DNA Structure

Discovery history

The very beginning of DNA discovery starts in the 1860s when Miescher discovered nucleic acids.  He called them nuclein because he isolated them from the nucleusThe control center of the cell that contains DNA and directs cellular activities..  Various experiments using bacteria further clarified knowledge about DNA.  Chargaff’s rules for base pairingThe specific hydrogen bonding between complementary bases (A-T, C-G in DNA). are based on his findings. He discovered that the number of adenineA purine nitrogenous base found in DNA and RNA, pairs with thymine (DNA) or uracil (RNA). nitrogenous bases always equaled the number of thymine nitrogenous bases. The same pairing occurred for guanine and cytosineA pyrimidine nitrogenous base that pairs with guanine in DNA and RNA.. 

My favorite story of DNA discovery is the final push to discovery of the shape of DNA in the 1950s. 

Watson and Crick experimented with physical models. They manipulated the components of DNA until they came up with the double helixThe twisted-ladder structure of DNA molecules. structure.  Picture 51, taken by Rosalind Franklin, helped their conclusions by providing a top down picture of the double helix.  Think of looking down a spiral staircase from the top.  Strangely, Rosalind Franklin died of cancer.  She shoulda worn her lead apron.

Nucleic Acids

Many terms that refer to DNA that get confusing for students. Back in chapter 2, we loosely defined the term nucleic acids. We included two types of nucleic acids. One has a deoxyribose sugar and is called DNA. The other has a riboseA five-carbon sugar found in RNA. sugar and is called RNA.  I have taught from other books. These books consider the molecule ATPThe energy currency of cells used for muscle contraction. to be a nucleic acidA substance that releases hydrogen ions (H⁺) in solution.. This is because it loosely meets the definition. 

To be classified as a nucleic acid, a molecule must consist of building blocks called nucleotidesThe building blocks of nucleic acids.. These are pictured here as little Lego pieces. RNA has only one stack of Lego pieces. DNA has 2 stacks of Lego pieces. They are bonded together by little black dots.  Kidding.  DNA has 2 strands of nucleotides that are bonded together by hydrogen bondsWeak attractions between hydrogen and electronegative atoms like oxygen or nitrogen..

What’s in a Nucleotide?

The nucleotides, the individual Lego pieces from the previous slide, also have their own three components. There is a phosphate group, which is very common in your body. There is also a sugar, which is also common. Lastly, there is a nitrogenous baseA component of nucleotides that includes adenine, guanine, cytosine, thymine (DNA), and uracil (RNA), common in everything you eat.  You may be familiar with these nitrogenous bases. You can correlate them to the AGGTCA sequence of letters associated with DNA.  Like the movie GATTACA. 

Nitrogenous Bases

There are 5 nitrogenous bases that are divided into 2 major groups called pyrimidines and purines. These groups separate the nitrogenous bases by shape.  These shapes allow the purines and pyrimidines to bond together with those hydrogen bonds that bind the DNA strands together.  The shapes of these moleculesGroups of atoms bonded together. are very specific. The purineA type of nitrogenous base with a two-ring structure (adenine and guanine). guanine will only form a hydrogen bond with the pyrimidines cytosine. Adenine will bond with both thymine and uracil.   Thymine is only found in a DNA molecule. It is crucial to note this point. On the other hand, uracil is only found in an RNA molecule.

Double helix

Let’s go back to our analogy with the Legos for a moment. We have one molecule of DNA with 2 strands of nucleotides that are bonded together by hydrogen bond. Let’s extend that analogy and think of a ladder.  The rails of the ladder are where you would put your hands. They are composed of the sugars and the phosphates in each of the individual nucleotides. The rungs of the ladder are where you would put your feet. These rungs are made up of bonded nitrogenous bases of the nucleotides. 

The specific nature of the bonding of the strands causes this structure to twist. It does not stay as a ladder. Instead, it forms a structure that is known as a double Helix.  The rails of the ladder are blue and yellow showing you the alternating sugar phosphate backbone. The rungs of the ladder are the nitrogenous bases paired with hydrogen bond. Why the hydrogen bonds?  They are weak.  This makes the DNA easy to break apart and reform in order to duplicate it or make proteinsLarge molecules made of amino acids with various functions in the body. from it.

DNA Packaging

In this picture here, we have a chromosome on the bottom which is a condensed structure of DNA.  DNA in this condensed form is tightly packed into a chromosome. This makes the sequence on the DNA inaccessible for replication or for making proteins.  It’s too tightly packed.  I once had a video that said that a molecule of DNA can be as long a 9 meters.  How, then can 46 of them fit inside the nucleus of one cell? 

Your DNA exists in your nucleiClusters of neurons in the CNS responsible for processing information. as these condensed, space saving structures.  To make these structures, the DNA winds around proteins called histones to make a combined structure called a nucleosome.  This is like rolling instead of folding your cloths to get them in a suitcase. Rolling condenses them more than folding, supposedly.  You can see a histone and its four parts here in the inset on the right.  Note how the DNA double helix is wrapping around these histones.  Histones complicated things in the beginning of DNA discovery.  Histones and DNA were isolated from nuclei. The question was: which one of these things was being passed down? Was it the nucleic acid or the protein?

This picture tries to show you too much in one shot, but there is something important that it shows you.  It shows a condensed chromosome and an unwound chromosome.  When a cell goes to divide, all the DNA will be condensed into chromosomes.  When a cell is just hanging out, it makes its proteins. The DNA is dispersed, allowing enzymesProteins that speed up chemical reactions in the body. to access the protein recipes.

Condensed Chromosome Anatomy

If I were to open the nucleus of one of your cellsThe basic structural and functional units of life. that is actively dividing, I would see DNA strands. These strings are called chromosomes.  In factA statement based on direct observation that is repeatedly confirmed., I would see 46 of these stringy things, or 23 pairs of these stringy things.  The pairs have the same length, but they also have the same placement of the centromereThe region of a chromosome where sister chromatids attach and spindle fibers bind..  A centromere is like the waist of a chromosome.  When a chromosome duplicates itself, it leaves the identical twin attached to itself at the centromere.  When duplicated, it’s like each of your chromosomes is a conjoined twin connected at the centromere. There are attachment points for separating the sister chromatids called kinetochores.