Cell biophysics

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Cell biophysics (or cellular biophysics) is a sub-field of biophysics that focuses on physical principles underlying cell function. Sub-areas of current interest include statistical models of intracellular signaling dynamics, intracellular transport, cell mechanics (including membrane and cytoskeletal mechanics), molecular motors, biological electricity and genetic network theory. [1] The field has benefited greatly from recent advances in live-cell molecular imaging techniques that allow spatial and temporal measurement of macromolecules and macromolecular function. Specialized imaging methods like FRET, FRAP, photoactivation and single molecule imaging have proven useful for mapping macromolecular transport, dynamic conformational changes in proteins and macromolecular interactions. Super-resolution microscopy allows imaging of cell structures below the optical resolution of light. Combining novel experimental tools with mathematical models grounded in the physical sciences has enabled significant recent breakthroughs in the field. Multiple centers across the world are advancing the research area [2] [3]

Biophysics is an interdisciplinary science that applies approaches and methods traditionally used in physics to study biological phenomena. Biophysics covers all scales of biological organization, from molecular to organismic and populations. Biophysical research shares significant overlap with biochemistry, molecular biology, physical chemistry, physiology, nanotechnology, bioengineering, computational biology, biomechanics, developmental biology and systems biology.

Cell (biology) the basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life. Cells are often called the "building blocks of life". The study of cells is called cell biology or cellular biology.

Cell mechanics is a sub-field of biophysics that focuses on the mechanical properties and behavior of living cells and how it relates to cell function. It encompasses aspects of cell biophysics, biomechanics, soft matter physics and rheology, mechanobiology and cell biology.

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Cytoplasm all of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures

In cell biology, the cytoplasm is all of the material within a cell, enclosed by the cell membrane, except for the cell nucleus. The material inside the nucleus and contained within the nuclear membrane is termed the nucleoplasm. The main components of the cytoplasm are cytosol – a gel-like substance, the organelles – the cell's internal sub-structures, and various cytoplasmic inclusions. The cytoplasm is about 80% water and usually colorless.

Integrin Defined set from Reactome

Integrins are transmembrane receptors that facilitate cell-extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.

Protein biological molecule consisting of chains of amino acid residues

Proteins are large biomolecules, or macromolecules, consisting of 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 three-dimensional structure that determines its activity.

Structural biology study of molecular structures in biology

Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on each molecule's basic composition, or "primary structure."

Cytoskeleton Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces interm

A cytoskeleton is present in the cytoplasm of all cells, including bacteria, and archaea. It is a complex, dynamic network of interlinking protein filaments that extends from the cell nucleus to the cell membrane. The cytoskeletal systems of different organisms are composed of similar proteins. In eukaryotes, the cytoskeletal matrix is a dynamic structure composed of three main proteins, which are capable of rapid growth or disassembly dependent on the cell's requirements.

Tight junction

Tight junctions, also known as occluding junctions or zonulae occludentes are multiprotein junctional complexes whose general function is to prevent leakage of transported solutes and water and seals the paracellular pathway. Tight junctions may also serve as leaky pathways by forming selective channels for small cations, anions, or water. Tight junctions are present only in vertebrates. The corresponding junctions that occur in invertebrates are septate junctions.

The Max Planck Institute for Biophysical Chemistry in Göttingen is a research institute of the Max Planck Society. Currently, 850 people work at the institute, about half of them are scientists.

Motor proteins are a class of molecular motors that can move along the cytoplasm of animal cells. They convert chemical energy into mechanical work by the hydrolysis of ATP. Flagellar rotation, however, is powered by proton pump.

Max Planck Institute for Medical Research

The Max Planck Institute for Medical Research in Heidelberg, Germany, is a facility of the Max Planck Society for basic medical research. Since its foundation, six Nobel Prize laureates worked at the Institute: Otto Fritz Meyerhof (Physiology), Richard Kuhn (Chemistry), Walther Bothe (Physics), André Michel Lwoff, Rudolf Mößbauer (Physics), Bert Sakmann and Stefan W. Hell (Chemistry).

Jennifer Lippincott-Schwartz American biologist

Jennifer Lippincott-Schwartz is a Senior Group Leader at Howard Hughes Medical Institute's Janelia Research Campus and a founding member of the Neuronal Cell Biology Program at Janelia. Previously, she was the Chief of the Section on Organelle Biology in the Cell Biology and Metabolism Program, in the Division of Intramural Research in the Eunice Kennedy Shriver National Institute of Child Health and Human Development at the National Institutes of Health from 1993 to 2016. Lippincott-Schwartz received her Ph.D. from Johns Hopkins University, and performed post-doctoral training with Dr. Richard Klausner at the NICHD, NIH in Bethesda, Maryland.

Thomas C. Südhof German biochemist

Thomas Christian Südhof, ForMemRS, is a German-American biochemist known for his study of synaptic transmission. Currently, he is a professor in the School of Medicine in the Department of Molecular and Cellular Physiology, and by courtesy in Neurology, and in Psychiatry and Behavioral Sciences at Stanford University.

The following outline is provided as an overview of and topical guide to biophysics:

Macromolecular assembly massive chemical structures such as viruses and non-biologic nanoparticles, cellular organelles and membranes and ribosomes, etc. that are complex mixtures of polypeptide, polynucleotide, polysaccharide or other polymeric macromolecules

The term macromolecular assembly (MA) refers to massive chemical structures such as viruses and non-biologic nanoparticles, cellular organelles and membranes and ribosomes, etc. that are complex mixtures of polypeptide, polynucleotide, polysaccharide or other polymeric macromolecules. They are generally of more than one of these types, and the mixtures are defined spatially, and with regard to their underlying chemical composition and structure. Macromolecules are found in living and nonliving things, and are composed of many hundreds or thousands of atoms held together by covalent bonds; they are often characterized by repeating units. Assemblies of these can likewise be biologic or non-biologic, though the MA term is more commonly applied in biology, and the term supramolecular assembly is more often applied in non-biologic contexts. MAs of macromolecules are held in their defined forms by non-covalent intermolecular interactions, and can be in either non-repeating structures, or in repeating linear, circular, spiral, or other patterns. The process by which MAs are formed has been termed molecular self-assembly, a term especially applied in non-biologic contexts. A wide variety of physical/biophysical, chemical/biochemical, and computational methods exist for the study of MA; given the scale of MAs, efforts to elaborate their composition and structure and discern mechanisms underlying their functions are at the forefront of modern structure science.

Photo-activated localization microscopy and stochastic optical reconstruction microscopy (STORM) are widefield fluorescence microscopy imaging methods that allow obtaining images with a resolution beyond the diffraction limit. The methods were proposed in 2006 in the wake of a general emergence of optical super-resolution microscopy methods, and were featured as Methods of the Year for 2008 by the Nature Methods journal. The development of PALM as a targeted biophysical imaging method was largely prompted by the discovery of new species and the engineering of mutants of fluorescent proteins displaying a controllable photochromism, such as photo-activatable GFP. However, the concomitant development of STORM, sharing the same fundamental principle, originally made use of paired cyanine dyes. One molecule of the pair, when excited near its absorption maximum, serves to reactivate the other molecule to the fluorescent state.

Bioelectrodynamics is a branch of medical physics and bioelectromagnetism which deals with rapidly changing electric and magnetic fields in biological systems, i.e. high frequency endogenous electromagnetic phenomena in living cells. Unlike the events studied by the electrophysiology, the generating mechanism of bioelectrodynamic phenomenon is not connected with currents of ions and its frequency is typically much higher. Examples include vibrations of electrically polar intracellular structures and non-thermal emission of photons as a result of metabolic activity.

Traction force microscopy (TFM) is an experimental method for determining the tractions on the surface of a biological cell by obtaining measurements of the surrounding displacement field within an in vitro extracellular matrix (ECM).

Force Spectrum Microscopy (FSM) is an application of active microrheology developed to measure aggregate random forces in the cytoplasm. Large, inert flow tracers are injected into live cells and become lodged inside the cytoskeletal mesh, wherein it is oscillated by repercussions from active motor proteins. The magnitude of these random forces can be inferred from the frequency of oscillation of tracer particles. Tracking the fluctuations of tracer particles using optical microscopy can isolate the contribution of active random forces to intracellular molecular transport from that of Brownian motion.

Cell-based models are mathematical models that represent biological cells as a discrete entities. They are used in the field of computational biology for simulating the biomechanics of multicellular structures such as tissues. Their main advantage is the easy integration of cell level processes such as cell division, intracellular processes and single-cell variability within a cell population.

References

  1. Phillips, Rob; Kondev, Jan; Theriot, Julie (2008). Physical Biology of the Cell. Garland Science, Taylor and Francis group.
  2. "Molecular and Cellular Biophysics" . Retrieved April 4, 2014.
  3. "Center for the Physics of Living Cells" . Retrieved April 4, 2014.