TNBGGA: The No Bullshit Guide to Genetic Analysis

In this book we mostly think of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. as an information molecule and not as an organic compound (Fig. Fig1), but we do need to know some basic concepts of the chemical structure of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. to get the idea that a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is a physical object.

How was DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. as the physical genetic material discovered? Below is a quick summary of the history. In 1923, a British physician named Frederick Griffith discovered that 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. Streptococcus pneunmoniae could be converted, or transformedplugin-autotooltip__default plugin-autotooltip_bigTransformation: in microbiology (including for yeasts), transformation is the alteration of phenotype due to uptake of external DNA into a cell. Not to be confused with “transformation” in the context of cell biology, where the definition is the alteration of a normal cell to a cancerous cell., from a non-disease-causing strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and (R) to a virulent (i.e., disease-causing) strainplugin-autotooltip__default plugin-autotooltip_bigStrain or line: refers to a pool or colony of individuals or cultured cells of a desired genotype or phenotype that is mostly homogeneous and can be bred and/or produced in perpetuity for research or commercial purposes. “Strain” tends to be used more for microorganisms and (S). To achieve this, he mixed heat-killed S 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. with live R 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. and found that the R 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. were now virulent. Not only did they become virulent, new 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. formed from these transformedplugin-autotooltip__default plugin-autotooltip_bigTransformation: in microbiology (including for yeasts), transformation is the alteration of phenotype due to uptake of external DNA into a cell. Not to be confused with “transformation” in the context of cell biology, where the definition is the alteration of a normal cell to a cancerous cell. R 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. were also virulent. In other words, they had acquired a new phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. that could be genetically inherited in future generations. Griffith didn't know what was causing this transformationplugin-autotooltip__default plugin-autotooltip_bigTransformation: in microbiology (including for yeasts), transformation is the alteration of phenotype due to uptake of external DNA into a cell. Not to be confused with “transformation” in the context of cell biology, where the definition is the alteration of a normal cell to a cancerous cell., but he named it the transforming principle.

Fast forward to 1945, and three scientists named Avery, MacLeod, and McCarty set out to isolate the so-called transforming principle that Griffith discovered. They tested whether different types of chemical components purified from the heat-killed 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. could function to transformplugin-autotooltip__default plugin-autotooltip_bigTransformation: in microbiology (including for yeasts), transformation is the alteration of phenotype due to uptake of external DNA into a cell. Not to be confused with “transformation” in the context of cell biology, where the definition is the alteration of a normal cell to a cancerous cell. R 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.. They found that 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., lipids, and carbohydrates did not transformplugin-autotooltip__default plugin-autotooltip_bigTransformation: in microbiology (including for yeasts), transformation is the alteration of phenotype due to uptake of external DNA into a cell. Not to be confused with “transformation” in the context of cell biology, where the definition is the alteration of a normal cell to a cancerous cell. R 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., but nucleic acids (and more specifically DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.) did. Initially, scientists had a hard time believing their results, because DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. was known to be chemically less complex than 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.. Most scientists at the time did not think the relatively simple DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. molecule could store all the instructions essential for life and many believed that 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. were more likely to be the genetic material. Between 1951-1952, Hershey and Chase devised experiments using live bacteriophageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria. and radioactively labeled proteinsplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes. and DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. to show that DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. and not 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. conferred heritability to the bacteriophageplugin-autotooltip__default plugin-autotooltip_bigBacteriophage: viruses that infect bacteria.. All this work collectively convinced scientists that DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. was indeed the genetic material. Still, no one knew how DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. stored information.

In rare cases of some viruses, genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) are made of RNAplugin-autotooltip__default plugin-autotooltip_bigRNA sequencing (RNAseq): an experimental technique that sequences all the RNAs in a sample. It is based off of converting RNAs into cDNAs with reverse transcriptase, followed by Illumina sequencing. – we do not discuss this further in this book.

In 1953, Watson and Crick, based on the X-ray crystallography data of Rosalind Franklin and their own modeling work, deduced that the structure of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is a double helix. The double helix consists of two molecules called single stranded DNAplugin-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. (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.). Sometimes we abbreviate this and just call each 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. a strand. Each strand is composed of a sequenceplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. of polymerized subunits called nucleotidesplugin-autotooltip__default plugin-autotooltip_bigNucleotide: molecules that are polymerized to form nucleic acids (DNA or RNA). Includes dNTPs and NTPs., of which there are four: 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), adenineplugin-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. (A), 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), and 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). Each strand is asymmetrical; one end (the end we usually think of as being the start) is called the 5' end (pronounced as “five prime end”), and the other end is called the 3' end (pronounced as “three prime end”). The two strands twist together in a helical shape and are held together by weak hydrogen bondsplugin-autotooltip__default plugin-autotooltip_bigHydrogen bond: a type of weak noncovalent bond that forms between atoms that are part of a dipole movement. 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. orientation; that is, if one strand is in a 5' to 3' left-to-right orientation, the other strand pairs with it in a 3' to 5' left to right orientation. The two strands held together forms double-stranded DNAplugin-autotooltip__default plugin-autotooltip_bigDouble-stranded DNA (dsDNA): DNA that consists of two complementary strands of ssDNA paired together via hydrogen bonds between the nitrogenous bases G, A, T, and C. (dsDNAplugin-autotooltip__default plugin-autotooltip_bigDouble-stranded DNA (dsDNA): DNA that consists of two complementary strands of ssDNA paired together via hydrogen bonds between the nitrogenous bases G, A, T, and C.).

It was not the helical structure itself but the discovery of base pairingplugin-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. of the four nucleotidesplugin-autotooltip__default plugin-autotooltip_bigNucleotide: molecules that are polymerized to form nucleic acids (DNA or RNA). Includes dNTPs and NTPs. in the chemical structure of the strands that revealed how information could be encoded in a molecule. Base pairingplugin-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. is the key feature of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. that allows it to store and propagate information. G and C always pair with each other, and A and T always pair with each other.

DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is able to make copies of itself with various enzymesplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. such as DNA helicaseplugin-autotooltip__default plugin-autotooltip_bigDNA helicase: an enzyme usually involved in DNA replication. Its main function is to unwind the two ssDNA strands of dsDNA. and 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 through semiconservativeplugin-autotooltip__default plugin-autotooltip_bigSemiconservative: a term used to describe how DNA replicates. Each time a dsDNA molecule is replicated to produce two “new” dsDNA moecules, one of the ssDNA strands of each “new” dsDNA actually is one the ssDNA strands from the starting dsDNA molecule. Thus, each “new” dsDNA molecule is only 50% new. 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. (Fig. 2), which is necessary for passing information from parents to progenyplugin-autotooltip__defaultProgeny: a synonym for offspring.. The strands are separated by DNA helicaseplugin-autotooltip__default plugin-autotooltip_bigDNA helicase: an enzyme usually involved in DNA replication. Its main function is to unwind the two ssDNA strands of dsDNA. and each old strand is used as a template 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 to synthesize a new strand by following basepairingplugin-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. rules.

Information from portions of the DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. (i.e., genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)) can be extracted by again taking advantage of complementary base-pairing to make a copy of the information copied onto an RNA molecule using an 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. called RNA polymeraseplugin-autotooltip__default plugin-autotooltip_bigRNA polymerase: the enzyme that carries out RNA transcription. There are many different types of RNA polymerase, but in this book we collectively refer to them as just “RNA polymerase” for simplicity.. This is known as 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. (Fig. 3). RNA is chemically less stable than DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth., and RNA can be thought of as a temporary copy of a portion of the DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.’s information. (Note that RNA uses uracilplugin-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. (U) in place of T.) RNAsplugin-autotooltip__default plugin-autotooltip_bigRNA sequencing (RNAseq): an experimental technique that sequences all the RNAs in a sample. It is based off of converting RNAs into cDNAs with reverse transcriptase, followed by Illumina sequencing. are also asymmetrical – they have a 5' and 3' end, and in fact are transcribedplugin-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. in a 5' to 3' direction.

There are many different kinds of RNA molecules, but here we are primarily concerned with messenger RNAplugin-autotooltip__default plugin-autotooltip_bigmessenger RNA (mRNA): an RNA molecule that codes for protein. (mRNAplugin-autotooltip__default plugin-autotooltip_bigmessenger RNA (mRNA): an RNA molecule that codes for protein.), which code for 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.. In eukaryotesplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus., mRNAsplugin-autotooltip__default plugin-autotooltip_bigmessenger RNA (mRNA): an RNA molecule that codes for protein. are transcribedplugin-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. in the nucleusplugin-autotooltip__default plugin-autotooltip_bigNucleus: in eukaryotes, the membrane-bound organelle in cells that contains the chromosomes.¹⁾, but are transported into the cytoplasm for translationplugin-autotooltip__default plugin-autotooltip_bigProtein translation: the process of using an mRNA as a template to synthesize a protein based on the genetic code, using ribosomes. into 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. (Fig. 5). A portion of the mRNAplugin-autotooltip__default plugin-autotooltip_bigmessenger RNA (mRNA): an RNA molecule that codes for protein. sequenceplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. called the 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). begins with the first RNA 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. AUG (the start codonplugin-autotooltip__default plugin-autotooltip_bigStart codon: usually the first AUG RNA sequence starting from the 5' end of the mRNA and reading in the 3' direction. AUG signals the ribosome to start translation. AUG also codes for the amino acid methionine.) that appears starting from the 5' end. Each set of three consecutive bases that are read after the AUG start codonplugin-autotooltip__default plugin-autotooltip_bigStart codon: usually the first AUG RNA sequence starting from the 5' end of the mRNA and reading in the 3' direction. AUG signals the ribosome to start translation. AUG also codes for the amino acid methionine. are called codonsplugin-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., each of which codes for a different amino acidplugin-autotooltip__default plugin-autotooltip_bigAmino acid: molecules that are polymerized to form proteins. (Fig. 4). The amino acidsplugin-autotooltip__default plugin-autotooltip_bigAmino acid: molecules that are polymerized to form proteins. are joined together in order via peptide bondsplugin-autotooltip__default plugin-autotooltip_bigPeptide bond: covalent bonds that connect amino acids to form a polypeptide.. This continues until a stop codonplugin-autotooltip__default plugin-autotooltip_bigStop codon: a codon that instructs the ribosome to terminate translation. Stop codons are UGA, UAG, or UAA in the universal genetic code. (UAA, UAG, or UGA) is reached. This process is called translationplugin-autotooltip__default plugin-autotooltip_bigProtein translation: the process of using an mRNA as a template to synthesize a protein based on the genetic code, using ribosomes. (Fig. 5) and it uses a large and complex 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. called a ribosomeplugin-autotooltip__default plugin-autotooltip_bigRibosome: a very large and complex enzyme formed from both protein and rRNA subunits. Its primary function is to catalyze translation. that reads mRNAplugin-autotooltip__default plugin-autotooltip_bigmessenger RNA (mRNA): an RNA molecule that codes for protein. in a 5' to 3' direction.

In most cases, “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” refers to 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. that is produced through 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. of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) and translationplugin-autotooltip__default plugin-autotooltip_bigProtein translation: the process of using an mRNA as a template to synthesize a protein based on the genetic code, using ribosomes. of mRNAsplugin-autotooltip__default plugin-autotooltip_bigmessenger RNA (mRNA): an RNA molecule that codes for protein.. 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. fold into complex three-dimensional shapes and can have many different functions. They can be enzymesplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. that catalyze biochemical reactions (an example would be the histidineplugin-autotooltip__default plugin-autotooltip_bigHistidine: Abbreviated as His or H; one of the 20 amino acids that are used to form proteins. biosynthetic enzymesplugin-autotooltip__default plugin-autotooltip_bigEnzyme: a macromolecule, usually a protein (but sometimes an RNA), that functions as a catalyst of some kind of biochemical reaction. in Chapter 02 Fig. 3); they can be structural 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 form cellular structures (examples include 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. such as myosin and actin, which make up muscle fibers); they can be membrane 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 facilitate transport (an example includes transmembrane glucose transporters that carry glucose from the digestive tract into intestinal epithelial cells); they can be secreted hormones (an example is insulin, which is used to regulate blood sugar levels); and so forth. 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. carry out the vast majority of biological functions and are therefore directly or indirectly responsible for the phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. we can observe in an organism.

Some RNAsplugin-autotooltip__default plugin-autotooltip_bigRNA sequencing (RNAseq): an experimental technique that sequences all the RNAs in a sample. It is based off of converting RNAs into cDNAs with reverse transcriptase, followed by Illumina sequencing. do not code for 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. and have some kind of direct biochemical function. In this case, the RNA is 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”. Examples of RNAsplugin-autotooltip__default plugin-autotooltip_bigRNA sequencing (RNAseq): an experimental technique that sequences all the RNAs in a sample. It is based off of converting RNAs into cDNAs with reverse transcriptase, followed by Illumina sequencing. with biochemical function include rRNAs, tRNAs, snRNAs, piwiRNAs, etc. These are beyond the scope of this book.

When genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) go through the process of 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. and translationplugin-autotooltip__default plugin-autotooltip_bigProtein translation: the process of using an mRNA as a template to synthesize a protein based on the genetic code, using ribosomes. to form a 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 (usually 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. but sometimes an RNAplugin-autotooltip__default plugin-autotooltip_bigRNA sequencing (RNAseq): an experimental technique that sequences all the RNAs in a sample. It is based off of converting RNAs into cDNAs with reverse transcriptase, followed by Illumina sequencing.) such that that 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 is providing some observable function to the organism, we say that the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is being 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.. A great deal of modern genetics research is devoted to understanding how 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. is controlled.

The 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). human 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 is approx. 3×10⁹ bp in size. This means that the average human chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. is $\frac{3\times10^9}{23}= 1.3 \times 10^8$ bp, or over one hundred million bp long – that is a very large molecule! Humans and most mammals have about 20,000 genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (which is surprisingly not that many more than Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research.). This means that on average each human chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. contains about 1000 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 :-) are typically 10³ - 10⁴ 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. in size, although they can be much larger.

For example, the human dystrophin geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is 2 x 10⁶ 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.. 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 dystrophin result in a debilitating disease called Duchenne muscular dystrophy (DMD), which affects humans but also dogs, especially Golden Retrievers. Interestingly, DMD is a sex-linkedplugin-autotooltip__default plugin-autotooltip_bigSex linkage: a gene is said to be sex-linked if it maps to a sex chromosome. trait in both humans and dogs - the dystrophin geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is on the $X$ chromosomeplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. in both species, and males are affected more than females (Fig. 6). Note that not all of 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. of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) may be 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).; that is, not all of 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. of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) may correspond to codonsplugin-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. for amino acidsplugin-autotooltip__default plugin-autotooltip_bigAmino acid: molecules that are polymerized to form proteins.. In fact, most DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is not geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) 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).. Most eukaryoticplugin-autotooltip__default plugin-autotooltip_bigeukaryote: organism whose cells have membrane bound organelles, including the nucleus. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (and in rare cases prokaryoticplugin-autotooltip__default plugin-autotooltip_bigProkaryote: an organism that does not have membrane bound organelles. In this book prokaryotes refer to bacteria. genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)) contain DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. 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. called intronsplugin-autotooltip__default plugin-autotooltip_bigIntron: sequences in a pre-mRNA that sit between exons and are removed by splicing. Formally speaking, introns are defined as being part of pre-mRNA, but the DNA sequence that codes for introns can also be informally described as introns.; when these intronplugin-autotooltip__default plugin-autotooltip_bigIntron: sequences in a pre-mRNA that sit between exons and are removed by splicing. Formally speaking, introns are defined as being part of pre-mRNA, but the DNA sequence that codes for introns can also be informally described as introns. 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 transcribedplugin-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. into RNA they are removed from the transcript by a process called splicingplugin-autotooltip__default plugin-autotooltip_bigIntron splicing: the act of remove introns and joining exons from pre-mRNA to form an mRNA. This occurs in the nucleus of eukaryotic cells and is catalyzed by an enzyme called the spliceosome. (see Chapter 12 for more details). However, the majority of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is non-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). in between genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) called intergenic regionsplugin-autotooltip__default plugin-autotooltip_bigIntergenic region: a region of DNA that sits between genes and does not contain other genes or coding sequences. Integenic regions usually contain various cis-acting regulatory elements that control the expression of nearby genes..

Now let us consider some terms we have seen before, but now in the context of understanding the physical nature of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-).

Allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. are different versions of the same geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). Different allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. are simply different variations or versions of the same geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-); different versions have differences in their DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. 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.. Often allelesplugin-autotooltip__default plugin-autotooltip_bigAllele: a version of a gene. Alleles of a gene are different if they have differences in their DNA sequence. are referred to as 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., but this usage is often incorrect, particularly when we discuss naturally occurring variants in a population. Differences in their 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. may or may not alter the amino acidplugin-autotooltip__default plugin-autotooltip_bigAmino acid: molecules that are polymerized to form proteins. sequenceplugin-autotooltip__default plugin-autotooltip_bigSequence: the precise order of monomers in a polymer. In DNA, it refers to the order of G, A, T, and C nucleotides. In RNA, it refers to the order of G, A, U, and C nucleotides. In proteins, it refers to the order of amino acids. of 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 encoded by the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). In fact, you can even define differences in non-coding intergenic regionsplugin-autotooltip__default plugin-autotooltip_bigIntergenic region: a region of DNA that sits between genes and does not contain other genes or coding sequences. Integenic regions usually contain various cis-acting regulatory elements that control the expression of nearby genes. (which are not part of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)! See Chap. 07) between individuals as different 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.. When a change in 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. does affect geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) function, that results in 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. (see Chap. 08).

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 an altered version of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) that have an altered phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. that is markedly different than most individuals in a population. Most of the time, the altered phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. is caused by a change in 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. function. If you are an evolutionary or population biologist, then you might use the term variation (or variant) instead of 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..

To examine these ideas more closely, let's look at 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 Drosophilaplugin-autotooltip__default plugin-autotooltip_bigDrosophila melanogaster: a fruit fly species used in genetics research. $shibire$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), which we first saw in Chapter 03 (Table 1). A particular 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. of $shibire$ codes for an altered heat sensitive 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 required for synaptic transmission (we can also call it a mutantplugin-autotooltip__default plugin-autotooltip_bigMutant: an individual that has a different phenotype than wildtype and likely contains one more mutations that cause this difference. proteinplugin-autotooltip__default plugin-autotooltip_bigProtein: a molecule that is formed by the translation of messenger RNAs (mRNAs). Functions that proteins provide are what usually give organisms their phenotypes.). When flies that carry this mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. are warmed up, they become paralyzed.

This example illustrates two powerful aspects of genetic analysis. First, we can follow molecular changes in the DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. (which are not easily observable) such as the $shibire$ 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. as they are revealed by easily observable consequences of 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. such as a paralyzed fly. This has a great deal of practical implication; even though technically it's possible to track different 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. by directly analyzing 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 practice this is much more difficult to do than simply looking at a phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism.. Second, we have a very precise way of studying the function of individual 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. by examining the consequences of altering just that one 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. function in an otherwise normal organism.

The physical definition of the geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is a very good one but there are many instances where we wish to study genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) whose DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. 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 not known. For example, we have isolated a new 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. fly that is also paralyzed, and we want to know whether this mutationplugin-autotooltip__default plugin-autotooltip_bigMutation: a change in the DNA of a gene that results in a change of phenotype compared to a reference wildtype allele. See also: mutant. is also in the $shibire$ geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). We can see from Chapters 02 and 03 that we can answer this question without knowledge of 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. either by a test for geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) function (complementation testplugin-autotooltip__default plugin-autotooltip_bigComplementation test: a genetic experiment that answers the question: how many different genes are represented within a collection of mutants?) or by a test of the chromosomalplugin-autotooltip__default plugin-autotooltip_bigChromosome: a structure that organizes dsDNA in a cell through interactions with various DNA binding proteins. position of 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. by recombinationplugin-autotooltip__default plugin-autotooltip_bigRecombination: Recombination can have slightly different meanings depending on context:

* In the context of genetic crosses (usually a dihybrid cross or a test cross), recombination refers to the phenomena where the phenotype of the F2 offspring is different than either parent (P generation). $lox$ mappingplugin-autotooltip__default plugin-autotooltip_bigGenetic mapping: a term describing a variety of different experimental approaches used to determine the physical locations of genes on chromosomes.. In practice, these other ways of defining genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) by function or by position can sometimes be more useful than a definition based on 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..

It's also important to note that we haven't actually defined a physical geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) yet! We've defined the physical material of genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) (DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.), the intermediate material between geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) and 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 (RNAplugin-autotooltip__default plugin-autotooltip_bigRNA sequencing (RNAseq): an experimental technique that sequences all the RNAs in a sample. It is based off of converting RNAs into cDNAs with reverse transcriptase, followed by Illumina sequencing.), and 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 itself that in most cases provides function (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.). Thinking of a typical mammal: if we have approximately 20,000 genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-), and the average size of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) is approximately 10,000 bp, that accounts for 2×10⁸ bp worth of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. (this is just back of the envelope math and not meant to be accurate). But a typical mammalian 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 (humans, for instance) is close to 3×10⁹ bp of DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth.. This rough calculation tells us that most of the 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 must not contain genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)²⁾! In other words, in a mammal most DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. is not part of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). In the next chapter we will see how we can analyze the 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 to find genesplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) within DNAplugin-autotooltip__default plugin-autotooltip_bigDNA: deoxyribonucleic acid. The genetic material for nearly all life on Earth. 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..

Conceptual question: We know that 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 :-) cause changes in observable phenotypesplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. controlled by that geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-). But why might some changes in 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. of a geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-) not alter the phenotypeplugin-autotooltip__default plugin-autotooltip_bigPhenotype: an observable feature or property of an organism. controlled by that geneplugin-autotooltip__default plugin-autotooltip_bigGene: read Chapters 02, 03, 04, 05, and 06 for a definition of gene :-)? There are lots of possible correct explanations!