2. Enzymes

Question 1

(2.1) What are the six different types of enzymes?

Answer 1

(Lil Hot)

• Lyase
• isomerase
• ligase
• hydrolase
• oxidoreductase
• transferase

Question 2

(2.1)How do Ligases work?

Answer 2

addition or synthesis reactions, generally between large molecules, often require ATP

Synthesis by smaller reactions with smaller molecules are usually accomplished by lyases.

Nucleic acid synthesis and repair is a common example.

Question 3

(2.1) How do Isomerases work?

Answer 3

Rearrange the bonds within a compound

Longer answer:
catalyze the interconversion of isomers, including both constitutional isomers and stereoisomers.

Some isomerases can also be classified as oxidoreductases, transferases, or lyases.

Question 4

(2.1) How do lyases work?

Answer 4

cleavage of a single molecule into two products, or synthesis of small organic molecules

Longer answer:
They catalyze or cleave without the addition of water and without the transfer of electrons. The reverse reaction (synthesis) is often more important biologically.

They don’t require water and do not act as oxidoreductase.

Because enzymes can go back and forth (i.e. it is not always reactant to product, but can be reversed), when the lyases work in the opposite direction, they are called synthases.

Question 5

(2.1) How do Hydrolases work?

Answer 5

Breaking of a compound into two molecules using the addition of water

Many hydrolases are named only for their substrate. For example, phosphatase, peptidase, nuclease, and lipases, all are hydrolases, and are named for what they break down.

Question 6

(2.1) How do Oxidoreductases work?

Answer 6

Catalyze oxidation-reduction reactions that involve the transfer of electrons

They often have a cofactor that acts as an electron carrier, such as NAD+ or NADP+

The electron donor is the reductant, and the acceptor is the oxidant.

Enzymes with the names dehydrogenase or reductase are usually oxidoreductases.

Question 7

(2.1) How do transferases work?

Answer 7

They move a functional group from one molecule to another.

Kinases are a type of transferase and catalyze the transfer of a phosphate group, generally from ATP to another molecule

Question 8

(2.1) What’s the difference between the ligase and synthase (or lyase)?

Answer 8

Ligase typically are used in large molecule processing and require ATP

lyase or (synthase) are used in small molecule processing.

Question 9

(2.1) How do enzymes function as biological catalysts?

Answer 9

Catalysts are characterized by two main properties: (1) they reduce the activation energy of a reaction, thus speeding up the reaction, and (2) they are not used up in the course of the reaction.

Enzymes improve the environment in which a particular reaction takes place, which lowers its activation energy.

They are also regenerated at the end of the reaction to their original form.

Question 10

(2.1) What is enzyme specificity?

Answer 10

Enzyme specificity refers to the idea that a given enzyme will only catalyze a given reaction or type of reaction.

For example, serine/threonine-specific protein kinases will only place a phosphate group onto the hydroxyl group of a serine or threonine residue.

Question 11

(2.1) In what ways do enzymes affect the thermodynamics versus the kinetics of a reaction?

Answer 11

Enzymes have no effect on the overall thermodynamics of the reaction; they have no effect on the ΔG or ΔH of the reaction,

However, they do lower the energy of the transition state, thus lowering the activation energy.

However, enzymes have a profound effect on the kinetics of a reaction. By lowering activation energy, equilibrium

Question 12

(2.1) Are reactions with enzymes endergonic or exergonic? Why?

Answer 12

They are exergonic because they release energy, the ∆G is negative

Question 13

(2.2) What is the:
1. Lock and Key Theory
2. Induced Fit Model

Answer 13

Lock and Key Theory

• active site of enzyme fits exactly around substrate
• There are no alterations to tertiary or quaternary structure of enzymes
• This is a less accurate model

Induced Fit Model

• Active site of enzyme molds itself around substrate only when substrate is present
• Tertiary and quaternary structure is modified for enzymes to function
• This is the more accurate model

Question 14

(2.2) What do cofactors and coenzymes do? How do they differ?

Answer 14

Cofactors and coenzymes both act as activators of enzymes. In both cases, these regulators induce a conformational change in the enzyme that promotes its activity.

They usually do so by carrying the charge through ionization, protonation, or deprotonation.

Cofactors tend to be inorganic (minerals)

Coenzymes tend to be small organic compounds (vitamins).

Question 15

(2.2) What are prosthetic groups on enzymes?

Answer 15

Prosthetic groups are tightly bound cofactors or coenzymes that are necessary for enzyme function

Question 16

(2.2) What’s the difference between a holoenzyme and an apoenzyme?

Answer 16

Apoenzymes - enzymes without cofactors
Holoenzymes - enzymes with cofactors

Question 17

(2.2) In what ways do enzymes work to provide a more favorable microenvironment to stabilize the transition state?

Answer 17

1. Affect the pH
2. Stabilize the transition state
3. Bring the reactive groups closer to one another

Question 18

(2.3) What is the equation for the Michaelis-Menten Equation?

Answer 18

[E] concentration of the enzyme
[S] concentration of the substrate
[P] concentration of the product
k ₁= the rate at which the enzyme-substrate complexes form
k_-1= the rate at which the enzyme-substrate complexes disassociate (the opposite reaction
k_cat= the rate at which the enzyme/substrate complex join dissociate and form the product

Qualitatively speaking, K_catmeasures the number of substrate molecules ‘turned over’ or converted to product, per enzyme molecule per second.

Question 19

IN the Michalis-Menten graph, what is the v_max and how can you increase or decrease it?

Answer 19

The v_max is the maximum rate at which an enzyme is converting a substrate to the product.

The only way to increase the v_max is to increase the enzyme concentration, which can be done by inducing the expression of the gene ending the enzyme.

Question 20

IN the Michalis-Menten graph, what is the K_m ?

What do high and low levels mean?

Answer 20

K_m-the substrate concentration at which half of the enzyme’s active sites are full. It is a measure of the affinity of the enzyme for the substrate

High K_m values= the enzyme has lower affinity for the substrate

Low K_m values= the enzyme has higher affinity for the substrate

Question 21

(2.3) Let’s say that one enzyme A has a higher K_m value than enzyme B. What does that tell you?

Answer 21

That enzyme B has a HIGHER affinity than enzyme A for the substrate.

Lower K_m values indicate higher affinity for a substrate

Question 22

(2.3) What is catalytic efficiency?

Answer 22

This describes a more efficient enzyme, and is calculated by the ratio of KK_cat/K_m.

A large K_cat or a small K_m will result in a higher catalytic efficiency.

FYI K_cat is the rate at which the enzyme/substrate complex join and dissociate and form the product.

Question 23

(2.3) On the Lineweaver-Burk Plots, what does the x-axis tell you and what does the Y axis tell you?

What is this graph useful for?

Answer 23

intercept with the x-axis give the value of 1/-K_m

intercept with the y-axis give the value of 1/v_max

It is useful for determining the type of inhibition that occurs whit an enzyme.

Question 24

(2.3) What is the shape that cooperative enzymes have?

Answer 24

They have a sigmoidal curve

Question 25

**(2.3)** What are the two states of an enzyme or binding site that undergoes cooperative binding?

Answer 25

Lwo-affinity tense state (T) High-affinity relaxed state (R)

Question 26

**(2.3)** What is the Hills coefficient? What does it mean when the coefficient is: >1 <1 =1

Answer 26

It is a coefficient that quantifies cooperativity. >1= positive cooperative binding <1 = negative cooperative binding =1= does not exhibit cooperative binding

Question 27

**(2.3)** What are the effects of increasing [S] on enzyme kinetics? What about increasing [E]?

Answer 27

**Increasing [S]**= Increasing [S] has different effects, depending on how much substrate is present to begin with. - When the substrate concentration is low, an increase in [S] causes a proportional increase in enzyme activity. - At high [S], however, when the enzyme is saturated, increasing [S] has no effect on activity because v_max has already been attained. **Increasing [E]**- will always increase v_max, regardless of the starting concentration of enzyme.

Question 28

**(2.3)** How are the Michaelis-Menten and Lineweaver-Burk plots similar? How are they different?

Answer 28

Similatirites: - Both the Michaelis–Menten and Lineweaver–Burk relationships account for the values of K_mand v_max under various conditions. - They both provide simple graphical interpretations of these two variables and are derived from the Michaelis–Menten equation. Differences: - However, the axes of these graphs and visual representation of this information is different between the two. - The Michaelis–Menten plot is v vs. [S], which creates a hyperbolic curve for monomeric enzymes. - The Lineweaver–Burk plot, on the other hand, is , which creates a straight line.

Question 29

**(2.3)** What does K_m represent? What would an increase in K_m signify?

Answer 29

K_m is a measure of an enzyme’s affinity for its substrate and is defined as the substrate concentration at which an enzyme is functioning at half of its maximal velocity. As K_m increases, an enzyme’s affinity for its substrate *decreases*.

Question 30

**(2.3)** What is enzyme cooperativity?

Answer 30

Cooperativity refers to the interactions between subunits in a multi-subunit enzyme or protein. The binding of substrate to one subunit induces a change in the other subunits from the T (tense) state to the R (relaxed) state, which encourages binding of substrate to the other subunits. In the reverse direction, the unbinding of substrate from one subunit induces a change from R to T in the remaining subunits, promoting unbinding of substrate from the remaining subunits.

Question 31

**(2.4)** How does temperature affect enzyme function?

Answer 31

For about every 10°C increase in temperature, the enzyme catalyzed reactions tend to double in velocity. After a certain temperature, however, the enzyme will denature quickly.

Question 32

**(2.4)** How does pH affect enzyme function?

Answer 32

pH effects enzyme function by affecting the ionization of the active site and because it may *denature* the enzyme. Enzymes are maximally active within a small pH range; outside of this range, activity drops quickly with changes in pH as the ionization of the active site changes and the protein is denatured.

Question 33

**(2.4)** How does salinity affect enzyme function?

Answer 33

Changes in salinity can disrupt bonds within an enzyme, causing disruption of tertiary and quaternary structure, which leads to loss of enzyme function. This generally only occurs in vitro, or in a laboratory setting.

Question 34

**(2.4)** What is the pH in the stomach? In the duodenum?

Answer 34

Stomach= 2 Duodenum= 8.5

Question 35

**(2.5)** What is the difference between **feedback inhibition** and **feed forward regulation**?

Answer 35

**Feedback inhibition** or negative feedback is a regulatory mechanism whereby the catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway. **Feed Forward Regulation**- products in one step encourage enzyme activity in the next step.

Question 36

**(2.5)** What are the four types of **reversible inhibition**?

Answer 36

1. competitive inhibition 2. noncompetitive inhibition 3. Mixed inhibition 4. uncompetitive inhibition.

Question 37

**(2.5)** In **competitive inhibition**: Where is the binding site? Impact on K_m? Impact on V_max? What does the graph look like?

Answer 37

**Binding Site**: active site **K_m**= increases **V_max**= no change It does not change the _max because if enough substrate is added, it will outcompete the inhibitor.

Question 38

**(2.5)** In **noncompetitive inhibition**: Where is the binding site? Impact on K_m? Impact on V_max? What does the graph look like?

Answer 38

**Binding Site**: allosteric site **K_m**= unchanged **V_max**= reduced because there is less enzyme to react

Question 39

**(2.5)** In mixed inhibition: Where is the binding site? Impact on K_m? Impact on V_max? What does the graph look like?

Answer 39

**Binding Site**: allosteric site, on enzyme and enzyme substrate complex, with different affinities for each. **K_m**= increases or decreases depending on the affinity for each. **V_max**= decreases *If it had an equal affinity for the enzyme and enzyme substrate, it would be called a non-competitive inhibitor. If it prefers to bind tot he enzyme, it increases the Km value (lowers affinity). If it has greater affinity for the enzyme substrate complex, it lowers the Km value (increasing affinity)

Question 40

**(2.5)** In **uncompetitive inhibition**: Where is the binding site? Impact on K_m? Impact on V_max? What does the graph look like?

Answer 40

**Binding Site**: allosteric site, only on the enzyme-substrate complex. It prevents release of the substrate. **K_m**= decreases **V_max**= decreases

Question 41

**(2.5)** What is **irreversible inhibition**?

Answer 41

**Irreversible inhibition** alters the enzyme in such a way that the active site is *unavailable for a prolonged duration or permanently*; new enzyme molecules must be synthesized for the reaction to occur again.

Question 42

**(2.5)** What are examples of **transient and covalent enzyme modifications**?

Answer 42

**Transient**: allosteric activation and inhibition **Covalent**: phosphorylation and glycosylation

Question 43

**(2.5)** Why are some enzymes released as zymogens?

Answer 43

Zymogens (tripsin-ogen) are precursors of active enzymes. It is critical that certain enzymes (like the digestive enzymes of the pancreas) remain inactive until arriving at their target site.