Brain BREAK! presents: DNA Structure.
Today, we’re taking the pretty double-helix and zooming in on one nucleotide – that is, one side of the “ladder.” It’s made of three molecular components: a phosphate group, a deoxyribose sugar, and a nitrogenous base (your A, T, G, or C).
The phosphate group is the same one you see in ATP and phospholipids – a phosphate atom surrounded by four oxygens. One of these oxygens bridges to a carbon and then our second major player, the deoxyribose sugar. This five-pointed sugar is named deoxyribose because ribose sugars contain an oxygen that this one doesn’t. It’s kind of like calling a sugar cookie non-chocolate-chip cookies. (RNA, the R meaning “ribose,” are your oxygen-rich chocolate chip cookies.)
Third, dangling off the opposite side of deoxyribose is a nitrogenous base. As you’d expect, there’s nitrogen aplenty in these rings – more detail on the types of bases in a minute. But there you have it! These three components make up our nucleotide. Hydrogen bonds link the base here to the base on the opposite helix. More phosphate groups link underneath deoxyribose, creating that “backbone” of a helix. On and on it goes.
So, to sum up: phosphate group + deoxyribose + base = nucleotide.
Nucleotide x a bajillion = deoxyribonucleic acid (DNA).
mRNA is single-stranded, as we know, so it only carries one strand of bases. Also, uracil replaces thymine as a nitrogenous base.
3 prime, 5 prime, Geidi Prime?!
You might wonder what these bewildering 3’ and 5’ (3 prime and 5 prime) designations are about. These are the “position” of the carbon atoms in deoxyribose, like an address. Where the P-group attaches gives each nucleotide an “up” and “down.” This is important to the enzymes involved in transcription and replication. An RNA polymerase ponders a crumpled map, saying, “I should have asked for directions at the nucleolus.”
Looking at a deoxyribose molecule, we start at the nitrogenous base link and count clockwise. The carbon linked to the nitrogenous base is 1’. Then comes 2’. Now, 3’ is important because it links to the next phosphate group “down” on the helix. Continuing to 4’, we come to an intersection: the O of the deoxyribose or the carbon that connects to the phosphate group “up.” This last carbon is 5’.
So, again, 3’ goes “down,” and 5’ goes “up.” That’s just how I’m saying it. Because the double helixes kind of mirror each other – as we said earlier – enzymes that work with the DNA strands need to know where to start and where to go. I like to think that if they went the wrong way, I would have a butt for a face.
Categorizing the bases
A and T (or U) align because they form two hydrogen bonds. G and C match up with three. We can also categorize these molecules in another way: purines and pyramidines.
Purines have a two-ring structure: a chemical pentagon connected to the deoxyribose, and a hexagon creating the hydrogen bonds across the way. A and G are purines. Pure silver (elemental symbol Ag) kills werewolves in fantasy stories.
Pyramidines have only the hexagon ring structure. This includes C, U, and T. Tutor Kamal has a great way of remembering this: you cut the pie (py-).
I think of pyramid mummies having their organs cut out. Is that odd? -CNx