Native stateIn biochemistry, the native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. The native state of a biomolecule may possess all four levels of biomolecular structure, with the secondary through quaternary structure being formed from weak interactions along the covalently-bonded backbone. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure.
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
Non-equilibrium thermodynamicsNon-equilibrium thermodynamics is a branch of thermodynamics that deals with physical systems that are not in thermodynamic equilibrium but can be described in terms of macroscopic quantities (non-equilibrium state variables) that represent an extrapolation of the variables used to specify the system in thermodynamic equilibrium. Non-equilibrium thermodynamics is concerned with transport processes and with the rates of chemical reactions.
ProteinProteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
Thermodynamic free energyIn thermodynamics, the thermodynamic free energy is one of the state functions of a thermodynamic system (the others being internal energy, enthalpy, entropy, etc.). The change in the free energy is the maximum amount of work that the system can perform in a process at constant temperature, and its sign indicates whether the process is thermodynamically favorable or forbidden. Since free energy usually contains potential energy, it is not absolute but depends on the choice of a zero point.
Equilibrium thermodynamicsEquilibrium Thermodynamics is the systematic study of transformations of matter and energy in systems in terms of a concept called thermodynamic equilibrium. The word equilibrium implies a state of balance. Equilibrium thermodynamics, in origins, derives from analysis of the Carnot cycle. Here, typically a system, as cylinder of gas, initially in its own state of internal thermodynamic equilibrium, is set out of balance via heat input from a combustion reaction.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
ThermodynamicsThermodynamics is a branch of physics that deals with heat, work, and temperature, and their relation to energy, entropy, and the physical properties of matter and radiation. The behavior of these quantities is governed by the four laws of thermodynamics which convey a quantitative description using measurable macroscopic physical quantities, but may be explained in terms of microscopic constituents by statistical mechanics.
Second law of thermodynamicsThe second law of thermodynamics is a physical law based on universal experience concerning heat and energy interconversions. One simple statement of the law is that heat always moves from hotter objects to colder objects (or "downhill"), unless energy in some form is supplied to reverse the direction of heat flow. Another definition is: "Not all heat energy can be converted into work in a cyclic process." The second law of thermodynamics in other versions establishes the concept of entropy as a physical property of a thermodynamic system.
Thermodynamic equilibriumThermodynamic equilibrium is an axiomatic concept of thermodynamics. It is an internal state of a single thermodynamic system, or a relation between several thermodynamic systems connected by more or less permeable or impermeable walls. In thermodynamic equilibrium, there are no net macroscopic flows of matter nor of energy within a system or between systems. In a system that is in its own state of internal thermodynamic equilibrium, no macroscopic change occurs.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Laws of thermodynamicsThe laws of thermodynamics are a set of scientific laws which define a group of physical quantities, such as temperature, energy, and entropy, that characterize thermodynamic systems in thermodynamic equilibrium. The laws also use various parameters for thermodynamic processes, such as thermodynamic work and heat, and establish relationships between them. They state empirical facts that form a basis of precluding the possibility of certain phenomena, such as perpetual motion.
Chemical thermodynamicsChemical thermodynamics is the study of the interrelation of heat and work with chemical reactions or with physical changes of state within the confines of the laws of thermodynamics. Chemical thermodynamics involves not only laboratory measurements of various thermodynamic properties, but also the application of mathematical methods to the study of chemical questions and the spontaneity of processes. The structure of chemical thermodynamics is based on the first two laws of thermodynamics.
Helmholtz free energyIn thermodynamics, the Helmholtz free energy (or Helmholtz energy) is a thermodynamic potential that measures the useful work obtainable from a closed thermodynamic system at a constant temperature (isothermal). The change in the Helmholtz energy during a process is equal to the maximum amount of work that the system can perform in a thermodynamic process in which temperature is held constant. At constant temperature, the Helmholtz free energy is minimized at equilibrium.
Gibbs free energyIn thermodynamics, the Gibbs free energy (or Gibbs energy as the recommended name; symbol ) is a thermodynamic potential that can be used to calculate the maximum amount of work, other than pressure-volume work, that may be performed by a thermodynamically closed system at constant temperature and pressure. It also provides a necessary condition for processes such as chemical reactions that may occur under these conditions. The Gibbs free energy is expressed as where p is pressure, T is the temperature, U is the internal energy, V is volume, H is the enthalpy, and S is the entropy.
Equilibrium unfoldingIn biochemistry, equilibrium unfolding is the process of unfolding a protein or RNA molecule by gradually changing its environment, such as by changing the temperature or pressure, pH, adding chemical denaturants, or applying force as with an atomic force microscope tip. If the equilibrium was maintained at all steps, the process theoretically should be reversible during equilibrium folding. Equilibrium unfolding can be used to determine the thermodynamic stability of the protein or RNA structure, i.e.
Chaperone (protein)In molecular biology, molecular chaperones are proteins that assist the conformational folding or unfolding of large proteins or macromolecular protein complexes. There are a number of classes of molecular chaperones, all of which function to assist large proteins in proper protein folding during or after synthesis, and after partial denaturation. Chaperones are also involved in the translocation of proteins for proteolysis. The first molecular chaperones discovered were a type of assembly chaperones which assist in the assembly of nucleosomes from folded histones and DNA.
First law of thermodynamicsThe first law of thermodynamics is a formulation of the law of conservation of energy, adapted for thermodynamic processes. A simple formulation is: "The total energy in a system remains constant, although it may be converted from one form to another." Another common phrasing is that "energy can neither be created nor destroyed". While there are many subtleties and implications that may be more precisely captured in more complex formulations, this is the essential principle of the First Law.
Zeroth law of thermodynamicsThe zeroth law of thermodynamics is one of the four principal laws of thermodynamics. It provides an independent definition of temperature without reference to entropy, which is defined in the second law. The law was established by Ralph H. Fowler in the 1930s, long after the first, second, and third laws had been widely recognized. The zeroth law states that if two thermodynamic systems are in thermal equilibrium with each other, and also separately in thermal equilibrium with a third system, then the three systems are in thermal equilibrium with each other.
Protein aggregationIn molecular biology, protein aggregation is a phenomenon in which intrinsically-disordered or mis-folded proteins aggregate (i.e., accumulate and clump together) either intra- or extracellularly. Protein aggregates have been implicated in a wide variety of diseases known as amyloidoses, including ALS, Alzheimer's, Parkinson's and prion disease. After synthesis, proteins typically fold into a particular three-dimensional conformation that is the most thermodynamically favorable: their native state.
