Foundations of Genetics

Chapter 10

Foundations of Genetics
Lecture Notes

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Foundations of Genetics
Mendel and the Garden pea
The father of modern Genetics is Gregor Mendel. Gregor Mendel (1822-1884) was an Austrian monk who lived in a monastery where the experiments with the garden pea were performed. Mendel’s work with the garden pea was the fundamental study which unveiled the laws that govern genetics and heredity. Mendel was the first to use the scientific method in a very systematic and analysed his results and observations statistically.

We know that British farmers performed experiments with the Garden Pea much earlier before Mendel. One of these was T. A. Knight who in the 1790’s performed crosses with purple and white flowers and made the observations that some traits have “stronger tendency” to show than others. However, Mendel counted every flower and offspring that exhibited a trait. Mendel also performed very detailed statistical analysis and carefully documented the results and mathematical relationships from one generation to the next. Gregor Mendel’s experiments and the results obtained allowed him to come up with simple but very powerful hypothesis. His predictions and explanation turned out to be scientifically significant and made modern genetics a reality. We now know that hereditary traits are specific and precise instruction laid out in the DNA of the parents.

Mendel’s Experimental systems
The choice of a garden pea to study genetics was appropriate because there were several characteristics that are very desirable. These include: 1. The pea has several varieties of which Mendel selected seven that had easily detectable characteristics or traits. 2. Mendel knew from previous work like Knight, some of the traits did not show in one generation or the other. 3. Peas are easy to study, mature quickly and small and therefore easily manipulated. 4. The flowers of peas are inside and if left alone do not open and fertilize themselves (with their own pollen).

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Mendel’s Experimental design
Mendel used the same method that Knight in the 1790’s. The key difference he introduced was that he counted all the offspring very carefully. In his studies Mendel followed the following steps. 1. Mendel let each pea variety to self fertilize for several generations to make sure that each variety he was working with is true-breeding (meaning, it produced only red flowers or they were all tall etc…). 2. Mendel then crossed two peas showing different traits, for example a pea producing white flowers were crossed with peas that were producing red flowers. The offspring from this generation was the F1 (first filial) generation. 3. Mendel then took the peas produced from the F1 generation and let them self fertilize to obtain the F2 (second filial) generation and counted the offspring.

Mendel’s Experiments

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Mendel repeated his crosses with several traits such as the color of lowers, color of seeds, and color of the pods and carefully counted the offspring and came out with the statistical predictions.

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Mendel’s Observations
Mendel experimented with seven traits in total (color of flower, color of seeds, color of pods, etc…). The results obtained from all of the experiments showed very similar results in terms of proportions. Here is a summary of what he found: • F1 generation: when Mendel crossed true-breeding purple flowered peas with white flowered peas all of the flowers were purple. This shows that purple is the dominant trait (trait that was expressed in F1) and white is the recessive trait (the trait that was not expressed in F1). F2 generation: when Mendel then self fertilized the purple flowered peas he obtained 75% of the flowers were purple and 25% of them were white. In other words 3:1 ratio.

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As Mendel counted the proportions of traits obtained in the F2 generation, he found the clue on the mechanism of laws that govern heredity. The genius thinking of Mendel was making the connection of the laws that govern heredity in a given proportion. Phenotypic and Genotypic ratios Mendel took the F2 generation offspring and let each one of them self-pollinate for several generations. His experiments demonstrated that the F2 generation offspring were: • • • 25% true breeding dominate 50% not true breeding dominant and 25% true breeding recessive.

These may also be expressed in terms of ratios as → 1:2:1 (25 : 50 :25 ).

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Mendel’s Theory
After his careful studies Mendel came out with what we today call Mendel’s theories. The theories turned out to be among the most important theories in the history of science. Mendel’s theories are composed of 5 hypothesises: 1. Parents transmit their genes or the “factors” that govern traits to their offspring. 2. Each parent carries two genes for each trait (one from each parent). The genes that code for a trait, for example color of flower, may be the same (homozygous) or different heterozygous. 3. Alternative alleles will produce alternative traits. Mendel used a capital letter for the dominant trait and lowercase letter for the recessive. For example if tall is dominant he would use (T) and short is recessive he would use (t). What we see on the offspring (outside appearance) we call phenotype and the genetic make up of the offspring is called genotype. 4. Each allele an offspring has is independent of the other. Each allele is also inherited independent of the other allele. 5. There is no guarantee whether a specific inherited trait will or will not be expressed as a result of the inheritance of an allele.

Analyzing Mendel’s Results
Each trait any organism exhibits is a result of alleles which are inherited from each parent. As you have seen earlier each gamete gets one copy of each chromosome during the meiotic division.

For example, a cross between the dominant purple flowered plants (P) with recessive white flowered plants (p) would result in all purple colored plants in F1 generation and 75% purple and 25% white in F2 generation. This can be expressed easily expressed using a Punnett square as show below.

Genes on homologous chromosomes

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Punnett square
A cross between two peas with a true breeding purple (PP) flower crossed with a true breeding white (pp) flower would result in the following possible offspring as shown in the Punnett square P (dominant) allele → Purple flowers p (recessive) allele → White flowers PP x PP → will always produce purple flowers (therefore true breeding purple) pp x pp → will always produce white flowers (therefore true breeding white) A cross between PP x pp is shown in the following Punnett square. Note the probabilities of the offspring are shown in percentages as 100%, or 75% or 50% or 25%. The probabilities can also be expressed in terms of ratios as → 3:1 or 4:0 or 1:2:1.

How Mendel analyzed flower color

Probability is 100%

Probability is 25%

50%

25%

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In the F1 Generation a cross between (PP x pp) will produce: • A genotypic ratio of 4:0 (all four will be Pp) and • A phenotypic ratio of 4:0 (all the flowers are purple). In the F2 Generation a cross between (Pp x Pp) will produce: • A genotypic ratio of 1:2:1. This means that one will be homozygous purple PP, two will be heterozygous purple Pp and one will be homozygous white pp. If this is expressed in terms of percentages it will be 25% homozygous purple 50% heterozygous purple and 25% homozygous white. A phenotypic ratio of 3:1 which means that three will be purple (one PP and two Pp and one pp). If this is expressed in terms of percentages it will be 75% will be purple and 25% will be white. 7

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Test Cross
In order to determine the genotype of the peas, i.e. which plants were homozygous purple (PP) and which peas were heterozygous purple (Pp) Mendel devised an elegant test known as a test cross. As he could not tell which plant is homozygous and which is heterozygous just by looking at them, Mendel took each purple plant from the F2 generation and crossed them with the recessive homozygous white (pp). • A cross between a white flowered plant (pp) and a homozygous purple (PP) would show all of the offspring being be purple. • A cross between a white flowered plant (pp) and heterozygous purple plant (Pp) would show 50% white and 50% purple flowers. In terms of ratios this would be (50:50 or 1:1).

A Testcross

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Test cross can also be used to test when two genes are involved in the inheritance of a trait. For example: • AABB trait A breeds true and • AaBB • AABa trait A breeds true • AaBb trait B breeds true trait B breeds true

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Mendelian Laws
The predictions that Mendel made from his careful and scientifically sound experiments are the basis of modern genetics. The statistical ratios and inheritance patterns have been observed in many other organisms other than peas. These finally resulted in creating what we now know as Mendel’s Laws. • Mendel’s first law: Mendel’s first law is known as the law of segregation states that only one allele (is responsible for a trait) is carried in each one of the gametes and the gametes are randomly segregated and combine randomly in forming offspring. Mendel’s second law: Mendel’s second law known as the law of independent assortment states alleles that govern traits located on different chromosomes are inherited independently of one another.

•

In order to find out the independent assortment of inheritance patters, Mendel performed detailed experiments using true breeding peas and then followed up with contrasting pairs of true breeding peas. For example: Mendel crossed homozygous peas with round and yellow seeds with homozygous wrinkled and green seeds. These are called dihybrid crosses. Mendel then let the dihybrid peas self pollinate and in the F2 generation of the dihybrid crosses he found out the ratios of offspring to be 9:3:3:1 as are predicted using the Punnett square.

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With these results Mendel concluded that each one of the four traits that he studied were inherited independently and the inheritance of one does not affect the inheritance of the other which is now referred as Mendel’s second law or law of independent assortment.

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Note: We now know that this is true only for genes that are not located close to each other on the same chromosome. Hence, Mendel’s second law now is re-stated as follows: “Genes located on different chromosomes are inherited independent of one another”.

Even though Mendel published his experimental results in 1866, it was not until 1900 which was 16 years after his death the real significance of his work was understood.
P generation Round, yellow Wrinkled, green

Analysis of a dihybrid cross

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How do genes influence traits:
As we have seen earlier each cell has DNA, the genetic material that contains blue print of what each organism is. The human genome is made of about 25,000 genes. These genes are located in 23 pairs of chromosomes. Each one of the chromosome has between 1000 to 2000 different genes. Each gene is read by enzymes and transcribed into messenger RNA (mRNA). The mRNA leaves the nucleus goes to the cytoplasm and is translated into proteins. In Eukaryotic cells the RNA contains extra material and before it is translated to proteins the RNA is edited, which means the extra material which is unnecessary for the manufacture of proteins is removed. For example one of the subunits of haemoglobin called the beta-subunit starts with 1,660 nucleotides and when the “editing” is done it ends up with 1,000 nucleotide mRNA and encodes a protein that has 146 amino acids.

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Formation of a protein from a gene
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How proteins determine the phenotype
When mRNA is translated it forms a chain of amino acids which will fold to form a three dimensional protein. The same happens with the beta haemoglobin protein also folds and joins with 3 other subunits to form a functional protein. Haemoglobin is a protein that is used to carry oxygen from the lungs to all parts of the body. The oxygen binding efficiency depends on what kind of protein is present in the body that will determine how the body will function.

Mutations

Play

A mutation may be defined as change in the nucleotide sequence in a gene which may result in a change in the amino acid sequence encoded. This can result in making the protein to be useless. Even a single amino acid change may result in devastating effect. Here is an example If the 6th amino acid of beta-haemoglobin changes from glutamic acid to valine, the resulting protein will form aggregates of rods that deform the red blood cells into sickle shape. Sickle shaped red blood cells cannot carry oxygen efficiently and cause severe sickness and can be fatal. Sickle celled red blood cells are resistant to malarial infections. However, even though it has this advantage its disadvantages are severe. 11

Polygenic inheritance
Determining phenotypes and phenotypic ratios is not always easy and straight foreword as it is in the inheritance patters of monohybrid and dihybrid inheritance patters. Some traits are influenced by multiple genes, hence, have polygenic inheritance. When several genes are involved the resulting phenotype will have a continuous variation. An example of this is height in humans. You will find a few people that are very tall a few very short and the majority being somewhere in the middle.

Pleiotropic Effects
When one allele has more than one effect on a phenotype it is called pleiotropic effect. One example of this is inheritance of yellow (dominant) color fur in mice. When the allele appears as homozygous, however, it is fatal. Therefore, a mouse carrying a homozygous for yellow fur will die. This is because the allele for yellow is pleiotropic i.e. it carries one phenotype for the yellow fur and one for a lethal developmental defect. Pleiotropic effects are common in human diseases. Examples are: • Cystic fibrosis and sickle cell anaemia. Cystic fibrosis causes clogged blood vessels, sticky mucus, salty sweat, liver and pancreatic failure etc… Cystic fibrosis is caused as a result of a pleiotropic effect of a single defect in a gene that encodes a chloride ion transmembrane channel. • Sickle cell anemia is a disease that causes heart failure, kidney failure enlargement of the spleen increased susceptibility to pneumonia etc… Sickle cell anemia is caused by a defect in the oxygen carrying haemoglobin molecule.

Incomplete dominance
Some alleles will not have dominance over the other. In this case the characteristics will be somewhere in the middle. For example: a cross between a red flower and a white flower produce pink flowered plants in the F1 generation. In the F2 generation the ratios will be 1:2:1 (one red, one pink and one white).
Incomplete dominance

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Environmental Effects
The degree of expression of some alleles depends on the environmental conditions like temperature. Arctic foxes make fur pigment only when the weather is warm. This helps it as a protection from predators.

In the winter this color is favoured to blend like the snow.

In the summer this color is favoured to Blend with the environment.

Epistasis
In some instances one gene interacts with other genes to either add or mask the phenotype of another gene. Epistasis is the condition where the interaction between the products in which the product of one gene modifies the phenotypic expression produced by the other gene. The phenotypic inheritance patterns that are today referred as epistasis were observed by the geneticist R. A. Emerson in 1918 when he crossed two true-breeding corn varieties with white kernels. What he got was that all of the F1 plants had purple kernels. He was very surprised with these results. He then crossed the purple kernel corn and in the F2 generation there results were 9 purple and 7 white. Emerson concluded that there were two genes involved for the inheritance of the color of the kernel in corn. His conclusion was correct. It turns out that either one of the genes that control the color of the kernel can block the expression of the other. If this was a normal dihybrid inheritance like what Mendel found the ratios would have turned out to be 9:3:3:1. However because this was epistasis the results turn out to be a 9:7. In both cases the possible gamete combinations are of course 16 (i.e. 9+3+3+1=16 and 9+7=16).

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To produce and have pigment there must be at least one copy of each of the dominant colors. As you can see 9 of the offspring in the above Punnett square have that and 7 do not.

Codominance
Many genes have several alleles. Sometimes both alleles are expressed and as a result the offspring will express more than one phenotype, hence the alleles are known as codominant.

Codominance
Unlike incomplete dominance, both alleles are expressed

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As you can see the horse shows both white and black color. Thus both colors are codominant. One of the codominant characters seen in cattle and horses is the roan color patterns. A roan animal expresses both colors at least in some parts of their body. In humans one of the genes that has Codominant alleles is the I gene that determines the ABO blood groups. The I gene codes for an enzyme that adds sugar molecules to lipids that act as recognition molecules on the surface of RBC. The three common alleles of the I gene are: • • • IA → adds galactosamine (IA and IB are codominant) IB → adds galactose Ii → adds neither of the sugars (this is the recessive gene).
Multiple alleles controlling the ABO blood groups
Possible alleles from female IA or IB or i

Possible alleles from male

IA or IB or i

IAIA

IAIB

IAi

IAIB

IBIB

IBi

IAi

IBi

ii

Blood types

A

AB

B

O

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IA IA → Homozygous group A IB IB → Homozygous group B IA IB → Heterzygous group AB (inherited codominantly) Ii Ii → Homozygous Group O IA Ii → Heterozygous group A IB Ii → Heterozygous group B The three alleles for blood types IA IB and Ii code for the 4 cell phenotypes that we know as the ABO blood systems or Karl Landsteiner blood groups

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Sex linked inheritance.
In many animals there are traits that are carried in sex chromosomes and are said to code for sex linked inheritance. One of these examples is the eye color in fruit fly (Drosophila melanogaster). The gene that carries the color of the eye is carried in the X-chromosome. This gene is absent in the Ychromosome. Therefore, a male fruit fly will show the recessive white eye color more than the female because the female will have the opportunity of one of the two XX being normal as opposed to the male which has only one X.

Morgan’s experiment

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Human Genome
The human genome has 23 pairs of chromosomes, of which 22 pairs are somatic and 2 pairs are sex chromosomes. Of the sex chromosomes a male carries XY and a female caries XX. Genes that are located on the Y chromosome determine males. In humans, the individual’s particular arrangement of chromosomes is known as the karyotype. The karyotype for all men is the same and that of all women is the same. Chromosomes sometimes do not separate (nondisjunction) during meiosis resulting in a condition known as aneuploidy which is an abnormal number of chromosomes. Humans who lose even one of the chromosomes (known as monosomy) will not be able to survive. If a human has one more chromosome (known as Trisomy), except for very few chromosomes, they will also not survive. If the trisomy is as a result of the small chromosomes, namely chromosomes 13, 15, 18, 21 and 22 the human will survive for some time with severe defects. In an individual born with three copies (instead of 2) of chromosome 13,
15 or 18 the developmental defects are so severe the individual will only survive a few months. If an individual has three copies of chromosome 21 (down syndrome) and more rarely chromosome 22 the individual will grow to

adulthood but will have severe muscle and mental developmental defects.

Non-disjunction can also occur in anaphase II Nondisjunction in anaphase I

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Down Syndrome
Caused by trisomy 21

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Nondisjunction of X chromosomes
Humans gametes can be X (eggs) or Y (sperms). Under normal conditions one Y fertilizes on X and produces a zygote with XY. If the X chromosome fails to separate during meiosis, one of the gametes will have XX and the other will be without a chromosome, designated as a “0”. At fertilization the following possibilities exist: XX x X → XX x Y → “O” x Y→ “O” x X → Fetus will be a female with XXX. Some of the females are normal, some are retarded or lower mental capacity. Fetus will be a male with XXY. This male will be sterile, carry many female characteristics and sometimes have diminished mental development. Fetus will be a male with OY. This zygote will die because humans cannot survive without the X chromosome. Fetus will be a female with OX. This female will be sterile, short in stature, have immature sex organs, webbed neck and have no changes at puberty. This condition is known as the Turner syndrome. 18

Nondisjunction of the X chromosome

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Nondisjunction of Y chromosomes
Under normal conditions one Y fertilizes on X and produces a zygote with XY. If the Y chromosome fails to separate during meiosis, one of the cells will have YY and the other will be without a chromosome, designated as a “0”. At fertilization the following possibilities exist: YY x X → Fetus will be male with YYX. This male will be fertile and generally have normal appearance, will tend to be taller and sometimes will be slightly retarded.

Mutations
A mutation may be defined as a change in the nucleotide sequence in a gene, which may result in a change in the amino acid sequence encoded. Mutation are rare events, however, when they happen they can cause severe problems. There are several human genetic diseases due to mutations.

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A general pedigree

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This diagram shows the pedigree of a recessive trait inheritance.

Sickle cell anemia
As described earlier, sickle cell anemia occurs as a result of a change of the 6th amino acid of betahaemoglobin from glutamic acid to valine. This change causes the resulting protein to form aggregates of rods that deform the red blood cells into sickle shape (normal red blood cells are spherical). The sickle celled red blood cells cannot carry oxygen efficiently and cause severe sickness and can be fatal. Sickle celled red blood cells are resistant to malarial infections. However, even though it has this advantage its disadvantages are severe.

Sickle-Cell Anemia: Recessive Trait
Smooth shape allows for easy passage through capillaries Irregular shape causes blockage of capillaries

Normal red blood cell

Sickled red blood cell

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Sickle-Cell Anemia: Recessive Trait

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Examples of genetic disorders in humans Hemophilia: Blood clotting occurs as a result of about 12 proteins that polymerize to form a clot and stop the bleeding. If a person lacks one of these proteins blood clotting will not occur and the person carrying this defect will be hemophiliac. Hemophilia is a recessive trait carried on the X (sex linked trait) chromosome. Any man that inherits a mutated X chromosome will be hemophiliac. As for women they will be carriers and transmit it to their offspring. For a woman to be hemophiliac she has to inherit two mutant alleles, one from each parent. This is very improbable to happen. One of the best known cases of hemophilia is the Royal family of Britain. Queen Victoria had 9 children and 3 of her boys received the defective chromosome carrying hemophilia.

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10 of Victoria’s male descendants had hemophilia

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Tay-Sachs disease: Another genetic disease is Tay-Sachs disease. This is an autosomal recessive trait in which the enzyme hexosaminidase A is defective. Babies that are affected with this disease cannot break down specific lipids and the lipids will accumulate in brain cells resulting in death. Babies that carry this disease start showing the disease by the 8th month. The children become blind within a year and rarely live more than the age of 5. This disease is very rare, however, it has high incidence in Ashkenazi Jews.

Huntington’s disease: Huntington’s disease is carried in the autosomal chromosome and is a dominant trait. This disease causes a slow deterioration of the brain cells. This disease is fatal, but because the onset of the disease is after the age of 30, it persists in human populations.

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Muscular dystrophy: Muscular dystrophy is a sex liked recessive trait that cause the wasting away of muscles due to the degradation of myelin coating of nerves stimulating muscles.

Hyperchlolesterolemia: Hyperchlolesterolemia is dominant trait that causes abnormal form of cholesterol cell surface receptor resulting in excessive cholesterol levels in blood that will lead to heart disease.

Phenylketonuria: This is a recessive genetic disorder which happens due to a defective, phenylalanine hydroxylase enzyme. Individuals that inherit this defect will have a failure in the development of their brain in infancy.

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CHAPTER 10
SUMMARY
  Gregor Mendel is the father of modern Genetics. He used the garden pea to study heredity (how genes are passed from parents to offspring). His experiments led him to make two elegant genetic laws  The first law was the law of segregation: alleles segregate during gamete formation.  The second law was the law of independent assortment: alleles on different chromosomes are inherited independently of one another. Mendel designated each generation with letters (symbols)  F1- first generation  F2- second generation  P- parents  Mendel named an allele recessive if it doesn’t show in the first generation from two true breeding varieties and dominant if all F1 are showing the same phenotype  F2 from dominant/recessive crosses (monohybrids) show a 3:1 phenotypic ratio for a character. Dihybrid cross- a cross between two parents for two distinct traits (9:3:3:1) Test cross – a cross between an F2 dominant phenotype with one of its recessive parents to distinguish between homozygous and heterozygous dominance Phenotype is the outward appearance and genotype is the genetic make up Other types of inheritance that don’t follow Mendelian pattern are:  Polygenic inheritance gives continuous variation.  Pleiotropic Effects When one allele has more than one effect.  Incomplete dominance- partial dominance where the F1 character is intermediate between parents.  Environmental Effects- genes are turned on or off by environment.  Epistasis: gene interaction in additive or masking manner to modify phenotype.  Codominance when both alleles are expressed (Human AB blood type). Genes on X chromosomes are Sex linked genes and their inheritance is different from autosomal chromosomes (22 pairs) Chromosomes sometimes do not separate (nondisjunction) during meiosis resulting in a condition known as aneuploidy. Example of aneuploidy are:  Down syndrome (Trisomy of chromosome 21)  Turner syndrome (female with one X chromosome - monosomy)



   

 

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Practice Quiz
1. The fundamental principles of heredity were described by a. Watson and Crick b. Gregor Mendel c. Charles Darwin 2. How many gametes are possible for an individual with Aa genotype? a. three b. only one c. two 3. Genetic makeup of an organism is designated by a. behavior b. phenotype c. genotype 4. An offspring with two different alleles for a trait is a. homozygous b. heterozygous c. recessive 5. The information within the central squares of a Punnett square represents a. offspring genotypes b. parental genotypes c. parental gametes 6. Characteristics such as shape, size and color are carried in genetic units are known as a. telomere b. genes c. centromers 7. colorblindness is? a. a trait/characteristics b. an allele c. a codominant 8. Which type of inheritance causes a continuous variation? a. polygenic inheritance b. pleiotropy c. X-linked 9. This is a situation where a single gene affects many phenotypic characteristics a. monohybrid b. polygenic c. pleiotropy 10. Monosomy refers to a. three extra chromosomes b. one chromosome less c. six extra chromosomes Answers: 1. a 2. c 3. c 4. b 5. a 6. b 7. a 8. a 9. c 10. b 25