Bioinorganic Chemistry: Ligands and Metal Binding
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Questions and Answers

What is the primary source of ligands in bioinorganic chemistry?

  • Chromatin
  • Amino-acid side chains and constituents of nucleic acids (correct)
  • Constituents of nucleic acids
  • Proteins in the matrix of a cell membrane

    • What does the coordination environment of residues in bioinorganic chemistry depend on?

  • The wrapping of DNA around the nucleosome core proteins in chromatin
  • The three-dimensional folding of proteins and the tertiary structures of nucleic acids (correct)
  • The positioning of proteins in the matrix of a cell membrane
  • The pH of the environment

    • What is the purpose of this chapter?

  • To provide the basic information about bioinorganic chemistry necessary to understand later chapters (correct)
  • To provide an in-depth analysis of metal-binding capabilities
  • To discuss the principles of enzyme kinetics
  • To explore gene cloning and expression

    • How many essential amino acids are there in proteins?

    <p>20</p> Signup and view all the answers

    What is the chirality at the α-carbon of naturally occurring amino acids?

    <p>S (or L)</p> Signup and view all the answers

    What can metal coordination at amino-acid side chains do?

    <p>Substantially diminish the effective pK, values</p> Signup and view all the answers

    What type of bonds join amino acids in a protein?

    <p>Peptide bonds</p> Signup and view all the answers

    What is the function of the one-letter code for amino acids?

    <p>To shorten the three-letter abbreviations</p> Signup and view all the answers

    Which of the following amino acids is NOT a commonly observed ligand?

    <p>Alanine</p> Signup and view all the answers

    What is the primary structure of a protein determined by?

    <p>The amino-acid sequence of the protein</p> Signup and view all the answers

    What type of bonds are typically found in the interior of a protein?

    <p>Hydrophobic bonds</p> Signup and view all the answers

    What is the function of the side chain of cysteine in metal ion binding?

    <p>To act as a bridging ligand</p> Signup and view all the answers

    What determines the three-dimensional structure of a protein?

    <p>The amino-acid sequence of the protein</p> Signup and view all the answers

    What type of interactions are important for protein structure?

    <p>All of the above</p> Signup and view all the answers

    What is the function of the three-letter code for amino acids?

    <p>To distinguish between similar amino acids</p> Signup and view all the answers

    What determines the orientation of ligand donor atoms in a metalloprotein?

    <p>The three-dimensional structure of the protein</p> Signup and view all the answers

    What refers to the local conformation of a few adjacent amino acids determined by specific hydrogen bonding patterns?

    <p>Secondary structure</p> Signup and view all the answers

    What is the term used to describe the overall course of a biopolymer chain that generates 'folds'?

    <p>Tertiary structure</p> Signup and view all the answers

    What refers to the assembly of different polypeptide chains to form larger units?

    <p>Quaternary structure</p> Signup and view all the answers

    What is the name of the protein that exists as a random coil with no unique secondary or tertiary structure in the absence of Zn2+?

    <p>Zinc finger</p> Signup and view all the answers

    What is the term used to describe the overall course of a biopolymer chain that generates 'folds'?

    <p>Tertiary structure</p> Signup and view all the answers

    What type of structure is essential for the function of Cu-Zn superoxide dismutase?

    <p>Quaternary structure</p> Signup and view all the answers

    What is the name of the enzyme that is required for assembly of the intact enzyme aspartate transcarbamoylase?

    <p>Zinc binding</p> Signup and view all the answers

    What ultimately determines the structure and properties of proteins?

    <p>Amino-acid sequence</p> Signup and view all the answers

    What is the first step in the pathway by which genetic information works?

    <p>Transcription</p> Signup and view all the answers

    What is the term used to describe the manipulation of proteins through the alteration of their amino acid sequences?

    <p>Gene cloning</p> Signup and view all the answers

    Which cellular component functions as the protein synthetic machinery?

    <p>Ribosomes</p> Signup and view all the answers

    What is the process of removing intervening sequences within the RNA and connecting the coding regions called?

    <p>Splicing</p> Signup and view all the answers

    What is the purpose of cloning a specific gene?

    <p>To isolate regions of DNA for sequencing and other characterization</p> Signup and view all the answers

    What is the term for the regions of DNA that encode the final protein?

    <p>Exons</p> Signup and view all the answers

    What is the process of identifying the member or members of the library that include the gene of interest called?

    <p>Screening</p> Signup and view all the answers

    What is the term for the initial RNA transcript that is processed into a mature messenger RNA?

    <p>Primary transcript</p> Signup and view all the answers

    What is the purpose of site-directed mutagenesis?

    <p>To carry out structure-function investigations</p> Signup and view all the answers

    What type of cells lack a nucleus?

    <p>Prokaryotes</p> Signup and view all the answers

    What is the term for the process of incorporating fragments of DNA into a vector?

    <p>Cloning</p> Signup and view all the answers

    What is the purpose of a library in gene cloning?

    <p>To identify the gene of interest</p> Signup and view all the answers

    What is the name of the bond that links the sugar and the base in a nucleoside?

    <p>Glycosidic bond</p> Signup and view all the answers

    What is the term for the unit comprising only a sugar and a base?

    <p>Nucleoside</p> Signup and view all the answers

    What is the type of RNA that carries genetic information from DNA to the ribosomes?

    <p>Messenger RNA (mRNA)</p> Signup and view all the answers

    What is the term for the process of determining RNA secondary structure by comparing homologous RNA sequences from different organisms?

    <p>Phylogenetic comparison</p> Signup and view all the answers

    What is the name of the base pairing scheme that is responsible for linking the two DNA strands into a double helix?

    <p>Watson-Crick base pairing</p> Signup and view all the answers

    What is the term for the RNA molecule that binds amino acids to its 3’ termini and carries them to the ribosome?

    <p>Transfer RNA (tRNA)</p> Signup and view all the answers

    What is the type of RNA that is a constituent of ribosomes?

    <p>Ribosomal RNA (rRNA)</p> Signup and view all the answers

    What is the term for the bond that links the sugar and the phosphate group in a nucleotide?

    <p>Phosphodiester bond</p> Signup and view all the answers

    What is the type of RNA that is best known for its structure?

    <p>Transfer RNA (tRNA)</p> Signup and view all the answers

    What is the term for the conformation of the sugar ring in RNA, where the C3’ carbon atom is on the same side of the plane defined by C4’-O-C1’ as the C5’ carbon?

    <p>C3’-endo</p> Signup and view all the answers

    What is the purpose of the gene for antibiotic resistance in a plasmid?

    <p>To allow the bacterial cell to survive antibiotic selection</p> Signup and view all the answers

    What is the result of the chemical transformation in the enzyme-substrate complex?

    <p>The formation of an enzyme-product complex</p> Signup and view all the answers

    What is the significance of the Vmax parameter in enzyme kinetics?

    <p>It is the maximal rate of the reaction in the presence of saturating levels of substrate</p> Signup and view all the answers

    What is the difference between the sugar-phosphate backbone of DNA and RNA?

    <p>There is no difference in the sugar-phosphate backbone of DNA and RNA</p> Signup and view all the answers

    What is the purpose of introducing specific changes into the nucleotide sequence of a gene?

    <p>To probe hypotheses about the structures and reactivity of metal sites in proteins</p> Signup and view all the answers

    What is the role of the origin of replication in a plasmid?

    <p>It is the site of initiation of DNA replication</p> Signup and view all the answers

    What is the phenomenon of substrate-saturation of the rate of the reaction?

    <p>The rate of the reaction reaches a maximum at high substrate concentrations</p> Signup and view all the answers

    What is the result of the process of protein overexpression via a plasmid?

    <p>The protein of interest is obtained in large amounts</p> Signup and view all the answers

    What is the name given to RNA enzymes that require metal ions for their activity?

    <p>Ribozymes</p> Signup and view all the answers

    What is the shape of the most common form of DNA?

    <p>Right-handed double helix</p> Signup and view all the answers

    What is the significance of the KM parameter in enzyme kinetics?

    <p>It is the concentration of substrate at which the reaction proceeds at half the maximal rate</p> Signup and view all the answers

    What is the purpose of the cloned DNA fragment in a plasmid?

    <p>To obtain the protein of interest in large amounts</p> Signup and view all the answers

    What is the approximate number of base pairs per turn of the helix in B-DNA?

    <p>8-10</p> Signup and view all the answers

    What is the sugar pucker conformation observed in A-DNA?

    <p>C3'-endo</p> Signup and view all the answers

    What is the reason for the poor metal-coordinating abilities of exocyclic amino groups in nucleoside bases?

    <p>Lone pairs are delocalized into the ring</p> Signup and view all the answers

    What is the characteristic feature of Z-DNA?

    <p>Left-handed double helix</p> Signup and view all the answers

    What is the type of RNA structure that is functionally very important?

    <p>Tertiary structure</p> Signup and view all the answers

    What is the name given to the metal-binding sites on nucleoside bases?

    <p>Endocyclic nitrogen atoms</p> Signup and view all the answers

    What is the reason for the sequence-dependent local variations in DNA structure?

    <p>Due to variations in sequence</p> Signup and view all the answers

    What is the characteristic feature of A-DNA?

    <p>Deep major groove</p> Signup and view all the answers

    What is the purpose of introducing a sulfur atom in nucleic acids?

    <p>To enhance the metal-binding properties</p> Signup and view all the answers

    What is the significance of s4U in bioinorganic chemistry?

    <p>It has a high affinity for soft metal ions like Hg(II) and Pt(II)</p> Signup and view all the answers

    What is the role of site-specific mutagenesis in metal-nucleic acid chemistry?

    <p>To study the metal-binding properties of nucleic acids</p> Signup and view all the answers

    What is the significance of the structure of s4U in bioinorganic chemistry?

    <p>It has a unique metal-binding site</p> Signup and view all the answers

    What is the common feature of modified nucleosides like s4U?

    <p>They are naturally occurring constituents of RNA molecules</p> Signup and view all the answers

    What is the significance of metal-nucleic acid interactions in bioinorganic chemistry?

    <p>They have potential applications in metal-based therapies</p> Signup and view all the answers

    Among the nucleic acid base heteroatoms, which atoms are the most likely to be metal-binding sites?

    <p>Nitrogen atoms</p> Signup and view all the answers

    What type of metal ions are likely to bind to the negatively charged oxygen atoms of the phosphodiester groups?

    <p>Hard metals such as those of the alkali and alkaline earth groups</p> Signup and view all the answers

    What is the estimated percentage of ATP in cells that is bound to Mg(II) ion?

    <p>90%</p> Signup and view all the answers

    What is the role of Mg(II) ion in the hydrolysis of the high-energy phosphate bond in ATP?

    <p>Mg(II) ion promotes the hydrolysis of the high-energy phosphate bond in ATP</p> Signup and view all the answers

    What is the function of Mg(II) ion in the binding of ATP to enzymes?

    <p>Mg(II) ion is a cofactor that enhances the binding of ATP to enzymes</p> Signup and view all the answers

    What is the role of metal ions in the stabilization of the tertiary structure of tRNA?

    <p>Metal ions stabilize the tertiary structure of tRNA</p> Signup and view all the answers

    What is the function of the nucleosomes in the structure of chromatin?

    <p>Nucleosomes are composed of histone proteins and wrapped DNA</p> Signup and view all the answers

    What is the purpose of synthesizing oligonucleotides with unique metal-binding properties?

    <p>To study the interactions between metal ions and nucleic acids</p> Signup and view all the answers

    What is the result of binding Pb(II) to tRNA?

    <p>Pb(II) promotes the cleavage of the sugar-phosphate backbone in tRNA</p> Signup and view all the answers

    What is the role of Mg(II) ion in the structure of chromatin?

    <p>Mg(II) ion has no effect on the structure of chromatin</p> Signup and view all the answers

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