Chromosomes and Inheritance - 1 Chromosome Theory of Inheritance Although Gregor Mendel did tremendous work in determining how genetic information was passed from generation to generation, he had no knowledge of chromosomes or the process of meiosis or that genes, the units of heredity, were located on chromosomes. Particularly important, we know today that we have far more genes than chromosomes. Mendel only addressed genes (his "paired factors") that were independently inherited, and fortuitously, each of the traits he studied was on separate chromosomes in the pea plant. Walter Sutton and Theodor Boveri made the correlation between Mendel's conclusions about genes (the inheritable traits of Mendel's "paired factors") and the behavior of chromosomes during mitosis and meiosis in 1902. Sutton is credited with first proposing the chromosome theory of inheritance, in which he connected Mendel's "paired factors" with the behavior of homologous chromosomes during meiosis. Chromosomes are in pairs and genes, or their alleles, are located on chromosomes. Homologous Chromosomes separate during meiosis so that alleles are segregated. Meiotic products have one of each homologous chromosome but not both. Fertilization restores the homologous pairs of chromosomes. Chromosomes and Segregation of Alleles in Meiosis
Chromosomes and Inheritance - 2 Genes Inherited Together Gene Linkage on Chromosomes From the time of Sutton's deduction that inheritance followed the behavior of chromosomes, genetic research had a "problem" to solve. Mendelian inheritance "required" genes to be inherited independently of each other, but there are far more genes than chromosome pairs. How can we have thousands of genes and not thousands of chromosomes? In 1908, researchers discovered a dihybrid cross in sweet peas that did not have the predicted Mendelian ratio of 9:3:3:1. 75% of the secondgeneration offspring had the same two traits as the dominant parent and 25% the same two traits found in the recessive parent, the 3:1 ratio expected for a monohybrid cross. But if flower color and pollen length (the genes observed) were on the same chromosome they could explain the 3:1 inheritance ratio. Since Sutton had hypothesized that we inherit chromosomes, it was logical to conclude that all of the genes on a chromosome are physically inherited together as a single linked group. Only genes that are located on different chromosomes have independent assortment during meiosis I and follow Mendel's independent assortment ratio (9:3:3:1 or 1:1:1:1 for a test cross). The inheritance ratio for linked genes is the same as the Mendelian 3:1 ratio for a monohybrid cross, or 1:1 for a test cross. For purposes of meiosis and inheritance all the genes on a chromosome are one connected (or linkage) unit. Linked Genes that Unlink Crossing-Over and Recombination After the "discovery" that genes were not always independently inherited, but all genes on a chromosome are inherited in the same combination (linkage unit) as the parents, many geneticists rushed to find genes that were linked. They would take two traits, do an inheritance test, and if the inheritance ratio was 9:3:3:1, or, with a test cross, a 1:1:1:1 ratio, they would conclude the genes were on separate chromosomes and followed Mendel's law of independent assortment. If the ratio was 3:1, or 1:1 for a test cross, they would conclude the genes were on the same chromosome, and linked. Life was good.
Chromosomes and Inheritance - 3 For proportion reasons, it was easier to do test crosses, and many were done. In a dihybrid test cross of linked genes, 50% of the offspring would be the same as one parent, and 50% the other parent. With independent assortment (genes on different chromosomes), 25% would resemble one parent, 25%, the second parent, and 25% would have one trait from one parent and one from the other parent and 25% would have also have the "other" traits from each parent for a total of 50% recombinant forms, offspring that differed from the parental allele combinations. Independent Assortment Ratio Linked Genes ratio Thomas Hunt Morgan and Fruit Flies in Genetics Thomas Hunt Morgan's research with fruit flies demonstrated linkage when his test cross of a heterozygous gray, normal-winged (wild type) fruit fly with a black vestigial-winged fruit fly did not yield the Mendelian predicted ratio of 1:1:1:1, but was closer to, but not exactly, the Mendelian Monohybrid test cross ratio. The crosses of linked genes produced some offspring that had a mix of the parental types, or recombinant forms but not in the proportions found in independent assortment ratios for the dihybrid crosses. Could genes somehow sometimes during meiosis? Recall that during our discussion of meiosis that crossing over occurs during Prophase I. Recombination results in chromatids that are not identical; some genes have been exchanged between non-sister chromatids so that each chromatid will have one or more genes from its homologous partner. Not all gametes will have the same linked genes as the parents. In other words, crossing over "unlinks" genes and recombinant chromatids and more genetic variation are the result. Recombination can readily be shown with the pea flower color and pollen length genes. Gamete Chromosomes
Chromosomes and Inheritance - 4 Morgan was among those who examined this hypothesis with his fruit flies, choosing two traits that were linked body color and wing size. Normal wings and gray were dominant; vestigial wings and black body were recessive mutants. About 17% of Morgan's test fruit flies were recombinant forms in contrast to the 50% expected for a dihybrid with independent assortment and 0% for gene linkage. The phenomenon of crossing-over with recombination was confirmed. Alleles on homologous chromosomes exchange places with their corresponding alleles during prophase I of meiosis, as we discussed in our unit on meiosis. Crossing over and Recombination in Meiosis
Chromosomes and Inheritance - 5 Crossing over can occur at several places (gene loci) along homologous chromosome pairs during meiosis. Being interested in finding gene loci, one of Morgan's students, Alfred Sturtevant, proposed that the frequency of recombination between any two linked genes is relative to the distance between their loci on the chromosome. The frequency of two genes close together on a chromosome crossing-over is small. The frequency of recombination is higher when the genes are farther apart on the chromosome. Sturtevant measured recombination frequency (very tediously) for a number of pairs of genes and used that data to locate the relative positions of genes on their respective chromosomes. This process of pinpointing specific genes on the chromosome is called chromosome mapping (or genetic mapping). Each map unit, called a centimorgan, is defined as the distance within which a cross-over is expected in 1% of the gametes. Sturtevant's Linkage Map
Chromosomes and Inheritance - 6 Chromosome mapping using recombination data was used extensively in the earlier part of the 20 th century despite limitations of knowing just relative positions and not being able to accurately map genes that are far from each other on a chromosome. Today we have much more sophisticated methods of dealing with chromosome mapping using cytogenetic characteristics, or making physical maps using DNA probes, where a known DNA fragment is used to compare with an unknown chromosome region. If the probe matches we can identify the region. The genomes of dozens of organisms have now been completed, including Arabidopsis, E coli, rice, the common yeast, the fruit fly and, of course, the human genome. (We will return to this subject later.) So far we have been discussing linked genes on autosomes, the chromosomes that physically match and have equivalent genetic information, but what about the sexdetermining chromosomes that pair, but don't have the exact same genes? The Special Case of the Sex-Determining Chromosomes and the Proof That Genes Are on Chromosomes By the early 1900's it was known that males and females of most organisms that have separate sexes have one pair of "notexactly-matching" homologous chromosomes, readily observed in karyotypes. The unmatched pair of chromosomes, or sometimes a single chromosome, determines the sex of the individual. These chromosomes are called the sex chromosomes. (Recall that the truly matching chromosomes are autosomes.) For many species, the sex-determining chromosomes will be homologous for one sex, usually female, and are conventionally called XX. The male will have unmatched chromosomes (XY). Some species, including birds, have a reverse pattern of sex chromosomes (Male = ZZ and female = ZW (just to not confuse letters)). Some species have one gender (female) with a pair of chromosomes and one gender (male) with a single unmatched chromosome (XX and X0 (It's OK to be confused with the letters. "O" = none)). Some insects, including bees, have haploid males and diploid female workers and the diploid queen.
Chromosomes and Inheritance - 7 In most cases the gender with the dissimilar pattern will determine the sex of the offspring. Human eggs, for example, are all "X". Sperm can be either "X" or "Y". In fruit flies, however, the ratio of X to Y chromosomes seems to determine gender and fertility. A fly with just one X chromosome will be a structural male, but sterile. Fertile males have both an X and a Y chromosome. Some females have two X chromosomes and a Y; others have two X chromosomes. It should be noted that many organisms do not have physically distinguishable sexes, as mentioned earlier with yeast genetic markers. In many plants male and female gametes might be produced in the same organ (bisexual) or in separate structures but on the same plant (monoecious). Plants that have their male and female reproductive structures on separate plants are called diocecious. (Flowering plant reproduction and development are discussed in Biology 213.) Interestingly, the first proof that a specific gene was located on a specific chromosome, hence validating the chromosome theory of inheritance, resulted from a mutation in Thomas Hunt Morgan's genetics lab that was inherited "differently" in male and female offspring. As were many other researchers in the early 1900's, Morgan was interested in validating (or disproving) Mendelian inheritance patterns and needed a convenient organism, and one with discernable traits. He chose the fruit fly, Drosophila melanogaster, for some very good reasons. Fruit Flies: Have a short generation time (inheritance research needs many generations) Are small and easy to keep in a laboratory Produce reasonably good numbers of offspring Have a number of easy to see inheritable characteristics Have a chromosome number of 8 (4 pairs of chromosomes) Proof of the Chromosome Theory of Inheritance using Sex-Linked Genes You may surmise that genes located on the sex chromosomes played a role in Morgan's proof that each gene is located on a specific chromosome. While seeking variants for his research Morgan happened upon a mutant male with white eyes. Morgan made several crosses using his white-eyed male, expecting the standard Mendelian results. He did not get them. While a 3:1 ratio of red-eyed offspring to white-eyed offspring was obtained, all of the white-eyed second-generation offspring were male flies. All F 2 females had red eyes. (25% of the F 2 males also had red eyes).
Chromosomes and Inheritance - 8 Initially, Morgan thought only males could have white eyes, but a test cross of F 1 females to the parental white-eyed male produced some females with white eyes. Moreover, the white-eyed females, when crossed with red-eyed males produced male offspring with white eyes and female offspring with red eyes. White-eyed females could pass the white-eye allele to their daughters, but if the father fly had red eyes, the eye color of the daughters would be red. The sons were all white-eyed, having received the white allele from the mother and the "Y" chromosome from their father. The proportion of and gender of offspring with white eyes depended on the genotypes of both parents. Morgan concluded that the gene for eye color in the fruit fly was located only on the X chromosome. The Y chromosome has no allele for eye color. Males pass the trait to their daughters (on their solitary X chromosome), which may or may not be expressed, depending on the eye color of the X chromosome the daughters receive from their mother, and sons express whatever eye color allele is on the X chromosome they receive from their mother. Homozygous white X red Heterozygous red X white Heterozygous red X red
Chromosomes and Inheritance - 9 Morgan's experiment demonstrated that a given genetic characteristic, in this case, eye color, was associated with a specific chromosome, in this case, the "X" chromosome, providing proof for the chromosome theory of inheritance. It also introduced the concept of sex-linked genes. Today we call a chromosome that is lacking genes found on its homologous chromosome, hemizygous. Human males are hemizygous for the genes on the X chromosome for which they have no alleles on their Y chromosome. They get just the one allele. The Role of Specific Sex-Linked Genes As assumed long before Morgan's work, sex-determining chromosomes have information that determines the sex of the individual. But how? Abnormal sex chromosome arrangements that result from non-disjunction during meiosis (to be discussed in our unit on gene mutations) provide data on how the X and Y chromosomes function. In humans the gene that triggers the hormonal conditions for the development of the testes is located on the Y chromosome. This gene, called the SRY gene (sex region of the Y chromosome), is activated in the embryo at about 2 months and is responsible for primary sex determination. Some other genes needed for normal male development are also on the Y chromosome; many others are on autosomes. In some species, the activation of the SRY gene is influenced by environmental conditions that can change how this gene gets expressed, hence altering the sex of the developing individual. Genes on autosomes are mostly responsible for the secondary sex determination, those characteristics associated with for normal male and female development, particularly at puberty. They are not all on the sex-determining chromosomes. However, no one thought the sex-determining chromosomes would have genes that coded for somatic traits until Thomas Hunt Morgan's "accidental" discovery of the selective inheritance of white eye in the fruit fly. These other traits are said to be sex-linked because they are inherited along with the sex of the individual. Because the X and Y chromosome are not exactly matching, the X chromosome has genes that are not located on the Y chromosome, and vice-versa. This is referred to as sex linkage and the sex-linked traits are hemizgous. One of the more common sex-linked traits in humans is red-green colorblindness.
Chromosomes and Inheritance - 10 A well-known sex-linked trait is hemophilia, carried in the European royal family. The human X chromosome has between 1000-2000 genes. The Y chromosome has about 78, most affecting sperm production and fertility, plus the SRY gene that determines the male sex, a gene sequence that codes for hairy ears and some ribosome proteins that are found only in males. A number of genetic disorders are associated with the X chromosome, including fragile X syndrome, one of the nucleotide repeat genetic disorders. (See later). Fragile X Note: A Special Feature of the X Chromosome, the Barr body, will be discussed in our section on gene regulation.
Chromosomes and Inheritance - 11 Exceptions to "Mendelian" Inheritance Patterns We have been discussing a variety of different inheritance patterns, all based on the inheritance of genes on homologous autosomal chromosomes or of genes on the sex-determining chromosomes. Although the genetic characteristics associated with the sex-determining chromosomes may depend on whether you inherit "X" or "Y" chromosomes, most alleles are the same no matter which parental chromosome you have inherited. This is not always the case. Some alleles on autosomes may be altered during gamete formation resulting in differential inheritance (discussed in our section on gene regulation). We also have genes in mitochondria and in chloroplasts that are inherited exclusively from the organelles in the egg cytoplasm, hence always passed from mother to all offspring. The paternal gamete does not transmit organelles. The expression of genes located in the organelles is known as extra-nuclear gene expression. In addition, proteins synthesized in the egg prior to fertilization needed for early development are coded only by the maternal genome. Extra-nuclear Gene Expression As stated previously, Mendelian inheritance addresses only the behavior of genes on chromosomes, but mitochondria and chloroplasts (and all plastids) have small circular pieces of DNA that are transcribed and translated within the organelle. These genes are often referred to as extranuclear genes precisely because they are not in the nucleus. Mitochondria and plastids are self-replicating. In sexual reproduction, only the egg cell's cytoplasm is passed to the zygote, so only maternal mitochondrial and chloroplast DNA will be transmitted from generation to generation. The genes in mitochondria and plastids are important for organelle function and cells might have hundreds of mitochondria or chloroplasts. The self-replicating organelles have a fairly high rate of mutation relative to the nuclear genome; multiple alleles are common in the chloroplast and mitochondria genomes. Some genetic disorders are traced to mutations in mitochondrial DNA that code for proteins in the electron transport chain. When mitochondrial DNA is defective, cells make less ATP. Mitochondrial diseases exhibit greater effects on muscle and nervous systems, since they are high energy demanding systems. Research is ongoing to determine if mitochondrial defects might also play a role in some diabetes, heart disease and diseases that debilitate the elderly, such as Alzheimer's. Some mutations in mitochondrial DNA may be one reason cells age. Fortunately, the frequency of mitochondrial gene "defects" is low so that mitochondrial diseases are rare in the population.
Chromosomes and Inheritance - 12 Some variegated leaf patterns or leaves produced without any chlorophyll are caused by mutations in chloroplast DNA that inhibit chlorophyll synthesis. Mutant chloroplasts from the egg cell are more or less randomly assorted in mitosis, so that different variegated patterns result. Chromoplasts may also be affected. As shown below, when the female parent has chlorophyll, all offspring will have chlorophyll. If the female parent lacks chlorophyll, none of the offspring produce chlorophyll. Parental presence or absence of chlorophyll has no effect on the offspring. Chloroplast inheritance in tomato, Hosta and Pelargonium leaves
Chromosomes and Inheritance - 13 Bacterial Gene Transmission and Recombination Bacteria (and Archaea) have one double-stranded, circular DNA molecule associated with specific proteins. It is tightly compacted to form the nucleoid, but lacks a membrane boundary. Bacteria may have multiple copies of their chromosome. Many bacteria also contain plasmids, small circular pieces of DNA with a few genes. Plasmids are also self-replicating. Bacteria are not diploid organisms and do not have meiosis and sexual reproduction that we find in diploid eukaryotes, processes that obtain and maintain genetic variation from generation to generation for eukaryotes. Most genetic variation in bacteria occurs by mutation. Their rapid reproduction rate by binary fission (discussed earlier) can result in many new mutant forms within a few hours or days when conditions for growth provide for rapid division. However, some bacteria do have genetic exchange and recombination of genes. Recall that recombination is defined as combining some portion of DNA from two sources into one individual. In some cases, the entire chromosome of one bacterium is passed to a second, with resultant recombination. Gene transfer and recombination occur by four methods in bacteria: Conjugation, transformation and transduction and plasmid gene transfer. We will now examine processes by which bacteria do genetic exchange. However, only conjugation involves genetic exchange between two bacteria. Conjugation Conjugation involves the direct transfer of DNA from one bacterium to a second. They can be the same or different types of bacteria. Conjugation requires specific structures, called pili (or pilus, singular) to facilitate the transfer of DNA from one bacterium to the second. The pilus is used to attach the two bacteria to each other. Conjugation is used most frequently to transfer plasmids, which adds the plasmid DNA to the recipient's genome (see plasmid gene transfer below), or to transfer portions of or the entire bacterial genome to the recipient, which results in recombination, a change in the recipient's DNA. The bacterium that sends the plasmid or chromosomal DNA is called a donor. The recipient bacterium receives the plasmid or chromosomal DNA. Once attached to the recipient by its pili, the donor bacterium grows a conjugation tube, which is a cytoplasmic bridge between the two cells, through which DNA passes.
Chromosomes and Inheritance - 14 Transduction Conjugation and Recombination Transduction requires a virus vector to bring the DNA into the host cell. Occasionally, when a virus incorporates a portion of it host cell's DNA into the viral genetic molecule. The new "virus" with its packaged host DNA fragment can attach to and be incorporated into a new bacterial host. Once the DNA fragment is in the new bacterial cell, recombination can occur resulting in variation. Note: Viruses that infect bacteria are called bacteriophages or phages.
Chromosomes and Inheritance - 15 T r a n s f o r m a t i o n In transformation, DNA from the environment is taken up by the bacterial cell and incorporated into the bacterium's genome. Recombination occurs between the donor DNA and the recipient's chromosomal DNA. Fred Griffith first demonstrated transformation in 1928, when the non-virulent form of Streptococcus pneumoniae bacteria he was studying changed to the virulent form when exposed to heat-killed virulent bacteria. He concluded that "something" that withstood heat was transferred from the mixture to the non-virulent bacteria "transforming" them into virulent bacteria. This landmark research led to the proof that DNA is the genetic molecule. (Griffith's research will be discussed in our unit on DNA structure and function) Not all bacteria do transformation. Those that have transformation have special proteins on their membrane that facilitate the uptake of the foreign DNA. E. coli can be stimulated to do transformation when Ca ++ ion concentration is high and the bacterium is subjected to rapid temperature changes. This temporary permeability of the membrane is call competency. Much recombinant DNA work uses transformation to incorporate genes from any number of donor sources into recipient, or host, bacteria.
Chromosomes and Inheritance - 16 Plasmid Gene Transfer In addition to the single chromosome, many bacteria have additional small pieces of self-duplicating DNA called plasmids, which contain just a few genes and move freely. Some bacteria can incorporate plasmids from other kinds of bacteria (plasmids are not necessarily species specific) and from their environment, which increases their genetic versatility and adds to the recipient's genome. When this occurs, the plasmid is called a gene vector. Vector is a term used when an intermediary is involved in a transfer of something. (Plasmids are often used in Recombinant DNA technology as gene vectors, a subject to be discussed in our genetic technology unit.) Some plasmids can be incorporated or integrated into the DNA molecule of the bacterium while other plasmids remain in the bacterial cytoplasm. o Plasmids that incorporate into the bacterial DNA molecule are duplicated with the DNA molecule. Integrated plasmids can also be excised to become free in the cytoplasm of the cell or re-integrate into new positions. During excision, an integrated plasmid may incorporate some chromosomal DNA along with its plasmid DNA, o As previously discussed, during conjugation, a plasmid can carry incorporated chromosomal DNA to the recipient bacterium. The chromosomal DNA brought with the plasmid then undergoes recombination with the recipient cell's complementary DNA. Two very important plasmids are the F plasmid, involved in bacterial recombination by c onjugation and the R plasmids. The R plasmid may have as many as ten antibiotic resistant genes as well as genes for the formation of pili. A population of bacteria exposed to antibiotics may rapidly become a resistant population if some of the bacteria contain the R plasmid. Bacterial Chromosome and Plasmid Plasmid Gene Transfer with Conjugation