Mitochondrial and chloroplast DNA

Mitochondrial and chloroplast DNA

1. BS. Biotechnology
Instructor
Sir Muzammel Rehman
Submitted By:
Rizwan Abbas (BsBt-13-f-043)


BAHAUDDIN ZAKARIYA UNIVERSITY LAHORE CAMPUS

Mitochondrial and Chloroplast’s DNA
About DNA of Mitochondria
ABSTRACT;
Chloroplast and DNA are organs of endosymbiotic origin and they have a small portion of
genome which has a vast effect on the genetics and the Structure and functioning of the organism
A short piece of such effects of these organelles are described here and presented as assignment
The references are also given with the table of contents

2. 1

Mitochondrial and Chloroplast’s DNA
Content and references


S.no

Tittle


Reference

Page


A

Introduction.
1. Endosymbiont theory


www.wikipedia.com/Evolutionary
Facts


02


B
Organelles of Endosymbiotic
origin in cells
1. Mitochondria
2. Chloroplast

A text book of cytology, genetics,
molecular by R.C Debary
S Chand publishers

03
04


C

About Mitochondrial DNA
1. Size and structure
2. Mitochondrial genes

3. www.genetics.com/Mitochondr
ial DNA - Genetics Home
4. ghr.nlm.nih.gov/chromosome/
MT

07
09


D

Inheritance of Mitochondrial
DNA
1. Effects
2. The mitochondrial genome:
www.sciencedirect.com/scienc
e/article/pii/S00052728980016
13


10


E

About Chloroplast DNA
1. History, Size
2. Genetics

Text book of cytology/Chapter 10
By
R.c .Debary

14
16


F


G

Effects of Chloroplast
1. On Phosphorylation
2. On proteins

Conclusion/summary

www.ncbi.com/genetic
/Mutations


selfie

18



21

3. 2

About DNA in Mitochondria and Chloroplast
A. Introduction:
1. Endosymbiont theory.
Scientists believe that mitochondria and chloroplasts were primitive cells without nuclei
(prokaryotes) that got inside of primitive cells with nuclei (eukaryotes) and then stayed
there. So they came in with their own DNA, and now they still have some of their own
DNA that carries the code for some of their own proteins. Simply we can say that,
Due to the environmental hurdles free living prokaryotes ancestors of chloroplasts and
mitochondria invaded plant and animal cells but provide useful function and so a
symbiotic relationship developed over time.
Mereschkowsky was the first scientist to propose the theory of symbiogenesis.
According to evolutionary point of view mitochondria and chloroplast are organ of
endosymbiotic origin hence they contain their own DNA carrying different genes for their
proper functioning
















B. An introduction to Organelles of Endosymbiotic origin in cells
1. The Mitochondrion
The term mitochondria originate from Greek word (mito =thread)
(Chondrion=granules). They are filamentous or granular cytoplasmic organelles of all
aerobic cells of higher animals and plants and also of certain micro-organisms including
Algae, Protozoa and Fungi but not present in bacteria. The number of mitochondria in a
cell depends on the type and functional state of the cell. It varies from species to
species. Mitochondria is known as power house of the cell as it has prime importance in
the energy production which is essential for survival and maintenance of cell.
Discovery of Mitochondria
The first scientists known to identify the existence of mitochondria were working during
the mid-1800s. In 1857, Albert von Kölliker described what he called “granules” in the
cells of muscles. The discovery of mitochondria in general came in 1886 when Richard
Altman, a cytologist, identified the organelles using a staining technique, and named
them “bio blasts.” He postulated that the structures were the basic units of cellular
activity. Carl Benda, in 1898, coined the term mitochondria.
l

4. 3

Shape and Structure.
The mitochondria may be filamentous or granular in shape and may change from one
form to another depending upon the physiological conditions of the cells. Thus, they
may be of club, racket, vesicular, ring or round-shape. Mitochondria are granular in
primary spermatocyte or rat, or club-shaped in liver cells. Mitochondria are double
membrane envelopes in which the inner membrane divides the mitochondrial space into
two distinct chambers: 1.The outer compartment, peri-mitochondrial space or the inter-
membrane space between outer membrane and inner membrane. This space is
continuous into the core of the crests or cristae. 2. The inner compartment, inner
chamber or matrix space, which is filled with a dense, homogeneous, gel-like
proteinaceous material, called mitochondrial matrix.














The mitochondrial matrix contains lipids, proteins, circular DNA molecules, 55S
ribosomes and certain granules which are related to the ability of mitochondria to
accumulate ions. Granules are prominent in the mitochondria of cells concerned with
the transport of ions and water
The outer membrane is quite smooth and has many copies of a transport protein called
porin which forms large aqueous channels through the lipid bilayer. The inner
membrane is not smooth but is impermeable and highly convoluted, forming a series of
inholdings, known as cristae, in the matrix space. The cristae greatly increase the area
of inner membrane, so that in liver cell mitochondria, the cristae membrane is 3–4 times
greater than the outer membrane area. Some mitochondria, particularly those from
heart, kidney and skeletal muscles have more extensive cristae arrangements than liver
mitochondria.
2. Chloroplast
Chloroplast belongs to the class of chromoplast (Green cooled) plastids. These are also
organelles of endosymbiotic origin.
The chloroplast (Gr., chlor=green plast=living) is most widely occurring chromoplast of
the plants. It occurs mostly in the green algae and higher plants. The chloroplast
contains the pigment chlorophyll a and chlorophyll b and DNA and RNA. They also play
important role in plant life activity.



DNA

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Discovery of Chloroplast
Russian botanist Konstantin Mereschkowsky was the first person to discover the
chloroplast. His discovery was the result of his work with lichens. In 1905, he began
arguing for the symbiotic origin of the chloroplast and nucleus. The botanist discovered
chloroplasts as he was studying Andreas Schimper's work with photosynthetic
organisms.
Location of Chloroplast
The chloroplasts are found in the cytoplasm of plant cells. But in certain cells, the
chloroplasts concentrated around the nucleus or just below the plasma membrane.
Chloroplasts are motile organelles, they show passive and active movements.
Size.
The size of the chloroplasts varies from species to species. The chloroplasts generally
measure 2–3μm in thickness and 5–10μm.The chloroplasts of polyploid plant cells are
comparatively larger than the chloroplasts of the diploid plant cells.
Shape.
Higher plant chloroplasts are generally biconvex or Plano-convex. However, in different
plant cells, chloroplasts may have various shapes,
Number.
The number of the chloroplasts varies from cell to cell and from species to species and
is related with the physiological state of the cell, but it usually remains constant for a
particularplant cell.

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Structure.
A chloroplast comprises the following three main structural components. Envelope,
Stroma and Thylakoids. The double membrane envelope present around chloroplast
and the exchange of molecules between chloroplast and cytosol via it. The stroma is a
kind of gel-fluid phase that surrounds the thylakoids (grana). It contains about 50 per
cent of the proteins of the chloroplast, most of which are soluble type. The stroma also
contains ribosomes and DNA molecules. The thylakoids (thylakoid = sac-like) consists
of flattened and closed vesicles arranged as a membranous network. The outer surface
of the thylakoid is in contact with the stroma, and its inner surface encloses an intra-
thylakoid space (the third compartment). Thylakoids may be stacked like a neat pile of
coins, forming grana or they may be unstacked, inter granal, or stromal thylakoids.

Mitochondrial life cycle.


C. About DNA of mitochondria.
According to the evolutionary point of view (Endosymbiotic hypothesis) the plastids and
mitochondria of cells have their own DNA unlike the Nuclear like present in nucleus in
form of chromatin (chromosome).
1. Mitochondrial DNA
Nuclear and mitochondrial DNA are thought to be of separate evolutionary origin. The
mitochondrial DNA is resulted due to the endosymbiotic relation which change over a
period of time but nuclear DNA is natural genetic material from origin of life. The DNA
located in mitochondria are also known as MTDNA.As mitochondria is power house of
the cell. In addition to energy production, mitochondria play a role in several other
cellular activities. For example, mitochondria help regulate the self-destruction of cells
(apoptosis)..All these process are carried out under several precise systems which are
regulated by the specialized organs and other factors which are produced, maintained,
regulate and efficiently perform function under influences of genes of MTDNA.

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Discovery of mitochondrial DNA
Mitochondrial DNA was discovered by Margit M. K. Nass and Sylvan Nass by electron
microscopy as DNases-sensitive thread inside mitochondria, and by Ellen Haslbrunner,
Hans Tuppy and Gottfried Schatz by biochemical assays on highly purified
mitochondrial fractions.
Difference between MT DNA and Nuclear DNA
There are three main differences between nuclear and mitochondria DNA (MTDNA):
1.) MTDNA is circular, whereas nuclear DNA is linear. (Both are double stranded)
2.) MTDNA is (generally) uni-parentally inherited, in most animals (not mussels though
for example), MTDNA is passed from mother to offspring.
3.) Nuclear DNA is diploid, whereas MTDNA exists in a state of ploidy. Each cell
contains numerous mitochondria hence many mitochondrial DNA molecules and refered
as heteroplasmy state.
Size?
MTDNA is the DNA located in mitochondria, cellular organelles within eukaryotic cells
that convert chemical energy from food into a form that cells can use, 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 nucleus and, in plants, in the
chloroplast. The human mitochondrial DNA (MTDNA) is a double-stranded, circular
molecule of 16 569 bp and contains 37 genes coding for two rRNAs, tRNAs and 13
polypeptides.
2. Structure and composition of mitochondrial DNA
Mitochondrial DNA is named MTDNA due to its specific location but there is not any
high chemical difference in composition with nuclear DNA. The mitochondrial as well as
Nuclear DNA constitute of a long chain of nucleotides that composed of a sugar,
nitrogenous base and phosphate group. The level of packing of mitochondrial
chromosome is similar to that of nuclear chromosome and also contain histones.
Mitochondrial DNA only has one chromosome, and this is organized like a circular
genome (similar to most prokaryotic DNA). This single chromosome is much shorter,
and codes for the specific proteins which are used in the metabolic processes.

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3. Structure and organization.
In most multicellular organisms, the MTDNA is organized as a circular, covalently
closed, double-stranded DNA. But in many unicellular there is four MTDNA as linearly
organized DNA double-stranded circular MTDNA molecule consists of 15,000-
17,000[19] base pairs. The two strands of a MTDNA re differentiated by their nucleotide
content, heavy strand (or H-strand) and a cytosine-rich strand referred to as the light
strand (or L-strand). The heavy strand encodes 28 genes, and the light strand
encodes 9 genes for a total of 37 genes. Of the 37 genes, 13 are for proteins
(polypeptides), 22 are for transfer RNA (tRNA) and two are for the small and large
subunits of ribosomal RNA (rRNA)., although in some cases one or more of the 37
genes is absent and the MTDNA size range is greater. Even greater 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).
About Mitochondrial genes
In humans, mitochondrial DNA can be assessed as the smallest chromosome coding
for 37 genes and containing approximately 16,600 base pairs.in plants there are about
120 genes assembled on MTDNA.
Human mitochondrial DNA
Human mitochondrial DNA was the first significant part of the human genome to be
sequenced. In most species, including humans, MTDNA s inherited solely from the
mother. Mitochondrial DNA contains 37 genes, all of which are essential for normal
mitochondrial function. Thirteen of these genes provide instructions for making enzymes
involved in oxidative phosphorylation. The remaining genes provide instructions for
making molecules called transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), which
are chemical cousins of DNA. These types of RNA help assemble protein building
blocks (amino acids) into functioning proteins.












MTDNA rearrangements
The majority of MTDNA rearrangement mutations are large-scale deletions, which vary
in size from 1.3 to 8 kb and span several genes. Single deletion MTDNA s occur
sporadically early in development, and the identical deletion is present in all cells within
affected tissues [87]. The occurrence of multiple MTDNA deletions of varying lengths in
affected tissues may be due to inherited mutations in nuclear genes, whose products
are involved in maintenance and replication

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D. Mitochondrial inheritance and effects
In 1909 Erwin Baur and Carl Correns found first cases of non-Mendelian heredity, in
plants. In most multicellular organisms, MTDNA is inherited from the mother (maternally
inherited) which is also termed as uniparental inheritance. Or extrachromosomal
inheritance. In animals, mitochondrial DNA inheritance is predominantly maternal. Some
concepts are here discussed below

















1. Laws of Organelle Genetics
Vegetative segregation: alleles of organelle genes segregate during mitotic as well as
meiotic divisions.
Uniparental inheritance: organelle genes are often transmitted from only one parent.
Mechanisms of Vegetative Segregation
Multiple factor hypothesis:
Two or more allele’s different pairs of alleles, with presumed cumulative effects, govern
the quantitative traits. Those alleles which contribute to the trait involved are called
contributing, effective or active alleles; those alleles which do not appear to do so are
referred to as non-contributing, on-effective, null alleles. A gene, individually exerting a
slight effect on the phenotype but along with a few or many genes, controls a
quantitative trait is palled polygene (a term by k.mather).sine there are usually many
genes of this kind forgone quantitative trait is called multiple factor hypothesis
In contrast, bi-parental inheritance is common in mussels of the genus Mylus. Females
inherit MTDNA only from their mother, but they transmit it to both daughters and sons.
Males inherit MTDNA from both parents, but they transmit to sons only the MTDNA they
inherited from their father are called cytoplasmic DNA transmission
Mitotic segregation
During mitosis, mitochondria are randomly segregated, and in heteroplasmic cells, the
proportion of mutant MTDNA in the daughter cells can thus shift. Should the mutant
load exceed the pathogenic threshold for that tissue, clinical expression of the disease
can occur? Conversely, mutant MTDNA may be lost, particularly in fast-dividing tissues.

10. 9

For example, an average annual 1% decrease in m.3243A > G mutation levels in blood
has been described.
Replication
Mitochondrial DNA transmit in life generation by passing replication .replication proceed
by binary fission as well as complete replication just like that of semiconservative
replication procedure of nuclear DNA.













VEGETATIVE SEGREGATION:
Vegetative segregation results from: Results from random replication and
partitioning of cytoplasmic organelles as with chloroplasts and mitochondria during
mitotic cell divisions and results in daughter cells that contain a random sample of the
Parent cell’s organelles e.g. Mitochondria of asexually replicating yeast cells
UNIPARENTAL INHERITANCE:
Occurs in extra nuclear genes when only one parent contributes organelles DNA to the
offspring
E.g. uniparental gene transmission is the maternal inheritance of human mitochondria.
At fertilization via the egg .
The father’s mitochondrial genes are not transmitted to the offspring via the sperm. Very
rare cases which require further investigation have been reported of paternal
mitochondrial inheritance in humans, in which the father’s mitochondrial genome is
found in offspring.
Chloroplast genes can also inherit uniparentally during sexual reproduction. They are
historically thought to inherit maternally, but paternal inheritance in many species is
increasingly being identified. The mechanisms of uniparental inheritance from species
to species differ greatly and are quite complicated.
For instance, chloroplasts have been found to exhibit maternal, paternal and biparental
mode seven within the same species.

BIPARENTAL INHERITANCE:
Occurs in extra nuclear genes when both parents contribute organelle DNA to the
offspring. It may be less common than uniparental extra nuclear inheritance, and usually
occurs in a permissible species only a fraction of the time.

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2. Effect of mitochondrial DNA
Animal mitochondrial DNA is a small, usually circular, DNA molecule that occurs in
mitochondria and contains genes that support aerobic respiration. Mitochondrial genes
and genomes are important tools in a variety of fields related to the study of animal
evolution, such as phytogeography, population genetics and phylogenetic.
A typical somatic cell contains 500–1000 mitochondria, whereas an oocyte contains
some 104–105 mitochondria, each with a few DNA molecules.
The effects of MTDNA on genetics, phenotypes and on other life processes are as
follows. Inheritance of MTDNA mutations etc.













MTDNA mutations
Mitochondrial genetics differ from nuclear genetics in three aspects. First, mitochondrial
genes are maternally inherited; they do not follow a Mendelian pattern of inheritance.
Second, the mitochondrial genome is polyploid. Normally, a state of homoplasmy exists
where only one form of MTtDNA is present. Mutation can lead to a state of
heteroplasmy where two or more forms of MTDNA coexist within a cell. Third, unlike a
diploid nuclear gene that can normally only assume three states (homozygous wild type,
heterozygous, or homozygous mutant), MTDNA heteroplasmy does not vary by discrete

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steps. The proportions of MTDNA species can vary with time or through mitotic
segregation as cells divide.











Point mutations
MTDNA point mutations are usually maternally inherited. They may occur within protein,
tRNA, or rRNA genes. However, more than half of disease-related point mutations
reported are located within MT-tRNA genes. Phenotypically, point mutations in
mitochondrial protein-coding genes specifically affect the function of the RC complex to
which the corresponding protein belongs, whereas MT-tRNA mutations may impair
overall mitochondrial translation by reducing the availability of functional MT-tRNAs.
Point mutations are mostly heteroplasmic, displaying considerable clinical
heterogeneity, and are considered highly recessive
MTDNA and aging
Mitochondrial functions influence and possibly control the rate of aging aging affects the
integrity of the mitochondrial genome. An increased production of reactive oxygen
species, often some evidence suggests a link between aging and mitochondrial genome
disfunctioning, mutations in MTDNA upset a careful balance of reactive oxygen species
(ROS) production and enzymatic ROS scavenging (by enzymes like superoxide
dismutase, catalase, glutathione peroxidase and others). There is thought to be a
positive feedback loop at work; as mitochondrial DNA accumulates genetic damage
caused by free radicals, the mitochondria lose function and leak free radicals into the
cytosol. A decrease in mitochondrial function reduces overall metabolic efficiency.
Susceptibility
MTDNA is particularly susceptible to reactive oxygen species generated by the
respiratory chain due to its proximity. Though MTDNA is packaged by proteins and
harbors significant DNA repair capacity, these protective functions are less robust than
those operating on nuclear DNA and are therefore thought to contribute to enhanced
susceptibility of MTDNA to oxidative damage. The outcome of mutation in MTDNA may
be alteration in the coding instructions for some proteins, which may have an effect on
organism metabolism and/or fitness.
Mutations of mitochondrial DNA can lead to a number of illnesses including exercise
intolerance and 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

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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, most mitochondria are present at the base of the sperm's tail, which is
used for propelling the sperm cells; sometimes the tail is lost during fertilization. The fact
that mitochondrial DNA is 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 accomplished on
human mitochondrial DNA by sequencing one or more of the hypervariable control
regions (HVR1 or HVR2) of the mitochondrial DNA, as with a genealogical DNA test.
HVR1 consists of about 440 base pairs.
Male inheritance
It has been reported that mitochondria can occasionally be inherited from the father in
some species such as mussels. Paternally inherited mitochondria have additionally
been reported in some insects such as fruit flies, honeybees and periodical cicadas.
Evidence supports rare instances of male mitochondrial inheritance in some mammals
as well.
GENETIC BOTTLENECK
A temporary reduction in population size that causes the loss of genetic variation.
These MTDNA molecules are likely to be immobile inside the mitochondrion because
they are attached to the mitochondrial inner membrane clustering into nucleoids. The
thousands of mitochondria found in each oocyte are probably derived from very few
mitochondria found in primordial germ cells. This phenomenon has been termed as
‘bottleneck’ or ‘sampling and amplification.















Homoplasmy and heteroplasmy
The polyploid nature of the mitochondrial genome — up to several thousand copies per
cell — gives rise to an important feature of mitochondrial genetics, homoplasmy and
heteroplasmy. In simple terms, homoplasmy is when all copies of the mitochondrial
genome are identical; heteroplasmy is when there is a mixture of two or more
mitochondrial genotypes. The value of these terms is apparent when we consider
MTDNA mutations that lead to disease. Some mutations affect all copies of the

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mitochondrial genome (homoplasmic mutation), whereas others are only present in
some copies of the mitochondrial genome (heteroplasmic mutation). In the presence of
heteroplasmy, there is a threshold level of mutation that is important for both the clinical
expression of the disease and for biochemical defects, as routinely demonstrated by the
cyto chemical assessment of cytochrome c oxidase (COX; complex IV) activity in an
individual cell Numerous single-cell and TRANSMITOCHONDRIAL CYBRID CELL


















Mitochondrial diseases with onset in early infancy/childhood
Leigh syndrome
Leigh syndrome is a progressive neurodegenerative condition, which particularly affects
the brainstem, diencephalon, and basal ganglia. There are characteristic
neuropathological features, but newer neuroimaging techniques can now easily detect
these lesions in life. Clinically, these infants and children have signs of brainstem and
basal ganglia dysfunction and often deteriorate in a stepwise manner. Leigh syndrome
is due to severe failure of oxidative metabolism and can be due to a variety of different
genetic defects affecting either the mitochondrial (e.g., m.8993T > C/G, m.10158T > C,
m.10191T > C) or nuclear genome (e.g., SURF1 gene).
Depletion syndromes
The clinical features associated with depletion syndromes depend upon the organ(s)
which have MTDNA depletion. On the whole, these are severe disorders and present in
childhood with severe muscle weakness, progressive encephalopathy, or liver failure.
There are a number of different genetic defects identified in these patients and the
clinical syndromes often reflect the genetic defect In view of the tissue-specific nature of
the defect, these patients may respond to organ transplantation.
Kearns–Sayre syndrome (KSS)
KSS is associated with the development of retinitis pigmentosa and progressive
external ophthalmoplegia occurring before the age of twenty. Clinical examination
usually detects a ‘salt and pepper’ retinopathy of the posterior fundus without the visual

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field defects, optic disk pallor, and attenuation of retinal vessels usually seen in retinitis
pigmentosa
Pearson syndrome
This is a rare disorder of infancy characterized by sidero-blastic anemia with
pancytopenia and exocrine pancreatic failure. The clinical course in these children can
be severe leading to early death. In those that survive the blood disorder improves but
they later develop the clinical features of KSS. In these children, there is a very high
level of large-scale single MTDNA deletion present in all tissues.

Mitochondrial diseases with onset in late childhood or adult life
Mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS)
These patients often present with stroke-like episodes with seizures. They particularly
affect the parietal-occipital region of the brain leading to visual field defects. Their
lesions do not match a recognized vascular distribution, highlighting that they are not
simple ischemic lesions. Seizures are frequent in these patients associated with the
episode or as isolated phenomena.
Chronic progressive external ophthalmoplegia (CPEO)
One of the most common presentations of MTDNA disease in adults is CPEO. CPEO is
characterized by a progressive paralysis of the eye muscles leading to impaired eye
movement and ptosis. Ptosis is frequently the presenting symptom and may be
asymmetrical; however, patients usually progress to bilateral disease. CPEO is typically
caused by sporadic large-scale single deletions or multiple MTDNA deletions
Neuropathy, ataxia, and retinitis pigmentosa (NARP)
Leber's hereditary optic neuropathy (LHON)
There are three primary LHON MTDNA mutations (m.11778G > A, m.3460G > A, and
m.14484T > C), which in total are present in at least 95% of LHON cases [56] and [124].
LHON is predominantly an organ-specific disease, targeting the retinal ganglion cells of
the optic nerve. Clinically, this presents with a sub acute or acute, painless, central
visual loss, which is typically unilateral with the other eye usually becoming affected
within the next 2 months
Myoclonic epilepsy and ragged red fibers (MERRF)
MERRF is a progressive, neurodegenerative disease caused most commonly by a point
mutation in the MT-TK gene, m.8344A > G [126], [127] and [128]. Clinically, MERRF is
a severe neurodegenerative disorder, which often presents in childhood or early
adulthood following normal development. The characteristic myoclonus is often the
presenting symptom. This progresses into a mixed picture of myopathy, often with
pronounced proximal muscle wasting in a limb-girdle distribution, and central
neurological features of focal and generalized epilepsy, cerebellar ataxia, optic atrophy,
pyramidal signs, and hearing loss.
Clinical syndromes
The clinical syndromes associated with MTDNA mutations are extremely variable and
patients can present at any stage in life. On the whole, the age of onset reflects the
level of mutation and the severity of the biochemical defect, but other factors
(presumably nuclear genetic or environmental) also effect the expression of disease.
For the purposes of this review, we will concentrate solely on primary MTDNA diseases,
the most common of which are depicted in together with their associated mutations.

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Threshold effect
Some deleterious MTDNA mutations are homoplasmic; however, the vast majority are
found in some but not all genomes. In the presence of heteroplasmy, the ratio of wild-
type to mutant MTDNA determines the onset of clinical symptoms. A minimum critical
proportion of mutated MTDNAs is necessary before biochemical defects and tissue
dysfunction become apparent.
Clonal expansion
Clonal expansion refers to the preferential amplification of MTDNAs mutations to a high
level in post-mitotic tissues and. This expansion is thought to be a result of random
genetic drift, dependent on relaxed replication of the mitochondrial genome.

E. About DNA of mitochondria and Chloroplast.

3. Chloroplast’s DNA
Plants are unique among higher organisms in that they meet their energy needs through
photosynthesis. The specific location for photosynthesis in plant cells is the chloroplast,
which also contains a single, circular chromosome composed of DNA. Chloroplast DNA
contains many of the genes necessary for proper chloroplast functioning.
A better understanding of the genes in chloroplast deoxyribonucleic acid (CPDNA) has
improved the understanding of photosynthesis, and analysis of the deoxyribonucleic
acid (DNA) sequence of these genes has been useful in studying the evolution.
Chloroplasts have their own DNA often abbreviated as CTDNA, or CPDNA. It is also
known as the plastomes when referring to genomes of other plastids.
Discovery
Its existence was first proved in 1962 and first sequenced in 1986—when two
Japanese research teams sequenced the chloroplast DNA of liverwort and tobacco.
Since then, hundreds of chloroplast DNAs from various species have been sequenced,
but they are mostly those of land plants and green algae—Glaucophytes, red algae, and
other algal groups are extremely underrepresented, potentially introducing some bias in
views of "typical" chloroplast.
Shape, Size and composition
Chloroplast DNAs are circular, and are typically 120,000–170,000 base pairs long They
can have a contour length of around 30–60 micrometers, and have a mass of about 80–
130 million Daltons
Most chloroplasts have their entire chloroplast genome combined into a single large
ring, though those of dinophyte algae are a notable exception—their genome is broken
up into about forty small plasmids, each 2,000–10,000 base pairs long. Each mini circle
contains one to three genes, but blank plasmids, with no coding DNA, have also been
found.
Chloroplast DNAs have long been thought to have a circular structure, but some
evidence suggests that chloroplast DNA more commonly takes a linear shape. Over
95% of the chloroplast DNA in corn chloroplasts has been observed to be in branched
linear form rather than individual circles. New chloroplasts may contain up to 100 copies
of their DNA, though the number of chloroplast DNA copies decreases to about 15–20
as the chloroplasts age. They are usually packed into nucleoids which can contain
several identical chloroplast DNA rings. Many nucleoids can be found in each

17. 16

chloroplast. Though chloroplast DNA is not associated with true histones,[ in red algae,
a histone-like chloroplast protein (HC) coded by the chloroplast DNA that tightly packs
each chloroplast DNA ring into a nucleoid has been found.
In green plants and green algae, the nucleoids are dispersed throughout the stroma.
The chloroplast genomes of higher plants contains about 120 genes More than 20 of
chloroplast genomes are sequenced .










Inverted repeats
Many chloroplast DNAs contain two inverted repeats, which separate a long single copy
section (LSC) from a short single copy section (SSC).The inverted repeats vary wildly in
length, ranging from 4,000 to 25,000 base pairs long each. Inverted repeats in plants
tend to be at the upper end of this range, each being 20,000–25,000 base pairs long.
The inverted repeat regions usually contain three ribosomal RNA and two TRNA
genes.

18. 17

F. Effects of Chloroplast DNA
Gene content and protein synthesis of chloroplast
The chloroplast genome most commonly includes around 100 geneswhich code for a
variety of things, mostly to do with the protein pipeline and photosynthesis. As in
prokaryotes, genes in chloroplast DNA are organized into operons. Interestingly, introns
are common in chloroplast DNA molecules, while they are rare in prokaryotic DNA
molecules (plant mitochondrial DNAs commonly have introns, but not human mtDNA
Chloroplast genome reduction and gene transfer
Over time, many parts of the chloroplast genome were transferred to the nuclear
genome of the host, a process called endosymbiotic gene transfer. As a result, the
chloroplast genome is heavily reduced compared to that of free-living cyanobacteria.
Chloroplasts may contain 60–100 genes whereas cyanobacteria often have more than
1500 genes in their genome.In land plants, some 11–14% of the DNA in their nuclei can
be traced back to the chloroplast, up to 18% in Arabidopsis, corresponding to about
4,500 protein-coding genes
Protein synthesis by chloroplast DNA
Protein synthesis within chloroplasts relies on an RNA polymerase coded by the
chloroplast's own genome, which is related to RNA polymerases found in bacteria.
Chloroplasts also contain a mysterious second RNA polymerase that is encoded by the
plant's nuclear genome. The two RNA polymerases may recognize and bind to different
kinds of promoters within the chloroplast genome. The ribosomes in chloroplasts are
similar to bacterial ribosomes.
RNA Editing in Plastids
RNA editing is the insertion, deletion, and substitution of nucleotides in a mRNA
transcript prior to translation to protein. The highly oxidative environment inside
chloroplasts increases the rate of mutation so post-transcription repairs are needed to
conserved functional sequences. The chloroplast editosome substitutes C -> U and U ->
C at very specific locations on the transcript. This can change the codon for an amino
acid or restore a non-functional pseudogene by adding an AUG start codon or removing
a premature UAA stop codon.
The editosome recognizes and binds to cis sequence upstream of the editing site. The
distance between the binding site and editing site varies by gene and proteins involved
in the editosome. Hundreds of different PPR proteins from the nuclear genome are
involved in the RNA editing process. These proteins consist of 35-mer repeated amino
acids, the sequence of which determines the cis binding site for the edited transcript.

19. 18

Protein targeting and import
The movement of so many chloroplast genes to the nucleus means that lots of
chloroplast proteins that were supposed to be translated in the chloroplast are now
synthesized in the cytoplasm. This means that these proteins must be directed back to
the chloroplast, and imported through at least two chloroplast membranes.

Phosphorylation, chaperones, and transport
After a chloroplast polypeptide is synthesized on a ribosome in the cytosol, ATP energy
can be used to phosphorylate, or add a phosphate group to many (but not all) of them in
their transit sequences. Serine and threonine (both very common in chloroplast transit
sequences—making up 20–30% of the sequence) are often the amino acids that accept
the phosphate group. The enzyme that carries out the phosphorylation is specific for
chloroplast polypeptides, and ignores ones meant for mitochondria or peroxisomes.
Phosphorylation changes the polypeptide's shape, making it easier for 14-3-3 proteins
to attach to the polypeptide.
The translocon on the outer chloroplast membrane (TOC)

The TOC complex, or translocon on the outer chloroplast membrane, is a collection of
proteins that imports pre-proteins across the outer chloroplast envelope. Five subunits
of the TOC complex have been identified—two GTP-binding proteins Toc34 and
Toc159, the protein import tunnel Toc75, plus the proteins Toc64 and Toc12.The first
three proteins form a core complex that consists of one Toc159, four to five Toc34s, and
four Toc75s that form four holes in a disk 13 nanometers across. The whole core
complex weighs about 500 kilo Daltons. The other two proteins, Toc64 and Toc12, are
associated with the core complex but are not part of it.



The translocon on the inner chloroplast membrane (TIC)

The TIC translocon, or translocon on the inner chloroplast membrane translocon is
another protein complex that imports proteins across the inner chloroplast envelope.
Chloroplast polypeptide chains probably often travel through the two complexes at the
same time, but the TIC complex can also retrieve preproteins lost in the intermembrane
space. Like the TOC translocon, the TIC translocon has a large core complex
surrounded by some loosely associated peripheral proteins like Tic110, Tic40, and

20. 19

Tic21. The core complex weighs about one million Daltons and contains Tic214, Tic100,
Tic56, and Tic20 I, possibly three of each.


Nuclear mutants of Chloroplast
Chloroplast gene expression
If a mutation in gene sequence of Chloroplast is mutated due to any effect following
issues may occur
a. pleiotropic effects on PSII accumulation
b. Chloroplast became unable to synthesize P6 polypeptide of PSII (product of the
psbD transcription rate is unaffected by the mutation psbD-psaA unprocessed
RNAs are unstable in the nac2
c. one-to-one correspondence between specific nuclear mutations and effects on
chloroplast gene
d. expression suggests that individual chloroplast transcription units can be
controlled by different sets of nuclear genes subunit
e. Inhibition of chloroplast function by inhibitors (Norflurazon) leads to a loss of s
subset of nucleus-encoded chloroplast enzymes.
f. Mutants deficient in carotenoids likewise lack a subset of nucleus-encoded
proteins.
g. Inhibitor studies implicate a need for chloroplast gene expression for signaling –
response of nuclear genes to chloroplast function is affected by inhibitors of
transcription and translation
h. Chloroplast-encoded proteins are not transported to the cytoplasm (or nucleus)
hypothesize that plastids produce metabolic signals that regulate the expression
of nuclear genes.

Xeroderma pigmentosum (XP),

Xeroderma pigmentosum (XP) meaning parchment pigmented skin, is a rare, autosomal
inherited neuro cutaneous disorder. XP patients are extremely sensitive to sun exposure
(ultraviolet radiation, UV): 45% develop skin cancer, comprising mostly basal and squamous cell
carcinomas, and to a lesser extent melanomas, angiomas, and sarcomas [47–49]. Besides skin
cancers, 20% of the XP patients can develop progressive neurological disabilities. These
patients are unable to repair UV-induced DNA damage because they are deficient in nucleotide-
excision repair pathway (NER).

Ataxia telangiectasia
(AT) is a rare human autosomal recessive neurodegenerative disorder that is
characterized by ataxic movements due to cortical cerebellar degeneration and ocular
and cutaneous telangiectasia (dilation of small blood vessels) [100, 101]. Other features
of the disease include increased risk of cancer, with ~70% of malignancies being
lymphomas and T cell leukemias immunodeficiency sterility, and extreme cellular and
chromosomal sensitivity to ionizing radiations

21. 20


Friedreich’s ataxia
(FA) is an autosomal recessive disease in humans. FA causes progressive cardio- and
neurodegeneration as well as skeletal muscle abnormalities, increased risk of diabetes,
and sometimes liver and renal failure.

This disorder is caused by a GAA triplet expansion, and/or a point mutation in the FA
gene, resulting in a deficiency in the expression of Frataxin is a nuclear-encoded
mitochondrial protein highly conserved across the evolution and with homologues found
in prokaryotes and eukaryotes. This protein is predominantly expressed in tissues with a
high energetic demand such as neurons and cardiac muscle. In addition, frataxin is
highly expressed in flowers, a high energy demand tissue in plants.

Summary/ Conclusion
The important key points are as follows
a. Every organism has a basic hereditary molecule in form of genome.
b. Every specie or organism have different number of mitochondria and chloroplast
in every cell.
c. Mitochondria and Chloroplast have its own DNA according to the evolutionary
concepts and had a vast effects on individual organism and on population.
d. Human Mitochondrial genome consist of a circular chromosome having 37
genes.
e. Plant’s mitochondrial genome varied to 120 genes
f. Chloroplast have also varied no of genes and its size and shape in different
species.
g. Mutation may occur in all sort of DNA
h. Inheritance is not only occurs at simple genetic level ( chromosomal level ) but it
also inherited by different methods which are,
1. Extra chromosomal
2. Uniparental and biparental
3. Mutated varying inheritance.
4. Environmental
i. Effect of mitochondrial DNA is extra nuclear /extra chromosomal inheritance
j. Every type of disease can be controlled and treated by analyzing its symptoms
and nature by use of molecular biological and biotechnological techniques.









The end