Unit 7: GeneticsGenetics is the scientific study of genes, discrete units or sequences of DNA that code for protein. Genes control many aspects of an organism including an organism's design and ability to reproduce. In this unit, we begin by examining Mendelian genetics, the simple patterns of inheritance laid out by "the father of genetics Greger Mendel" before moving on to more advanced and complicated patterns of inheritance such as codominance. We will utilize tools known as pedigrees to visualize and model how certain traits are inherited through family lines. And finally, we will explore a number of concepts related to biotechnology, the practice of deliberately manipulating genetic material through technology. This will include a number of scientific achievements such as gel electrophoresis and DNA fingerprinting and the Human Genome Project as well as some more controversial topics including genetically modified organisms (GMOs), cloning and genetic manipulation through CRISPR/Cas9.
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Mendelian Genetics
Greger Mendel
Greger Mendel was an Austrian Monk who ultimately became the father of modern genetics: the study of genes and inheritance in living organisms. Mendel worked with pea plants, carefully breeding plant with different phenotypes and recording his results. He worked with pea plants because they grew quickly and the plants were self-pollinating meaning the sperm of one flower could fertilize an egg of the very same flower. This meant the plants were "true-breeding" the parent plant and daughter plant were identical and would have the same traits. This allowed Mendel to have full control over his research as he generated various strains of pea plants like those than only grew very tall or those that only grew very short. As Mendel continued his work he began to cross breed the different pea plant types. For example, he would breed a yellow and green plant together to see what would happen. During cross breeding, the parents are known as the P generation and the resulting plant offspring are known as the F1 generation. The F1 gives rise to the F2 generation and so on. Mendel found interesting results in the F1 generation as he crossed the various pea plant types. When breeding the tall and short plants, he found that all of the individuals in the F1 generation exhibited the tall trait, but none exhibited the short trait. But when Mendel cross bred the F1 generation plants with each other, he found a whole new set of results in the F2 generation. Now, there was a single short plant for every 3 tall ones (3:1 ratio tall to short) In truth, Mendel was lucky in the fact that he worked with pea plants as they exhibit a relatively simple system of genetic inheritance. Other organisms, including humans, are far more complicated and would have baffled Mendel. None the less, Mendel's work had major ramifications and laid down the foundation of modern genetics. Mendel's work even provided a mechanism Darwin's still young Theory of Evolution, which originally did not explain how inheritance operated or how traits were passed from one generation to the next. |
Genetics
Genetics is a branch of science that studies genes and heredity in living organisms. Virtually every aspect of an organism is determined by its genes and every organism inherited those genes from at least one parent. Genes are segments of DNA that code for specific proteins. Genes themselves are controlled by alleles or versions of a particular gene. For example, the gene that controls the color of an organism could be controlled by multiple alleles. In diploid organisms like ourselves, there are two copies of each chromosome- a paternal and a maternal chromosome. Each chromosome will code for the same gene as its homologous counterpart but each individual chromosome can contain a different allele. It is the combination of these alleles (inherited from the parent) that ultimately determines what the organism will look like. The total variety of genes within a population of organisms is know an as a gene pool. The more available types or combinations of alleles and hence genes within a population, the deeper the gene pool and more diverse the population.
For example, consider the following: in a certain gene pool of pea plants there are two alleles that control the gene for color: G and g. The G allele codes for a green organism, while the g allele codes for a yellow organism. Because pea plants are diploid they can have up to three distinct allelic combinations for the gene that controls color: GG, Gg and gg. (Note, Gg and gG are both considered to be the same genotype, the order of the alleles does not matter).
According to genetics, every organisms has a specific phenotype, which is determined by its genotype. A phenotype refers to the physical, observable characteristics of an organism, while a genotype refers to the genetic make up of an organism or more specifically the allelic combination of each gene. In the above example, there are two possible phenotypes: green and yellow, but three possible genotypes: GG, Gg and gg. This apparent imbalance of 2 possible phenotypes and 3 possible genotypes exists because not all alleles are the same. Some alleles are more dominant or controlling than others. In genetics, dominant alleles are represented by upper case letters while recessive alleles are represented by lower case alleles. In the example, the G (green) allele is dominant over the recessive g (yellow) allele. Traits coded for by recessive alleles are only expressed when both alleles are recessive, but traits code for by dominant alleles only require a single allele to be present.
Returning again to our example gene pool, we can see that two genotypes code for the same phenotype: GG and Gg both code for green organisms. Whenever an organism has two dominant alleles, it is considered homozygous dominant-both alleles are dominant at a particular gene, in this case the gene that controls the color of the organism. However, an organism with the genotype Gg would be considered heterozygous since it contains two different alleles. In terms of phenotype, it does not matter if the organism is homozygous dominant or heterozygous, the phenotype will be identical in both. However, the genotype of the organism will have important implications later when we discuss offspring and inheritance. Lastly, the final genotype in the example, gg, is known as homozygous recessive since it has two recessive alleles. To remember these terms better, consider the prefixes: "homo" = same and "hetero" = different. A heterozygote is literally a zygote (offspring) with different alleles at a particular gene (Gg). And homozygous genotypes have the same alleles present at a gene, either all dominant (homozygous dominant) or all recessive (homozygous recessive).
Genetics is a branch of science that studies genes and heredity in living organisms. Virtually every aspect of an organism is determined by its genes and every organism inherited those genes from at least one parent. Genes are segments of DNA that code for specific proteins. Genes themselves are controlled by alleles or versions of a particular gene. For example, the gene that controls the color of an organism could be controlled by multiple alleles. In diploid organisms like ourselves, there are two copies of each chromosome- a paternal and a maternal chromosome. Each chromosome will code for the same gene as its homologous counterpart but each individual chromosome can contain a different allele. It is the combination of these alleles (inherited from the parent) that ultimately determines what the organism will look like. The total variety of genes within a population of organisms is know an as a gene pool. The more available types or combinations of alleles and hence genes within a population, the deeper the gene pool and more diverse the population.
For example, consider the following: in a certain gene pool of pea plants there are two alleles that control the gene for color: G and g. The G allele codes for a green organism, while the g allele codes for a yellow organism. Because pea plants are diploid they can have up to three distinct allelic combinations for the gene that controls color: GG, Gg and gg. (Note, Gg and gG are both considered to be the same genotype, the order of the alleles does not matter).
According to genetics, every organisms has a specific phenotype, which is determined by its genotype. A phenotype refers to the physical, observable characteristics of an organism, while a genotype refers to the genetic make up of an organism or more specifically the allelic combination of each gene. In the above example, there are two possible phenotypes: green and yellow, but three possible genotypes: GG, Gg and gg. This apparent imbalance of 2 possible phenotypes and 3 possible genotypes exists because not all alleles are the same. Some alleles are more dominant or controlling than others. In genetics, dominant alleles are represented by upper case letters while recessive alleles are represented by lower case alleles. In the example, the G (green) allele is dominant over the recessive g (yellow) allele. Traits coded for by recessive alleles are only expressed when both alleles are recessive, but traits code for by dominant alleles only require a single allele to be present.
Returning again to our example gene pool, we can see that two genotypes code for the same phenotype: GG and Gg both code for green organisms. Whenever an organism has two dominant alleles, it is considered homozygous dominant-both alleles are dominant at a particular gene, in this case the gene that controls the color of the organism. However, an organism with the genotype Gg would be considered heterozygous since it contains two different alleles. In terms of phenotype, it does not matter if the organism is homozygous dominant or heterozygous, the phenotype will be identical in both. However, the genotype of the organism will have important implications later when we discuss offspring and inheritance. Lastly, the final genotype in the example, gg, is known as homozygous recessive since it has two recessive alleles. To remember these terms better, consider the prefixes: "homo" = same and "hetero" = different. A heterozygote is literally a zygote (offspring) with different alleles at a particular gene (Gg). And homozygous genotypes have the same alleles present at a gene, either all dominant (homozygous dominant) or all recessive (homozygous recessive).
Inheritance
Just as an organism's genotype determines its phenotype, genotype also determines the possible gametes that an organism can form using meiosis for sexual reproduction. During meiosis, alleles are segregated or separated from one another. Again, using our example with color for pea plants we had three possible genotypes: GG, Gg and gg. A heterozygous green pea plant can only provide one allele for color per gamete. This means that each gamete will contain either a G allele OR a g allele, not both. This means that the genotype of an organism will have a major impact on the offspring of that organism. The gametes produced by a homozygous dominant green pea plant will contain only the G allele because that is the only allele available, while the gametes produced by a homozygous recessive yellow pea plant will only contain the g allele because that is the only allele available. This is the law of segregation. |
Punnett Squares
As you can imagine, genetics draws very heavily on probability. For example, when two heterozygous individuals mate, what is the probability that their offspring will also be heterozygous? Could the offspring be homozygous dominant? Recessive? Punnett squares allow us to calculate all of this in a simple, easy way. The first step when using Punnett squares is to identify the genotype of the parents. Let's try an example. In a particular type of flower, the gene for flower color is controlled by 2 allele: B and b where B codes for violet coloration and b codes for white coloration. Imagine we cross two heterozygotes. The parents will both be violet because the allele for violet is dominant. However, the gametes from each parent can contribute either B or b since they are both heterozygotes. In the punnett square (like the one of the right), you place these alleles in each column or row and then write out the possible genotypic combinations of the offspring as shown. In this case, there is a 1 in 4 chance the offspring will be homozygous dominant, a 2 in 4 for chance the offspring will be heterozygous and a 1 in 4 chance the offspring will be homozygous dominant for flower coloration, a 1:2:1 ratio. Stated another way, there will be 3 violet offspring for every 1 white offspring, a 3:1 ratio. These ratios are universal when heterozygotes are interbred or "crossed" and you will find many such patterns as you get more experience with punnett squares. |
Punnett squares can be used to calculate the genotypes and phenotypes of offspring with more than one gene at a time. Instructions for monohybrid crosses (one gene, like in the above example) and dihybrid crosses (two genes) are shown below. For dihybrid crosses, be sure to follow the law of independent assortment: alleles from different genes are not connected, they will be assigned to gametes in a random manner. For instance, in an organism with the genotype AaBb, each gamete can contain A and B or A and b; the A allele is not tied to any other allele.
Here is an example of a dihybrid cross: Imagine again our pea plant gene pool where G coded for green color and g coded for yellow color. Now let's add a second gene for height where the allele T codes for tall plants and t codes for short plants where T is dominant to t. A heterozygous pea plant would have the genotype TtGg and a tall and green phenotype. When 2 heterozygous pea plants are crossed the following gametes are possible: TG, Tg, tG, tg because of the laws of independent assortment and segregation. Using these gametes, it is possible to determine all the possible genotypes of the offspring as shown below. In this situation a 9:3:3:1 phenotypic ratio emerges for the offspring: 9 tall green plants (TTGG, TTGg, TtGG, TtGg) : 3 tall yellow plants (TTgg, Ttgg) : 3 short green plants (ttGG, ttGg) : 1 short white plant (ttgg). This ratio is true of any dihybrid cross of heterozygotes.
Here is an example of a dihybrid cross: Imagine again our pea plant gene pool where G coded for green color and g coded for yellow color. Now let's add a second gene for height where the allele T codes for tall plants and t codes for short plants where T is dominant to t. A heterozygous pea plant would have the genotype TtGg and a tall and green phenotype. When 2 heterozygous pea plants are crossed the following gametes are possible: TG, Tg, tG, tg because of the laws of independent assortment and segregation. Using these gametes, it is possible to determine all the possible genotypes of the offspring as shown below. In this situation a 9:3:3:1 phenotypic ratio emerges for the offspring: 9 tall green plants (TTGG, TTGg, TtGG, TtGg) : 3 tall yellow plants (TTgg, Ttgg) : 3 short green plants (ttGG, ttGg) : 1 short white plant (ttgg). This ratio is true of any dihybrid cross of heterozygotes.
Advanced Genetics
Incomplete Dominance and Codominance
So far we have only discussed Mendelian genetics, a simple form of genetics in which every gene codes for a single phenotype and each gene is controlled by just two alleles. But life is never simple and straight forward, it is often complicated and messy as is genetics. Alleles do not always follow the clean cut dominant-recessive rules we have seen so far, often they exhibit more interesting patterns. For example, alleles that exhibit incomplete dominance actually blend their traits. Imagine that in a species of plant known as the "four-o-clock" the gene for flower color is determined by two alleles: R and W where R codes for red flowers and W codes for white flowers. However, neither allele is dominant over the other. So RR individuals exhibit red color flowers, WW individuals exhibit white flowers but RW individuals exhibit a new phenotype- pink, a blend of both phenotypes. This new, blended phenotype will be homogenous or uniform. |
In other cases, alleles can be codominant and both alleles are expressed simultaneously. This may sound the same as incomplete dominance but it is actually very different. Consider again the "four-o-clock" plant. We will continue to use R (red) and W (white) but this time alleles will be codominant, not incompletely dominant. Now heterozygous individuals (RW) will exhibit the red and white phenotype together: the phenotype is not homogenous/uniform but actually heterogenous. This leads to a spotted or speckled phenotype that uses both colors. This can be seen in the Rhododendron to the left and even in certain species of chickens.
The key difference between incomplete dominance and codominance is in the phenotype of heterozygotes. When alleles are incompletely dominant, the heterozygote expresses a new, blended phenotype. In codominace there is not really a new phenotype but rather both original phenotypes are expressed at the same time. |
Multiple Alleles and Human Blood Type
Blood types in humans actually provides a great example of both codominance and another new genetic concept, multiple alleles. Again, life is complicated and it will not always be the case that a gene is controlled by just two alleles, there can often be three or more alleles that control a gene. In humans, blood type is controlled by three alleles: A, B and i (Note: in reality the alleles are I^A, I ^B and i, but this software does not allow me to form superscripts and write the alleles correctly so I^A and I^B will be written as A and B respectively for the sake of simplicity. Please understand and the correct nomenclature). A and B are codominant to each other, but each is dominant over i. A codes for the A type antigen on blood cells, B codes for the B type antigen on blood cells and i codes for no antigens on blood cells. Antigens are structures found on cells used for identification, allowing the body to differentiate between human cells and infectious microbes like bacteria, fungi and even viruses. If the body encounters a foreign antigen, like a B antigen in a person with type A blood, the foreign antigen will illicit an immune response.
The presence of these three alleles (A, B and i) allows for four unique phenotypes: A, B, AB and O blood types. People with the A blood type have the genotype AA or Ai and express the A antigen. Similarly, people with the B blood type have the genotype BB or Bi and exhibit the B antigen. AB and O are more interesting, however. A person with a blood type of AB has the genotype of...AB, no other genotype is possible. An individual with type AB blood expresses both A and B antigens together (codominance). An individual with type O blood must have the genotype ii and no antigen are expressed.
Blood types in humans actually provides a great example of both codominance and another new genetic concept, multiple alleles. Again, life is complicated and it will not always be the case that a gene is controlled by just two alleles, there can often be three or more alleles that control a gene. In humans, blood type is controlled by three alleles: A, B and i (Note: in reality the alleles are I^A, I ^B and i, but this software does not allow me to form superscripts and write the alleles correctly so I^A and I^B will be written as A and B respectively for the sake of simplicity. Please understand and the correct nomenclature). A and B are codominant to each other, but each is dominant over i. A codes for the A type antigen on blood cells, B codes for the B type antigen on blood cells and i codes for no antigens on blood cells. Antigens are structures found on cells used for identification, allowing the body to differentiate between human cells and infectious microbes like bacteria, fungi and even viruses. If the body encounters a foreign antigen, like a B antigen in a person with type A blood, the foreign antigen will illicit an immune response.
The presence of these three alleles (A, B and i) allows for four unique phenotypes: A, B, AB and O blood types. People with the A blood type have the genotype AA or Ai and express the A antigen. Similarly, people with the B blood type have the genotype BB or Bi and exhibit the B antigen. AB and O are more interesting, however. A person with a blood type of AB has the genotype of...AB, no other genotype is possible. An individual with type AB blood expresses both A and B antigens together (codominance). An individual with type O blood must have the genotype ii and no antigen are expressed.
When it comes to donating and receiving blood, not all blood types are equal. This is because all blood types have unique combination of antigens, the structures the body uses to identify itself from other microbes. A person with type A blood can only handle A antigens; B antigens would not be recognized by the body. Providing type B blood to a person with type A blood would cause an immune response and the body would reject the blood. Similarly, someone with type B blood cannot accept type A because their body will not recognize the A antigen. However, an individual with AB blood can accept AB, A or B type blood because their body is equipped to identify both the A and B antigen. This makes the AB blood type the universal acceptor. In contrast, the O blood type is often called the universal donor because O blood lacks antigens entirely. This means it is impossible for the body to form an immune response and reject O blood. But because their bodies
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are not equipped to identify the A or B antigen as "self" a person with type O blood can only accept type O blood. The graphic on the right summarizes which blood types cannot donate and receive blood to and from other blood types respectively.
Blood Transfusions and Compatibility
In addition to the 4 blood types listed above, there is another phenotypic trait called Rh factor. Rh is yet another protein found on the blood cells: those who have the protein are considered Rh positive and those lacking the Rh protein are consider Rh negative. This creates a total of 8 blood types: A positive, A negative, B positive, B negative and so on. Again, we must be careful when determining which blood types re compatible. Those with that are Rh positive can safely donate to other individuals who are Rh positive, but not to those who are Rh negative. In this regard, Rh negative is similar to the O blood type- those who are Rh negative lack an antigen to illicit an immune response. So while Rh negative can donate to any blood type, they can only accept blood from other Rh negative individuals.
In instances where a person needs extra blood supplied to them, a blood transfusion can be performed. Blood is injected into the patient using an IV and integrated into the cardiovascular system. If the patient is provided a blood transfusion of an incompatible blood type the side effects can be severe. In such a case, the host's immune system rejects the blood cells because of the antigens present on the transfused blood cells. Symptoms include fever, blood in the urine and chills. Left untreated, the patient can suffer kidney failure, pulmonary (lung) complications, anemia (reduced blood supply) and even shock.
In addition to the 4 blood types listed above, there is another phenotypic trait called Rh factor. Rh is yet another protein found on the blood cells: those who have the protein are considered Rh positive and those lacking the Rh protein are consider Rh negative. This creates a total of 8 blood types: A positive, A negative, B positive, B negative and so on. Again, we must be careful when determining which blood types re compatible. Those with that are Rh positive can safely donate to other individuals who are Rh positive, but not to those who are Rh negative. In this regard, Rh negative is similar to the O blood type- those who are Rh negative lack an antigen to illicit an immune response. So while Rh negative can donate to any blood type, they can only accept blood from other Rh negative individuals.
In instances where a person needs extra blood supplied to them, a blood transfusion can be performed. Blood is injected into the patient using an IV and integrated into the cardiovascular system. If the patient is provided a blood transfusion of an incompatible blood type the side effects can be severe. In such a case, the host's immune system rejects the blood cells because of the antigens present on the transfused blood cells. Symptoms include fever, blood in the urine and chills. Left untreated, the patient can suffer kidney failure, pulmonary (lung) complications, anemia (reduced blood supply) and even shock.
Sex Linked Traits
In humans, gender is controlled by the sex chromosomes X and Y. An individual with the genotype XX is female and XY is male. However, the X and Y chromosomes are not equal, the Y chromosome is significantly smaller than the X chromosome and carries few alleles on it (none for the purposes of this class). This creates interesting patterns of inheritance called sex-linked traits, traits that affect males and female in different proportions because they are coded for by genes on the sex chromosomes. Traits that are not coded for by genes on the sex chromosomes are known as autosomal traits. Red-green color blindness is a sex-linked recessive trait found on the X chromosome controlled by the alleles R and r. R codes for an individual with normal eye sight, while r codes for a color blind individual and R is dominant over r. Females are at a lower risk of being color blind because they require two copies of the r allele to express the disorder. But because males have a Y chromosome which does not carry the allele for color blindness, they only have one allele for the gene that controls color blindness. This means that a male only requires a single r allele to be color blind, raising their risk of the disorder. |
In the example above, a mother and father with normal vision are crossed. The mother is a heterozygote and does contain the r allele (although it is not expressed) and is hence a carrier of the r allele. This means that 50% of the male offspring will have the red-green color blindness disorder, while in this situation, none of the female offspring will (50% of the females will be carriers though).
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Polygenic Traits
As the name implies, polygenic traits are traits that are controlled by multiple genes. Examples of polygenic traits in humans include eye color, skin color and even height.
As the name implies, polygenic traits are traits that are controlled by multiple genes. Examples of polygenic traits in humans include eye color, skin color and even height.
Genetic Disorders
Genetic Disorders
There are a wide variety of disorders in humans that are inherited genetically: sickle cell anemia, Tay-Sachs, Huntington's disease and cystic fibrosis to name a few, all of which are recessive conditions- these disorders only affect homozygous recessive individuals. Some notable examples are summarized in the table below.
There are a wide variety of disorders in humans that are inherited genetically: sickle cell anemia, Tay-Sachs, Huntington's disease and cystic fibrosis to name a few, all of which are recessive conditions- these disorders only affect homozygous recessive individuals. Some notable examples are summarized in the table below.
Because genetic disorders are often fatal, it is very rare for them to be dominant traits. If these disorders were dominant, they would most likely kill the individual off before they could have offspring and ultimately be bred out of the gene pool. As such, genetic disorders are typically recessive, only killing individuals who are homozygous recessive and remain hidden in carriers (heterozygous individuals), allowing the disease to persist in the gene pool. A notable exception is Huntington's disease, a degenerative brain disorder. The reason Huntington's disease can be dominant and not be bred out of the gene pool is because the disease does not present itself until later in life in the mid 30's. This means that an individual that has Huntington's disease can pass it onto their children before they are ever aware they have the disease, allowing the Huntington's gene to pass into the next generation.
Heterozygote Advantage
Another reason genetic disorders persist within a gene pool is that sometimes their alleles confer an advantage to heterozygous individuals.
The allele that causes cystic fibrosis also produces a special protein that blocks the bacteria that causes Typhoid from entering the body. Because individuals who are heterozygous for the gene that causes cystic fibrosis do not experience the disease, heterozygotes have an advantage relative to both homozygous dominant and recessive individuals. In other words, heterozygote advantage refers to a condition in which a heterozygote has a higher fitness (ability to survive and reproduce) relative to homozygous individuals. Individuals who are heterozygous for the gene that controls sickle cell anemia also exhibit heterozygote advantage because they are healthy (no sickle cell disorder) and are resistant to malaria.
Another reason genetic disorders persist within a gene pool is that sometimes their alleles confer an advantage to heterozygous individuals.
The allele that causes cystic fibrosis also produces a special protein that blocks the bacteria that causes Typhoid from entering the body. Because individuals who are heterozygous for the gene that causes cystic fibrosis do not experience the disease, heterozygotes have an advantage relative to both homozygous dominant and recessive individuals. In other words, heterozygote advantage refers to a condition in which a heterozygote has a higher fitness (ability to survive and reproduce) relative to homozygous individuals. Individuals who are heterozygous for the gene that controls sickle cell anemia also exhibit heterozygote advantage because they are healthy (no sickle cell disorder) and are resistant to malaria.
Sickle Cell Anemia
Sickle cell anemia is an autosomal recessive genetic disorder that causes an individual's red blood cells to become misshaped. Normal, healthy red blood cells are smooth and circular, but in sickle cell anemia, the red blood cells become crescent or sickle shaped. This is the result of mutations in the hemoglobin protein at the core of these cells that binds and holds oxygen. One of the key functions of your circulatory |
system is to distribute oxygen along with other resources and nutrients to the cells in your body. With these misshaped sickle-cells, that task becomes more difficult.
A person with sickle-cell anemia experience fatigue and dizziness as a result of poor blood circulation. While having sickle cell anemia is obviously not a good thing, what is interesting is that is does offer an advantage in at least one way. The crescent shaped blood cells are resistant to malaria, a disease caused by the protist Plasmodium, which is spread by mosquito bites. About 350-500 million people contract malaria each year, experiencing flu-like symptoms and even death for as many a 1 million people annually. So being a carrier of sickle cell anemia can be a powerful advantage since heterozygotes do not typically experience the disease, but still have the added benefit of resisting malaria. This gives carriers an edge over both the "normal" and "sick" phenotypes produced by the respective homozygous conditions.
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Cystic Fibrosis
Cystic fibrosis is another autosomal recessive genetic disorder in humans. Those who are unfortunate enough to have the disorder experience an excessive build up of mucus in the respiratory and digestive tracts as well as other vital organs like the pancreas. The mucus effectively clogs vital airways and can ultimately cause death by asphyxiation. But just as with sickle cell anemia, there is a small advantage to cystic fibrosis- the allele that causes the disorder also codes for a protein that block the infection of the bacteria Salmonella, which causes typhoid fever and is typically spread via contaminated food and water. Once again, carriers have an advantage over both homozygote types (dominant and recessive) since they do not experience the actual cystic fibrosis disorder (seen in homozygous recessive individuals) , but they are resistant to Typhoid infections (absent in homozygous dominant individuals).
Cystic fibrosis is another autosomal recessive genetic disorder in humans. Those who are unfortunate enough to have the disorder experience an excessive build up of mucus in the respiratory and digestive tracts as well as other vital organs like the pancreas. The mucus effectively clogs vital airways and can ultimately cause death by asphyxiation. But just as with sickle cell anemia, there is a small advantage to cystic fibrosis- the allele that causes the disorder also codes for a protein that block the infection of the bacteria Salmonella, which causes typhoid fever and is typically spread via contaminated food and water. Once again, carriers have an advantage over both homozygote types (dominant and recessive) since they do not experience the actual cystic fibrosis disorder (seen in homozygous recessive individuals) , but they are resistant to Typhoid infections (absent in homozygous dominant individuals).
Pedigrees
Pedigrees
In genetics, a pedigree is used to track different genotypes and phenotypes through a familial lineage across generations. In the pedigree, males are represented by squares and females by circles. These shapes can be colored in to illustrate which individuals are affected by a particular trait or disorder and heterozygotes are often illustrated by a half-filled shape or another fill color. Individuals connected by a horizontal line are mates, they bred and had children. Individuals directed connected to these mating parents are the offspring. Unless the key specifies something different always assume that shaded figures are affected and have the indicated trait.
In genetics, a pedigree is used to track different genotypes and phenotypes through a familial lineage across generations. In the pedigree, males are represented by squares and females by circles. These shapes can be colored in to illustrate which individuals are affected by a particular trait or disorder and heterozygotes are often illustrated by a half-filled shape or another fill color. Individuals connected by a horizontal line are mates, they bred and had children. Individuals directed connected to these mating parents are the offspring. Unless the key specifies something different always assume that shaded figures are affected and have the indicated trait.
Pedigrees offer us the opportunity to practice looking for patterns in inheritance. For example, consider the pedigree to the left. This pedigree shows the inheritance of the forelock trait across three generations. Notice that the pedigree does not indicate if the forelock trait is dominant or recessive. Fear not- we can determine this information by observing the patterns of inheritance. First, identify were two organisms with the same phenotype interbreed. This occurs in the second generation of the left hand side. If the forelock trait (blue, shaded) is recessive then the offspring of this pair should all have the forelock trait. This is not what happens as one of the offspring lacks the forelock (white, unshaded), indicating that the forelock trait is not recessive but rather dominant. This means that both parents were heterozygous and carried a single copy of the recessive allele allowing the appearance of of child without the forelock trait.
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Below is a pedigree of the royal family that focuses on hemophilia, a condition in which the blood fails to clot properly. The disorder is X-linked recessive: the allele that codes for hemophilia is found on the X chromosome and is recessive to the normal allele. Because the hemophilia allele is X-linked, it affects males and females in different proportions. Females have two X chromosomes can require two copies of the hemophilia allele in order to actually have hemophilia. A female with only one copy of the hemophilia allele will be a carrier for the disease, but not actually express hemophilia. Males however have only a single X chromosome and hence only require a single copy of the hemophilia allele to express the disorder. It is impossible for a male to be a carrier of the disorder.
In the pedigree of the royal family, we can see the lineage begins with Queen Victoria (represented by a white circle) and Albert (represented by a purple square) at the top. Because they are connected by a horizontal line, we know they bred and their children are connected to them by the branching lines. Because Queen Victoria is colored white, we know she carried the allele for hemophilia, although she did not have the disorder, and because Albert is a normal male he did not have the hemophilia allele present at all. The punnett square to the right summarizes the possible genotypes of the offspring. H represents the normal allele, while h represents the hemophilia allele since hemophilia i a recessive trait. These letters are placed as superscripts on the X chromosome because hemophilia is X-linked. As you can see, male offspring had a 50% chance of being hemophilic and a 50% of being normal, while female offspring had a 50% chance of being a carrier and 50% of being completely normal (no hemophilia allele present at all).
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Biotechnology
Gel electrophoresis
Gel electrophoresis is a technology used to separate nucleic acids, generally DNA, based on their molecular size. Because DNA has a small negative charge , it is possible to separate strands of DNA based on their size using a positively charged electrode and a gel matrix. In the first step of gel electrophoresis, a DNA molecule is cut into smaller pieces of various length using restriction enzymes. These enzymes target specific DNA sequences, meaning each unique DNA molecule is "cut up" in a specific manner. Next, Polymerase Chain Reaction (PCR) is used to replicate the DNA sequences, amplifying the material for use in gel electrophoresis. After being cut up and replicated, the DNA is loaded into an agar gel- a porous, jelly-like substance obtained from algae frequently used as a growing medium. In gel electrophoresis, the agar gel contains a series of wells, indentations where the DNA is placed into the agar, along one side of the agar gel. Again, the agar gel is porous, it is composed of a dense matrix through which the DNA fragments can move. However, larger fragments take longer to move through the gel than shorter ones. In other words, DNA fragments can be separated according to their length allowing us to generate a "DNA fingerprint". |
DNA fingerprinting is a useful tool for forensics as it can be used to match an individual to a crime scene. Consider the following example: a murder has occurred at the local bakery. Rather than use macromolecule clues like we did earlier in the year, we can use gel electrophoresis and DNA fingerprinting to match a suspect to the crime scene. All we require is a DNA sample left at the scene- usually from blood or possibly a hair follicle (hair itself does not contain DNA, but the root or follicle of a hair will contain DNA). This DNA sample will be treated with restriction enzymes and run through gel electrophoresis along with DNA samples from the suspects. We can then use the DNA fingerprint to match a suspect to the sample from the crime scene. The example to the right shows that Suspect 2's DNA was found at the crime scene.
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Gel electrophoresis and DNA fingerprinting technology can not guarantee that a suspect committed the crime, but it can guarantee that their DNA was found at a crime scene if there is a match.
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Human Genome Project
The Human Genome Project was a 13 year, international effort to sequence the entire human genome of over 3 billion base pairs that began in 1990. The project has yielded a wealth of knowledge about genes and heredity, not just of the human species, but of all species and has paved the way for huge advances in technology and medicine for treating genetic disorders. To make the research more manageable, DNA was broken down into pieces using restriction enzymes and major regions were identified using markers, specific DNA sequences in separate regions. Once these smaller sequences were interpreted and their sequences catalogued, researchers used computers to pieces together the original DNA molecule, providing a complete picture of the human genome. |
The Human Genome Project was officially completed in 2003 and has opened up new fields of research such as Bioinformatics (the application of mathematics and computer science to store, retrieve, and analyze biological data) and the more specialized field of Genomics (the study of genomes). The Human Genome Project is free to everyone, copies of the human genome sequence as well as many other organisms are freely available online. The Human Genome Project has delivered a wealth of knowledge: only 2% of our genome codes for proteins and as much as 50% of our DNA comes directly from viruses. Moving forward, researches will continue to refine existing technologies and expand our genomic library of knowledge.
Cloning
As our understanding of genetics expands, humans have developed new technologies to manipulate organisms. Cloning is an example of one such technology. During cloning, the nucleus of a fully formed organism is isolated and inserted into a "blank", unfertilized egg cell from a female organism of the same species. The egg cell is blank because its nucleus has been artificially removed and will be replaced with the nucleus isolated from the other organism. This egg cell is then placed back into the uterine wall of a female and permitted to grow and develop into a fetus, eventually being born. |
The technology for cloning has existed since 1957, when the first tadpoles were cloned, but the first successful case of mammalian cloning was accomplished in 1996 (announced in 1997) by Ian Wilmut. Wilmut shocked the world by announcing he had successfully cloned a sheep named Dolly. Dolly lived until 2003 when she died at the age of 6 (most lambs live between 10-12 years). Today cows, mice, pigs and even cats have been successfully cloned. Obviously this technology raises ethical questions. Should humans be cloned? What are the ramifications and health consequences of being cloned? Just because we can do something, does it mean we should? These questions will continue to be debated by society over the coming years. Remember, true science is purely objective and lacks ethics; science is simply knowledge. Science tells us what we can do, what is possible, but it is the role of society to determine what should be done.
While cloning would provide invaluable advances in agriculture and farming, allow us to generate clones of the heartiest, healthiest, highest yielding crops and animals and expand food production. However, cloning so far has been seen to lower the life expectancy of cloned organisms and there are therefore questions about the quality of life of these cloned organisms. Some argue that entire clone armies could be developed and the entire issue of cloning is easily overshadowed by eugenics. Eugenics is the belief that the human genome should be improved by removing lesser quality genes from the gene pool. Why this may sound fair, it is a perversion of evolution advocating hatred and intolerance. In practice, eugenics saw the persecution of the handicapped and represents a dark blemish on science and society.
While cloning would provide invaluable advances in agriculture and farming, allow us to generate clones of the heartiest, healthiest, highest yielding crops and animals and expand food production. However, cloning so far has been seen to lower the life expectancy of cloned organisms and there are therefore questions about the quality of life of these cloned organisms. Some argue that entire clone armies could be developed and the entire issue of cloning is easily overshadowed by eugenics. Eugenics is the belief that the human genome should be improved by removing lesser quality genes from the gene pool. Why this may sound fair, it is a perversion of evolution advocating hatred and intolerance. In practice, eugenics saw the persecution of the handicapped and represents a dark blemish on science and society.
Genetically Modified Organisms
Genetically modified organisms (GMOs) are organisms that have had their genomes deliberately and directly altered by humans through the use of biotechnology. There are a number of different GMOs that have been produced for economic reasons by the food industry. One such example is Bt corn, a genetically modified type of corn that expresses genes from the bacteria --Bacillus thuringiensis. These genes allow the corn to produce toxins that kills insects that try to eat the corn. This means that farmers do not need to use insecticides on their crops. There are many other types of genetically modified crops including drought resistant corn, soybean and cotton. Much of the debate surrounding GMOs concerns their safety. Much of the public believes that genetically modified food is unsafe to eat and may cause cancer or some other unforeseen consequence. It is important to acknowledge however, that currently there is no scientific evidence to suggest that GMOs are unsafe for human consumption. Another major concern centers around biodiversity. Since genetically modified organisms do not exists naturally and often have enormous advantages over their natural counterparts, GMOs can drastically reduce biodiversity, lowering the overall health of the biosphere. |
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Currently, GMOs are created using recombinant DNA technology that splices together the genome of two organisms (like the corn and Bacillus thuringiensis). This process is slow, expensive and technologically demanding, which has limited its application; right now, genetic modification is too expensive for the general public and the length of the process has limited its application. One of the major drawbacks though is that recombinant DNA technology utilizes restriction enzymes to cut apart the DNA in order to insert the gene. While these enzymes are be highly effective at their job, it is difficult to program where they will cut the DNA. However, CRISPR holds the power to change all of that and make genetic modification simple, convenient and available to everyone.
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CRISPR
While they may not seem particularly sophisticated, bacteria are actually pretty complex. Like ourselves, many bacteria have an immune system to help prevent and fight infection. You might ask yourself: bacteria infect humans and other organisms, so what infects bacteria? While it is true that bacteria do not infect other bacteria, there is another threat to these microorganisms: viruses, specifically bacteriophages. Bacteriophages are viruses infect bacteria cells. A virus is really nothing more than a genome (of DNA or RNA) surrounded by a protein coat, which means the virus really cannot do anything on its own. In order to replicate, the bacteriophage will enter the bacteria cell and highjack the cell's internal machinery (its organelles) in order to replicate itself. This requires the virus to shed its protein coat upon entering the bacteria cell, exposing its genetic material which then integrates into the host bacteria cell's genome (DNA). This can be disastrous for the bacteria cell, as it is forced to replicate the virus over and over again until the bacteria cell eventually ruptures and dies.
While they may not seem particularly sophisticated, bacteria are actually pretty complex. Like ourselves, many bacteria have an immune system to help prevent and fight infection. You might ask yourself: bacteria infect humans and other organisms, so what infects bacteria? While it is true that bacteria do not infect other bacteria, there is another threat to these microorganisms: viruses, specifically bacteriophages. Bacteriophages are viruses infect bacteria cells. A virus is really nothing more than a genome (of DNA or RNA) surrounded by a protein coat, which means the virus really cannot do anything on its own. In order to replicate, the bacteriophage will enter the bacteria cell and highjack the cell's internal machinery (its organelles) in order to replicate itself. This requires the virus to shed its protein coat upon entering the bacteria cell, exposing its genetic material which then integrates into the host bacteria cell's genome (DNA). This can be disastrous for the bacteria cell, as it is forced to replicate the virus over and over again until the bacteria cell eventually ruptures and dies.
To better protect and defend themselves from infection, the bacteria have developed a simple immune system called CRISPR: clustered, regularly-interspaced short palindromic repeats. That may sound like a mouthful but let's take a look at how CRISPR works. Within the bacteria's DNA are short palindromes (sequences that read the same no matter which they are read like AATTCCTTAA) that are repeated throughout the bacteria's DNA. In between these palindromic DNA segments are unique sequences of DNA that are viral in origin. In this way CRISPR functions as a library of known viral genetic material to support immunity for the bacteria cell. Now whenever a virus enters the cell, its DNA can be compared to the CRISPR library and if there is a
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match, the cell will activate Cas proteins. These Cas proteins (Cas stands for CRISPR associated systems) come in a variety of different forms and types with many different, highly specialized functions including helicases (unwind DNA) and endonucleases (cut DNA at specific locations). The Cas proteins will use the viral DNA from the CRISPR library (which is actually converted to RNA and referred to as CRISPR RNA) to identify incoming, infectious viral DNA and ultimately destroy it. The Cas proteins can even expand the CRISPR library by collecting new viral DNA that has not been previously recognized by the cell and adding that material into the bacterial genome.
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But perhaps the most important Cas protein is Cas-9 which was discovered in Streptococcus pyogenes. Cas-9 is an endonuclease, meaning it cut DNA at specific locations, locations that are determined by CRISPR in Streptococcus pyogenes. The reason this is so exciting is because scientists have actually been able to use Cas-9 for our own purposes: we can feed any genetic material we want into Cas-9 (not just CRISPR derived RNA) and use it to identify that sequence and cut a DNA sequence. In other words, the CRISPR/Cas-9 system is programmable, a huge advantage over restriction enzymes. This is tremendously useful and effective for genetic modification; scientists can now identify a gene that they want to alter, create a copy of it, feed
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that into Cas-9 and then use Cas-9 to modify the genome of any organism. Deleterious genes can be broken and rendered inoperable or we could use Cas-9 to genetically modify the organism by altering the gene or outright inserting a whole new gene. CRISPER opens up opportunities for gene modification in which we alter genes that already exist in an organism to behave in specific ways. This contrasts with genetic engineering in which foreign DNA is inserted into an organism's genome as is the case with GMOs leading to the GMO becoming transgenic. The difference between genetic modification and genetic engineering may seem slight but it poses huge implications regarding a controversial subject. For example, using CRISPR we can modify a genes not just to be on or off but also control the degree to which they are active, roughly the equivalent of upgrading a simple light switch to a dimmer that allows to adjust the brightness of the room not just if the lights are on or off.
But, the fundamental issue that this CRISPR/Cas-9 system raises isn't so much can we do these things, but rather should we be using this technology? Using CRISPR/Cas-9 will make it technologically easy and cheap to begin genetically modifying organisms including humans on a previously unimaginable scale. It is therefore important to exercise restraint and careful thought before we begin to use this technology, because once the flood gates open and we begin modifying, there may be no way to ever stop again and who knows what the ramifications will be. Science tells us what we can do, but it is society that tells us whether or not we should do it.
But, the fundamental issue that this CRISPR/Cas-9 system raises isn't so much can we do these things, but rather should we be using this technology? Using CRISPR/Cas-9 will make it technologically easy and cheap to begin genetically modifying organisms including humans on a previously unimaginable scale. It is therefore important to exercise restraint and careful thought before we begin to use this technology, because once the flood gates open and we begin modifying, there may be no way to ever stop again and who knows what the ramifications will be. Science tells us what we can do, but it is society that tells us whether or not we should do it.