Mating seasons and reproductive physiology
Genes: Mendelian models for heredity
Castle-Hardy-Weinberg Equilibrium
Nucleic acids and the genetic code
Translation of the DNA code to phenotype
Genetic engineering, embryo transplants, and clones
An understanding of evolution begins with knowledge of reproduction and of the chemistry of life. This understanding also includes the mechanics of evolution as a process, the importance of variation, the nature of adaptation, and the difficulty of defining a species. This section is written from the top down, that is, starting with behavior, and progressing to anatomy, cells, chromosomes, and then nucleic acids.
Certain features of human reproductive biology and behavior are better understood by viewing humanity as a primate species whose reproductive traits differ from those of nonprimates. This approach provides us with a comparative perspective for studying ourselves, a general model that helps us discover processes and appreciate functional relationships. Additionally, this approach produces models for experimentation, foundations for modern biotechnology. Primate reproductive processes provide excellent examples of how we can use the tools of scientific method to study ourselves. Finally, but no less importantly, this approach provides a vantage point that functions to reject superstitions about ourselves that blind us to the realities, and sometimes to the beauty, of our world. (return to outline)
Mating seasons and reproductive physiology
Most primate species have a clearly defined breeding or mating season; that is, most mating behavior and copulations occur in a definable period of the year. In some primate species, mating behavior may be confined to a few weeks out of the year. For most species however, it is a period of several months during which behaviors are quite different from those at other times of the year. Each species has its own characteristic pattern, and each can be modified somewhat by environmental circumstances. (Variation in day length with the passage of seasons is the best documented stimulus among nonprimate mammals.) Seasonal mating behavior reflects a synchrony of hormonal cycles of group members. Although we presume that non-human infants born outside of the birth season are less likely to survive, there is little direct evidence of the controlling mechanisms that shape synchrony in humans. Whatever their original functions, these mechanisms are still clearly seen in human cycling.
| September | 16.1 |
| October | 2.6 |
| November | - |
| December | - |
| January | - |
| February | 2.5 |
| March | 2.3 |
Average number of days deviating from the population mean for the beginning of menstrual cycles of 76 college women living in close proximity for seven months. Data from December and January were incomplete because of Christmas vacation. (From B.B. Little, D.S. Guzick, R.M. Malina, and M.C. Rocha Ferreria 1989 Environmental influences cause menstrual synchrony, not pheromones. Am. J. Human Biology 1:53-57.)
Behavioral changes that accompany mating seasons in primates include marked increases in aggressive behavior, attention to sexual behavior among males, and sexual receptivity among females. Both sexes experience hormonal changes. With elevated spermatogenesis in males, testes size increases measurably. Rising androgen concentrations produce color changes in the skin of the scrotum, face, chest, and/or perianal regions of males of some primate species. Male behaviors can also be markedly different at this time; some species become more aggressive and quarrelsome, others more gregarious.
With rising estrogens associated with mating season, certain skin areas of females may exhibit color changes. Females of many primate species, including those as closely related to humans as chimpanzees, retain water and are highly vascularized (have an increased blood supply), producing a colored swelling that signals reproductive status. If copulation and conception occur, hormonal changes alter this sexual skin color of some species, announcing the pregnancy. Copulation patterns of some human groups correlate with hormonal cycles and some do not.
Though these characteristics are not unique among mammals, primate reproduction does have several unusual features. Mothers sustain an unusually large buildup of blood vessels that carry nutrients and oxygen across the placental wall to the developing infant. Primates also have unusually long gestation periods and ordinarily produce no more than one infant per year per mother. A few primate species regularly have twins or triplets, stimulating unusual parental care-taking behaviors such as paternal transport (father carrying the infants) or parking infants (hiding them) while the mother forages. Thus, each primate mother raises a relatively small number of progeny during her life span.
One of the obvious sequelae of a mating season is a birth season. Some advantages to synchronizing births to a restricted time period include: 1) Infants are born with peers that play an important part in each other's social development. 2) For a brief part of the year, a troop can modify its daily round and behavior to emphasize the demanding needs of infant caretaking. Predators, especially birds of prey, give special attention to primate groups during birth seasons. Small, defenseless juveniles and infants are ideal targets for predation. Troop activities and attention may, for a time, emphasize maternal activities, caretaking, and defensive behaviors. 3) Births seem to be timed to allow lactation and weaning to occur during seasons when food resources are most available.
It is important to appreciate that both sexes undergo cyclic changes that are controlled by the brain and endocrine system. Hormonal events are coordinated by the hypothalamus, a structure at the base of the brain, which has access, via nerve tracts, both to internal body chemistry and to sensory input from the environment. The hypothalamus regulates functions such as temperature, arterial pressure, blood fluid balance, electrolyte content of body fluids, feeding, gastrointestinal activity, coordination of endocrine glands, wakefulness and sleep, alertness, and excitement. The hypothalamus also has close structural relationships to areas of the brain concerned with sensations of pleasure or pain and with emotions such as rage.
Female hormonal cycles are usually counted from the day of the first evidence of menstruation, since this is usually readily defined. With estrogen and progesterone titers relatively low, the uterine lining sheds its built-up tissues, the discharge recognized as vaginal bleeding. After a few days, the hypothalamus initiates a hormonal cycle by producing gonadotropic releasing hormones, GnRH. These hormones stimulate the anterior pituitary gland (adenohypophysis), a small structure also located at the base of the brain, to produce follicle stimulating hormone (FSH) and luteinizing hormone (LH). FSH and LH are distributed throughout the body by the circulatory system. At the onset of the cycle, FSH titers are relatively high, then decrease slightly for the first 10 days. LH concentration remains relatively stable. FSH affects the ovary, particularly the follicles, a few of which begin to mature rapidly and secrete estrogens. Estrogens influence almost all body cells by affecting regulation of water, sodium, calcium, lipid metabolism, food intake, secretory functions of skin, body temperature, liver function, blood clotting, intraocular pressure, and sensitivity to other hormones.
Rising titers of estrogens also produce a myriad of physical and behavioral changes:
1) The uterine lining (endometrium) exhibits a build-up of vascularization in anticipation of implantation of a fertilized egg.
2) There are increases in metabolic rate, in protein deposition, and in fat deposition in the breasts.
3) The female is more aggressive, more active, and more receptive to sexual behavior. This temporary receptivity to sexual behavior, a consequence of rising titers of estrogen, is called estrus.
4) The sexual skin may swell and undergo color changes.
5) The anterior pituitary, again stimulated by the hypothalamus, this time produces a surge of LH and FSH, which has a synergistic effect to promote accelerated growth of ovarian follicular tissues and estrogen production.
At birth, a female has many primordial follicles in her ovarian capsules. About 300,000 follicles exist at puberty, each containing an ovum. At the beginning of each menstrual cycle, several follicles enlarge, forming a cavity around each ovum. One ovum begins growing about day 6; the others regress. The maturing ovarian follicle, called the Graafian follicle, reaches a size of about 15mm and is a primary source of estrogens. About day 14, the ovum is extruded from the ruptured follicle (ovulation). Some individuals may experience follicular bleeding and pain at this time. Cells from the follicular lining proliferate and the clotted blood is replaced with yellowish luteal cells that form the corpus luteum, which secretes estrogens and progesterone. If the ovum is not fertilized, the corpus luteum begins to degenerate about four days before the next menses (day 24). The remaining scar tissue is called the corpus albicans.
The most important function of progesterone is to maintain and promote changes in the uterine lining. It also decreases the frequency of uterine contractions which might dislodge the implanted ovum, produces secretions in the Fallopian tubes that may assist the ovum in its transit, and stimulates swelling and development of alveoli in the breasts. There is an immediate surge of progesterone production and concurrent diminution of LH, FSH, and estrogen levels at this time. If conception and implantation do not occur, levels of progesterone are reduced, resulting in menstruation, the shedding of vascular tissues that have built up on the uterine lining in anticipation of pregnancy. The hypothalamus, presumably in response to lowered levels of FSH and LH in the bloodstream, initiates a new cycle by again stimulating production of FSH. Cycles of this type show varying degrees of elevated titers of the hormones involved and varying degrees of physical changes. Indeed, some cycles may be anovulatory when cyclic variation of FSH and LH is not so extreme, failing to induce development of a corpus luteum.
If implantation and pregnancy occur, the uterus and placenta secrete large quantities of estrogens, progesterone, and at least two other hormones, chorionic somatomammotropin (CS) and chorionic gonadotrophin (CG). CS stimulates general growth and milk production. CG functions similarly to LH and under its stimulation, the corpus luteum secretes even larger quantities of progesterone and estrogen. About the fourth month of pregnancy, placental progesterone replaces that formerly produced by the corpus luteum.
Male primates undergo similar cycles, the major difference being that the targets of the pituitary hormones are the testes, rather than the ovary and uterus. In a male cycle, the hypothalamus stimulates the anterior pituitary to produce FSH. Primary spermatocytes are produced from spermatogonia. FSH regulates spermatogenesis by stimulating conversion of primary spermatocytes into secondary spermatocytes in the seminiferous tubules of testes. Each secondary spermatocyte divides to form two spematids which eventually become four spermatozoa. FSH thus initiates the proliferative process of spermatogenesis, but it will not proceed unless testosterone is secreted simultaneously by Leydig cells in the testes. Normal adult males produce spermatozoa in large numbers. The average male ejaculates 3.5 ml of semen (range is .5 ml to 11 ml), containing 120,000,000 spermatozoa per ml or an average of about 400,000,000 per ejaculate. A man is considered infertile if his ejaculate yields less than 20,000,000 spermatozoa.
The hypothalamus also stimulates the anterior pituitary of the male to produce LH (sometimes called interstitial cell stimulating hormone, ICSH, in males). LH promotes production of testosterone in interstitial cells of the testes (Leydig cells), apparently proportional to the amount of LH available. Testosterone appears to be necessary for spermatogenesis to proceed to completion, i.e. to produce mature spermatozoa. Production of testosterone during fetal development induces development of male sexual organs on a mammalian fetus in which the basic body plan is female. Fetal testosterone exposure suppresses the female cycling of hypothalamic and pituitary secretion. In the absence of this hormonal exposure, female morphology persists. Production of testosterone later in life gives rise to secondary masculine sex characteristics (facial hair, lower voice, etc.) that distinguish adult males from adult females. Androgens have behavioral effects quite similar to those of estrogens.
Neuroendocrine cycles related to sexual behavior of both sexes are vulnerable to stress. Severe stresses of many types may inhibit the hypothalamus such that spermatogenesis is decreased or synchronization of sexual cycles among members of a social group is disrupted. Extreme conditions (such as those found in a concentration camp, poor nutrition, long distance running, etc.) can disrupt hormonal cycles in either sex.
Although psychological stimuli play an important role in sexual acts, functioning of sex organs and orgasm are controlled by reflex mechanisms in the sacral and lumbar spinal cord. Men who have suffered spinal damage above the lumbar region can sometimes achieve ejaculation by genital stimulation. Male sexual stimulation produces erection and secretion of a small amount of lubricating mucus from the glands of Littré and the bulbo-urethral glands. At climax, peristaltic contractions expel spermatozoa into the urethra where they mix with seminal fluid and prostatic fluid to form semen. Rhythmic impulses from the spinal cord produce ejaculation. The ejaculate has a pH of approximately 7.5 and a milky, mucoid appearance. At first spermatozoa are relatively immobile, but enzymes in semen break down the mucoid consistency. Shortly after ejaculation, spermatozoa undergo their final stage of maturation (capacitation) and become motile, moving 3-5mm per minute. After ejaculation, sperm survive only a day or two at body temperature, but they can be stored for long periods at temperatures below -100' C. Female ova deteriorate quickly, probably remaining viable for no more than about 12 hours after ovulation. If fertilization involving "old" ova or spermatozoa occurs, the incidence of abnormal zygotes rises. It takes about three days for an ovum, assisted by peristaltic contractions of muscles in the Fallopian tube (oviduct), to travel the three inches between the follicle and uterus.
Control of sexual responses in females follows similar mechanisms with perhaps a male emphasis on visual and a female emphasis on tactile stimuli. Psychological and sexual stimulation of females produces engorgement of erectile tissue homologous to that of males, and results in secretion of mucus, primarily from the vaginal mucosa, the major source of lubrication during intercourse. Female orgasm may function to facilitate transport and fertilization of the ovum. In both sexes, orgasm affects the cerebrum to satisfy the sexual drive. (return to outline)
Fertilization, fusing of male and female gametes to form a zygote, usually occurs in the widest part of the uterine tubes near the ovary. Spermatozoa deposited in the vagina after coitus must travel through the female reproductive tract and intercept the ovum in its first day of passage. The conceptus continues the journey through the Fallopian tube. About three days after fertilization and three or four mitotic divisions, the zygote enters the uterus. It then consists of an inner cell mass that will give rise to tissues of the embryo and an outer cell mass that will form the placenta. Fluid penetrates its intercellular spaces, inflating the cavity within the outer cell mass, producing a blastocyst. By the end of the first week after fertilization, the blastocyst has embedded itself in the endometrium of the uterus, an event called implantation. The expected length of human pregnancy is about 280 days after the onset of last menstruation or 266 days (38 weeks) after fertilization.
This process can be interrupted by birth control measures at any stage. Indeed the rate of natural fetal loss is reported to be as high as 30% of all conceptions. In general, the conceptus is fragile in its early stages of development. The slightest disturbance of the uterine environment or abnormality may result in a spontaneous shedding of the conceptus. In contrast, advanced pregnancies are robust. The mother is often able to carry the fetus to term even under concentration camp levels of stress and great nutritional privation. (return to outline)
In 1839 a German botanist Schwann Schleiden observed that all living things are constructed of cells. Thus, cells are the smallest living structures. Living cells are enclosed by an outer membrane that limits the passage of materials into and out of the cell. A matrix of material called cytoplasm, in which specialized structures called organelles are suspended or move, fills this membrane.
There are two groups of cellular organisms, prokaryotes and eukaryotes. Bacteria and cyanobacteria, organisms that appear to have relatively simple and presumably primitive organization, comprise the prokaryotes. Prokaryote cytoplasm contains only one well-defined type of organelle, protein-generating structures called ribosomes. Prokaryote genetic material is one continuous molecule, a chromosome, and is concentrated into a region, the nucleoid, but there is no membrane surrounding the nucleoid. Chromosomes contain long strands of nucleic acids that carry the information necessary for cell activities such as metabolism, growth, and reproduction.
All other organisms have eukaryotic cells. In contrast to prokaryotic cells, eukaryotes have extensive internal membranes that function to partition the cell and organelles into compartments and to increase the internal membrane surface area. One of these membrane systems, the endoplasmic reticulum (ER) encloses a series of compartments. Eukaryotic cells have a great variety of organelles:
1. Nucleus - surrounded by a membrane, it contains the chromosomes, the hereditary material.
2. Ribosomes - the sites at which protein synthesis occurs (also found in prokaryotes).
3. Mitochondria - where cellular respiration occurs. They manufacture fuel in the form of ATP (adenosine triphosphate), a molecule that releases free energy when its phosphate bonds are broken.
4. Microbodies - compartments for various metabolic reactions require isolation.
5. Golgi apparatus - a membrane system whose compartments are specialized to receive, modify, store, and secrete substances.
6. Lysosomes - compartments of potent enzymes (such as digestive enzymes) that can break down substances.
7. Vacuoles - large membrane-bound sacs that store food or other substances, serve as disposal sites for metabolic by-products, or function to collect excess water.
A network of fibers, a cytoskeleton, gives cells shape and strength. A mesh of microfilaments of contractile proteins allows cell movements and shape changes. Microtubules change length allowing organelles attached to them to move inside the cell.
Plant cells generally differ from those of animals in several ways. Their cell membranes are bounded by cell walls of cellulose, giving the cell structural rigidity. Plants have a class of organelles called plastids, that may contain important pigments or serve as storage areas for substances such as starch. Disk-shaped chloroplasts are plastids that contain the green pigment chlorophyll. Their function is similar to that of mitochondria, except chloroplasts use light energy to generate ATP, and then uses ATP to synthesize sugar from carbon dioxide and water, a process called photosynthesis. (return to outline)
The primary genetic material, those structures that pass characteristics from parents to child, and which directs metabolism, is found in chromosomes, linear structures in cell nuclei. [An additional type of heredity, associated with passage of mitochondria from mother to child, will be discussed later.] Each eukaryotic species has a characteristic number of chromosomes. A normal human somatic (body) cell has a nucleus that contains 46 chromosomes in which genetic information is coded, whereas chimpanzees and gorillas have 48. Chromosomes consist of nucleic acids and various other substances, some of which are proteins that readily stain when exposed to different preparations, darkening the chromosome and producing bands of darker and lighter appearance. Stains make chromosome morphology observable with a microscope. Chromosome shape and appearance changes markedly during different phases of cell activity and stages of cell division. Chromosomes are most easily observed near the beginnings of cell division when they are tightly coiled, shorter and thicker. At this stage they are small double strands, each chromatid and its duplicate sister chromatid connected at a structure called a centromere. Variations in chromosome length, centromere location, and bands allow identification of individual chromosomes.
Though these chromosomes can be observed with a microscope, a more useful way to study them is to select a cell at the appropriate stage of mitotic development, stain the chromosomes with biological reagents, and photograph them. The photograph is then enlarged and the image of each chromosome is cut out, sorted by size and type, and re-photographed. The number and type of chromosomes represented is called a karyotype. A karyotype of normal human body cells has 22 paired chromosomes and one set that may be odd, for a total of 46. The odd pair of chromosomes, sex chromosomes, determines gender of the individual. Sex chromosomes are of two forms, the long straight X and a shorter bent Y. Individuals whose karyotype includes the XX combination are female; XY individuals are male if growth has been normal.
Two different kinds of cell division, mitosis vs. meiosis, occur in the two different kinds of cells, body cells vs. sex cells, respectively. Growth, replication, and repairs of body tissues are accomplished by mitotic cell divisions in which new cells retain the full complement of 46 chromosomes, diploidy. However, production of gametes (spermatozoa or ova) involves meiotic cell division, a process whereby only one of each pair of chromosomes is transmitted to any one progeny. Meiosis produces a cell with only 23, or half the normal number of chromosomes, a condition known as haploidy. At fertilization, sperm and ovum join to form a zygote and restore diploidy, the full complement of 46 chromosomes. Since a female produces only X chromosomes, all ova contain an X chromosome. If a male produces an equal number of X and Y spermatozoa, one would expect an equal number of male and female zygotes in a large human population. In fact, there appears to be a positive bias for Y spermatozoa and the sex ratio at fertilization may be as extreme as 140 boys:100 girls, perhaps because y-bearing sperm may move faster. Male conceptuses are however, less viable than female and the ratio of male:female drops to 105:100 at birth. The male:female ratio reaches 1:1 during the teenage years, and afterward the proportion of women increases steadily.
Genetic recombination, one of the most important features of sexual reproduction is produced in two ways -
(1) by independent assortment of chromosomes, the chance passage of one chromosome of each diploid pair to a gamete, and
(2) crossing-over. Pairs of homologous chromosomes are aligned during meiosis. If breaks occur in the paired strands, it is possible for segments to reunite with segments from sister chromosomes. The result is a cross over, an exchange of genetic information between chromosomes. This crossing over, along with independent assortment produce genetic recombination, combinations of genes different from those that occurred in the parents.
Mistakes can occur at any step during the reproductive or growth processes, but errors in meiosis are especially destructive since they produce abnormal karyotypes. These processes can be disturbed by agents from outside the cell (radiation, chemical agents,...) or by internal defects. Substantial deviations from a normal karyotype are usually deleterious. Over 2300 inherited disorders associated with karyotype abnormalities have been cataloged. One of the most common is Down's syndrome, a condition associated with an extra 21st chromosome (Trisomy 21), producing an individual with 47 chromosomes. A small percentage of affected individuals have extra fragments of the chromosome rather than complete trisomy. Individuals with Down's syndrome have certain characteristic body features, various internal disorders, a vulnerability to certain cancers, some mental retardation, and an unusually happy, friendly disposition. The rate of Trisomy 21 varies with maternal (and slightly with paternal) age, producing an overall rate of about 1 per 750 conceptions.
Rate of Down's Syndrome and Maternal Age
Age of mother (years) Rate (Trisomy 21 per live births) 20 years 1/1925 25 1/1205 30 1/885 35 1/366 40 1/110 45 1/32 50 1/12
Incidence is much higher than this at conception, but a majority are spontaneously aborted, and about 1 in 6 of those born alive will die in their first year of life. The rise of Trisomy 21 in children of older mothers seems to correlate with a decrease in the mechanisms of maternal detection and a consequent decrease in spontaneous abortion rather than an increase in trisomy occurrence. The older female appears more likely to carry a fetus with abnormal karyotype to term. Other trisomies have even higher fatality rates. A general rule is that a greater divergence from a usual karyotype complement produces more devastating consequences. Total absence of an X chromosome is generally lethal, but almost any other combination is possibly viable. An XX/XY karyotype produces true hermaphroditism (both ovaries and testes). A pregnant woman with access to good medical services can have her physician perform amniocentesis, a procedure in which fetal cells are collected from amniotic fluid, cultured, and a fetal karyotype prepared, allowing abnormal karyotypes to be identified. Incidence of abnormal genotypes not detectable by examination of the karyotype through amniocentesis does not rise with older maternal ages. Table 3-3 lists the more common numerical variations in chromosomes due to errors during meiosis.
A high rate of spontaneous abortion (between 33 and 40% of all conceptions) reflects the fallibility of human replicating mechanisms. Most of these abortions are not recognized. A miscarriage is defined by the World Health Organization as a conceptus born dead after the end of 22 complete weeks, weighing 500 g, or with a crown-heel length of at least 25 cm. Most women detect their pregnancies about week 6 after their last menstrual period, the fourth week of pregnancy. About 10% of recognized pregnancies end as spontaneous abortions. These estimates of spontaneous abortion, most of which have gross chromosomal anomalies, are drawn from Sweden where public education, health services, and prenatal care exceed standards for most of the world, including the United States. (return to outline)
GENES: MENDELIAN MODELS FOR HEREDITY
The characteristics of an animal or plant that we directly observe or measure (height, hair color, blood type, sex,...) comprise that individual's phenotype. If a characteristic is inherited, we presume that it is influenced by genetics; that is, the characteristic is controlled by units of heredity acquired at conception known as the genotype. It is convenient, but not wholly accurate, to think of a Mendelian gene as a unit of function that controls or determines a particular phenotypic characteristic. The idea of a gene was not initially based upon the study of chromosomes (or genes), but upon the study of phenotypic characters passed from parent to offspring. (return to outline)
The science of genetics began with Gregor Mendel [1822-1884], an Augustinian monk, who performed experiments with 34 varieties of peas. Mendel, interested in plant reproduction, controlled pollination of garden pea plants so he could study heredity. He studied the changes in phenotype from generation to generation and hypothesized about the hereditary mechanisms that would account for the observed variation. One thing that made his work unique was that he counted and studied all offspring from his hybrid experiments and constructed a quantitative model of heredity. He was knowledgeable enough to appreciate that chance events would approach the expected rates, but would not be exactly the predicted values. He appears to have bred peas long enough to have formed an hypothesis about pea inheritance and to have formulated his classic experiment to show his discoveries. His work was published in 1866, but the mathematical language of its presentation and the failure of Mendel's contemporaries to appreciate its significance relegated it to obscurity. This may not be surprising since chromosomes had not been discovered at that time. His observations that led to a gene hypothesis were simple but profoundly important.
Mendel's choice of experimental varieties and the use of them as both stock for the experiments and as a control group is best explained in his own words:
In all, thirty-four more or less distinct varieties of Peas were obtained from several seedsmen and subjected to a two year's trial. In the case of one variety there were noticed, among a larger number of plants all alike, a few forms which were markedly different. These however, did not vary in the following year, and agreed entirely with another variety obtained from the same seedsman; the seeds were therefore doubtless merely accidentally mixed. All the other varieties yielded perfectly constant and similar offspring; at any rate, no essential difference was observed during two trial years. For fertilization twenty-two of these were selected and cultivated during the whole period of the experiments. They remained constant without any exception. (Mendel, 1865; translated and reprinted in Peters, 1959; pages 1-20).
Mendel selected seven characters for a careful experiment:
1. form of ripe seeds (round vs. wrinkled)
2. color of the seed cotyledons (yellow vs. green)
3. color of seed coat (brown vs. white)
4. form of ripe seed pods (inflated vs. constricted between seeds)
5. color of unripe seed pods (green vs. yellow)
6. position of flower on stem (axial vs. terminal)
7. length of stem (6 ft. vs. 1 ft.)
In his first crossings, he conducted 287 controlled pollinations on 70 plants. In each pollination, a parent of one type was mated with a parent of a different type; for example round with wrinkled seed pods. The resulting seeds grew into plants, which he called the F1 generation. Dominant characteristics of the F1 generation were:
1. round seed
2. yellow cotyledons
3. brown seed coats
4. inflated seed pods
5. green unripe seed pods
6. axial flowers (along the stem)
7. long stems (longer than either parent)
Traits that disappeared in the F1 generation were labeled recessive. Members of the F1 generation were self-pollinated to produce seeds, which when planted, became the plants of the F2 generation. The characteristics of the resulting F2 generation included:
1. From 253 plants; 5,474 round and 1,850 wrinkled - a ratio of 2.96 to 1
2. From 258 plants; 6,022 yellow and 2,001 green - a ratio of 3.01 to 1
3. From 929 plants; 705 brown and 224 white - a ratio of 3.15 to 1
4. From 1,181 plants; 882 inflated and 299 constricted - a ratio of 2.95 to 10
5. From 580 plants; 428 green and 152 yellow - a ratio f 2.82 to 1
6. From 858 plants; 651 axial and 207 terminal - a ratio of 3.14 to 1
7. From 1,064 plants; 787 long and 277 short - a ratio of 2.84 to 1
Overall the ratio of dominant to recessive characters was 2.98 to 1, a value that Mendel perceived as approaching 3:1.
Mendel then produced an F3 generation by self-pollinating 100 plants exhibiting the dominant trait for each character. He found a consistent ratio for dominant:hybrid:recessive to be 1:2:1 for each character. The brilliance of Mendel's work lay in his recognition of the ratios and his development of models of heredity that explained them. Although he did not use the term gene, he recognized that there are alternate forms for each character. Each organism has two such units for each character, one inherited from each parent. If the two are different on an organism, one (the dominant one) may be expressed and the other (the recessive one) fully masked. This explains the 1:0 ratios (dominant:recessive) in the F1 generation, the 3:1 ratios (dominant+hybrid:recessive) in F2, and the 1:2:1 ratios (dominant:hybrid:recessive in subsequent generations.
Relationships between genotypes and phenotypes are easily visualized with the use of a Punnett square, a logical device invented after the turn of the century. For example, in experiment 1 (round vs.. wrinkled ripe seed), the round parents can only produce gametes containing the gene for the round character. Since this gene is dominant, it is represented with a capitol letter, "R." Parents with wrinkled ripe seed can only produce gametes containing the gene for the wrinkled character. Since wrinkled is recessive, it is represented with a lower case "r."
The Punnett squares below illustrate the type of gametes each parent can produce and the genotypes of their offspring (the F1 generation):
Genotypes of F1/ Phenotypes of F1
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F1 (first filial) generation Round x wrinkled ripe seed
-Round parents produce only round genes.
-Wrinkled parents produce only wrinkled genes.
-All progeny receive a Round gene from one parent anda wrinkled gene from the other.
-Thus all progeny have the genotype Rr.
-Rr genotypes produce a phenotype with round ripe seed..
In experiment 1, Mendel produced an F2 generation by self pollinating plants from the F1:
Genotypes of F2 :
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-Each parent can produce both R and r genes
Phenotypes of F2
F2 (second filial) generation round x round
-Since there three ways to produce round phenotypes (RR, Rr and rR), the ratio between the phenotypes among progeny is 3:1, (3 round: 1 wrinkled).
Mendel sampled some of the F2 generation and determined that 1/3 of the dominant phenotypes (round) would produce only round progeny, while the other 2/3 produced both round and wrinkled progeny in a ratio of 2:1 (round:wrinkled). Thus he established the frequency of genotype in this F2 generation as 1:2:1 (RR:Rr:rr).
Evident in Mendel's work are two general principles, sometimes called Mendel's Laws:
1) The principle of segregation is that each gamete carries but one character (gene), producing a paired condition in the organism. These paired units segregate during gamete formation and are restored to a paired condition at fertilization.
2) The principle of independent assortment recognizes that the genes of different characters segregate independently during gamete production.
This second principle is demonstrated by an experiment combining seed shape and seed color:
The observed ratio among the phenotypes (Round, Yellow: Round, green: wrinkled, Yellow: wrinkled,green) is similar to the predicted ratio of is 9:3:3:1. Furthermore the ratio of round to wrinkled is 3.18:1 and the ratio of yellow to green is 2.97:1, confirming the principle of independent assortment - one character does not effect the heritability of another character. Any phenotypic character that behaves in a manner that can be modeled as inheritance of single genes from each parent is called a Mendelian characteristic.
Alternate forms of a gene are called alleles, i.e., R and r are alleles of a gene that effects the shape of pea seeds. A polymorphic gene has two or more alleles. Homozygous individuals are those who have a double dose of the same allele (RR, rr,...), whereas heterozygous individuals have unlike alleles (Rr). The RrYy x RrYy mating that produced the F2 generation above, a crossing of two individuals identically heterozygous for two genes, is called a dihybrid cross.
At the turn of the century, several scientists, Hugo de Vries [1848-1935], Carl Correns [1864-1935], and Eric Von Tschermak [1871-1962], rediscovered and repeated Mendel's experiments. (return to outline)
Castle-Hardy-Weinberg Equilibrium
In 1903, W.E. Castle [1867-1962] postulated that gene frequencies remain the same from generation to generation in the absence of selection. The same mathematical observation was made independently in 1908 by G.H. Hardy [1877-1947] and W. Weinberg [1862-1937], the latter two publishing it independently in that year. The stability expected from generation to generation in a large randomly mating population is due to a statistical effect called the Castle-Hardy-Weinberg equilibrium. The key word is random and it is surprising how random the net effects of mating usually appear. Any mechanism or force that upsets random gamete exchange in a breeding population violates the Castle-Hardy-Weinberg assumption and causes relative frequencies of alleles to change. Evolution can be defined as a change in frequency of alleles in a population that occur through time; consequently, anything that violates the Castle-Hardy-Weinberg equilibrium is an evolutionary force.
Further, this model can provide a basis for estimating gene frequencies among the gametes that produced the progeny being counted. To do this, we must make three assumptions.
1. Using the example of Mendel's experiment #1, the percentage of R gametes plus the percentage of r gametes equals 100% of the gametes from which the progeny are derived. This can be written as R% + r% = 100% or p+q=1. The letters p and q represent the frequencies of the R gametes and the r gametes, respectively. Since each gamete has only one allele for this gene, p and q also represent the frequencies of R and r alleles.
2. The probability of acquiring an R gamete by chance is equal to the frequency of R gametes in the population of gametes.
3. The probability of two independent events occurring together is the product of each event by itself. Thus the probability of producing an Rr individual is the probability of acquiring an R gamete times the probability of acquiring a r gamete.
Thus from assumption 1:
p + q = 1 so 1 - p = q, where
p = the proportion of R gametes
q = the proportion of r gametes
1 = (p + q)2 produces 1 = p2 + 2pq + q2
This is a useful model. We estimate that 49% of the progeny are homozygous round pea seeds, 42% [21%+21%] are heterozygous round, and only 9% are homozygous wrinkled. The latter is a number that also could be arrived at by counting wrinkled phenotypes in the garden. Since wrinkled pea seeds in this model are homozygous for the r allele, the frequency of wrinkled seed bearing plants is the square of the frequency of gametes with r in the population of gametes that produced the plants:
q = q2 or .3 = .09
This model provides estimates of allele frequencies from observed counts of phenotypes. It is an intellectual tool that permits estimation of genotype frequencies from counts of phenotypes in populations. It is an idea of great importance in medicine, biology, and agriculture. (return to outline)
A more relevant application of Mendel's concepts involving human issues is the ABO blood system. In 1900, the physician Karl Lansteiner (1868-1943) described four major blood groups (A,B, AB, and O) that appear to fit a Mendelian model of inheritance. Characteristics of the ABO blood system also illustrate some of the properties of the human immune system, our bodies' defense against disease. Invaded by a microorganism, our body tissues must first identify the invader as foreign material before they can respond. Each protein bears unique molecular characteristics, called antigens, by which tissues are able to classify them as host or non-host.
Thus, antigens are properties of proteins that permit them to be identified. The human body manufactures a variety of cells that function to attack, accumulate, or destroy foreign proteins. These defensive tissues are called antibodies. When antigens of a non-host molecule are detected, antibodies are manufactured that are molecularly tailored to target the non-host antigens.
Antigen/antibody reactions are used to understand the ABO blood system. Blood groups are variations in red cell coat proteins that produce immunologic responses when the red blood cells of one person mix with the serum of another. In a hypothetical experiment suggestive of Lansteiner's research, a human blood sample is spun in a centrifuge, separating whole blood into components on the basis of cell density. The heaviest tissues, the red blood cells, lie at the bottom of the centrifuge tube. Some of these red blood cells are carefully extracted and injected into a live rabbit. The rabbit's immune system identifies the human red blood cells as non-rabbit, and manufactures antibodies to attack them. In a few days, a sample of blood is drawn from the rabbit, centrifuged and the clear serum (containing antibodies that have been tailored specifically to attack human red blood cells) is extracted. Since this is our first test serum, we will call it "A."
A small amount of test serum "A" mixed with a few drops of blood from the original human donor, results in a clumping reaction between the donor red blood cells and test serum antibodies. This agglutination (clumping) of red blood cells is readily observed under a low power microscope. The next step is to test blood from a series of human donors. Though samples from some donors clump, those from many donors are unaffected by test serum "A." The process is repeated, isolating red blood cells from a donor who does not react to serum "A," injecting them into a different rabbit, and extracting a second test serum, "B." Serum "B" reacts with some of the donors who were unaffected by serum "A," but there remain some donors, whose red blood cells are not affected by either "A" or "B." In addition, some donor samples react to both serum "A" and serum "B."
The chart below summarizes the behavior of red blood cell phenotypes in this experiment (+ indicates that agglutination occurs; - indicates that agglutination does not occur):
When red blood cells from one donor are mixed with serum samples from another donor, we find that the sera of phenotype A individuals have anti-B antibodies and the sera of phenotype B donors have anti-A antibodies. This Mendelian model of ABO blood groups illustrates the behavior of these phenotypes:
| Phenotype | Genotype |
Agglutination |
Agglutination |
ABO antibodies |
|
|
|
|
|
anti-B |
|
|
|
|
|
anti-A |
|
|
|
|
|
anti-A |
|
|
|
|
|
none |
|
|
|
|
|
anti-A & anti-B |
|
|
|
|
|
anti-B |
Information conveyed by this model is extremely useful. Gene alleles A and B are co-dominant; that is, both alleles of a pair are fully expressed in a heterozygote. Allele O is recessive; that is, it is masked in the presence of either of the dominant alleles, A or B. Thus the phenotypes of AO and BO heterozygotes cannot be distinguished from AA and BB homozygotes except by examining the phenotypes of their offspring or parents.
However, the ABO alleles produce different plasma antibodies. It is logical therefore, that the sera of AB phenotypes contain neither anti-A or anti-B, otherwise their red blood cells would be attacked by their own antibodies. Likewise, phenotype O can have both types of serum antibodies since its red blood cells are not agglutinated by either anti-A or anti-B. Additional alleles are possible in the ABO system. For example, there are two A subtypes (A1 and A2) with A1 being dominant over A2.
The ABO system is also expressed in other body tissues and fluids, but the ability to secrete ABO characteristics in fluids such as saliva or gastric juice is controlled by an independent gene, the Secretor gene, Se. The ABO system appears to be under selection pressure by disease processes. For example, it is possible, but not certain, that ABO variation correlates with variation in vulnerability to alpha-hemolytic streptococcus, influenza, polio, Escherichia coli, smallpox, and other infectious agents.
These concepts have direct applications to human problems. Blood transfusions and organ transplants have become life-saving procedures in modern medicine. Prompt blood transfusions sometimes can mean life to a patient in hemorrhagic shock (reduced blood volume and insufficient cardiac output). Type O red blood cells generally can be given to any host in the ABO series, because they will not be attacked by host antibodies. Thus, phenotype O is known as the universal donor. Conversely, phenotype AB is the universal recipient. Since blood transfusions carry the risk of transmitting diseases from donor to host (recipient), they are used only in life-threatening conditions. Blood donors are screened carefully and the donor blood pool tested extensively to make it as safe as possible.
An irrational fear of AIDS temporarily reduced blood stocks in blood banks, because some misinformed people mistakenly thought the disease could be contracted by donating blood. That fear has generally been corrected through education, and an adequate, relatively safe supply is maintained by donors. Another myth to be dispelled was that some desperate people routinely and repeatedly sell blood to blood banks. In this case, the public confused the life-saving blood bank system with businesses that provide blood products (mostly serum, not red blood cells) to industry. Human blood components, especially serum proteins, are widely used in the cosmetic industry. Shampoos and soaps that supply "body" and "condition" to hair often contain blood components. No reputable blood bank purchases blood. (return to outline)
A polymorphic condition is the existence of two or more alleles of a gene in a population. Natural selection acts to promote some alleles and to inhibit others, depending upon the system and circumstances. However, many variations may be equivalent or neutral and thus not subject to selection pressure. Whether or not we understand its significance, genetically based phenotypic variation is an important feature of human biology. An estimate of this genetic variation in a population is calculated as the percentage of proteins that show variation. A survey of 62 human proteins produces a total heterozygosity of 14.8% (Avers, 1989 page 282). When the sample is analyzed by population, 91.2% of this variability is within populations. Only 8.8% of this variation represents diversity between population. The high within population variance reflects the diversity that we see between each individual, and much of the between population variation may reflect selection in contrasting environments.
There are more than 30 human blood group systems known and at least 160 red cell antigens documented. It is not clear whether this genetic diversity is a result of selection by disease or a consequence of chance mutations that were retained in the absence of selection pressure.
Another blood variant, formerly the Rhesus system (named after the rhesus monkey in which it was first discovered), is currently designated the anti-LW system after its discoverers, Landsteiner and Wiener. This anti-LW system can produce hemolytic disease in newborns if the mother is Rh-negative and the child is Rh-positive. Since transplacental hemorrhage can immunize a mother and cause her to produce antibodies to fetal tissues, the risk of maternal immunization increases with successive pregnancies. The incidence of Rh hemolytic disease of neonates among American whites was 1 per 200 births prior to the development of medical techniques of prevention. Rh-negative phenotypes seem to have an elevated incidence of a variety of diseases, including typhoid, paratyphoid, tuberculosis, sarcoidosis, mumps, infectious mononucleosis, and viral meningitis.
The MN blood group system is useful to scientists as an example of a polymorphism that, like ABO, is easily tested and studied in human populations. It seems to have little relationship to disease agents. In contrast, the Duffy blood group system, known to have three alleles, Fy,Fya, and Fyb, includes a Duffy negative genotype, FyFy, which is completely resistant to one form of malaria, Plasmodium vivax.
More than a 100 variants of human hemoglobin are known, some of which represent important health problems. Over 100,000 deaths per year are attributed to sickle cell anemia, HbSHbS. The sickle cell character is produced by an allele that codes for a difference in the structure of hemoglobin (a structural change). However, if the defect is in the production of one or more of the globin chains, a regulatory change that suppresses the formation of normal quantities of normal globins, the resulting abnormal hemoglobin is called thalassemia. About 50 different thalassemias are known, and homozygous thalassemia phenotypes are characterized by anemia, fever, hyperuricemia, and skeletal pathologies. Relatively high frequencies of thalassemia alleles in the Mediterranean region suggests some sort of heterozygote advantage in a malarial environment. Likewise, unusually high frequencies of the sickle cell character are seen in the malarial areas of Africa.
Another red blood cell disorder that correlates with the distribution of malaria, deficiency of the enzyme glucose-6-phosphate dehydrogenase (G6PD), was discovered after American black soldiers reacted badly to the antimalarial drug, primaquine. Since the gene locus for G6PD is X-linked, the disorder is most often seen in males (they have only one X chromosome and the Y chromosome lacks the gene).
The most polymorphic of all known human systems are the human leukocyte antigens, HLA. Unlike other blood cell types, leukocytes (white blood cells) recognize and attack foreign or damaged cells within our bodies. Antigenic properties that are the bases for that recognition determine histocompatibility between tissues in the body. Although controlled by a small number of genes on chromosome six, more than 20 million different phenotypes are possible. Tissue histocompatibility is the body's first line of defense against parasites and microorganisms, but it also makes organ donations difficult and errors in the HLA system can be the basis for allergies or other immunopathic disorders.
Milk is a normal part of the mammalian diet only during the time of breast feeding, the first few years of life in humans. By age four, production of the enzyme lactase, needed to digest lactose (milk sugar), ceases in most humans. However, human populations that have long been exposed to dairy products have high frequencies of lactase-producing adult phenotypes. Availability of milk sugars in adult diets appears to select for genotypes that can digest them, producing population variation in production of the enzyme lactase. (return to outline)
Some characteristics behave in a Mendelian manner but are under the control of more than one gene. One allele may be masked or modified by action of another, a condition called epistasis. Table 3-4 (modified from Klug & Cummmings) illustrates a normal dihybrid cross and examples of deviations from the expected 9:3:3:1 ratio due to epistasis. It is also possible for an allele to effect more than one character, a condition termed pleiotropy. (return to outline)
If genes are functional locations on chromosomes, each of the 46 human chromosomes should bear numerous genes. Since chromosomes are inherited as units, genes found on a particular chromosome will be "linked" to each other and, except in cases of chromosome damage, they will be inherited as units. In 1905, William Bateson [1861-1926] and R.C. Punnett [1875-1967] demonstrated linkage in certain pea genes. The simplest areas on which to search for linked genes are the sex chromosomes, since sex-related traits in a phenotype are relatively easy to detect. T.H. Morgan [1866-1945] (1910) described a sex-linked character, eye color in fruit flies. Although eyes were normally red in the culture of fruit flies (Drosophila) that he was studying, a white-eyed male appeared. When this white-eyed male was bred with his red-eyed sisters, the offspring had red eyes. When these F1 hybrids were inbred, all female offspring were red-eyed; half the male offspring were red-eyed and half were white-eyed. Morgan crossed the white-eyed male with his red-eyed daughters to produce all four classes (red-eyed females, red-eyed males, white-eyed females, and white-eyed males) in approximately equal numbers.
One of the earliest recognized human X-linked characters is a disease known as Hemophilia A, a major symptom of which is uncontrollable bleeding after an injury. The most famous family to exhibit this disease is that of Queen Victoria [1819-1901], who ruled the United Kingdom of Great Britain and Ireland. An X-linked recessive trait, Hemophilia A is expressed in any male who has the allele on his single X chromosome. One feature of an X-linked character is that it can be transmitted from father to daughter, but never from father to son, since males acquire their X chromosome from their mother. Consequently a heterozygous female would be expected to contribute an X chromosome with a Hemophilia A gene to half of her children. Half of the sons of a heterozygous female and a normal father should be hemophiliacs and half of their daughters should be heterozygotes (carriers of the gene but not exhibiting the disease). A hemophiliac female is therefore homozygous, having acquired the gene from both parents.
This is a partial list of phenotypic characters that are thought to be controlled in part by genes on the X chromosome.
Phenotypic conditions controlled in Part by Genes on the X
Chromosome
(modified from Sutton, 1965, page167)
1. partial color blindnessk deutan series
2. partial color blindnessk protan series
3. total color blindness (note most cases are autosomal)
4. glucose-6-phosphate dehydrogenase structure
5. Xg blood group system
6. Duchenne type muscular dystrophy
7. muscular dystrophy of Becker
8. hemophilia A (AHG deficiency)
9. hemophilia B (Christmas disease; PTC deficiency)
10. agammaglobulinemia
11. gargoylism (Hurler syndrome - note there is also an autosomal form)
12. Hypoparathyroidism
16. diabetes insipidus, nephrogenic type
17. diabetes insipidus, neurohypophyseal type
18. Lowe syndrome
19. hereditary hypochromic anemia
20. angiokeratoma diffusum corporis
21. dyskeratosis rongenita
22. hereditary bullous dystrophy, macular type
23. keratosis follicularis spinulosa decalvans cum ophiasi
24. ichthyosis vulgaris
25. anhidrotic ectodermal dysplasia...
(return to outline)
Mendelian traits can be represented by a relatively uncomplicated model. If a genotype can be identified and if there are few alleles for that gene locus, prediction is straightforward. Unfortunately, most heritable characteristics are more complex and are affected by more than one locus. An example that illustrates this complexity is inheritance of the ability to taste phenylthiocarbamide (PTC). People vary in the concentration of PTC that they can taste, a characteristic that is relatively easy to measure in an experiment:
A series of 13 small cups is prepared, with different dilutions of PTC in water. Cup 1 is the strongest solution (0.13 %) and the concentration is reduced by half in each succeeding cup. Volunteers are asked which cups have PTC and which cups are simply water. The most dilute solution of PTC that is detectable is recorded as the threshold at which the individual can taste PTC.
It is evident that polygenic influence on phenotypic characteristics can produce continuous variation, an effect demonstrated mathematically by Ronald A. Fisher in 1918. . Distinctions between genotypic classes become even more blurred when environmental variation is added. In reality, few phenotypic characteristics can be modeled by a simple Mendelian approach. On the other hand, many traits that appear continuous (such as height, weight, skin pigmentation,...) can be explained by relatively simple polygenic models. (return to outline)
Nucleic acids and the genetic code
As evidence that pointed to chromosomes as carriers of genes accumulated, the primary quest of cytogenetics became the search to understand the chemical nature of the gene. About 1900, Phoebnus Aaron Levene [1869-1940] worked out the chemistry of "nuclein" (deoxyribonucleic acid or DNA), a compound that had been isolated in 1873 by Johann Friedrich Miescher [1844-1895]. Levene demonstrated that DNA was composed of equal amounts of four bases. This seemed an unlikely candidate for the genetic code, since it was too simple - a molecule with only four known variants. Later, Hershey and Chase (1952) demonstrated that a virus particle was composed primarily of DNA. In 1953, James D. Watson and Francis Crick, assisted greatly by X-ray crystallographic data from Rosalind Franklin, proposed a model for DNA that explained the structure and chemistry of DNA. This structure implied a mechanism of replication and explained how DNA could function in inheritance. Working out how DNA controlled metabolism by coding for proteins followed quickly, and led to a formulation the "Central Dogma" of molecular biology, DNA -> RNA -> protein.
An important component of human chromosomes, deoxyribonucleic acid (DNA) is the primary genetic material. Additionally, a small quantity of DNA is also found in mitochondria, small self-reproducing organelles within the cytoplasm of cells that produce most of a cells' energy.
A DNA strand is formed by stringing together a series of molecules called nucleotides. A nucleotide consists of three components; a five carbon sugar (deoxyribose), a nitrogenous base, and phosphoric acid. There are five different nitrogenous bases found in nucleic acids, adenine, guanine, cytosine, thymine, and uracil (abbreviated A, G, C, T, and U). A, G, and C are found in both RNA and DNA, but T occurs only in DNA and is functionally replaced by U in RNA. One of these bases is bonded to each sugar unit. The phosphate component provides a high-energy bond which links sugars together to make a long chain of nucleotides called a polynucleotide. Another nucleic acid found in cells, ribonucleic acid (RNA), is based on a slightly different sugar (ribose). The sequence of bases along polynucleotide strands is the genetic code that is passed from parent to progeny.
DNA strands are usually double and tightly coiled around each other like two wires twisted together. The paired strands are held together by weak bonds between the bases on opposing strands. However, the sequence of bases along the two coiled strands is complementary because of the number of bonds formed. A only pairs with T (A:T or T:A) and C only pairs with G (C:G or G:C). Consequently, the sequence of bases down a strand is recorded in complementary pairs in its associated homologous strand. The genetic code therefore is the sequence of ATGC... in DNA strands associated with chromosomes. One vital property of DNA is that if two homologous coiled strands are separated, their code (sequence of bases) serves as a template for the formation of new strands of nucleic acids (either RNA or DNA) through complementary pairing of bases. This is the process by which new nucleic acid replicates the original code - the sequence of bases.
RNA is similar in structure to DNA, except that RNA contains U instead of T and the sugar, deoxyribose, is replaced by ribose. There are three functionally defined classes of RNA, messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). Each is produced by complementary pairing from a parent DNA strand except that U is substituted for T.
Ribosomes, small organelles in the cytoplasm of cells, are largely composed of rRNA, and they are the site at which amino acids, mRNA, tRNA, and growing polypeptide strands interact to produce proteins. Messenger RNA bears copied segments of code from a cell's primary DNA that are necessary to specify a particular protein, and migrates to a ribosome outside the cell nucleus where it is decoded. The mRNA code specifies the sequence in which amino acids will be linked to form a protein. Thus proteins (polypeptides) are strings of amino acids.
Each code word, or codon, consists of three adjacent nucleotides. Since each nucleotide could have any of four bases, there are 64 possible words (4 x 4 x 4 = 64). This is more than enough vocabulary to specify each of the 20 amino acids that are the building blocks of proteins. Accordingly, some codons are redundant, for example, UUU and UUC both indicate phenylalanine. Every mRNA message begins with the codon AUG, which serves as the message START. STOP is specified by UAA, UAG, or UGA. The message string that codes for a protein or polypeptide sequence is called a cistron or, alternatively, a structural gene. Some DNA codons produce RNA segments that do not lead to the production of proteins, but instead control the actions of other DNA segments. These genes that do not produce polypeptides are called regulatory genes. Repetitive sequences that do not seem to code for anything are called interons.
Transfer RNA bonds to a particular amino acid, migrates to an appropriate ribosome, then bonds to rRNA at a position specified by mRNA. Since tRNA and mRNA bond through base-pairing, they must each have complementary forms of the codon for that amino acid, a process called codon and anticodon matching. When protein synthesis is initiated, the first amino acid incorporated is always methionine, since AUG codes both for START and methionine. Typical polypeptide strings are hundreds of amino acids long. When movement of the next tRNA with its amino acid brings it near the position at the ribosome, it is bonded into place and the process continued until a STOP codon is encountered.
Thus the inherited genetic code is the nuclear DNA of a cell. This code controls protein synthesis through manipulation of RNA codons. The characters and activities of cells and the organisms they comprise are a consequence of this polypeptide synthesis by structural and regulatory genes. In terms of DNA, the concept of gene changes from the imagined unit used in Mendelian genetics to a functional set of codons within a DNA molecule. (return to outline)
Life is a software package, written in nucleic acid code. Organisms are the hardware that "run the code". A primary function of the hardware is to sustain the software, replicate it, and pass it on with as few errors as practical. Thus when organisms reproduce, they do not create life. They pass it on.
Our culture sometimes confuses "life"
with "organism." We also have a tendency to imagine
the process as more foolproof than we should. Many of our myths
can be attributed to ignorance about biology and biological systems.
But our knowledge is getting better.
Organic molecules on planet Earth are CHNOPS compounds; that is, they are largely built of carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur. Since most organic molecules are built around a string of carbon atoms, our biosystem can be considered carbon-based. Consequently, in chemistry, molecules containing carbon atoms are called organic molecules (except for CO2 and some of the acids and salts formed by CO2). The term inorganic refers to CO2 and molecules that do not contain carbon. Colloquially organic also means "organic in origin" or "derived from living organisms." The reader must decide from context which meaning of the term organic is implied. The laboratory synthesis of urea in 1828, the first laboratory synthesis of a naturally occurring organic compound, demonstrated that chemical reactions in living organisms are not different from chemical reactions in inanimate substances. This was an important refutation of vitalism, the theory that a vital force unique to living organisms controlled chemical reactions and activities inside living things. An alternative school of thought, mechanism, argued that processes within organisms follow the same rules of physics and chemistry seen in the inanimate world.
A carbon atom forms four strong bonds to other atoms around it. Carbon-based molecules are considered to be relatively stable since it requires 80 kcal/mole to break a carbon bond. Carbon's nearest rival as a candidate for producing organic molecules is silicon, which also forms four bonds, but only 40 kcal/mole are required to break a silicon bond. Thus, silicon-based molecules are more fragile than those of carbon.
The simplest of organic molecules, the hydrocarbons, are composed of strings of hydrogen and carbon. If there are fewer hydrogen atoms than bonds, carbon chains may bend into closed rings. Hexagonal and pentagonal rings are common and important in many organic molecules. If a hydroxyl (-OH) is added to one of these rings, an alcohol is produced. Addition of a carboxyl (-COOH) to a carbon ring produces an acid. An acid is a compound that produces hydrogen ions (H+) when dissolved in water (H2O); a base is a compound that contributes hydroxide ions (OH-).
The sugars in nucleic acid are five carbon rings called pentoses. The difference between deoxyribose (found in DNA) and ribose (found in RNA) is the presence of a hydrogen atom in position 2 on the carbon ring in deoxyribose versus a hydroxyl group (-OH) in ribose.
The bases C, T, and U are six-membered rings of nitrogen and carbon. A and G are slightly larger and more complex.
DNA is a series of deoxyribose units held together by phosphoric acid and bonded to a homologous strand of deoxyribose units by the complementary bases. (return to outline)
Major energy pathways in cells employ a molecule closely related to DNA, adenosine monophosphate (AMP). Thus the chemistry that controls and powers cellular activities is based upon simple organic compounds similar to nucleotides. The addition of phosphates to AMP produces energy-rich compounds. Then when a phosphate is surrendered, a relatively large amount of chemical energy becomes available for cell metabolism. Conversion from adenosine triphosphate (ATP) to adenosine diphosphate (ADP) provides most of a cell's energy. A major component of metabolism is respiration, in which energy (in the form of ATP) is generated from the catabolism (degradation) of carbohydrates, lipids, and sometimes amino acids. In humans the end products (ammonia, carbon dioxide, urea, and water) are excreted through kidneys, lungs, and skin. (return to outline)
Amino acids, the elementary units of proteins, are relatively simple. A protein is a series of amino acids joined together to make a large molecule. Each of the thousands of different kinds of proteins has a specific sequence of amino acids. For example, myoglobin, a protein that carries oxygen molecules in muscles is constructed of 153 amino acids. A large molecule, made by joining many smaller molecules through identical bonds, is called a polymer. An enzyme that synthesizes polymers is called a polymerase. Nucleic acids and proteins are polymers. Proteins form structures, enzymes, and hormones, the substances that make up organisms and control their metabolism. (return to outline)
Translation of the DNA code to phenotype
All of these processes are aided by specific enzymes and powered by energy from ATP or other similar molecules. A large molecule called an RNA polymerase locates and bonds to a certain sequence of bases on a DNA strand. The polymerase moves down the strand, unzipping the complementary homologous DNA strands. RNA nucleotides in the surrounding medium attach themselves to the unzipped DNA segment by complementary pairing of bases and copy a segment of the genetic code. When an end sequence on the DNA strand is encountered, the process stops. The mRNA segment with the transcription, the coded RNA formed by complimentary base pairing with the DNA template, separates and DNA recoils. However, many sequences of the transcribed message either do not code for any known process or amino acid, appear to be meaningless noise, or are redundant copies. These are recognized and deleted by other enzymes. Sometimes these intervening sequences (IVSs) are hundreds of bases long and some genes have dozens of IVSs. The edited mRNA strand migrates out of the cell nucleus into cytoplasm and eventually encounters a ribosome.
The fluid or matrix inside cells contains large numbers of raw materials for cell processes, including many amino acids. Transfer RNA is a folded (sometimes cloverleaf-shaped) strand of RNA. One of its two poles will bond only to a specific amino acid (with the assistance of one of 20 enzymes tailored for this purpose). The other tRNA pole (anticodon) recognizes the specific codon for that amino acid in mRNA and, by complementary pairing, attaches the amino acid to the position specified by mRNA. The resulting string of amino acids is a protein (a polypeptide chain of a hundred or more amino acids). When the mRNA codon for termination (UAA, UAG, or UGA) is read, the protein molecule is completed and released.
The simple genetic code has extraordinary power to produce complexity in organisms, but the fundamental chemistry of Earth life is singular - the same in all beings. If extraterrestrials with a non-earth biochemistry were to study our planet, they should note the continuity of nucleic acids in life on earth. It would be logical from this perspective to consider all earth life a single biochemical entity. (return to outline)
The primary structure of a normal adult hemoglobin (HbA) molecule provides a useful example of a protein. It is composed of a protein unit and four heme groups. Heme is a complex iron-containing chemical ring structure that enables the molecule to combine with oxygen. The protein unit consists of four strands, two identical alpha chains of 141 amino acids and two identical beta (ß) chains of 146 amino acids. These chains fold together to produce a characteristic three-dimensional shape around the hemes. Changes in the amino acid sequence alter a proteins function, for example the amino acid in position 6 of the beta chain is glutamic acid (Glu). Substitution of valine (Val) at this position changes the properties of the globin unit and ultimately the characteristics of hemoglobin. In low-oxygen environments, these hemoglobin molecules are attracted to each other and aggregate, forming polymers of hemoglobin. This distorts the shape of the red blood cell and changes it from its normal disk shape. This abnormal hemoglobin is called sickle-cell hemoglobin (HbS). Discovery of this relationship between amino acid substitution and Hbs in 1957 became the first example of a relationship between one gene and a specific polypeptide chain.
Substitution of lysine (Lys) for glutamic acid (Glu) in position 6 of the beta chain produces another type of hemoglobin, Hemoglobin C. If the same substitution (lysine for glutamic acid) occurs in position 26, it produces yet another hemoglobin, Hemoglobin E. Dozens of such hemoglobin variants are known, each with slightly different properties. Indeed, fetal hemoglobin (HbF) has a different structure from that of HbA. At birth, the proportion of HbF red blood cells varies from 60% to 90%, but it is entirely replaced by HbA by four months of age in normal infants.
Genes respond to epigenetic (developmental) circumstances. Different genes are activated in skin cells than in muscle cells, with the result that cells produce proteins appropriate to their specialization. Control of ontogeny (growth and development) occurs in part by alterations in gene reading. The mechanisms involved in turning genes on and off, and controlling ontogeny are poorly known and are a major area of current research.
Thus the model of a gene that was applied to Mendelian genetics must be modified in light of our expanding knowledge of DNA. A gene is a locus or region (or regions) on a nucleotide strand that controls the synthesis of some particular protein or gene product (tRNA, rRNA,...). A large polypeptide chain may contain thousands of base pairs and some proteins may consist of more than one chain (as in the hemoglobin molecule). Production of organisms with genes tailored to some industrial purpose (genetic engineering) will be greatly enhanced if genes that control the enzymes of a particular protein pathway are located close to each other so that they may be copied or manipulated as a group. (return to outline)
Mitochondria, the organelles in the cytoplasm responsible for most energy production, have their own DNA, a single large chromosome coiled into a loop as is often seen in bacteria. They are semiautonomous with their own genetic system, their own synthesis of amino acids into mitochondrial proteins, and their own asexual reproduction. This autonomy led to the hypothesis that mitochondria may be derived from ancient aerobic bacteria that were captured by larger predatory cells and eventually developed a symbiotic relationship. Mitochondria are apparently passed from mother to child in the cytoplasm of the ovum. Mitochondrial DNA, therefore, is an example of strict maternal inheritance.
Mitochondrial DNA (mtDNA), small, and relatively simple in structure, is the best known DNA since it is easier to purify than nuclear DNA. It is particularly interesting for phylogenetics since portions of it are thought to evolve five to ten times faster than nuclear DNA, it appears to be haploid, and also appears to be inherited primarily from the mother. The ovum contains thousands of maternal mitochondria, and spermatozoon mitochondria appear rarely to be incorporated into the zygote. A pair of breeding humans might transmit four haploid sets of nuclear genes, but only one haploid genotype of mtDNA. Generally in animals (and a few protozoans) mtDNA is a stable double-stranded circular DNA about 15 kilobases in length that has 37 genes specifying 22 tRNAs, 13 mRNAs (for enzymes involved in electron transport or ATP synthesis), and 2 rRNAs (Moritz, Dowling and Brown, 1987). Mitochondrial DNA evolved from a more complex genome by progressive transfer of genetic functions to nuclear DNA and there is close interaction between mtDNA and nuclear DNA. (return to outline)
Centrioles show paternal inheritance, perhaps drawing their origins from the basal bodies of sperm flagella. Centrioles allow ova, which have been suspended in mid-meiosis, to finish dividing since they produce the spindle apparatus. Flagella are also probably endosymbiots, reminants of an organism took up permanent residence in other cells and over time have become a single organism (Margolis). They have RNA of their own. Conversion of flagella RNA into DNA so the centrioles can replicate, may be why cells have reverse transcriptase, an enzyme that synthesizes DNA on a template of RNA. Reverse transcriptase functions in the replication of RNA viruses, some of which are major pathogens such as HIV. (return to outline)
Genetic engineering, embryo transplants, and clones
Most people from industrialized countries think of genetic engineering in a context of new plant phenotypes or oil-eating bacteria. Production in the 1970s of a vervet monkey with rabbit hemoglobins was a portent of the future. One great problem with gene modification of mammals was the need to sustain the new individual through the complex and lengthy process of fetal development. This problem has now been solved by embryo transplants.
This technology can be important without changing the genotype. Assume that there is a shortage of chimpanzee infants, but an adequate supply of another species, such as baboons. The reproductive cycles of a female baboon and a female chimpanzee could be synchronized by hormone treatment and both inseminated on the same day. Blastocysts from both mothers can be collected by uterine lavage (flushing the uterus with water). In both blastocysts, the developing individual is represented by a small cell mass; the rest of the tissues will become placental membranes. Microsurgery allows removal and disposal of the baboon fetal cell mass and its replacement with a chimpanzee cell mass. The modified blastocyst is then placed back in the uterus of the baboon to implant and develop. Maternal tissues will not attack the chimpanzee fetus because the placental membranes are those of the baboon. Body size differentials may prevent normal delivery (chimpanzee infants are bigger than baboon infants), but a cesarean delivery could produce a healthy ape infant. In this way, a single chimpanzee female may foster several infants per year, borrowing baboon uteri for the slow process of fetal development. Similar techniques permit rearing of clones and experimentally altered zygotes of almost any mammal, including higher primates. The initial success of Oregon scientists to clone monkeys and Scottish scientist to clone sheep utilized this technology.
The relative ease at which cloning of mammals was accomplished makes it likely that the technology will be utilized for commercial production of rare or valuable phenotypes.
The most widely used technique to manipulate the genotype is recombinant DNA. This technique uses enzymes to cut segments of DNA from a genome and other enzymes to join segments of the genome to DNA from another species. For example, we have strains of a bacterium, E. coli, that have been modified to produce human somatotrophin that can then be extracted and purified in commercial quantity.
The power of this technology to transform our world is difficult to appreciate. Our culture, our ethics, our ignorance, and our economy are likely to be greater obstacles to progress than technical problems. For example, imagine the discovery of a microorganism which, with slight modification, eliminates a human problem ( such as AIDS or cholesterol build-up from fatty diets). One exposure and you receive life-time protection. Such therapies may not be economical in our modern world since costs of research, development, testing, and marketing might not be offset by large income from sales of pharmaceuticals. In our current business economy, it might be more cost-effective to isolate and synthesize beneficial enzymes from our hypothetical microorganism and market them as weekly diet supplements. (return to outline)
Table of Contents
11 June 2006
Department of
Department
of Anthropology, College
of Liberal Arts , UT Austin
Comments to cbramblett@mail.utexas.edu