Protein structure principles

Published on April 19, 2020 Reviewed on November 27, 2022   48 min

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Greetings. Welcome to this Principles of Biochemistry lecture series. My name is Jerry Feigenson. I am a professor in the Department of Molecular Biology and Genetics at Cornell University in the USA. In the second lecture, you saw some properties of each of the 20 amino acid residues that are found in proteins. You saw the peptide bond formation that creates the protein polymer and you saw the hydrophobic effect that drives water soluble proteins to fold, and you saw that once we start to examine a real protein, myoglobin, we see the need to know the three-dimensional structure.
In this third lecture, you will learn before finding the protein three-dimensional structure, just knowing the amino acid sequence is useful, and you will see how x-ray diffraction is used to find protein 3D structure. I will show you the six categories of interactions that determine protein structure and action and you will see the structural consequences of the peptide bond and the real size of atoms.
Prior to finding the three-dimensional structure, we can find the primary protein structure, which means the amino acid sequence. It used to be that researchers used protein-based methods. They would start with protein, put it into an automated protein sequenator, and find the sequence of amino acids in the actual protein. This was a very useful research method, but it's actually very difficult to do this. Let's label this method difficult. It might surprise you that most amino acid sequences are determined nowadays in a different way. In fact, what's done nowadays is to find the sequence of amino acids. We first find the part of DNA that codes for this protein and then sequence the nucleotides. The nucleotides are far easier to measure their sequence than it is for amino acids in a protein. So we sequence the nucleotides and we call this method easy. So that's how we find the amino acid sequence. So let's do that. Well, we run into an interesting behavior and here's a bit of jargon. We use the term isozyme or equivalent isoenzyme or isoform. It means from the same organism, analytically and structurally similar enzymes, but the amino acid sequence is slightly different. Let me give you an example. Suppose we determine the amino acid sequence for myoglobin from many different tissues. Well, no matter what's the source of myoglobin, we find the same amino acid sequence. If we do this for some other proteins, we find a different result. For example, the enzyme hexokinase from different tissues, we find different amino acid sequences. That means, different isoforms or isozymes.