4 20.9 The yeast mitochondrial genome, consisting of 78,000 bp, contains much noncoding DNA.
consists of noncoding sequences. Yeast mitochondrial genes are separated by long intergenic spacer regions that have no known functions. The genes encoding polypeptides often include regions that encode 5' and 3' untranslated regions of the mRNA; there are also short repetitive sequences and some duplications.
www.whfreeman.com/pierce Information on the Fungal Mitochondrial Genome Project (FMGP), whose goals are to sequence and analyze complete mitochondrial genomes from all major groups of fungi
20.8 The human mitochondrial genome, consisting of 16,569 bp, is highly economic in its organization. (a) The outer circle represents the heavy (H) strand, and the inner circle represents the light (L) strand. The origins of replication for the H and L strands are ori H and ori L, respectively. (b) Electron micrograph of isolated mtDNA. (Part b, CNRI/Photo Researchers.)
www.whfreeman.com/pierce Information on genes of the human mitochondrial genome
Yeast mtDNA The organization of yeast mtDNA is quite different from that of human mtDNA. Although the yeast mitochondrial genome with 78,000 bp is nearly five times as large, it encodes only six additional genes, for a total of 2 rRNAs, 25 tRNAs, and 16 polypeptides (< Figure 20.9). Most of the extra DNA in the yeast mitochondrial genome
Flowering plant mtDNA Flowering plants (angiosperms) have the largest and most complex mitochondrial genomes known; their mitochondrial genomes range in size from 186,000 bp in white mustard to 2,400,000 bp in muskmelon. Even closely related plant species may differ greatly in the sizes of their mtDNA.
Part of the extensive size variation in the mtDNA of flowering plants can be explained by the presence of large direct repeats, which constitute large parts of the mitochondrial genome. Crossing over between these repeats can generate multiple circular chromosomes of different sizes. The mito-chondrial genome in turnip, for example, consists of a "master circle" consisting of 218,000 bp that has direct repeats (iFigure 20.10). Homologous recombination between the repeats can generate two smaller circles of 135,000 bp and 83,000 bp. Other species contain several direct repeats, providing possibilities for complex crossing-over events that may increase or decrease the number and sizes of the circles.
120.10 Size variation in plant mtDNA can be generated through recombination between direct repeats. In turnips, the mitochondrial genome consists of a "master circle" of 218,000 bp, which has direct repeats that are separated by 135,000 bp on one side and 83,000 bp on the other. Crossing over between the direct repeats produces two smaller circles of 135,000 bp and 83,000 nucleotide pairs.
In the vast majority of bacterial and eukaryotic DNA, the same codons specify the same amino acids (see p. 000 in Chapter 15). However, there are exceptions to this universal code, and many of these exceptions are in mtDNA (Table 20.2). There is not a "mitochondrial code"; rather, exceptions to the universal code exist in mitochondria, and these exceptions often differ among organisms. For example, AGA specifies arginine in the universal code, but AGA codes for serine in Drosophila mtDNA and is a stop codon in mammalian mtDNA.
The mitochondrial genome consists of circular DNA with no associated histone proteins. The size and structure of mtDNA differ greatly among organisms. Human mtDNA exhibits extreme economy, but mtDNAs found in yeast and flowering plants contain many noncoding nucleotides and repetitive sequences. Mitochondrial DNA in most flowering plants is large and typically has one or more large direct repeats that can recombine to generate smaller or larger molecules.
Replication, Transcription, and Translation of mtDNA
Mitochondrial DNA does not replicate in the orderly, regulated manner of nuclear DNA. Mitochondrial DNA is synthesized throughout the cell cycle and is not coordinated with the synthesis of nuclear DNA. Which mtDNA molecules are replicated at any particular moment appears to be random; within the same mitochondrion, some molecules are replicated two or three times, whereas others are not replicated at all. Furthermore, the two strands in human mtDNA may not replicate synchronously. Mitochondrial DNA is replicated by a special DNA polymerase called DNA polymerase 7 (gamma). Presumably, helicases and topoiso-merases are required for mitochondrial DNA replication, just as they are in eubacterial and nuclear DNA replication.
The processes of transcription and translation of mito-chondrial genes exhibit extensive variation among different organisms. In human mtDNA, eubacterial-like operons are absent, and there are two promoters, one for each nucleotide strand, within the D loop. Transcription of the two strands proceeds in opposite directions, generating two giant precursor RNAs that are then cleaved to yield individual rRNAs, tRNAs, and mRNAs. As the tRNAs are transcribed, they fold up into three-dimensional configurations. These configurations are recognized and cut out by enzymes. The tRNA
Table 20.2 Nonuniversal codons found in
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