The Mneumonics of Nucleotide Structure

Posted by 5x5 on September 12, 2009 under Biochemistry | Be the First to Comment

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A nucleotide consists of three components:

The nucleoside portion

1. Either a ribose or 2-deoxyribose sugar
2. A DNA/RNA base (Purine related: Adenine, Guanine versus Pyrimidine related: Cytosine, Uracil, Thymine)

and

3. A phosphate group

To make these basic components of life easier to remember, they can be related to love, romance and a really bad soap opera.

Pyrimidines are the purest of the two.  They like to keep things simple, having only 1 ring and 6 atoms.

Purine is not as pure as it says and keeps an extra pyramid on the side making it 2 rings of 9 atoms.

Pyrimidine, being a longer name with a “y” has a longer, CUT throat following: Cytosine, Uracil and Thymine.  All of them see to (C2) a bond loss for O and gaiN a H.

Only Cytosine is willing to let amino (NH₂) on top.  While Uracil and Thymine prefer to loose another bond in order to have O on top with and extra H on the side.

Thymine likes to fart (methane CH₃) and sees to giving it a high 5 (C-5).

RNA molecules find this disgusting and do not participate in this habit, using Uracil instead of Thymine.

Since sugar is sweet, the other two nucleotide components want to attach to it.  The base is the 1st (C1) to attach N, showing off its Chi angle with free 360 degree rotation.  They are in love and form a glycosidic bond.

Time passes and when the base is showing off its 360 degree rotation, the sugar forms a new phosphodiester bond with a phosphate.  When discovered, the base is not happy about the arrangement, but decides as long as the phosphate stays on the 5′ end, he can live with the situation.  As more time passes, several nucleotides run into each other.  The phosphate attached to the 5′ end feels a bit neglected. Rather than leaving, it creates another phosphodiester bond with a 3′ hydroxyl of one of the other nucleotides.

Every time three of these nucleotides attach, a codon is born.

Another way to memorize nucleotides structure is to use their chemical names and the chemical naming convention rules.  You may find it slightly less interesting, but most certainly straight forward.

Adenine – 6-amino-purine (amino group on 6th ring constituent in structure)

Guanine – 2-amino-6-oxo-purine (amino group on the 2nd ring constituent and oxygen on the 6th)

Cytosine – 2-oxo-4-amino-pyrimidine (oxygen on the 2nd and an amino group on the 4th ring constituent)

Thymine – 2,4-dioxo-5-methyl-pyrimidine (oxygen on the 2nd and 4th and a methyl group on the 5th ring constituent)

Uracil – 2,4-dioxo-pyrimidine (oxygen on the 2nd and 4th ring constituent)

Have you found any mneumonics to help you remember nucleotide structure? If so, post ‘em here!