A report on Gene and Mitochondrion

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

- Gene

The proteins employed in mtDNA repair are encoded by nuclear genes, and are translocated to the mitochondria.

- Mitochondrion
Gregor Mendel

11 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.

Gene transfer from a deltaproteobacterium to an archaeon led to the methanogenic archaeon developing into a nucleus.

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

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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
Impure DNA extracted from an orange

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 information carried by DNA is held in the sequence of pieces of DNA called genes.

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.

Onion (Allium cepa) root cells in different phases of the cell cycle (drawn by E. B. Wilson, 1900)

Cell (biology)

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Basic structural and functional unit of life forms.

Basic structural and functional unit of life forms.

Onion (Allium cepa) root cells in different phases of the cell cycle (drawn by E. B. Wilson, 1900)
Structure of a typical prokaryotic cell
Structure of a typical animal cell
Structure of a typical plant cell
Detailed diagram of lipid bilayer of cell membrane
A fluorescent image of an endothelial cell. Nuclei are stained blue, mitochondria are stained red, and microfilaments are stained green.
Deoxyribonucleic acid (DNA)
Human cancer cells, specifically HeLa cells, with DNA stained blue. The central and rightmost cell are in interphase, so their DNA is diffuse and the entire nuclei are labelled. The cell on the left is going through mitosis and its chromosomes have condensed.
Diagram of the endomembrane system
Prokaryotes divide by binary fission, while eukaryotes divide by mitosis or meiosis.
An outline of the catabolism of proteins, carbohydrates and fats
An overview of protein synthesis.
Within the nucleus of the cell (light blue), genes (DNA, dark blue) are transcribed into RNA. This RNA is then subject to post-transcriptional modification and control, resulting in a mature mRNA (red) that is then transported out of the nucleus and into the cytoplasm (peach), where it undergoes translation into a protein. mRNA is translated by ribosomes (purple) that match the three-base codons of the mRNA to the three-base anti-codons of the appropriate tRNA. Newly synthesized proteins (black) are often further modified, such as by binding to an effector molecule (orange), to become fully active.
Staining of a Caenorhabditis elegans highlights the nuclei of its cells.
Stromatolites are left behind by cyanobacteria, also called blue-green algae. They are the oldest known fossils of life on Earth. This one-billion-year-old fossil is from Glacier National Park in the United States.
Robert Hooke's drawing of cells in cork, 1665

The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria also contain some DNA.

All cells (except red blood cells which lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin) possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery.

HeLa cells stained for nuclear DNA with the blue fluorescent Hoechst dye. The central and rightmost cell are in interphase, thus their entire nuclei are labeled. On the left, a cell is going through mitosis and its DNA has condensed.

Cell nucleus

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In cell biology, the nucleus (pl.

In cell biology, the nucleus (pl.

HeLa cells stained for nuclear DNA with the blue fluorescent Hoechst dye. The central and rightmost cell are in interphase, thus their entire nuclei are labeled. On the left, a cell is going through mitosis and its DNA has condensed.
Diagram of the nucleus showing the ribosome-studded outer nuclear membrane, nuclear pores, DNA (complexed as chromatin), and the nucleolus.
A cross section of a nuclear pore on the surface of the nuclear envelope (1). Other diagram labels show (2) the outer ring, (3) spokes, (4) basket, and (5) filaments.
A mouse fibroblast nucleus in which DNA is stained blue. The distinct chromosome territories of chromosome 2 (red) and chromosome 9 (green) are stained with fluorescent in situ hybridization.
An electron micrograph of a cell nucleus, showing the darkly stained nucleolus
A generic transcription factory during transcription, highlighting the possibility of transcribing more than one gene at a time. The diagram includes 8 RNA polymerases however the number can vary depending on cell type. The image also includes transcription factors and a porous, protein core.
Macromolecules, such as RNA and proteins, are actively transported across the nuclear membrane in a process called the Ran-GTP nuclear transport cycle.
An image of a newt lung cell stained with fluorescent dyes during metaphase. The mitotic spindle can be seen, stained green, attached to the two sets of chromosomes, stained light blue. All chromosomes but one are already at the metaphase plate.
Human red blood cells, like those of other mammals, lack nuclei. This occurs as a normal part of the cells' development.
Oldest known depiction of cells and their nuclei by Antonie van Leeuwenhoek, 1719
Drawing of a Chironomus salivary gland cell published by Walther Flemming in 1882. The nucleus contains polytene chromosomes.

The genes within these chromosomes are structured in such a way to promote cell function.

A small fraction of the cell's genes are located instead in the mitochondria.

A series of codons in part of a messenger RNA (mRNA) molecule. Each codon consists of three nucleotides, usually corresponding to a single amino acid. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosome to synthesize a protein according to this code.

Genetic code

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Set of rules used by living cells to translate information encoded within genetic material into proteins.

Set of rules used by living cells to translate information encoded within genetic material into proteins.

A series of codons in part of a messenger RNA (mRNA) molecule. Each codon consists of three nucleotides, usually corresponding to a single amino acid. The nucleotides are abbreviated with the letters A, U, G and C. This is mRNA, which uses U (uracil). DNA uses T (thymine) instead. This mRNA molecule will instruct a ribosome to synthesize a protein according to this code.
The genetic code
Reading frames in the DNA sequence of a region of the human mitochondrial genome coding for the genes MT-ATP8 and MT-ATP6 (in black: positions 8,525 to 8,580 in the sequence accession NC_012920 ). There are three possible reading frames in the 5' → 3' forward direction, starting on the first (+1), second (+2) and third position (+3). For each codon (square brackets), the amino acid is given by the vertebrate mitochondrial code, either in the +1 frame for MT-ATP8 (in red) or in the +3 frame for MT-ATP6 (in blue). The MT-ATP8 genes terminates with the TAG stop codon (red dot) in the +1 frame. The MT-ATP6 gene starts with the ATG codon (blue circle for the M amino acid) in the +3 frame.
Examples of notable mutations that can occur in humans.
Axes 1, 2, 3 are the first, second, and third positions in the codon. The 20 amino acids and stop codons (X) are shown in single letter code.
Genetic code logo of the Globobulimina pseudospinescens mitochondrial genome by FACIL. The logo shows the 64 codons from left to right, predicted alternatives in red (relative to the standard genetic code). Red line: stop codons. The height of each amino acid in the stack shows how often it is aligned to the codon in homologous protein domains. The stack height indicates the support for the prediction.

The vast majority of genes are encoded with a single scheme (see the RNA codon table).

That scheme is often referred to as the canonical or standard genetic code, or simply the genetic code, though variant codes (such as in mitochondria) exist.

DNA damage resulting in multiple broken chromosomes

DNA repair

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

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

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.

Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes.

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

The Oxford Dictionary suggests the name is a blend of the words gene and chromosome.

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

The interaction of tRNA and mRNA in protein synthesis.

Transfer RNA

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Adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins.

Adaptor molecule composed of RNA, typically 76 to 90 nucleotides in length (in eukaryotes), that serves as the physical link between the mRNA and the amino acid sequence of proteins.

The interaction of tRNA and mRNA in protein synthesis.
Secondary cloverleaf structure of tRNAPhe from yeast.
Tertiary structure of tRNA. CCA tail in yellow, Acceptor stem in purple, Variable loop in orange, D arm in red, Anticodon arm in blue with Anticodon in black, T arm in green.
3D animated GIF showing the structure of phenylalanine-tRNA from yeast (PDB ID 1ehz). White lines indicate base pairing by hydrogen bonds. In the orientation shown, the acceptor stem is on top and the anticodon on the bottom
Bulge-helix-bulge motif of a tRNA intron

Other modified nucleotides may also appear at the first anticodon position—sometimes known as the "wobble position"—resulting in subtle changes to the genetic code, as for example in mitochondria.

Organisms vary in the number of tRNA genes in their genome.

General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome).

Proteome

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Entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time.

Entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time.

General schema showing the relationships of the genome, transcriptome, proteome, and metabolome (lipidome).
The proteome can be used to determine the presence of different types of cancers.
This image shows a two-dimensional gel with color-coded proteins. This is a way to visualize proteins based on their mass and isoelectric point.
An Orbitrap mass spectrometer commonly used in proteomics

For instance, the mitochondrial proteome may consist of more than 3000 distinct proteins.

In eukaryotes this becomes much more complicated as more than one protein can be produced from most genes due to alternative splicing (e.g. human proteome encodes about 20,000 proteins, but some estimates predicted 92,179 proteins out of which 71,173 are splicing variants).