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--- chapter_02 [2024/08/26 21:20] – [The yeast lifecycle] mike
+++ chapter_02 [2025/01/29 08:32] (current) – [The complementation test can be used to group different mutants into unique genes] mike
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-<typo fs:x-large>**Chapter 02: Defining genes by function**</typo>
+<- chapter_01|Chapter 01^table_of_contents|Table of Contents^chapter_03|Chapter 03 ->
+<typo fs:x-large>**Chapter 02: Defining %%genes%% by function**</typo>
 ===== What is a gene? Why do we care? =====
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 ==== The yeast lifecycle ====
 In the laboratory, we can grow yeast either on a Petri dish (Fig. {{ref>Fig1}}) or in some kind of liquid media in a container such as an Erlenmeyer flask or test tube. Yeast can reproduce sexually, but instead of saying they have two sexes (such as male and female) we say there are two mating types. Yeast cells can exist as haploids of either mating type α ($MATα$) or mating type a ($MATa$). Haploid cells of different mating types when mixed together will fuse to form a diploid cell. Both haploid and diploid cells can undergo mitosis to make more clones of themselves. Diploid cells can also undergo meiosis and form four ascospores that can germinate and become four haploid cells. Two of these cells will be $MATα$ and the other two will be $MATa$ (Fig. {{ref>Fig2}}).
 <figure Fig2>
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 </caption>
 </figure>
-Each intermediate compound in the pathway is converted to the next compound through a chemical reaction catalyzed by an enzyme (A is converted to B, B is converted to C, etc.). If there is a mutation that somehow affects the function of enzyme 3, then intermediate C cannot be converted to intermediate D and ultimately the cell cannot make histidine. Such a mutant will only grow if histidine is provided in the growth medium. This type of mutant is known as an auxotroph or auxotrophic mutant. This type of mutation is known as an auxotrophic mutation. A strain refers to a collection of individual organisms of a particular genotype (in the case of yeast, individual cells) that can be propagated in perpetuity. It's easy to maintain most yeast strains – all you need to do is provide them with food (sugars) and they will go through mitosis to make more copies of themselves.
+Each intermediate compound in the pathway is converted to the next compound through a chemical reaction catalyzed by an enzyme (A is converted to B, B is converted to C, etc.). If there is a change in a gene (i.e., a mutation) that somehow affects the function of enzyme 3, then intermediate C cannot be converted to intermediate D and ultimately the cell cannot make histidine. Such a mutant will only grow if histidine is provided in the growth medium. This type of mutant is known as an auxotroph or auxotrophic mutant. This type of mutation is known as an auxotrophic mutation. A strain refers to a particular genetic variant of an organism that can be propagated in perpetuity. It's easy to maintain most yeast strains – all you need to do is provide them with food (sugars) and they will go through mitosis to make more copies of themselves.
 ==== Defining dominant and recessive alleles ====
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 </table>
-Having performed this cross: if the two mutants don't complement, we conclude that they are mutant in the same gene.  ((In rare cases, just because two mutants do not complement each other does not automatically mean that the mutants have mutations in the same gene. There can be situations called "non-allelic non-complementation" where mutations in different genes do not complement each other. You can show that non-complementing mutations are in different genes by mapping their position ([[chapter_05|Chapter 05]]). When two different genes show non-allelic non-complementation, that can be an indication that the gene products of the two genes (usually the proteins encoded by the genes) have some sort of physical interaction.)) Another way we say this is that "$hisX$ is allelic to $his3$". Conversely, if they do complement, we conclude that they are mutant in different genes. For instance, $hisX$ might be a mutation in the $his4$ gene. To understand the reasoning behind this conclusion, look at the genotypes of the diploid in the two possible outcomes of this experiment.
+Having performed this cross: if the two mutants don't complement, we conclude that they are mutant in the same gene.  ((In rare cases, just because two mutants do not complement each other does not automatically mean that the mutants have mutations in the same gene. There can be situations called "non-allelic non-complementation" where mutations in different genes do not complement each other. You can show that non-complementing mutations are in different genes by mapping their position ([[chapter_05|Chapter 05]]). When two different genes show non-allelic non-complementation, that can be an indication that the gene products of the two genes (usually the proteins encoded by the genes) have some sort of physical interaction.)) Another way we say this is that "$hisX$ is allelic to $his3$". Conversely, if they do complement, we conclude that they are mutant in different genes. For instance, $hisX$ might be a mutation in the $his4$ gene.
-This works because in row 2 of Table {{ref>Tab4}}, the $his3$ haploid parent is presumed to be mutant only in the $his3$ gene and therefore implicitly carries the wildtype $HISX$ allele, and similarly the $hisX$ haploid parent is presumed to be mutant only in this one gene and thus implicitly carries the wildtype $HIS3$ allele. Therefore, the diploid produced from the cross will be heterozygous for both the $his3$ and $hisX$ genes and therefore provide normal function for both genes. It is important to know that this test only works for recessive mutations.
+To understand the reasoning behind this conclusion, look at the combination of alleles (i.e., the genotype) of the diploid in the two possible outcomes of this experiment. In row 2 of Table {{ref>Tab4}}, the $his3$ haploid parent is presumed to be mutant only in the $his3$ gene and therefore implicitly carries the wildtype $HISX$ allele, and similarly the $hisX$ haploid parent is presumed to be mutant only in this one gene and thus implicitly carries the wildtype $HIS3$ allele. Therefore, the diploid produced from the cross will be heterozygous for both the $his3$ and $hisX$ genes and therefore provide normal function for both genes. It is important to know that this test only works for recessive mutations.
 The beauty of the complementation test is that the trait can serve as a read-out of gene function even without knowledge of what the gene is doing. We can simply define a gene based on its function, and we can distinguish between different genes (assuming we have recessive mutant alleles of those genes) using the complementation test. In fact, you can even use the complementation test for mutants that have different phenotypes! The only requirement for the complementation test is that the two mutants must be recessive.