This tutorial is Part 3 of a 10 part series.
Part 1, What is mtDNA?
Part 2, Facts about mtDNA
Part 3, Structure of mtDNA <<== You are here
Part 4, Ancestral Markers in mtDNA
Part 5, Detecting Markers in mtDNA
Part 6, Tracing Ancestry with mtDNA
Part 7, The Cambridge Reference Sequence
Part 8, mtDNA Test Types
Part 9, mtDNA Haplogroup Determination
Part 10, mtDNA Subclades
Understanding the structure of mtDNA will help you to understand the different types of mtDNA tests available.
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”. The pairing of A from one strand with T from the other strand and the pairing of C from one strand with the G from the other strands leads to the term "base pairs".
Let’s take a closer look at the regions of the mtDNA
The mtDNA consists of 3 regions: HVR1, HVR2 and Coding Regions. HVR1 and HVR2 are "hypervariable regions" which have no known function and do not code for protein. The Coding Region is very important for survival and codes for rRNA, tRNA and protein.
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 between the HVR1 and HVR2 regions.
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 that contains the most ancestral markers and is the starting point for ancestral studies.
The D-Loop contains two regions, the HVR1 region which spans locations 16,000 to 16569, and the HVR2 region which spans locations 1 to 400. Unlike all of the other regions of the mtDNA, the D-Loop does not contain any functional genes.
Many ancestral markers are found in the HVR1 and HVR2 regions.
The HVR1 and HVR2 regions are considered non-vital parts of the mtDNA because they do not have a useful biological function. Thus, whenever a mutation occurs in the HVR1 or HVR2 region (we will discuss ancestral markers and mutations later), the individual does not die and survives to pass the mutation along to future generations. However, the Coding region contains many important genes which are essential for the survival of the individual, so usually, whenever a mutation occurs in the Coding region, it is often lethal and the organism dies. Thus, very few mutations which occur in the Coding region can be passed down to future generations. For this reason, over a period of thousands of years, many mutations have accumulated in the HVR1 and HVR2 regions, but a much smaller number of mutations can be found in the Coding region. When tracing ancestry, scientists usually begin by testing the HVR1 and HVR2 regions because of its abundance of mutations or “ancestral markers”.