Protein Folding

The Rules, Models that Illustrate Them, and the Link Between Genotype and Phenotype


Background and Review


Amino acids

Hydrophobic and hydrophilic effects

            Quickie concept quiz

The Link Between Genotype and Phenotype

Build and Fold a Model Protein

Hydrophobic Collapse


Final Shape

The Backbone

Effects of Mutation on the Protein

Effects of Mutations on Organismal Phenotypes

Back to top


Let's review what we know about proteins...


* They are made by assembling amino acids into polymers

* A single protein can contain tens, hundreds, or thousands of amino acids

* All species use the same 20 amino acids to build their proteins

* What makes different types of proteins different from each other is the sequence in which the amino acids occur

* The sequence of amino acids in proteins is determined by the sequence of bases in DNA, in the genes that encode the proteins

* The process of gene expression, involving messenger RNA, ribosomes, etc. is the mechanism by which proteins are assembled

* Somehow the string of amino acids produced by a ribosome folds into a final shape that is determined by the amino acid sequence...and this somehow contributes to the characteristics of the organism.

Back to top


Let's review what we know about amino acids...


* They all have a common core structure, from which they get their name:




The NH2 group (written here as H2N-) is an amino group.  The COOH group is a carboxylic acid group.  Therefore, "amino acid."


* Each of the 20 different amino acids has a particular chemical structure, indicated above by the X.  When a protein has been built by bonding amino acids together, it is, in essence, a string with a particular sequence of different X groups coming off of it.  The X's are the "side chains."

*  Some amino acid side chains are positively charged; some are negatively charged; some are neutral; some are hydrophobic; some are hydrophilic.

Back to top


When put into water...


What do hydrophilic molecules do?

They dissolve in the water.  Hydrophilic molecules are polar, and can join the Hydrogen Bond network that polar water molecules form.

What do hydrophobic molecules do?

They do not dissolve.  The Hydrogen Bond network forces non-polar molecules away.  [A potentially-useful animation]

What if a molecule is a polymer with many sidechains, some of which are hydrophobic, and some of which are hydrophilic?

Another way to phrase this is:

Which of these three different shapes is this amino acid polymer most likely to adopt in water?


Why is B correct? 

The insoluble, hydrophobic amino acids cannot be pushed out of the water altogether the way oil is, because they are attached to the soluble, hydrophilic amino acids.  All they can do is group together, forming a droplet of oil in the middle of the protein--with a surrounding shell of soluble amino acids.

Back to top


So What? 

...and how does this help us understand the link between genotype and phenotype?


First, it helps to build a model.  Here's one:

It's made of Styrofoam balls on a string (representing the backbone) with various side-groups protruding from it.  It's impossible to tell from looking at it that this has any particular information for "folding."  Does it?

Back to top


The first event: collapse into a globule that buries the hydrophobic amino acids away from water.  This occurs extremely rapidly:

Back to top


Step 2: jiggling and sorting until the hydrophobic side chains are packed together in the most stable way (i.e. the lowest energy conformation).  In the model, we'll hold it in this shape using small Velcro tabs on the hydrophobic amino acids.  The hydrophilic amino acids face away from the hydrophobic core:

Back to top


Step 3: more jiggling and sorting, as other kinds of interactions occur.  Here, we've modeled two interactions between side chains with + and - charges:

Back to top


This is much easier to see with an actual model.  It's also much easier to see that the shape is not rigid.  It flops and wiggles in the water surrounding it, just as the model flops and wiggles as you move it around.  But, the hydrophobic interactions and the charge interactions hold it together.  If we draw a picture of the backbone itself (and imagine it with a shadow), it would look like this:


Let's draw in the positions of the two types of forces holding the protein together:

Back to top


Let's consider one more thing: a mutation


What would happen if there were a mutation in the gene for this protein, such that one of the charged amino acids is replaced by a neutral amino acid?


The portions of the protein that should be held in place by that charge interaction would be free to wiggle and wobble.  Sometimes they might be in the normal locations, but most of the time they will be "out of place."  If this protein is an enzyme, then sometimes it will be able to catalyze a reaction, but most of the time it will not.  The mutant protein will have less activity than the non-mutant protein.


Simulate such a mutation with the model.  Hold it up and wiggle it around.  You can see that sometimes, the shape can be normal, but most of the time it is not.

                        Non-Mutant                                                                Mutant

Back to top


Consequences for Phenotype


This might be illustrated best with a table, so we can consider several different genes. For each one, we'll consider 3 different alleles: non-mutant, a mutation such as that mentioned above with only 10% of normal activity, and a mutation that interferes with protein folding so much that the enzyme has no activity at all.


Here is the table, identifying several genes and these three types of alleles.  What phenotypes would be shown?








Drosophila white gene

Allows accumulation of red eye pigment



10% activity mutant


Loss-of-function mutant





Human gene responsible for producing brown hair pigment



10% activity mutant


Loss-of-function mutant





Human gene responsible for producing brown skin pigment



10% activity mutant


Loss-of-function mutant





Aster gene responsible for producing blue flower pigment



10% activity mutant


Loss-of-function mutant



If you really need to see the answer, check here.

Back to top