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EVOLUTION OF LIFE

There are 5 universal elements in bio active molecules; carbon, nitrogen, oxygen, sulfur and phosphorous. Phosphorous has same 5 electron outer shell as Nitrogen in the periodic table, and sulfur has the same shell as oxygen. They naturally bonds to carbon polymers such as proteins. In N2, the two nitrogen atoms form a triple bond. It is because of nitrogen’s small size that it is able to form pπ-pπ bonds with itself and is surprisingly stable. This property is not exhibited by atoms such as phosphorus. Thus, phosphorus is more reactive than nitrogen. Author Isaac Asimov once called phosphorus "life's bottleneck," because it makes up 1 percent of an organism but is only present in 0.1 percent of minerals on Earth.

https://www.sciencenews.org/article/phosphorus-earth-earliest-life-forged-lightning-chemistry

The phosphorus of the primitive Earth was present as phosphates. The primitive Earth was deficient in the total available phosphorus until a sufficient quantity of phosphorus weathered from the igneous rocks in which it was entrapped. One path to bio accessible phosphorous is through lightening strikes.

https://pubmed.ncbi.nlm.nih.gov/917502 &https://www.gondwanatalks.com/l/did-lightning-provide-phosphorus-to-ancient-life/

The best guess was that it all started with the "primordial soup" hot or cold. New research shows that precursors of ribonucleotides, amino acids and lipids can all be derived by a reducing reaction that adds carbon and nitrogen compounds to hydrogen cyanide and some of its derivatives, and thus that all the cellular subsystems could have arisen simultaneously through common chemistry. The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant.

https://phys.org/news/2015-03-chemists-riddle-life-began-earth.html

A cell is a isolated biochemical factory. Cell walls are made of phospho-lipids, with the hydrophilic phosphate head and two hydrophobic (polyethylene like) tails. The 2 tails, means that they do not naturally form spherical tail-in micelles, but instead self assemble into roughly flat bilayers. A bilayer lipid isolates the water in the cell from the outside world. There are portals that allow passage into and out of the cell, and receptors for messaging. Inside the cell are the template (DNA) with a sugar phosphate backbone, the means for replication, and to generate energy using tri-phosphate to di-phosphate cycles.

Primitive protocells were the precursors to today's unicellular organisms. Although the origin of life is largely still a mystery, in the currently prevailing theory, known as the RNA world hypothesis, early RNA (single helix) molecules would have been the basis for catalyzing organic chemical reactions and self-replication.

The energy transfer molecule in cells is ATP - a "triphosphate". The core process in metabolism is oxidation using energy from ATP to remove acid groups from precursors. In the case of photosynthesis in plants, light is absorbed and reacts with water to make ATP and oxygen is the byproduct. The ATP is then used to fix carbon from carbon dioxide into biomolecules.

Once there was a process for building biomolecules, a process evolved for using biomolecules as food by breaking them down by oxidation in the citric acid cycle to create ATP that could be used for locomotion, sensing, and replication by the creation of specialist molecules such as proteins.

The most earliest common ancestor was probably a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. A thermophile is an organism that thrives at relatively high temperatures, between 41 and 122 °C (106 and 252 °F). Thermophiles are found in various geothermally heated regions of the Earth, such as hot springs like those in Yellowstone National Park and deep sea hydrothermal vents, as well as decaying plant matter, such as peat bogs and compost.

The enzymes in thermophiles function at high temperatures and are a component in DNA replication, even used in PCR. PCR employs two main reagents—primers (which are short single strand DNA fragments known as oligonucleotides that are a complementary sequence to the target DNA region) and a DNA polymerase (thermophile enzyme).

Bacteria evolved from thermophiles and are microbes with a cell structure simpler than that of many other organisms. Their control centre, containing the genetic information, is contained in a single loop of DNA. Some bacteria have an extra circle of genetic material called a plasmid rather than a nucleus. The plasmid often contains genes that give the bacterium some advantage over other bacteria. For example it may contain a gene that makes the bacterium resistant to a certain antibiotic.

The fossil record starts around 3.5By years ago with cyano-bacteria in the form of Stromatolites, which are layers of sand and rock glued together by residues from cyano-bacteria. Cyano-bacteria absorbed carbon dioxide and seeded the earth with oxygen. Cyano-bacteria are unicellular. All the oxygen that makes the atmosphere breathable for aerobic organisms originally comes from cyanobacteria or their later descendants.

Plants evolved with superior photosynthesis from green pigment chloroplasts. Fungi followed with the ability to digest carbohydrates such as cellulose. Jellyfish were the first with basic locomotion. The first with mobility were the Molluscs with egg layers with exoskeletons, and copper based blood that flows throughout the body. Within the molluscs are a staggering variety of insects, and shellfish. The cephalons, squid and octopus, evolved closed circulation that delivered oxygen to key organs. Octopus show remarkable intelligence and are a true intelligent alien. The hard exoskeleton limits the size of insects. The soft exoskeletons limit the protection against predators and their load bearing capability.

The evolution of fish began about 530 million years ago with lampreys and then early fish with developed the skull and the vertebral column, leading to the first craniates and vertebrates.

Around 400 M years ago, a great increase in fish variety occurred. It was from the lobe-finned fish that the first amphibians (tetrapods) evolved as four-limbed vertebrates . Meanwhile, the insects ruled on land until the fish evolved into amphibians.

The devastating Permian–Triassic extinction event (252 M years ago) wiped out an estimated 96% of all marine species and 70% of terrestrial vertebrate species. The scientific consensus is that the main cause of extinction was the large amount of carbon dioxide emitted by the volcanic eruptions that created the Siberian Traps, which elevated global temperatures, and in the oceans led to widespread anoxia and acidification. The Siberian traps are a massive igneous rock outflow covering 7 M squ km.

There is evidence that survivors of the Permian extinction were warm blooded based on isotopes of oxygen in the bones and teeth. The assumption is that they were better able to survive the temperature changes associated with the extinction.

https://theconversation.com/more-than-252-million-years-ago-mammal-ancestors-became-warm-blooded-to-survive-mass-extinction-79961

Evidence from crocodiles and their extinct relatives suggests that elevated metabolisms could have developed in the earliest archosaurs, which were the common ancestors of dinosaurs and crocodiles.

Dinosaurs diverged from their archosaur ancestors during the Middle to Late Triassic epochs, roughly 230 million years. The Triassic/Jurassic extinction (volcanic) event, 205 M years ago, left fairly untouched; plants, crocodylomorphs, dinosaurs, pterosaurs and mammals. The dinosaurs thrived.

The fabulously diverse dinosaurs dominated for over 200My. The dinosaurs have roughly 80% of DNA in common with humans, which accounts for the recognizable "architecture" of dinosaur skeletons.

The dinosaurs were egg layers. The egg limits the amount of energy available to the fetus before birth, at which point it needs to be able metabolize adult food. The ancestral mammals, led to Monotremes as egg layers who suckle their young, and marsupials who give birth to a "fetus" that suckles and develops in a protected pouch. The most successful were the Eutherans who are placental mammals who develop inside the mothers body directly fed using mother blood through a placenta. After birth the placentals suckled their young. These variants allowed unlimited access to energy and over 2 years of development before metabolizing adult food. These variants appeared while dinosaurs dominated.

The K-T meteor 66My ago changed the trajectory of evolution. Nothing larger than 50 lbs survived an explosion that released the same energy as 100 teratonnes of TNT more than a billion times the energy of the atomic bombings of Hiroshima and Nagasaki.

Shrews survive the meteor, mammal species explode, and birds evolved as the survivors of the dinosaur line.

The role of extinctions can be seen in diversity, measured as the count of different "families" changing overtime. The similarities between species from their common ancestor can be seen in their limb bone structure.

Around 7My ago, Hominids split from Great Apes and by 200Ky ago humans appeared with 99.5% of the DNA of the common Great Ape ancestor. Humans have been around 40Ky.

The increasing size of the brain case is one of the most notable changes in the evolving humans as seen in these skulls at the "cradle of humanity" in South Africa. There is also evidence that intelligence also seems to be linked to an alternative source of changes in DNA. DNA changes by mutation, and also courtesy of "transposons" that move sections of DNA around by writing the information back into a cells DNA, presumably changed which bits get expressed. The DNA sequence of hundreds of individual neurons from human cadavers show that cells in the same brain are, indeed, genetically distinct from one another. This suggests a new level of specialization in brain cells.

https://www.newyorker.com/tech/annals-of-technology/the-strangers-in-your-brain

The early humans were hunter - gatherers who spent their travelling around following food sources. There are many surviving native communities that survived to modern times such as native americans, eskimos. For practical reasons, there was no incentive to develop permanent dwellings.

During the last ice age, from (c. 115,000 – c. 11,700), hunter gatherers leave Africa and populate all the major land masses using land bridges formed by ice and low sea levels.

The end of the last ice age around 10Ky ago, uncovered the Fertile Crescent which became one the first centers of settled farming. Once people could grow more than they needed, cities and a ruling class emerged in Babylon. The Fertile Crescent is most famous for its sites related to the origins of agriculture. The western zone around the Jordan and upper Euphrates rivers gave rise to the first known Neolithic farming settlements (referred to as Pre-Pottery Neolithic A (PPNA)), which date to around 9,000 BCE and includes very ancient sites such as Göbekli Tepe, Chogha Golan, and Jericho (Tell es-Sultan). During the Neolithic period from a lifestyle of hunting and gathering to one of agriculture and settlement, making an increasingly large population possible. These settled communities permitted humans to observe and experiment with plants, learning how they grew and developed. This new knowledge led to the domestication of plants into crops.

The Fertile Crescent had many diverse climates, and major climatic changes encouraged the evolution of many annual plants, which produce more edible seeds than perennial plants. The Fertile Crescent was home to the eight Neolithic founder crops important in early agriculture (i.e., wild progenitors to emmer wheat, einkorn, barley, flax, chick pea, pea, lentil, bitter vetch), and four of the five most important species of domesticated animals—cows, goats, sheep, and pigs; The Fertile Crescent flora comprises a high percentage of plants that can self-pollinate, but may also be cross-pollinated. These plants, called "selfers", were one of the geographical advantages of the area because they did not depend on other plants for reproduction.

This region, also saw the emergence of early complex societies during the succeeding Bronze Age. There is also early evidence from the region for writing and the formation of hierarchical state level societies. This has earned the region the nickname "The cradle of civilization".

As soon as ruling classes emerge with wealth and resources, fights between rulers to increase their wealth and influence became the norm that has lasted to this day - unfortunately. Over 3000 years, the Egypt of the Pharoes was invaded by the Persians, Greeks, and Romans without disturbing the religious establishment.

By 500BC, trans-continental trade over the Silk Road to the far east and India, and the Incense Route to Africa and Arabia brought exotic goods. Petra stood at a crossroads of these routes and brought wealth to the Nabateans, a semi nomadic Arabian tribe that ran many of the trans Arabia routes.

Food availability allowed populations to grow, while urbanization increased the mortality from disease. The Black death 700y ago (1300's) killed around 50% of city dwellers.

Trade in the 1200's between Europe and the Middle East flowed through Venice. Marco Polo was a resident of Venice. The onset of long distance sailing exploration sidelined Venice.

The competition between European powers changed to empire building through exploration. Discovery by Columbus, Magellan, and Drake followed by invasions by Cortes, Cartier, the Pilgrims and others led to slavery and mass genocide of native populations in the name of commerce and religious conversion. The voyages of discovery and empire building by the Europeans naval powers in the 500-600y ago (1400-1500's), brought new contacts with the indigenous hunter gatherers and resulted in genocide of 90% of the indigenous people from diseases that they had no immunity for.

The scientific revolution changed the trajectory of life on earth through modern medicine, hygiene and nutrition.

Pre industrial revolution the population increased at 0.15% a year, post it has increased to 1.7% a year equivalent to 3 children per couple per generation. This has lead to the massive consumption of land for food and fossil fuels.

A-The-double-stranded-structure-of-DNA-B-The-DNA-backbone-consists-of-phosphate.png

10tonsScientificNaturalHistoryMuseumPrag

The evolutionary tree

The first attempt to lay out evolutionary history as a progression based on anatomy was Ernst Haeckel's Biogenetic Law (1866). His tree "Pedigree of Man" had the correct sequence of Primitive - Invertebrate - Vertebrate - Mammals.

We now have much more fossil history, biochemical information and DNA. A tree based on Mitochondrial DNA was recently compiled giving a more detailed view of relationships. The family tree drawing was inspired by a linear diagram of species differentiation in cytochrome C from a biochemistry textbook, Lehninger. Cytochrome C is a genetic protein common in all living things. The organic curved branches is humans centered but not at the top of the tree. Canines evolved with better smell, whales with bigger brains, and eagles with better vision.

https://scitechconnect.elsevier.com/africa-retracing-human-evolution-migration-dna

https://rsscience.com/the-biological-classification-of-paramecium-name-history-and-evolution/

Personal communication from Mark Hom MD

I annotated the evolution tree with the key functions of metabolism, energy distribution, structure and reproduction, that enabled the different branches. Life started with cyanobacteria and plants that use photosynthesis to absorb CO2 fix carbon and produce oxygen, seeding earths atmosphere. Decomposers such as mushrooms then evolved that took plant proteins and produce carbon dioxide and energy. The first oxygen users were the mollusks (insects, crustaceans, octopus) that had copper based blood that flowed through their body cavity. Octopus evolved a closed blood distribution that enabled oxygen to be delivered to key organs. Iron based blood (hemoglobin) in a closed circulation system then became universal in vertebrates from lampreys and fish onwards. Warm blood evolved in dinosaurs on, enabling much faster metabolism. The final step increases the development of their young. Eggs provide a finite amount of energy to the developing fetus. Octopus' actively protect their eggs, sharks let them develop in their bodies for protection, and monotremes suckle their young after hatching. The placental mammals provide unlimited time and access to energy to maximize fetal development.

The key functions that appear as the species evolve can be overlayed on the Mitochondrial tree proving a much more detail of the expansion of functionality.

It starts with a bacteria lipid walled, single cell with a ring of DNA. Cloroplasts evolved that could absorb sunlight. The first big branch is to plants with multiple cellulose walled cells with full DNA functionality in including Mitochondria. Mitochondria provide energy to the eukaryote cell by oxidizing sugars or fats and releasing energy as ATP. These two are responsible for the oxygen atmosphere. Mitochondrial DNA is inherited only from the mother and contains only information needed for the mitochondria to work.

Next up are the Fungi, which are the clean up crew as decomposers of protein and cellulose. The users of oxygen starts with sponges which evolved as fixed growths in the water that filtered nutrients from the flowing water. Then locomotion starts with the Jelly fish.

The next branch was very significant, Mollusks appeared with an exoskeleton and a whole body circulation of oxygen using "Hemolymph" and copper based blood. Snails and crustations evolved first and the insects evolved from crustations as pollinators of the plants that appeared around 400 M years ago. The snails evolved into squids and octopus with closed circulation of a copper containing blood, which enables oxygen to be delivered to key organs. While the octopus still used eggs, the female protects the eggs as they develop. The octopus evolved a genome as complex as humans. The DNA is 45% transposed (reorganized within the animal) a feature that has been linked to intelligence in humans. The octopus has demonstrated remarkable intelligence in problem solving and ability to self camouflage in color and texture. The octopus seems be a real "alien" intelligence on this planet with completely different design, and biochemistry.

There were no land based creatures so a huge niche was empty. Insects took over and ruled the land until the amphibians showed up. They show some amazing collective capabilities. Butterfly's evolved around 50 M years ago post KT extinction. Butterflies have the unique migration from Mexico to Alaska, travelling north over 4-5 generations each lasting 2 months using the sun as a guide, following the flowering of milkweed. They then fly south in a single 8 month generation. Bees have developed signals to show each other the direction to food. Ants are herbivores that demonstrate large scale communication and cooperative action.

https://www.nationalgeographic.com/animals/article/monarch-butterfly-migration

Lampreys were the first to evolve a closed circulation system with iron containing blood - hemoglobin. This enables oxygen to be delivered to key organs.

The vertebrates first appeared with fish such as tuna and carp, the sharks evolved keeping their eggs inside their bodies until they hatched to protect their young. The amphibians marked the transition onto land, leading to cold blooded dinosaurs. It is thought that warm blooded dinosaurs evolved to better survive the volcanic created extinctions 250 and 205 M years ago.

The dinosaur era lasted 200M years and was the cradle of most of todays species. There were a dizzying array of dinosaurs that led to birds, and reptiles. Squid and octopus evolved with remarkable intelligence. Small placental mammals first appeared.

The monotremes were the first mammals who laid eggs but suckled their young. The first placental mammals were shrew - like and small enough to be ignored by the dinosaurs. To this point all species of animals used eggs for reproduction with a limited energy supply before the fetus had to be viable. The placenta allowed much longer time for the fetus to develop with unlimited energy supply. This enabled much more complex species.

The KT meteor extinction killed off anything over 50 lbs which included all large dinosaurs. The dinosaurs that were left evolved into warm blooded birds and cold blooded reptiles.

After the KT extinction, the birds and mammals exploded to occupy all the empty niches. Of the birds, the crows emerged as intelligent tools users and makers. The mammals also rapidly evolved with great variety. Around 200 K years ago humans appeared and are now for better or worse are the dominant species.

It appears that the recipe for intelligence is a creature with locomotion, a closed circulation oxygen deliver system for key organs, and a complex gene structure that can be locally reorganized.

Match to Human DNA

Plants (18%) 1.5 B years for 82% change 18 My/%

Insects (44%) 500M years 66% 6 My/%

Birds (80%) 200 M years for 20% 10 My/%

Rodents (93%) 60 M years for 7% 9 My/% Apes (99%) 7 M years for 1% 7 My/%

Humans (100%)

It took 1.5 By for plants to evolve to Dinosaurs (80% human DNA), who then lasted for 200My. Insects have 60% human DNA. It took 60My for Shrews (93% human DNA) to evolve to Apes (99.5% human DNA). It took 7M years for Apes to evolve to Humans. The DNA differences represent a "round trip", so the mutation rate is around 20M years for 1% DNA change in gene location.

Function evolution

Metabolism

Metabolism started with bacteria and plants evolving photosynthesis that used light energy to combine carbon dioxide and water to fix carbon produce oxygen and grow the full range of biomolecules, catalyzed by enzymes.

Next digesters such as fungi evolved that use oxygen and enzymes to breakdown carbohydrates into carbon dioxide and energy using the citric acid cycle.

Animals evolved to combine these 2 steps using sugars as the energy source in the citric acid cycle to generate ATP energy and use ATP energy to grow and live.

In bio systems, energy is stored and released in the exchange between ADT "diphosphate" and ATP "triphosphate". Cyanobacteria use photosynthesis as an energy source to support replication leading to stromatolites and oxygen. This includes creating a wide range of molecules in their cells such as DNA, lipids, proteins. In photosynthesis, plants use the energy of sunlight to make ATP and then the Calvin cycle fixes carbon to create glucose, and a full range of biomolecules. There are also nitrogen fixing bacteria.

The Calvin cycle uses CO2 and energy from ATP in a process of taking a 5 carbon bi-phosphate, making two 3 carbon phosphates one of which is used and the other recycled. The key enzyme of the cycle is called RuBisCO, another bi-phosphate. After 5 cycles, the five 3 carbon phosphates are reorganized into three more of the 5 carbon bi phosphates, completing the cycle.

Plants expanded their metabolism to grow cellulose shells for huge multicellular structures, and added more efficient energy generation from chloroplasts to become prolific oxygen generators.

Fungi were the first "digesters" that could breakdown carbohydrates into heat, carbon dioxide and water. Fungi use the citric acid (Krebs) cycle to break down biomolecules and release the energy as heat. The citric acid cycle is found in species as diverse as the unicellular bacterium Escherichia coli, fungi, and huge multicellular organisms like elephants. They breath in oxygen and breath out carbon dioxide.

The citric acid energy cycle starts with citric acid (5 carbon, 3 acid ,1 ketone molecule). It gets oxidized to remove 2 carbons leaving succinic acid, (4 carbon 2 acid molecule) plus energy as ATP. The succinic acid then combines with acetyl (2 carbon 1 acid molecule) to regenerate citric acid. The acetyl molecules are peeled off glucose. Additional byproducts of the cycle are a number of bio precursors.

Fungi also fabricate new biomolecules to grow. The engine for building sequences is the ribosome that uses messenger RNA to provide the template, and the t-RNA bound to amino acids to build a peptide chain.

Animals evolve ways convert the biomolecules in plants and animals in food to glucose using their new specialized organs. They use the glucose in the citric acid (Krebs) cycle to produce usable energy in the form of ATP. Animals expanded their metabolism to include oxygen supply using blood, in using energy to trigger molecular reconfiguration in muscles, and electrical transfer in nerves and neurons, and the growth of biomolecules. These reactions combine monosaccharides to form polysaccharides, fatty acids to form triglycerides, amino acids to form proteins, and nucleotides to form nucleic acids. These processes require energy in the form of ATP molecules generated by catabolic reactions. Anabolic reactions, also called biosynthesis reactions, create new molecules that form new cells and tissues, and revitalize organs.

The first animals were all cold blooded. The evolution of warm blood enables higher metabolic rates with enhanced unloading of oxygen by hemoglobin. This relationship is helpful as metabolically-active peripheral tissues such as exercising skeletal muscle which often display supra-normal temperatures. Because of this increased temperature, oxygen unloading by hemoglobin is enhanced in these metabolically-active tissues, thus improving oxygen transport to areas which require it most.

https://courses.lumenlearning.com/suny-ap2/chapter/energy-and-heat-balance/

https://portlandpress.com/essaysbiochem/article/64/4/607/226177/Metabolism

Transport

The animals use blood to concentrate and deliver oxygen. Copper blood carries 1/4 of the oxygen as iron blood (haemoglobin), but works better at low temperature and may have less tendency to clot.

Copper blood first appeared in mollusks with open circulation throughout their body cavity.

Closed circulation with arteries and veins evolved to better deliver oxygen and nutrients to key organs in vertebrates and cephalopods like octopus.

The vertebrates then evolved with more efficient iron based blood.

Finally amphibians evolved lungs that enabled complex air breathing life.

Structure

Bacteria started with dual lipid based cell walls.

Plants added a cellulose superstructure that enabled large trees.

Exoskeletons appeared with the first mollusks that provided physical protection and a structure for load bearing and locomotion. The big limitation was that the skeleton does not grow, it must be shed and regrow for the animal to grow larger.

The evolution of vertebrates with an internal support structure started with fish and continues today. The basic bone architecture has been retained for hundreds of millions of years. The internal structure allows growth and training changes.

Reproduction

It starts with cell division in bacteria. Plants use seeds usually spread annually.

The first animals reproduced through large numbers of fertilized eggs, that were left to fend for themselves. Eggs provide a limited energy supply and when it is used the fetus must be self supporting.

An improved survival strategy appeared where eggs are protected by parents (octopus) before birth. Warm blooded animals had to keep the eggs warm as well (birds). After birth, the infants are often fed by parents until self-supporting.

Another survival strategy appeared in monotremes. After eggs are hatched, the infants are supported by mothers milk

One way to improve survival appeared when eggs were allowed to develop protected inside the mothers body, for example in sharks.

The final evolution occurred in placental mammals, where the fetus develops with unlimited energy and time, with energy supplied by the placenta inside the mother, and then is supported after birth by mothers milk.

Genes

The Mendelian gene is a basic unit of heredity and the molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and noncoding genes.[3][4][5][6]

During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. Most biological traits are under the influence of polygenes (many different genes) as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or the number of limbs, and some are not, such as blood type, the risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

The concept of gene continues to be refined For example, regulatory regions of a gene can be far removed from its coding regions, and coding regions can be split into several exons. Some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression.[9][10]

The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes. A chromosome consists of a single, very long DNA helix on which thousands of genes are encoded.[46]: 4.2 The region of the chromosome at which a particular gene is located is called its locus. The chromosomal or genomic location of a gene or any other genetic element is called a locus (plural: loci) and alternative DNA sequences at a locus are called alleles. Each locus contains one allele of a gene; however, members of a population may have different alleles at the locus, each with a slightly different gene sequence.

Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication. The length of the telomeres decreases each time the genome is replicated and has been implicated in the aging process.

All genes are associated with regulatory sequences that are required for their expression. First, genes require a promoter sequence.

Sets of three nucleotides, known as codons, each correspond to a specific amino acid.[46]: 6 The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961. There are 64 possible codons (four possible nucleotides at each of three positions, hence 43 possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms.

Alleles at a locus may be dominant or recessive; dominant alleles give rise to their corresponding phenotypes when paired with any other allele for the same trait, whereas recessive alleles give rise to their corresponding phenotype only when paired with another copy of the same allele. If you know the genotypes of the organisms, you can determine which alleles are dominant and which are recessive. For example, if the allele specifying tall stems in pea plants is dominant over the allele specifying short stems, then pea plants that inherit one tall allele from one parent and one short allele from the other parent will also have tall stems.

The error rate in eukaryotic cells can be as low as 10−8 per nucleotide per replication,[83][84] whereas for some RNA viruses it can be as high as 10−3.[85] This means that each generation, each human genome accumulates 1–2 new mutations. If it takes roughly 10 M years for a new species, and a generation lasts 10 years. There are 1-2 M DNA differences between nearest species.

The relationship between genes can be measured by comparing the sequence alignment of their DNA.[46]: 7.6 The degree of sequence similarity between homologous genes is called conserved sequence.

Jumping genes

A transposable element (TE, transposon, or jumping gene) is a nucleic acid sequence in DNA that can change its position within a genome, sometimes creating or reversing mutations and altering the cell's genetic identity and genome size. Transposition is responsible for some diseases such as Hemophilia skipping generations.

Fifty percent of the DNA in each human cell is in the form of mobile jumping genes—strands of DNA called transposable elements (TE) that have the ability to sew themselves in and out of DNA as well as move to different sections and to place copies in different sections. The mobile strands of DNA in the jumping gene can create new types of proteins, disrupt the entire genetic process and provide new sources of regulation of DNA through many kinds of RNA effects. The jumping gene can provide new epigenetic changes, as well. Previous posts noted that these jumping genes and alternative messenger RNA splicing are especially critical for the human brain and its evolution.

mRNA transposition in humans is 98% of the jumping genes, representing almost half of the entire human DNA. Recent dramatic findings show that jumping genes are very active in the brain. These SINEs and LINEs are actively altering and regulating neurons and other cells. Some of the changes have been incorporated into day-to-day functions. There is strong evidence that these jumping genes and their effects on alternative functions have been significant in the development of the human brain. This goes along with the evidence that the human brain uses the most alternative messenger RNA splicing. While these findings are still too complex to fully understand, it does appear to be part of the picture that has developed where jumping genes and cellular defense against them are crucial for evolution in general and especially so for the evolution of the human brain.

https://jonlieffmd.com/blog/jumping-genes-regulation-of-the-brain

Cell components

Bio- phosphates such as lipids, ATP, DNA, RNA, many metabolic cycle components.

Polysaccharides such as cellulose. Cellulose is an organic compound consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units.

Proteins built from combinations of 12 amino acids. Amino acids are organic compounds that contain both amino and carboxylic acid functional groups.[1] Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins.[2] Only 22 alpha amino acids appear in the genetic code

Proteins perform a vast array of functions within organisms, including enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, which form a system of scaffolding that maintains cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for metabolic use.

Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. The basic folding pattern is thought to be controlled by the grouping of hydrophobic amino acid residues, leaving the hydrophilic on the outside providing the functionality. The folding can be preserved by hydrogen bonds or crosslinks. The outward facing hydrophilic groups will ensure that the protein is water soluble. When the protein "denatures", it unfolds and becomes water insoluble.

Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes.

Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells.