RNA

A hairpin loop from apre-mRNA. Notice its nitrogen-rich (blue) bases and oxygen-rich (red) backbone.

Ribonucleic acid or RNA is a nucleic acid, consisting of many nucleotides that form a polymer. Each nucleotide consists of a nitrogenous base, a ribose sugar, and a phosphate. RNA plays several important biological roles, including many processes involving translation of genetic information from deoxyribonucleic acid (DNA) into proteins. One type of RNA, messenger RNAribosomes, whereas ribosomal RNAs form vital portions of the structure of ribosomes and transfer RNAs act as essential carrier molecules for amino acids to be used in protein synthesis. It has also been known since the 1990s that several types of RNA regulate which genes are active. (mRNA), carries information from DNA to the protein synthesis complexes known as

RNA is very similar to DNA, but differs in a few important structural details: in the cell RNA is usually single stranded, while DNA is usually double stranded. RNA nucleotides contain ribose while DNA contains deoxyribose (a type of ribose that lacks one oxygen atom), and RNA uses the nucleotide uracil in its composition, instead of thymine which is present in DNA. RNA is transcribed from DNA by enzymes called RNA polymerases and is generally further processed by other enzymes. Some of these RNA processing enzymes contain their own RNAs.

Structure

Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)

Each nucleotide in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, generally adenine, cytosine, guanine or uracil. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each at physiological pH, making RNA a charged molecule (polyanion). The bases may form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil.^[1] However other interactions are possible, such as a group of adenine bases binding to each other in a bulge,^[2] or the GNRA tetraloop that has a guanine–adenine base-pair.^[1]

Chemical structure of RNA

An important structural feature of RNA that distinguishes it from DNA is the presence of a hydroxylA-form geometry rather than the B-form most commonly observed in DNA.^[3] This results in a very deep and narrow major groove and a shallow and wide minor groove.^[4] A second consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone.^[5] group at the 2' position of the ribose sugar. The presence of this ********al group enforces the C3'-endo sugar conformation (as opposed to the C2'-endo conformation of the deoxyribose sugar in DNA) that causes the helix to adopt the

RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil),^[6] but there are numerous modified bases and sugars in mature RNAs. Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T), are found in various places (most notably in the TΨC loop of tRNA).^[7] Another notable modified base is hypoxanthine, a deaminated guanine base whose nucleoside is called inosine. Inosine plays a key role in the wobble hypothesis of the genetic code.^[8] There are nearly 100 other naturally occurring modified nucleosides,^[9] of which pseudouridine and nucleosides with 2'-O-methylribose are the most common.^[10] The specific roles of many of these modifications in RNA are not fully understood. However, it is notable that in ribosomal RNA, many of the post-tran******ional modifications occur in highly ********al regions, such as the peptidyl transferase center and the subunit interface, implying that they are important for normal ********.^[11]

Secondary structure of an RNA from a telomerase

The ********al form of single stranded RNA molecules, just like proteins, frequently requires a specific tertiary structure. The scaffold for this structure is provided by secondary structural elements which are hydrogen bonds within the molecule. This leads to several recognizable "domains" of secondary structure like hairpin loops, bulges and internal loops.^[12] There has been a significant amount of research directed at the RNA structure prediction problem.

Comparison with DNA

RNA and DNA differ in three main ways. First, unlike DNA which is double-stranded, RNA is a single-stranded molecule in most of its biological roles and has a much shorter chain of nucleotides. Secondly, while DNA contains deoxyribose, RNA contains ribose, (there is no hydroxyl group attached to the pentose ring in the 2' position in DNA, whereas RNA has two hydroxyl groups). These hydroxyl groups make RNA less stable than DNA because it is more prone to hydrolysis. Thirdly, the complementary nucleotide to adenine is not thymine, as it is in DNA, but rather uracil, which is an unmethylated form of thymine.^[13]

The 50S ribosomal subunit. RNA is in orange, protein in blue. The active site is in the middle (red).

Like DNA, most biologically active RNAs including tRNA, rRNA, snRNAs and other non-coding RNAs are extensively base paired to form double stranded helices. Structural analysis of these RNAs have revealed that they are highly structured. Unlike DNA, this structure is not long double-stranded helices but rather collections of short helices packed together into structures akin to proteins. In this fashion, RNAs can achieve chemical catalysis, like enzymes.^[14] For instance, determination of the structure of the ribosome – an enzyme that catalyzes peptide bond formation – revealed that its active site is composed entirely of RNA.^[15]

Synthesis

Synthesis of RNA is usually catalyzed by an enzyme—RNA polymerase—using DNA as a template. Initiation of synthesis begins with the binding of the enzyme to a promoter sequence in the DNA (usually found "upstream" of a gene). The DNA double helix is unwound by the helicase^[16] activity of the enzyme. The enzyme then progresses along the template strand in the 3’ to 5’ direction, synthesizing a complementary RNA molecule with elongation occurring in the 5’ to 3’ direction. The DNA sequence also dictates where termination of RNA synthesis will occur.

There are also a number of RNA-dependent RNA polymerases as well that use RNA as their template for synthesis of a new strand of RNA. For instance, a number of RNA viruses (such as poliovirus) use this type of enzyme to replicate their genetic material.^[17] Also, it is known that RNA-dependent RNA polymerases are required for the RNA interference pathway in many organisms.^[18]

Types of RNA

Overview

Structure of a hammerhead ribozyme, a ribozyme that cuts RNA

Messenger RNA (mRNA) is the RNA that carries information from DNA to the ribosome sites of protein synthesis (translation) in the cell. The coding sequence of the mRNA determines the amino acid sequence in the protein that is produced.^[19]

RNA genes are genes that encode RNA which is not translated into a protein, known as non-coding RNA or small RNA. Non-coding RNAs can also derive from introns.^[20] The most prominent examples of non-coding RNAs are transfer RNA (tRNA) and ribosomal RNA (rRNA), both of which are involved in the process of translation.^[13] There are also non-coding RNAs involved in gene regulation, RNA processing and other roles. Certain RNAs are able to catalyse chemical reactions such as cutting and ligating other RNA molecules,^[21] and the catalysis of peptide bond formation in the ribosome;^[15] these are known as ribozymes.

Double-stranded RNA (dsRNA) is RNA with two complementary strands, similar to the DNA found in all cells. dsRNA forms the genetic material of some viruses (double-stranded RNA viruses). In eukaryotes, long double-stranded RNA such as viral RNA can trigger RNA interference, where short dsRNA molecules called siRNAs (small interfering RNAs) can silence the expression of genes.^[22]

In translation

Messenger RNA (mRNA) carries information about a protein sequence to the ribosomes, the protein synthesis factories in the cell. It is coded so that every three nucleotides (a codon) correspond to one amino acid. In eukaryotic cells, once precursor mRNA (pre-mRNA) has been transcribed from DNA, it is processed to mature mRNA before being exported from the nucleus into the cytoplasm, where it is bound to ribosomes and translated into its corresponding protein form with the help of tRNA. In prokaryotic cells, which do not have nucleus and cytoplasm compartments, mRNA can bind to ribosomes while it is being transcribed from DNA. After a certain amount of time the message degrades into its component nucleotides with the assistance of ribonucleases.^[19]

Transfer RNA (tRNA) is a small RNA chain of about 80 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding.^[20]

Ribosomal RNA (rRNA) is the catalytic component of the ribosomes. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. In the cytoplasm, ribosomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time.^[19] rRNA is extremely abundant and makes up 80% of the 10 mg/ml RNA found in a typical eukaryotic cytoplasm.^[23]

In gene regulation

Several types of RNA can downregulate gene expression by being complementary to a part of a gene. MicroRNAs (miRNA; 21-22 nt) are found in eukaryotes and act through RNA interference^[24] Some miRNAs upregulate genes instead (RNA activation).^[25] While small interfering RNAs (siRNA; 20-25 nt) are often produced by breakdown of viral RNA, there are also endogenous sources of siRNAs.^[26] siRNAs act through RNA interference in a fashion similar to miRNAs, including RNA activation.^[27] Animals have Piwi-interacting RNAs (piRNA; 29-30 nt) which are active in germline cells and are thought to be a defense against transposons and play a role in gametogenesis.^[28][29] X chromosome inactivation in female mammals is caused by Xist, an RNA which coats one X chromosome, inactivating it.^[30]Antisense RNAs are widespread among bacteria; most downregulate a gene, but a few are activators of tran******ion.^[31] (RNAi), where an effector complex of miRNA and enzymes can break down mRNA which the miRNA is complementary to, block the mRNA from being translated, or cause the promoter to be methylated which generally downregulates the gene.

Uridine to pseudouridine is a common RNA modification.

In RNA processing

Many RNAs are involved in modifying other RNAs. Introns are spliced out of pre-mRNA by spliceosomes, which contain several small nuclear RNAs (snRNA).^[13] RNA can also be altered by having its nucleotides modified to other nucleotides than A, C, G and U. In eukaryotes, modifications of RNA nucleotides are generally directed by small nucleolar RNAs (snoRNA; 60-300 nt),^[20] found in the nucleolus and cajal bodies. snoRNAs associate with enzymes and guide them to a spot on an RNA by basepairing to that RNA. These enzymes then perform the nucleotide modification. rRNAs and tRNAs are extensively modified, but snRNAs and mRNAs can also be the target of base modification.^[32][33]

DNA

From Wikipedia, the free encyclopedia

The structure of part of a DNA double helix

Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions used in the development and ********ing of all known living organisms. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules. The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

Chemically, DNA is a long polymer of simple units called nucleotides, with a backbone made of sugars and phosphate groups joined by ester bonds. Attached to each sugar is one of four types of molecules called bases. It is the sequence of these four bases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called tran******ion.

Within cells, DNA is organized into structures called chromosomes. These chromosomes are duplicated before cells divide, in a process called DNA replication. Eukaryotic organisms such as animals, plants, and fungi store their DNA inside the cell nucleus, while in prokaryotes such as bacteria it is found in the cell's cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

Physical and chemical properties

The chemical structure of DNA. Hydrogen bonds are shown as dotted lines.

DNA is a long polymer made from repeating units called nucleotides.^[1][2] The DNA chain is 22 to 26 Ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit is 3.3 Å (0.33 nm) long.^[3]chromosome, chromosome number 1, is 220 million base pairs long.^[4] Although each individual repeating unit is very small, DNA polymers can be enormous molecules containing millions of nucleotides. For instance, the largest human

In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules.^[5][6] These two long strands entwine like vines, in the shape of a double helix. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. In general, a base linked to a sugar is called a nucleoside and a base linked to a sugar and one or more phosphate groups is called a nucleotide. If multiple nucleotides are linked together, as in DNA, this polymer is called a polynucleotide.^[7]

The backbone of the DNA strand is made from alternating phosphate and sugar residues.^[8] The sugar in DNA is 2-deoxyribose, which is a pentose (five-carbon) sugar. The sugars are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms of adjacent sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of DNA strands are referred to as the 5′ (five prime) and 3′ (three prime) ends. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar ribose in RNA.^[6]

The DNA double helix is stabilized by hydrogen bonds between the bases attached to the two strands. The four bases found in DNA are adenine (abbreviated A), cytosine (C), guanine (G) and thymine (T). These four bases are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.

These bases are classified into two types; adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines.^[6] A fifth pyrimidine base, called uracil (U), usually takes the place of thymine in RNA and differs from thymine by lacking a methyl group on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine.

Major and minor grooves

Animation of the structure of a section of DNA. The bases lie horizontally between the two spiraling strands. Large version^[9]

The double helix is a right-handed spiral. As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see animation). There are two of these grooves twisting around the surface of the double helix: one groove, the major groove, is 22 Å wide and the other, the minor groove, is 12 Å wide.^[10] The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like tran******ion factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.^[11]

Base pairing

Further information: Base pair

Each type of base on one strand forms a bond with just one type of base on the other strand. This is called complementary base pairing. Here, purines form hydrogen bonds to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides binding together across the double helix is called a base pair. The double helix is also stabilized by the hydrophobic effect and pi stacking, which are not influenced by the sequence of the DNA.^[12] As hydrogen bonds are not covalent, they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.^[13] As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the ********s of DNA in living organisms.^[1]

Top, a GC base pair with three hydrogen bonds. Bottom, an AT base pair with two hydrogen bonds. Hydrogen bonds are shown as dashed lines.

The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). The GC base pair is therefore stronger than the AT base pair. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have stronger-interacting strands, while short helices with high AT content have weaker-interacting strands.^[14] In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT Pribnow box in some promoters, tend to have a high AT content, making the strands easier to pull apart.^[15] In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their melting temperature (also called T_m value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single common shape, but some conformations are more stable than others.^[16]

Sense and antisense

Further information: Sense (molecular biology)

A DNA sequence is called "sense" if its sequence is the same as that of a messenger RNA copy that is translated into protein. The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the ********s of these RNAs are not entirely clear.^[17] One proposal is that antisense RNAs are involved in regulating gene expression^[18] through RNA-RNA base pairing.

A few DNA sequences in prokaryotes and eukaryotes, and more in plasmids and viruses, blur the distinction made above between sense and antisense strands by having overlapping genes.^[19] In these cases, some DNA sequences do double duty, encoding one protein when read 5′ to 3′ along one strand, and a second protein when read in the opposite direction (still 5′ to 3′) along the other strand. In bacteria, this overlap may be involved in the regulation of gene tran******ion,^[20] while in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.^[21]

Supercoiling

Further information: DNA supercoil

DNA can be twisted like a rope in a process called DNA supercoiling. With DNA in its "relaxed" state, a strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.^[22] If the DNA is twisted in the direction of the helix, this is positive supercoiling, and the bases are held more tightly together. If they are twisted in the opposite direction, this is negative supercoiling, and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymestopoisomerases.^[23] These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as tran******ion and DNA replication. called ^[24]

From left to right, the structures of A, B and Z DNA

Alternative double-helical structures

Further information: Mechanical properties of DNA

DNA exists in many possible conformations.^[8] However, only A-DNA, B-DNA, and Z-DNAmetal ions and polyamines.^[25] Of these three conformations, the "B" form described above is most common under the conditions found in cells.^[26] The two alternative double-helical forms of DNA differ in their geometry and dimensions. have been observed in organisms. Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of

The A form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.^[27][28] Segments of DNA where the bases have been chemically-modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.^[29] These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of tran******ion.^[30]

Structure of a DNA quadruplex formed by telomere repeats. The conformation of the DNA backbone diverges significantly from the typical helical structure^[31]

Quadruplex structures

Further information: G-quadruplex

At the ends of the linear chromosomes are specialized regions of DNA called telomeres. The main ******** of these regions is to allow the cell to replicate chromosome ends using the enzyme telomerase, as the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes.^[32] These specialized chromosome caps also help protect the DNA ends, and stop the DNA repair systems in the cell from treating them as damage to be corrected.^[33] In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.^[34]

These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable G-quadruplex structure.^[35] These structures are stabilized by hydrogen bonding between the edges of the bases and chelation of a metal ion in the centre of each four-base unit.^[36] Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a long circle stabilized by telomere-binding proteins.^[37] At the very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.^[35]

Natural selection and evolution

Main article: Evolution

Mutations produce organisms with different genotypes, and those differences can result in different phenotypes. Many genetic mutations, called "neutral mutations", have a negligible effect on an organism's phenotype, health, and reproductive fitness. Mutations which do have an effect are often deleterious, but occasionally mutations arise which are beneficial in the current environmental context of the organism.

A genetic tree of eukaryotic organisms, constructed by comparison of several orthologous gene sequences

Population genetics research studies the distributions of these genetic differences within populations and how the distributions change over time. Changes in the frequency of an allele in a population can be influenced by natural selection, where a given allele's higher rate of survival and reproduction causes it to become more frequent in the population over time. Genetic drift can also occur, where chance events lead to random changes in allele frequency.

Over many generations, the genomes of organisms can change, resulting in the phenomenon of evolution. Mutations and the selection for beneficial mutations can cause a species to evolve into forms that better survive their environment, a process called adaptation. New species are formed through the process of speciation, a process often caused by geographical separations that allow different populations to genetically diverge.

As sequences diverge and change during the process of evolution, these differences between sequences can be used as a molecular clock to calculate the evolutionary distance between them. Genetic comparisons are generally considered the most accurate method of characterizing the relatedness between species, an improvement over the sometimes deceptive comparison of phenotypic characteristics. The evolutionary distances between species can be combined to form evolutionary trees. These trees are commonly considered the most accurate representation of relatedness, although the transfer of genetic material between unrelated species (known as "horizontal gene transfer" and most common in bacteria) cannot be represented by the tree.

Mutations

Main article: Mutation

Gene duplication allows diversification by providing redundancy: one gene can mutate and lose its original ******** without harming the organism.

During the process of DNA replication, errors occasionally occur in the polymerization of the second strand (these error rates are generally extremely low, 1 error in every 10-100 million bases).^[43][44] These errors, called mutations, can have an impact on the phenotype of an organism, especially if they occur within the protein coding sequence of a gene. Processes which increase the rate of changes in DNA are called "mutagenic": mutagenic chemicals promote errors in DNA replication, often by interfering with the structure of base-pairing, while UV radiation induces mutations by causing damage to the DNA structure.^[45] Chemical damage to DNA occurs naturally as well, and cells use DNA repair mechanisms to repair mismatches and breaks in DNA -- nevertheless, the repair sometimes fails to return the DNA to its original sequence.

In organisms which use chromosomal crossover to exchange DNA and shuffle genes, errors in alignment during meiosis can also cause mutations.^[46] Errors in crossover are especially likely when similar sequences cause partner chromosomes to adopt a mistaken alignment, which makes some regions in genomes more prone to mutating in this way. These errors create large structural changes in DNA sequence -- duplications, inversions or deletions of entire regions, or the accidental exchanging of whole parts between different chromosomes (called "translocation").

Discrete inheritance and Mendel's laws

Main article: Mendelian inheritance

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".^[11] This property was first observed by Gregor Mendel, who studied the segregation of heritable traits in pea plants.^[4][12] 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.^[13] 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.^[14] 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.^[15]

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".