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Medicinal Chemistry and Molecular Biology (CHEM2011) > Neil Thomas > Flashcards

Neil Thomas Flashcards

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1
Q

What is process to determine Gram positive and negative bacteria?

A

A heteroaroatic purple stain (crystal violet) sticks to the outer membrane of bacteria. After decolourisation with an organic solvent:
Gram negative bacteria are RED,
Gram positive bacter are PURPLE.

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2
Q

What type of bacteria is this? Is it Gram positive or negative?

https://cdn.mos.cms.futurecdn.net/kiwgs7oBBeHx78X6r6FNr-1920-80.jpg.webp

A

Streptococci
(Chains)

Gram positive

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3
Q

What type of bacteria is this? Is it Gram positive or negative?

https://upload.wikimedia.org/wikipedia/commons/thumb/d/d3/Staphylococcus_aureus_VISA_2.jpg/1200px-Staphylococcus_aureus_VISA_2.jpg

A

Staphylococci
(Round clusters of cells)

Gram positive

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4
Q

What type of bacteria is this? Is it Gram positive or negative?
https://media.sciencephoto.com/image/c0370100/800wm

A

Coccobacilli
(Intermediate between cocci (spherical bacteria) and bacilli (rod-shaped bacteria))

Gram-variable

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5
Q

What type of bacteria is this? Is it Gram positive or negative?

http://www.ucmp.berkeley.edu/bacteria/treponemapal.gif

A

Spirochetes

(Helically coiled - corkscrew-shaped or spiraled - cells)

Gram-negative.

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6
Q

What type of bacteria is this? Is it Gram positive or negative?

https://images.nationalgeographic.org/image/upload/t_edhub_resource_key_image/v1652340959/EducationHub/photos/e-coli.jpg

A

Escherichia coli

(Isolated round cells)

Gram-negative.

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7
Q

What is the definition of a prodrug?

A

A prodrug is a precursor to an active drug that is formed in vivo.

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8
Q

What is an anti-metabolite?

A

An anti-metabolite is a compound that blocks enzymes involved in metabolic pathways.

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9
Q

What is a bacteriostatic drug?

A

A bacteriostatic drug is a compound that inhibts growth and replication but do not directly kill.

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10
Q

What is a synergistic mixture and why are they used?

A

A synergistic mixture is a mix of two different drugs where the activity of the two drugs combined is greater than the sum of the activity if the drugs are used on their own.

Synergistic mixtures are used to overcome resistance, the idea being that if one drug can no longer inhibit its target enzyme, because of a mutation, the other will.

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11
Q

What is reversible competitive inhibition?

A

In reversible competitive inhibition an enzyme can either bind to a substrate or a inhibitor. The inhibitor binds tighter to the enzyme so the reaction will proceed down this pathway. A Enzyme-Inhibitor, non-covalent, complex is then formed so no product is formed.

In the case of sulfanilamide, the amine group is a poor nucleophile so the biosynthesis of folic acid cannot go ahead.

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12
Q

What does QSAR stand for and what is it?

A

Quantitative structure-activity relationship (QSAR) are mathematical relationships linking chemical structure and pharmacological activity in a quantitative manner for a series of compounds. Methods which can be used in QSAR include various regression and pattern recognition techniques.

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13
Q
  1. What is the main functional group of this molecule?
  2. What type of agent is this?
  3. What are the modifiable groups on this molecule?
  4. How does the lone pair on the nitrogen affect the stability of the molecule?
    https://ibb.co/5c3P5Fv
A
  1. B-lactam/cylic amide.
  2. An anti-staphylococcal agent.
  3. Sulpur, the geminal dimethyl groups, and R group of the carbonyl.
  4. No delocalisation of N lone pair because the molecule cannot be flattened out. Meaning no resonance forms are available. The carbonyl is therefore more similar to that of ketone than amide; it is much more electrophilic so more susceptible to hydrolysis.
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14
Q
  1. What is the main functional group of this molecule?
  2. What type of agent is this?
  3. What are the modifiable groups on this molecule?
  4. How does the lone pair on the nitrogen affect the stability of the molecule?
    https://ibb.co/5c3P5Fv
A
  1. B-lactam/cylic amide.
  2. An anti-staphylococcal agent.
  3. Sulpur, the geminal dimethyl groups, and R group of the carbonyl.
  4. No delocalisation of N lone pair because the molecule cannot be flattened out. Meaning no resonance forms are available. The carbonyl is therefore more similar to that of ketone than amide; it is much more electrophilic so more susceptible to hydrolysis.
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15
Q

Explain the key differences between mammalian, Gram positive, and Gram negative cell membranes.

A

Mamallian membranes:
- Phospholipid bilayer. Fatty acid tail which is hydrophobic and a polar head group which is hydrophilic.
- It is semi-permeable. Meaning it must have ion channels to allow molecules in and out
- Cholesterol is ONLY FOUND IN THE MAMMALLIAN MEMBRANE. Cholesterol makes the membrane fluid and flexible
- The membrane has a more simple structure than bacteria. This is because mammalian cells do not suffer from osmotic stress as the salt levels inside the cell are not as high as the levels in bacterium cells. Therefore there is no need to strengethen the membrane.

Gram +ve:
- Have a THICK layer of peptidoglycan between the cell exterior, and the cytoplasmic membrane as a way of strengthening the cell. It is a mesh of carbohydrates in one direction and peptides in the other. It is highly crosslinked in Gram +ven bacteria because they have a higher salt concentration, in their cytoplasm, than Gram -ve bacteria.
- The type of phospholipids differs from those found in the mammalian membrane.
- B-lactamases are secreted from the bacteria and dilute away very quickly.

Gram -ve:
- These have two membranes: the cytoplasmic membrane and the outer membrane.
- They also have the periplasmic space - this is formed of peptidoglycan but it is a thinner amount and is less crosslinked than that found in Gram +ve bacteria.
- The periplasmic space also contains lipoproteins (proteins with a fatty acid attached). These allow salts and vitamins (and other polar molecules) to pass through the membrane.
- B-lactamases are found between the two membranes. Meaning a concentrated layer of the B-lactamases are found. Therefore, are much more effective at degrading penicillins.

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16
Q

What is the role of transpeptidases?

A

Transpeptidases are enzymes which cross-link the peptidoglycan chains to form rigid cell walls. Transpeptidases are the target for pencillins.

17
Q

What are B-lactamases?

A

B-lactamases are enzymes secreted by bacteria which provides antibiotic resistance by breaking the antibiotics’ structure.

18
Q
  1. What is a suicidal substrate?
  2. What is the mechanism of B-lactam inhibition of transpeptidases?
  3. How does the permanent deactivation of transpeptidases lead to cell rupture?
A
  1. Suicide substrates are compound that behaves as a normal enzyme substrate until a highly reactive intermediated is generated and it then irreversibly diverges from the normal catalytic mechanism to form the permanent covalent bond with enzyme/co-enzyme
  2. B-lactam is such a good mimic of the D-Ala-D-Ala motif on the peptide (which would usually be used to form crosslinked peptidoglycan) water cannot hydrolyse the ester bond on the acyl-enzyme intermediate.
    Intermediate stays stuck in the form with the acylated serine residue. i.e. it is irreversibly inhibited. This kills the activity of the enzyme.
  3. The permament deactivation of transpeptidases causes the number of crosslinks in peptidoglycan to be reduced which causes the cell to rupture due to osmotic pressure.
19
Q

Describe combination therapy.

A

Combination therapy is using a B-lactamase inhibitor in combination with a pencillin. For example Augmentin is a combination of amoxocillin and clauvanic acid. It is effective because clauvanic acid removes all B-lactamases from the system. This is an example of a synergistic mixture.

20
Q
  1. What does MIC stand for?
  2. What does it mean about the quality of antibiotics.
A
  1. MIC stands for Minimum Inhibitory Concentration. I.e. the lowest antibiotic concentration that prevents growth of bacteria on petri dishes.
  2. The lower the MIC value, the better the antibiotic.
21
Q

What is the definition of bacteriocidal?

A

A bacteriocidal compound is one whose mechanism of action directly leads to cell death.

22
Q

1.What is the binding sites on ionophores?
2. Explain the selectivity of ionophores.

A
  1. The binding sites on ionophores are the oxygen atoms on the saturated heterocycles.
  2. The binding sites on ionophores wrap around different ions. The size and structure of the compounds means they have different selectivity (for examples Nigericin prefers to bind to K+ over Na+). This ‘coat’ around the ions is very hydrophobic allowing the ion to be shuttled across the hydrophobic core of the cell membrane.
23
Q

What is the mechanism of action of glycopeptide antibiotics (e.g. Vancomycin)?

A

Glycopeptides surround and smother the D-Ala-D-Ala unit and stop it binding to the transpeptidase enzyme. Similarly to penicillins, this reduces the amount of crosslinking in the peptidoglycan which ultimately leads to the cell rupturing due to osmotic pressure.

24
Q

What is a nucleoside?

A

A nucleoside is formed when the anomeric hydroxyl group at the 1C position on the 2-deoxyribose sugar has been subsituted with one of the four bases but is still missing a phosphate group.

25
Q

Explain the binding positions on DNA.

A
  1. G-C has 3 H-bonds (these have a higher melting point, are shorter, and this region is narrower and more compact than the AT region). A-T has 2 H-bonds.
  2. All atoms are aromatic (have pi electrons). The base pairs are stacked but slightly offset. Pi orbitals do not sit above one another, they instead overlap and are slightly twisted. Forming a duplex.
  3. The DNA bases form a hydrophobic, aromatic core structure. These are connected by the phosphate-diester backbone. This backbone is negatively charged therefore neutral/positvely charged molecules can bind to it.
  4. Spacing between adjacent turns are different in size (minor grooves vs major grooves). These have different widths. Small molecules can bind to the minor grooves. Proteins that bind to the DNA bind in the major grooves.
  5. Planar aromatic/heteroaromatic molecules can slip inbetween the base pairs and can act as a molecular glue stopping DNA duplex strands from seprating. This stops the replication process.
26
Q

Where is the strongest nucleophile found in DNA?

A

The strongest nucleophile in DNA is N-7 of Guanine. This is where DNA alkylating agents are going to react.

27
Q

What are DNA intercalating agents?

A

DNA intercalating agents have heteroaromatic rings which allows the moecules to slot in between the bases in the DNA duplex.
Quinine, an example of a intercalating agent, binds to the DNA of malarial parasites preferentially over human DNA. This stops the parasitic DNA from replicating.

28
Q

What causes GT mismatch?

A

GT mismatch is caused when an alkylated N-7 guanine coverts the tautomer from the preferred keto form to the enol form. A mutation in the DNA sequence occurs. Usually, the cell will recognise this and begin the process of apoptosis - programmed cell death. Depurination

29
Q

Name the purines and the pyrimidines.

A

Purines:
Adenine and Guanine

Pyrimidines:
Cytosine, Thymine, and Uracil.

Medicinal Chemistry and Molecular Biology (CHEM2011) (2 decks)

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