TNBGGA: The No Bullshit Guide to Genetic Analysis

In Chapter 12 we considered the structure of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. organisms and discussed a general strategy for identifying and cloningplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of S. cerevisiae genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that are transcriptionallyplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. regulated in response to a change in environment. The ability to regulate geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. in response to environmental cues is a fundamental requirement for all living cells, both prokaryoticplugin-autotooltip__default plugin-autotooltip_bigProkaryote: an organism that does not have membrane bound organelles. In this book prokaryotes refer to bacteria. and eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus..

We also considered how many genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) each organism has: about 4,000 for E. coliplugin-autotooltip__default plugin-autotooltip_bigEscherichia coli: an enteric bacterium used both as a model organism and as a utility organism in genetics research. E. coli is commonly used to host various cloning vectors, such as plasmids, cosmids, F factors, and bacterial artificiak chromosomes (BACs)., 6,000 for yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 and a little over 20,000 for mice and humans (Chap. 12 Fig. 1). But only a subset of these genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is actually expressedplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. at any one time in any particular cell. For multicellular organisms this becomes even more apparent; it is obvious that skin cells must be expressing a different set of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) than liver cells, although of course there must be a common set of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that are expressedplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. in both cell types (these are often called housekeeping genesplugin-autotooltip__default plugin-autotooltip_bigHousekeeping gene: a gene that is always expressed in all cell types, usually that has some function that is universal to all cells. “Housekeeping gene” tends to be used in the context of multicellular organisms; “constitutive” tends to be used more for unicellular organisms.).

There are a number of ways that geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) regulation in eukaryotesplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. differs from geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) regulation in prokaryotesplugin-autotooltip__default plugin-autotooltip_bigProkaryote: an organism that does not have membrane bound organelles. In this book prokaryotes refer to bacteria.. For example:

• Eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are (usually) not organized into operonsplugin-autotooltip__default plugin-autotooltip_bigOperon: two or more genes that are transcribed together on an mRNA from a single promoter. Most commonly seen in bacteria; very rare in eukaryotes. .
• Eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. regulatory genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are not usually linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. (i.e., map closely) to the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) they regulate.
• Some eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. regulatory proteinsplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. must ultimately be compartmentalized to the nucleusplugin-autotooltip__default plugin-autotooltip_bigNucleus: in eukaryotes, the membrane-bound organelle in cells that contains the chromosomes., even when signaling begins at the cell membrane or in the cytoplasm.
• Eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is wrapped around histonesplugin-autotooltip__default plugin-autotooltip_bigHistone: in eukaryotes, histones are proteins that are used to organize DNA within the nucleus. Eight different individual histone proteins come together to form a structure called the histone octamer. to form nucleosomesplugin-autotooltip__default plugin-autotooltip_bigNucleosome: In eukaryotes, approximately 146 bp of chromosomal DNA wraps around a histone octamer to form a nucleosome. The nucleosome is the basic unit of chromatin. and chromatinplugin-autotooltip__default plugin-autotooltip_bigChromatin: the collective structure of all proteins and DNA in the nucleus of a eukaryotic cell. Nucleosomes are stacked in different configurations to form chromatin structures of different density. Chromatin structure is regulated by a variety of chromatin modifying enzymes..

Today we will consider how one can use genetics to begin to analyze the mechanisms by which geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. can be regulated. For this we will take the example of the yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 $GAL$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in S. cerevisiae. This chapter assumes some familiarity with tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A.. Please review Appendix A on tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A. before reading this chapter.

Yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are named with three letters followed by a number. By convention, wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype. type allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. of yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 are indicated by all caps and italics ($GAL4$). Mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. are in lowercase and italics ($gal4$), and sometimes a specific alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. number is included ($gal4\text{-}1$). Phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. are indicated by just the letters with the first letter capitalized (wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 is Gal⁺; both $gal4$ and $gal1$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. are Gal^-). Proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. produced from the $GAL4$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) would be written as Gal4 (sometimes as Gal4p to clearly identify proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes.). A mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. can be written as Gal4^- or Gal4p^-. Sometimes the +/- superscript can be used to emphasize the wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. or mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. status of an alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence., such as $GAL4^+$ or $gal4^-$, but this is not standard.

Galactose is a 6-carbon monosaccharide that yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 can metabolize and use as its sole carbon source for growth. Galactose must first be converted to other compounds so that it can enter the glycolysis pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose.. There are several enzymesplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. that are used in this process, and as expected you can isolate mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that are defective for these enzymesplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. and therefore auxotrophicplugin-autotooltip__default plugin-autotooltip_bigAuxotroph: a mutant that cannot synthesize one more essential nutrient from minimal media needed for survival or proliferation. for galactose. Examples of such mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. include $gal1$, $gal7$, and $gal10$ (Fig. 1). $gal1$ codes for the enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. galactokinase, and Gal1p galactokinase activity is inducedplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. by the addition of galactose¹⁾. A more “genetics” way of saying this is that galactose inducesplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. (you could also frame the statement in a “genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)” perspective - “galactose inducesplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. $gal1$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. Either way is appropriate).

Once a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (such as $gal1$) has been identified as being inducibleplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. under certain conditions (in this case by the addition of galactose), we can begin to dissect its regulatory mechanism by isolating mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that defective in the regulatory process, i.e., mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that constitutively express the $GAL$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) even in the absence of galactose, and mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that have lost the ability to induceplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. the $GAL$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in the presence of galactose. If we were studying galactose regulation today, we would probably use a $lacZ$ reporterplugin-autotooltip__default plugin-autotooltip_bigReporter gene: a gene whose gene product has an easily observed function and that can be used to indirectly measure the level of transcription determined by a promoter or other cis-acting regulatory elements. system similar to what we discussed in Chap. 12.

Historically, however, when the Gal regulatory system was first genetically dissected, it was done by directly measuring the inductionplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. of $GAL1$-encoded galactokinase enzymeplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. activity, so this is how we will discuss the genetic dissection of the system²⁾. For instance, here are some common Gal mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference.:  

From Table 1, we see that $gal4$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. are uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). and $gal80$ and $gal81$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. constitutively express the $GAL1$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Let’s analyze each mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. in turn:

$gal4$: It was first established that, like $gal1$, the $gal4$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. is recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele., because heterozygousplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. diploidsplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. generated by mating $gal4$ to $GAL4$ (i.e., $\frac{gal4}{GAL4}$ diploidsplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent.) have normal regulation of $GAL1$ galactosidase expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. It was then established that the mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in the $gal4$ strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and lies in a new geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), and not simply in the $GAL1$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-); this was shown by complementationplugin-autotooltip__default plugin-autotooltip_bigComplementation: a concept where an additional allele of a gene (usually a wildtype allele) can provide normal function to an organism with a recessive loss of function mutation in that gene. The concept of complementation underlies the complementation test. analysis (i.e., $\frac{GAL1}{gal1};\frac{gal4}{GAL4}$ diploidsplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. obtained from mating $gal4$ with $gal1$ are Gal⁺) and the fact that the $gal4$ and $gal1$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are unlinkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. was established by tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A.. You should think about what the tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I. from the aforementioned diploidsplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. would look like.

Taken together, the simplest model is that Gal4p is a positive regulatorplugin-autotooltip__default plugin-autotooltip_bigPositive regulator: in the context of gene regulation, a positive regulator is a gene whose activity increases the expression of another gene. Compare to transactivator/activator. of $GAL1$. The + sign in the diagram below indicates that Gal4p increases $GAL1$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. but does not indicate whether this is direct or indirect.

$gal80$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference.: The next useful regulatory mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. isolated was $gal80$, in which the $GAL1$-encoded galactokinase is expressedplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. even in the absence of galactose and is not further inducedplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. in its presence. In other words, $gal80$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. are constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state.. Again, heterozygousplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. diploidsplugin-autotooltip__default plugin-autotooltip_bigDiploid: a term that describes a cell or organism that has two copies of similar genetic information, usually obtaining one copy from a male parent and the other copy from a female parent. ($\frac{gal80}{GAL80}$) showed that $gal80$ is recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele., and mappingplugin-autotooltip__default plugin-autotooltip_bigGenetic mapping: a term describing a variety of different experimental approaches used to determine the physical locations of genes on chromosomes. by tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A. showed that $gal80$ is not linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. to $gal1$, $gal4$ or any other $gal$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). If a mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. $gal80$ results in constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places., the simplest model to explain the data is that $GAL80$ negatively regulates Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. Since $GAL4$ positively regulates and $GAL80$ negatively regulates Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places., we have to figure out how these two geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) products work together to achieve such regulation. Assuming that $GAL4$ and $GAL80$ act in series (that is, in a linear genetic pathwayplugin-autotooltip__default plugin-autotooltip_bigPathway: a series of reactions or events that occur in sequence with some common goal or purpose.), there are two formal possibilities:

Model 1 is that Gal4p positively regulates Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places., and that Gal80p negatively regulates Gal4p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.; the presence of galactose somehow inhibits Gal80p function thus releasing Gal4p to positively activate Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. Model 2 is that Gal80p negatively regulates Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places., and Gal4p negatively regulates Gal80p; here the presence of galactose positively activates Gal4p which in turn negatively regulates Gal80p, thus relieving inhibition of Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places..

Logically, both models seem to make sense. How can we use genetic analysis to determine which model is more likely to be correct?

We can distinguish between these two models by doing an epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test (see Chapter 11) to establish the epistaticplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. relationship between $gal4$ and $gal80$. To review the epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test: this involves making a double $gal4$; $gal80$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and. The phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. will indicate which of the two models is most likely to be true; take a look at the two models in Figure 4 to predict what phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. should have. If Model 1 is correct, then the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. would become uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all).; if Model 2 is correct, then the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. should be constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state.. We discuss how to make the double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and below, but let's first think about how the interpretation of the epistasisplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. test works by looking more closely at Fig. 4.

• First, assume that Model 1 is correct; if there is loss of functionplugin-autotooltip__default plugin-autotooltip_bigLoss of function: a general term used to describe mutant alleles that have less activity than wildtype. Amorphic and hypomorphic mutations are loss of function mutations. in both $gal4$ and $gal80$, then Gal4p cannot be inhibited by Gal80p, but that is irrelevant because there won't be any functional Gal4p to begin with. Therefore, Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. can never be inducedplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive..
• On the other hand, assume that Model 2 is correct; in this case, if there is loss of functionplugin-autotooltip__default plugin-autotooltip_bigLoss of function: a general term used to describe mutant alleles that have less activity than wildtype. Amorphic and hypomorphic mutations are loss of function mutations. in both $gal4$ and $gal80$ then Gal80p can never be inhibited by Gal4p, but this is irrelevant because there won't be any functional Gal80p to begin with. Therefore, Gal1p will constitutively be expressedplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places..

We could make the $gal4$; $gal80$ double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and using molecular engineering approaches (such as by first cloningplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of and then knocking out $gal4$ and $gal80$; see Chapter 14), but an easier way is to let yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 meiosisplugin-autotooltip__default plugin-autotooltip_bigMeiosis: a process involving two sequential cell divisions that usually produces four gametes (reproductive cells such as sperm or eggs). do the job for you (cloningplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of and knocking out genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 is not super hard but tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A. is much easier). If we mate the $gal4$; $GAL80$ haploidplugin-autotooltip__default plugin-autotooltip_bigHaploid: a term that describes a cell or organism that has only one copy of genetic information. Haploid cells typically arise from meiosis (or mitosis of a haploid mother cell). strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and with the $GAL4$; $gal80$ haploidplugin-autotooltip__default plugin-autotooltip_bigHaploid: a term that describes a cell or organism that has only one copy of genetic information. Haploid cells typically arise from meiosis (or mitosis of a haploid mother cell). strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and we should obtain double mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. among the tetratype and non-parentalplugin-autotooltip__default plugin-autotooltip_bigRecombinant: (adj.) Describing something that has undergone recombination, e.g., recombinant DNA or recombinant offspring. “Non-parental” is a synonym when referring to organisms. (n.) Something that has undergone recombination, e.g., “This fly is a recombinant.” ditype tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I. that result from this cross (remember that this chapter assumes a basic familiarity with tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A.; see Appendix A for details).

Since we already know that $gal4$ and $gal80$ are unlinkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes., we know that the ratio of PD:NPD:TT = 1:1:4. We also can easily identify PD tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I., because we know the $gal4$ and $gal80$ single mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. definitively. We can also identify the TT tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I., because the $gal4$; $gal80$ double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. will be either uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). or constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. (thus, TT tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I. will either have uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all).: constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state.: wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. = 2:1:1 or 1:2:1). Any tetradplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I. that is not a PD or a TT then must be NPD by default. NPD tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I. must contain 2 sporesplugin-autotooltip__default plugin-autotooltip_bigSpore: in fungi (including yeast), ascospores (spores) are the equivalent of the four daughter cells of meiosis. that are wildtypeplugin-autotooltip__default plugin-autotooltip_bigWildtype: a reference strain of an organism that scientists operationally define as “normal” to which mutants are compared. Not to be confused with wild organisms. (inducibleplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive.), and by elimination the remaining 2 sporesplugin-autotooltip__default plugin-autotooltip_bigSpore: in fungi (including yeast), ascospores (spores) are the equivalent of the four daughter cells of meiosis. must be the desired $gal4$; $gal80$ double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. (marked by ??? in Table 2). Tetrad analysisplugin-autotooltip__default plugin-autotooltip_bigTetrad analysis: an experimental method to analysis meiosis in yeasts and other fungi. See Appendix A. allows us to easily construct a double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. without a priori knowledge of its phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism..

When this experiment was actually done, the $gal4$; $gal80$ double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. wound up being uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all).. Since this is the same phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. as $gal4$, we say that $gal4$ is epistaticplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. to $gal80$. These results suggest that Model 1 is correct; $gal4$ positively regulates $gal1$, while $gal80$ negatively regulates $gal4$. This was later substantiated with additional molecular and biochemical experiments.

Now let's consider a new class of mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. that turned out to be quite informative. $gal81$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference., like $gal80$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference., are constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. for Gal1 expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places.. But unlike $gal80$, $gal81$ is dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele.. That is, $\frac{gal81}{GAL81}$ heterozygotesplugin-autotooltip__default plugin-autotooltip_bigHeterozygous: a state for a diploid organism wherein the two alleles for a gene are different from each other. are constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state.. An obvious question to ask is whether $gal81$ mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. are still constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. in a $gal4$ background, as it was already established that Gal4p positively regulates Gal1p (and the other Gal genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)). In other words, what is the epistaticplugin-autotooltip__default plugin-autotooltip_bigEpistasis: describes a relationship between two mutant alleles $a$ and $b$. If the phenotype of a double mutant $a \cdot b$ is the same as the single mutant $a$ we say that $a$ is epistatic to $b$, and that $a$ likely functions after $b$ in a pathway. relationship between $gal81$ and $gal4$? To test this, we can attempt to make a $gal4$·$gal81$ double mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. by crossing the single mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference.:

$$ gal81 \cdot GAL4 \times gal4 \cdot GAL81 $$

A surprising finding from this cross was that all the tetradsplugin-autotooltip__default plugin-autotooltip_bigTetrad: In the context of yeast genetics, a tetrad refers to the four ascospores from a single ascus, which represents the four products of a single meiotic event. In the context of meiosis in general, a tetrad refers to the four chromatids from a set of replicated homologous chromosomes lined up at metaphase I. were of the parental ditype (PD); there were no tetratypes (TT) or nonparental ditypes (PD), indicating that $gal81$ and $gal4$ are very tightly linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes.³⁾. Indeed, it turns out that $gal81$ maps to the coding region of the $gal4$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). In other words, $gal81$ is an alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. of $gal4$; we say that “$gal81$ is allelic to $gal4$”. The $gal81$ mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. was therefore renamed as $gal4^{81}$. Essentially $gal4^{81}$ behaves as a super-activatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator. that is impervious to the negative effects of $gal80$. $gal4^{81}$ thus activates Gal1p expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. independently of galactose and Gal80p.

After cloningplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of and sequencingplugin-autotooltip__default plugin-autotooltip_bigSequencing: the procedure used to determine the sequence of a biological polymer such as DNA, RNA, or protein. Although there are indeed biochemical techniques that can be used to directly sequence RNA or protein, these methods are almost never used in modern molecular genetics research - instead, RNA $gal4^{81}$ and lots of other biochemical experiments, scientists learned that the $gal4^{81}$ mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. is a missenseplugin-autotooltip__default plugin-autotooltip_bigMissense mutation: a mutation that causes a change in an the amino acid specified at a particular location in the gene sequence. mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. that alters the amino acidplugin-autotooltip__default plugin-autotooltip_bigAmino acid: molecules that are polymerized to form proteins. sequenceplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. of the region of the Gal4p proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. that normally interacts with Gal80p. This mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. prevents Gal80p from interacting with Gal4p. This was a very satisfying result, as genetics (a discipline concerned with abstract ways of thinking about biology) was used to learn biochemical knowledge about how two geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) products (proteinsplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes.) physically interact with each other to regulate geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places..

These and many other genetic, molecular, and biochemical experiments led to the following model (Figure 5) to explain Gal geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) regulation. Upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of of the $GAL1$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (and other Gal genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)), two cisplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-acting DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. elements are needed for transcriptionalplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. activation: the promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA, and upstream activator sequencesplugin-autotooltip__default plugin-autotooltip_bigUpstream activator sequence (UAS): In a general sense, a UAS is a cis-acting regulatory element, usually located significantly upstream of the promoter and TATA box, to which transactivators bind to activate transcription of nearby genes.

Although the term “UAS” can in principle be used to describe any cis-acting upstream sequence that activates transcription, in practice the term enhancer is used more often to describe these $GAL1$ (UASsplugin-autotooltip__default plugin-autotooltip_bigUpstream activator sequence (UAS): In a general sense, a UAS is a cis-acting regulatory element, usually located significantly upstream of the promoter and TATA box, to which transactivators bind to activate transcription of nearby genes.

Although the term “UAS” can in principle be used to describe any cis-acting upstream sequence that activates transcription, in practice the term enhancer is used more often to describe these $GAL1$).

First, TATA binding proteinplugin-autotooltip__default plugin-autotooltip_bigTATA binding protein: a protein that binds to the TATA box that helps to initiate transcription in eukaryotes. (TBPplugin-autotooltip__default plugin-autotooltip_bigTATA binding protein: a protein that binds to the TATA box that helps to initiate transcription in eukaryotes.) binds to a DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. sequenceplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. called the TATA consensus siteplugin-autotooltip__default plugin-autotooltip_bigTATA box: a short DNA sequence (usually just 6 bp long) that is part of most eukaryotic promoters located around 35-40 bp upstream of the transcription start site. It is the binding site for TATA binding protein (TBP). (also called a TATA boxplugin-autotooltip__default plugin-autotooltip_bigTATA box: a short DNA sequence (usually just 6 bp long) that is part of most eukaryotic promoters located around 35-40 bp upstream of the transcription start site. It is the binding site for TATA binding protein (TBP).), which is located just in front (upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of⁴⁾) of the $GAL1$ transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. start site. TBPplugin-autotooltip__default plugin-autotooltip_bigTATA binding protein: a protein that binds to the TATA box that helps to initiate transcription in eukaryotes. bound to the TATA boxplugin-autotooltip__default plugin-autotooltip_bigTATA box: a short DNA sequence (usually just 6 bp long) that is part of most eukaryotic promoters located around 35-40 bp upstream of the transcription start site. It is the binding site for TATA binding protein (TBP). forms a scaffold for a very large RNA polymeraseplugin-autotooltip__default plugin-autotooltip_bigRNA polymerase: the enzyme that carries out RNA transcription. There are many different types of RNA polymerase, but in this book we collectively refer to them as just “RNA polymerase” for simplicity. complex. The area of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. immediately upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of of the transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. start site of GAL1 that contains the TATA boxplugin-autotooltip__default plugin-autotooltip_bigTATA box: a short DNA sequence (usually just 6 bp long) that is part of most eukaryotic promoters located around 35-40 bp upstream of the transcription start site. It is the binding site for TATA binding protein (TBP). is also called the promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA; the promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA is usually around 40-50 bp of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. in size. Note that the word “promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA” is also used to describe cisplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-regulatory sequencesplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. in E. coliplugin-autotooltip__default plugin-autotooltip_bigEscherichia coli: an enteric bacterium used both as a model organism and as a utility organism in genetics research. E. coli is commonly used to host various cloning vectors, such as plasmids, cosmids, F factors, and bacterial artificiak chromosomes (BACs). (Chap. 10); however, prokaryoticplugin-autotooltip__default plugin-autotooltip_bigProkaryote: an organism that does not have membrane bound organelles. In this book prokaryotes refer to bacteria. promotersplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA and eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. promotersplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA do not work in the same way.

RNA polymeraseplugin-autotooltip__default plugin-autotooltip_bigRNA polymerase: the enzyme that carries out RNA transcription. There are many different types of RNA polymerase, but in this book we collectively refer to them as just “RNA polymerase” for simplicity. binding to TBPplugin-autotooltip__default plugin-autotooltip_bigTATA binding protein: a protein that binds to the TATA box that helps to initiate transcription in eukaryotes. alone does not enable transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription.; the complex must be activated by a kind of proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. called a transcriptionalplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. activatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator. (or transactivatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator.), which in this case is Gal4p. Gal4p binds to another DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. sequenceplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. further upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of of the $GAL1$ transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. start site called the upstream activator sequenceplugin-autotooltip__default plugin-autotooltip_bigUpstream activator sequence (UAS): In a general sense, a UAS is a cis-acting regulatory element, usually located significantly upstream of the promoter and TATA box, to which transactivators bind to activate transcription of nearby genes.

Although the term “UAS” can in principle be used to describe any cis-acting upstream sequence that activates transcription, in practice the term enhancer is used more often to describe these $GAL1$ (UASplugin-autotooltip__default plugin-autotooltip_bigUpstream activator sequence (UAS): In a general sense, a UAS is a cis-acting regulatory element, usually located significantly upstream of the promoter and TATA box, to which transactivators bind to activate transcription of nearby genes.

Although the term “UAS” can in principle be used to describe any cis-acting upstream sequence that activates transcription, in practice the term enhancer is used more often to describe these $GAL1$). The region of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. that contains UASplugin-autotooltip__default plugin-autotooltip_bigUpstream activator sequence (UAS): In a general sense, a UAS is a cis-acting regulatory element, usually located significantly upstream of the promoter and TATA box, to which transactivators bind to activate transcription of nearby genes.

Although the term “UAS” can in principle be used to describe any cis-acting upstream sequence that activates transcription, in practice the term enhancer is used more often to describe these $GAL1$ is usually several hundred bp upstreamplugin-autotooltip__default plugin-autotooltip_bigUpstream/downstream: These descriptors have different meanings depending on context:

* In genetics, these are terms used to describe directions on DNA, usually relative to the transcription start site of a gene. DNA sequences that are located in the same direction as the direction of from the promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA (see Chap. 14) and is more generally called an enhancerplugin-autotooltip__default plugin-autotooltip_bigEnhancer: a more inclusive term for a UAS. One reason this is a more inclusive term is because not all enhancers are located upstream of genes; some enhancers are located downstream of a gene, and in some cases can even be located inside a gene.. In the absence of galactose, Gal80p physically prevents Gal4p from activating RNAP. In the presence of galactose, the Gal80 proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. changes conformation and binds to a different region of Gal4p, unveiling the ability of Gal4p to activate RNAP. The mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. in the $gal4^{81}$ alleleplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. interferes with Gal80p binding, thereby allowing mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. Gal4⁸¹p proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. to recruit and activate RNAP all the time even in the absence of galactose.

It is important to know that, while minor details will be different in different genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) and organisms, the model shown in Fig. 5 generally holds true for all eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). This includes mammalian and human genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that may have biomedical or economic relevance.

A final comment about the model for inductionplugin-autotooltip__default plugin-autotooltip_bigInducible: a term describing a pattern of gene expression, wherein genes or operons are not expressed until some kind of condition is met, e.g., inducer is present. Not all genes are naturally inducible; some genes are naturally constitutive. of the Gal genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) by galactose: For many years it was assumed that galactose binds directly to Gal80p, thus preventing it from inhibiting Gal4p from activating $GAL1$ transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription.. However, one extra proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. is involved in this chain of events. The Gal3 proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. turns out to directly bind galactose. This allows Gal3p to move from the cytoplasm into the nucleusplugin-autotooltip__default plugin-autotooltip_bigNucleus: in eukaryotes, the membrane-bound organelle in cells that contains the chromosomes., upon which the galactose/Gal3p moiety binds to Gal80p to facilitate moving Gal80p to a different site on Gal4p, thus allowing Gal4p to activate transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription.. While the model as written in Fig. 5 does not include Gal3p, the models are still formally correct.

In the next chapter we will be looking at structures of some of these regulatory proteinsplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. and cisplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-regulatory elements, and how to genetically analyze them in more detail.

Conceptual question: If you were one of the original scientists studying Gal geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) regulation and you had a $gal4$ mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference., how could you cloneplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of $gal4$ by complementationplugin-autotooltip__default plugin-autotooltip_bigComplementation: a concept where an additional allele of a gene (usually a wildtype allele) can provide normal function to an organism with a recessive loss of function mutation in that gene. The concept of complementation underlies the complementation test.? Your only tool you have for measuring phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. is measuring galactokinase activity (see footnote 2). Similarly, how could you cloneplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of $gal80$ by complementationplugin-autotooltip__default plugin-autotooltip_bigComplementation: a concept where an additional allele of a gene (usually a wildtype allele) can provide normal function to an organism with a recessive loss of function mutation in that gene. The concept of complementation underlies the complementation test.?

Exercise 1: In the chapter, we discuss that $gal81$ was shown to be allelic to $gal4$ by linkageplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes., followed by cloningplugin-autotooltip__default plugin-autotooltip_bigClone: Depending on the context, this word can have a few different meanings:

* In the context of genes, cloning means that the physical identity of a gene has been found, and the gene has been sequenced. * In the context of DNA, a cloned DNA fragment is one that has been inserted into some kind of and sequencingplugin-autotooltip__default plugin-autotooltip_bigSequencing: the procedure used to determine the sequence of a biological polymer such as DNA, RNA, or protein. Although there are indeed biochemical techniques that can be used to directly sequence RNA or protein, these methods are almost never used in modern molecular genetics research - instead, RNA. Could scientists have established that gal81 is allelic to gal4 using the complementation testplugin-autotooltip__default plugin-autotooltip_bigComplementation test: a genetic experiment that answers the question: how many different genes are represented within a collection of mutants?? Why or why not?

Exercise 2: $gal4^{81}$ and $gal80$ are both constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. mutantsplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. (although one is dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. and one is recessiveplugin-autotooltip__default plugin-autotooltip_bigRecessive: used to describe an allele, usually in comparison to wildtype. Recessive alleles do not exhibit their phenotype when combined with a wildtype allele.). Devise an experiment to show that $gal4^{81}$ and $gal80$ are not allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. of the same geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-).

Conceptual question: How does regulation of Gal genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in yeastplugin-autotooltip__default plugin-autotooltip_bigYeast: in this book, refers to Saccharomyces cerevisiae, a single-celled eukaryotic microbe used as a model genetic organism. See Chapter 02 compare to regulation of Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in E. coliplugin-autotooltip__default plugin-autotooltip_bigEscherichia coli: an enteric bacterium used both as a model organism and as a utility organism in genetics research. E. coli is commonly used to host various cloning vectors, such as plasmids, cosmids, F factors, and bacterial artificiak chromosomes (BACs). (seen in Chap. 10)? This is an important thing to think about!