Whether larger than life or smaller that the eye can see, the most important goal for all living organisms is staying alive! It takes a constant input of energy to stay alive. In the most fundamental sense, in addition to water, all life requires three basic things in order to stay alive:
Energy--(e.g., from food, sunlight or can even get from eating rocks!)
Carbon--because all living creatures from bears to bacteria are ~ ½ carbon.
3.A way to breathe! OR a steep hill!--this is so that the energy can flow, like electricity through a wire or water over a dam and ultimately, make ATP. In a world with nothing moving/flowing (including energy), life would come to a grinding halt! The hill is needed, because the easiest, most natural direction of movement is downhill not uphill.
A basic understanding of atomic structure is essential to understanding the concept of how energy is extracted from the foods that living things eat and used to perform bodily functions like jumping and playing, and in order to introduce electrons as the way "energy" truly exists and gets transferred from food and light to cells and then converted to ATP.
Energy, Electrons, and…..Basic Atomic Structure
Matter is composed of atoms. Atoms themselves are composed of three basic particles: protons (with a positive electrical charge), electrons (with a negative electrical charge), and neutrons (with no electrical charge). Protons and neutrons are bundled together in the center of the atom, an area called the nucleus. Here, they are protected from the outside world and are not involved in ordinary chemical processes/reactions, only nuclear reactions like in an atomic bomb or nuclear power reactor. Electrons move around the nucleus in an orbit, like the moon around the earth. In these outer orbits, electrons in one atom can interact (e.g. swap/exchange) with electron orbits of neighboring atoms; this is basically how chemical reactions occur.
The atom made up of one proton and one electron is called hydrogen. The proton and electron stay together because just like two magnets, the opposite electrical charges attract each other. The particles in an atom are not still. The electron is constantly spinning around the nucleus. The centrifugal force of the spinning electron keeps protons and electrons from coming into contact with each other, much as the earth's rotation keeps it from plunging into the sun.
Positively and Negatively Charged Atoms -- "Ions"
Each atom of the same element is characterized by a certain number of protons in the nucleus, known as the atomic number. In pure elemental form, like on the periodic table, atoms have the same number of electrons in orbit around the nucleus, thus the amount of positive charge from protons exactly balances or cancels out the amount of negative charge from electrons to give a neutral atom with no net/excess + or -- charge.
Atoms can have electrical charges. This results when the number of protons and electrons is not exactly balanced. Some atoms can either gain or lose electrons (the number of protons never changes in an atom). If an atom gains electrons, the atom becomes negatively charged. If the atom loses electrons, the atom becomes positively charged (because the number of positively charged protons will exceed the number of electrons). An atom that carries an electrical charge is called an ion.
Cations (positively-charged ions) and anions (negatively-charged ions) are formed when atoms lose or gain electrons. The electrostatic attraction between the positives and negatives brings the particles together and creates an ionic compound, such as sodium chloride, NaCl, or table salt.
In an electrically neutral atom, the positively charged protons are always balanced by an equal number of negatively charged electrons. Hydrogen is the simplest atom with only one proton and one electron. Helium is the second simplest atom. It has two protons in its nucleus and two electrons spinning around the nucleus. With helium, the third particle is introduced. Because the two protons in the nucleus have the same charge on them, they would tend to repel each other, and the nucleus would fall apart. To keep the nucleus from pushing apart, helium has two neutrons in its nucleus. As neutrons have no electrical charge on them, they act as a sort of nuclear glue, holding the protons, and thus the nucleus, together.
An electron shell may be thought of as the orbit followed by electrons around an atom's nucleus. Each shell can contain only a fixed number of electrons and must fill completely before electrons can be added to an outer shell. The electrons in the outermost shell determine the chemical properties of the atom.
Electrons and the Chemical Reactions of Life
The most important chemical property of atoms controlled by electrons is whether or not and how an element reacts--no matter where it is--the soil, ocean or in our bodies! Elements with completely filled electron shells, those at the end of each row of the periodic table--He, Ne, Ar, are happily replete and thus, not willing to give up or take on any more electrons. These elements are very inert and do not like to participate in chemical reactions. They also all happen to be gases called the "noble gases".
Living organisms gain energy for life through "Redox reactions"
There are many different types of chemical reactions, but the basic and most important chemical reaction in living systems is the "redox" reaction. This term comes from the two concepts of reduction and oxidation. Oxidation is the loss of electrons, or an increase in oxidation state by a molecule, atom, or ion. Reduction is the gain of electrons or a decrease in oxidation state by a molecule, atom, or ion. Reduction and oxidation always occur together in the same reaction: they are 2 halves of a whole.
An example of a redox process is the formation of rust:
Fe (iron metal as in steel) + O
(rust or iron oxide)
The Fe starts out with an oxidation number of zero (0) and ends up having an oxidation number of +3. It has been oxidized from a neutral iron atom to a positively-charged iron ion.
also starts out with an oxidation number of zero (0), but it ends up with an oxidation number of 2--. It has been reduced by the Fe to give oxygen anions, O
The substance bringing about the oxidation of the iron atoms is the oxygen, making the oxygen the oxidizing agent. In other words, the oxidizing agent is being reduced (undergoing reduction). The substance bringing about the reduction of the oxygen is the iron metal, making the iron metal the reducing agent. In other words, the reducing agent is being oxidized (undergoing oxidation). Oxidation is always accompanied by reduction. Reactions in which oxidation and reduction are occurring are usually called redox reactions.
It is through such redox reactions in which electrons (= energy) are swapped and transferred from one atom to another, that energy flows from food/sunlight/rocks to our cells!
An important and familiar example of a redox process is photosynthesis which involves the reduction of carbon dioxide into sugars coupled to the oxidation of water into molecular oxygen. The reverse reaction, respiration, oxidizes sugars to produce carbon dioxide and water all over again!
Metabolism is the term used to describe the chemical processes that fuel, or support, life (i.e. eating and digesting food to gain energy), and as described above, the most fundamental chemical process/reaction in metabolism is the redox reaction. Substances called metabolites (e.g. food, nutrients) that include both organic substances and inorganic matter such as oxygen, nitrogen and even metals like iron and manganese, are used during metabolism. Metabolism is linked to all other bodily processes by providing energy or by building and maintaining structures necessary for them to function. There are two components of metabolism.
Catabolism breaks down the large molecules that produce energy for activity. This basically works in three main stages. First, large organic molecules such as proteins or lipids are digested into smaller components outside the cells. Next, these smaller molecules are taken up by the cells and converted to yet smaller molecules, which release some energy. Finally, these smaller molecules are oxidized to water and carbon dioxide in the citric acid cycle and the stripped electrons are carried over to the electron transport chain by NADH (a soluble electron carrier in cells) where energy that is stored in NADH is released and converted to ATP (adenosine triphosphate).
Anabolism uses metabolites to build new tissue for healing, growth and reproduction. This process uses energy to construct complex molecules from simple ones. Anabolism involves three basic stages. First is the production of precursors, such as amino acids and monosaccharides. The next step involves their activation into reactive forms using energy from ATP. The third stage is the assembly of these precursors into complex molecules such as proteins and lipids.
Metabolic Classification of Microbes
Unlike larger eukaryotic organisms which are classified based on their morphology and behavior (e.g. predator, prey, consumer), microorganisms--which are mostly prokaryotes=single--celled bacteria and archaea, are classified based on their metabolism. They are identified by their energy source (light or preformed molecules), by their electron donor (organic or inorganic compounds) and their carbon source (again, organic or inorganic).
Bacteria are classified based on what they eat (or carbon and energy sources). Autotrophs (Latin for self/grow) are able to make their own food from light or chemical sources of energy using only inorganic CO
and include plants, algae, diatoms and phototrophic bacteria like cyanobacteria and purple bacteria, as well as most bacteria that get their energy from inorganic chemicals, minerals and rocks called chemolithotrophs. Heterotrophs (other/grow) obtain their carbon from the tissues or body fluids of other organisms (animals and plants). Chemolithotrophs are organisms that get their energy from inorganic chemicals, rocks/minerals; most chemolithotrophs are also autotrophs and thus use CO
as a carbon source. Heterotrophs get their carbon from pre-formed organic matter; they may also get their electrons from the same organic matter (= chemoorganotrophs), if they instead get electrons from inorganic chemicals and carbon from organic matter, they are called "mixotrophs". They break down complex organic compounds that they take in from around them in order to make them more available (digestible) as food. Each type of heterotroph needs specific conditions and the right kind of organic material. Some bacteria can even decompose organic material at temperatures below freezing. If conditions are right, this heat will be enough to set the stage for the next group of bacteria that live at more moderate mid-range temperatures (~15- 40°C) called mesophiles.
Saprobic bacteria are heteroptrophs that live on decaying material such as a dead body. By decomposing organic material for energy, these microorganisms help recycle nutrients like nitrogen and carbon back into the environment. If it were not for these decomposers, the organic carbon in dead and rotting organisms would remain locked underground, effectively stopping the carbon cycle. The carbon dioxide in the air would be quickly depleted, and there would be none left for plants to carry out photosynthesis. Saprobic bacteria are, therefore, one of the most important links in the carbon cycle.
How life "breathes"--many variations on a theme
Cellular respiration allows organisms to use energy stored in the chemical bonds of organic compounds like glucose (C
) (or inorganic substances like iron and sulfur). The energy in glucose is used to produce ATP. Cells use ATP to supply their energy needs. In respiration, glucose is oxidized and this releases energy. Oxygen is reduced to form water. The carbon atoms of the sugar molecule are released as carbon dioxide CO
. We exhale this water and carbon dioxide.
+ 6 O
→ 6 CO
+ 6 H
The citric acid cycle is a series of chemical reactions of central importance in all living cells that use oxygen or other substitutes in place of oxygen (e.g., sulfate, nitrate, Fe3+or rust-remember that anaerobic respiration also uses the citric acid cycle to make ATP) as part of cellular respiration. In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion. In aerobic organisms, the citric acid cycle is part of a metabolic pathway involved in the chemical conversion of carbohydrates, fats and proteins into carbon dioxide and water to generate a form of usable energy, ATP.
The focus now moves from the background information on the fundamental requirements for staying alive-energy in the form of electrons, electron transfers in the form of redox reactions and organic or inorganic fuels to drive metabolism, to the environmental context of living organisms on a large scale and the relevant nutrient/elemental cycles occurring in natural environments.
Photosynthesis is the process by which plants and mostly bacteria convert sunlight into energy. The organisms that carry it out are called phototrophs. Photosynthesis evolved early in the evolutionary history of life on Earth when all forms of life were microorganisms and the atmosphere had no oxygen and much more carbon dioxide. Plants are not the major primary producers on the planet--these are marine phototrophic bacteria. Phototrophic bacteria like the cyanobacteria use the energy from sunlight to make ATP, the fuel used by all living things. The conversion of sunlight energy into usable chemical energy is associated with the actions of pigments like chlorophylls--there are many different types of chlorophylls that come in many colors other than green (e.g., purple). Generally, the photosynthetic process uses water and releases the oxygen that we must have to stay alive. The first organisms to do this were the cyanobacteria over 2 billion years ago.
Plants are the only photosynthetic organisms to have leaves (and not all plants have leaves). A leaf operates as a solar collector crammed full of photosynthetic cells. The raw materials of photosynthesis, water and carbon dioxide, enter the cells of the leaf, and the products of photosynthesis, sugar and oxygen, leave the leaf.
Water enters the root and is transported up to the leaves through specialized plant cells known as xylem. Land plants must guard against drying out (desiccation) and so have structures known as stomata to allow gas to enter and leave the leaf. Carbon dioxide cannot pass through the protective waxy layer covering the leaf (cuticle), but it can enter the leaf through an opening flanked by two guard cells. Likewise, oxygen produced during photosynthesis can only pass out of the leaf through the opened stomata. Unfortunately for the plant, while these gases are moving between the inside and outside of the leaf, a great deal of water is also lost. Scientists study fossil leaves and count the number of stomata to tell what the carbon dioxide level of Earth's atmosphere was in the past.