RNA Processing
This enzyme adds a stretch of ~250 adenosine residues to the 3' end of eukaryotic mRNAs and does not require a template for its polymerization activity.
What is poly(A) polymerase?
The number of codons in the "standard" genetic code that specifies the incorporation of an amino acid in a polypeptide chain
What is 61?
Enzymes work, in part, by stabilizing this molecular intermediate, which represents the highest point of free energy on the reaction coordinate.
What is the transition state?
This nucleotide is as a precursor in the synthesis of nucleic acids, but it also has an important role in its free form in driving a large number of energetically unfavorable reactions and processes in cells.
What is ATP?
In the Li et al. paper, FISH-IF was used to detect this repetitive sequence of chromosomal DNA in order to study the localization and function of TZAP.
What is telomeric DNA?
The formation of this structure is required for the splicing of eukaryotic mRNAs, but it is ultimately degraded after the second transesterification of the splicing reaction takes place.
What is the lariat?
The activation and editing sites of these enzymes are critical to ensuring that tRNAs are charged with the correct amino acids so that translation takes place with a high degree of accuracy.
What are aminoacyl-tRNA synthetases?
This type of catalytic mechanism is suggested (but not proven) by sensitivity to pH changes and involves the transfer of a proton to and from one or more of the reacting species.
What is acid-base catalysis?
Of the following three forces, the one that contributes least to the stability of nucleic acids: base pairing, stacking interactions, cation shielding
What is base pairing?
Prior to the Li et al., 2017 paper, these were the only two protein containing complexes known to specifically and stably associate with telomeric DNA.
What are the shelterin complex and telomerase?
In addition to alternative splicing and poly(A) site selection, the alternative use of these regulatory sequences contributes significantly to diversity at the level of mature mRNA transcripts.
What are promoters (alternative promoters)?
In E. coli, the initiator tRNA carrying N-formylmethionine binds to the start codon of the mRNA adjacent to this conserved sequence in order to initiate translation.
What is the Shine-Dalgarno sequence?
This Michaelis-Menten parameter is commonly used in the literature to compare the catalytic efficiencies of enzymes and reflects both the binding step and the catalytic step of an enzyme-catalyzed reaction.
What is Kcat/Km?
In this form of double-stranded DNA, the base pairs are tilted by about 20 degrees with respect to the helical axis and the deoxyribose sugars are in the C-3' endo conformation.
What is A-DNA?
In chromatin immunoprecipitation (ChIP), proteins are crosslinked to DNA, the cells are lysed, and the chromatin is then fragmented using one of these two methods.
What is sonication or nuclease digestion?
The loading of this protein complex onto the mRNA during the splicing process serves to mark the sites of exon splicing and is involved in mRNA transport via the nuclear pore complex.
What is the exon junction complex?
The antibiotic tetracycline blocks the binding of aminoacyl-tRNAs to this site on bacterial ribosomes, thereby arresting translation and killing the bacterial cells.
What is the A site?
This type of catalysis involves an inorganic cofactor that commonly acts to "shield" the negative charge that is present on one or more of the reacting species.
What is metal ion catalysis?
Chaotropic agents such as urea and ethanol destabilize nucleic acids be interfering with this noncovalent force, which results from van der Waals interactions between the nitrogenous bases.
What are stacking interactions?
FISH and ChiP (which is also apparently the name of a restaurant in Burlington) was primarily used in the Li et al. paper to show that TZAP has this biochemical activity at telomeres.
What is telomere trimming (or shortening)?
The activity of this template-independent polymerase is required for the proper maturation of eukaryotic tRNAs and requires CTP and ATP as substrates.
What is CCA-adding polymerase?
These "E3" enzymes bind to target substrates and modify them with ubiquitin chains, which often, but not always, results in degradation of the substrate proteins by the 26S proteasome.
What are ubiquitin ligases?
This type of inhibition, a form of competitive inhibition, results from the diffusion of a product into the active site of an enzyme and represents a "natural" form of inhibition used to control enzyme activity.
What is product inhibition?
The approximate number of helical turns that would be present in a 240 bp fragment of double-stranded DNA in the Z-DNA form
What is 20 (12 bp/turn for Z-DNA)?
IF is similar in principle to immunostaining, which was used in the Luk et al. 2012 study to detect the presence of tyrosine hydroxylase, a marker for this cell type that is directly linked to Parkinson's disease.
What are dopamine (or dopaminergic) neurons?