Saturday, December 3, 2022

Your genetic blueprint: Genome, chromosomes, DNA, and genes

Your genome is unique to you. It is made up of chromosome that come from your father and mother. The chromosomal DNA is made up of genes, which are coded with base–pairs.

Executive Summary

Your genome is the entire set of genetic instructions each of your cells has. It tells them how to make various proteins, how to function, and in general, how to respond to various life situations.

Your genome contains your chromosomes, which have your DNA. Your DNA molecule is made up of genes and some other matter. Genes, in turn, are made of 4 simple compounds. By using various permutations and combinations of these compounds, your genome tells all of your cells everything they need to know about how to produce proteins.

Read the full article for a fascinating journey into this master blueprint of your life.

Our bodies are intricate, refined by billions of trials and errors by Mother Nature. Yet, all that millions of years of work is boiled down into a long, 6-billion alphabet script: your Genome.

This article will give you some insight into this vast topic. This delicate blueprint can easily get damaged by an incorrect lifestyle. That can lead to early ageing or cancer. So, read on.

Our genome

Your genome means your entire genetic material, the complete blueprint. It is unique to you. Every single cell in your body has a copy of it. I have a different genome, of similar length as yours. And, every single cell of my body has a copy of it.

Each of us has this very long genetic recipe. It is the master blueprint, with instructions for all types of cells. Each cell retains a full copy, but executes only the part that is relevant to it.

Differences in genomes

As per a 2012 article in the journal Nature, nearly 99.9% of the genome, is identical to you and me. That is what makes us humans. We have similar locations for eyes and feet. And we grow to similar heights.

The remaining 0.1% makes us all different. It gives us different physical attributes, such as height and hair colour. It also leads to differences in something called receptors in our cells. That changes our disposition to some diseases, causing one more vulnerable to heart disease, and another to diabetes.

We share an even lesser percentage of the blueprint with a giraffe. It has eyes and a mouth like us. But something in its blueprint tells its cells that it should have a loooooong neck.

There is a still lesser percentage of blueprints that we share with earthworms. They breathe, eat, and move around like us. But, they don’t have legs or shoulders like us.

Our closest cousins are chimpanzees. Cousins, as in ‘related living beings on the evolution tree’! A 2005 article in the journal Genome Research showed that chimpanzees share about 96% of our genetic blueprint.

You tell me your 6 billion alphabet genome and, theoretically, I can ‘construct’ you physically. Well, ‘theoretically’ because we still don’t know what makes you alive and functioning. But, I can surely know if your eyes would be hazel in colour, whether your hair would be curly, and if you would have a long nose.

That blueprint, that genome, of yours is the ‘You’.

How is the genome stored?

There is no central place in the clouds for storing your genome. The genome thing happened before modern ‘cloud computing’ took form.

So, each cell in your body has a copy of it — the full 6 billion character long. How inefficient! It is like all school children having just one textbook for everything that they will ever need to learn in their life. The kids just need to refer to the appropriate chapter each time.

This genome is stored inside the nucleus of each cell in your body. One can predict your life’s story knowing your genome.

What can the genome predict?

Of course, the genome does not know that one day, you will slip and fall on a staircase, breaking a wristbone. But, it knows how your body will go about repairing that fracture.

The genome does not know the environment around you, whether a car will hit you, or you will eat a macaroon tomorrow. But, it knows how your body will respond to each of those situations.

In that sense, your genome is not your destiny. It decides your disposition, which in turn can decide the fate of your health.

Our chromosomes

Our genome is made up of chromosomes. 46 of them, to be precise.

A chromosome is nothing but a very, very long molecule wound around a protein base in a coil.

Parental genetic material

The chromosomes come in pairs—23 of them. Each pair has one chromosome that comes from your biological father. And the other chromosome comes from your mother. That is why it is said that you carry the genetic imprint of your parents.

The chromosomes of a pair contain similar instructions. The father chromosome will have instructions on what your cells should do and so does the mother chromosome. As a result, in each cell, you carry a 3–billion alphabet instruction manual from your dad, and another 3–billion character one from your mom.

Both the chromosomes in a pair are almost the same length. While they are very long — 130 million characters long —, they contain instructions meant for similar purposes at almost the exact same location on the two strands.

Depending on the type of instructions, environmental factors, and certain other controlling instructions, your cells listen to one of the two sets of instructions. Happens in real life, too? Whom did you listen to — dad or mom — when they disagreed?

The entire science of genetics revolves around how different cells listen to one or the other sets of instructions, and how we can make them listen to something else.

Thus, inside each cell nucleus, there are 23 pairs of chromosomes. These are 23 pairs of ‘books’ that contain your life’s entire recipe, with different aspects neatly stored in different books.

Almost like having a history encyclopedia, a geography encyclopedia, etc. To make that more dramatic, you have two encyclopedias for everything. For example, dad’s history encyclopedia and mom’s history encyclopedia.

Large parts of those encyclopedias say the same thing, such as Julius Caesar ruled the Roman Empire. But, they don’t agree on some parts, such as whether Cleopatra committed suicide. Now, whom do you listen to? That is all governed by the science of genetics.

Each of these ‘books’ is 130 million alphabets long, on average. Some are longer; some shorter.

For the sake of completeness, the chromosomes in the 23rd pair are called the sex chromosomes. They determine your gender. They are much smaller in length than those in the other 22 pairs of chromosomes.

What makes you genetically different from your siblings?

Your father contributes 23 of his 46 chromosomes to you. And, so does your mother. But, the same is true for your brothers and sisters, too. Even they have the same father and mother. So, why aren’t you genetically identical to your siblings?

Your father had 46 chromosomes. And, when you were conceived, 23 chromosomes came from your father? But, which 23 of his 46?

The sperm, which comes from the father, has those 23 chromosomes. The egg, which comes from the mother, has 23 chromosomes.

Out of the 6–billion alphabet scripts of your father’s genome, some 3 billion alphabets were randomly selected (though based on some basic rules) for the 23 chromosomes in the sperm. Ditto for your mother’s egg.

Thus, your 6–billion character script was constructed only from the alphabet in your parents’ scripts. But, those alphabets were chosen randomly. So, your siblings will have a different script, though the two original ‘books’ were the same — your father’s and mother’s genomes.

But why siblings look similar?

The sperm and the egg do not contain randomly selected alphabets from the two scripts. They contain randomly selected ‘chapters’, or whatever equivalent of a chapter is, from the two genome ‘books’, figuratively.

That is why your siblings look different from you, but also look somewhat similar. Given that there are thousands of possible chapters in those long books, it is impossible to have an identical genetic makeup to your siblings.

It turns out, statistically, you share about 50% genetic makeup with your siblings. This should be logical. For selecting the genetic material, randomness selects either your grandpa matter or your grandma matter in your father’s sperm and in your mother’s egg.

Unless you have an identical twin, that is.

Identical twins

In identical twins, the entire 6 billion character script is exactly the same.

First, a baby’s genome is created the normal way. Then, it splits into two identical copies, and one each goes to you and your identical twin. This happens when you two are really small, even before you become about 1 cell in size each. 🙂

That is why identical twins look very similar. Whatever differences you see in them are all environmentally driven.

Their genetic fate is identical as they begin life. But, as destiny hands them different circumstances, they evolve slightly differently. And, the difference grows, as they live more and more years of life.

Our DNA

Chromosomes are long strands of molecules. All these molecules taken together over 46 chromosomes are called our DNA. The molecules of each chromosome are wrapped around a protein called Histone. Thus, each chromosome has a part of DNA molecule and some protein base, around which the molecule is wound in a coil shape.

Rotating helix of a DNA
GIF image credit: brian0918, from Wikimedia. Public Domain

On the left, is a beautiful GIF animation of what the helical structure of a DNA strand looks like. It is about 12 ‘alphabets’ long in the animation.

Our full DNA is, obviously, 6-billion alphabets long, spread over 46 chromosomes. Thus, it is nearly 500 million times longer than this. So, kindly don’t ask me for an image of DNA. 🙂 When fully stretched, our DNA is 2 meter long.

And, each chromosome is 4 cm long, on average. However, it is tightly coiled and wound around the histone protein. This helps them fit inside a 4–6 µm space, which is the size of a typical cell nucleus. That is a 1,000 times reduction in length!

What does DNA look like?

DNA is all our chromosomes taken together. And different chromosomes have different shapes. So, let us restrict ourselves to just understanding how densely packed our DNA is. We will not worry about the exact shape.

Take a 40-meter-long string, made of some really thin material. Tie one end somewhere in an open ground. Start twisting the other end. At some point, the string will curl into a coil.

Keep twisting it some more. You will notice that it is becoming smaller in length. Eventually, the coil will get coiled onto itself. Now, you have a coil of a coil.

Keep twisting the string. Now, you have a pathetically messed up coil. This is a coil, of a coil, of a coil.

By now, you have missed your meal, and your family is debating your sanity. But, keep twisting it further. It will keep coiling on to itself more and more. The twisted string will be real short now, perhaps a meter long. Keep going.

Assuming the string material was really thin and sturdy, one day, you will get the string down to 4 millimeters in length. By now, you have missed many dinners. But, you have in front of you a 1,000 times larger replica of what your chromosome looks like.

Not very pretty, I agree. But, it works. Remember what the theory of evolution says:

It is the survival of the fittest, not of the prettiest, nor of the strongest, nor even of the most capable.

— Charles Darwin

Ok, Darwin did not say the whole thing. But, you get the point.

6 billion alphabets. 23 pairs of books, with an average of 130 million alphabets each. A script, literally having more twists and turns than all Hollywood suspense movies ever released, combined.

Our genes

Each chromosome has between 200 to 2,000 genes (except Y-chromosome, which has 50 genes), with an average of 900 genes.

Each gene is an instruction template for certain cells to manufacture a specific protein. Using an intricate process, our cells make proteins using these recipes.

Protein synthesis

The cells use certain organic matter called amino acids as raw material. There are 22 different amino acids. Then, using the recipe, the cells string those amino acids to form something called polypeptides. These polypeptides are further combined in the body to form thousands of proteins.

Thus, each recipe is the sequence in which amino acids are to be strung, and the total length of that string. Each gene is this sequence list.

If you add up the genes on half of our DNA (23 strands), we have 21,000 genes. Of course, to be precise, the 23 dad strands have 21,000 dad genes and 23 mom strands have some other 21,000 mom genes.

So, you can roughly say that our bodies have instructions for making 21,000 proteins. Other proteins have to be made in the body from these starting proteins. Or, eaten. Or, recombined from amino acids extracted from the proteins we eat.

Now, something more. Here is a 2005 article in the journal Science that says that nearly 98.5% part of our DNA contains something called non-coding RNA genes, regulatory DNA sequences, and sequences for which as yet no function has been determined.

The genes that help our cells make protein are called protein-coding genes, which are about 1.5% of the total matter on our DNA.

Thus, our 46 books have 3 million chapters altogether. Out of these, nearly 2.96 million chapters don’t contain instructions for making proteins.

Redundancy in nature

Imagine 2.96 million chapters whose purpose we don’t know, yet. And, each of our trillions of cells has a copy of all of them. Perhaps, you are beginning to marvel less at the beauty of nature. So much wastage.

In engineering, we have a term for it: The brute force method. Mother nature has simply tried quintillions (1 quintillion = 1 million, million, million, million, million; so, obviously, I have not counted them) of permutations and combinations. No wonder this brute force approach has got it right eventually. Or, somewhat right. 🙂

Millions of years of evolution have made trillions and trillions of mistakes, making organisms extinct left, right, and centre. And, all that is left out of that trial and error is, well, you. So, give yourself a pat on your back.

And, that traffic jam yesterday? Didn’t you ask in sheer exasperation at the end of it, “Why me?” Well, now you know. Because you are the lucky one, perfected from those quintillion tries.

Genes common to all humans

Out of those active 21,000 genes, 99% or about 20,800 genes, are identical in all human beings. So, they make identical proteins that are common to all of us. For example, insulin, albumin, and hemoglobin are proteins common to all our bodies.

To repeat, we have 42,000 genes in each of our cells — 21,000 dad genes, and 21,000 mom genes. But, since only one of the two genes, dad’s or mom’s, is active in us, we are referring to 21,000 as the number of genes we have.

Of course, this is just a rough example. Our body does not make hemoglobin from genes, for example. The heme part is synthesized inside a cell’s mitochondria and the globin part is a protein is synthesized by the body separately, but not directly from a gene.

As an aside, that is one reason you don’t want to blindly keep eating iron-rich food to get your hemoglobin levels up. If you are deficient in protein, how will you get the globin component? In that case, your hemoglobin will not rise, in spite of having adequate iron in the body.

Genes that are different in humans

The remaining 200–odd proteins, which our cells make, are different in each of us. For example, our eye colours are different. Certain gene helps in making eye colour-related proteins. That gene is different in different people.

Apologies again. There are multiple genes that together determine your eye colour, not just one gene. But, you get the point.

Thus, all of us have 20,800 chapters out of our 21,000 chapter blueprint of life the same. How boring! The only difference between you and me is, then, the 200 chapters. The real thriller of each of our lives just differs in 200 chapters.

The humdinger: the remaining 2.9996 million chapters that each of your ten trillion cells have, contain the same or irrelevantly different, information compared to the similar 2.9996 million chapters in each of my ten trillion cells.

Imagine the sheer excess storage. And, the utter redundancy of lugging those coils around in our bodies. But, it has got us where we are today.

Each of those extra alphabets that you lug around in each cell weighs about 3 femtograms or 3 x 10-15 g. Imagine how light we would be without that extra weight! 🙂

The real difference between you and the rest of the world

If you have a sharp eye, you must have noted the following:

At the start of the article, I said that 0.1% of our genetic material differs between humans. Now, I am saying that 200 genes out of 1.5 million gene–like chapters on DNA differ in humans, which is 0.013%. Which percentage is correct?

Frankly, don’t look for precise numbers. Mankind still does not fully understand what precise purpose each part of our genetic code serves.

So, some fragments of our genome, which are not counted as genes, maybe differ in different people. Just remember the concept — your chromosomes have only about 200 genes that are different from other people on earth.

And, that is the maximum number. Often, it will be much less as some genes will be the same in unrelated people. You may have brown eyes and curly hair. And, someone else may have brown eyes and straight hair.

So, all that sets you apart from the rest of the 7 billion people on this planet is a unique combination of 200 different proteins that your cells make.

None of those 200 proteins are unique to you. But, their combination in you is unique. You are the only one, who was ever born with that combination. Unless you have an identical twin, that is.

Our nucleotides

Each gene is made up of anything between a few hundred to 2 million of something called nucleotides. An average gene should be about 2,000 nucleotides, or alphabets, long.

These are the most basic blocks of our genetic material. They are the alphabets that write our life’s scripts. And, there are just 4 of them.

The ‘alphabets’ are Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). So, you can say that our entire genetic code is written with 4 characters.

Thus, each gene is a 2,000 character–long ‘chapter’, on an average. What do you expect with just 4 alphabets? 🙂

A typical gene, which is a recipe for making a specific protein, may look like this:
A T T G C T A C G ………. 2,000 alphabets ……. A G C T A C

What an exciting chapter!

Double helix

For some interesting reasons, these alphabets (nucleotides) have a further redundancy. Yes, more redundancy. But not a wasteful one, this time.

Instead of a single DNA molecule strand, there are two strands next to each other. So, the DNA helix, or coil, is actually a double helix.

The two helixes (or, is it helices?) are copies of each other, except for one interesting twist. Pun intended!

The other, duplicate helix does not have the same alphabet in the same place. In fact, it has a complementary alphabet. Alphabet (nucleotide) A is always, always paired with a T. Similarly, a C is always, always paired with a G.

Base pairs

A and T form a pair. So do C and G. Wherever one helix has an A, the other helix will have a T. And vice versa. Ditto for C and G.

Thus, these single alphabets are called base pairs. At any location, they appear as pairs: one alphabet on one helix, and the complementary, or paired, alphabet on the other helix.

So, if one helix is showing a gene as A T T G C…, the other helix will show it as T A A C G…

Recreating a broken DNA

This redundancy is useful because if by any error or accident, one strand of your DNA gets damaged, your body can recreate it from the other strand.

For example, take a hypothetical DNA strand A T G T C G A A G. In it, if the ‘characters’ from 2 to 5 are lost due to some environmental stress, the damaged strand would look like A • • • • G A A G.

Now, nature does not have to know what part was lost. It simply has to take the other DNA strand, which looks like T A C A G C T T C. And, throw a soup, or a mixture, of alphabets A, T, C, and G, at that complementary strand.

At the locations where the first strand is broken, the alphabets T, G, T, and C, respectively, would simply stick to the exposed part of the complementary strand, viz., — A C A G —. And, the broken DNA strand would be repaired back to its original state.

Alphabets in pairs

Think about it! There are not too many molecules in the organic world that would attract the same molecules to them. So, it is hard to find molecular alphabets such as A, T, G, and C, which can be rebuilt from the other strand.

However, there are plenty of molecules that attract some other molecules and bind to them. So, it helps to have the alphabets of the genetic code in complementary pairs.

Simply brilliant! Our Mother Nature deserves a Nobel Prize for that. In fact, it did get one. In 1962, Dr. Crick, Dr. Watson, and Dr. Wilkins were awarded the Nobel Prize in Medicine for discovering the molecular structure of DNA and how it helps transfer information in living beings.

Now, just to bring to your notice: Each of the 6 billion alphabets in our DNA is actually a duplicate. That is, each alphabet on our DNA has a complementary alphabet on the second helix of the DNA strand, we have 12 billion characters in our genetic code, and not 6 billion, as we have discussed all along.

Summary

Thus, in summary, our genetic material has 2 x 3 billion base pairs. And, each cell has these same 2 x 3 billion pairs. You will probably have 2 x 400,000 of these different from mine, while all the rest may be identical, or redundant, in us humans. These, 800,000 alphabets, or base pairs, written in on about 400 genes, or chapters, will separate you from the rest of the 7 billion of us.

In conclusion

Your genome is the entire set of genetic instructions each of your cells has. It tells them how to make various proteins, how to function, and in general, how to respond to various life situations.

Your genome contains your chromosomes, which have your DNA. Your DNA molecule is made up of genes and some other matter. Genes, in turn, are made up of 4 simple compounds. By using various permutations and combinations of these alphabets, your genome tells each of your cells everything they need to know about how to work.

Edited for technical accuracy: Mr. Arvind Pendse, Retd. Scientist, National Chemical Laboratory, India

First published on: 27th July 2019
Image credit: Gerd Altmann from Pixabay
Last updated on: 3rd May 2022

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