The organization of information, energy and substance flow in a cell

A cell is an open self-regulating system, which has an information, energy and substance flow. On a level of organism and on a level of a cell it may be distinguished external and internal substance exchange. An external exchange in organism - is exchange with external environment that means incoming of food substances and outcoming of waste substances.

An internal exchange in organism occurs by assimilation and dissimilation. Accordinary with assimilation type organisms may be divided on heterotrophic, mixotrophic and autotrophic; accordinary with dissimilation type organisms may be divided on aerobic and anaerobic.

Pic. 3.11. The cell as self-regulating system

Energy is defined as the ability to bring about change, or, more generally, as the capacity to do work. Accordinary to exchange type with environment living systems may be divided on: isolated - without any exchange, adiabatic - there is no substance exchange, but there is energy one, excluding heat energy, closed - there is no substance exchange, but there is energy one in any form, open - any exchange is possible.

The energy flow of organism is presented by cellular energy producing processes such as photosynthesis, chemosynthesis, fermentation and respiration. During photosynthesis in plant cells, the sun’s energy is converted to energy of chemical bonds of ATP and NADP.H2. Then this energy is used in a plastic processes. During chemosynthesis the transformation of one type of chemical bond to another occurs. So, nitrificaiing bacteria oxidize ammonium to nitrites and then to nitrates; sulfur bacteria oxidize H2S to sulfic acid; ferrobacteria oxidize iron ions. The energy liberating from oxidation is used for carbon dioxide reduction to organic substances.

In the heterotrophic organism cells, the energy flow is provided by respiration and fermentation processes. During fermentation, products dissimilate to organic substance still having a lot of energy in its bonds. So, that is why the energy outcome from fermentation is small. This process occurs in hyaloplasm.

The major role in energy exchange in heterotrophic organisms is respiration. With help of this process such low' energy substance as glucose, fatty acids; amino acids are dissimilated to carbon dioxide. The energy liberating from oxidation of these substances is used for synthesis of ATP. The ATP synthesis occurs on inner membrane and crysts of mitochondrion, containing enzymes of citric acid cycle. The energy of ATP converts to some work type - chemical, mechanical, regulating, osmotic, and electric.

Anaerobic glycolisis is a less effective process providing cell energy supplyment. The products of glycolisis (pyruvates) come to mitochondrion. There they ARE subject to oxidation linked with ADP phosphorilation to ATP. From systems converting energy of ATP to mechanical work, the mechanical-chemical system of muscle is studied better than anything. It consists of contractive proteins actine and myosin and adenosintriphosphatase enzyme, splitting ATP with energy liberating. Energy supplying mechanisms of cell are very effective. The coefficient of useful action of chloroplast and mitochondrion are 25% and 4560% subsequently. It is more than steam engine (8%) and internal combustion engine (17%) have.

Each cell as each organism has an information exchange (information flow). Cells and organisms receive information about their environment - about light, food, sexual partner, enemy etc. (external information). The other information flow always outcome from organism. THE organism serves as a transmitter of these signals (internal information). The information cannot be defined neither as matter nor as energy. But material or energy transmitters carry it. During hormone regulation hormone can get to any part of an organism but only some of them are able to accept it. For example, thyrotropic hormone of anterior pituitary acts only on thyroid gland. During nervous regulation, the information parameter is impulse rate (number of impulses per time unit). A cell accepts external information flow from intercellular matrix with help of receptors on a cell surface.

The information flow in an organism is performed with help of brain cortex and endocrine glands. In a cell, internal information is written in DNA. In internal information flow nucleus and cytoplasm DNA, mRNA, cytoplasm apparatus of translation takes part. The internal information flow provides the heredity of species signs from generation to generation. In eukaryotic cell, the genomes of chloroplasts and mitochondria also take part in internal information flow.

“Living matter” or “living state” - is, firstly, not a structure. It is a process. The living structures aren’t stable; they are always under destroying and rebuilding. This renewing (the substance flow) occurs with different speed. The measure to determine substance flow is period of renewing. It is a time required to change half molecules of substance to new molecules. The substance flow is characterized by plastic exchange in a cell - photosynthesis, chemosynthesis, protein biosynthesis etc. All three types of RNA take part in protein biosynthesis. The sequence of polypeptide chain synthesis processes may be concluded in following.

1. Amino acid activation by specific enzyme in a presence of ATP following to aminoaciladenilat formation.
2. Attachment of activated amino acid to specific tRNA liberating AMP.
3. Binding of aminoacil-tRNA (tRNA with amino acid) to ribosome. Then, incorporation of amino acids to protein liberating tRNA.

In the ribosomes, there are two furrows, one for growing polypeptide chain, second for mRNA. Also in ribosome, there are two sites for tRNA binding. A-site is for tRNA carrying amino acid, P-site for tRNA carrying polypeptide chain.

There are three phases in translation: initiation, elongation and termination of polypeptide synthesis (pic 3.13).

Pic. 3.13. The elongation (a) and termination (b) of protein synthesis (by V.N. Yarygin 1997)

The initiation phase. It provides the beginning of protein synthesis. During this phase occurs merging of two previously separated rRNA subunits on definite mRNA site and attachment to it first aminoacil-tRNA. In a mRNA molecule near the-end is a complementary site to rRNA sequence of small subunit. The mRNA binds with small ribosome subunit to put start codon (AUG) in P-site. When the first aminoacil-tRNA is positioned over the first AUG codon sequence of mRNA, the large ribosomal subunit binds, forming the A and P sites, and polypeptide synthesis begins.

There is aminoacil-tRNA in the P-site, but А-site contains next mRNA codon. The initiation processes are catalyzed by initiation factors. These factors bind with small ribosome subunit. When initiation phase is over, initiation factors leave ribosome subunit.

The elongation phase. It is a sequence of cyclic repeating events. During this phase occur specific recognizing of next codon in А-site by aminoacil-tRNA and complementary binding of codon and anticodon. While this binding, a transported amino acid is in the А-site nearby previously incorporated in protein structure amino acid in the P-site.

Then two amino acids undergo a chemical reaction, in which previously incorporated in protein structure amino acid is released from its tRNA and it’s attached instead by a peptide bond to incoming amino acid. The abandoned tRNA falls from its site on the ribosome, leaving that site vacant. Then ribosome moves along mRNA molecule a distance corresponding three nucleotides.

This movement reposition growing chain and exposes the next codon to tRNA. Then subsequent tRNA recognizes the next codon bringing a new amino acid to the polypeptide chain. The actions listed above have been repeated until codon-terminator appears at on А-site of ribosome.

The termination phase. It is also called finishing of polypeptide chain synthesis. It start from encounting one of codon-terminators. There is no tRNA, which is able to bind with this codon. Instead of tRNA this codon is recognized by special release factor. The molecule of water is bounded to terminal amino acid and protein chain is released from ribosome. After that, ribosome breaks in two subunits.

A ceil as open biological system has a substance exchange with external environment. A passive transport occur due to kinetic energy, however for active transport the metabolic energy is needed.

The plamolemm selectively regulate substance exchange.

While free transport molecules or ions pass through membrane passively at the original state. During a transport with transmitters, they pass through membrane bounded with membrane transmitters.

Diffusion is a net movement of molecules to regions of lower concentration as a result of random spontaneous molecular motions. Gases, as oxygen consumpted for cellular respiration, and carbon dioxide formed as a result of respiration, in solutions are subject to active diffusion through membranes.

They move from the regions of higher concentration to the regions of lower concentration by diffuse gradient. Diffusion through membrane occurs less actively because membrane lipids serve as a barrier, limitating diffusion.

According to a two ways theory, or theory of lipid filter, the lipid soluble molecules can diffuse directly through lipid bilayer. The rest of substances may pass only through slight imperfections in the sheet of lipid molecules. They passing speed of bigger particles depend on not only their molecular weight but also on their solubility.

The water diffusion through semipermeable membrane is called osmosis. During this process occur free water concentrations decreasing in a cell, which may be explained by solutant (dissolved molecules) influence and by action of structured components (macromolecules, cell wall capillaries etc.). Osmotic water consumption leads to increasing animal cell volume. For example, erythrocytes in a clear water increase in volume until the cell burst. In a plant, cell hypotonic conditions lead only to slight increasing cell in volume. The osmotic water consumption leads to creation of high turgor pressure in a vacuole, which acts conversely to that consumption.

The plasmolemm contains transport proteins, which carry substrates through membrane. There are different transporters with different mechanism of action and different specificy to substrate (pic 3.14).

Pic. 3.14. The transport of substances through plasma membrane: A - catalyzing membrane passing: 1 - substrate attachment, 2 - conformation shift, 3 - substrate release, 4 - conformation shift (substrate is blade, transport proteins are crossed). В - active transport: 1 - substrate attachment, 2 - ATP bounding, 3 - ATP hydrolysis, giving up ADP and energy, 4 - substrate release, S - conformation shift. C - different types of catalyzing passing: S - unique substrate, S1 and S2 two substrates of one transport protein. D - “proton pump”, on a right side is parallel passing of second substrate S2 (from Kompendum der allegemeinen biologe editedby G. Elisabeth et al., 1982)

The passive transport with transport protein according to concentration gradient is called catalyzed transport or facilitated diffusion. By this way sugars, amino acids and other substances pass through membrane (pic 3.14a).

The coupled transport is a specific case of facilitated diffusion. Some transporters carry two different substrates together in one direction or in controversial directions.

The active transport - it is transport of molecules and ions across membrane against concentration gradient driven by the expenditure of chemical energy. There is energy requirement because a substance has to move against its natural intention to diffuse in controversial direction. The transport ATPases - are transport proteins, which is able to degrade ATP liberating energy. This process may be considered as an engine of active transport. By this way, protons (proton pump) and ions (ion pump) enter to a cell. For example, a secretion of HC1 in mammalian stomach and wide spread sodium-potassium pump, transporting K+ inside and Na+ outside of a cell, use active transport.

The unbalanced states - the electrochemical potentials - are made on a surface of a cell with help of proton and ion pumps. They are used for performing parallel (or antiparallel) transport and they carry different molecules against their concentration gradient. Examples are transportation Na+ and sugar in animal cells in the same direction and same transportation of H+ and sugar in a plant cells.

The active transport may be performed by endocytosis and exocytosis.

The endocytosis - is a membrane vesicles formation by membrane invagination while consumption of soluble substances (pinocytosis) and solid substances (phagocytosis) (pic 3.15).Such vesicles are called pinosomes or phagosomes. Using endocytosis ovicell consume yolk proteins, leucocytes engulf foreign substances and immunoglobulines, a cell of renal tubules adsorb proteins from primary urine.

Pic. 3.15. The endocytosis, exocytosis and lysosome functions: A - endo- and exocytosis; В - simple phagocytosis; C - exocytosis of Golgi vesicle; D - two phases of exocytosis (1 - membrane and vesicle still not fused, 2 - lipid bilayers fusion); E - heterophagocytosis, F - autophagocytosis (1 - endocytosis, 2 - endocytosis vesicle, 3 - Golgi complex, 4,5 - primary and secondaiy lysosomes; 6 - residual bodies, 7 - organelle consumption; regions with lysosome enzymes are crossed)./( from Kompendum der allegemeinen biologe editedby G. Elisabeth et al., 1982)

The exocytosis - is a process that is controversial to endocytosis. Different vesicles from Golgi complex fuse with plasma membrane and eject contains. Them vesicle membrane may stay as a part of plasmolemm or come back to cytoplasm in a form of a vesicle. Today the data were received that lysosomes takes part in removing whole cell or their organelles from an organism. That means that lysosomes perform autophagocytosis processes.