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Encyclopedia of Biology

Encyclopedia of Biology

Keywords: Encyclopedia of Biology

234 Murphy, William Parry Once the body was dehydrated, the abdominal and
chest cavities were then washed with palm oil and aromatic
Egyptian Mummies: spices. The abdominal incision site was sewn together, and
Brief History and Radiological Studies a metallic amulet, inscribed with the sacred eye of the god
Horus, was placed over the incision. The body was then
(continued) covered with a mixture of cedar oil and spices. A protective
coating of dark-colored resin was poured over the body as
During the 21st dynasty (1085 to 945 B.C.E.) embalmers a sealant to prevent moisture from entering the body. The
began wrapping the internal organs with long strips of linen body was anointed with oil mixed with spices and perfumes.
and then replacing them back into the body as “visceral Finally the corpse was wrapped in numerous turns of linen
packages.” This may have been done to dissuade grave bandages. Laid out end-to-end, the linen would measure
robbers from opening or destroying canopic jars in search hundreds of yards long.
for jewels and treasures. With this technique there was no
need for a canopic jar, and imitation one-piece canopic jars At the time of burial the body was adorned with gold,
were sometimes placed in the tombs. jewels, and amulets. The amulets were prescribed by the
Book of the Dead and were supposed to aid the deceased
The dehydrating agent used in mummification was on his journey to the underworld. These valuable objects,
natron, a naturally occurring salt composed of sodium car- which were placed beneath the wrappings, would become
bonate, sodium bicarbonate, and sodium chloride (table the targets of grave robbers over the ensuing centuries.
salt). The two chief sources of natron in ancient Egypt were
El Kab, a city in Upper Egypt, and the Wadi Natrun, an area The coating resin imparted a dark color to the skin
just outside Cairo. In Arabic the word wadi means “dry river of the mummies. Foreign travelers to Egypt mistakenly
bed.” The chemical symbol for sodium, Na, is derived from assumed that the blackened, solidified resin covering the
the word natron. mummies was bitumen, the mineral formed from pitch. Since
the major source of bitumen was a mountain in Persia
The body was placed on a slanted embalming table and (Iran), where the substance was called “mummia,” these
completely covered with natron. A groove in the dependent embalmed bodies eventually became known as “mummies.”
end of the table allowed the fluids to drain off. The human
body is about 70 percent water, and during mummification The process of mummification has been studied for
there is considerable loss of weight due to loss of water. It centuries. Visual inspection necessitates that the mummy
was very likely that embalming took place outside in a tent, be unwrapped from its burial cloth. Anatomic dissection of
which allowed better ventilation. Anubis, the jackal-headed a mummy results in the irrevocable destruction of the
god of embalming, is often referred to as being “in his tent.” “intact body” and violates the ancient Egyptians’ desire to
remain whole in the hereafter. With the advent of the X ray,
This female mummy at the Albany Institute of History and mummies could be studied without destroying or even dis-
Art has never been unwrapped and has only been “seen” turbing them. The first published radiograph of mummified
by X ray and CT. Once believed to be a male priest, the 1988 remains appeared in 1898, only three years after the discov-
X-ray and CT studies performed by Dr. Wagle proved it to ery of the X ray by Wilhelm Konrad Röntgen in 1895. Other
be the body of a female. She is five feet tall. (Courtesy of reports followed.
William Wagle, M.D.)
With the invention of computed tomography (CT) in
1972, a much more powerful nondestructive tool became
available to scientists and Egyptologists interested in study-
ing human and animal mummies.

CT provides excellent detail of the inside of a mummy.
A collaborative project performed between the author and
the Albany Institute of History and Art (AIHA) in Albany,
New York, in November 1988, involved the plain film and CT
analysis of two ancient human Egyptian mummies. Both
mummies have been part of AIHA’s Egyptian collection
since their purchase from the Cairo Museum in 1909. The
mummies came from the ancient community of Thebes on
the upper Nile, and they lived during the 21st Egyptian
dynasty, which was from 1085 to 945 B.C.E.

One of the mummies had been obtained uncovered Murphy, William Parry 235
from the waist up. X rays performed in the Radiology
Department at Albany Medical Center showed that this The amputation site was covered with skin, indicating that it
mummy had a male pelvic structure. The other mummy was an intravital (during life) amputation. This prosthesis was
was completely wrapped in the original burial bandage composed of three separate components. The main compo-
(3,000 years old), and it had always been assumed that this nent consisted of a perfectly shaped wooden corpus (12 × 3.5
was another male priest. X rays, however, demonstrated a × 3.5 cm), which resembled a big toe including the nail. This
female pelvic structure, proving this to be the mummy of a was attached to two small wooden plates that were fixed to
woman. According to the hieroglyphics on the side of the each other by seven leather strings. According to the
wooden coffin containing the male mummy, he was a authors, there were clear marks of use on the sole of the
priest named Ankhefenmut. Since the coffin was not prosthetic toe, indicating that it had been used during life.
sealed at the time it was obtained by the AIHA, absolute
identification of this mummy could not be certain. The In early 1989 a collaborative study was performed
name and station in life of the female mummy remain a between the AIHA, the author, and William Lorensen, Ph.D.,
mystery to this day. of the General Electric Corporate Research & Development
in Schenectady, New York. The CT data obtained from the
X rays of each mummy included the skull, spine, pelvis, November 1988 mummy studies was used to perform the
and lower extremities. Skeletal structures were amazingly first-ever computer-assisted “unwrapping” of a mummy.
well preserved. The 3,000-year-old bones had an apparently Using a proprietary surface-algorithm program developed
normal density and were not eroded or fractured. CT stud- by Dr. Lorensen, the mummy’s facial linen was removed in a
ies visualized the thoracic and abdominal cavities, cranial computer program capable of sensing differences in sur-
vault, and spinal canal. As described in other studies face shading. (The original study is in the archives of GE
including anatomic dissection and CT, the oval-shaped Corporate Research & Development.) When multiple
objects in the thoraco-abdominal cavities contained the images from this study are viewed in ciné mode, there is
dried-out inner organs wrapped in multiple layers of linen, clearly the visual impression that the linens are actually
which created a “jelly-roll” appearance on CT. The skull being removed.
was filled with air and a solidified liquid that corresponds to
the resin used in the mummification process. Because the (continues)
cranial vault and the spinal canal are contiguous, the resin
had flowed into both and had solidified. Computed tomography (CT) shows the prosthesis on a
mummy’s foot. The prosthesis is composed of a high-density
The most novel finding of this study was the discovery U-shaped holder and a low-density “toe.” The mummy has
of a well-crafted, two-component great-toe prosthesis (arti- never been unwrapped, and only X ray and CT have
ficial toe) in the female mummy. This prosthesis attaches provided images of one of the most carefully constructed
directly to the first metatarsal bone of the right foot. The dis- toe prostheses ever seen. This appears in an article written
tal portion of the prosthesis has a CT density measurement by Dr. Wagle for the American Journal of Roentgenology in
of –600 Hounsfield units, which is that of air. This is probably April 1994. (Courtesy of William Wagle, M.D.)
some low-density air-filled shell that looks like a toe. The
more proximal socketlike portion, which holds the toe, mea-
sures +1,318 Hounsfield units. This is very high-density
material, but it does not appear to be metal on X ray. It may
be some form of high-density ceramic, which exactly fits
the “toe” and rests upon the first metatarsal bone of the
foot. This prosthesis has only been visualized with X ray and
CT because the female mummy has never been unwrapped
from her burial cloth. The reason for the artificial toe stems
from the ancient Egyptian belief that one should enter the
hereafter “whole.”

A recent report in the British medical journal The Lancet
describes a wooden prosthesis of the great right toe of a
female mummy from the 21st or 22nd dynasty (ca. 1065–740
B.C.E.), which is the same time period as the AIHA mummy.

236 mu (µ) symbol Analysis with DNA sampling is extremely accurate
and will open up new avenues of detective work that
Egyptian Mummies: have not been available for the past 3,000 years. It may
Brief History and Radiological Studies someday be possible to link mummies that now reside in
different countries and may also allow Egyptologists to
(continued) date mummies from different dynasties. We may learn that
Ankhefenmut has relatives in other museums throughout
In a 2002 published report, state-of-the-art helical CT the world.
provided color three-dimensional reconstructed images so
detailed that even braided hair could be seen. Sequential —William A. Wagle, M.D., is a professor in
three-dimensional fly-through images allowed visualization the Department of Radiology,
of the thoraco-abdominal cavity in such a way that the
viewer feels as though he is inside the cavity and “looking Albany Medical Center, Albany, New York.
around.” The technique provides an endoscopic journey
throughout the cavity.

Department of Anatomy. At Harvard Medical School, Whipple, the Nobel Prize in physiology or medicine for
in Boston, he received an M.D. in 1922. 1934. Murphy’s treatment of the subject was published
as Anemia in Practice: Pernicious Anemia (1939). In
In 1924 he was appointed assistant in medicine at 1958 he was granted emeritus status at both Harvard
Harvard, and from 1928 until 1935 he was an instruc- and the Peter Bent Brigham Hospital. He died at home
tor in medicine. From 1935 until 1938 he was associate in Brookline, Massachusetts, on October 9, 1987.
in medicine at Harvard, and from 1948 until 1958 he
was a lecturer in medicine, becoming in 1958 a senior mu (µ) symbol See BRIDGING LIGAND.
associate in medicine and subsequently emeritus lectur-
er in that subject. mutagen An agent that causes a permanent heritable
change (i.e., a mutation) into the DNA (deoxyribonu-
In 1923 he practiced medicine and engaged in cleic acid) of an organism.
research on diabetes mellitus and on diseases of the
blood, and he used intramuscular injections of extract of See also MUTATION.
liver for the treatment of pernicious and hypochromic
anemia and for granulocytopenia. He was associated mutagenesis The introduction of permanent herita-
with George Richards MINOT and George Hoyt WHIPPLE ble changes, i.e., MUTATIONs into the DNA of an
in work on pernicious anemia and the treatment of it by
means of a diet of uncooked liver. For this work he was
awarded, with George Richards Minot and George Hoyt

TA C A C T GA T CT

3'

AT G C G A C T A G A C G 5'

Mutagenesis involves the replacement of one nucleotide in a DNA sequence by another nucleotide or the replacement of one amino acid
in a protein by another amino acid. (Courtesy of Darryl Leja, NHGRI, National Institutes of Health)

organism. In the case of site-directed mutagenesis, the Deletion Duplication mycorrhizae 237
substitution or modification of a single amino acid at a
defined location in a protein is performed by changing Inversion
one or more BASE PAIRS in the DNA using recombinant
DNA technology.

mutation A heritable change in the NUCLEOTIDE
SEQUENCE of genomic DNA (or RNA in RNA virus-
es), or in the number of GENEs or chromosomes in a
cell, that can occur spontaneously or be brought
about by chemical mutagens or by radiation (induced
mutation).

mutualism A state where two different species ben- Insertion
efit from their association. Two types exist: symbiotic
and nonsymbiotic mutualism. Examples include chromosome
lichens (algae and fungi), mycorrhizae and rooting 20
plants, yucca plant pollination by the yucca moth, and
bees and flowers. In symbiotic mutualism, both indi- chromosome chromosome
viduals interact physically, and their relationship is 4 20
biologically essential for survival, e.g., the fungus–
alga relationship. The more common nonsymbiotic chromosome
mutualism is when individuals live independent lives 4
but cannot survive without each other, e.g., bees and
flowering plants. Translocation

mutual prodrug The association in a unique chromosome derivative
molecule of two, usually synergistic, DRUGs attached to 20 chromosome
each other, one drug being the carrier for the other and
vice versa. 20

mycelium Threadlike tubes, filaments, or hyphae; derivative
the roots of mushrooms; the thalus or vegetative part chromosome
of a fungus. Bacteria (Actinomycetales) also produce
branched mycelium. 4

mycorrhizae A symbiotic (mutualism) connection chromosome
between plant roots and the mycelia of some fungi 4
species. The fungus provides water and mineral nutri-
ents to the plant, and the plant provides energy to the A permanent structural alteration in DNA. In most cases, DNA
fungus. Ectomycorrhizae form between tree species changes either have no effect or cause harm, but occasionally a
and basidiomycete fungi, and the fungus provides a mutation can improve an organism’s chance of surviving and
sheath around the root that it penetrates. Endomycor- passing the beneficial change on to its descendants. (Courtesy
of Darryl Leja, NHGRI, National Institutes of Health)

238 myelin

rhizae form when the fungus hyphae grow between
and within the cells of the plant roots. Many species
cannot grow without their mycorrhizae connections.

myelin A lipid that forms a multilayered sheath
around some nerve fibers (axons) in the central, auto-
nomic, and peripheral nervous systems.

myelin sheath Multilayered specialized Schwann cells
(nonconducting glial cells) that help provide the efficient
movement of signals by coating and insulating sections
(internodes) of neurons (axons) in the nervous system.

myiasis An infection caused by fly maggots. Primary
myiasis is when a fly deposits eggs on the host and the
maggots feed upon living tissue. Secondary myiasis
occurs first when there is a break in the skin that
allows maggots the access to tissue.

myocrysin See GOLD DRUGS.

myofibril A long, cylindrical, contractile filament Transmission electron micrograph of part of a striated muscle fiber
within muscle or muscle fiber that makes up striated (cell) from the human neck. Striated muscle cells are elongated,
muscle. Each myofibril contains intertwined filaments hence their description as fibers. Each cell has several nuclei
of muscle proteins, myosin, and actin; called a (not visible) positioned just below the sarcolemma, the name given
sacromere. The myofibril bundles have alternate light to the cell membrane of muscle cells. Running the length of each
and dark bands (thick and thin) that contain these pro- fiber are contractile protein filaments (actin and myosin myofila-
tein filaments responsible for the muscle’s contractile ments) arranged in bunches called myofibrils (20–30 myofibrils
ability, and these give it the characteristic striated look are visible here). The arrangement of the two types of myofilament
under a microscope. causes the prominent transverse banding, which gives striated
muscle its name. Magnification: ×8, 100 at 8 × 10-inch size.
(Courtesy © Science Photo Library/Photo Researchers, Inc.)

myoglobin A monomeric dioxygen-binding heme- myosin A thick contractile protein found in myofib-
protein of muscle tissue, structurally similar to a SUB- rils that interacts with actin, another protein, to create
UNIT of HEMOGLOBIN. contraction in a muscle cell. It is the most abundant
protein in muscles fibrils.
myopia (nearsightedness; shortsightedness) An inher-
ited disorder where a refractive error in the eye means myriapods A group of organisms comprising cen-
that the shape of the eye does not bend light correctly, tipedes and millipedes, which are long, flattened,
resulting in a blurred image; inability to see distant segmented predators; each segment bears a pair of legs.
objects clearly because the images are focused in front Centipedes evolved during the Silurian period, and
of the retina.

myrmecophile 239

there are about 2,800 species alive today; there are
about 10,000 species of millipedes.

myrmecophile An organism, such as a beetle, that
lives within an ant nest and is either being cared for by
the ants or preying upon the ants or their brood for
food. Myrmecophile is Greek for “ant loving.”

An Arthropoda and an example of a myriapod from New York’s
Catskills. Its oviduct is located in the anterior, on the side of
the neck. Shown ovipositing in this picture. (Courtesy of Tim
McCabe)



N

NAD+ Oxidized form of nicotinamide adenine dinu- natural killer cell (NK cell; NK lymphocyte) A
cleotide. Note that despite the plus sign in the symbol, large granular lymphocyte killer cell that attacks and
the COENZYME is anionic under normal physiological kills tumorous, cancerous, and virus-infected cells
conditions. NAD+ is a coenzyme derived from the B vita- through phagocytosis and by using chemicals that
min niacin. It is transformed into NADH when it accepts destroy the abnormal cells. They are not specifically
a pair of high-energy electrons for transport in cells and targeted to any antigen the way other lymphocytes are,
is associated with catabolic and energy-yielding reactions. and therefore they do not need additional stimulation
to attack and kill. Part of the innate immune response.
NADH Reduced form of nicotinamide adenine dinu-
cleotide (NAD). Called coenzyme I, it is an electron See also LYMPHOCYTE.
donor essential for a variety of oxidation-reduction
reactions. natural selection Survival and reproduction of a
genotype that leaves more progenies who possess
NADP+ Oxidized form of nicotinamide adenine di- attributes of fitness, survivability, and adaptation to
nucleotide phosphate. Note that despite the plus sign in their environment over that of another genotype. Those
the symbol, the COENZYME is anionic under normal better adapted to their environment are likely to
physiological conditions. An enzyme commonly associ- increase in frequency over a number of generations
ated with biosynthetic reactions. NADP is a hydrogen over those that are less adapted, and this difference is
carrier in a wide range of redox reactions. not due to chance. It is the environment’s strong influ-
ence on the reproductive success of individuals in a
NADPH Reduced form of nicotinamide adenine di- population; one of the major forces of evolution. First
nucleotide phosphate. An energy-rich compound pro- promoted by Charles Darwin in the 19th century.
duced by the light-reaction of photosynthesis. It is used
to synthesize carbohydrates in the dark-reaction. See also EVOLUTION.

NCE See NEW CHEMICAL ENTITY.

naiad (larva, nymph) Used to describe the interme- NDA (new drug application) The process of submit-
diate stage, between egg and adult, of a dragonfly’s ting a new drug for approval. After a new drug appli-
development. cation (NDA) is received by the federal agency in

241

242 Neanderthal

charge, it undergoes a technical screening generally outer skin. Most feed on bacteria, fungi, and other soil
referred to as a completeness review and is evaluated to organisms; however, some are parasitic, obtaining their
ensure that sufficient data and information have been nutrients from animals (dog heartworm), humans (pin-
submitted in each area to justify the filing. worm), and plants. There are 15,000 known species.
They are related to the arthropods and are part of a
Neanderthal An early type of human (Homo sapiens newly recognized group, the Ecdysozoa, which includes
neanderthalensis) that evolved in Europe about the arthropods and nematodes.
250,000 years ago and spread to the Middle East. By
the last Ice Age, fossil remains reveal a people with neo-Darwinism See DARWINISM.
faces that had distinct eyebrow ridges, flattened noses,
and heavy jaws. Their bodies were short and well built, neoteny The retention of immature features in the
all features that may have been adaptations to the cold adult stage.
conditions of the last Ice Age. They appear to have sur-
vived in parts of Europe until some time after 30,000 See also PAEDOGENESIS.
years ago and lived for a time side by side with present-
day-type humans. Neotropic Geographical region including the West
Indies, South America, and Central America north to
See also CRO-MAGNON. the northern edge of tropical forests in Mexico.

Nearctic Biogeographic region including arctic, tem- nephron A microscopic coiled tubular structure
perate, and subtropical North America, reaching south found in each kidney that consists of a GLOMERULUS, a
to the northern border of the tropical rain forest in mass of capillaries that filters the blood, and a renal
Mexico. tubule that produces urine for elimination. Each kidney
is estimated to contain about 1 million nephrons.
necrosis Condition describing dead plant or animal
tissue due to injury, disease, or treatment.

negative feedback Describes a situation where an neritic zone The part of ocean that covers all water
action produces a consequence that affects, or feeds to a depth of 600 feet. The entire ocean is called the
back on, the action. In negative feedback, the conse- pelagic zone and is divided into two major zones, the
quence stops or reverses the action. In biology, for oceanic and neritic. The oceanic covers depths below
example, the stopping of the synthesis of an enzyme by 600 feet, while the neritic zone covers depths from 0 to
the accumulation of the products of the enzyme-medi- 600 feet.
ated reaction is a negative feedback reaction.
net primary productivity (NPP) The primary pro-
nematocyst A small harpoonlike structure or sting- ductivity of any community is the total amount of
ing capsule located in a cnidoblast that coils out; used biomass that is produced through photosynthesis per
by coelenterates (e.g., jellyfish) to deliver a toxin to unit area and time by the primary producers—plants. It
stun or kill its prey. is usually expressed in units of energy or in units of dry
organic matter. The annual primary production around
nematode Roundworms, simple worms of micro- the world is more than 240 billion metric tons of dry
scopic size, consisting of an elongate stomach with a plant biomass. Productivity is further divided into gross
reproduction system inside a resistant outer cuticle or and net primary productivity. Gross primary productiv-
ity (GPP) is the total energy fixed by plants in a com-
munity through photosynthesis. However, a portion of

neurosecretory cells 243

the energy is used in plant respiration, so by subtract- lamus that react to other nerve cells and that have
ing this from the gross primary production, the net pri- characteristics of both neurons and endocrine cells
mary productivity (NPP) is deduced, and this and release hormones (neurohormones) directly into
represents the rate of production of biomass available body fluids or storage areas. There are two classes of
to be consumed by animals and other organisms. The neurosecretory cells in the hypothalamus. They are
most productive areas on the Earth are those that have located in the median eminence near the adenohy-
higher temperatures, abundant soil nitrogen, and water. pophysis, the anterior glandular lobe of the pituitary,
These ecosystems include the tropical rain forest, and in the neurohypophysis, the posterior lobe of the
swamps, marshes, estuaries, and deciduous forests. gland.

neural crest The neural crest is formed only in verte- The adenohypophysis arises from epithelial tissue
brate embryos during the final stages of neurulation, a at the roof of the mouth and includes the pars distalis,
process in vertebrates where the ectoderm of the future pars tuberalis, and pars intermedia.
brain and spinal cord—the neural plate—develops
folds (neural folds) and forms the neural tube. The neu- The median eminence is an enlarged area of the
ral crest consists of paired dorsal lateral streaks of cells infundibulum, the part of the brain between the
that migrate away from the neural tube and spread brainstem and cerebrum. Here nerve cells secrete
throughout the organism to differentiate into many cell their releasing and inhibitory hormones that get
types that contribute to the development of systems absorbed into the blood capillaries in the median
such as skin, heart, endocrine, bones of the skull, teeth, eminence and carried on in the venous blood down
and even parts of the peripheral nervous system, to along the infundibulum to the anterior pituitary
name a few. gland.

neuron The basic data processing unit of the nervous The adenohypophysis secretes FSH (follicle-
system; a specialized cell that carries information elec- stimulating hormone), LH (luteinizing hormone),
trically from one part of the body to another by spe- ACTH (adrenocorticotropic hormone), TSH (thyroid-
cialized processes or extensions called dendrites and stimulating hormone), GH (growth hormone), and
axons. Widely branched dendrites carry nerve impulses prolactin.
toward the cell body, while axons carry them away and
speed up transmitting nerve impulses (conduction) The neurohypophysis, or the posterior lobe of the
from one neuron to another. Each neuron has a nucleus pituitary, is connected to the hypothalamus by the
within a cell body. stalklike infundibulum and receives two hormones
released by the neurons in the hypothalamus, oxy-
Neuroptera An order of insects with 18 families tocin (OT) and vasopressin or ADH (antidiuretic hor-
worldwide comprising dobsonflies, fishflies, alderflies, mone). Oxytocin and ADH are stored in the posterior
spongillaflies, owlflies, snakeflies, ant lions, and pituitary. The neurohypophysis is an outgrowth of
lacewings. They are characterized by having usually nervous tissue from the floor of the brain in the region
similar membranous wings with many veins, held in a of the hypothalamus. It is made up of the pars ner-
rooflike position, and chewing or sucking mouthparts. vosa and is connected to the brain by the infundibu-
They undergo complete metamorphosis, and they are lum. Oxytocin acts on myoepithelial cells in the
insectivorous. mammary glands and uterine muscles, causing both to
contract. ADH stimulates the kidneys to reabsorb
neurosecretory cells Modified nerve cells that more water.
have endocrine functions. Nerve cells in the hypotha-
The hypothalamus contains mammillary bodies,
the median eminence, and infundibulum. It contains
nuclei that produce the neurohormones. In the
supraoptic region are cell bodies of neurons in the par-
aventricular nucleus that synthesize oxytocin, while
those in the supraoptic nucleus synthesize ADH.

Neurosecretory cells are also found in other ani-
mals such as mollusks, nematodes, and platy-
helminthes, to name a few.

244 neurotransmitter

neurotransmitter A chemical made of amino acids local medical school, where he studied for three years
and peptides that switch on or off nerve impulses and then began working in Paris hospitals.
across the synapse between neurons. Excitatory neuro-
transmitters stimulate the target cell, while inhibitory He received his M.D. degree in 1893 and returned
ones inhibit the target cells. Examples of neurotrans- to Rouen, becoming director of the bacteriological lab-
mitters are acetylcholine, dopamine, noradrenaline, oratory in 1896. He left in 1903 to become director of
and serotonin. the Pasteur Institute in Tunis, a position he held until
his death in 1936.
Acetylcholine is the most abundant neurotransmit-
ter in the body and the primary neurotransmitter Early in his career, Nicolle worked on cancer, and
between neurons and muscles. It controls the stomach, at Rouen he investigated the preparation of diphtheria
spleen, bladder, liver, sweat glands, blood vessels, heart, antiserum. In North Africa, under his influence, the
and others. Dopamine is essential to the normal func- Institute at Tunis quickly became a world-famous cen-
tioning of the central nervous system. Noradrenaline, ter for bacteriological research and for the production
or norepinephrine, act in the sympathetic nervous sys- of vaccines and serums to combat most of the prevalent
tem and produce powerful vasoconstriction. Serotonin infectious diseases.
is associated with the sleep cycle.
He discovered in 1909 that the body louse trans-
neutral variation Genetic diversity that appears to mits typhus fever, and this discovery was vital to pre-
offer no selective advantage. vention of the disease during the two world wars. He
also made several contributions on knowledge and pre-
neutron An atomic particle found in the nuclei of vention of Malta fever, tick fever, scarlet fever, rinder-
atoms that is similar to a proton but has no electric pest, measles, influenza, tuberculosis, and trachoma. In
charge. 1928 he was awarded the Nobel Prize in physiology or
medicine for his work on typhus.
See also ELECTRON.
Nicolle wrote several important books, including
new chemical entity A compound not previously La Nature, conception et morale biologiques (1934);
described in the literature. Responsabilités de la Médecine (1936), and La Des-
tinée humaine (1937).
niche A habitat providing a particular set of environ-
mental conditions needed for the survival of a given He was also a philosopher and writer of stories,
species. Species that occupy different niches may coex- such as Le Pâtissier de Bellone (1913), Les Feuilles de
ist side by side in a stable manner with no competition. la Sagittaire (1920), La Narquoise (1922), Les Menus
However, if two species occupy the same niche, i.e., if Plaisirs de l’Ennui (1924), Les deux Larrons (1929),
they require the same resources, there will be competi- and Les Contes de Marmouse et ses hôtes (1930). He
tion, and the weaker of the two will become extirpated. died on February 28, 1936, in Tunis (Tunisia).
Evolutionary effects can make a species adapt to a spe-
cialized niche that has a particular set of abiotic and nif A set of about 20 GENEs required for the assembly
biotic factors within the habitat. of the NITROGENASE ENZYME complex.

Nicolle, Charles-Jules-Henry (1866–1936) French nitrate reductase A METALLOENZYME, containing
Biologist Charles-Jules-Henry Nicolle was born in molybdenum that reduces nitrate to nitrite.
Rouen, France, Seine-Maritime, on September 21,
1866, to Eugène Nicolle, a local doctor. He entered a nitrite reductase A METALLOENZYME that reduces
nitrite. DISSIMILATORY nitrite reductases contain copper
and reduce nitrite to nitrogen monoxide. Assimilatory
nitrite reductases contain SIROHEME and IRON-SULFUR
CLUSTER and reduce nitrite to ammonia.

See also ASSIMILATION.

nodes of Ranvier 245

nitrogenase An ENZYME complex from bacteria that soil, which plants can then use. Cyanobacteria (blue-
catalyzes the reduction of dinitrogen to ammonia: N2 green algae) and bacteria (e.g., Rhizobium spp.; Azoto-
+ 8e– +10H+   2NH4 + H2 with the simultaneous bacter spp.) associated with legumes (like peas) can fix
HYDROLYSIS of at least 16 ATP molecules. The electron N2 by reducing it to ammoniacal (ammonialike) N,
donor is reduced FERREDOXIN or flavodoxin. Dihydro- mostly in the form of amino acids.
gen is always a coproduct of the reaction. Ethyne
(acetylene) can also be reduced to ethene (ethylene) The ASSIMILATION of dinitrogen through microbial
and in some cases ethane. All nitrogenases are IRON- reduction to ammonia and conversion into organoni-
SULFUR PROTEINS. Three different types, which differ in trogen compounds such as amino acids. Only a limited
the type of COFACTOR present, have been identified: number of microorganisms are able to fix nitrogen.
molybdenum-nitrogenase (the most common, which
contains the iron-molybdenum cofactor), vanadium- See also NITROGENASE.
nitrogenase, and iron-only nitrogenase.
NMR See NUCLEAR MAGNETIC RESONANCE SPEC-
See also FEMO-COFACTOR; REDUCTION. TROSCOPY.

nitrogen fixation The natural process where atmo- nocturnal An animal or plant that is active during
spheric nitrogen, N2, is converted to compounds that the night rather than the day.
can be easily utilized by plants. All organisms require
nitrogen compounds, but few are able to utilize N2, a node A point on a plant stem where a leaf is attached.
relatively inert and unreactive form and, unfortunately,
the most readily available. Most organisms require nodes of Ranvier These are gaps or segments
fixed forms such as NH3, NO3, NO2, or organic N. between the neuron’s myelin sheath wrapped around
Bacteria perform nitrogen fixation by combining the
nitrogen with hydrogen to form nitrates (NH3) in the

N2
free nitrogen in
atmosphere

fixation bacteria
by denitrification
lightning decay leguminous ANIMALS
assimilation nodules (protein)
nNiOtr3a–tes
PLANTS feeding
(protein)

nitrification

industrial denitrification
fertilizers
(Haber process) NO 4 decay
ammonium
compounds

The circulation of nitrogen between organisms and the environment.

246 nomenclature

an axon. The nodes contain voltage-sensitive sodium nonclassical isostere See BIOISOSTERE.
channels or gates that generate action potentials. The
neural signal jumps from node to node by a process noncompetitive inhibitor An inhibitor that binds to
called saltatory conduction, which creates a faster an enzyme at some location other than the active site
transmission than if the action potential traveled the and changes the enzyme’s shape so that it becomes
entire length of the axon. inactive or less active; binding to a location remote
from the active site and changing its conformation so
nomenclature See BINOMIAL. that it no longer binds to the substrate.

1 23 45 678 9

10 11 12 13 14 15 16 17 18

19 20 21 22 XX

Monosomy is the condition of possessing only one copy of a particular chromosome instead of the normal two copies. (Courtesy of
Darryl Leja, NHGRI, National Institutes of Health)

nuclear envelope 247

noncyclic electron flow The first stage of photo- norm of reaction An expression or variation in
synthesis; begins when light energy enters a cluster of pattern among phenotypes produced by a single
pigment molecules (called the photosystem) located in genotype caused by a variation in environmental con-
the thylakoid. The light-induced flow of electrons from ditions. While phenotypes are an expression of genes
water to NADP in oxygen-evolving photosynthesis in an organism that give it certain traits and charac-
involving both photosystems I and II. Photosystems ters (anatomical structure, physiology, and behavior)
are large complexes of proteins and chlorophyll that that can be measured, sometimes the traits are actual-
capture energy from sunlight. Both systems I and II ly norms of reaction, i.e., traits expressed in different
include special forms of chlorophyll A. Photosystem I, ways in different environments. For example, human
or P-700, includes chlorophyll A pigment with a spe- body weight or height is different in identical envi-
cific absorbance of 700 nm (red light). Photosystem II, ronments or on different diets. Take a set of genes
or P-680, contains the reaction center responsible for that produce a particular trait together, list all the
oxygen evolution and contains a special chlorophyll A possible environmental conditions that they can sur-
that absorbs light at 680 nm (red light). If the photo- vive in, and the norm of reaction is the total variation
chemical reactions in photosystem II are inhibited, in that trait in all of the survivable environmental
photosystem I is inhibited as well. conditions.

noncyclic photophosphorylation The formation of notochord A rodlike cord, a rudimentary skeleton,
ATP by NONCYCLIC ELECTRON FLOW. composed of stiff cartilage in chordates that runs
lengthwise under the dorsal (top) surface of the body.
nondisjunction The failure of paired chromosomes It forms the support structure of the body, supporting
to separate normally and migrate to opposite poles the nerve cord. It is replaced by the vertebral column
after cell division, thereby giving rise to cells that have later in the development of most chordates; it persists
too many or too few chromosomes. This results in in primitive fishes such as hagfish, coelacanth, and chi-
monosomy, where one member of a chromosome pair maeras. The phylum Chordata comprises animals
is missing, or trisomy, where there is an extra chromo- characterized by bodies that have elongated bilateral
some in any of the chromosome pairs. symmetry and that, in some part of their development,
have a notochord and gill slits (or pouches), and usual-
nonpolar covalent bond A covalent bond formed ly have a head, tail, and digestive system with open-
by the equal sharing of electrons between two atoms ings at both ends. Chordates include the fish,
with the same electronegativity. Electronegativity is the amphibians, reptiles, birds, and mammals, but not all
tendency of an atom to attract electrons to itself in a chordates are vertebrates, e.g., invertebrate tunicates
covalent bond. and lancelets.

N-terminal amino acid residue See AMINO ACID
RESIDUE.

nonsense mutation A mutation where one of the nuclear envelope (nuclear membrane) A two-
mRNA sequences (UAA, UAG, UGA) signals the termi- membrane structure that surrounds the nucleus. The
nation of translation, the process whereby the genetic space between the two membranes is referred to as
code carried by mRNA directs the synthesis of proteins the perinuclear space. The outermost membrane meets
from amino acids; a codon is changed to a stop codon, the rough endoplasmic reticulum and has ribosomes
prematurely stopping polypeptide chain synthesis. attached. The inner membrane lies next to a dense
These three nonsense codons are amber (UAG), ocher filamentous network called the nuclear lamina and
(UAA), and opal (UGA). surrounds the nucleus, except where there are nuclear

See also MESSENGER RNA.

248 nuclearity

pores. Nuclear pores are found where the inner and of a nucleus is expressed in parts per million (ppm) by
outer membranes are joined. The space is filled with its frequency, νn, relative to a standard, νref, and
filamentous material. The pores are involved in regulat- defined as δ = 106 (νn – νref)/νo, where νo is the operat-
ing the transport of materials between the nucleus and ing frequency of the spectrometer. It is an indication of
the cytoplasm. the chemical state of the group containing the nucleus.
More information is derived from the SPIN–SPIN COU-
nuclearity The number of CENTRAL ATOMs joined in PLINGs between nuclei, which give rise to multiple pat-
a single COORDINATION entity by BRIDGING LIGANDs or terns. Greater detail can be derived from two- or
metal-metal bonds is indicated by dinuclear, trinuclear, three-dimensional techniques. These use pulses of radi-
tetranuclear, polynuclear, etc. ation at different nuclear frequencies, after which the
response of the spin system is recorded as a free-induc-
nuclear magnetic resonance (NMR) spectroscopy tion decay (FID). Multidimensional techniques, such as
NMR spectroscopy makes it possible to discriminate COSY and NOESY, make it possible to deduce the
nuclei, typically protons, in different chemical environ- structure of a relatively complex molecule such as a
ments. The electron distribution gives rise to a chemical small protein (molecular weight up to 25,000). In pro-
shift of the resonance frequency. The chemical shift, δ, teins containing paramagnetic centers, nuclear HYPER-
FINE interactions can give rise to relatively large shifts
of resonant frequencies, known as contact and pseudo-

Prepare cDNA probe Prepare microarray

“normal” tumor

RT/PCR

label with
fluorescent

dyes

combine equal
amounts

hybridize probe scan
to microarray

The nucleic acid probe provides a new way of studying how large numbers of genes interact with each other and how a cell’s regulatory
networks control vast batteries of genes simultaneously. The method uses a robot to precisely apply tiny droplets containing functional
DNA to glass slides. Researchers then attach flourescent labels to DNA from the cell they are studying. The labeled probes are allowed
to bind to complementary DNA strands on the slides. The slides are put into a scanning microscope that can measure the brightness of
each fluorescent dot. The brightness reveals how much of a specific DNA fragment is present, an indicator of how active it is. (Courtesy
of Darryl Leja, NHGRI, National Institutes of Health)

nucleolus 249

contact (dipolar) shifts, and considerable increases in nucleolus A somewhat round structure in the nucle-
the nuclear spin relaxation rates. From this type of us that forms at the nuclear organizer, a specific chro-
measurement, structural information can be obtained mosomal region, consisting of ribosomal RNA (rRNA)
about the paramagnetic site. and protein. It disappears during nuclear division in
late prophase, is completely absent during meta and
nuclear pores Openings in the membrane of a cell’s anaphase, and then reappears during telephase. The
nuclear envelope that allow the exchange of materials nucleus controls the synthesis of proteins in the cyto-
between the nucleus and the cytoplasm. plasm through messenger RNA (mRNA). Messenger

nucleation The process by which nuclei are formed; sugar- Deoxyribonucleic acid (DNA) sugar-
defined as the smallest solid-phase aggregate of atoms, phosphate base pairs phosphate
molecules, or ions that is formed during a precipitation backbone backbone
and that is capable of spontaneous growth.

nucleic acid probe (DNA probe) A single strand P A T
of DNA that is labeled or tagged with a fluorescent or S hydrogen
radioactive substance and binds specifically to a com- bonds S
plementary DNA sequence. It is used to detect its P P
incorporation through hybridization with another S GC
DNA sample. Nuclear acid probes can provide rapid S
identification of certain species like mycobacterium. P TA P
S
nucleic acids Macromolecules composed of AT S
SEQUENCEs of NUCLEOTIDES that perform several func- P P
tions in living cells—e.g., the storage of genetic infor- S C G
mation and its transfer from one generation to the next base pair C S
(DNA), and the EXPRESSION of this information in pro- P P
tein synthesis (mRNA, tRNA)—and can act as func- S G
tional components of subcellular units such as S
RIBOSOMEs (rRNA). RNA contains D-ribose, while P nucleotide P
DNA contains 2-deoxy-D-ribose as the sugar compo- S
nent. Currently, synthetic nucleic acids can be made S
consisting of hundreds of nucleotides. P

See also GENETIC CODE; OLIGONUCLEOTIDE.

nucleobases See NUCLEOSIDES.

nucleoid The irregularly shaped, aggregate mass of One of the structural components, or building blocks, of DNA and
DNA that makes up the chromosome in a prokaryotic RNA, a nucleotide consists of a base (one of four chemicals: ade-
cell; not bound by a membrane. Found in the nucleoid nine, thymine, guanine, and cytosine) plus a molecule of sugar
region of the cell. and one of phosphoric acid. (Courtesy Darryl Leja, NHGRI,
National Institutes of Health)

250 nucleosides

RNA is produced in the nucleolus of the cell and trav- 2-deoxy-D-ribose or of D-ribose, but without any
els to the cytoplasm through the pores of the nuclear phosphate groups. The common nucleosides in biologi-
envelope. cal systems are adenosine, guanosine, cytidine, and uri-
dine (which contain ribose), and deoxyadenosine,
nucleosides Compounds in which a purine or pyrim- deoxyguanosine, deoxycytidine, and thymidine (which
idine base is ß-N-glycosidically bound to C-1 of either contain deoxyribose).

See also NUCLEOTIDES.

The nucleus is the central cell structure that houses the chromosomes. (Courtesy Darryl Leja, NHGRI, National Institutes of Health)

nymph 251

nucleosome A beadlike subunit of chromatin, the 3. A positively charged core of an atom containing
material chromosomes are made of, consisting of about protons and neutrons.
150–200 base pairs of DNA wrapped around a core
complex of eight histone proteins (two molecules each 4. The frozen center of a comet’s head that contains
of histones H2a, H2b, H3, and H4). Histones are a most of the comet’s mass.
type of protein associated with DNA in chromosomes
in the nucleus, and they function to coil the DNA into null cell A class of lymphocytes characterized by a
nucleosomes. lack of surface markers specific for either T or B lym-
phocytes.

nucleotides Nucleosides with one or more phos- numerical taxonomy See PHENETICS.
phate groups esterified mainly to the 3- or the 5- posi-
tion of the sugar moiety. Nucleotides found in cells are nuptial flight The mating flight of insects (e.g.,
adenylic acid, guanylic acid, uridylic acid, cytidylic queen with males).
acid, deoxyadenylic acid, deoxyguanylic acid, deoxy-
cytidylic acid, and thymidylic acid. A nucleotide is a nut A simple, dry, indehiscent fruit with a bony shell.
nucleoside in which the primary hydroxy group of
either 2-deoxy-D-ribose or of D-ribose is esterified by nyctinasty A movement made by a plant partly in
orthophosphoric acid. response to a nondirectional stimulus such as day and
night conditions.
See also ADENOSINE 5’-TRIPHOSPHATE; NAD+;
NADP+; NUCLEOSIDES.

nucleus There are four definitions:

1. The round structure within a cell enclosed in a nymph A development stage in insects that is imma-
double membrane containing chromosomes in ture and undergoes incomplete metamorphosis. Does
which DNA replication and transcription take place. not have a pupal stage.

2. A collection of nerve cells in the brain.



O

obligate aerobe Any organism that must utilize OEC See OXYGEN-EVOLVING COMPLEX.
atmospheric oxygen in its metabolic pathways and for
cellular respiration, and cannot survive without it. The olfaction The process of smell. In humans, chemore-
adjective obligate refers to an environmental factor. ceptors are located in a patch of tissue about the size of
a postage stamp, called the olfactory epithelium, that is
See also AEROBE. located high in the nasal cavity.

obligate anaerobe Any organism where atmospheric oligochaete Worms of the phylum Annelida, class
oxygen is toxic to its growth; growth can occur only in Oligochaetae. Chiefly terrestrial and freshwater worms
an anaerobic environment. The adjective obligate refers with distinct body segmentation and no apparent head.
to an environmental factor. The earthworm is a familiar example.

See also ANAEROBE. oligogyny Multiple egg-laying queens that each have
their own territory within a colony.
oceanic zone The ocean is divided into zones. The
whole mass of water is called the pelagic. This is divid- oligonucleotide Macromolecules composed of short
ed into two major subzones: the neritic zone, which SEQUENCEs of NUCLEOTIDES that are usually syntheti-
covers all water to a depth of 600 feet, and the oceanic cally prepared and used, for example, in site-directed
zone, which covers all water below 600 feet. The MUTAGENESIS.
oceanic zone is further divided into subzones. The
mesopelagic (semidark waters) covers the depths from oligotrophic lake A condition of a lake that has
650 feet to 3,200 feet, which is the middle layer low concentrations of nutrients and algae resulting in
between the upper (sunlit 650 feet) epipelagic and the clear blue conditions. Contrast with mesotrophic
lower (cold and dark) bathypelagic. lakes, which have a moderate nutrient condition,
and eutrophic lakes, which have excessive levels of
See also PELAGIC ZONE. nutrients.

octahedron See COORDINATION.

ODMR See OPTICALLY DETECTED MAGNETIC
RESONANCE.

253

254 ommatidium

ommatidium A single unit, or visual section, of a sels and the heart. Examples include horseshoe crabs,
compound eye such as that found in insects. It resem- lobsters, and insects.
bles a single simple eye that descends directly into the
eye core. Each ommatidium contains a corneal lens, operant conditioning A type of associative learning
crystalline cone, and pigment and retinula cells and behavior also called trial-and-error learning, or instru-
functions as a single eye sending an image to the brain. mental conditioning. It is a method to modify behavior
The insect’s brain must take all the messages from each (an operant) that utilizes contingencies between the
ommatidia and piece the image together. response and the presentation of the reinforcer. Based
on the 1938 experiments of Burrhus Friederich Skinner
omnivore An animal that eats both plant and animal (rats pressing lever for food) and published in his book
material. Humans are omnivores. The Behavior of Organisms.

See also CARNIVORE.

oncogene A normal cellular gene that, when inap- operon A functional unit consisting of a PROMOTER,
propriately expressed or mutated, can transform an operator, and a number of structural GENEs, found
eukaryotic cells into tumor cells. A gene that controls mainly in PROKARYOTEs. An example is the operon NIF.
cell growth but also is responsible for directing the The structural genes commonly code for several func-
uncontrolled growth of tumor or cancer if it is dam- tionally related ENZYMEs, and although they are tran-
aged by means such as an inheritance defect, mutation, scribed as one (polycistronic) mRNA, each has its
or environmental exposure such as to carcinogens. separate TRANSLATION initiation site. In the typical
There are dozens of oncogenes known, and they func- operon, the operator region acts as a controlling ele-
tion in a variety of ways, but their commonality is the ment in switching on or off the synthesis of mRNA.
overexpression that interferes with the normal regula-
tion of cell growth. Also refers to a group or sequence of closely linked
genes that function as a unit in synthesizing enzymes
ontogeny The life history of one individual and its needed for biosynthesis of a molecule and that is con-
stages as it evolves from zygote to adult. The opposite trolled by operator and repressor genes; common in
of phylogeny, which is the history of a group. bacteria and phages. An operator gene is the region of
the chromosome, next to the operon, where a repressor
oogamy A process such as the fusion or union protein binds to prevent transcription of the operon.
between a small motile or flagellated sperm (gamete) The repressor gene protein binds to an operator adja-
and large nonmotile egg (gamete). cent to the structural gene, preventing the transcription
of the operon.
oogenesis The process and development of producing a
female ovum; developing a diploid cell into a haploid egg. opsonization The modification of the surface of a
bacterium by coating or deposition of an opsonin (an
antibody or complement), which is a group of proteins
that lyse organisms. An opsonin coats a bacterium in
order to enhance its ability to be eaten (phagocytosis) by
macrophages and other leukocytes; an immune response.

open circulatory system A type of circulatory sys- optically detected magnetic resonance (ODMR)
tem where the internal transport of blood flows A double-resonance technique in which transitions
through the body cavity and bathes the organs directly between spin sublevels are detected by optical means.
and not through a system of vessels. Humans have a Usually these are sublevels of a triplet, and the transi-
closed circulatory system, which is a type of circulatory tions are induced by microwaves.
system where the blood flows through a system of ves-

osmosis 255

order A taxonomic grouping between class and fami- orgasm An involuntary and rhythmic contraction
ly. The order consists of groups that are more alike characterized by strong feelings of pleasure by both
than those in a class. sexes during human sexual activity; the highest point of
sexual excitement.
See also TAXON.

organ A specialized combination of two or more dif- orphan drug A DRUG for the treatment of a rare dis-
ferent tissues that performs a particular function. Sever- ease for which reasonable recovery of the sponsoring
al organs work together in an organ system to perform firm’s research and development expenditure is not
a set of coordinated functions. There are ten major expected within a reasonable time. The term is also
organ systems in the human body, and each system is used to describe substances intended for such uses.
made up of one or more organs. These systems include
the circulatory, digestive, endocrine, integumentary, osmoconformer Not actively changing internal
muscular, nervous, reproductive, respiratory, skeletal, osmolarity (total solute concentration) because an ani-
and urinary systems. mal is isotonic (body fluids are of equal concentration
with respect to osmotic pressure) with the environment.
organelle The “organs” of the cell. Any membrane-
bound or nonmembrane-bound structure that is spe- osmolarity Solute concentration expressed as molar-
cialized in performing a specific role in the cell. ity. Molarity is the moles of solute dissolved in 1 liter
Examples of organelles are chloroplasts, centrosomes, of solution. A solute is, in the case of a gas or solid dis-
Golgi apparatus, ribosomes, mitochondria, and even solved in liquid, the gas or solid, but in other examples
the nucleus. it is the part that has the smaller amount. For example,
a beaker of salt water would have the water as the sol-
organic chemistry The study of carbon (organic) vent and the salt as the solute. The mole is defined as
compounds; used to study the complex nature of living the number of carbon 12 atoms in 12 grams of carbon
things. Organic compounds are composed mostly of 12. It allows scientists to weigh substances and tell how
carbon, hydrogen, oxygen, and nitrogen atoms bonded many particles are in that substance.
together. One of two main divisions of chemistry. The
other is inorganic chemistry. Branches of these two See also MOLARITY.
include analytical, biochemical, and physical chemistry.
osmoregulation A process to control water balance
organism A living entity. in a cell or organism with respect to the surrounding
environment using osmosis. The ability by which
organ of Corti The organ within the cochlea that organisms maintain a stable solute concentration by
contains thousands of hairlike receptor cells that maintaining osmotic pressure on each side of a
respond to different sound frequencies and convert semipermeable membrane.
them to nerve impulses through the auditory nerve to
the brain. osmoregulator An organism that must take in or
discharge excess water because its body fluids have a
different osmolarity than the environment.

organogenesis The formation and advanced period osmosis The diffusion or movement of water across
of embryonic development of plants and animals when a selectively permeable membrane from one aqueous
organs are formed from the primary germ layer. Its system to another of different concentration. Water
study is called organogeny.

256 osmotic pressure

moves from areas of high-water/low-solute concentra- it is related to the taxon under study, but it has an
tion to areas of low-water/high-solute concentration. ancestor in a more distant past than the taxon being
classified.

osmotic pressure Pressure that is generated by a ovarian cycle Determines the menstrual cycle in
solution moving by osmosis into and out of a cell and the ovary; a regular cyclic event that comprises two
caused by a concentration gradient. phases and ovulation: the follicular phase (before
ovulation), ovulation itself, and the luteal phase
Osteichthyes A class of fish—“bony fish”; Oste- (after ovulation but before a new follicular phase). It
ichthyes is the largest and most diverse taxon of all ver- normally lasts for 11 to 16 days and is regulated by
tebrates. Found as early as the lower Devonian period, hormones.
there are two subclasses, Actinopterygii (e.g., ray fin:
sturgeon, tuna, catfish) and Sarcopterygii (fleshy fin: ovary The female organ or gonad, located on each
lungfish, coelacanths). Two of the most successful side of the uterus, that produces oocytes that develop
groups of vertebrates ever known, with some species into mature eggs. The ovaries are connected by the
adapted to breathe air. Their endoskeleton is made of fallopian tubes, also called the oviducts. They also
bone. produce female estrogens (estradiol and proges-
terone) that are responsible for secondary sexual
osteoporosis A decrease in bone mass and bone den- characteristics.
sity with associated increased risk of fracture, especial-
ly of wrists, hips, and spines. Of the 10 million oviduct Another name for fallopian tubes, hollow
Americans estimated to have osteoporosis, 8 million organs about 12 centimeters long (about 6 inches) that
are women and 2 million are men. join the ovary to the uterus and that transport the
ovum.
ostracoderm A primitive and extinct fish without
jaws and encased in an armor of bony plates and der- oviparous Refers to a process in which a female ani-
mal scales. It lived from the early Ordovician to the late mal produces eggs that develop and hatch outside the
Devonian (470 to 370 million years ago). Also known body. In oviparous species, fertilization occurs when
as agnathans, fossils have been found in both North the sperm meet the ova as they pass through the
America and Europe. Pteraspids, cyathaspids, and oviduct. Insects such as butterflies and moths are
amphiaspids are examples. oviparous. They lay their eggs on leaves in which the
larvae hatch.
ostracods Aquatic crustaceans with seven pairs of
appendages, each specialized for different tasks, that ovotransferrin An iron-binding protein from eggs,
live inside a calcified carapace made of two valves. structurally similar to the TRANSFERRINs.
Sexually dimorphic, i.e., males and females are differ-
ent shapes. There are more than 50,000 named ovoviviparous Animals that reproduce by eggs that
species. remain in the mother’s uterus until they are ready to
hatch. The young emerge alive with only a membrane
outgroup During a phylogenetic analysis, an out- to break away from. There is no umbilical cord
group is any group that is not included in the study attached to a placenta. Some fish and reptiles are
group but is related to the group under study. Used for ovoviviparous.
comparative purposes. An outgroup is chosen because

oxidoreductase 257

ovulation The process in which a mature ovary folli- charge number is a number in parentheses written
cle opens and releases an egg (secondary oocyte) without a space immediately after the name of an ion,
enclosed in a mucouslike material. In mammals, one and whose magnitude is the ionic charge. Thus the
egg is released each menstrual cycle. number may refer to cations or anions, but never to
neutral species. The charge is written in Arabic
See also OVARY. numerals and followed by the sign of the charge.

ovule A protective structure in seed plants where the In a COORDINATION entity, the oxidation number
female gametophyte develops, and where fertilization of the CENTRAL ATOM is defined as the charge it would
occurs. The integument, a layer of tissue, surrounds the bear if all the LIGANDs were removed along with the
ovule and it becomes a seed. electron pairs that were shared with the central atom.
Neutral ligands are formally removed in their closed-
ovum Alternative term for egg. It is the secondary shell configurations. Where it is not feasible or reason-
oocyte in mammals. Unfertilized haploid nonmotile able to define an oxidation state for each individual
egg cell. member of a group or CLUSTER, it is again recommend-
ed that the overall oxidation level of the group be
oxidase An ENZYME that catalyzes the oxidation of defined by a formal ionic charge, the net charge on the
SUBSTRATEs by O2. coordination entity.

oxidation A process where one or more electrons are See also MIXED VALENCY.
lost, and the oxidation state of some atom increases. It
can occur only in combination with reduction, a pro- oxidative addition The INSERTION of a metal of a
cess where electrons are gained and the oxidation state COORDINATION entity into a covalent bond involving
of some atom decreases. formally an overall two-electron loss on one metal or a
one-electron loss on each of two metals.
oxidation number The oxidation number of an
element in any chemical entity is the number of oxidative phosphorylation An aerobic process of
charges that would remain on a given atom if the energy harnessing by the production of ATP (energy)
pairs of electrons in each bond to that atom were in mitochondria by enzymatic phosphorylation of
assigned to the more electronegative member of the ADP coupled to an electron transport chain (ETC).
bond pair. The oxidation number of an element is The ETC is a series of mitochondrial enzymes (pro-
indicated by a roman numeral placed in parentheses tein carrier molecules) in the mitochondrial mem-
immediately following the name (modified if neces- branes. As high-energy electrons are shuttled down
sary by an appropriate ending) of the element to the chain via NADH and FADH2 (flavin adenine di-
which it refers. The oxidation number can be positive, nucleotide) to oxygen molecules, they produce ATP
negative, or zero. Zero, not a roman numeral, is rep- and water.
resented by the usual cipher, 0. The positive sign is
never used. An oxidation number is always positive oxidizing agent An atom or ion that causes another
unless the minus sign is explicitly used. Note that it to be oxidized, and therefore the agent to become
cannot be nonintegral. Nonintegral numbers may reduced. It is a reactant that accepts electrons from
seem appropriate in some cases where a charge is another reactant. Oxygen, chlorine, ozone, and perox-
spread over more than one atom, but such a use is not ide compounds are examples of oxidizing agents.
encouraged. In such ambiguous cases, the charge
number, which designates ionic charge, can be used. A oxidoreductase An ENZYME of EC class 1, which
catalyzes an oxidation-reduction reaction.

See also EC NOMENCLATURE FOR ENZYMES.

258 oxygen

oxygen One of the most important elements for ozone (O3) A form of oxygen containing three atoms
biological systems and for other processes, such as instead of the common two; formed by ultraviolet radia-
reacting with other substances to release energy. One tion reacting with oxygen. Ozone accounts for the dis-
tree can produce enough oxygen in one week to meet tinctive odor of the air after a thunderstorm or around
the demands of a person’s daily oxygen need. Oxygen electrical equipment, first reported as early as 1785;
is needed in oxidation-reduction reactions within ozone’s chemical constitution was established in 1872.
cells. Cellular respiration is the process that releases The ozone layer in the upper atmosphere blocks harmful
energy by breaking down food molecules in the pres- ultraviolet radiation that normally causes skin cancer.
ence of oxygen. Atomic symbol is O; atomic number Ozone is an oxidizer and a disinfectant, and it forms
is 8. hydrogen peroxide when mixed with water. The Earth’s
ozone layer protects all life from the sun’s harmful radia-
oxygen-evolving complex (OEC) The ENZYME tion, but human activities have damaged this shield. The
that catalyzes the formation of O2 in PHOTOSYNTHE- United States, in cooperation with over 140 other coun-
SIS. Contains a CLUSTER of probably four manganese tries, is phasing out the production of ozone-depleting
ions. substances in an effort to safeguard the ozone layer.

See also OXYGEN.

P

pacemaker Another name for the sinoatrial (SA) to 248 million years ago) through the JURASSIC PERIOD
node. (206 to 144 million years ago). Pangaea began to break
apart during the Jurassic, forming two more large conti-
See also SA NODE. nents, GONDWANALAND and LAURASIA. Gondwanaland,
or Gondwana, formed the southern supercontinent, and
paedogenesis The ability to reproduce while still in its remnants are now the continents South America,
immature or larval stage; acceleration of reproductive Africa, India, Australia, and Antarctica. Laurasia, the
ability. northern supercontinent, has as its remnants current
North America, Europe, Asia, Greenland, and Iceland.

paedomorphosis Retainment of ancestral juven- paraphyletic Refers to a group of individuals
ile characteristics in the adult form. Can occur (taxon) that includes the most recent common ancestor
through neoteny or progenesis (acceleration of gonad of all of its members, but does not include all of the
development). descendants of that most recent common ancestor.

paleontology The scientific study of past life forms, parasite Any plant or animal that lives on or in
both plant and animal, in their geological and paleoen- another organism, the host, to obtain its nutrients and
vironmental context. It can be in the form of study of eventually harming or killing the host; only the parasite
fossils of organisms or their by-products. The field has benefits. Examples of parasites are ticks, fleas, trema-
several subdisciplines, including micropaleontology, todes, lice, Giardia lamblia, Sacculina, and plants such
paleobotany, palynology, invertebrate and vertebrate as rafflesia and dodder (Cuscuta sp.) Parasites can be
paleontology, human paleontology or paleoanthropolo- ectoparasites (living on the host, e.g., tick) or endopar-
gy, taphonomy, and ichnology. James Hall (1811–98), asites (living within the host, e.g., tapeworm).
New York State’s first paleontologist, is considered the
father of American paleontology. parasitism The symbiotic relationship between two
organisms where one species, the parasite, benefits, but
See also GEOLOGICAL TIME. the other, the host, is harmed. If the parasite kills the
host it endangers its own survival.
Pangaea The name given to the one huge landmass,
or supercontinent, that existed during the Permian (280

259

260 parasitoid

parasitoid An organism that lives in or on the body cells of a plant’s “ground tissue,” composed of
of a single host individual during its development and parenchyma cells that function in assimilation and
eventually kills the host. Falls between a predator and a storage, are called assimilates. Parenchyma tissues
true parasite. are the mesophyll, an important assimilation tissue;
the palisade parenchyma, directly beneath the epider-
parasympathetic division (craniosacral division) mis of the upper part of a leaf; and the spongy
One of two divisions of the autonomic nervous system. parenchyma, which fills the spaces beneath the pal-
The parasympathetic deals with conserving energy, isade parenchyma. Parenchyma are the only cells
digestion of food, and excretory functions; encourages that can engage in mitosis and are the only type of
sedentary functions as opposed to the sympathetic divi- cell found in apical meristems. Parenchyma found in
sion; increases the nutrient content in the blood, which the air-filled floating leaves of aquatic plants are
stimulates growth and storage of energy reserves. Other called aerenchyma.
responses include a decreased heart rate and airway
and pupil diameters. parthenogenesis A form of reproduction in many
lower animals in which the egg develops into a new
parathyroid glands A set of four glands, two in the individual without fertilization. In certain social
left lobe of the thyroid gland and two in the right lobe. insects, such as ants and honeybees, the unfertilized
They function to control blood calcium levels by secret- eggs develop into male drones.
ing parathyroid hormone (PTH). If too much calcium
is allowed in the blood, a condition known as hyper- partial agonist An AGONIST that is unable to induce
parathyroidism occurs; if the blood calcium is too low, maximal activation of a RECEPTOR population, regard-
a condition known as hypoparathyroidism can exist. less of the amount of DRUG applied.
The parathyroid hormone also stimulates absorption of
food by the intestines and conservation of calcium by See also INTRINSIC ACTIVITY.
the kidneys.
partial pressure Each gas in a mixture of
Parazoa The animal subkingdom of sponges, the gases exerts a pressure called the partial pressure. It
phylum Porifera. Mostly mouthless marine multicellu- is the pressure exerted by one gas in a mixture of
lar sessile animals that feed by drawing in microorgan- gases.
isms through their pores (suspension feeders). Four
classes of sponges exist: Calcarea (calcareous sponges), passive transport (diffusion) A molecule or ion
Hexactinellida (glass sponges), and Demospongiae (the that crosses a biological membrane by moving down a
largest and most diverse, 90 percent of known species), concentration or electrochemical gradient with no
and Sclerospongiae (mostly fossil records). There are expenditure of metabolic energy. Passive transport, in
about 5,000 species of sponges. the same direction as a concentration gradient, can
occur spontaneously, or proteins can mediate passive
parenchyma One of the three types of plant tis- transport and provide the pathway for this movement
sue; unspecialized, composed of large thin-walled across the lipid bilayer without supplying energy for
cells forming the greater part of leaves, roots, the the action. These proteins are called channels if they
pulp of fruit, and the pith of stems; Has an abun- mediate ions and permeases if they mediate large
dance of plastids, chloroplast-containing cells able to molecules. This type of transport always operates from
perform photosynthesis in leaves and stems (when regions of greater concentration to regions of lesser
filled with chloroplasts, called chlorenchyma). The concentration.

See also ACTIVE TRANSPORT.

Pavlov, Ivan Petrovich 261

pattern formation The direction given to cells to the most important centers of physiological research.
form a specific three-dimensional structure in shaping Also, in 1890 he was appointed professor of pharma-
the development of an organism and its parts. cology at the Military Medical Academy, and five years
later he was appointed to the then-vacant chair of
pattern recognition The identification of patterns in physiology, which he held until 1925.
large data sets using appropriate mathematical method-
ologies. Between the years 1891 and 1900, Pavlov did
the bulk of his research on the physiology of diges-
Pavlov, Ivan Petrovich (1849–1936) Russian Physi- tion at the Institute of Experimental Medicine and
ologist Ivan Petrovich Pavlov was born on September demonstrated that the nervous system played the
14, 1849, in Ryazan, to Peter Dmitrievich Pavlov, a vil- dominant part in regulating the digestive process.
lage priest. He was educated first at the church school Pavlov promoted his research in lectures that he
in Ryazan, the Ryazan Ecclesiastical High School, and delivered in 1895 and published under the title Lekt-
then at the local theological seminary. sii o rabote glavnykh pishchevaritelnyteh zhelez
(Lectures on the function of the principal digestive
Pavlov abandoned religion for science when he glands) in 1897.
was inspired by the progressive ideas of the Russian
literary critic D. I. Pisarev, by Ivan M. Sechenov, the His research on the physiology of digestion led to
father of Russian physiology, and by the works of the development of the first experimental model of
Charles Darwin. In 1870 he enrolled in the physics learning, called classical conditioning. Pavlov’s research
and mathematics faculty to take the course in natural into the physiology of digestion led to the study of con-
science. ditioned reflexes. In a now-classic experiment, he
trained a hungry dog to salivate at the sound of a bell,
Pavlov became interested in physiology. While tak- which was previously associated with the sight of food.
ing the course in natural science, he and a fellow stu- He implanted small stomach pouches in dogs to mea-
dent wrote a treatise on the physiology of the sure the secretion of gastric juices produced when the
pancreatic nerves that won wide acclaim, and Pavlov dogs began to eat.
was awarded a gold medal.
In 1901 he was elected a corresponding member of
In 1875 Pavlov received the degree of candidate of the Russian Academy of Sciences, and in 1904 he was
natural sciences. However, his overwhelming interest in awarded a Nobel Prize for his work in digestion. In
physiology forced him to continue his studies and 1907 he was elected academician of the Russian Acade-
attend the Academy of Medical Surgery. Pavlov won a my of Sciences, and in 1912 he was given an honorary
fellowship at the academy, and with a position as direc- doctorate at Cambridge University. He held many other
tor of the physiological laboratory at the clinic of the honorary memberships of various scientific societies
famous Russian clinician, S. P. Botkin, he was able to abroad. Finally, upon the recommendation of the Med-
continue his research work. In 1881 Pavlov married ical Academy of Paris, he was awarded the Order of
Seraphima (Sara) Vasilievna Karchevskaya, a teacher, the Legion of Honor (1915).
the daughter of a doctor. They had four sons and a
daughter. In 1883 he presented his thesis, entitled “The After the Russian Revolution, a special government
centrifugal nerves of the heart,” and laid down the decree signed by Lenin on January 24, 1921, noted
basic principles on the trophic function of the nervous “the outstanding scientific services of Academician I. P.
system. Pavlov showed that there existed a basic pat- Pavlov, which are of enormous significance to the
tern in the reflex regulation of the activity of the circu- working class of the whole world.”
latory organs.
The Communist Party and the Soviet government
In 1890 Pavlov organized and directed the depart- gave Pavlov and his collaborators unlimited scope for
ment of physiology at the Institute of Experimental scientific research and built him a laboratory. Pavlov
Medicine and spent the next 45 years making it one of summarized his discoveries in his book, Conditioned
Reflexes. Pavlov died in Leningrad on February 27,
1936.

262 pedigree

male affected male deceased male
female affected female deceased female

A simplified diagram of a family’s genealogy that shows family members’ relationships to each other and how a particular trait or
disease has been inherited. (Courtesy Darryl Leja, NHGRI, National Institutes of Health)

pedigree The line of descent; a documented list or peptidoglycan A thick, rigid-layer, cross-linked
table of ancestors, as in a genealogical record of an ani- polysaccharide-peptide complex that is found in the
mal or person. walls of bacteria. It is composed of an overlapping
lattice of two sugars, N-acetyl glucosamine (NAG)
pelagic zone The ocean is divided into zones. The and N-acetyl muramic acid (NAM), that are cross-
whole mass of water is called the pelagic. This is divid- linked by amino acid bridges that are found only in
ed into two major subzones: the neritic zone, which the cell walls of bacteria. This elaborate, covalently
covers all water to a depth of 600 feet, and the oceanic cross-linked structure provides great strength of the
zone, which covers all water below 600 feet. The cell wall.
oceanic zone is further divided into subzones. The
mesopelagic (semidark waters) covers the depths from peptidomimetic A compound containing nonpep-
650 feet to 3,200 feet, which is the middle layer tidic structural elements that is capable of mimicking or
between the upper (sunlit 650 feet) epipelagic and the antagonizing the biological action(s) of a natural par-
lower (cold and dark) bathypelagic. ent peptide. A peptidomimetic no longer has classical
peptide characteristics, such as enzymatically scissille
peptide bond The bond that links amino acids peptidic bonds.
together. Created by a condensation reaction between
the alpha-amino group of one amino acid and the See also PEPTOID.
alpha-carboxyl group of another amino acid; a cova-
lent bond. peptoid A PEPTIDOMIMETIC that results from the
oligomeric assembly of N-substituted glycines.

peripheral nervous system 263

perception The brain’s interpretation of a sensory periderm Secondary tissue produced by the cork
stimulus; conscious mental awareness. cambium that, when mature, is made up of dead cells
(called cork) that are composed of a waterproof sub-
perennial A plant that lives through many seasons, stance called suberin. Acts as a protective shield against
such as a tree. water loss, extreme temperatures, and as a pathogen
barrier. Usually called bark.

pericycle Plant cells just inside the endodermis of the peripheral nervous system Part of the nervous
root that remain meristematic, allowing new lateral system that consists of (a) sensory neurons composed
roots to grow (only the pericycle cells nearest the inter- of stimulus receptors that notify the central nervous
nal xylem poles perform this function). Located between system that stimuli have occurred and (b) motor
the endodermis and phloem. One of four outer layers of neurons, called effectors, that travel from the central
the root (the others being epidermis, cortex, endodermis) nervous system to make muscles and glands react.
that surround the vascular tissue in the middle of a root. The peripheral nervous system is subdivided into the

growing polypeptide amino acid
chain of amino acids tRNA

peptide bond

anti-codon
codon

translation mRNA

ribosome
Two or more amino acids joined by a peptide bond. (Courtesy Darryl Leja, NHGRI, National Institutes of Health)

264 periplasm

sensory-somatic nervous system and the autonomic
nervous system.

periplasm The fluid occupying the space between the
inside and outside cellular membranes of bacteria.

peristalsis Involuntary rhythmic waves or move-
ments of longitudinal and circular muscles in the diges-
tive tract (stomach, intestines, esophagus) in short or
long duration.

peroxidase A heme protein (donor: hydrogen perox- Scanning electron micrograph (SEM) of a macrophage, a white
ide OXIDOREDUCTASE, EC class 1.11.1) that catalyzes blood cell (upper right), engulfing a protozoan, Leishmania mexi-
the one-electron oxidation of a SUBSTRATE by dihydro- cana (lower left). This parasitic protozoan causes the disease
gen peroxide. Substrates for different peroxidases leishmaniasis. Here, the macrophage has extended part of its body
include various organic compounds, CYTOCHROME-c, to surround and capture the Leishmania. This process is called
halides, and Mn2+. phagocytosis. Leishmaniasis is transmitted by the bites of infected
sandflies, causing a skin ulcer at the site of the bite. The more
See also EC NOMENCLATURE FOR ENZYMES. serious form, kala-azar, can be fatal. Macrophages are part of the
immune system that keep the body free of invading organisms.
peroxisome A single-membrane enzyme-containing Magnification unknown. (Courtesy © Science Photo
organelle present in most eukaryotic cells. The perox- Library/Photo Researchers, Inc.)
isome is involved in metabolic processes such as the
ß-oxidation of long- and very-long-chain fatty acids,
bile acid synthesis, cholesterol synthesis, plasmalogen
synthesis, amino acid metabolism, and purine
metabolism.

petiole A leaf stalk that attaches to the stem. phagocytosis The act of ingestion and digestion of
microorganisms, insoluble particles, damaged or dead
Pfeiffer’s rule States that in a series of chiral com- host cells, and cell debris by specific types of cells
pounds the EUDISMIC RATIO increases with increasing called phagocytes (e.g., macrophages, neutrophils); a
POTENCY of the EUTOMER. form of endocytosis.

See also ENDOCYTOSIS.

phage (bacteriophage) A type of virus that attacks pharmacokinetics The study of absorption, distri-
bacteria. bution, METABOLISM, and excretion (ADME) of bioac-
tive compounds in a higher organism.
See also BACTERIA.
See also DRUG DISPOSITION.

phagocyte A cell that is able to ingest, and often to pharmacophore (pharmacophoric pattern) The
digest, large particles such as bacteria and dead tissue ensemble of steric and electronic features that is neces-
cells.

phospholipase A 265

sary to ensure the optimal supramolecular interactions represented a nonphylogenetic approach to biological
with a specific biological target structure and to trigger classification.
(or to block) its biological response.
phenotype The outward observable features, func-
A pharmacophore does not represent a real tions, or behaviors of an organism, based on the coding
molecule or a real association of functional groups of the genotype.
but, rather, is a purely abstract concept that accounts
for the common molecular interaction capacities of a See also GENOTYPE.
group of compounds toward their target structure.
The pharmacophore can be considered as the largest pheromone A volatile chemical secreted and sent
common denominator shared by a set of active externally by an organism to send information to mem-
molecules. This definition discards a misuse often bers of the same species via olfactory senses that induce
found in the MEDICINAL CHEMISTRY literature, which a physiological or behavioral response, such as sexual
consists of naming as pharmacophores simple chemi- attraction.
cal functionalities such as guanidines, sulfonamides,
or dihydroimidazoles (formerly imidazolines), or typi- phloem The principal food-conducting living tissue
cal structural skeletons such as flavones, phenoth- of vascular plants; one of the vascular tissues in plants,
iazines, prostaglandins, or steroids. the other being the xylem, that make up the vascular
bundle. Composed of food-conducting sieve elements:
pharmacophoric descriptors Used to define a sieve cells and sieve-tube members. Sieve cells are found
PHARMACOPHORE, including H-bonding and hydropho- in gymnosperms, while angiosperms have sieve-tube
bic and electrostatic interaction sites, defined by atoms, members.
ring centers, and virtual points.
See also XYLEM.
pharynx A short section of fibromuscular tube that
is the common opening for the digestive and respira- phosphatase An ENZYME that catalyzes the hydrolysis
tory systems. Located in the throat at the convergence of orthophosphoric monoesters. Alkaline phosphatases
of the nasal passage and oral cavity it opens to the (EC 3.1.3.1) have an optimum pH above 7 and are zinc-
larynx (respiratory system) and the esophagus (diges- containing proteins. Acid phosphatases (EC 3.1.3.2)
tive system). Composed of three parts: the nasophar- have an optimum pH below 7, and some of these con-
ynx (behind the nose and above the soft palate; tain a dinuclear center of iron, or iron and zinc.
tonsils), the oropharynx (back of the mouth and soft
palate, tonsils, and posterior third of the tongue wall See also EC NOMENCLATURE FOR ENZYMES;
of the throat), and the hypopharynx or laryngophar- NUCLEARITY.
ynx (lower part of the throat behind the larynx and
above the esophagus). The pharynx receives air from phosphate group Oxygenated phosphorus (–PO4)
the nasal cavity, while air, food, and water enter from that is attached to a carbon chain; important in energy
the mouth. transfer from ATP in cell signal transduction, the bio-
chemical communication from one part of the cell to
phenetics (numerical taxonomy) A former school of another; also part of a DNA nucleotide.
taxonomy that classified organisms on the basis of
overall morphological or genetic similarity that phospholipase A (phosphatide acylhydrolase) Cat-
involved observable similarities and differences with- alyzes the hydrolysis of one of the acyl groups of phos-
out considering whether or not the organisms were phoglycerides or glycerophosphatidates. Phospholipase
related. It involved clustering groups into types and

266 phospholipases

A1 hydrolyzes the acyl group attached to the 1-posi- photoautotroph An organism that uses sunlight to
tion, while phospholipase A2 hydrolyzes the acyl group provide energy and uses carbon dioxide as the chief
attached to the 2-position. source of carbon, such as photosynthetic bacteria,
cyanobacteria, algae. Green plants are photoau-
phospholipases A class of enzymes that catalyze the totrophs.
hydrolysis of phosphoglycerides or glycerophosphati-
dates. photoheterotroph Like photoautotrophs, any organ-
ism that uses light as a source of energy but must use
phospholipids The main component of cell walls; an organic compounds as a source of carbon, for example,
amphiphilic molecule (lipid). A glycerol skeleton is green and purple nonsulfur bacteria.
attached to two fatty acids and a phosphate group, and
onto the phosphate is attached one of three nitrogen photolysis A light-induced bond cleavage. The term is
groups, so both phosphate and nitrogen groups make often used incorrectly to describe irradiation of a sample.
the “polar head” larger and more polar. The phosphate
part of the molecule is water soluble, while the fatty photon Name given to a quantum or packet of ener-
acid chains are fat soluble. The phospholipids have a gy emitted in the form of electromagnetic radiation. A
polar hydrophilic head (phosphate) and nonpolar particle of light and gamma and X rays are examples.
hydrophobic tail (fatty acids). When in water, phospho-
lipids sort into spherical bilayers; the phosphate groups photoperiodism The physiological response to
point to the cell exterior and interior, while the fatty length of day and night in a 24-hour period, such as
acid groups point to the interior of the membrane. the flowering or budding in plants.

Examples include lecithin, cephalin and sphin- photophosphorylation The process of creating
gomyelin, phosphatidic acid, plasmalogen. Two types adenosine 5-triphosphate (ATP) from ADP and phos-
of phospholipids exist: glycerophospholipid and sphin- phate by using the energy of the sun. Takes place in the
gosyl phosphatide. A synthetic phospholipid, thylakoid membrane of chloroplasts.
alkylphosphocholine, has been used in biological and
therapeutic areas.

Structurally, phospholipids are similar to triglyc-
erides, except that a phosphate group replaces one of
the fatty acids.

phosphorylation A process involving the transfer photorespiration A process that decreases photo-
of a phosphate group (catalyzed by ENZYMEs) from synthesis and occurs when carbon dioxide levels are
a donor to a suitable acceptor; in general, an ester link- low inside a plant’s leaves; a process that uses oxygen,
age is formed, for example: ATP + alcohol   ADP + releases carbon dioxide, and generates no ATP in the
phosphate ester process. Occurs on hot days when oxygen concentra-
tions in leaves exceed carbon dioxide levels due to
photic zone The upper layer within bodies of water, closed stomata.
reaching down to about 200 meters, where sunlight
penetrates and promotes the production of photosyn- photosynthesis A metabolic process in plants and
thesis; the richest and most diverse area of the ocean. A certain bacteria that uses light energy absorbed by
region where photosynthetic floating creatures (phyto- CHLOROPHYLL and other photosynthetic pigments for
plankton) are primary producers as well as a major the reduction of CO2, followed by the formation of
food source. The littoral zone and much of the sublit- organic compounds.
toral zone fall within the photic zone.
See also METABOLISM; PHOTOSYSTEM.

pineal gland 267

photosystem A membrane-bound protein complex that would otherwise infect them; e.g., pisatin (pro-
in plants and photosynthetic bacteria, responsible for duced by peas), phaseollin (produced by beans [Phase-
light harvesting and primary electron transfer. Com- olus]), camalexin (produced by Arabidopsis thaliana),
prises light-harvesting pigments such as CHLOROPHYLL; resveratrol (grapes).
a primary electron-transfer center and a secondary
electron carrier. In green-plant photosynthesis, photo- phytochelatin A peptide of higher plants consisting
system I transfers electrons from PLASTOCYANIN to of polymers of 2–11 glutathione (γ, glutamyl, cysteinyl,
a [2FE-2S] FERREDOXIN and contains IRON-SULFUR glycine) groups, which binds heavy metals.
PROTEINS. Photosystem II transfers electrons from the
OXYGEN-EVOLVING COMPLEX to plastoquinone and phytochrome (red-light-sensitive system) Photore-
contains an iron center. ceptor proteins that regulate light-dependent growth
processes; absorbs red and far-red light in a reversible
See also PHOTOSYNTHESIS. system; one of the two light-sensing systems involved
in photoperiodism and photomorphogenesis. Plant
phototropism Growth movement by plants that is responses regulated by phytochrome include
induced by light. If growth is toward the light source it photoperiodic induction of flowering, chloroplast
is called positive phototropism; if it is away from the development (minus chlorophyll synthesis), leaf
source it is termed negative phototropism. senescence, leaf abscission, seed germination, and
flower induction.
pH scale The concentration of hydrogen ions in a
solution, based on a scale from 0 to 14. Low pH corre- picket-fence porphyrin A PORPHYRIN with a pro-
sponds to high hydrogen ion concentration, and high tective enclosure for binding oxygen at one side of the
pH refers to low hydrogen concentration. A substance ring that is used to mimic the dioxygen-carrying prop-
added to water that increases the concentration of erties of the HEME group.
hydrogen ions (i.e., lowers the pH) is called an acid,
while a substance that reduces the concentration of See also BIOMIMETIC.
hydrogen ions (i.e., raises the pH) is called a base. Acid
in the stomach has a pH of 1, while a liquid drainer pilus A hairlike projection, composed of a protein
has a pH of 14. Pure water is neutral with a pH of 7. pilin and found on the surface of certain gram-negative
Compounds called buffers can be added to a solution bacteria, that functions to adhere to carbohydrate
that will resist pH changes when an acid or base is receptors on host cells. Specialized sex pili conjugate
added. with other bacteria to transfer DNA. Also called fim-
briae.
See also ACID; BASE.
pineal gland (pineal body; epiphysis) A small
phylogeny The evolutionary tree that connects a endocrine gland shaped like a pine cone and located in
group of organisms. the middle of the brain. It functions as a regulator of the
biological clock. At night, the hormone serotonin con-
phylum A taxonomic category between kingdom verts into melatonin (n-acetyl-5-methoxy-tryptamine
and class. [NA-5-MT]) by enzymatic interaction. Melatonin is a
neurotransmitter and neurohormone.
See also TAXON.
The pineal helps to regulate the function of all
phytoalexin A toxic substance that acts like an organs of the endocrine system in the body (pituitary
antibiotic that is produced by plants to inhibit or kill gland, thyroid + parathyroid glands, thymus, pancreas,
the growth of microorganisms, such as certain fungi

268 pinocytosis

and ovaries/testes) that secrete their hormones to the placebo An inert substance or dosage form that is
blood. The pituitary gland stimulates the secretion of identical in appearance, flavor, and odor to the active
these hormones, but the pineal gland stops it via mela- substance or dosage form. It is used as a negative con-
tonin. If there is too much hormone, the pineal releases trol in a BIOASSAY or in a clinical study.
melatonin to counteract; too much stress in the body,
serotonin triggers the release of adrenaline. The pineal placenta A structure that develops in the uterus dur-
is also sensitive to light, and it releases melatonin at ing pregnancy that provides a blood supply and nutri-
night and is inhibited during the day. ents for the fetus and eliminates waste; formed from
the uterine lining and embryonic membranes. In
New studies regarding the effect of electromagnetic humans, it is also referred to as the afterbirth because it
frequency (EMF) on the body (from cell phones, high is ejected after the baby in a normal vaginal birth. If the
voltage lines, etc.) also relates to the pineal gland, placenta is abnormally low in the uterus and covering
which is sensitive to EMF and seems to suppress the the uterus, a pregnancy-related condition called placen-
activity of the pineal gland by reducing melatonin pro- ta praevia occurs and usually necessitates delivery by a
duction. cesarean section.

The pineal gland is suspected to play a role in a placental mammal Any mammals that bear their
number of problems including cancer, sexual dysfunc- young live and are nourished before birth in the moth-
tion, hypertension, and the decline in melatonin has er’s uterus through a placenta. There are about 4,000
been suggested to be a trigger for the aging process. species, from bats to cats to humans.

pinocytosis An active transport process by which placoderm A member of an extinct class of early
liquids or very small particles are ingested into the cell hinged-jaw fishlike vertebrates covered with a tough
by endocytosis. The cytoplasmic membrane invaginates outer body armor of bony plates with paired fins; lived
(forms “pockets”), fills with liquid or material, and during the Silurian and Devonian periods (438 to 360
pinches off into a pinocytic vesicle or vacuole that can million years ago). Examples include the antiarchs and
then be transported. dinichthyids.

pith The core of plant stems; location of vascular sys-
tems containing parenchyma cells and ground tissue.
Also to kill by severing the spinal cord.

pituitary gland A two-lobed, pea-size gland at the plankton Plankton includes mostly small-sized
base of the brain and attached to the hypothalamus plants called phytoplankton (e.g., diatoms) and ani-
that controls the endocrine system. The major divisions mals called zooplankton (e.g., radiolarians) that drift
of the gland are the anterior lobe, or adenohypophysis, and float along with the tides and currents of water
and the posterior lobe, the neurohypophysis. Each lobe bodies. Their name comes from the Greek meaning
produces hormones. The anterior lobe produces “drifter” or “wanderer.” Phytoplankton produce their
growth hormone, thyroid-stimulating hormone, own food by photosynthesis and are primary produc-
adrenocorticotropic hormone, prolactin, luteinizing ers and food supply for a host of other organisms.
hormone (LH), and follicle-stimulating hormone Plankton are also an oxygen producer, generating
(FSH), the last two called gonadotropins because they according to some estimates as much as 80 percent of
stimulate the gonads. The posterior lobe releases anti- the Earth’s oxygen supply.
diuretic hormone (vasopressin) and oxytocin. These
hormones regulate many body functions from growth planula The free-swimming, flat, ciliated larvae of
to birth contractions. the coelenterates.

pleated sheet 269

plasma In biology, this term has the following three plasmolysis A process caused by diffusion when the
meanings: cell membrane shrinks away from its cell wall, with
the resulting vacuole and cytoplasm shrinking due to
1. Fluid component of blood in which the blood cells the presence of a foreign material, like salt, becoming
and platelets are suspended (blood plasma). Note too abundant; water is drawn from the cell into the
the distinction between plasma, which describes a extracellular area, and the cell becomes flaccid after
part of the blood (the fluid part of blood, outside losing its internal turgor.
the blood cells), and serum, which describes a frac-
tion derived from blood by a manipulation (the fluid plastid A type of plant cytoplasmic organelle that
that separates when blood coagulates). develops from a precursor small and colorless undiffer-
entiated organelle, the proplastid. During cell differentia-
2. Fluid component of semen produced by the accesso- tion, proplastids differentiate into particular plastid
ry glands, the seminal vesicles, the prostate, and the types according to the type of cell in which they are
bulbourethral gland. located in response to the particular metabolic demands.
Plastids are essential components for plant cell function.
3. Cell substance outside the nucleus (CYTOPLASM).
Plastids develop into specialized functional types.
plasma cell An antibody-producing B cell that has They divide by binary fission or budding. Several types
reached the end of its differentiation pathway. B cells of plastids exist: amyloplast or leucoplast (starch syn-
are white blood cells that develop from B stem cells thesis and storage), chloroplast (photosynthesis), chro-
into plasma cells that produce immunoglobulins (anti- moplast (plant color), etioplast (night plants, can
bodies). develop chloroplasts), proteoplast or proteinoplast
(storage), elaioplast (oil storage).
plasma membrane An interface and permeability-
limiting membrane composed of lipids and proteins plastocyanin An ELECTRON TRANSFER PROTEIN, con-
that act as a selective barrier for the cell’s interior cyto- taining a TYPE 1 COPPER site, involved in plant and
plasm. cyanobacterial PHOTOSYNTHESIS, which transfers elec-
trons to PHOTOSYSTEM I.
plasmid An extrachromosomal GENETIC element
consisting generally of circular double-stranded DNA, platelet (thrombocyte) Disk-shaped, colorless blood
which can replicate independently of chromosomal cells produced by the bone marrow (from megakary-
DNA. R plasmids are responsible for the mutual trans- ocytes); contains numerous proinflammatory mediators
fer of antibiotic resistance among microbes. Plasmids and functions to stop bleeding and allow damaged
are used as vectors for CLONING DNA in bacteria or areas to clot. A normal platelet count is
yeast host cells. 150,000–400,000 mm3 (millimeters cubed).

See also CLONING VECTOR. See also BLOOD.

plasmodesma Living bridges between cell walls; platelet-activating factor (PAF) A cytokine media-
small tubes or openings lined with plasma membrane tor of immediate hypersensitivity, perhaps even the
between cell walls that connect each cell to one another most important, which produces inflammation.
and are believed to allow molecules to pass through.

plasmogamy A process of cytoplasm fusion between pleated sheet (beta pleated sheet) One type of sever-
two cells; the first step in syngamy (sexual reproduction). al secondary structures, the three-dimensional arrange-

270 pleiotropy

ments (folding, twisting, coiling) of polypeptide chains either the ancestral (or plesiomorphic) character state
in a protein. They can be in the form of a helix, ran- or the derived (apomorphic) character state for a par-
dom coil, or pleated sheet; linked by hydrogen bonds in ticular character.
the peptide backbone; sheets are formed when the
polypeptide chains fold back and forth, or when two pluripotent stem cell (stem cell) Primitive blood
parts are parallel to each other and bonded; also called cells found in the bone marrow, circulating blood-
the beta pleated sheet. stream, and umbilical cord that are capable of repro-
ducing and differentiating to make all varieties of
pleiotropy The ability of a single gene to affect many mature blood cells (white blood cells, red blood cells,
phenotypic traits. Jonathan Hodgkin from the MRC and platelets). This means that all blood cells originate
Laboratory of Molecular Biology, in Cambridge, Unit- from this single type of cell. Pluripotent stem cells are
ed Kingdom, has characterized several types of usually referred to as stem cells.
pleiotropy:

Artefactual Adjacent but functionally unrelated genes pneumatophore (breathing roots) A specialized root
affected by the same mutation, e.g., claret. structure that has numerous pores or lenticels over its
surface, allowing gas exchange, and that grows up into
Secondary Simple primary biochemical disorder lead- the air, e.g., mangroves.
ing to complex final phenotype, e.g., phenylke-
tonurea. pocosin A swamp on the coastal plain of the south-
eastern United States.
Adoptive One gene product used for quite different
chemical purposes in different tissues, e.g., e-crys- poikilotherm An organism (e.g., fish or reptile)
tallin. whose body temperature varies or fluctuates with the
temperature of its surroundings; an ectotherm.
Parsimonious One gene product used for identical
chemical purposes in multiple pathways, e.g., gpb-1. point mutation When the base sequence of a codon
is permanently changed. Four types exist:
Opportunistic One gene product playing a secondary
role in addition to its main function, e.g., sisB/ Missense A change in base sequence converts a codon
AS-C. for one amino acid to a codon for a different amino
acid.
Combinatorial One gene product employed in vari-
ous ways, and with distinct properties, depending on Nonsense A codon for a specific amino acid is
its different protein partners, e.g., unc-86. converted to a chain-terminating codon.

Unifying One gene, or cluster of adjacent genes, Silent Conversion of a codon for an amino acid to
encoding multiple chemical activities that support a another codon that specifies the same amino acid.
common biological function, e.g., cha-1 unc-17.
Frameshift A nucleotide is deleted or added to the
plesiomorphic character The ancestral character of coding portion of a gene.
a homologue; the descendant character is termed the
apomorphic character. Two characters in two taxa are poison plants (poison ivy; poison oak; poison sumac)
homologues if they are the same as the character that is The poison ivy plant is known as Toxicodendron radi-
found in the ancestry of the two taxa, or if they have cans in the eastern United States and T. rydbergii in
characters that have an ancestor/descendant relation- the midwestern United States. Historically it has been
ship described as preexisting or novel (plesiomorphic
and apomorphic character).

All taxa are mixtures of ancestral and derived char-
acters. Ancestral character states are those similar to
the remote ancestor, while derived characters are those
that have undergone recent change. Taxa can show

polydentate 271

called Rhus toxicodendron. Western poison oak is that can vary depending on the plant, climate, and
known as Toxicodendron diversilobum. region.

These plants can cause a skin reaction. No reaction pollen allergy A hypersensitive reaction to pollen.
usually occurs the first time the skin is exposed to the While grass pollens are generally the most common
plant. Subsequent contact with the plant or plant resin, cause of hay fever (seasonal allergic rhinitis), other
however, can result in an allergic skin reaction that pollen types are also important. These include tree pol-
usually appears seven to 14 days after contact. Subse- lens such as alder, hazel, birch, beech, cypress, pine,
quent contact results in a more rapid reaction, usually chestnut, and poplar, and weed pollens such as plan-
within two to five days postcontact. The severity of the tain, mugwort, and ragweed. The relative importance
reaction is related to the amount of plant material that of the kinds of pollen that can cause hay fever varies
comes in contact with the skin, as well as to the degree between different climatic and vegetation zones. For
of allergic sensitivity of the individual. The allergen example, ragweed pollen, although very common in
(irritant from the plant) is often transferred from the North America, is present in Europe only in the French
hands or clothing to other parts of the body. Rhône valley and some areas of Eastern Europe, while
the pollen most associated with seasonal allergy in
The poison ivy plant and its relatives are common Mediterranean regions is the olive tree. A person aller-
throughout the United States. Poison ivy leaves are coat- gic to one pollen is generally also allergic to members
ed with a mixture of chemicals called urushiol. When of the same group or family (e.g., Betulaceae). Pollen-
people get urushiol on their skin, it causes allergic con- induced reactions include extrinsic asthma, rhinitis,
tact dermatitis. The body’s immune system treats urushi- and bronchitis.
ol as foreign and attacks the complex of urushiol
derivatives with skin proteins. The irony is that urushiol, pollination The first step in plant reproduction.
in the absence of the immune attack, would be harmless. Occurs when the male germ cell of a plant, a pollen
grain, reaches the female reproductive part, or stigma,
Poison ivy can affect two out of three Americans, of the same species of plant. This happens by wind
and of these, 15 percent may have severe allergic reac- transportation or by animal carriers, although 90 per-
tions that require medical treatment. Millions of Amer- cent of flowering plants rely on animal delivery.
icans yearly seek remedies for the irritation caused by
poison ivy, oak, and sumac. polyandry A rare mating system where one female
mates with more than one male, although each male
polar covalent bond A type of chemical bond, mates with only one female. Two types of polyandry
based on electron affinity, where electrons shared by exist: simultaneous polyandry, where each female
atoms spend a greater percentage of time closer to an maintains a large territory that contains smaller nesting
oxygen nucleus rather than a hydrogen nucleus; bonds territories of two or more males who care for the eggs
are polar, i.e., they have a partial electric charge across and tend to the young; and sequential polyandry, where
the molecule due to their geometry and the electronega- a female mates with a male, lays eggs, and terminates
tivity difference between the two atoms (hydrogen is the relationship and leaves that male. While the male is
positive, oxygen is negative); in organisms, they can left to incubate the eggs, she repeats the sequence with
form weak hydrogen bonds. Water is an example, but another male. The latter is more common. In human
peptide bonds and amines also form polar covalent society, it is the practice of a woman to have more than
bonds; these molecules can attract each other. one husband at a time.

polar molecule A molecule that has both a positive
and a negative end, such as water.

pollen Microscopic grains produced by plants in polydentate See CHELATION; DONOR ATOM SYMBOL.
order to reproduce. Each plant has a pollinating period

272 polygenic inheritance

polygenic inheritance The interaction of several polymorphonuclear leukocyte (PMN; granular
genes on a phenotype trait. A series of genes at multiple leukocyte; granulocyte; inflammatory granulocyte;
loci where each contributes a small additive effect on a polymorphonuclear cell) A subgroup of leukocytes
plant’s phenotype, for example, height in tobacco plants. (white blood cells) filled with granules of toxic chemi-
cals that enable them to digest microorganisms by
polygyny A mating system where one male mates phagocytosis. Examples of granulocytes are neu-
with more than one female, while each female mates trophils, eosinophils, and basophils.
with only one male; believed to be the normal mating
system in animals.

polyhedral symbol The polyhedral symbol indicates original double-stranded DNA
the geometrical arrangements of the coordinating
atoms about the CENTRAL ATOM. It consists of one or separate strands
more capital italic letters derived from common geo- and anneal primers
metric terms (tetrahedron, square plane, octahedron, 5' 3'
etc.), which denote the idealized geometry of the LIG- primers
ANDs around the COORDINATION center, and an Arabic 3' 5'
numeral that is the coordination number of the central
atom. The polyhedral symbol is used as an affix, 5' 3'
enclosed in parentheses, and separated from the name 3' 5'
by a hyphen. Examples are T-4, SP-4, TBPY-5, SPY-5,
OC-6, and CU-8. 3' new primers 5'
5' 3'
polymer A macromolecule of high relative molecular
mass composed of many similar or identical monomers new strands
linked together in chains. Plastics are polymers.

polymerase chain reaction (PCR) A laboratory
technique used to rapidly amplify predetermined
regions of double-stranded DNA. Generally involves
the use of a heat-stable DNA polymerase.

polymorphic Refers to a phenotypic expression desired
occurring in a number of forms appearing within an fragment
interbreeding population, such as fur coloration. strands

polymorphism Difference in DNA sequence among Polymerase chain reaction (PCR) is a fast, inexpensive technique
individuals in a plant or animal population expressed for making an unlimited number of copies of any piece of DNA.
as two or more distinct forms of individuals in the Sometimes called “molecular photocopying,” PCR has had an
same population. Polymorphisms can be inherited or immense impact on biology and medicine, especially genetic
environmentally created (polyphenism). Examples research. (Courtesy of Darryl Leja, NHGRI, National Institutes of
include sickle cell anemia and the caste system of bees. Health)

postzygotic barrier 273

polyp A cnidarian body form that is the sessile porins A class of proteins that create water-filled
reproductive stage; the alternate is the mobile medusa channels across cell membranes.
stage. In medicine, a polyp is a small stalked benign
growth or tumor protruding from a mucous mem- porphyrin A macrocyclic molecule that contains
brane; can be precursors of cancer. four pyrrole rings linked together by single carbon
atom bridges between the alpha positions of the pyr-
polypeptide A polymer chain of amino acids linked role rings. Porphyrins usually occur in their dianionic
by covalent peptide bonds. One or more polypeptides form coordinated to a metal ion.
form proteins. Each polypeptide has two terminal ends;
one, called the amino terminal or N-terminal, has a free See also COORDINATION.
amino group, while the other end is called the carboxyl
terminal or C-terminal with a free carboxyl group. positional information Cells send signals indicating
their locations relative to each other in the embryo
polyphyletic Refers to a group of organisms that development process; positional information is commu-
might have some similarities but that do not include the nicated through gap junctions, specific cell-cell adhe-
most recent common ancestor of all the member organ- sions, or diffusible signal molecules; part of the process
isms due to that ancestor lacking some or all character- of determining cell fate.
istics of the group. Polyphyletic groups are not
recognized in accepted taxonomies. positive feedback When a change occurs in a vari-
able during homeostasis, the response is to reinforce
polyploidy When the number of chromosomes in a the change in the variable. Examples include nerve
cell gets doubled; two complete chromosome sets; a impulse conduction, blood clotting, female ovarian
mutation. Polyploidy is very common in plants, where cycles, labor and birth, and immune responses. A
30 percent to 70 percent of modern angiosperms are resulting NEGATIVE FEEDBACK may need to take over to
believed to be polyploids. Polyploidy is rare in animals halt the process.
but is found in some insects, amphibians, reptiles, and
one mammal (a rat in Argentina). postsynaptic membrane The presynaptic mem-
brane is at the tip of each nerve ending. A small cleft
polyribosome (polysome) A cluster of ribosomes called the synaptic cleft separates the presynaptic
translating on one messenger RNA molecule. membrane from the postsynaptic membrane, a special
area on the receiving cell. When the presynaptic nerve
polysaccharide A carbohydrate (polymer) made by ending receives nerve impulses, it sends neurotransmit-
polymerizing any of more than 1,000 monosaccha- ters stored in synaptic vesicles into the synaptic cleft
rides; a complex sugar. (the synapse), which in turn diffuse across and trans-
mit the signal to the postsynaptic membrane receptor
population Any group of interbreeding individuals of molecules, which are specialized molecules that open
a particular species living in a specific geographic area. or close certain ion channels when activated by the
correct neurotransmitter.
population viability analysis (PVA) A process to
evaluate the likelihood of a population surviving and to postzygotic barrier A species-isolating mechanism
identify threats facing the species. Used in endangered preventing hybrids that are produced by two
species recovery and management. different species from developing into fertile and
viable adults.

See also PREZYGOTIC BARRIER.

274 potency

potency A comparative rather than an absolute primary germ layers After gastrulation, develop-
expression of drug activity. Drug potency depends on ment of the three germ layers—ectoderm, mesoderm,
both AFFINITY and EFFICACY. Thus, two AGONISTs can endoderm—occurs, and these eventually develop into
be equipotent but have different intrinsic efficacies, all parts of the animal.
with compensating differences in affinity. Potency is the
dose of DRUG required to produce a specific effect of primary growth Growth initiated by the apical
given intensity as compared with a standard reference. meristem that takes place relatively close to the tips of
roots and stem and that involves extending the length
potential energy Stored energy that can be released of the plant.
or harnessed to do work.
primary immune response The immune response
power saturation A phenomenon used in ELECTRON (cellular or humoral) to a first encounter with an anti-
PARAMAGNETIC RESONANCE SPECTROSCOPY to estimate gen. The primary response is generally small, has a long
the electron-spin relaxation times, thus providing infor- induction phase or lag period, consists primarily of IgM
mation about distances between PARAMAGNETIC centers. antibodies, and generates immunologic memory.

predator An animal that preys on or eats other primary producer An autotroph that acts as a food
animals. source for the next level up in the food chain. Green
plants are primary producers.

predisposition, genetic A latent susceptibility to primary productivity The rate at which new plant
disease, at the genetic level, that can be activated under biomass is formed by photosynthesis. Gross primary
certain conditions. productivity is the total rate of photosynthetic produc-
tion of biomass; net primary productivity is gross pri-
prevalence The number of all new and old cases of a mary productivity minus the respiration rate.
disease in a defined population at a particular point in
time. primary structure The amino acid SEQUENCE of a
protein or the NUCLEOTIDE sequence of DNA or RNA.

prezygotic barrier There are two types of reproduc- primary succession Occurs when communities
tive isolation mechanisms: prezygotic (before gamete develop in a newly exposed habitat that had no former
union) and postzygotic (after gamete union). A form of life (e.g., bare rock, newly deposited sand).
prezygotic barrier is mechanical isolation, which deals
with the mechanics of the reproductive organs and primate Mammals that include humans and other
physically prevents sexual intercourse between two dif- species that are closely related. There are two main
ferent species. Temporal (two species reproduce at dif- groups: the anthropoids (humans, apes, monkeys) and
ferent times of day) and habitat isolation (two prosimians (aye-ayes, galagos, lemurs, lorises, pottos,
overlapping species in same range live in different habi- and tarsiers).
tats) are also prezygotic barriers.

See also POSTZYGOTIC BARRIER.

primary consumer Any animal that eats grass, algae, primer A short preexisting polynucleotide chain to
and other green plants in a food chain; a herbivore. which new deoxyribonucleotides can be added by
DNA polymerase.

prophage 275

primordial germ cells Fetal cells that develop in the prognosis Prediction of the future course of a disease.
early fetus and that will develop into the gametes, the
male sperm or female eggs. prokaryote A unicellular organism characterized by
the absence of a membrane-bound nucleus.
principle of allocation Each organism has a limited,
finite energy budget that is used for living out its life See also EUKARYOTES.
processes of growth, reproduction, obtaining nutrients,
predator flight, and adjusting to environmental promoter The DNA region, usually upstream from
changes. the coding SEQUENCE of a GENE or OPERON, that binds
and directs RNA polymerase to the correct transcrip-
prion The smallest infectious particle known tional start site and thus permits TRANSCRIPTION at a
(though its existence is challenged by some scientists), specific initiation site. (In catalysis, a promoter is used
consisting of hydrophobic protein without any nucle- differently: a cocatalyst usually present in much smaller
ic acid. There are a number of prion-caused diseases. amounts than the catalyst.)
Scrapie, found in sheep and goats, causes those ani-
mals to lose coordination, and eventually they prophage A phage (bacteriophage, a virus that
become incapacitated and develop an intense itch infects bacteria) chromosome that has been inserted
that leads them to scrape off their wool or hair on a specific part of the DNA chromosome of a
(hence the name “scrapie”). Other diseases are trans- bacterium.
missible mink encephalopathy, chronic wasting dis-
ease of mule deer and elk, feline spongiform Comparison of Prokaryotic and Eukaryotic Cells
encephalopathy, and bovine spongiform encephalopa-
thy (mad cow disease). Kuru has been seen among the Occurrence Prokaryotic Eukaryotic
Fore highlanders tribesmen of Papua New Guinea, bacteria animals, plants, and
the result of cannibalism (but has almost disap- Average diameter
peared). Creutzfeldt–Jakob disease affects one person Nuclear material 1µm fungi
in a million. The other two human prion diseases are not separated 20µm
Gerstmann–Straussler–Scheinker disease and fatal DNA bounded by nuclear
familial insomnia. from cytoplasm
Nucleolus by membrane membrane
probability The statistical measure of an event’s like- Cell division circular and
lihood. forming only one linear and divided into
Cytoplasmic linkage group a number of chromo-
procambium A primary meristem tissue that differ- streaming - somes
entiates into the vascular bundle and vascular tissues amitotic
(xylem and phloem). Vacuoles +
Plastids - usually by mitosis or
prodrug Any compound that undergoes BIOTRANS- Ribosomes
FORMATION before exhibiting its pharmacological Endoplasmic - meiosis
effects. Prodrugs can thus be viewed as DRUGs contain- - +
ing specialized nontoxic protective groups used in a reticulum smaller (70S)
transient manner to alter or to eliminate undesirable Golgi apparatus - +
properties in the parent molecule. +
- larger (80S)
See also DOUBLE PRODRUG. +

+

+ indicates presence; - indicates absence

276 prophase

prophase During prophase, the chromosomes are
identical chromatids that are connected at the center by
a centromere (x-shaped). The mitotic spindle, which is
used to maneuver the chromosomes about the cell, is
formed from excess parts of cytoskeleton and initially
set up outside the nucleus.

The cell’s centrioles are then duplicated to form
two pairs of centrioles, with each pair becoming a part
of the mitotic center forming the focus for the aster, an
array of microtubules. The two asters lie side by side
and close to the nuclear envelope while near the end of
prophase; the asters then pull apart and the spindle is
formed.

prophylaxis Measures taken (treatment, drugs) to Breaking down unneeded proteins is accomplished by the
prevent the onset of a particular disease (primary pro- orderly action of several multiprotein complexes. At the heart
phylaxis) or recurrent symptoms in an existing infec- of this process is a multiprotein complex called the proteasome.
tion that have been brought under control (secondary These machines of destruction consist of a tunnellike core with
prophylaxis, maintenance therapy). Preventive treat- a cap at either or both ends. The core is formed by four stacked
ment. Treatment intended to preserve health and pre- rings surrounding a central channel that acts as a degradation
vent the occurrence or recurrence of a disease. Taking a chamber. The caps recognize and bind to proteins targeted by
drug to prevent yourself from getting an illness. the cell for destruction, then use chemical energy to unfold the
Chemoprophylaxis is prevention of disease by chemical proteins and inject them into the central core, where they are
means. broken into pieces. This is a fundamental kind of machine that
has been highly conserved during evolution. Some form of it
proprioreceptor Part of the sensory system. A sense is found in organisms ranging from simple bacteria to humans.
organ that detects the relative position about body (Courtesy of U.S. Department of Energy Genomes to Life program:
positions and movement. www.DOEGenomesToLife.org)

prostaglandin (PG) A lipid mediator, synthesized by have been tagged for elimination by a smaller protein,
the action of the enzyme phospholipase A2, which ubiquitin, in a process called ubiquitination. Ubiquitin
breaks down cell membrane components into arachi- covalently attaches to lysines of the other proteins, tag-
donic acid and then into prostaglandin by cyclooxyge- ging them for proteolysis (cleavage of proteins by pro-
nase. Highly proinflammatory, bronchospastic, and teases) within the proteasome.
vasodilatory.

prosthetic group A tightly bound, specific non- protein A molecule composed of many amino
polypeptide unit in a protein that determines and is acids and with a complex structure. For example,
involved in its biological activity. immunoglobulin, casein.

See also COFACTOR. See also AMINO ACID.

proteasome A large, protein-complex protease protein kinase A kinase is an enzyme that transfers
found inside cells that degrades other proteins that a phosphate group from ATP to some molecule. A pro-

amino acids

Primary protein structure
is a sequence of a chain of amino acids

pleated alpha
sheet
helix Secondary protein structure
occurs when the sequence of amino acids are

linked by hydrogen bonds

pleated Tertiary protein structure
sheet occurs when certain attractions are present

alpha between alpha helices and pleated sheets
helix

Quaternary protein structure
is a protein consisting of more than one amino

acid chain

Protein is a large complex molecule made up of one or more chains of amino acids. Proteins perform a wide variety of activities in the
cell. (Courtesy of Darryl Leja, NHGRI, National Institutes of Health)

278 protein machines

tein kinase phosphorylates a protein, using ATP, and Protonephridium consists of a network of two or more
the phosphorylation modulates the shape and activity closed longitudinal branched tubules running the length
of proteins. Protein kinase A and protein kinase C are of the body. The tubular system drains into excretory
involved in intracellular signal transduction in most ducts that empty into the environment through nephrid-
human cells. iopores, small external openings.

See also PROTEIN PHOSPHATASE.

protein machines Genomes are “brought to life” by proton motive force Energy or force created by the
being read out or “expressed” according to a complex transfer of protons (hydrogen ions) on one side only of a
set of directions embedded in the DNA sequence. The cell membrane and across the membrane during chemios-
products of expression are proteins that do essentially mosis; an electrochemical gradient that has potential
all the work of the cell: they build cellular structures, energy. This force can be channeled to operate rotating
digest nutrients, execute other metabolic functions, and flagella, generate ATP, and other needed activities.
mediate much of the information flow within a cell and
among cellular communities. To accomplish these proton pump Proton pumps are a type of active
tasks, proteins typically work together with other pro- transport that use the energy of ATP hydrolysis to force
teins or nucleic acids as multicomponent “molecular the transport of protons out of the cell, thus creating a
machines,” structures that fit together and function in membrane potential.
highly specific, lock-and-key ways.

protein phosphatase (phosphoprotein phosphatase) proto-oncogene A normal gene that can become an
An enzyme that removes a phosphate group from a active oncogene, one that is capable of causing cells to
protein by the use of hydrolysis; opposite effect of a change into cancer cells, by mutation or insertion of
PROTEIN KINASE. viral DNA.

proteoglycan A type of glycoprotein with high car- protoplasm The living material within cells.
bohydrate content; component in the extracellular
matrix of animal cells. Composed of one or more gly- protoplast Any cell from which the outer cell wall
cosaminoglycans, long polysaccharide chains covalent- or membrane has been removed, leaving only the cell
ly linked to protein cores. contents.

protoderm One of the three primary meristem tis- protoporphyrin IX The PORPHYRIN LIGAND of HEME
sues differentiated from the apical meristem; the outer- b. Heme b is a Fe(II) porphyrin complex readily isolated
most tissue. The protoderm differentiates into the from the hemoglobin of beef blood, but it is also found
plant’s epidermis of the roots and shoots. in other proteins, including other HEMOGLOBINs, MYO-
GLOBINs, CYTOCHROME P-450, CATALASEs, PEROXIDAS-
proton An atomic particle found in the nuclei of Es, as well as b type CYTOCHROMEs. Protoporphyrin IX
atoms along with a neutron, but the proton has a posi- contains four methyl groups in positions 2, 7, 12, and
tive electric charge. 18, two vinyl groups in positions 3 and 8, and two pro-
pionic acid groups in positions 13 and 17.

protonephridium An example of primitive kidneys for protostome Any of the group of coelomates, such as
osmoregulation and excretion among platyhelminthes. annelids, mollusks, and arthropods, whose embryonic

pseudopodium 279

blastopore becomes a mouth and who have spiral and
determinate cleavage.

protozoan The simplest forms of animal life, con- The Vorticella is a protist (protozoan) and belongs to the phyllum
sisting of aquatic single cells or colonies of single cells, Ciliophora. A protist that turns as it moves. (Courtesy of Hideki
such as amoeba and paramecium. The “protists” Horikami)
ingest food and live in both fresh and marine waters as
well as inside animals, and most are motile. Estimates Other protozoans such as Naegleria fowleri cause
of the number of species of protozoa are between meningitis; Trypanosoma cruzi causes African sleeping
12,000 to 19,000 species. Many protozoans are sickness and Chagas disease; and Plasmodium spp.
known to cause human disease, such as Giardia lam- causes malaria.
blia, a flagellated organism that can infect via water or
be contracted via contaminated foods. It causes giar- provirus Term given to a retrovirus DNA when it is
diasis, the most frequent cause of nonbacterial diar- integrated into the infected host cell genome. It can
rhea in North America. Cryptosporidium parvum has remain inactive for periods of time and can be passed
a strong association between cases of cryptosporidiosis to each of the infected cell’s daughter cells.
and immunodeficient individuals (such as those with
AIDS). Cyclospora cayetanensis infection results in a proximate causation Explains how organisms
disease with nonspecific symptoms: usually one day of respond to their immediate environment (through
malaise, low fever, diarrhea, fatigue, vomiting, and behavior, physiology, and other methods) and the
weight loss. Cryptosporidium parvum causes intesti- mechanics of those responses.
nal, tracheal, or pulmonary cryptosporidiosis. Acan-
thamoeba spp., Naegleria fowleri, and other amoebae
are responsible for primary amoebic meningoen-
cephalitis (PAM). Naegleria fowleri is associated with
granulomatious amoebic encephalitis (GAE), acan-
thamoebic keratitis, and acanthamoebic uveitis. Enta-
moeba histolytica causes amoebiasis (or amebiasis),
resulting in various gastrointestinal upsets, including
colitis and diarrhea. In more severe cases, the gastroin-
testinal tract hemorrhages, resulting in dysentery.

pseudocoelomate Any invertebrate whose body cav-
ity is not completely lined with mesoderm. The embry-
onic blastocoel persists as a body cavity and is not
lined with mesodermal peritoneum (the lining of the
coelom); therefore it is called a pseudocoel (“false cavi-
ty”). Examples include nematodes, rotifers, acantho-
cephalans, kinorhynchs, and nematomorphs.

Amoebas are protozoans, which are the simplest form of animal pseudopodium A dynamic protruding structure of
life. Photo of Amoeba proteus. (Courtesy of Hideki Horikami) the plasma membrane used by amoeboid-type cells
used for locomotion and phagocytosis.

280 pterin

pterin 2-amino-4-hydroxypteridine. pupa The stage preceding the adult in a holometa-
See also MOLYBDOPTERIN. bolous insect, for example, the stage in a butterfly or
moth when it is encased in a chrysalis and undergoing
punctuated equilibrium A part of evolutionary metamorphosis.
theory that states that evolution works by alternating
periods of spurts of rapid change followed by long
periods of stasis.

Q

quadruped An animal that moves using four-footed the growth and movement of Northern Hemisphere
locomotion; moves using all four limbs. continental glaciers and the Ice Age.

See also GEOLOGICAL TIME.

quantitative character (polygenic character; polygenic quaternary structure There are four levels of struc-
inheritance) An inherited character or feature in a ture found in polypeptides and proteins. The first or
population whose phenotypes have continuous varia- primary structure of a polypeptide or protein deter-
tion, such as height or weight, and whose distribution mines its secondary, tertiary, and quaternary structures.
follows small discreet steps and can be numerically The primary structure is the amino acid sequence. This
measured or evaluated; expressed often from one is followed by the secondary structure, how the amino
extreme to another. The effects are due to both envi- acids adjacent to each other are organized in the struc-
ronment and the additive effect of two or more genes. ture. The tertiary or third structure is the folded three-
dimensional protein structure that allows it to perform
quantum evolution A rapid increase in the rate of its role, and the fourth or quaternary structure is the
evolution over a short period of time. total protein structure that is made when all the sub-
units are in place. Quaternary structure is used to
quarantine A way to control or prevent importing, describe proteins composed of multiple subunits or mul-
exporting, or transporting of plants, animals, agricul- tiple polypeptide molecules, each called a monomer. The
tural products, and other items that may be able to arrangement of the monomers in the three-dimensional
spread disease or become a pest. protein is the quaternary structure. A considerable
range of quaternary structure is found in proteins.

quasisocial Refers to a situation where members of queen A member of the reproductive caste in semiso-
the same generation share a nest and care for the cial or eusocial insect species.
brood.

Quaternary period The most recent geologic period queenright A colony that contains a functional
of the Cenozoic era. It began 2 million years ago with queen. A monogynous colony in which one morpho-
logically different female ant is the only reproducer.

281

282 queen substance

queen substance A pheromone secreted by queen which may suggest a mechanism that links gene expres-
bees and given to worker bees that controls them from sion with patterning. It is the region in the apical meris-
producing more queens. tem that has little activity, and cells rarely divide or do so
very slowly. However, cells can be encouraged to divide
quiescent center A region of cells behind the root cap by wounding of the root. The quiescent center (QC) con-
that contains a population of mitotically inactive cells; sists of a small group of cells at the tip called the initials.
precedes the organization of a root meristem and con- It is the initials that divide very slowly and create the qui-
tains high levels of the enzyme ascorbic acid oxidase, escent center. Cells around the QC divide rapidly and
form the majority of the cells of the root body.

R

raceme An inflorescence, a flower structure, in (infrared, visible light, ultraviolet, electromagnetic) or
which stalked flowers are borne in succession along an ionizing (alpha, beta, gamma, and X rays). Ionizing
elongate axis, with the youngest at the top and oldest radiation can have severe effects on human health, but
at the base. it is also used in medical diagnostic equipment and
can be used to provide a host of other economic
racemic Pertaining to a racemate, an equimolar mix- benefits from electrical power generation to smoke
ture of a pair of ENANTIOMERs. It does not exhibit opti- detectors.
cal activity.
radical A molecular entity possessing one or more
radial cleavage A form of embryonic development unpaired electrons, formerly often called “free radical.”
where cleavage planes are either parallel or perpendicu- A radical can be charged positively (radical cation) or
lar to the vertical axis of the embryo. Found in negatively (radical anion). Paramagnetic metal ions are
deuterostomes, which include echinoderms and chor- not normally regarded as radicals.
dates.
radicle An embryonic plant root.

radial symmetry A body shape characterized by radioactive isotope An isotope is an element with a
equal parts that radiate outward from the center like a different amount of neutrons than protons. Isotopes
pie. Found in cnidarians and echinoderms. are unstable and spin off energy and particles. There
are radioactive and nonradioactive isotopes, and some
Radiata The animal phylum that includes cnidarians elements have both, such as carbon. Each radioactive
and ctenophores; radially symmetric. isotope has its own unique half-life, which is the time it
takes for half of the parent radioactive element to
radiation Released energy that travels through decay to a daughter product. Some examples of
space or substances as particles or electromagnetic radioactive elements, their stable daughters, and half-
waves and includes visible and ultraviolet light, heat, lives are: potassium 40–argon 40 (1.25 billion years);
X rays, and cosmic rays. Radiation can be nonionizing rubidium 87–strontium 87 (48.8 billion years); thorium
232–lead 208 (14 billion years); uranium 235–lead 207

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