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Mitochondrial DNA is the circular molecule in the diagram above and is the basis for my world building project

The beginning of the first circle begins at Zero Hours

Zero Hours marks the beginning of a series of events  that need to happen in order to transform oneself and one’s world to convert one’s body and one’s consciousness into pure energy so that it can travel into another area of existence

There’s also the transition of a world into a new era that is believed to be glorious

it’s a long process, but to advance the entire civilization of Organelle from a type zero civilization into a type one and further it’s necessary 

Below will be the basics of the Cosmic Wheel for now and will be later transformed into a guide for self transformation

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Transfer RNA:

Phenylalanine

Phenylalanine is involved in the production of the neurotransmitters

norepinephrine (Helps you wake up)

dopamine (When you experience something pleasurable, dopamine signals that something important has happened)

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D Loop

D-loop is a triple-stranded region in the mitochondrial genome that contains transcription and replication elements

The D-loop is located in the major non-coding region (NCR) of mtDNA 

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HSP2

HSP2 is a promoter in human mitochondrial DNA (mtDNA) that regulates the transcription of polycistronic transcripts

HSP2 is one of three promoters in mtDNA, along with HSP1 and LSP

HSP2 produces a transcript that includes almost the entire mitochondrial genome

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HSP1

HSP1 drives the expression of 12 mRNAs that code for OXPHOS proteins, two rRNAs, and 14 tRNA

The transcription factor A, mitochondrial (TFAM) activates transcription at HSP1 

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LSP

LSP is involved in the process of making primers that start the replication of mtDNA. 

Transcribes eight tRNAs and the mitochondrial gene MT-ND6 

Makes the primer that starts the leading strand mtDNA replication 

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Transfer RNA:

Proline

Proline is an amino acid with a unique structure that includes a secondary amine group and a rigid ring

Proline's side chain is a ring with three carbon atoms

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Threonine

 It's a linear molecule that's polar due to its side chain, which contains a hydroxyl group

Threonine has a carboxyl group, an amino group, and a hydrogen attached to a central carbon

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CytB

Cytochrome b is part of complex III, which transfers electrons from ubiquinol to cytochrome c

The gene produces a protein made of a long chain of amino acids

An integral membrane protein with hydrophobic properties

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Transfer RNA:

Glutamic acid

helps nerve cells in the brain send and receive information from other cells

a naturally occurring amino acid and the primary excitatory neurotransmitter

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ND6

ND6 is a subunit of the enzyme NADH dehydrogenase

And is part of the first step of the electron transport process

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ND5

accepts electrons from NADH and transfers them to ubiquinone

The MT-ND5 gene is a mutational "hot spot"

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Transfer RNA:

Leucine

serving as a signaling molecule involved in appetite control

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Serine

a key component of many enzymes and contributing to protein structure, particularly by providing sites for phosphorylation; it is also a vital source of one-carbon units for various metabolic pathways, including the synthesis of nucleotides and the methylation process, and has important functions in cell signaling and neurotransmission

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Histidine

The side chain of histidine is an imidazole ring that contains nitrogen atoms

The ring is aromatic, which makes it stable and apolar at physiological pH

The ring can undergo protonation and deprotonation, resulting in three possible states

The ring is responsible for proton buffering, metal ion chelating, and antioxidant properties

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ND4

 a mitochondrial gene that provides instructions for making the NADH dehydrogenase 4 protein

part of the mitochondrial genome, which is a small circular molecule that contains only 37 genes

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Transfer RNA:

Arginine

Arginine is an alpha-amino acid

The side chain of arginine is a 3-carbon aliphatic chain with a guanidinium group at the end

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ND3

The MT-ND3 gene is 345 nucleotides long and contains no introns

It begins with the AUG methionine codon and ends with the U of the UAA stop codon

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Transfer RNA:

Glycine

the simplest and most stable amino acid, with a single hydrogen atom as its side chain

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COIII

The MT-CO3 gene is one of the mitochondrial genes that encodes cytochrome c oxidase subunits

The MT-CO3 gene encodes a single polypeptide and lacks introns

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ATP6

The MT-ATP6 gene encodes the intramembrane subunit 6 (or A) of the ATP synthase

The ATP synthase enzyme is made up of two major components, the soluble F1 and the membrane-bound F0

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ATP8

A gene that encodes a subunit of the ATP synthase enzyme

The enzyme uses the energy from protons flowing across a membrane to convert adenosine diphosphate (ADP) to ATP

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Transfer RNA:

Lysine

lysine is a long chain with a reactive amino group at its end

The side chain is amphipathic, with a hydrophobic part near the backbone and a positively charged end

Lysine side chains are often found where part of the side chain is buried, but generally prefer to be on the outside of proteins

Lysine side chains form ionic bonds with negatively charged groups of acidic amino acids

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COII

a gene that can be used to identify species and study human evolution

COII sequences have been used to identify species of aphids and honeybees

used in genetic studies due to its relatively fast evolutionary rate, making it valuable for tracing evolutionary relationships between species

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Transfer RNA:

Aspartic acid

Aspartate and glutamate are considered negative because they are negatively charged at physiological pH. In other words, they have already been deprotonated, and their functional group ~cannot~ as an acid by donating its hydrogen (because it doesn't have one at this pH)

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Serine

a key component of many enzymes and contributing to protein structure, particularly by providing sites for phosphorylation; it is also a vital source of one-carbon units for various metabolic pathways, including the synthesis of nucleotides and the methylation process, and has important functions in cell signaling and neurotransmission

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COI

 a gene that encodes a protein that helps with oxidative phosphorylation

A 658 bp fragment of the mtDNA COI gene is used as a "DNA barcode" to identify species

The COI gene is used to infer phylogenies, especially the region near the 5'-end

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Transfer RNA:

Tyrosine

It's an aromatic amino acid that contains a hydroxyl group and a benzene ring

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Cysteine

its structure includes a thiol group, an amino group, and a carboxylic acid group

It's chiral, meaning it has an L and a D form

The L-form is the protein monomer in all living things

The D-form acts as a signaling molecule in mammalian nervous systems

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Asparagine

It has an alpha-amino group, an alpha-carboxylic acid group, and a side chain carboxamide

Asparagine is a polar, aliphatic amino acid

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Alanine

Alanine is a nonpolar, aliphatic amino acid

It's encoded by all codons that start with GC

It exists in isomeric forms, L-alanine

The L-isomer is the one that's incorporated into proteins

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Tryptophan

an amino acid with a side chain that includes an indole ring fused to a pyrrole ring. It's a polar molecule that's essential for humans and many other animals

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ND2

Helps with mitochondrial respiration and oxidative phosphorylation

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Transfer RNA:

Methionine

Methionine has an amino group, a carboxyl group, and a side chain

The amino and carboxyl groups, and the central carbon, form the amino acid backbone

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Glutamine

It's a linear molecule that's polar, meaning it has both positive and negative charges

It contains a carboxylic acid group

It can exist in two forms, L-glutamine and D-glutamine, but only the L-form occurs in nature

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Isoleucine

an amino acid with a branched side chain

Isoleucine is an α-amino acid, which means it has an α-amino group and an α-carboxylic acid group

Its side chain is a branched 4-carbon structure, or sec-butyl group

Isoleucine is a non-polar, hydrophobic amino acid

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ND1

provides instructions for making the NADH dehydrogenase 1 protein which is part of the enzyme complex complex I

Complex I is involved in the first step of the electron transport chain, which transfers electrons from NADH to ubiquinone

This process creates an electrical charge that provides energy for ATP production

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Transfer RNA:

Leucine

is an essential amino acid with a branched-chain structure. It contains an isobutyl group, an α-amino group, and an α-carboxylic acid group

Leucine is a non-polar aliphatic amino acid

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16s

16S rRNA is a component of all self-replicating systems

The 16S rRNA gene is one of two mitochondrial ribosomal RNA genes

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Transfer RNA:

Valine

Valine is a branched-chain amino acid

It's a non-polar aliphatic amino acid

It's hydrophobic and usually found in the interior of proteins

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12s

12S rRNA is necessary for translating messenger RNAs into mitochondrial proteins

It's a component of the mitochondrial ribosome's SSU rRNA

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The Book Of Life

The gateway to higher knowledge is believed by the people to exist in dna

Multiple belief are created to explain the knowledge attained by the elite’s hypothesis and their findings 

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The Book of Life

Nucleotides

The heterocyclic ring system

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This is the law:

Purines:

Purines have a distinctive structure consisting of two rings fused together

Adenine always pairs with thymine

Pyrimidines:

A single ring

cytosine always pairs with guanine

Purines go with pyrimidines and pyrimidines go with purines

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Types of six-membered rings: 

Pyridine

A ring composed of five carbon atoms and one nitrogen atom

This group is characterized by having five members together and one stand alone 

(contains N)

N is asparagine. It has an alpha-amino group

An alpha amino acid is an amino acid in which the amino group and the carboxyl group are both bonded to the same carbon atom, known as the alpha carbon

Both groups are “Bonded” to a single member 

an alpha-carboxylic acid group,

refers to a carboxylic acid where the carbon bearing the carboxyl group (COOH) is directly attached to an amino group (NH2), commonly found in alpha-amino acids

All information gathered goes directly to that one member 

and a side chain carboxamide

A side chain is a chemical group attached to the main chain or backbone of a molecule

Those who follow this group:

The core of a carboxamide is an amide group

Which is crucial, forming the peptide bond that links amino acids together in a chain, resulting in proteins

Understand the importance of linking together what is necessary in order for society to result in creation

where a carbonyl carbon (C=O) is linked to a nitrogen atom 

The leading member works with the stand alone not against them, while they are linked they are not the same 

The concept of nations and allies is created, along with the concept that the stand alone and the leading member of the group are to work together. However they are understanding they will never be the same 

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pyran

While the ring contains alternating single and double bonds, the presence of the oxygen atom disrupts the perfect cyclic electron system that's necessary for aromaticity. Specifically, the oxygen atom breaks the resonance structure that is characteristic of aromatic compounds

A ring that is a non-aromatic, heterocyclic ring composed of five carbon atoms and one oxygen atom

A group of five members together and one stand alone

(contains O)

O is pyrrolysine 

the 22nd naturally occurring proteinogenic amino acid, is encoded by the amber codon UAG in some archaea and bacteria and is essential for methanogenesis (methane production)

thiane

Thiane is a heterocyclic compound and an organosulfur compound

A ring with five carbon atoms and one sulfur atom

A group of five members together and one stand alone 

(contains S)

S is Serine. An α-amino acid that is used in the biosynthesis of proteins. It contains an α-amino group, a carboxyl group, and a side chain consisting of a hydroxymethyl group, classifying it as a polar amino acid 

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Types of five-membered rings: 

Pyrrole 

containing four carbon atoms and one nitrogen atom in a ring

(contains N)

N is asparagine. It has an alpha-amino group, an alpha-carboxylic acid group, and a side chain carboxamide

furan

Contains four carbon atoms and one oxygen atom

(contains O)

Pyrrolysine a non-standard amino acid found in some archaeal species and synthesized into proteins by ribosomes has a side chain that is similar to lysine but with a pyrroline ring attached, making it a derivative of lysine with a unique pyrroline structure

thiophene

containing four carbon atoms and one sulfur atom

(contains S)

The defining feature of serine's side chain is the presence of a hydroxyl group (OH) attached to a methylene group

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Chromosomes

spindle fibers

Spindle fibers are made of tubulin proteins, which are arranged in polymers called microtubules

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Satellite DNA

a large collection of repeated DNA sequences

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TTAGGG

is a DNA sequence that forms the telomeres of human chromosomes

Telomeres prevent chromosomes from fraying or tangling

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G-rich

G-rich sequences are found in:

telomeres

Telomeres shorten with each cell division, eventually preventing the cell from dividing and leading to cell death

minisatellites

Minisatellites are DNA sequences that are made up of repeating units of DNA

promoters

A promoter is a DNA sequence that controls the start of gene transcription

G-rich sequences are prone to folding into G-quadruplex structures

G-quadruplexes are made up of four guanine residues held together by hydrogen bonds

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Shelterin

protects the telomeres from degradation, prevents the activation of unwanted repair systems, and regulates the activity of telomerase

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TRF1

TRF1 is a core component of the telomere protein complex, also known as shelterin, which is involved in regulating telomere length and protecting telomeres from DNA damage. 

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TRF2

telomeric repeat-binding factor 2, is a protein that plays a crucial role in telomere protection and maintenance, acting as a component of the shelterin complex and binding to telomeric DNA repeats

TRF2 is a telomere-binding protein that specifically binds to the double-stranded telomeric TTAGGG repeats

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POT1

POT1 is a subunit of the shelterin telomere binding complex 

POT1 contains domains, including:

OB1

typically refers to the OB-fold domain 1, a structural motif in proteins that binds to DNA, particularly in the context of proteins involved in DNA binding and repair

OB2

refers to an Oligonucleotide/Oligosaccharide Binding (OB) fold domain found in proteins, particularly in the context of telomere maintenance

OB3

OB3 may have application AD-like dementia by interrupting the cascade of insulin resistance, neuro-inflammation, and neurodegeneration

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TCAB1

A gene that encodes a protein crucial for telomerase function, specifically its localization to Cajal bodies and subsequent trafficking to telomeres

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The Nations Of Organelle

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The Nature of Nuc

Nucleolus: An organelle within the nucleus

The nucleolus is a spherical structure in the nucleus of a cell that produces ribosomes. It's made of RNA and protein, and it's not surrounded by a membrane

The nucleolus has three main parts: 

the fibrillar center:

contains non-transcribed copies of ribosomal DNA

Non-transcribed means not captured in a written record

In the early days of Organelle Nuc has not produced written history yet and rely on spoken word 

In more modern times the Nucleolus is a community of great minds dedicated to studying the DNA and RNA of the creatures in their environment following the hypothesis that the answers to life’s biggest questions exist in the DNA code 

where the genes for pre-rRNA

the precursor molecule to mature ribosomal RNA (rRNA) - type of non-coding RNA 

is a functional RNA molecule that is not translated into a protein

Translation is the process by which a cell makes proteins using the genetic information carried in messenger RNA

proteins are large molecules made of amino acids that perform many essential functions in cells

In the early days of Nuc Amino Acids have not yet been discovered 

The discovery of Amino Acids is huge and is to be an important step in Organelle’s development 

It is transcribed directly from ribosomal DNA (rDNA) within the nucleus, specifically in a region called the nucleolus

Is expressed. Meaning:

Pre-rRNA is transcribed from ribosomal DNA (rDNA) by RNA polymerase 

RNA polymerase is an enzyme that copies DNA into RNA

DNA is copied into RNA through a process called transcription. 

Transcription is the first step in gene expression,

the process by which the information encoded in a gene is turned into a function

which is the process of using a gene's DNA to create a functional product

Stories that have been passed down are used to explain a function in the world. These stories are far from myth and contain valuable information passed down through generations

The creation stories:

The DNA is unwound to expose the bases on each strand

The story about strings takes place in a world built by the god of creation. Everything that has existed in this world was spun together from strings.

One day one of the people living in the city discovered a loose thread, so they pulled it. Everything unraveled and secrets were revealed.

The people looked down at the string and noticed it was flat and strong. The people decided to draw on the string what was revealed and then they spun the string into the structures for the new city. Now everything in creation has the code of life within it as the ribbon gets twisted into hollow tubes becoming the strings of life 

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The stories are unpacked and analyzed and a hypothesis is born. One that believes the secrets of the universe are written in DNA

RNA polymerase attaches to the DNA strand, called the template strand that is used to create messenger RNA 

The mRNA travels to the cytoplasm, where ribosomes read the mRNA sequence

In the creation story: The string spins into creatures called “Messengers” who carry the secrets of the universe in their bodies as they travel outside the city into the unknown where it is believed they came into contact with “Creator Spirits”

RNA polymerase binds to the DNA at a region called the promoter

Promoters are typically found directly upstream of the transcription initiation site of a gene

the process of starting the synthesis of RNA from DNA

It locally melts the DNA double helix

The images that have been drawn in this myth are passed down through visions they have been interpreted as well as misinterpreted. The creations have never been seen before by those who received these visions. So they compared it with what was familiar to them in their environment. The result is mysterious creatures and inventions. Throughout the ancient times of Nuc there has been a handful of people who got more than just visions. They would disappear for days where, as they claimed, heard the law spoken to them. They would return to the people to deliver the message.

RNA polymerase translocates along the DNA, polymerizing ribonucleotides to create RNA

During transcription, ribonucleotides are the building blocks used by RNA polymerase to create a complementary RNA strand:

The first law of creation:

A complementary DNA strand is one where, in a double-stranded DNA molecule:

forming the nucleotides:

the genetic instructions for all living beings

Those who have heard the voice and have seen the visions are told “The following is the law, the instructions on how build a society”

The people of Nuc are introduced to what is called the Book of Life 

It is explained to them simply that creation is not only strings but also rings and that they are to form their society in accordance with this. They are told that the two fused rings ONLY are to pair up with the single ring and vice versa. Two of the same never do. Socially what this means has a mixed reaction. 

from

a DNA template:

complementarily pairs with the code so it can be used as a template upon which to build mRNA with the correct code

via hydrogen bonding and then forming covalent phosphodiester bonds

RNA polymerase uses the template strand to create a complementary RNA molecule

The RNA chain is elongated one nucleotide at a time

Transcription ends when sequences in the RNA signal that the transcript is finished 

the dense fibrillar component

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the site where newly transcribed pre-ribosomal RNA (pre-rRNA) is processed and modified after its initial transcription in the fibrillar center 

 and the granular component

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Chromatin: Long, entangled structures of chromosomes that contain DNA

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Nuclear lamina: A network of intermediate filaments that provides structural support and maintains the nucleus's shape

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Nuclear pore complex: A gatekeeper that controls the flow of molecules across the nuclear envelope

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Nuclear membrane: A double layer that separates the nucleus from the cell's cytoplasm

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Nucleoplasm: The matrix inside the nucleus

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The first circle of Nuc

The second circle of Nuc

The third circle of Nuc

The fourth circle of Nuc