Biochem Exam 2 - Enzymes

what are the 3 ways to inc the rate of a chemical reaction

inc temp, inc conc of reacting substances, add catalyst

what is the exception to enzymes are usually proteins

ribozymes are rna molecules that act as a catlyst not proteins

what is the typical rate of enhancements for typical enzymes

10^8 to 10^12

what is the exception to most enzymes have high specificity for substrates

chymotrypsin has a broad specificity
hydrolyzes peptide, amide, or ester bonds after phe, tyr, trp

what are the six major classifications of enzymes

oxidoreductases = ox-red reactions
transferases = transfer or functional groups
hydrolases = hydrolysis reaction
lyases = group elim to form double bonds
isomerases = isomerization reactions
ligases = bond formation coupled with atp hydrolysis

what is the enzyme class for pyruvate decarboxylase

lyase

what determines the rate of a reaction

the height of the activation energy barrier

what are the three mechanisms for enzyme catalysis

acid base, covalent catalysis, metal ion catalysis

describe acid catalysis

H+ transfer from an acid lowers the free energy of the transition state

describe base catalysis

H+ is abstracted by a base to lower free energy of the transition state

which amino acids can act as an acid or base in acid-base reactions

asp, glu, his, lys, cys, tyr

describe covalent catalysis

accelerate reactions by forming a covalent bond between E and S during the formation of a transition state
enzymes that use this undergo a 2 part reaction process

describe metal ions as catalysts

mediates ox-red reactions

what type of catalysis does chymotrypsin’s catalytic triad participate in

acid-base and covalent

chymotrypsin is considered what and contains which amino acids in its active site

is a serine protease
contains asp 102, his 57, and ser 195

what is the function of asp 102 in chymotrypsin’s catalytic triad

anchors his 57

what is the function of his 57 in chymotrypsin’s catalytic triad

acts as a base and then later on an acid

what is the function of ser 195 in chymotrypsin’s catalytic triad

acts as a nucleophile

what is the scissile bond

the bond on the substrate to be cleaved by hydrolysis is positioned near ser 195

what are the first 6 steps of the serine protease mechanism

1. peptide substrate binds to the active site so that the scissile bond is near ser 195

2. his57 acts as a base and deprotonates ser195

3. ser195 turns into a strong nucleophile

4. asp102 stabilizes the now positively charged his57

5. O- of ser195 attacks the peptide carbonyl C = forms a tetrahedral intermediate

6. intermediate stabilized by oxyanion hole

what are steps 7-12 of the serine protease mechanism

7. his57 acts as a acid and donates a proton to the N of the scissile bond

8. peptide bond breaks and creates acyl-enzyme/covalent intermediate and a fragment N terminal product leaves

9. water enters active site and his57 acts as a base deprotonating water to generate a hydroxide nucleophile

10. OH- attacks the carbonyl carbon of the acyl-enzyme = forms another tetrahedral intermediate, which is stabilized in the oxyanion hole

11. his57 acts as an acid again and donates a proton to the ser195 oxygen

12. the second peptide fragment the c terminal product is released

what is the relationship between nucleophilicity and the acidity of an amino side chain

the greater the acidity, the less nucleophilic the group

explain the proximity and orientation effect

when enzymes bind substrates, the substrates are brought into proximity and in the correct orientation to make a chemical reaction more favorable

explain induced fit

when hexokinase binds to glucose (the substrate), a conformational change occurs in the enzyme to fit the substrate better

describe the specificity of chymotrypsin

gly226, gly216, ser189 at bottom

describe the specificity of trypsin

gly226, gly216, asp189 at bottom

describe the specificity of elastase

val226 and thr216

A specificity pocket lined with Gly residues and with an Asp
residue at the bottom of the pocket is characteristic of…?

trypsin

A specificity pocket lined with Val and Thr residues accommodates what?

small hydrophobic side chains

Asp189 lies at the base of the specificity pocket of trypsin. In site-directed mutagenesis studies this residue was replaced by Lys. What would be the substrate specificity of the mutant enzyme?

acidic residues