Base pair

Depiction of the adenine–thymine Watson–Crick base pair

Fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds.

- Base pair
Depiction of the adenine–thymine Watson–Crick base pair

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Alpha

Illustration of a bacterium showing chromosomal DNA and plasmids (Not to scale)

Plasmid

Small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.

Small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently.

Illustration of a bacterium showing chromosomal DNA and plasmids (Not to scale)
There are two types of plasmid integration into a host bacteria: Non-integrating plasmids replicate as with the top instance, whereas episomes, the lower example, can integrate into the host chromosome.
Overview of bacterial conjugation
Electron micrograph of a DNA fiber bundle, presumably of a single bacterial chromosome loop
Electron micrograph of a bacterial DNA plasmid (chromosome fragment)
A schematic representation of the pBR322 plasmid, one of the first plasmids to be used widely as a cloning vector. Shown on the plasmid diagram are the genes encoded (amp and tet for ampicillin and tetracycline resistance respectively), its origin of replication (ori), and various restriction sites (indicated in blue).

The size of the plasmid varies from 1 to over 200 kbp, and the number of identical plasmids in a single cell can range anywhere from one to thousands under some circumstances.

Blending inheritance leads to the averaging out of every characteristic, which as the engineer Fleeming Jenkin pointed out, makes evolution by natural selection impossible.

Centimorgan

Unit for measuring genetic linkage.

Unit for measuring genetic linkage.

Blending inheritance leads to the averaging out of every characteristic, which as the engineer Fleeming Jenkin pointed out, makes evolution by natural selection impossible.

The number of base pairs to which it corresponds varies widely across the genome (different regions of a chromosome have different propensities towards crossover) and it also depends on whether the meiosis in which the crossing-over takes place is a part of oogenesis (formation of female gametes) or spermatogenesis (formation of male gametes).

Gregor Mendel

Gene

Basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

Basic unit of heredity and a sequence of nucleotides in DNA that encodes the synthesis of a gene product, either RNA or protein.

Gregor Mendel
Fluorescent microscopy image of a human female karyotype, showing 23 pairs of chromosomes. The DNA is stained red, with regions rich in housekeeping genes further stained in green. The largest chromosomes are around 10 times the size of the smallest.
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
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.
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.
A sequence alignment, produced by ClustalO, of mammalian histone proteins
Evolutionary fate of duplicate genes.
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.
Gene functions in the minimal genome of the synthetic organism, Syn 3.
Comparison of conventional plant breeding with transgenic and cisgenic genetic modification.

Two chains of DNA twist around each other to form a DNA double helix with the phosphate-sugar backbone spiraling around the outside, and the bases pointing inwards with adenine base pairing to thymine and guanine to cytosine.

Pinner's 1885 structure for pyrimidine

Pyrimidine

Aromatic heterocyclic organic compound similar to pyridine.

Aromatic heterocyclic organic compound similar to pyridine.

Pinner's 1885 structure for pyrimidine
The pyrimidine nitrogen bases found in DNA and RNA.

These hydrogen bonding modes are for classical Watson–Crick base pairing.

Illustration of three types of point mutations to a codon.

Point mutation

Genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome.

Genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome.

Illustration of three types of point mutations to a codon.
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. When one of these codons is changed by a point mutation, the corresponding amino acid of the protein is changed.
A to G point mutation detected with Sanger sequencing
Transitions (Alpha) and transversions (Beta).

In Neurospora crassa, repeat sequences of at least 400 base pairs in length are vulnerable to RIP.

This nucleotide contains the five-carbon sugar deoxyribose (at center), a nucleobase called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a <u title="Nucleotide">Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a <u title="Deoxyadenosine monophosphate" href="deoxyadenosine monophosphate">nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.

Nucleotide

Nucleotides are organic molecules consisting of a nucleoside and a phosphate.

Nucleotides are organic molecules consisting of a nucleoside and a phosphate.

This nucleotide contains the five-carbon sugar deoxyribose (at center), a nucleobase called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a <u title="Nucleotide">Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a <u title="Deoxyadenosine monophosphate" href="deoxyadenosine monophosphate">nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.
Showing the arrangement of nucleotides within the structure of nucleic acids: At lower left, a monophosphate nucleotide; its nitrogenous base represents one side of a base-pair. At the upper right, four nucleotides form two base-pairs: thymine and adenine (connected by double hydrogen bonds) and guanine and cytosine (connected by triple hydrogen bonds). The individual nucleotide monomers are chain-joined at their sugar and phosphate molecules, forming two 'backbones' (a double helix) of nucleic acid, shown at upper left.
Structural elements of three nucleo tides —where one-, two- or three-phosphates are attached to the nucleo side (in yellow, blue, green) at center: 1st, the nucleotide termed as a nucleoside mono phosphate is formed by adding a phosphate (in red); 2nd, adding a second phosphate forms a nucleoside di phosphate; 3rd, adding a third phosphate results in a nucleoside tri phosphate. + The nitrogenous base (nucleobase) is indicated by "Base" and "glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).
The synthesis of UMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(128,0,0);">inorganic molecules
The synthesis of IMP. The color scheme is as follows: enzymes, <span style="color: rgb(219,155,36);">coenzymes, <span style="color: rgb(151,149,45);">substrate names , <span style="color: rgb(227,13,196);">metal ions , <span style="color: rgb(128,0,0);">inorganic molecules

In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA.

Figure 1. During meiosis, homologous recombination can produce new combinations of genes as shown here between similar but not identical copies of human chromosome 1.

Homologous recombination

Type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids .

Type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids .

Figure 1. During meiosis, homologous recombination can produce new combinations of genes as shown here between similar but not identical copies of human chromosome 1.
Figure 2. An early illustration of crossing over from Thomas Hunt Morgan
Figure 3. Homologous recombination repairs DNA before the cell enters mitosis (M phase). It occurs only during and shortly after DNA replication, during the S and G2 phases of the cell cycle.
Figure 4. Double-strand break repair models that act via homologous recombination
Figure 5. The DSBR and SDSA pathways follow the same initial steps, but diverge thereafter. The DSBR pathway most often results in chromosomal crossover (bottom left), while SDSA always ends with non-crossover products (bottom right).
Figure 6. Recombination via the SSA pathway occurs between two repeat elements (purple) on the same DNA duplex, and results in deletions of genetic material. (Click to view animated diagram in Firefox, Chrome, Safari, or Opera web browsers.)
Figure 7. Crystal structure of a RecA protein filament bound to DNA. A 3' overhang is visible to the right of center.
Figure 8A. Molecular model for the RecBCD pathway of recombination. This model is based on reactions of DNA and RecBCD with ATP in excess over Mg2+ ions. Step 1: RecBCD binds to a double-stranded DNA end. Step 2: RecBCD unwinds DNA.  RecD is a fast helicase on the 5’-ended strand, and RecB is a slower helicase on the 3'-ended strand (that with an arrowhead) [ref 46 in current Wiki version].  This produces two single-stranded (ss) DNA tails and one ss loop.  The loop and tails enlarge as RecBCD moves along the DNA.  Step 3:  The two tails anneal to produce a second ss DNA loop, and both loops move and grow.  Step 4:  Upon reaching the Chi hotspot sequence (5' GCTGGTGG 3'; red dot) RecBCD nicks the 3’-ended strand.  Further unwinding produces a long 3'-ended ss tail with Chi near its end.  Step 5:  RecBCD loads RecA protein onto the Chi tail.  At some undetermined point, the RecBCD subunits disassemble.  Step 6:  The RecA-ssDNA complex invades an intact homologous duplex DNA to produce a D-loop, which can be resolved into intact, recombinant DNA in two ways.  Step 7:  The D-loop is cut and anneals with the gap in the first DNA to produce a Holliday junction.  Resolution of the Holliday junction (cutting, swapping of strands, and ligation) at the open arrowheads by some combination of RuvABC and RecG produces two recombinants of reciprocal type.  Step 8:  The 3' end of the Chi tail primes DNA synthesis, from which a replication fork can be generated.  Resolution of the fork at the open arrowheads produces one recombinant (non-reciprocal) DNA, one parental-type DNA, and one DNA fragment.
Figure 8B. Beginning of the RecBCD pathway. This model is based on reactions of DNA and RecBCD with Mg2+ ions in excess over ATP. Step 1: RecBCD binds to a DNA double strand break.  Step 2: RecBCD initiates unwinding of the DNA duplex through ATP-dependent helicase activity.  Step 3: RecBCD continues its unwinding and moves down the DNA duplex, cleaving the 3' strand much more frequently than the 5' strand. Step 4: RecBCD encounters a Chi sequence and stops digesting the 3' strand; cleavage of the 5' strand is significantly increased. Step 5: RecBCD loads RecA onto the 3' strand. Step 6: RecBCD unbinds from the DNA duplex, leaving a RecA nucleoprotein filament on the 3' tail.
Schematic representation of the s2m RNA secondary structure, with tertiary structural interactions indicated as long range contacts.
Figure 9. Joining of single-ended double strand breaks could lead to rearrangements
Figure 10. Protein domains in homologous recombination-related proteins are conserved across the three main groups of life: archaea, bacteria and eukaryotes.
Figure 11. As a developing embryo, this chimeric mouse had the agouti coat color gene introduced into its DNA via gene targeting. Its offspring are homozygous for the agouti gene.

These sites are non-randomly located on the chromosomes; usually in intergenic promoter regions and preferentially in GC-rich domains These double-strand break sites often occur at recombination hotspots, regions in chromosomes that are about 1,000–2,000 base pairs in length and have high rates of recombination.

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.

RNA

Polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

Polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes.

A hairpin loop from a pre-mRNA. Highlighted are the nucleobases (green) and the ribose-phosphate backbone (blue). This is a single strand of RNA that folds back upon itself.
Three-dimensional representation of the 50S ribosomal subunit. Ribosomal RNA is in ochre, proteins in blue. The active site is a small segment of rRNA, indicated in red.
Watson-Crick base pairs in a siRNA (hydrogen atoms are not shown)
Structure of a fragment of an RNA, showing a guanosyl subunit.
Secondary structure of a telomerase RNA.
Structure of a hammerhead ribozyme, a ribozyme that cuts RNA
Uridine to pseudouridine is a common RNA modification.
Double-stranded RNA
Robert W. Holley, left, poses with his research team.

This antisense-based process involves steps that first process the RNA so that it can base-pair with a region of its target mRNAs.

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).

Protein

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues.

A representation of the 3D structure of the protein myoglobin showing turquoise α-helices. This protein was the first to have its structure solved by X-ray crystallography. Toward the right-center among the coils, a prosthetic group called a heme group (shown in gray) with a bound oxygen molecule (red).
John Kendrew with model of myoglobin in progress
Chemical structure of the peptide bond (bottom) and the three-dimensional structure of a peptide bond between an alanine and an adjacent amino acid (top/inset). The bond itself is made of the CHON elements.
Resonance structures of the peptide bond that links individual amino acids to form a protein polymer
A ribosome produces a protein using mRNA as template
The DNA sequence of a gene encodes the amino acid sequence of a protein
The crystal structure of the chaperonin, a huge protein complex. A single protein subunit is highlighted. Chaperonins assist protein folding.
Three possible representations of the three-dimensional structure of the protein triose phosphate isomerase. Left: All-atom representation colored by atom type. Middle: Simplified representation illustrating the backbone conformation, colored by secondary structure. Right: Solvent-accessible surface representation colored by residue type (acidic residues red, basic residues blue, polar residues green, nonpolar residues white).
Molecular surface of several proteins showing their comparative sizes. From left to right are: immunoglobulin G (IgG, an antibody), hemoglobin, insulin (a hormone), adenylate kinase (an enzyme), and glutamine synthetase (an enzyme).
The enzyme hexokinase is shown as a conventional ball-and-stick molecular model. To scale in the top right-hand corner are two of its substrates, ATP and glucose.
Ribbon diagram of a mouse antibody against cholera that binds a carbohydrate antigen
Proteins in different cellular compartments and structures tagged with green fluorescent protein (here, white)
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing heme units

The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes.

Escherichia coli

Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms.

Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms.

Model of successive binary fission in E. coli
Redistribution of fluxes between the three primary glucose catabolic pathways: EMPP (red), EDP (blue), and OPPP (orange) via the knockout of pfkA and overexpression of EDP genes (edd and eda).
A colony of E. coli growing
E. coli on sheep blood agar.
E. coli growing on basic cultivation media.
Scanning electron micrograph of an E. coli colony.
An image of E. coli using early electron microscopy.
Escherichia coli bacterium, 2021, Illustration by David S. Goodsell, RCSB Protein Data Bank This painting shows a cross-section through an Escherichia coli cell. The characteristic two-membrane cell wall of gram-negative bacteria is shown in green, with many lipopolysaccharide chains extending from the surface and a network of cross-linked peptidoglycan strands between the membranes. The genome of the cell forms a loosely-defined "nucleoid", shown here in yellow, and interacts with many DNA-binding proteins, shown in tan and orange. Large soluble molecules, such as ribosomes (colored in reddish purple), mostly occupy the space around the nucleoid.
Helium ion microscopy image showing T4 phage infecting E. coli. Some of the attached phage have contracted tails indicating that they have injected their DNA into the host. The bacterial cells are ~ 0.5 µm wide.

It is a circular DNA molecule 4.6 million base pairs in length, containing 4288 annotated protein-coding genes (organized into 2584 operons), seven ribosomal RNA (rRNA) operons, and 86 transfer RNA (tRNA) genes.