Chapter - III BACTERIAL GENETICS Genetic Recombination Gene Expression: Transcription and Translation From genes to proteins Allele: An alternate form of a gene. Alleles occur at loci on chromosomes. 1 Genetic Recombination Genetic material, otherwise known as DNA (DeoxyriboNucleic Acid) is composed of millions of genetic instruction sets. Each "set" is actually a specific ordered sequence of only four different amino acids (Adenine, Thymine, Guanine, and Cytosine). Each instruction set may be several hundred acid molecules long. A "set" of instruction "code" (as it is sometimes referred to) is known as an Allele. Connect a large number of alleles together into a long "strand" and you have half of a Chromosome. When you put two matching chromosome strands together, the "genetic code" or alleles match up on both sides, and together the two alleles are referred to as a Gene. In most body cells, chromosomes occur in pairs. This is what leads to the term "gene pair". Each "gene", therefore, is actually comprised of a pair of alleles. A particular area or location on a chromosome, is called a "locus" (plural = "loci"). The combination of both alleles at a specific locus determine a particular Trait or Characteristic of the animal. Hair color and eye color are examples of traits. Most of the cells in the body contain all of chromosomes. The chromosomes act as "instruction sets" which both tell the body how it will grow, develop and operate the traits of the individual. Fig.1. Each "color band" pair represents a Locus. The two alleles at each location, together represent a Gene. When both alleles are the same, they are referred to as homozygous. When each allele within a pair is different, it is known as heterozygous. Since the chromosomes occur in pairs, each "half" of the chromosome pair has the same order/arrangement of loci as the other. The exception to this, is the chromosome pair known as the Sex Chromosomes in the specialized sex cells used for reproduction. These chromosomes are often referred to as the X and Y chromosomes. The Y chromosome is shorter and contains less material than the X chromosome. The specific combination of the 2 sex chromosomes determine the gender or sex of the individual. Two X chromosomes (XX) will result in a female. The XY combination will result in a male. The reproductive cells, known as gametes, (which take the form of ova in females or spermatozoa in males) carry only half of the animal's genes. In all the higher species (such as mammals) the offspring will receive only one half of a gene pair from each parent. In the process of cell division that creates these gametes, the existing chromosomes of the parent are allowed to "cross-over". That is, some of the alleles found on one side of the chromosome pair will randomly trade places with the alleles found on the other side. After this exchange, the cell divides, and each resulting gamete cell has only half of the genetic material of the parent. As a result, each gamete contains a unique grouping of half of the genes of the parent animal. This special process of recombining the alleles to form gametes is known as Meiosis. Genetic recombination is the name given to a group of reactions during which cellular machinery uses DNA to alter or "recombine" with a similar (homologous) sequence. The process involves pairing between complementary strands of DNA, and results in a physical exchange of chromosome material. Genetic information is recombined by the cell for several reasons including the repair of damaged DNA, and the production of population variability during sexual reproduction. In some cases, recombination is known to change genes, adding new alleles to the population. Creationists generally believe that this mechanism was designed to generate the tremendous variety that is evident within each kind, whereas evolutionists attribute such variability ultimately to random mutagenesis. However, many creationists contend that recombination processes add nothing new to the gene pool. The position at which a gene is located on a chromosome is called a locus. In a given individual, one might find two different versions of this gene at a particular locus. 3 These alternate gene forms are called alleles. During Meiosis, when the chromosomes line up along the metaphase plate, the two strands of a chromosome pair may physically cross over one another, and during these events genetic recombination is performed by the cell. Recombination results in a new arrangement of maternal and paternal alleles on the same chromosome. Although the same genes appear in the same order, the alleles are different. This process explains why offspring from the same parents can look so different. In this way, it is theoretically possible to have any combination of parental alleles in an offspring, and the fact that two alleles appear together in one offspring does not have any influence on the statistical probability that another offspring will have the same combination. This theory of "independent assortment" of alleles is fundamental to genetic inheritance. The frequency of recombination is actually not the same for all gene combinations. This is because recombination is greatly influenced by the proximity of one gene to another. If two genes are located close together on a chromosome, the likelihood that a recombination event will separate these two genes is less than if they were farther apart. Linkage describes the tendency of genes to be inherited together as a result of their location on the same chromosome. Linkage disequilibrium describes a situation in which some combinations of genes or genetic markers occur more or less frequently in a population than would be expected from their distances apart. Scientists apply this concept when searching for a gene that may cause a particular disease. They do this by comparing the occurrence of a specific DNA sequence with the appearance of a disease. When they find a high correlation between the two, they know they are getting closer to finding the appropriate gene sequence. Evolutionary Assumptions Chromosomes have genes arranged along their length. During meiosis, it is believed the intended function of recombination is to leave existing genes unchanged by performing reacting in the neutral regions between reading frames. 4 Recombination within genes is able to create new alleles, however, it has been assumed this is not the cell's intent, and any changes to gene sequence are believed to be mutations resulting from mistakes during recombination or replication. The theory of evolution has led to the assumption that recombination originally occurred by mistake, instead of being an intelligently designed process. During sexual reproduction, gametes (egg, sperm) are produced during a cell division process called meiosis. Prior to meiotic division, homologous chromosomes unite at the axis before dividing to opposite poles. It is believed that this homologous pairing was originally performed simply to insure an equivalent division of genetic information. But, an exchange of DNA accidentally occurred during this process, which provided beneficial variability and was naturally selected to became a regular part of gamete formation. It remains generally assumed that recombination events are rather random, and therefore, the phenotypes produced by these reaction are also random. The DNA used for meiotic recombination possess homology or sequences that are very similar, and also code for variations of the same characteristic. Before the chromosomal DNA is distributed into new daughter cells, the homologues pair and are spliced together at multiple locations. During these interactions, entire regions and many genes are frequently exchanged. Offspring are always genetically unique due to recombination. However, it is now clear that recombination is a powerful source of new alleles. The knowledge of recombination comes predominantly from the bacteria E. coli, and its effect during sexual reproduction (meiosis) has been studied mostly using lower eukaryotes such as baker's yeast, as well as fruit flies. Recent work with mice has provided additional information from mammals, and shown that substantial differences exist between unicellular and multicellular organisms. The basic details and many genes involved in homologous recombination (HR) appear conserved among the multitude of life forms on earth. It is now widely recognized that genetic editions through HR are part of a highly coordinated process involving a cascade of specific macromolecule interactions (genes), and controlled by highly organized regulatory systems. Non-Random Recombination It was assumed that gene crossovers during meiosis occurred at random intervals along chromosomes. It was believed that the frequency of gene crossovers was directly related to the distance between genes, but a variety of discoveries have illustrated the existence of differential recombination rates and patterns, and forced a revision of map distances. It is now a well-known fact that recombination frequency is not constant in any one particular cell. Reactions occur more frequently in some regions of the genome than in others with variations of several orders of magnitude observed. These 5 hyperactive regions have been termed as "hot spots" as opposed to inert "cold spots" where little to no exchange is found. The frequencies of recombination events are also non-random. The rates are found to be significantly higher when comparing germ-line with somatic cell types. Sex- specific differences in recombination frequency have also been elucidated. Standard linkage analysis was used to confirm that females have a higher recombination rate than males, and males recombine preferentially in the distal regions of the chromosome. In addition to exchanges during cell division, HR is involved with many other forms of genomic DNA editing. For example, recombination is induced or shut off as a preprogrammed cell function during differentiation and development. It is also used to perform error-free DNA repair, which in this case serves to prevent unintentional variability.