Enzymes

Enzymes

Proteins that function as biological catalysts

Catalysts

It accelerates process

Reduces

Catalysts offers alternative pathway which (increases/reduces) activation energy (Ea)

Yeast

What does “zyme” mean in enzyme (greek etymology)

“ferments”

What is the former name of enzymes

Globular proteins

Most enzymes are ______ proteins

Simple

A ______ enzyme is composed of only amino acid chain

Conjugated

A _______ enzyme has a non protein part in addition to a protein part (protein part + non protein part)

Apoenzyme

The protein part of an enzyme and is inactive in itself

Cofactor

It is the nonprotein organic or inorganic (cofactor/co-enzyme) moiety

Holoenzyme

= apoenzyme + cofactor

Active site

It is the site where catalysis happens

Substrate

These are compounds being catalyzed

• H-bonds

• Salt links

• Van der Waals Interaction

• Hydrophobic Effect

What are the interactions between the active site and substrate?

Contact Binding Residues

(Amino Acid Residue Bonding)

• It binds reversibly

• Directly affects binding partner

• Weak interaction ( H and ionic bonds)

Auxiliary Residues

(Amino Acid Residue Bonding)

• Only stabilizes the substrate

• Metal coordination/structural/indirect stabilization

1. Class of enzyme

2. Type of bond, functional group, or chemical donor

3. Specific mechanism, acceptor molecule, or co-substrate

4. Unique Identifier

What does each of the 4 digit classification number of enzymes mean?

Oxidoreductases

Class of enzyme that does:

• Redox Reactions

• Transfer or Electrons

Transferases

Class of enzyme that does:

• Transfer of chemical groups

• Commonly transfers bio-energetic molecules

Hydrolases

Class of enzyme that does:

• Hydrolysis (bond cleavage with the transfer of functional group to water)

Lyases

Class of enzyme that does:

• Non-hydrolytic bond cleavage

Isomerases

Class of enzyme that does:

• Intramolecular group transfer (orientation in space/ isomerism)

Ligases (synthases)

Class of enzyme that does:

• Synthesis of new covalent bond between substrates, using ATP hydrolysis

Alcohol Dehydrogenase

Example of Oxidoreductases

OA: NAD⁺

RA: CH₃CH₂OH

OP: CH₃CHO

RP: NADH + H⁺

Oxidizing and reducing agent?

Oxidized and reduced product?

Hexokinase

Example of Transferases

1. Hydrolysis - removal of water from a larger molecule to make a smaller molecule

2. Condensation/ dehydration synthesis - removal of water from smaller molecules to form a larger macromolecule

Hydrolases involves two types. What are those?

Acetylcholinesterase (by hydrolysis)

Example of Hydrolases

Pyruvate decarboxylase

Example of Lyases

Triose Phosphate Isomerase

Example of Isomerases

Coenzyme

Organic type of cofactor

Metal-ion

Inorganic type of cofactor

Lock and Key Model

(Enzyme Model)

• Fixed geometrical conformation

• “only substrate of specific shape can bind with the active site, just like a lock and a key”

Induced Fit

(Enzyme Model)

• Usually has the tendency to attach to the conformational changes based on the substrate

• Both the substrate enzyme’s active site undergoes conformational changes up until the substrate is fully attached to the enzyme.

True

T/F

All given functional groups can act as acids or bases

Covalent catalysis

General acid-base catalysis is usually combined with ______ catalysis

donates

A bronsted acid (donates/accepts) protons

accepts

A bronsted base (donates/accepts) protons

General acid catalysis

This enzyme mechanism involves an amino acid donating a hydrogen ion, as in the reaction

General base catalysis

This enzyme mechanism involves an amino acid taking a hydrogen ion from one of the substrates, such as the reaction:

True

T/F

Acid catalysis can accelerate hydrolysis and other bond-cleavage reactions.

True

T/F

Base Catalysis can activate water, alcohols, and thiols for nucleophilic attack

Metal Ions (Metal-ion catalysis)

(Mechanism of Action)

_______ enhances the rate of chemical reactions by acting as Lewis acids, forming complexes with reactants, and stabilizing transition states.

Adducts (from formation of coordinate covalent bonds)

_______ are products of a direct addition reaction between two or more distinct molecules, where all atoms from the original components are retained in the resulting single molecule.

Scissile bonds

These are bonds susceptible to cleavage.

• metal coordination can withdraw electron density from a substrate, altering bond polarity and making cleavage easier.

Covalent Catalysis

(Mechanism of Action)

Involves the formation of a covalent bond between the enzyme and at least one of the substrates involved in the reaction.

• often, this involves nucleophilic catalysis