Proteins 3/15/19

By Richard E. Bleil

Proteins fascinate me. They are the work horses of the body, and are often named after the job they perform. For example, calbindin is a protein the, you guessed it, binds to calcium. Calcium is necessary for the cell to live, but the concentration it needs is higher than the calcium concentration in the extracellular fluid, so Calbindin will bind four calcium ions outside of the sell, move across the cellular membrane and release them inside the cell.

People have heard of genetics, and know that our genes are encoded in our DNA. That genetic code is nothing more (as far as science currently knows) than the “road map” of how to build proteins. Here’s how it works.

Proteins are made of 20 known amino acids. DNA is made of four nucleic acids. The nucleic acids in DNA are arranged into “codons”, which is a grouping of three nucleic acid. Each codon represents one amino acid, plus one “start” codon, and one “stop”. In essence, DNA uses code, but instead of being binary like the computer I am working on today, it is quaternary (four amino acids). This is how we can “decode” DNA; basically we look for the “start” codons, and “read” the codons to determine the amino acid sequence for each known protein to the nearest “stop” codon.

The body does the same thing. It doesn’t work off the the DNA, though, since the DNA is just the source code. In essence, the DNA is like the equivalent of a hard drive on a computer. It contains the code on how to do things, but the programs don’t actually run off of the hard drive. Instead, the code is uploaded to the computer’s memory. The same thing happens in the body. Proteins will slide along the DNA until they find the “start” codon, in which case they begin replicating the DNA forming a type of RNA called a “messenger RNA”, or m-RNA. This m-RNA just reflects the code. Another RNA, the “Ribosomal RNA” then “reads” the m-RNA, and creates a space where the new protein is made. This is like the CPU on a computer, reading one codon at a time and literally putting the protein together. It does this by working with transfer RNA’s, known as t-RNA. Each t-RNA binds with one amino acid, and when the ribosomal RNA needs that specific amino acid, it allows the t-RNA in. The ribosomal RNA takes this amino acid, and adds it to the fragment of protein it had already formed. Quite an elegant process, actually.

Proteins exist in two states, the “native state” and “denatured”. For a protein to work, it must be in the native state. This means the shape must be exactly right. Think of having a beaded necklace, with twenty styles of colors of beads (representing each of the 20 amino acids). If you throw the necklace into the air and let it land on the ground, it will have some kind of folded configuration, or shape. But, of every possible shape it could possibly have, one, and only one, shape will let the protein do its work. Imagine throwing that necklace in the air a thousand times, and have it fall into that exact same shape every single time.

You’ve probably seen this. Egg white is made of a protein called “Albumin”. In its native state, albumin is a thick, clear, colorless fluid. When you cook it, the albumin turns into a white solid, the “egg white”. It’s the heat that caused the protein to denature. As it turns out, protein is very sensitive to the conditions of its surroundings, and easy to denature. When milk goes bad, lactose oxidizes to form lactic acid, which causes the acidity of the milk to increase (drops the pH). This acidic surrounding causes the milk’s protein, Casein (which is responsible for the white color of the milk, not calcium which is a common misperception) to denature and form solid. This is a process in which the albumin “precipitates out” as a solid, causing that chunky solid of bad milk.

Temperature and pH both cause proteins to denature, so what happens when the body’s temperature of pH is off? We see this during high fevers, or when hyperventilating or other pH issues. When temperature is too high, proteins begin to denature, and cells in the brain begin to die which is why extremely high fever is dangerous and can lead to brain damage or death. When one hyperventilates, pH raises in the body resulting in a condition called “alkalosis” (too basic, or, not acidic enough). This causes proteins to denature, leading to muscle cramps.

There are three levels of protein structure. All three must be correct for proteins to actually perform their function. Primary structure is just that order of amino acids. In other words, that’s the order of the beads in our allegorical necklace. This is created in the ribosomal RNA. The second level of structure are internal short structures that are part of the protein structure, but not overall. These can be helical, or straight segments, or segments of two portions of the protein either going in the same direction or opposite. This is the “secondary protein structures”. Tertiary protein structure is the overall structure. Notice that each level of structure incorporates the previous. Technically, there is a fourth structure, called the “quaternary protein structure” which occurs when two or more proteins work in conjunction with each other. Quaternary structure refers to the overall structure of all cooperating proteins. For example, the “hemoglobin” protein, which holds the Heme molecule to transfer oxygen and carbon dioxide in our blood, works with four different proteins, and the quaternary structure must be correct for it to function.

Proteins are extremely long “polymers”, meaning long molecules of repeating units. One protein that you have in your body right now, the “Titan” protein, consists of over then thousand amino acids. As it turns out, amino acids are used, and created, in other functions as well. For example, enzymes are made of the same twenty amino acids, but are much shorter. Enzymes are “catalysts”, which means they speed up chemical reactions, but cannot cause them. For example, sugar will naturally hydrolyze in the body (break down with water), but it will occur at a rate too slow to be of practical use in our metabolic process. So, as a result, there is an enzyme that speeds up this reaction, but it cannot create sugar in our body because that reaction would not occur naturally. Enzymes are like mini proteins, so they also must have proper primary, secondary and tertiary structures to function as well.

One enzyme specifically seeks out and destroys peroxide compounds. Peroxides are highly damaging to organic matter, like your cells. This is why hydrogen peroxide is such a great anti-septic for injuries. If you pour hydrogen peroxide on blood, it breaks down to release oxygen, causing the “fizzing” that you will see. This breakdown is occurring faster than it normally would because of that enzyme in our blood that breaks it down.

And there you go! Far more knowledge of proteins than you thought you might ever know!!!

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