Lesson #4 Chromosomes and gene action.

It is interesting to note that the mid nineteenth century produced two of the greatest biologist of all time, each of which would eventually revolutionize the way we look at biology. What is even more interesting is that Darwin, with his theory of evolution, would cause an uproar while Mendel's work would go unnoticed for 34 years. Darwin could clearly see that plants and animals evolved, but he didn't have any idea of the mechanism. It is interesting to speculate on what might have happened had Darwin been acquainted with Mendel's work. Even if Darwin had been acquainted with Mendel's "particles of inheritance" there would still have been a missing element - where were these particles. At the time Mendel published his results chromosomes had yet to be named or even studied to any extent. However, by the late nineteenth century the basic biology of chromosomes, cell division, meiosis and fertilization were well understood, with one big exception. What did the chromosomes do, what was their role in the cell? It was assumed that they played some major role because there was always a regular process by which they divided, the way the gametes had half the number of chromosomes and that fertilization restored the chromosome number. When Mendel's paper was rediscovered in 1900 it quickly became apparent that chromosomes were the carriers of Mendel's particles which eventually became know as genes.

A detailed analysis of the structure and biochemistry of chromosomes and genes isn't necessary to understand basic Mendelian inheritance. However, a basic understanding of chromosomes and genes is necessary to fully understand some of the more complex aspects of Mendelian inheritance that we will cover in future lessons.

Chromosomes are made up mostly of histones, complex proteins; and DNA, deoxyribonucleic acid. It is the DNA which is the chemical that carries the genetic information that makes all living things what they are. DNA is a sequence of nucleotides lined up in a long linear string. There are 4 different nucleotides that can be combined in various sequences and different lengths. These nucleotides are adenine (A), guanine (G), cytosine (C) and thymine (T). Through a complex biochemical process these nucleotides are "read" in groups of three with different groups of three being translated into specific amino acids. The sequence AAG gets translated to one amino acid while CTG gets translated to a different amino acid. This is a very simplified picture, but it provides the basics of what we need to know.

A gene is a specific sequence of DNA that cells translate into a special class of proteins that are called enzymes. Enzymes are special types of proteins that act as catalysts - chemicals that help mediate a specific chemical reaction. All living things are made up of complex organic chemicals and it is enzymes that control how these organic chemicals get combined to form more complex chemicals. Thus, each gene corresponds to a specific enzyme.

Proteins, and hence enzymes, are made up of 20 different amino acids. Amino acids have a structure that allows these chemicals to link up to each other in long linear chains. A enzyme can have hundreds to thousands of amino acids and with 20 possible amino acids at each location there are a lot of different possible enzymes possible.

There are three levels of organized structure that each enzyme has. The first or primary structure is the linear sequence of amino acids. The secondary structure is the spatial orientation of the amino acids relative to each other. The third or tertiary structure, and the one we are most interested in, is the three dimensional structure that a enzyme assumes as a result of the folding and super folding of the chain of amino acids. This folding comes about because some of these amino acids can form strong chemical bonds between themselves while other amino acids form weaker hydrogen bonds resulting from slight differences in the electric charge of the amino acids. These bonds that amino acids can form have significant effects on the tertiary structure of a enzyme, and as we will see later, can have significant effects on how genes act.

The easiest way to visualize how enzymes work is to think in terms of a lock and key. When we put the right key into a certain lock the key will open the lock. If the key is too small or doesn't have the right notches it won't open the lock. If the key is too big it won't fit into the lock and hence not work. Enzymes can be considered as the lock and various chemical substrates are the key. The chemical fits into the tertiary structure of the enzyme and the enzyme then preforms some function that then results in a new chemical. For example, daylilies can produce cyanidin, an anthocyanidin pigment that produces rose/red color. If a certain enzyme is present it will take that cyanidin compound and add a hydroxyl group and convert it to delphinidin which is a lavender/purple pigment. However, this enzyme has to have a certain tertiary structure such that it "locks" with cyanidin in such a way that it can add the necessary hydroxyl group at the right location.

It should now be easy to see how recessive genes come about. Lets for example make a very simple example. Lets take a linear sequence of 100 amino acids. At location numbers 25 and 75 we have two amino acids that can form a strong bond with each other. This linear chain is now folded in half in a "U" shape. In our simple example the cyanidin compound can fit into the inside of the "U" and the two amino acids at locations numbers 1 and 100 then add the necessary hydroxyl group to produce delphinidin.

Now, lets modify our enzyme somewhat. First, if we eliminate the two amino acids at locations 25 and 75 then the linear chain won't form the necessary "U" shape and hence the enzyme won't function. A daylily that had two copies of this allele of the delphinidin gene would not be able to convert cyanidin to delphinidin and we would say it was a recessive allele of the delphinidin gene.

Now, lets restore the two amino acids at locations 25 and 75 so the linear chain forms the necessary "U" shape. However, now lets remove the two amino acids at locations 1 and 100. The cyanidin molecule will still fit into the "U" shape, but now there is no reactive site to add the necessary hydroxyl group that will convert cyanidin to delphinidin. This allele of the delphinidin gene will also appear as a recessive gene.

Any radical change in the primary sequence of a enzyme that results in a significant change in the tertiary structure, or a radical modification of the reactive site will result in a enzyme that becomes non-functional and hence will appear as a recessive trait when we make the necessary crosses. In the example present here there are two different alleles that are non-functional. Actually, these are different alleles of the same gene, but both of them are non-functional and hence both appear as recessive. However, we can't distinguish these two different alleles because both appear as recessive.

How do these changes in the enzyme structure come about? Each gene is a linear sequence of nuceotides that gets translated into a enzyme. These nuceotides are "read" in groups of three. When cells divide they generally replicate their chromosomes faithfully and the DNA gets accurately copied so that the daughter cells have identical copies of the DNA. However, sometimes, things don't work out quite correctly. A DNA sequence of ATG might get changed to AGG. The sequence AGG translates to a different amino acid than ATG. This change may significantly change the tertiary structure or the reactive site to make the gene non-functional, and we might eventually see this change as a recessive allele.

When we study Mendelian genetics we usually consider genes in isolation, but in reality all genes exist in complex interactions in a total living system. One gene produces a enzyme that preforms a certain function and the product of that reaction becomes the substrate for a second enzyme which in turns becomes the substrate for another enzyme and so on. We can visualize this as A > B > C > D. What happens if the gene that converts B to C becomes homozygous recessive? Now C is not produced. Now, even if the enzyme that converts C to D is present, we still don't get D because the necessary substrate that is required is lacking. Just because a dominant allele is present doesn't mean that it will be expressed.

The environment can also effect the phenotype. Wild rabbits have white fat but certain domestic rabbits have yellow fat. Crossing white fat rabbits with yellow fat rabbits reveals this as a simple Mendelian trait with white fat being dominant. Rabbits eat plants that contain xanthophylls, which are yellow compounds. White fat rabbits convert xanthophylls to a colorless compound so that it doesn't show up in the fat. Yellow fat rabbits lack the necessary enzyme to convert xanthophylls to colorless compounds and some of the xanthophylls are deposited in the fat giving the fat a yellow color. However, if yellow fat rabbits are fed a diet free of xanthophylls then they have white fat. If we didn't know that these rabbits were being fed a xanthophyll free diet we wouldn't know they were recessive for this gene. Although this is an extreme example, environmental factors can effect many traits in ways that can make it difficult to accurately classify traits. Temperature sensitive genes in particular can be quite frustrating.