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Exploring Mitochondrial DNA 

Explaining the science using folklore

D Loop

a triplex structure within the non-coding region of mitochondrial DNA (mtDNA). It's formed by a short DNA strand (7S DNA) displacing one strand of the usual double-stranded DNA, creating a loop. This region is crucial for mtDNA replication and transcription, acting as the origin of replication for the heavy strand and as a promoter for both the heavy and light strands

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Amino Acid Codes:

proline 

Proline has a secondary amine, making it the only proteinogenic amino acid with this characteristic. Its side chain forms a ring, giving it a rigid structure and impacting its behavior in proteins

threonine

Threonine has an α-amino group, a carboxyl group, and a side chain with a hydroxyl group

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CytB

Complex III, including cytochrome b, facilitates the transfer of electrons from ubiquinol to cytochrome c, a crucial step in oxidative phosphorylation

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Amino Acid Codes:

Glutamic acid

Plays a crucial role in the nervous system as an excitatory neurotransmitter

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ND6

ND6 is part of NADH dehydrogenase, a complex that catalyzes the transfer of electrons from NADH to ubiquinone, a crucial step in the electron transport chain. This process helps generate energy in the form of ATP, the cell's primary energy currency

ND5

provides instructions for making a protein called NADH dehydrogenase 5. This protein is part of a large enzyme complex known as complex I, which is active in mitochondria

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Amino Acid Codes:

Leucine 

Leucine is one of the three branched-chain amino acids an amino acid having an aliphatic side-chain with a branch used as a source of energy. 

The side chain is the non-polar, hydrophobic "R group" the side chain attached to the central alpha carbon

The alpha carbon is the core of each amino acid, linking all the essential functional groups all connected to this central alpha carbon

Serine

It's classified as a polar amino acid

Polar amino acids are a group of amino acids with hydrophilic side chains

those that are attracted to water and have a strong affinity for aqueous environments

that can form hydrogen bonds with water

due to its hydroxyl group side chain. Serine is also a precursor for other amino acids like glycine

Three amino acids (serine, threonine, and tyrosine) have a hydroxyl group in their side chain. 

Serine and threonine have aliphatic hydroxyl groups, while tyrosine has a hydroxyl group on an aromatic ring, making it a phenol

Histidine

A precursor for histamine, a neurotransmitter involved in various bodily functions. 

Histidine also has unique acid/base properties due to its imidazole side chain

The only standard proteinaceous amino acid containing an imidazole functional group is histidine

its imidazole ring plays a crucial role in the process of maintaining a stable pH by neutralizing excess acids or bases

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ND4

the ND4 protein, which is essential for complex I's function in the electron transport chain

The transport chain is a series of protein complexes embedded in the inner mitochondrial membrane

that facilitates the transfer of electrons from electron donors to electron acceptors

substances that give up electrons during a chemical reaction, essentially acting as reducing agents. They are involved in redox reactions, where electrons are transferred from the donor to an electron acceptor

a substance that can receive electrons from another molecule, typically during a redox (reduction-oxidation) reaction

ultimately leading to the generation of ATP through oxidative phosphorylation.

 This process is essential for cellular respiration and involves a series of redox reactions that create an electrochemical gradient, driving ATP synthesis

 Complex I is responsible for transferring electrons and protons, generating a gradient that drives ATP synthesis, the process by which cells produce energy

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Amino Acid Codes:

Arginine

The molecule features a guanidino group appended to a standard amino acid framework. At physiological pH, the carboxylic acid is deprotonated and both the amino and guanidino groups are protonated, resulting in a cation

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ND3

The ND3 gene encodes a subunit of NADH dehydrogenase, an enzyme that catalyzes the transfer of electrons from NADH to ubiquinone, a crucial step in the electron transport chain

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Amino Acid Codes:

Glycine

Glycine has the simplest structure of all proteinogenic amino acids, with a hydrogen atom as its side chain

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COIII

the COIII gene of Schizophyllum uses TGG exclusively. Translation requires no deviation from the universal code

ATP6

encodes a subunit of the ATP synthase enzyme complex, specifically subunit 6 of the F0 portion. This subunit is crucial for the final step of oxidative phosphorylation, the process that generates ATP, the cell's main energy source

ATP8

encodes a subunit of mitochondrial ATP synthase. involved in oxidative phosphorylation

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Amino Acid Codes:

Lysine

a precursor to many proteins. Lysine contains an α-amino group, an α-carboxylic acid group, it is classified as a basic, charged, aliphatic amino acid. It is encoded by the codons AAA and AAG.

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CoII

the gene coding for cytochrome oxidase subunit II, a protein involved in cellular respiration. used in DNA barcoding for species identification

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Amino Acid Codes:

Aspartic acid

It exists in two forms: L-aspartic acid, a building block of proteins, and D-aspartic acid, which plays a role in the nervous and reproductive systems

Serine 

Playing a vital role in various cellular processes, including protein synthesis, cell proliferation, and the synthesis of other molecules. It's synthesized in the body from 3-phosphoglycerate. Serine also exists in a D-form, which has unique metabolic significance

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COI

The COI gene is used in DNA barcoding, a technique that uses short, standardized DNA sequences to identify species. Researchers analyze a specific region (the "Folmer region") of the COI gene to distinguish between different species

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Amino Acid Codes:

tyrosine

Tyrosine is an alpha-amino acid, an aromatic amino acid, and a polar amino acid and plays a role in the synthesis of neurotransmitters and hormones

cysteine

Cysteine is a sulfur-containing amino acid with a thiol (-SH) group in its side chain, enabling it to form disulfide bonds. It's one of the 20 standard amino acids and is chiral, but L-cysteine is the form found in proteins

Asparagine

Asparagine has a polar side chain (carboxamide) and is considered an aliphatic amino acid Asparagine is involved in the N-glycosylation of proteins, a process where sugar molecules are attached to the protein

Alanine

Alanine has a central carbon atom connected to an amino group, a carboxyl group, a hydrogen atom, and a methyl group (CH3) Alanine can act as an inhibitory neurotransmitter in the brain, similar to other inhibitory amino acids like GABA, taurine, and glycine

tryptophan

Tryptophan is an alpha-amino acid with a unique indole side chain, a six-membered benzene ring fused to a five-membered pyrrole ring

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ND2

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Amino Acid Codes:

M

Q

I

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ND1

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Amino Acid Codes:

L

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16s

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Amino Acid Codes:

V

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12s

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Amino Acid Codes:

F