Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

G:24 Glossary
pathogen (adjective pathogenic) An organism, cell, virus, or
prion that causes disease.
pathogen-associated molecular patterns (PAMPs)
Microbe-associated molecules, either not present or
sequestered in the host organism, that often occur in repeating
patterns that are recognized by pattern recognition receptors
(PRRs) in or on cells of the innate immune system. PAMPs are
present in various microbial molecules, including nucleic acids,
lipids, polysaccharides, and proteins.
pattern recognition receptor (PRR) Receptor present on
or in cells of the innate immune system that recognizes and is
activated by microbial pathogen-associated molecular patterns
(PAMPs).
PDZ domain Protein-binding domain present in many
scaffold proteins, and often used as a docking site for
intracellular tails of transmembrane proteins. (Figure 19–22)
pectin Mixture of polysaccharides rich in galacturonic acid
which forms a highly hydrated matrix in which cellulose is
embedded in plant cell walls. (Figure 19–63)
peripheral (secondary) lymphoid organ Lymphoid organ
in which T cells and B cells interact and respond to foreign
antigens. Examples are spleen, lymph nodes, and mucosalassociated
lymphoid organs. (Figure 24–12)
peroxins Form a protein translocator that participates in the
import of proteins into peroxisomes.
peroxisome Small membrane-bounded organelle that uses
molecular oxygen to oxidize organic molecules. Contains some
enzymes that produce and others that degrade hydrogen
peroxide (H 2 O 2 ). (Figure 12–27)
pH scale Common measure of the acidity of a solution: “p”
refers to power of 10, “H” to hydrogen. Defined as the negative
logarithm of the hydrogen ion concentration in moles per liter
(M). pH = –log [H + ]. Thus a solution of pH 3 will contain 10 –3 M
hydrogen ions. pH less than 7 is acidic and pH greater than 7 is
alkaline.
phagocytosis Process by which unwanted cells, debris, and
other bulky particulate material is endocytosed (“eaten”) by a
cell. Prominent in carnivorous cells, such as Amoeba proteus,
and in vertebrate macrophages and neutrophils. From Greek
phagein, to eat.
phagosome Large intracellular membrane-enclosed vesicle
that is formed as a result of phagocytosis. Contains ingested
extracellular material. (Figure 13–61)
phase variation The random switching of phenotype and
expression of proteins involved in infection at frequencies much
higher than mutation rates.
phase-contrast microscope Type of light microscope that
exploits the interference effects that occur when light passes
through material of different refractive indices. Used to view
living cells. (Figure 9–7)
phenotype The observable character (including both physical
appearance and behavior) of a cell or organism.
(Panel 8–2, p. 486)
phosphatidylinositol 4,5-bisphosphate [PI(4,5)P 2 , PIP 2 ]
Membrane inositol phospholipid (a phosphoinositide) that is
cleaved by phospholipase C into IP 3 and diacylglycerol at the
beginning of the inositol phospholipid signaling pathway. It can
also be phosphorylated by PI 3-kinase to produce PIP 3 docking
sites for signaling proteins in the PI-3-kinase–Akt signaling
pathway. (Figures 15–28 and 15–53)
phosphoglyceride Phospholipid derived from glycerol,
abundant in biomembranes. (Figures 10–2 and 10–3)
phosphoinositide A lipid containing a phosphorylated inositol
derivative. Minor component of the plasma membrane, but
important in demarking different membranes and for intracellular
signal transduction in eukaryotic cells. (Figure 15–52)
phosphoinositide 3-kinase (PI 3-kinase) Membrane-bound
enzyme that is a component of the PI-3-kinase–Akt intracellular
signaling pathway. It phosphorylates phosphatidylinositol
4,5-bisphosphate at the 3 position on the inositol ring to
produce PIP 3 docking sites in the membrane for other
intracellular signaling proteins. (Figure 15–53)
phosphoinositides (PIPs; phosphatidylinositol
phosphates) A lipid containing a phosphorylated inositol
derivative. Minor component of the plasma membrane, but
important in demarking different membranes and for intracellular
signal transduction in eukaryotic cells. (Figure 13–10)
phospholipase C (PLC) Membrane-bound enzyme that
cleaves inositol phospholipids to produce IP 3 and diacylglycerol
in the inositol phospholipid signaling pathway. PLCβ is activated
by GPCRs via specific G proteins, while PLCγ is activated by
RTKs. (Figure 15–55)
phospholipid The main category of lipids used to construct
biomembranes. Generally composed of two fatty acids linked
through glycerol (or sphingosine) phosphate to one of a variety
of polar groups. (FIgure 10–3, and Panel 2–5, pp. 98–99)
phosphorylation Reaction in which a phosphate group is
covalently coupled to another molecule.
photoactivation Technique for studying intracellular
processes in which an inactive form of a molecule of interest
is introduced into the cell, and is then activated by a focused
beam of light at a precise spot in the cell. (Figure 9–28)
photochemical reaction center The part of a photosystem
that converts light energy into chemical energy in
photosynthesis. (Figure 14–44)
photosynthetic electron-transfer reactions Light-driven
reactions in photosynthesis in which electrons move along an
electron-transport chain in a membrane, generating ATP and
NADPH.
photosystem Multiprotein complex involved in
photosynthesis that captures the energy of sunlight and
converts it to useful forms of energy: a reaction center plus an
antenna (Figure 14–45)
phototropin Photoprotein associated with the plant plasma
membrane that senses blue light and is partly responsible for
phototropism.
phragmoplast Structure made of microtubules and actin
filaments that forms in the prospective plane of division of a
plant cell and guides formation of the cell plate. (Figure 17–49)
phytochrome Plant photoprotein that senses light via a
covalently attached light-absorbing chromophore, which
changes its shape in response to light and then induces a
change in the protein’s conformation. Plant phytochromes are
dimeric, cytoplasmic serine/threonine kinases, which respond
differentially and reversibly to red and far-red light to alter cell
behavior.
PI-3-kinase–Akt pathway Intracellular signaling pathway
that stimulates animal cells to survive and grow. (Figure 15–53)
pinocytosis Literally, “cell drinking.” Type of endocytosis
in which soluble materials are continually taken up from the