Catalytic Mechanisms

Question 1

How do enzymes lower the activation energy barrier?

Answer 1

They do this stabilizing the transition state using weak bounds and interactions between the enzyme and substrate. Binding energy is ost effective in the transition state, lowering the activation energy barrier.

Question 2

What factors contribute to the activation barrier?

Answer 2

• Entropy- the random order of molecuoles increases entropy(disorder). Reduces productivity
• Solvation shells: water moelcules form shells around biomolecules. This needs to be broken
• Substrate Distortion: Some reactions need the og substrate to be distorted. This does require energy
• Alignment of Catalytic Groups: the catalytic groups on enzyme (active site) need to be in the proper alignment

Question 3

What is “constraint” in relation to overcoming the activation energy barrier?

Answer 3

Enzymes bind and constrain substrates in a specfifc orientation, which reduces entropy and increases productivity

Question 4

What is “desolvation” in relation to overcoming thw activation energy barrier?

Answer 4

Enezymes dissolve the solvation shell, facillitating interactions between the enzyme and substrate

Question 5

How do enzymes overcome the substrate distortion to overcome the activation barrier?

Answer 5

Enzymes undergo conformational changes when the substrate binds. They optimize the catalytic groups alignemnt and promot the formation of the transition state.

Question 6

What is acid-base catalysis?

Answer 6

The transfer of protons (H+) between the enzyme and substrate

Question 7

What is Covalent catalysis?

Answer 7

Formation of transient covalent bond between enzyme and substrate, a;tering reaction pathway. This requires a nucleophile like reactive serine, thiolate, amine, or carboxylate

Question 8

What is metal ion catalysis?

Answer 8

uses metak ions bound to the enzyme to facilitate substrate binding, stabile negative charges, or participate in redox reactions.

Question 9

What is the difference between general and specific acid-base catalysis?

Answer 9

General - involves proton transder from or to an amino acid side chain that acts as a general acid or base
Specific - uses the acidic or basic properties of water molecules to facilitate proton transfer.

Question 10

What amino acids are important for general acid-base catalysis?

Answer 10

amino acids with ionizable side chains play crucial roles in general acid-base catalysis because they can donate or accept protons.

Question 11

What is the function of proteases?

Answer 11

these are enzymes that cleave(break) peptide bonds in a peptide

Question 12

Why are proteases important?

Answer 12

They digest dietary proteins, they activation zymogens, and regulate protein function

Question 13

What are zymogens?

Answer 13

inactive enzyme precursors

Question 14

What are serine proteases? What are some examples?

Answer 14

They use a serine residue in their active site for catalysis. Examples are chymotrypsin and trypsin

Question 15

What are cysteine proteases?

Answer 15

have a cysteine residue in their active site for catalysis

Question 16

What are aspartyl proteases? What are examples?

Answer 16

They use 2 aspartate residues in their active site for catalysis. Examples include HIV protease and pepsin.

Question 17

What are metalloproteases?

Answer 17

They use a metal ion, like zinc, for catalysis

Question 18

Where is the specific location that chymotrypsin is able to cleave on a protein?

Answer 18

cleave peptide bonds immediately following and adjacent to aromatic amino acids

Question 19

What are the important residues of chymotrypsin?

Answer 19

Catalytic triad: Ser195, His57, and Asp102 form a hydrogen-bonding network essential for catalysis.

Gly193: stabilizes the enzyme-transition state complementarity

Question 20

What type of catalysis does chymotrypsin employ?

Answer 20

Both acid-base and covalent catalysis

Question 21

What is the oxyanion hole?

Answer 21

It is a region in the active site of chymotrypsin that stabilizes the negative charge (oxyanion) that develops on the carbonyl oxygen of the substrate during the transition state.

Question 22

What is a hydrophobic pocket?

Answer 22

Accomadates the aromatic side chain of the substrate, contributing to substrate specificity

Question 23

What are the tetrahedral intermediates?

Answer 23

They are formed during the reaction mechanism and are stabilized by the oxyanion hole

Question 24

What is the acylated enzyme form?

Answer 24

It is a form formed when the enzyme becomes covalently attached to the substrate during the reaction

Question 25

WHat is the deacylated enzyme form?

Answer 25

it is the form regenerated after the release of the product, restoring the enzyme to og state

Question 26

WHat is the substarte of the HIV protease?

Answer 26

Viral polyproteins, specifically cleaving between Phe and Pro residues

Question 27

WHAt are the important residues of the HIV protease?

Answer 27

Asp25 and Asp25’(from other subunit of dimeric enzyme) form the catalytic center

Question 28

How do HIV protease inhibiters block the active site?

Answer 28

The mimic the tetrahedral intermediate of the normal reaction, effectively blocking the active site.

Question 29

What do HIV protease inhibitors contain?

Answer 29

They contain benzyl rings that target the hydrophobic binding pockety and adjacenct OH group, which mimics the negatively charged oxyygen in the tetrahedral intermediate

Question 30

What property does the hexokinase illustrate? (How)

Answer 30

The concept of induced for and the importance of multiple substrates for enzyme activity.

Question 31

WHat two substrates does hexokinase require?

Answer 31

Glucose and ATP. binding of glucose causes conformational change of hexokinase, creating binding site for ATP

Question 32

WHat type of catalysis is the enolase enzyme?

Answer 32

metal ion

Question 33

What is the importance of the metal ion (specifically Mg2) in the enolase catalysis?

Answer 33

it stabilizes the transition state and facilitates proton removal.

Question 34

What are the important active site residues of enolase?

Answer 34

Lys345 and Glu211

Question 35

WHat is peptidoglycan used for?

Answer 35

Essential compoents of bacterial cell walls. Provides structural integrity and protection against osmotic stress

Question 36

What is the structure of peptidoglycans?

Answer 36

Are polymers consisting of repeating disaccharide units cross-linked by peptide

Question 37

WHat are on active site residues of the lysozyme?

Answer 37

Glu35 and Asp52

Question 38

Where does the lysozyme cleave?

Answer 38

cleaves B(1->4) glycosidic bond between N-acetylmuramic acid (Mur2Ac) and N-acetylglucoamine (GlcNAc) in peptidoglycans, specifically between sites D and E in the substrate

Question 39

What is used to identify active site residues on lysozymes?

Answer 39

X-ray crystallography studies with substrate analogs bound to lysozume revealed the location of the active site residues. Specifically, the C-1 carbon of substarte analog is positioned between Glu35 and Asp52, suggesting their involvement in catalysis

Question 40

How is crucial for inhibitory activity in penicillin?

Answer 40

a B-lactam ring

Question 41

How does penicillin inhibit bacterial cell wall synthesis?

Answer 41

It irreversibly inactivates transpeptidase by mimicing it’s substrate D-Ala-D-Ala. It forms a convalent bond with the active site serine residue

Question 42

What is the role of B-lactamases?

Answer 42

bacterial/antibiotic resistance.
some bacteria express this enzyme, which cleaves the b-lactam ring of penicillin, making it inactive

Question 43

What is the result of inhibiting transpeptidase?

Answer 43

penicillin disrupts bacterial cell wall synthesis, leading to cell lysis and bacterial death