Many are catalysts (enzymes, permeases, signal molecules) that control the formation of a 'final' product. Normal and abnormal destruction kinetics apoptosis.Ribosomes copy instructions in mRNA into proteins. MRNA translationmRNA's are generated by transcription, destroyed by a first-order reaction, exist at a steady-state level. (Constituitive genes)Inducing and repressing transcription factorsAttenuation"Cross-talk" among genes. Gene transcriptionone or two genes are transcribed to mRNA by RNAP's controlled by transcription factors. The Goodwin Equations Gene transcription mRNA translation Product synthesis. GenomicsThe concept of the genome and the cells.Regulation of homeostasisControl of DevelopmentReversibility of the normally unidirectional development pathway. But one must measure what is defined, or define what is measured!The art (kunst) that must be added to the science (wissenschaft) of macroscopic analysis is picking the right compartments and the right "entities" to follow. Macroscopic Problems: Cell Aggregates, Organs All basic representations are useful if properly reinterpreted:What goes in, plus what is made, minus what goes out, is always what accumulates. When is a cell not one compartment? When it is a nerve cellWhen its "organelles" must be considered:NucleusMitochondriaProcessing elementsWhen related chemical species are considered: finite-rate chemical transformations define compartments, too. Steady State All variables of interest have the same value at all moments of observationSteady state is a property of the system and the frame of reference.Steady state means, at the most fundamental level, no change in accumulation.Cyclic and "practical" steady states.Ĭells A cellCohorts of cells normally asynchronous synchronization cyclic and sequential behavior is concealed in cohort-scale measurements. May be important especially in neural cells.Ĭooperativity Desirable biological function that supports homeostasis. Ionic equilibria and membranes Not considered in these lectures. Models exist for both facilitated (not active) and active transport. Unlike enzymes, permeases do show reversible behavior. Permeases Can be regarded as enzymes that facilitate transport rather than reactions. Enzymes are catalysts they never change an equilibrium only the rate. Regulatible ('allosteric effectors') Substrate dependencies: First-order at low concentration Zero-order at high concentration Enzyme reactions are usually irreversible. Others equilibrate either with reactants or products of rate-limiting processes.In processes involving both reaction and transport, rate-limiting step may be of either type.Įnzyme reactions Linear in enzyme concentration. Reaction A few reactions among many are rate limiting. Reaction: equilibrium, power-law, enzymatic. Molecular MotionConvectionDiffusionConvective diffusionCompartmentsĬompartment RepresentationsInput and output via convection, permeation passive, permease-driven, active and coupled transportAccumulation with and without volume change Compare with path-particularized systems. Molecular delivery is particularized by packaging what is to be delivered (message or material) so that only intended recipients are reached. Molecules deliver:MessagesMaterial mass, energy All larger-scale entities acquire their ultimate meaning and explanation in molecules. Molecules They can only do two things:They reactThey move They are the most important elements in biological systems. Transport and Rate Phenomena in Biological SystemsRedux
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