L25 - Making And Breaking Biological Molecules

Question 1

What is the importance of chemistry in biology?

Answer 1

• generate energy amd transfer into useful form (ATP, ion, metabolite grads)
• partition molecules into dif compartments
• catalyse reaction - occure on a meaningful timescale
• maintain molecular structure
• regulate activity of other molecules
• transmit and store info

Question 2

What does some of this chemistry rely on?

Answer 2

• making and breaking of covalent bonds (catalysis, energy gen in ATP, storage of info)
• weak forces stabilising protein 3 struc (molecular structure, ion/metabolite grad)

Question 3

What type of chemistry is it when protein kinase catalyses the transfer of a phosphate group from ATP to a threonine residue?

Answer 3

Covalent chemistry

Question 4

What type of chemistry is it when negatively charged DNA is tightly wrapped around positively charged histone proteins enabling effective packaging in the nucles of the cell?

Answer 4

Non-covalent chemistry

Question 5

What does the specificity of molecular interactions rely on?

Answer 5

• molecular shape
• chemical complementarity
• spatiotemporal overlap

Question 6

How does molecular shape affect specificity in molecular interactions?

Answer 6

Different molecules fitting togehter like a 3D jigsaw

Question 7

How does chemical complementarity affect specificity in molecular interactions?

Answer 7

+ve charges interacting with -ve charges
- hydrogen bonding potential fulfilled
- cluters of hydrophobic moieties

Question 8

How does spatiotemporal overlap affect specificity in molecular interactions?

Answer 8

Molecules being in the same place at the same time

Question 9

Where do interactions occur?

Answer 9

Protein surface or in active site

Question 10

What are B-lactam antibiotics?

Answer 10

Most prescribed antibiotic class
- penicillins, cephalosporins, carbapenems, monobactams

Question 11

What do B-lactam antibiotics target?

Answer 11

enzymes known as penicillin-binding proteins (PBPs)

Question 12

What are PBPs involved in?

Answer 12

Biosynthesis of the cell wall of gram-negative bacteria
- irreversibly inhibited by B-lactam antibiotics

Question 13

Where are B-lactamases found in?

Answer 13

Gram-negative bacteria

Question 14

What do B-lactamases hydrolyse?

Answer 14

Amide bond of the four-membered B-lactam ring in many antibiotics
- can no longer bind to target = loss of activity

Question 15

What happens if an antibiotic has no activity in its target bacteria?

Answer 15

Bacteria is resistant to the antibiotic
- B-lactam hydrolysis is a mechanism of antimicrobial resistance

Question 16

What happens to the molecular shape of benzylpenicillin binding to PC1 B-lactamase from S.aureus?

Answer 16

• penicillin binds in a pocket on surface of PC1
• fits well in its binding pocker
• bound drug displaces so binding site visible

Question 17

What are interactions in chemical complementarity of benzylpenicillin binding to PC1 B-lactamase form S.aureus?

Answer 17

• Hydrogen bonding to Gln237 backbone
• Hydrogen bonds to solvent (water)
• Hydrogen bond to Asn132 side chain
• Hydrophobic residues around benzene ring
• ring stacking between benzine ring and Tyr105 sidechain

Question 18

Comparing B-lactamase binding pocket with that in a PBP?

Answer 18

• both pockets form H bonds to same chem groups
• PBP forms covalent bonds to sidechain of Ser434 = acyl-enzyme

Question 19

What happens to the mutant PBP enzyme which Asn489 mutated to Asp?

Answer 19

Mutation leads to a reduction of number of H bonds/interactions
- bind more weakly

Question 20

What is the covalent chemistry in B-lactam hydrolysis?

Answer 20

• deprotenated serine acts as nucleophil to B-lactam
• hydrolysis of covalent bond between C-N with OSer
• reaction stops in PCP enzyme (Acyl-enzyme covalently inhibited)
• H in H2O protenated
• OH to C=O
• LG of OSer
  = hydrolysed B-lactam
• H-O-Ser regenated

Question 21

What makes it difficult to design new antibiotics?

Answer 21

Similar interactions in both target and off-target enzymes