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Related Concept Videos

SN2 Reaction: Mechanism02:27

SN2 Reaction: Mechanism

The kinetic studies of SN2 reactions suggest an essential feature of its mechanism: it is a single-step process without intermediates. Here, both the nucleophile and the substrate participate in the rate-determining step.
The presence of the more electronegative halogen in the substrate creates a polarized carbon-halide bond. The halide pulls the electron cloud generating an electrophilic center at the carbon atom. Thus, the carbon atom carries a partial positive charge while the halide has a...
Nucleophiles02:30

Nucleophiles

The word “nucleophile” has a Greek root and translates to nucleus-loving. Nucleophiles are either negatively charged or neutral species with a pair of electrons in a high-energy occupied molecular orbital (HOMO). As these species tend to donate electron pairs, nucleophiles are considered Lewis bases as well. Negatively charged species, like OH−, Cl−, or HS−, with one or several pairs of electrons, are typically nucleophiles. Similarly, neutral species such as ammonia, amines, water, and alcohol...
Nucleophilic Substitution Reactions02:34

Nucleophilic Substitution Reactions

Historical perspective
In 1896, the German chemist Paul Walden discovered that he could interconvert pure enantiomeric (+) and (-) malic acids through a series of reactions. This conversion suggested the involvement of optical inversion during the substitution reaction. Further, in 1930, Sir Christopher Ingold described for the first time two different forms of nucleophilic substitution reactions, which are known as SN1 (nucleophilic substitution unimolecular) and SN2 (nucleophilic substitution...
SN2 Reaction: Kinetics02:14

SN2 Reaction: Kinetics

Kinetic Studies and Significance
In a chemical reaction, a relationship exists between the concentration of reactants and the rate at which the reaction proceeds. The study to measure this relationship is known as the kinetics of a chemical reaction. Kinetic studies are used to deduce the rate law of a chemical reaction, which provides information about the species involved during the transition state of the rate-determining step. Thus, kinetic studies help to derive the mechanism of a reaction.
Predicting Products: SN1 vs. SN202:27

Predicting Products: SN1 vs. SN2

Nucleophilic substitution reactions of alkyl halides can proceed via an SN1 or an SN2 mechanism. While in SN2 reactions, the nucleophile attacks the substrate simultaneously as the leaving group departs, in SN1 reactions, the substrate first dissociates to give the carbocation intermediate. Various factors such as the structure of the substrate, the strength of the nucleophile, and the nature of the solvent promote one mechanism over the other.
With increased substitution on the alkyl halide,...
Leaving Groups02:14

Leaving Groups

The nature of leaving groups strongly influences the outcome of a nucleophilic substitution reaction.
In general, in a nucleophilic substitution reaction, a nucleophile displaces a functional group, called the leaving group, from the substrate to give a substituted product. A leaving group departs the substrate molecule through heterolytic cleavage, taking the pair of electrons with it to become a relatively stable weak base in the form of an anion or a neutral molecule.  
In a nucleophilic...

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Single-Molecule F&ouml;rster Resonance Energy Transfer Methods for Real-Time Investigation of the Holliday Junction Resolution by GEN1
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Two distinct components of release factor function uncovered by nucleophile partitioning analysis.

Jeffrey J Shaw1, Rachel Green

  • 1Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Molecular Cell
|November 13, 2007
PubMed
Summary

Release factor proteins (RFs) aid in terminating protein translation. RF1 specifically uses water for peptide release, a process critical for protein synthesis accuracy.

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Area of Science:

  • Molecular Biology
  • Protein Synthesis
  • Biochemistry

Background:

  • Translation termination releases completed polypeptide chains via hydrolytic reactions catalyzed by release factors (RFs).
  • The precise catalytic mechanism of peptide release by RFs remains incompletely understood.
  • Conserved active-site nucleotides and the GGQ tripeptide motif in RFs are known to be important for function.

Purpose of the Study:

  • To investigate the kinetic contributions of RFs to the rate and specificity of peptide release.
  • To elucidate the role of specific RF components, such as the GGQ motif, in catalysis.

Main Methods:

  • Pre-steady-state kinetic experiments were employed.
  • Nucleophile competition assays were performed to assess specificity.

Main Results:

  • Unacylated tRNA non-discriminately stimulates peptide release.
  • Release Factor 1 (RF1) exhibits high specificity for water as a nucleophile.
  • Amino acid Q235 within the RF1 GGQ motif is essential for this water specificity.

Conclusions:

  • RFs contribute to peptide release through a two-part mechanism: general activation of the catalytic center and specific selection of water.
  • The Q235 residue of RF1 plays a crucial role in facilitating the specific selection of water, ensuring accurate termination.