1.
Sunday, November 13, 2022
Kurdistan Regional Government – Iraq
Ministry of Higher Education & Scientific Research
University of Zakho
Faculty of Science
Biology Department
Mitochondrial DNA
Subject (Genetics I)
5th Semester
Prepared By
Rahma Hishyar
Rasol haji Ahmed
Dunya Miqdad
Ruwayda Abdullqadir
Supervised By
Prof. Dr. Yousif Mohammed

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Abstract
Mitochondrial DNA (mtDNA) is the physical embodiment of the genetic
information encoded in the mitochondrion. Technically, the term ‘mitochondrial
DNA’ encompasses not only the mitochondrial genome per se, but additional DNA
types (e.g., small linear plasmid-like DNAs) that are present in the mitochondria of
some organisms. As its name implies, mtDNA is compartmentalized within the
mitochondrion and is therefore physically and transcriptionally separate from the
main nuclear genome of the eukaryotic cell. As well as being transcriptionally
distinct from the nuclear genome, the mitochondrial genome and other types of
mtDNA molecules are distinct in evolutionary origin, with the main mitochondrial
genome having been derived from a eubacterial ancestor through a process of
endosymbiosis.

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List of Contents
1. Introduction..........................................................................................................1
2. Genome structure and diversity...........................................................................2
2.1 Animal...........................................................................................................3
2.2 Plants and fung ..............................................................................................3
2.3 Protists...........................................................................................................4
3. Replication...........................................................................................................4
4. Genes on the human mtDNA and their transcription..........................................5
5. Regulation of transcription ..................................................................................5
6. Mitochondrial inheritance....................................................................................6
6.1 Female inheritance ........................................................................................7
6.2 Male inheritance............................................................................................8
7. The mitochondrial bottleneck..............................................................................9
8. Mitochondrial donation .....................................................................................10
9. Mutations and disease........................................................................................10
10. Causes:............................................................................................................11
11. Symptoms:......................................................................................................11
12. Test and diagnosis ..........................................................................................12
13. Susceptibility ..................................................................................................12
14. Genetic illness.................................................................................................13
15. Use in evolutionary biology and systematic biology mtDNA in nuclear DNA
13
16. Mitochondrial vs. Nuclear DNA ....................................................................14
17. Reference........................................................................................................16

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Table of Figure
No. Figure Figure Page No.
1
Illustration of the location of mitochondrial
DNA in human cells
2
2 mtDNA replication and transcription 6
3 Mitochondria inheritance 8
4 Mitochondrial bottleneck 9
5 Mutation of mtDNA 11

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1. Introduction
Mitochondrial DNA (mtDNA or mDNA) isthe DNA locatedin mitochondria,
cellular organelleswithin eukaryotic cells that convert chemical energy from food
into a form that cells can use, such as adenosine triphosphate (ATP). Mitochondrial
DNA is only a small portion of the DNA in a eukaryotic cell; most of the DNA can
be found in the cell nucleusand, in plants and algae, also in plastids such as
chloroplasts. Nuclear and mitochondrial DNA are thought to be of separate
evolutionary origin, with the mtDNA being derived from the circular genomes of
bacteriaengulfed by the early ancestors of today's eukaryotic cells. This theory is
called the endosymbiotic theory. In the cells of extant organisms, the vast majority
of the proteins present in the mitochondria (numbering approximately 1500 different
types in mammals) are coded for by nuclear DNA, but the genes for some, if not
most, of them are thought to have originally been of bacterial origin, having since
been transferred to the eukaryotic nucleus during evolution. The reasons
mitochondria have retained some genes are debated.
The existence in some species of mitochondrion-derived organelles lacking a
genome suggests that complete gene loss is possible, and transferring mitochondrial
genes to the nucleus has several advantages. The difficulty of targeting remotely-
produced hydrophobic protein products to the mitochondrion is one hypothesis for
why some genes are retained in mtDNA colocalisation for redox regulation is
another, citing the desirability of localised control over mitochondrial machinery
Recent analysis of a wide range of mtDNA genomes suggests that both these features
may dictate mitochondrial gene retention.( Johnston & Williams,2016)

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2. Genome structure and diversity
Across all organisms, there are six main genome types found in mitochondrial
genomes, classified by their structure (i.e. circular versus linear), size, presence of
introns or plasmid like structures, and whether the genetic material is a singular
molecule or collection of homogeneous or heterogeneousmolecules. In many
unicellular organisms (e.g., the ciliateTetrahymena and the green alga
Chlamydomonas reinhardtii), and in rare cases also in multicellular organisms (e.g.
in some species of Cnidaria), the mtDNA is found as linearly organized DNA. Most
of these linear mtDNAs possess telomerase-independent telomeres (i.e., the ends of
the linear DNA) with different modes of replication, which have made them
interesting objects of research because many of these unicellular organisms with
linear mtDNA are known pathogens. (Manicom et al., 1987).
Mitochondrial DNA is the small circular chromosome found
inside mitochondria. These organelles, found in all eukaryotic
cells, are the powerhouse of the cell. The mitochondria, and
thus mitochondrial DNA, are passed exclusively from mother
to offspring through the egg cell.
0:33
Illustration of the location of mitochondrial DNA in
human cells
Figure 1 mtDNA

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2.1 Animal
Most animals, specifically bilaterian animals, have a circular mitochondrial genome.
Medusozoa and calcarea clades however have species with linear mitochondrial
chromosomes. In terms of base pairs, the anemone Isarachnanthus nocturnus has
the largest mitochondrial genome of any animal at 80,923 bp. In February 2020, a
jellyfish-related parasite – Henneguya salminicola – was discovered that lacks
mitochondrial genome but retains structures deemed mitochondrion-related
organelles. Moreover, nuclear DNA genes involved in aerobic respiration and in
mitochondrial DNA replication and transcription were either absent or present only
as pseudogenes. This is the first multicellular organism known to have this absence
of aerobic respiration and lives completely free of oxygen dependency.
2.2 Plants and fung
There are three different mitochondrial genome types found in plants and fungi. The
first type is a circular genome that has introns and may range from 19 to 1000 kbp
in length. The second genome type is a circular genome (about 20–1000 kbp) that
also has a plasmid-like structure (1 kb) The final genome type that can be found in
plants and fungi is a linear genome made up of homogeneous DNA molecules Great
variation in mtDNA gene content and size exists among fungi and plants, although
there appears to be a core subset of genes that are present in all eukaryotes (except
for the few that have no mitochondria at all).in Fungi, however, there is no single
gene shared among all mitogenomes. Some plant species have enormous
mitochondrial genomes, with Silene conica mtDNA containing as many as
11,300,000 base pairs. Surprisingly, even those huge mtDNAs contain the same
number and kinds of genes as related plants with much smaller mtDNAs. The
genome of the mitochondrion of the cucumber (Cucumis sativus) consists of three

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circular chromosomes (lengths 1556, 84 and 45 kilobases), which are entirely or
largely autonomous with regard to their replication.
2.3 Protists
Protists contain the most diverse mitochondrial genomes, with five different types
found in this kingdom. Type 2, type 3 and type 5 mentioned in the plant and fungal
genomes also exist in some protists, as do two unique genome types. One of these
unique types is a heterogeneous collection of circular DNA molecules while the
other is a heterogeneous collection of linear molecules Genome each range from
1–200 kbp in size.The smallest mitochondrial genome sequenced to date is the 5,967
bp mtDNA of the parasite Plasmodium falciparum. Endosymbiotic gene transfer, the
process by which genes that were coded in the mitochondrial genome are transferred
to the cell's main genome, likely explains why more complex organisms such as
humans have smaller mitochondrial genomes than simpler organisms such as
protists.
3. Replication
Mitochondrial DNA is replicated by the DNA polymerase gamma complex which is
composed of a 140 kDa catalytic DNA polymerase encoded by the POLG gene and
two 55 kDa accessory subunits encoded by the POLG2 gene. The replisome
machinery is formed by DNA polymerase, TWINKLE And mitochondrial SSB
proteins. TWINKLE is a helicase, which unwinds short stretches of dsDNA in the
5' to 3' direction All these polypeptides are encoded in the nuclear genome.
During embryogenesis, replication of mtDNA is strictly down-regulated from the
fertilized oocyte through the preimplantation embryo The resulting reduction in per-
cell copy number of mtDNA plays a role in the mitochondrial bottleneck, exploiting
cell-to-cell variability to ameliorate the inheritance of damaging mutations.

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According to Justin St. John and colleagues, "At the blastocyststage, the onset of
mtDNA replication is specific to the cells of the trophectoderm. In contrast, the cells
of the inner cell mass restrict mtDNA replication until they receive the signals to
differentiate to specific cell types."
4. Genes on the human mtDNA and their transcription
The two strands of the human mitochondrial DNA are distinguished as the heavy
strand and the light strand. The heavy strand is rich in guanine and encodes 12
subunits of the oxidative phosphorylation system, two ribosomal RNAs (12S and
16S), and 14 transfer RNAs (tRNAs). The light strand encodes one subunit, and 8
tRNAs. So, altogether mtDNA encodes for two rRNAs, 22 tRNAs, and 13 protein
subunits, all of which are involved in the oxidative phosphorylation process.
Between most (but not all) protein-coding regions, tRNAs are present (see the
human mitochondrial genome map). During transcription, the tRNAs acquire their
characteristic L-shape that gets recognized and cleaved by specific enzymes. With
the mitochondrial RNA processing, individual mRNA, rRNA, and tRNA sequences
are released from the primary transcript. Folded tRNAs therefore act as secondary
structure punctuations.
5. Regulation of transcription
The promoters for the initiation of the transcription of the heavy and light strands
are located in the main non-coding region of the mtDNA called the displacement
loop, the D-loop. There is evidence that the transcription of the mitochondrial rRNAs
is regulated by the heavy-strand promoter 1 (HSP1), and the transcription of the
polycistronic transcripts coding for the protein subunits are regulated by HSP2.
Measurement of the levels of the mtDNA-encoded RNAs in bovine tissues has

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shown that there are major differences in the expression of the mitochondrial RNAs
relative to total tissue RNA. Among the 12 tissues examined the highest level of
expression was observed in heart, followed by brain and steroidogenic tissue
samples. As demonstrated by the effect of the trophic hormone ACTH on adrenal
cortex cells, the expression of the mitochondrial genes may be strongly regulated by
external factors, apparently to enhance the synthesis of mitochondrial proteins
necessary for energy production. Interestingly, while the expression of protein-
encoding genes was stimulated by ACTH, the levels of the mitochondrial 16S rRNA
showed no significant change.
6. Mitochondrial inheritance
In most multicellular organisms, mtDNA is inherited from the mother (maternally
inherited). Mechanisms for this include simple dilution (an egg contains on average
200,000 mtDNA molecules, whereas a healthy human sperm has been reported to
contain on average 5 molecules), degradation of sperm mtDNA in the male genital
tract and in the fertilized egg; and, at least in a few organisms, failure of sperm
mtDNA to enter the egg. Whatever the mechanism, this single parent (uniparental
inheritance) pattern of mtDNA inheritance is found in most animals, most plants and
Figure2
mtDNA replication and transcription

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also in fungi.In a study published in 2018, human babies were reported to inherit
mtDNA from both their fathers and their mothers resulting in mtDNA heteroplasmy.
6.1 Female inheritance
In sexual reproduction, mitochondria are normally inherited exclusively from the
mother; the mitochondria in mammalian sperm are usually destroyed by the egg cell
after fertilization. Also, mitochondria are only in the sperm tail, which is used for
propelling the sperm cells and sometimes the tail is lost during fertilization. In 1999
it was reported that paternal sperm mitochondria (containing mtDNA) are marked
with ubiquitin to select them for later destruction inside the embryo. Some in vitro
fertilization techniques, particularly injecting a sperm into an oocyte, may interfere
with this.The fact that mitochondrial DNA is mostly maternally inherited enables
genealogical researchers to trace maternal lineage far back in time. (Y-chromosomal
DNA, paternally inherited, is used in an analogous way to determine the patrilineal
history.) This is usually accomplished on human mitochondrial DNAby sequencing
the hypervariable control regions(HVR1 or HVR2), and sometimes the complete
molecule of the mitochondrial DNA, as a genealogical DNA test HVR1, for
example, consists of about 440 base pairs. These 440 base pairs are compared to the
same regions of other individuals (either specific people or subjects in a database)
to determine maternal lineage. Most often, the comparison is made with the revised
Cambridge Reference Sequence. Vilà et al. have published studies tracing the
matrilineal descent of domestic dogs from wolves. The concept of the Mitochondrial
Eve is based on the same type of analysis, attempting to discover the origin of
humanity by tracking the lineage back in time.

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6.2 Male inheritance
Male mitochondrial DNA inheritance has been discovered in Plymouth Rock
chickens. Evidence supports rare instances of male mitochondrial inheritance in
some mammals as well. Specifically, documented occurrences exist for mice, where
the male-inherited mitochondria were subsequently rejected. It has also been found
in sheep and in cloned cattle. Rare cases of male mitochondrial inheritance have
been documented in humans. Although many of these cases involve cloned embryos
or subsequent rejection of the paternal mitochondria, others document in vivo
inheritance and persistence under lab conditions doubly uniparental inheritance of
mtDNA is observed in bivalve mollusks. In those species, females have only one
type of mtDNA (F), whereas males have F type mtDNA in their somatic cells, but
M type of mtDNA (which can be as much as 30% divergent) in germline cells.
Paternally inherited mitochondria have additionally been reported in some insects
such as fruit flies, honeybees, and periodical cicadas.
Figure3 mitochondria inheritance

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7. The mitochondrial bottleneck
Entities subject to uniparental inheritance and with little to no recombination may
be expected to be subject to Muller's ratchet, the accumulation of deleterious
mutations until functionality is lost. Animal populations of mitochondria avoid this
through a developmental process known as the mtDNA bottleneck. The bottleneck
exploits random processes in the cell to increase the cell-to-cell variability in mutant
load as an organism develops: a single egg cell with some proportion of mutant
mtDNA thus produces an embryo in which different cells have different mutant
loads. Cell-level selection may then act to remove those cells with more mutant
mtDNA, leading to a stabilisation or reduction in mutant load between generations.
The mechanism underlying the bottleneck is debated, with a recent mathematical
and experimental metastudy providing evidence for a combination of the random
partitioning of mtDNAs at cell divisions and the random turnover of mtDNA
molecules within the cell.
Figure 4 mitochondrial bottleneck

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8. Mitochondrial donation
An IVF technique known as mitochondrial donation or mitochondrial replacement
therapy (MRT) results in offspring containing mtDNA from a donor female, and
nuclear DNA from the mother and father. In the spindle transfer procedure, the
nucleus of an egg is inserted into the cytoplasm of an egg from a donor female which
has had its nucleus removed, but still contains the donor female's mtDNA. The
composite egg is then fertilized with the male's sperm. The procedure is used when
a woman with genetically defective mitochondria wishes to procreate and produce
offspring with healthy mitochondria. The first known child to be born as a result of
mitochondrial donation was a boy born to a Jordanian couple in Mexico on 6 April
2016.
9. Mutations and disease
Mitochondrial disorders impair the function of mitochondria, the tiny compartments
in every cell of the body that produce the energy needed by cells. Depending on
which cells have fewer or lower-functioning mitochondria, different symptoms may
occur. Organs and other parts of the body that require more energy, such as the heart,
muscles and brain, are often affected. Mitochondrial disease is the name for a large
number of mitochondrial disorders, with different genetic causes and
presentations.Mitochondrial disease may be caused by genetic mutations in the
body’s nuclear DNA (the DNA found in the nucleus of cells) or by genetic mutations
or deletions in the body’s mitochondrial DNA (mtDNA < the DNA found in cells’
mitochondria). mtDNA common mutation syndromes are mitochondrial disorders
caused by recurrent mtDNA mutations in unrelated families and populations.
Despite the name, these are rare conditions; “common” means that these specific
mutations recur across families and ethnic groups.

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10.Causes:
mtDNA common mutation syndromes are often inherited from the mother. Only
women pass mtDNA mutations on to their children through the oocyte. Men with
mtDNA mutations may be affected by the conditions, but do not pass them on to
their children.In some cases, mtDNA mutations are spontaneous (de novo) in the
affected individual and are not inherited.
11.Symptoms:
mtDNA common mutation syndromes vary widely by type and from case to case.
There is also a great deal of overlap in symptoms among different mitochondrial
conditions. Doctors now consider them to represent a broad spectrum of features and
severity in diagnosis and treatment. Two patients may have the same symptoms with
different genetic causes, and will therefore be diagnosed with different
mitochondrial disorders. And two patients with the same genetic disorder may have
very different symptoms and require different treatment.Listed here are the most
common symptoms for each of the classical clinical mtDNA mutation syndromes.
Figure 5 mutation of mtDNA

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12.Test and diagnosis
If a mtDNA common mutation syndrome is suspected based on the patient’s physical
symptoms and history, additional tests are performed to make a diagnosis. These
tests may include:
-Blood tests to look for high concentrations of lactic acid and other
abnormalities
-Cerebrospinal fluid (CSF) analysis to look for elevated protein levels
MRI of the brain and/or spinal cord
-Electrocardiography (ECG or EKG) to detect heart rhythm abnormalities
-Echocardiography (Echo) to detect cardiomyopathy
-Muscle biopsy to obtain tissue in which to measure biochemical function,
perform DNA testing, and detect ragged red fibers characteristic of MELAS
syndrome and MERRF
-Genetic testing using blood, muscle, skin, urinary sediment or other tissue
samples to look for mutations in mtDNA and nuclear DNA
13.Susceptibility
The concept that mtDNA is particularly susceptible to reactive oxygen species
generated by the respiratory chain due to its proximity remains controversial.
mtDNA does not accumulate any more oxidative base damage than nuclear DNA. It
has been reported that at least some types of oxidative DNA damage are repaired
more efficiently in mitochondria than they are in the nucleus.
mtDNA is packaged with proteins which appear to be as protective as proteins of the
nuclear chromatin. Moreover, mitochondria evolved a unique mechanism which
maintains mtDNA integrity through degradation of excessively damaged genomes
followed by replication of intact/repaired mtDNA. This mechanism is not present in

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the nucleus and is enabled by multiple copies of mtDNA present in mitochondria
The outcome of mutation in mtDNA may be an alteration in the coding instructions
for some proteins, which may have an effect on organism metabolism and/or fitness.
14.Genetic illness
Mutations of mitochondrial DNA can lead to a number of illnesses including
exercise intoleranceand Kearns–Sayre syndrome (KSS), which causes a person to
lose full function of heart, eye, and muscle movements. Some evidence suggests that
they might be major contributors to the aging process and age-associated
pathologies. Particularly in the context of disease, the proportion of mutant mtDNA
molecules in a cell is termed heteroplasmy. The within-cell and between-cell
distributions of heteroplasmy dictate the onset and severity of diseaseand are
influenced by complicated stochastic processes within the cell and during
development. Mutations in mitochondrial tRNAs can be responsible for severe
diseases like the MELAS and MERRF syndromes. Mutations in nuclear genes that
encode proteins that mitochondria use can also contribute to mitochondrial diseases.
These diseases do not follow mitochondrial inheritance patterns, but instead follow
Mendelian inheritance patterns.
15.Use in evolutionary biology and systematic biology mtDNA in
nuclear DNA
Sequencing the genomes of more than 66,000 people revealed that most of them had
some mitochondrial DNA inserted into their nucleargenomes. More than 90% of
these nuclear-mitochondrial segments (NUMTs) were inserted into the nuclear
genome within the last 5 or 6 million years, that is, after humans diverged from apes.
It appears that organellar DNA is much more often transferred to nuclear DNA than

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previously thought. This observation also supports the idea of the endosymbiont
theory that eukaryotes have evolved from endosymbionts which turned into
organelles while transferring most of their DNA to the nucleus so that the organellar
genome shrunk in the process.
16.Mitochondrial vs. Nuclear DNA
Similar to the nuclear genome, the mitochondrial genome is built of double-stranded
DNA, and it encodes genes However, the mitochondrial genome differs from the
nuclear genome in several ways Many interesting features distinguish human
mitochondrial DNA from its nuclear counterpart, including the following:
• The mitochondrial genome is circular, whereas the nuclear genome is
linear
• The mitochondrial genome is built of 16,569 DNA base pairs, whereas
the nuclear genome is made of 3.3 billion DNA base pairs.
• The mitochondrial genome contains 37 genes that encode 13 proteins,
22 tRNAs, and 2 rRNAs.
• The 13 mitochondrial gene-encoded proteins all instruct cells to
produce protein subunits of the enzyme complexes of the oxidative
phosphorylation system, which enables mitochondria to act as the
powerhouses of our cells.
• The small mitochondrial genome is not able to independently produce
all of the proteins needed for functionality; thus, mitochondria rely heavily on
imported nuclear gene products.
• One mitochondrion contains dozens of copies of its mitochondrial
genome. In addition, each cell contains numerous mitochondria. Therefore, a

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given cell can contain several thousand copies of its mitochondrial genome,
but only one copy of its nuclear genome.
• The mitochondrial genome is not enveloped, and is it not packaged into
chromatin.
• The mitochondrial genome contains few, if any, noncoding DNA
sequences. (Three percent of the mitochondrial genome is noncoding DNA,
whereas 93% of the nuclear genome is noncoding DNA).
• Some mitochondrial coding sequences (triplet codons) do not follow
the universal codon usage rules when they are translated into proteins.
• Some mitochondrial nucleotide bases exhibit functional overlap
between two genes; in other words, the same nucleotide can sometimes
function as both the last base of one gene and the first base of the next gene.
• The mitochondrial mode of inheritance is strictly maternal, whereas
nuclear genomes are inherited equally from both parents. Therefore,
mitochondria-associated disease mutations are also always inherited
maternally.
• Mitochondrial genes on both DNA strands are transcribed in a
polycistronic manner: Large mitochondrial mRNAs contain the instructions
to build many different proteins, which are encoded one after the next along
the mRNA. In contrast, nuclear genes are usually transcribed one at a time
from their own mRNA.

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