Extranuclear Inheritance

We have already encountered one major exception to Mendel's concepts, namely linkage, which is an exception to his Law of Independent Assortment. The other major exception is the presence of genes in the cytoplasm, primarily in mitochondria and chloroplasts. Mendel's laws are all based on nuclear gene heredity--that is meiosis (although he knew nothing about meiosis). Cytoplasmic genes do not segregate to daughter cells according to meiosis, so do not obey his laws. For that reason, the inheritance of these cytoplasmic genes is often referred to as non-Mendelian genetics.
Organelle Genetics: There are two separate Genetic Systems involved in the production of mitochondria and chloroplasts: The Nuclear System: Most proteins found in mitochondria and chloroplasts are coded for by nuclear genes, made on cytoplasmic ribosomes, then transported into mitochondria. The Organelle System Some proteins in these organelles are coded for by organelle DNA and made on organelle ribosomes.
Organelle Genomes: Mitochondria and chloroplasts have their own small DNA molecules that are usually circular (except in some algae and protozoa) and are present in multiple copies in each organelle. Mitochondrial DNA (mtDNA): Animal mtDNA molecules are usually about 16-19 kb in size (about 1/100,000 of the nuclear genome, altogether about 1% of cellular DNA). Plant mtDNA is 10 - 150 times larger than animal mtDNA (150 - 2500 kb). Since plant mtDNA codes for about the same number of genes as animal mtDNA and there is sometimes great variability in size even within closely related plants, the excess may be "junk DNA." DNA replication begins from the D-loop regions and replicates one strand, then when reaching the D-loop again, the other strand is replicated in the opposite direction. mtDNA codes for tRNAs, rRNAs and a few proteins. There are two promoters on the heavy strand, which has 28 genes including the two rRNA genes, and one promoter on the light strand, which has 9 genes, 8 of which are tRNA genes. Transcripts are processed into the appropriate RNAs. In vertebrate mitochondria "AGA" and "AGG" are stop codons, but not "UGA", which codes for tryptophan instead. "AUA" codes for isoleucine in most organisms but for methionine in vertebrate mitochondrial mRNA. mtDNA has a nucleotide substitution (mutation) rate that is about 10 times higher than nuclear genomes, making mtDNA comparisons useful taxonomically. Some mtDNA genomes have introns. (..but, wait a minute..."For decades, scientists thought they had a handle on the mitochondrial chromosome: 13 genes for proteins, two for rRNAs and 22 for tRNAs, all tightly packed with no introns." ... but now "it appears to contain small open reading frames that are hidden inside the other genes.") Summary: Animal mtDNA is circular and usually about 16,000 - 19,000 bp long. The D-loop is the replication origin region of this molecule. It has an unusual method of replication. DNA replication begins from the D-loop regions and replicates one strand, then when reaching the D-loop again, the other strand is replicated in the opposite direction.In humans, there are two strands, H and L, with two promoter on the H strand and one on the L strand. Therefore, three RNA are transcribed then cut into the appropriate mRNAs, rRNAs, or tRNAs. The mtDNA includes 13 genes for proteins involved in oxidative phosphorylation, 2 rRNA genes, and 22 tRNA genes. Mitochondrial DNA uses a genetic code which is slightly different from the nuclear code. Most of the proteins needed to make a mitochondrion are coded for by nuclear genes. These proteins are imported into the mitochondria.
Chloroplast DNA (ctDNA or cpDNA): Plant chloroplast DNA molecules are about 120 - 180 kb in size. Higher plant ctDNA codes for about 120 genes, including rRNAs, 30 tRNAs, several rProteins, an RNA polymerase subunit, several respiration-related proteins, plus other 40 proteins. ctDNA has introns. Summary: ctDNA is much larger than animal mtDNA and may be circular or linear.
Organelle Division: Mitochondria and chloroplasts are never made de novo, but always come from pre-existing organelles. DNA replication occurs throughout the cell cycle. Organelle division occurs by furrowing of the inner membrane with DNA molecules being distributed between the daughter organelles.
Organellar Inheritance: Inheritance of mitochondrial and chloroplast genes is non-Mendelian (cytoplasmic inheritance, extranuclear inheritance). In yeast, this leads to random segregation of traits. In higher organisms, non-Mendelian inheritance is seen as maternal inheritance, since mitochondria and chloroplast are usually inherited via the ovum only. Heteroplasmy and lead to mosaicism. Why are mitochondria only inherited from the mother?: http://science.sciencemag.org/content/early/2016/06/22/science.aaf4777.abstract Summary: Mitochondrial and chloroplast trait are inherited maternally, resulting in a unique pedigree.
Other Extranuclear Genes: Endosymbionts like kappa (killer) in Paramecium.
Human Mitochondrial Traits Many are lethal and only seen with heteroplasmy (some normal mitochondria present).