intermolecular Bonds

Question 1

which bond is the strongest?

Answer 1

electrostatic or ionic bonds

Question 2

between what groups does the ionic bond take place?

Answer 2

having opposite charges: carboxylate ion and aminium ion

Question 3

in what condition ionic bonds are the strongest between hydrophobic and polar environments?

Answer 3

hydrophobic

Question 4

generally binding sites of macromolecules are more _ in nature than the surface

Answer 4

hydrophobic

Question 5

A heteroatom is an atom within an organic compound that is not _ or hydrogen.

Answer 5

carbon

hydrogen

Question 6

A hydrogen bond can vary substantially in strength and normally takes place between an _ and an _

The electron-deficient H is usually attached to a _

Answer 6

electron-rich hetero-atom (the hydrogen bond acceptor(HBA))

electron-deficient hydrogen (the hydrogen bond donor (HBD))

heteroatom (O or N)

Question 7

what common atoms are usually HBA

Answer 7

oxygen and nitrogen

Question 8

_ are the strongest type of covalent bond

Answer 8

Sigma bonds

Question 9

aromatic rings and alkynes are only likely to be significant (HBA) if they interact with a _ such as an alkylammonium

Answer 9

strong hydrogen bond donor

Question 10

electron density in pi systems in aromatic rings and alkynes are regions of _ but electron density is _ so _

Answer 10

high electron density

diffuse

a week HBA

Question 11

which amino acids have hydrophobic side chains? so then they interact with each other

Answer 11

valine, leucine, isoleucine, phenilalanine, proline

Question 12

which amino acids have polar functional groups but also have substantial hydrophobic character?

Answer 12

methionine, tryptophan, threonine, tyrosine

Question 13

which amino acids can form ionic bonds?

Answer 13

basic and acidic amino acids when they are in close proximity.

These amino acids have side chains that can be charged at physiological pH.

Question 14

which amino acids cannot be involved in ionic interactions

Answer 14

nonpolar amino acids

Question 15

what charge on DNA?

Answer 15

negatively charged phosphate groups of DNA

Question 16

Hydrogen bonding interactions may occur between proflavine and DNA _.

Answer 16

bases

Question 17

_ a key target for medicines designed to fight bacterial infections.

Answer 17

DNA gyrase

Question 18

DNA gyrase:

Answer 18

bacterial enzyme responsible for introducing negative supercoils into DNA.

Question 19

Fluoroquinolones bind to the _, particularly to _.

Answer 19

DNA gyrase enzyme

its A subunit

Question 20

Phosphorylation, the _(def), can occur on several amino acids in proteins, most commonly on _ residues. These three amino acids contain _ groups in their side chains, which can serve as attachment points for the phosphate group.

Answer 20

addition of a phosphate group to a molecule.

serine, threonine, and tyrosine

hydroxyl (-OH)

Question 21

3 major classes of transmembrane receptors:

Answer 21

• GPCRs
• Enzyme receptors
• ion channel reeceptors

Question 22

Example of chemical antagonism:

Answer 22

Gastic acid reflux in eosophagus, take Rennie, composed of (CO3)^(2-) (calcium carbonate) to neutralize H+

Question 23

Neuromuscular blockers (NMBs), such as _, prevent ACh from binding to _, causing muscle relaxation or paralysis. Neostigmine, an _, increases ACh levels, which competes with the blocker and reactivates nAChR, leading to muscle contraction again.

Answer 23

Rocuronium

nAChR

acetylcholinesterase inhibitor

Question 24

covalent bond- inter- or intramolecula?

Answer 24

intra

Question 25

_ are the most important initial interactions as a drug enters the binding site

Answer 25

Ionic bonds

Question 26

hydrogen bonds: Weaker than _ but stronger than _ interactions

Answer 26

ionic van der Waals

Question 27

The electron deficient H is called a _ The electron rich heteroatom is called _

Answer 27

H-bond donor a H-bond acceptor

Question 28

When there is O with a double bond:

Answer 28

it does not form Hydrogen-bonds but can accept H

Question 29

dipole-dipole interactions' Strength decreases with distance more quickly than with _, but less quickly than with _

Answer 29

electrostatic interactions van der Waals interactions

Question 30

ion-dipole interactions' strength: falls off _(more or less) rapidly with distance than for a dipole-dipole interaction

Answer 30

less

Question 31

example of induced dipole interactions:

Answer 31

a quaternary ammonium ion and an aromatic ring

Question 32

When hydrophobic regions of the drug and target interact, the _ are released, leading to an _ (disorder). This is thermodynamically _ because nature tends toward increased disorder.

Answer 32

structured water molecules increase in entropy favorable

Question 33

The release of ordered water molecules upon hydrophobic binding contributes _ to the binding energy, making the overall drug-target interaction more _.

Answer 33

positively favorable

Question 34

list all of the intermolecular interactions:

Answer 34

electrostatic / ionic bond Hydrogen bond van der Waals dipole-dipole ion-dipole induced dipole hydrophobic

Question 35

list the Non-receptor/Enzyme Drug Targets

Answer 35

Transporters Structural Proteins Protein Synthesis Inhibitors Lipids and Sterols (Rocuronium) DNA RNA

Question 36

Transporters Function: Involved in _ Drug Targets: _ target _, inhibiting _. _ acts as a reuptake inhibitor of Noradrenaline and Dopamine, used in ADHD treatment.

Answer 36

the reuptake of neurotransmitters, Cocaine and tricyclic antidepressants dopamine and noradrenaline transporters reuptake Ritalin

Question 37

(Protein Synthesis Inhibitors) Puromycin: An _ that acts as a _ during protein synthesis --> _

Answer 37

antibiotic chain terminator stopping translation.

Question 38

Proflavine and Doxorubicin: _ and _ drugs that intercalate between DNA bases, preventing _ and _

Answer 38

Antibiotics antitumor replication transcription