Amino acid residue (in a polypeptide) When two or more amino acids combine to form a peptide, the elements of water are removed, and what remains of each amino acid is called amino acid residue. Amino acid residues are therefore structures that lack a hydrogen atom of the amino group (-NH-CHR-COOH), or the hydroxy moiety of the carboxy group (NH2-CHR-CO-), or both (-NH-CHR-CO-); all units of a peptide chain are therefore amino acid residues. (Residues of amino acids that contain two amino groups or two carboxy groups may be joined by isopeptide bonds, and so may not have the formulas shown.) The residue in a peptide that has an amino group that is free, or at least not acylated by another amino acid residue (it may, for example, be acylated or formylated), is called N-terminal; it is the N-terminus. The residue that has a free carboxy group, or at least does not acylate another amino acid residue (it may, for example, acylate ammonia to give -NH-CHR-CO-NH2), is called C-terminal.
The following is a list of symbols for amino acids (use of the one-letter symbols should be restricted to the comparison of long sequences):
|
A |
Ala |
Alanine |
|
B |
Asx |
Asparagine or aspartic acid |
|
C |
Cys |
Cysteine |
|
D |
Asp |
Aspartic acid |
|
E |
Glu |
Glutamic acid |
|
F |
Phe |
Phenylalanine |
|
G |
Gly |
Glycine |
|
H |
His |
Histidine |
|
I |
Ile |
Isoleucine |
|
K |
Lys |
Lysine |
|
L |
Leu |
Leucine |
|
M |
Met |
Methionine |
|
N |
Asn |
Asparagine |
|
P |
Pro |
Proline |
|
Q |
Gln |
Glutamine |
|
R |
Arg |
Arginine |
|
S |
Ser |
Serine |
|
T |
Thr |
Threonine |
|
V |
Val |
Valine |
|
W |
Trp |
Tryptophan |
|
Y |
Tyr |
Tyrosine |
|
Z |
Glx |
Glutamine or glutamic acid |
Aminoacyl-tRNA synthetases (aaRSs) When ribo-somes pair a tRNA (transfer ribonucleic acid) with a codon (three bases in a DNA or RNA sequence), an amino acid is expected to be carried by the tRNA. Since each tRNA is matched with its amino acid before it meets the ribosome, the ribosome has no way of knowing if the match was made. The match is made by a family of enzymes called aminoacyl-tRNA synthetases. These enzymes charge each tRNA with the proper amino acid via a covalent ester bond, allowing each tRNA to make the proper translation from the genetic code of DNA into the amino acid code of proteins. Cells make at least 20 different aminoacyl-tRNS synthetases, one for each of the amino acids.
Aminoacyl-tRNA synthetases belong to two classes, depending on which amino acid they specify. Class i enzymes usually are monomeric and attach to the carobxyl of their specific amino acid to the 2′ OH of adenosine 76 in the tRNA molecule. Class ii enzymes are either dimeric or tetrameric and attach to their amino acids at the 3′ OH. These enzymes catalyze first by activating the amino acid by forming an aminoacyl-adenylate. Here the carboxyl of the amino acid is linked to the alpha-phosphate of ATP, displacing pyrophosphate. After the corrected tRNA is bound, the aminoacyl group of the aminoacyl-adenylate is transferred to the 2′ or 3′ terminal OH of the tRNA.
Recent studies have shown that aminoacyl-tRNA synthetases can tell the difference between the right and the wrong tRNA before they ever start catalysis, and if the enzyme binds aminoacyl-adenylate first, it is even more specific during tRNA binding. Previous studies have also proved that aminoacyl-tRNA synthetases reject wrong tRNAs during catalysis. Other research has shown that specific aaRSs play roles in cellular fidelity, tRNA processing, RNA splicing, RNA trafficking, apoptosis, and transcriptional and translational regulation. These new revelations may present new evolutionary models for the development of cells and perhaps opportunities for pharmaceutical advancements.
Amino group (-NH2) A functional group (group of atoms within a molecule that is responsible for certain properties of the molecule and reactions in which it takes part), common to all amino acids, that consists of a nitrogen atom bonded covalently to two hydrogen atoms, leaving a lone valence electron on the nitrogen atom capable of bonding to another atom. it can act as a base in solution by accepting a hydrogen ion and carrying a charge of +1. Any organic compound that has an amino group is called an amine and is a derivative of the inorganic compound ammonia, NH3. A primary amine has one hydrogen atom replaced, such as in the amino group. A secondary amine has two hydrogens replaced. A tertiary amine has all three hydrogens replaced. Amines are created by decomposing organic matter.
Amniocentesis Amniocentesis is the removal of about two tablespoons of amniotic fluid via a needle inserted through the maternal abdomen into the uterus and amniotic sac. This is done to gain information about the condition, and even the sex, of the fetus. The fluid contains cells from the fetus and placenta.
Some women have a greater chance of giving birth to a baby with a chromosome problem, and amniocente-sis can provide the answers if performed at about 16 weeks gestation (second trimester) or later. Chromosome analysis and alpha-fetoprotein (AFP) tests are two such tests, and these check for chromosome abnormalities such as Down’s syndrome and whether there are any openings in the fetal skin, such as in the spine, that could lead to neural-tube defects like spina bifida or anen-cephaly, or inherited disorders such as cystic fibrosis.
While the procedure is relatively safe, some problems that can occur are miscarriage (1 in 200, or 0.5 percent chance), cramping, and infections (less than 1 in 1,000).
Amniocentesis can also be performed during the second and third trimesters to determine fetal lung maturity, to verify the health of the fetus in cases of Rh sensitivity, and to identify any infections.
First used in 1882 to remove excess amniotic fluid, it is often used in late pregnancy to test for anemia in fetuses with Rh disease and to check if the fetal lungs are advanced enough for delivery to occur.
Amnion The amnion is a thin, but tough, transparent membranous sac and innermost of the four extra embryonic membranes (allantois, yolk sac, chorion) that encloses the embryo of reptiles, birds, and mammals. These membranes hold the amniotic fluid and form a protective layer for the fetus, insulating it from bacteria and infection.
Amniotes Any of the vertebrates such as reptiles, birds, and mammals that have an amnion surrounding the embryo.
Amniotic egg A calcium based or leathery shelled water-retaining egg that enables reptiles, birds, and egg-laying mammals, such as the monotremes (duck billed platypus and two species of echidna, spiny anteaters), to complete their life cycles on dry land.
Amoebic dysentery Dysentery caused by a protozoan parasite (Entamoeba histolytica), mostly caused by poor sanitary conditions and transmitted by contaminated food or water.
Amphibian Cold-blooded, or ectothermic, vertebrates in the class Amphibia. These include the frogs and toads (order Anura, or Salientia), salamanders and newts (order Urodela, or Caudata), and the caecilians, limbless amphibians (order Apoda, or Gymnophiona). There are more than 11,000 species of amphibians, and they are believed to be the first vertebrate species to live on land.
Located between the fish and reptiles on the evolutionary scale, they are the most primitive of the terrestrial vertebrates and undergo a metamorphosis from water-breathing limbless larva (tadpole) to land-loving, or partly terrestrial, air-breathing four-legged adult.
Eggs are typically deposited in water or a wet protected place, although some do lay eggs in dry places. The eggs are not shelled and do not possess the membranes that are common in reptiles or higher vertebrates. Adults have moist skins with no scales or small scales, and they are specialized in living habitats. Each has its own evolutionary adaptations from the jumping ability (over 17 feet in some cases) of frogs and toads, to the limbless caecilians, to the long tails of the salamanders and newts. For example, frogs can enter aestivation, a period of dormancy similar to hibernation, when experiencing long periods of heat or drought conditions, and they can breathe through their skin in a process called cutaneous gas exchange. The most poisonous frog known, Phyllobates terribilis, only needs 0.00000007 ounce of skin secretion to kill a predator, while an antibiotic secreted from the African clawed frog (Xenopus laevis) may someday be used to treat burns and cystic fibrosis.
Over the last 50 years, many species of amphibians around the world have declined markedly in numbers; some species have become extinct. In many instances, these declines are attributable to adverse human influences acting locally, such as deforestation, draining of wetlands, and pollution.
However, in 1988, herpetologists (scientists who study amphibians) from many parts of the world reported declines in amphibian populations in protected, or pristine, habitats such as national parks and nature reserves, where such local effects could not be blamed. This suggested that there may be one or more global factors that are affecting climatic and atmospheric changes and adversely affecting amphibians, such as increased UV-B radiation, widespread pollution, acid rain, and disease. In effect, the decline could be the result of human-induced changes to the global ecosystem and could have far-reaching consequences for human survival.
Amphipathic molecule A molecule that has both a hydrophilic (water soluble, polar) region and a hydrophobic (water hating, nonpolar) region. The hydrophilic part is called the head, while the hydropho-bic part is called the tail. Lipids (phospholipids, cholesterol and other sterols, glycolipids [lipids with sugars attached], and sphingolipids) are examples of amphi-pathic molecules.
Amphipathic molecules act as surfactants, materials that can reduce the surface tension of a liquid at low concentrations, and are used in wetting agents, demisters, foaming agents, and emulsifiers.
Anabolism The processes of metabolism that result in the synthesis of cellular components from precursors of low molecular weight.
Anaerobic Any organism or environmental or cellular process that does not require the use of free oxygen. Certain bacteria such as Actinomyces israeli, Bacteroides fragilis, Prevotella melaninogenica, Clostridium difficile, and Peptostreptococcus are anaerobes.
In effect, an anaerobic organism does not need oxygen for growth. Many anaerobes are even sensitive to oxygen. Obligate (strict) anaerobes grow only in the absence of oxygen. Facultative anaerobes can grow either in the presence or in the absence of oxygen.
Anagenesis A pattern of evolutionary change along a single, unbranching lineage involving the transformation of an entire population, sometimes so different from the ancestral population that it can be called a separate species. Examples would be one taxon replacing another or the transformation of a single ancestral species into a single descendant species. Anagenesis is also known as phyletic evolution and is the opposite of cladogenesis.
In medicine, it refers to the regeneration of tissue or structure.
Analog A drug whose structure is related to that of another drug but whose chemical and biological properties may be quite different.
Analogy The similarity of structure between two species that are not closely related; usually attributed to convergent evolution. Structures that resemble each other due to a similarity in function without any similarity in underlying structure (or origin) are called analogous structures. For example, birds and bats each have their forelimbs modified as wings. They are analogous because they evolved independently after the earliest birds and bats diverged from their common ancestor, who did not have wings. However, the details of their structures are quite different.
A photomicrograph of Clostridium botulinum, a strictly anaerobic bacterium, stained with Gentian violet. The bacterium C. botulinum produces a nerve toxin that causes the rare but serious paralytic illness botulism.
Anation Replacement of the ligand water by an anion in a coordination entity.
