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VIII How life works http://sgoodwin.staff.shef.ac.uk/phy229.html 8.0 Introduction What are the processes of life? How does Earth life use free energy to produce complexity and internal order? How does Earth life store information? What aspects of Earth life might be found elsewhere? 8.1 The cell The cell is the fundamental unit of life (and often included as a requirement for life). Cells have several properties: Cells are surrounded by a cell wall/membrane (made of lipids and proteins) that separate the interior of the cell from its surroundings and moderate the flow of material into/out of the cell (homeostatis). Cells metabolise, taking-in raw materials and /or energy and converting them to more complex molecules/energy or decompose them (anabolism or catabolism). Cells contain genetic material (DNA or RNA) which is used to build proteins that are used by the cell. Cells reproduce by cell division (asexual or sexual). 8.1 Prokaryotic cells The simplest cells are prokaryotic cells, thought to be the first cells to have developed. Prokaryotic cells contain three main structures: Nucleoid: the genetic material of the cell. Cell wall/membrane: separating the internal components and liquid (cytoplasm) from the external environment. Ribosomes: molecular structures that assemble the proteins required by the cell. They also often have flagella to move, and various molecular machinery. 8.1 Eukaryotic cells Multi-celled organisms, and many single-celled organisms, are made of more complex eukaryotic cells. They contain organelles – specialised sub-units that perform specific functions and allow cells to specialise (and so allow the development of multi-celled organisms). Eukaryotic cells have their DNA stored in a nucleus and have more and more specialised organelles than prokaryotic cells. Some organelles (e.g. mitochondria) have their own DNA and are thought to once have been separate organisms. 8.2 Proteins Proteins perform many functions: They catalyse reactions (enzymes), attack foreign bodies (antibodies), transport information (some hormones), transport material, and form structures (e.g. hair), regulate ion levels etc. etc. etc. 8.2 Producing proteins: Reading DNA The process of converting the information stored in DNA into a protein is very complex and the details are not important to us in this course. The basic route is: TRANSCRIPTION: TRANSCRIPTION A length of DNA that carries the information that will eventually result in a single protein is a gene. DNA is separated into its two strands and a particular enzyme (protein) locates the region of DNA to be transcribed. It then links nucleic acid bases floating around in the cell onto a messenger RNA strand (mRNA) matching the nucleic acid sequence on the gene (but replacing T with A and A with U bases). DNA contains start and stop base sequences to tell the enzyme when to start and stop a transcription. 8.2 Producing proteins: Reading DNA TRANSLATION: TRANSLATION once a mRNA strand has been created it must convert amino acids into the desired protein. The mRNA connects itself to a ribosome which attaches amino acids in the correct order to produce the precise protein (via transfer RNA). Note that the order of the bases is important and DNA and mRNA/tRNA have directions, for instance the sequence UUC tells the ribosome to add a phenylalanine amino acid to the protein, while the CUU sequence tells the ribosome to add a leucine amino acid. The number of amino acids in a protein varies from 2 to several thousand, thus the total number of proteins that can be assembled from the base set of 20 amino acids is vast. Aside: Epigenetics Recently it has become clear that something odd is happening in genetics... We inherit our DNA as a mix of our parent's DNA. In each cell (and globally) various genes are 'switched on' (expressed). Different cells express different genes depending on their type. Stem cells can become any type of cell, and their chemical environment acts to tell them which genes to express and which not. But once they are a particular cell type they are fixed (except some pluripotent cells). It was always thought that what genes were expressed was written into your DNA as well – your DNA set what genes you have and which would be expressed. The only change could come from random mutations. But recent developments suggest that environment plays a role, and environment can change what genes are expressed in a field known as epigenetics. 8.2 The function of proteins After a protein has been produced by a ribosome using the information carried by the mRNA the molecule folds into a complex shape. The shape is determined by the self-interaction of the amino acids as well as interactions with the environment and is not encoded in the DNA. The shape of the protein determines how it will interact with other molecules which may be other proteins (to build structures), 'factors' (e.g. vitamins) that takepart in chemical reactions, foreign molecules, or DNA during replication. 8.3 Evolution and illness If a gene is incorrectly copied it will encode a different sequence that will do a different thing. If an organism is 'lucky' the new protein will do a better or new job and this is one driver of evolution. If an organism is 'unlucky' the new protein cannot do a vital job and the organism is ill or dies. Lactose intolerance is due to a lack of the lactase protein used to break-down the lactose disaccharide carbohydrate found in milk. Rare in northern Europeans (<5%), very common in Africa, Asia and the Americas (>90%). This is encoded on two genes which used to switchoff after infancy but various ethnic groups have developed the ability to stop the switch-off. 8.3 Important cell processes There are various key components to cells. Obviously there needs to be DNA to store information and ribosomes and other machinery to produce proteins. The cell also needs mechanisms to produce, store, and release energy, and do any other jobs that are required. 8.3 Sources of energy Organisms can be divided into two broad classes: Autotrophs: able to fix carbon: the conversion of inorganic carbon into organic molecules. Photosynthesis uses light as an energy source, chemosynthesis uses chemical energy (an electron donor). Heterotophs: require organic molecules as their raw materials (and can then convert this using energy from light or chemical reactions). An example is humans (heterotrophs) eating carbohydrates in something like corn (a photosynthesising autotroph). 8.4 Chloroplasts and photosynthesis Chloroplasts are organelles that conduct photosynthesis. They contain their own DNA and are thought to have their origin as originally separate prokaryotic cells (cyanobacteria). The basic chemical reaction of photosynthesis is: 6CO2 + 12H2O + light ---> C6H12O6 + 6O2 +6H2O Photosynthesis occurs in two stages: the first uses light to produce high-energy molecules, the second uses CO2 to convert these molecules into sugars. The basic structure in photosynthesis is the 'magnesium ring' in chlorophyll a which means that Mg is a crucial element in plants (or cyanobacteria). 8.4 Chloroplasts and photosynthesis Photons excite electrons in the photosynthetic chemical (in most cases chlorophyll) to a high state. A series of transport reactions moves this excited electron through a series of intermediary molecules until it forms ATP and NADPH – two energy storing chemicals. Photosynthesis is uses either red or blue photons rather than the peak wavelengths of Solar radiation. It is thought that they evolved in the sea, and so evolved to use the light available at depths of a few meters. The energy stored in ATP or NADPH can be used to synthesise sugars as a long-term energy store in a reaction that does not require light. 8.4 Energy storage in cells Life stores energy in the form of chemical bonds. The most common form in eukaryotic cells is as adenosine triphosphate (ATP). Energy is released through a reaction with a particular enzyme which removes a phosphate group: ATP + H2O -> ADP + HPO4 the reverse reaction occurring when the organism is at rest and not requiring immediate energy. 8.4 Respiration There are two main ways in which energy is turned into ATP in cells. Anaerobic respiration (no oxygen) where sugars (glucose C6H12O6) are turned into ATP and lactic acid. Producing 2 ATP per glucose with a usable energy of ~120kJ per mole of glucose. glucose Aerobic respiration (with oxygen) where sugar and oxygen combine producing H2O and CO2 as waste products from a process that produces 36 ATP per glucose – which produces ~2160kJ per mole of glucose. glucose Clearly aerobic respiration is a far more efficient energy producer than anaerobic respiration and provides a huge advantage to those organisms that can use it (see the oxygen catastrophe later). Summary The basic components of living organisms on the Earth is the cell. The fundamental components of a cell are the cell wall/membrane, genetic material, and ribosomes. This is all prokaryotic cells contain, whilst eukaryotic cells are far more advanced and contain internal structures called organelles. Ribosomes synthasise proteins from a set of 20 amino acids using information encoded on DNA or RNA via messenger RNA. The complex structure of a protein determines how it will interact with other molecules, many proteins act as catalysts in important biochemical reactions (these are known as enzymes). What does this mean for astrobiology? Terrestrial life depends on the cell and complex biochemical reactions that take place in a water solution (cytoplasm) within that cell. Energy for most organisms comes from Solar radiation – directly into organisms that can photosynthesise light into sugars, and indirectly into organisms that take-in these sugars and convert them into energy (e.g. animals). This is not the only source of energy, some organisms survive without light, using other sources of energy (we will come to these later, as they extend the range of possible environments for life). What does this mean for astrobiology? Therefore the basic requirements for Terrestrial life are water to act as a solvent, complex molecules to store energy and information, and an energy source to drive the reactions (in most cases, ultimately sunlight). So the conditions in which biochemical life (as we know it, or can imagine it) has some ultimate limitations: The temperature must be low enough for liquids to exist, and low enough for highly complex molecules to form and remain stable. Probably <400K. The temperature must be high enough for liquids to exist and for molecules to have higher energy states excitable. Probably >100K. Is it a coincidence that we exist exactly in the middle of this range?