Cytoskeleton in the context of Cell biophysics

The cell membrane (also known as the plasma membrane or cytoplasmic membrane, and historically referred to as the plasmalemma) is a semipermeable biological membrane that separates and protects the interior of a cell from the outside environment (the extracellular space). The cell membrane is a lipid bilayer, usually consisting of phospholipids and glycolipids; eukaryotes and some archaea typically have sterols (such as cholesterol in animals) interspersed between them as well, maintaining appropriate membrane fluidity at various temperatures. The membrane also contains membrane proteins, including integral proteins that span the membrane and serve as transporters, and peripheral proteins that attach to the surface of the cell membrane, acting as enzymes to facilitate interaction with the cell's environment. Glycolipids embedded in the outer lipid layer serve a similar purpose.

The cell membrane controls the movement of substances in and out of a cell, being selectively permeable to ions and organic molecules. In addition, cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity, and cell signaling and serve as the attachment surface for several extracellular structures, including the cell wall and the carbohydrate cell coat called the glycocalyx, as well as the intracellular network of protein fibers called the cytoskeleton. In the field of synthetic biology, cell membranes can be artificially reassembled.

Proteins 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.

A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, and they often associate to form stable protein complexes.

The chlorarachniophytes are a small group of exclusively marine algae widely distributed in tropical and temperate waters. They are typically mixotrophic, ingesting bacteria and smaller protists as well as conducting photosynthesis. Normally they have the form of small amoebae, with branching cytoplasmic extensions that capture prey and connect the cells together, forming a net. These extensions are dependent on the presence of light and polymerization of the actin cytoskeleton. They may also form flagellate zoospores, which characteristically have a single subapical flagellum that spirals backwards around the cell body, and walled coccoid cells.

The chloroplasts were presumably acquired by ingesting some green alga. They are surrounded by four membranes, the outermost of which is continuous with the endoplasmic reticulum, and contain a small nucleomorph between the middle two, which is a remnant of the alga's nucleus. This contains a small amount of DNA and divides without forming a mitotic spindle. The origin of the chloroplasts from green algae is supported by their pigmentation, which includes chlorophylls a and b, and by genetic similarities. The only other groups of algae that contain nucleomorphs are a few species of dinoflagellates, which also have plastids originating from green algae, and the cryptomonads, which acquired their chloroplasts from a red alga.

In excitotoxicity, nerve cells suffer damage or death when the levels of otherwise necessary and safe neurotransmitters such as glutamate become pathologically high, resulting in excessive stimulation of receptors. For example, when glutamate receptors such as NMDA receptors or AMPA receptors encounter excessive levels of the excitatory neurotransmitter, glutamate, significant neuronal damage might ensue. Different mechanisms might lead to increased extracellular glutamate concentrations, e.g. reduced uptake by glutamate transporters (EAATs), synaptic hyperactivity, or abnormal release from different neural cell types. Excess glutamate allows high levels of calcium ions (Ca) to enter the cell. Ca influx into cells activates a number of enzymes, including phospholipases, endonucleases, and proteases such as calpain. These enzymes go on to damage cell structures such as components of the cytoskeleton, membrane, and DNA. In evolved, complex adaptive systems such as biological life it must be understood that mechanisms are rarely, if ever, simplistically direct. For example, NMDA, in subtoxic amounts, can block glutamate toxicity and induce neuronal survival. In addition to abnormally high neurotransmitter concentrations, also elevation of the extracellular potassium concentration, acidification and other mechanisms may contribute to excitotoxicity.

Excitotoxicity may be involved in cancers, spinal cord injury, stroke, traumatic brain injury, hearing loss (through noise overexposure or ototoxicity), and in neurodegenerative diseases of the central nervous system such as multiple sclerosis, Alzheimer's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, alcoholism, alcohol withdrawal or hyperammonemia and especially over-rapid benzodiazepine withdrawal, and also Huntington's disease. Other common conditions that cause excessive glutamate concentrations around neurons are hypoglycemia. Blood sugars are the primary energy source for glutamate removal from inter-synaptic spaces at the NMDA and AMPA receptor site. Persons in excitotoxic shock must never fall into hypoglycemia. Patients should be given 5% glucose (dextrose) IV drip during excitotoxic shock to avoid a dangerous build up of glutamate. When 5% glucose (dextrose) IV drip is not available high levels of fructose are given orally. Treatment is administered during the acute stages of excitotoxic shock along with glutamate receptor antagonists. Dehydration should be avoided as this also contributes to the concentrations of glutamate in the inter-synaptic cleft and "status epilepticus can also be triggered by a build up of glutamate around inter-synaptic neurons."

In biology, a protein filament is a long chain of protein monomers, such as those found in hair, muscle, or in flagella. Protein filaments form together to make the cytoskeleton of the cell. They are often bundled together to provide support, strength, and rigidity to the cell. When the filaments are packed up together, they are able to form three different cellular parts. The three major classes of protein filaments that make up the cytoskeleton include: actin filaments, microtubules and intermediate filaments.

Actin is a family of globular multi-functional proteins that form microfilaments in the cytoskeleton, and the thin filaments in muscle fibrils. It is found in essentially all eukaryotic cells, where it may be present at a concentration of over 100 μM; its mass is roughly 42 kDa, with a diameter of 4 to 7 nm.

An actin protein is the monomeric subunit of two types of filaments in cells: microfilaments, one of the three major components of the cytoskeleton, and thin filaments, part of the contractile apparatus in muscle cells. It can be present as either a free monomer called G-actin (globular) or as part of a linear polymer microfilament called F-actin (filamentous), both of which are essential for such important cellular functions as the mobility and contraction of cells during cell division.

In hematology, erythrocyte deformability refers to the ability of erythrocytes (red blood cells, RBCs) to change shape under a given level of applied stress without hemolysing (rupturing). This is an important property because erythrocytes must change their shape extensively under the influence of mechanical forces in fluid flow or while passing through microcirculation (see hemodynamics). The extent and geometry of this shape change can be affected by the mechanical properties of the erythrocytes, the magnitude of the applied forces, and the orientation of erythrocytes with the applied forces. Deformability is an intrinsic cellular property of erythrocytes determined by geometric and material properties of the cell membrane, although as with many measurable properties the ambient conditions may also be relevant factors in any given measurement. No other cells of mammalian organisms have deformability comparable with erythrocytes; furthermore, non-mammalian erythrocytes are not deformable to an extent comparable with mammalian erythrocytes. In human RBCs there are structural supports that aid resilience, which include the cytoskeleton: actin and spectrin that are held together by ankyrin.

Intracellular transport is the movement of vesicles and substances within a cell. Intracellular transport is required for maintaining homeostasis within the cell by responding to physiological signals. Proteins synthesized in the cytosol are distributed to their respective organelles, according to their specific amino acid's sorting sequence. Eukaryotic cells transport packets of components to particular intracellular locations by attaching them to molecular motors that haul them along microtubules and actin filaments. Since intracellular transport heavily relies on microtubules for movement, the components of the cytoskeleton play a vital role in trafficking vesicles between organelles and the plasma membrane by providing mechanical support. Through this pathway, it is possible to facilitate the movement of essential molecules such as membrane‐bounded vesicles and organelles, mRNA, and chromosomes.

Intracellular transport is unique to eukaryotic cells because they possess organelles enclosed in membranes that need to be mediated for exchange of cargo to take place. Conversely, in prokaryotic cells, there is no need for this specialized transport mechanism because there are no membranous organelles and compartments to traffic between. Prokaryotes are able to subsist by allowing materials to enter the cell via simple diffusion. Intracellular transport is more specialized than diffusion; it is a multifaceted process which utilizes transport vesicles. Transport vesicles are small structures within the cell consisting of a fluid enclosed by a lipid bilayer that hold cargo. These vesicles will typically execute cargo loading and vesicle budding, vesicle transport, the binding of the vesicle to a target membrane and the fusion of the vesicle membranes to target membrane. To ensure that these vesicles embark in the right direction and to further organize the cell, special motor proteins attach to cargo-filled vesicles and carry them along the cytoskeleton. For example, they have to ensure that lysosomal enzymes are transferred specifically to the golgi apparatus and not to another part of the cell which could lead to deleterious effects.

In biology, the nuclear matrix is the network of fibres found throughout the inside of a cell nucleus after a specific method of chemical extraction. According to some it is somewhat analogous to the cell cytoskeleton. In contrast to the cytoskeleton, however, the nuclear matrix has been proposed to be a dynamic structure. Along with the nuclear lamina, it supposedly aids in organizing the genetic information within the cell.

The exact function of this structure is still disputed, and its very existence has been called into question. Evidence for such a structure was recognised as long ago as 1948, and consequently many proteins associated with the matrix have been discovered. The presence of intra-cellular proteins is common ground, and it is agreed that proteins such as the Scaffold, or Matrix Associated Proteins (SAR or MAR) have some role in the organisation of chromatin in the living cell. There is evidence that the nuclear matrix is involved in regulation of gene expression in Arabidopsis thaliana.

Telonemia is a phylum of microscopic eukaryotes commonly known as telonemids. They are unicellular free-living flagellates with a unique combination of cell structures, including a highly complex cytoskeleton unseen in other eukaryotes.

Telonemia shares several distinctive features with its related group, the SAR supergroup. Among these features are cortical alveoli, small sacs beneath the cell's surface that act as cushions, providing support and helping to maintain the cell's shape. Additionally, they possess tripartite mastigonemes, complex three-part hair-like structures on their flagella, the whip-like tails used for movement. These structures enhance their swimming capabilities by increasing resistance against water. Furthermore, Telonemia is equipped with filopodia, very thin, thread-like projections extending from the cell body. These projections can serve various purposes, such as aiding in movement or capturing food particles by wrapping around them. Together, the two lineages compose the TSAR clade.

Biological crosstalk refers to instances in which one or more components of one signal transduction pathway affects another. This can be achieved through a number of ways with the most common form being crosstalk between proteins of signaling cascades. In these signal transduction pathways, there are often shared components that can interact with either pathway. A more complex instance of crosstalk can be observed with transmembrane crosstalk between the extracellular matrix (ECM) and the cytoskeleton.

Intermediate filaments (IFs) are cytoskeletal structural components found in the cells of vertebrates, and many invertebrates. Homologues of the IF protein have been noted in an invertebrate, the cephalochordate Branchiostoma.

Intermediate filaments are composed of a family of related proteins sharing common structural and sequence features. Initially designated 'intermediate' because their average diameter (10 nm) is between those of narrower microfilaments (actin) and wider myosin filaments found in muscle cells, the diameter of intermediate filaments is now commonly compared to actin microfilaments (7 nm) and microtubules (25 nm). Animal intermediate filaments are subcategorized into six types based on similarities in amino acid sequence and protein structure. Most types are cytoplasmic, but one type, Type V is a nuclear lamin. Unlike microtubules, IF distribution in cells shows no good correlation with the distribution of either mitochondria or endoplasmic reticulum.

Microtubules are biopolymers of tubulin that form part of the cytoskeleton to provide structure and shape to a eukaryotic cell. Microtubules can be as long as 50 micrometres, as wide as 23 to 27 nm and have an inner diameter between 11 and 15 nm. They are formed by the polymerization of a dimer of two globular proteins, alpha and beta tubulin into protofilaments that can then associate laterally to form a hollow tube, the microtubule. The most common form of a microtubule consists of 13 protofilaments in the tubular arrangement.

Microtubules play an important role in a number of cellular processes. They are involved in maintaining the structure of the cell and, together with microfilaments and intermediate filaments, they form the cytoskeleton. They also make up the internal structure of cilia and flagella. They provide platforms for intracellular transport and are involved in a variety of cellular processes, including the movement of secretory vesicles, organelles, and intracellular macromolecular assemblies. They are also involved in cell division (by mitosis and meiosis) and are the main constituents of mitotic spindles, which are used to pull eukaryotic chromosomes apart.

Extracellular vesicles (EVs) are lipid bilayer-delimited particles that are naturally released from almost all types of cells. EVs range in diameter from near the size of the smallest physically possible unilamellar liposome (around 20–30 nanometers) to as large as 10 microns or more, although the vast majority of EVs are smaller than 200 nm. EVs can be divided according to size and synthesis route into exosomes, microvesicles and apoptotic bodies. The composition of EVs varies depending on their parent cells, encompassing proteins (e.g., adhesion molecules, cytoskeletons, cytokines, ribosomal proteins, growth factors, and metabolic enzymes), lipids (including cholesterol, lipid rafts, and ceramides), nucleic acids (such as DNA, mRNA, and miRNA), metabolites, and even organelles. Most cells that have been studied to date are thought to release EVs, including some archaeal, bacterial, fungal, and plant cells that are surrounded by cell walls. A wide variety of EV subtypes have been proposed, defined variously by size, biogenesis pathway, cargo, cellular source, and function, leading to a historically heterogenous nomenclature including terms like exosomes and ectosomes.

Numerous functions of EVs have been established or postulated. The first evidence for the existence of EVs was enabled by the ultracentrifuge, the electron microscope, and functional studies of coagulation in the mid-20th century. A sharp increase in interest in EVs occurred in the first decade of the 21st century following the discovery that EVs could transfer nucleic acids such as RNA from cell to cell. Associated with EVs from certain cells or tissues, nucleic acids could be easily amplified as markers of disease and also potentially traced back to a cell of origin, such as a tumor cell. When EVs are taken up by other cells, they may alter the behaviour of the recipient cell, for instance EVs released by colorectal cancer cells increase migration of fibroblasts and thus EVs are of importance in forming tumour landscapes. This discovery also implied that EVs could be used for therapeutic purposes, such as delivering nucleic acids or other cargo to diseased tissue. Conversely, pharmacological inhibition of EV release, through Calix[6]arene, can slow down progression of experimental pancreatic cancer. The growing interest in EVs as a nexus for therapeutic intervention was paralleled by formation of companies and funding programs focused on development of EVs as biomarkers or therapies of disease, the founding of an International Society for Extracellular Vesicles (ISEV), and establishment of a scientific journal devoted to the field, the Journal of Extracellular Vesicles.

In cell biology, a bleb (or snout) is a bulge of the plasma membrane of a cell, characterized by a spherical, "blister-like", bulky morphology. It is characterized by the decoupling of the cytoskeleton from the plasma membrane, degrading the internal structure of the cell, allowing the flexibility required for the cell to separate into individual bulges or pockets of the intercellular matrix. Most commonly, blebs are seen in apoptosis (programmed cell death), but they are also seen in other non-apoptotic functions, including apocrine secretion (cell secretion by disintegration of part of a cell). Blebbing, or zeiosis, is the formation of blebs.