Gene

Some genetic traits are instantly visible, such as eye color or the number of limbs, others are not, such as blood type, the risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

Therefore in this book I will consider genes as DNA sequences encoding information for functional products, be it proteins or RNA molecules.

First, in order for a nucleotide sequence to be considered a true gene, an open reading frame (ORF) must be present.

[26][27][28] 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.

[29] 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] From 1857 to 1864, in Brno, Austrian Empire (today's Czech Republic), he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring.

Charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan ("all, whole") and genesis ("birth") / genos ("origin").

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.

[40][41] In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities arranged like beads on a string.

[42][43] Collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA.

[46] The theories developed in the early 20th century to integrate Mendelian genetics with Darwinian evolution are called the modern synthesis, a term introduced by Julian Huxley.

He proposed that the Mendelian gene is a unit of natural selection with the definition: "that which segregates and recombines with appreciable frequency.

"[48]: 24  Related ideas emphasizing the centrality of Mendelian genes and the importance of natural selection in evolution were popularized by Richard Dawkins.

[50] This led to the construction of phylogenetic trees and the development of the molecular clock, which is the basis of all dating techniques using DNA sequences.

DNA consists of a chain made from four types of nucleotide subunits, each composed of: a five-carbon sugar (2-deoxyribose), a phosphate group, and one of the four bases adenine, cytosine, guanine, and thymine.

Nucleic acid synthesis, including DNA replication and transcription occurs in the 5'→3' direction, because new nucleotides are added via a dehydration reaction that uses the exposed 3' hydroxyl as a nucleophile.

Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the "words" in the genetic "language".

Telomeres are long stretches of repetitive sequences that cap the ends of the linear chromosomes and prevent degradation of coding and regulatory regions during DNA replication.

[51]: 14.4  Prokaryotes sometimes supplement their chromosome with additional small circles of DNA called plasmids, which usually encode only a few genes and are transferable between individuals.

[26] The structure of a protein-coding gene consists of many elements of which the actual protein coding sequence is often only a small part.

[60] The mature messenger RNA produced from protein-coding genes contains untranslated regions at both ends which contain binding sites for ribosomes, RNA-binding proteins, miRNA, as well as terminator, and start and stop codons.

[61] In addition, most eukaryotic open reading frames contain untranslated introns, which are removed and exons, which are connected together in a process known as RNA splicing.

The poly(A) tail protects mature mRNA from degradation and has other functions, affecting translation, localization, and transport of the transcript from the nucleus.

The transcription of an operon's mRNA is often controlled by a repressor that can occur in an active or inactive state depending on the presence of specific metabolites.

[51]: 6  The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961 using frameshift mutations in the rIIB gene of bacteriophage T4[74] (see Crick, Brenner et al. experiment).

The RNA molecule produced by the polymerase is known as the primary transcript and undergoes post-transcriptional modifications before being exported to the cytoplasm for translation.

Mendel's work demonstrated that alleles assort independently in the production of gametes, or germ cells, ensuring variation in the next generation.

[102] The initial draft sequences of the human genome confirmed the earlier predictions of about 30,000 protein-coding genes however that estimate has fallen to about 19,000 with the ongoing GENCODE annotation project.

Symbols are preferably kept consistent with other members of a gene family and with homologs in other species, particularly the mouse due to its role as a common model organism.

Photograph of Gregor Mendel
Gregor Mendel
DNA chemical structure diagram showing how the double helix consists of two chains of sugar-phosphate backbone with bases pointing inward and specifically base pairing A to T and C to G with hydrogen bonds.
The chemical structure of a four base pair fragment of a DNA double helix . The sugar - phosphate backbone chains run in opposite directions with the bases pointing inward, base-pairing A to T and C to G with hydrogen bonds .
Micrographic karyogram of human male, showing 23 pairs of chromosomes. The largest chromosomes are around 10 times the size of the smallest. [ 53 ]
Schematic karyogram of a human, with annotated bands and sub-bands . It shows dark and white regions on G banding . It shows 22 homologous chromosomes , both the male (XY) and female (XX) versions of the sex chromosome (bottom right), as well as the mitochondrial genome (at bottom left).
Further information: Karyotype
An RNA molecule consisting of nucleotides. Groups of three nucleotides are indicated as codons, with each corresponding to a specific amino acid.
Schematic of a single-stranded RNA molecule illustrating a series of three-base codons . Each three- nucleotide codon corresponds to an amino acid when translated to protein.
A protein-coding gene in DNA being transcribed and translated to a functional protein or a non-protein-coding gene being transcribed to a functional RNA
Protein coding genes are transcribed to an mRNA intermediate, then translated to a functional protein . RNA-coding genes are transcribed to a functional non-coding RNA ( PDB : 3BSE , 1OBB , 3TRA ​).
Illustration of autosomal recessive inheritance. Each parent has one blue allele and one white allele. Each of their 4 children inherit one allele from each parent such that one child ends up with two blue alleles, one child has two white alleles and two children have one of each allele. Only the child with both blue alleles shows the trait because the trait is recessive.
Inheritance of a gene that has two different alleles (blue and white). The gene is located on an autosomal chromosome . The white allele is recessive to the blue allele. The probability of each outcome in the children's generation is one quarter, or 25 percent.
Depiction of numbers of genes for representative plants (green), vertebrates (blue), invertebrates (orange), fungi (yellow), bacteria (purple), and viruses (grey). An inset on the right shows the smaller genomes expanded 100-fold area-wise. [ 87 ] [ 88 ] [ 89 ] [ 90 ] [ 91 ] [ 92 ] [ 93 ] [ 94 ]
Gene functions in the minimal genome of the synthetic organism , Syn 3 [ 105 ]
Comparison of conventional plant breeding with transgenic and cisgenic genetic modification