Life's Ratchet: How Molecular Machines Extract Order from Chaos (44 page)

enzyme
Protein-based catalyst; protein that can facilitate a reaction by lowering the reaction’s activation barrier.

equilibrium
In thermodynamics, the state at which entropy is maximum, free energy is minimum, and no more useful work can be extracted from a system. Characterized by uniform temperature and pressure.

evolution
Process by which new proteins, molecular machines, or organisms arise. Novelty is produced by mutations, which are then acted upon by selection. Acts like a “ratchet,” leading to increasing complexity.

feedback loop
The interaction of products of a process with the precursors of a process via allostery, whereby the amount of product is controlled. Feedback loops are the basic component of the chemical “circuitry” that regulates cells.

Feynman’s ratchet
An automated version of Maxwell’s demon, which could extract energy from a system at equilibrium, thus violating the second law of thermodynamics. Shown to be impossible.

first law of thermodynamics
Law of energy conservation, which explicitly includes heat as a type of energy.

fluorescence
Emission of longer-wavelength light by a molecule in response to excitation by shorter-wavelength light.

fluorophore
Molecule that emits visible light when excited by light of shorter wavelength (fluorescence). Used to label molecules so that their behavior can be observed in an optical microscope.

food calorie
Energy unit, equals 4,184 joules.

force
A push or pull that either deforms an object or changes its state of motion. The unit of force is the newton (N).

free energy
Energy that is available to do work. Equals total energy minus unusable, dispersed energy. The latter is given by the product of entropy and temperature.

Gedankenexperiment
Posing a hypothetical situation to see if a physical theory makes sense. From a German word meaning “thought experiment.”

gene
A unit of hereditary information. A complete sequence of information in the genome, encoded in DNA.

genetic code
The code that DNA uses to encode amino acid sequences of proteins.

head
Term for the motor domain of a motor protein, specifically, the part on which it walks.

helicase
Molecular machine that untwists and separates DNA strands during replication.

holism
The view that systems have to be studied as a whole, without being broken into parts.

hydrophilic
Molecules that lower their free energy when dissolved in water. Can either form hydrogen bonds with water, or are charged.

hydrophobic
Molecules that experience an increase in free energy when placed in water, and do therefore not dissolve in water.

irritability
The property of living tissue to react to external stimuli such as electrical currents.

kinesin
Family of molecular motors that move on microtubules. Responsible for moving cargo or assisting in cell division.

kinetic theory
A precursor to statistical mechanics; the application of statistics to the motion of atoms in gases.

Landauer’s limit
The minimum energy required to erase one bit of information.

laser tweezers
Laser-based force measurement technique using a small bead suspended in focused laser light.

ligase
Enzyme that splices parts of DNA together.

lipids
Amphiphilic molecules, which form micelles or vesicles and are the main constituent of cell membranes. Consist of a hydrophobic fatty acid bound to a hydrophilic head group.

loose coupling
The ability of a molecular motor to move variable distance for each ATP consumed. Such a motor must periodically detach from the track and move as a Brownian ratchet.

Loschmidt’s demon
A hypothetical creature that could reverse time.

macrostate
The externally measurable state of a system, which is necessarily an average over many atoms and molecules. Usually described in terms of macroscopic quantities like temperature or pressure.

Maxwell’s demon
Hypothetical creature that could sort molecules and violate the second law of thermodynamics. Shown to be impossible.

messenger RNA (mRNA)
RNA that carries the information to make a protein from DNA in the cell nucleus to the ribosomes outside the nucleus.

micelle
Spherical assembly of amphiphilic molecules.

micrometer
One-millionth of a meter. Typical size of a bacterium.

microstate
The exact state of a system; includes the location and speeds of all atoms in the system.

microtubules
Stiff, protein-based fibers that make up part of the skeleton of the cell. Kinesin and dynein move on microtubules. Microtubules play an important role during cell division.

mitochondria
Power plants of cells. This is where sugar is broken down and the energy contained is transferred to ATP.

mitosis
Cell division.

MMP (matrix metalloprotease)
An enzyme that breaks down the extracellular matrix and frees up cells so they can move. Some MMPs have been shown to be molecular machines that derive their energy from eating collagen.

molecular machine
Molecule that can transform energy from one form to another.

molecular motor
Molecular machine that transforms chemical into mechanical energy.

molecular storm
Random thermal motion of atoms and molecules.

molecule
Tightly bonded assembly of at least two atoms. In biological cells, some molecules, such as DNA or proteins, can be very large, containing many thousands of atoms.

mutation
Irreversible change in a gene; the result of a chemical reaction of DNA with an ion or a radical (atoms, molecules, or ions with unpaired electrons).

myosin
Family of molecular motors that move on actin. Myosin II is responsible for muscle contraction, while myosin V transports cargo within cells.

nanobots
Hypothetical nanoscale machines that can perform complex tasks, especially with medical applications.

nanometer
One-billionth of a meter. Typical size of a small molecule.

nanoscale
The scale of the nanometer.

nanoscience
The science of nanoscale objects.

nanotechnology
Technology that involves nanoscale structures or materials.

normal distribution
Distribution expected for measurements that depend on several statistically independent influences. This universal distribution is found in physics, biology, economics, and other fields.

nucleotide
Molecule that makes up a “letter” in the genetic code. Part of DNA and RNA. There are four nucleotides in DNA: adenine, guanine, thymine, and cytosine, denoted by the letters A, G, T, and C.

open system
Systems that can exchange energy or matter, or both, with the environment; as opposed to isolated systems.

perpetuum mobile
Machine that could violate the first, or at least the second, law of thermodynamics. Found to be impossible.

polymerase
Molecular machine that makes (polymerizes) DNA or RNA.

power
Rate of transformation of energy into a different form, or rate of work performed. Energy per second. The unit of power is the watt (W); 1 watt = 1 joule per second.

pressure
Force per unit area. In a gas, pressure is the result of many collisions of atoms with a wall.

probability
The likelihood of the occurrence of an event; given by the number of ways the event could occur, divided by all possible outcomes.

processivity
The ability of a molecular motor to move on a molecular track for long distances without detaching.

protein
A large molecule consisting of a folded strand of amino acids connected by peptide bonds. Proteins fold into specific shapes, which allow them to fulfill many tasks in cells, including acting as enzymes, molecular machines, or structural elements (collagen, actin, etc.).

protein folding
Physical process in which a chain of amino acids folds into its lowest free-energy state to form a functional protein.

quantum mechanics
Physical theory that describes atoms, electrons, and subatomic particles. Fundamentally based on probabilities.

reductionism
A method in which systems are analyzed by breaking them into smaller parts.

replication
The copying of DNA during cell division.

ribosome
RNA-based machine in our cells that produces proteins according to instruction contained in DNA.

RNA (ribonucleic acid)
Molecule that can both carry information and act as a catalyst. Plays many roles in cells, from information carrier to protein production machines (ribosome).

scanning probe microscopy
Type of microscopy where a sharp probe “feels” a surface to generate an image or to measure surface properties.

scanning tunneling microscopy
A type of scanning probe microscopy that measures tunneling currents between a sharp metallic needle and a conducting surface. Can provide images of atoms.

second law of thermodynamics
Law that states that in a closed system, entropy can never decrease, but generally tends to increase during energy transformations. There are many alternative formulations of this law.

statistical mechanics
The application of statistical methods to the motions of atoms and molecules. Averaging over many atoms and molecules leads to the macroscopic science of thermodynamics.

systems biology
Mathematical theory of regulation and computation in living cells.

temperature
The average kinetic energy of atoms or molecules in a system at equilibrium.

thermodynamics
The science of heat and energy, volume, pressure, and temperature.

tight coupling
The exact coupling of ATP hydrolysis to the motion of a molecular motor. Typically implies that one ATP is hydrolyzed for each step taken by the motor. Associated with motors that have at least one part of the motor attached to the track at all times. As opposed to loose coupling.