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Glossary

Glossary – all lectures combined

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

A

A-factor
Also known as frequency factor and pre-exponential factor. It is the factor, conventionally designated A, which precedes the exponential term in the Arrhenius equation. It is dependent on temperature and represents the frequency of collision between reacting molecules. Its units vary according to the order of the reaction, having dimensions time–1 (usually s–1) for first order reactions and [concentration–1] [time–1] for second order reactions.
Acid
A compound containing an atom (or atoms) that can donate protons to water, forming hydronium ions (H3O+) . Also see base.
Activator
A type of transcription factor that enhances the transcription of a gene.
ADP (adenosine diphosphate)
The biological molecule which ATP is usually synthesised from, and converts back to when it loses the third phosphate during hydrolysis, a process which also releases free energy.
ATP (adenosine triphosphate)
A nucleotide that is of fundamental importance as a carrier of chemical energy in all living organisms. It consists of adenine linked D-ribose (i.e. adenosine); the D-ribose component bears three phosphate groups, linearly linked together by covalent bonds.
Ab initio wavefunction methods (quantum chemistry)
These are theoretical approaches that allow one to calculate molecular wavefunctions, typically by employing computational quantum chemistry techniques. From these fundamental calculations, molecular properties important to electron transfer theory can be calculated such as electronic couplings and reorganisation energies.
Accessory bacteriochlorophyll
Accessory antennas (including bacteriochlorophyll) are supplementary light-harvesting systems that are additional to core antennas. They are present in variable amounts (e.g. more may be necessary for organisms existing in low levels of sunlight). They are generally mobile within the organism, and are often involved in regulatory processes. The one appearing in Biological Energy Lecture 3, Slide 17, is a specific case.
Acid-base equilibrium
A chemical reaction between an acid and a base that has achieved equilibrium between a conjugate acid-base pair takes the following general form
HA + H2O ↔ H3O+ + A-
where HA is an acid (proton donor) and A is a base (proton acceptor).
Acidity constant, Ka
Also known as acid dissociation constant and defined as
Ka = [H3O+][A-]/[HA]
i.e. the ratio of the concentrations of the products to the acid in an acid-base equilibrium reaction involving a conjugate acid-base pair:
HA + H2O ↔ H3O+ + A
Actin
A globular protein found in cells; it is the monomer and fundamental unit of two types of filaments – microfilaments (component parts of the cytoskeleton) and thin filaments (part of the contractile apparatus in muscle cells). Actin participates in many important cellular processes, including muscle contraction, cell motility, cell division and cytokinesis, vesicle and organelle movement, cell signalling and the establishment and maintenance of cell junctions and shape.
Actin filament
A narrow, flexible fibre around 7 nanometres in diameter made by polymerising the protein actin. Part of the cytoskeleton within cells. Are dynamically assembled and disassembled into various structures in a living cell, giving rise to cell shape, mechanical stability and assisting with division and motion.
Activated complex
A collection of intermediate structures in a chemical reaction. During the course of the reaction, groups of atoms may pass through a range of transient configurations, not all of which will progress from reactants to products. The one configuration with the highest potential energy that can proceed to form products is termed the transition state.
The terms activated complex and transition state are frequently interchanged in texts.
Activation energy
Microscopically, it is the energy Δε required to break the existing chemical bonds of colliding reactant molecules. Macroscopically, it can be thought of as the energy barrier ΔE that must be overcome for a chemical reaction to commence, or as the minimum energy required to start a chemical reaction. ΔE is often expressed in units of in kJ mol–1.
ΔE = NA Δε, where NA is the Avogadro number.
Activationless region
That regime in the solution of the Marcus-Hush equation where the driving force ΔE0 is equal to the reorganisation energy λ,this being the regime where the most rapid electron transfer occurs.
Activator
A type of transcription factor that enhances the transcription of a gene by binding to a region of DNA called an enhancer.
Active diffusion
Diffusion where particles are driven to take steps of larger distance before their direction is randomised. In the case of motors bound to microtubules, the pre-randomisation step depends on how long the motors remain bound to the microtubule before detaching and on how fast the motors proceed along the microtubule. See also Passive Diffusion.
Acto-myosin
The molecular motor giving rise to muscle movement. Actin thin filaments and myosin thick filaments are arranged into acto-myosin fibrils which provide the apparatus for muscle contraction. By hydrolysing ATP molecules to release energy, myosin heads undergo a cycle during which they attach to thin actin filaments, exert a tension, and perform a power stroke causing the thin filaments to slide past thus shortening the muscle. Other types of non-muscle myosin also move along actin filaments during active transport inside many types of cell.
Acto-Myosin Molecular Motor
The molecular motor giving rise to muscle movement. Actin thin filaments and myosin thick filaments are arranged into acto-myosin fibrils which provide the apparatus for muscle contraction. By hydrolysing ATP molecules to release energy, myosin heads undergo a cycle during which they attach to thin actin filaments, exert a tension, and perform a power stroke causing the thin filaments to slide past thus shortening the muscle. Other forms of non-muscle myosin also exert force on actin filaments, driving active transport within many types of cells.
Adiabats, adiabatic surfaces
Curves or energy surfaces which can be plotted as a function of the reaction coordinate.In reality they are represented in a (3N–6)-dimensional space (N is the number of atoms), but diagrammatically, often plotted against a single effective coordinate. Adiabatic curves do not intersect and represent physical realitiesthat correspond to the real states (e.g. S0, S1, S2, etc.) of the molecule. Adiabatic states can be thought of as the ground and excited state energy surfaces of a molecule. Mathematically, they diagonalise the Hamiltonian.
AFM (Atomic Force Microscope)
A type of scanning-probe microscope used as an imaging device where a sharp tip on the end of a spring-like cantilever scans a surface and produces a contour map of that surface. A feedback signal is used to move the tip up and down keeping one chosen component of the interaction between the tip and the surface, for example the force, constant. It is possible to achieve sub-nanometre lateral and vertical resolution depending on the sharpness of the tip. AFM can also be used to measure the mechanical properties of individual molecules and high-speed AFM can capture the behaviour of individual molecules in considerable detail.
Aggregate
A collection of molecules or particles, combined to make an overall formation or mass.
Aggregation number
The number of molecules present in a micelle once the critical micelle concentration has been achieved.
Aliphatic
Non- aromatic carbon compounds.
Alpha carbon atom, Cα
The first carbon that attaches to a functional group. The alpha carbon in an amino acid is attached to the amino group, the carboxyl group, a hydrogen atom and the side-chain.
Alpha helix
The most common form of secondary structure in proteins, in which the polypeptide chain is coiled into a helix. The helical structure is held in place by weak hydrogen bonds between the N–H and C=0 groups in successive turns of the helix.
Amino-acid
Any of a group of water-soluble organic compounds that possess both a carboxyl (–COOH) and an amino (–NH2) group attached to the same carbon atom, called the α–carbon.
Amphiphile
An organic compound that contains both hydrophilic (having water affinity) and hydrophobic (having no water affinity) portions (amphi = both). The molecule is therefore both hydrophilic and lipophilic (fat loving), Examples include surfactants, detergents, soaps and phosopholipids. Such a compound is known as amphiphilic or amphipathic.
Amphiphilic
See amphiphile.
Anaphase
The latter stages of mitosis where two sets of identical chromosomes are pulled apart towards the pole of a mitotic spindle, the protein connections between sister chromatids being synchronously cleaved only when every chromosome has the correct attachments to each spindle pole.
Antenna complex
Antenna complexes in biological systems are protein-based supra-molecular structures that embody light-absorbing molecules, such as chlorophyll and carotenoids, in optimal positions and orientationsfor the efficient harvesting of sunlight and its onward transmission towards a common reaction centre where the chemistry of photosynthesis begins.
Antibodies
Large Y-shaped proteins, also known as immunoglobulins, produced by a type of white blood cell called B-cells. They have highly variable tips thus allowing millions of variants to exist.
Aromatic
Organic compound polymers possessing benzene or equivalent heterocyclic rings. Atoms in these rings are alternately single- and double-bonded to one another, and the rings are stabilized because electrons of the double bonds are free to cycle around the rings. These bonds may also be seen as a hybrid of a single bond and a double bond, each bond in the ring being identical to every other.
Arrhenius equation
An equation for the rate constant, k, of a chemical reaction expressed in terms of a pre-exponential A-factor and an exponential term containing the temperature (T), the activation energy and either the Boltzmann constant (kB) or the universal gas constant (R) depending on the scales involved.

k = A exp(–Δε/kBT)
k = A exp(–ΔE/RT)
Arrhenius plot
A plot of the natural logarithm of the rate constant, ln(k), against the reciprocal of temperature, 1/T. For a reaction with an A-factor independent of temperature, such a plot yields yields a straight line with gradient –( ΔE /R) and intercept on the y–axis of ln(A) from which activation energy, ΔE, and A may be deduced, respectively.
Asters
Star-like structures formed when a complex of molecular motors bind to clusters of microtubules: this allows microtubules to interact with each other through the motor complexes. When only plus-end directed motor complexes are bound to microtubules, spherical structures are formed with microtubules arranged radially around a central concentration of motor complexes with the microtubules' plus-ends also at the centres and their minus-ends point outwards. When only minus-end directed motors are bound to microtubules, the inverse structures are formed, with the microtubules' minus-ends at the centre while the motor complexes and the microtubules' plus-ends are distributed radially.
Each pole of the mitotic spindle has the structure of an aster. If spindle assembly is interfered with in cells, asters can arise as a result of only one spindle pole correctly forming.
Attenuation coefficient, β
In long range electron transfer processes it is the coefficient, β, in the exponential factor of the rate equation which describes the decay in the electron transfer rate with separation distance between donor and acceptor species. A larger b represents a greater fall off of the electron transfer rate with distance between the chromophores. For most molecules, the value of this coefficient lies in the range 8–12 nm–1 and for proteins is about 10 nm–1.
Avoided crossing
An energy gap between the ground and excited states of a molecule where two diabatic surfaces couple to one another to give rise to ground and excited state adiabatic surfaces. The diabatic surfaces effectively avoid one another, hence the term 'avoided crossing'. The magnitude of the energy gap between the two surfaces is twice the magnitude of the electronic coupling.
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B

Bacteriochlorophyll
Discovered in 1932, this is a structurally similar equivalent of chlorophyll in plants, algae and cyanobacteria (blue-green bacteria). It occurs in certain groups of bacteria such as purple bacteria that do not produce oxygen when they photosynthesise.
Bacteriophage lambda
A bacteriophage is a virus that preys on bacteria. Phage lambda is a temperate phage (i.e. it can remain dormant in its host cell after initial infection by integrating its DNA into the host's chromosome) that infects the cells of the bacterium Escherichia (E.) coli.
Bacteriopheophytin
The first electron carrier intermediate in the reaction centre of purple bacteria. After the initial excitation of the bacteriochlorophyll or the special pair of chlorophylls, this molecule accepts an electron and becomes negatively charged, leaving the special pair of chlorophylls positively charged – acharge transfer event. That electron rapidly moves to a nearby molecule of menaquinone and subsequently onto ubiquinone, thus facilitating the chemistry of photosynthesis.
Base
1) a substance that can accept protons, and can be thought of as the chemical opposite of acids. 2) specific nitrogen-containing constituents of nucleic acids that are also chemical bases: adenine, thymine, uracil, guanine or cytosine. Also see acid.
Basic
Containing a base, in the sense of opposite to an acid.
Bend, β
One of three measures of thin rod deformation (together with stretch and twist density) defined as the rate of change of the rod's tangent vector t with respect to the rod's length (ds): β= dt/ds. It is a vector quantity.
bending energy, f0:
the energy required for bending unit area (e.g. of a membrane), which is directly related to the curvature
Bending rigidity, κ
The force couple required to bend a non-rigid structure to unit curvature. Also known as flexural rigidity.
Beta pleated sheets
A form of secondary structure in proteins in which the extended polypeptide chains lie parallel or anti-parallel to each other and are linked by hydrogen bonds between the N–H and C=O groups. These sheets may occur in globular proteins and link polypeptides of the same type in certain fibrous proteins.
Bilayer
A structure, especially a thin film or membrane, consisting of two molecular layers. A lipid bilayer is a thin membrane of two layers made up of lipid molecules, where the membranes are flat sheets that form a continuous barrier around cells.
Bimolecular
See molecularity.
Bimolecular reaction
A reaction which involves just two reacting molecules.
Binding pocket
A region on a protein, DNA or RNA to which other specific molecules and ions bind (this binding may be via chemical bonds or other attractive interactions).
Biochemical noise
Random fluctuations in the components of a biological cell (eg the number of a specific protein molecule present). These fluctuations can cause differences between individual organisms that are genetically identical. The ability to buffer variations generated by molecular noise is referred to as robustness.
Bistable switch
A regulatory network having two stable states, corresponding to two distinct outcomes.
Born-Oppenheimer approximation
A mathematical technique whereby a molecular system's wavefunction can be separated into a nuclear (vibrational, rotational) component and an electronic component, the total wavefunction simply being the product of the two. Such a separation is justified by the fact that the proton is 2000 times larger in mass than the electron and hence the electron can 'instantaneously' adjust to changes in the nuclear geometry.
Bridge-mediated electron transfer
Also see superexchange. Electron transfer from a donor to acceptor species facilitated by the presence of a chemical structure bridging the two. Two processes are identifiable – one where the electron can be localised within the bridge (electron transport) and one where it cannot be localised in the bridge and travels directly from donor to acceptor(electron transfer).
Brownian motion
The irregular motion in all directions experienced by small particles suspended in a liquid , It is caused by collisions between the suspended particles and those in the medium. Easily observable in an optical microscope for particles of the order 1μm diameter.
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C

C-terminal
The end of a protein or polypeptide chain, terminated by a free carboxyl group (–COOH). When a protein is translated from messenger RNA, it is created from an N–terminal to a C-terminal. Protein sequences are usually written from N- to C-terminal. Also known as a carboxyl-terminus, carboxy-terminus, C-terminus, or COOH-terminus.
Canonical partition function, Z
A partition function that describes all the statistical properties of a system of particles in thermodynamic equilibrium. There are different types of partition function, used depending on the statistical ensemble it is describing. The canonical partition function applies to a canonical ensemble in which the system can exchange heat with the environment, at a fixed temperature, volume and number of particles. The Helmholtz free energy can be obtained from the canonical partition function. From this all other thermodynamic properties can be derived.
Carotenoid
A second important class of light-harvesting molecule found in the antenna systems of photosynthetic organisms, together with chlorophyll. It comes in many forms and is one of those chemicals that gives root vegetables such as carrots their distinctive colour. A common structural feature is that it forms an extended linear molecule and hasa delocalised π-system of bonding molecular orbitals. Carotenoids have three main functions: the collection of light; the regulation of energy transfer in antenna complexes; photo-protection by rapidly quenching(electronically deactivating) triplet excited states of chlorophyll molecules and singlet states of oxygen molecules whenever formed.
Catalyst
A substance that participates in a chemical reaction but whose concentration is unchanged as a result of the reaction. It participates in the reaction's intermediate stages, effectively lowering the relevant activation energy.
Catalytic Core
A chemically active region at the centre of a myosin motor head that can bind to actin filaments and hydrolyse ATP.
Catastrophe
The rapid depolymerisation or shrinking at the end of a microtubule caused by the loss of a GTP cap at the end of the microtubule. The conversion from GTP to GDP is believed to cause a shape or conformation change in the linked dimer which prevents subsequent polymerisation and destabilises the microtubule structure. However, the microtubule can be rescued if the depolymerisation reaches a GTP-rich region whose conformation is stable, and polymerisation can recommence.
Cell
A fundamental, usually sub-millimetre, unit of life having both structure and function. Enables complicated biochemistry essential to life, maintains structural integrity and mechanical properties, admits and imparts forces that allow motion and shape changes. Can exist independently as unicellular life forms or in conjunction with others to form differentiated tissues and organs in multi-cellular life forms. Generally a cell is bounded by a plasma membrane. Two main types of cell are recognised: prokaryotic (without nucleus) and eukaryotic (with nucleus).
Cellulose
a polysaccharide that consists of long unbranched chain of glucose units. The organisation of the monosaccharide repeats differ from that in starch (amylose and amylopectin) so that there is a high degree of intra- and inter-chain hydrogen bonding, rendering the molecule insoluble in aqueous solvents.
Central Dogma (of molecular biology)
The postulate that genetic information resides in the nucleic acid and is passes to the protein sequence, but cannot flow from protein to nucleic acid.
Central Dogma
The central set of concepts in molecular cell biology: genetic information is stored in DNA (the genome), and can be replicated in cell division, or copied to RNA and then into proteins. Short sequences or templates of DNA are copied by a protein called polymerase into messenger RNA (mRNA) in a process known as transcription; in eukaryotes this occurs within the cell nucleus or near its nuclear membrane. The messenger RNA is transported to specialised protein assemplies within the cytoplasm called ribosomes, where the genetic information is decoded and proteins are formed in a process known as translation.
Centromere
The point in between pairs of identical chromosomes at which they are held together prior to cell division.
Centrosomes
Two points located outside the nucleus where microtubules nucleate; the polymerisation of overlapping microtubules that occurs in between the centrosomes pushes them apart to form the mitotic spindle.
Chaperones
Protein molecules that assist other protein molecules to fold correctly.
Chaperone
A cytoplasmic protein that binds non-covalently to a newly formed polypeptide and ensures its correct folding and transport. The chaperone does not form part of the finished protein.
Chargaff's rule
A rule stating that natural DNA contains equal numbers of guanine and cytosine bases and equal numbers of adenine and thymine bases. This is a consequence of the base pairing of guanine with cytosine, and adenine with thymine, in dsDNA
Chemical equilibrium
A state in which the rates of the forward and reverse reactions are equal. Reactants and products are thus present at concentrations which do not vary with time. See dynamic equilibrium.
Chemical master equation
An equation for the rate of change of the probability of finding a stochastic system described by chemical reactions in a given state at a given time.
Chemical Potential, μ
A measure of the (Gibbs) free energy associated with a given chemical species under given conditions and hence of its relative ability to perform work.
Chemical potential, m
The change in a system's energy that occurs when one particle is added to the system, while all the other thermodynamic parameters are held constant.
Chemiosmotic coupling
An energy transduction mechanism which links the chemical synthesis of ATP during oxidative phosphorylation to the protonmotive force.
Chemotaxis
Cell motion or motility in response to a chemical gradient.
Chiral centre
The central atom in a group that consists of the central atom bound to a set of sub-groups, in a spatial arrangement that is not superimposable on its mirror image.
Chitin
A polysaccharide comprising of chains of N-acetyl-D-glucosamine, a derivative of glucose.
chlorophyll
The primary class of light-harvesting molecule found in the antenna systems of photosynthetic organisms, together with carotenoids.Although appearing in many types, the general architecture of a chlorophyll molecule is that of an almost flat square, about 1 nm along its side, with a phytol tail or side-chain. At the centre of the square is a magnesium atom which is coordinated to four nitrogen atoms.
Chloroplast
Any of the chlorophyll-containing organelle, found in large numbers in those plant and algal cells undergoing photosynthesis.
Circle of curvature
See osculating circle
Citric Acid Cycle
A cyclical series of biochemical reactions that is fundamental to the metabolism of aerobic organisms. The enzymes for the cycle are located in the mitochondria and are in close association with the components of the electron transport chain. Also known as the Kreb's cycle.
Chromophores
Light-absorbing molecules e.g. chlorophyll and carotenoids, or electronically distinct components of larger molecules.In the sphere of photobiology, chromophores participate in the harvesting of sunlight and its onward transmission via several steps towards the reaction centre.
Codon
A triplet of nucleotides within a molecule of messenger RNA that functions as a unit of genetic coding (the triplet code), usually by specifying a particular amino acid during the synthesis of proteins in a cell.
Collagen
An insoluble fibrous protein found extensively in the connective tissue of the skin, tendons, and bone.
Collision cross-section
The area πdAB2 where dAB is collision diameter.
Used to define an effective collision volume (cylindrical) or corridor within which the collision frequency per unit volume can be estimated. In simple collision theory, one particle (of type A or B) is considered to sweep out such a volume as it moves through a fliud. It collides with all particles (of type B or A) whose centres lie within that volume.
Collision diameter, dAB
The minimum approach distance between the centres of two particles A and B needed to bring about a reaction between them. In simple collision theory, it is the sum of the individual radii (rA + rB) of the particles of reacting substances A and B.
Used to calculate collision cross-section.
Collision theory
A model, used to describe encounters between particles, in which the particles are assumed to be solid, spherical and electrically neutral. Conventionally, the frequency of collisions per unit volume between particles of substances A and B is denoted ZAB.
Only those collisions involving particles with energies greater than some activation energy will result in a reaction. Increasing the concentration of the reactant(s), or raising the system's overall temperature, will normally increase the collision frequency thus increasing the reaction rate.
Complex fluid
See Soft condensed matter
Complex reaction
A reaction which proceeds from reactants to products via an activated complex in a sequence of elementary reactions. The overall rate equation cannot be deduced from the stoichiometry of the reaction and the reaction orders of intermediate reactions must be deduced experimentally, giving rise to the possibility of non-integer reaction orders.
Concentration
The amount of a substance per unit volume. Can be presented in a number of ways including:

  • number density: number of particles per unit volume;
  • molar concentration: number of moles per unit volume.

  • Chemical concentration is often denoted using square brackets e.g. [H+] which refers to the concentration of hydrogen ions in this case. If this convention is used, the units are normally assumed to be mol dm–1.
    In a rate equation, c is often used to represent concentration with an appropriate subscript (e.g. cH+) to indicate the substance of interest.
    Condensins
    Protein complexes at least partly responsible for giving rise to chromosome condensation in the nucleus, they are thought to act by modifying the cross-linking and supercoiling properties of the DNA
    Conjugate acid-base pair
    The components of a proton-exchange equilibrium reaction where the acid donates a proton (H+) and becomes a conjugate base and that proton is accepted by the base which becomes a conjugate acid. For example:
    HA (acid) + H2O (base) ↔ H3O+ (conjugate acid) + A–Â (conjugate base)
    Conservative substitution
    The substitution of amino acids whose side chains have similar biochemical properties.
    Contour length
    Can be calculated as an incremental length integrated over the original unstretched length (L0) of a rod:
    Lcontour = ∫ [1 + u(s)]ds0
    where u(s) is the stretch. Can be understood as the length of a chain of molecules or monomers in a fully extended state.
    Critical micelle concentration (CMC)
    The concentration of surfactants above which they spontaneously form micelles.
    Curvature (at a point)
    The rate of change at that point in the angle the tangent makes to a fixed axis relative to the arc length.
    Cytokinesis
    During the latter stages of mitosis, when the two sets of chromosomes are fully separated, the cell membrane contracts and is pinched-in where the metaphase plate was located; thought to occur via positive feedback between acto-myosin monomers, driving a change in shape in the membrane. Two new nuclei are formed by contracting rings of actin and myosin closing around the now separated sets of chromosomes and pinching them off into separate cells.
    Cytoskeleton
    A network of semi-rigid protein (mainly actin and tubulin) filaments that extends throughout the cytoplasm of eukaryotic cells. It provides the structural framework of the cell, mechanically supports organelles, facilitates cell movement and provides tracks on which molecular motors carry material directionally within a cell.
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    D

    Dalton, Da
    One twelfth of the mass of an atom of the isotope carbon-12, equal to 1.66033 × 10–27kg. Also known as the atomic mass unit or the unified mass unit. The mass of a molecule in daltons is close to the number of protons plus neutrons contained in its constituent atoms.
    Decay coefficient, β
    See attenuation coefficient.
    Degree of freedom
    An independent parameter that characterises a given system. The number of degrees of freedom indicates the number of independent quantities required to specify the system's complete state and a complete set could be used to derive all the properties of that system.
    Delocalised π-system
    A molecular orbital extending over a molecule. Where a series of p-orbitals on neighbouring atoms can all overlap laterally, they form a delocalised molecular orbital ('pi' or p-orbital) over all of the involved atoms.In the case of occupied π -orbitals, this, effectively, spreads their charge over a larger region of space, lowering the energy of the system and making the molecule more stable.
    Density matrix
    In the Heisenberg representation of quantum mechanics, the density matrix is equivalent to the wavefunction in the Schrödinger picture. The density matrix has the advantage that it can be used to represent statistical mixtures, as well as pure states, and therefore is useful for describing relaxation and dephasing during quantum dynamical processes.
    Dextrorotary
    A chemical compound that rotates the plane of polarisation of plane-polarised light to the right (clockwise as observed by someone facing the oncoming radiation). The rotation occurs when the molecules of substances are asymmetric; so that they can exist in two different structural forms (enantiomers) each being a mirror image of the others. Also see laevorotatory.
    Diabats, diabatic surfaces
    Curves of changing molecular potential energy that appearas intersecting parabolae when plotted on reaction coordinate diagrams; they describe the reactant (non charge-transfer) and product (charge-transfer) states. Despite being intuitively useful calculational tools, diabatic states do not represent physical realities.
    Diastereomers
    Molecules that are stereoisomers (molecules with the same molecular formula and sequence of bonded atoms, but different three-dimensional spatial arrangement of their atoms) but are not enantiomers. Unlike enantiomers, diastereomers typically have different physical properties.
    Diffusion coefficient, D
    A proportionality constant describing the rate at which a diffusing substance is transported between two planes of unit area in a system where there is s concentration difference between them. The larger the diffusion coefficient, the faster the diffusion. Also known as diffusivity. See Fick's law and Stokes-Einstein equation.
    Diffusion flux, J
    A quantity describing the rate of movement of molecules across a unit area (see Fick's law).
    Diffusivity
    See diffusion coefficient.
    Diffusion potential
    The voltage between both sides of a membrane where the electrochemical potential is the same on both sides of the membrane. It is the voltage required to bring the electrical and chemical potentials into equilibrium with each other. Also known as the Nernst Potential.
    Directional curvature
    A curvature that depends only on the direction of a curve.
    Disaccharides
    A sugar consisting of two linked monosaccharide molecules.
    Dissociation constant, Kd
    The equilibrium constant for a dissociation process: the breaking down of a molecular complex into its component molecules or atoms. It is commonly applied to the dissociation of acids in water, and to the dissociation of transcription factors from their DNA binding sites.
    Disulfide bonds
    Covalent S-S bonds. They normally occur in extracellular protein environments where they are stable but are relatively unstable in the more reducing environment within a cell. They are formed by covalent cross-links between residues of the amino acid cysteine and are present to stabilise some types of protein structures. A disulfide bond can be broken by chemical reduction (adding hydrogen) giving, for example, two S-H bonds and the free energy change associated with this reaction is fairly low being of the order of a few kJ mol–1.
    Disulfide bond
    The bond that is formed between two sulfydryl groups of cysteine and which stabilises the secondary structure of proteins.
    DNA
    Deoxyribonucleic acid. A linear polymer of covalently linked deoxyribo-nucleotides. In cells DNA is usually in the form of long macromolecules, each constructed of two linear polymer strands coiled around each other in a ladder-like double helix structure. The strands are joined by hydrogen bonds between the complementary bases in the nucleotides. DNA carries the genetic information for an individual cell.
    Donor-bridge-acceptor (DBA) systems
    Chemical systems where the donor and acceptor molecules are covalently bound to an intervening chemical “bridge". The bridge facilitates the transfer of electrons.
    Downstream processes
    In this set of lectures (Biological energy Lectures 3, 4 and 5), by downstream processes, we are referring to the later processes of photosynthesis where the chemical production of carbohydrates actually commences in the reaction centre.
    Dissociation constant, Kd
    A type of equilibrium constant that describes the reversible splitting of a chemical species. For example, the dissociation constant for the reaction
    AB ↔ A + B
    is
    Kd = [A][B]/[AB]
    Driving force
    Energy change of a reaction,ΔE0, as the system moves from reactants to products.
    ds-DNA
    Double-stranded DNA. Also see ss-DNA.
    Dynamic equilibrium
    A special case of chemical equilibrium referring to a closed system. In a closed system, left to itself, concentrations will eventually settle down in such a way that there is dynamic equilibrium between the forward and reverse reactions; that is, their rates are equal, and the concentrations remain constant.
    Dynamic unhomogeneity
    When observing biochemicals (e.g. enzymes) at work during a chemical reaction, the condition where the behaviour of a given molecule during successive catalytic cycles is correlated at short times – the molecules appear to exhibit memory, which is consistent with slow conformational fluctuations.
    Dynamic instability
    The phenomenon where microtubules randomly switch between rapidly growing and rapidly shrinking phases linked to the differing polymerisation and depolymerisation properties of the microtubules.
    Dynein
    A large, multi-protein complex consisting of chemical sub-units for ATP hydrolysis, microtubule binding and cargo recognition. This molecular motor is minus-end directed and allows the localisation of proteins which is critical for correct cellular function.
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    E

    Einstein equation
    A relation defining a particle's diffusion coefficient in terms of the particle's mobility, the Boltzmann constant and temperature. It is a simple example of a fluctuation-dissipation relation.
    Elasticity
    The property of a material or body that enables it to return to (or near to) its original dimensions when the external agent causing its deformation is removed. Several types of elasticity can be defined, depending on the mode of deformation and on the origin of the driving force that restores the configuration. See enthalpic elasticity, entropy-dominated elasticity.
    Electrochemical Potential, μ*
    A chemical potential that explicitly includes an electrostatic component.
    Electron acceptor chromophore
    A colour-imparting chemical species which accepts an electron during a charge transfer process.
    Electron donor chromophore
    A colour-imparting chemical species which donates an electron during a charge transfer process.
    Electron transfer theory
    A theory describing the movement of an electron from one chemical species (a Donor molecule) to a second chemical species (an acceptor molecule). To provide a more complete understanding of this complex process, the theory draws together ideas from quantum physics and from semi-classical physics.
    Electron transfer
    In general, the movement of an electron from a donor molecule to an acceptor molecule – it can occur through space, through a solvent or through a bond – and is fundamental to photosynthesis.In the case of bridge-mediated electron transfer, it is the process of electron relocation where the electron does not travel through the molecular orbitals on the bridge andoccurs, via the 'superexchange mechanism'wherethe energy levels of the bridge's orbitals are significantly different to those of the donor and acceptor.
    Electron transfer
    Electron transfer is a process whereby an electron is transferred from an electron donating group to an electron accepting group, giving rise to a change in charge distribution for the molecule. That is, there is a net loss of one electron from the donor making it positively charged and a net gain of one electron in the acceptor making it negatively charged. Typically, it involves the initial absorption of a photon giving rise to an excited state in a Donor molecule where an electron is promoted from the Highest Occupied Molecular Orbital to the Lowest Unoccupied Molecular Orbit (LUMO). Subsequently, the electron transfers from the Donor LUMO to the Acceptor LUMO which is lower in energy. It is a fundamental reaction in photosynthesis.
    Electron transport
    In the case of bridge-mediated electron transfer, it is the process of electron relocation where the electron travels through the orbitals of the bridge's chemical species; it occurs when the energy levels of the bridge's orbitals are similar to those of the donor and acceptor.
    Electron transport chain
    A series of molecules which actively participate in the transfer of electrons towards the reaction centre; this chain separates and stabilises the resulting oxidised and reduced chemical species prior to the onset of the downstream processes which result in long-term energy storage by the production of sugars/carbohydrates.
    Electron transport reactions
    Chemical processes in which the transfer of energy is described in terms of transfer of electrons between molecules with different electron affinity.
    Electrostatic interactions
    In the context of protein folding, sequence-specific forces which act only on certain parts of a protein molecule in order to stabilise it when folded. (By contrast, generic forces act on all parts of a protein to bring about stabilisation.) Examples of electrostatic interactions are the ionic interaction and the dipolar interaction, with hydrogen bonds often also considered as largely electrostatic interactions.
    Electrostatic interaction
    The exchange of forces between stationary electric charges and the fields associated with them.
    Elementary reaction
    A chemical reaction in which one or more chemical species react directly to form products in a single reaction step with a single transition state.
    Enantiomer
    (One of) two molecules that are mirror images of each other and are non-superposable.
    Endoplasmic reticulum
    An extensive network of membrane-enclosed tubules and sacs within the cytoplasm of cells, linking the plasma membrane with the nuclear membrane. There are two parts: rough endoplasmic reticulum (with ribosomes attached to its surface manufacturing proteins which are transported to the Golgi complex) and smooth endoplasmic reticulum (which manufacture lipids and fatty acids).
    Energy transfer
    On capture of a photon, a chromophore may enter an electronically excited state. This electronically excited energy may be transferred between chromophores via the Coulomb interaction; most commonly the associated mechanism is known as Förster resonance energy transfer.
    Enthalpic elasticity
    The commonly understood meaning of elasticity in solids, where bonds stretch and relax such as in the moderate flexing of a metal plate or stretching of a spring. Formally, this is explained using a free energy of the system such as the Gibbs free energy (G) which comprises an enthalpy term (H) and an entropy term (TS):
    G = H – TS
    Enthalpy is defined in terms of the system's internal energy (U), pressure (p) and volume (V):
    H = U + pV
    Hence enthalpic elasticity is understood as a change in the system's internal energy.
    Enthalpy, H
    The sum of the total internal energy required to create a system, and an extra term for the amount of energy required to make room for it (by displacing volume and pressure). Therefore during an isobaric (same pressure) process, the change in enthalpy is equal to the heat transferred during the process. It is an extensive quantity. Its absolute value cannot be directly measured (only changes in enthalpy can be measured directly).
    Entropic spring
    An elastic element that exerts a restoring force when its shape is changed from its equilibrium state because the equilibrium state represents a maximum in entropy. In a conventional spring, the equilibrium state represents a minimum in energy. With the definition of free energy as (Energy – Temperature × Entropy), the equilibrium state of an entropic spring is a minimum in free energy.
    Entropy-dominated elasticity
    A form of elasticity exhibited by softer materials such as gels and rubbers, where deformation results in a loss of entropy within the system as the number of possible conformations admitted by the new constraints is reduced. In terms of the Gibbs free energy:
    G = H – TS
    the entropy term now dominates and it is possible to define an elastic constant which is proportional to system's temperature.
    Entropy, S
    A measure of the amount of energy in a physical system that cannot be used to do work during a thermodynamic process; it is therefore a measure of the disorder of a system. The entropy depends on the state of the system and is an extensive variable, has an arbitrary zero and for a closed system is either constant or increasing.
    Equilibrium constant, Kc
    When a given pair of forward-reverse reactions attains chemical equilibrium, the equilibrium constant, Kc is defined as the product of the products' concentrations divided by the product of the reactants' concentrations. For example, for the reactions
    aA + bB ↔ pP + qQ
    we have
    Kc ={[P]p[Q]q [/A]a[B]b}equ
    The units of Kc depend on the stoichiometry of the reaction.
    Equipartition theorem
    The principle that the mean energy of each degree of freedom is ½ kBT in equilibrium, where kB is the Boltzmann constant and T is the thermodynamic temperature. For example applies to of the molecules of a gas, where kinetic energy is equally divided among the various degrees of freedom.
    Eukaryotic
    A cell containing a nucleus within which most of its DNA is resident. Plant cells and animal cells are of this type.
    Exciton
    An excited electronic state of a chromophore unit or molecule, brought about by the absorption of a photon,where an electron transits to one of the lowest unoccupied molecular orbitals leaving behind a hole in the highest occupied molecular orbital. The electron-hole pair can be referred to as a molecular exciton. It is a bound state having a lifetime of the order of nanoseconds,able to participate in resonance energy transfer where the exciton transfers from one molecule to another suitable neighbouring molecule.
    Exciton acceptor
    A molecule which accepts electronic excitation energy from an exciton donor. The acceptor is initially in the electronic ground (lower energy) state before accepting transferred energy from a nearby donor molecule which is in an excited (higher energy) electronic state. Post-transfer, the acceptor achieves an excited state and the donor returns or “decays" back to the ground state. This process is central to the transfer of solar energy to the reaction centre in photosynthesis.
    Exciton donor
    A molecule that absorbs a photon to give rise to an excited electronic state.This excited state can be transferred to an exciton acceptor, through the exchange of a virtual photon. Post-transfer, the donor returns or “decays" back to the ground state and leaves the acceptor in an excited state.
    Extensive (variable, quantity, number or parameter)
    A property of a system that depends on the size of the system (e.g. volume is an extensive property). Such a property can be expressed as a sum of the properties of constituents of the system.
    Extrinsic noise
    The contribution to biochemical noise caused by “whole cell" factors such as number of ribosomes or RNA polymerase.
    Eyring theory
    Sometimes known as the Eyring-Polanyi theory. It represents a further development in reaction kinetic theories giving a more precise understanding of activation energy and the pre-exponential factor at a molecular level. It is applicable, for example, to bimolecular reactions, electronic transitions and light absorption. Formally, it follows from transition state theory and derives the following equation:
    k = kBT/h exp(–ΔG*/RT)
    where all variable have the same meaning as in the Arrhenius equation but with h being the Planck constant and ΔG* the molar Gibbs energy of activation for the transition state. ΔG* can be written as
    ΔG* = ΔH* TΔS*

    where ΔH* is the molar enthalpy of activation for the transition state and ΔS* is the molar entropy of activation for the transition state.
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    F

    F1FO ATP-synthase
    An enzyme complex that catalyses the formation of ATP from ADP and inorganic phosphate, using the energy stored as the protonmotive force. It occurs in the inner mitochondrial membrane and is responsible for oxidative phosphorylation during respiration.
    Fat
    See Lipid.
    Fermi's Golden Rule
    In the context of biological energy transfer, this rate relation, derived from time-dependent quantum mechanics, defines the rate of energy transfer in terms of the strength of the coupling between the donor and acceptor molecules, and the density of the final energy states achieved by this mechanism.
    The coupling is furthermore dependent on the relative orientation of the donor and acceptor transition dipole moments, and the distance between the coupled molecules. The density of states can be interpreted in terms of the correlation between the fluorescence characteristics of the donor and the absorption characteristics of the acceptor.
    Fick's (first) law
    The simplest law describing diffusion of quantities or objects that do not interact with each other, e.g. heat or dilute particles. It postulates that flow occurs from areas of high to low concentration, with a flux proportional to the gradient of the diffusing quantity.
    First order reaction
    A reaction that proceeds at a rate depending on the concentration, c, of only one reactant. Examples include the decomposition of a single molecule (a unimolecular reaction) and radioactive decay. A general first order rate equation is:
    J = kc,
    The rate constant, k, of a first order reaction has dimensions [time–1].
    Fischer Projection
    The simplest way of representing a sugar in linear form. The Fischer projection is a two-dimensional representation of a three-dimensional organic molecule by projection.
    Flicker spectroscopy
    The process used to measure the fluctuation spectrum by measuring the spatial and sometimes temporal correlations in fluctuation modes, and investigating their spectra.
    Fluctuation
    A change in a variable or variables from one condition or phase to another, usually around an average value.
    Fluctuation dissipation theorem
    A theorem used to relate the amplitude of thermal fluctuations at thermodynamic equilibrium to the dissipation properties of a system. Dissipation is a property of non-equilibrium thermodynamical systems, describing how the energy of the system is irreversibly lost as heat.
    Fluctuation spectrum
    The mean square amplitude of fluctuation spatial modes. See also static structure factor.
    Fluorescence localisation
    Attaching a fluorescent molecule as a label or tag to another molecule of interest so that it can be made visible against a large background of non-fluorescent molecules. Fluorescent molecules absorb photons and re-emit longer wavelength (lower energy) photons with a delay or lifetime of nanoseconds. Fluorescence microscopes use filters to distinguish between excitation and emission wavelengths and if the background light is reduced sufficiently, the detectors are sensitive enough to be able to detect single fluorescent molecules.
    Fluorophores
    A type of fluorescent dye used to stain proteins, cells and tissues with a fluorescent label for viewing by a microscope. The dye's molecules absorb energy at one wavelength (Excitation) and re-emit energy at another longer wavelength (Emission). Excitation energy has higher frequencies (shorter wavelengths) whilst re-emitted energy has lower frequencies (longer wavelengths).
    Fluorophore
    A group of atoms which give a molecule fluorescent properties.
    Fluorescence resonance energy transfer (FRET)
    Also known as Förster Resonance Energy Transfer.
    Allows the detection of nanometre-scale relative motions between two fluorophores and sometimes the absolute measurement of distances to within a few nanometres. This method is based on the resonant coupling of two different fluorophores – one donor and one acceptor – attached to the molecule under investigation.
    The donor is generally a 'bluer' fluorophore than the acceptor and may be selectively excited by a laser or a continuous light source fitted with a suitable interference filter. When excited, the donor decays from its excited energy state by transferring energy to the acceptor through non-radiative dipole-to-dipole coupling (if closer than about 10 nm). This mechanism is termed “Förster resonance energy transfer" after the German scientist Theodor Förster and does not involve direct photon transfer as in radiative decay. FRET is sometimes referred to as Resonance Energy Transfer (RET) or Electronic Energy Transfer (EET).
    FMO (Fenna-Matthews-Olson) complex
    A chemical complex serving as a light-harvesting antenna within certain bacteria (e.g. green sulphur bacteria) which enables the transfer of excitation energy to the reaction centre embedded in the cell membrane.
    Fokker-Planck equation
    A partial differential equation describing the temporal change in the probability density P(x,t) of a particular mechanical state in terms of the spatial change of the probability flux, J(x,t) under forced diffusion conditions. Chemical transitions are excluded. It contains two “mechanical" terms: one includes the Diffusion Coefficient, the other includes the Drag Coefficient and the forcing function.
    Förster distance
    Sometimes referred to as the Förster Radius (R0), thisdefinesthat distance between the donor and acceptor at which there is an equal probability of the excited donor decaying back down to its ground state via either spontaneous decay or via resonant energy transfer to the acceptor.
    Förster Radius
    The distance between donor and acceptor fluorophores at which FRET energy transfer is 50% efficient. Designated R0, in the formula for Energy Transfer Efficiency: E = 1 /[ 1 + (r/R0)6 ], it is the separation distance where 50% of excited donors are deactivated by the FRET mechanism i.e. when r becomes R0, E becomes ½ or 50%.
    The magnitude of R0 is determined by the distance between the donor and acceptor fluorophores, the orientation of their respective dipole moments and the spectral overlap of the donor emission spectrum and the acceptor absorption spectrum. The Förster Radius, Ro, is typically in the range 2˜6 nm enabling distances in the 1˜10 nm range to be observed.
    Free energy transduction
    Non-equilibrium Thermodynamics presents us with a picture of forces acting on physical systems and giving rise to changes within those systems which are measured as conjugate fluxes. However, the coupling of non-conjugate forces with associated fluxes gives rise to free energy transduction where, for example, a molecular motor converts the chemical energy (a non-mechanical force) of an ATP molecule to the mechanical energy of motion of a cell (a mechanical flux or change).
    free enthlapy
    See Gibbs energy
    Freely jointed chain (FJC)
    The simplest model to describe a polymer. In this model, monomers are rigid rods of a fixed length, and their orientation is completely independent of the orientations and positions of all other monomers. The FJC thus models a polymer as a random walk, and neglects any kind of interactions among monomers. Also known as an Ideal Chain.
    Frequency factor
    See A-factor.
    Functional group
    A specific groups of atoms within a molecule that is responsible for the characteristic chemical reactions of that molecule.
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    G

    Gaussian bending rigidity, κG
    The property that defines the resistance to creating Gaussian curvature in a membrane.
    Gaussian curvature (at a point)
    The product of the two principal curvatures at that point. Also known as the total curvature.
    Gene
    A unit of heredity composed of DNA. In classical genetics a gene is visualised as a discrete particle forming part of a chromosome that determines a particular characteristic. In molecular biology, a gene usually refers to a section of DNA that codes for a single protein.
    Gene
    The smallest sequence within the genome that carries some function, e.g. the code to make a protein. It is the molecular unit of heredity. The genome as a whole holds the information to build and maintain an organism's cells and pass genetic traits to offspring.
    Generalised electron transfer coordinate
    A specially devised reaction coordinate which simplifies the plots of energy surfaces on a reaction coordinate diagram. The 3N–6 internal degrees of freedom of the molecule are projected onto a single dimension, making the electron transfer reaction easier to visualise.
    Gibbs (free) energy,G
    Measures the useful work obtainable from a thermodynamic system at constant temperature and pressure and gives the ability of a system to do non-mechanical work and in a chemical reaction the change in G is zero when equilibrium has been reached. Also known as free enthalpy.
    Glucosamines
    An amino sugar derivative.
    Glucose
    A white crystalline sugar occurring widely in nature.
    Glycolysis
    The series of biochemical reactions in which glucose is broken down to pyruvate with the release of usable energy in the form of ATP and other chemical species.
    Glycosidic bond
    The type of chemical linkage between the monosaccharide units of disaccharides, oligosaccharides, and polysaccharides, which is formed by the removal of a molecule of water (i.e. a condensation reaction).
    Golgu apparatus
    See Golgi complex
    Golgi complex
    Sometimes known as Golgi apparatus, an organelle in the cytoplasm comprising an assembly of vesicles and folded membranes. Proteins arrive after being manufactured in the endoplasmic reticulum and are further processed prior to being sorted into vesicles either for storage, immediate secretion out through the plasma membrane or transport to lysosomes.
    GTP
    Guanosine Triphosphate – a molecule linked to each (alpha and beta) tubulin dimer which mediates polymerisation or microtubule growth by the large free energy change when GTP is to guanosine diphosphate, GDP.
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    H

    Hamiltonian
    The Hamiltonian is the quantum mechanical operator corresponding to the total energy of the system. It includes terms that fully describe the kinetic and potential energies of the molecules, both intramolecular and intermolecular. Specifically, electronic couplings between chromophores are included, which are responsible for driving the energy transfer process.
    Haworth projection
    A three-dimensional model of the ring structure of a sugar is constructed by treating the ring as planar;the bonds of pendant carbon atoms are drawn perpendicular to the plane, either up or down. It is a common way of representing cyclic structure of monosaccharides with a three-dimensional perspective.
    Helfrich nodel
    The first successful quantitative description of the energy required to distort membranes (phospholipid bilayers). The starting point for calculating shapes and dynamics of vesicles and cell membranes.
    Helmholtz free energy,F or A
    A thermodynamic function of a system, which, measures the useful amount of work obtained by an isolated system at a constant volume and temperature. The change in the Helmholtz free energy between two states gives the maximum amount of work that could be obtained if the path followed between the two states is optimum. Also known as the Helmholtz function.
    Heterodimer
    A macromolecular complex composed of two different molecules such as alpha-tubulin and beta-tubulin; this complex is the heterodimer or monomer sub-unit that assembles in numbers to form microtubule polymers.
    Hydrogen bonds
    Considered to be broadly electrostatic interactions. They occur between a weakly acidic donor and an acceptor carrying a lone pair of electrons, and can be viewed as a hydrogen atom shared between two electronegative atoms. The donor is the atom most closely linked to the hydrogen and the donor-hydrogen bond is polarised giving rise to a fractional positive charge on the hydrogen that attracts the acceptor. Interaction between the hydrogen and the lone pair on the acceptor gives the bond some covalent character. Hydrogen bonds, for example between O and NH, are common in cells and although they make only small contributions to the stability of a folded protein, they can help to distinguish between correctly and incorrectly folded states. Bond distance is usually in the range 0.27 – 0.31 nm and formation energies are in the range –(12–40) kJ mol–1.
    Hydrogen bond
    A type of electrostatic interaction between electronegative (a property quantifying a particle's ability to attract electrons, forming negative ions) atoms in one molecule and hydrogen atoms bound to electronegative atoms in another molecule. It is a weak inter- or intramolecular force a results from the interaction of a hydrogen atom bonding with a lone pair of electrons. It is important in associate liquids (particularly water), and in polyamides and is responsible for much of the tertiary structure of proteins.
    Hydrophilic
    Having affinity for water; readily absorbing or dissolving in water.
    Hydrophobic
    Lacking affinity for water; repelled from water;
    Hydrophobic effect
    A type of generic force which acts on the whole protein molecule to help stabilise it after folding. Protein folding in aqueous environments involves burying hydrophobic side chains in the interior away from water. The hydrophobic effect is a relatively weak effect but it is important because it is summative. The free energy change of removing one CH2 group from water is only about –3 kJ mol–1 but a folded protein may bury many such groups, potentially as many as 100. Therefore, hydrophobic interactions are the main reason that folded proteins are stable.
    Hydrophobic force
    The entropy-based driving force due to the orientational constrains imposed on water molecules adjacent to the surface of a solute. As some water molecules are released into the bulk of the water entropy is increased; this is the bases of the “attraction" between hydrophobic objects in water.
    Hydrophobicity
    Lacking an affiinity for water
    Hypervariable residues
    A specific location within a protein where many alternative amino-acids are to be found.
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    I

    Inner sphere relaxation (reorganisation energy)
    The energy change associated with the relaxation of the molecular structure after electron transfer has occurred.
    Intensive (variable, quantity, number or parameter)
    A property of a system that does not depend on the size of the system (e.g. pressure is an intensive property).
    Interaction partner
    A molecule that can specifically bind to another. The binding of an interaction partner can dramatically change the behaviour of the original molecule e.g. a protein may bind to DNA only when a ligand is bound, causing changes in gene regulation.
    Internal energy, U
    The sum of the potential energies of the molecular interactions and the kinetic energies of the molecular motions of all the particles of the system. The total energy of a thermodynamic system.
    Intrinsic noise
    The contribution to biochemical noise caused by the inherent stochastic (random) nature of the chemical reactions involved in gene expression.
    Ion-motive force
    The change in the electrochemical potential of a charge when it crosses a membrane, which quantifies the free energy given up by an ion as it crosses a membrane that is out of equilibrium.
    Ionic
    Pertaining to or associated with gaseous or electrolytic ions, where an ion is an atom or molecule with a resultant electric charge.
    Ionic interaction
    A type of sequence-specific force which acts only on certain parts of a protein molecule in order to stabilise it when folded. If the dielectric constant at the interior of a folded protein is taken to be 4 and a pair of ions embedded within are separated by about 0.4 nm, the electrostatic energy is –86 kJ mol–1. It turns out, however, that there is little free energy difference between an unsolvated pair of ions buried within a protein and a solvated pair of ions at the protein surface in an aqueous environment. Therefore, although ionic interactions are strong, they are not usually important in stabilising folded proteins.
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    K

    Keratin
    Any of a group of fibrous proteins occurring in hair, feathers, hooves, and horns. Keratins have a coiled polypeptide chains that combine to form supercoils of several polypeptides linked by disulphide bonds between adjacent cysteine amino acids.
    Kinesin
    A family of at least 39 molecular motors, most of which are plus-end directed. They allow the localisation of proteins which is critical for correct cellular function.
    Kinetochore
    The complex of proteins which mediates the interaction between microtubules and chromosomes.
    kJ per mole, kJ mol–1
    The energy unit that is used in this lecture. One kJ mol–1 is equivalent to 1.66 × 10–21 J per molecule, or just under half the mean thermal kinetic energy, kBT per molecule, at room temperature.
    Kratky-Porod model
    See Worm-like chain (WLC)
    Kuhn length, b
    A real polymer chain can treated as being theoretically divided into N Kuhn segments, each with Kuhn length, b. These segments can then be treated as the elements of a freely jointed chain to give a simple model of the polymer. Each segment is then joined with each other and the chain can orient in any direction, without the influence of any forces and independent of the direction of other segments. Also known as the effective segment length.
    Kymograph
    A representation of microscopy images used to visualise the movement and velocity of a chemical motor. An example of this is the use of Total Internal Reflection Fluorescence to measure the intensity of reflected light along the length of a microtubule and displays it as a vertical column of pixels. The system under study could be a quantum dot bound to a kinesin complex. Subsequent columns of intensity are plotted adjacently at 50–200 ms time intervals thus building up a picture of events such as linear motion (diagonal lines), acceleration (curved lines), stalling (horizontal lines) and unbinding (terminating lines).
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    L

    Lac operon
    The operon that regulates the genes for lactose metabolism in the bacterium Escherichia (E.) coli. An operon is a unit containing several genes whose proteins are produced simultaneously.
    Laevorotatory
    A chemical compound that rotates the plane-polarised light to the left (anticlockwise for someone facing the oncoming radiation). Also see dextrorotatory.
    Langevin equation
    A stochastic (randomly determined) differential equation which describes the time evolution of a set of degrees of freedom for example describing the dissipation of a macroscopic disturbance with respect to the fluctuations of a physical quantity.
    Le Chatelier's principle
    The principle that any closed system in chemical equlibrium will respond to changes in such a way as to tend to restore that equlibrium. For example, adding more reactants increases the forward reaction rate; this results in products being produced at an increased rate until the forward and reverse reaction rates again become equal and equilibrium is restored.
    Levinthal's Paradox
    For a protein of say 100 residues, the time taken to explore all possible configurations before adopting a stable form is 70 orders of magnitude longer than the age of the universe. Therefore, the probability of correct protein folding by a random search is vanishingly small; yet correctly folded proteins are very common in nature. This paradox is resolved by noting that protein sequences contain information on folding paths as well as on the stability of folded structures. Protein folding is believed to be progressive and hierarchical where the end state is approached by some sort of ordered pathway accompanied by sharply increasing conformational stability.
    Levinthal's paradox
    A thought experiment regarding the theory of protein folding. There is a very large number of degrees of freedom in an unfolded polypeptide chain; therefore the molecule has a large number of possible configurations. If a protein were to attain its correctly folded configuration by sequentially sampling all the possible conformations, it would require a time longer than the age of the universe to find its natural figure- even if sampled at nano- or picosecond rates. Paradoxically however, most proteins fold spontaneously in a milli- or microsecond.
    Lipid
    Any of a group of organic compounds, including the fats, oils, waxes, sterols, and triglycerides, that are insoluble in water but soluble in nonpolar organic solvents, are oily to the touch, and together with carbohydrates and proteins constitute the principal structural material of living cells
    Lipid membrane
    A soft membranes composed of lipids which envelope structures like the nucleus, Golgi complex, endoplasmic reticulum and the cell itself which is encompassed by the plasma membrane, a lipid bilayer. Lipids can be complex (fatty acids) or simple (steroids), have hydrophilic heads and hydrophobic tails. Although lipid membranes are susceptible to deformation by thermal fluctuations, energies greater than the thermal kBT are required to bend lipid bilayers into closed spheres. Apart from roles in forming cell and organelle membranes, lipids also have a part to play as food-energy stores, in cell signalling and in the immune system.
    Liposome
    See vesicle
    Liquid state
    A phase of matter that is characterised by ease of flow and near incompressibility. Liquids possess only short-range structural regularity and bundles of atoms, molecules, or ions can move relative to each other.
    Lithotrophe
    An organism which obtains energy from reactions between available chemicals that have no biological origin.
    Lysis
    The destruction of a cell by splitting apart. Bacteriophages eventually cause lysis of their host cells, releasing multiple progeny phages.
    Lysogeny
    The relationship between a temperate phage and bacterium. A bacterium whose chromosome contains an integrated phage genome is called a lysogen.
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    M

    Marcus inverted region
    That regime in the solution of the Marcus-Hush equation where the driving force ΔE0 is greater than the reorganisation energy λ.This regime is important in stopping back-transfer or reverse reactions in the photosynthetic reaction centre.
    Marcus-Hush Theory
    A well-known semi-classical theory of electron transfer relating the rate of electron transfer to the energy of reaction, the reorganisation energy and the square of the electronic coupling (a quantity which takes the dimensions of energy).
    Mean-square displacement
    If a set of points is defined by taking their displacements each from a reference point, the mean-square displacement is the value obtained by taking this set, squaring its elements and taking its average.
    Mechanical coordinate
    One of two abstract variables to which the complexity of the model describing the action of acto-myosin can be reduced. It related to the mechanical aspects of the model and is a measure of the distance along the muscle between two arbitrarily chosen markers along the actin and myosin filaments. Also see Reaction coordinate.
    Menaquinone
    A participant in the electron transfer process of bacterial photosynthesis which accepts an electron from the bacteriopheophytin before donating it onwards to ubiquinone.Sometimes identified in the general literature as Vitamin K2.
    Messenger RNA
    Messenger RNA is responsible for carrying the genetic code transcribed from DNA to specialised sites within the cell (known as ribosomes) where the information is translated into protein composition. Also known as mRNA.
    Metaphase plate
    The plane, equidistant from each pole of the mitotic spindle, where chromosomes align due to the pulling forces from each pole of the spindle.
    Micelle
    An aggregate particle formed by a group of surfactants which can typically form when compounds such as soaps or detergents are added to aqueous solution.
    Microtubules
    Biological polymers which play a key role in the structure and function of cells. Typically they are tubular arrangements of 13 microfilaments themselves consisting of dimers of alpha-tubulin and beta-tubulin molecules assembled together end-to-end. Due to this dimeric property, the microtubules exhibit a form of polarity, having a “plus" and “minus" end enabling appropriately configured molecular motors to move in preferred directions along the microtubules.
    Microtubule
    A rigid, hollow rod around 24 nanometres in diameter made by polymerising the protein tubulin. The most rigid component of the cytoskeleton within cells. Have a role to play in maintaining cell shape, movement of organelles, transport of materials within the cell and in cell division.
    Mitochondria
    Structures within the cytoplasm of eukaryotic cells that carry out aerobic respiration: the site of the Krebs cycle and electron transport chain, and therefore the cell's energy production.
    Mitosis
    The process by which a cell replicates and divides into two identical daughter cells.
    Mitotic spindle
    During cell division, the micrometre-scale structure which ensures that chromosome are equally divided between the two daughter cells.
    Molar concentration
    Concentration expressed moles per litre (mol l–1or mol dm–3). 1 mole comprises NA particles, where NA is Avogadro number = 6.02 × 1023 mol–1. Traditionally, a solution containing 1 mole of a substance in 1 litre of solution is referred to as a 'molar solution' and denoted 1M. Similarly a 2M (2 molar) solution has 2 moles in 1 litre of solution, and so on.
    Mole fraction
    The ratio of the number of moles of a given component to the total number of moles of all components in a mixture.
    Molecular binding
    An attractive interaction between two molecules where two specific molecules bond with one another forming a molecular complex.
    Molecular orbital (MO)
    The application of the orbital concept –originallyused to describe the motion or presence of electrons around the nucleus of an atom –tomolecular structures.It is a mathematical construct describing the quantum behaviour of an electron in a molecule and can be used to calculate the probability of finding an electron in a region encompassing all the nuclei in the molecule, rather than being centred on a single nucleus as in the case of an atom.A molecular orbital describes the behaviour of an electron moving in the average potential field of all nuclei and other electrons which are present in its system.
    Molecular machines
    A molecular assembly – usually of proteins – giving rise to most processes occurring in living cells such as motility, transport of needed cargo within the cell and expulsion of unwanted materials out of the cell. Due to their tiny size, molecular machines operate at energies near the thermal energy, kBT (where kB is the Boltzmann constant and T the absolute temperature). Accordingly, these minute machines are subject to continual thermal fluctuations which must be taken into account when trying to understand their behaviour.
    Molecular motor
    A type of molecular machine that gives rise to movement, one example being acto-myosin in muscle cells. Such motors can be modelled by combining the mathematical formalisms of diffusion and chemical reactions.
    Molecular motor
    A protein assembly that generates force and movement as a result of chemical reactions. Some (e.g. myosin) can move in one direction along an actin filament; others (kinesin and dynein) can move in opposite directions along microtubules.
    Molecular orbital (MO) picture
    A theoretical description of the electronic structure of molecules. The molecular orbitals are formed by linear combination of atomic orbitals (LCAO), which gives rise to bonding and anti-bonding orbitals.
    Molecular Phylogeny
    The molecular evolution of an organism or group of related organisms.
    Molecularity (of a reaction)
    The number of molecules of the reactants coming together (via one intermediate transition state in the case of an elementary reaction) to form the eventual chemical product. A bimolecular reaction refers to two molecules or particles coming together and a unimolecular reaction involves the decay or disintegration of a single particle or chemical species.
    Monge parameterization
    Arepresentation of a curved surface, in which the height h above a reference plane is expressed as a function of orthonormal coordinates x and y. One of the simplest parameterisations (maps) of curved surfaces.
    Monosaccharides
    Monosaccharides, or a simple sugar is a carbohydrate that cannot be split into smaller units by the action of dilute acids.
    Monte Carlo method
    Numerical modelling using sequences of random numbers to generate a sequence of representative events based on probability distributions for all possible events. One use is in simulating the motion of molecular motors. A crucial feature of the method is the selection of an appropriately small timescale for the calculations such that the motor can be considered to be in one chemical state and at one spatial position during each time step. The method can be computer intensive and require long calculation runs when modelling average properties such as motor speed, but it does quite successfully reveal the microscopic behaviour of the motor.
    Motility
    The ability of cells to change shape to bring about a number of effects including transitional motion, division and the internal transportation of organelles and materials.
    Muscle contraction
    Being composed of long proteins such as actin and myosin which are organized into thin filaments and thick filaments, striated muscles such as skeletal and cardiac muscles contract when the thin (actin) and thick (myosin) filaments slide along one another. According to the Sliding Filament Theory of muscle contraction, these actin and myosin filaments do not change length, but simply slide past each other.
    (Muscle) Myosin
    A molecular motor (protein) comprising head and tail sections that produces muscle contraction by moving relative to a track or filament of actin. It is a dimer with two identical but independent motor heads capable of exerting motive forces on actin filaments. By hydrolysing (using water molecules to split) ATP molecules it releases and converts (transduces) their stored chemical energy into mechanical energy to bring about motion. Also known as Myosin II.
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    N

    N-terminal
    The start of a protein or polypeptide terminated by a free amine group (–NH2). When a protein is translated from messenger RNA, it is created from an N-terminal to a C-terminal. Protein sequences are usually written from N- to C-terminal. Also known as an amino-terminus, N-Terminus, NH2-terminus or amine-terminus.
    NAD+
    NAD+ or nicotinamide adenine dinucleotide, is a coenzyme found in all living cells.
    NADH
    The reduced form of NAD+ (nicotinamide adenine dinucleotide), a coenzyme which serves as an electron acceptor for many dehydrogenases. NADH donates its electrons to the electron transport chain.
    Nanometry
    The observation and measurement of phenomena existing at nanometer dimensions. Techniques and instruments developed in the latter decades of the twentieth century have enabled progressively smaller dimensions to be examined. In Biological sciences, this has led to the observation and understanding of the behaviour of individual biomolecules machines in real time and to an incredible level of detail.
    Ncd
    A mitotic motor which moves towards the minus end of microtubules and is a member of the Kinesin family of molecular motors. Shortened form of “nonclaret disjunctional" arising from the effect, or phenotype, of removing the gene from the fruit fly drosophila melanogaster.
    Negative autoregulation
    The use of negative feedback in a biochemical or physiological system. Negative feedback occurs when the output of a system acts to counteract its own production: e.g. a repressor protein which represses its own gene.
    Nernst Potential
    See Diffusion Potential
    Network
    See cytoskeleton
    Neutral drift
    Accumulated genetic changes that are selectively neutral.
    Normal curvature (at a point)
    The curvature of a line formed by the intersection of a curved surface and a plane containing the normal to that surface at the point under consideration. Also see principal curvature.
    Normal region
    That regime in the solution of the Marcus-Hush equation where the driving force ΔE0 is less than the reorganisation energy λ.
    Nucleic acids
    A group of long, linear macromolecules, that carry genetic information directing all cellular functions, composed of either one or two chains of linked nucleotides. The two main types of nucleic acids are DNA and RNA.
    Nucleotide
    The basic structural components of biological nucleic acids. Nucleotides consist of a pentose sugar (ribose or deoxyribose), a nitrogenous base (nucleobase), a ribose sugar, and a phosphate group.
    Nucleotide binding pocket
    A cavity in the catalytic core of a myosin motor head that binds ATP and links its hydrolysis to overall shape changes in the protein molecule.
    Number density
    The number of particles (e.g. molecules, atoms, ions, nuclei – in chemistry the term 'molecule' is often used for all such entities) per unit volume. Usually represented by the symbol n with a subscript denoting the relevant particle e.g. nH for hydrogen atoms. It has dimensions of [volume–1], typically m–3 for higher densities and cm–3 for lower densities.
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    O

    Oligopeptides
    Short polymers with typically 10–20 amino acids. May be synthesised but often occur naturally. Also see polypeptide, and note that there is no precise number of amino-acids that defines the distinction between oligopeptie and polypeptide.
    Oligosaccharides
    Carbohydrates containing a small number (2–10) of monosaccharide units linked together, with elimination of water.
    One-step model (for gene expression)
    A model in which “one step" (transcription and translation combined) is used to represent the production of a protein from a gene.
    Oparin-Haldane hypothesis
    The theory that UV radiation from the sun or lightning discharges caused reactions in the primordial atmosphere to produce the molecules that are the building blocks of life- amino acids, nucleic acid bases and sugars.
    Optical activity
    The ability of certain substances to rotate the plane of plane-polarized light as it passes through a crystal, liquid, or solution.
    Optical microscopy
    Microscopy using incident, reflected and refracted light in the visible part of the electromagnetic spectrum i.e. wavelengths in the 440 – 740 nm range.
    Optical tweezers
    A tightly-focused laser beam capable of holding micro- and nano-particles stable in a tiny 3-dimensional space known as a “trap". It is a means of studying single molecules by exerting miniscule forces – picoNewtons – on a dielectric bead that has been attached to a molecule of interest such as DNA, a protein or an enzyme.
    The narrowest point of the focused beam, or waist, contains a very strong electric field gradient. The bead is attracted along the gradient to the region of strongest electric field at the beam's centre due of its properties as a dielectric (an insulator capable of being polarised by an electric field). The position of the bead can be detected optically by measuring scattered light from the trapping laser and a spatial resolution of 0.1 nm is possible. Near-infra-red wavelengths are often used because bio-specimens are almost transparent in this spectral region and because the low photon energy minimises photochemical damage. This technique has revolutionised the study of molecular motors by allowing direct manipulation and measurement of their movements.
    Order (of a reaction)
    The power or index to which the concentration of a reactant is raised in the rate equation. For an elementary reaction, the reaction order is given by the stoichiometry of the reaction. For example, in the case
    2A + B → C
    with a rate equation,

    J = k[A]2[B]1
    the reaction is order 2 with respect to A , and order 1 with respect to B, giving an overall reaction order of 3. For complex reactions, reaction orders may not necessarily equal their respective stoichiometric coefficients.
    Ordinary differential equation
    An equation involving only total differentials (not partial differentials).
    Organotrophe
    An organism which obtains its energy from the organic chemicals that are produced by phototrophes.
    Osculating circle
    A circle that closely touches a curve around a given point and whose centre is the centre of curvature at that point. Also known as the circle of curvature.
    Oxidative phosphorylation
    A reaction occurring during the final stages of aerobic respiration, in which ATP is formed from ADP and phosphate coupled to electron transport in the electron transport chain.
    Outer sphere relaxation (reorganisation energy)
    The energy change associated with the relaxation of any surrounding solvent molecules after the electron transfer process has occurred.
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    P

    Particle tracking
    The attachment of visible labels such as micron-sized beads or gold nanoparticles to molecules of interest enabling their motion to be visualised by the scattering light. A useful, non-invasive method of observation with optical microscopy.
    Passive diffusion
    Diffusion where the direction of motion of a particle is randomised by collisions with other particles at high frequency. See Active Diffusion.
    Persistence length
    A geometric property quantifying the mechanical stiffness of a polymer, such as DNA. It is the distance along a the rigid polymer over which the direction changes statistically. It can also be regarded as the length over which the polymer naturally stays straight when subject to thermal fluctuations.
    Sometimes defined as the distance along a rod over which the direction or rotation angle changes statistically. More formally defined as that length (lp) over which the tangent vectors of tiny length-segments (ds) along the rod lose correlation – the “memory" is lost and bending and twisting can occur. It is the length-scale over which the rod remains rigid.
    For length-segments shorter than the persistence length, the molecule chain behaves like an elastic rod exhibiting standard physical properties of matter. For length-segments greater than the persistence length, the behaviour of the molecule chain must be described by statistical methods.
    Persistence length, A
    A way to quantify the stiffness of a polymer or string. If a polymer is shorter than the persistence length it will behave like a flexible elastic rod, while polymers much longer than the persistence length can only be described statistically. If θ is angle between the directions of the polymer chain at 2 points separated by a contour length L, A is defined by the relation 〈cos θ = e–L/A, where the angled brackets denote the average over all pairs of points.
    pH
    Defined as the common logarithm (base 10) of the concentration of the hydronium ion in solution preceded by a minus sign:
    pH = –log10[H3O+]
    In pure water:
    [H3O+] = [OH] = 10–7 mol dm–3
    and hence pH = 7.
    Phenotype
    The distinctive physical appearance of an entity such as a cell (e.g. blood, hair, skin, bone, muscle, nerve) which is caused by each type being in a different steady-state of protein expression.
    Phosphate
    An inorganic chemical which is a salt or ester of phosphoric acid (an inorganic acid comprising hydrogen, phosphorus and oxygen).
    Photoprotectors
    Light absorbing molecules (chromophores) which act as absorbers that remove excess energy, preventing system overload under intense light conditions.
    Photosynthesis
    The process by which plants, algae and certain bacteria absorb sunlight and, through a complicated and elegant series of chemical and physical events, produce carbohydrates which store that energyfor food by combining water and carbon dioxide, releasing oxygen as a by-product.
    Photosynthetic bacterial reaction centre
    The reaction centrewithin bacteria where photosynthetic chemistry takes place.
    Phototrophe
    An organism which obtains its energy from sunlight.
    Phylogenetics
    Describing a system of classification of organisms that aims to demonstrate their evolutionary history.
    Phylogenetic tree
    A diagram in which each branch point indicates the probable existence of a common ancestor of all the organisms above it.
    phytol tail
    Part of the chlorophyll molecule – a tail or side-chain containing phytol, anacyclic diterpene alcohol with formula C20H40O.
    Poisson distribution
    The probability distribution for the number of occurrences of particular event in a particular time period, when the occurrence of the event is a Poisson process.
    Poisson process
    A stochastic (random) process in which the probability of an event occurring depends only on the current state of the system.
    Polypeptide
    A peptide comprising about ten or more amino acids, where a peptide is a group of two or more amino acids linked by peptide bonds. The properties of the polypeptide are determined by the sequence of its constituent amino acids.
    Polypeptide chain
    See polypeptide.
    Polysaccharides
    Any of a group of carbohydrates comprising long chains of monosaccharide (simple sugar) molecules. Important examples are starch, glucose, and cellulose.
    Primary structure
    Protein molecules consist of one or several long chains (polypeptides) of amino acids linked in a characteristic sequence; this is known as the primary structure.
    Pre-exponential factor
    See A-factor.
    Principal directions
    The directions at which the principal curvatures occur.
    Principal curvatures
    Parameters that measure how much a surface bends at a given point, in different directions; they are the maximum and minimum normal curvatures at that point.
    Principle of detailed balance
    The principle that, when a system is in dynamic equilibrium, the forward and reverse reaction rates of a chemical reaction are equal.
    Principle of detailed balance
    The principle of Detailed Balance, also known as Microscopic Reversibility, states that if a system is in equilibrium then each of its degrees of freedom is separately in equilibrium. By allowing us to consider equilibrium between any two states of any system, this principle requires that forwards and backwards rate constants for any transition are related by Boltzmann's law, k1k2 = exp (ΔG kbT ), where k1 and k2 are the forward and backward rate constants, ΔG is the free energy difference between the states, kb is the Boltzmann constant, and T the absolute temperature.
    Probability
    The likelihood of a particular event occurring.
    Prokaryotic
    A cell without a nucleus where its DNA is resident throughout its cytoplasm. All bacteria cells (and the less familiar archea cells) are of this type. Such cells also lack cytoplasmic organelles, and have little or no cytoskeleton.
    Prometaphase
    A mid-phase of mitosis where the nuclear membrane disintegrates and microtubules emanating from the spindle poles attach to the centromere of each chromosome. For correct division, each chromosome requires one of its sister chromatids to be attached to each spindle pole.
    Promotor
    The region of DNA molecule that controls the start of transcription (the first step in the process of protein synthesis in which genetic information is transferred from DNA to RNA).
    Prophase
    The first phase of mitosis where the nuclear DNA condenses from a random polymer into distinct chromosomes. The DNA has been duplicated prior to cell division.
    Protein
    A type of polymer comprising a large number of monomers – a range of up to 20 amino acids – all connected by identical peptide links (covalent C-N bonds). Proteins are of three main types: globular proteins which are water-soluble (enzymes, antibodies, haemoglobin, insulin); membrane proteins which are particularly amphiphilic; fibrous proteins (keratin, collagen, actin, myosin, fibrin) which have a strong tendency to assemble into linear aggregates .
    Protein
    One or several long biological polypeptide chains with specific amino-acid sequences. The polypeptide chains in proteins are usually folded into well defined 3-dimensional shapes, and the separate chains in a protein with more than one polypeptide are usually packed together with well-defined orientations. Proteins are classified broadly into globular proteins and fibrous proteins; globular proteins are usually compact, rounded and water-soluble and fibrous proteins are generally insoluble in water and consist of long coiled strands or flat sheets.
    Proton motive force (pmf)
    The electrochemical gradient which is consists of a membrane potential together with a proton gradient across the membrane. This is the primary form of biological free energy.
    Purple photobacteria
    Purple bacteria are well-studied organisms capable of producing energy through photosynthesis. Contrary to the impression given by the nomenclature, theyhave colours ranging from purple through a variety of reddish hues. Structurally, they containring-shaped light-harvesting rings arranged around a central light-harvesting ring, within which resides the reaction centre. They were the first bacteria discovered to photosynthesize without using water as the reducing agent (some forms use hydrogen sulphide, other forms use hydrogen); in consequence no oxygen is produced as a by-product.
    Pyrrole ring
    A hetrocyclic aromatic molecule comprising a ring of 5 atoms, four of which are carbon, the other being nitrogen. It is a central building block of the chlorophyll family of molecules.
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    Q

    Quantum dots
    Semiconductor particles of nanometre dimensions which exhibit optical and electrical properties of a different character to the same material in bulk form. Typical materials might be Cadmium Selenide or Zinc Sulphide with particles ranging from 2 to 10 nanometres in diameter, roughly the length of 40–50 atoms.
    One of their most important characteristics is the emission of light in the visible range after they have been excited by another energy source – the wavelength of the emitted light depending on the size of the quantum dot as well as on its material. By controlling the size of a quantum dot, quantum dots can be “tuned" to emit a particular colour of light making use of a phenomenon known as the “size quantisation effect". The smaller the quantum dot, the emitted light is nearer to the blue (high energy) end of the spectrum; conversely the larger the quantum dot, the emitted light is nearer to the red (low energy) end of the spectrum. It is also possible to tune quantum dots into the infra-red or into the ultra-violet regions of the electromagnetic spectrum.
    Quantum electrodynamics (QED)
    QED describes how light and matter interact, and is the first theory fully to combine quantum mechanics and special relativity. It mathematically describes phenomena involving electrically charged particles interacting by means of photon exchange, and can be thought of as the quantum counterpart of classical electromagnetism.
    Quaternary structure
    The three-dimensional structural relationship of the component polypeptides in a multi-subunit protein or protein complex.
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    R

    Ramachandran plot
    A plot of the torsional angles phi and psi against each other for the residues in a folded protein, useful for displaying elements of secondary structure.
    Random walk
    The path taken by an object that moves in steps where each step is determined randomly.
    Rate constant
    The parameter k in the rate equation. Sometimes referred to as the rate coefficient on the grounds that it can be temperature dependent and therefore not a true constant.
    The dimensions of k depend on the reaction order.
    Zeroth order rate constant: [k] = [concentration] [time–1].
    First order rate constant: [k] = [time–1] e.g. s–1
    Second order rate constant: [k] = [concentration] [time–1 ]
    Third order rate constant: [k] = [concentration2] [time1]
    Rate constant
    A parameter that relates the rate of product formation in a chemical reaction) to the concentrations of the various reactants. The symbol k is most common, but other symbols (e.g. q) are also used. Also called rate parameter.
    Rate coefficient
    See rate constant.
    Rate equation
    An equation relating the reaction rate J to the concentrations, c, of reactants e.g. for a reaction betweenn A and B:
    J = kcAxcBy.
    where k is the rate constant and × and y are the reaction orders with respect to each reactant.
    Reaction centre
    A nanoscale region to which absorbed sunlight is transported where, after electron transfer and the separation of differently charged chemical species occur, the onset of full photosynthetic chemistry takes place for the production of carbohydrates. A major function of the reaction centre is to keep the positively and negatively charged species located as far away from one another as possible, similar to a capacitor, so that unintended charge recombination does not occur prior to carbohydrate production.
    Reaction coordinate
    A quantity plotted along the x-axis of a reaction coordinate diagram denoting the progress of a chemical reaction from reactants to products. The actual variable plotted may differ according to the reaction and could for example be distance between particles, bond length, bond angle or bond order. The chosen quantity gives direction to the reaction according to its value e.g. a particular bond angle might be small at the start of a reaction becoming large when reactants have converted to products.
    Reaction coordinate
    One of two abstract variables to which the complexity of the model describing the action of acto-myosin can be reduced. It related to the chemical aspects of the model and describes progress in the overall reaction of ATP hydrolysis. Also see Mechanical Coordinate.
    Reaction coordinate diagram
    A diagram describing the journey of a chemical reaction from reactants through intermediate complexes to products. A plot of (potential) energy along the y-axis against reaction coordinate on the x-axis.
    Reaction-diffusion equation
    This is the Fokker-Planck Equation with chemical transitions included. It is a partial differential equation containing the same two “mechanical" terms describing the motor movement whilst in a general state i plus a third “chemical" term describing chemical transitions into and out of state i at position x. Such chemical transitions are considered to be instantaneous and are defined by rate constants which are functions of position x.
    Reaction kinetics
    The study of the rates of chemical reactions. Sometimes referred to as chemical kinetics. Takes into account factors such as the physical state of the reactants, their concentration and the local temperature. Information yielded from such investigations can include reaction rate, rate constant, reaction mechanism and transition states.
    Reaction rate
    The rate at which the concentration of a given substance changes with time during a chemical reaction. Usually represented as J (sometimes v). Can be understood as the rate of increasing concentrations of products or the rate of decreasing concentrations of reactants.
    Reaction scheme
    A sequences of chemical reactions where the products of one reaction go on to take part in further reactions e.g.
    A + B à C
    then
    C + D à E
    Concentrations are given by sets of simultaneous differential equations some admitting analytical solutions, others requiring numerical analysis.
    Redox reaction
    All chemical reactions in which atoms have their oxidation number changed.
    Redox potentials
    A measure of the tendency of a chemical species to acquire electrons and thereby be reduced.
    (Gene) Regulation
    The act of controlling the rate of kind and rate of cellular processes by controlling the activity of individual genes leading to an increase or decrease in activity in one or more proteins.
    (Gene) Regulatory networks
    A collection of genes which interact with each other indirectly through RNA and protein expression products. These interactions can control such behaviours as a cell deciding whether to turn into a muscle or nerve. These regulatory networks combine the results of many molecular binding events to make calculations about the state of the cell and its environment, and use the results to determine how the cell behaves.
    Relaxation
    The process by which a particle or chemical species returns back to an electronic state of lower energy (usually the ground state)from a temporary excited state by releasing a photon,transferring its energy onto a neighbouring entity, or dissipating the excess energy as heat.
    Repressor
    A protein that can prevent the expression of a gene.
    Residue
    A specific monomer in a polymer chain (a polysaccharide, protein or nucleic acid). The name arises from the fact that polymerisation often discards a small part of the building blocks, and only the residue of the building block ends up in the finished polymer.
    Respiratory chain
    The final electron transport chain in aerobic respiration.
    Respiratory enzyme complexes
    Three large groups of enzymes in the respiratory chain.
    Reorganisation energy, λ
    A key component of the Marcus-Hush theory which represents – in a single simplifying variable – the otherwise complicated behaviour of many intra-and inter-molecular vibrational degrees of freedom. It can be determined by conducting experiments in different polar solvents. It is thought of as the energy change associated with the relaxation of the molecular structure (inner sphere relaxation) and any surrounding solvent molecules (outer sphere reorganisation?) after the electron transfer process has occurred.
    Replication
    Duplication of genetic material, usually prior to cell division.
    Representation of states
    The two types of representation are:[1] the diabatic representation, where the charge delocalised and charge transfer states are represented by intersecting parabolae, and [2] the adiabatic representation, where ground state and excited state energy surfaces because of mixing of the diabatic states at the intersection of theparabolae. The choice of representation employed in calculations depends on the specific application.
    Repressor
    A type of transcription factor that blocks the transcription of a gene by binding to a region of DNA .
    Resonance energy transfer (RET)
    The mechanism of energy transfer between chemical species, such as donors and acceptors, which obeys energy conservation and employs the interaction between the dipole moment of the donor and the dipole moment of the acceptor as its principal means of operation.
    Resonance energy transfer (RET)
    The mechanism of energy transfer between chemical species, such as donors and acceptors, which obeys energy conservation and employs the interaction between the dipole moment of the donor and the dipole moment of the acceptor as its principal means of operation.
    Ribosome
    A small spherical body within a living cell that is the site of protein synthesis.
    Ribosome
    A small spherical body within a cell, which is the site of protein synthesis. Sometimes described as a protein machine or factory and usually attached to the endoplasmic reticulum but may occasionally be free in the cytoplasm. Comprises RNA and protein. It reads the genetic information already copied (transcribed) into messenger-RNA and use it to create proteins in a process known as translation – i.e. the ribosome translates the genetic information from the mRNA into proteins by moving along the mRNA, reading its amino acid sequence and producing a corresponding chain of amino acids.
    Ribosome
    A large and evolutionarily well-conserved molecular machine that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by a nucleotide sequence of an RNA molecule.
    Ribozyme
    An RNA molecule that can function as a catalyst. The name comes from the contraction of ribonucleic acid enzyme.
    Rise time, trise
    The time it takes for the concentration of a protein to reach half of its steady state value.
    RNA
    Ribonucleic acid. A linear polymer of covalently linked ribo-nucleotides. In cells DNA is usually in the form of single-stranded chains of nucleotides that can fold into a variety of shapes. RNA has the same chemical composition as DNA except the sugar ribose replaces deoxyribose, and the pyrimidine base uracil replaces thymine. RNA plays a key part in protein synthesis.
    RNA polymerase
    An enzyme that catalyses the elongation of a polymeric RNA molecule. RNA polymerases (types I and III) catalyse the synthesis of RNA using as a template either an existing DNA strand or an RNA strand.
    RNA world
    A hypothesis that proposes that life based on RNA predates the current world of life based on DNA, RNA and proteins.
    Robust
    Maintaining function in the face of perturbations or fluctuations. For example, gene regulatory networks may be robust to changes in the number of protein molecules present.
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    S

    Sarcomere
    The basic repeating unit of a muscle comprising long fibres of protein (key ones being myosin and actin) which slide past one another giving rise to muscle contraction and relaxation. Sacromeres, approximately 2 micrometers in length, join end-to-end to form myofibrils or muscle fibrils and chains of these form tubular muscle cells or myocytes.
    Second order reaction
    A reaction in which the reaction rate is proportional to each of the concentrations of two reactants, e.g. in a reaction such as
    A + B à P
    or to the square of the concentration of a single reactant e.g. in a reaction such as.
    A + A à P
    Also see order of a reaction.
    Second order reaction
    Same as bimolecular reaction.
    Secondary structure
    Local folding pattern in a polymer. In proteins, the most common secondary structures are the alpha helix and beta sheet.
    Selectively neutral
    Pertaining to a mutation that is neither advantageous nor disadvantageous.
    Shear modulus, G
    A basic elastic constant, defined as the shear stress divided by the shear strain.
    Single-molecule experiment
    An experiment tracking the production of single protein molecules in individual cells.
    Sister chromatids
    The many pairs of identical chromosomes which have condensed from the two copies of a cell's DNA formed prior to cell division. Each chromatid is joined to its sister by cohesion protein complexes. During mitosis, the cohesion links are cleaved and the sisters are pulled apart so that the two new cells have an identical set of chromosomes.
    Soft condensed matter
    A sub-set of condensed matter which comprises physical systems and states that are easily altered by thermal stress or fluctuations. Typical examples are colloidal suspensions, polymer solutions, foams and emulsions; these materials are commonly called complex fluids in N.America.
    Spectroscopic gradient
    A gradient of decreasing energy levels encountered by harvested light during transfer across successive acceptors on its journey; the excited state of each subsequent acceptor will usually be slightly lower than the previous donor. Hence the next acceptor in line receives energy at a longer wavelength (lower frequency and hence energy) than the preceding acceptor, now a donor.
    A small amount of energy is also lost through intramolecular vibrational relaxation prior to each energy transfer step. As a result of these two principles, the overlap integral for forward transfer is much larger than the overlap integral for back transfer, signifying that the gradient gives the excitationa preferred direction of travel (towards the reaction centre), making the return journey very unlikely.
    Spindle assembly checkpoint
    Sometimes known as the spindle checkpoint where the DNA lines up until every chromosome is attached to both spindle poles, ready for separation into two new cells. A cascade of protein degradation forms a strong feedback mechanism preventing the onset of anaphase until every chromosome is correctly attached to the spindle. Then the spindle elongates and pulls the chromosomes apart, ready for cytokinesis where two cells are formed.
    Spontaneous curvature (of a membrane), K0
    The curvature which appears spontaneously and is determined by the details of the membrane.
    Spring constant, λ
    Constant of proportionality between restoring force and displacement in a linear spring.
    ss-DNA
    Single-stranded DNA A single strand of the DNA double helix that contains all the information in the double-stranded sequence (ds-DNA). ss-DNA molecules usually form random coils in solution.
    Starch
    A polysaccharide consisting of proportions of two glucose polymers, amylose (a linear molecule) and amylopectin (highly branched).
    Static structure factor
    A mathematical description of how a material scatters incident radiation. For a membrane, this is equivalent to the mean square amplitude of membrane modes..
    State parameter
    See Thermodynamic variables.
    State variable
    See Thermodynamic variables.
    Static inhomogeneity
    When observing a large group of molecules (e.g. enzymes) at work, for example during a chemical reaction, the condition where each molecule behaves in the same way over time, all are qualitatively the same, but the rate constants associated with individual molecules are different.
    Statistical mechanics
    The branch of physics concerned with determining the average (macroscopic) properties of a physical system made up of a large number of components, from the knowledge of microscopic behavior. This is done by applying probability theory to the constituent particles of the system. Also called Statistical thermodynamics.
    Statistical thermodynamics
    See Statistical mechanics.
    Statistical weight, w(E)
    The relative probability of a particular feature of a state e.g. energy. If a system has a number of possible quantised states and more than one distinct state has the same energy level, this energy level is said to be degenerate and its statistical weight is the number of states having that energy level.
    Steady state
    A situation in which concentration remains unchanged. For example, the concentration of a given substance remains in a steady state when the reaction rates for its production and removal are equal.
    Stem cell
    Found in all multi-cellular organisms; can divide and differentiate into many specialised cell types and can self-renew to produce more stem cells. Two basic types are: embryonic stem cells (found in early stage embryos, can differentiate into any cell type in the body indefinitely – pluripotent) and adult stem cells (undifferentiated, replenish dead cells and repair damaged tissue).
    Stochastic
    A process that contains a random element.
    Stochasticity
    The randomness associated with physical processes at the length scales of atoms and molecules where their numbers, locations and interactions are difficult to predict; an understanding requiring recourse to probabilistic ideas and methods.
    Stoichiometry
    The relative proportions of reactants in a chemical reaction. In a hypothetical elementary reaction such as
    A + 3B à 2C
    the stoichiometry of the reaction is given by the 1:3:2 i.e the ratios of the numbers of paticles, or moles, of A, B and C taking part in the reaction.
    Stokes-Einstein equation
    A relation defining the diffusion coefficient of a spherical object in terms of the radius of the particle and the viscosity of the fluid that surrounds it. Can be used to determine an effective hydrodynamic radius of any particle suspended in a solution.
    Stretch, u
    One of three measures of thin rod deformation (together with bend and twist density) defined as the incremental change in a rod's length relative to its length:
    u(s) = r(ds)/ds.
    A scalar quantity, sometimes referred to as extensional deformation and is akin to strain.
    Stretching modulus, Kstretch
    Tensile tress divided by tensile strain (commonly known as the Young modulus).
    Stroma
    A colourless, aqueous fluid inside chloroplasts which contains enzymes that catalyse one of the two half-reactions of photosynthesis, where carbon dioxide is reduced and incorporated into precursor units of carbohydrates.Within the liquid stroma are flat thylakoidswhere the other half-reaction of photosynthesisproceeds: stacks of thylakoids are known as grana. Photosynthesis commenceson the surface membranes of thylakoids before being completed in the stroma.
    Subwavelength resolution
    The ability to separate images of objects on scales that are smaller than the wavelength of the light or other electromagnetic radiation used to generate them. For visible light in the 100s of nanometres wavelength range, such resolution would fall into the units-to-tens of nanometres range. This can be achieved by localising single fluorescent molecules and it is possible to determine the position of a single fluorophore down to 1 nm length scales. Ultimately the resolution is limited by either by the integration time required to form the image or by the lifetime of the fluorophore.
    Sugar
    A class of simple, water-soluble carbohydrates (saccharose) including sucrose, lactose and fructose.
    Superexchange
    The mechanism by which electron transfer occurs using the presence of a chemical bridge: During the electron transfer process, the electron does not localise within the molecular orbitals of the bridge. Rather, the bridge orbitals couple to the orbitals of the Donor and Acceptor and give rise to a relatively long range (greater than 1 nanometre) means of through-bond-mediated electron transfer.
    Surfactant
    A substance that acts to reduce the surface tension of the liquid it is immersed in, which has both a hydrophobic and a hydrophilic end. It also reduces the interfacial tension between two liquids or a liquid and a solid and therefore increases the solubility of organic compounds. Examples of surfactants include detergents, foaming agents and dispersants. Also known as a surface-active or wetting agent.
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    T

    Templated polymerization
    The process by which polymer chains are allowed to grow along template macromolecules for the greater part of their lifetime. A template is any molecule that acts as a pattern for the synthesis of a new molecule, and polymerization is the process of reacting monomer molecules together in a chemical reaction to form three-dimensional networks or polymer chains.
    Templated polymerization
    The process by which the DNA double helix is copied. If the strands are separated, each single strand can act as a template for copying the other strand. Polymerisation is the process by which monomer molecules are joined to form polymer chains.
    Tertiary structure
    The large-scale three-dimensional shape of a polymer chain, in particular of a polypeptide or RNA molecule.
    Thermodynamic equilibrium
    A state in which the variables that specify the quantities of the system (e.g. pressure and temperature) all remain constant over time in an isolated system, for example there are no net flows or phase transitions. It is achieved when the appropriate potential is minimised.
    Thermodynamic potential
    A measure of the energy of a system which represents the amount of work obtainable when the system undergoes a change.
    Thermodynamic variable
    One of order to specify the state of a system. Once these variables have been met all other properties of the system can be determined. Also known as state parameters or state variables.
    Thio-
    Prefix denoting a compound in which a sulfur atom occupies a position normally filled by an oxygen atom.
    Thylakoid
    A membrane-bound flat sac containing chlorophyll found inside chloroplasts and cyanobacteria, where the light-dependent reactions of photosynthesis occur.Within the thylakoid membrane, one of the two half-reactions of photosynthesis proceeds where oxygen is released and water is absorbed: the other half-reaction proceeds within the stroma.
    TIRF Total Internal Reflection Fluorescence
    In TIRF Microscopy, the sample is illuminated by an evanescent light field near a glass-water (or glass-cell membrane) interface. The bright, highly collimated exciting laser radiation is incident at an angle greater than the critical angle and so is totally internally reflected. The evanescent light field extends into the sample by only 100 nm or so, decaying exponentially with distance into the water. TIRF facilitates the measurement of fluorescence from single molecules immobilised at the glass surface or diffusing or transported into the thin illuminated layer. The limited penetration of the exciting light greatly reduces the background resulting from fluorescence of molecules in solution away from the interface.
    The evanescent field is produced by total internal reflection of a laser beam introduced either through an objective lens of numerical aperture greater than that of water, or through a prism above the sample on the opposite side of the objective lens. The latter avoids laser light scattered inside the objective and that emitted by the fluorescence of the immersion oil or of the glass in the objective. However, it requires a closed sample and extra optical components above the sample, and observation of the surface furthest from the objective – so “through-objective" TIRF is more commonly employed.
    Torsional angles
    Measures of the rotation of one chemical group relative to an adjacent group about a chemical bond. In polypeptide chains there are two important torsional angles for each amino acid: phi (f) measures rotation about the Ca–N bond, psi (y) measures rotation about the Ca–CO bond.
    Total curvature
    See Gaussian curvature.
    Trafficking
    The directional transport of cellular components and fuel through the body of the cell to those sites within the cell where they are needed.
    Transcription
    The process of living cells in which the genetic information of DNA is transferred to a molecule of messenger RNA (mRNA) as the first step of protein synthesis. Transcription is regulated by transcription factors and in eukaryotes takes place in the cell nucleus or nuclear region .
    Transcription
    The process by which the genetic information of a DNA template is transferred to a molecule of messenger-RNA as the first step in protein synthesis. In eukaryotes, transcription mainly takes place inside the nucleus and is governed by a group of proteins called transcription factors.
    Transcription factor
    Any of a group of proteins that can regulate gene activity by increasing or decreasing the binding of RNA polymerases to the DNA molecule during the process of transcription.
    Transfer RNA
    Involved in the assembly of amino acids in a protein chain being synthesized at a ribosome, also known as tRNA. Each tRNA is specific for an amino acid and bears a triplet of bases complementary with a triplet of mRNA. It therefore decodes the genetic code, physically matching each codon to its specific amino acid.
    Transition state
    See activated complex.
    Translation
    The process of living cells in which the genetic information encoded in messenger RNA (mRNA) in the form of a sequence of nucleotide triplets is copied to make the corresponding polypeptide chain. Each triplet codes for one amino acid in the polypeptide, which typically folds into a protein.
    Triglycerides
    An ester of glycerol (propane-1,2,3-triol) in which all three hydroxyl groups are esterified with a fatty acid. The three fatty acid residues need not be identical.
    Twist density, ω
    One of three measures of thin rod deformation (together with bend and stretch) defined as the rate of change of the angle of rotation (φ ) relative to the principal axis with respect to the rod's length (ds):
    ω = dφ/ds.
    It is a scalar quantity and is sometimes known as torsional deformation.
    Two-dimensional Fourier transform electronic spectroscopy
    An experimental technique using pulsed lasers and diffraction optics that has enabled the real-time monitoring of the energy transfer process. Snapshots of the process are taken at short time intervals, as small as 20 femtoseconds (10–15 s), over a picosecond (10–12 s) total period.
    Two-step model (for gene expression)
    A model in which the production of a protein from a gene is represented by two steps: transcription and translation.
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    U

    Ubiquinone
    A participant in the electron transfer process of bacterial photosynthesis, which accepts an electron from menaquinone prior to the onset of full photosynthetic chemistry and the production of carbohydrates. This oil-soluble, vitamin-like substance is present in most eukaryotic cells, primarily in the mitochondria.In its completely oxidized form (ubiquinone) it is a conduit in the electron transfer process and in its completely reduced form (ubiquinol) it performs as an antioxidant.
    Unimolecular
    See molecularity.
    Unit evolutionary period
    The time for sequences of protein mutations to have diverged by 1%.
    Upstream processes
    In this set of lectures, upstream processes are those that occur during photosynthesis just prior to the production of carbohydrates. They include the absorption of sunlight and its transfer to the reaction centre and also the electron transfer processes that lead to the charge transfer and the separation of active chemical species within the reaction centre.
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    V

    van der Waals interactions
    A type of generic force which acting on the whole protein molecule aiding stabilisation after folding. Arises due to dipole-dipole attraction where one dipole is the result of a spontaneous fluctuation on one atom or molecule and the other is the polarization induced on a neighbouring atom or molecule. In the balance between a weak attractive interaction and a stronger but shorter-range repulsive interaction (as atoms become so close that their electron shells overlap) an energy minimum is achieved which signifies a stable configuration. At this minimum, the van der Waals bonding energy is of order 2–4 kJ mol–1 per pair of atoms in close contact, defined by a centre-to centre separation equal to the sum of their van der Waals radii. Folded proteins contain many atoms in close contact and van der Waals interactions are important in determining their conformations and are also important when proteins dock with other proteins or bind small molecules.
    van der Waals interaction
    An attractive force between atoms or molecules, which is caused by: dipole-dipole interaction (electrostatic interaction between two molecules with a permanent dipole moment), dipole-induced dipole interactions, in which a dipole of one molecule polarises a neighbouring molecule, and dispersion forces arising from small instantaneous dipoles in atoms. This force is typically small on a macroscopic scale, but very significant on molecular and colloidal scales.
    Vesicle
    A small, usually fluid-filled, membrane-bound sac within the cytoplasm of a living cell. Can be replicated in the lab, and is known as “giant" when its diameter is over a few microns. Also known as liposome.
    Virtual photon
    A theoretical construct for quanta of electromagnetic coupling, which cannot be physically measured because of their ultrashort lifetime. The concept is fundamental to the resonant transfer of energy process between coupled chemical species separated by distances shorter than the Förster distance. As the separation distance between the species increases significantly, the virtual photon increasingly acquires the characteristics of a real photon transferred from donor to acceptor species, in the more comprehensive quantum mechanical understanding of the energy transfer mechanism.
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    W

    Waxy mutants
    A plant species in which there is no amylose present in the starch granules.
    Wireframe
    A representation of a molecular structure that includes only bonds between atoms, which are shown as thin lines.
    Worm-like chain (WLC)
    A model in polymer physics used to describe the behavior of semi-flexible polymers, also known as the Kratky-Porod model. The WLC is an inextensible, isotropic rod that is continuously flexible. It is particularly suited for describing stiffer polymers with successive segments pointing roughly in the same direction. At room temperature the WLC is a conformational ensemble that is smoothly curved, at 0 K it is straight and rigid. The WLC model accurately describes the mechanical stretching of DNA,
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    Z

    Zeroth order reaction
    A reaction whose reaction rate is independent of the concentration of the reactant – increasing or decreasing its concentration will not speed up or slow down the reaction. An example could be a substance diffusing into a cell from an external source.
    Also see order of a reaction.
    Zwitterion
    An ion that has a positive and negative charge on the same group of atoms. Zwitterions can be formed from compounds that contain both acid groups and basic groups in their molecules. Also known as ampholyte ions.