PROMOTER, BASE PAIR

of poly A containing at least 200 AMP residues is enzymatically attached to the 3′ end of mRNA in the nucleus of the cell. The mRNAs with the “tail” are then transferred to the cytoplasm and the tail enzymatically removed to form the functional mRNAs. It is believed that the poly A tail aids in the transfer of the complex and/or targets the complex to the cytoplasm. See also POST-

TRANSLATIONAL MODIFICATION OF PROTEIN

mRNA, rRNA, tRNA.

Post-Translational Modification of Protein

Enzymatic processing of a polypeptide chain after its translation from its mRNA, i.e., addition of carbohydrate moieties to the protein or the removal of a portion of the polypeptide chain in order to produce a functional protein in the correct environment.

See also POLYPEPTIDE (PROTEIN), MOIETY, MES-

SENGER RNA (mRNA), ENZYME, RIBOSOMES, CAR-

BOHYDRATES, GLYCOPROTEIN.

Potato Late Blight A fungal disease of the potato plant (Solanum tuberosum) caused by the fungus Phytophthora infestans. During the 1840s, this plant disease struck the potato crops of Ireland and Europe, leading to the starvation of more than one million people (principally in Ireland, because that nation was very dependent on potatoes for food). See also FUNGUS.

PPPA See PLANT PROTECTION ACT.

PPFM See P I N K P I G M E N T E D F A C U L T A T I V E

METHYLOTROPH.

PPO Acronym for Protoporphyrinogen Oxidase. See also ACURON™ GENE.

PR Proteins See PATHOGENESIS RELATED PROTEINS.

Prebiotics Chemical compounds or microorganisms (e.g., yeasts) — administered alone or in combination (e.g., in the feed rations of animals) — that (generally) act to stimulate growth of beneficial types of bacteria within the digestive system of animals (e.g., livestock). Those compounds can include some organic acids (propionic acid, malic acid, etc.). For example, adding certain strains of yeast (culture) and malate (malic acid) to cattle feed rations has been shown to stimulate Selenomonas ruminantium bacteria (growth) in the rumen (i.e., the “first stomach” in cattle). Selenomonas ruminantium tend to constitute 22–51% of the total bacteria

in a typical rumen, and are important for optimal digestion (e.g., of the grass eaten by that animal).

Inulin, and several fructose oligosaccharides, etc. act as prebiotics in the human digestive system (e.g., by stimulating growth of Bifidus species of bacteria in the digestive system). For animal feed rations, in addition to fructose oligosaccharides, transgalacto-oli- gosaccharides may be added, to also act as prebiotics. See also PROBIOTICS, YEAST, BAC-

TERIA, BIFIDUS, INULIN, FRUCTOSE OLIGOSACCHA-

RIDES, TRANSGALACTO-OLIGOSCCHARIDES, STRAIN.

Pribnow Box T h e c o n s e n s u s s e q u e n c e T-A-T-A-A-T-G centered about 10 base pairs before the starting point of bacterial genes. It is a part of the promoter and is especially important in binding RNA poly-

merase. See also RNA POLYMERASE, TATA HOMOLOGY, HOMEOBOX,

(bp).

Primary Structure Refers to the sequence of amino acids in a protein “molecular” chain, or to the linear sequence of nucleotides in a polynucleotide (RNA or DNA) molecular

chain. See also POLYPEPTIDE (PROTEIN), AMINO ACID, PROTEIN, STRUCTURAL GENE, STRUCTURAL

GENOMICS, NUCLEOTIDE, PROTEOMICS, DEOXY-

RIBONUCLEIC ACID (DNA), RIBONUCLEIC ACID

(RNA).

Primer (DNA) A short sequence deoxyribonucleic acid (DNA) that is paired with one strand of the template DNA, in the Polymerase Chain Reaction (PCR) technique. In PCR testing (e.g., a paternity test), the primer is selected to be complementary to the analytically relevant sequence of DNA. It is the growing end of the DNA chain and it simply provides a free 3′-OH end at which the enzyme DNA polymerase adds on deoxyribonucleotide units (monomers). Which deoxyribonucleotide is added is dictated by base pairing to the template DNA chain. Without a DNA primer sequence a new DNA chain cannot form, since DNA polymerase is not able to initiate DNA chains. See also

DEOXYRIBONUCLEIC ACID (DNA), SEQUENCE (OF

A DNA MOLECULE), TEMPLATE, COMPLEMENTARY

(MOLECULAR GENETICS), DOUBLE HELIX, POLY-

MERASE, POLYMERASE CHAIN REACTION (PCR),

© 2002 by CRC Press LLC

ICS),

POLYMERASE CHAIN REACTION (PCR) TECHNIQUE,

NESTED PCR.

Prion Proteinaceous structures (molecules) found in the plasma membrane (surface) of cells, in the brains of all vertebrate animals. In 1982, Dr. Stanley Prusiner discovered that misshapen (mutated) versions can cause the neurodegenerative disease Bovine Spongiform Encephalopathy (BSE) in cattle, and the neurodegenerative diseases CreutzfeldJakob Disease (CJD), kuru, Gerstmann- Straussler-Scheinker Syndrome, and Fatal Familial Insomnia (FFI) in humans. Dr. Prusiner named these molecules prions for “proteinaceous infected particle,” because, unlike infectious pathogenic bacteria or viruses, prions do not contain DNA. The dye named Congo Red, and IDX (a derivative of the chemotherapeutic doxorubicin) have shown some ability to slow prion-caused neurodegeneration. See also

PROTEIN, CELL, PLASMA MEMBRANE, MUTANT,

BACTERIA, DEOXYRIBONUCLEIC ACID (DNA),

PROTEIN STRUCTURE, BSE, PROTO-ONCOGENES,

STRESS PROTEINS, MONOCLONAL ANTIBODIES.

Proanthocyanidins The chemical components within North American cranberries (Vaccinium macrocarpon) and blueberries (genus Vaccinium) that impart health benefits to humans who consume those cranberries/blueberries. For example, when humans consume cranberries, these chemical compounds prevent Escherichia coli bacteria from adhering to the cells lining the human urinary tract (thereby helping to prevent some urinary tract infections). See also

ANTHOCYANIDINS, PHYTOCHEMICALS, NUTRACEU-

TICALS, CELL, ESCHERICHIA COLIFORM (E. COLI).

Probe A relatively small molecule that can be used to sense the presence and condition of a specific protein, DNA fragment, RNA fragment, or nucleic acid by a unique interaction with that macromolecule. See also

DNA PROBE, HYBRIDIZATION (MOLECULAR GENET-

BACTERIAL ARTIFICIAL CHROMOSOMES

(BAC), YEAST ARTIFICIAL CHROMOSOMES (YAC),

HUMAN ARTIFICIAL CHROMOSOMES (HAC),

MARKER ASSISTED SELECTION, SOUTHERN BLOT ANALYSIS, FLUORESCENCE IN SITU HYBRIDIZATION

(FISH).

	Probiotics Compounds that (generally) act to
	stimulate growth of beneficial types of bac-
	teria within the digestive system of animals
	(e.g., livestock). For example, organic acids
	(propionic acid, acetic acid, lactic acid, citric
	acid, etc.) act to inhibit the growth/multipli-
	cation of pathogens (disease-causing micro-
	organisms) in the digestive system of
	monogastric (i.e., single-stomach) animals
	such as poultry and swine. Those acids are
	able to pass through the outer cell membrane
	(plasma membrane) of pathogenic bacteria
	and fungi. Once inside those pathogens’
	cells, the acids dissociate, and acidify the
	cells’ interior (which disrupts the cells’ pro-
	tein synthesis, growth, and replication of the
	pathogen). See also PREBIOTICS, BIFIDUS, CIT-
	RIC ACID, FRUCTOSE OLIGOSACCHARIDES, PATHO-
	GEN, MICROORGANISM, BACTERIA, FUNGUS, CELL,
	ACID, PLASMA MEMBRANE.
	Procaryotes Simple organisms that lack a dis-
	t i n c t n u c l e a r m e m b r a n e a n d o t h e r
	organelles. Many structural systems are dif-
	ferent between procaryotes and eucaryotes,
	including the DNA arrangement, composi-
	tion of membranes, the respiratory chain, the
	photosynthetic apparatus, ribosome size, the
	presence or lack of cytoplasmic streaming,
	the cell wall, flagella, the mode of sexual
	reproduction, and the presence or lack of
		P
	vacuoles. Some representative procaryotes
	are the bacteria and blue-green algae. See
	also EUCARYOTE.
	Process Validation (for production of a phar-
	maceutical) Defined by the U.S. Food and
	Drug Administration (FDA) as “Establishing
	documented evidence which provides a high
	degree of assurance that a specific process
	will consistently produce a (pharmaceutical)
	product meeting pre-determined specifica-
	tions and quality characteristics.” See also
	FOOD AND DRUG ADMINISTRATION (FDA), GOOD
	MANUFACTURING PRACTICES (GMP), GOOD LABO-
	RATORY PRACTICES (GLP), cGMP.
	Progesterone A female sex hormone, secreted
	by the ovaries, that supports pregnancy and
	lactation (milk production). See also HOR-
	MONE, PITUITARY GLAND, ESTROGEN.
	Programmed Cell Death S e e p 5 3 G E N E ,
	APOPTOSIS.
	Prokaryotes See PROCARYOTES.

© 2002 by CRC Press LLC

CYCLOOXYGENASE,

Promoter The region on DNA to which RNA polymerase binds and initiates transcription (of RNA). The promoter “promotes” the transcription (expression) of that gene, but the promoter’s impact on the timing/degree of gene expression is itself regulated by the molecules that bind to the promoter. For example, the “binding” of RNA polymerase causes transcription of RNA to begin, and the “binding” to promoter of other STATs (i.e., signal transducers and activators of transcription) can regulate the degree to which a given gene is expressed. A promoter is a region of DNA (deoxyribonucleic acid) which lies “upstream” of the transcriptional initiation site of a gene. The promoter controls where (which portion of a plant, which organ within an animal, etc.) and when (which stage in the lifetime of an organism) the gene is expressed. For example, the promoter named “Bce4” is “seed-specific” [i.e., it only “promotes” the expression of a given gene’s product (protein, fatty acid, amino acids, etc.) within a plant’s seed]. See also

POLYMERASE, GENE, EXPRESS, RNA POLYMERASE,

CONTROL SEQUENCES, GENE EXPRESSION, BCE4,

PLASTID, DEOXYRIBONUCLEIC ACID (DNA), POLY-

GENIC, TRANSCRIPTION, CAULIFLOWER MOSAIC

VIRUS 35S PROMOTER, SIGNAL TRANSDUCERS AND

ACTIVATORS OF TRANSCRIPTION (STATs).

PProof-Reading Any mechanism for correcting

errors in nucleic acid synthesis that involves scrutiny of individual (chemical) units after they have been added to the (molecular) chain. This function is carried out by a 3′ to 5′ exonuclease, among others. Proof-reading dramatically increases the fidelity of the base pairing mechanism. See also SEQUENCING (OF

DNA MOLECULES).

Propionic Acid See PROBIOTICS, BIFIDUS. Prostaglandin Endoperoxide Synthase A n

enzyme that can exist in several different forms within the human body to catalyze the production of prostaglandins. See also

ENZYME, CYCLOOXYGENASE, ARACHIDONIC ACID,

ISOZYMES, PROSTAGLANDINS, HIGHLY UNSATUR-

ATED FATTY ACIDS (HUFA).

Prostaglandins A group of cyclic (i.e., circleshaped) fatty acids that act as hormones in the body (promote inflammation during

infections, help promote maintenance of the tissues of the stomach/kidney/intestines, etc.). Originally isolated from sheep and human prostates, prostaglandins are synthesized (manufactured) by the body via chemical reactions catalyzed by the enzymes cyclooxygenase/prostaglandin endoperoxide synthase; usually from arachidonic acid (also docosahexanoic acid). See also PROSTAGLANDIN

ENDOPEROXIDE SYNTHASE,

ARACHIDONIC ACID, FATTY ACID, HORMONE,

ENZYME, HIGHLY UNSAURATED FATTY ACIDS

(HUFA), DOCOSAHEXANOIC ACID (DHA).

Prostate The gland in the body of males that produces the liquid which carries sperm into the females (during mating). In older human males, the prostate will often become enlarged (e.g., by “antagonism” when estrogen molecules circulating in the blood contact its surface). Via the selective estrogen effect, isoflavones (e.g., from soybeans) consumed by such males can displace and replace those estrogen molecules from the surface of the prostate (thereby preventing enlargement). See also ESTROGEN, ISOFLA-

VONES, SELECTIVE ESTROGEN EFFECT.

Prostate-Specific Antigen (PSA) An antigen whose concentration increases significantly 5 to 10 years prior to the (clinical) diagnosis of prostate cancer. This means that PSA level measurements can be utilized in diagnosis of prostate cancer before symptoms appear. However, a series of tests is required in order to accurately gauge the probability of cancer because PSA levels can also be elevated when a man develops a noncancerous enlarged pros-

tate. See also ANTIGEN, TUMOR, TUMOR-ASSOCI-

ATED ANTIGENS, PROSTATE.

Prosthetic Group A heat-stable metal ion or an organic group (other than an amino acid) that is covalently bonded to the apoenzyme protein. It is required for enzyme function. The term is now largely obsolete. See also

ION, AMINO ACID, PROTEIN, ENZYME, APOENZYME,

COENZYME.

Protease An enzyme that catalyzes the hydrolytic cleavage (breakdown) of proteins. By analogy, the enzyme breaks the link (peptide bond) holding a chain together. Proteases represent a whole class of protein-degrading

© 2002 by CRC Press LLC

enzymes. See also HYDROLYTIC CLEAVAGE,

ENZYME, PEPTIDE BOND, TRYPSIN, CHYMOT-

RYPSIN, LACTOFERRIN.

Protease Nexin I (PN-I) A protein that acts as an inhibitor of protease. See also PROTEASE,

PROTEIN, PROTEASE NEXIN II (PN-II).

Protease Nexin II (PN-II) A protein that is thought to regulate important activities in the body and brain by inhibiting specific enzymes and interacting with certain body cells. PN-II is formed from a precursor molecule known as beta-amyloid, via metabolic processing of the beta-amyloid. Recent research indicates that incorrect metabolic processing of betaamyloid by the body results in amyloid plaques in the brain. The amyloid plaques are generally found in victims of Alzheimer’s disease, and directly correlate (in number) with the degree of dementia. See also PROTEASE

NEXIN I (PN-I), REGULATORY ENZYME, PROTEIN,

ENZYME, INHIBITION, METABOLISM.

Proteasomes Refers to enzymatic/catalytic bodies present within all mammal cells that activate certain transcription factors, are involved in causing the cell to “present” antigens (i.e., from pathogens that invaded that cell) on the cell’s surface, and perform various other cellular functions. For example, the 26S proteasome degrades (breaks down) all ubiquinated (ubiquitin-“tagged”) proteins in that cell. See also ENZYME, PROTEIN, CELL,

TRANSCRIPTION FACTORS, ANTIGEN, PATHOGEN,

UBIQUITIN.

Protein Coined in 1838 by Jons Berzelius. From the Greek word proteios, meaning the first or the most important or of the first rank. Any of a class of high molecular weight polymer compounds composed of a variety of α-amino acids joined by peptide linkages. Via the synthesis (of this “chain”) performed by ribosomes, each protein is the ultimate expression product of a gene. More than one protein can be expressed from a given gene (the particular protein expressed is determined by factors such as the cell’s temperature or other environmental variable, presence of STATs — some of which themselves are proteins, presence of certain bacteria, etc.). During their synthesis (after emerging from the cell’s ribosome), proteins

	may also be phosphorylated (i.e., a “phos-
	phate group” is added to the protein mole-
	cule), glycosylated (i.e., one or more
	oligosaccharides is added onto the protein
	molecule), acetylated (i.e., one or more
	“acetyl groups” is added to the protein mol-
	ecule), farnesylated (i.e., a “farnesyl group”
	is added to the protein molecule),
	ubiquinated (i.e., a ubiquitin “tag” is added
	to the protein molecule), sulfated (i.e., a
	“sulfate group” is added to the protein mol-
	ecule), or otherwise chemically modified.
	Proteins are the “workhorses” of living sys-
	tems and include enzymes, antibodies,
	receptors, peptide hormones, etc. Proteins in
	living organisms respond to changing envi-
	ronmental and other conditions by changing
	their location within cells, by getting cut into
	(specific) pieces, by changing which (other)
	molecules they will bind (adhere) to, etc. All
	of the amino acids commonly found in (each
	and every one of the) proteins have an asym-
	metric carbon atom, except the amino acid
	glycine. Thus the protein is potentially chiral
	in nature. See also AMINO ACID, GENE, PEPTIDE,
	ABSOLUTE CONFIGURATION, STEREOISOMERS,
	CHIRAL COMPOUND, EXPRESS, OLIGOMER, PRO-
	TEIN FOLDING, MESSENGER RNA (mRNA), RIBO-
	SOMES, POLYRIBOSOME (POLYSOME), ORGANISM,
	CELL, SIGNAL TRANSDUCERS AND ACTIVATORS OF
		P
	TRANSCRIPTION (STATs), CENTRAL DOGMA (NEW),
	PHOSPHORYLATION, UBIQUITIN, GLYCOSYLATION
	(TO GLYCOSYLATE), FARNESYL TRANSFERASE.
	Protein Arrays See PROTEIN MICROARRAYS.
	Protein Bioreceptors See RECEPTORS.
	Protein C An anticlotting (glyco) protein that
	prevents post-operative arterial clot forma-
	tion when administered intravenously. May
	be synergistic (in its anticlotting effect) with
	tissue plasminogen activator (tPA). See also
	THROMBOMODULIN, TISSUE PLASMINOGEN ACTI-

VATOR (tPA), PROTEIN, GLYCOPROTEIN.

Protein Chips See PROTEIN MICROARRAYS.

Protein Digestibility-Corrected Amino Acid Scoring (PDCAAS) A method of expressing the quality of a given (food) protein source, in terms of its digestible protein (amino acid constituents’) ability to support growth in young growing humans (i.e., if that protein supplies all needed essential

© 2002 by CRC Press LLC