Part I: Water
Part II: Base Pairing
Part III: Salt, pH and Temperature
Part IV: Proteins and RNA
I told Kastle awhile ago I could write a post explaining what DNA was. This is an attempt at explaining the basics.
DNA Part I: The Most Important Structural Element of DNA
Here is a molecular model of DNA. It has a deoxyribose sugar and phosphate backbone and nitrogenous bases. What is missing from this picture?
Think about the structure of the Eiffel Tower. What do you think when you see this?
Our tremendous size biases us. When we think about structures, we often think about freestanding structures in air. Most people don’t think of the air around and inside the Eiffel Tower as part of the Eiffel Tower. Indeed, if the Eiffel Tower was moved to the Moon, it would pretty much look the same.
That is not the case at the molecular level. The most important structural element of DNA is water. Part I of this will be about water, hydrophilic (“water loving”) molecules and hydrophobic (“water hating”) molecules.
The Concept of Electronegativity
In molecules, different atoms have different affinities for the negatively charged electrons. The relative affinity for electrons is called “electronegativity.” Here is a chart of electronegativity:
Oxygen is much more electronegative than hydrogen (3.5 v 2.1). That means water is a polar molecule: the hydrogen side of a water molecule is more positive than the molecule as a whole, and the oxygen side is more negatively charged than the molecule as a whole.
This property allows it to dissolve charged ions such as salt (the green ones are negative chloride ions and the white ones are positive sodium ions):
It also allows it to dissolve other highly polar molecules like the sugars ribose and deoxyribose. Deoxyribose has carbons, oxygens and hydrogens. The oxygen atoms (3.5 electronegativity) are partially negative and the hydrogen (2.1 electronegativity) and carbon (2.5 electronegativity) atoms bonded to the oxygens are partially positive.
Another highly polar molecule is phosphate. Oxygen is partially negative and phosphate is partially positive because oxygen is more electronegative than phosphorus (3.5 v 2.2):
Non-polar molecules lack strong electronegativity differences within the molecules. “oil and water don’t mix.” Here is an oil, a kind of triglyceride:
Here are the nitrogenous bases of DNA:
They are a kind of compound called “aromatic molecules.” No, those don’t necessarily smell, but what you need to know for this is they are all highly hydrophobic. There are also a few little polar groups (see the oxygens and nitrogens?) on those hydrophobic molecules. Therefore, they are called “amphiphilic molecules” meaning they have both hydrophilic and hydrophobic parts. That will become important in a later post when I talk about “base pairing.” For now, don’t worry about those.
Amphiphilic molecules behave in a funny way in water. They self-organize so the hydrophobic parts stay away from the water and the hydrophilic parts face the water. Here are detergent molecules in a “micelle”:
^The yellow strands are carbons and hydrogens and the red heads are phosphates.
Here is a drawing of a cell membrane:
Notice how the hydrogen/carbon chains stay out of the water while the phosphate heads stay in the water.
DNA Is All About Excluding Water
Here is the structure of DNA again:
It cannot form a micelle. However, it can have the bases “stack” on each other and pair up to exclude the water and have the hydrophilic sugar and phosphate backbone stay in the water. Here is a space filling model that shows there is no room for water on the inside of DNA:
Not very visually appealing, huh? Here is a someone more schematic picture:
Every property of DNA follows from water: hydrophilic backbone and hydrophobic bases. There are other minor details which I will be covering in the next few posts.