Amino acids are the basic building blocks of peptides. All natural occuring
amino acids have the basic structure: H2N–CHR–CO2H, where
R is called the "side-chain" and the carbon adjacent to the COOH is the L
diastereometer. There are twenty naturally occuring sidechains.
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Domain is a word that is used rather loosely when refering to biopolymers. The
general concept behind "domain" is that a long biopolymer is made up of a
series of structural units that comprise designatable stretches of the
sequence. Domains are usually named based on their functions, e.g., an
"SH2 binding domain" of a protein. It is also used frequently in lab jargon to
refer to any part of a protein. Because the designation of a domain is a
fundamental process in the annotation of a biopolymer, the <domain>
element (and its nucleic acid relatives <ddomain> and <rdomain>)
has a very special place in BIOML.
DeoxyRibonucleic Acid: a biopolymer constructed from deoxyribonucleotides, by
linking the 5' phosphate group of one deoxy-ribonucleotide to the 3' hydroxyl
of another deoxyribonucleotide by a phosphodiester bond.
Deoxyribonucleotides are the basic building blocks of DNA. They are composed of
three parts: one beta-D-2-deoxyribose molecule (a sugar), a base
(thymidine, guanine, cytosine or adenine) attached at the 1' position of the
deoxyribose, and a phosphate group attached at the 5' position of the ribose.
The molecular object responsible for the inheritance of a trait. The idea is
now narrowed to include only the DNA strand responsible for the production of a
single polypeptide chains.
Messenger RNA is an RNA molecule that is constructed from a DNA template by a
complicated molecular machine. mRNA is then transported to the ribosome, where
it is translated into a peptide sequence. In prokaryotic organisms, such as
bacteria, the mRNA is a directly read from the DNA template. In eukaryotic
organisms, such as animals and plants, an initial translation of the DNA is
made into RNA, which is then edited to remove non-coding stretches of RNA
(called introns). Once the editing is complete, the resulting RNA molecule is
designated as mRNA and sent to the ribosomes for translation into peptides.
A peptide is formed by linking together amino acids by peptide (amide) bonds.
Once a peptide has been created by a ribosome, it may require further chemical
groups to be added or removed from its component amino acids in order for it to
function correctly. These chemical changes that occur after translation are
called post-translational modifications.
A concept that describes the object responsible for a particlar type of
function in a cell. The idea is now narrowed to included only complexes of
folded and modified linear polypeptide chains.
RiboNucleic Acid: biopolymer constructed from ribonucleotides, by linking the
5' phosphate group of one ribonucleotide to the 3' hydroxyl of another
ribonucleotide by a phosphodiester bond.
Ribonucleotides are the basic building blocks of RNA. They are composed of
three parts: one beta-D-ribose molecule (a sugar), a base (uridine,
guanine, cytosine or adenine) attached at the 1' position of the ribose, and a
phosphate group attached at the 5' position of the ribose.
Subunit is a word that is rather loosely defined, and it is frequently used in
lab jargon to mean a variety of closely related things. For the purposes of
BIOML, a subunit is a high-order building block for a protein defined as the
largest component polypeptide of a protein that is completely held together by
covalent bonds. Subunits associate with each other to form a protein via
non-covalent interactions. Many proteins contain only one type of subunit. A
protein composed of two copies of an identical subunit is refered to as a
"homodimer". If a protein is composed of one copy each of two different
subunits, it is refered to as a "heterodimer".