Activation of amino acids is carried out by a two step process catalyzed by aminoacyl-tRNA synthetases. Each tRNA, and the amino acid it carries, are recognized by individual aminoacyl-tRNA synthetases. This means there exists at least 20 different aminoacyl-tRNA synthetases, there are actually at least 21 since the initiator met-tRNA of both prokaryotes and eukaryotes is distinct from non-initiator met-tRNAs. Activation of amino acids requires energy in the form of ATP and occurs in a two step reaction catalyzed by the aminoacyl-tRNA synthetases. First the enzyme attaches the amino acid to the a-phosphate of ATP with the concomitant release of pyrophosphate. This is termed an aminoacyl-adenylate intermediate. In the second step the enzyme catalyzes transfer of the amino acid to either the 2'� or 3'�OH of the ribose portion of the 3'-terminal adenosine residue of the tRNA generating the activated aminoacyl-tRNA. Although these reaction are freely reversible, the forward reaction is favored by the coupled hydrolysis of PPi.
Accurate recognition of the correct amino acid as well as the correct tRNA is different for each aminoacyl-tRNA synthetase. Since the different amino acids have different R groups, the enzyme for each amino acid has a different binding pocket for its specific amino acid. It is not the anticodon that determines the tRNA utilized by the synthetases. Although the exact mechanism is not known for all synthetases, it is likely to be a combination of the presence of specific modified bases and the secondary structure of the tRNA that is correctly recognized by the synthetases.
It is absolutely necessary that the discrimination of correct amino acid and correct tRNA be made by a given synthetase prior to release of the aminoacyl-tRNA from the enzyme. Once the product is released there is no further way to proof-read whether a given tRNA is coupled to its corresponding tRNA. Erroneous coupling would lead to the wrong amino acid being incorporated into the polypeptide since the discrimination of amino acid during protein synthesis comes from the recognition of the anticodon of a tRNA by the codon of the mRNA and not by recognition of the amino acid.
Most microorganisms and plants can biosynthesize all 20 standard amino acids, while animals (including humans) must obtain some of the amino acids from their diet. The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids. Key enzymes that synthesize certain amino acids are not present in animals � such as aspartokinase, which catalyzes the first step in the synthesis of lysine, methionine, and threonine from aspartate. If amino acids are present in the environment, microorganisms can conserve energy by taking up the amino acids from their surroundings and downregulating their biosynthetic pathways.
In animals, amino acids are obtained through the consumption of foods containing protein. Ingested proteins are broken down through digestion, which typically involves denaturation of the protein through exposure to acid and hydrolysis by enzymes called proteases. Some ingested amino acids are used for protein biosynthesis, while others are converted to glucose through gluconeogenesis, or fed into the citric acid cycle. This use of protein as a fuel is particularly important under starvation conditions as it allows the body's own proteins to be used to support life, particularly those found in muscle.
Humans can produce 10 of the 20 amino acids. The others must be supplied in the food. Failure to obtain enough of even 1 of the 10 essential amino acids, those that we cannot make, results in degradation of the body's proteins�muscle and so forth�to obtain the one amino acid that is needed. Unlike fat and starch, the human body does not store excess amino acids for later use�the amino acids must be in the food every day. The 10 amino acids that we can produce are alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine. Tyrosine is produced from phenylalanine, so if the diet is deficient in phenylalanine, tyrosine will be required as well. The essential amino acids are arginine (required for the young, but not for adults), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino acids are required in the diet.
Now we shall finish this page with several special topics:
Mentioned in passing are viruses. These are strands or segments of nucleic acids encased in a lipid and/or protein coating. They are not living matter although they can reproduce in cells. Although some viruses are beneficial, most disrupt chromosomes, and can insert themselves into DNA or RNA, causing infections. The best known virus today is HIV, which through AIDS destroys the body's ability to overcome disease and cancer. These belong to the class of organic materials known as antigens. In animals, the antigens that threaten their well-being are attacked by antibodies, generated by immune response systems (e.g., lymphocytes)
A brief comment about how living organisms derive energy needed to function, usually through metabolism, which describes several possible chemical reactions. A general way is any process that releases energy when bonds are broken. In plants, photosynthesis is an endothermic reaction involving interaction of sunlight with chloroplasts. In animals, respiration and fermentation release energy when appropriate organic molecules are catabolized (degraded or broken down). About half that energy is stored in a group of molecules, chief of which is ATP (Adenosine TriPhosphate) synthesized naturally from ribose sugar, an adenine base, and phosphate molecules. Here is its structural formula:
At the beginning of this page we pointed out that there are three fundamental life forms: Bacteria, Plants, and Animals. Bacteria cells are, as was shown, fairly simple. Plant and animal cells are more complex, as summarized by these diagrams:
Plants are very important in that they are the largest source of "food" which provides both the material and the energy needed to create and sustain life. The basic process involves photosynthesis in which the energy sources is (usually) the Sun. Solar photons (hν) energize a reaction between CO2 and H2O to yield glucose and Oxygen, according to this formula:
This diagram describes the photosynthesis process:
Oxygenic photosynthesis is carried out in two steps, 1) the light reactions which use pigments to capture solar energy and 2) the dark reactions which use the energy from the light reactions to fix atmospherically derived carbon (CO2) into organic carbon (sugars). It should be noted that the final product is not actually glucose as depicted in the equation above,we just don't usually discuss the last step when we talk about photosynthesis. Glucose does result from photosynthesis, but it usually present in polymeric form either as sucrose (a dimer) or starch (a polymer).
The organic molecule Chlorophyll is the essential agent in plant photosynthesis. It consists of a porphyrin ring and a hydrophobic phytol tail, as shown in this structural formula.
The process is centered within the chloroplasts. It is interesting to note the structural similarities between chlorophyll and hemoglobin, a molecule found in higher order animals.
Hemoglobin is involved in one of the most vital processes in the human body (and in other higher animals) - respiration. Oxygen from the air attaches to hemoglobin carried in the blood and reacts with various molecules to catabolically break them down, releasing energy. Aerobic oxidation is expressed in this formula:
Some animals and plants can obtain energy without the use of Oxygen. This is an anaerobic process.
Plants and animals interact with each other as sources of life-sustaining food. Plants form the base of the food chain. Next are the herbivores - animals that consume only plants. At the top are the omnivores - animals that eat both plants and other animals. Food chains can also be described in terms of producers and consumers, predators and prey, or trophic levels. The sequence of consumption will vary with the different ecosystems involved. Here is one example:
Twenty-first century humankind has a sophisticated food chain system in terms of its infrastructure. Consider this example which starts with a farm (upper left) and shows food production as illustrated by chickens (it could be cows or pigs or crops) as it moves to its final destination - people - through modern food distribution centers.
Now, armed with this general background in Biology/Biochemistry, we will proceed to the next page, which covers the origin and history of life (primarily on Earth) and the tenets of Evolution.