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35 Cards in this Set

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What are the polar amino acids?
DEHCYKRS
What is the reactive group of H?
imidazole
What is the reactive group of arginine?
guanidinium

What amino acids have the principle functions of cation binding and proton transfer?

DE

What amino acid has the principle function of proton transfer?

H

What amino acids have the principle function of covalent binding of acyl groups?

CS
What amino acid has the principle function of hydrogen bonding to ligands?
Y

What amino acid has the principle functions of anion binding and proton transfer?

K

What amino acid has the principle function of anion binding?

R

How is the active site pressured by evolution?

It's pressured to put a group that can accept and donate protons there.

What catalytic residue is most common in the active sites of enzymes?

His (18%)
What is more likely to be found in an active site and why: hydrophilic or hydrophobic residues?
hydrophilic because they are functional

How does triose phosphate isomerase interconvert the two tautomers DHAP and G3P?

through a series of proton transfers
What two key residues does triose phosphate possess in the active site?
Glu165 and His95

What is the pH optimum for triose phosphate isomerase given the pKa values for Glu165 and His95?

> 6.5, when both are protonated and active

What cleave the peptide bond?
proteases

True or false: breaking a peptide bond is thermodynamically unfavorable.

false, favorable

True or false: breaking a peptide bond is very slow in the absence of catalysis.

true (half-life ~500 years)
What are three members of the serine protease family?

chymotrypsin


trypsin


elastase

What unites members of the serine protease family?

same fold and mechanism
Describe the catalytic triad framework. (4)

Asp polarizes histidine




Other nitrogen on histidine becomes a strong base




Basic nitrogen hydrogen bonds to serine




Oxygen of serine is nucleophilic

What happens when serine oxygen attacks carbonyl?
proton transfer to histidine

What does chymotrypsin cleave after?

aromatic residues

What do antibiotics often target?

cell wall

What is cell wall made out of?

peptidoglycan

What is peptidoglycan?

repeating polymer of di-saccharide, tetra-peptide repeats cross-linked into a 3D matrix
What interfere with cell wall biosynthesis of Gram-positive bacteria?
beta-lactam antibiotics

What are two examples of Gram-positive bacteria?

staphylococci


streptococci

How do beta-lactams inhibit glycopeptide transpeptidase?

by mimicking its substrate, the terminal D-Ala---D-Ala
How is enzyme deactivated by the inhibition of transpeptidase by beta-lactam?
Transpeptidase attacks the beta-lactam ring of penicillin, forming a covalent bond that is slow to hydrolyze.

What irreversibly blocks enzyme by mimicking D-Ala---D-Ala and being very stable when bound to enzyme?

penicillin

A protein that is optimally active at pH=5 is likely to have which in the active site?




NE


HS


GY
RE
KR

NE
imidazolium
acid

imidazole

base

Beta lactamase is an enzyme that hydrolyses the beta-lactam of penicillin. Why does this protein allow cells to grow in the presence of penicillin?

Reduces the concentration of the inhibitor.