Goldfarb D. Biophysics DeMYSTiFied
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352 Biophysics D e mystifieD
Cooperative unit length In a polymer undergoing a cooperative transition, the
number of residues that tend, on average, to undergo the transition together.
Cooperativity
The occurrence of separate events together in a nonindepen-
dent, relatively all-or-none manner.
Cotransport Active transport that involves transporting more than one type of
molecule or ion.
Cotransporter
A transport protein that mediates the simultaneous transport
(cotransport) of more than one type of molecule or ion.
Covalent bond A bond that holds two atoms together by virtue of one or more
pairs of valence electrons being shared by the two atoms.
Cristae
Membranous folds that fold in toward the center of a mitochondrion.
Critical flow velocity The velocity at which fluid flow changes from laminar to
turbulent.
Cross-linking
A covalent connecting of otherwise distant parts of a
molecule.
Crystal An orderly, three-dimensional, repeating arrangement of atoms or mol-
ecules.
Cumulative probability
The combined probability (the sum of the probabili-
ties) of one or more states or distributions of a system, from the first state or
distribution, up to and including a specified state or distribution of the sys-
tem. For cumulative probability to be meaningful, the sequence of the states
or distributions (i.e., the definition of first, last, and how to get from first to
last) must be specified.
Current clamp
A technique used in electrophysiology to measure and char-
acterize electric voltages across cell membranes by holding the current
constant.
Cytoplasm
The inside of a cell (excluding the inside of membrane-bound
organelles; although membrane-bound organelles, such as the nucleus and
mitochondria, are themselves in the cytoplasm, the insides of membrane-
bound organelles are typically not considered part of the cytoplasm).
Cytoskeleton
Fibrous tubelike and ropelike, sometimes interconnected, struc-
tures inside cells that support, transmit, or apply forces within the cell. (See
also microtubule, intermediate filament, microfilament, and tubulin.)
Degeneracy
In statistical mechanics, for a particular energy level, the number
of different states of a system that have that same particular energy.
Glossary 353
Delocalized electrons Electrons that are able to move about an entire mol-
ecule, or section of a molecule (as opposed to being held within the
region surrounding only one atom, or two adjacent covalently bonded
atoms).
Denatured
The state of a protein or nucleic acid that has unfolded, so that it
is no longer in its native state.
Denaturing agent
A substance or environmental condition that destabilizes a
higher-order structure (quaternary, tertiary, and/or secondary structure) in
proteins or nucleic acids, causing them to unfold out of their native state.
Deoxycarbohydrate
A carbohydrate that is missing one oxygen atom, that is, a
molecule made of carbon, hydrogen, and oxygen, in the ratio C
n
H
2n
O
n21
. See
also carbohydrate.
Deoxyribose
A 5-carbon deoxycarbohydrate, whose ring form is commonly
found in nucleotides.
Destructive interference The interference of two or more waves specifically in
a way that results in a smaller or less intense wave (the distance between the
peaks and troughs becomes smaller).
Dielectric constant
A measure of how easily a medium (material or substance)
is polarized by an electric field. The dielectric constant therefore also mea-
sures how easily a material or substance conducts electricity. Dielectric con-
stant is also called permittivity.
Differential scanning calorimeter
An instrument that can measure the heat
capacity of a sample as a function of temperature.
Differentiation
The process of a cell specializing and becoming a particular
type of cell.
Diffraction A phenomenon whereby light waves pass through an ordered
arrangement of openings and subsequently interfere with each other on the
other side.
Diffusion
The process of molecules or particles spreading out as a result of
their random motion. In diffusion, molecules or particles always move (over
time) from a region of higher concentration to one of lower concentration,
however, not necessarily directly or straight away, but rather somewhat grad-
ually as the result of random motion.
Dipole moment
The magnitude of the charge at either end of an electric dipole
times the fixed distance between the two charges at the opposite ends of the
electric dipole.
354 Biophysics DemystifieD
Disaccharide Two monosaccharides covalently bonded together into a single
molecule.
Disorder
In thermodynamics and statistical mechanics, order and disorder re-
late directly to the number of different ways of accomplishing one particular
thing. An ordered system is one in which there is a small number of ways to
accomplish a particular state of the system. A disordered system is one in
which there are many ways to accomplish a particular state of the system.
Dispersion forces
Intermolecular forces that arise from synchronized fluctuat-
ing charge distributions.
Distribution
In statistical mechanics, a specification of how the total energy of
a system is divided up among the particles or molecules of the system, in
terms of how many molecules have specified amounts of energy.
Disulfide bond
A covalent bond between two sulfur atoms, attaching two
cysteine residues together.
DNA (deoxyribonucleic acid) A nucleic acid whose nucleotides contain deoxy-
ribose.
DNA melting
Unwinding or denaturing of the DNA helix.
DNA polymerase An enzyme that catalyzes the biochemical reaction of cova-
lently connecting together deoxyribonucleotides to form DNA.
DNA replication
The processes whereby a cell makes a copy of its DNA.
Double bond A covalent bond in which two pairs of electrons are shared
between two atoms.
Double helix
The most common secondary structure in DNA, consisting of
two helical strands wound around each other.
Eddies Small fluid currents that flow backward, or in a partial circular motion,
opposite the direction of the overall fluid flow.
Electric dipole
Two equal and opposite charges separated by a fixed distance.
Electrolyte solution A solution containing a relatively high concentration of
ions, so that it easily conducts electricity.
Electronegative
Having the quality of a strong pull on electron clouds. Electro-
negative atoms have a tendency to form polar bonds when covalently bonded
to less electronegative atoms.
EM spectroscopy Electromagnetic spectroscopy. A technique that involves
sending some form of electromagnetic radiation into a sample, and measuring
various properties of the electromagnetic radiation that emerges from the
Glossary 355
sample. The measured property is then plotted as a function of the wave-
length or frequency of the radiation; the resulting plot is called a spectrum
(plural: spectra). See also spectroscopy.
Endocytosis
A process whereby a portion of the cell membrane folds in toward
the cell, engulfing some molecule or molecules from outside the cell. This
portion of membrane then breaks off from the membrane, forming a vesicle
that carries the engulfed contents into the cell.
Endomembrane system
A set of membranous organelles that work together
in eukaryotic cells; the endomembrane system includes the endoplasmic
reticulum, Golgi apparatus, nuclear envelope, and other membranous
organelles.
Endoplasmic reticulum
A network of folded membranes, in eukaryotic cells,
that provides a surface on which various biochemical reactions are carried
out.
Energy path
How the energy of a system changes (ups and downs) over the
course of time or throughout the duration of a process.
Enthalpy
A thermodynamic quantity equal to internal energy plus pressure-
volume energy.
Enthalpy driven A spontaneous (favorable) process in which the change in
enthalpy makes a favorable contribution to the Gibbs energy change, but the
entropy change is either unfavorable or negligible. The enthalpy change is
primarily responsible for the favorable Gibbs energy change.
Entropy
The amount of energy contained in a system that cannot be trans-
formed into work. Entropy is also a measure or the amount of disorder in a
system: the more disordered the energy of a system is, the less of that energy
can be transformed into work.
Entropy driven
A spontaneous (favorable) process in which the change in en-
tropy makes a favorable contribution to the Gibbs energy change, but the
enthalpy change is either unfavorable or negligible. The entropy change is
primarily responsible for the favorable Gibbs energy change.
Environmental biophysics
The branch of biophysics that deals with physics of
the relationship between organisms and their environment.
Enzyme
A protein that acts as a catalyst.
Ester A type of carbonyl group very similar to carboxyl, but where the hy-
droxyl hydrogen or the carboxyl group has been replaced with a carbon
atom.
356 Biophysics DemystifieD
Eukaryote An organism that has eukaryotic cells.
Eukaryotic The quality of having a cell nucleus.
Excitable tissue
Cell types, in an organism, that create or conduct electric
impulses.
Exocytosis A process whereby a vesicle inside the cell fuses with the plasma
membrane, releasing its contents to the environment outside the cell.
Expression
Transcription of a gene’s sequence into mRNA, followed by transla-
tion of the mRNA into the polypeptide or protein.
Extinction coefficient (or molar extinction coefficient) A measure of absorbance
that accounts for both the concentration and the thickness of the sample
being studied; the absorbance is expressed in units that are per concentration
and per length (M
21
cm
21
).
Fatty acid A long chain hydrocarbon with a carboxyl (carboxylic acid) group
at one end. (See also saturated, unsaturated, and polyunsaturated fatty acid.)
Favorable
A process is favorable, or spontaneous, if the Gibbs energy
change for that process is negative; that is, if the process decreases the
Gibbs energy.
First law of thermodynamics
Any change to the amount of energy contained
in a system is equal to the amount of energy put into the system minus the
amount of energy taken out of the system. In other words, energy cannot be
created or destroyed.
Fluid mosaic model
A model that describes biological membranes as composed
of a phospholipid bilayer with other molecules scattered about within the
plane of the bilayer.
Fluorescence
The emission of light, or electromagnetic radiation, from a mol-
ecule or substance.
Fluorescent tagging A technique in which a fluorophore is attached to
another molecule in order to follow that molecule through some biological
process.
Fluorophore
A molecule or the specific part of a molecule that is responsible
for the fluorescence.
Folding moderators
Molecules that assist in protein folding. Also called
chaperones.
Free energy
Energy that can be transformed into work, where work equals
force times distance. Also called available energy and Gibbs energy.
Glossary 357
Freely jointed chain A model in which each segment or residue of a chain is
free to angle and rotates relative to its adjacent segments or residues.
Fuel
A source of potential energy for a motor.
Functional group A specific group of atoms within a molecule that confers
certain functional characteristics to that molecule.
Gel A fluid that has a molecular structure that gives it properties similar to a
solid.
Gel electrophoresis
A technique used to sediment molecules through a gel via
the application of an electric field.
Gel phase
The relatively solid state of a lipid bilayer.
Gene A section of a DNA molecule that specifies the amino acid sequence for
a given protein.
Genome All of a cell’s genes (on all of its chromosomes or chromatin) taken
together as a whole.
Gibbs energy
Energy that can be transformed into work, where work equals
force times distance. Also called available energy and free energy.
Gibbs energy change The enthalpy change minus the quantity of the absolute
temperature times the entropy change DG 5 DH 2 TDS where DH is the en-
thalpy change, T is the absolute temperature, and DS is the entropy change.
Glyceride
Any of a class of molecules consisting of a glycerol molecule with a
fatty acid attached to one or more of glycerol’s three carbon atoms. The result
is a monoglyceride, diglyceride, or triglyceride.
Glycerol
A small, three-carbon carbohydrate, with a hydroxyl group attached
to each carbon atom.
Ground state
The lowest energy state of a system.
Gyrase A type of topoisomerase that catalyzes an increased negative writhe by
reducing the linking number.
Heat capacity The amount of heat required to raise the temperature of a sam-
ple by one degree.
Heat energy
Energy that results from the kinetic energy and random motion
of molecules.
Heat engine
A motor that converts heat energy into motion.
Helical repeat
In a helical polymer, the number of residues in a single turn of
the helix.
Helicase An enzyme that catalyzes the unwinding of DNA.
358 Biophysics DemystifieD
Helix-coil transition A conformational transition from a helix conformation to
a random-coil conformation; unwinding of the helix.
Heterogeneous sequence
A sequence that varies throughout the molecule and
is not repetitive.
Heteropolymer A polymer in which the residues are not all identical.
High-energy intermediate If a process causes a system to go through interme-
diate states along the way from its initial state to its final state and if one or
more intermediate states are higher in energy than the initial and end states,
then those intermediate states that are higher in energy than the initial and
end state are called high-energy intermediates.
Histone
A cluster (quaternary structure) of certain proteins that are involved
in DNA packaging by having the DNA bound to and wrapped around
them.
Homogenous sequence
A simple and repetitive sequence throughout the
molecule.
Homopolymer A polymer in which the residues are all identical.
Hydrocarbon
A molecule made up of only hydrogen and carbon.
Hydrocarbon chain A hydrocarbon molecule in which the carbon atoms are
covalently connected to one another in a line, like links in a chain.
Hydrogen bond
The attractive force between a hydrogen atom with a partial
positive charge and another atom with a partial negative charge. The two
atoms participating in the hydrogen bond (i.e. the hydrogen and the other
atom) are not directly covalently bonded together, nor are they ever cova-
lently bonded with only a single atom between them.
Hydrophilic
Having polar properties that allow a molecule to interact favor-
ably (i.e., with a negative Gibbs energy change) with water, for example,
forming hydrogen bonds with the water.
Hydrophilic force
A close-range repulsive force keeping the two hydrophilic
surfaces apart, due to a layer of water molecules between them, that results
from their strong tendency to hydrogen-bond with water.
Hydrophobic
Having nonpolar properties, and thus interacting unfavorably
(i.e., with a positive Gibbs energy change) with water.
Hydrophobic effect or hydrophobic interaction
An interaction between water
and a nonpolar substance like oil that results in configurations that minimize
contact between the water and the nonpolar substance.
Glossary 359
Hydroxyl group An oxygen atom with one hydrogen atom covalently
attached.
Immunoglobulins
Also called antibodies, proteins that can recognize and bind
to foreign objects (such as viruses and bacteria).
Induced dipole A distortion of the electron cloud of a neutral, nonpolar molecule
due to the presence of an electric field, so that the molecule becomes a dipole.
Interference
The combining of two or more waves in a specific location result-
ing in increased or decreased wave height at that location. See also construc-
tive and destructive interference.
Intermediate filament
A mid-sized tubelike or ropelike structure that is part of
the cytoskeleton.
Interphase The phase of the cell cycle where most of the cell’s energy goes into
growth and DNA replication.
Ion
An atom or molecule with a charge, due to one or more missing electrons
or due to one or more extra electrons.
Ion channel A type of transport protein that spans the bilayer and folds in a
way to create a hydrophilic tunnel through which ions and other small
hydrophilic molecules can pass.
Ionic bond
A bond that holds two atoms together due to each atom being an
ion, one positive (cation) and one negative (anion).
Ketone
A carbonyl carbon that is also directly connected to two other atoms
neither of which is hydrogen.
Laminar flow
Fluid flow in which the velocity of the fluid varies in layers, or
according to the distance from the vessel walls, due to friction.
Left-handed helix A helix that turns counterclockwise as you move along the
length of the helix.
Ligand
A smaller molecule or atom that binds to a larger molecule.
Ligand binding An association of one or more ligands (smaller molecules) with
a larger molecule, held together by non-covalent forces.
Linking number (Lk)
The number of times that one closed curve is linked to
another closed curve.
Lipid Fat or oil. A molecule characterized by being not soluble in water and
soluble in nonpolar solvents.
Lipid vesicle
A small hollow sphere of lipid molecules. The lipid molecules
making up the vesicle are organized into a lipid bilayer.
360 Biophysics De mystifieD
Lipoprotein A complex of protein and lipid, used to carry lipids to where they
are needed and able to carry lipids through places where the lipids would
otherwise be insoluble.
Liposome
A lipid bilayer sphere with a void in the middle, also called a vesicle
or lipid vesicle.
Liquid crystalline phase The relatively fluid phase of a lipid bilayer.
Lysosome
A vesicle that contains enzymes (called lysozymes) that specialize in
breaking down or digesting larger molecules.
Machine A device that can alter the direction and/or size of a force
Macromolecule
A very large molecule, often a polymer such as DNA, proteins,
carbohydrates, and phospholipids. Although there is no clear cutoff in size
that defines a molecule as a macromolecule, common usage of the word is
typically reserved for molecules that contain more than 1000 atoms.
Mechanics
The branch of physics that deals with the application of forces to
physical objects.
Membrane A thin flexible sheetlike structure that separates things. In the case
of a biological cell, membranes separate between the cell and the outside
world or within the cell between different regions of the cell.
Membrane protein
A protein that has formed a quaternary structure with a
membrane so as to become part of the membrane.
Membrane transport protein
A membrane protein that is involved (passively
or actively) in transporting other molecules across the membrane.
Micelle
A lipid ball with the hydrocarbon chains pointed in toward the center,
and the polar head groups at the surface of the ball.
Microfilament The smallest of several tubelike or ropelike structures that are
part of the cytoskeleton.
Microtubule
The largest of several tubelike structures that are part of the cy-
toskeleton.
Mitochondrion (plural: mitochondria) An organelle that carries out the role of
generating ATP molecules for use as energy currency throughout the cell.
Model
A hypothesis, guess, or theory, with some details about the mechanism
of how a system undergoes a certain process.
Molar extinction coefficient See extinction coefficient.
Molecular and subcellular biophysics
The branch of biophysics that deals with
the behavior of biomolecules and the workings of individual cells.
Glossary 361
Molecular binding An association of two or more molecules, or subunits, held
together by non-covalent forces.
Molecular interpretation
An explanation of what the molecules or particles
of a system are doing, when the system undergoes some overall change.
Monosaccharide A single unit carbohydrate (not a polymer), also called a sim-
ple sugar. (See also disaccharide, oligosaccharide, and polysaccharide.)
Most probable distribution
In statistical mechanics, the distribution that has
the largest number of ways to arrange the molecules, that is, the largest num-
ber of permutations.
Motor
A machine that also has the ability to convert potential energy into me-
chanical energy (motion).
mRNA (messenger RNA) A single-stranded RNA molecule that contains a
complementary copy of the sequence of nucleotides in a particular section of
DNA.
Native state
The state of a protein or nucleic acid that has folded into its cor-
rect functional shape where its Gibbs energy has been minimized. The native
state can include one or a small number of conformations.
Nearest-neighbor approximation
An approximation that assumes only adja-
cent residues can influence each other, but residues at a distance (or nonad-
jacent) cannot.
Negatively supercoiled
A superhelix in which writhe is negative.
Nicked duplex DNA (ndDNA) A circular, double-helical DNA with one or
more breaks in one or more strands.
Nitrogenous base
A class of organic base compounds containing nitrogen and
owing their property as a base (a compound that reduces H
+
ions) to a pair of
nonbonded electrons on a nitrogen atom. Nucleic acids contain nitrogenous
bases with aromatic ring structures categorized as purines and pyrimidines.
Nonpolymeric lipid
A lipid that is not a polymer or that does not contain a
polymer as a major portion of its structure. A nonpolymeric lipid is also called
a nonsaponifiable lipid, meaning that it cannot be broken down by the chem-
ical process of hydrolysis.
Nuclear envelope
A structure that includes both the inner and outer mem-
branes of the nucleus and the perinuclear space.
Nuclear lamina
A network of intermediate filaments, just inside the inner nu-
clear membrane, that plays a role similar to the cytoskeleton.