Pyrimidines

Purines

We leave out uracil (U) from this tutorial because it is an RNA nitrogenous base.

BASE PAIRING

Adenine-Thymine

The hydrogen atom on N3 of THYMINE bonds with N1 of ADENINE.
An amino group hydrogen on C6 of ADENINE bonds with the carbonyl oxygen on C4 of THYMINE.

Cytosine-Guanine

as follows:

An amino group hydrogen on C2 of GUANINE bonds with the carbonyl oxygen on C2 of CYTOSINE.
The hydrogen atom bound to N1 of GUANINE bonds with N3 of CYTOSINE.
An amino group hydrogen on C4 of CYTOSINE bonds with the carbonyl oxygen on C6 of GUANINE.

BASIC ORGANIZAION

Sugar-phosphate backbones

5' to 3' Strand

With the sugar in-place, we add a phosphate at the 5' end, which establishes the directionality of the strand of DNA – let's see how the rest, now, falls into place.
At the 3' carbon, add an oxygen.
Show that it forms a phosphate, which then connects to the next deoxyribose

We can cap the strand, though, at the 3' hydroxyl, because, we understand the pattern.
Draw the 5' (phosphate) to 3' (hydroxyl) orientation.

Note that we have not, yet, addressed the nitrogenous bases that attach to the 1' carbons on these sugars.

3' to 5' Strand

Now, let's skip to the opposite side, which presents in opposing (antiparallel) orientation.
Draw the deoxyribose (upside down in reference to the first one we drew).
Attach a phosphate to its 5' carbon.
At the 3' carbon, attach a phosphate.
Show that it attaches to another deoxyribose.

DNA Base Pairing

Sugar-Phosphate Backbone

DNA has a fixed backbone that comprises units of:

These give each DNA strand directionality: 5' to 3' vs 3' to 5'.

The Nitrogenous Bases

Denote the 4 nitrogen bases.

To remember the purines, think: Larger & think about ATP/GTP (adenine, guanine).

The pyrimidines: Thymine & Cytosine (Uracil is in RNA, only*).

To remember the pyrimidines, think: Smaller & think about the chemistry of UMP to dTMP (thymine) & CTP (cytosine).

Base Pairing