04 - Enzymes

Oxidation-reduction rxns; mostly use coenzymes such as NAD⁺, NADP⁺, FAD, coenzyme Q, or molecular oxygen as e^- acceptors

Transfer a chemical group (amino, phosphoryl, carboxyl, etc.) from a donor to an acceptor; transaminases, kinases, etc.

Hydrolytic cleavage of covalent bonds between C and some other atom; peptidases, proteases, phosphatases, etc.

Non-hydrolytic cleavage of covalent bonds between C and some other atom; decarboxylases, dehydratases, aldolases, etc.

Non-hydrolytic cleavage of covalent bonds between C and some other atom; decarboxylases, dehydratases, aldolases, etc.

Formation of covalent bonds between C and other atoms such as sulfur, nitrogen or oxygen; frequently uses ATP or GTP as an energy source; carboxylases, thiokinases, etc.

Required for enzymes to perform their function; bound very tightly by covalent or noncovalent interactions; heme, Fe, Cu, Se, etc.; many are derived from vitamins

Thiamin pyrophosphate from thiamin, FAD and FMN from riboflavin, NAD⁺ and NADP⁺ from Niacin, and Coenzyme A from pantothenic acid

Non-protein components that are not absolutely essential for enzyme activity but are needed for maximal activity of the enzymes; most common cofactors are metal ions

Increase the velocity of the forward and reverse reaction at equilibrium, though it does not change the concentration of [S] or [P]; Keq remains the same

It is the free energy of the product (G_P) minus the free energy of the substrate (G_S); when the free energy of the rxn (ΔG) is negative the rxn is spontaneous

The standard free energy change (ΔG°) is where the [S] and [P] are kept at 1M at the beginning of the rxn

• ΔG*, E_act or ΔG^‡, it is the free energy change
• from S to the transition state

Lower E_act but do not alter ΔG° or ΔG

They bind the transition state in preference to the substrate while forming the ES complex

The rxn velocity at infinite [S]

K_m; this is the [S] that gives a rxn velocity equal to ½ V_max

  

When K_m­ is high the affinity of the enzyme for its substrate is low; when K_m­ is low the affinity of the enzyme for its substrate is high

A genetic mutation in aldehyde dehydrogenase (Lys for Glu) which decreases the affinity of aldehyde dehydrogenase for NAD⁺; may be responsible for undesirable side effects of alcohol and may protect against alcoholism

• Since the inhibition is overcome by increasing the [S], V_max­­ does not change; however it increases the K_m for a given substrate, meaning that in the presence of the inhibitor, more substrate is needed to
• achieve ½ V_max
• 
• 

• It can bind either the free enzyme or the ES complex; K_m­ is unchanged; V_max is decreased even at high substrate concentrations
• 
• 

• Antifreeze contains ethylene glycol, and some alcoholics drink this to support their drinking habit, but it is toxic; ethanol is administered to these individuals because ethanol competes for the active site on ADH and thus prevents its metabolism and the generation of its toxic metabolites (glycolic
• acid and oxalic acid); similar for methanol (its metabolite is formic acid)

Glycolic acid and oxalic acid

Formic acid

• 
• Remember as K_m goes up the affinity of the enzyme for the substrate goes down; K_i is the inhibition constant

2 (1+200/0.2)=2*1001=2002µM

Catalysis by proximity, catalysis by strain, acid-base catalysis, and covalent catalysis

The active site assemble subsrates to within close bond-forming distance of one another, the higher [S] the more likely they will occupy the active site in close proximity to enhance catalysis

This is typically how enzymes that break covalent bonds work; they put the bond needing to be broken in a thermodynamically unfavorable position so it will undergo cleavage

There are ionizable functional groups at the active side which serve as acid or bases

Pepsin hydrolyzes peptide bonds at the carboxyl end of large hydrophobic AAs in proteins using water; it has two aspartic acid residues at its active site which serve as acids and bases

Generates a transient covalent bond between an active side reside and one or more substrates; once the rxn is complete the intermediate disappears

Chymotrypsin; it is s serine protease (has a serine as a residue); it has the three residues Asp-12, His-57, and Ser-195; these three residues form a charge-relay network; they hydrolyze peptide bonds at the carboxyl end of aromatic AAs in proteins using water

Sigmoidal curve because the active site of one enzyme can affect the active site in the same enzyme

• Affect K_m but not V_max­; binds at an allosteric
• site which then affects the affinity of substrate binding

Alter V_max but not K_m

• 
• where n is the Hill coefficient and is equal to the number of substrate binding
• sites on the enzyme

An allosteric enzyme involved it the biosynthesis of pyrimidine nucleotides; CTP is one of the end products of the biosynthetic pathway, and allosterically inhibits aspartate transcarbamoylase; ATP stimulates this pathway; both are K-class effectors

Enzymes which occur in more than one molecular form but catalyze the same rxn; can have different kinetic properties for Km and/or Vmax­; ΔG and ΔG° remain the same but ΔG^‡ will be different for each one

For example LDH exists in 5 different isoforms, with LDH1 being predominant in the heart, whereas LDH5 is predominate in erythrocytes, skeletal muscle, and liver; when tissues are destroyed the intracellular enzymes are released into blood; therefore serum levels of LDH1 vs LDH5 can be used as an indicator of where the damage occurred