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--- chapter_02 [2026/10/25 00:45] – mike
+++ chapter_02 [2026/10/25 00:54] (current) – [Growing yeast in the lab] mike
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-The fact that scientists already know the answer to "what is a gene" begs the next question: "why do we care?" The "we" in this question is referring to you, the reader, who presumably is a student of biology. From that perspective, there are several answers to this question. First, it is useful for students of biology not just to know what something is; it is much more important to know how we know. In some fields of biology, you may learn about experimental techniques, such as how to use a microscope or how to dissect a specimen. In comparison, genetics involves thought experiments that give a great deal of insight into how biologists (especially geneticists) conceptually think about problems. Second, genetics can be used as a tool for studying biology. Even though the laboratory technologies have changed, the ideas that classical geneticists of the 20th century used to study and define the gene can still be applied to answering new questions about how things work in biology. Many modern advances in medicine are built upon knowledge gained from studying the genetics of diseases.
+After asking "What is a gene?" the next obvious question is: "Why do we care?" The "we" in this question is referring to you, the reader, who presumably is a student of biology. From that perspective, there are several answers to this question. First, it is useful for students of biology not just to know what something is; it is much more important to know how we know. In some fields of biology, you may learn about experimental techniques, such as how to use a microscope or how to dissect a specimen. In comparison, genetics involves thought experiments that give a great deal of insight into how biologists (especially geneticists) conceptually think about problems. Second, genetics can be used as a tool for studying biology. Even though the laboratory technologies have changed, the ideas that classical geneticists of the 20th century used to study and define the gene can still be applied to answering new questions about how things work in biology. Many modern advances in medicine are built upon knowledge gained from studying the genetics of diseases.
-The answer to the question "what is a gene?" will take some effort to answer because there are actually several different definitions that are appropriate in different contexts. The definitions we use in this book are first given here:
+Explaining "What is a gene?" will take some effort because there are actually several different definitions that are appropriate in different contexts. The definitions we use in this book are first given here:
   - Genes are sources of information that provide some observable biological function.
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   - Genes are defined sequences of DNA that code for RNA or protein.
-We first think about genes in the context of their function.
+We will first think about genes in the context of their function.
 ===== Bakers' yeast as a model genetic organism =====
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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}}).
+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 yeast 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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 In yeast, haploids and diploids are isomorphic – meaning that if there is a change in a gene (i.e., a mutation ) that affects some function of the yeast cells, then essentially the same change will be observed in both haploid and diploid cells. This allows us to look at the effect of having two different alleles (i.e., versions) of the same gene in the same diploid cell. For instance, a haploid yeast cell might carry a mutant allele of the $his3$ gene, whereas a diploid might carry two identical $his3$/$his3$ mutant alleles or two different alleles such as $his3$/$HIS3$.
-All yeast needs to grow in the lab (other than water and warmth) are salts, minerals, and glucose; growth media that contains only these things is called minimal media. Using the compounds contained in minimal media, normal yeast cells can synthesize all the molecules that are needed to construct a cell, such as amino acids (including histidine) and nucleotides. Organisms that are able to do this are called prototrophs. In a laboratory context, we define normal yeast cells that can grow on minimal media as wildtype. Note that "wildtype" and "wild" do not mean the same thing!
+All that yeast needs to grow in the lab (other than water and warmth) are salts, minerals, and an organic carbon source (usually a sugar, but even glycerol can work!); growth media that contains only these things is called minimal media. Using the compounds contained in minimal media, normal yeast cells can synthesize all the molecules that are needed to construct a cell, such as amino acids (including histidine) and nucleotides. Organisms that are able to do this are called prototrophs. In a laboratory context, we define normal yeast cells that can grow on minimal media as wildtype. Note that "wildtype" and "wild" do not mean the same thing!
 ===== Genes are functionally defined by mutations that alter their function =====