PHSC1212 Biochemistry - Lecture 7: Enzyme Catalysis pt 2

Catalytic and non-catalytic

two primary roles of the side chains of amino acids within enzyme active sites

Amino acids with polar and charged R-groups

What type of amino acids can participate in catalytic mechanisms?

Serine, threonine, tyrosine

amino acids that can participate in catalytic mechanisms due to a hydroxyl group

Cysteine

amino acid that can participate in catalytic mechanisms due to a thiol group

Glutamine and asparagine

amino acids that can participate in catalytic mechanisms due to amide group

Glutamate and aspartate

amino acids that can participate in catalytic mechanisms due to carboxylate group

Lysine

amino acid that can participate in catalytic mechanisms due to amine group

Arginine

amino acid that can participate in catalytic mechanisms due to guanidinium group

Histidine

amino acid that can participate in catalytic mechanisms due to imidazole group

Non-polar side chains

play a non-catalytic role by properly orienting the substrate in the active site

Non catalytic

What type of role do nonpolar side chains play?

Orientation of substrate in active site

What does a noncatalytic role of an amino acid in enzyme function involve?

Cofactors

non-protein components of a functional enzyme

Metal ions and coenzymes

two types of cofactors

Mg2+, Zn2+

metal ion cofactor examples

NAD, FADH, ATP

coenzyme cofactor examples

Chemical versatility

What do cofactors add to an enzyme?

Permanently or transiently

two types of cofactor binding

Prosthetic group

a cofactor permanently bound to the enzyme

Co-substrate

a cofactor transiently bound to the enzyme

Substrate binding or stabilizing negatively charged intermediate

What are alkali and alkaline earth metals involved in?

Oxidation reduction reactions

What can transition metals participate in?

Alkali metals

group 1 in periodic table

Alkaline earth metals

group 2 in periodic table

Transition metals

metals that can have multiple oxidation states

Coenzymes

nonprotein components of enzymes that may be permanently bound to the enzyme or temporarily bound, and their structures are changed by reaction and must be regenerated

Structural change requiring regeneration

What happens to coenzymes during a reaction?

Vitamins

most coenzymes are derived from these

Electron transfer, group transfer, high energy transfer potential

three groups of coenzymes

Electron transfer

coenzyme that transfers electrons and promote redox reactions

Group transfer

coenzyme that transfers a functional group

High-energy transfer potential

enzymes that transfer a phosphate group from the nucleotide and results in energy release

In the catalytic cycle

When are permanently bound coenzymes regenerated?

After release as product and by different enzyme

When are temporarily bound coenzymes regenerated?

Temperature

affects every chemical reaction, can speed up until a certain point

Speeds up, then denatures

role of temperature in enzyme function

pH

can affect the ionization of the active site amino acids and the substrate

React or bind substrate

pH and ionization are important in enzyme function because the gain or loss of protons in an active site can alter the enzyme's ability to do what?

Denature enzymes

How can tertiary protein structure be affected by pH?

Narrow pH

What are biological systems are buffered to maintain?

Oxidoreductases

enzymes involved in oxidation/reduction reactions (loss or gain of electrons)

Transferases

enzymes that transfer small molecular groups (like phosphate or ATP)

Hydrolases

enzymes that cleave bonds in a way that uses water

Lyases

enzymes that eliminate groups to form a double bond; can also add groups to a double bond to form single bonds

Isomerases

enzymes that catalyze intramolecular rearrangements (like L form to D form)

Ligases

enzymes that catalyze the joining of two molecules by forming new bonds (require ATP)

ATP

required by ligase class of enzymes to function

Elimination or addition

reactions catalyzed by lyases