Basic Science #5: Discovery of DNA Structure

Good friends of mine were trying to understand chemistry and they asked me this question: How can you see molecules?  How do they know about atoms?
Here is my answer on many levels. 

Lets start with this early x-ray picture of the DNA molecule next to Rosalind Franklin who succeeded in producing it:

The steps leading to this image were first and foremost the basic curiosity: We want to know!  Then those curious people start looking and finding things out step by step. 

Discoveries in science are always based on previous knowledge.   Most of the time it takes a team of people cooperating with their shared curiosity and intelligence to figure out the most astounding facts of nature. In the case of DNA there were the previous methods to isolate the genetic material from Bacteria.  It was known how to label it with radioactive material.  The newest technology was x-ray crystallography.  Rosalind Franklin was a bright researcher trained in this technique.  She produced these now famous images and was just about to decipher them. After working for years with the unsafe radiation she developed ovarian cancer and died before she could get any recognition.
An additional level in all this is the personalities of these bright researchers.  Often we find that the most studious hard working researcher is looked over and someone new with a strong ego takes over and takes all the credit.  James Watson an American molecular
biologist and Francis Crick the Physicist from UK were working on this project at the same time.  They got hold of Rosalind Franklin's x-ray images and worked together to discover the detailed structure of the DNA double helix:



This was not a simple task.  It involved the knowledge that this genetic material includes the four nucleic bases.  These four basic structures are found in the nucleus of the bacteria cell, and that is why they are named nucleic bases.  The initials are A, G, C, T. 
You will find these letters in DNA sequences.

They also knew that the DNA material includes the sugar ribose with one less oxygen (deoxyribose) and phosphate.

They had to build the model of these bases and figure out the structure so that it will fit the x-ray image. James Watson and Francis Crick were the firsts to publish this result and win the Nobel Prize.  The Nobel Prize in Physiology or Medicine 1962 was awarded jointly to Francis Harry Compton Crick, James Dewey Watson and Maurice Hugh Frederick Wilkins "for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material".
The most amazing part of this research is that this structure predicts that every 3 nucleic bases will be a code for one amino acid.  This is how the genetic material in the cell nucleus is translated to proteins in the cell.  The proteins that are part of the structure of the cell and have many metabolic activities.
This discovery has connected chemistry and biology!  
Fifty years later Francis Crick predicted that the next breakthrough in science will be the connection between bilogy and behavior!

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Basic Science #4: Amino acids as building blocks for proteins.

Amino acids are the basic building blocks of proteins.  Proteins can be very complex, up to thousands of amino acids attached to each other in a chain to make a protein.  Here is a simple amino acid: Alanine.  As I showed you it has an amino group NH₂ which is basic (blue) in pH and a carboxyl group COOH which is acidic (red.)

Two amino acids are connected to each other in a peptide bond.  The next amino acid will be connected to the previous peptide via the carboxyl group, so that each chain of amino acids bound together will have an amino end and a carboxyl end.

To understand the complexity of proteins I will bring here a table of the 20 amino acids in life.  The names of the acids were given by the Greeks historically according to their source (like Serine was isolated from silk) or their color (Leucine for white.)  But it is more important to understand their diversity in structure. The position of the amino acid in the protein will determine how the protein will interact with its surroundings and what will be its activity. 

To envision this check the following table.  The amino acids are categorized in 5 groups.  First by their interaction with water: a hydrophilic amino acid  will be in a water environment and a hydrophobic amino acid (turquoise) will be in a fat environment as a cell membrane of a fat cell.

Next the hydrophilic amino acids can be polar but uncharged (grey.) They can be basic with two amino groups (blue) or acidic with two carboxyl groups (red.)

The order of the amino acids in the chain is just the primary structure of the protein.

The next level of complexity is the secondary structure, the way this amino acid chain twists and turns, as a helix.  Sometimes to the right, sometimes to the left and this is called a and b helix.

The next level is the tertiary structure, this is caused by bridges of bonds between two different parts of the protein.  These bridges are made with di-sulfide bonds between two amino acids that contain sulfur: Cysteines. 

There is a Quaternary structure as well by combining a whole folded protein with another similar (or different) sub-unit to make a dimer, a trimer and so on.  All the different possible combinations exist.  This is one way to show how we have such an amazing beautiful diversity in life!

Why are you Still Alive?

I heard about this article published by the Readers Digest last November.  This should interest all of us as we are hearing about the zika virus affecting the babies born to women infected by the virus.
We should remember that just one hundred fifty years ago life expectancy in humans was no longer than forty years.  People did not always live to see their grandchildren, let alone great grandchildren.  These days people in the developed world live into their eighties and nineties and are still healthy and active.
It is important to understand the progress that brought about this long life expectancy.  On the top of the list is the fact that we learned to cure bacterial and viral diseases.  Smallpox was a viral disease that killed more people than any other illness or factor.

Smallpox-1894

We also managed to abolish disease as bacterial TB and cholera which causes loss of water.
Next on the list is the fact that we learned to use soap to clean up and mainly wash our hands.  We learned to avoid touching bacteria and transferring them to anything we touch.
The houses in which we live protect us from the weather, rain storms, winds and heat.  Modern houses are well  air conditioned unlike the  poor huts in the third world.
At last we should appreciate the clean running water in our modern homes.  This is thanks to the governments who provide this service of providing running water.  And note where the government of Michigan failed its citizens in Flint.  It is not taken for granted that governments can always be trusted.
It is important to remember what is keeping us alive and healthy for so long!