Enzyme Structure and Function (BIO, BC)

Question 1

What is the function of enzymes in catalyzing biological reactions?

Answer 1

Enzymes function to lower the activation energy of reactions (do not get used up!)

Question 2

Enzyme Structure determines function 🡪Thus a change in structure result in a ?

Answer 2

change in function

Question 3

Enzyme are categorozed by 6 reaction types, list them.

Answer 3

6 Types of Enzymes:

L : Ligase

I : Isomerase

L : Lyase

H : Hydrolase

O : Oxidoreducatase

T : Transferase

Question 4

What is Ligase Rxn? And What is another name?

Answer 4

Join two large biomolecules, often of the same type.

A + B 🡪 AB

Sometimes joins two molecules through a condensation rxn ( release of H20)

Another name is SyntheTase which means it USES ATP

Example: Carboxylase, Synthetase

Question 5

What is a Lyase Rxn? Due to the reversal of this rxn, what is another name?

Answer 5

Lyases cleave without the addition of water and without the transfer of electrons. Example : A 🡪 B + C (does not use water, or oxidation/reduction)

HOWEVER, the reverse reaction, synthesis, aka synthase: join two molecules together and don’t need ATP.

A + B –> AB (does not use ATP to join molecules)

Example : Synthase, Decarboxylase

Question 6

Synthetase vs Synthase

Answer 6

Question 7

Hydrolases fxn?

Answer 7

Cleavage with the addition of water

Examples : pepsin, amylase, lipase, petidase, nuclease, phosphatase, esterase, glycosylase

A + H2O 🡪 B + C

Question 8

Isomerase Fxn?

Answer 8

Isomerase is the Interconversion of isomers, including both constitutional and stereoisomers. Examples : Mutase, Epimerase

A 🡪 B

Question 9

Transferase Fxn?

Answer 9

Move a functional group from one molecule to another

A + BX 🡪 AX + B

Example : Kinases, Phosphorylase

Question 10

Oxidoreductase Fxn?

Answer 10

Catalyze oxidation-reduction reactions that involve the transfer of electrons

Oxidase = oxidizing or taking away electrons from a molecule

Reductase = reducing or giving electrons to a molecule

A + B: 🡨🡪 A: + B

Examples : Dehydrogenase, Oxidase, Peroixdase

Question 11

Reduction of activation energy needed for what? & achieved by?

Answer 11

Enzymes lower the activation energy of the reaction (making it easier for the reactants to transition to form products)

Acid/Base catalysis = enzymes use acidic/basic properties to make rxns go faster by proton transfer

Covalent catalysis = enzymes covalently bind to help with electron transfer

Electrostatic catalysis = charged molecules or metal ions used to stabilize big positive or negative charges

Proximity/Orientation effects = enzymes make collisions between reacting molecules happen more often

Transition state = highest energy point from path A to B (in A🡪 B)

Where you also find most instability (high energy = more unstable)

Question 12

How did Induced Fit Model get it’s name?

Answer 12

Called the induced fit because both the enzyme and substrate have changed their shape a little so they bind together really tightly (catalyzing reaction at full force)

Question 13

Binding between reactant and enzyme STRONGEST at which state?

Answer 13

Binding between reactant and enzyme STRONGEST at the transition state

Question 14

Cofactors & Mechanism of catalysis

Answer 14

Directly involved in the enzyme’s catalytic mechanism (might be stabilizing the substrates, or helping the reaction to convert substrates from one form to another) (e.g. Mg2+)

Question 15

Coenzymes & Mechanism for Catalysis

Answer 15

Organic carrier molecules (i.e. NADH, CoA)

Question 16

Water-soluble vitamins & Mechanism for Catalysis

Answer 16

Need to obtain from the diet

Vitamins 🡪 organic cofactors and coenzymes

e. g. Vitamin B3 is precursor for NAD
e. g. Vitamin B5 is precursor for CoA

Question 17

Example of Effects of pH changes on enzyme activity :

Answer 17

e.g. DNA 🡪 Negatively charged 🡪 DNA Polymerase binds Mg2+ cofactor to stabilize negative charge on DNA

In normal conditions, DNA Pol holds onto Mg ion through electrostatic interaction between magnesium and one of its aspartate residues, which would be deprotonated and thus negatively charged at neutral pH values

If you took DNA Pol and put it in environment with reduced pH, the aspartate residue would become protonated since pH has dropped so much, and protonated form has no negative charge, so can’t bind Mg ion cofactor

DNA Pol cannot do job properly in low pH environment

Question 18

Effects of temperature changes on Enzyme Activity

Answer 18

Effects of temperature changes:

Proteins fold from primary 🡪 secondary 🡪 tertiary 🡪 quaternary structures to function properly

Significant changes in temp cause protein to lose its functionality (loses its shape)

e.g. when we get sick and our body temperature goes up, our digestive enzymes cannot work properly and consequently we cannot eat food as well