TNBGGA: The No Bullshit Guide to Genetic Analysis

In Chapters 01-06 we have been focusing on eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. model genetic 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, Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research., and to a lesser extent humans. In Chapters 08-11, we will start thinking about the bacteriumplugin-autotooltip__default plugin-autotooltip_bigBacteria: Single-celled organisms that also utilize DNA and the standard genetic code as all organisms on earth, but unlike eukaryotes do not have intracellular membranes and membrane-bound organelles. In this book we use bacteria and prokaryote interchangeably. Escherichia 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). as a model genetic organism. Although the biology of 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). is very different from the aforementioned eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. organisms, many of the underlying genetic principles for geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) function and analysis of geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) function are the same in all organisms. 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). is historically relevant because much of what we know about genetics and molecular biologyplugin-autotooltip__default plugin-autotooltip_bigMolecular biology: the study of nucleic acids, specifically DNA and RNA. was discovered using 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). as a model organism, and because researchers today still use 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). as a tool in the laboratory to perform various routine tasks, such as molecular 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 (Chap. 09).

Similar to baker's 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 (introduced in Chapter 02), 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). can be grown in the laboratory either in Petri dishesplugin-autotooltip__default plugin-autotooltip_bigPetri dish: a round dish, usually 5-10 cm in diameter, that can contain growth media to grow cells in vitro. or in liquid media (Fig. 1). However, the similarities end there. First, 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 a much more friendly-smelling organism. 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 a eukaryoteplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. and is used to make things like bread, beer, and wine – a 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 lab often smells like a bakery. 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 be either 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). or diploidplugin-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.. 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 mitosisplugin-autotooltip__default plugin-autotooltip_bigMitosis: a type of cell division that generates two genetically identical daughter cells. is very rapid for a eukaryoteplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. - it has a doubling time of 3-6 hours depending on growth conditions. 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). 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 cells are roughly round-shaped and about 5 μm in diameter. Finally, 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). 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 have 16 linear chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins., around 6000 total genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), and a 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). genomeplugin-autotooltip__default plugin-autotooltip_bigGenome: a dataset that contains all DNA information of an organism. Most of the time, this also includes annotation and curation of that information, e.g., the names, locations, and functions of genes within the genome. As an adjective (“genomic”), this usually is used in the context of size of about 1.2×10⁷ bp of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth..

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)., on the other hand, is an enteric bacteriumplugin-autotooltip__default plugin-autotooltip_bigBacteria: Single-celled organisms that also utilize DNA and the standard genetic code as all organisms on earth, but unlike eukaryotes do not have intracellular membranes and membrane-bound organelles. In this book we use bacteria and prokaryote interchangeably. (a prokaryoteplugin-autotooltip__default plugin-autotooltip_bigProkaryote: an organism that does not have membrane bound organelles. In this book prokaryotes refer to bacteria.) that lives in our large intestines - it basically smells like poop. While 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 grows fast, 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). grows even faster; its doubling time can be as fast as 20 minutes under ideal laboratory conditions. It does not divide via mitosisplugin-autotooltip__default plugin-autotooltip_bigMitosis: a type of cell division that generates two genetically identical daughter cells.; instead, it uses a mechanism called binary fission (Fig. 1) and has very different mechanisms to regulate its cell division compared to eukaryotesplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus.. Finally, 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). is 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). only, and it has a single circular chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. of about 5×10⁶ bp of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. and around 4,500 genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Finally, 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). cells are rod-shaped and are about 1 μm in length; by comparison, 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 cells are about 10 μm in diameter and are spherical. Because 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). is an obligate 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)., it makes some aspects of genetic analysis easier, and other aspects somewhat more complicated.

If you spread 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). cells on an agar media surface on a Petri dishplugin-autotooltip__default plugin-autotooltip_bigPetri dish: a round dish, usually 5-10 cm in diameter, that can contain growth media to grow cells in vitro. at a low enough density such that individual cells are separated from each other (usually less than 200 cells/10 cm diameter dish; see Fig. 1 left panel), then as those cells go through binary fission more and more new daughter cellsplugin-autotooltip__default plugin-autotooltip_bigMother/daughter cells: in cell division, a mother cell divides to form two daughter cells. are formed near the original mother cellplugin-autotooltip__default plugin-autotooltip_bigMother/daughter cells: in cell division, a mother cell divides to form two daughter cells. (laboratory 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). can swim in liquid but are essentially non-motile on agar media in a Petri dishplugin-autotooltip__default plugin-autotooltip_bigPetri dish: a round dish, usually 5-10 cm in diameter, that can contain growth media to grow cells in vitro.). When enough daughter cellsplugin-autotooltip__default plugin-autotooltip_bigMother/daughter cells: in cell division, a mother cell divides to form two daughter cells. are formed, you can see them on the surface of the agar without a microscope – they form a visible lump called a colonyplugin-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. Each colonyplugin-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 contains up to 10⁹ 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). cells! All the cells in the colonyplugin-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 are (essentially) genetically identical to each other; each colonyplugin-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 is made up of clonesplugin-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 (we often use shorthand language and say that the colonyplugin-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 is a 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, which is not technically accurate but easier to say). The concept of clonesplugin-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 on a Petri dishplugin-autotooltip__default plugin-autotooltip_bigPetri dish: a round dish, usually 5-10 cm in diameter, that can contain growth media to grow cells in vitro. also applies to 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 (Chap. 02) and mouse embryonic stem cellsplugin-autotooltip__default plugin-autotooltip_bigEmbryonic stem cell: totipotent stem cells derived from preimplantion embryos that can be grown in vitro in a Petri dish. (Chap. 16).

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). genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are named with three lowercase letters and a capital letter and written in italics, such as $lacZ$. Usually, when nothing else is explicitly specified, “$lacZ$” represents the wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype.-type 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.. Wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype. type can also be explicitly indicated with a superscript +, such as $lacZ^+$. 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 a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) use numbers after the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) name ($lacZ1$, $lacZ2$, etc). Officially, you are not supposed to use a superscript “-” to indicate 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. 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. ($lacZ^-$/ is formally discouraged), but if you write it that way people will understand you. The 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 by the $lacZ$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is written as LacZ (first letter capitalized, no italics). You can also use 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. name to describe the gene productplugin-autotooltip__default plugin-autotooltip_bigGene product: the molecule that is produced based on information contained within a gene and provides function to the organism. Most of the time, a gene product is a protein. Sometimes gene products can also be an RNA molecule. In forward genetic analysis, we can't formally tell if a gene product is; for instance, the $lacZ$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) codes for β-galactosidase. Phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. are written without the final letter; for instance, wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype. type 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). are Lac⁺, and both $lacY$ and $lacZ$ 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 Lac^-.

Let’s say that we are investigating the lacZ geneplugin-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)., which encodes the lactose hydrolyzing 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. β-galactosidase. There is a special compound known as X-galplugin-autotooltip__default plugin-autotooltip_bigX-gal: an abbreviation for 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, a colorless chemical that turns blue when it is hydrolyzed by β-galactosidase. (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside) that normally is colorless but can be hydrolyzed by β-galactosidase to produce a blue pigment. When X-galplugin-autotooltip__default plugin-autotooltip_bigX-gal: an abbreviation for 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, a colorless chemical that turns blue when it is hydrolyzed by β-galactosidase. is added to the growth medium in Petri dishesplugin-autotooltip__default plugin-autotooltip_bigPetri dish: a round dish, usually 5-10 cm in diameter, that can contain growth media to grow cells in vitro. (also called plates; note that “plate” can be used both as a noun and a verb), Lac⁺ 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). coloniesplugin-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 turn blue, whereas Lac^- coloniesplugin-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 with mutationsplugin-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 lacZ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) remain white. By screeningplugin-autotooltip__default plugin-autotooltip_bigScreen: a screen is a process through which a researcher looks through a population of individuals in an attempt to find rare individuals with certain phenotypes, usually with no obvious way to enrich for the rare individuals. contrast to a selection. (see Info Box below) many coloniesplugin-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 on such plates, it is possible to isolate a collection of 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). 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. with alterations in the lacZ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (of course, you might find 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. in other lac genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) as well). PCRplugin-autotooltip__default plugin-autotooltip_bigPolymerase chain reaction (PCR): An experimental technique invented by Kary Mullis used to exponentially amplify DNA in vitro. PCR made obtaining large quantities of DNA for analysis much faster and easier than using traditional cloning methods. amplification of the lacZ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) from 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. followed by DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. 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 (Chap. 7) allows the DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. base changes that cause the Lac^- phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. to be determined. A very large number of different lacZ mutationsplugin-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. can be found, but they can usually be categorized into three general types based on how the coding sequenceplugin-autotooltip__default plugin-autotooltip_bigCoding sequence: refers to the portion of DNA or mRNA in a gene that contains direct information on the gene product. In most cases, this means a portion of DNA or mRNA that correlates to codons. Note that not all parts of a gene will necessarily be coding sequence (e.g., intron sequences). has been altered: 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., nonsenseplugin-autotooltip__default plugin-autotooltip_bigNonsense mutation: a mutation that converts a regular (amino acid-coding) codon into a stop codon., and frameshiftplugin-autotooltip__default plugin-autotooltip_bigFrameshift mutation: an indel mutation in which the net number of base pairs added or removed is not a multiple of three. This disrupts the open reading frame and drastically alters the amino acid sequence past the site of the indel; this usually results in a premature stop codon. mutationsplugin-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. (Table 1).

Geneticists can characterize mutationsplugin-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. even if they don't know the precise change to the 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. in a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). We can do this by assessing geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) activity. Using our $lacZ$ example, let's say we have a way to quantitatively measure how much geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) activity there is for different 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. of $lacZ$. For instance, we might have a way to measure how much blue pigment is produced, or how quickly it is produced. Let's define 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. $lacZ$ as having 100% activity. We can categorize different 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. as follows:

Note that the categorizations in Tables 1 and 2 are not mutually exclusive. They are simply ways to describe 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. using different tools and different perspectives. It's also useful to think about how the concepts in Table 2 relate to the concept of 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 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. 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. (see Exercise 3 in Questions and exercises below.

Mutationsplugin-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. occur spontaneously in nature; this is the driving force behind evolution. Naturally occurring mutationsplugin-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. can occur due to the inherent error rate of DNA polymeraseplugin-autotooltip__default plugin-autotooltip_bigDNA polymerase: an enzyme that is usually involved in DNA replication. This enzyme uses deoxyribonucleotides (dNTPs) and a primed template as a substrate to synthesize a new strand of ssDNA that pairs with its template to form dsDNA. There are many different kinds of DNA polymerase, but in this book we collectively refer to them as or naturally occurring mutagensplugin-autotooltip__default plugin-autotooltip_bigMutagen: a chemical or source of ionizing radiation that has the potential to damage DNA such that the DNA sequence will be altered. from environmental sources such as natural sources of radiation or certain kinds of foods. However, natural 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. rates are very low. As an interesting historical note, the Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. $white$ 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. we learned about in Chapter 04 was a spontaneous 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 Morgan found by sheer luck (although he was smart enough to recognize its value). But Morgan quickly realized that if he wanted more 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. to study, he would have to increase 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. rate experimentally.

The frequency with which mutationsplugin-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. occur can be increased as much as 10³-fold by treatment of cells with a chemical mutagenplugin-autotooltip__default plugin-autotooltip_bigMutagen: a chemical or source of ionizing radiation that has the potential to damage DNA such that the DNA sequence will be altered., a substance that generates changes to DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. (Table 3).

• Base analogs are chemicals that resemble deoxyribonucleotides and can be incorporated into DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. by DNA polymeraseplugin-autotooltip__default plugin-autotooltip_bigDNA polymerase: an enzyme that is usually involved in DNA replication. This enzyme uses deoxyribonucleotides (dNTPs) and a primed template as a substrate to synthesize a new strand of ssDNA that pairs with its template to form dsDNA. There are many different kinds of DNA polymerase, but in this book we collectively refer to them as. However, they mis-pair with regular dNTPsplugin-autotooltip__default plugin-autotooltip_bigDeoxyribonucleotide triphosphates (dNTPs): the collective name for four different molecules (dGTP, dATP, dTTP, dCTP) that are substrates for DNA polymerase and are used to form DNA. These are sometimes abbreivated as “deoxynucleotides” (which clearly refers to dNTPs) or just, so after a round of DNA replicationplugin-autotooltip__default plugin-autotooltip_bigDNA replication: usually the process of starting with a dsDNA molecule and ending with two identical copies of that dsDNA molecule. In most cases, “replication” implies DNA replication. the wrong dNTPplugin-autotooltip__default plugin-autotooltip_bigDeoxyribonucleotide triphosphates (dNTPs): the collective name for four different molecules (dGTP, dATP, dTTP, dCTP) that are substrates for DNA polymerase and are used to form DNA. These are sometimes abbreivated as “deoxynucleotides” (which clearly refers to dNTPs) or just is incorporated into the newly synthesized ssDNAplugin-autotooltip__default plugin-autotooltip_bigSingle-stranded DNA (ssDNA): a polymerized chain of deoxyribonucleotides that is not paired with a complementary polymer. Usually formed by denaturing dsDNA with heat or other methods. strand.
• Base modifying agents are chemicals that react with the G, A, T, or C bases and alter their structure such that they mis-pair regular dNTPsplugin-autotooltip__default plugin-autotooltip_bigDeoxyribonucleotide triphosphates (dNTPs): the collective name for four different molecules (dGTP, dATP, dTTP, dCTP) that are substrates for DNA polymerase and are used to form DNA. These are sometimes abbreivated as “deoxynucleotides” (which clearly refers to dNTPs) or just. For instance, ethyl methanesulfonate (EMS) is an alkylating agent that reacts with the guanineplugin-autotooltip__default plugin-autotooltip_bigNitrogenous bases: ringed chemical structures that are part of nucleotides. They include adenine (A), guanine (G), thymine (T), and cytosine (C) in DNA, and uracil (U) that substitutes for thymine in RNA. (G) bases in DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth., converting them to O⁶-ethylguanine). This modified base pairsplugin-autotooltip__default plugin-autotooltip_bigBase pair: a term used to describe how nitrogenous bases (G, A, T/U, and C) in nucleic acids interact with each other via hydrogen bonds to form double-stranded molecules (including dsDNA, dsRNA, and DNA/RNA hybrids). G always pairs with C, and T/U always pairs with A. with a T, whereas G normally pairs with C. This means that after a round of DNA replicationplugin-autotooltip__default plugin-autotooltip_bigDNA replication: usually the process of starting with a dsDNA molecule and ending with two identical copies of that dsDNA molecule. In most cases, “replication” implies DNA replication., a G/C pair will change into an A/T pair. EMS is very commonly used in genetics research to generate 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..
• Intercalating agents do not chemically modify DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.. Instead, they cause DNA polymeraseplugin-autotooltip__default plugin-autotooltip_bigDNA polymerase: an enzyme that is usually involved in DNA replication. This enzyme uses deoxyribonucleotides (dNTPs) and a primed template as a substrate to synthesize a new strand of ssDNA that pairs with its template to form dsDNA. There are many different kinds of DNA polymerase, but in this book we collectively refer to them as to slip or stutter so that it randomly adds or deletes bases while replicating DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.. Proflavin was famously used by Francis Crick in ridiculously complicated bacteriophageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. genetic experiments to demonstrate that the genetic codeplugin-autotooltip__default plugin-autotooltip_bigGenetic code: the code that matches codons with specific amino acids. Since each codon is 3 nucleotides long (i.e., the genetic code is a triplet code) and there are 4 different RNA nucleotides (G, A, U, and C), the genetic code could in theory specify up to $4^3=64$ different amino acids. But since there are only 20 different is a continuous triplet code.

In addition to chemicals, DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.-damaging ionizing radiation such as UV light or X-rays can be used as a mutagenplugin-autotooltip__default plugin-autotooltip_bigMutagen: a chemical or source of ionizing radiation that has the potential to damage DNA such that the DNA sequence will be altered.. UV light can cause pyrimidine dimersplugin-autotooltip__default plugin-autotooltip_bigPyrimidine dimer: a structure formed by adjacent pyrimidine bases in DNA as a result of exposure to UV light. to form. The bases cytosineplugin-autotooltip__default plugin-autotooltip_bigNitrogenous bases: ringed chemical structures that are part of nucleotides. They include adenine (A), guanine (G), thymine (T), and cytosine (C) in DNA, and uracil (U) that substitutes for thymine in RNA. (C) and thymineplugin-autotooltip__default plugin-autotooltip_bigNitrogenous bases: ringed chemical structures that are part of nucleotides. They include adenine (A), guanine (G), thymine (T), and cytosine (C) in DNA, and uracil (U) that substitutes for thymine in RNA. (T) that make up DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. are called pyrimidines. When 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. has two consecutive pyrimidine bases, UV light can cause covalent bonds to form between the pyrimidine bases. This is a type of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. damage that prevents normal DNA replicationplugin-autotooltip__default plugin-autotooltip_bigDNA replication: usually the process of starting with a dsDNA molecule and ending with two identical copies of that dsDNA molecule. In most cases, “replication” implies DNA replication.. Cells have mechanisms to repair this damage, but the repair mechanism is error-prone, which leads to mutationsplugin-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.. These mutationsplugin-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. can include single base changes but can also include indels.

X-rays are a stronger kind of ionizing radiation than UV light and cause more intense damage to DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.. Specifically, X-rays can cause chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. to actually break into fragments. Cells have mechanisms to repair chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. breaks, but these repair mechanisms are also error-prone, leading to indels. X-rays can also cause chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. rearrangements when the repair mechanisms lose track of where broken fragments should be reattached to each other (Table 4). While most mutationsplugin-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. only affect single genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. arrangements can affect hundreds of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) simultaneously.

Rearrangements also alter the map positions of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). In some cases, the position of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) can affect its 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., so altering the position of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) may also alter its function (this is called the position effect). In some cases, when breakpoints occur within different genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), the rejoining of the broken ends with the wrong partner can result in the creation of new fusion proteinsplugin-autotooltip__default plugin-autotooltip_bigChimeric protein: a protein that is the result of artificially joining together parts of two or more unrelated proteins. Also called a fusion protein.; this occurs in some kinds of cancers such as chronic myelogenous leukemia, where the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) BCR and ABL are fused together in the so-called Philadelphia chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins.. The 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. created by the fusion of $BCR::ABL$ causes white blood cells to proliferate uncontrollably.

In mammals, a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) called $p53$ controls (among other things) cells' ability to repair chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. breaks such as those caused by X-rays. Among its other functions, $p53$ also regulates cell cycle control (in brief, it can prevent mitosisplugin-autotooltip__default plugin-autotooltip_bigMitosis: a type of cell division that generates two genetically identical daughter cells. from happening if there is unrepaired DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. damage). In some cancers, the $p53$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is mutated, thus resulting in tumors forming through uncontrolled cell division (the cells will go through mitosisplugin-autotooltip__default plugin-autotooltip_bigMitosis: a type of cell division that generates two genetically identical daughter cells. even when unrepaired DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. damage is present). In some cases, these cancers can be treated through radiation therapy by directing beams of radiation towards tumor tissue. This will cause extensive chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. damage to these tumor cells; large fragments of chromosomesplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. will be broken away from centromeresplugin-autotooltip__default plugin-autotooltip_bigCentromere: a locus on a chromosome that marks where spindle fibers attach during mitosis and meiosis.. Because $p53$ is mutated in these cells, the damage cannot be repaired even with error-prone mechanisms. These tumor cells will then die after mitosisplugin-autotooltip__default plugin-autotooltip_bigMitosis: a type of cell division that generates two genetically identical daughter cells. due to losing too much DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.; chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. fragments that are not attached to centromeresplugin-autotooltip__default plugin-autotooltip_bigCentromere: a locus on a chromosome that marks where spindle fibers attach during mitosis and meiosis. cannot be moved to daughter cellsplugin-autotooltip__default plugin-autotooltip_bigMother/daughter cells: in cell division, a mother cell divides to form two daughter cells. during anaphaseplugin-autotooltip__default plugin-autotooltip_bigAnaphase: a phase of mitosis or meiosis during which chromosomes start to be pulled apart. and are lost. The clinical tradeoff here is that X-rays may cause additional mutationsplugin-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. or chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. alterations in nearby healthy cells. Tumors that are wildplugin-autotooltip__default plugin-autotooltip_bigWild: refers to organisms that grow in wild populations. Not to be confused with wildtype. type for $p53$ cannot be treated with radiation, because the repair mechanisms are still intact. Tumors can now be genotyped using technologies such as PCRplugin-autotooltip__default plugin-autotooltip_bigPolymerase chain reaction (PCR): An experimental technique invented by Kary Mullis used to exponentially amplify DNA in vitro. PCR made obtaining large quantities of DNA for analysis much faster and easier than using traditional cloning methods., DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. microarrays, or NGSplugin-autotooltip__default plugin-autotooltip_bigNext generation sequencing (NGS): DNA sequencing technologies that were developed after Sanger sequencing and are much more higher throughput than Sanger sequencing. Includes methods such as Illumina sequencing, 454 pyrosequencing, Nanopore sequencing, etc. (Chapter 7).

Another interesting story on cancer, mutationsplugin-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., and $p53$ involves elephants. Since naturally occurring mutationsplugin-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. are random and can arise whenever DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is replicated, and since cancer is caused by mutationsplugin-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 genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that regulate cell cycle control, it logically should follow that larger animals with more cells (and therefore naturally have more cell division) should get cancer more frequently. Interestingly, increased cancer rates are not observed in large animal species. This is called Peto's paradox. While human mortality to cancer is estimated to be around 25%, elephants succumb to cancer at only around 5%, despite being much larger than humans. It turns out that elephants have 20 copies of the $p53$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), and this presumably provides elephants with much stronger resistance to tumor formation.

A classical and powerful mode of genetic analysis is to investigate the types of mutationsplugin-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 can reverse the phenotypicplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. effects of a starting 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.. These are called suppressor mutationsplugin-autotooltip__default plugin-autotooltip_bigSuppressor mutation: a mutation that causes the mutant phenotype of another mutation to revert to wildtype.. Say that you start with an 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). $lacZ$ 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 does not stain blue after exposure to X-galplugin-autotooltip__default plugin-autotooltip_bigX-gal: an abbreviation for 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, a colorless chemical that turns blue when it is hydrolyzed by β-galactosidase.. After plating a large number of 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). cells, rare revertants can be isolated by looking for bacteriaplugin-autotooltip__default plugin-autotooltip_bigBacteria: Single-celled organisms that also utilize DNA and the standard genetic code as all organisms on earth, but unlike eukaryotes do not have intracellular membranes and membrane-bound organelles. In this book we use bacteria and prokaryote interchangeably. that now stain blue. These revertants could have either been mutated such that the starting 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 reversed (for instance, a 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 changed an A to a T has that T changed back to an A), or they could have acquired a new 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. (either in the same geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) or in a different geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)) that somehow compensates for the starting 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.. The possibilities are:

1. back 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., also called a true revertant: reverts back to 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. intragenic suppressorplugin-autotooltip__default plugin-autotooltip_bigIntragenic suppressor: a mutation in a gene that acts as a suppressor mutation for a different mutation in the same gene.: compensating 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 same geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)
3. extragenic suppressorplugin-autotooltip__default plugin-autotooltip_bigExtragenic_suppressor: a mutation in a gene that acts as a suppressor mutation for a mutation in a different gene.: compensating 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 different geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)

These possibilities can be distinguished from each other because a revertant that arose by suppression will still carry the starting 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. (now masked by the suppressor mutationplugin-autotooltip__default plugin-autotooltip_bigSuppressor mutation: a mutation that causes the mutant phenotype of another mutation to revert to wildtype.), whereas a back 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. will produce a true 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.. Assuming mutationsplugin-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. are 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., the general test is to cross the revertant to 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. 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). (Fig. 4). The details for how to actually do this experiment 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). are partially described in Chapter 09, so we will not elaborate on the details here – what we care about is the concept.

In this experiment, we want to see whether there are recombinantsplugin-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.” (progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. that are different from the parent) from the outcome of this cross. In essence we are using 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., or a test of geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) position, to see if we are looking at one or two genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) in our revertants (Fig. 4). If there are many Lac^- recombinantsplugin-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.”, that indicates that there likely is an extragenic suppressorplugin-autotooltip__default plugin-autotooltip_bigExtragenic_suppressor: a mutation in a gene that acts as a suppressor mutation for a mutation in a different gene.. If there are many Lac⁺ recombinantsplugin-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.”, that indicates that it is either an intragenic suppressorplugin-autotooltip__default plugin-autotooltip_bigIntragenic suppressor: a mutation in a gene that acts as a suppressor mutation for a different mutation in the same gene. or a back 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 practice, intragenic suppressorsplugin-autotooltip__default plugin-autotooltip_bigIntragenic suppressor: a mutation in a gene that acts as a suppressor mutation for a different mutation in the same gene. will be very difficult to distinguish from back mutationsplugin-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. using this approach. For example, an intragenic suppressorplugin-autotooltip__default plugin-autotooltip_bigIntragenic suppressor: a mutation in a gene that acts as a suppressor mutation for a different mutation in the same gene. that lies very close to the original Lac^- 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. may be able to produce Lac^- recombinantsplugin-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.” in principle, but these recombinantsplugin-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.” may be too rare to be easily observed (ask yourself: why would these recombinantsplugin-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.” be rare?). Intragenic revertants can be found in organisms where enormous numbers of progenyplugin-autotooltip__defaultProgeny: a synonym for offspring. can be produced to identify rare events. This usually means using bacteriophageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. (phageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. genetics are not studied much anymore) or under very specific circumstances in organisms like 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)..

Generally speaking, we are most interested in extragenic suppressorsplugin-autotooltip__default plugin-autotooltip_bigExtragenic_suppressor: a mutation in a gene that acts as a suppressor mutation for a mutation in a different gene.. This is because the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) products of extragenic suppressorsplugin-autotooltip__default plugin-autotooltip_bigExtragenic_suppressor: a mutation in a gene that acts as a suppressor mutation for a mutation in a different gene. often interact with the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) products of the original 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. geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). For example, if $mutA$ is suppressed by $supB$, then the MutA and SupB 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. might physically interact with each other. Knowing that two 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. interact with each other gives us important information about how they function. Usually geneticists will collaborate with biochemists to further confirm this interaction (assuming the genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) have all been cloned). Our example here uses 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)., but suppressor analysis can be and is used in other model genetic organisms as well, including 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, Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research., and others.  

A useful class of extragenic suppressorplugin-autotooltip__default plugin-autotooltip_bigExtragenic_suppressor: a mutation in a gene that acts as a suppressor mutation for a mutation in a different gene. mutationsplugin-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. can suppress nonsenseplugin-autotooltip__default plugin-autotooltip_bigNonsense mutation: a mutation that converts a regular (amino acid-coding) codon into a stop codon. mutationsplugin-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. by changing the ability of the cells to read a nonsenseplugin-autotooltip__default plugin-autotooltip_bigNonsense mutation: a mutation that converts a regular (amino acid-coding) codon into a stop codon. codonplugin-autotooltip__default plugin-autotooltip_bigCodon: a three nucleotide sequence that is read by the ribosome and specifies an amino acid that is added to a growing poplypeptide chain based on the genetic code. as a regular codonplugin-autotooltip__default plugin-autotooltip_bigCodon: a three nucleotide sequence that is read by the ribosome and specifies an amino acid that is added to a growing poplypeptide chain based on the genetic code. instead. These kinds of suppressors are called nonsense suppressorsplugin-autotooltip__default plugin-autotooltip_bigNonsense suppressor: a mutation in a tRNA gene wherein the anticodon loop sequence has mutated such that it is complementary to a stop codon. This has the effect of being able to suppress some nonsense mutations.. Such extragenic revertants were originally isolated by selectingplugin-autotooltip__default plugin-autotooltip_bigSelection: There are two distinct but somewhat related definitions for this term:

In model organism research, a selection is a process through which a researcher is attempting to find rare individuals with certain phenotypes and has some way of enriching for the rare individuals by killing off all other individuals that do not match the search criteria. Contrast to a (see Info Box in this chapter above) for reversion of nonsenseplugin-autotooltip__default plugin-autotooltip_bigNonsense mutation: a mutation that converts a regular (amino acid-coding) codon into a stop codon. mutationsplugin-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. named $amber$ (UAG) mutationsplugin-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 two different bacterialplugin-autotooltip__default plugin-autotooltip_bigBacteria: Single-celled organisms that also utilize DNA and the standard genetic code as all organisms on earth, but unlike eukaryotes do not have intracellular membranes and membrane-bound organelles. In this book we use bacteria and prokaryote interchangeably. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Since simultaneous back mutationsplugin-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. at two different lociplugin-autotooltip__default plugin-autotooltip_bigLocus (plural form: loci): a physical location of a gene; often used as a synonym for a gene. is highly improbable, the most frequent mechanism for suppression is a single 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 geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) for a tRNA that changes the codonplugin-autotooltip__default plugin-autotooltip_bigCodon: a three nucleotide sequence that is read by the ribosome and specifies an amino acid that is added to a growing poplypeptide chain based on the genetic code. recognition portion of the tRNA. For example, one of several possible nonsense suppressorsplugin-autotooltip__default plugin-autotooltip_bigNonsense suppressor: a mutation in a tRNA gene wherein the anticodon loop sequence has mutated such that it is complementary to a stop codon. This has the effect of being able to suppress some nonsense mutations. occurs in the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) for a serine tRNA (tRNA^ser). One of six tRNA^ser genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) normally contains the anticodon 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. CGA which recognizes the serine codonplugin-autotooltip__default plugin-autotooltip_bigCodon: a three nucleotide sequence that is read by the ribosome and specifies an amino acid that is added to a growing poplypeptide chain based on the genetic code. UCG (by convention, 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. are given in the 5’ to 3’ direction; note that CGA will base pair with UCG in an antiparallelplugin-autotooltip__default plugin-autotooltip_bigAntiparallel: a term used to describe how the orientation of the two strands of dsDNA are opposite to each other. direction). A 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 changes the anticodon to CUA allows the 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. tRNA^ser to recognize a UAG codonplugin-autotooltip__default plugin-autotooltip_bigCodon: a three nucleotide sequence that is read by the ribosome and specifies an amino acid that is added to a growing poplypeptide chain based on the genetic code. and insert serine when a UAG codonplugin-autotooltip__default plugin-autotooltip_bigCodon: a three nucleotide sequence that is read by the ribosome and specifies an amino acid that is added to a growing poplypeptide chain based on the genetic code. appears in a coding sequenceplugin-autotooltip__default plugin-autotooltip_bigCoding sequence: refers to the portion of DNA or mRNA in a gene that contains direct information on the gene product. In most cases, this means a portion of DNA or mRNA that correlates to codons. Note that not all parts of a gene will necessarily be coding sequence (e.g., intron sequences)..

The combined use of amber mutationsplugin-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. and an amber suppressor produces a conditional mutantplugin-autotooltip__default plugin-autotooltip_bigConditional mutant: a mutant that displays a mutant phenotype only under certain conditions. Some examples include:

* a temperature sensitive mutant that is mutant only at increased temperatures. * a nonsense mutation that exhibits a mutant phenotype only when a nonsense suppressor is absent. * an auxotrophic mutant that can only grow if a specific nutrient is provided., which is 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. whose 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 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. under some circumstances but not under others. Here, the condition that determines whether the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. of an amber 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 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. or not is the presence or absence of the amber suppressor. Conditional mutantsplugin-autotooltip__default plugin-autotooltip_bigConditional mutant: a mutant that displays a mutant phenotype only under certain conditions. Some examples include:

* a temperature sensitive mutant that is mutant only at increased temperatures. * a nonsense mutation that exhibits a mutant phenotype only when a nonsense suppressor is absent. * an auxotrophic mutant that can only grow if a specific nutrient is provided. are especially useful for studying mutationsplugin-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 essential genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that are required for life), because otherwise the 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 just be dead, and you would have no way to study it.

Another kind of conditional 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 temperature sensitive 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. for which the 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 exhibited at high temperature but not at low temperature. Temperature-sensitive mutationsplugin-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. often affect 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. folding - the 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. structure might be stable at lower temperatures, but higher temperatures the 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. might unfold or misfold and therefore lose function. In Chapter 06 we discussed a temperature sensitive 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 $shibire$ in Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research., which is another example of a conditional mutantplugin-autotooltip__default plugin-autotooltip_bigConditional mutant: a mutant that displays a mutant phenotype only under certain conditions. Some examples include:

* a temperature sensitive mutant that is mutant only at increased temperatures. * a nonsense mutation that exhibits a mutant phenotype only when a nonsense suppressor is absent. * an auxotrophic mutant that can only grow if a specific nutrient is provided.. Temperature sensitive 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. can be isolated from all model genetic organisms and are extremely useful for studying essential genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) or genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that, when mutated, result in very sick organisms that are difficult to study.

Finally, auxotrophicplugin-autotooltip__default plugin-autotooltip_bigAuxotroph: a mutant that cannot synthesize one more essential nutrient from minimal media needed for survival or proliferation. mutationsplugin-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. such as we saw in Chapter 02 are in a sense also conditional because auxotrophicplugin-autotooltip__default plugin-autotooltip_bigAuxotroph: a mutant that cannot synthesize one more essential nutrient from minimal media needed for survival or proliferation. 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. can be grown in the presence of the required nutrient, but the 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. will not grow when the nutrient is not provided.

Exercise 1. Given the introductory information on 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). in this chapter, estimate how long it will take for a visible colonyplugin-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 to form on a Petri dishplugin-autotooltip__default plugin-autotooltip_bigPetri dish: a round dish, usually 5-10 cm in diameter, that can contain growth media to grow cells in vitro. starting from plating cells at single cell density. You will need to use exponents and logarithms to solve this.

Conceptual question: Based on your prior knowledge, what kinds of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. alterations from Table 1 are most likely to occur for the types of mutationsplugin-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. described in Table 2? What kind of mutagenplugin-autotooltip__default plugin-autotooltip_bigMutagen: a chemical or source of ionizing radiation that has the potential to damage DNA such that the DNA sequence will be altered.(s) would you use to generate these 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.? Justify your answers!

Conceptual question: Take a look at the different kinds of 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. grouped by change in functionality (Table 2). Which of these do you think will be 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.? Which will be 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.? The answer is not as straightforward as you might initially think! Remember that we define 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. as 100% activity, meaning that each 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. 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. is providing 50% activity. What if 75% activity still looks “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.” but 50% activity looks “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.”?

Conceptual question: Using Table 2, how might you characterize the $p53$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) duplication in elephants?