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Basic Genetics Concepts The Basics • Genes are the units of heredity: they determine all aspects of our bodies and how they work. • Note: we are talking about genes as abstract entities here, not about the physical details of DNA sequences. • We are the product of our genes, but there are many event and interactions between our genes and our physical bodies. That is, the phenotype of an individual is not always obvious from the genotype. • Genotype: our genetic constitution. Ultimately, this means our DNA sequence. • Phenotype: our physical appearance and condition. • We humans are diploid: we have 2 copies of every gene, one copy from the mother and one copy from the father. • Diploidy implies that every trait is determined (or “conditioned”) by 2 copies of a gene, which might not be identical. • Alleles: different versions of a gene (as we now know, different alleles have slightly different DNA sequences) • Homozygous: both copies of a gene are identical: same allele • Heterozygous: the two copies of a gene are different: different alleles. Dominance • Dominance is a description of how 2 different alleles interact, the phenotype associated with different possible genotypes at a single gene. • For convenience in these examples, we will call one allele A and the other allele a. • Complete dominance: the phenotype of the heterozygote is the same as one of the homozygotes: AA and Aa have the same phenotype, which is different from aa. This is the type of dominance seen by Mendel. • In this example, A is the dominant allele (whose phenotype is seen in the heterozygote) and a is the recessive allele (phenotype seen in aa homozygotes but not in the heterozygote). • Many human genetic diseases are recessive: only the homozygotes show a mutant phenotype, while the heterozygotes appear normal. That is, the normal allele is completely dominant to the disease allele. • The heterozygotes for recessive disease are called carriers. More Dominance • Partial dominance (sometimes called incomplete dominance): when the heterozygote has a phenotype different from either homozygote: AA, Aa, and aa all have distinctly different phenotypes. • Often the heterozygote’s phenotype is intermediate between the two homozygotes. • A common example: an AA plant has red flowers, and aa plant has white flowers, and an Aa plant has pink flowers (intermediate between red and white). • Most dominant genetic disease in humans are actually partially dominant: the heterozygote has a mutant phenotype, while the dominant homozygote either dies before birth or is extremely defective with very low chances of survival. More Dominance • Co-dominance: when the heterozygote shows the phenotypes of both parents. • Co-dominance is mostly seen at the level of molecular markers: if you are a heterozygote for a given gene, DNA sequencing will detect the 2 different sequences. • Also often seen with proteins that have slightly different properties such as mobility on an electrophoresis gel, or different blood types. Penetrance as a Confounding Variable • Penetrance: the percentage of individuals with a mutant genotype that express the mutant phenotype. • The expression of many genes is affected by various environmental conditions and by other genes in the genome. • Often, individuals who have a genotype that should give them a mutant phenotype appear normal instead. A gene that displays this phenomenon is said to have incomplete penetrance. • Incomplete penetrance is very common in humans, which causes a lot of difficulties in determining dominance and inheritance patterns. Offspring ratios are not what they should be, for instance. • Closely related: variable expressivity = the degree of expression of the mutant gene is variable. The Sexual Cycle • We reproduce sexually: every individual has two different parents. • Cloning means having only 1 parent, with the offspring genetically identical to the parent. • Cloning is common in plants and some lower animals, and can be done artificially in some mammals. However, it is not currently possible in humans. • We are diploid, but to reproduce we need haploid gametes. • Gametes: sperm or eggs • Haploid: 1 copy of each gene • The sexual cycle of humans (and most other eukaryotes): • A diploid cell is reduced to haploid by the cell division process of meiosis. • Two haploid cells combine to form a new diploid cell by the process of fertilization. The first diploid cell of the next generation, the fertilized egg, is called a zygote. Segregation of Genes into Gametes • The two copies of each gene go randomly and equally into the gametes, which then combine at random to form the next generation. • Each gamete gets one copy of each gene, chosen randomly. As a consequence, both copies of the gene have an equal chance of ending up in a gamete. • Mendel’s Law of Segregation • A consequence of meiosis. • Leads to simple, easily recognized inheritance patterns • Two heterozygotes (normal carriers) of a recessive trait produce 1/4 mutant offspring and 3/4 normal. • A heterozygote for a dominant trait mating with a homozygous normal person produces 1/2 affected offspring and 1/2 normal offspring. • Some variants: • Two heterozygotes for a dominant trait should produce 3/4 affected offspring, but if the dominant homozygous condition is lethal, the ratio is reduced to 2/3. • A heterozygote for a recessive trait mating with a homozygous normal individual produce all normal offspring. This is a way to avoid producing children with mutant phenotypes. Independent Assortment and Linkage • Within a species, genes are found in fixed positions: at the same chromosomal location in all individuals. • Even between closely related species, most genes are in the same relative positions. • When looking at 2 different genes, their alleles go into gametes independently of each other (usually). That is, they assort independently. • Mendel’s Law of Independent Assortment, which generates the classic 9:3:3:1 ratios in crosses involving 2 genes. • However, genes that are close together on the same chromosome tend to go into gametes together: genes that do not assort independently are linked. • How frequently 2 genes stay together is a function of how far apart they are on the chromosome: the closer they are, the more tightly they are linked. • Mendel did not observe linkage: he didn’t look at enough genes. • Linkage is the basis for gene mapping Recombination • The two copies of each chromosome (one from each parent) are called homologues. • During prophase of the first meiotic division, the homologues pair up, and at several random locations on every chromosome, they break and rejoin, so each chromosome after this is a mixture of segments from the two parents. This is the process of recombination, also called crossing-over. • Linkage can be seen when 2 genes close together are both heterozygous: for example when the alleles on one chromosome are A and B, and the alleles on the other chromosome are a and b. That is: A B / a b • If a crossover event occurs between these two genes, the resulting chromosomes will be A b and a B. These are called recombinant chromosomes. • If no crossover occurred between the 2 genes, the resulting chromosomes will be A B and a b. These are called parental chromosomes, because the alleles are in the same configuration as in the original parents. More Recombination • The closer 2 genes are to each other, the more likely it is they there will not be a recombination event between them. That is, the offspring will have more A B and a b parental chromosomes than A b and a B recombinant chromosomes. In this case, genes A and B are said to be linked. • However, when 2 genes are far enough apart, there can be multiple crossovers between them. Since you can’t detect these events directly, 2, 4, or 6 crossovers give the same result as 0 crossovers (parental configuration), and any odd number of crossovers between 2 genes looks like a single crossover (recombinant configuration). • Two consequences of this: 1. The maximum percentage of recombinant offspring is 50%. The frequency of A B and a b parental chromosomes in the offspring is the same as the frequency of A b and a B recombinant chromosomes. In this cases, genes A and B are unlinked. 2. Genes far enough apart on the same chromosome appear to be unlinked. Gene Mapping • When mapping an organism like Drosophila, one usually examines flies containing several different mutant genes. However, it is rare for any human to have 2 mutant genes that give clear visible phenotypes. • Rather than map genes relative to each other, genes are usually mapped relative to various genetic markers. Genetic markers are loci (sites at specific locations; singular of loci is locus) on the chromosome that have a different sequence in different individuals. • Most common markers today are single nucleotide polymorphisms (SNPs), where many people will have one nucleotide, say a G, while many others have another nucleotide, say an A. • Genetic markers are inherited between generations, and they can be detected and used for maps just like visible mutant phenotypes. • Most genetic markers have no obvious effect on the person’s phenotype. • There are several million different SNP markers known, so there are always several near any gene. • Using genetic markers it is possible to build up a map of all the chromosomes, knowing where all the markers are relative to each other , to the genes, and to the known DNA sequence of the chromosomes. • Compared to Drosophila, humans have very few offspring, and they don’t mate in a controlled fashion. Special techniques are needed to map human genes, combining the information from many crosses together. Genes on the X and Y Chromosomes • The X and Y chromosomes determine sex in humans: the usual condition is that males have an X and a Y (XY) and females have 2 X chromosomes (XX). • The X chromosome has many genes on it, most of which have nothing to do with sex. • There are only a few genes on the Y chromosome • Genes on the X chromosome are called sex-linked, because their inheritance goes along with the inheritance of sex. • Since males have only 1 X chromosome, any mutations on that chromosome are expressed, whether dominant or recessive. • The effect is that most sex-linked mutations are seen in 10 times (or more) as many males as females. • Genes present in only 1 copy, such as genes on the X in males, are called hemizygous. • Sex-linked genes have a unique pattern of inheritance. • Because of this, the first human genes to be mapped to a chromosome were all sex-linked. Chromosomes • Key features of a chromosome: centromere (where spindle attaches), telomeres (special structures at the ends), arms (the bulk of the DNA). • Chromosomes come in 2 forms, depending on the stage of the cell cycle. The monad form consists of a single chromatid, a single piece of DNA containing a centromere and telomeres at the ends. The dyad form consists of 2 identical chromatids (sister chromatids) attached together at the centromere. • Chromosomes are in the dyad form before mitosis, and in the monad form after mitosis. • The dyad form is the result of DNA replication: a single piece of DNA (the monad chromosome) replicated to form 2 identical DNA molecules (the 2 chromatids of the dyad chromosome). • Diploid organisms have 2 copies of each chromosome, one from each parent. The two members of a pair of chromosomes are called homologues. • Each species has a characteristic number of chromosomes, its haploid number n. Humans have n=23, that is, we have 23 pairs of chromosomes. Drosophila have n=4, 4 pairs of chromosomes. Cell Cycle • The cell cycle is a theoretical concept that defines the state of the cell relative to cell division. • The 4 stages are: G1, S, G2, and M. • M = mitosis, where the cell divides into 2 daughter cells. The chromosomes go from the dyad (2 chromatid) form to the monad (1 chromatid) form. That is, before mitosis there is 1 cell with dyad chromosomes, and after mitosis there are 2 cells with monad chromosomes in each. • S = DNA synthesis. Chromosomes go from monad to dyad. • G1 = “gap”. Nothing visible in the microscope, but this is where the cell spends most of its time, performing its tasks as a cell. Monad chromosomes. • Cells not actively dividing are said to be in the G0 state, which is just like G1 with monad chromosomes • G2 (also “gap”). Dyad chromosomes, cell getting ready for mitosis. • G1, S, and G2 are collectively called “interphase”, the time between mitoses Mitosis • Mitosis is ordinary cell division among the cells of the body. During mitosis the chromosomes are divided evenly, so that each of the two daughter cells ends up with 1 copy of each chromosome. • For humans: start with 46 dyad chromosomes in 1 cell, end with 46 monads in each of 2 cells. • Stages: prophase, metaphase, anaphase, telophase. Stages of Mitosis • Prophase: --chromosomes condense --nuclear envelope disappears --centrioles move to opposite ends of the cell --spindle forms • Metaphase: --chromosomes are lined up on cell equator, attached to the spindle at the centromeres • Anaphase: --centromeres divide. Now chromosomes are monads --the monad chromosomes are pulled to opposite poles by the spindle. • Telophase: --cytokinesis: cytoplasm divided into 2 separate cells --chromosomes de-condense --nuclear envelope re-forms --spindle vanishes Meiosis • Meiosis is the special cell division that converts diploid body cells into the haploid gametes. Only occurs in specialized cells. • Takes 2 cell divisions, M1 and M2, with no DNA synthesis between. • In humans, start with 46 chromosomes (23 pairs) in dyad state. • After M1, there are 2 cells with 23 dyad chromosomes each. • After M2 there are 4 cells with 23 monad chromosomes each. First Meiotic Division (M1) • Prophase of M1 is very long, with a number of sub-stages. • Main event in prophase of M1 is crossing over, also called recombination. • In crossing over, homologous chromosomes pair up (this pairing is called synapsis), and exchange segments by breaking and rejoining at identical locations. • Several crossovers per chromosome, with random positions. This is the basis for linkage mapping. • In metaphase of M1, pairs of homologous chromosomes line up together. • In mitosis and M2, chromosomes line up as single individuals. • Anaphase of M1: the spindle pulls the two homologues to opposite poles. However, the centromeres don’t divide, and the chromosomes remain dyads. • Telophase of M1: cytoplasm divided into 2 cells, each of which has 1 haploid set of dyad chromosomes Second Meiotic Division (M2) • Meiosis 2 is just like mitosis. • In prophase, the chromosomes condense and the spindle forms. • Metaphase of M2: dyad chromosomes line up singly on the cell equator. • Anaphase of M2: centromeres divide, chromosomes are now monads which get pulled to opposite poles. • Telophase: cytoplasm divided into 2 cells. • After M2: total of 4 cells from the original cell. Each contains one haploid set of monad chromosomes Gene Balance and Chromosome Rearrangement • For many genes, it is necessary to have exactly 2 functional copies present. Having 1 copy or 3 copies leads to abnormalities. • The amount of gene product needs to be carefully balanced against products form other genes • Not all genes need this • Having equal numbers of every gene and every chromosome is called euploid. Not having equal numbers of all genes and chromosomes is aneuploid. • There are some special rules for genes on the X chromosome • Two main ways to become aneuploid: • Gain or lose a whole chromosome through non-disjunction in meiosis • Chromosome structural changes Non-disjunction • In meiosis 1, the homologous chromosomes are paired. Normally, one member of the pair goes to each of the spindle poles when the chromosomes separate in anaphase 1. • In meiosis 2, the dyad chromosomes split into 2 monad chromosomes in anaphase. One monad of each pair of monads migrates to each of the spindle poles. • In non-disjunction, both members of a pair migrate to the same pole. • Happens spontaneously • Can occur in meiosis 1 or meiosis 2 • Results in aneuploid gametes: a gamete with either 0 or 2 copies of a chromosome instead of 1. Chromosome Structural Changes • Chromosomes are long and fragile, and sometimes they break. The cell has mechanisms to re-attach broken ends, but sometimes the wrong ends get attached together. This results in structural changes: inversions, deletions, duplications, and translocations. • • • • Inversion: a piece of chromosome is inserted backwards Deletion: a piece of chromosome is missing Duplication: a piece of chromosome is present in 2 copies Translocation: a piece of chromosome has been moved to a different chromosome • Between species, chromosomal rearrangements are common, and they often prevent the production of viable hybrid offspring. More Structural Changes • Most chromosome structural changes involve several or many genes. Some genes can tolerate aneuploidy, while others are very sensitive to it. • The chromosome breaks themselves can cause genetic harm, if they break a gene in half. Otherwise, any genetic harm is due to aneuploidy. • Most of the time, a person is heterozygous for the unusual chromosomes: they also have a set of normal chromosomes . • Organisms that are heterozygous for deletions and duplications are aneuploid: they have 1 copy or 3 copies of the genes involved. • Inversions and translocations are often euploid initially, but the offspring end up aneuploid due to crossing over and chromosome segregation in meiosis. Some Population Genetics Concepts • A population is a group of individuals from the same species who interbreed freely. • There is only 1 human population, but some species have several non-overlapping habitats, creating different populations. • Many genes are polymorphic: at least 2 alleles present in the population. • In human genetics, 2 or more alleles have to be present in at least 1% of individuals. • The ABO blood group is a polymorphic genes: 3 alleles are all present in the human population at reasonably high frequencies. • Allele frequency and genotype frequency. For a gene with 2 alleles, A and a, there are 3 possible genotypes: AA, Aa, and aa. • Genotype frequency = the number of individuals with a given genotype divided by the total number of individuals in the population. Genotype frequency is directly observed. • Allele frequency = number of genes with a given allele divided by the total number of genes in the population. Since we are diploid, the allele frequency is derived from the genotype frequencies. The frequency of allele A equals the frequency of AA individuals plus half the frequency of Aa heterozygotes. Hardy-Weinberg Equilibrium • If a gene is not being acted upon by any evolutionary forces, the allele frequencies are related to the genotype frequencies by a simple equation. • These frequencies are stable from generation to generation. • If the genotype frequencies predicted from the allele frequencies don’t match the actual genotype frequencies, the population is evolving, by violating one or more of the 5 conditions necessary for Hardy-Weinberg equilibrium: 1. 2. 3. 4. 5. No mutations No migration in or out of the population Random mating Very large population No selection favoring one genotype over another Selection • The most interesting of the H-W conditions is “no selection”. Darwin’s theory of evolution by natural selection says that most major changes come from natural selection in favor of one trait compared to other traits. • In population genetics terms, this means one genotype has a higher fitness (ability to survive and reproduce) than other genotypes • Common selection patterns: • Selection against a recessive homozygote. The frequency of the less fit allele decreases every generation • Selection in favor of the heterozygote. Both alleles are maintained in the population. A good example is sickle cell anemia, where the AS heterozygous genotype is the most fit genotype in places where malaria is prevalent. A = normal beta globin and S = sickle cell beta-globin (which causes malaria resistance). Genetic Drift • Also important for H-W equilibrium is population size. In small isolated populations, allele frequencies can change very rapidly due to random events: who mates with who, fatal accidents, … • Genetic drift: random changes in allele frequencies within a population. • Genetic drift has its largest effects on small populations. • If a population goes through a bottleneck (gets reduced to a very small number), only those alleles present among the survivors get into future generations. • This can also be called the founder effect: only the alleles present in the founders of a new population occur in future generations. • Can lead to otherwise rare alleles being common in small isolated populations • Genetic drift can lead to fixation of an allele: all members of the population are homozygous for that allele, and there are no other alleles present. • Neutral mutations are alleles that are not affected by natural selection: they are selectively neutral. However, genetic drift can cause neutral mutations to decrease or increase their frequency, and even become fixed in the population. • Both selection and drift are important forces in evolution. Which force is more important depends on the circumstances. Quantitative Genetics • Many traits are clearly inherited, but show continuous variation rather than having 2 distinctly different alleles: height, skin color, intelligence for example. • Traits that show continuous variation are called quantitative traits. • Quantitative traits usually show a normal distribution (also called a Gaussian distribution or a bell shaped curve) • The phenotype of quantitative traits is affected by both genetics and the environment: the bottom line of quantitative genetics • Mathematically, the total phenotypic variance is the sum of the variance due to genetics plus the variance due to the environment • VT = VG + VE • The proportion of the variance due to genetics is called the heritability • H = VG / VT • Often the genetic part is polygenic: many genes involved, each contributing a small part of the phenotype • Sometime oligogenic: a few genes involved, each contributing to the phenotype. Principles of Development • How to get from a single cell, the zygote, to a multicellular organism. • General events: • cell division and growth • differentiation: cells develop different phenotypes • pattern formation: overall development of body axes, the general body plan, and structure of individual organs • morphogenesis: changes in shape Canalization of Development • Cells become increasingly specialized during development. Their range of possible fates (final cell type) decreases. This is called the canalization of development. • Initially, cells of the embryo are totipotent: can develop into any embryonic cell. After a while, embryo is divided into a trophoblast and an inner cell mass. Inner cell mass become the embryo while trophoblast becomes outer membranes and placenta. Cells in ICM can become any embryonic tissue, but they can’t become trophoblast cells: these cells are pluripotent. As development proceeds, embryonic cells become increasingly specialized and can no longer become any final cell type: they become multipotent and finally unipotent when they can only become one final cell type. • At some point, a cell is determined to be a particular cell type. Determination is followed by differentiation, changes of form and function, into that cell type. • decisions about determination are caused by a cell’s lineage: previous decisions, by its position in the embryo, and by signals passed between the cells. Stem Cells • Stem cells are self-renewing cells that differentiate into a variety of cell types. After a stem cell divides, one daughter cell typically remains a stem cell, while the other one starts to differentiate into a final cell type: this is called asymmetric cell division. • There are many types of stem cell in adults, and they are generally rare and hard to find. Some differentiate into a single cell type, while others can have multiple fates. • Embryonic stem cells are the pluripotent cells of the inner cell mass, which can become any kind of embryonic cell. Pattern Formation • How does the basic body plan get formed • axes: dorsal-ventral (back-front), cranial-caudal (head-tail), left-right. • position within an organ: e.g. how to get 5 different fingers on a hand • axis development: based partly an uneven distribution of components in the egg and partly on external events. • sperm entry point determines boundary between trophoblast and inner cell mass, which in turn determines the dorsal-ventral axis • cranial-caudal axis probably determined by position of second polar body exit relative to sperm entry point • morphogen gradients. Certain cells secrete chemicals that act as morphogens: signals that allow other cells in that tissue to determine their position in the tissue. The farther a cell is from the morphogen secretion site, the lower the concentration of the morphogen. • a well known example is the zone of polarizing activity, which occurs in limb buds. Cells nearest the ZPA become the little finger or toe, while those farthest away become the thumb or big toe. Hox genes • Animal development along an axis, from Drosophila to humans, is largely determined by clusters of homeobox (Hox) genes. • Different members of the Hox clusters are activated in different parts of the morphogen gradient, in an overlapping pattern • The Hox gene products then stimulate the activity of other genes that cause the cells to differentiate into the proper type. Fertilization • Egg is surrounded by two layers of extracellular matrix, the vitelline membrane and the zona pellucida. The sperm cells must dissolve their way through these layers to get to the egg. Sperm contain an acrosome at their tips that contains the necessary enzymes. • When a sperm reaches the egg membrane, the membranes fuse, putting the sperm nucleus inside the egg. • Egg membrane then depolarizes and cortical granules release their contests to push all other sperm cells away. • Meiosis 2 occurs and the second polar body exits opposite the sperm entry point. • the male and female pronuclei then undergo mitosis together, and the resulting nuclei fuse. • Fertilization occurs in the Fallopian tubes. After fertilization, the embryo takes about a week to reach the uterus. Early Development • The early cell divisions of the embryo occur without any overall growth. These divisions, the cleavage divisions, result in the morula, a ball of 16 or more cells. Each cell is called a blastomere. • After a few more divisions, cells on the outside of the morula flatten out, and the inside develops into a hollow ball, the blastocyst. • On one side of the blastocyst a clump of cells, the inner cell mass, forms. The inner cell mass develops into the embryo and the amnion, the inner membrane. • The other cells of the blastocyst are called the trophoblast (trophoectoderm), The trophoblast forms the chorion, the outer membrane of the embryo, and the embryonic part of the placenta (which is also composed of maternal tissues). • At about 5 days after fertilization, the blastocyst hatches by releasing itself from the zona pellucida that surrounded the egg, Then implantation into the uterine wall occurs, about 6 days postfertilization. Gastrulation • Lewis Wolpert: “It is not birth, marriage, or death, but gastrulation, which is truly the important event in your life.” • About 3 weeks after fertilization, the cells of the inner cell mass undergo a series of movements that end up producing the three fundamental germ layers of the body: ectoderm, mesoderm, and endoderm. Also, body orientation gets established. • ectoderm turns into skin and nervous system • mesoderm turns into muscle, bone, circulatory system, kidneys • endoderm turns into gut lining, endocrine glands, most internal organs • Cells in one area of inner cell mass develop a primitive streak, an area where the cells start to move inward. The cells that end up inside become the endoderm, while the cells that remain outside become the ectoderm. The mesoderm develops last, from cells near the primitive streak. • The primitive streak is replaced by the notochord, a rod of cartilage that is the defining characteristic of the chordates (which includes the vertebrates). Neurulation • After gastrulation finishes, about 4 weeks after fertilization, the nervous system starts to form, • The first event is the induction of the neural tube (beginning of the spinal cord) by the notochord interacting with the ectoderm above it. If the tube fails to close, spina bifida or anencephaly (absence of a brain) results. • Induction is a developmental process in which cells of one type touch cells of another type and induce them to differentiate into a new pattern. • Neural crest cells form at the margins of the neural tube. These cells migrate laterally, forming the peripheral nervous system, melanocytes (pigment cells). • This period ends after about 8 weeks, after which the embryo is called a fetus, which grows and develops further. Twinning • 2 basic types: dizygotic (fraternal): develop from 2 separate eggs fertilized by separate sperm. Nothing more than siblings who happen to share a womb. • monozygotic (identical): develop from one fertilized egg, with the embryo splitting into 2 early in development. Cause is unknown. • Cells up to the 4 cell stage are pluripotent: any single cell can develop into a whole person. This limits identical siblings to quadruplets. • splitting the embryo after about 12 days of development can be incomplete, resulting in conjoined twins. The joined region can include almost any area of the body and any degree of completeness. • A split before 4 days gives separate placentas • 4-8 day gives a shared placenta but separate amniotic sacs • 8-12 day split gives shared amniotic sacs, but still two separate individuals • 13-15 day splits are usually incomplete, resulting in conjoined twins. • A competing theory says that you start with a fertilized egg, the embryo splits completely, and then stem cells seeking similar cells cause them to re-fuse.