Team:Peking R/Notebook/Vocabulary

Vocabulary

TPP
thiamine pyrophosphate is a thiamine (vitamin B1) derivative which is produced by the enzyme thiamine pyrophosphatase.

theophylline
Theophylline, also known as dimethylxanthine, is a methylxanthine drug used in therapy for respiratory diseases such as COPD and asthma under a variety of brand names.

RBS(Ribosomal Binding Site)
A ribosomal binding site (RBS) is a sequence on mRNA that is bound by the ribosome when initiating protein translation.

Ribozyme
A ribozyme is an RNA molecule with a well defined tertiary structure that enables it to catalyze a chemical reaction. Ribozyme means ribonucleic acid enzyme. It may also be called an RNA enzyme or catalytic RNA. Many natural ribozymes catalyze either the hydrolysis of one of their own phosphodiester bonds (self-cleaving ribozymes), or the hydrolysis of bonds in other RNAs. Some have been found to catalyze the aminotransferase activity of the ribosome. Examples of ribozymes include the hammerhead ribozyme, the VS ribozyme and the hairpin ribozyme.

Riboswitch
In molecular biology, a riboswitch is a part of an mRNA molecule that can directly bind a small target molecule, and whose binding of the target affects the gene's activity.Thus, an mRNA that contains a riboswitch is directly involved in regulating its own activity, in response to the concentrations of its target molecule. The discovery that modern organisms use RNA to bind small molecules, and discriminate against closely related analogs, significantly expanded the known natural capabilities of RNA beyond its ability to code for proteins or to bind other RNA or protein macromolecules.

c-di-GMP
Cyclic di-GMP (also called cyclic diguanylate and c-di-GMP) is a second messenger used in signal transduction in a wide variety of bacteria. Cyclic di-GMP is not known to be used by eukaryotes or archaea. The biological role of cyclic di-GMP was first uncovered when it was identified as an allosteric activator of a cellulose synthase found in Gluconacetobacter xylinus.

Intron
An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene. The term intron refers to both the DNA sequence within a gene, and the corresponding sequence in RNA transcripts. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are found in the genes of most organisms and many viruses, and can be located in a wide range of genes, including those that generate proteins, ribosomal RNA (rRNA), and transfer RNA (tRNA). When proteins are generated from intron-containing genes, RNA splicing takes place as part of the RNA processing pathway that follows transcription and precedes translation.

Aptamer
Aptamers are oligonucleic acid or peptide molecules that bind to a specific target molecule. Aptamers are usually created by selecting them from a large random sequence pool, but natural aptamers also exist in riboswitches. Aptamers can be used for both basic research and clinical purposes as macromolecular drugs. Aptamers can be combined with ribozymes to self-cleave in the presence of their target molecule. These compound molecules have additional research, industrial and clinical applications.

Self-Splicing RNA
In molecular biology and genetics, splicing is a modification of an RNA after transcription, in which introns are removed and exons are joined. This is needed for the typical eukaryotic messenger RNA before it can be used to produce a correct protein through translation. For many eukaryotic introns, splicing is done in a series of reactions which are catalyzed by the spliceosome, a complex of small nuclear ribonucleoproteins (snRNPs), but there are also self-splicing introns.

Gibbs Free Energy△G
In thermodynamics, the Gibbs free energy (IUPAC recommended name: Gibbs energy or Gibbs function; also known as free enthalpy to distinguish it from Helmholtz free energy) is a thermodynamic potential that measures the "useful" or process-initiating work obtainable from a thermodynamic system at a constant temperature and pressure (isothermal, isobaric). Just as in mechanics, where potential energy is defined as capacity to do work, similarly different potentials have different meanings. Gibbs energy is the capacity of a system to do non-mechanical work and ΔG measures the non-mechanical work done on it. The Gibbs free energy is the maximum amount of non-expansion work that can be extracted from a closed system; this maximum can be attained only in a completely reversible process. When a system changes from a well-defined initial state to a well-defined final state, the Gibbs free energy ΔG equals the work exchanged by the system with its surroundings, minus the work of the pressure forces, during a reversible transformation of the system from the same initial state to the same final state.

Shine-Dalgarno sequence
The Shine-Dalgarno sequence (or Shine-Dalgarno box), proposed by Australian scientists John Shine and Lynn Dalgarno, is a ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG; in E. coli, for example, the sequence is AGGAGGU. This sequence helps recruit the ribosome to the mRNA to initiate protein synthesis by aligning it with the start codon. The complementary sequence (CCUCCU), is called the anti-Shine-Dalgarno sequence and is located at the 3' end of the 16S rRNA in the ribosome. The eukaryotic equivalent of the Shine-Dalgarno sequence is called the Kozak sequence.
Mutations in the Shine-Dalgarno sequence can reduce translation. This reduction is due to a reduced mRNA-ribosome pairing efficiency, as evidenced by the fact that complementary mutations in the anti-Shine-Dalgarno sequence can restore translation.
When the Shine-Dalgarno sequence and the anti-Shine-Dalgarno sequence pair, the translation initiation factors IF2-GTP, IF1, IF3, as well as the initiator tRNA fMet-tRNA(fmet) are recruited to the ribosome.