What is the BEST description of an enzyme?

a. It allows a chemical rxn to proceed extremely fast

b. It increases the rate at which a chemical rxn approaches equilibrium relative to is uncatalyzed rate
c. It makes a rxn thrmodynamically favorable
b. It increases the rate at which a chemical rxn approaches equilibrium relative to is uncatalyzed rate
Approximately how much does staphylococcal nutclese (Table 11-1) decrease the activation free energy (G++) of its rxn
(the hydrolysis of a phophodiester bond) at 25C
At 25C, every 10-fold increase in rate correstponds to a decrease of about 5.7 kJ -mol in G++. For the nuclease, thwi a
rate enhancement on the order of 10, G++ is lowered about 14 x 5.7 kJmol. ALternatively sinces the rate
enhancement K is given by..............SEE ANSWER IN BOOK
The covalent catalytic mechanism of an enzyme depends on a single active site Cys whose pK is 8. A mutation in a nearby
residue alters the microenviornment so tha this pK increases to 10. Would the mutation cause the rxn rate to increase or
decrease? Explain
The active form of the enzyme contains the thiolate ion. The increased pK would increase the nublophilicity of the thiolate
and thereby increase the rate of the rxn catalyzed by the active form of the enzyme. HOwever, at physiological pH there
would be less of the active form of the enzyme and therefore the overall rate would be decreased.
Explain why enzymes are stereospecific
The protein (or RNA) enzyme is a chiral molecule whose binding clefts and catalytic residues are arranged in a specific 3-D
asymmetry array. Hence, only substates with the appropriate stereochemistry can bind to the enzyme, and the enzyme
transofrms the substrate to product according to the spatial arrangement of enteracting fxnl groups
What is an apoenzyme and how does it differ from a holoenzyme? Which form is active?
An apoenzyme is the protein protion of an enzyme that has lost its cofactor (a metal ion or coenzyme). A holoenzyme is an
active enzyme containing both the protein and the cofactor.
If a protonated His residue acts as the proton donor in and acid-catalyzed enzymatic rxn, what happens to the enzyme;s
activity as the pH increases to a value that exceeds the pKR of that residue?
As the pH approaches the PKR, the His become progressively deprotonated and less effective as an acid catalyst. When pH
= pKR, 50% of the His residues are deprotonated and the enzyme is half-active. When the pH significantly exceeds pKR,
the His is slmost completely deprotonated and the enzyme is inactive.
What is the role of Zn i carbonic anhydrase? Hin: see interactive exercise 7
The Zn in carbonic anyhydrase polarizes a water molecule and thereby causes it to ionize. The resulting Zn--OH is the
nublophile that attacks carbon dioxide, converting it to HCOTHe metal ion stabilizes the negative chage of the OH,
which would otherwise not form at neutral pH.

What type of enyzme catalyzes the following rxn?

Isomerase

What type of enzyme catalyzes the following reactions

b. Lysase (group elimination to form double bond)
c. Oxidoreductase (oxidation reaction)
d. Ligase (bond formation coupled with ATP. Hydrolysis
Approximately how much does staphylococcal nuclease (table 11-1_ decrease the activation free energy (G++) of it
reaction (the hydrolysis of a phosphodiester bond at 25C?
At 25C, every 10-fold increase in rate corresponds with a decrease of ~5.7kjmol. For a nuclease with rate enhancement
of 10, G os ;pwered 14x5.7kJmol or ~80 kJmol
or k= e ^(Gcat/RT)
lnK = Gcat/(8.3145 x [273 + 25]) = 80kJmol
Studies at different pHs show that an enzyme has two catalytically important residues whos pKs are ~4 and ~10. Chemical
modicfication expericments indicate that a Glu and Lys residue are essential for activity. Match the residues to theri pKs
and explain whether they are likely to act as acid or base catalysts.
Glu has a pK of ~ 4, in its ionized form it acts as a base catalyst (see book)
Lys has a pK ~9, in its protonized form acts as an acid catalyst
The pK values of 2 essential catalytic residues in RNAse are 5.4 to 6.4. Which corresponds to His12 and which to His 119
(see figure 11-10)
His12 has pK of 5.4, since it is active when unprotonated. It would lose activity when the pH decreases.
His 119 has a pK of 6.4 since it is active when protonated. It would lose activity when the pH increases.

The pK values of 2 essential catalytic residues in RNAse are 5.4 to 6.4. Which corresponds to His12 and which to His 119
(see figure 11-10). Draw the tritration curve for these two residues.
Explain why lysozyme cleaves the artificial substrate (NAG)~4000 times more slowly than it cleaves (NAG)
Lysozyme cleaves between the 4th and 5th sugar and will
preferably bind (NAG) and distort the conformation of the
4th sugar (D) accelerates the reaction.
The lysozyme active site is arranged to cleave oligosaccharides between the 4th and 5th residues. Moreover, since the
lysozyme active site can bind at least six monosaccharide units, (NAG) would be more tightly bound to the enzyme than
(NAG) and this additional binding free energy would be applied to distorting the D ring to its half-chair conformation,
thereby facilitating the reaction
Lysozyme residues Asp 101 and Arg 114 are requried for efficient catalysis, althought they are located at some distance
from the active site GLue 35 and Asp 52. Substituting Ala for either Asp 101 or Arg 114 does not significantly alter the
enzymes tertiary structure, but it significantly reduces its catalytic activity. Explain
Asp 101 and Arg 114 form hydrogen bonds with the substrate molecule (fig 11-19). Ala cannot form theses hydrogen bonds
so the substituted enzyme is less active

Diagram the hydrogen-bonding interactions of the catalytic triad His-Lys-Ser during catalysis in a hypothetical hydrolytic
enzyme
Predict the effect of mutating Asp 102 of trypsin to Asn on substrate binding.
Little or no effect

Predict the effect of mutating Asp 102 of trypsin to Asn on catalysis

Catalysis would be much slower because the mutation disrupts to function of the catalytic triad. Asn i s not charged.