Protein Synthesis

I have approached the topic of information flow through the ecosystem in a rather unconventional format. This is partly to stir up your mind, if you are bored with the mantra. It is also because I believe the logic of the ecosystem is better expressed in this way. It’s easy enough to float you a metaphor or to oversimplify the complexity of the biological system in an effort to clearly present the overall beautify of its organization. Or to become poetic instead of scientific when trying to express that beauty. But I think this implies that you can not think for yourself. Of course, you can. If you know the facts.

Science is about facts. Science is not necessarily about details, but it often happens that people need the details in order to make a clear picture of the logic. I am trying to weave a pathway between the factual details and their relationship to the beautiful system(s) that maintains life on earth. So, for information that is commonly available and accurately presented by reliable sources on the web I assume you will go to the web if you want more detail. The first and second laws of thermodynamics, for example, that we discussed in chapter one. The chemistry of the molecular interactions. The details of DNA replication. All of those you can find on the web. What may not be on the web are the well established relationship between these details and the survival of life on earth. Speculation abounds, in spite of the facts that are so well established. Similarly, with protein synthesis, you can go to the web for the details, which are elegant, complex, and well established. But I will try to overview the process.

The process of information flow in individual cells and/or organisms branches from the genetic code in two directions. The first serves the important role of maintaining the code and passing it on to the next generation of cells or organisms. This function is served by the process of DNA replication followed by cell division. We have talked about mitosis and cell division to make genetically identical daughter cells. Later we will talk about the manner in which DNA replication is followed by meiosis and fertilization in eukaryotic organisms to make fertilized eggs. Either way, and also in prokaryotic organisms, DNA replication preserves the genome (the genome is all the genes in one individual) so the cell can make more cells that are genetically the same as itself. Sometimes we refer to these as clones. Your body is a clone of cells that were produced in this manner.

To stay alive — to do its processes, the cell must make many different kinds of proteins, when and where they are required. To do this, the cell uses structural genes, that carry the code of the protein, and regulatory genes that determine when and where the protein will be produced. We don’t need to talk about regulatory genes. Now – very, very briefly, protein synthesis.

We have already said that the chromosomes are double stranded. They are in the nucleus (if it’s a eukaryotic cell) and they stay there, well protected. On one strand of the DNA is the genetic code and on the other strand is the copy of the code. The two strands remain bonded together with weak bonds unless they are needed to do DNA replication or protein synthesis. Because all the nucleotides are bonded end to end with strong covalent bonds, the sequence of the code does not shift around. Because the two strands are held together with weak bonds, these can come apart when the chromosome needs to replicate or a gene is needed to code for a protein. When the strands are together, the code is kept safe, it cannot replicate until the correct time, and it cannot make proteins in the wrong times/places. When it is time for the chromosome to copy itself, and all the genes of which it is composed, the two sides come apart and DNA replication occurs in a very controlled fashion. This happens just before cell division.

During the remainder of the cell’s life, it needs to use the genes at various times to do protein synthesis. Protein synthesis is the production of a protein, within the cell, using the code of a structural gene. Then the two strands of the DNA double helix open up only at the location of the gene that is needed to make a protein.

Remember the two strands of DNA that preserve the genetic code are composed of four nucleotide molecules that are arranged in the sequence of the code. The four nucleotides are adenine, thymine, guanine and cytosine. When a protein is required, the gene opens up and a different sort of copy is made of the gene. The code is the same, the covalent bonds never come apart, but the weak bonds between the two strands open up and the code is copied as RNA rather than DNA. DNA and RNA are both nucleic acids and they are both large molecules composed of smaller nucleotide molecules.

RNA is a nucleic acid molecule made of small nucleotide molecules that are bonded end to end by strong covalent bonds, to preserve the code. But instead of thymine, RNA uses a different nucleotide named uracil.

So for example if the DNA code is:


A DNA copy would be TTATGCCG

And an RNA copy would be UUAUGCCG

This means very little to you and me, but to the cell, it is the code for a protein.
Except that it is not a code for a protein. For one thing I just made it up and it probably has an invalid code. For another, proteins are very big molecules with dozens or hundreds of subunits. Proteins are large organic molecules made of smaller amino acid molecules that are fastened together end to end by strong covalent bonds. There are more or less 20 amino acids involved with this process. The RNA code identifies one amino acid with every three of its nucleotides. Therefore if a protein is small, only 100 amino acids, the RNA that carries the code would have to be 300 nucleotides in length (at least, but actually more because there are also signal sequences in the DNA and the RNA).

Next comes a very complicated, and almost incredible sequence of processes the cell uses, first to take the RNA copy of the gene out of the nucleus and into the cytoplasm, and then to use that code to make a protein. The energy for this large job will come from ATP molecules, and they got the energy — basically it comes from photosynthesis as we described earlier.

Besides energy, the cell requires many enzymes and different sorts of RNA molecules to grab hold of the message (the messenger RNA) and carry it out of the nucleus and match it up with the right amino acids and then make the covalent bonds between the amino acids to create the primary structure of that specific kind of protein that is encoded on that specific gene. The gene meanwhile can keep making more, or it can curl back up inside the nucleus and rest while the protein is doing its job somewhere else in the cell.

There are at least three kinds of genes involved in this process:

A structural gene is a gene that codes for the sequence of amino acids in a protein;
A regulatory gene is involved somehow in turning genes on and off;
And there are genes that encode the many kinds of molecules that are used to do all the processes that are required to do protein synthesis.

Stripped to its bare bones, a protein is produce inside a cell as follows:

DNA code → RNA code → Protein primary structure → then the protein folds up as we described earlier and is able to do its job
because of its shape (physical shape and distribution of energy charges).

If a genetic defect occurs so that there is no protein produced then one of the jobs of staying alive does not get done. For an example we used earlier, if there is no tyrosinase, then no pigment will form in the pigment cells and the result will be an albino animal. If the defective gene encoded a cell surface receptor, then if the receptor is not produced the cell can not respond to whatever signal the receptor was designed to detect.

And I am glad we are finished trying to overview the details of why this works the way it does. As incredible and marvelous as these facts are, the really most interesting part of this story is the way the information that is coded in the genes keeps the entire ecosystem alive and able to respond to changing circumstances.

Bare Bones Biology 003 – World Views

Bare Bones Biology – 100425

Earth day was great. The weather held, and all these people hustled around trying to find their best way to contribute to our common goals. I’m pretty sure most of them believe that we all have the same worldview, working to the same goal, thinking the same way they do. I used to believe that too, until I finally figured out that almost nobody thinks like I do. So today instead of talking about science, I’ll talk about worldviews.

I believe the human brain is hard wired to be logical. With giraffes, it’s the neck; with peacocks it’s the feathers; with us, it’s a well-developed innate capacity for logic. Everyone who starts life with a normal brain, the most normal thing about it is, the brain is always working to make a worldview that is logical.

Surely we’ve all had the experience of walking into a room, stopping and looking around because something doesn’t feel right. Something is not part of the normal logic of this room, and we feel uncomfortable until we figure out what it is. That feeling of discomfort drives all people, I believe, to build a logical worldview within which they can live in some comfort. Or, if they already have one they like, they will cling to it like their lives depend on their own worldview being accurate. We all need to have a worldview that makes logical good sense.

Well, of course there is a problem with this. At least two problems with this. The first is that we have to build our view of the world around our experience of the world. Everyone has a somewhat different environment, and also the environment keeps changing; therefore everyone has a somewhat different worldview. The result, if my worldview comes up against your world view, is Culture Shock! Culture shock is very uncomfortable, but it’s also exciting, and when we work our way through — it takes about a year for a big culture shock — we end with such a sense of competence and security compared with the time when we were afraid of people who are different. Or if we didn’t know that we can handle situations of difference.

So a good understanding of how to handle culture shock is something we can learn, and we can teach it to our children. In today’s world it’s a good thing to do. Go someplace different, live there for a year and listen to the logic of the new place. Or, actually, you can do this without ever leaving home, but you do have to listen to the internal logic in other people’s heads.

Of course the second problem is that everything logical is not necessarily real and true. A good many people don’t know this, but just because your worldview is pristinely logical doesn’t mean it is true. For example, in my introductory economics course I was told that the whole economic model is based on four pillars of solid reality, and it’s true, if you believe in the four pillars, the whole construct is beautifully logical.

Unfortunately, I guess they don’t know about the fifth one, and that’s too bad. We could have avoided these economic collapses if their worldview were more like the real world.

And of course that’s also true of our own worldviews. Nobody knows everything; everybody is wrong about some things, so we can never build a truly accurate worldview. Probably if we did, nobody would believe it. But it’s worth trying to get as close as possible to reality, because the safest worldview is one that is both logical and true. If we have logical reasons to believe that we can fly, for example, that doesn’t mean we really can, and we would be safer if our worldview were closer to reality.

So even though culture shocks and other attacks on our world view can be profoundly uncomfortable, I think it’s worth it. Anyhow, the moral of this story for you and me is that we are better off with a bit more safety and a bit less comfort. In a world that is full of exciting ideas and scary propaganda, it’s worth the effort to listen carefully to the logic of others, because there is always the chance they are right about some things at least. If they are, then our worldview needs to be tweaked a little. If we want to live in a safer world.

And now that you have had the lesson — imagine all the different turning on and turning off of a zillion genes and proteins over 11 months to make a baby horse.

Proteins in Action

So why are we going into all this tedious detail about how proteins function?

Because I want to explain how the genes control the information of the individual organisms and of the whole ecosystem. Maybe you only need to know that a gene can “turn on” and “turn them off,” and that’s how they control when and where the functions happen. Pigmentation happens only in pigment cells by producing the enzyme that causes pigment to form. Only in pigment cells. Or that most hormones influence cells, even though the hormone is outside the cell, because the cell has a protein on its cell surface that can respond to the hormone. Or that you can’t have the structures of your muscles (or their functions) unless the genes turn on (in muscle cells) that make the necessary proteins. Also none of these things can happen without organic energy that is available in the form of ATP that we have already discussed.

Protein functions depend upon their shapes. Every different kind of protein has a different shape.

Imagine here that the gray shape is a protein. Remember that “shape” means the physical distribution of the atoms and also the distribution of the energy. Physically the shape of the interacting molecules must fit together. In addition, energy interactions depend on the energy charges that are distributed over the surface of the molecule (or not). Positive charges attract negative charges. Similar charges repel each other. If there is no charge, the molecule usually is not inclined to interact.

Now imagine that the gray protein, on one of its sides, has an area that exactly attracts the black molecule. So whenever a black molecule is in the neighborhood it will pop right into the gray protein and stay there as long as conditions permit. And because the two molecules are attracted to each other, the energy relationships settle into a slightly new organization. As the energy relations over the protein readjust slightly to cuddle up to the black molecule, this causes all of the gray molecule to slightly shift. The shift moves charges and shapes all over the molecule until in this example the other side of the molecule is molded into a perfect “shape” to attract a third molecule. In the presence of ATP to provide the energy, these changes cause an important function to happen in the cell. And that function causes the gray protein to spit out both other molecules and return to normal. So it can do the same thing over again.

Or a receptor protein may be floating in the lipids of the membrane that surrounds the cell. The cell is maybe in an ovary and a hormone floats by. If the receptor is just the right shape to grab hold of the hormone, then the receptor-hormone complex will form and the receptor protein will be changed just enough that it activates something inside the cell.

In this way, and in other ways, the “shapes” of proteins are specific to their functions, and because they are specific they can be used to carry information from the gene to perform some action. Or proteins may be part of the structure of the cell. But to say again (and somewhat oversimplify), the point is that nothing happens unless the gene turns on to produce the protein and organic energy is available to activate the function of the protein.

The flow of information through the cell, the organism and the ecosystem is coded in the genes — the flow of energy discussed in chapter one is required for any work — the two paths cross to regulate almost everything that happens in life.

Social Justice Poster

I have learned a new skill.  Apparently you can click on the link above and download the poster.

Protein Structure

A protein is a molecule that consists of amino acids joined together by covalent bonds. The code for this sequence of amino acids is preserved in a gene.

Last time we said the second 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. 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 idea of “shape,” I am embarrassed to tell you this, is something of a metaphor for a set of characteristics that make up a protein in it’s final configuration, and also make it capable of adjusting to the conditions around it so that it can do its function(s) in an automatic response to those conditions.

Of course, we can’t really see what a protein is doing, so we require models that are based on the unchanging natural laws of chemistry and physics and the behaviors of the proteins, as they can be measured in various kinds of environments. I will try to describe a model for protein shapes.

Proteins are made of amino acids. Proteins are usually big molecules. Amino acids are rather small molecules. Molecules are atoms joined together with energy bonds, or they are bigger molecules made by joining together smaller molecules.

We should remember that atoms and molecules cannot be joined in just any old combination, but that every kind of atom is different in its distribution of energy. Some kinds of atoms join with others more strongly or less strongly or not at all. The distribution of energy in an atom, if the atom is part of a molecule, influences the distribution of energy in the molecule. And that is influenced by the energy of the environment. The environmental energy is usually measured as pH (that is, whether the environment more acid or more basic).

So. It is complicated.

We do not need to discuss all those complications. We only need to know they exist and understand that the “shape” of a molecule depends on the energy interactions among the atoms in the molecule and also the pH of the environment. We also need to know that the energy reactions are of two major sorts:

1. Covalent energy bonds are very strong and do not change without the help of an enzyme;
2. Weak energy bonds are constantly readjusting themselves depending on local conditions.

The primary structure of proteins consists mostly of the covalent bonds that attach one amino acid to the next amino acid in a long (or sometimes shorter) string of amino acids. These are the essential amino acids that we must eat in our diets in order to be healthy.

AminoAcid → AminoAcid → AminoAcid → AminoAcid → AminoAcid
(those arrows are strong covalent bonds)

The genetic code determines which amino acid will be where in this string and how long the string will be. Every different kind of protein has its own unique sequence of the specific kinds of amino acids, because it is made by its own specific gene.  The gene carries the code for the primary structure of the protein. We will discuss this later, but we have already said the function of many or most genes is to preserve this code and also to make sure the proteins are produced at the right time and place in the cell.

Once the sequence of the protein is firmly fastened together by covalent (strong) energy bonds that join the amino acids end to end, then there may or may not be one or a few covalent bonds created that join the sides of one or a few amino acids.  If these are present, they bend the protein molecule into its secondary structure.

The protein is then released into the cell where it folds up into a tertiary structure or shape. The tertiary structure of a protein.  The covalent bonds are formed by enzymes, but the tertiary structure is automatic as the protein folds up in response weak energy bonds that form among the various amino acids.

The weak bond is shown between the sides of two amino acids by the gray arrow; the strong bonds between their ends as black arrows. There are several different kinds of weak bonds.  Some weak bonds are stronger than others, all of them can be influenced by the pH of the environment.  The ends of every amino acid are the same.  This is why every amino acid as able to make a strong covalent bond with every other amino acid.  The sides of every kind of amino acid are different.  The proteins fold up, after the strong bonds are formed, because the sides of some of the amino acids will attract each other, some will repel each other and they will all finally settle into the configuration that is most comfortable for them all together.

Sometimes proteins pair up with other proteins by weak bonding or strong bonding.  Hemoglobin is an example. It consists of four molecules of protein — two of one kind and two of another kind.  These function together to carry red blood cells in the blood. If a protein consists of more than one chain of amino acids (polypeptide chain), its final structure is referred to as  its quaternary structure.

So, that is why proteins come in different shapes. The thing to remember from all this information is that each protein has the right shape to do one specific function in the cell. The covalent bonds make sure the primary structure is strong, and the weak bonds of the protein can adjust themselves to make the shape change just slightly when the conditions change.