DNA Lesson Series: The mtDNA and its role in Ancestry
mtDNA Part I - mtDNA 101
mtDNA Part II - Facts about mtDNA
mtDNA Part III - mtDNA Structure  <<– you are here
mtDNA Part IV - Ancestral Markers
mtDNA Part V - Detecting Mutations in the mtDNA
mtDNA Part VI - mtDNA Ancestral Markers
mtDNA Part VII - The Cambridge Reference Sequence
mtDNA Part VIII - mtDNA Test Types
mtDNA Part IX - mtDNA Haplogroup Determination
mtDNA Part X - mtDNA Subclades
mtDNA Part XI - mtDNA Haplogroup H
mtDNA Part XII - Subclades of mtDNA Haplogroup H
mtDNA Part XIII - Distribution of Subclades of H
mtDNA Part XIV - Descendents of Maria-Theresa
mtDNA Part XV - Luke the Evangelist
mtDNA Part XVI - Empress Feodorovna
mtDNA Part XVII - James “Earthquake McGoon” McGovern

In this blog, we will talk about the structure of the mtDNA.  Understanding the structure of the mtDNA will help you to understand the types of ancestral markers found in it.   

mtDNA is a circular loop of DNA.  DNA is the chemical that carries genetic information.  DNA looks like a long ladder twisted into a “double helix”.  The sides of the ladder are the ”backbone”, and the rungs of the ladder consist of “nucleotide bases”.  There are 4 types of bases:  A, C, T, and G.  “A” is always connected to “T”, and “C” is always connected to “G”. 

Let’s take a closer look at the mtDNA loop.  The mtDNA has 4 main regions:  1) D-Loop, 2) rRNA, 3) tRNA and 4) genes that code for protein.  The regions that code for rRNA, tRNA and protein are called the “coding region”.   

The mtDNA loop is 16,569 base pairs in length.  The location of each base pair in the mtDNA can be specified with an accession number according to its position in the mtDNA.  When numbering the base pairs, we start at the “origin”.  The origin is arbitrarily located in the D-Loop region. 

The position of any base pair in the mtDNA is relative to the origin.  The position of any base pair in the mtDNA is designated by counting from “1″ clockwise around the mtDNA.  Thus, the positions are named 1 to 16,569 (remember this because it is important when we start talking about ancestral markers).

Let’s take a closer look at the D-Loop Region (aka Hypervariable Region) of the mtDNA since it is the region most frequently tested for ancestral studies. 

The D-Loop contains two regions, the HVR1 region which spans locations 16,000 to 16569, and HVR2 region which spans locations 1 to 400.  Unlike all of the other regions of the mtDNA, the D-Loop does not have any functional genes. 

Most of the ancestral markers are found in the D-Loop.  The D-Loop is considered a non-vital part of the mtDNA because it does not have a useful biological function.  Thus, whenever a mutation occurs in this region (we will discuss ancestral markers and mutations in the next blog), the individual does not die and survives to pass the mutation along to future generations.  However, the coding region of the mtDNA is considered essential for the survival of the individual, so usually, whenever a mutation occurs in this region, it is often lethal and the organism dies.  Thus, mutations which occur in the coding region are usually not passed down to future generations.  For this reason, over a period of thousands of years, many mutations accumulate in the D-Loop, but very little are found in the coding region.  Mutations are found at a much lower frequency in the coding region because only the mutations which do not end up being lethal are passed down.  When tracing ancestry, scientists usually begin by testing the D-Loop because of its abundance of mutations or “ancestral markers”.

In Part IV, we will continue this topic by discussing the types of ancestral markers which are found in the HVR1, HVR2 and coding regions of the mtDNA.