BCHM Exam 3 Before Going on

Describe how enzymes differ from other catalysts.

enzymes …

• are usually proteins, some exceptions (ex. catalytic RNA, ribosomal subunit)

• are specific, have an active site where their substrate bonds

  • moonlighting enzymes: can bind to more than one substrate (have a main reaction and a secondary reaction

• can be regulated (turn up/down, on/off)

  • aren’t always active

• work at mild conditions

  • works at physiological pH and ambient temperature

  • can’t increase temperature of environment because it risks denaturing proteins

  • can’t increase concentration of the reactants because there is no space

Explain how enzymes exhibit specificity for their substrates and products. 

2 theories

1) lock and key theory

• substrate has a shape that matches the active site, the two molecules bind 

2) induced fit theory

• more accurate model

• the active site of the enzyme is flexible and will mold to the shape of the substrate

• moonlighting enzymes can mold to the shape of multiple substrates (why they can catalyze different reactions)

- fact- it would take 20 years for a peptide bond to break without an enzyme (chymotrypsin)

Describe how enzymes are classified.

3 types

• addition, removal, rearrangement

• but translocase is exception, its function is transport

1) oxidoreductase

• oxidation-reduction reactions

• add/remove electrons

• always have an electron carrier (ex. NADH, FAD, FADH2)

• oxidation- loss of electrons

• reduction- gain of electrons

2) transferases

• transfer a functional group from one molecule to another

• do NOT use ATP for energy

3) hydrolases

• cleave bonds by adding a water molecule, splits into two molecules

• ex. phospholipase A2 (PLA2)  

4) lyases

• remove functional groups via non-hydrolysis reactions

  • NO WATER

• result in the addition/removal of a double bond

5) isomerases

• rearrange functional groups within a molecule

• mutases: transfer functional groups from one position to another

• epimerases: invert functional groups about asymmetric carbons

6) ligases

• use ATP to break bonds

  • ADP and P are released, P is not added to molecule

• form C-C, C-S, C-O, and PO3²- ester bonds

7) translocases

• move molecules (usually) across the membrane

• ex. integral proteins (ATP-ADP translocase)

Relate a reaction’s activation energy to its rate.

• activation energy is the energy needed for a reaction to reach its transition state and begin a chemical reaction

• lower activation energy increases the rate of the reaction

Describe an enzymes effect on activation energy and the change in energy of a reaction. 

• enzymes decrease activation energy through the stabilization of the transition state

  • the transition state is where the enzyme is bound tightest to the substrate

• the active site brings the reactants closer together, making product formation quicker

• have no effect in the change in energy of a reaction (therefore no effect on exergonic/endergonic)

Describe the roles of the different cofactors in catalysis.

• cofactors work with an enzyme to aid in the catalysis

• they can be organic/inorganic

• metal ions

  • inorganic cofactors

  • used for oxidation/reduction

• coenzymes

  • organic cofactors

  • 2 types

    • cosubstrates: temporarily associate with the enzyme (ex. NAD+, NADH)

    • prosthetic groups: covalently linked to the enzyme, more permanent

Identify the three types of chemical catalytic mechanisms.

1) acid-base catalysis

• proton is transferred (accepted/donated, some have both) between the enzyme and substrate to stabilize the transition state

• acid catalyst- proton is donated

• base catalyst- proton is accepted

• remember that the enzyme must end how it started, know where H goes at end

2) covalent catalysis

• covalently bond to a substrate during the transition state

• transient/temporary covalent bond

• nucleophile (in enzyme active site) forms the bond in search of an electron poor center

• two-part reaction process with intermediate between them, first part is covalent bond forming, second part is it breaking (usually higher energy bump)

3) metal ion catalysis

• mediate oxidation-reduction reactions to promote reactivity of other groups in enzyme’s active site through electrostatic effects

• stabilize the transition state

Assign roles to specific amino acid side chains during catalysis.

1) acid-base catalysis

• AAs with ionizable side chains

• Asp, Glu, His, Lys, Cys, Tyr

• Not Arg

2) covalent catalysis

• Ser, Tyr, Cys, Lys, His

• deprotonated form because they are great nucleophiles