MBIO 2730 ENZYMES

What are catalysts?

substances that speed up chemical reactions

Are catalysts consumed?

catalysts are not consumed in the process

What biomolecule are most biological catalysts?

most biological catalysts are proteins

What are some biological catalysts? Besides protein…

RNA

What catalyzes peptide bond formation?

peptide bond formation is catalyzed by ribosomal RNA

What do some enzymes require to function?

some enzymes require organic coenzymes and/or metal ions

What is an apoenzyme/apoprotein?

the protein portion of a holoenzyme

What is a holoenzyme?

protein and coenzyme

How do we name enzymes?

add -ase to its activity

What do oxidoreductases do?

transfer electrons as H or H-

What do transferases do?

group transfer of functional groups

What do hydrolases do?

bond breakage through the addition of water

What do lyases do?

addition to or formation of double bonds

What do isomerases do?

group transfer yielding isomers

What do ligases do?

formation of C-C; C-S; C-O; C-N bonds coupled to ATP cleavage

Why are enzymes necessary?

to speed up reaction rates; reactions still occur but too slowly; enzymes help reactions occur at appropriate speed

At what temperature and pH are most biological molecules stable?

most biomolecules are stable at pH 7 and 37°C in water

How much do enzymes accelerate bond formation and breakage?

enzymes accelerate reactions by 10^2–10^17

Are enzymes specific or non-specific? Are there side reactions?

enzymes are specific; usually no side reactions

Enzymes can be ___.

regulated

Do enzymes have a half-life?

enzymes have a half-life; useful enzymes have longer half-lives; less-used enzymes have shorter half-lives

Are enzymes easily denatured? If yes by what?

enzymes are easily denatured

by temperature, pH, mechanical

Enzymes function via changes in ________

conformation; dynamic not static; atoms constantly in motion

Describe specificity of enzymes

specific reactant molecules (substrates) bind to the enzyme active site and are converted to product

How does the active site fit the substrate?

the active site fits the substrate like a hand in glove

Describe the action of phosphofructokinase

transfers a phosphate from ATP to fructose-6-phosphate forming fructose-1

How do trypsin, chymotrypsin, and elastase recognize different amino acids?

trypsin, chymotrypsin and elastase recognize different amino acid classes based on the size and shape of their binding sites

How is aconitase specific?

aconitase distinguishes between the two ends of citrate even though there is no chiral carbon

How is aconitase able to distinguish between the two ends of citrate?

enzyme is 3D with three different sites of interaction

In some cases enzymes are _______ specific and are able to interact with multiple different substrates.

less

What are some examples of more general less specific enzymes?

hexokinase ---> phosphorylates glucose, fructose, mannose

What is the function of hexokinase?

phosphorylates glucose; fructose; mannose (transfer of a phosphate group from a donor to an acceptor, Or the addition of phosphate group to another molecule)

Enzymes provide a binding site that is ________ to the steric and electronic features of the substrate. “hand in glove”

complementary

How do enzymes work? What kind of environment do they provide?

enzymes provide an environment where bond formation and breakage is easier

We can keep track of G changes by what kind of diagram?

reaction coordinate diagram

What does a reaction coordinate indicate?

indicates free energy changes as a reaction progresses from substrate to product

What must be added to stretch bonds to the point of breaking?

free energy (G)

What is the transition state?

point where bonds of reactants and products are equally probable at reforming (hardest spot to break)

What do enzyme catalysts lower?

activation energy (Ea)

How much faster is the reaction catalyzed by carbonic anhydrase than by itself in water?

10^7 times faster

Is Keq affected by a catalyst?

no; equilibrium constant unchanged

Does the position of substrate and product energy change when enzyme is used?

no change

The smaller the delta G of the transition state the larger ___ is.

k

What increases delta G of the transition state? Does this make the reaction faster or slower?

tight binding of E to S increases delta G‡; slows reaction

What does the enzyme bind tightly instead of substrate to lower the delta G?

the transition state of the substrate

What does formation of bonds between enzymes and transition state release?

binding energy

What is binding energy also used for?

entropy reduction; desolvation; strain reduction; induced fit

How does binding energy contribute to entropy reduction?

enzyme holds substrates close in correct orientation

How does binding energy contribute to desolvation?

removes water shell around substrate

How does binding energy contribute to strain reduction?

overcomes steric or electronic strain

How does binding energy help with induced fit?

enzyme changes conformation to align active site properly

Enzymes usually also participate in the chemical transformation by their _ side chains.

amino acid

What type of enzyme is chymotrypsin?

a proteolytic enzyme that cleaves peptide bonds at Trp; Tyr; Phe

What do the side chains of His, Asp, Ser in the chymotrypsin active site form?

the side chains of His, Asp, Ser in the chymotrypsin active site form a catalytic triad

In the first step of a chymotrypsin enzymatic reaction E binds to what?

E binds to S

In the second step of chymotrypsin enzymatic reaction what happens?

electron flow from general base into substrate; forms first transition state

What is an oxyanion?

a polyatomic ion containing oxygen

What happens in the third step of chymotrypsin enzymatic reaction?

electrons flow from substrate to general acid; C-terminal peptide is released

How is the N-terminus released in chymotrypsin reaction?

by hydrolysis

Attack in first half of reaction?

serine

Attackee in first half of reaction?

carbonyl carbon

Attacker in second half of reaction?

water

Attackee in second half of reaction?

carbonyl carbon

What amount of enzymes uses metal cofactors?

about one-third

What do metal cofactors do?

metals stabilize charged transition states; help orient/bind substrate; accept/donate electrons in redox reactions. Ex is zinc in carbonic anhydrase