PAGE
Polyacrylamide gel electrophoresis. Separation of molecules through a polyacrylamide gel matrix in an electric field. Separation may depend upon size and charge of the molecules.

Palindrome
A sequence of DNA that reads the same in the 5' to 3' direction on the complementary strands. For example -
5' GATC 3'
3' CTAG 5'

Often described as inverted repeats or sequences with dyad symmetry. Many DNA-binding proteins recognize palindromic sequences. Note that the grammatical usage of this term is differnet than the way it is used in genetics and molecular biology - in gramme r it is used to describe a word string that reads the same if read from right to left as if read from left to right.

Papillae
Small colonies that appear within or at the edge of a colony. For example, blue Lac+ papillae may occur in a white Lac- colony on X-gal plates. (For an excellent example of a papillation assay, see Nghiem et al. 1988. Proc. Natl. Acad. Sci. USA 85: 2709-2713.)

Paralogous
Genes that descended from an original copy of the gene that duplicated within an ancestral genome, and thus each copy of the gene could diverge independently. Because paralogous genes can vary within a species as much as between species, such genes are useful tools for studying protein evolution but not for constructing phylogenetic trees.

Partial digestion
Treatment of a DNA molecule with a restriction endonuclease under such conditions that only a fraction of all the recognition sites are cleaved. Commonly used to produce a random collection of DNA fragments for construction of gene libraries.

Partitioning
Separation of chromosomes or plasmids into daughter cells following DNA replication and cell division.

Pathogenecity island (PAI)
A region of a bacterial chromosome that seems to have been acquired via horizontal gene transfer and includes a group of genes encoding virulence factors. Evidence of horizontal gene transfer may be comparison with genomes from related nonpathogenic bacteria, or by flanking genes that suggest transfer via phage, conjugation, or transpositiion. The GC content and codon usage of PAI is often different from the rest of the chromosome.

PCR
Polymerase chain reaction. A method for amplifying a particular region of DNA by a sequence of denaturation, annealing of specific primers, and synthesis. Use of a thermostable DNA polymerase (such as Taq polymerase) allows the reactions to be perfo rmed in a thermocycler that automatically adjusts the temperature to the optimal for each reaction through many cycles. The concentration of the amplified DNA fragment increases exponentially with each cycle.

Penicillin (Pen)
An antibiotic that inhibits crosslinking of peptidoglycan chains in the cell wall of bacteria. Cells growing in the presence of penicillin synthesize weak cell walls, causing them to burst due to the high internal osmotic pressure. PenR usually results from expression of periplasmic -lactamase that breaks the Beta-lactam ring of the antibiotic. A large variety of penicillin derivatives are available. Ampicillin is a commonly used derivative of penicillin.

Peptidoglycan
The structural component of most bacterial cell walls.

Permease
An enzyme system concerned with the transport of specific substances, usually nutrients, through the cytoplasm membrane.

Permissive conditions
A particular environmental condition which allows the growth of an organism with a conditional mutation. For example, for temperature sensitive mutations 30 C is typically a permissive temperature and 42 C is the nonpermissive condition.

PFGE
See Pulsed field gel electrophoresis.

PFU
Abbreviation for plaque forming unit.

Phage (also called Bacteriophage)
A bacterial virus.

Phage head
The capsid which contains the phage nucleic acid. Often used to describe icosahedral capsid. The pressure inside an icosahedral head from a typical dsDNA phage is about 60 ATM.

Phagemid
A plasmid that contains a portion of a phage genome. Upon co-infection of the host with a Helper phage, the plasmid can be packaged into phage particles. A commonly used type of phagemid is packaged as ssDNA into phage M13 particles.

Phage induction
A treatment which stimulates prophage to enter; the lytic cycle; eventually the host cell lyses and releases free phage.

Phage tail
Proteins that extend from a phage head and mediate adsorption to receptors on the host cell.

Phase variation
A mechanism which results in variable expression of surface antigens. An example is the switch between H1 and H2 flagellar antigens by an invertable switch in Salmonella.

Phenocopy
An environmental condition that results in a phenotype different that that usually observed for a certain mutant. For example, the surfact properties of F+ bacteria can be altered to mimic F- bacteria when grown to stationary phase in medium with glucose as a carbon source.

Phenol extraction
A method commonly used to remove proteins from aqueous DNA samples. Phenol denatures proteins. The denatured proteins partition into the organic phase or remain at the interphase but the DNA remains in the aqueous phase.

Phenotype
The appearance or other observable characteristics of an organism. The phenotype expressed by an organism depends upon the particular forms of its genes (e.g. its wild-type or mutant alleles) and the environmental conditions.

phoA
The gene encoding alkaline phosphatase. Alkaline phosphatase is inactive unless it is exported outside of the cytoplasm where it becomes oxidized. Thus, gene fusions to phoA are commonly used to identify protein domains that are translocated outside of the cytoplasm (including cytoplasmic membrane protein domains exposed to the periplasm, periplasmic proteins, outer membrane proteins, or excreted proteins).

Phosphodiester bond
The covalent bond joining the 3' hydroxyl of the sugar moiety of one (deoxy)ribonucleotide to the 5' hydroxyl of the adjacent sugar.

Photoreactivation
The repair of ultraviolet irradiated DNA by the cleavage of pyrimidine dimers. Catalyzed by the photoreactivating enzyme, an enzyme that requires post-irradiation exposure to visible light.

Phylogeny
The classification of organisms according to evolutionary criteria.

Physical map
The linear order of genes and distance between them (usually expressed in base pairs or kilobases). Physical maps are constructed from in vitro characterization of the DNA (e.g. by restriction mapping or DNA sequencing).

Physiological suppression
A second mutation that affects an aspect of cell physiology and thereby restores the function of a primary mutation. For example, a mutation in a protease may allow accumulation of a partially active mutant protein, thereby restoring sufficient function to repair the mutant phenotype; a second mutation that increases accumulation of a limiting substrate may restore function of a primary mutant that has poorer substrate binding; a mutation that increases proline accumulation may suppress a primary mutant with a protein folding defect; etc.

Pilus
A filamentous protein polymer protruding from the cell surface. Usually involved in attachment to other cells or surfaces. For example, the F-pilus expressed in E. coli cells that carry the F-plasmid is involved in attachment to F- cells prior to conjugation. The plural of pilus is pili.

Plaque
A clear area in a lawn of bacterial cells caused by the lysis of infected cells by a phage.

Plaque forming unit
A virus particle capable of forming a plaque, indicating that it is able to infect, reproduce, and kill host cells.

Plasmid
A molecule of extrachromosomal DNA existing as an autonomous replicon in the cytoplasm. Most plasmids are covalently closed circular (CCC) DNA, although examples of linear plasmids are known.

Pleiotropic
A single mutation that simultaneously changes several apparently unrelated phenotypes.

Point mutation
A mutation involving the substitution, addition, or deletion of a single base pair .

Poisson distribution
A statistical test developed by Simeon Poisson . The Poisson equation describes the probability distribution of random events -- for example, the probability that random mutations in a cell will affect a particular gene, or the average number of viruses to infect a single cell at a particular multiplicity of infection.

Polar mutation
A mutation which affects not only the gene in which it is located but other genes located immediately downstream on the DNA molecule. See Rho dependent polarity .

Polyacrylamide gel electrophoresis
See PAGE.

Polycistronic
An mRNA that encodes several discrete gene products.

Polylinker
A short, synthetic DNA sequence containing several restriction enzyme recognition sites. Polylinkers facilitate cloning into plasmid or phage vectors.

Polymerase chain reaction
See PCR.

Polysome
An mRNA molecule that is in the process of being translated by multiple ribosomes simultaneously.

Polytopic
Commonly used to describe membrane proteins that span the membrane multiple times, such that different regions of the protein are exposed on opposite sides of the membrane. ("Topic" refers to the topology of the protein in the membrane.)

Positive supercoiling
Additional coiling of the circular duplex DNA molecule in the same direction as the winding of the double helix.

Post-meiotic segregation
The type of segregation produced when a recombinant DNA molecule contains an uncorrected mismatched base pair; at the next replication, normal base pairing occurs producing one mutant progeny and one wild-type progeny.

Post-replication repair
A DNA repair process which occurs after DNA replication.

Post-replication repair
A DNA repair process which occurs after DNA replication.

Post-transcriptional regulation
Regulation of gene expression after the gene has been transcribed into mRNA. For example, by regulation of translation, regulation of protein activity, or regulation of protein turnover.

Post-translational modification
The modification of proteins after the protein has been synthesized. Proteins may be modified in a wide variety of ways, including phosphorylation (addition or a phosphate group), adenylation (addition of an adenine group), glycosylation (addition of a sugar group), acylation (addition of a lipid group), proteolysis (removal of the initiator methionine, cleavage of a signal sequence, or cleavage of a pro-peptide), etc. are subject to a multitude of modification steps. These modifications can have profound, sometimes reversible effects on protein structure and function.

Post-translational regulation
Regulation of gene expression after the gene has been transcribed into mRNA and translated into protein. For example, by regulation of protein activity by covalent modification or proteolysis.

Primase
An enzyme that synthesizes ribonucleotide primers for lagging strand DNA synthesis of Okazaki fragments. Polymerizes ribonucleotide triphosphates in the 5' to 3' direction.

Primer
A short oligonucleotide complementary to a strand of DNA or RNA that is used to initiate synthesis of the complementary DNA strand. The primer provides a 3'OH end which is required by DNA polymerases to initiate synthesis of the complementary DNA.

Primosome
A complex of primase and helicase that initiates synthesis of RNA primers on the lagging DNA strand during DNA replication.

Probe
A fragment of DNA labeled with radioactivity or chemiluminescence and used to hybridize to another DNA molecule to identify complementary base sequences.

Procaryote
An organism lacking a nuclear membrane and certain organelles such as mitochondria. Refers to both Bacteria and Archae. This term was used synonymously with bacteria before the differences between Bacteria and Archae were understood. Although prokaryotes share some common features because of the lack of membrane bound organelles (e.g., coupled transcription and translation are possible in prokaryotes but not in eukaryotes), overall the Archae are more similar to the Eukarya than they are to Bacteria.

Processivity
The ability of an enzyme to continue to act on a polynucleotide for a long distance without dissociating.

Promiscuous plasmid
A plasmid with a broad host-range.

Promoter
A sequence on DNA that functions as the RNA polymerase binding site, thus defining the transcription start site. Promoter recognition is largely determined by the sigma factor associated with RNA polymerase and the interaction of RNA polymerase with positive regulatory proteins. The consensus sequence for a promoter depends upon the sigma factor associated with RNA polymerase.

Prophage
A temperate phage genome whose lytic functions are repressed and which replicates in synchrony with the bacterial chromosome. A prophage may be integrated into the host chromosome (as with phage lambda) or exist as an autonomously replicating plasmid (as with phage P1).

Proflavin
An intercalating agent used as a frameshift mutagen.

Proofreading
Removal of mismatched base pairs during DNA replication by the 3' to 5' exonuclease activity of DNA polymerase, followed by resynthesis.

Protease
An enzyme that degrades proteins to peptides or amino acids.

Proteolysis
The degradation of proteins to peptides or amino acids catalyzed by proteases.

Proteomics
The large-scale study of proteins, using biochemical or physical methods. Approaches include two-dimensional electrophoresis of proteins expressed under particular conditions or in particular cell compartments, Mass spectometry of proteins, use of hybrid approaches to identify protein-protein interactions, large scale crystallography of cellular proteins, etc. This approach complements the analysis of genome sequences (genomics) because it identifies the protein gene products that perform the cellular functions encoded by genes; The analysis of all (or most) of the proteins encoded by a genome. Some of the techniques used to characterize the proteins on this scale include bioinformatics, 2-dimensional gel electrophoresis, mass spectrometry, and protein microarrays.

Prototroph
A microorganism that is able to grow on minimal medium containing only a carbon source and inorganic salts.

Pseudogene
An inactive gene derived from an ancestral active gene. Pseudogenes are often recognized by nonsense or frameshift mutations that disrupt an open reading frame that encodes a functional protein in a related genome.

Pseudoreversion
Reversion of a mutant phenotype caused by a second mutation at a different site that partially or fully restores the wild-type phenotype. See suppression.

Pseudorevertant
A revertant that retains the original mutation but has a second mutation at a different site that partially or fully restores the wild-type phenotype. See suppressor.

Pulsed field gel electrophoresis
A gel electrophoresis technique that employs an electric field that alternates between two different vectors to achieve separation of very large molecules of DNA.

Puromycin
An antibiotic that inhibits protein synthesis. Puromycin is an analog of charged tRNA that binds to the ribosome, and is transferred to the growing peptide chain. The polypeptide is released from the ribosome resulting in premature translation termination. Puromycin inhibits protein synthesis in Bacteria, Eukarya, and Archae.

Pyrimidine dimers
Covalent bonds formed between two adjacent pyrimidines on the same strand of DNA induced by Ultraviolet irradiation.