Question

The mitochondrial genome is an interesting mix of eukaryotic and prokaryotic elements. Address the major aspects of mtDNA (in terms of organization, replication, transcription and translation. Use a table to organize your answers.

Answer 1

Feature	Discussion
Organisation	The human mitochondrial DNA (mtDNA) is double-stranded and circular molecule. It consists of 16,569 bp. It contains 37 genes which code for 2 rRNAs, 22 tRNAs and 13 polypeptides.
Replication	The mechanism of mt DNA replication is quite different from that of bacterial chromosomal replication and DNA replication in the nucleus. Replication takes place via a strand-asynchronous mechanism involving two unidirectional, independent origins. Synthesis starts at the origin of H-strand (heavy strand) replication in the D-loop and proceeds along the parental L-strand (light strand) to produce a full daughter H-strand. When the second origin at two thirds of the way around the genome is reached, DNA synthesis of the L-strand initiates in the opposite direction.
Transcription	The human mt transcription machinery consists of three components: mtRNA polymerase (POLRMT), TFAM and mitochondrial transcription factor either B1 or B2. Promoter recognition and transcription initiation require the simultaneous presence of these three factors. Termination of transcription appears to be regulated by multiple termination factors. Transcription in mt is started by a DNA-dependant RNA polymerase called POLRMT, which is structurally similar to RNA polymerases in T3 and T7 bacteriophages. However, in contrast with bacteriophage polymerases, which can recognize promoter regions without auxiliary proteins, additional factors are required to perform this function by POLRMT.
Translation	Although most of the proteins present in mitochondria are encoded by the nuclear DNA, a few are encoded by the mtDNA and are synthesized by its own translation system. The human mitochondrial DNA codes for 22 tRNAs, 2 rRNAs and 13 polypeptide subunits of the enzyme complexes I, III, IV, and V. The mitochondrial translation more closely resembles with its prokaryotic part than its eukaryotic cytoplasmic counterpart. The protein-synthesizing system of mitochondria has following characteristics not observed in prokaryotes or the eukaryotic cell cytoplasm. (1) mitochondria use a genetic code that has several distinct differences from the universal code. For example, human mitochondria use the universal arginine codons AGG and AGA, in addition to UAA and UAG for termination of translation. Also, UGA serves as a codon for tryptophan rather than as a stop codon. AUA has been assigned to Met rather than serving as an Ile codon. (2) The mitochondrial mRNAs have unusual features: they contain no or very few 5' untranslated nucleotides, are uncapped, and contain a poly(A) tail that immediately follows or even forms part of the stop codon. (3) Mitochondria use a simplified decoding mechanism that allows translation of all codons with only 22 tRNAs instead of the 31 predicted by Crick’s wobble hypothesis. (4) Mitochondria use a tRNA single for both the initiation and elongation phases (depending on the presence or absence of a formyl group, resp.), whereas not only in the prokaryotic and eukaryotic cytoplasmic translation systems but also in the mitochondria of most lower eukaryotes two specialized tRNA species exist.