A report on DNA and Mitochondrion

The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.
Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy
Chemical structure of DNA; hydrogen bonds shown as dotted lines. Each end of the double helix has an exposed 5' phosphate on one strand and an exposed 3' hydroxyl group (—OH) on the other.
Simplified structure of a mitochondrion.
A section of DNA. The bases lie horizontally between the two spiraling strands ([[:File:DNA orbit animated.gif|animated version]]).
Cross-sectional image of cristae in a rat liver mitochondrion to demonstrate the likely 3D structure and relationship to the inner membrane
DNA major and minor grooves. The latter is a binding site for the Hoechst stain dye 33258.
Electron transport chain in the mitochondrial intermembrane space
From left to right, the structures of A, B and Z DNA
Transmission electron micrograph of a chondrocyte, stained for calcium, showing its nucleus (N) and mitochondria (M).
DNA quadruplex formed by telomere repeats. The looped conformation of the DNA backbone is very different from the typical DNA helix. The green spheres in the center represent potassium ions.
Typical mitochondrial network (green) in two human cells (HeLa cells)
A covalent adduct between a metabolically activated form of benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA
Model of the yeast multimeric tethering complex, ERMES
Location of eukaryote nuclear DNA within the chromosomes
Evolution of MROs
T7 RNA polymerase (blue) producing an mRNA (green) from a DNA template (orange)
The circular 16,569 bp human mitochondrial genome encoding 37 genes, i.e., 28 on the H-strand and 9 on the L-strand.
DNA replication: The double helix is unwound by a helicase and topo­iso­merase. Next, one DNA polymerase produces the leading strand copy. Another DNA polymerase binds to the lagging strand. This enzyme makes discontinuous segments (called Okazaki fragments) before DNA ligase joins them together.
Interaction of DNA (in orange) with histones (in blue). These proteins' basic amino acids bind to the acidic phosphate groups on DNA.
The lambda repressor helix-turn-helix transcription factor bound to its DNA target
The restriction enzyme EcoRV (green) in a complex with its substrate DNA
Recombination involves the breaking and rejoining of two chromosomes (M and F) to produce two rearranged chromosomes (C1 and C2).
The DNA structure at left (schematic shown) will self-assemble into the structure visualized by atomic force microscopy at right. DNA nanotechnology is the field that seeks to design nanoscale structures using the molecular recognition properties of DNA molecules.
Maclyn McCarty (left) shakes hands with Francis Crick and James Watson, co-originators of the double-helix model.
Pencil sketch of the DNA double helix by Francis Crick in 1953
A blue plaque outside The Eagle pub commemorating Crick and Watson
Impure DNA extracted from an orange

Although most of a cell's DNA is contained in the cell nucleus, the mitochondrion has its own genome ("mitogenome") that is substantially similar to bacterial genomes.

- Mitochondrion

Eukaryotic organisms (animals, plants, fungi and protists) store most of their DNA inside the cell nucleus as nuclear DNA, and some in the mitochondria as mitochondrial DNA or in chloroplasts as chloroplast DNA.

- DNA
The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right.

12 related topics with Alpha

Overall

Eukaryote

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Eukaryotes are organisms whose cells have a nucleus enclosed within a nuclear envelope.

Eukaryotes are organisms whose cells have a nucleus enclosed within a nuclear envelope.

The endomembrane system and its components
Simplified structure of a mitochondrion
Longitudinal section through the flagellum of Chlamydomonas reinhardtii
Structure of a typical animal cell
Structure of a typical plant cell
Fungal Hyphae cells: 1 – hyphal wall, 2 – septum, 3 – mitochondrion, 4 – vacuole, 5 – ergosterol crystal, 6 – ribosome, 7 – nucleus, 8 – endoplasmic reticulum, 9 – lipid body, 10 – plasma membrane, 11 – spitzenkörper, 12 – Golgi apparatus
This diagram illustrates the twofold cost of sex. If each individual were to contribute the same number of offspring (two), (a) the sexual population remains the same size each generation, where the (b) asexual population doubles in size each generation.
Phylogenetic and symbiogenetic tree of living organisms, showing a view of the origins of eukaryotes and prokaryotes
One hypothesis of eukaryotic relationships – the Opisthokonta group includes both animals (Metazoa) and fungi, plants (Plantae) are placed in Archaeplastida.
A pie chart of described eukaryote species (except for Excavata), together with a tree showing possible relationships between the groups
The three-domains tree and the Eocyte hypothesis
Phylogenetic tree showing a possible relationship between the eukaryotes and other forms of life; eukaryotes are colored red, archaea green and bacteria blue
Eocyte tree.
Diagram of the origin of life with the Eukaryotes appearing early, not derived from Prokaryotes, as proposed by Richard Egel in 2012. This view implies that the UCA was relatively large and complex.

Eukaryotic cells typically contain other membrane-bound organelles such as mitochondria and Golgi apparatus; and chloroplasts can be found in plants and algae.

Eukaryotic DNA is divided into several linear bundles called chromosomes, which are separated by a microtubular spindle during nuclear division.

Bacteria

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Bacteria (singular bacterium, common noun bacteria) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

Bacteria (singular bacterium, common noun bacteria) are ubiquitous, mostly free-living organisms often consisting of one biological cell.

Rod-shaped Bacillus subtilis
Phylogenetic tree of Bacteria, Archaea and Eucarya. The vertical line at bottom represents the last universal common ancestor.
Bacteria display many cell morphologies and arrangements
The range of sizes shown by prokaryotes (Bacteria), relative to those of other organisms and biomolecules.
Structure and contents of a typical Gram-positive bacterial cell (seen by the fact that only one cell membrane is present).
An electron micrograph of Halothiobacillus neapolitanus cells with carboxysomes inside, with arrows highlighting visible carboxysomes. Scale bars indicate 100 nm.
Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
Bacillus anthracis (stained purple) growing in cerebrospinal fluid
Many bacteria reproduce through binary fission, which is compared to mitosis and meiosis in this image.
A culture of ''Salmonella
A colony of Escherichia coli
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.
Transmission electron micrograph of Desulfovibrio vulgaris showing a single flagellum at one end of the cell. Scale bar is 0.5 micrometers long.
The different arrangements of bacterial flagella: A-Monotrichous; B-Lophotrichous; C-Amphitrichous; D-Peritrichous
Streptococcus mutans visualised with a Gram stain.
Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Here bacteria are represented by three main supergroups: the CPR ultramicrobacterias, Terrabacteria and Gracilicutes according to recent genomic analyzes (2019).
Overview of bacterial infections and main species involved.
Colour-enhanced scanning electron micrograph showing Salmonella typhimurium (red) invading cultured human cells
In bacterial vaginosis, beneficial bacteria in the vagina (top) are displaced by pathogens (bottom). Gram stain.
Antonie van Leeuwenhoek, the first microbiologist and the first person to observe bacteria using a microscope.

This involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya (sometimes in highly reduced form, e.g. in ancient "amitochondrial" protozoa).

Bacteria do not have a membrane-bound nucleus, and their genetic material is typically a single circular bacterial chromosome of DNA located in the cytoplasm in an irregularly shaped body called the nucleoid.

Diagram of a typical prokaryotic cell

Prokaryote

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Single-celled organism that lacks a nucleus, and other membrane-bound organelles.

Single-celled organism that lacks a nucleus, and other membrane-bound organelles.

Diagram of a typical prokaryotic cell
Phylogenetic ring showing the diversity of prokaryotes, and symbiogenetic origins of eukaryotes
Phylogenetic and symbiogenetic tree of living organisms, showing the origins of eukaryotes and prokaryotes
Diagram of the origin of life with the Eukaryotes appearing early, not derived from Prokaryotes, as proposed by Richard Egel in 2012. This view, one of many on the relative positions of Prokaryotes and Eukaryotes, implies that the universal common ancestor was relatively large and complex.
Comparison of eukaryotes vs. prokaryotes
Phylogenetic tree showing the diversity of prokaryotes. 
This 2018 proposal shows eukaryotes emerging from the archaean Asgard group which represents a modern version of the eocyte hypothesis. Unlike earlier assumptions, the division between bacteria and the rest is the most important difference between organisms.

Besides the absence of a nucleus, prokaryotes also lack mitochondria, or most of the other membrane-bound organelles that characterize the eukaryotic cell.

The division between prokaryotes and eukaryotes reflects the existence of two very different levels of cellular organization; only eukaryotic cells have an enveloped nucleus that contains its chromosomal DNA, and other characteristic membrane-bound organelles including mitochondria.

A label diagram explaining the different parts of a prokaryotic genome

Genome

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All genetic information of an organism.

All genetic information of an organism.

A label diagram explaining the different parts of a prokaryotic genome
An image of the 46 chromosomes making up the diploid genome of a human male. (The mitochondrial chromosome is not shown.)
Part of DNA sequence - prototypification of complete genome of virus
Composition of the human genome
Log-log plot of the total number of annotated proteins in genomes submitted to GenBank as a function of genome size.

It consists of nucleotide sequences of DNA (or RNA in RNA viruses).

Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in the mitochondria.

Gregor Mendel

Gene

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Gregor Mendel
Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes. The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.
Schematic of a single-stranded RNA molecule illustrating a series of three-base codons. Each three-nucleotide codon corresponds to an amino acid when translated to protein
Protein coding genes are transcribed to an mRNA intermediate, then translated to a functional protein. RNA-coding genes are transcribed to a functional non-coding RNA.
Inheritance of a gene that has two different alleles (blue and white). The gene is located on an autosomal chromosome. The white allele is recessive to the blue allele. The probability of each outcome in the children's generation is one quarter, or 25 percent.
A sequence alignment, produced by ClustalO, of mammalian histone proteins
Evolutionary fate of duplicate genes.
Depiction of numbers of genes for representative plants (green), vertebrates (blue), invertebrates (orange), fungi (yellow), bacteria (purple), and viruses (grey). An inset on the right shows the smaller genomes expanded 100-fold area-wise.
Gene functions in the minimal genome of the synthetic organism, Syn 3.
Comparison of conventional plant breeding with transgenic and cisgenic genetic modification.

In biology, a gene (from γένος, ; meaning generation or birth or gender) is a basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

Subsequently, the sequencing in the Human Genome Project indicated that many of these transcripts were alternative variants of the same genes, and the total number of protein-coding genes was revised down to ~20,000 with 13 genes encoded on the mitochondrial genome.

Diagram of a replicated and condensed metaphase eukaryotic chromosome. (1) Chromatid – one of the two identical parts of the chromosome after S phase. (2) Centromere – the point where the two chromatids touch. (3) Short arm (p). (4) Long arm (q).

Chromosome

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Diagram of a replicated and condensed metaphase eukaryotic chromosome. (1) Chromatid – one of the two identical parts of the chromosome after S phase. (2) Centromere – the point where the two chromatids touch. (3) Short arm (p). (4) Long arm (q).
Organization of DNA in a eukaryotic cell
The major structures in DNA compaction: DNA, the nucleosome, the 10 nm "beads-on-a-string" fibre, the 30 nm fibre and the metaphase chromosome.
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Human chromosomes during metaphase
Stages of early mitosis in a vertebrate cell with micrographs of chromatids
The 23 human chromosome territories during prometaphase in fibroblast cells
Karyogram of a human male
In Down syndrome, there are three copies of chromosome 21.

A chromosome is a long DNA molecule with part or all of the genetic material of an organism.

Each eukaryotic chromosome consists of a long linear DNA molecule associated with proteins, forming a compact complex of proteins and DNA called chromatin. Chromatin contains the vast majority of the DNA of an organism, but a small amount inherited maternally, can be found in the mitochondria.

Figure 1: Ribosomes assemble polymeric protein molecules whose sequence is controlled by the sequence of messenger RNA molecules. This is required by all living cells and associated viruses.

Ribosome

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Ribosomes, also called Palade granules (after discoverer George Palade and due to their granular structure), are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation).

Ribosomes, also called Palade granules (after discoverer George Palade and due to their granular structure), are macromolecular machines, found within all cells, that perform biological protein synthesis (mRNA translation).

Figure 1: Ribosomes assemble polymeric protein molecules whose sequence is controlled by the sequence of messenger RNA molecules. This is required by all living cells and associated viruses.
Ribosome rRNA composition for prokaryotic and eukaryotic rRNA
Figure 2: Large (red) and small (blue) subunit fit together.
Figure 3: Molecular structure of the 30S subunit from Thermus thermophilus. Proteins are shown in blue and the single RNA chain in brown.
Figure 4: Atomic structure of the 50S subunit from Haloarcula marismortui. Proteins are shown in blue and the two RNA chains in brown and yellow. The small patch of green in the center of the subunit is the active site.
Figure 5: Translation of mRNA (1) by a ribosome (2)(shown as small and large subunits) into a polypeptide chain (3). The ribosome begins at the start codon of RNA ( AUG ) and ends at the stop codon ( UAG ).
Figure 6: A ribosome translating a protein that is secreted into the endoplasmic reticulum.

The sequence of DNA that encodes the sequence of the amino acids in a protein is transcribed into a messenger RNA chain.

In eukaryotes, ribosomes are present in mitochondria (sometimes called mitoribosomes) and in plastids such as chloroplasts (also called plastoribosomes).

The bacterium Escherichia coli (E. coli), is a single-celled prokaryote

Organism

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Organism is any organic, living system that functions as an individual entity.

Organism is any organic, living system that functions as an individual entity.

The bacterium Escherichia coli (E. coli), is a single-celled prokaryote
An amoeba is a single-celled eukaryote
Polypore fungi and angiosperm trees are large multicellular eukaryotes.
Precambrian stromatolites in the Siyeh Formation, Glacier National Park. In 2002, a paper in the scientific journal Nature suggested that these 3.5 Gya (billion years old) geological formations contain fossilized cyanobacteria microbes. This suggests they are evidence of one of the earliest known life forms on Earth.
LUCA may have used the Wood–Ljungdahl or reductive acetyl–CoA pathway to fix carbon.

Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles (such as mitochondria in animals and plants and plastids in plants and algae, all generally considered to be derived from endosymbiotic bacteria).

It is generally the phenomena of entire organisms that determine their fitness to an environment and therefore the survival of their DNA-based genes.

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.

Mitochondrial DNA

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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.
Electron microscopy reveals mitochondrial DNA in discrete foci. Bars: 200 nm. (A) Cytoplasmic section after immunogold labelling with anti-DNA; gold particles marking mtDNA are found near the mitochondrial membrane (black dots in upper right). (B) Whole mount view of cytoplasm after extraction with CSK buffer and immunogold labelling with anti-DNA; mtDNA (marked by gold particles) resists extraction. From Iborra et al., 2004.
Human mitochondrial DNA with the 37 genes on their respective H- and L-strands.
Human mitochondrial DNA with groups of protein-, rRNA- and tRNA-encoding genes.
The involvement of mitochondrial DNA in several human diseases.
Animal species mtDNA base composition was retrieved from the MitoAge database and compared to their maximum life span from AnAge database.

Mitochondrial DNA (mtDNA or mDNA) is the DNA located in mitochondria, cellular organelles within eukaryotic cells that convert chemical energy from food into a form that cells can use, such as adenosine triphosphate (ATP).

DNA damage resulting in multiple broken chromosomes

DNA repair

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DNA damage resulting in multiple broken chromosomes
Structure of the base-excision repair enzyme uracil-DNA glycosylase excising a hydrolytically-produced uracil residue from DNA. The uracil residue is shown in yellow.
Double-strand break repair pathway models
DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide ester bond between the phosphate backbone and the deoxyribose nucleotides.
DNA repair rate is an important determinant of cell pathology
Most life span influencing genes affect the rate of DNA damage
A chart of common DNA damaging agents, examples of lesions they cause in DNA, and pathways used to repair these lesions. Also shown are many of the genes in these pathways, an indication of which genes are epigenetically regulated to have reduced (or increased) expression in various cancers. It also shows genes in the error-prone microhomology-mediated end joining pathway with increased expression in various cancers.

DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.

In human cells, and eukaryotic cells in general, DNA is found in two cellular locations – inside the nucleus and inside the mitochondria.