TNBGGA: The No Bullshit Guide to Genetic Analysis

Jacob and Monod found that the physical location of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) relative to each other affected their function. Unlike eukaryotesplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus., 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). only has a single chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins.. Therefore, all genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) on the chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. are on the same DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. molecule. Note in Table 1 that $lacI^{-d}$ is dominantplugin-autotooltip__default plugin-autotooltip_bigDominant: used to describe an allele, usually in comparison to wildtype. Dominant alleles will express their phenotype when combined with a wildtype allele. no matter whether it is on the same piece of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. as $lacZ^+$ (on the 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). chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins.; another way to say this is “in cisplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different”) or a different piece of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. as $lacZ^+$ (on the $F'$ plasmidplugin-autotooltip__default plugin-autotooltip_bigPlasmid: a circular episome found in bacteria and yeast. Plasmids are commonly used as cloning vectors.; another way to say this is “in transplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different”). By contrast, $lacO^c$ is only 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. if it acts in cisplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different; that is, $lacO^c$ only exhibits its 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. effect when it is on the same piece of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. as $lacZ^+$. Jacob and Monod explained this by theorizing that the $lacI$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) must produce a proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. that is able to diffuse and attach to either chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. or $F'$ plasmidplugin-autotooltip__default plugin-autotooltip_bigPlasmid: a circular episome found in bacteria and yeast. Plasmids are commonly used as cloning vectors. DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.. They further hypothesized that $lacO$ (which they also knew was very closely linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. to $lacZ$) represented not a 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.-producing geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) but rather 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. that controlled $lacZ$ expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. - and it only worked if $lacO$ was physically linkedplugin-autotooltip__default plugin-autotooltip_bigLinkage: two loci are linked to each other if they are less than 50 m.u. apart. Two loci are unlinked if they are either (1) greater than 50 m.u. apart on the same chromosome, or; (2) are on separate chromosomes. to $lacZ$ on the same piece of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth..

The concept of cisplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different- and transplugin-autotooltip__default plugin-autotooltip_bigCis and trans: In genetics, cis and trans are terms used to describe the relative physical locations of genes or genetic elements. If two genes are in cis, this means that they are physically located on the same DNA molecule. If two genes are in trans, this means that they are physically located on two different-activating factors applies to eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) regulation as well. In fact, 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. that bind to DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. and activate geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) transcriptionplugin-autotooltip__default plugin-autotooltip_bigRNA transcription: the process of RNA polymerase using the DNA sequence of a gene as a template to form an mRNA (in prokaryotes) or pre-mRNA (in eukaryotes). In most cases, “transcription” implies RNA transcription. (even in eukaryotesplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus.) are sometimes called transactivatorsplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator.. So far, we've seen that the Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon. is negatively regulated; that is, the default state of the Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon. is that it 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., but the $lacO$ repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator. inactivates 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. unless an inducerplugin-autotooltip__default plugin-autotooltip_bigInducer: a molecule that triggers the expression of a gene or genes. Examples in E. coli include lactose and IPTG, which induce expression of the Lac operon in E. coli, and maltose, which induces expression of the Mal operon. An example in yeast is galactose, which induces expression of Gal genes. is present. In the next section, we will see an example of a transactivatorplugin-autotooltip__default plugin-autotooltip_bigTransactivator (activator): a DNA binding protein that binds to promoter sequences to activate the transcription of nearby genes. In the context of gene expression, “activator” is usually a synonym for transactivator. Compare with positive regulator. 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). called MalTplugin-autotooltip__default plugin-autotooltip_bigMalT: a protein encoded by the $malT$ gene that acts as a transactivator for the Mal operon..

To understand positive regulation, we first need a little more background information on uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). 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 Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon.. Until now we have been mostly considering 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 lead to constitutiveplugin-autotooltip__default plugin-autotooltip_bigConstitutive: a term describing a pattern of gene expression, wherein the gene is always expressed no matter what. For some genes, constitutive expression is normal (see housekeeping gene). For inducible genes or operons, constitutive is a mutant state. synthesis of β-galactosidase. It is also possible to get 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 are uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all).¹⁾. For example, 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. in the promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA ($lacP^-$) is uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). (Table Tab5). $lacP^-$ promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA 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 the Lac operonplugin-autotooltip__default plugin-autotooltip_bigLac operon: an operon in E. coli that contains the cis-acting regulatory elements $lacP$ and $lacO$, and the protein coding genes $lacZ$, $lacY$, and $lacA$. The Lac operon is an example of a negatively-regulated operon. can be distinguished from simple $lacZ^–$ 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. since promoterplugin-autotooltip__default plugin-autotooltip_bigPromoter: has multiple closely related but subtly different meanings depending on context:

* In bacteria, a promoter is a cis-acting DNA sequence near the transcription start site of a gene or operon that binds to bacterial RNA polymerase. * In eukaryotes, the formal definition of a promoter (also called a basal promoter) is a RNA 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. affect the $lacY$ and $lacA$ genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) as well.

Another type of uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). 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 in $lacI$, where a Lac repressor proteinplugin-autotooltip__default plugin-autotooltip_bigLacI: the protein encoded by the $lacI$ gene; also called the Lac repressor protein. Binds to lactose or IPTG; upon binding, it loses the ability to bind to $lacO$. is formed that binds to the $lacO$ operatorplugin-autotooltip__default plugin-autotooltip_bigOperator: in bacterial genetics, an operator is a cis-acting genetic element that negatively regulates the expression of nearby genes. $lacO$ of the Lac operon is an example of an operator. DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. but does not bind inducerplugin-autotooltip__default plugin-autotooltip_bigInducer: a molecule that triggers the expression of a gene or genes. Examples in E. coli include lactose and IPTG, which induce expression of the Lac operon in E. coli, and maltose, which induces expression of the Mal operon. An example in yeast is galactose, which induces expression of Gal genes.. These so-called “super repressorplugin-autotooltip__default plugin-autotooltip_bigRepressor: a DNA binding protein that binds to negatively acting cis-acting elements such as operators in bacteria to inhibit transcription. Compare to negative regulator.” 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 designated as $lacI^s$ (Table 3). Finding uninducibleplugin-autotooltip__default plugin-autotooltip_bigUninducible: a mutant state wherein normally inducible genes are no longer inducible (and in fact may no longer be expressed at all). 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 a regulatory geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) such as $lacI$ suggests the possibility that there might be positive regulatory mechanisms for geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) expressionplugin-autotooltip__default plugin-autotooltip_bigExpression: a term used to describe the idea that the function of a gene is apparent and can be observed. Genes may not always be expressed all the time in all places. in other genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-).