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Drugs > ELM 6 Drug-target Bonds > Flashcards

ELM 6 Drug-target Bonds Flashcards

1
Q

Q: What is the primary structure of a protein?

A

A: The primary structure is the linear amino acid sequence of a protein.

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2
Q

Q: What defines the secondary structure of a protein?

A

A: The secondary structure involves the folding of sections of the protein into regular patterns like alpha helices.

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3
Q

Q: What does the tertiary structure of a protein refer to?

A

A: The tertiary structure refers to the overall folding pattern of a protein monomer.

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4
Q

Q: What is the quaternary structure of a protein?

A

A: The quaternary structure is the assembly of protein monomers to form a functional protein.

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5
Q

Q: What is a peptide bond?

A

A: A peptide bond is the basic chemical bond that holds amino acids together in a protein.

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6
Q

Q: What is the role of an R group in an amino acid?

A

A: The R group is the side chain of an amino acid that determines its chemical properties.

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7
Q

Q: What is a pharmacophore?

A

A: A pharmacophore is the minimum set of chemical features a drug must have to bind to its target protein.

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8
Q

Q: What characterizes a covalent bond in the context of drug-target interactions?

A

A: A covalent bond is a strong bond where atoms share electrons, and it is uncommon in drug-target interactions.

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9
Q

Q: What is an ionic bond?

A

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).

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10
Q

Q: What is a dipole?

A

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.

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11
Q

Q: Describe a hydrogen bond.

A

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.

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12
Q

Q: What is a hydrogen bond acceptor?

A

A: A hydrogen bond acceptor is the electronegative atom that supplies the lone pair in a hydrogen bond.

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13
Q

Q: What is a hydrogen bond donor?

A

A: A hydrogen bond donor is the electronegative atom that supplies the hydrogen in a hydrogen bond.

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14
Q

Q: What is hydrophobic bonding?

A

A: Hydrophobic bonding is a weak interaction between two hydrophobic molecules, arising due to a gain in entropy.

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15
Q

Q: What are van der Waals forces?

A

A: Van der Waals forces are weak interactions between dipoles.

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16
Q

Q: How many different R groups are there in amino acids?

A

A: There are 21 different R groups in amino acids.

17
Q

Q: How are peptide bonds formed?

A

A: Peptide bonds are formed by a condensation reaction between a carboxyl group and an amine group.

18
Q

Q: In a dipeptide structure, what are the N terminus and C terminus?

A

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.

19
Q

Q: What is a binding domain in a protein?

A

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.

20
Q

Q: What is a pharmacophore?

A

A: A pharmacophore is the minimum requirement of a drug to fit into a binding site, including the correct charge, size, and structure.

21
Q

Q: What is a proteinogenic amino acid?

A

A: A proteinogenic amino acid is an amino acid used in proteins.

22
Q

Q: What are non-proteinogenic amino acids?

A

A: Non-proteinogenic amino acids are amino acids that aren’t used in proteins, such as GABA.

23
Q

Q: What is the valence shell of electrons?

A

A: The valence shell of electrons is the outermost shell of an atom.

24
Q

Q: How do the strengths of ionic bonds compare to covalent bonds?

A

A: Ionic bonds aren’t as strong as covalent bonds.

25
Q

Q: What is a cation-pi interaction?

A

A: A cation-pi interaction is when a cation interacts with the electron cloud on aromatic rings of amino acids.

26
Q

Q: How do the strengths of hydrogen bonds compare to ionic bonds?

A

A: Hydrogen bonds aren’t as strong as ionic bonds.

27
Q

Q: What conditions are necessary for hydrogen bonds to occur?

A

A: For hydrogen bonds to occur, there must be a lone pair of electrons and an electronegative atom (nitrogen, oxygen, or fluorine) covalently bonded to hydrogen.

28
Q

Q: What is hydrophobic bonding, and why does it occur?

A

A: Hydrophobic bonding occurs when nonpolar molecules like oil come together in water, resulting in a gain in entropy as the water molecules become less ordered, thus increasing energy levels.

29
Q

Q: How do van der Waals forces work?

A

A: Van der Waals forces are weak interactions between dipoles; molecules must be at an optimal distance to attract without repelling.

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