Biochem Chap 3

Question 1

What are 3 characteristics of enzymes?

Answer 1

• lowers Ea of reaction
• Affects kinetics but not thermodynamics Delta G or equilibrium
• Regenerates itself

Question 2

What are the two models used to describe enzymes?

Answer 2

Two models to describe ES: 1) lock and key and 2) induced fit (more accepted).

Question 3

What is an isomerase?

Answer 3

Catalyzes isomerization reaction - rearrangement of bonds

Question 4

What is a ligase?

Answer 4

Catalyzes joining of molecules

Question 5

What is a transferase?

Answer 5

Catalyzes transfer of a functional group from one molecule to another

Question 6

What is a lyase?

Answer 6

Catalyzes breaking of molecule without water

Question 7

What is a hydrolase?

Answer 7

Catalyzes breaking of molecule by adding water

Question 8

What is an oxidoreductase?

Answer 8

Catalyzes transfer of electrons between molecules

Question 9

What are cofactors/coenzymes?

Answer 9

bind to active site and assist in catalysis - can be ions or water-soluble ions.

Question 10

What is a prosthetic group? Holoenzyme? Apoenzymes?

Answer 10

When cofactor/coenzyme is bound extremely tightly to enzyme it is a prosthetic group - with their cofactors they are called holoenzymes and without they are apoenzymes.

Question 11

What are characteristics of nonpolar hydrophobic amino acids in enzymes?

Answer 11

Nonpolar hydrophobic amino acids are less likely to be catalytically important amino acids as they cannot directly engage in certain chemistry. They are more important for forming enzyme cores.

Question 12

What is a Michaelis-Menten plot?

Answer 12

two specific conditions: enzyme concentration held constant and substrate concentration increased. The reaction velocity is plotted vs. substrate concentration

Question 13

How do you calculate Vmax?

Answer 13

Vmax=[E] x kcat

Question 14

What is Km?

Answer 14

is the substrate concentration at 1/2 Vmax. Is the binding affinity of substrate for the enzyme. If a substrate can bind enzyme with a higher affinity, it is more likely to be captured by the enzyme and converted into product. Small Km = high substrate affinity.

Question 15

What is catalytic efficiency and how do you calculate?

Answer 15

Catalytic efficiency is how effective an enzyme is at converting substrate to product: catalytic efficiency = kcat/Km

Question 16

What is a Lineweaver-Burk plot?

Answer 16

reciprocal of each axis.

Question 17

Describe competitive inhibition? See graph

Answer 17

In competitive inhibition an inhibitor binds to enzymes active site preventing substrate from binding. Amount of substrate is increased, and effect of the inhibitor decreases, Vmax can be reached. If inhibitor is blocking binding site, binding affinity will be worse and Km will increase.

Question 18

Describe uncompetitive inhibition. See graph.

Answer 18

In uncompetitive inhibition the inhibitor binds selectively to ES. If add more substrate, enzyme will not work as fast - Vmax decreases. A decrease in ES causing increase in affinity - Km decreases.

Question 19

Describe mixed inhibition. See graph

Answer 19

In mixed inhibition the inhibitor binds to allosteric site, or non-active site regulatory pocket. Often this binding is biased towards one another ie. 70% of inhibitors may bind enzyme and 30% may bind ES.

Question 20

Describe noncompetitive inhibition. See graph

Answer 20

Non-competitive inhibition occurs when 50% of inhibitors bind the enzyme alone and 50% bind the ES complex. Vmax decreases but Km will stay the same

Question 21

What are 6 ways to regulate enzyme activity?

Answer 21

Local environment conditions, covalent modification, allosteric regulation, zymogens, feedback regulation and cooperativity

Question 22

Describe regulating via local environment conditions.

Answer 22

The two main are temp and pH
To a point, increasing temp increases kinetic energy of E + S - but once too high, enzyme is denatured.
pH - amino acids at active sites are often charged - depend on pH of solution. Their protonation status can determine whether or not enzyme will work. Diff enzymes function differently at diff pH’s but overall they function best around 7-8.

Question 23

Describe allosteric regulation.

Answer 23

Many enzymes have allosteric sites - bind allosteric activators or inhibitors

Question 24

What are zymogens?

Answer 24

Zymogens are inactive enzyme forms that must be cleaved to be activated. ie. trypsinogen - must be cleaved into trypsin to be active

Question 25

Describe covalent modification

Answer 25

Many enzymes are regulated via post-translational modifications (PTMs) that are added to proteins - include phosphorylation, acetylation, glycosylation and methylation.

Question 26

What is feedback regulation? See image

Answer 26

Most common form is negative regulation - enzymes product or downstream product can inhibit enzyme. Positive (feed-forward) regulation - substrate or product upstream can activate enzyme.

Question 27

Describe cooperativity.

Answer 27

Many enzymes have multiple binding sites or form multi-domain proteins and can bind more than one substrate which can affect affinity for others.

Cooperativity example: hemoglobin - 4 subunits that bind 1 oxygen. After first binds oxygen, the next is much more likely to bind another - pattern continues. Cooperativity is often described by Hill coefficient - If < 1 it is negative cooperativity and the first binding decreases the binding of subsequent. If > 1 then it is positive - binding of first increases binding of subsequent. If = 1 then there is no cooperativity, and the binding of first has no effect on subsequent.

Question 28

How does cooperativity look in a [s] vs. reaction velocity graph?

Answer 28

sigmoidal.