P

packet: messages sent between computers, containing the actual message data, the data type, the data's length, the sender's computer, network, and socket, the destination's computer, network, and socket, and error-control information.

Images courtesy of www.thinkquest.org

parallel machine: a computer which utilizes multiple processors working together

parallel processing: type of distributed computing which, instead of distributing the workload across multiple computers, distributes the workload across multiple processors within one computer.

parallel virtual machine: refers to distributed computing over the Internet. A parallel machine uses parallel processing — or multiple processors belonging to different computers over the Internet.

Paralogous Homologous sequences within a single species that arose by gene duplication.

Peptide bond An amide bond making up the backbone of a peptide or protein.

Phenotype is the observable traits or characteristics of an organism, for example hair color, weight, or the presence or absence of a disease. Phenotypic traits are not necessarily genetic.

Polar compound is either ionic (e.g. sodium chloride-table salt) or that has molecules with a large permanent dipole moment (e.g. water)

Polar coordinates A coordinate system based on a sphere.

Polar Solvents are compounds such as water and liquid ammonia, which have dipole moments and consequently high dielectric constants. These solvents are capable of dissolving ionic compounds or covalent compounds that ionize.

Polymer a large molecule made of many small units (monomers) joined each other through organic reactions.

Polymerase Chain Reaction (PCR) is a fast, inexpensive technique for making an unlimited number of copies of any piece of DNA. Sometimes called "molecular photocopying," PCR has had an immense impact on biology and medicine, especially genetic research.

polymerization: the chemical reaction in which high molecular mass molecules are formed from monomers.
Image courtesy of Mauro Boero, Michele Parrinello

Polypeptide - More than 10 amino acids joined by peptide bonds

Primer is ashort oligonucleotide sequence used in a polymerase chain reaction.

Probe is apiece of labeled DNA or RNA or an antibody used to detect the function of a gene.

Prochiral A molecule which is not chiral but which has a particular shape whereby it has, in effect 4 different functional groups arranged close to tetrahedrally in space. Such a molecule is frequently a ring system; e.g. valium, a benzodiazepine.

Profile A table that lists the frequencies of each amino acid in each position of protein sequence. Frequencies are calculated from multiple alignments of sequences containing a domain of interest.

Promoter is the part of a gene that contains the information to turn the gene on or off. The process of transcription is initiated at the promoter.

Pronucleus is the nucleus of a sperm or an egg prior to fertilization. Sperm and egg cells carry half the number of chromosomes of other nonreproductive cells. When the pronucleus of a sperm fuses with the pronucleus of an egg, their chromosomes combine and become part of a single nucleus in the resulting embryo, containing a full set of chromosomes.

propagation: the continuous successive chain extension in a polymer chain reaction

Proteasome is a protein that digests other proteins. Breaking down unneeded proteins is accomplished by the orderly action of several multiprotein complexes. At the heart of this process is a multiprotein complex called the proteasome. These machines of destruction consist of a tunnel-like core with a cap at either or both ends. The core is formed by four stacked rings surrounding a central channel that acts as a degradation chamber. The caps recognize and bind to proteins targeted by the cell for destruction, then use chemical energy to unfold the proteins and inject them into the central core, where they are broken into pieces. This is a fundamental kind of machine that has been highly conserved during evolution. Some form of it is found in organisms ranging from simple bacteria to humans.

protein complexes: To date scientists have studied proteins largely as discrete entities, yet most proteins operate collectively as part of protein complexes or pathways. A deeper understanding of protein interactions will assist in validating novel drug targets and may extend the usefulness of existing drug targets.

Protein is polymer of Amino Acids. It is a complex molecule consisting of a particular sequence of amino acids (peptides) that are joined to form a protein (polypeptides). All proteins consist of carbon, hydrogen, oxygen and nitrogen. Proteins vary in structure according to their function, with the 3 types of protein being fibrous, globular and conjugated proteins.

The Protein Data Bank (PDB) is the worldwide repository for these atom-level representations of proteins. The PDB collects, validates, and distributes as widely as possible these experimental models of proteins so that researchers can use them to better understand how we as humans function and are affected by disease and infection.

protein dynamics: Certain parts of a particular protein will be rigid, but others may be flexible and change their shape, even when bound. ... NMR has the unique ability to characterize protein fluctuations quantitatively, much more so than crystallography can. [CHI Structural proteomics report]

Understanding the function of a protein is fundamental for gaining insight into many biological processes. Proteins are stable mechanical constructs that allow certain internal motions to enable their biological function. Structural properties of a protein can be obtained with X-ray crystallography or NMR acquisition techniques. Molecular dynamics (MD) simulations at pico/ nano- second time scales output one or more trajectory files which describe the coordinates of each individual atom over time.

protein folding simulations: Atomistic simulations of protein folding starting purely from sequence have been a major goal of computational biology. One great challenge associated with protein folding simulation is the relatively long time scales (tens to hundreds of microseconds) compared with typical atomistic simulation time scales (nanoseconds). Using novel algorithms and a cluster of over 40,000 computer processors ("Folding@Home" http://folding.stanford.edu), we have simulated over a millisecond of atomistic molecular dynamics simulation- several orders of magnitude greater than the previous state of the art. For the first time, we have used molecular dynamics to fold proteins and, moreover, to predict protein folding rates. These predictions of protein structure and rates compare well with recent experiments.

Protein Secondary Structure: The protein chain from initial extended sequence of amino acids undergo coiling (alpha helix) and pleating (beta sheet) which is called the secondary structure. Below is computer representation of secondary structures.

Backbone=red, a-helix = yellow, b-sheet = blue

Protein Synthesis
A process where information is taken from DNA to acts as a blue print for creating a particular protein that is in demand by the body. This blueprint will allow the construction of the protein with the various materials required in its production.

proteomics represents the effort to establish the identities, quantities, structures and biochemical and cellular functions of all proteins in an organism, organ, or organelle, and how these properties vary in space, time and physiological state

proteomics technologies: Major types include protein separation, ultrafiltration, 1D and 2D gel electrophoresis, liquid chromatography, capillary electrophoresis, mass spectrometry, protein informatics, protein arrays, protein quantification, protein localization, and protein- protein interactions.

proteomimetics - small molecule: The interaction between proteins is fundamental to many receptor- ligand, enzyme- substrate, and protein-protein interactions that have been linked to human disease states. Given the large number of novel protein targets emerging from the genome and the dearth of small molecules known to bind to and antagonize these targets, the challenge presented to the pharmaceutical industry is in the identification of novel agents effecting these novel targets. Traditional screening methods can be augmented by directed discovery efforts that seek to capture the essence of a protein's binding epitope in the context of a small molecule. These "proteomimetics" may have enhanced specificity and safety based on the evolution of the protein's epitope for a singular biological function.

proteonomics: Expression systems that can rapidly produce high levels of recombinant proteins are a critical link between the discovery of new genes and the identification of targets and molecules for drug development. Advances in the baculovirus expression technology makes it the system of choice in the emerging field of proteonomics where rapid production and high yields of biologically active complex proteins are essential in the discovery of new drug targets, vaccines, and biotherapeutics.

Pseudogene is asequence of DNA that is very similar to a normal gene but that has been altered slightly so it is not expressed. Such genes were probably once functional but over time acquired one or more mutations that rendered them incapable of producing a protein product.

Author: Tug Sezen