**7. Nomenclature**

**cDNA library:** The collection of single-stranded DNA products generated by reverse tran‐ scription using total RNAs isolated from an organism as templates.

**Gibbs free energy: T**he thermodynamic potential of a system at a certain temperature and pressure. In this chapter, Gibbs free energy indicates the stability of a certain hairpin structure.

**Heat shock response:** The coordinated production of several proteins and other essential cellular components by a cell that work together to facilitate survival when the cell is exposed to an environmental temperature that is higher than its ideal surviving temperature.

**Hydration shell:** A shell-like structure formed by water molecules surrounding a molecule.

**Melting temperature (Tm):** The temperature at which half of the double-stranded molecules within a population assume a single-stranded conformation.

**Quorum sensing**: The coordinated regulation of bacterial gene expression in response to a secreted signal molecule that indicates the population density. When the signal molecule reaches a threshold amount, the cascade of signal-induced regulation occurs.

**Riboswitch:** A *cis-*encoded regulatory RNA element that functions to modulate target gene expression via switching between two mutually different secondary structures. Conforma‐ tional changes within a riboswitch are induced by binding to a metabolite or other small molecule at a specific ligand-binding region.

**RNA thermometer**: A *cis*-encoded RNA element that represses translation via incorporation of the ribosome-binding site within an inhibitory hairpin at non-permissive temperatures. With increased temperature, the inhibitory structures within an RNA thermometer is desta‐ bilized, the ribosome-binding site is exposed, and translation proceeds.

**Shine-Dalgarno (SD) sequence**: Also known as the ribosome-binding site, the Shine-Dalgarno sequence is a sequence on an mRNA molecule to which the ribosome binds. Binding of a ribosome to an SD sequence on a transcript is necessary for the initiation of translation.

**Sigma factor:** A protein factor that facilitates the sequence-specific binding between an RNA polymerase and specific promoter regions on the DNA. Sigma factors are necessary for transcription initiation.

**Structurome:** The collective determination of the secondary structure of each transcript present in a given organism or cell type.

**Transcriptome:** The total population of RNA molecules present in a given organism or cell type.

**5′ Untranslated region (5′ UTR):** The region of a protein-encoding transcript that is located upstream of the translation start site. The 5′ UTR thus does not containing amino acid-coding sequences but rather contains the ribosome-binding site and often houses regulatory elements, such as RNA thermometers.
