Properties of enzymes

Question 1

define enzymes

Answer 1

usually soluble proteins which catalyze chemical reactions by lowering the activation energy of these reactoins

Question 2

Describe enzymes

Answer 2

Accelerate reactions at human body temperatures and at pH conditions found in cells or body compartments

• Bind substrates, form an enzyme-substrate and then an enzyme-product complex, and release the products
• Provide a means for regulating the rate of metabolic pathways depending on the need of the whole body

Question 3

what are the two names for each enzyme?

Answer 3

• The short recommend name has often the suffix “-ase” and is mainly describing the reaction that is carried out. It can describe the substrates or products which can lead to two correct recommended names
• The systemic name follows a classification thagt includes a name and an Enzyme Commission (EC) number. As a result, there are six major classes and each has numerous subgroups

Question 4

What is the active site of enzymes?

Answer 4

A relatively small part of a three-dimensional pocket or cleft formed by amino acids that come from different parts of the primary structure

Question 5

What is the catalytic efficiency of a reaction as opposed to an uncatalyzed reaction?

Answer 5

The catalytic efficiency of enzymes ranges from 10^3-10^8 times faster than uncatalyzed reactions/

Question 6

What is the specificity of enzymes?

Answer 6

The specificity of enzymes is very high and includes recognition of optical configuration of the substrates. are needed for the breakdown of nutrients in order to generate energy when needed (catabolism)

Question 7

what are holo and apoenzymes?

Answer 7

Some enzymes need coenzymes/cofactors from vitamins or minerals(holoenzymes)

Apoenzymes are enzymes without the coenzymes

Question 8

what is anabolism?

Answer 8

allow synthesis and assembly of cellular building blocks

Question 9

summarize how enzymes work

Answer 9

All reactions: catalyzed or uncatalyzed have to go through a transition state

the enzyme can stabilize the transition state. the active site of the enzyme can provide catalytic groups that favor the formation of the transition state.

Enzymes provide an alternate reaction pathway and as a result, can reduce the energy of activation

Note: Enzymes do not change the Gibbs energy or the delta G of the overall reaction

Question 10

what is enzyme kinetics?

Answer 10

the study of product formation under specific conditions such as different substrate concentrations, pH, and temperature.

this offers insight into the affinity of the enzyme for different substrates and also for drugs.

The rate of reaction is product formation over time expressed as the actual amount in g.

The velocity of reaction

Question 11

What is the velocity of a reaction?

Answer 11

The velocity is product formation over time expressed in concentrations and is used in Biochemistry.

Question 12

What is the effect of substrate concentration on the velocity?

Answer 12

The velocity increases at higher substrate concentration for any enzymatic catalyzed reaction until Vmax is reached

At Vmax all available binding sites on the enzyme are saturated with substrate and the product formation cannot be increased any further.

Question 13

what is the effect of temperature on the velocity?

Answer 13

The velocity increases with hgiher temperature except when the temperature rises above 40 degrees celcius. This causes the human enzymes to be denatured

Thermophilic bacteria found in hot springs have theior optimal velocity at higher temperatures at 70 degrees. Their purified enzymes are used for experiments

Question 14

What is the effect of pH on velocity?

Answer 14

A. The concentration of hydrogen ions affects the reaction velocity. The enzyme and substrate have chemical groups that need to be either ionized or unionized in order to interact.

B. An extreme pH can denature the enzyme

C. Different enzymes can have different optimal pH. Examples of enzymes that function at different pH’s in the human body

Question 15

what is the function of Pepsin?

Answer 15

Cleaves dietary proteins and acts in the lumen of the stomach under acidic conditions

Question 16

What is the function of Trypsin?

Answer 16

cleaves dietary proteins in the duodenum

Question 17

what is the function of alkaline phosphatase?

Answer 17

cleaves phosphate groups from nucleotides and proteins

Question 18

how can the regulation of enzymes be achieved?

Answer 18

A. Concentration of substrates and/or products
B. Modulation of enzyme concentration
C. Covalent modification of enzymes
D. Allosteric regulation: modulation of a metabolic pathway

Question 19

What is the role of rate limiting step of pathways ?

Answer 19

1. Feedback inhibition

Down-regulation of the pathway:

• allosteric feedback inhibition of the present enzyme (decreased affinity for the substrate, larger K0.5)
• reduced gene expression

2. Feed-forward activation (less common)
   Upregulation of the pathway:
   -allosteric activation of the present enzyme (smaller K0.5)
   -activated gene expression

Question 20

Contrast the types of allosteric enzymes changing their affinity for the substrate

Answer 20

1. Feed-forward activation:
   The positive allosteric effector leads to a conformational shift of the allosteric enzyme. This changes the affinity for the substrate and leads to higher affinity
2. Feed-back inhibition:
   The negative allosteric effector leads to a conformational shift of the allosteric enzyme. This changes the affinity for the substrate and leads to lower affinity

Question 21

Describe allosteric enzymes

Answer 21

These often regulated enzymes of pathways, they have allosteric binding site for specific molecules (effectors)

Binding leads to a reversible conformational shift and and can reduce or increase the activity of the enzyme. In most cases it changes the affinity for the substrate

Often composed of 2-4 protein subunits and more product can be formed when mor Substrates bind to the different subunits

Question 22

Covalent modification of an enzyme…

Answer 22

Irreversible proteolytic activation is used for the activation of:

A. Blood clotting enzymes (clotting cascade)

B. Digestive enzymes that could. Cause damage if activated prematurely

Question 23

Give trypsinogen as an example of proteolytic activation

Answer 23

The inactive trypsinogen is synthesized in the pancreas, released into the pancreatic juice abs enters the duodenum lumen

Trypsin is a powerful protease and shall be active only in the lumen of the small intestine

Trypsinogen (inactive pancreatic zymogen)

Enteropeptidase in the duodenum recognizes trypsinogen and cuts it to trypsin

The shorter protein folds to trypsin (active enzyme), while the peptide is degraded