Mitochondrion

Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy
Simplified structure of a mitochondrion.
Cross-sectional image of cristae in a rat liver mitochondrion to demonstrate the likely 3D structure and relationship to the inner membrane
Electron transport chain in the mitochondrial intermembrane space
Transmission electron micrograph of a chondrocyte, stained for calcium, showing its nucleus (N) and mitochondria (M).
Typical mitochondrial network (green) in two human cells (HeLa cells)
Model of the yeast multimeric tethering complex, ERMES
Evolution of MROs
The circular 16,569 bp human mitochondrial genome encoding 37 genes, i.e., 28 on the H-strand and 9 on the L-strand.

Double-membrane-bound organelle found in most eukaryotic organisms.

- Mitochondrion
Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy

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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.

Mitochondrial DNA

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).

The cytosol is a crowded solution of many different types of molecules that occupy up to 30% of the cytoplasmic volume.

Cytosol

One of the liquids found inside cells ).

One of the liquids found inside cells ).

The cytosol is a crowded solution of many different types of molecules that occupy up to 30% of the cytoplasmic volume.
Intracellular fluid content in humans
Carboxysomes are protein-enclosed bacterial microcompartments within the cytosol. On the left is an electron microscope image of carboxysomes, and on the right a model of their structure.

For example, the mitochondrial matrix separates the mitochondrion into many compartments.

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.

DNA

Polymer composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses.

Polymer composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses.

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.
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.
A section of DNA. The bases lie horizontally between the two spiraling strands ([[:File:DNA orbit animated.gif|animated version]]).
DNA major and minor grooves. The latter is a binding site for the Hoechst stain dye 33258.
From left to right, the structures of A, B and Z DNA
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.
A covalent adduct between a metabolically activated form of benzo[a]pyrene, the major mutagen in tobacco smoke, and DNA
Location of eukaryote nuclear DNA within the chromosomes
T7 RNA polymerase (blue) producing an mRNA (green) from a DNA template (orange)
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

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.

The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow.

Enzyme

Enzymes are proteins that act as biological catalysts (biocatalysts).

Enzymes are proteins that act as biological catalysts (biocatalysts).

The enzyme glucosidase converts the sugar maltose into two glucose sugars. Active site residues in red, maltose substrate in black, and NAD cofactor in yellow.
Eduard Buchner
Enzyme activity initially increases with temperature (Q10 coefficient) until the enzyme's structure unfolds (denaturation), leading to an optimal rate of reaction at an intermediate temperature.
Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black.
Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow.
Chemical structure for thiamine pyrophosphate and protein structure of transketolase. Thiamine pyrophosphate cofactor in yellow and xylulose 5-phosphate substrate in black.
The energies of the stages of a chemical reaction. Uncatalysed (dashed line), substrates need a lot of activation energy to reach a transition state, which then decays into lower-energy products. When enzyme catalysed (solid line), the enzyme binds the substrates (ES), then stabilizes the transition state (ES‡) to reduce the activation energy required to produce products (EP) which are finally released.
The metabolic pathway of glycolysis releases energy by converting glucose to pyruvate via a series of intermediate metabolites. Each chemical modification (red box) is performed by a different enzyme.
In phenylalanine hydroxylase over 300 different mutations throughout the structure cause phenylketonuria. Phenylalanine substrate and tetrahydrobiopterin coenzyme in black, and Fe2+ cofactor in yellow.
Hereditary defects in enzymes are generally inherited in an autosomal fashion because there are more non-X chromosomes than X-chromosomes, and a recessive fashion because the enzymes from the unaffected genes are generally sufficient to prevent symptoms in carriers.

For example, fatty acids are synthesized by one set of enzymes in the cytosol, endoplasmic reticulum and Golgi and used by a different set of enzymes as a source of energy in the mitochondrion, through β-oxidation.

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

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.

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

Diagram of a typical prokaryotic cell

Prokaryote

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.

(A) Electron micrograph of Halothiobacillus neapolitanus cells, arrows highlight carboxysomes. (B) Image of intact carboxysomes isolated from H. neapolitanus. Scale bars are 100 nm.

Organelle

Organelle is a specialized subunit, usually within a cell, that has a specific function.

Organelle is a specialized subunit, usually within a cell, that has a specific function.

(A) Electron micrograph of Halothiobacillus neapolitanus cells, arrows highlight carboxysomes. (B) Image of intact carboxysomes isolated from H. neapolitanus. Scale bars are 100 nm.
Structure of Candidatus Brocadia anammoxidans, showing an anammoxosome and intracytoplasmic membrane

They include structures that make up the endomembrane system (such as the nuclear envelope, endoplasmic reticulum, and Golgi apparatus), and other structures such as mitochondria and plastids.

Internal symbiont: mitochondrion has a matrix and membranes, like a free-living alphaproteobacterial cell, from which it may derive.

Symbiogenesis

Leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms.

Leading evolutionary theory of the origin of eukaryotic cells from prokaryotic organisms.

Internal symbiont: mitochondrion has a matrix and membranes, like a free-living alphaproteobacterial cell, from which it may derive.
Konstantin Mereschkowski's 1905 tree-of-life diagram, showing the origin of complex life-forms by two episodes of symbiogenesis, the incorporation of symbiotic bacteria to form successively nuclei and chloroplasts.
One model for the origin of mitochondria and plastids
Modern endosymbiotic theory posits that simple life forms merged, forming cell organelles, like mitochondria.
Kwang Jeon's experiment: [I] Amoebae infected by x-bacteria [II] Many amoebae become sick and die [III] Survivors have x-bacteria living in their cytoplasm [IV] Antibiotics kill x-bacteria: host amoebae die as now dependent on x-bacteria.
Mitochondria of a mammal lung cell visualized using Transmission Electron Microscopy
Diagram of endomembrane system in eukaryotic cell
The human mitochondrial genome has retained genes encoding 2 rRNAs, 22 tRNAs, and 13 redox proteins.
Simplified chart showing the three main mergers of the endosymbiotic theory

The theory holds that mitochondria, plastids such as chloroplasts, and possibly other organelles of eukaryotic cells are descended from formerly free-living prokaryotes (more closely related to bacteria than to archaea) taken one inside the other in endosymbiosis.

The redox reactions of nicotinamide adenine dinucleotide.

Nicotinamide adenine dinucleotide

Coenzyme central to metabolism.

Coenzyme central to metabolism.

The redox reactions of nicotinamide adenine dinucleotide.
UV absorption spectra of NAD and NADH.
Some metabolic pathways that synthesize and consume NAD in vertebrates. The abbreviations are defined in the text.
Salvage pathways use three precursors for NAD+.
Rossmann fold in part of the lactate dehydrogenase of Cryptosporidium parvum, showing NAD in red, beta sheets in yellow, and alpha helices in purple.
In this diagram, the hydride acceptor C4 carbon is shown at the top. When the nicotinamide ring lies in the plane of the page with the carboxy-amide to the right, as shown, the hydride donor lies either "above" or "below" the plane of the page. If "above" hydride transfer is class A, if "below" hydride transfer is class B.
A simplified outline of redox metabolism, showing how NAD and NADH link the citric acid cycle and oxidative phosphorylation.
The structure of cyclic ADP-ribose.
Arthur Harden, co-discoverer of NAD

In eukaryotes the electrons carried by the NADH that is produced in the cytoplasm are transferred into the mitochondrion (to reduce mitochondrial NAD) by mitochondrial shuttles, such as the malate-aspartate shuttle.

Gregor Mendel

Gene

Basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

Basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

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.

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.