Origins 8: Why do we need proteins and what are they?
Welcome to the amazing and wonderful world of proteins. DNA uses a large part of its genes to give building instructions for proteins. What are they, and why do we need them?
First let’s talk about how the body uses them. Proteins are built into the cell wall. Without proteins, there would be no way to get nutrients, oxygen, and energy into the cell and no way to get waste and carbon dioxide out. Proteins also control electric charge motion in and out of the cell. Hormones are made of proteins that control many other reactions in the body like emotions and sensory stimulation. Enzymes are also proteins that help us digest food and speed up (catalyse) chemical reactions in the cell. Proteins control various parts of DNA, activating some parts and blocking others. Cells use proteins to read and translate DNA, and all proteins in the body are constructed by other complex proteins. Cells use proteins to keep DNA and amino acids from changing into undesirable forms. In fact, proteins are the working molecule in the cell.
What are proteins? All proteins are made of building blocks called “amino acids”. There are twenty amino acids used in proteins. Think of the amino acids like an alphabet. Instead of spelling words and sentences amino acids “spell” proteins.
Here is a picture of the general structure of all amino acids.
Black spheres represent carbon, reds oxygen, blues nitrogen, and whites are hydrogen atoms. The unconnected bond is where any organic structure can be bonded to make a particular amino acid.
Here is the structure of glycine on the left. Alanine is on the right.
The simplest amino acid, glycine, has another hydrogen on the stick, but there are an infinite number of possible amino acids, and only twenty are used by the body (and all other life forms).
But there is more. The amino acids can be combined together in many ways, but all proteins are structured with only one allowed bonding pattern. The only allowed bonding site is the OH bond on the end of the amino acid. It must bond with one of the hydrogen atoms bonded to the nitrogen atom at the other end to produce a protein and a water molecule. This allowed bond is called a “peptide” bond.
Proteins used in life can have as few as 24 amino acid building blocks. Adrenaline is an example. But this is rare. The average protein is made of 300 amino acids, and some, like titin, have almost 27,000 amino acids. Titin is an elastic protein that builds muscle.
So, if the smallest word in the protein language is made of 24 letters (amino acids), the longest would take almost thirty-eight pages of type. In English, if a spelling mistake occurs we can usually make sense of the words, but if too many mistakes are made, the sentence is gibberish. This is the same for proteins. A few errors can be tolerated without losing much function, but too many and the protein is useless. Even small errors can degrade function. There are some places in the protein chain where any substitution makes the protein useless.
The body needs to produce two million red blood cells a second, and a single red blood cell has 170 million hemoglobin molecules. Hemoglobin is a protein. Wow! Each hemoglobin molecule has 574 amino acids in four protein chains. Thus, the body has to build twenty thousand trillion (20,000,000,000,000,000) peptide bonds per second for a functioning blood supply.
Our bodies use about one hundred thousand (100,000) different proteins to function properly. And interestingly, proteins are constructed by other proteins (ribosomes) in the body. Ribosomes contain both RNA and proteins. They build protein from scratch using a blueprint from DNA. (We’ll talk about ribosomes, RNA, and DNA in more detail in a later blog.
Many parts of DNA are coded for constructing proteins, but we need proteins to build the proteins. We also need proteins to interpret the DNA. About fifty proteins are involved in building proteins. Who built the proteins that interpret the DNA so that they can build proteins? It’s an interesting kind of chicken and egg problem.
We can build proteins in the laboratory. Here is a quote from MIT News (May 28, 2020): “Their tabletop automated flow synthesis machine can string together hundreds of amino acids, the building blocks of proteins, within hours.” We are not even close to keeping up with the ribosomes who string together three to five amino acids each every second (over 14,000 an hour) to build the proteins we need in every cell.
The protein is just a molecule, like sugar or baking soda. Yet this molecule, using only a string of amino acids, can decode the DNA (actually, it is first translated into RNA) and then build complete proteins in seconds. To me, that is amazing!