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.

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.

Human chromosomes (grey) capped by telomeres (white)

Telomere

Region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes.

Region of repetitive nucleotide sequences associated with specialized proteins at the ends of linear chromosomes.

Human chromosomes (grey) capped by telomeres (white)
Lagging strand during DNA replication.
Shelterin co-ordinates the T-loop formation of telomeres.
Synthesis of chromosome ends by telomerase
The average cell will divide between 50 and 70 times before cell death. As the cell divides the telomeres on the end of the chromosome get smaller. The Hayflick limit is the theoretical limit to the number of times a cell may divide until the telomere becomes so short that division is inhibited and the cell enters senescence.

It has since been questioned whether the last lagging strand primer is placed exactly at the 3'-end of the template and it was demonstrated that it is rather synthesized at a distance of about 70-100 nucleotides which is consistent with the finding that DNA in cultured human cell is shortened by 50-100 base pairs per cell division.

A furanose (sugar-ring) molecule with carbon atoms labeled using standard notation. The 5′ is upstream; the 3′ is downstream. DNA and RNA are synthesized in the 5′-to-3′ direction.

Directionality (molecular biology)

End-to-end chemical orientation of a single strand of nucleic acid.

End-to-end chemical orientation of a single strand of nucleic acid.

A furanose (sugar-ring) molecule with carbon atoms labeled using standard notation. The 5′ is upstream; the 3′ is downstream. DNA and RNA are synthesized in the 5′-to-3′ direction.
In the DNA segment shown, the 5′ to 3′ directions are down the left strand and up the right strand
Phosphodiester bonds (circled) between nucleotides

In a DNA double helix, the strands run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information.

Diagram of a replicated and condensed metaphase eukaryotic chromosome. (1) Chromatid – one of the two identical parts of the chromosome after S phase. (2) Centromere – the point where the two chromatids touch. (3) Short arm (p). (4) Long arm (q).

Chromosome

Long DNA molecule with part or all of the genetic material of an organism.

Long DNA molecule with part or all of the genetic material of an organism.

Diagram of a replicated and condensed metaphase eukaryotic chromosome. (1) Chromatid – one of the two identical parts of the chromosome after S phase. (2) Centromere – the point where the two chromatids touch. (3) Short arm (p). (4) Long arm (q).
Organization of DNA in a eukaryotic cell
The major structures in DNA compaction: DNA, the nucleosome, the 10 nm "beads-on-a-string" fibre, the 30 nm fibre and the metaphase chromosome.
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Human chromosomes during metaphase
Stages of early mitosis in a vertebrate cell with micrographs of chromatids
The 23 human chromosome territories during prometaphase in fibroblast cells
Karyogram of a human male
In Down syndrome, there are three copies of chromosome 21.

The chromosomes of most bacteria, which some authors prefer to call genophores, can range in size from only 130,000 base pairs in the endosymbiotic bacteria Candidatus Hodgkinia cicadicola and Candidatus Tremblaya princeps, to more than 14,000,000 base pairs in the soil-dwelling bacterium Sorangium cellulosum.

Model of hydrogen bonds (1) between molecules of water

Hydrogen bond

Primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group, and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac).

Primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group, and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac).

Model of hydrogen bonds (1) between molecules of water
AFM image of naphthalenetetracarboxylic diimide molecules on silver-terminated silicon, interacting via hydrogen bonding, taken at 77  K. ("Hydrogen bonds" in the top image are exaggerated by artifacts of the imaging technique. )
An example of intermolecular hydrogen bonding in a self-assembled dimer complex. The hydrogen bonds are represented by dotted lines.
Intramolecular hydrogen bonding in acetylacetone helps stabilize the enol tautomer.
Examples of hydrogen bond donating (donors) and hydrogen bond accepting groups (acceptors)
Cyclic dimer of acetic acid; dashed green lines represent hydrogen bonds
Crystal structure of hexagonal ice. Gray dashed lines indicate hydrogen bonds
Structure of nickel bis(dimethylglyoximate), which features two linear hydrogen-bonds.
The structure of part of a DNA double helix
Hydrogen bonding between guanine and cytosine, one of two types of base pairs in DNA
Para-aramid structure
A strand of cellulose (conformation Iα), showing the hydrogen bonds (dashed) within and between cellulose molecules

For example, the double helical structure of DNA is due largely to hydrogen bonding between its base pairs (as well as pi stacking interactions), which link one complementary strand to the other and enable replication.

The DNA replication fork. RNA primer labeled at top.

Primer (molecular biology)

Short single-stranded nucleic acid used by all living organisms in the initiation of DNA synthesis.

Short single-stranded nucleic acid used by all living organisms in the initiation of DNA synthesis.

The DNA replication fork. RNA primer labeled at top.
Diagrammatic representation of the forward and reverse primers for a standard PCR

In solution, the primer spontaneously hybridizes with the template through Watson-Crick base pairing before being extended by DNA polymerase.

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.

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.

Wobble base pairs for inosine and guanine

Wobble base pair

Wobble base pairs for inosine and guanine

A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules.