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35 Cards in this Set
- Front
- Back
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What are the polar amino acids?
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DEHCYKRS
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What is the reactive group of H?
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imidazole
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What is the reactive group of arginine?
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guanidinium
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What amino acids have the principle functions of cation binding and proton transfer? |
DE
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What amino acid has the principle function of proton transfer? |
H
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What amino acids have the principle function of covalent binding of acyl groups? |
CS
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What amino acid has the principle function of hydrogen bonding to ligands?
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Y
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What amino acid has the principle functions of anion binding and proton transfer? |
K
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What amino acid has the principle function of anion binding? |
R
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How is the active site pressured by evolution? |
It's pressured to put a group that can accept and donate protons there.
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What catalytic residue is most common in the active sites of enzymes? |
His (18%)
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What is more likely to be found in an active site and why: hydrophilic or hydrophobic residues?
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hydrophilic because they are functional
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How does triose phosphate isomerase interconvert the two tautomers DHAP and G3P? |
through a series of proton transfers
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What two key residues does triose phosphate possess in the active site?
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Glu165 and His95
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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 |
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What cleave the peptide bond?
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proteases
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True or false: breaking a peptide bond is thermodynamically unfavorable. |
false, favorable
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True or false: breaking a peptide bond is very slow in the absence of catalysis. |
true (half-life ~500 years)
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What are three members of the serine protease family?
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chymotrypsin trypsin elastase |
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What unites members of the serine protease family? |
same fold and mechanism
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Describe the catalytic triad framework. (4)
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Asp polarizes histidine Other nitrogen on histidine becomes a strong base Basic nitrogen hydrogen bonds to serine Oxygen of serine is nucleophilic |
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What happens when serine oxygen attacks carbonyl?
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proton transfer to histidine
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What does chymotrypsin cleave after? |
aromatic residues
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What do antibiotics often target? |
cell wall
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What is cell wall made out of? |
peptidoglycan
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What is peptidoglycan? |
repeating polymer of di-saccharide, tetra-peptide repeats cross-linked into a 3D matrix
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What interfere with cell wall biosynthesis of Gram-positive bacteria?
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beta-lactam antibiotics
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What are two examples of Gram-positive bacteria? |
staphylococci streptococci |
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How do beta-lactams inhibit glycopeptide transpeptidase? |
by mimicking its substrate, the terminal D-Ala---D-Ala
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How is enzyme deactivated by the inhibition of transpeptidase by beta-lactam?
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Transpeptidase attacks the beta-lactam ring of penicillin, forming a covalent bond that is slow to hydrolyze.
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What irreversibly blocks enzyme by mimicking D-Ala---D-Ala and being very stable when bound to enzyme? |
penicillin
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A protein that is optimally active at pH=5 is likely to have which in the active site? NE HS GY |
NE
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imidazolium
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acid
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imidazole |
base
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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.
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