Genetics with an "M"
Jennie R. Willis
Department of Molecular Biology
This article is copyright to the author. Federal law may prohibit the copying or unauthorized use of the article without express permission of the author.
Mystery, Myths and Magic
Historically, there are many written accounts indicating the interest, yet lack of knowledge that ancient peoples had regarding the transmission of traits between living beings, whether they be people, animals, or plants. One story of interest is recorded in the Bible in the 30th chapter of the Book of Genesis. Beginning in verse 29, we find an account of a business deal between Laban (an underhanded real estate broker) and Jacob, his nephew. Submerged in a history of family turmoil, Jacob reluctantly agrees to tend Laban's herds, but requests a unique method of payment for his services. He will be allowed to take all of the speckled goats out of the herd and keep them for himself. It must be noted that in Syria, at that period, a large percentage of the goats were solid black and they were deemed most valuable. Laban agreed to this transaction, but he wanted to make sure Jacob had nothing to start with, so he immediately removed all of the speckled goats from his herd and moved them far away so that they could not interbreed. Jacob, however, had his own little devious ideas. He took the young shoots and rods of the local trees and carved white stripes into them so that they appeared "speckled". Then he placed the rods before the watering hole where the goats mated, with the hope that the coloring of the young might be subject to prenatal influence. He also chose the stronger animals to be mated so that he would get offspring that were not only speckled, but also more hardy. Jacob, in fact, was successful and he eventually became wealthy, but not because of his magic plot. The black goats did bear speckled offspring, and because he chose to mate the strongest animals, the kids were healthy and virile, so his herd increased. Since Jacob had no idea that his success was due to recessive genes, rather than speckled rods, we can hardly acclaim him as the first geneticist, but perhaps we should give him credit for identifying the first "heterozygous-goat".
Throughout ancient history people made observations that suggested an orderly transmission of traits, such as disease that tended to "run in families", children tended to resemble their parents, and breeding of good animals or plants required starting with good stock or seeds. But the scientists and philosophers of the times were never able to prepare sound theories to explain these mysteries. Gradually, over the centuries, scientific truths began to emerge and accumulate along with the practical observations made primarily by farmers and stock breeders, so that by the 1800's the sexual nature of living organisms had been largely resolved, and some basic principles of genetics were becoming evident. It was clear from agricultural experience that stable varieties would breed true, that sometimes mating parents from different varieties would produce a hybrid (i.e., mule), that occasional "monsters" or gross deformities would occur, and that all results still seemed to be a matter of trial and error. However, despite the efforts of multiple investigators, no truly general laws of inheritance were established, and the quagmire of myths, mysteries and magic continued into the 19th century.
Mendel - the Monk
The mechanisms of heredity were first described in the 1860's by an Austrian monk named Gregor Mendel. His experiments dealt with the hybridization of garden peas, and led to the conclusion that there are hereditary particles contributed by each parent. We now call those "particles' genes. Several important principles of genetics were established by Mendel's observations of his pea plants. It might be helpful to introduce a few terms at this point. The genetic structure that contains the genes is the chromosome. Genes on the chromosome exist as one of two distinct types of alleles (one allele is contributed from each parent). If both alleles for a gene are the same the organism is said to be homozygous. If the alleles are different the organism is said to be heterozygous. Some traits are dominant. In Mendel's experiments he found that true breeding tall plants crossed with true breeding short plants yielded all tall plants. Therefore, tallness is dominant to shortness. We call the non-dominant trait recessive. Dominant traits are usually represented by capital letter (A), and recessive traits by lower case letters (a).
Examining Mendel's experiment:
The two alleles of a true-breeding tall plant would be AA and the two alleles of a true breeding short plant would be aa. If we now cross these plants
AA x aa ---> the observed result is all tall plants
This is because one allele is contributed by each parent so that all hybrid plants have one A and one a - since A (tall) is dominant all the plants look tall, but in fact, their genes (Aa) are not the same as either parent. Therefore, we must distinguish between the way an organism appear to us - called phenotype, and the actual composition of the genes or alleles it has - called genotype.
Principle of Segregation:
Following the initial cross of tall x short plants, Mendel's next step was to cross the heterozygous offspring (Aa) of the first mating. Although the parent (Aa) of the second mating all appeared tall, the observed offspring from the mating included not only the appearance of tall plants, but also the appearance of short plants. What has happened? Remember that each parent (Aa) will contribute either A or a, giving these possible combinations:
The phenotype shows 3 tall plants and 1 short plant. This has been established as the phenotypic Mendelian ratio of 3:1 for a single heterozygous trait. However, of the 4 total offspring we have 3 genotypes: AA, 2Aa, and aa, so the genotypic Mendelian ratio is 1:2:1.
The different genotypes represented in this cross are referred to as:
AA - homozygous dominant
Aa - heterozygous
aa - homozygous recessive
From this type of experiment by Mendel is derived the Principle of Segregation which states that during sex cell formation the members of a pair of allelic genes are separated from one another to pass into different gametes that are produced in equal numbers. Fertilization between gametes is random.
Principle of Independent Assortment:
The next step in Mendel's experimentation involved crossing plants that differed in 2 characteristics. We can illustrate this by taking our tall vs. short trait and adding to it a smooth vs wrinkled gene. The question we are asking is whether one trait will always be transmitted with the other, or are the traits transmitted independently of each other. In other words, will you always have tall and smooth together, or is it possible to get combinations of tall and wrinkled or short and smooth. Let's look at the cross:
|tall = A||smooth = S|
|short = a||wrinkled = s|
Again, crossing true breeders we have:
It is easier now to project the offspring combinations by using a Punnett Square. The possible gamete combinations from each parent are:
You work out the genotype. What is the genotypic ratio? What are the phenotypes? The phenotypic ratio?
Your answer should have been:
This turned out to be the result that Mendel observed. Obviously, the inheritance of the two traits, tall and smooth, were independent of each other. This type of experiment demonstrated what is called the Principle of Independent Assortment - the alleles of one gene sort out independently of the alleles of another.
Another basic and important concept derived from Mendel's work involves sex-linked inheritance. The sex chromosomes are designated X for the female and Y for the male. The actual determination of the sex of an individual (for most animals including humans and dogs) is a result of a combination from the parents of XX which designates female, or XY which designates male. Since a female possesses 2 X chromosomes, any trait located on the X can be transmitted to her offspring. a male will also contribute traits on his X chromosome, but if he donates Y (thus producing a male), no trait on the X chromosome will be contributed. Genetic traits transmitted on these chromosomes (X or Y) are said to be sex-linked and are subject to unique patterns of inheritance. Any chromosome other than the sex chromosome is called an autosome. Combining several terms we have now learned, we can describe a few of the basic patterns of inheritance:
Autosomal dominant - alleles are located on an autosomal chromosome and exist in a heterozygous state. One parent must exhibit the trait. All offspring of homozygotes and 50% offspring of heterozygotes will exhibit the trait.
Autosomal recessive - alleles are located on an autosomal chromosome and must exist in a homozygous state. Both parents are heterozygous carriers and will produce 25% homozygous recessive (affected) offspring, 50% heterozygous carriers, and 25% homozygous dominant (not affected) offspring.
Sex-linked - alleles are located on the X chromosome. Trait is most often expressed in males, females carry the trait but usually do not express it.
Although Mendel's investigations remained obscure until 50 years after his death, eventual acceptance of his careful observations, along with a snowballing acquisition of knowledge in the area of cellular biology, led to a dynamic breakthrough in our understanding of the mechanisms and molecules involved in the function of the cell. However, one of the questions remaining in the forefront was: "What is the gene?" The answer was to come in the 20th century with the birth and exponential growth of the science of molecular biology.
In order to describe a gene and its function, it may be easier to look at the end product for which it is responsible and work backwards. Whole living organisms such as people, dogs and trees are complex systems consisting of tissues like bone, skin, hair, leaves, etc. Tissues are made of sub-units called cells which consist of organized structures composed of macromolecules. The most important macromolecules fall into four categories:
- Carbohydrates - compounds made up of carbon, hydrogen, and oxygen; they are sugars and they serve as food supplies. Examples are starch and cellulose.
- Lipids - compounds made up of long chain fatty acids; they are a major component of cell membranes. Examples are animal fat and vegetable oil.
- Protein - compounds made up of amino acids; they provide structure and enzymatic function for the cell.
- Nucleic acids - compounds made up of a sugar, a purine or pyrimidine base, and phosphate. They contain and carry the genetic information.
For our consideration the two macromolecules we need to describe in some detail are the proteins and the nucleic acids.
A protein molecule has one of two functions:
- Structural - it provides the physical material that gives an organism shape and form. Examples are bone, hair, and muscle.
- Catalytic - it is the component of enzymes - the molecules that accelerate and control all of the biochemical reactions in the living cell. In other words, all that a living organisms is and can be is dependent on the enzymes it possesses.
The sub-units of proteins are amino acids. There are 20 amino acids. Try to visualize a protein alphabet with 20 letters, where the various combinations of letters (amino acids) will define the word (protein). Here is a list of the amino acids with designated abbreviations in parentheses:
|glycine (gly)||serine (ser)||arginine (arg)||phenylalanine (phe)|
|alanine (ala)||threonine(thr)||aspragine (asn)||tyrosine (tyr)|
|valine (val)||aspartic acid (asp)||glutamine (gla)||tryptophan (try)|
|leucine (leu)||glutamic acid (glu)||cysteine (cys)||histidine (his)|
|isoleucine (ile)||lysine (lys)||methionine (met)||proline (pro)|
There are two molecules classified as nucleic acids - DNA and RNA.
DNA - deoxyribonucleic acid consists of deoxyribose (a 5 carbon sugar), a base (either adenine, guanine, cytosine, or thymine), and a phosphate (PO4) backbone. it usually exists as a double strand arranged in a double helix. Both strands are able to replicate themselves to preserve the genetic information for the future generations. One of the two strands will also function to transmit the genetic message for protein synthesis to the cell.
RNA - ribonucleic acid consists of ribose (a 5 carbon sugar), a base (either adenine, guanine, cytosine, or uracil), and a phosphate (PO4) backbone. It exists as a single strand and functions as the carrier of genetic information to the organelles that will perform protein synthesis.
The gene determining sub-units of nucleic acids are the bases. Each nucleic acid has four bases. Therefore, we need to visualize a nucleic acid alphabet with 4 letters. The letters are A, C, G, and T for DNA and A, C, G, and U for RNA. The question we now ask is how can we store and utilize the genetic information needed to create and maintain cell life using the molecules we have just described.
The Miracle Molecule
Since there are only 4 nucleotide bases and at least 20 amino acids to define a given protein, it is obvious that some combination of the 4 bases is necessary to code for 20 amino acids. Neither 1 base (4 combinations), nor 2 bases (16 combinations) is sufficient. A combination of 3 bases, however, gives 64 "code words", called codons, which is more than enough for 20 amino acids. The genetic code is a triplet code, and it is all contained in the DNA molecules that are a component of the chromosomes that comprise the cells of all living organisms. The bases are arranged along the DNA strands in a specific sequence. DNA is a double-stranded molecule with strands being complementary to each other in relation to the order of the bases. A pairs with T; C pairs with G.
1 strand is used only to replicate the code when the cell reproduces
1 strand (sense strand) gives the message to make a protein)
Here's a hypothetical molecule:
The top strand will be used to replicate the code, the bottom strand will give the message for a protein with each codon (triplet) describing one amino acid. The entire sequence codes for a gene. The gene contains the information for one protein (enzyme). Each enzyme is responsible for catalyzing a step in a biochemical reaction. The sum total of these reactions builds tissue and maintains the functions of our body.
All genes together constitute the genome. The genome consists of all of the DNA contained in the chromosome (genetic structure). Humans have 23 pairs of chromosomes; dogs have 39.
Now that we know how and where the architectural plan for the organism is stored, the question to ask is how do we use the blueprint to build the house? The answer comes from our partner nucleic acid - RNA. RNA functions as the carrier of the DNA code to the organelle that will assemble the desired protein (enzyme). Let us look again at our hypothetical message strand of DNA:
(Remember, in RNA the base uracil substitutes for thymine - thus, uracil will pair with adenine).
The complementary RNA strand will be:
Figure 1. The Genetic Code. Four nucleotides in RNA, taken three at a time, can form the 64 combinations shown: 61 correspond to amino acids in protein; the other 3 are stop(termination) codons. (Drlica, Understanding DNA and Gene Cloning; P. 35)
Looking at the table (figure 1) we can decode this message and find the designated amino acid sequence to be:
methionine - proline - serine - leucine - arginine - glycine - histidine - stop
where the first codon (AUG) and the last codon (UAG) serve as punctuation marks. From this hypothetical example we have decoded a genetic message for a protein consisting of 6 amino acids. Cellular proteins are certainly of much greater length and also have 3 dimensional folding - the example given is to demonstrate the mechanism of transferring the DNA message to RNA. That process is called transcription. The RNA molecule that has transcribed the message is called messenger RNA or m-RNA.
Once the message has been transcribed to m-RNA the next task is to carry the message to the part of the cell that assembles the protein. This organelle is named the ribosome. In order for the ribosome to make the desired protein it must have at its disposal the necessary sub-units (amino acids) to put in place. Another RNA molecule, called transfer RNA (t-RNA), has the task of picking up the correct (specific) amino acid, carrying it to the ribosome and putting it into place as the m-RNA prescribes the proper order. The process of transferring the message encoded in m-RNA to the production line in the ribosome is called translation. The end result is the production of the protein molecule originally called for by the code in the DNA.
Figure 2. Flow of Genetic Information. From Drlica, Understanding DNA and Gene Cloning. (A larger image of this figure is also available.)
We can now define what is termed the central dogma of molecular biology. Central dogma is the concept describing the flow of hereditary information. With one generation information flows from DNA to RNA to protein to produce the ultimate phenotype. Between generations, DNA replicate itself precisely.
Mutation - a Mistake
If all the sequences of the genes replicate with fidelity, then all of the cells of the body develop and function properly. If, however, a mistake is made in replication, then the sequence will be altered. This is called a mutation. Let's go back to our hypothetical DNA strand - the code strand reads:
Let us suppose that in the third codon the second base (G) is accidentally deleted and, therefore, not replicated in the next generation. Reading the bases three at a time the strand sequence becomes
The reading frame has been shifted so that the complementary message strand made will now be different, and the m-RNA made will code for amino acids other than those required for the proper protein. We now have a nonsense message. Perhaps it would be better to explain with real words. Let's substitute 3 letter words for the DNA codons:
Again, if we delete the second letter (E) from the third codon (word), the next generation strand will read:
IT IS NONSENSE!
A gene that contains a mutation may be sufficiently altered so that the product it codes for is either made improperly, or in some cases not made at all. A change in the product (enzyme) will alter the body function and if it is a serious change may lead to a disease state (genetic order).
Since DNA strands replicate the code, a mutation or mistake during replication will reproduce from generation to generation. Therefore, mating animals with mutations perpetuates the mutation. The obvious evidence of mutation is exhibited in the phenotype (expression of the gene) of the organism. This is the level where we recognize dominance and recessiveness of traits. We know that to mate two diseased animals will produce and perpetuate the fault. We know not to do this because we can physically visualize the problem in phenotype. BUT - what about the carrier state? Carriers are individuals which do not exhibit the trait, but carry a copy of the mutated sequence in their genome. We cannot see this until a mating with another carrier produces the disorder. Statistically, the expression of the fault may be rare, but the mutated sequence is still passed on and on - and at some point in time, when an unlucky mating occurs, it will be expressed. By then we have implanted that mutated sequence in who knows how many siblings, and we are faced with a "poisoned population" in our gene pool along with a greatly increased probability of reproducing the fault.
Clearly, it would be of greater advantage to have a method of looking at the genetic material directly, so that a mutated sequence can be identified before the animal is ever bred. This raises the question of how to identify an aberration in the chromosome at the molecular level. Fortunately, this type of research is being presently pursued for both humans an dogs, and it will be a subject of supplemental material for this manual. There is hope on the horizon for expecting a day when DNA from blood or tissue samples can be analyzed and carrier states identified. Stay tuned!
It is not the purpose of this article to provide an exhaustive treatise on basic genetics, but rather to lay a foundation upon which an increasing knowledge of the science can be built, so that proper applications of these principles can be made in the pursuit of our hobby of breeding dogs. It is absolutely essential for all breeders to take the responsibility of educating themselves to the best of their abilities in order to protect the future of our dogs. The days of trial and error breedings must be history; we cannot afford to further pollute our gene pool. The days of gossip and innuendo must also be history; our dogs deserve better than the pit of pettiness and paranoia we so easily descend into. The mandate is clear: if our breed is to be healthy and hardy in years to come, we, as breeders, must be willing to face the truth and make tough decisions, we must be open to new ideas and change, and above all, we must be honest with ourselves and each other.
In the Book of Ecclesiastes the wise King Solomon writes:
"There is a right time for everything:
A time to find; a time to lose;
A time for keeping; a time for throwing away;
A time to tear; a time to repair;
A time to be quiet; a time to speak up "
For dog lovers and breeders it is:
A time to think; a time to act.
The Book, Tyndale House Publishers, Wheaton, Illinois 1971
Drlica, K., Understanding DNA and Gene Cloning, 2nd Edition, John Wiley and Sons, New York, NY, 1992
Farnsworth, M.W., Genetics, 2nd Edition, Harper and Row, New York, NY, 1988
Gonik, L. and Wheelis, M., The Cartoon Guide to Genetics, Updated Edition, Harper Collins, New York, NY, 1991
Goodenough, U., Genetics, 3rd Edition, Saunders College Publishing, Philadelphia, PA, 1984
Maxson, L.R. and Daugherty, C.H., Genetics - A Human Perspective, William C. Brown, Dubuque, IA, 1985
Pfeiffer, C.F. and Harrison, E.F., editors, The Wycliffe Bible Commentary, Moody Press, Chicago, IL, 1975