P

Package:

In recombinant DNA procedures, refers to the step of incorporation of cosmid or other lambda vector DNA with an insert into a phage head for transduction of DNA into host.
Palindromic Sequence: A nucleotide sequence which is the same when read in either direction, usually consisting of adjacent inverted repeats. Restriction endonuclease recognition sites are palindromes:

5'-->3'

GAATTC EcoRI recognition site

CTTAAG

3'<--5'

pBR322:

A plasmid vector.

Peptide:

A molecule formed by peptide bonds covalently linking two or more amino acids. Short peptides (generally less than 60 amino acid residues, and usually only half that length) can be chemically synthesized by one of several different methods; larger peptides (more correctly, polypeptides) are usually expressed from recombinant DNA.

Peptide Bond:

A covalent bond between two amino acids, in which the carboxyl group of one amino acid (X1--COOH) and the amino group of an adjacent amino acid (NH2--X2) react to form X1-CO-NH-X2 plus H2O.

Peptide-Binding Groove:

That region of a Class I or II MHC molecule that is responsible for binding processed antigen peptides for presentation.

Peptidyl Transferase:

An enzymatic activity of the ribosome responsible for formation of the peptide bond between the nascent polypeptide chain and the amino acid carried by the charged tRNA in the A site of the ribosome. In so doing, the ribosome is moved along the mRNA by one codon.

Paratope:

That region within the antigen-binding site of an immunoglobulin molecule responsible for recognition of epitope structure.

Passive Reference (Reference Dye):

A fluorescence dye that provides an internal reference to which the reporter dye signal can be normalized during data analysis by the software. This type of normalization is necessary to correct for fluctuations from well to well caused by changes in concentration or volume. ROX is the most commonly used passive reference dye.

Peltier Element:

The element used for heating and cooling in a qPCR machine.

Penetrance:

Refers to the proportion of individuals heterozygous for a given dominant allele that express the phenotype of that dominant allele.

Phage:

A virus of bacteria, phage such as lambda have been used to introduce foreign DNA into bacteria. Because of its infectious nature, the transfection (introduction) efficiency into the bacterial host is usually two orders of magnitude greater for phage over that of plasmids.

Physical Map:

A map of the locations of identifiable landmarks on DNA (e.g., restriction enzyme cutting sites, genes), regardless of inheritance. Distance is measured in base pairs. For the human genome, the lowest- resolution physical map is the banding patterns on the 24 different chromosomes; the highest- resolution map would be the complete nucleotide sequence of the chromosomes.

Polyacrylamide Gel Electrophoresis (PAGE):

A gel of polyacrylamide used for separating DNA. It can also be used to separate proteins.

Phenotype:

The physical properties of an organism. Genotype is the largest influencing factor in the development of phenotype. But even for two organisms with identical genotypes (i.e. identical twins), they will not have identical phenotypes. Environmental factors can have a strong influence on a particular phenotype.

Point Mutation:

A single nucleotide substitution within a gene; there may be several point mutations within a single gene. Point mutations do not lead to a shift in reading frames, thus at most cause only a single amino acid substitution.

PolyA Tail:

After an mRNA is transcribed from a gene, the cell adds a stretch of A residues (typically 50-200) to its 3' end. It is thought that the presence of this "polyA tail" increases the stability of the mRNA.

Polycistronic:

Refers to a form of gene organization resulting in transcription of an mRNA that contains the coding sequences for multiple gene products, each of which is independently translated from the mRNA.

Polymorphism:

Differences between individuals in a population.

Polynucleotide Kinase:

Enzyme which catalyzes the transfer of the terminal phosphate of ATP to 5' hydroxyl termini of polynucleotides, either DNAor RNA. Usually derived from T4 bacteriophage.

Polyprotein:

A giant polypeptide that contains multiple individual protein sequences embedded within it and which must be proteolytically cleaved to yield the individual proteins.

Polyadenylation:

Following transcription of a gene, a specific signal near the 3' end of the primary transcript (AATAAA) signals that a polyadenine tail be added to the newly formed transcript. The tail may be up to several hundred nucleotides long. The precise function of the poly A tail is uncertain but it seems to play a role in stability of the mRNA and perhaps in its metabolism through the nuclear membrane to the ribosome.

Post-Translational Processing:

The reactions which alter a protein's covalent structure, such as phosphorylation, glycosylation or proteolytic cleavage.

Post-Translational Regulation:

Any process which affects the amount of protein produced from a gene, and which occurs AFTER translation in the grand scheme of genetic expression. Actually, this is often just a buzz-word for regulation of the stability of the protein. The more stable a protein is, the more it will accumulate.

Post-Transcriptional Regulation:

Mechanisms of gene regulation that do not involve transcriptional enhancement or silencing and include altering the rate of mRNA degradation, the efficiency of translation or post-translational modification, or transportation of the polypeptide out of the cell.

Precursor mRNA:

Primary transcript that is precursor of mature mRNA.

Primary Transcript:

Unprocessed RNA product of RNA transcription.

Primase:

An DNA-dependent RNA polymerase function that synthesizes a short RNA primer used during DNA replication by DNA polymerase. Primase does not require a primer, only a template.

Primer:

A short oligonucleotide complementary to target DNA and acts as the leader for DNA extension. Also refers to short oligonucleotide used to primer reverse transcription of RNA to DNA in reverse transcription reactions.

Promoter:

The first few hundred nucleotides of DNA "upstream" (on the 5' side) of a gene, which control the transcription of that gene. The promoter is part of the 5' flanking DNA, i.e. it is not transcribed into RNA, but without the promoter, the gene is not functional. Note that the definition is a bit hazy as far as the size of the region encompassed, but the "promoter" of a gene starts with the nucleotide immediately upstream from the cap site, and includes binding sites for one or more transcription factors which can not work if moved farther away from the gene.

Proto-Oncogene:

A gene present in a normal cell which carries out a normal cellular function, but which can become an oncogene under certain circumstances. The prefix "c-" indicates a cellular gene, and is generally used for proto-oncogenes (examples: c-myb , c-myc , c-fos , c-jun , etc).

Proteasome:

A protein complex which degrades ubiquitinated proteins.

Protein Translation:

This term is applied to the assembly of a polypeptide sequence from mRNA.

Protein Array:

A library of proteins (e.g., peptides, antibodies, purified proteins, or unknown protein samples) is spotted on microscopic slides. They are usually used to identify novel proteins or protein-protein interactions.

Pseudotyped Virus:

These take advantage of the powerful expression levels obtainable by murine retroviral backbones, yet are packaged in an envelope that allows docking and uptake by human target cells. An example is the popular MFG vector that utilizes a murine leukemia retroviral backbone and an amphotropic packaging cell line to produce infectious particles.

Pulsed-Field Gel Electrophoresis (PFGE):

An electrophoresis technique for separation of large DNA. Alternating electrical field is applied to run DNA through a low density agarose gel matrix.