Genetics

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File:ADN static.png
DNA, the molecular basis for inheritance. Each strand of DNA is a chain of nucleotides, matching each other in the center to form what look like rungs on a twisted ladder.

Genetics is the science of heredity and variation in living organisms.<ref name=Griffiths_et_al> {{

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}}.{{ #if: |  “{{{quote}}}” }}  854 pages. ISBN 0-7637-1511-5. </ref> Knowledge of the inheritance of characteristics has been implicitly used since prehistoric times for improving crop plants and animals through selective breeding. However, the modern science of genetics, which seeks to understand the mechanisms of inheritance, only began with the work of Gregor Mendel in the mid-1800s.<ref name=Weiling>{{#if:Weiling F

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}}{{#if:
 |[{{{url}}} Historical study: Johann Gregor Mendel 1822-1884]
 |Historical study: Johann Gregor Mendel 1822-1884

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}}</ref> Although he did not know the physical basis for heredity, Mendel observed that inheritance is fundamentally a discrete process with specific traits that are inherited in an independent manner — these basic units of inheritance are now called genes.

Following the rediscovery of Mendel's observations in the early 1900s, research in 1910s yielded the first physical understanding of inheritance — that genes are arranged linearly along large cellular structures called chromosomes. By the 1950s it was understood that the core of a chromosome was a long molecule called DNA and genes existed as linear sections within the molecule. A single strand of DNA is a chain of four types of nucleotides; hereditary information is contained within the sequence of these nucleotides. Solved by Watson and Crick in 1953, DNA's three-dimensional structure is a double-stranded helix, with the nucleotides on each strand physically matched to each other. Each strand acts as a template for synthesis of a new partner strand, providing the physical mechanism for the inheritance of information.

The sequence of nucleotides in DNA is used to produce specific sequences of amino acids, creating proteins — a correspondence known as the "genetic code". This sequence of amino acids in a protein determines how it folds into a three-dimensional structure, this structure is in turn responsible for the protein's function. Proteins are responsible for almost all functional roles in the cell. A change to DNA sequence can change a protein's structure and behavior, and this can have dramatic consequences in the cell and on the organism as a whole.

Although genetics plays a large role in determining the appearance and behavior of organisms, it is the interaction of genetics with the environment an organism experiences that determines the ultimate outcome. For example, while genes play a role in determining a person's height, the nutrition and health that person experiences in childhood also have a large effect.

History of genetics

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File:Sexlinked inheritance white.jpg
Morgan's observation of sex-linked inheritance of a mutation causing white eyes in Drosophila led him to the hypothesis that genes are located upon chromosomes.

Although the science of genetics has its origins in the work of Gregor Mendel in the mid-1800s, various theories of inheritance preceded Mendel. These theories generally assumed that there existed an inheritance of acquired characteristics (also known as "soft inheritance"): the belief that individuals inherit traits that have been strengthened in their parents. Today, the theory is commonly associated with Jean-Baptiste Lamarck, who used this pattern of inheritance to explain the evolution of various traits within species (these changes are now understood to be the product of natural selection rather than a product of soft inheritance).

Mendelian and classical genetics

The modern science of genetics traces its roots to the observations made by Gregor Johann Mendel, a German-Czech Augustinian monk and scientist who made detailed studies of the nature of inheritance in plants. In his paper "Versuche über Pflanzenhybriden" ("Experiments on Plant Hybridization"), presented in 1865 to the Brunn Natural History Society, Gregor Mendel traced the inheritance patterns of certain traits in pea plants and showed that they could be described mathematically.<ref name="mendel">{{#if:Mendel, GJ

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}} (in English in 1901, J. R. Hortic. Soc. 26: 1–32) translation available online</ref> Although not all features show these patterns of Mendelian inheritance, his work suggested the utility of the application of statistics to the study of inheritance.

The significance of Mendel's observations was not understood until early in the twentieth century, after his death, when his research was re-discovered by other scientists working on similar problems. The word "genetics" itself was coined in 1905 by William Bateson, a significant proponent of Mendel's work, in a letter to Adam Sedgwick <ref>Online copy of William Bateson's letter to Adam Sedgwick</ref>. The adjective "genetic" (derived from the Greek word "genno" γεννώ: to give birth) predates the noun, dating back to the 1830's and first used in the biological sense in 1859 by Charles Darwin in the The Origin of Species.<ref>genetic, a. and n. pl., Oxford English Dictionary, 2nd ed. (1989)</ref> Bateson publicly promoted and popularized usage of word "genetics" to describe the study of inheritance in his inaugural address to the Third International Conference on Plant Hybridization in London, England, in 1906.<ref name="bateson_genetics">{{#if: Bateson, W

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Although the conference was titled "International Conference on Hybridisation and Plant Breeding", Wilks changed the title for publication as a result of Bateson's speech.</ref>

In the decades following rediscovery and popularization of Mendel's work, numerous experiments sought to elucidate the molecular basis of DNA. In 1910 Thomas Hunt Morgan argued that genes reside on chromosomes, based on observations of a sex-linked white eye mutation in fruit flies. In 1913 his student Alfred Sturtevant used the phenomenon of genetic linkage and the associated recombination rates to demonstrate and map the linear arrangement of genes upon the chromosome.

File:FirstSketchOfDNADoubleHelix.jpg
Francis Crick's first sketch of a DNA double helix.

Molecular genetics

Although chromosomes were known to contain genes, chromosomes were composed of both protein and DNA — it was unknown which was critical for heredity or how the process occurred. In 1928, Frederick Griffith published his discovery of the phenomenon of transformation (see Griffith's experiment); sixteen years later, in 1944, Oswald Theodore Avery, Colin McLeod and Maclyn McCarty used this phenomenon to isolate and identify the molecule responsible for transformation as DNA.<ref name=Avery_et_al>{{#if:Avery OT, MacLeod CM, and McCarty M

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 |[{{{url}}} Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III]
 |Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III

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}}35th anniversary reprint available</ref> The Hershey-Chase experiment in 1952 identified DNA (rather than protein) as the genetic material of viruses, further evidence that DNA was the molecule responsible for inheritance.

James D. Watson and Francis Crick resolved the structure of DNA in 1953, using the X-ray crystallography work of Rosalind Franklin that indicated the molecule had a helical structure. Their double-helix model paired a sequence of nucleotides with a "complement" on the other strand. This structure not only provided a physical explanation for information contained within the order of the nucleotides, but also a physical mechanism for duplication through separation of strands and the reconstruction of a partner strand based on the nucleotide pairings. Although the structure explained the process of inheritance, it was still unknown how DNA influenced the behavior of cells. In the following years many scientists sought to understand how DNA controls the process of protein production within ribosomes, eventually discovering the transcription of DNA into messenger RNA and uncovering the genetic code which links the nucleotide sequence of messenger RNA to the amino acid sequence of protein.

With this molecular understanding of DNA, an explosion of research based on this understanding of the molecular nature of DNA became possible. The development of chain-termination DNA sequencing in 1977 enabled the determination of nucleotide sequences on DNA,<ref name=sanger_et_al> {{#if:Sanger F, Nicklen S, and Coulson AR

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 |[{{{url}}} Enzymatic Amplification of β-Globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia]
 |Enzymatic Amplification of β-Globin Genomic Sequences and Restriction Site Analysis for Diagnosis of Sickle Cell Anemia

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}} </ref> These and other techniques, through the pooled efforts of the Human Genome Project and parallel private effort by Celera Genomics, culminated in the sequencing of the human genome in 2001.

Features of inheritance

Discrete inheritance and Mendel's laws

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File:Punnett square mendel flowers.svg
A Punnett square depicting a cross between two pea plants heterozygous for purple (B) and white (b) blossoms.

At its most fundamental level, inheritance in organisms occurs by means of discrete traits, called "genes".<ref> {{

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}}.{{ #if: |  “{{{quote}}}” }}  Chapter 2 (Patterns of Inheritance): Introduction </ref> This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants.<ref name="mendel" /><ref> {{

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}}.{{ #if: |  “{{{quote}}}” }}  Chapter 2 (Patterns of Inheritance): Mendel's experiments </ref> In his experiments studying the trait for flower color, Mendel observed that the flowers of each pea plant were either purple or white — and never an intermediate between the two colors. These different, discrete versions of the same gene are called "alleles".

In the case of pea plants, each organism has two alleles of each gene, and the plants inherit one allele from each parent.<ref> {{

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}}.{{ #if: |  “{{{quote}}}” }} Chapter 3 (Chromosomal Basis of Heredity): Mendelian genetics in eukaryotic life cycles </ref> Many organisms, including humans, have this pattern of inheritance. Organisms with two copies of the same allele are called "homozygous", while organisms with two different alleles are "heterozygous".

The set of alleles for a given organism is called its genotype, while the visible trait the organism has is called its "phenotype". When organisms are heterozygous, often one allele is called "dominant" as its qualities "dominate" the phenotype of the organism, while the other allele is called "recessive" as its qualities "recede" and are not observed. Dominant alleles are often abbreviated with a capital letter, while recessive alleles are given a lowercase version of the same letter.<ref>This form of notation is especially common in plants. There are other types of notation, you can read more here.</ref> Some alleles do not have complete dominance and instead have incomplete dominance by expressing an intermediate phenotype, or codominance by expressing both alleles at once.<ref> {{

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}}.{{ #if: |  “{{{quote}}}” }}  Chapter 4 (Gene Interaction): Interactions between the alleles of one gene </ref>

When parents breed to produce children, their children randomly inherit one of the two alleles from each parent. The outcome of these crosses can be visualized by use of a Punnett square. These observations of discrete inheritance and the segregation of alleles are collectively known as "Mendel's first law" or the "Law of Segregation".

Assortment and interactions of multiple genes

File:Galton-height-regress.jpg
Human height is a complex genetic trait. Francis Galton's data from 1889 shows the relationship between offsping height as a function of mean parent height. While correlated, the remaining variation in offspring heights indicates environment is also an important factor in this trait.

Organisms have thousands of genes, and in sexually reproducing organisms assortment of these genes are generally independent of each other. This means that the inheritance of an allele for yellow or green pea color is unrelated to the inheritance of alleles for white or purple flowers. This phenomenon, known as "Mendel's second law" or the "Law of independent assortment", means that the alleles of different genes get shuffled between parents to form children with many different combinations. (Some genes do not assort independently, demonstrating genetic linkage, a topic discussed later in this article.)

Often different genes can interact in a way that influences the same trait. In the blue-eyed Mary, for example, there exists a gene with alleles that determine the color of flowers: blue or magenta. Another gene, however, controls whether the flowers have color at all: color or white. When a plant has two copies of this white allele, its flowers are white — regardless of whether the first gene has blue or magenta alleles. This interaction between genes is called "epistasis", with the second gene epistatic to the first.<ref> {{

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}}.{{ #if: |  “{{{quote}}}” }}  Chapter 4 (Gene Interaction): Gene interaction and modified dihybrid ratios</ref>

Many traits are not discrete features (eg. purple or white flowers) but are instead continuous features (eg. human height and skin color). These "complex traits" are the product of interactions of many genes.<ref>{{#if:Mayeux R

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}}.{{ #if: |  “{{{quote}}}” }}  Chapter 25 (Quantitative Genetics): Quantifying heritability</ref> Measurement of the heritability of a trait is relative, though — in a more variable environment, the environment has a bigger influence on the total variation of the trait. For example, human height is a complex trait with a heritability of 89% in the United States. In Nigeria, however, where people experience a more variable access to good nutrition and health care, height has a heritability of only 62%.<ref>{{#if:Luke A, Guo X, Adeyemo AA, Wilks R, Forrester T, Lowe W Jr, Comuzzie AG, Martin LJ, Zhu X, Rotimi CN, Cooper RS

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|{{#if:|, |, and }}[[{{{6}}}|{{{6}}}]]}}{{#if:
|{{#if:|, |, and }}[[{{{7}}}|{{{7}}}]]}}{{#if:
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|{{#if:|, |, and }}[[{{{9}}}|{{{9}}}]]}}{{#if:
|, and [[{{{10}}}|{{{10}}}]]}}{{#if: | (too many parameters in {{main}})}}