Phosphodiester what? The biochemistry of the DNA backbone

Picture it: You're sitting in class and you keep hearing some stuff about phopsphodiester bonds... um... what? You know it forms links in the DNA deoxyribose backbone but... wait, what? If you have not had much chemistry start reading here; if you've taken organic chem feel free to skip ahead. Let's take it from the top.

You always hear that all life is organic... Wait, Like Organic Chemistry? Yup! Organic refers to carbon. So now that we know we're talking about carbon bonds here, what do they look like? Well, like this:

See how the red dots on the hydrogen atoms become shared with carbon atoms in pairs? These are your basic covalent bonds; or bonds that share electrons between atoms. Take it from me, after you have enough chemistry you get real tired of drawing all of those dots real quick so we can just draw little lines instead; it means the same exact thing: covalent bond.

Now, carbon bonds can make a few different shapes depending on the number and type of atoms. Let's take a look at C6H12 (6 carbon atoms and 12 hydrogen atoms). It can form a linear structure or what is called a cyclic structure, also called a ring structure. Take a look:

Notice the double line in the straight structure? That is called a double bond. That means that there are extra electrons shared there. It is a super strong bond. C6H12 can look exactly like either of these two things. Now that we know what a cyclohexane (the ring structure of C6H12) structure looks like, what could cyclopentane look like? Like this:

Pretty simple right? Cyclo means ring and pent means 5, so it's 5 carbons making a ring. Now this would be a big pain in the ass to keep drawing all of these C's, H's, and lines right? Want some shorthand? Of course you do! Check this out:

That means the same exact thing! Cyclopentane. Each change in direction means a carbon, and we just imagine the hydrogens in their places. Saves a lot of time! This is what kind of shorthand you see when we draw the DNA backbone!

Now that we're up to speed, what is ribose? Well, this:

It's just like cyclopentane, but with more stuff! Just replace the top carbon on the pentagon with an oxygen and add some more atoms to the other carbons. That's all ribose is; it is a sugar. Any word that ends in -ose is a sugar. Now we're getting somewhere! The DNA backbone is a whole bunch of these sugars (the ones missing an O, or deoxyribose) linked by phosphorus.

So what do we call a bond between phosphorus and two deoxyribose molecules? You guessed it! Phosphodiester bond! Check it out:

Now the yellow P bonded to the O's is the phospho- part of the bond, and the O's bonded to the ribose are part of the ester part of the bond. See the other cyclic molecules attached to the top right side of our two deoxyribose molecules? Know what they are? Purine and Pyrimidine bases.

A phosphodiester bond is nothing more than a PO4 molecule linking together the sugars on the DNA backbone! Know where Ligase gets the PO4 from to link these deoxyribose molecules together? ATP!

So what do you think? The chemistry of DNA seem a little less overwhelming?


Franklin A.

Energetic and fun science tutor

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