ELM 6 Drug-target Bonds Flashcards
(29 cards)
Q: What is the primary structure of a protein?
A: The primary structure is the linear amino acid sequence of a protein.
Q: What defines the secondary structure of a protein?
A: The secondary structure involves the folding of sections of the protein into regular patterns like alpha helices.
Q: What does the tertiary structure of a protein refer to?
A: The tertiary structure refers to the overall folding pattern of a protein monomer.
Q: What is the quaternary structure of a protein?
A: The quaternary structure is the assembly of protein monomers to form a functional protein.
Q: What is a peptide bond?
A: A peptide bond is the basic chemical bond that holds amino acids together in a protein.
Q: What is the role of an R group in an amino acid?
A: The R group is the side chain of an amino acid that determines its chemical properties.
Q: What is a pharmacophore?
A: A pharmacophore is the minimum set of chemical features a drug must have to bind to its target protein.
Q: What characterizes a covalent bond in the context of drug-target interactions?
A: A covalent bond is a strong bond where atoms share electrons, and it is uncommon in drug-target interactions.
Q: What is an ionic bond?
A: An ionic bond is an interaction between a cation (an atom that has lost an electron) and an anion (an atom that has gained an electron).
Q: What is a dipole?
A: A dipole is a molecule in which the electrons are unevenly distributed, resulting in one part of the molecule having a slight positive charge and another region having a slight negative charge.
Q: Describe a hydrogen bond.
A: A hydrogen bond is an interaction between a hydrogen covalently bonded to an electronegative atom such as oxygen, and the lone pairs of electrons of another electronegative atom such as nitrogen.
Q: What is a hydrogen bond acceptor?
A: A hydrogen bond acceptor is the electronegative atom that supplies the lone pair in a hydrogen bond.
Q: What is a hydrogen bond donor?
A: A hydrogen bond donor is the electronegative atom that supplies the hydrogen in a hydrogen bond.
Q: What is hydrophobic bonding?
A: Hydrophobic bonding is a weak interaction between two hydrophobic molecules, arising due to a gain in entropy.
Q: What are van der Waals forces?
A: Van der Waals forces are weak interactions between dipoles.
Q: How many different R groups are there in amino acids?
A: There are 21 different R groups in amino acids.
Q: How are peptide bonds formed?
A: Peptide bonds are formed by a condensation reaction between a carboxyl group and an amine group.
Q: In a dipeptide structure, what are the N terminus and C terminus?
A: In a dipeptide structure, the N terminus is the side with the amine group, and the C terminus is the side with the carboxyl group. The chain extends by adding to the C terminus.
Q: What is a binding domain in a protein?
A: A binding domain is the area where a drug binds within a protein, and it typically has several points at which the drug can interact.
Q: What is a pharmacophore?
A: A pharmacophore is the minimum requirement of a drug to fit into a binding site, including the correct charge, size, and structure.
Q: What is a proteinogenic amino acid?
A: A proteinogenic amino acid is an amino acid used in proteins.
Q: What are non-proteinogenic amino acids?
A: Non-proteinogenic amino acids are amino acids that aren’t used in proteins, such as GABA.
Q: What is the valence shell of electrons?
A: The valence shell of electrons is the outermost shell of an atom.
Q: How do the strengths of ionic bonds compare to covalent bonds?
A: Ionic bonds aren’t as strong as covalent bonds.
