Human Biochemistry, Volume 2 - Murray R. 1993

Structure, Function, and Replication of Informational Macromolecules
DNA Organization and Replication
Alterations and Rearrangements of Genetic Material

Alterations in The sequence of purine and pyrimidine bases caused by the substitution, deletion, or insertion of one or more NUCLEOTIDES can lead to a modified product of the Gene in question—most commonly a protein. The consequences of such genetic material changes (Mutations) are described in Chapter 40.

Chromosomal Recombination

Homologous Chromosomes in PROKARYOTES AND EUKARYOTES can exchange genetic material. This exchange, or recombination, occurs in mammalian Cells primarily during Meiosis. This event is preceded by the pairwise alignment of homologous chromosomes, a process that typically takes place with extremely high precision. The Crossing-over process is schematically illustrated in Fig. 38.9. It consists of an equivalent reciprocal exchange of Genetic information between homologous chromosomes. If homologous chromosomes carry different alleles of the same gene, crossing-over can result in a noticeable and heritable trait modification. In rare cases where homologous chromosomes do not align entirely precisely during conjugation, unequal crossing-over may occur, resulting in a non-equivalent exchange of information. As a result, one of the chromosomes loses a portion of its genetic information and thus carries a deletion. The second chromosome acquires an increased amount of material and consequently bears an insertion or duplication (Fig. 38.9). Unequal crossing-over in humans is exemplified by the Hemoglobins designated Lepore and anti-Lepore. It can occur within tandem regions of repetitive DNA, such as globin gene sequences or sequences belonging to more abundant repetitive DNA families (Fig. 38.10). This phenomenon is responsible for the expansion or contraction of copy numbers within a given repeat family.

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Fig. 38.9. The process of crossing-over between homologous chromosomes and The formation of recombinant chromosomes.

Chromosomal Integration

Certain bacterial Viruses (Bacteriophages) are capable of recombining with host DNA such that the phage DNA is integrated in a linear form into the bacterial genome. Bacteriophage integration proceeds via a mechanism depicted in simplified form in Fig. 38.11, involving the breakage and joining of both DNA molecules while maintaining polarity. Consequently, integration is accompanied by linearization—the transition of the circular bacteriophage DNA molecule into a linear form. Two mechanisms of bacteriophage genome integration with the bacterial genome are known. If the bacteriophage DNA contains regions homologous to the bacterial DNA, a mechanism analogous to homologous chromosome recombination is utilized. Alternatively, integration is carried out by bacteriophages that synthesize Proteins directing the specific binding of particular sequence regions (sites) on the bacterial chromosome to non-homologous sites within the phage DNA. Integration via this mechanism is termed site-specific.

Fig. 38.10. Unequal crossing-over within the structural genes of human hemoglobins. Products of unequal crossing-over: delta-beta Lepore and beta-delta anti-Lepore globin genes. The given Examples show the locations of the crossover regions. (Reproduced, with permission, from Clegg J. B., Weatherall D. J. ß⁰-thalassemia: Time for reappraisal? Lancet 1974, 2: 133.)

Many animal viruses, particularly Oncogenic Viruses, can integrate into the mammalian genome either directly or, in the case of RNA viruses, via DNA transcripts. The integration of viral DNA into animal chromosomes is generally not site-specific.

Fig. 38.11. Integration of a circular genome (containing genes A, B, C) into a host DNA molecule (containing genes 1 and 2) and the gene arrangement order in the recombinant DNA strand.

Transpositions

The eukaryotic genome contains small DNA elements that are not proviruses, yet are capable of independently excising themselves from the host genome and subsequently integrating into various other regions, thereby affecting the Functions of adjacent DNA sequences. These mobile elements, sometimes referred to as "jumping DNA," can translocate chromosomal DNA fragments and thus profoundly influence genome evolution. As noted above, the family of short Alu repeats is characterized by structural similarities with the terminal sequences of Retroviruses, which enable the latter to integrate into and exit from the mammalian genome.

Direct Evidence for the transposition of other small DNA elements within The Human Genome came from the discovery of so-called processed immunoglobulin genes, a-Globins, and several others. Processed genes are identical or nearly identical to the mature mRNA sequences of these genes. They consist of an untranslated 5' region, a coding region devoid of introns, and a poly(A) tail at the 3' end. The Emergence of processed genes can only be explained by the integration of reverse transcripts corresponding to the respective mature mRNAs. Apparently, the only possible mechanism for the insertion of such reverse transcripts is transposition. Indeed, both ends of processed genes are flanked by short repeats similar to those found in mobile elements of lower organisms. Some processed genes contain randomly distributed sequence variations accumulated over the course of evolution. Such alterations frequently lead to the formation of nonsense codons that prevent expression (see Chapter 40). Such processed genes are termed pseudogenes.

Gene Conversion

In addition to unequal crossing-over and transpositions, a third mechanism of rapid genetic material modification exists. Identical sequences of homologous or non-homologous chromosomes can form random pairs, while mismatched regions are excised. As a result, a specific repeat variant within a family becomes fixed. This process is known as gene conversion.

Diploid cells of eukaryotic organisms (including humans), upon completing the S phase of the Cell Cycle, contain a tetraploid set of chromosomes. Each sister chromatid (chromosomal pair) carries identical genetic information because both are the result of semi-conservative Replication of the parental DNA molecules. Crossing-over can occur between these genetically identical chromatids. The EXCHANGE OF GENETIC information between sister chromatids (Fig. 38.12) manifests as equal crossing-over and has no genetic consequences.

Fig. 38.12. Sister chromatid exchange in humans. Giemsa staining of chromosomes after two rounds of replication in the presence of bromodeoxyuridine. (Courtesy of S. Wolff and J. Bodycote.)

Certain interesting genetic rearrangements occur in mammalian cells during normal development and differentiation. For instance, in the mouse germline, the V_L and C_L genes encoding a single chain of an immunoglobulin molecule (see Chapter 41) are located at a considerable distance from one another in The Genome. In the DNA of mature immunoglobulin-producing (plasma) cells, these same genes are brought into much closer proximity and are transcribed as part of a single primary transcript. However, even after DNA rearrangement during differentiation, the sequences of these genes are not directly contiguous. An intervening non-coding sequence (intron) of approximately 1,200 Base Pairs lies between them, which is removed from the primary transcript during Processing in the course of mRNA maturation (see Chapters 39 and 41).