Supernovae and Life

Part 9 - Nano-machines

Inside every cell are molecules which collect, break down, transport or remake other molecules to provide the cell with nutrients and energy and permitting it to grow and replicate itself. In effect the cell is a tiny manufacturing plant filled with nano–machines.

One of the structures in most cells is the nucleus which contains deoxyribonucleic acid (DNA), a molecule similar to RNA except that it is a long, string-like chain of nucleotides, wound in a double helix. DNA encodes the genetic instructions used in the growth and reproduction of all living organisms. An average human DNA molecule is about 5cm (2 inches) long but it is tightly coiled permitting the 3 billion base pairs in each cell to fit into a space just 6000 nanometres across.

(A nanometre is1000th of a micrometre which is 1000th of a millimetre which is 1000th of a metre and there are 25.4 millimetres in one inch).

RNA, DNA, lipids, proteins and carbohydrates constitute the main macromolecules essential for all living organisms.

Another structure that is a part of every modern cell (and virtually identical in every living organism) is the ribosome, a small furry ball that contain ribonucleic acid (RNA) and about 60 proteins in even the simplest cell. (RNA is a long chain molecule essential in coding, decoding and regulating genes).

Ribosomes are tiny complex machines, essential for the production of protein, which are a part of every cell on Earth. (Which implies that every living organism is descended from a single, extinct common ancestor, a microbe).

To make proteins, ribosomes follow a template encoded in DNA. A messenger RNA molecule transfers the information, for a specific protein, from the DNA, the ribosome 'reads' the information from the messenger RNA and uses a third RNA molecule (attached to a specific amino acid) to build up the protein one amino acid at a time. This process is amazingly efficient. A ribosome can add between 10 and 20 amino acids per second. Then the completed protein finds its proper place within the cell.

Proteins are a vital part of every process within cells. They are needed to catalyze metabolic reactions, replicate DNA and transport molecules from one place to another. They also transfer information within and between cells and respond to chemical signals from other cells.Most fibrous proteins, like collagen and elastin, provide rigidity to biological components and are critical components of connective tissue such as cartilage. Keratin is found in nails, hair, hooves and feathers. Some globular proteins, like actin and tubulin, form long, stiff fibres that make up the cytoskeleton, which allows the cell to maintain its shape and size.

Motor proteins generate the forces exerted by contracting muscles and are essential for the motility of single celled organisms and the sperm of many multicellular organisms which reproduce sexually.

Normally, cell membranes are impermeable to charged molecules but membrane proteins contain internal channels that allow trans-membrane proteins to transport a particular ion (typically potassium and sodium) to enter and exit the cell.

Many proteins are involved in cell (quorum) signalling. Some, such as insulin, are extra-cellular proteins that transmit signals from the cell in which they were synthesized to other cells in distant tissues. Others are membrane proteins that act as receptors with the purpose of binding a signalling molecule from another cell and inducing a biochemical response in the receptor cell. One of the ligand-binding proteins is haemoglobin, which transports oxygen from the lungs and releases it to other organs and tissues in all vertebrates.

Antibodies are proteins of the immune system with the function of binding to foreign substances in the body, thereby targeting them for destruction.

All animals need proteins in their diet to provide the essential amino acids that cannot be synthesized by the animal. Digestion breaks the proteins down so that they can be use in the metabolism.

Proteins in mammalian cells have an average life ranging from minutes to years, with an average of only 1–2 days, before they are degraded and recycled by the nano machines.

ATP (Adenosine triphosphate) is used as a source of energy for all living organisms. It consists of three components, a nitrogenous base (adenine), the sugar ribose, and a triphosphate. It is a precursor of DNA and RNA, used to make protein, and is an essential component of muscles and nerves.

In photosynthetic eukaryotic cells such as algae and higher plants, it is produced by mitochondria which use the energy of sunlight to strip electrons from hydrogen atoms. This maintains an electrical gradient across cell membranes permitting the mitochondria to form molecules of ATP using the electrical current to drive a molecular motor (known as a coupling factor). This operates rather like a rechargeable battery which stores sunlight energy in the form of ATP but can operate in reverse, consuming ATP to provide energy.

Animals, of course, cannot produce ATP using sunlight, so they must get energy from food some of which is converted into ATP. It is regenerated in prodigious quantities by coupling factors so that the human body recycles the equivalent of its own body weight of ATP each day.

Reaction centres are the nano-machines of the most complex biological reactions in nature. In photosynthesis the energy of a light photon knocks an electron out of a molecule (typically chlorophyll) and the missing electron is quickly replaced by another supplied by a quartet of manganese atoms on one side of a membrane. In turn, the manganese atoms acquire four electrons by breaking down nearby water molecules using the energy supplied by sunlight. The hydrogen ions (hydrogen atoms minus their electron) are shunted to one side of a membrane while the oxygen from the water molecule is released to search for more electrons. Meanwhile the electrons are shunted off to make sugars like ATP.

Rubisco is the acronym for ribulose biphosphate carboxylase/oxygenase. It is a protein complex responsible for fixing carbon dioxide in all oxygen producing photo-synthetic organisms. It is probably the most important protein on Earth as it produces about 99% of the organic material upon which all life depends. We (and all animals) are totally dependent on it for our existence.It is a very ancient molecule, that evolved when the concentration of carbon dioxide was greater, and it is very inefficient. About 30% of the time it mistakes oxygen for carbon and wastes energy producing a useless molecule. And it is slow. It make a product about five times a second compared to other cell enzymes that are about a 100 times faster. Evolution does not always produce the most efficient devices, merely those that work.