Sindicacion RSS :: Escuchar Musica mientras nos lees

.

In the macroscopic world every product is assembled following a blueprint and using a set of assemblers with fixed bricks and boards. In bionanomachines the same principle is used, the assembler is the ribosome and the blueprints is the DNA. There is stored the information needed to construct different kinds of products. The process is simple and universal, for every organism on Earth is done as described in previous chapters.

The polymerases are the enzimes used for DNA replication. They can be helped by “clamps” that improve the processivity increasing it 500,000 times. Ribosomes themselves are clamps that closes around the RNA message.

There are a lot of other enzimes that modify and interact with the nucleic acids, like:

  • polymerases

  • nucleases: cut acid strands.

  • Ligases: connect nucleic acid strands.

  • Repressors, transcription factors, enhancer proteins and another regulatory proteins: regulate the use of the information

  • Base-excision nucleases: remove bases from nucleic acid strands.

  • Topoisomerases: solve the topological problems of long strands of DNA.

  • Recombinases: swap DNA portions of different DNA strands.

  • Spliceosomes: edit RNA removing pieces

  • Nucleosomes and other proteins: package nucleic acids for storage.

All this tools are helpful for editing nucleic acids to write the blueprint for custom proteins.

There is an intermediate step between the DNA and the proteins. DNA first is coded in messengerRNA (mRNA) and then ribosomes produce proteins from that information. There are some virus that skip that step, but that is not usual. That can be an evolutionary legacy.

That step is called transcription. Each DNA base correspond to a RNA base. RNA polymerases display the DNA strand and connect the RNA bases.

Then the ribosomes translate that RNA into proteins. That is a translation from one language to another. That translation is done by the transfer RNA (done itself by RNA). The genetic code is based on sequential triplets. Each 3 nucleotides form a codon and specify one of 20 possible amino acids. There is also some of them that codes the “start” and “stop” states.

The ribosome is a complex machine. It gets the codons, one of a time, and assemble the associated amino acid into the protein. Then moves to the next codon and repeat the process. It can assembly around 1000 amino acids per second. This extraordinary machine is composed primarily of RNA.

All this information is stored in 4 different bases, what is 2 bits. About 30 atoms are needed per base, so 15 bases are needed for store 1 bit. But the retrieval of that information is 1million times slower than in modern computers.

Many reactions in nano scale require energy, it can come from electrical, light or chemic reactions. In cells the energy used is not as in the macroscopic world, where we waste a lot of it, instead the energy used is the required, because all the heat is rapidly dissipated so it isn't useful (although it can be useful to raise the temperature of the organism). The reactions inside the cell work together to be possible. One process can be not favorable, but with another one can change, so both together are possible.

In cells the energy is stored in molecules. Those molecules are instable and provides the energy needed in many reactions. They are the fuel of the organisms. The most common is the ATP. It is created with energy from the light or from the breakdown of the food. Then release that energy in unfavorable biomolecular processes.

The ultimate energy source of almost all life is the Sun. The light is captured by small molecules called photosynthetic reaction centers. They get a photon and create a high-energy electron which is used for power. This electron is properly stored to avoid its energy lose and then is placed on a carrier molecule. The hole then is filled by another low-energetic electron usually provided by water.

Photosynthetic organisms absorb a lot of different wavelengths using chlorophyll and carotenoid molecules.

The charge transport is important in macroscopic world because it allows multiple machines to work. Cells also can conduct electrons, but instead of do it on bulk thanks to a potential difference do it electron by electron. For this purpose there are carriers that tunnel the electrons in distances between them less than 1.4 nm. If the total distance needed is more than that chains of carriers are used. This is used for two main purposes: the bulk delivery of electrons for chemical reactions and for powering other processes. Although this is possible there is no use of the single-electron computation. The biological computation is performed by hard-wired and biochemical networks and at the micro scale by programmable nerve networks.

DNA can conduct, but it is really difficult to experiment with it because getting a single strand of DNA, isolate it and apply two electrodes is a major challenge. It is supposed to conduct about 10E+12 electrons per second, not bad for a single molecule of DNA. But this is not used for anything in nature.

It is possible to store energy in a difference of charges. Ions instead of electrons. Membranes impermeable to ions can act as the medium between the different charges. The ions are pumped across the membrane to the other side and then the flow back is used to perform chemical or mechanical work.

Chemical transformations are done in cells with the help of catalysts, the enzimes. They minimize the necessary energy of the process and speed it controlling the side products. In the active site of the enzyme specific amino acids are placed to stabilize the transition state of the molecule undergoing.

To speed up the reactions, enzimes reduce the entropy. It is done in the active site, which is separated in two regions, a specificity pocket that recognizes the proper substance and binds to it and the catalytic machinery that performs the chemical transformation. They can be very specific, separating molecules with differences in a single atom or stereoscopic differences. They also stabilize transition states modifying the target to make it more active.

There are some possibilities to control the regulation of the processes. We already talked about the power control using ATP, but there are another mechanisms.

Allosteric motions are used for regulation. A protein can adopt two (sometimes more) possible states: one relaxed (R state) when the protein binds tightly to substrate molecules, and another tense (T state) when the protein resists the binding. We can force the protein to adopt one of these states, turning it on or off. It is also possible cooperative binding, so when binding to one substrate the protein increases the affinity for binding additional molecules at the remaining sites.

There are two different sites in an allosteric complex, one for the substrate and another one for binding a regulatory molecule. Binding to this second site changes the shape of the other site, changing the affinity of the substrate binding site. The control depends on the linking of the two sites within the protein complex. This mechanism provides a vast number of possibilities for regulation.

The action of biomolecules can be also changed by changing the groups bonded to them. If positive or negative charges are added to them the key chemical groups can be altered. So it can be used to activate or deactivate the function of the proteins.

Biomaterials are not as the materials of the macroscopic world, they are not constructed to last for a long time. Instead they are always being constructed and destructed to construct another things to give a dynamic response to the environment.

Filaments are an important biomaterial. They are created by binding a protein with different copies of itself forming structures. They can form linear filaments, microtubules or other structures. It depends of this conformation the rigidity or flexibility of the structures.

Some other bigger structures are possible. They can be built with subunits combined. They can form networks strong but resilient at the same time, porous and permeable to water and small molecules. The most common is a though two-dimensional membrane to cover the lipid membranes. They can also form a network of proteins inside a cell or create a three-dimensional network used for support and transportation.

Some minerals can be combined with biomaterials to get additional strength or another properties like sense the gravity, the magnetic field of Earth or for vision. Biomineralization is the process of growing crystals on demand. There are some methods, but all of them follow the same patron: get a space to grow the crystals, transport ions inside, nucleate crystals or aggregates of the mineral and finally control the growth and orientation of the mineral.

This use of organic-inorganic materials is very important for bionanotechnology because it is possible to combine the strength with the resilience. It is still being studied, but now it is better understood, although is still a challenge.

There are elastic proteins that are formed by disordered chains that may be stretched and distorted. They have multiple uses in organisms.

Another biomaterial is adhesives. They have to follow two criteria: stick to the surfaces and form a tough solid to be stable themselves. They can be compromised by water, because it can solve them.

Motors are rare in organisms, but there are a few. They are used for several tasks, like: separate the chromosomes or the remodeling of cell organelles. To the first one the two best exampled studied are myosin and kinesin. They use ATP to energize the process.

Another motors are the rotary motors, like in flagellar movement. These motors use also ATP to provide the energy necessary.

The brownian ratchets are motors that use the thermal motion. They use a barrier that allow protons to go pass in one direction, but not in the other one.

All the bionanomachines inside the cell are freely diving, so it is necessary a container. That's the membrane. They are impermeable to those molecules but permeable to others. A complete sealed membrane would be useless for a cell. To provide that permeability the membrane use channels that are passive transport devices. They allow the flow of molecules through membranes. They can work with a specific molecule and can be gated, closing or opening in response to some signal.

To transport proteins an active approach is needed. Usually a molecule is binded to the protein to force the molecule across in the process. In some cases ATP is used, but light can also be used. The most common types of transport are the ABC transporters. The name refers to ATP-binding cassette and use a flip-flop mechanism. They are like boxes open to the outside of the cell. A molecule goes inside and then cross to the cell.

For sensing the environment receptor proteins are used. They change the shape or change the charges distribution. Then those changes are amplified and are transformed into intracellular changes or initiate nerve impulses.

Bionanomachines are particularly good recognizing taste and smell. In order to accomplish that goal they can recognize specific molecules using proteins. Mammals have about 1000 genes to encode odorant receptors that can be combined to sense billions of different odors.

Light is sensed by monitoring light-sensitive motions in retinal. They change when absorb a photon.

Mechanosensors are still being studied. They can detect touch, acceleration and sound. They are thought to be ion channels that open quickly to allow many ions to pass. They are adaptable so forces like gravity are ignored and only changes in forces produce signals. This is done by relaxing the channel progressively.

Bacteria use a temporal sensing mechanism. They are too small to sense changes in the gradient of nutrients from one side to the other, so they are sensing the concentration and comparing it with the previous data. Their flagellar motor is working to impulse the cell in one direction, if the data says there is less concentration then it reverses and the cell tumbles, picking a new direction.

Self-replication is needed to create macroscopic objects with nanomachines. There are too many molecules in a gram, so a machine that can replicate itself is the best because in a sort period of time many nanomachines can be working. This is a good promise but also it is dangerous.

Cells are self-replicators, the parts include:

  • Information-driven assembler: they construct new molecules using the ribosomes.

  • Information storage medium: DNA is the storage of the information for the ribosomes.

  • Duplicator: DNA polymerase duplicate the information storage in modern cells.

  • Chemical processors: They convert available raw materials into building blocks. There are thousands of these enzymes to perform these transformations.

  • Infrastructure: They support the cell but also allows transportation inside it. The most famous is the lipid membrane.

It is thought that the most possible living organism (in laboratory conditions) has between 250 and 350 genes. The simplest living organism has 550 but lives inside other cells and uses many of their processes. But not only genes are enough, the blueprint is important but also a map of the structure of a living cell is also important.

This approach is like this because of evolution, but if we create nanomachines without the competition factor then we can make them without some of the parts, like the containers or other characteristics and we can make them more efficient.

In bionanothechnology machine-phase matter is used, it is the combination of multiple nanomachines to perform a task. They are composed of many modular machines, each very stable and functionally efficient. They are redundant, with many copies of the type of nanomachine.

Muscle sarcomeres are one example of machine-phase matter. They combine the action of many myosin to create macroscopic motion.

Neurons are programmable electrical components. They have an input layer (cell body and associated dentrites), an output layer (terminal branches) and a high-speed electrical communication (axons). They can act in an analog to digital schema. They encode the magnitude of the signal into a frequency of action potentials.

Compártelo