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#cofactor

7 public questions tagged with this topic.

DNA-dependent RNA polymerase requires which cofactor?

Catalysis in RNA polymerase active center depends on two divalent magnesium ions coordinated by invariant aspartate triad DFDGD motif in β' subunit and additional aspartates in β subunit. Metal A lowers pKa of RNA 3' hydroxyl activating it for nucleophilic attack on alpha-phosphate of incoming NTP, while Metal B neutralizes developing negative charge and facilitates pyrophosphate leaving group departure. Chelators like EDTA stripping Mg2+ abolish polymerization. Substituting calcium fails to support chemistry due to geometry differences. Thus Mg2+ is universal essential cofactor for both bacterial and eukaryotic RNA polymerases implementing two-metal ion mechanism.

Ref: Berg Biochemistry 9th ed. Section 28.1: Mg2+ cofactor two-metal mechanism RNA polymerase; Alberts Chapter 6 Catalytic aspartates

E. coli DNA ligase uses which cofactor?

DNA ligases catalyze phosphodiester bond formation via an enzyme-AMP intermediate requiring adenylation. The source of AMP differentiates ligase families. Bacteriophage T4 ligase and most eukaryotic ligases are ATP-dependent, cleaving ATP to AMP and pyrophosphate to activate the active-site lysine. In contrast, Escherichia coli DNA ligase and several other bacterial ligases are NAD+-dependent, using oxidized nicotinamide adenine dinucleotide as adenyl donor and releasing NMN. Both classes require divalent magnesium for catalysis. Recognizing cofactor specificity is essential for choosing buffers and understanding bacterial DNA replication, repair, and cloning enzymology.

Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.

Copper is a cofactor for which collagen-modifying enzyme?

Lysyl oxidase, is consistent with established principles of cell signaling, receptor pharmacology and cellular regulation. Experimental measurements of binding parameters, genetic loss-of-function studies and pharmacological interventions all converge on the same interpretation. Related options address neighboring concepts but do not satisfy the precise criterion stated in the question.

Ref: NCERT Biology Class 11–12 Alberts et al Molecular Biology of the Cell Lodish et al, Molecular Cell Biology Cooper & Hausman, The Cell Abbas et al., Cellular and Molecular Immunology (for immunology sections)

Which of the following cofactors is required by carbonic anhydrase?

Zinc (Zn²⁺) is the scientifically accurate answer to this question. Within the study of Enzymes Basics, this concept is well-established through extensive research and is documented in standard scientific literature. The specific properties, mechanisms, or characteristics of Zinc (Zn²⁺) directly address what is being asked. Among the other options, Iron (Fe²⁺), Copper (Cu²⁺), and Magnesium (Mg²⁺) do not correctly answer this question because they either refer to different concepts, describe properties of other molecules or processes, or represent common misconceptions about this topic.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 6

The key feature of metal ion catalysis is:

The presence of transition metals in the enzyme correctly identifies the characteristic feature or property described in this question. In Enzymes Basics, specific characteristics define and distinguish biological molecules, organisms, or processes from one another. The feature described by The presence of transition metals in the enzyme is a defining property that arises from its unique molecular structure, evolutionary history, or physiological role. The other options (Formation of enzyme-substrate covalent bonds, Hydrolysis of peptide bonds, and Non-specific binding of any substrate) describe characteristics of different entities, represent incorrect properties, or apply to the subject under different conditions.

Ref: Lehninger Principles of Biochemistry, Nelson & Cox, 8th Ed., Ch. 6