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March 14th, 2012

The protein of story: a study in structure

I was bending my husband's ear about the issues I'm having with the revision of my current work-in-progress and he made a comment about protein structure. Yeah, I know, we're like that in our house. But it got me thinking, and then I read this post about the double helix of plot and character over at Project Middle Grade Mayhem. So here's what I came up with.

Proteins have four levels of structure. The primary structure is the sequence of amino acids, the order in which the beads are strung along the chain. It's the direct translation of the genetic code in the DNA and it is what makes each protein unique. This is like the prose, the order of words in a book. It's linear. It goes from point a to point b, from "Once upon a time" to "happily ever after," from the amino terminus to the carboxyl terminus. Changing the primary structure is like line editing, getting the order of words in each sentence right.

The secondary structure of a protein includes common structural motifs, like alpha helices and beta sheets. They arise from the way the individual amino acids interact with other amino acids in their general proximity. These are like the rhythm, tone, and voice. It's how the words and sentences flow together, the patterns that they make. It's how the characters think and talk and behave.

Tertiary structure is like the plot. It's how the amino acids interact with other amino acids in other parts of the protein chain. There are twists and turns. Things fold back on each other. Lines intersect. Some amino acids can even form chemical bonds with each other, joining parts of the protein chain together, connecting them at particular points along the line. The tertiary structure gives the protein/book its shape. Foreshadowing, flashback, conflict, surprise, epiphany. These are all tertiary structural elements of the story, and they ultimately make the protein perform its function. They make the story work.

Quaternary structure is only relevant in some proteins, those made up of subunits. It's how the different protein molecules fit together to form a functional unit. So maybe that's like a series. Or maybe it's how a bunch of different subplots fit together.

How do you change the structure of a protein? Mutations. How do you change the structure of a book? Edits and revision.
Some mutations change only the primary structure. They add, delete, or substitute single amino acids in such a way that the higher levels of structure are not affected. They don't really change the shape or function of the protein as a whole. Line edits can be like that. They make a sentence flow more smoothly or clarify a point, but they don't change anything about the voice or rhythm or plot.

Bigger edits, like taking out or adding scenes, can certainly change the overall structure of the book/protein and those changes depend on the size, position, and composition of the insertion/deletion. Even simple changes, single words, can have a profound effect on the secondary or tertiary structure, if they are the right changes in the right place.

Right now I'm working on the secondary and tertiary structure of my story. It's easy to get bogged down in the primary structure--rewriting and rewording a sentence over and over until it's just right. But if the changes I make in that sentence don't affect the rhythm, voice or plot, I must resist the urge to polish it, because I'm still working on the shape of the protein/story as a whole. The changes I make need to fold, spiral, bulk up, and flatten out the story until it's in its most functional shape.

Ultimately, though, it's the sequence of amino acids that make a protein function.
It's the right words strung together in the right order that make a story work.


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Jacqueline Houtman
I'm a freelance science writer based in Madison, WI. I also write sciency fiction for kids. My award-winning debut novel, THE REINVENTION OF EDISON THOMAS, was published by Front Street/Boyds Mills Press in March 2010.

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  • 21 Apr 2015, 21:32
    I thought The Fourteenth Goldfish might work, but apparently the grandfather learns how to reverse aging and becomes a teenager. Speculative elements not allowed on the list. I'll look into Life on…
  • (Anonymous)
    21 Apr 2015, 17:27
    Hi Jacqueline. Suzy G. here. I just got these 2 new titles in at my library: "Life On Mars" by Jennifer Brown and "The Fourteenth Goldfish" by Jennifer L. Holm. Haven't read them yet, but they look…
  • 25 Sep 2013, 21:30
    A more up-to-date listing can be found on my website:

  • (Anonymous)
    25 Sep 2013, 21:14
    According to your page nothing has been going on since 3 Feb 11. Is that true? Did the world stop and I haven't been informed?

    Not to be a pest

  • 10 Oct 2012, 21:08
    Thanks for your comment, Beth.
    It's actually a shower curtain (brand new, never used for a shower). It's the same one they use on The Big Bang Theory. I think I got mine through ThinkGeek.

    Good luck…
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