Key terms Flashcards
bacteriorhodopsin
Pigmented protein found in abundance in the plasma
membrane of the salt-loving archaeon Halobacterium
halobium; pumps protons out of the cell, fueled by light
energy.
cell cortex
Specialized layer of cytoplasm on the inner face of the
plasma membrane.
cholesterol
Short, rigid lipid molecule present in large amounts in the
plasma membranes of animal cells, where it makes the lipid
bilayer less flexible.
detergent
Soapy substance used to solubilize lipids and membrane
proteins.
fat droplet
Large cluster of hydrophobic fats or oils that forms inside
the cells.
glycocalyx
Protective layer of carbohydrates on the outside surface
of the plasma membrane formed by the sugar residues of
membrane glycoproteins, proteoglycans, and glycolipids.
lipid bilayer
Thin pair of closely juxtaposed sheets, composed mainly of phospholipid molecules, that forms the structural basis for
all cell membranes.
membrane domain
Functionally and structurally specialized region in the membrane of a cell or organelle; typically characterized by
the presence of specific proteins.
membrane protein
Voltage difference across a membrane due to a slight
excess of positive ions on one side and of negative ions on
the other.
phosphatidylcholine
phosphatidylcholine
Common phospholipid present in abundance in most cell
membranes; uses choline attached to a phosphate as its
head group.
phospholipid
A major type of lipid molecule in many cell
membranes. Generally composed of two fatty
acid tails linked to one of a variety of phosphatecontaining
polar groups.
plasma membrane
The protein-containing lipid bilayer that surrounds a living
cell.
saturated
Describes an organic molecule that contains a full
complement of hydrogen; in other words, no double or
triple carbon–carbon bonds.
unsaturated
Describes an organic molecule that contains one or more
double or triple bonds between its carbon atoms.
action potential
Traveling wave of electrical excitation caused by rapid,
transient, self-propagating depolarization of the plasma
membrane in a neuron or other excitable cell; also called
a nerve impulse.
active transport
The movement of a solute across a membrane against its
electrochemical gradient; requires an input of energy, such
as that provided by ATP hydrolysis.
antiport
Type of coupled transporter that transfers two different
ions or small molecules across a membrane in opposite
directions, either simultaneously or in sequence.
axon
Long, thin extension that conducts electrical signals away
from a nerve cell body toward remote target cells.
Ca2+ pump
Enzyme that phosphorylates target proteins in response to
an increase in Ca2+ ion concentration through its interaction
with the Ca2+-binding protein calmodulin.
channel
A protein that forms a hydrophilic pore
across a membrane, through which
selected small molecules or ions can
passively diffuse.
dendrite
Short, branching structure that extends from the surface of
a nerve cell and receives signals from other neurons.
depolarization
A shift in the membrane potential, making it less negative
on the inside of the cell.
electrochemical gradient
Driving force that determines which way an ion will move
across a membrane; consists of the combined influence
of the ion’s concentration gradient and the membrane
potential.
gradient-driven pump
A protein that uses energy stored in the electrochemical
gradient of ions to actively transport a solute across a
membrane.
H+ pump
A protein or protein complex that uses energy supplied by
ATP hydrolysis, an ion gradient, or light to actively move
protons across a membrane.
ion channel
Transmembrane protein that forms a pore across the lipid
bilayer through which specific inorganic ions can diffuse
down their electrochemical gradients.
k+ leak channel
Ion channel permeable to K+ that randomly flickers between
an open and closed state; largely responsible for the resting
membrane potential in animal cells.
ligand gated channel
An ion channel that is stimulated to open by the binding of
a small molecule such as a neurotransmitter
mechanically-gated channel
An ion channel that allows the passage of select ions across
a membrane in response to a physical perturbation.
membrane potential
Voltage difference across a membrane due to a slight
excess of positive ions on one side and of negative ions on
the other.
membrane transport protein
A protein associated with the lipid bilayer of a cell
membrane.
Na+ pump
Transporter found in the plasma membrane of most animal
cells that actively pumps Na+ out of the cell and K+ in using
the energy derived from ATP hydrolysis.
Nernst equation
An equation that relates the concentrations of an inorganic
ion on the two sides of a permeable membrane to the
membrane potential at which there would be no net
movement of the ion across the membrane.
nerve terminal
Structure at the end of an axon that signals to another
neuron or target cell.
Neuron
ormation as part of the nervous system; a nerve cell.
Neurotransmitter
Small signaling molecule secreted by a nerve cell at a
synapse to transmit information to a postsynaptic cell.
Examples include acetylcholine, glutamate, GABA, and
glycine.
Optogenetics
Technique that uses light to control the activity of neurons
into which light-gated ion channels have been artificially
introduced.
Osmosis
Passive movement of water across a cell membrane from
a region where the concentration of water is high (because
the concentration of solutes is low) to a region where the
concentration of water is low (and the concentration of
solutes is high).
Passive transport
oncentration gradient across a cell membrane via a
membrane transport protein, such as a channel or a
transporter.
Patch-clamp recording
Technique used to monitor the activity of ion channels in a
membrane; involves the formation of a tight seal between
the tip of a glass electrode and a small region of cell
membrane, and manipulation of the membrane potential
by varying the concentrations of ions in the electrode.
pump
Transporter that uses a source of energy, such as ATP
hydrolysis or sunlight, to actively move a solute across a
membrane against its electrochemical gradient.
resting membrane potential
Voltage difference across the plasma membrane when a
cell is not stimulated.
symport
A transporter that transfers two different solutes across a
cell membrane in the same direction.
synapse
Specialized junction where a nerve cell
communicates with another cell (such as
a nerve cell, muscle cell, or gland cell),
usually via a neurotransmitter secreted by
the nerve cell.
synaptic vesicle
Small membrane-enclosed sac filled with neurotransmitter
that releases its contents by exocytosis at a synapse.
transmitter-gated ion channel
Transmembrane receptor protein or protein complex that
opens in response to the binding of a neurotransmitter,
allowing the passage of a specific inorganic ion; its
activation can trigger an action potential in a postsynaptic
cell.
transporter
Membrane transport protein that moves a solute across a
cell membrane by undergoing a series of conformational
changes.
voltage-gated channel
Channel protein that permits the passage of selected ions,
such as Na+, across a membrane in response to changes
in the membrane potential. Found primarily in electrically
excitable cells such as nerve and muscle cells.
voltage-gated Na+ channel
rotein in the plasma membrane of electrically excitable
cells that opens in response to membrane depolarization,
allowing Na+ to enter the cell. It is responsible for action
potentials in these cells.
autophagy
Mechanism by which a cell “eats itself,” digesting molecules
and organelles that are damaged or obsolete.
clathrin
Protein that makes up the coat of a type of transport vesicle
that buds from either the Golgi apparatus (on the outward
secretory pathway) or from the plasma membrane (on the
inward endocytic pathway).
coated vesicle
Small membrane-enclosed sac that wears a
distinctive layer of proteins on its cytosolic
surface. It is formed by pinching-off of a
protein-coated region of cell membrane.
endocytosis
Process by which cells take in materials through an
invagination of the plasma membrane, which surrounds
the ingested material in a membrane-enclosed vesicle. (See
also pinocytosis and phagocytosis.)
endomembrane system
Interconnected network of membrane-enclosed organelles
in a eukaryotic cell; includes the endoplasmic reticulum,
Golgi apparatus, lysosomes, peroxisomes, and endosomes.
endoplasmic reticulum
Labyrinthine membrane-enclosed
compartment in the cytoplasm of
eukaryotic cells where lipids and
proteins are made.
endosome
Membrane-enclosed compartment of a eukaryotic cell
through which material ingested by endocytosis passes on
its way to lysosomes.
exocytosis
Process by which most molecules are secreted from
a eukaryotic cell. These molecules are packaged in
membrane-enclosed vesicles that fuse with the plasma
membrane, releasing their contents to the outside.
golgi apparatus
Membrane-enclosed organelle in eukaryotic cells that modifies the proteins and lipids made in the endoplasmic reticulum and sorts them for transport to other sites.
lysosome
Membrane-enclosed organelle that breaks down worn-out
proteins and organelles and other waste materials, as well
as molecules taken up by endocytosis; contains digestive
enzymes that are typically most active at the acid pH found
inside these organelles.
membrane-enclosed organelle
Any organelle in a eukaryotic cell that is surrounded by a
lipid bilayer—for example, the endoplasmic reticulum, Golgi
apparatus, and lysosome.
nuclear envelope
Double membrane surrounding the nucleus. Consists of
outer and inner membranes, perforated by nuclear pores.
nuclear pore
Channel through which selected large
molecules move between the nucleus
and the cytoplasm.
peroxisome
Small membrane-enclosed organelle that contains enzymes
that degrade lipids and destroy toxins.
phagocytic cell
A cell such as a macrophage or neutrophil that is specialized
to take up particles and microorganisms by phagocytosis.
phagocytosis
The process by which particulate material is engulfed
(“eaten”) by a cell. Prominent in predatory cells, such as
Amoeba proteus, and in cells of the vertebrate immune
system, such as macrophages.
pinocytosis
Type of endocytosis in which soluble materials are taken
up from the environment and incorporated into vesicles for
digestion. (Literally, “cell drinking.”)
rab protein
One of a family of small GTP-binding proteins present on
the surfaces of transport vesicles and organelles that serves as a molecular marker to help ensure that transport vesicles
fuse only with the correct membrane.
receptor-mediated endocytosis
Mechanism of selective uptake of material by animal cells
in which a macromolecule binds to a receptor in the plasma
membrane and enters the cell in a clathrin-coated vesicle.
rough endoplasmic reticulum
Region of the endoplasmic reticulum
associated with ribosomes and involved in
the synthesis of secreted and membranebound
proteins.
secretion
Production and release of a substance from a cell.
signal sequence
Amino acid sequence that directs a protein to a specific
location in the cell, such as the nucleus or mitochondria.
SNARE
One of a family of membrane proteins responsible for the
selective fusion of vesicles with a target membrane inside
the cell.
tethering protein
Filamentous transmembrane protein involved in the
docking of transport vesicles to target membranes
transport vesicle
Membrane vesicle that carries proteins from one
intracellular compartment to another—for example, from
the endoplasmic reticulum to the Golgi apparatus.
unfolded proteins response
Molecular program triggered by the accumulation of
misfolded proteins in the endoplasmic reticulum. Allows
cells to expand the endoplasmic reticulum and produce
more of the molecular machinery needed to restore proper
protein folding and processing.
vesivular transport
Movement of material between organelles in the eukaryotic
cell via membrane-enclosed vesicles.
active site
Region on the surface of an enzyme that binds to a substrate
molecule and catalyzes its chemical transformation.
allosteric
Describes a protein that can exist in multiple conformations
depending on the binding of a molecule (ligand) at a
site other than the catalytic site; such changes from one
conformation to another often alter the protein’s activity or
ligand affinity.
alpha helix
Folding pattern, common in many proteins, in which a
single polypeptide chain twists around itself to form a rigid
cylinder stabilized by hydrogen bonds between every fourth
amino acid.
amino acid sequence
The order of the amino acid subunits in a protein chain.
Sometimes called the primary structure of a protein.
antibody
Protein produced by B lymphocytes in response to a foreign
molecule or invading organism. Binds to the foreign
molecule or cell extremely tightly, thereby inactivating it or
marking it for destruction.
antigen
Molecule or fragment of a molecule that is recognized by
an antibody.
Beta sheet
olding pattern found in many proteins in which neighboring regions of the polypeptide chain associate side-by-side with each other through hydrogen bonds to give a rigid, flattened structure.
binding site
Region on the surface of a protein, typically a cavity or
groove, that interacts with another molecule (a ligand)
through the formation of multiple noncovalent bonds.
C-terminus
The end of a polypeptide chain that carries a free carboxyl
group (–COOH).
chromatography
Technique used to separate the individual molecules in a
complex mixture on the basis of their size, charge, or their
ability to bind to a particular chemical group. In a common
form of the technique, the mixture is run through a column
filled with a material that binds the desired molecule, and
it is then eluted from the column with a solvent gradient.
coiled-coil
Stable, rodlike protein structure formed when two or more
α helices twist repeatedly around each other.
conformation
Precise, three-dimensional shape of a protein or other
macromolecule, based on the spatial location of its atoms
in relation to one another.
coenzyme
Small molecule that binds tightly to an enzyme and helps it
to catalyze a reaction.
cryoelectron microscopy
Technique for observing the detailed structure of a
macromolecule at very low temperatures after freezing
native structures in ice.
disulfide bond
Covalent cross-link formed between the sulfhydryl groups
on two cysteine side chains; often used to reinforce a
secreted protein’s structure or to join two different proteins
together.
electrophoresis
Technique for separating a mixture of proteins or DNA
fragments by placing them on a polymer gel and subjecting
them to an electric field. The molecules migrate through
the gel at different speeds depending on their size and net
charge.
enzyme
A protein that catalyzes a specific chemical reaction.
feedback inhibition
A form of metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an
enzyme early in the pathway.
fibrous protein
A protein with an elongated, rodlike shape, such as collagen
or a keratin filament.
globular protein
Any protein in which the polypeptide chain folds into a
compact, rounded shape. Includes most enzymes.
GTP-binding protein
Intracellular signaling protein whose activity is determined
by its association with either GTP or GDP. Includes both
trimeric G proteins and monomeric GTPases, such as Ras.
helix
An elongated structure whose subunits twist in a regular
fashion around a central axis, like a spiral staircase.
intracellular condensate
A large aggregate of phase-separated macromolecules that
creates a region with a special biochemistry without the use
of an encapsulating membrane.
intrinsically disordered sequence
Region in a polypeptide chain that lacks a definite structure.
ligand
General term for a small molecule that binds to a specific
site on a macromolecule.
lysozyme
Enzyme that severs the polysaccharide chains that form the
cell walls of bacteria; found in many secretions including
saliva and tears, where it serves as an antibiotic.
mass spectrometry
Sensitive technique that enables the determination of the
exact mass of all of the molecules in a complex mixture.
michaelis constant
The concentration of substrate at which an enzyme works
at half its maximum velocity; serves as a measure of how
tightly the substrate is bound.
motor protein
Protein such as myosin or kinesin that uses energy derived
from the hydrolysis of a tightly bound ATP molecule to
propel itself along a protein filament or polymeric molecule.
N-terminus
The end of a polypeptide chain that carries a free α-amino
group.
nuclear magnetic resonance
Technique used for determining the three-dimensional
structure of a protein in solution.
peptide bond
Covalent chemical bond between the
carbonyl group of one amino acid and the
amino group of a second amino acid.
polypeptide, polypeptide chain
Linear polymer composed of multiple amino acids. Proteins
are composed of one or more long polypeptide chains.
polypeptide backbone
Repeating sequence of the atoms (–N–C–C–) that form the core of a protein molecule and to which the amino acid side
chains are attached.
primary structure
The amino acid sequence of a protein.
protein
Macromolecule built from amino acids that provides cells
with their shape and structure and performs most of their
activities.
protein domain
Segment of a polypeptide chain that can fold into a compact,
stable structure and that often carries out a specific function.
protein family
A group of polypeptides that share a similar amino acid
sequence or three-dimensional structure, reflecting a
common evolutionary origin. Individual members often
have related but distinct functions, such as kinases that
phosphorylate different target proteins.
protein kinase
Enzyme that catalyzes the transfer of a phosphate group
from ATP to a specific amino acid side chain on a target
protein.
protein machine
Assembly of protein molecules that operates as a
cooperative unit to perform a complex series of biological
activities, such as replicating DNA.
protein phosphatase
Enzyme that catalyzes the removal of a phosphate
group from a protein, often with high specificity for the
phosphorylated site.
protein phosphorylation
The covalent addition of a phosphate group to a side chain
of a protein, catalyzed by a protein kinase; serves as a form
of regulation that usually alters the activity or properties of
the target protein.
quaternary structure
Complete structure formed by multiple, interacting
polypeptide chains that form a larger protein molecule.
scaffold protein
Protein with multiple binding sites for other macromolecules,
holding them in a way that speeds up their functional
interactions.
secondary structure
Regular local folding pattern of a polymeric molecule. In
proteins, it refers to α helices and β sheets.
side chain
Portion of an amino acid not involved in forming peptide
bonds; its chemical identity gives each amino acid unique
properties.
substrate
A molecule on which an enzyme acts to catalyze a chemical
reaction.
subunit
A monomer that forms part of a larger molecule, such as an
amino acid residue in a protein or a nucleotide residue in
a nucleic acid. Can also refer to a complete molecule that
forms part of a larger molecule. Many proteins, for example,
are composed of multiple polypeptide chains, each of which
is called a protein subunit.
tertiary structure
Complete three-dimensional structure of a fully folded
protein.
transition state
Transient structure that forms during the course of a
chemical reaction; in this configuration, a molecule has the
highest free energy; it is no longer the substrate, but is not
yet the product.
turnover number
The maximum number of substrate molecules that an
enzyme can convert into product per second.
Vmax
The maximum rate of an enzymatic reaction, reached when
the active sites of all of the enzyme molecules in a sample
are fully occupied by substrate.
x-ray crystallography
Technique used to determine the three-dimensional
structure of a protein molecule by analyzing the diffraction
pattern produced when a beam of x-rays is passed through
an ordered array of the protein.
acetyl CoA
Activated carrier that donates the carbon atoms in its readily
transferable acetyl group to many metabolic reactions,
including the citric acid cycle and fatty acid biosynthesis;
the acetyl group is linked to coenzyme A (CoA) by a
thioester bond that releases a large amount of energy when
hydrolyzed.
Acid
A molecule that releases a proton when dissolved in water;
this dissociation generates hydronium (H3O+) ions, thereby
lowering the pH.
Actin filament
Thin, flexible protein
filament made from
a chain of globular actin molecules; a major constituent of
all eukaryotic cells, this cytoskeletal element is essential for
cell movement and for the contraction of muscle cells.
Actin-binding protein
Protein that interacts with actin monomers or filaments
to control the assembly, structure, and behavior of actin
filaments and networks.
Activated carrier
A small molecule that stores energy or chemical groups
in a form that can be donated to many different metabolic
reactions. Examples include ATP, acetyl CoA, and NADH.
activation energy
The energy that must be acquired by a molecule to undergo
a chemical reaction.
adaptation
Adjustment of sensitivity following repeated stimulation;
allows a cell or organism to register small changes in a
signal despite a high background level of stimulation.
Adenyl cyclase
Enzyme that catalyzes the formation of cyclic AMP from
ATP; an important component in some intracellular
signaling pathways.
adherens junction
Cell junction that helps hold together epithelial cells in a
sheet of epithelium; actin filaments inside the cell attach to
its cytoplasmic face
ADP
Nucleoside diphosphate produced by hydrolysis of the
terminal phosphate of ATP.
allele
An alternative form of a gene; for a given gene, many alleles
may exist in the gene pool of the species.
alternative splicing
The production of different mRNAs (and proteins) from the
same gene by splicing its RNA transcripts in different ways.
alu sequence
Family of mobile genetic elements that comprises about
10% of the human genome; this short, repetitive sequence is
no longer mobile on its own, but requires enzymes encoded
by other elements to transpose.
amino acid
Small organic molecule containing both an amino group
and a carboxyl group; it serves as the building block of
proteins.
aminoacyl-tRNA synthase
During protein synthesis, an enzyme that attaches the
correct amino acid to a tRNA molecule to form a “charged”
aminoacyl-tRNA.
amphipatic
Having both hydrophobic and hydrophilic regions, as in a
phospholipid or a detergent molecule
anabolic pathway
Series of enzyme-catalyzed reactions by which large
biological molecules are synthesized from smaller subunits;
usually requires an input of energy.
anabolism
Set of metabolic pathways by which large molecules are
made from smaller ones.
anaphase
Stage of mitosis during which the two sets of chromosomes
separate and are pulled toward opposite ends of the dividing
cell.
anaphase-promoting complex (APC/C)
A protein complex that triggers the separation of sister
chromatids and orchestrates the carefully timed destruction
of proteins that control progress through the cell cycle; the
complex catalyzes the ubiquitylation of its targets.
antenna complex
In chloroplasts and photosynthetic bacteria, the part of
the membrane-bound photosystem that captures energy
from sunlight; contains an array of proteins that bind
hundreds of chlorophyll molecules and other photosensitive
pigments.
anticodon
Set of three consecutive nucleotides in a transfer RNA
molecule that recognizes, through base-pairing, the threenucleotide
codon on a messenger RNA molecule; this
interaction helps to deliver the correct amino acid to a
growing polypeptide chain.
apical
Describes the top or the tip of a cell, structure, or organ; in an epithelial cell, for example, this surface is opposite the
base, or basal surface.
apoptosis
A tightly controlled form of programmed cell death that
allows excess cells to be eliminated from an adult or
developing organism.
archaeon
Microscopic organism that is a member of one of the
two divisions of prokaryotes; often found in hostile environments such as hot springs or concentrated brine.
Asexual reproduction
Mode of reproduction in which offspring arise from a
single parent, producing an individual genetically identical
to that parent; includes budding, binary fission, and
parthenogenesis.
Aster
Star-shaped array of microtubules emanating from a
centrosome or from a pole of a mitotic spindle.
Atom
The smallest particle of an element that still retains its
distinctive chemical properties; consists of a positively
charged nucleus surrounded by a cloud of negatively
charged electrons.
atomic weight
The mass of an atom relative to the mass of a hydrogen
atom; equal to the number of protons plus the number of
neutrons that the atom contains
ATP
Activated carrier that serves as the principal carrier of
energy in cells; a nucleoside triphosphate composed of
adenine, ribose, and three phosphate groups
ATP synthase
Abundant membrane-associated enzyme complex that
catalyzes the formation of ATP from ADP and inorganic
phosphate during oxidative phosphorylation and
photosynthesis.
Avogadro’s number
The number of molecules in a mole, the quantity of
a substance equal to its molecular weight in grams;
approximately 6 × 1023.
bacterium
Microscopic organism that is a member of one of the two
divisions of prokaryotes; some species cause disease.
The term is sometimes used to refer to any prokaryotic
microorganism, although the world of prokaryotes also
includes archaea, which are only distantly related to each
other.
Basal
Situated near the base; opposite of apical.
Basal lamina
Thin mat of extracellular matrix, secreted by epithelial cells,
upon which these cells sit.
Base
Molecule that accepts a proton when dissolved in water;
also used to refer to the nitrogen-containing purines or
pyrimidines in DNA and RNA.
base pair
Two complementary nucleotides in an RNA or a DNA
molecule that are held together by hydrogen bonds—
normally G with C, and A with T or U.
Bcl2family
Related group of intracellular proteins that regulates
apoptosis; some family members promote cell death, others
inhibit it
