancer, etc., a number of samples are needed. What is the frequency of the genes that cause this trait in different populations? For example, in North America, the frequency of the allele that causes the disease is 0.2. Based on this genetic frequency, we need to determine our sample size and sample size for our study. 2 Termor congenital: These are diseases that the fetus shows at birth that can have a root GeneticIt can beNon- geneticand is affected by medications taken by the mother or environmental factors or trauma to the fetus Be. Molecular genetics topics: The simplest living organism is a bacterium, and all its characteristics areIt is divided into daughter cells at once. When the cell wants to divide, all the DNA is In a eukaryotic cell, the moleculeDNA is broken into different pieces called chromosomes. During cell division, this replication of moleculesand distribution between daughter cells can be disrupted. DNA That's why we have diseases caused by a whole molecule.Or we don't have chromosomes in prokaryotic cells, but we do have DNA in the cell. In eukaryotic cells, we have chromosomal abnormalities. We talked about the origin of shared genes. In eukaryotic cells, the different chromosome molecules that exist in eukaryotic cells, including humans, cause the organism to have, in addition to defects that occur in numerical changes,occurs, more sources to be affected by DNA modification factors It may contain mutations or mutating factors. All living organisms undergo changes under the influence of chemical and mutagenic environmental factors. Bacterial cells undergo a large amount of changes due to their thick coating.It is from a eukaryotic cell and condenses (condenses) DNA. A single moleculeIt is larger and less condensed. It does not have more coverage around the DNA. In eukaryotes, the DNA molecule We don't have a cell except for the plasma membrane. So the changes we see are considered different from bacteria. Molecule Chromosomes are a linear string of genes distributed on a chromosome. But they are not all in the same direction. DNA For example, if the geneOn the other hand. No arrangement can have B on one side and A next to each other to model C, B, and A. Special in that the moleculeOr how genes are arranged on chromosomes. That is, they can process DNA Their patterns may be in the opposite or same direction. There is a special class of molecules involved in gene expression in eukaryotic cells. If we focus on genes that code for proteins, these are controlled by only one molecule.RNA polymeraseIIThere are those who can emulate. In humans, there are about There are 25,000 genes. How many are there inside a living cell?There must be a polymerase that can be used in each RNA at the time needed. Can a cell model its own proteins? 3 HermoleculeRNA polymerase and DNA polymerase have a volume and space and require energy. In a nucleus in a human cell, RNA polymerase and DNA That's about 2 meters!!!We have and along with the nucleosome network, how much space is left? [Negative question -] DNA In totalWhich is located inside the cell, I call it the genome. The science of studying the sequence, number, position, and components of genes in DNA We call it the level of a living being.GenomicsWe say. A series of sciences (omics) have emerged that help us understand various aspects of medical and biological sciences. Inside a eukaryotic cell like a human, we have different types of cells. 98% of normal cellsn2. But gamete cells Chromosomes. Cells in different human tissues, such as liver and muscle, have different numbers of nuclei and genetic material. We don't even have any genetic material inside the active red blood cell. If it exists, it is an indicator of disease. The genome has different definitions depending on the organism and the individual. But the human genome means in the common cells thatnThere are 2. In prokaryotes, we do not have this diversity, but we have other issues to compare the relationship of bacterial cells with human diseases. We need to study the microbial flora on the surface of the skin. Here the concept of genomics changes. For example, for psoriasis or diabetic ulcers or bedsores, different types of bacteria can cause disease on the surface of the skin. If we want to identify bacteria, we need to extract the entire genome of the bacteria that are at the site of the injury andsequence Let's separate bacteria based on specific criteria, which are usually based on fixed sequences.srRNA16 Bacteria use each other to identify bacteria. Transcriptomics:The study of the number or type of transcripts or patterns produced in a cell. They call it transcriptomics. Here, too, we have diversity for a creature like a human. We have general transcriptomics for humans, where they take a collection of cells from their body, analyze them, and say what genes are expressed in the human body. In the human body and other multicellular creatures, they have created specific tasks for different organs and tissues, for example, the eye works on its own, the ear works on its own, and the muscle works on its own. Despite the cells that are in different tissues and make up the tissues and organs, the source of genetic information is the same. But the way the information is expressed is different. Transcriptomics is a bit different, and we say the transcriptome of the heart, eye, and brain, etc. But if we look more closely, each organ has a series of micro-tissues. In our body, we have 5 main types of tissues, but we have more diverse micro-tissues. We have between 50 and 55 types of tissues. For example, connective tissue that holds different parts together. How many types of tissues do we have in our face? The tissue of the upper lip and nose, under the eye and above the eye, shoulder and earlobe is not the same. The amount of elasticity is different. What is the reason for the difference in the amount of elasticity? They are all the outer skin tissue, but their underlying structure is different. The skin on the palm and the back of the hand are epidermal tissues. But they're not the same. So when we talk about the transcriptome of a tissue, it's very broad. 4 ProteomeIt is the sum of the proteins of a cell and an organism. The difference is that ifIf we have 25,000 genes, the total number of transcriptomes in the human body is about 40,000, and the number of proteins in the human body is about 55,000 to 60,000. This means that we have a cascade state, and some genes produce more than one type of transcriptome and protein. What changes the relationships between these and can create different expression patterns in different tissues are regulatory mechanisms that operate at the gene level and changes that occur at the nucleotide level. We have a series of changes that are outside the nucleotide sequence.It occurs but can affect the function of genetic material under the influence of DNA. Let's call them epigenetic changes. It mainly acts through changes in the genome and affects the transcriptome and proteome. This three-part set of genomics, transcriptomics and proteomics examines the set of information inside the genome. The transcriptome and proteome are tools that help the genome toMetabolomeCheck the set of specific reactions within a cell or tissue, MetabolomeThey say that inside the heart tissue, we have a specific metabolome that is specific to the heart tissue, which is divided into different parts, for example, the metabolome of the heart valves, the metabolome of the aorta, the metabolome of muscle tissue, and the metabolome of nervous tissue, and what leads to the phenotype is the result of the function of the metabolome. For example, a person has a short nose or a long one because of the metabolome. Metabolome 3 categoriesGlycomicsOrSugars interactionLipidomicsAll of these together form a science called FluxomixIn the body, skin tissue, heart, kidney, bone,HeartThe intensity of metabolic function is higher and the intensity of activity is higher, and the bones and skin are the least affected. In the heart, bone, skin and liver tissue, the mechanism of using fixed glucose and producing protein and sugar is the same. But the intensity is different. The study and comparison of the differences in the intensities that exist in the metabolic functions inside the cell is called fluxomics. (The difference in the intensities of metabolic activities and their comparison with each other.) Example: What is the difference in the intensity of the influx of sugar energy, metabolism, etc. in cells. We considered the metabolome in general. When we look at it in detail, for example, lipidomics and glycomics have specific applications. Lipidomics is related to heart disease. Glycosmics is usually liver diseases. Looking at it in detail, inside our cells, some of these metabolic activities are carried out by proteins that are multimers and have several subunits. Example: BacteriaThe polymerase has a number. This one enzyme has to copy different genes. In bacteria, different genes are RNA. For example, genes are related to replication, division, chemotaxis, and specific metabolisms.Is this all RNA polymerase? Does it transcribe simultaneously or is it categorized? Where and which part of the enzyme does this classification relate to? The enzyme has subunits alpha, beta, betaprim, omega [I didn't hear omega in the voice]. These 4 only have polymerase properties. But they don't know where to model it. In order for the apoenzyme to know which operon to express, it needs the sigma subunit. If it attaches to the polymerase 5 It tells you where to pattern. It determines the patterning of genes in the bacterial cell. SigmaPolymerase core [The sound stopped here, I don't know exactly] The sigma subunit gives you specificity. So at the molecular and atomic level and the level of protein structure,RNA polymeraseIt has 4 subunits, each with a specific and fixed protein structure. Structurally, they are placed together and at the atomic level, they establish molecular connections with each other. The sigma subunit cannot attach to the others with a specific bond, in fact, it can establish connections through structure. So, protein molecules with multiple subunits, usually through the hinge of their structure, are placed together and form a larger protein complex. What creates the phenotype is the interaction between protein structures that must fit together to perform a specialized function. Interactions are the science of studying how protein molecules fit together to perform their function.InteractumWe say. Something we see in a particular phenotype.InteractumIt is like sickle cell anemia. This disease is caused by a mutation inWe know that an amino acid is encoded at a single gene position.6 chains. This is the genetic dimension and at the level ofIt is a nucleotide change. A nucleotide change occurs at the level of the DNA transcriptome. ThenIt is translated into protein. We have the map protein, but when it goes into an environment where there is low oxygen or mRNA He takes oxidant drugs, such as broad beans, and shows the sickle cell phenotype. What works is the structure that is created in hemoglobin. The interaction that the subunit containing the mutation in the beta chain makes with the other subunits. The structural change that is created in the protein causes the red blood cell to be shaped from the outside. Its set of internal interactions makes it sickle-shaped. Hemoglobin must be able to take up oxygen in the air sac andAnd when it goes into the body tissue, it has to be the opposite of Co2. to act. To know where to get oxygen and whereIt goes back to the structure of protein molecules that have the CO2 subunit. The connection of the alpha and beta chains and the prosthetic group makes hemoglobin, and its stable structure suggests that the molecule can be active. ScienceInteractumIt examines how hemoglobin subunits interact to perform biological functions while also forming the structure of hemoglobin. Dozens of proteins must work together to perform, for example, replication. For example, dozens ofDNA must be single strand binding protein Slow,The polymerase sits down so that the primase can do its job. All of these structures must interact with each other to make the DNA process work. Modeling is done. They tell how the different components and proteins do this in coordination.Interactum. Now let's look at it more closely. They say that the cause of cancer is a mutation that is passed from parent to child. A mutation changes the genetic material, thenNext, protein. If we want to understand the mechanism of various diseases, we need to understand the relationship between gene structure and RNA. Let's communicate the phenotype we see. For example, let's say we want to create a disease. And bring it down to the molecular level. In medical genetics, we usually see a disease based on phenotypic symptoms. For example, his hand is wrinkled. A person with Down syndrome is a phenotype. 6 Short nose bridge, protruding tongue, light eyes, short neck, bare skin. We diagnose that the person has Down syndrome. The doctor diagnoses that you have the flu and a cold. For genetic counseling, we need to establish a connection between the person's phenotype and the person's genotype. That is, based on the clinical symptoms and phenotype that the person shows, we need to determine which part of the genetic material is changing so that we see this phenotype. We need to diagnose in addition to the gene change, we need to see where that gene has changed. In order for a gene to do its job properly and produce a normal phenotype and function, three things are very important, and for each gene, you must define three characteristics.When? Where? How much? Where is the concept?In which tissue is each gene expressed? Are all genes expressed in all tissues/or are some expressed in some tissues/ Some in all cells/some very specific. For example, genes related to glucose metabolism are expressed in all cells and tissues because the energy source of all cells in our body is glucose. So the genes related to metabolizing glucose should be expressed in all cells. But are the neurotransmitter nerve messages that want to be transmitted expressed in all cells or only in the nervous tissue? In the nervous tissue. While all cells in the body have their genes. In the liver, genes related to the production and breakdown of glucose are active. In other cells, the genes are also present, but they are not active. In different tissues, we have the same genes but different expression patterns. We call it where. Where a gene is expressed and where it is not. If our phenotype is to be natural and normal, genes must be expressed in our body in a specific pattern. Whose concept?For example, in our body, is the amount of digestive enzymes produced in the stomach always the same? No! Only when We need it to digest food. For example, enzymes related to the glycogen synthesis cycle are activated after eating food. After we finish eating, glycogen is broken down in the liver and released into the bloodstream as needed. A group of our genes need to know when to be expressed if they are to do their job smoothly. How much is the concept?In heart and liver tissue, we need more energy than in skin tissue. Energy production in both cells comes from There is a mechanism and women are similar. But the intensity of their function in different tissues is not the same. To study each gene and determine the relationship between phenotype and genotypephenotype genotype.correlation analysis studyIn addition to examining the phenotype well to find the gene, we must also look for a candidate gene. We use that adjective to answer 3 questions: when, where, how much! If we see the patient's phenotype, we should use this path to see where the gene is not working. Let's give an example. Suppose: A monozygotic disease like beta thalassemia. We don't know anything about this disease. We go for a test before marriage. From the blood sample, they say that both of you have a mutation and you can't get married. What did they analyze in the blood? They lyse hemoglobin, electrophoresis 7 They put protein, the amountThey check and diagnose that you have thalassemia minor. That is, on the woman's A to 2 A1 Your beta coder, Mutaswin, is there. Minors usually have a phenotype that is usually a little weaker than the norm in society. They have less flexibility in physical movement and can do less heavy exercise. (Of course, based on the location of the mutation.) Image: Suppose the structure of the globin gene Question: In beta thalassemia minor, the number of red blood cells is lower. If the number is lower or its functional capacity is low, what does the beta gene refer to? For example, a normal red blood cell can take a thousand oxygen molecules in the lungs and return them to the tissue. In someone with beta thalassemia, this thousand varies between 500 and 900 based on the type of mutation. Let's assume we have 800. Now we translate the phenotype into gene structure. In order for the red blood cell to function less, where in the gene expression must be reduced? Each red blood cell has 250 hemoglobin molecules, and each hemoglobin has 4 oxygen-carrying and releasing capacities..has Co2 If they say it can transport 1,000 oxygen molecules, how many hemoglobins does it have? In medicine, we see the phenotype and give medicine to return it to a normal phenotype. In genetics, we see the phenotype and we have to translate it into a genotype and into molecules.Let's translate DNA and changes at the DNA level. What are the possible reasons that could reduce the capacity from 1,000 to 800? In other words, if the number is to be reduced, where should it be affected? In each gene, partWe have a regulator that includes exons and introns. A structural part Promoter and regulatory regions. We don't say hemoglobin is low, we don't say it is absent. Whether we say that the amount of gene expression is low or that it is not expressed at all are two different phenotypes and the causes are completely different. Under normal circumstancesEach RNA polymeraseIt transcribes every 5 minutes. What if it could be every 7 minutes? The expression becomes less.In order for the polymerase to recognize the promoter, it must first read the RNA.How does it recognize that area if it sets every 5 minutes? 98% of the time,We have B-DNA. Nucleoside: Base and sugar. If phosphate is attached, it becomes a nucleotide. There are 3 types of nucleotides: monophosphate, diphosphate, and triphosphate. The monophosphate type in the structureIt is RNA and DNA, and triphosphate is the starting material and substrate of RNA and DNA. 8 InIt can also form G with T and C with A. They bond together. In this case, the diameter of the molecule is equal to AT and GC, DNA. It can give a link, but it does not have the usual diameter structure.It is a DNA with RNA or RNA hybrid. In the hybrid, we have two DNAs, A- and Z- DNA. In the promoter region, A, BZ, three DNA structures In each complete round of B-DNAIt is 34 angstroms high and 10Important note: The diameter of the molecule is constant and bpIt is 2 nanometers. If the structure of the moleculeand the genes are arranged in order, let's consider each B-DNA gene as all DNA According to the building we showed, there is a promotional part and aThe promotional part is supposed to be structured. Control the expression of information in the structural part. The direction of the expression pattern is left to right based on the shape we have. The enzyme recognizes the promoter and copies it. If the direction is the opposite, it rotates. So in the structure of the genome, if we focus, the genes are not all copied from the same path. Later inWe show ncbi. Let's assumeWe are polymerase and the structure of RNA2 metersNow we want our B-DNA region to be linear and all DNA. Identify a promoter. What do we do? We need to answer these 3 questions. When? Where? How much? In all cells.The polymerase is the same in all RNA and DNA. Cells are the same. For example, something calledWe do not have RNA polymerase in adipose and liver tissue. In a TATA negative bacterial cell and a TATA negative human cell, the position of the GC box and TATA boxIt is 35. DutyIt causes transcription to start at the right position. When it says box it doesn't mean a dot and TATA box It is a box and it is a functional range.T and A are located in a specific region that contains TATA box-rich sequences. It is. 9 The promoter of the gene that wants to be expressed must beDNA polymerase is being detected at the RNA level. RNA polymerase It's movement. I say +1 from the first nucleotide where the patterning starts.And until the end of the initiation point numbering We do. I would show the parts that are modeled with a positive number. The upstream part andNegative number regulator It is. That is, TATA box35 nucleotides left to startThe sequence minus the TATA box and the initiation point where transcription is supposed to begin.25 to minus 45. A sequence of 10Since T and A are specific nucleotides rich in bp It's hard to say the range is minus 25 and minus 45, they say minus 35. Also in some genes, GC box negativeIt is 85 and rich.But in principle minus.GC75 to minus 95. This area is 10.bp or bp20, is separated from the rest based on its specific sequence. DNA domain: Sequences that have a different composition from the surrounding spots. They have a meaning due to the composition of the game they have inside them. What is their function in the gene, what does it interfere with? When, where, how much? Answer: None. GenesIf they are to determine when, where, and how much the problem is, they have GC, not TATA, not GC less or TATA less. It will be. Connection pointThe polymerase wants to start its work. This is the movement of RNA polymerase. When RNA enters the gene, the GC box and TATA box polymerase, after the decision has been made upstream to express the gene. In fact, RNA Common on the surfaceIt has to settle down and start from one point and the DNA changes. It has to come and somewhere in the DNA It copies the template because its job is to polymerize. But it doesn't know where to start. (For example, in bacteria, the sigma subunit did this.) We have something similar at the human level. The promoter is between 2It is long. In the range of Kb to tens of Kb. Promoter, we have elements that specify who, where, and how much? The thing that specifies who, where, and how much is upstream of this [probably meaning promoter] (i.e. from minus 100 to popin). These elements that are downstream of this [probably meaning promoter] are of two types.A bunchSpecific sequenceDNA domainare known as transcription binding sites. Inside the human cell 150 typesWe have transcription factors. 10 These are proteins whose genes are located somewhere in the genome, for example, chromosome 1. They are regulated and expressed from there. But this transcription has to go to different places in the genome, which is why it is calledtrans element factorWe say. The factor that replaces It is produced and coded, but it works elsewhere. For a transcription factor to bind to a gene, it needs a sequence that is upstream of the promoter. These sequences are adomain They are and have a specific sequence. Transcription factors don't stick everywhere, they only stick to specific places. That specific sequence is where transcription factors bind,cis elementWe say. In regulating the expression of each gene, to say when and where How much? FactorsPolymerases say the upstream decided to express it. Now we say where the RNA expression comes from. Only the structure that is lower and closer to the GC box and TATA box is involved. But the trans and cis Kenny. If we have 25,000 genes, it doesn't make sense that 25,000We need to have polymerase. It must be produced when needed. When will the need be determined? RNA Does it? Answer: When, where, how much? (I mean the elements). Where to express it? Answer:.TATA box and GC box [The part where the professor showed his picture] For an enzyme to work, the enzyme's conformation is initially stationary. When it decides to express the gene, the motor conformation must change and assume the polymerase conformation. When the enzyme moves, its bottom part mustIn fact, the composition of the TATA box and the GC box can be touched and felt by DNA. It is a game that is in the heart.(Of course, if it is located right under the GC box. When the end of the enzyme is on the DNA Okay, it's sitting right, and its conformation is in the part where it's on.DNA wrist moves with DNA conformation complete and stable) This standing conformation changes to a lying one. That is, the moleculeThe head is the first place where DNA (the end of the DNA) is now lying on the surface of the DNA. He sleeps on the molecule.The TATA box sleeps with a footprint on its head. This footprint is on DNA. The end of the enzymeThe polymerase, which is a protein structure, has a conformation that must be matched to the RNA. What determines where a molecule goes and what it does is its structure.Two RNA polymerases, one at the bottom and one at the top It has structure. When it comes to the surfaceWhich arrived, because it moves spatially complementary to GC and scans it into DNA They are stuck together. What provides the space? The upstream part. If it is to be expressed,between trans elements They sit upstream and go to the partsThey bind, they change conformation, and this region opens up and is in cis. (Under normal conditions, the region is closed.) The gene that wants to be expressed, the conformational changes it finds here with bindingThis region opens. Then the enzyme that passes the trans activator element and the cis elements and the trans It does, now it sees (it didn't see before because it was closed and it was a nucleosome.) Now that it's open, it knows its end. If it knows the right place for expression, if the enzyme wants to sleep, where should the head part be? Its length (its head) should be on.fit. If it fits, the conformation changes to the conformation it should model. Now it won't separate. TATA box 11 Now that you have a firm footing, speak from here. SoOnly the starting point of the pattern is shown. For the GC and TATA genes Those that are wonderfulAnd it must be expressed in a controlled manner. If it is expressed involuntarily, it changes the fate of the cell. Specific expression And the starting point is extremely controlled. It does not open the outer conformation of DNA to read. When it wants to read RNA, it recognizes the TATA box and GC polymerase. It recognizes and does not open the gaps, and it does not open two strings at all. Conclusion: ThisIt is, at the nanoscale level, it transmits a series of information through our B-DNA, despite the fact that DNA The composition of the game and that changes in each area. That isBut when you get down to the atomic level, it's called B-DNA. It has. Regulator molecules screen the surface of the molecule (like touching). (Like we recognize objects in the dark by touch. These molecules also recognize by touch. For example, the armrest of a chair has a specific conformation.) InWhen a mutation occurs and the game composition changes, it changes the conformation and DNA interaction. Regulatory molecules are disrupted. Mutations or changes not only change the information code, they can also change the conformation at the molecular level. They disrupt it. They create DNA, DNA regulatory molecule interactions. 12 Fourth session In this session we will talk about human genetics and traits. When we talk about a phenotype, we need to be able to find the genetic factors that cause this trait. In genetics, we have two ways to do this: 1- We can reach genes through phenotypic analysis. 2 2- From Move the gene and reach the phenotype (we explained this situation before and will quickly review it) In the case of the human model, if you remember, if there is a genetic trait on the gene, we must have an animal model. If we look at it the other way around, that is, we have a candidate gene and we want to study the function of the gene, the best way is to create an animal model for the candidate gene. It is natural that if any phenotype that exists is shown, if we apply all the standard conditions, the role of that gene in the phenotype is determined. But in human genetics and when humans are studied, this is a bit difficult and we have to go from phenotype to genotype. In the previous session, we presented an example: If the amount of homocysteine decreases, which parts of the gene would change to change its amount? About the promoter andWe talked about polymerases and examined their role, while the RNA gene For a gene to be expressed, the upstream regulatory region must undergo structural changes to allow it to be expressed. Someone with an anemic trait may have a promoter change that affects function. In the last session, we said that a person has anemia and has a low amount of hemoglobin in their red blood cells, and to get to the gene, we checked the promoter region.and the GC box and TATA box parts We talked about the upstream, but we didn't talk very specifically about why gene expression in an individual is lower than in the rest of the population. The structure of each gene contains the necessary elements for the gene to be expressed at the appropriate level under physiological conditions. Now, if an individual carries a mutation within their gene, for example in the promoter region, that changes the function of the gene, that is, increases or decreases gene expression, it can affect the phenotype. In the promoter, upstream, there are factors that regulate which tissues the gene is expressed in or not. And in the upstream part that decides whether the gene should be expressed or not, there are partsThere are CAAT box and TATA box. That's the place to sit.RNA polymerase and initiation Modeling and guidance are the things that exist. 1 It is what we said.They are present in the -85 region, and the CAAT box is present in the -35 region, and the TATA box is present in the -35 region. We said this distance is very important because the moleculeWhen the polymerase jumps and decides to copy this RNA The area is set to sit. We told you in advance how fast the area will sit.Two-stranded RNA polymerase It has an end. The end part is supposed to beDNA sticks and when it lies flat on the surface of the GC box The upper part was placedThe polymerase is the same in all genes. What is variable? RNA polymerase is constant in all genes and must sit on all genes so the RNA structure part binds to it so it can do its job. TATA box sequence Nucleotide sequence in the upstream regulatory region Interaction betweenThe polymerase and promoter determine whether the RNA is in the correct region or not. We have two concepts: something sticks to an area and the other is how fast and how strongly it sticks. If it wants to endWhat does it need to bind quickly and accurately? GC box RNA polymerase We expect the sequence to appear on the surfaceThe polymerase is perfectly matched and whatever RNA is spatially aligned with the DNA This matching can be done more quickly, the connectionRNA polymerase to this region occurs faster And when it sits and settles down faster, it means the end.Be careful when transferring DNA polymerase with RNA. The active conformation is when this molecule starts to lie on theAnd the DNA part His head is withTATA box will communicate faster. On the other hand, the more TATA box The closer the sequence, the stronger the bond, the faster the conformational change, and the more stable the molecule.RNA polymerase Goes to patterning faster inside living cellsThey have the GC box and TATA box sequences. They have a standard, but in fact they do not have the same sequence in all genes. They vary and can have one or two nucleotides inThe polymerase changes the RNA domain of these regions and consequently the speed of DNA binding. Or slow down. Different genes are regulated in one way, how quickly they are patterned in the heart.The polymerase starts RNA where it comes from, the stability of the TATA box, the GC box in the DNA region. Modeling provides a framework. ✓ If a person has fewer hemoglobin molecules than the normal population, one of the reasons is This could be the sequence thatThe hemoglobin of all humans is in this person CAAT box Changed or sequencedWhich is in the genome sequence of this person has changed, resulting in the TATA box in the person Normal if in a unit of time, for example, every minuteIt takes 3 patterns, in this person it takes 2 patterns, so Molecule reductionRNA polymerase could be the reason for a person's hemoglobin drop So if we want to look for a genetic change that could explain why a person's hemoglobin molecule is low, one of the places we should look is the areaIt is -1 to -80. Second point: The mutations that occur can be open changes that cantransition purine to purine or pyrimidine to pyrimidine) orAny of these changes can be (transversion) (be effective in regulatory sequences) During the evolution and physiology of every living organism, a series of information codes are encoded on the molecular level. DNA The regulation of each gene is somewhat specific, meaning the structure of the proteins that are involved. 2 They perform a function such asPolymerase is stable but RNA polymerase binds to promoters It must be able to change based on different physiological conditions. There are two types of promoters: 1- Strong: Produces more products in less time. 2- Weak: Produces fewer products per unit of time. If the structureIf the polymerase is stable, then what increases or decreases the strength of the promoter is RNA. ✓ How to connectHow fast and how accurately does the polymerase recognize the site of RNA docking? ✓ How fast does it model? Both of these have the function and the final product and output of how many moleculesIn mRNA They create units of time. So one of the places where we see that in the phenotype of the patient or the phenotype that we study, the amount of protein is low is that the binding sites on the surfaceLet's check. From the DNA We said that changes that can change positionsis (base substitution) base subsituation One base replaces another, and changes in the structure of a domain can change the position of that domain or the information that that domain carries in the outer three-dimensional part of the molecule.and change it to DNA This deviceRNA polymerase binds to a promoter with varying intensity or stringency In normal society, we expect a person to have a certain amount of hemoglobin to meet the norm. Norm does not mean that the red blood cells are necessarily full of hemoglobin or that it is below a certain level. If you pay attention to biological tests, such as blood sugar tests, it is said that if blood sugar isSo if it's 80 to 100, it's normal. We determine a range that more or less of it causes different diseases. Promoters or functional regions within promoters can contribute to these changes by the changes they cause. Two points: We said weConsider -1 to -100 in the region of the two segments -35 and -85 for binding RNA polymerase and It is important to start modeling.-35 to -85 (the central points of the second) are 50 nucleotides apart, which is 50 times the length of RNA polymerase, and RNA polymerase is about 50 nucleotides (a little more) long, which It has to sit and settle down to function. The head of the molecule, if it sits properly, points to a point where patterning should begin, so these sequences are important in terms of spacing and sequence. ✓ If the mutationFor example, insertion is done at 25 - that is, how many nucleotides are added to this region. What happens (or for example)35- becomes 37- and 85- becomes 87-) The distance between them is still 50. Stay and actThe polymerase sits and settles in the region, but the head of the RNA molecule It does not refer to a specific region, i.e. the start of nucleotide patterning that should form the first nucleotide of the transcript.2 bases are swapped, if the base is not an adenine or guanine, the pattern The vector can be problematic.Stop the polymerase and allow RNA to progress. 3  ✓ If the mutation inoccurs and two nucleotides are lost, the structure is pulled forward deletion-25 To be-35 becomes -33 and -85 becomes -83. What happens? It doesn't start at +1 and It starts with the next two, and that copy is not the original copy, and those physiological conditions are not appropriate. ✓ If betweenIf a base is added between -85 and -35, RNA polymerase will not bind to the TATA box and The whole pattern is disrupted. ✓ If between85- and 35- are also disrupted if one base is removed. ❖ After the mutations that can affect this areabase subsituation Its effects are less harmful and can be a tendencyThe polymerase changes the promoter RNA amount. Change the patterning, but deletion and addition mutations can have destructive effects, which of course depends on where the mutation occurs, i.e. if the deletion or addition occurs in the nucleotide100- Does it have any effect on modeling? Main positions Consider the difference between the open change in promoter function and the100 – or 60 – Which has a more harmful effect?60- So we must learn whether a mutation is a deletion, an addition, or a translocation. Each one can have different beneficial or detrimental effects depending on the region where it occurs, so both the type and location of the mutation are important. In some people, the blood is thick, meaning the amount of hemoglobin in the red blood cells can be higher or the number of red blood cells per unit volume of blood can be higher. ❖ If the first case is that the amount of hemoglobin in the red blood cells is high, which gene should be changed? Slow? The amount of patterning must be changed to produce more. One reason could be that the number of patterning times has increased and the moleculeRNA polymerase is designed to change very quickly so that the promoter has more GC boxes and TATA boxes, and one of the reasons for this is that the RNA site Give. For example, suppose it's an in-person class. From the time we leave home until we reach university, we are students, but we don't have the strength to learn. We had to get to university, enter the faculty, sit on a chair, then when we calm down, we take out a handout and start. Now, the more comfortable the chair, the sooner we will become stable, or if it was wooden? Whatever the sequenceIf the polymerase is wet, the RNA polymerase complex sits on its surface with the RNA structure. The initial phase is formed faster and patterning occurs faster, so the amount of hemoglobin can increase. ❖ At the heart of the moleculeA mutation occurs that shortens the lifespan of the mRNA molecule, making the mRNA molecule slower. After these molecules are patterned, they stick together and the RNA molecule becomes 4 Based on physiological conditions, there is something hidden in the genetic code for each gene, meaning it is possible that in my genetics, it is due to the gene.So that the protein code 10 B codes for four proteins and from the mRNA gene on A And this goes back to the signals on it. Some of these signals go back to where the ribosome sits, where the ribosome makes the initiation code, and some of them go back to the structure inside. Returns mRNA That at the heart of this moleculeWhether it has a stabilizing or non-stabilizing sequence, and now if there is an mRNA mutation LifespanNow if a mutation occurs that changes the mRNA, it will show a phenotype. Lifespanincrease and allow too much protein coding, do we have a change in the exon or mRNA Intron? Exon? Because Molecule mRNA Translation May To be Face splicing May Two introns stick together and The final form is formed, so if we want to increase lifespan, we need to make a mutation in the red mRNA structure. The color will occur so that it can last longer. When we want to go from phenotype to genotype, we need to look at each individual gene region that can be involved in creating the phenotype and see the phenotypic effects. Or, before we find the phenotypic effects of a gene, we need to know what happens if each part of the gene changes. A process called modeling andWe have splicing. Splicing occurs due to the presence of a series of specific sequences at the beginning and end of introns.If A mutation occurs in an intron that prevents it from being removed correctly or a nucleotide from being moved. What effect does this mutation have on theDoes it have a final mRNA? If the mutation occurs at the intron level, the number of moleculesWhich is created according to the mRNA conditions It is physiological, but the function of each moleculehas changed. Humans have 2 alleles for each gene mRNA One from the father and one from the mother, both of whom did not have the mutation, but one changed. Such a person is heterozygous and can have the same number of molecules.Let's say NGS is the same as a normal person in terms of the number of transcripts, but when RNA-Seq is consistent with a normal person, and if the mRNA Let's study and sequence When we check the mRNA in the patient's body, we see that half of the mRNA molecules They have extra sequences, but what did we see in terms of phenotype? (For example, in hemoglobin) The person is anemic. When we want to study a phenotype, we can easily find the candidate gene for the trait and predict the type of changes in the gene structure. This prediction is very important because we must be able to prove this change in the individual's genome. 5 We have different techniques to measure the structure and function of genetic material, such as: ✓ To measure the genome sequence Sequencing or NGS ✓ Let's measure the number of RNA sequences that have increased or decreased. ✓ Western Blot to see if an RNA molecule is doing its job ✓ Northern blot to see if the number of transcripts has changed Regardless of which technique we use to study, we must have a preconceived idea of which technique will provide us with more complete information. A gene is mapped to a protein-coding gene. If a mutation occurs in the region Phenotypic effects occur when the 3'UTR or CDS is completely 3'UTR or when the 5'UTR is completely 5'UTR. It's different and has nothing to do with the promoter, especially when we have some additional mechanisms. such as epigenetic changes, the connection between interactionsCheck mRNAs with lncRNA and miRNA Let's do it. Example: Let's assume that this gene has a healthy promoter structure and that the template is also being copied and the introns are being removed correctly, only in theThe phenotype that the individual exhibits is transformed from ATT to ATG, the start codon. What does it give? MoleculemRNA is not translated at allWhat technique should we use for diagnosis? Is it possible to compare the number of molecules?Does it help us? No, because mRNA is transcribed but not translated. So we need to examine the proteins and sequence them to confirm.Perform DNA-sequencing and not everywhere in the gene, just in the part.mRNA A subtle point: sequencing techniques can be on the entire genome, such asIt can be at the level of exons and coding. Now in this example, the whole exon. Genome Sequencing Whole It is necessary. Now suppose the middle partHave a base-changing mutation that changes an acidic amino acid in the CDS What behavior do you expect from a protein? The protein structure is disrupted and may not be able to react with other proteins, and the phenotype is shortness of breath and shortness of breath, and the proteins cannot function properly. Change and the protein continues instead of ending. Phenotypic effect? Stop codonFramework for change It is added that it can have very destructive changes based on the phenotype type, for example, if it is a cell surface protein that has a different function inside the cell than on the surface, such as cell surface receptor proteins, which are usually part of theIt has a biological function and the cell does not receive signals. C-terminal 6 These examples and phenotypes are for when our protein functions as a monomer. If this protein has to function as a dimer, it is either homo (two identical subunits stick together) or hetero (two subunits from two different genes stick together). In the hemoglobin example we gave, the active protein has a tetrameric structure and4 subunits, 2 α and 2 β Now, what happens if one of the two β subunits is damaged? We have a change in the total protein. So when we want to get from the phenotype level to the genotype, we need to know the structure and function of the protein carefully so that we can then find the corresponding gene. Example:A child has come to us who, since he was born and started eating, has had spots on his hands when he eats tomatoes and is allergic to the food. If the cause of this trait is a gene, how do we find this gene? And what changes have occurred in that gene that have caused the person to be allergic to tomatoes? (The baby did not have allergies when drinking breast milk while the mother was consuming tomatoes). In gene function, the promoter, structure, deletion, addition, and mutation each have effects, and these effects can have different effects based on the position in which the gene is altered. In order to relate the phenotype to the genotype, we must be able to predict what each part does and what the function is. If that part changes, we can see the effects at the phenotype level. ChangesSplicing can be physiological or pathogenic. Physiological: We have a protein inside the cell that must be distributed in different parts of the cell. It is natural that the producing gene must be able to produce it, both in the nucleus and in the cytoplasm and on the surface of the membrane.have those who can transcribe They are concentrated in different parts, meaning that signal peptides are attached to their heads so that the protein molecules, which are all encoded in the cytoplasm, go to the target areas after production and are located in that area. So if these signals change or change This localization has a problem with splicing. Proteins in the cell are disrupted and this Neuroligin is a gene that can cause a number of diseases, for example, the localization gene 1. It has a high number of copies, initially in people with schizophrenia andHe was nominated and mental retardation They said they had a problem and even named it as a biomarker. Then they saw that this gene is not only in the nervous system, not just on the surface of the nerve cell membrane, it is also in the nucleus. Then they saw that it is also in the tissue and blood. But the difference between a normal person and a sick person is in the amount of function of this gene, and they realized that the signals thatsplicing It guides and controls the distribution of proteins. If it changes, it can cause disease. So we should not necessarily look for a decrease or increase in protein. It can also happen that the protein is not in its proper place. 7 can cause disease. So the signals that control protein positioning are also involved in disease. If we want to identify these regions, for example, the first nucleotide of the first exon, the second nucleotide of the first intron,And... what do they mean? CDS Badr here introduces the system.We will discuss the nucleotide sequence nomenclature. The nucleotide nomenclature system is how nucleotides are named and tracked. In the gene structure, I saw that we had a promoter and a patterned part, where the patterned part has exon and intron sequences, and we have a part that afterThe mRNA naming system was splice. And the markings for these are not the same. Simple example: This One Moleculeis that mRNA Part coding into two regions sequence Black is divided. System If labeling On the surfacemRNA work Let's do: the first nucleotidewhich is the start code to the last nucleotide which is the stop code is a code behind ATG It is a head, so if this areaIt codes for 100 amino acids, in fact it is a region of 300 nucleotides (nucleotides 1 to 300) named with numbers. If we want to refer to the nucleotide in the UTR part, if If it was upstream, we indicate it with negative numbers, and if it was downstream, we add * to the numbers. For the gene structure, we can use the siteLet's use NCBI and search for the gene. 8  Gene information in other databases And in All Positioning On the genome Other names for the gene Full name of the gene Living organisms that have this gene express the gene. We see the naming system for each organism in the red box, and for reporting we need to know that for humans and cows, all the letters of the gene are written in uppercase.For mice and rats, the first letter is capitalized, the rest of the letters are ITPA. SmallWe also have (green box) like the national ID code and there are a number of contracts and an.Itpa 9 We have two parts, left and right, after clicking on the gene. The right part is a summary of the complete information explained on the left. Summary of gene function Orthologs are genes that are structurally and functionally similar but are expressed in different organisms. Position in the genome Number of known exons of the gene: but not necessarily all at once, it can be less or more Other thanWe have other databases that have information similar to what is displayed here, based on NCBI. The information is all over the world. ✓ It is more detailed and private, supported by California (UCSC, similar to NCBI in the US). It is wet) ✓ England University of Oxford Sanger Center ✓ Sakura (blossom) Japan All inare stored in NCBI Purple box: Every few years, they review the entire genome information and post the output on the site, and the number indicates which is the most up-to-date.and they leave the old one that GRCh38 If someone was working on the previous system, they wouldn't lose any data. Pink box: Gene location on the chromosome whose length and nucleotide position change with each update. 10  For each gene sequenceIt is proposed and for the sound DNA/RNA/Pr It is necessary to use a specific code for each, for example, we use a code that shows us that we are talking about a gene or the code that we use for a peptide. Usually, the genome sequence is written with letters.G or C It is shown. NC: number/Gene Numbers mean genes.They sorted them and gave each one a number. The number before the dot is the gene itself, and the number after the gene indicates the gene version. It is natural that the more information a gene has, the more it is likely to be used. The newer the version, the higher it gets, so at the top of the version11 and at the bottom is 10, which means information. They upgraded, perfected, and updated the gene. In this sectionGenetic regions/products that have the position and number of transcripts for each gene It shows the genes that are encoded in this region, in the part that we selected. In the case of this gene, or any other gene,There are various transcripts. Yes,They indicate the protein it encodes with the letter NP, and the letter mRNA with the letter NM. To isolate the gene fromUsed NC/NG What Appearance This figure shows the difference in colors. The green and purple colors are visible in the figure. The purple colors indicate whether this gene encodes a sequence that is not translated into protein.They show that it is normal and if it codes with NR, it is called non-coding mRNA? And this is noc coding that if it codes for a protein then,Okay, we don't have anything called protein, we have noncoding, but if NP Another point: a series ofThe collected data from NR are shown as a series with NM. There are various databanks that provide a series of results throughObtained a series of Sequencing Test mediatorThey did this based on the sequencing of the domains and a series of experimental genomes. and genome sequences predict and estimate that part of the gene is encoded by a protein orIt is converted into mRNA. From the databank for which dataIt exists and we can use it, valid and experimental. And it is the most complete withIt has been experimental and we show it as a predict, but if the data is NM 11 Let's not talk about it.It is shown that X is represented by the letter mRNA. It is natural that when X Protein is also a letter.There are and we do not have laboratory data. Prediction is shown and both X In the geneWe have (in purple) noncoding as we can see in the figure, 2 ITPA ,4 predicted sequences and 8 transcripts Note: From here we can identify the geneDoes it have a splicing variant or not? This gene has a splicing variant. Note: In Figure 1and a box line We see.Where there is a flash box It shows the direction of patterning and shows in which direction the gene is expressed. In neighboring genes, the direction of transcription is opposite (our gene is in red in the figure). At the heart of thisThere are some notes on the transcript. Each of the vertical boxes represents an exon. For example, in the gene above,The first transcript has eight exons. All the exons of our geneThere are 12, but it doesn't necessarily mean that all transcripts have 12 exons. It means that from the known gene regions, 12 are It has the ability to be exonerated. But.s do not necessarily have 12 transcripts For example, the latest copyIt has 7 exons and the fourth transcript has 9 exons, now in these 9 exons The first exon is made up of two colors: light and dark green. Light green Expressiveand dark green represents the 5'UTR CDS It is natural that at the end of itThat's why the end of this 3'UTR transcript It is also two-color. So the coding parts are shown in dark color and the non- coding parts are shown in light color. 12 If on anyWe go, a box opens up that shows us the protein sequence of the transcript. How much is it, what is its name? Where is it located? How many nucleotides? PartHow many CDS are there? aligned Nucleotide? How many amino acids does it code for? FormatFASTA or non-FASTA? There is also other information in this database. For example, gene expression information shows how much the gene under study is expressed in a tissue in a normal human. This gene is expressed in all tissues. are expressed, so we can say that the geneishousekeeping AlsoThose in variation The textures are also evident in the schematic form. 13 Session 6: Human Genetics In everyday life, when we want to distinguish people from each other, we have several parameters. For example, in college, one of the distinctions is how many women and how many men we have. In order to distinguish people from each other, we use a series of characteristics as a basis for distinction, for example, we say those who are taller and those who are shorter. If we want to separate people based on their phenotype, regardless of their name, we must use parameters. Now, when we look at the appearance of people, there are different characteristics that allow us to distinguish people from each other, but when we want to talk about genetics, genetic diseases, and genetic traits, the appearance of people can no longer be the basis. There, we are dealing with a sample of people who do not have any of these phenotypes. For example, let's take blood samples from everyone in our class and then separate the lymphocytes from the whole blood (red and white blood cells and serum). Consequently, if we want to separate you based on the sample we take from you, we need some characteristics or molecular markers based on which we can distinguish individuals from each other. Usually, markers that are used at the molecular level are used to distinguish individuals from each other and to distinguish different species from each other. One of the places where you can be employed in the future is organizations and bodies that are responsible for checking the import of food and agricultural products into the country. For example, a shipment of corn flour is imported. Now we need to be able to identify whether this shipment is corn or whether it contains different things, and if it is corn, what species and gender it is. When we are dealing with flour, we no longer see the cell and the plant to distinguish it from the leaves and color. The same is true for humans. When we are dealing with your example, friends, at the cellular and molecular level, we naturally need markers that can distinguish individuals from each other. Molecular characteristics that can distinguish individuals and species from each other, if in the futureAnd they are genetic material, they are given DNA genetic markers. We say that these can separate people. ExampleA: In order to be able to separate people, one characteristic is that if we want to separate a man's blood sample from a woman's, we examine their sex chromosomes. Women have two.And gentlemen xx and OneSo we can't separate people based on gender, but there are many differences between men and women. We need to refine the marker. To refine this marker, we need to look at the cellular and differentiation stages. ExampleSuppose we come from a human being.We take 3 samples, one from the liver, one from the skin, one from the blood, then We provide you with these samples and say that these all belong to one human being and that we have taken biopsies from different tissues. Now, orPreparation of a solid biopsy: We take a biopsy from blood or from solid tissue, liquid. How do we distinguish these tissues from each other? In a human body, we know that the genetic material that has reached it from the zygote is present in all the cells of the body in equal amounts.And the content is the same in terms of sequence. How do we get DNA? Separate specific tissues? Someone could say that you took samples from specialized tissues, so if you come and analyze the transcriptome, because the transcriptome is the basis for distinguishing tissues from each other and shows which genes are active in each tissue, we can separate them. This is the correct answer. But we need to compare a specific set of genes in the transcriptome, which is supposed to be all the genes that are expressed in a cell. We have a part inside all healthy cells called the -which is responsible for maintaining the body's natural homeostasis of cells (sugar-lipid-glycoprotein metabolism) which is called housekeeping It is present in all cells, but the amount varies, and this amount can be a basis for distinguishing tissues from each other. So one way to identifyDifferent tissues compare their transcriptomes. Now origin If they tell us that we can't analyze the transcriptome, it meansWe can't pull out the tissues that have RNA. The ones you have are from a long time ago, and they have been fixed since then. For example, they were taken in paraffin and fixed, and before that they were in liquid nitrogen, so they have lost their structure. We expect that every tissue has a We can have specific immunostaining of tissues and with organization But the tissue that goes into liquid nitrogen immediately after being removed will also have its structure destroyed. Now, what is the way to identify the origin of these tissues? One of the topics we discussed in class was that the differentiation that needs to take place is the first step, which is during the multiple divisions during the embryonic period.It regulates the organization of the cell. That is, in each cell, it directs cell division, both the opening and closing of the DNA molecule, and the DNA, based on the genes it needs. It brings the middle of the nucleus where the active patterning centers are located, and it moves the weights that are not needed to the lateral parts or near the nuclear membrane. So we can compare the location of specific genes that are characteristic of the activity of a tissue using the techniqueFISHOr a technique that uses nucleic acid probes They use acid.It detects the DNA molecule inside the nucleus and understands this cellular organization. Where does the material we are studying come from? In studies on tissue and cells, we don't need toDNA andIt is enough to check the position or organization of this DNA. We extract only RNA. It belongs to the body of an individual, but when we come to find markers in the bodies of different people, it is natural that we should expectGenome means the location of genomes in nuclei in the organization. The same tissues are the same in different people; that is, if we were to take skin samples from all of you and analyze them in terms of the location of skin-determining genes, all the genes would be in the central region, so between different peopleOr the expression pattern of position genes in the same tissues is very similar. So organization It cannot be a specific marke