With all my talk on protein terminology I didn’t want RNA and DNA to feel left out, so here are some nucleic acid mnemonics and intuition tips for those having any doubt! If you want a detailed discussion, see this post: http://bit.ly/nucleicacids2 But here’s an overview so we are on the same page and then some bullet points:
Nucleic acids (DNA and RNA) are polymers made up of nucleotide monomers, which are themselves made up of key components.
Nulceotides contain
- a nitrogenous (nitrogen-containing) base (aka nucleobasee)
- a pentose (5-carbon sugar) – either ribose (in RNA) or deoxyribose (in DNA)
- 1 or more phosphates (negatively-charged)
building nucleic acids up from their parts…
BASE (aka NUCLEOBASE)
BASE + SUGAR = nucleoSIDE (remember nucleoside has a side of sugar)
BASE + SUGAR + PHOSPHATE = nucleoTIDE
NUCLEOTIDE + NUCLEOTIDE + NUCLEOTIDE . . . = NUCLEIC ACID
There are 5 common nitrogenous bases (nucleobases, often just called “bases”). 3 are found in *both* RNA & DNA (but attached to different sugars) – and these 3 shared ones are adenine (A), guanine (G), & cytosine (C). Then you have thymine (T), which is only found in DNA & uracil (U), which is only found in RNA.
There are two main classifications we give to nucleobases – they can be a purine (A & G) or a pyrimidines (C, T, U).
Now we get into some memory tricks and intuitive thinking thoughts
Nucleobases
- you can use the mnemonic PURe As Gold to recall that the purines are adenine and guanine (so the other 3 have to be pyrimidines)
- Purines have 2 rings (1 6-membered, 1 5-membered) (I remember this by thinking of purines as “pure” – having it all) as opposed to pyrimidines which only have 1 ring (6-membered)
- changes from pyrimidine to pyrimidine (U→C or C→U) or purine to purine (A→G or G→A) are called transitions (you’re transitioning between within a form)
- changes from pyrimidine to purine or vices versa are called transversions (you’re changing across versions)
- N stands for aNy Nucleobase
- R stands for a puRine (A or G)
- Y stands for a pYrimidine (C, T, or U)
Nucleosides
- When those bases hook up to a Sugar (through a glycosidic bond) they become nucleoSides. (Remember side of sugar)
- The “weddings” of nucleobase to sugar also come with name changes
- purines → end in “-sine” (e.g. adenine becomes adenosine)
- pyrimiDines → end in “-Dine” (e.g. cytosine becomes cytidine)
Nucleotides
- You get nucleoTides when you hook phosphate group(s) onto a nucleoside
- 1 gives you a nucleoside monophosphate, 2 a nucleoside diphosphate, and 3 a nucleoside triphosphate
- It may look confusing that the nucleoTides have nucleoSide in their name as written above, but that’s because it’s written as its parts – nucleoSide + phosphate (nucleoTide has the phosphate so if we wrote nucleoTide monophosphate, etc. that would be “redundant”
Nucleic acids
- Now we have our monomers (nucleotides) – time to stick them together to form a polymer (nucleic acids).
- Nucleotides join together through phosphodiester bonds, which are strong covalent (electron-sharing) linkages that leave a backbone of nucleic acids consisting of alternating phosphate & pentose residues w/nitrogenous bases as “side groups” joined to the backbone at regular intervals.
- Nucleotides come to be added (by enzymes called DNA or RNA polymerases) in their triphosphate form, but 2 phosphates are lost as energy payment, so you end up with a single phosphate in between each letter in the chain.
- The sugar-phosphate backbone is charged & hydrophilic (water-loved) but nucleobases are hydrophobic (water-avoided). So nucleic acids try to form secondary structures that minimize exposure of bases to water & maximize exposure of the backbone to water
- DNA usually does this through forming double-stranded DNA (dsDNA) consisting of a double helix made up of 2 DNA strands running in opposite directions (antiparallel)
- The width of the helix is constant because 1 purine (2-ringed base) & one pyrimidine (1-ringed base) always join together: C to G & A to T (remember the letters G and C look similar, like they’d fit together nicely).
- The actual nucleobases pair in this way because they have complementary hydrogen bonding opportunities on their “edges.”
- GC-rich regions of strands are more tightly stuck together – think “G”, Glue
- A & T (or U) only form 2 H-bonds w/each other BUT G & C can form 3 H-bonds when they “Velcro together” so they’re stronger (at least that’s the simple incomplete explanation. As explained in the video, G-C rich regions of DNA are actually also stronger mainly for more complicated reasons involving base stacking interactions https://sandwalk.blogspot.com/2007/07/measuring-stacking-interactions.html, https://youtu.be/PM3lIvFoLAg).
- Back to the helix – See a DNA double helix, put your right thumb up. If the twist follows your fingers your graphic designer is in luck! The first thing I do when I see a graphic of DNA is give it a thumbs up. Not *just* because I’m happy to see it (though it is *groovy*) but because I’m checking to make sure it’s right-handed! In order to complement the base pairing, the strands adopt a right-handed helical form (to see that it’s right handed, give a thumbs up w/right hand – the direction your fingers are curling is direction DNA curls)
- The most common double helix in DNA is “B-form” It has 2 grooves – a larger major groove, & narrower minor groove. These grooves can act like windows for other molecules to “read” their sequence without having to unzip them. RNA can also form double helixes (though usually a more compact “A-form”) & it also forms a variety of structures w/in single strands
- In the major groove you can distinguish all 4 base pairs, but in the minor groove you can only tell GC or CG vs AT or TA. I still remember the mnemonic I came up with when taking molecular bio in undergrad… AHA! ADAM ATe A TAMADA! (see pic)
And remember, memory tricks can be great but don’t *just* memorize! Understand the concepts! And then use the memory tricks to help with the terms and stuff you do just have to memorize. Hope this helped with both!
