Genetica per Scienze Naturali a.a. 05-06 prof S. Presciuttini 1. From Genes to Phenotypes Mendel was fortunate to have chosen some of the most genetically

Genetica per Scienze Naturalia.a. 05-06 prof S. Presciuttini

1. From Genes to Phenotypes Mendel was fortunate to have chosen some of the most genetically Mendel was fortunate to have chosen some of the most genetically

simple of characters in the garden pea for his seminal experiments simple of characters in the garden pea for his seminal experiments that laid the foundation for the science of genetics.that laid the foundation for the science of genetics.

Differences between traits were determined by single gene Differences between traits were determined by single gene substitutions on different chromosomes, and each trait behaved as substitutions on different chromosomes, and each trait behaved as clearly dominant or recessive in this experimental system. This clearly dominant or recessive in this experimental system. This allowed Mendel to recognize the pattern of inheritance of the allowed Mendel to recognize the pattern of inheritance of the individual genes.individual genes.

However, the experimental situation devised by Mendel was rather a However, the experimental situation devised by Mendel was rather a particular case, that of unlinked loci with biunivocal correspondence particular case, that of unlinked loci with biunivocal correspondence between homozygous genotypes and dichotomous phenotypes.between homozygous genotypes and dichotomous phenotypes.

Most of the major advances in genetics have come from laboratory Most of the major advances in genetics have come from laboratory studies on characters having a simple, one-to-one correspondence of studies on characters having a simple, one-to-one correspondence of genotype to phenotype. However, in natural populations, phenotypic genotype to phenotype. However, in natural populations, phenotypic variation generally shows a more complex relationship to genotype variation generally shows a more complex relationship to genotype and not a one-to-one correspondence. and not a one-to-one correspondence.


2. Interactions Between the Alleles of One Gene One important generalization of Mendel’s theory concerns the One important generalization of Mendel’s theory concerns the

interactions of the different alleles of a locus in producing a interactions of the different alleles of a locus in producing a phenotypephenotype

A) Intermediate dominanceA) Intermediate dominance Four-o'clocksFour-o'clocks are plants native to tropical America. Their name are plants native to tropical America. Their name

comes from the fact that their flowers open in the late afternoon. comes from the fact that their flowers open in the late afternoon. When a wild-type four-o'clock plant with red petals is crossed with a When a wild-type four-o'clock plant with red petals is crossed with a pure line with white petals, the Fpure line with white petals, the F11 has pink petals. If an F has pink petals. If an F22 is produced is produced

by selfing the Fby selfing the F11, the result is, the result is


3. Intermediate dominance Because of the 1:2:1 ratio in the FBecause of the 1:2:1 ratio in the F22, ,

we can deduce an inheritance pattern we can deduce an inheritance pattern based on two alleles of a single gene. based on two alleles of a single gene. However, the heterozygotes (the FHowever, the heterozygotes (the F11

and half the Fand half the F22) are intermediate in ) are intermediate in

phenotype, suggesting an incomplete phenotype, suggesting an incomplete type of dominance. Inventing allele type of dominance. Inventing allele symbols, we can list the genotypes of symbols, we can list the genotypes of the four-o'clocks in this experiment as the four-o'clocks in this experiment as cc++//cc++ (red), (red), c/cc/c (white), and (white), and cc++//cc (pink).(pink).


4. Incomplete dominance

B) Incomplete dominanceB) Incomplete dominance Incomplete dominance describes the general situation in which the phenotype of a Incomplete dominance describes the general situation in which the phenotype of a

heterozygote is intermediate between the two homozygotes on some quantitative heterozygote is intermediate between the two homozygotes on some quantitative scale of measurement.scale of measurement.

This fThis figure gives terms for all the theoretical positions on the scale, but in practice it igure gives terms for all the theoretical positions on the scale, but in practice it is difficult to determine exactly where on such a scale the heterozygote is located. In is difficult to determine exactly where on such a scale the heterozygote is located. In cases of full dominance, in the wild-type/mutant heterozygote either half of the cases of full dominance, in the wild-type/mutant heterozygote either half of the normal amount of transcript and product is adequate for normal cell function (the normal amount of transcript and product is adequate for normal cell function (the gene is haplo-sufficient), or the wild-type allele is "up-regulated" to bring the gene is haplo-sufficient), or the wild-type allele is "up-regulated" to bring the concentration of transcript up to normal levels.concentration of transcript up to normal levels.


5. CodominanceC) CodominanceC) Codominance The human ABO blood groups are determined by three alleles of one gene that The human ABO blood groups are determined by three alleles of one gene that

show several types of interaction to produce the four blood types of the ABO show several types of interaction to produce the four blood types of the ABO system. The allelic series includes three major alleles, system. The allelic series includes three major alleles, ii, , IIAA, and , and IIBB, but of course any , but of course any person can have only two of the three alleles (or two copies of one of them). There person can have only two of the three alleles (or two copies of one of them). There are six different genotypes, the three homozygotes and three different types of are six different genotypes, the three homozygotes and three different types of heterozygotes:heterozygotes:

In this allelic series, the alleles In this allelic series, the alleles IIAA and and IIBB each determine a unique antigen, which is each determine a unique antigen, which is deposited on the surface of the red blood cells. These are two forms of a single deposited on the surface of the red blood cells. These are two forms of a single protein. However, the allele protein. However, the allele ii results in no antigenic protein of this type. In the results in no antigenic protein of this type. In the genotypes genotypes IIAA/i/i and and IIBB/i/i, the alleles , the alleles IIAA and and IIBB are fully dominant to are fully dominant to ii. However, in the . However, in the genotype genotype IIAA/I/IBB each of the alleles produces its own antigen, so they are said to be each of the alleles produces its own antigen, so they are said to be codominant.codominant.


6. Relativity of dominance relationships The human disease sickle-cell anemia gives interesting insight into dominance. The The human disease sickle-cell anemia gives interesting insight into dominance. The

gene concerned affects the molecule hemoglobin, which transports oxygen and is gene concerned affects the molecule hemoglobin, which transports oxygen and is the major constituent of red blood cells. The three genotypes have different the major constituent of red blood cells. The three genotypes have different phenotypes, as follows:phenotypes, as follows:

In regard to the presence or absence of anemia, the HbA allele is obviously In regard to the presence or absence of anemia, the HbA allele is obviously dominant. In regard to blood cell shape, however, there is incomplete dominance. dominant. In regard to blood cell shape, however, there is incomplete dominance. Finally, in regard to hemoglobin itself there is codominanceFinally, in regard to hemoglobin itself there is codominance, as the two hemoglobin , as the two hemoglobin molecules molecules HbA and HbS HbA and HbS can be visualized simultaneously by means of can be visualized simultaneously by means of electrophoresiselectrophoresis

Sickle-cell anemia illustrates that the terms dominance, incomplete dominance, and codominance are somewhat arbitrary. The type of dominance inferred depends on the phenotypic level at which the observations are being made, organismal, cellular, or molecular. Indeed the same caution can be applied to many of the categories that scientists use to classify structures and processes; these categories are devised by humans for convenience of analysis


7. Sickle cell anemia

The red blood cells of people with sickle cell disease contain The red blood cells of people with sickle cell disease contain an abnormal type of hemoglobin, the oxygen-carrying an abnormal type of hemoglobin, the oxygen-carrying pigment, called hemoglobin S. The deficiency of oxygen in the pigment, called hemoglobin S. The deficiency of oxygen in the blood causes hemoglobin S to crystallize, distorting the red blood causes hemoglobin S to crystallize, distorting the red blood cells into a sickle shape, making them fragile and easily blood cells into a sickle shape, making them fragile and easily destroyed, leading to anemia.destroyed, leading to anemia.

Electrophoresis of hemoglobin from an individual with sickle-cell anemia, a heterozygote (called sickle-cell trait), and a normal individual. The

smudges show the posi-tions to which the hemoglobins migrate on the starch gel.


8. The complexity of the phenotype At one level, geneticists tend to think of genes in isolation. In reality, At one level, geneticists tend to think of genes in isolation. In reality,

genes don't act in isolation. The proteins and RNAs they encode genes don't act in isolation. The proteins and RNAs they encode contribute to specific cellular pathways that also receive input from contribute to specific cellular pathways that also receive input from the products of many other genes. Furthermore, expression of a single the products of many other genes. Furthermore, expression of a single gene is dependent on many factors, including the specific genetic gene is dependent on many factors, including the specific genetic backgrounds of the backgrounds of the organismorganism and a range of environmental and a range of environmental conditionsconditions, , temperature, nutritional conditions, population density, temperature, nutritional conditions, population density, and so on. and so on.

Gene actionGene action is a term that covers a very complex set of events, and is a term that covers a very complex set of events, and there is probably no case where we understand all the events that there is probably no case where we understand all the events that transpire from the level of expression of a single gene to the level of transpire from the level of expression of a single gene to the level of an organism's phenotype. an organism's phenotype.

Two importantTwo important generalizations about the complexity of gene action generalizations about the complexity of gene action:: 1. There is a one-to-many relationship of genes to phenotypes.1. There is a one-to-many relationship of genes to phenotypes. 2. There is a one-to-many relationship of phenotypes to genes.2. There is a one-to-many relationship of phenotypes to genes.


9. One-to-many relationship of genes to phenotypes This relationship is called This relationship is called pleiotropypleiotropy. Pleiotropy is inferred . Pleiotropy is inferred

from the observation that mutations selected for their effect from the observation that mutations selected for their effect on one specific character are often found to affect other on one specific character are often found to affect other characters of the organism. This might mean that there are characters of the organism. This might mean that there are related physiological pathways contributing to a similar related physiological pathways contributing to a similar phenotype in several tissues.phenotype in several tissues. For example, the white eye-color mutation in For example, the white eye-color mutation in DrosophilaDrosophila results in results in

lack of pigmentation not only in compound eyes but also in ocelli lack of pigmentation not only in compound eyes but also in ocelli (simple eyes), sheaths of tissue surrounding the male gonad, and (simple eyes), sheaths of tissue surrounding the male gonad, and the Malpighian tubules (the fly's kidneys). In all these tissues, the Malpighian tubules (the fly's kidneys). In all these tissues, pigment formation requires the uptake of pigment precursors by pigment formation requires the uptake of pigment precursors by the cells. The white allele causes a defect in this uptake, thereby the cells. The white allele causes a defect in this uptake, thereby blocking pigment formation in all these tissues.blocking pigment formation in all these tissues.


10. Gene mutations may affect apparently unrelated traits Often, pleiotropy involves multiple events that are not Often, pleiotropy involves multiple events that are not

obviously physiologically related.obviously physiologically related. For example, the dominant For example, the dominant DrosophilaDrosophila mutation mutation DichaeteDichaete causes causes

the wings to be held out laterally but also removes certain hairs on the wings to be held out laterally but also removes certain hairs on the back of the fly; furthermore, the mutation is inviable when the back of the fly; furthermore, the mutation is inviable when homozygous. homozygous. This example shows a real limitation in the way This example shows a real limitation in the way dominant and recessive mutations are named.dominant and recessive mutations are named. The reality is that The reality is that a single mutation can be both dominant and recessive, depending a single mutation can be both dominant and recessive, depending on which aspect of its pleiotropic phenotype is under on which aspect of its pleiotropic phenotype is under consideration. In general, genetic terminology is not up to the task consideration. In general, genetic terminology is not up to the task of representing this level of pleiotropy and complexity in one of representing this level of pleiotropy and complexity in one symbol, and there is a certain arbitrary or historical aspect as to symbol, and there is a certain arbitrary or historical aspect as to how we name alleles.how we name alleles.


11. Phenylketonuria (PKU)Another example is human Another example is human phenylketonuria, in which loss of an phenylketonuria, in which loss of an enzyme involved in the breakdown enzyme involved in the breakdown of excess phenylalanine causes of excess phenylalanine causes pleiotropic effects that include pleiotropic effects that include elevated phenylalanine levels in the elevated phenylalanine levels in the blood plasma, urinary excretion of blood plasma, urinary excretion of intermediate products of intermediate products of phenylalanine breakdown, severely phenylalanine breakdown, severely reduced IQ, changes in hair color, reduced IQ, changes in hair color, and changes in head size. and changes in head size.

FigureFigure. Frequency distributions of . Frequency distributions of phenylketonurics (right) compared with phenylketonurics (right) compared with controls (left). A: controls (left). A: d/sd/s = 13, where = 13, where dd is the is the difference in the means and difference in the means and ss is the average is the average standard deviation of the two distributions. standard deviation of the two distributions. B: B: d/sd/s = 5.5; C: = 5.5; C: d/sd/s = 2.0; D: = 2.0; D: d/sd/s = 0.7 = 0.7


12. The discovery of PKU In 1934, Asjbørn Følling, a Swedish physician, recognized that a In 1934, Asjbørn Følling, a Swedish physician, recognized that a

certain type of mental retardation was caused by elevated levels of certain type of mental retardation was caused by elevated levels of phenylalanine in body fluids. He identified the disease as an phenylalanine in body fluids. He identified the disease as an autosomal recessive condition. autosomal recessive condition.

In the 1940s, Lionel Penrose in the UK introduced the idea that PKU In the 1940s, Lionel Penrose in the UK introduced the idea that PKU was not randomly distributed in human populations and could be was not randomly distributed in human populations and could be treatable.treatable.

In the mid-1950s, it was demonstrated that individuals with PKU had In the mid-1950s, it was demonstrated that individuals with PKU had a deficiency of hepatic cytosolic phenylalanine hydroxylase (PAH) a deficiency of hepatic cytosolic phenylalanine hydroxylase (PAH) enzyme activity. Next it was shown that affected individuals enzyme activity. Next it was shown that affected individuals responded to dietary restriction of the essential nutrient phenylalanine.responded to dietary restriction of the essential nutrient phenylalanine.

During the 1980s, the human PAH gene was mapped and cloned, and During the 1980s, the human PAH gene was mapped and cloned, and the first mutations identified. In the 1990s, in vitro expression the first mutations identified. In the 1990s, in vitro expression analysis was being used to study the effects of different PAH alleles analysis was being used to study the effects of different PAH alleles on enzyme function and the crystal structure of PAH was elucidated.on enzyme function and the crystal structure of PAH was elucidated.


13. Screening and treatment of PKU By the 1960s, a microbial inhibition assay was used for mass By the 1960s, a microbial inhibition assay was used for mass

screening of newborns, providing early diagnosis and access to screening of newborns, providing early diagnosis and access to successful treatment. successful treatment.

In the 1970s, it was discovered that not all cases of hyperphenyl-In the 1970s, it was discovered that not all cases of hyperphenyl-alaninemia (HPA) was PKU. Some forms of HPA were caused by alaninemia (HPA) was PKU. Some forms of HPA were caused by disorders of synthesis and recycling of the cofactor disorders of synthesis and recycling of the cofactor [tetrahydrobiopterin (BH4)] involved in the phe hydroxylation [tetrahydrobiopterin (BH4)] involved in the phe hydroxylation reaction (genetic heterogeneity). reaction (genetic heterogeneity).

HPA is treatable. Affected individuals can lead normal lives. HPA is treatable. Affected individuals can lead normal lives. Continuous efforts are made to improve the taste and convenience of Continuous efforts are made to improve the taste and convenience of the current synthetic dietary supplements. Research to improve the the current synthetic dietary supplements. Research to improve the current treatment with restrictive phenylalanine diets, supplemented current treatment with restrictive phenylalanine diets, supplemented by medical formula, is still ongoing.by medical formula, is still ongoing.


14. Distribution of blood phenylalanine concentration The phenylalanine tolerance test. A short time after administering a measured amount The phenylalanine tolerance test. A short time after administering a measured amount of phenylalanine to the subject, the concentration of phenylalanine in the blood plasma of phenylalanine to the subject, the concentration of phenylalanine in the blood plasma is measured. The level is usually substantially higher in people who carry one PKU is measured. The level is usually substantially higher in people who carry one PKU gene (even though they show no signs of disease) than in individuals who are gene (even though they show no signs of disease) than in individuals who are homozygous for the unmutated genehomozygous for the unmutated gene


15. The complexity of “simple” Mendelian traits Phenylalanine hydroxylase deficiency is a 'multifactorial disorder' in

that both environment (dietary intake of phe) and genotype (mutation of the PAH gene) are necessary causal components of disease. Because each individual has a personal genome, even those with similar mutant PAH genotypes may not have similar 'PKU' phenotypes.

Variability of metabolic phenotypes in PAH deficiency is caused primarily by different mutations within the PAH gene. Whereas the genotype does predict the biochemical phenotype (i.e., by phe loading tests), it does not always predict the clinical phenotype (i.e., occurrence of mental retardation).

PAH deficiency is therefore a 'complex' disorder at the cognitive and metabolic levels.


16. A single amino acid substitution The The compounded compounded consequences consequences of one amino of one amino acid acid substitution in substitution in hemoglobin to hemoglobin to produce sickle-produce sickle-cell anemia. cell anemia.

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Genetica per Scienze Naturali a.a. 05-06 prof S. Presciuttini 1. From Genes to Phenotypes Mendel was fortunate to have chosen some of the most genetically