I am an aficionado of proteins. An undergraduate course in Biochemistry opened my eyes to the simplicity and wonder of the grand "central dogma" of biology. It occurred to me at the time that macromolecules might be interesting to Micronesian students.
Macromolecules are chain polymers. And, wonder of wonders!, three of the important categories of macromolecules are chain polymers. Proteins and Nucleic Acids are never branched. Their entire existence and function is based upon a motif: a linear sequence.
In Biology classes I placed strong emphasis on the molecular background of the significant biological molecules. My curriculum began with Natural Selection, then started constructing a model of a living organism as---not a mechanism, but---understandable as a system, at some level, of macromolecules. I had to start from the beginning, telling a story about my mother explaining to me that everything is made of atoms. I dare say that most of my students had not recieved this piece of the puzzle.
Proteins are central.
Life is, at some level, a system of proteins interacting in various ways, among themselves, and Nucleic Acids (which carry the blueprint for their production), fueled by carbohydrates, and constrained within membranes made of lipids (which also serve other functions.). It is, of course much more complicated that this, but this is the core idea of life as a process, of a functioning organism.
The following is a short list of some kinds of proteins in a living organism, from the simplest to the most complex.
- Enzymes: catalysts of chemical reactions.
- Action proteins: muscle, flagella, cilia all operate through the agency of proteins.
- Transport: Motor proteins carry packets of other molecules (many of them proteins) around in the cell. Hemaglobin carries Oxygen.
- Antibodies
- Structural protein: hair, keratin, nails, claws, barbs and arrowheads, protective spines.
- Regulatory proteins
- venoms and toxins
- membrane channels
- Signalling proteins: Hormones (insulin,
- pheromones: messages that are external to the organism, between organisms: cat scents, mating signals---sex pheromones, alarm pheromones, trail pheromones (in ants),
A protein is a chain of one of about 20 Amino Acids in a very specific order determined by the DNA that codes for it. Each of these Amino Acid has unique properties. Some are charged, either + or -. Some love water (are hydrophilic), and others abhor water (are hydrophobic). These and other properties of Amino Acids cause the chain to fold upon itself in certain ways. Imagine a giant spaghetti monster made up of one extremely long strand of spaghetti, a chain of Amino Acids with different properties that cause certain links in this chain to attract or repel one another, or fold away from the water inside the cell, or to embrace it. In the end, the strand of spaghetti folds into a precisely determined shape, it's structure. The shape of this blob of spaghetti determines it's function. Structure determines function.
Remarkably, this is exactly how it all works. Thousands of blobs of spaghetti shaped each in it's own unique way, interact with one another. A digestive enzyme may break starch---chains of sugars---by breaking these sugars apart. The enzyme to break the starch chain has a pocket that precisely fits a starch molecule in a specific configuration, between two sugars, the sub-molecules of that starch chain. The bond between these two sugars is now placed under stress and weakened, and caused to break. If even one of the Amino Acids making up this chain were changed, say from positively charged to neutral, the shape would lose its integrity; the enzyme (amylase, in this instance) would not operate at peak efficiency., or perhaps fail to work at all.
Each protein achieves its function through the precise ordering of its Amino Acid components, which determines the manner in which the chain folds into it's 3-dimensional structure. DNA is a chain 4 sub-molecules, Nucleotides, in a specific order. This order providing the code for the Amino Acid sequence in a proteins is a gene.
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Today I want to look at diagrams that have been devised to help us see and understand the structures of proteins. Structure Diagrams, . protein is a straight chain of amino acids.
Proteins, after all, attain every aspect of their functions from their shapes. Their shapes are written in a linear code.
At Lawrence Berkeley National Laboratory (LBNL) I observed a poster wrapped around a column, touting that the shapes of over 8,000 proteins had been characterized at that facility.
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8,714 Proteins. A Poster in the Advanced Light Source of LBNL.
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Close up showing protein structure diagrams. The double helices are proteins! |
Today I decided to dive into the dark waters of these diagrams, that I have never understood. I discovered something wonderful: A Wikipedia guide to proteins structure diagrams! Put a pin in that. I also stumbled upon an article about the LBNL Advanced Light Source, written in April 2025:
Today, the nine structural biology beamlines at the ALS passed a major milestone of collectively depositing over 10,000 protein structures into the Protein Data Bank (PDB), a worldwide, open-access repository of protein structures.
WOW!
Here, then, is a link to the Wikipedia Page about Ribbon Diagrams.
On this page I learned about early ribbon diagrams, hand drawn by Jane Richardson, such as this one.
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| Triose P isomerase monomer |
Here is another one: A Prealbumin Dimer:
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The following is different kind of model, a space filling model: an animation of Salivary Amylase breaking the bond between sugars in a starch chain. Shown is it's active pocket. Starch nestles into the pocket, is broken apart by the enzyme, and is spit out in two parts. Click in the lower right hand corner to enlarge it. This is a different form of model, a space filling model. Note the attribution. My profound gratitude for the enormous amount of work that went into this.
