Protein Functions

Your genes are collectively your DNA, the genetic code of life that is at the core of your chromosomes. Your genes use the genetic code (they are the genetic code) to make proteins. Protein synthesis is the process by which each specific kind of gene provides the information to make one particular kind of protein, and we will get to the basic biochemistry of that process eventually. First we want to emphasize the specificity and its relationship to the code. The protein is produced in the right cell at the right time and place where the specific protein is needed to do its function. And the production of this protein may direct the production of another protein, or it might do something else that changes conditions in the cell.

This is the very root nature of life. One thing happens that changes another thing, on and on until the cycle comes round to begin again, but with a new carrier cell or organism to keep it going for yet another cycle. Without the cycle, life could not continue because life needs energy to carry on. Otherwise, it would just be a big pile of DNA, and DNA does nothing outside of a cell.

In the cell, the DNA codes for the proteins that permit life to use energy to do work (chapter one, Bare Bones Ecology, download under book chapter to right on this blog). The work that it does is to maintain life, that is, to make more cells with more DNA, or to maintain the complex organization of life in a universe where things naturally tend to become unorganized. The DNA can not function without the cells that it lives in; to live, it must maintain the life of the cell. The cell then does the work (using the proteins encoded in the DNA) of staying alive. Obviously, the DNA must have some way to interact with (communicate with) the cell or all this life cycle can’t happen.

Protein synthesis is a kind of communication between the DNA, that is the code for life inside the nucleus of the cell, and everything else in the cell that maintains the life of the cell. And the death of cells, because death is also encoded in the DNA and is also necessary for life to continue down the generations. Communication of information is necessary to maintain life.

Communication, according to your favorite dictionary, is “the communicating of information.” Right. So what does communicating mean? I once saw radio communication diagram that emphasized speakers and receivers. Speaker on the left side with arrows coming out of it into the air, indicating that the speaker has changed electrical impulses into sound waves, and a big ear on the right side with the sound waves going into it showing that the sound waves have changed to whatever functions happen in your head that makes sound. That’s a fair description of communication. Information (gene) generates a different kind of information (protein) that is able to travel and is “received” in the sense that the protein makes something happen. And there you have it, the whole flow of information of the ecosystem. Hard to believe, and of course not nearly that simple, but mostly accurate. The proteins are primarily responsible for the flow of information in the ecosystem.

For the most part, each protein has one function. For example, we will now talk about the pigment cell, where there is a protein named “tyrosinase” that is an enzyme. Tyrosinase is a protein that is made only in pigment cells, because that is where your tyrosinase gene “turns on.” Under the influence of something that happened before, it begins to release the code to make the tyrosinase protein. Tyrosinase has only one primary function, and that function is to kick-start the process of pigment formation in the pigment cell. It does this by being an enzyme. An enzyme is a protein that is a catalyst; a catalyst is anything that makes a chemical reaction happen predictably. In the case of tyrosinase, the summary chemical reaction is something like this:

Tyrosine + energy + enzyme → Melanin pigment + enzyme

You see that the enzyme is not used up in the chemical reaction. Its function is only, as I said, to “kick start” the reaction and then stick around and do it again, over and over. Tyrosinase the enzyme is critical to pigmentation because tyrosine (the substrate of the reaction) is a small molecule that is found floating around in all the cells, and we do not want pigment in all the cells. Only in the pigment cells. Melanin pigment is what makes your hair and skin black (or yellow or red or whatever color it is). Melanin is an unpleasant sticky sort of substance that would gum up the works of the cell if it were not carefully controlled. The reaction to produce melanin happens only in the presence of the enzyme. Tyrosinase is an enzyme that ensures the pigment is made at the right time in the right cell and in the right part of the cell.

But of course it is not that simple. There are at least fifteen other proteins, each with its own specific function, that do various jobs to make certain the tyrosinase is not activated until it is in the right location of the cell. That location is an organelle that is found only in pigment cells and is called a pigment granule. The pigment granules (melanosomes) are in the cytoplasm of the pigment cells. Cytoplasm is the liquid parts of the cell that are outside the nucleus. So we have already three functions of proteins; first, the tyrosinase; then the tyrosinase is “escorted” by a whole set of other proteins that move it from where it is made to the melanosome and make sure it is inactive until it gets to the destination; then there are many different kinds of proteins involved with making the structure of the melanosome.

And just so you know the rest of the story, the pigment begins to form and continues until it covers up the entire pigment granule with black or red gooey melanin. This inactivates the tyrosinase and the melanosome is mature. Then other proteins in the cell carry it off to the very tippy ends of the pigment cell, where it is transferred into a growing hair, or into some other cell of the skin.

There is only one kind of gene that carries the code to make a tyrosinase protein. If this gene is missing, or if the code is wrong, you will not have skin/hair/eye pigment. You will be an “albino.” So for many years this particular gene was named the albino gene. Science has been busy trying to understand the functions of other genes involved with all this activity by studying which process is disabled if specific genes are defective, but that is a different story.

The point of all this detailed discussion is to give you an idea of the coordinated flow of information that is required inside the cell, from the genes that carry the code for all these many proteins to functions that are the result. Proteins can function to make chemical reactions happen at the right time and place in the cell; proteins can function to move things around in the cell; proteins can function as components of the structure of cells. But remember that every protein has essentially one function and that function happens because of the genetic code (OK, we skipped a bunch of steps there that we will come back to later).

Enzyme = a protein that functions as a catalyst
Structural protein = a protein that functions as part of the structure of the cell
Helper proteins of various sorts with various names are proteins that help the enzymes and structural proteins to do their functions.

And proteins have yet more jobs to do to keep the ecosystem alive.

Next Wednesday.

Genetic Code: Job Two

We have described the first job of the genetic code that is carried by the chromosomes. Chromosomes are the organelle(s) inside the nucleus of the cell that contain and preserve the genetic code and pass the code on to the next generation of cells. The first job of the chromosomes is to make an exact copy of the code — normally with no mistakes — just before the cell replicates in the process of mitosis. Mitosis is the process of cell division that gives rise to two daughter cells that are genetically the same as the original cell before it divided.  We described mitosis in recent posts.

Life does not arise spontaneously. Life on earth today is descended from pre-existing life in the form of cells, organs, organisms, ecosystems and the whole big blue marble of the living earth. All of the uncountable numbers of cells (there are billions of cells, just in your own body — so you can imagine how many make up the body of the whole earth ecosystem) all are descended from other cells, and all those cells together make up the information content of the ecosystem.

Today we will introduce the second job of the information of life, and that is to make the life function, or permit it to function. Every plant knows to turn to the sun (or away from it, depending on the plant or the plant part). Every finger can learn to type on this keyboard, using signals from the brain to the nerves. These capabilities of plants and animals are studied by the science of physiology.

Physiology is a fairly minor subdivision of biology in terms of overall significance, because biology includes the whole ecosystem and physiologists are interested primarily in the organismal level of organization (for discussion of levels of organization see Bare Bones Ecology, available as a pdf download, look under the links to the right or below this column). For this reason and because it is easy to find information about physiology, we will not describe it very much.  We now are talking about the information flow of the whole ecosystem.

Every cell can communicate with its environment or it would not survive, and the entire ecosystem “knows” what all its parts are doing, rather in the same sense that your body “knows” (without you knowing) what all its various parts are doing and how they all relate with their environment. And all the parts, the cells, the bodies, the ecosystems and the whole earth ecosystem — all of them are able to respond to the conditions in which they find themselves, both internally and externally.

Wo.

That must be a lot bigger than physiology.

And it is the genetic code that carries the primary responsibility for all this communication. It does this mostly by preserving and passing on the code that the cell uses to make proteins. And by making sure that the appropriate protein is produced inside the correct cell(s) at the right time in the right place in the organism so that (for example) the plants can turn toward or away from the sun and the cells can survive in this enormous life until they are no longer needed, and they know when to survive and when not to survive, and the entire “big blue marble” of our earth stays blue and green — alive — rather than being one big red storm like Mars.

Wo.

It’s too much to describe in one blog.

Next Thursday we will talk about proteins.

Meantime —

Happy Easter! Use it well, your miracle of life.

Mitosis

Inside the nucleus of each of your cells is an exact copy of the DNA that you received from your parents. As you know, every eukaryotic cell consists of molecules — water, proteins, lipids, carbohydrates nucleic acids and some other things — all organized inside a membrane. The membrane is referred to as “semi-permeable.” This means some things can cross the membrane and other things can not. In a normal environment, the cell controls what is inside and what is outside of itself. The organization inside the eukaryotic cell is complex, and includes many organelles. Organelles are lipid-bound structures that contain molecules organized to do specific functions, for example photosynthesis in plants, cellular respiration in nearly all cells, and my favorite, pigment granules inside pigment cells. Prokaryotic cells (like bacteria) are equally well designed, but they don’t have membrane-bound organelles inside themselves.

The nucleus of eukaryotic cells is the central core of the cell. It has two membranes around it, and it contains the DNA. DNA is the genetic material that is passed from generation to generation as a coded molecule made of nucleotides (we discussed in the last few posts). DNA is a physical molecule that is kept safe in the nucleus of your cells and copied exactly every time a new cell is made. It does not shift around or change its code (unless there is a mistake, which is very rare). It also does not leave the nucleus of the cell.

DNA has nothing to do with our political lives and is not found in our behaviors or our social structures — Bill Moyers notwithstanding, and if anyone knows Bill Moyers I hope he will read this little book so he can do a more accurate job of representing biology. Our understanding of the limiting parameters of biology (and our response to those limits) will determine whether or not humans on earth can continue the lifestyle to which we have become accustomed. So to Bill Moyers I say:

“Democracy does not contain DNA, and biology is not a whim of human language. Biology is a fact of  nature that will be here whether or not humans continue on this earth. It is far more important to our survival than either our democracy or our ability to make cute metaphors.”

Oh, oops, I got off on a rant, but you get the point. DNA is not a social reality. DNA in nature is designed to maintain the code of life and to regulate the biology of the cell. The DNA molecule carries the coded instructions for operating your body, cell by cell, and that’s all that it does. And that is one reason DNA is so carefully controlled in the cell, so it should not make mistakes in the code or wander out of the nucleus of the cell.

In the past few posts we have given an overview of DNA replication. DNA replication happens inside the nucleus of each cell when it comes time for the cell to replicate (that is when one cell divides to make two cells). To divide, the cell gets bigger, stretches out longer, and then pinches itself in half in the middle. Before it divides, the cell must make another copy of the genetic code, and then it must have a way to make sure that each new cell gets one of each of the chromosomes (the genetic code), so the two new cells are genetically identical. So that is when DNA replication occurs. We explained DNA replication in the last couple of posts.

After the DNA replicates, then the cell has two exact copies of each chromosome. Each chromosome is one enormously long DNA molecules, plus some proteins and other things that cluster around the DNA. All the DNA in all the chromosomes are your genetic code.

Because it is so long, the chromosome has to wind itself up into a shorter space before it replicates. These shorter, wound up (condensed) chromosomes are what you may have seen in pictures. The original chromosome and the copy chromosome (of each) remain attached to each other, and they all are still in the nucleus of the cell. Then, just before the cell begins to pinch itself into two cells, the nucleus dissolves. The condensed chromosomes line up in a space like a flat circle that is referred to sometimes as a “plate” between the two ends, preparing for mitosis.

Mitosis is the process of cell division that gives rise to two identical daughter cells.

The double chromosomes line up across the middle of the elongated cell, so that one of the duplicated chromosomes faces each end. Structures (microtubules, they are made of molecules) form in each end of the cell that look like little strings. The copy chromosomes are still attached to the original. The microtubules from one end attach to one of each duplicated chromosome, and those from the other end of the elongated cell attach to the other of each duplicated chromosome. Then one of each different chromosome is pulled to the left and the other is pulled to the right. The cell pinches itself in the middle until there are two cells that each have one of every different kind of chromosome, a nucleus forms around the chromosomes, and they stretch out long again so they are no longer condensed. The two daughter cells are genetically identical to each other and to the original cell.

This is the process of mitotic cell division (mitosis) and I’m sure you can find it on the web and in many books, in great detail, with lots of names for all the different stages of division. The detail is not as important to us as the bottom line, which is:

1. Every chromosome must replicate its DNA so each new cell will have the exact genetic code as the parent cell;

2. The replicate chromosome stays attached to the original chromosome while they line up in the center of the elongated replicating cell.

3. One copy of each chromosome is pulled to the left and another copy is pulled to the right in the elongated cell.

4. If all these processes are done properly, then each new cell has an exact copy of the DNA code of the original cell.