82 Questions
What is the primary source of ligands in bioinorganic chemistry?
Amino-acid side chains and constituents of nucleic acids
What does the coordination environment of residues in bioinorganic chemistry depend on?
The three-dimensional folding of proteins and the tertiary structures of nucleic acids
What is the purpose of this chapter?
To provide the basic information about bioinorganic chemistry necessary to understand later chapters
How many essential amino acids are there in proteins?
20
What is the chirality at the α-carbon of naturally occurring amino acids?
S (or L)
What can metal coordination at amino-acid side chains do?
Substantially diminish the effective pK, values
What type of bonds join amino acids in a protein?
Peptide bonds
What is the function of the one-letter code for amino acids?
To shorten the three-letter abbreviations
Which of the following amino acids is NOT a commonly observed ligand?
Alanine
What is the primary structure of a protein determined by?
The amino-acid sequence of the protein
What type of bonds are typically found in the interior of a protein?
Hydrophobic bonds
What is the function of the side chain of cysteine in metal ion binding?
To act as a bridging ligand
What determines the three-dimensional structure of a protein?
The amino-acid sequence of the protein
What type of interactions are important for protein structure?
All of the above
What is the function of the three-letter code for amino acids?
To distinguish between similar amino acids
What determines the orientation of ligand donor atoms in a metalloprotein?
The three-dimensional structure of the protein
What refers to the local conformation of a few adjacent amino acids determined by specific hydrogen bonding patterns?
Secondary structure
What is the term used to describe the overall course of a biopolymer chain that generates 'folds'?
Tertiary structure
What refers to the assembly of different polypeptide chains to form larger units?
Quaternary structure
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+?
Zinc finger
What is the term used to describe the overall course of a biopolymer chain that generates 'folds'?
Tertiary structure
What type of structure is essential for the function of Cu-Zn superoxide dismutase?
Quaternary structure
What is the name of the enzyme that is required for assembly of the intact enzyme aspartate transcarbamoylase?
Zinc binding
What ultimately determines the structure and properties of proteins?
Amino-acid sequence
What is the first step in the pathway by which genetic information works?
Transcription
What is the term used to describe the manipulation of proteins through the alteration of their amino acid sequences?
Gene cloning
Which cellular component functions as the protein synthetic machinery?
Ribosomes
What is the process of removing intervening sequences within the RNA and connecting the coding regions called?
Splicing
What is the purpose of cloning a specific gene?
To isolate regions of DNA for sequencing and other characterization
What is the term for the regions of DNA that encode the final protein?
Exons
What is the process of identifying the member or members of the library that include the gene of interest called?
Screening
What is the term for the initial RNA transcript that is processed into a mature messenger RNA?
Primary transcript
What is the purpose of site-directed mutagenesis?
To carry out structure-function investigations
What type of cells lack a nucleus?
Prokaryotes
What is the term for the process of incorporating fragments of DNA into a vector?
Cloning
What is the purpose of a library in gene cloning?
To identify the gene of interest
What is the name of the bond that links the sugar and the base in a nucleoside?
Glycosidic bond
What is the term for the unit comprising only a sugar and a base?
Nucleoside
What is the type of RNA that carries genetic information from DNA to the ribosomes?
Messenger RNA (mRNA)
What is the term for the process of determining RNA secondary structure by comparing homologous RNA sequences from different organisms?
Phylogenetic comparison
What is the name of the base pairing scheme that is responsible for linking the two DNA strands into a double helix?
Watson-Crick base pairing
What is the term for the RNA molecule that binds amino acids to its 3’ termini and carries them to the ribosome?
Transfer RNA (tRNA)
What is the type of RNA that is a constituent of ribosomes?
Ribosomal RNA (rRNA)
What is the term for the bond that links the sugar and the phosphate group in a nucleotide?
Phosphodiester bond
What is the type of RNA that is best known for its structure?
Transfer RNA (tRNA)
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?
C3’-endo
What is the purpose of the gene for antibiotic resistance in a plasmid?
To allow the bacterial cell to survive antibiotic selection
What is the result of the chemical transformation in the enzyme-substrate complex?
The formation of an enzyme-product complex
What is the significance of the Vmax parameter in enzyme kinetics?
It is the maximal rate of the reaction in the presence of saturating levels of substrate
What is the difference between the sugar-phosphate backbone of DNA and RNA?
There is no difference in the sugar-phosphate backbone of DNA and RNA
What is the purpose of introducing specific changes into the nucleotide sequence of a gene?
To probe hypotheses about the structures and reactivity of metal sites in proteins
What is the role of the origin of replication in a plasmid?
It is the site of initiation of DNA replication
What is the phenomenon of substrate-saturation of the rate of the reaction?
The rate of the reaction reaches a maximum at high substrate concentrations
What is the result of the process of protein overexpression via a plasmid?
The protein of interest is obtained in large amounts
What is the name given to RNA enzymes that require metal ions for their activity?
Ribozymes
What is the shape of the most common form of DNA?
Right-handed double helix
What is the significance of the KM parameter in enzyme kinetics?
It is the concentration of substrate at which the reaction proceeds at half the maximal rate
What is the purpose of the cloned DNA fragment in a plasmid?
To obtain the protein of interest in large amounts
What is the approximate number of base pairs per turn of the helix in B-DNA?
8-10
What is the sugar pucker conformation observed in A-DNA?
C3'-endo
What is the reason for the poor metal-coordinating abilities of exocyclic amino groups in nucleoside bases?
Lone pairs are delocalized into the ring
What is the characteristic feature of Z-DNA?
Left-handed double helix
What is the type of RNA structure that is functionally very important?
Tertiary structure
What is the name given to the metal-binding sites on nucleoside bases?
Endocyclic nitrogen atoms
What is the reason for the sequence-dependent local variations in DNA structure?
Due to variations in sequence
What is the characteristic feature of A-DNA?
Deep major groove
What is the purpose of introducing a sulfur atom in nucleic acids?
To enhance the metal-binding properties
What is the significance of s4U in bioinorganic chemistry?
It has a high affinity for soft metal ions like Hg(II) and Pt(II)
What is the role of site-specific mutagenesis in metal-nucleic acid chemistry?
To study the metal-binding properties of nucleic acids
What is the significance of the structure of s4U in bioinorganic chemistry?
It has a unique metal-binding site
What is the common feature of modified nucleosides like s4U?
They are naturally occurring constituents of RNA molecules
What is the significance of metal-nucleic acid interactions in bioinorganic chemistry?
They have potential applications in metal-based therapies
Among the nucleic acid base heteroatoms, which atoms are the most likely to be metal-binding sites?
Nitrogen atoms
What type of metal ions are likely to bind to the negatively charged oxygen atoms of the phosphodiester groups?
Hard metals such as those of the alkali and alkaline earth groups
What is the estimated percentage of ATP in cells that is bound to Mg(II) ion?
90%
What is the role of Mg(II) ion in the hydrolysis of the high-energy phosphate bond in ATP?
Mg(II) ion promotes the hydrolysis of the high-energy phosphate bond in ATP
What is the function of Mg(II) ion in the binding of ATP to enzymes?
Mg(II) ion is a cofactor that enhances the binding of ATP to enzymes
What is the role of metal ions in the stabilization of the tertiary structure of tRNA?
Metal ions stabilize the tertiary structure of tRNA
What is the function of the nucleosomes in the structure of chromatin?
Nucleosomes are composed of histone proteins and wrapped DNA
What is the purpose of synthesizing oligonucleotides with unique metal-binding properties?
To study the interactions between metal ions and nucleic acids
What is the result of binding Pb(II) to tRNA?
Pb(II) promotes the cleavage of the sugar-phosphate backbone in tRNA
What is the role of Mg(II) ion in the structure of chromatin?
Mg(II) ion has no effect on the structure of chromatin
Learn about the role of amino acid side chains and nucleic acid constituents as ligands in bioinorganic chemistry, and how their coordination environment is influenced by protein folding and nucleic acid structure. Explore the modulation of metal-binding capabilities by complex structural elements.
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