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A Thread on how DNA encodes the genetic code, what the genetic code does, how DNA replicates and the use of DNA can help understand human migrations and evolution
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This thread is an attempt by the author to understand the basics of DNA, its functioning and its usefulness in understanding human migrations.

Interest in understanding this was triggered while reading @tjoseph0010's book Ancient Indians.
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I am not an expert on the subject.

Please treat this thread as Notes written to understand a topic of my interest.

There may be mistakes in my understanding. I welcome information on such mistakes in the Comments.
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We know that “DNA” determines the physical characteristics of an organism as it develops from a single cell to a fully developed individual.

But what is DNA, and how does it work?
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Think of DNA as an ingenious technology for “storing” the “program” which controls the development and sustenance of the living being.

Just like a disk drive stores software for driving a computer.
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There is one more important characteristic of DNA. It can replicate itself. The new DNA produced after replication also has a complete replica of the “program” stored in the original DNA.

This self replication property of DNA is what makes the organism a “living organism”.
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Three questions.

1. What does the “program” stored in DNA control?
2. How is the program “encoded” and “stored” in DNA, and how does it work?
3. How does DNA replicate?
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1. WHAT DOES THE “PROGRAM” STORED IN DNA CONTROL?

It controls production of proteins in the cell.

Proteins are one of the most important building blocks of the body.

They are complex molecules, built by combining simpler molecules called “amino acids”.
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Assembly of amino acids into proteins is done by cell structures called “Ribosomes”.

But Ribosomes need instructions for when to start assembling a protein, which amino acid to use next, when to stop assembly.

These instructions are what are encoded in DNA.
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2. HOW IS THE PROGRAM ENCODED IN DNA AND HOW DOES IT WORK?

This is where things get really cool.

The description below is a little detailed, but is well worth your patience, if only for understanding the awesomeness of nature's scheme!
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Any “program” needs symbols to encode individual instructions of the program.

Computer software, for example, use the symbols “1” and “0” for encoding instructions which ultimately get executed by the CPU.
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The set of instructions for Ribosomes stored in DNA uses chemical “symbols” to encode individual instructions.

These symbols are based on organic molecules called “Nucleotides”.

How? Read on.
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The centre piece of a nucleotide is a “Deoxyribose sugar group”.

Its generic formula is C5 H10 O4 (5 Carbon atoms, 10 Hydrogen atoms, 4 Oxygen atoms per molecule of the sugar).
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In typical sugars the number of Oxygen atoms is half the number of Hydrogen atoms. By that yardstick, one oxygen atom is missing here.

Hence the “de-oxy”.

(Absence of one Oxygen atom is what gives flexibility to DNA, allowing it to be coiled, looped, etc.)
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On one side the Deoxyribose Sugar group described above is bonded to a “Phosphate group” (PO4).

On the other side it is bonded with an organic (carbon containing) “Base”.

Together, these three groups comprise the “Nucleotide”.
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Let us now come to the Phosphate group.

As we saw, it is bonded with the Deoxyribose sugar group of the nucleotide.

However the Phosphate group can also bond with the sugar group of another nucleotide.
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This means that two nucleotides can get connected through the Phosphate group to form a “chain” of nucleotides.

This chain is shown as a straight chain in the diagram, but it actually twists around in the shape of a helix.
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The two bonds formed by the phosphate group, one with its own sugar group and another with the sugar group in the next nucleotide, are called “phosphodiester” bonds.

In a way, these bonds are the basis of life.
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Now the third group in the nucleotide– the Base.

These bases can be of four types - Adenine (A), Guanine (G), Thymine (T) or Cytosine (C).

Depending on which base is present, there can therefore be four different types of nucleotides.
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We already know that on one side the base bonds with the Sugar group in the nucleotide.

The other side of the base can also bond, but only with another base, and that too, selectively.
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Adenine, for example, will bond only with (“pair” with) Thymine. A-T. Or T-A.

Gunanine will only pair with Cytosine. G-C. Or C-G.

So if a nucleotide chain has A at one point, it can link up with another chain which has T at the corresponding point.
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The two nucleotide chains can thus get joined, forming a stable, ladder-like structure.

However since a chain of nucleotides is not straight but twisted in a helix, when two such chains get linked they form the classic “double helix” of DNA.
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We started by saying that the four nucleotides work as symbols to encode the identity of the amino acid to be used next by the Ribosome in protein assembly.

How is this encoding achieved?
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Since each nucleotide can have one of 4 bases – A, T, G or C - the total number of permutations for a sequence of 3 successive nucleotides is 4x4x4 = 64.

These 64 permutations can thus be used to tell the Ribosome which of the 20 standard amino acids to use next.
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This group of 3 successive nucleotides is called a “Codon”.

With 64 permutations possible for the “value” of a Codon, and only 20 amino acids to be uniquely identified, some amino acids can be coded by more than one value of the Codon.
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The Ribosome also needs to be told to Start or Stop protein assembly.

Some of the 64 permutations of the value of the 3-Base Codons are used to tell the Ribosome when to start or stop protein synthesis.
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For example, Codons GCT, GCC, GCA, GCG, all code for adding amino acid Alanine.

GTT, GTC, GTA, GTG code for adding Valine.

TAA, TGA, TAG are STOP Codons, while ATG is the START Codon
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The segment of DNA containing the full sequence of nucleotides necessary to encode a complete protein is called a “Gene”.

Humans have about 20,000 – 23,000 genes.

The two strands of the double helix carry separate genes.
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DNA carrying the Genes resides in “Chromosomes” in the cell nucleus.

There can be hundreds or thousands of genes on a chromosome.

Humans have 23 pairs of Chromosomes – 23 each from the mother and the father].
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The “Genotype” (or “Genome”) is the individual's complete set of Genes - instructions on how that person’s body synthesizes proteins and thus how that body is supposed to be built and function.
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Many genes had some function earlier in evolution, but none at present. Diet, environment, illnesses may also mean that a gene is “unexpressed”- the protein it encodes is not made.

Genes which are actually expressed are what constitute our “Phenotype”.
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Now that we know how the amino acids are encoded in DNA, let us see how this information is transmitted to Ribosomes, where it is actually needed?

This is done by the process of “Transcription” and uses RNA (Ribonucleic Acid) as the “courier”.
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Like DNA, RNA is also a chain of Nucleotides. Only in place of Thymine, the base Uracil is used in RNA.

Also the sugar groups in RNA are Ribose sugars and not Deoxyribose.

RNA is not inherited but made when needed, as described below.
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When information in some DNA Codons is to be sent to a Ribosome, the corresponding segment of the DNA double helix unwinds and opens.

Using the open segment as a template, a strand of RNA forms by pairing free bases with the exposed bases.
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This complementary (because it carries bases complementary to those on the unwound DNA) strand of RNA is called “Messenger RNA (mRNA)”.

mRNA separates from DNA, leaves the nucleus, and attaches to a Ribosome in the cell.
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When mRNA reaches the Ribosome, a process of “Translation” takes place. The Ribosome therefore knows the type and sequence of amino acids as per the information brought by mRNA.
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Another, smaller type of RNA, called “Transfer RNA (tRNA)” now brings the required amino acid to the Ribosome, molecule by molecule, for the Ribosome to assemble the protein out of them.
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So this is how the instructions for protein synthesis are encoded in DNA, transmitted to the Ribosome's protein making machinery and utilised in the Ribosome to actually synthesise proteins. One last question remains:
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3. HOW DOES DNA REPLICATE
This replication is the essence of life. DNA inherited by the individual has to be copied into each new cell as the cell is created. This happens by using a procedure similar to mRNA Transcription.
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Only now the entire double helix unwinds, opens up and splits into two.

Bases on each open strand bind with complementaryp bases floating near by (A with T, G with C, etc.) leading to two new, identical double helixes.
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Billions of Base Pairs are involved in replication.

Mistakes can happen while duplicating.

A base may get wrongly paired.

Or it may get missed.

There are mechanisms for “proof reading” DNA during replication.
There are also repair mechanisms.
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Mistakes may be spontaneous, or because of environmental or medical factors. Most mistakes are corrected. They do not repeat in subsequent DNA replications.

However if a mistake does repeat in subsequent copies it is called a “Mutation”.
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A mutation is inherited by the offspring of an individual only if it affects the reproductive cells (eggs or sperm).

Mutations affecting other cells are no inherited, and affect only the descendants of that cell (e.g., some cancers).
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A mutation that goes on to later be found in a sizable number of the population, are called a “Polymorphism”.

Different blood groups among humans are an example.

However Polymorphisms rarely affect the Phenotype of the person.
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Occasionally, only one nucleotide may be affected by a mutation in the reproductive cells.

If later this mutation becomes a polymorphism (found in >1% of the population) then a new “Haplogroup” is said to have emerged.
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By examining the DNA of contemporary members of that Haplogroup it is possible to find out how long back that mutation first occurred.

This then becomes an important modern tool for understanding human evolution and population migrations.
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Ref:
1. msdmanuals.com
2. ncbi.nlm.nih.gov
3. nature.com

-- ENDS --

-- Thank you --
As alert reader @BindalShradha pointed out, the name of @tjoseph0010 's book is Early Indians and not Ancient Indians.

Sorry about the error.

And thanks, @BindalShradha.
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