Gene Key 57

[Cesar Sergeantson]

Agene is the basic physical and functional unit of heredity. Genes are made up of DNA. Some genes act as instructions to make molecules called proteins, which are needed for the body to function. However, many genes do not code for proteins, instead they help control other genes.

The information in DNA is encoded in genetic building blocks called base pairs. In humans, genes vary in size from a few hundred DNA base pairs to more than 2 million base pairs. Between 1990 and 2003, an international research effort called the Human Genome Project worked to sequence all of the DNA in a human (known as the human genome). The project estimated that humans have between 20,000 and 25,000 genes that provide instructions for making proteins. Later studies sought to build on the work of the Human Genome Project and have provided additional details on the genome sequence. We now know that the human genome contains about 19,900 genes used to produce proteins.

Scientists keep track of genes by giving them unique names. Because gene names can be long, genes are also assigned symbols, which are short combinations of letters (and sometimes numbers) that represent an abbreviated version of the gene name. For example, one of the genes on chromosome 7 is called the cystic fibrosis transmembrane conductance regulator because variants in this gene can cause cystic fibrosis. The symbol for this gene is CFTR.

The National Human Genome Research Institute provides information on the Human Genome Project and Telomere 2 Telomere, two studies that were pivotal in providing a complete sequence of the human genome. The National Human Genome Research Institute also includes additional information about gene and the genome.

In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protein-coding genes and non-coding genes.[1][2][3]

The transmission of genes to an organism's offspring, is the basis of the inheritance of phenotypic traits from one generation to the next. These genes make up different DNA sequences, together called a genotype, that is specific to every given individual, within the gene pool of a population of a given species. The genotype, along with environmental and developmental factors, ultimately determines the phenotype of the individual.

A gene can acquire mutations in its sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a gene, which may cause different phenotypical traits.[4] Genes evolve due to natural selection or survival of the fittest and genetic drift of the alleles.

The term gene was introduced by Danish botanist, plant physiologist, and geneticist Wilhelm Johannsen in 1909.[5] It is inspired by the ancient Greek: γόνος, gonos, that means offspring and procreation.

There are many different ways to use the term "gene" based on different aspects of their inheritance, selection, biological function, or molecular structure but most of these definitions fall into two categories, the Mendelian gene or the molecular gene.[1][6][7][8][9]

The Mendelian gene is the classical gene of genetics and it refers to any heritable trait. This is the gene described in The Selfish Gene.[10] More thorough discussions of this version of a gene can be found in the articles Genetics and Gene-centered view of evolution.

Very early work in the field that became molecular genetics suggested the concept that one gene makes one protein (originally 'one gene - one enzyme').[12][13] However, genes that produce repressor RNAs were proposed in the 1950s[14] and by the 1960s, textbooks were using molecular gene definitions that included those that specified functional RNA molecules such as ribosomal RNA and tRNA (noncoding genes) as well as protein-coding genes.[15]

The primary function of the genome is to produce RNA molecules. Selected portions of the DNA nucleotide sequence are copied into a corresponding RNA nucleotide sequence, which either encodes a protein (if it is an mRNA) or forms a 'structural' RNA, such as a transfer RNA (tRNA) or ribosomal RNA (rRNA) molecule. Each region of the DNA helix that produces a functional RNA molecule constitutes a gene.[16]

We define a gene as a DNA sequence that is transcribed. This definition includes genes that do not encode proteins (not all transcripts are messenger RNA). The definition normally excludes regions of the genome that control transcription but are not themselves transcribed. We will encounter some exceptions to our definition of a gene - surprisingly, there is no definition that is entirely satisfactory.[17]

A gene is a DNA sequence that codes for a diffusible product. This product may be protein (as is the case in the majority of genes) or may be RNA (as is the case of genes that code for tRNA and rRNA). The crucial feature is that the product diffuses away from its site of synthesis to act elsewhere.[18]

The important parts of such definitions are: (1) that a gene corresponds to a transcription unit; (2) that genes produce both mRNA and noncoding RNAs; and (3) regulatory sequences control gene expression but are not part of the gene itself. However, there's one other important part of the definition and it is emphasized in Kostas Kampourakis' book Making Sense of Genes.

Therefore in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules. With 'encoding information', I mean that the DNA sequence is used as a template for the production of an RNA molecule or a protein that performs some function.[6]

The emphasis on function is essential because there are stretches of DNA that produce non-functional transcripts and they do not qualify as genes. These include obvious examples such as transcribed pseudogenes as well as less obvious examples such as junk RNA produced as noise due to transcription errors. In order to qualify as a true gene, by this definition, one has to prove that the transcript has a biological function.[6]

In spite of the fact that both protein-coding genes and noncoding genes have been known for more than 50 years, there are still a number of textbooks, websites, and scientific publications that define a gene as a DNA sequence that specifies a protein. In other words, the definition is restricted to protein-coding genes. Here is an example from a recent article in American Scientist.

... to truly assess the potential significance of de novo genes, we relied on a strict definition of the word "gene" with which nearly every expert can agree. First, in order for a nucleotide sequence to be considered a true gene, an open reading frame (ORF) must be present. The ORF can be thought of as the "gene itself"; it begins with a starting mark common for every gene and ends with one of three possible finish line signals. One of the key enzymes in this process, the RNA polymerase, zips along the strand of DNA like a train on a monorail, transcribing it into its messenger RNA form. This point brings us to our second important criterion: A true gene is one that is both transcribed and translated. That is, a true gene is first used as a template to make transient messenger RNA, which is then translated into a protein.[22]

This restricted definition is so common that it has spawned many recent articles that criticize this "standard definition" and call for a new expanded definition that includes noncoding genes.[23][24][25] However, this so-called "new" definition has been around for more than half a century and it is not clear why some modern writers are ignoring noncoding genes.[editorializing]

Although some definitions can be more broadly applicable than others, the fundamental complexity of biology means that no definition of a gene can capture all aspects perfectly. Not all genomes are DNA (e.g. RNA viruses),[26] bacterial operons are multiple protein-coding regions transcribed into single large mRNAs, alternative splicing enables a single genomic region to encode multiple district products and trans-splicing concatenates mRNAs from shorter coding sequence across the genome.[27][28][29] Since molecular definitions exclude elements such as introns, promotors, and other regulatory regions, these are instead thought of as "associated" with the gene and affect its function.

An even broader operational definition is sometimes used to encompass the complexity of these diverse phenomena, where a gene is defined as a union of genomic sequences encoding a coherent set of potentially overlapping functional products.[30] This definition categorizes genes by their functional products (proteins or RNA) rather than their specific DNA loci, with regulatory elements classified as gene-associated regions.[30]

Prior to Mendel's work, the dominant theory of heredity was one of blending inheritance,[32] which suggested that each parent contributed fluids to the fertilization process and that the traits of the parents blended and mixed to produce the offspring. Charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan ("all, whole") and genesis ("birth") / genos ("origin").[33][34] Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction.

Mendel's work went largely unnoticed after its first publication in 1866, but was rediscovered in the late 19th century by Hugo de Vries, Carl Correns, and Erich von Tschermak, who (claimed to have) reached similar conclusions in their own research.[35] Specifically, in 1889, Hugo de Vries published his book Intracellular Pangenesis,[36] in which he postulated that different characters have individual hereditary carriers and that inheritance of specific traits in organisms comes in particles. De Vries called these units "pangenes" (Pangens in German), after Darwin's 1868 pangenesis theory.

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