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Applications of Organic and Bioinorganic Chemistry > Cell Structure & Bonding > Flashcards

Cell Structure & Bonding Flashcards

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1
Q

What kind of cells are human, animal and plant cells ?

A

They are eukaryotic cells

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2
Q

What happens at the rough endoplasmic reticulum ?

A

The location of protein synthesis

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3
Q

Out of sodium and potassium, which has a higher concentration outside the cell membrane and inside the cell membrane ?

A
  • Outside the cell membrane, the sodium concentration is high
  • Inside the cell membrane, the potassium concentration is high
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4
Q

How do the hydrophobic tails interact with each other?

A

The hydrophobic tails interact with each other by van der Waals interactions and are
hidden from the aqueous media

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5
Q

Drug targets are large molecules (macromolecules). What is smaller than this ?

A

Drugs

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6
Q

Usually what are the binding sites ?

A

Typically hydrophobic hollows or clefts on the surface of macromolecules

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7
Q

Binding interactions typically involve ?

A

Intermolecular bonds

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8
Q

Explain the binding groups ?

A

Functional groups on the drug are involved in binding interactions

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9
Q

What are binding regions ?

A

Specific regions within the binding site that are involved in binding interactions

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10
Q

What is Pharmacodynamics ?

A

What a drug does to the body

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11
Q

What is Pharmacokinetics ?

A

What the body does to a drug

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12
Q

What do binding interactions usually result in ?

A

An induced fit where the binding site changes shape to accommodate the drug

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13
Q

What does this induced fit alter?

A
  • The overall shape of the drug target

- Important to the pharmacological effect of the drug

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14
Q

Explain Electrostatic/Ionic bond?

A
  • Strongest of the intermolecular bonds (20-40 kJ mol-1)
  • Takes place between groups of opposite charge
  • The strength of the ionic interaction is inversely proportional to the distance between the two charged groups
  • Ionic bonds are the most important initial interactions as a drug enters the binding site
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15
Q

Explain Hydrogen bond?

A
  • Weaker than electrostatic interactions but stronger than van der Waals interactions (12-16 kcal mol-1)
  • A hydrogen bond takes place between an electron deficient hydrogen and an electron
    rich heteroatom (N or O)
  • The electron deficient hydrogen is usually attached to a heteroatom (O or N)
  • The electron deficient hydrogen is called a hydrogen bond donor (HBD)
  • The electron rich heteroatom is called a hydrogen bond acceptor (HBA)
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16
Q

What are some examples of strong hydrogen bond acceptors ?

A
  • Carboxylate ion RCO2-
  • Phosphate ion RPO32-
  • Tertiary amine NR3
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17
Q

What are some examples of moderate hydrogen bond acceptors ?

A
  • Carboxylic acid RCOOH
  • Amide oxygen RNHCOR
  • Ketone R2CO
  • Ester RCOOR
  • Ether ROR
  • Alcohol
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18
Q

What are some examples of poor hydrogen bond acceptors ?

A 
- Sulphur RSR
Fluorine RF
- Chlorine RCl
- Aromatic ring Ar
- Amide nitrogen RNHCOR
- Aromatic amine such as aniline
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19
Q

What are some examples of good hydrogen bond donors?

A
  • Alkylammonium ion NHR3+
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20
Q

Explain Van der Waals interactions ?

A
  • Very weak interactions (2-4 kJ mol-1)
  • Occur between hydrophobic regions of the drug and the target
  • Transient areas of high and low electron densities cause temporary dipoles
  • Interactions drop off rapidly with distance
  • Drug must be close to the binding region for interactions to occur
  • The overall contribution of van der Waals interactions can be crucial to binding
21
Q

Explain Ion-dipole interactions?

A
  • Can occur if the drug and the binding site have dipole moments
  • Dipoles align with each other as the drug enters the binding site
  • Dipole alignment orientates the molecule in the binding site
  • Orientation is beneficial if other binding groups are positioned correctly with respect to the corresponding binding regions
  • Stronger than a dipole-dipole interaction
  • Strength of interaction falls off less rapidly with distance than for a dipole-dipole
    interaction
22
Q

Explain induced dipole interactions ?

A
  • Occur where the charge on one molecule induces a dipole on another
  • Occur between a quaternary ammonium ion and an aromatic ring
23
Q

Explain Desolvation penalties?

A
  • Polar regions of a drug and its target are solvated prior to interaction
  • Desolvation is necessary and requires energy
  • The energy gained by drug-target interactions must be greater than the energy required for desolvation
24
Q

Explain in detail how the hydrophobic interactions ?

A
  • Hydrophobic regions of a drug and its target are not solvated
  • Water molecules interact with each other and form an ordered layer next to
    hydrophobic regions - negative entropy
  • Interactions between the hydrophobic regions of a drug and its target ‘free up’ the
    ordered water molecules
  • Results in an increase in entropy
  • Beneficial to binding energy
25
Q

What is logP ?

A

Ratio of concentrations of a compound in n-octanol compared with water
(immiscible phases)

26
Q

What is the equation for logP?

A

LogP =

log{[solute]octanol/[solute]water}

27
Q

What does a higher logP value mean for the compound?

A

The higher the value the more lipophilic (“fat liking”) or hydrophobic (“water hating”)
the compound

28
Q

So, what does a low logP ?

A

Low logP compounds are very hydrophilic (water liking)

29
Q

For oral absorption of a drug it must pass ?

A

The intestinal epithelium but not be too hydrophobic not to partition out again

30
Q

What does Log P = 1 mean ?

A

10:1, organic:aqueous

31
Q

What does LogP = 0 mean ?

A

1:1, organic:aqueous

32
Q

What does Log P = -1 mean ?

A

1:10, organic: aqueous

33
Q

What does logP influence ?

A

logP influences the ADME Tox (Absorption, Distribution, Metabolism, Elimination -Toxicity)

34
Q

What does logD measure ?

A

logP at a given pH

35
Q

What is Absorption related to?

A

To bioavailability (fraction of an administered dose of unchanged drug that reaches the systemic circulation

36
Q

What is the bioavailability for intravenous administration ?

A

100% bioavailability

37
Q

What is the Distribution ?

A

This is the reversible transfer of a drug between one compartment to another. Some factors affecting drug
distribution include blood flow rates, molecular size,
polarity and binding to serum proteins e.g. albumin

38
Q

What is meant by Elimination?

A

Drugs/metabolites have to be excreted from the body often as urine (kidney) or faeces (after liver)

39
Q

Otherwise the accumulation of foreign substances can have a harmful affect ?

A

On normal metabolism

40
Q

How can excretion also occur?

A

Excretion can also occur through the lungs e.g. anaesthetic gases

41
Q

What is meant by metabolism?

A
  • Drugs are chemically modified the body, mostly in the liver by redox (cytochrome p450) enzymes to give metabolites.
  • These can be pharmacologically inert, effectively lowering the dose of the parent drug and its effects. However, sometimes metabolites can be more active than the parent drug (we will see prodrugs later)
42
Q

What does the ionisation state (pKa) affect ?

A

How the compound is able to diffuse across the membrane as well as known obstacles e.g. the blood-brain barrier (BBB)

43
Q

So, the drugs that ionise easily will ?

A

Not pass through lipophilic membranes e.g. BBB

44
Q

For acids, a high pKa means?

A

a high pka means the species is predominantly unionised, is a bad proton donor, and a weak acid

45
Q

But for an acid, what does a low pKa mean ?

A

a low pKa means the species is predominantly ionised, is a good proton donor, and a strong acid

46
Q

For bases, a high pKa means?

A

a high pKa means the species is predominantly ionised, is a good proton acceptor, and a strong base

47
Q

For bases, a low pKa means?

A

a low pka means the species is predominantly unionised, is a bad proton acceptor, and a weak base

48
Q

What does High Throughput Screening (HTS) screen for ?

A

HTS screens a library (collection) of compounds for preliminary in vitro activity- hits

Applications of Organic and Bioinorganic Chemistry (6 decks)

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