On-Line Biology Book: GLOSSARY

P Q

pacemaker.  See sinoatrial node.

Pacinian corpuscles  Sensory receptors located deep in the epidermis that detect pressure and vibration.

paleontology The study of ancient life by collection and analysis of fossils.

Paleozoic Era  The period of time beginning 570 million years ago ending 245 million years ago; falls between the Proterozoic and Mesozoic Eras and is divided into the Cambrian, Ordovician, Silurian, Devonian, Carboniferous, and Permian Periods. PICTURE

palindrome  A sequence that reads the same in either direction; in genetics, refers to an enzyme recognition sequence that reads the same on both strands of DNA.

palisade Layer of mesophyll cells in leaves that are closely placed together under the epidermal layer of the leaf. Palisade parenchyma: Columnar cells located just below the upper epidermis in leaves the cells where most of the light absorbtion in photosynthesis occurs. PICTURE 1 | PICTURE 2

palynology The study of palynomorphs and other acid-resistant microfossils usually produced by plants, protists, and fungi.

palynomorph Generic term for any object a palynologist studies.

pancreas  A gland in the abdominal cavity that secretes digestive enzymes into the small intestine and also secretes the hormones insulin and glucagon into the blood, where they regulate blood glucose levels. A digestive organ that produces trypsin, chymotrypsin and other enzymes as a pancreatic juice, but which also has endocrine functions in the production of the hormones somatostatin, insulin, and glucagon.

pancreatic islets  Clusters of endocrine cells in the pancreas that secrete insulin and glucagon; also known as islets of Langerhans.

Pangaea The name proposed by German meteorologist Alfred Wegener for a supercontinent that existed at the end of the Paleozoic Era and consisted of all the Earth's landmasses.

parallel evolution  The development of similar characteristics in organisms that are not closely related (not part of a monophyletic group) due to adaptation to similar environments and/or strategies of life.

parasites  Organisms that live in, with, or on another organism. The parasites beneÞt from the association without contributing to the host, usually they cause some harm to the host.

parasitism  A form of symbiosis in which the population of one species beneÞts at the expense of the population of another species; similar to predation, but differs in that parasites act more slowly than predators and do not always kill the host. A type of symbiosis in which one organism benefits at the expense of the other, for example the influenza virus is a parasite on its human host. Viruses, are obligate intracellular parasites.

parasympathetic system  The subdivision of the autonomic nervous system that reverses the effects of the sympathetic nervous system. Part of the autonomic nervous system that controls heartbeat, respiration and other vital functions.

parenchyma  One of the three major cell types in plants. Parenchyma cells have thin, usually multisided walls, are unspecialized but carry on photosynthesis and cellular respiration and can store food; form the bulk of the plant body; found in the þeshy tissue of fruits and seeds, photosynthetic cells of leaves, and the vascular system. Generalized plant cells whose numerous functions include photosynthesis, storage, bulk of herbaceous stem tissues, lateral transport in woody stems. Parenchyma are variously shaped but are characterized by thin walls and remain alive at functional maturity. PICTURE

parietal lobe  The lobe of the cerebral cortex that lies at the top of the brain; processes information about touch, taste, pressure, pain, and heat and cold. PICTURE

passive transport  Diffusion across a plasma membrane in which the cell expends no energy.

pectin  A substance in the middle lamella that cements adjoining plant cells together.

pectoral girdle  In humans, the bony arch by which the arms are attached to the rest of the skeleton; composed of the clavicle and scapula. PICTURE

pedigree analysis  A type of genetic analysis in which a trait is traced through several generations of a family to determine how the trait is inherited. The information is displayed in a pedigree chart using standard symbols.

pelagic zone  One of the two basic subdivisions of the marine biome; consists of the water above the sea þoor and its organisms.

pelvic girdle  In humans, the bony arch by which the legs are attached to the rest of the skeleton; composed of the two hipbones. PICTURE

pelvis  The hollow cavity formed by the two hipbones. PICTURE

penicillin The first of the so-called wonder drugs; discovered by Sir Alexander Fleming.

pepsin  An enzyme produced from pepsinogen that initiates protein digestion by breaking down protein into large peptide fragments. An enzyme, produced by the stomach, that chemically breaks down peptide bonds in polypeptides and proteins.

pepsinogen  An inactive form of pepsin; synthesized and stored in cells lining the gastric pits of the stomach.

peptic ulcer  Damage to the epithelial layer of the stomach lining; generally caused by bacterial infection.

peptide bond  A covalent bond that links two amino acids together to form a polypeptide chain. A covalent bond between the amine end of one amino acid and the acid end of another amino acid. PICTURE

peptides  Short chains of amino acids.

perichondrium  A layer of connective tissue that forms around the cartilage during bone formation. Cells in the perichondrium lay down a peripheral layer that develops into compact bone.

perennials Plants that persist in the environment for more than one year (as in the case of annuals).

period The fundamental unit in the hierarchy of time units; a part of geologic time during which a particular sequence of rocks designated as a system was deposited. Units of geological time that are the major subdivisions of Eras.

periosteum  A Þbrous membrane that covers bones and serves as the site of attachment for skeletal muscles; contains nerves, blood vessels, and lymphatic vessels.

peripheral nervous system  The division of the nervous system that connects the central nervous system to other parts of the body. Components of the nervous system that transmit messages to the central nervous system.

peristalsis  Involuntary contractions of the smooth muscles in the walls of the esophagus, stomach, and intestines that propel food along the digestive tract. Waves of muscle contraction in the esophagus that propel food from the oral cavity to the stomach. PICTURE

Permian Period The last geologic time period of the Paleozoic Era, noted for the greatest mass extinction in earth history, when nearly 96% of species died out. PICTURE

peroxisomes  Membrane-bound vesicles in eukaryotic cells that contain oxidative enzymes.

pesticides Chemicals that are applied to agricultural crops or domesticated plants and which kill or inhibit growth of insects.

petals  Usually brightly colored elements of a þower that may produce fragrant oils; nonreproductive structures that attract pollinators. Sterile leaf-like (white, colorless, but usually colored) structures in flowers that serve to attract pollinators. PICTURE

petiole The generally non-leafy part of the leaf that attaches the leaf blade to the stem; celery and rhubarb are examples of a leaf petiole that we use as food. The stalk connecting the leaf blade to the stem. PICTURE

petrifaction Mode of fossilization where f organic matter is replaced with silica.

PGA (phosphoglycerate)  A three-carbon molecule formed when carbon dioxide is added to ribulose biphosphate (RuBP) during the dark reaction of photosynthesis (Calvin, or Calvin-Benson Cycle). PGA is converted to PGAL, using ATP and NADPH.

PGAL (phosphoglyceraldehyde)   A substance formed from PGA during the dark reaction of photosynthesis. Some PGAL leaves the cycle and can be converted to glucose, while other PGAL molecules are used to reform ribulose biphosphate (RuBP) to continue the dark reaction.

pH The negative logarithm of the H+ ion concentration. The pH is a measure of the acidity or basic character of a solution. Since it measures a fraction, the larger the pH number, the less H ions are present in a solution. PICTURE

phagocytes  White blood cells that can engulf (by phagocytosis) and destroy microorganisms including viruses and bacteria; cells in this category include neutrophils and monocytes.

phagocytosis  A form of endocytosis in which white blood cells surround and engulf invading bacteria or viruses. PICTURE

pharynx  The passageway between the mouth and the esophagus and trachea. Food passes from the pharynx to the esophagus, and air passes from the pharynx to the trachea.

phenotype  The observed properties or outward appearance of a trait. The physical expression of the alleles posessed by an organism.

pheromones  Chemical signals that travel between organisms rather than between cells within an organism; serve as a form of communication between animals.

phloem  Tissue in the vascular system of plants that moves dissolved sugars and other products of photosynthesis from the leaves to other regions of the plant. Phloem tissue consists of cells called sieve tubes and companion cells. Cells of the vascular system in plants that transport food from leaves to other areas of the plant. PICTURE 1 | PICTURE 2 | PICTURE 3

phosphate group A chemical group composed of a central phosphorous bonded to three or four oxygens. The net charge on the group is negative. PICTURE

phospholipids  Asymmetrical lipid molecules with a hydrophilic head and a hydrophobic tail. Lipids with a phosphate group in place of one of the three fatty acid chains. Phospholipids are the building blocks of cellular membranes. Phospholipids have hydrophilic heads (glycerol and phosphate) and hydrophobic tails (the non-polar fatty acids). PICTURE

phosphorylation The chemical attachment of phosphorous to a molecule, usually associated with the storage of energy in the covalent bond that is also formed. Example: attachment of the third phosphate group to ADP in the formation of the higher energy form, ATP. Photophosphorylation is a type of phosphorylation associated with the formation of ATP in the photosynthesis process.

photic zone  The layer of the ocean that is penetrated by sunlight; extends to a depth of about 200 meters.

photoperiodism  The ability of certain plants to sense the relative amounts of light and dark in a 24-hour period; controls the onset of þowering in many plants.

photosynthesis  The process by which plant cells use solar energy to produce ATP. The conversion of unusable sunlight energy into usable chemical energy, associated with the actions of chlorophyll. PICTURE

photosystems  Clusters of several hundred molecules of chlorophyll in a thylakoid in which photosynthesis takes place. Eukaryotes have two types of photosystems: I and II. The series of green photoreceptive pigments involved in the light reactions, which occur in the thylakoids of the chloroplast (in eukaryotes). Energy from light is passed to the electrons as they move through the photosystem pigments. PICTURE 1 | PICTURE 2 | PICTURE 3 | PICTURE 4

phototrophs  Organisms that use sunlight to synthesize organic nutrients as their energy source; e.g., cyanobacteria, algae, and plants.

phototropism  The reaction of plants to light in which the plants bend toward the light. Plant response to light by unequal growth caused by concentration of the plant hormone Indole Acetic Acid (IAA, an auxin) on the darker side of the plant shoot. PICTURE

phycocyanin An accessory pigment found in cyanobacteria and the chloroplasts of red algae.

phycoerythrin An accessory pigment found in cyanobacteria and the chloroplasts of red algae.

phylogeny 1) the study of evolutionary relationships within a monophyletic group. 2) evolutionary hypotheses represented as a dendrogram or branching diagram. PICTURE 1 | PICTURE 2

phylogenetic Pertaining to a phylogeny.

phylum  The broadest taxonomic category within kingdoms (pl.: phyla). PICTURE

phytochrome  A pigment in plant leaves that detects day length and generates a response; partly responsible for photoperiodism.

phytoplankton  A þoating layer of photosynthetic organisms, including algae, that are an important source of atmospheric oxygen and form the base of the aquatic food chain.

pilus Projection from surface of a bacterial cell (F+) that can donate genetic material to another (F-).

pineal gland  A small gland located between the cerebral hemispheres of the brain that secretes melatonin.

pioneer community  The initial community of colonizing species.

pistil Female reproductive structures in flowers, consisting of the stigma, style, and ovary. Also known as a carpel in some books. PICTURE 1 | PICTURE 2

pith Central area in plant stems, largely composed of parenchyma tissue modified for storage. PICTURE 1 | PICTURE 2

pituitary gland  A small gland located at the base of the brain; consists of an anterior and a posterior lobe and produces numerous hormones. The master gland of the endocrine system, the pituitary releases hormones that have specific targets as well as those that stimulate other glands to secrete hormones. Part of the pituitary is nerve tissue, the rest is glandular epithelium. PICTURE 1 | PICTURE 2

placenta  An organ produced from interlocking maternal and embryonic tissue in placental mammals; supplies nutrients to the embryo and fetus and removes wastes.

placental mammals One of three groups of mammals that carry their young in the mother's body for long periods during which the fetus is nourished by the placenta. Humans are placental mammals.

planaria  Small free-living þatworms (Phylum Platyhelminthes) with bilateral symmetry and cephalization. The freshwater type is often used as an experimental organism.

planktonic organisms  "Floaters"; one of the two main types of organisms in the pelagic zone of the marine biome.

Plantae The plant kingdom; nonmobile, autotrophic, multicellular eukaryotes. Kingdom of the plants, autotrophic eukaryotes with cellulose in their cell walls and starch as a carbohydrate storage product, with chlorophylls a and b as photosynthesis pigments. PICTURE

plasma  The liquid portion of the blood. Along with the extracellular þuid, it makes up the internal environment of multicellular organisms.

plasma cells  Cells produced from B cells that synthesize and release antibodies. PICTURE

plasmids  Self-replicating, circular DNA molecules found in bacterial cells; often used as vectors in recombinant DNA technology. Small circles of double-stranded DNA found in some bacteria. Plasmids can carry from four to 20 genes. Plasmids are a commonly used vector in recombinant DNA studies. PICTURE

plasmodesmata  Junctions in plants that penetrate cell walls and plasma membranes, allowing direct communication between the cytoplasm of adjacent cells (sing.: plasmodesma).

plasmolysis Osmotic condition in which a cell loses water to its outside environment.

plastids  Membrane-bound organelles in plant cells that function in storage (of food or pigments) or food production. Term for any double membrane-bound organelle. Chloroplasts contain the chemicals for photosynthesis, amyloplasts (also known as leukoplasts) store starch, chromoplasts contain colorful pigments such as in the petals of a flower or epidermis of a fruit.

platelets  In vertebrates, cell fragments that bud off from the megakaryocytes in the bone marrow; carry chemicals needed for blood clotting. Cell fragment functioning in blood clotting.

plate tectonics  The movement of the plates that make up the surface of the Earth. The revolutionary paradigm in geology that the earth's crust is composed of rigid segments (plates) in constant (although considered slow in a human-scale time frame) motion (tectonics) relative to each other.

pleiotropic A term describing a genotype with multiple phenotypic effects. For example: sickle-cell anemia produces a multitude of consequences in those it affects, such as heart disease, jidney problem, etc.

Pleistocene The first geologic epoch of the Quaternary Period of the Cenozoic Era that ended 10,000 years ago with the retreat of the last glaciers. PICTURE

pleura  A thin sheet of epithelium that covers the inside of the thoracic cavity and the outer surface of the lungs.

pleural cavity  The space between the sheets of pleura (one covering the inside of the thoracic cavity, the other covering the outside of the lungs).

polar covalent bond  A covalent bond in which atoms share electrons in an unequal fashion. The resulting molecule has regions with positive and negative charges. The presence of polar covalent bonds allows other polar molecules to surround molecule: example: glucose sugar in water.

pollen grains  The containers for male gametophytes of seed plants produced in a microsporangium by meiosis. Microspores produced by seed plants that contain the male gametophyte. PICTURE

pollen tube Structure produced by the tube nucleus in the pollen grain through which the sperm nucleus (or nuclei in angiosperms) proceed to travel through to reach the egg. PICTURE

pollination The transfer of pollen from the anthers to the stigma by a pollinating agent such as wind, insects, birds, bats, or in a few cases the opening of the flower itself.

polygenic inheritance  Occurs when a trait is controlled by several gene pairs; usually results in continuous variation. PICTURE

polymer Organic molecule composed of smaller units known as monomers. A large molecule composed of smaller subunits, for example starch is a polymer of glucose, proteins are polymers of amino acids.

polymerase chain reaction (PCR)  A method of amplifying or copying DNA fragments that is faster than cloning. The fragments are combined with DNA polymerase, nucleotides, and other components to form a mixture in which the DNA is cyclically amplified.

polynucleotides  Long chains of nucleotides formed by chemical links between the sugar and phosphate groups.

polyp  The sessile form of life history in cnidarians; e.g., the freshwater hydra.

polyploidy  Abnormal variation in the number of chromosome sets. The condition when a cell or organism has more than the customary two sets of chromosomes. This is an especially effective speciation mechanism in plants since the extra chromosomes will establish reproductive isolation with the parental population(s), an essential for speciation. PICTURE 1 | PICTURE 2

polysaccharides  Long chains of monosaccharide units bonded together; e.g., glycogen, starch, and cellulose. PICTURE

pons  The region that, with the medulla oblongata, makes up the hindbrain, which controls heart rate, constriction and dilation of blood vessels, respiration, and digestion. PICTURE

population  A group of individuals of the same species living in the same area at the same time and sharing a common gene pool. A group of potentially interbreeding organisms in a geographic area.

population dynamics  The study of the factors that affect the growth, stability, and decline of populations, as well as the interactions of those factors.

portal system  An arrangement in which capillaries drain into a vein that opens into another capillary network.

positive feedback Biochemical control where the accumulation of the product stimulates production of an enzyme responsible for that product's production.

positive feedback control  Occurs when information produced by the feedback increases and accelerates the response.

precambrian Informal term describing 7/8 of geologic time from the beginning of the earth to the beginning of the Cambrian Period of the Paleozoic Era. During this time the atmosphere and oceans formed, life originated (or possibly "colonized" Earth), eukaryotes and simple animals evolved and by the end of the precambrian they began to accumulate hard preservable parts, the common occurrence of which marks the beginning of the Cambrian. PICTURE

precipitation  The part of the hydrologic cycle in which the water vapor in the atmosphere falls to Earth as rain or snow.

predation  One of the biological interactions that can limit population growth; occurs when organisms kill and consume other living organisms.

predatory release  Occurs when a predator species is removed from a prey species such as by great reduction in the predator's population size or by the migration of the prey species to an area without major predators. The removal of the predator releases the prey from one of the factors limiting its population size.

prehensile movement  The ability to seize or grasp.

prenatal testing  Testing to detect the presence of a genetic disorder in an embryo or fetus; commonly done by amniocentesis or chorionic villi sampling.

presymptomatic screening  Testing to detect genetic disorders that only become apparent later in life. The tests are done before the condition actually appears, such as with Huntington disease.

prey switching  The tendency of predators to switch to a more readily available prey when one prey species becomes rare; allows the Þrst prey population to rebound and helps prevent its extinction.

primary cell wall  The cell wall outside the plasma membrane that surrounds plant cells; composed of the polysaccharide cellulose.

primary body Those parts of a plant produced by the shoot and root apical meristems.

primary compounds Chemicals made by plants and needed for the plant's own metabolism.

primary growth Cells produced by an apical meristem. The growth a plant by the actions of apical meristems on the shoot and root apices in producing plant primary tisues.

primary macronutrients  Elements that plants require in relatively large quantities: nitrogen, phosphorus, and potassium.

primary meristems The apical meristems on the shoot and root apices in plants that produce plant primary tissues.

primary root  The Þrst root formed by a plant.

primary structure  The sequence of amino acids in a protein. PICTURE

primates The taxonomic order of mammals that includes prosimians (lemurs and tarsiers), monkeys, apes, and humans; characteristics include large brain, stereoscopic vision, and grasping hand.

principle of independent assortment  Mendel's second law; holds that during gamete formation, alleles in one gene pair segregate into gametes independently of the alleles of other gene pairs. As a result, if enough gametes are produced, the collective group of gametes will contain all combinations of alleles possible for that organism.

principle of segregation  Mendel's Þrst law; holds that each pair of factors of heredity separate during gamete formation so that each gamete receives one member of a pair.

prions  Infectious agents composed only of one or more protein molecules without any accompanying genetic information.

producers  The Þrst level in a food pyramid; consist of organisms that generate the food used by all other organisms in the ecosystem; usually consist of plants making food by photosynthesis.

progesterone One of the two female reproductive hormones secreted by the ovaries.

prokaryote  Type of cell that lacks a membrane-bound nucleus and has no membrane organelles; a bacterium. Prokaryotes are more primitive than eukaryotes. Cells lacking membrane-bound organelles and having a single circular chromosome, and ribosomes surrounded by a cell membrane. Prokaryotes were the first forms of life on earth, evolving over 3.5 billion years ago.

prolactin  A hormone produced by the anterior pituitary; secreted at the end of pregnancy when it activates milk production by the mammary glands.

promoter  The speciÞc nucleotide sequence in DNA that marks the beginning of a gene. PICTURE

prophase  1) The Þrst stage of mitosis during which chromosomes condense, the nuclear envelope disappears, and the centrioles divide and migrate to opposite ends of the cell. 2) The first stage of mitosis and meiosis (although in meiosis this phase is denoted with either a roman numeral I or II) where the chromatin condenses to form chromosomes, nucleolus dissolves, nuclear envelope dissolves, and the spindle begins to form. PICTURE

prostaglandins  A class of fatty acids that has many of the properties of hormones; synthesized and secreted by many body tissues and have a variety of effects on nearby cells.

prostate gland  A gland that is located near and empties into the urethra; produces a secretion that enhances sperm viability. Gland involved in the reproductive system in males, the prostate secretes a sperm activating chemical into the semen during the arousal/ejaculation response. PICTURE

proteinoids  Polymers of amino acids formed spontaneously from inorganic molecules; have enzyme-like properties and can catalyze chemical reactions.

proteins  Polymers made up of amino acids that perform a wide variety of cellular functions. One of the classes of organic macromolecules that function as structural and control elements in living systems. Proteins are polymers of amino acids linked together by peptide bonds.

prothallus  In ferns, a small heart-shaped bisexual gametophyte. PICTURE

Protista The taxonomic Kingdom from which the other three eukaryotic kingdoms (Fungi, Animalia and Plantae) are thought to have evolved. The earliest eukaryotes were single-celled organisms that would today be placed in this admittedly not monophyletic group. The endosymbiosis theory suggests that eukaryotes may have evolved independently several times.

protists  Single-celled organisms; a type of eukaryote. Protista

proton  A subatomic particle in the nucleus of an atom that carries a positive charge. The positively charged (+1) subatomic particle located in the atomic nucleus and having a mass slightly less than that of a neutron. Elements differ by the number of protons in their atoms.

protostomes  Animals in which the Þrst opening that appears in the embryo becomes the mouth; e.g., mollusks, annelids, and arthropods.

protozoa Single-celled protists grouped by their method of locomotion. This group includes Paramecium, Amoeba, and many other commonly observed protists. PICTURE 1 | PICTURE 2

proximal tubule  The winding section of the renal tubule where most reabsorption of water, sodium, amino acids, and sugar takes place. PICTURE

pseudocoelom  In nematodes, a closed þuid-containing cavity that acts as a hydrostatic skeleton to maintain body shape, circulate nutrients, and hold the major body organs.

pseudocoelomates  Animals that have a body cavity that is in direct contact with the outer muscular layer of the body and does not arise by splitting of the mesoderm; e.g., roundworms.

pseudopodia  Temporary cytoplasmic extensions from a cell that enables it to move (sing.: pseudopodium). PICTURE

pulmonary artery  The artery that carries blood from the right ventricle of the vertebrate heart to the lungs. Artery carrying oxygen-poor blood from the heart to the lungs. PICTURE

pulmonary circuit  The loop of the circulatory system that carries blood to and from the lungs. PICTURE

pulmonary vein  The vein that carries oxygenated blood from the lungs to the left atrium of the heart. Veins carrying oxygenated blood from the lungs to the heart. PICTURE

punctuated equilibrium  A model that holds that the evolutionary process is characterized by long periods with little or no change interspersed with short periods of rapid speciation.

purine One of the groups of nitrogenous bases that are part of a nucleotide. Purines are adenine and guanine, and are double-ring structures. PICTURE

pyloric sphincter  The ring of muscle at the junction of the stomach and small intestine that regulates the movement of food into the small intestine. PICTURE

pyrimidine One of the groups of nitrogenous bases that are part of a nucleotide. Pyrimidines are single ringed, and consist of the bases thymine (in DNA), uracil (replacing thymine in RNA), and cytosine. PICTURE

quantum models of speciation  Models of evolution that hold that speciation sometimes occurs rapidly as well as over long periods, as the classical theory proposed.

Quaternary Period The most recent geologic period of the Cenozoic Era, the Quaternary began 2 million years ago with the growth of northern hemisphere continental glaciers and the ice age. PICTURE

quaternary structure  In some proteins, a fourth structural level created by interactions with other proteins. Aspect of protein structure determined by the number and arrangement of polypeptides in a large protein such as hemoglobin. PICTURE


Text ©1992, 1994, 1995, 1997, 1998, 1999, 2000, M.J. Farabee, all rights reserved.

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