A crash course in DNA, Amino Acids and Proteins – How the code of life produces the stuff that makes you and your brain

The four DNA nucleotides

The four DNA nucleotides

What is DNA?
Deoxyribonucleic Acid (DNA) is the language used for the blueprint of an organism. It is a digital code, in some ways similar to the sequence of 0s and 1s used in binary computer code. For example, in binary coding, the sequence 0-1-0-0-0-0-1-0 represents the letter “B” whereas  0-1-0-0-1-1-0-1 represents the letter “M”. DNA, on the other hand, makes use of 4 different chemicals called nucleotides, which code for a vast multitude of organic compounds which make us.

What is DNA made of? How is DNA structured?
The nucleotides in DNA are chemical compounds of carbons, nitrogens and phosphate groups. Adenine, Thymine, Guanine and Cytosine are the 4 nucleotides which comprise the DNA code abbreviated by A, T, G and C. A’s bind with T’s and G’s bind with C’s making the DNA sequence complementary. The DNA is structured in a double helix which allows a process of unravelling. Taken together, this structural arrangement, immediately indicates a mechanism for DNA’s potential for duplication and therefore heritability.

What does the DNA code produce?
The sequence of As, Ts, Gs and Cs along the DNA double helix determines which amino acid is produced, and subsequently which protein is produced in response to chemical cues and cellular messengers. For example, the DNA sequence T-A-T codes for the production of the amino acid Tyrosine and T-G-G codes for the amino acid Tryptophan. Amino acids are biological compounds composed of carbon, hydrogen, oxygen and nitrogen. In humans there are 20 amino acids coded by various 3-letter combinations of As, Ts, Gs and Cs and are the building blocks of proteins. A linked chain of amino acids is what forms proteins.

DNA strand suspended across two pillars.

DNA strand suspended across two pillars.

What is the function of these proteins?
There are hundreds of thousands of proteins in the human body which are folded into precise 3D shapes. Proteins perform a huge array of functions in the human body. They play a major role in the scaffolding and structure of all cells. Most enzymes (biological molecules which aid biochemical reactions) are made of proteins. A few other functional roles of proteins include the formation of hair cells, muscle fibers, neurotransmitters and are the single constituents of ion channels and receptors found in nerve cells.

What is a gene? What is the genome?
A sequence of DNA which is heritable and performs a particular function, producing a particular protein, is termed a gene. There are approximately 20,500 protein coding genes in humans. The totality of genes in an organism is termed the genome. The genome is densely packed with information on how the body and its various organs and individual cells grow and function. In humans, the genome contains roughly 700mb of data weighing about 0,000,000,000,006 grams and if unravelled and stretched out, is about 2.5 metres long.

First microscopic image of double helix of DNA - Published November 2012.

First microscopic image of double helix of DNA – Published November 2012.

How is DNA packaged?
Because DNA is incredibly small and tightly bound this allows the complete DNA of the organism to be contained in each cell of your body. It is housed in the nucleus of a cell and repeatedly wrapped in a fractal like pattern allowing for its tiny footprint. The wrapping begins around molecules known as histones, together the DNA and histones make up nucleosomes. The nucleosomes are packaged into a thread and form a fibre known as chromatin. Chromatin is coiled and looped again leading to the final shapes known as chromosomes. Chromosomes are formed around the time two copies of the cells DNA are separated.

How is DNA copied among cells?
Humans, begin as a single cell – a sperm-fertilised-egg containing half the genetic information from the father and half from the mother. As development proceeds, cellular division takes place. The DNA is first duplicated in the parent cell before dividing into 2 daughter cells. These daughter cells themselves divide into 4 and so on. The DNA is duplicated through biochemical nanomachines. Helicase unwinds the DNA into two strands fast as a jet engine. One strand is copied continuously, the other needs to be copied in reverse.

How does a cell differentiate into a neuron or a cardiac cell?
Once the DNA has been copies, the cells then divide and they may subsequently differentiate into specialised cells and migrate to particular locations according to which genes in the cell are expressed. The activation or expression of genes within the cell is dependent on the chemical environment and messengers which surrounds the cell. Different cells divide at different rates, and cell death takes place to control cell number and dispose of dysfunctioning cells.

How are genes expressed?
The expression of genes, in our computer metaphor, is equivalent to the running of the code. The genes housed in the nucleus of a cell need to be interpreted for the production of proteins or functional Ribonucleic Acids (RNAs). This occurs through the processes of transcription and translation of DNA into RNA and subsequent production of proteins. RNA is chemical cousin of DNA made up of As, Us (not Ts), Gs and Cs and can be thought of as the major group of molecules involved with interpretation and communication of the primary DNA store.

DNA Transcription Process

DNA Transcription Process

Gene expression begins when a chemical signal derived inside or received from outside the cell triggers a cascade of intracellular signalling and events. The “transcription” phase of gene expression begins with “initiation”. Intracellular signalling in the form of transcription factors bind to and regulate an enzyme called DNA polymerase which itself attaches to a specific promoter region of DNA dependent on the transcription factors. Once attached “elongation” begins where the RNA polymerase complex, acts like a zipper, and slides along the DNA and unwinds the DNA making a copy of the template strand of DNA. This occurs through free-roaming As, Us, Gs and Cs which bind to the coding strand and create the messenger RNA (mRNA) in the process. As the DNA polymerase slides along the DNA, it unwinds the DNA at the front and stitches up the DNA at the back, until it reaches the specific terminating region and detaches from the DNA completing the “termination” phase. The RNA produced here, may be subject to further processing such as “splicing” where some introns (non-amino-acid coding regions of DNA) may be removed placing the exons (amino-acid coding regions of DNA) adjacent to each other.

DNA Translation Process

DNA Translation Process

Once the mRNA has been completed it travels outside the nucleolus and through a pore in the nuclear envelope where it binds with ribosomes. Ribosomes are the protein making machinery found in cells. The mRNA is fed through the ribosomes like ticker-tape and the process of “translation” begins. Free roaming transfer RNA (tRNA) are 3-letter RNA molecules which attach to the coded amino-acid. While the mRNA is being fed through the ribosome, when the correctly corresponding tRNA / amino acid complex binds to the currently processed mRNA code section, the tRNA disperses, and the amino acid is sequentially added to the linked amino acid chain forming the protein. Once the protein is made it is chaperoned to a machine where the protein is folded into a particular shape. The protein is then released into the cell and potentially transported in vesicles to its intended destination. This process is happening in billions of your cells at any given moment.

The central dogma of molecular biology
These described processes form the central dogma of molecular biology as suggested by Francis Crick in 1970. DNA replicates to make more DNA –> RNA is produced through transcription of the DNA –> RNA is translated into protein –> Proteins make us.

Conclusion
I have now explained the fundamental tenets of molecular biology. It’s remarkable how a set of signaling, encoding, decoding, manufacturing and logistic operations are able to explain our fundamental biological workings. However, these operations are special in that they take place at an unimaginably tiny scale with vast amounts of detail and depth. Perhaps the most remarkable aspect of this system is that what it assembles, has come to understand it.

I highly recommend watching these videos for a fuller and added dimension of understanding.


References and Image Sources:

What is Neuroscience?

Neuroscience is the scientific study of the nervous system. It involves investigations into the biological workings of the nervous system and how its activity produces thoughts, feelings and behaviour.

It is made up of the ‘neuro’ part of fields like:

  • Anatomy, giving rise to Neuroanatomy – study of the structure of the nervous system
  • Physiology, giving rise to Neurophysiology – study of the function of the nervous system
  • Computer Science and Artificial Intelligence giving rise to the fields of Neural Networks – using artifical neural networks, modelled on biological neural networks, to process data
  • Computational Modelling, giving rise to Computational Neuroscience – the modelling of biological neural systems
  • Psychology – study of mind using the study of behaviour gives rise to Neuropsychology – the study of neurobiology relating to specific psychological processes and behaviour
  • Medicine giving rise to Neurology – branch of medicine dealing with disorders of the nervous system
  • Zoology focusing on the nervous system enables comparison of animals nervous systems
  • Linguistics, giving rise to Neurolinguistics – studying how neural mechanisms enable comprehension, production and acquisition of language
  • Pharmacology, giving rise to Neuropharmacology – study of how drugs affect nervous system functioning at the cellular level
  • Molecular Biology, giving rise to Molecular Neuroscience – study of biochemistry and genetics related to the nervous system
  • Genetics, giving rise to Neurogenetics – study of genetics related to the development and function of the nervous system

That’s a large number of exciting interdisciplinary fields. This means, there’s a great chance, one can bridge one’s love for neuroscience, with another special area of interest.

The Most Important Thing To Study

Anything you ever learn in life occurs through a physical change in the wiring of your brain. The brain is the final processing centre of the streams of new information received through your senses. The books you read, the words you hear and the movements you make are converted into electrical signals which travel to your brain for processing.

Further, the brain has a top-down influence on learning too. Previous experiences which have shaped your brain and the current conscious state your brain is in, act to influence how new information is experienced and stored. In this sense, the brain is a true integrator of all our new knowledge.

Your creativity, reasoning, planning, debating and socialising are brain based processes too. Your motivation to study, whatever it is you wish, comes from the limbic areas of your brain – not some abstract, mythical place or entity. The decision you took to pick a particular career or area of study was carried out with your noggin.

The brain is where everything significant happens; it is the final determinant of your cares and decisions and is the main player in determining what you study and which career you choose. The brain is the tool you use to make any decision; its physiological state determines what motivates and interests you, simulates scenarios, balances pros and cons and outputs its decision. The brain decides whether you study Law, Computer Science or Spanish. However, surely there is no more interesting or beneficial thing to understand than the physical tool which determines everything meaningful about your life – the brain.

Not convinced? Other reasons Neuroscience is the most important thing to study:

1)      Neuroscience is the final frontier. Humans have mapped the earth, much of nearby space, deciphered the human genome and understood the workings of most of our biology. However, it is the most fascinating organ of ours, the brain, which remains most mysterious.

2)      Neuroscience offers huge benefits in medicine for many. Estimates suggest, over 1 in 3 people will suffer from a mental illness at one point in their lifetime. Treatments remain in their infancy and predominantly treat symptoms, not cause. Often, researchers do not fully understand why treatments which work, do. Also, dementia is on the rise with ever-increasing lifespans. By 2050, the incidents of Alzheimers are forecast to quadruple worldwide. Advances in neurological therapeutics have not kept pace with advances in some other areas of medicine.

3)      Neuroscience research helps us improve our own brains. From the non-invasive processes of changing the way we think by becoming aware of an improved way of thinking, to installing biological neuroprosthetics which may enable a ‘memory upgrade’ or a ‘pattern recognition enhancer’.

4)      Neuroscience understanding will advance Artificial Intelligence (AI) research. Understanding how we are intelligent enables us to make machines intelligent. Advancing machine intelligence has the potential to solve many of man’s problems, with machines performing many tasks for humans and speeding up human development.

5)      Understanding neuroscience, helps you understand yourself. Who are you? I would say you are a puddle of thoughts, memories, goals, feelings, sensations, cares and conscious awareness. All of these phenomena are the result of brain based physiological processes. If you understand how these work, you will understand yourself better.

6)      Any drive you have is the result of how your brain is currently wired. This, neuroscientific enquiry can help understand. Studying neuroscience may provide an avenue to look into your own drive and psych and, in the distant future, possibly tamper with it for your own good.

Hence, to spell it out, I believe neuroscience is the most important thing to study.

Your Brain Is You

Francis Crick, Co-Discoverer of DNA and Neuroscience ResearcherYour brain is what creates your reality. It receives information fed to you through your senses and forms a model of your world. It produces your perception, creates motivations and defines your personality. This biological organ is the final determinant of your loves, your wants, your desires, your sorrows, your ambition, your priorities and your entire existence. Perhaps no one sums this school of thought better than the late Francis Crick in his “Astonishing Hypothesis”.

“You, your joys and your sorrows, your memories and your ambitions, your sense of personal identity and free will, are in fact no more than the behaviour of a vast assembly of nerve cells and their associated molecules” – Francis Crick (Co-discoverer of DNA and Neuroscience Researcher)

It was a significant moment when I first fully understood and believed the concept that my brain was everything I am – my very being, my reality. Little bits of the puzzle which I had been gathering through the years were all sort of fitting together. Physical changes in brain tissue resulted in different psychological subjective experiences. That cup of coffee which elevates ones mood is not doing anything mystical when elevating your mood – it is simply increasing the activation of specific brain circuitry related to uplifting ones mood and making them talk faster. Additionally, I came across a host of evidence which showed that physical, structural changes in someone’s brain had profound affects on their personality and subjective experience of the world. Some evidence was even centuries old – the classic case of Phineas Gage having a complete personality transformation and the lose of many higher human like behaviours as a result of frontal lobe trauma. Such evidence has been backed up through brain imaging analysis with certain brain areas found to be responsible for profound characteristics, such as those thought to be uniquely human, such as moral behaviour and spirituality. Previously these were believed to be part of some abstract, and potentially supernatural phenomenon.

It meant, all I had wondered and questioned about the world, human complexity, consciousness and my reality was the result not of some mystical abstract concept, but understandable physiological processes in a biological organ, taking place on an immensely vast scale.

Questions for truth, meaning and understanding took on a different meaning. Questions like: why we’re here? What is one’s purpose? Why do we care about the things we care about? What is the most important thing to do? How can we become content? These questions were to now have radically different answers.

After stumbling upon neuroscience, together with an increased understanding of evolution, I believe one can look to scientific pursuit of these and associated fields to answer these questions. We do not have to look down the paths of religion or philosophy.  We have not found the needle, but neuroscience is the haystack.

This haystack includes: everything I think, everything I feel, everything I do is a result of trillions of meticulously arranged, enormously complex cells, harnessing a combined computing power we have not been able to replicate (at this time). And when we have developed our technology a little further, and understood the brain a lot more, we have the ability to replicate and improve brains and with that, solve many of man’s problems.

How extraordinary and valuable is that?