Companion to the "Abiogenesis for the Birdwatcher" page
One of the bases which make up the genetic code in DNA and RNA.
A period of 1000 million years. (Which the Americans persist in illogically calling a billion years. 1000 million is actually a milliard, a very useful term which is still regularly used in Dutch but seems unfortunately to be dying out in English).
An important group of molecules, 20 of which form the jigsaw pieces out of which all proteins are built. They consist of an amino group (NH2), a carboxyl group (COOH) which gives them their acidic properties, and a side chain. As a result they look like this.
H-N-H
|
O=C--C--- side chain
| |
H-O H
A key component of many organic reactions. A pungent smelling gas, with a formula of NH3.
The smallest possible piece of an element. For the purposes of chemistry and biology, atoms can be regarded as little balls which are indivisible and unchanging. (Atomic physicists know different.)
Adenosine tri-phosphate. A vital component of the energy provision in cells.
Generally speaking, an alkaline compound (= opposite of acidic).
In this context, one of the four carriers of genetic information in DNA (adenine, cytosine, guanine, thymine). Two of these (cytosine and thymine) are pyramidines and the other two are purines.
In RNA, the thymine is replaced by another base: uracil.
A compound with the general structure:
H H H | | | H-C-C-C- ... | | | O O O | | | H H HThe name comes from the fact that the repeating unit consists of a carbon atom plus a molecule of water.
An inorganic substance that speeds up a chemical reaction, without changing the nature of the reaction or changing the catalyst itself. In some cases the reaction may, without the catalyst, be so slow that it effectively does not happen at all.
Chemical substances are represented by a formula showing how many atoms of each element are present in each molecule. For example water, as most people know, is H2O - each molecule consists of two atoms of hydrogen and one of oxygen.
The commonest elements in organic chemistry are all represented by their initial letter - Carbon, Oxygen, Hydrogen and Nitrogen - as are also Sulphur and Phosphorus. But since there are 92 elements, most of them require two letters, eg Ca for Calcium and Mg for Magnesium. Some metals however have abbreviations which may seem obscure as they come from Latin or German. For example:
Na Sodium K Potassium Fe Iron W TungstenWith organic chemistry it is fairly common for the formula to also convey some basic information on the structure. For example ethyl alcohol - the alcohol in beer, whisky etc - looks like this:
H H | | H-C-C-O-H | | H HOne might suppose the formula would be written C2H6O, but it is actually written C2H5OH - C2H5 being the ethyl group and the OH group being a distinctive feature of alcohols.
H-C=C-H(that should actually be a triple-bond in the middle, not a double). Replace one of the hydrogens by a cyanide group and you get cyano-acetylene:
H-C=C-C-N
Deoxyribonucleic acid. The carrier of genetic information in all living things. This is a nucleic acid where the sugar component is a sugar called deoxyribose. DNA has the structure of two chains twisted around each other - the famous double helix. Each chain is made up of nucleotides.
The essence of DNA is its complementary chains: every occurrence of the base adenine in one chain is matched by the base thymine in the other, and every occurrence of cytosine in one is matched by the base glycine in the other.
All matter, including all of the thousands of known chemicals and millions of living organisms, is made up of a small number of elements - 92 of them. (There are also another dozen or so which have been manufactured in nuclear reactors). Indeed only about forty of the 92 are at all common or well known: for example oxygen, carbon, hydrogen, iron, lead, copper and so on.
A protein that acts as a catalyst, speeding up a biochemical reaction, but not altering its nature.
Plants, animals and in fact all multicellular organisms are eukaryotes, and so are some single-celled organisms.
O=C-- | HFormaldehyde is well-known for being the common preservative fluid used for biological specimens.
This is the means by which the sequence of amino acids in a protein is coded in DNA. Each amino acid is represented by a "codon triplet" - a sequence of three bases.
As there are four different bases (adenine, cytosine, guanine and thymine), this gives 4x4x4 = 64 possible combinations. As there are only 20 amino acids, some acids are coded for by several triplets. In addition some triplets do not code for any amino acid, but give the signal to stop coding when a protein is complete.
A nine-step process which converts glucose into pyruvate and also releases ATP. This process occurs in all living organisms. With one extra step added it is the process that yeast uses for converting sugar to alcohol.
The pyruvate can be used in other processes (such as the citric-acid cycle) which release still more ATP.
A lipid molecule consists of a small head and a long tail. The small head is a charged group of atoms, such as a phosphate or sugar, while the tail is a hydrocarbon chain, which carries no charge. The head attracts water, while the tail repels it. Lipids are also known as fats.
The simplest hydrocarbon: CH4. A colourless, odourless gas; the main component of the natural gas used for cooking in much of Europe.
A molecule is the smallest possible unit of a chemical compound. It is made up of atoms. Molecules are described by chemical formulae.
A single sub-unit of a polymer.
A long chain molecule, so called because the first nucleic acids were discovered in the nucleus of cells. Composed of nucleotides.
Part of a nucleotide: a sugar molecule combined with a base.
One of the basic repeating units of DNA or RNA. Consists of a combination of a phosphate, a sugar (deoxyribose in DNA or ribose in RNA) and a base.
An oxidising environment is (surprise!) one in which oxygen is available, either in the form of free oxygen or molecules which readily release oxygen. (Actually some other elements are also oxidisers, but that can be ignored here.) The opposite of oxidising is reducing.
A (negatively charged) group of one phosphorus and four oxygen atoms: PO4
Process by which plants harness the energy of the sun. Carbon dioxide and water are converted into carbohydrates, and oxygen is released. It is carried out by chlorophyll, which gives plants their green colour
A long chain molecule made up of repeating sub-units (called monomers). For example, if you string a large number of ethene molecules (C2H4) together, you get polythene.
And if you string together a large number of sugar monomers, you get starch.
A peptide consists of two or more amino acids joined together; a polypeptide is a long chain of amino acids. Polypeptides are precursors of proteins.
A prebiont or protobiont is an aggregate of organic material that manages to maintain an internal environment different from its surroundings. It could also be called a protocell.
prior to the existence of living organisms
An infectious agent that consists only of protein, with no nucleic acid. Notorious for causing BSE or 'mad cow disease' and Creutzfeld-Jakob disease. The name derives loosely from 'proteinaceous infectious particle'.
A prokaryotic cell is a comparatively simple cell, containing no nucleus or other organelles (unlike a eukaryotic cell).
Bacteria are prokaryotes.
One of the most important classes of molecule in biochemistry. A protein consists of one or more polypeptides, where a polypeptide is in its turn a chain of amino acids. Proteins are required for both the structure and function of cells and body organs.
A base containing a single ring. For example, cytosine looks like this (to within the limitations of ASCII art):
H-N-H H
\ /
C--C
/ \
N C-H
\ /
C--N
/ \ (In DNA, this H is
O H replaced by the
sugar molecule)
Purines, on the other hand, contain a double ring.
Iron Sulphide, FeS2. Commonly known as 'fools gold'.
A negative ion, C3H3O3, looking as below. Combine it with a hydrogen ion, and you get pyruvic acid. Pyruvate is an important part of energy-generating processes in cells.
H | H-C-H | C=O | C=O | O
Essentially an environment with an excess of hydrogen. The opposite of oxidising. Free oxygen cannot exist in a reducing environment, as it gets converted to water.
An RNA molecule that can act as an enzyme.
Ribonucleic acid. Similar to DNA, but with the sugar ribose instead of deoxyribose and with the base uracil instead of thymine. Normally found as a single chain, unlike DNA.
An enzyme used in the construction of molecules. The aminoacyl tRNA synthetases are the substances which build proteins by attaching amino acids to an RNA molecule.