Dr. Paul's Virtually Biology Show.

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Parapatric speciation. Parapatric speciation is speciation involving geographical isolation and divergence of two or more populations from a parent species. The speciation process is completed with the evolution of species isolating mechanisms which prevent mistaken interbreeding. Parapatric speciation is different than allopatric speciation in that the completion of speciation involves the evolution of post zygotic species isolating mechanisms. However the distinction between allopatric and parapatric speciation isn't always clear.

Parasitism. A type of symbiosis where one partner benefits and the other one is harmed.
Passive immunity. A type of apparent resistance to a foreign antigen obtained by injecting the patient with an appropriate set of antibodies produced by another organism. Passive immunity is temporary and used in situations when the patient's own immune system could not mount a defense in time to save the individual.
Passive transport. The passage of substances through a plasma membrane without the use of cellular energy.

Pathogen. A pathogen is a disease causing organism or virus. In addition to viruses, some bacteria and protista are important pathogens as are certain fungi and animals.

Pepsin. An enzyme in the stomach that digests proteins down to the level of small polypeptides. Enzymes that break down peptide bonds are also called Peptidases.
Peptide bond. A bond between the amino end of one amino acid and the carboxyl end of the next amino acid. The term peptide is also used for a short chain of amino acids strung together by peptide bonds...while polypeptide is another term for protein.
Permeable. Able to let other substances pass through. Used to describe a membrane. Contrast semi-permeable.
Permease. A protein that serves as a gateway or channel to allow diffusion of substances through a plasma membrane. May refer to a gated or ungated channel. This type of diffusion is called faciliated diffusion.
Peroxisome. A small organelle containing oxidative enzymes involved with the intracellular digestion of lipids and amino acids.
Phagocytosis. The active ingesting of solid particles, including other cells, by a cell.
Phosphoglycerate(PGA). A three carbon intermediate important in the Calvin-Benson cycle in the part of the cycle leading to the production of PGAL.
Phosphoglyceraldehyde(PGAL). A three carbon compound found as an intermediate both in glycolysis and in the Calvin-Benson cycle of photosynthesis. Surplus PGAL harvested by the chloroplast is the true end product of the Calvin Benson cycle and in tern is used by the plant cell to produce fructose, then glucose and from there do all the other things that plants and the rest of the living world needs to do.
Phosphorylation. The process of adding a phosphate group to a molecule. The phosphate may be transferred from another organic molecule as in substrate level phosphorylation or be gotten as inorganic phosphate in the solution where the reaction is taking place as in electron transport phosphorylation. Phosphorylation is important in the production of ATP from ADP and phosphate.
Photosynthesis. A two step process by which plants and other organisms take light energy, transfer it to electrons and use the electrons plus hydrogen ions to reduce carbon dioxide to produce sugars. In most modern forms of photosynthesis, oxygen is a waste product.
pH Scale. This scale is a logarithmic scale for expressing the concentration of hydrogen ions in a solution involving water. Each step increase in pH means a ten fold decrease in the concentration of hydrogen ions in the solution. Thus a solution of pH 6 has 10 times the concentration of hydrogen ions than one at pH 7 and 1000 times the hydrogen ion concentration as one at pH 8.0

Phenotype. The phenotype is the physical or chemical appearance of an organism with respect to both the expression of its genetic material and environmental influences on its appearance.

Pheromone. A chemical produced by an organism that influence the behavior or physiology of another member of the same species. Thus the chemicals ants use for their ant trails would be pheromones. People tend to think of pheromones as sex attractants but most pheromones work in other contexts. Also humans do have sex pheromones but because of our relative intelligence, attraction involves a few more characteristics than the right smell. Phloem. The set of complex plant tissues involved in the transport of sugars and other organic compounds throughout the plant. Contrast xylem.
Phospholipid. A compound consisting of two fatty acid chains linked to a glycerol molecule. The top position in the glycerol molecule is occupied by a polar group consisting in part of a phosphate functional group along with any one of a number of other functional groups. The result is a molecule with two hydrophobic tails(the fatty acids) and a polar head(the phosphate containing group).
Photon. A discrete packet or quantum of light energy. Remember light can viewed as a wave or a particle. When we talk about light as being absorbed by electrons many time we treat light as a photon.
Photolysis. The process by which water is split during the light dependent reactions of photosynthesis. The purpose of this process is to replenish electrons lost by the photosystems. In addition the process produces hydrogen ions which are used to help make ATP by electron transport phosphorylation and oxygen which has been exploited by many organisms for cellular respiration.

Photosystem. A series of pigments called antenna pigments and with a chlorophyll molecule that absorb light which boosts electrons to a high energy level where they can be picked up by NADP+ as part of the light dependent reactions of photosynthesis.
Phototropism. The bending of a plant toward or away from light. The shoot is typically positively phototropic while the roots are often negatively phototropic.
Phosphate. An important functional group consisting of a phosphorus atom and three oxygen's.
Phylogeny. The evolutionary history of a species or other group of organisms.

Pigment. A compound that appears white, black or colored due to the patterns of absorption and reflection of light hitting the molecules of the compound. Examples include various dyes, chlorophyll, and melanin

Pineal gland. An endocrine gland in the vertebrate forebrain that secretes melatonin and is involved with regulation of daily rhythms.
Pinocytosis. The active taking in of bulk fluids by a cell using endocytosis. The term literally means "cell drinking."
Pistil. The female reproductive parts of the flower and consisting of one or more carpels.
Pituitary gland. An important endocrine gland associated with and largely controlled by, the hypothalamus that secretes a wide range of hormones largely for the control of other endocrine glands.

Plantae. One of the five recognized kingdoms. Most plants except for a few parasitic plants are photosynthetic autotrophs and carry out photosynthesis using specialized organelles called chloroplasts. All plants have Eukaryotic cells and have cell walls made of a polysaccharide called cellulose. Plant life cycles involve alternation of generations. This type of life cycle gets its name because it alternates between spore producing sporophytes and gamete producing gametophytes.

Plasma. The fluid portion of blood.
Plasmodesmata. Channels through the cell walls of a plant cell that allow movement of chemicals between adjacent plant cells. Thus the cytoplasm of a whole series of plant cells may be continuously interconnected by the plasmodesmata. Such an interconnected group of cells called a symplast is critical for sugar transport.
Plasma membrane. A phospholipid bi-layer and associated proteins that serves either as an outer cell membrane or one of the cell's internal membranes.
Plasmid. A small circular piece of DNA found in bacterial cells and that can be swapped with plasmids from other bacterial. Plasmids are important in genetic engineering because they can take up DNA from other organisms.
Plasmolysis. The shrinking away of the cell membrane from the cell wall of plants by osmosis when the plant cell is placed in a hypertonic solution.
Plastid. Any of several DNA containing organelles found in plants and some protists that are involved in photosynthesis, starch storage and pigmentation.
Pleiotropic. Refers to a gene having more than one affect on the phenotype of an organism.
Polar covalent bond. A bond involving atoms that have a relatively strong tendency to grab electrons and atoms with a tendency to give up electrons. The premier example is water. The oxygen molecule has a strong tendency to take electrons and hydrogen has a strong tendency to give it electron up. The result is a molecule that is slightly negative on one side and slightly positive on the other side.

Polar molecules are molecules in which one end has a positive charge, another end has a negative charge. Polar molecules can also arise from the presence of ions.
Polygenic inheritance refers to a situation where a trait such as height or weight is controlled not by genes at a single locus, but by inputs from many loci. Many seemingly continuous phenotypic characteristics are controlled at least in part in this way.
Polymer. A polymer is a large molecule made out of repeating molecular subunits. These subunits may be exactly the same as in cellulose which is made out of thousands of repeating glucose subunits, or they may be similar as in the case of proteins which are made out of slightly different amino acid subunits strung together like slightly different box cars of a train.

Polymerases. A series of enzymes responsible for taking nucleotides and producing nucleic acids. DNA polymerase catalyses the formation of DNA during DNA replication. RNA polymerase is responsible for catalyzing the production of the RNA transcript during transcription.

Polypeptide. A series of many amino acids linked together by peptide bonds. Larger polypeptides are called proteins but to a large degree the terms are used interchangeably.

Polyploidy. A situation where the cells of an organism have more than two of each kind of homologous chromosome. This is common in plants. The triploid(three copies of each chromosome) and tetraploid(four copies) are the most common forms of polyploidy

Population A population is a group of organisms of the same species living in a well defined area.

Portal system. Refers to two sets of capillaries connected by a vein as in hepatic portal system.
Primary structure. A description of a protein solely in terms of the sequence of amino acids and the position of certain chemical bonds, usually disulfide bonds. Insulin is shown here. Note that it consists of two polypeptide chains:

Chain 1 GLY- ILE -VAL- GLU -GLN -CYS -CYS -THR- SER -ILE -CYS- SER -LEU - TYR -GLN -LEU -GLU -ASN -TYR -CYS -ASN

Chain 2 PHE -VAL -ASN-GLN -HIS -LEU -CYS- GLY- ASP -HIS -LEU- VAL- GLU- ALA -LEU- TYR -LEU- VAL- CYS- GLY- GLU- ARG -GLY- PHE -PHE -TYR - THR -PRO -LYS -THR

Data from the Brookhaven Protein Data Base.

Principle of Superposition The idea that in deposits of sedimentary rock the oldest deposits are on the bottom and the youngest deposits are on the top. This an important concept in dating the relative age of fossils and in reconstructing geological history.
Prokaryotic cell. Refers to a cell that lacks a nucleus and other membrane bound membranes. Bacteria and archea are prokaryotes. Contrast with eukaryotic cell.
Protein. A protein is a compound made from smaller molecules called amino acids. The amino acids are strung together by specialized chemical bonds called peptide bonds. Proteins serve many important functions in the organism.

Protista. One of the currently recognized kingdoms of living things. The protista are single celled or primitively multicellular organisms, characterized by having membrane bound organelles and a true nucleus. Paramecium, Euglena, Amoeba, Stentor, Algae and Diatoms are representative Protists. The Protists are considered to be a catch all group for organisms that don't fit into the other kingdoms.

Proton. A positively charged particle found in the nucleus of an atom. The number of protons in the nucleus of the atom is equal to the number of electrons surrounding the nucleus.

Punctuated equilibrium. Refers to the idea that the evolutionary history of species has long periods where no evolution happens interspersed with brief bursts of evolutionary change.
Pure covalent bond. A chemical bond between two or more atoms that involves a more or less equal sharing of electrons among the atoms. Carbon is capable of forming large covalently bonded structures.
Pyruvic acid(pyruvate). A three carbon organic acid that is a product of glycolysis.