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At typical physiological pHs glutamate does exist as glutamate. Broadly the acidity in the digestive track is enough to reduce glutamate to glutamic acid. The stomach for example has a healthy pH of between 1.5 to 3.5. Canadianer points out in the comments that the active site during catalysis are protonated. There are obviously a lot of examples of this ...


Short answer: there are no restrictions in principle on which amino acids can follow which. That means that in principle you can have polypeptide in any configuration: AAAA, WQWQWQ etc. Problem is that polypeptides must be functional and, because they are in aqueous solution, it puts restrictions on how polypeptide form secondary and tertiary structure. It ...


@MadScientist: Certain functions require every single one of these 20 amino acids. However, in isolated cases a selected subset of amino acids might very well lead to an active protein.


To answer your question: No, there are no restrictions to what amino acid is next ("a nearest neighbor") to its N-terminal or C-terminal neighbor.


We can look at the list of amino acids on wikipedia for a start. And we can look at this L-alanine: What makes your image confusing is that it's a Fischer Projection, and I hate those because you have to remember what way the stereochemistry goes. In Fischer Projections, vertical lines face away from you, while horizontal lines face towards you. So if we ...

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