Why Do Purines Bond With Pyrimidines, Why Do Purines Pair With Pyrimidines

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What are Purines and Pyrimidines?: The Basics

Each DNA strand has a ‘backbone’ that is made up of a sugar-phosphate chain. Attached to each one of these sugars is a nitrogenous base that is composed of carbon and nitrogen rings. The number of rings this base has determines whether the base is a purine (two rings) or a pyrimidine (one ring). The purines on one strand of DNA form hydrogen bonds with the corresponding pyrimidines on the opposite strand of DNA, and vice versa, to hold the two strands together. Within DNA molecules, this is their most important function and is known as base pairing. Because hydrogen bonds are not as strong as covalent bonds, base pairings can easily be separated, allowing for replication and transcription.

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Because purines always bind with pyrimidines – known as complementary pairing – the ratio of the two will always be constant within a DNA molecule. In other words, one strand of DNA will always be an exact complement of the other as far as purines and pyrimidines go.This phenomenon is known as Chargaff’s Rule, named after Irwin Chargaff, who first noticed it. This complementary pairing occurs because the respective sizes of the bases and because of the kinds of hydrogen bonds that are possible between them (they pair more favorably with bases with which they can have the maximum amount of hydrogen bonds).

There are two main types of purine: Adenine and Guanine. Both of these occur in both DNA and RNA. There are three main types of pyrimidines, however only one of them exists in both DNA and RNA: Cytosine. The other two are Uracil, which is RNA exclusive, and Thymine, which is DNA exclusive. One strategy that may help you remember this is to think of pyrimidines like pyramids that have sharp and pointy tops. So sharp and pointy in fact, that they might CUT (Cytosine, Uracil, Thymine) you.

Which purines pair with which pyrimidines is always constant, as is the number of hydrogen bonds between them:

ADENINE pairs with THYMINE (A::T) with two hydrogen bondsGUANINE pairs with CYTOSINE (G::C) with three hydrogen bonds

One way to remember which bases go together is to look at the shapes of the letters themselves. The letters made up of only straight lines (A and T) are paired with each other, while the letters that are made up of curves (G and C) also go together. Just make sure you don’t write your A’s in cursive!

These specific pairings also factor into Chargaff’s Rule, which we mentioned before. The number of adenines in a DNA molecule will always be equal to the number of thymines. The same goes for guanines and cytosines. Because of this, if you know the percentage of one nitrogen base within a DNA molecule, you can figure out the percentages of each of the other three as well – its complementary pair will have the same percentage, and each of the other two bases will be the sum of the first pair subtracted from 100% and divided by two. Expect a question asking you to calculate something similar to this on the exam.

If what we have covered so far is confusing to you, make sure you go back and review your notes on DNA/RNA structure before moving on to studying the differences between purines and pyrimidines.

Purines vs. Pyrimidines

When it comes identifying the main differences between purines and pyrimidines, what you’ll want to remember is the ‘three S’s’: Structure, Size, and Source. The very basics of what you need to know are in the table below, but you can find more details about each one further down.

  Purines Pyrimidines
Structure Double carbon-nitrogen ring with four nitrogen atoms Single carbon-nitrogen ring with two nitrogen atoms
Size Bigger Smaller
Source Adenine and Guanine in both DNA and RNA Cytosine in both DNA and RNAUracil only in RNAThymine only in DNA

The most important difference that you will need to know between purines and pyrimidines is how they differ in their structures.

The purines (adenine and guanine) have a two-ringed structure consisting of a nine-membered molecule with four nitrogen atoms, as you can see in the two figures below.


Chemical Structure of Adenine in vector format. Image Source: Wikimedia CommonsStructure of guanine. Image Source: Wikimedia Commons

The pyrimidines (cytosine, uracil, and thymine) only have one single ring, which has just six members and two nitrogen atoms.


Cytosine chemical structure. Image Source: Wikimedia CommonsStructure of uracil. Image Source: Wikimedia CommonsSkeletal chemical structure of Thymine. Image Source: Wikimedia Commons

Because purines are essentially pyrimidines fused with a second ring, they are obviously bigger than pyrimidines. This size difference is part of the reason that complementary pairing occurs. If the purines in DNA strands bonded to each other instead of to the pyrimidines, they would be so wide that the pyrimidines would not be able to reach other pyrimidines or purines on the other side! The space between them would be so large that the DNA strand would not be able to be held together. Likewise, if the pyrimidines in DNA bonded together, there would not be enough space for the purines.

Test Yourself!

Question 1: Which of these is a pyrimidine used to produce DNA?

A. Adenine

B. Cytosine

C. Uracil

D. Thymine

E. Both B and C

F. Both B and D

Question 2: The diagram below shows examples of which of the following?

kinds of purine. Image Source: Wikimedia Commons

A. Sugar-phosphate backbones

B. Amino acids

C. Uracil and Thymine

D. Purines

Question 3: Which of the following options is true of the differences between purines and pyrimidines in DNA?

A. The purines, adenine and thymine, are smaller two-ringed bases, while the pyrimidines, cytosine and uracil, are larger and have a single ring.

B. The pyrimidines, cytosine and uracil, are smaller and have a single ring, while the purines, adenine and guanine, are larger and have two rings.

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C. The purines, adenine and guanine, are larger and have two a one-ringed structure, while the pyrimidines, thymine and cytosine, have two rings and are smaller.

D. The pyrimidines, cytosine and thymine are smaller structures with a single ring, while the purines, adenine and guanine, are larger and have a two-ring structure.

E. The purines, adenine and cytosine, are large with two rings, while the pyrimidines, thymine and uracil, are small with one ring.

Answers and Explanations:

Question 1: The correct choice is F: both B and D. Cytosine and Thymine are both used to produce DNA. Be careful with questions like these! If the wording had been “which of these is a pyrimidine used only to produce DNA,”the answer would have been ‘D: Thymine’ instead.

Question 2: The correct choice is D: Purines. The diagram shows adenine and guanine, which you can identify by their two-ringed structure. Even if you did not remember this, you could rule out the other options like this: the sugar-phosphate backbones contain no nitrogen, amino acids must have amine, and uracil and thymine only have one ring.

Question 3: The correct choice is D. This was a tough one, so if you got it right, give yourself a pat on the back – you’ve learned the main differences between purines and pyrimidines! A key point to notice in this question is that it asks specifically about purines vs. pyrimidines in DNA. If you were confused about why option B was incorrect, this is the reason (uracil is found only in RNA, not DNA). The exam will often have trick answers like this early on in the options, which is why it is crucial that you read ALL the options before choosing.


Congratulations on making it through the whole guide! Here’s a quick recap of the main points we’ve covered in this review:

Purines and pyrimidines are the nitrogen bases that hold DNA strands together through hydrogen bonds.They pair together through complementary pairing based on Chargaff’s Rule (A::T and G::C).The purines in DNA are adenine and guanine, the same as in RNA.The pyrimidines in DNA are cytosine and thymine; in RNA, they are cytosine and uracil.Purines are larger than pyrimidines because they have a two-ring structure while pyrimidines only have a single ring.

You should now feel confident in your ability to identify and differentiate between purines and pyrimidines, as well as in your knowledge of what role they play in DNA structure. Make sure you don’t just focus in on the small details though – don’t forget to look at the big picture or how this all plays into biology as a whole!

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