The Most Important Thing About Proteins

This is where the rubber meets the road — Oops, that’s another metaphor. Where the flow of energy that we spent all of chapter one talking about, meets the flow of information. Anything that important just has to be complicated, and indeed it is mind-boggling if we think only of the individual processes. But it’s incredibly beautiful if we look at the big picture.

The first most important thing we need to know about proteins is they are made inside the cells at the right time in the right place because of the genetic code. We introduce this idea in the past few weeks and will return to it soon.

The second most important thing we need to know about proteins is that each different kind of protein has a specific three-dimensional “shape” that is well designed to direct it’s own specific job for maintaining the life of that cell. Every kind of protein has it’s own perfect shape that is preserved in its own gene. The shape of the protein is perfect for whatever job it is supposed to do and is also perfect to interact with the source of energy that is needed to do that job.

The third most important thing we need to know about proteins is that they function at the intersection of information and energy in the cell, and also in the ecosystem.

Today we will talk about the relationship between the shape of the protein, the specific job the protein is designed to do, and the energy source that is necessary to do any work in the cell. We will concentrate on the latter two and talk more about conformation (shape) next Thursday.

Some important proteins are the same in all cells (nearly all). Some, like your muscles, are in specialized cells. Some proteins, when they are mature and fully structured, attach to other proteins of the same kind, some to proteins of a different kind. All proteins and most other molecules get the energy from cellular respiration to do whatever specific work they do. The energy is released in mitochondria. It is circulated by ATP. We need an example to visualize these processes, so we will use muscles. If you want to know specifically how muscles work, that information is on the web. We are talking about the relationship between work and energy and the specificity of the proteins.

Muscles are composed of more than two kinds of proteins attach together, but the two major ones are actin protein and myosin protein. Of course the proteins are microscopic, but they organize together in large bundles, and the final result is a muscle. Move your hand to your face. The muscles on the inside of your arm become shorter (contract) because actin and myosin interact with each other. They actually move across each other so the two ends of the muscle come closer together (contract). Of course, it is work to contract a muscle. If you stop doing the work of holding the muscle short, then your arm can fall loose again. If you need to pull your arm up behind you, then a different set of muscles on the back side of your arm will contract. Muscles don’t do work to expand. They can use energy to contract or they can stop using energy and let the muscle get longer again.

It works like this. My brain is attached to my various nerves and the various nerves are attached to many things, but this particular nerve we are talking about is attached to a muscle in my arm. Big long nerve, runs all the way down my arm. When I put my hand on the hot stove, nerves in my hand send signals up to my brain (or maybe only as far as my spinal nerve). My brain thinks “ouch” and at the same time (actually faster than the ouch) it sends a signal down a different nerve to my arm that contracts the arm muscles that remove my hand from the stove. Every step of this process requires specialized proteins (and other sorts of molecules) and also requires energy that we discussed in chapter one. (The PDF of chapter one is available on the right of this blog.)

What do the proteins have to do with this? There are hundreds of different kinds of proteins. Each kind has a different conformation (shape) that makes it suitable to do a specific function, but nearly all of the actions require energy. Energy is the ability to do work. The energy comes from cellular respiration, and the energy gets into the molecules in the first place by the process of photosynthesis that happens in plants. Cellular respiration occurs in mitochondria. It is the process that breaks down a larger organic molecule, glucose, so that energy is released, and then it captures the energy. The energy is moved from the mitochondria to the location where energy is needed by a molecule named ATP. The ATP contains the energy as an energy bond.

The energy bond is carried around in the cell by a phosphate group. A phosphate group is so important it has a shorthand designation Ⓟ. It is a very tiny little group of atoms that can be carried around inside the cell as part of a larger (but still small) molecule that is called ATP (adenosine triphosphate). Adenosine plus three phosphate groups fastened end to end, or A~Ⓟ~Ⓟ~Ⓟ. The trick is that the third phosphate group on this tri-phosphate molecule can be transferred to any other molecule that needs the energy. For example a muscle molecule. When the third phosphate group is transferred to the muscle molecule, along with the energy bond that attaches it, the muscle molecule changes its shape in the tiniest but most important fashion that causes the muscle to contract. How exactly?

How exactly is not the most important part of this story. There are two most important parts to the story.

First, every protein molecule is a different and very specific shape, and that shape is just perfect for it to do its job(s). One part of the muscle job is to be able to attach to a phosphate group. When it attaches to the muscle, the phosphate group changes the “shape” (it changes the relationships among many of the energy bonds) of the muscle molecules so the actin moves a teeninsy bit across the myosin and the muscle is that little bit shorter. That little job of work changes the “shape” of the proteins back again to what they were, as the work absorbs the added energy, so the phosphate group falls off and floats away in the cell. Then the muscles will repeat this process millions of time to do their work. This is happening all over the muscle when it needs to contract. Lots of ATP molecules bring lots of phosphate groups to the muscle.

So to summarize, A~Ⓟ~Ⓟ~Ⓟ actually transfers the third phosphate group ~Ⓟ to the muscle, so it uses its energy to bond with the muscle proteins. We might think of this as muscle~Ⓟ. This changes the energy relationships inside the muscle proteins so their “shape” changes. As the work is done, the energy is lost, and the Ⓟ falls off the muscle. The tiniest bit of work has been done and the energy and the phosphate group are gone away, a bit of energy is changed to heat, and the muscle returns to its resting “shape.” (That’s why your muscles get warm when you are doing work.)

Now the muscle cannot do any more work until it gets more energy. The ATP has become ADP (A~Ⓟ~Ⓟ) that is adenosine di-phosphate (tri means three, di means two). It is no longer a high-energy a molecule. It returns to the mitochondrion.

The mitochondrion is an organelle (an organelle is an intracellular structure that contains many molecules that work together to perfom some particular function of the cell) inside of eukaryotic cells that has the function to break apart high-energy organic molecules and capture some of the energy that is released. That captured energy is used to re-attach phosphate groups to ADP molecules so they become ATP again and can then go back to the muscle and give it more energy so it can do more work. As we have seen before (chapter two), the molecules (physical things) cycle and cycle over again, while the energy does not. The energy is changed from a high-energy form to a low energy form and then is lost from the system as heat. This is the basic story of all life on earth at all the levels of organization.

In chapter one (available as a download on the right side of this blog) we explained WHY energy is required to maintain any kind of life including our whole living earth ecosystem. We have just now described HOW it happens. But let us summarize, because we should never forget that all of the energy for life on this earth comes from plants.

1. The plants use energy from the sun to make the high-energy bonds of organic molecules. This is the process of photosynthesis.

2. We eat the plants, or we eat some animal that ate the plants, because the only energy we can use to stay alive is organic energy, that is, the energy bonds that do the work of bonding together the atoms of organic molecules.

3. After we eat the high-energy organic molecules (carbohydrates, proteins, lipids and nucleic acids), they are broken down in a long trail of events that make the molecules for our for our bodies from the raw materials we eat. Energy is also released and is manipulated in the mitochondria, where larger carbohydrate molecules are broken apart to release smaller, low-energy molecules, water and carbon dioxide.

4. Much of the energy is captured and used to attach phosphate groups to ADP molecules, thus energizing them to become ATP.

5. The small ATP molecules are able to float around in the cell and interact with all the molecules that require energy to do work. Most of these are proteins.

6. This is done by transferring the phosphate and its energy to the protein (or wherever it’s needed). The protein then absorbs the energy, causing work to happen by changing the energy relationships (“shape”) inside the protein. The energy is gone from the phosphate into the protein, so the phosphate is no longer bonded to the protein and it falls off.

6. The result is work plus ADP plus an unattached phosphate group.

7. The ADP and the Ⓟ return to the mitochondria. The energy that was used to do the work is converted to a lower form, heat energy, that can’t be used in biochemical processes and so radiates out of the system.

So, we are at the intersection between the flow of energy, and the flow of information through the ecological system. Energy flows through space, from a higher form to a form that can be used by life, to a lower form that goes away never to return. Information also does not recycle, but it flows along through time, within the system. Only the materials recycle.

So now we have again described the flow of energy through the living system and away. This time in a cell. But we have added the idea that the proteins, by being specific for particular jobs, direct the way in which the energy is used in the cell. We used an example of muscle proteins, but every protein has its own specific function. And each kind of protein does its functions because of the genetic code that determines how how each will be “shaped,” and also determines when and where each will be produced in the cells.

Next Thursday we will talk about how the proteins are “shaped.”