Lecture 18 Enzymes I

Question 1

Enzyme

Answer 1

A protein (or protein-based molecule) that speeds up a chemical reaction in a living organism.

Question 2

Enzyme acts as

Answer 2

A catalyst for specific chemical reactions, converting a specific set of reactions (substrates) into specific products

Question 3

Catalysis

Answer 3

Increasing the speed of chemical reactions
Ex. O2 + iron = rust (takes centuries)
Add H2O and takes days

Question 4

Enzymes and the energy of activation

Answer 4

Enzymes lower the energy of activation by forming an enzyme-substrate complex by allowing products of the enzyme reaction to be formed and released much faster

Question 5

ES

Answer 5

Enzyme-substrate complex

Intermediate

Question 6

Sir Archibald Edward Garrod

Answer 6

-inborn errors of metabolism
alkaptonuria - relation between disease and fundamental errors in biochemical reactions
-enzymes must be a link

Question 7

Enzyme Specificity

Answer 7

3D structure of enzyme protein contributes to specificity of reaction
-lock and key

Question 8

Active Site

Answer 8

Substrate binds, undergoes chemical alteration

Question 9

Enzyme substrate complex

Answer 9

Lock and key VS. Induced fit

Question 10

Evidence of an enzyme substrate complex

Answer 10

With a constant concentration of enzyme and increasing concentration of substrate, reaction rates increased to maximum
-Indirect evidence of ES complex

Question 11

The limit in reaction rate is due to

Answer 11

Substrate occupying all the available catalytic sites

Question 12

Maximal Velocity

Answer 12

Substrate is saturated all the enzymes

Question 13

Evidence of an enzyme substrate complex

Answer 13

-X-ray crystallography

Ex. cytochrome P450 bound to its substrate camphor

Question 14

Active Site

Answer 14

3D cleft or crevice formed from the residues of various protein regions and occupies small total volume
–shape dictates specificity
Specificity of binding depends on the precisely defined arrangement of atoms in the active site

Question 15

Active site microenvironment

Answer 15

Active site contains a unique microenvironment, usually void of water and controls the proper shape, pH and polarity for substrate binding and chemical reactivity

Question 16

Trypsin cleaves after

Answer 16

Arginine

Question 17

1st Law of Thermodynamics

Answer 17

Conservation of energy

-in biochemical reactions - E is transferred from one form to another

Question 18

Transition State

Answer 18

Intermediate structure that is not the substrate and not yet the product

• unstable and highest free energy
• double cross denotes the transition state

Question 19

Gibbs Free Energy of Activation

Answer 19

The difference in free energy of the transition state and the substrate
Enzymes function to lower the activation energy

Question 20

Delta G =

Answer 20

Free energy of substrate-free energy of product

Question 21

Enzymes and reactions

Answer 21

Enzymes accelerate reactions by facilitating the formation of the transition state/lower activation energy

Question 22

Cofactors

Answer 22

Small molecules that contribute to the chemical reaction of the enzyme

• many different roles in catalysis
• enzymes that use the same cofactor share similar mechanisms of catalysis
• Apoenzyme
• Haloenzyme

Question 23

Apoenzyme

Answer 23

Enzyme without its cofactor

Question 24

Haloenzyme

Answer 24

Cofactor bound and catalytically active

Question 25

Metal Cofactors

Answer 25

Positively charged Stable coordination of active site groups Contribute to chemical reactivity Ex. Zinc activates H2O to form OH- nucleophile

Question 26

Coenzymes

Answer 26

Small organic molecules often derived from vitamins (bigger than ions) When bound tightly called a prosthetic group

Question 27

Prosthetic Group

Answer 27

When coenzymes are bound tightly

Question 28

2 Types of Cofactors

Answer 28

1 Metals | 2 Coenzymes

Question 29

Scurvy

Answer 29

Cofactor deficiency | Vitamin C

Question 30

Ariboflavinosis

Answer 30

Cofactor deficiency | Riboblavin (B2) required for FAD synthesis

Question 31

NAD+ binding site of dehydrogenases

Answer 31

Binds the active site in a well-defined arrangement for substrate activation

Question 32

6 Major Classes of Enzymes

Answer 32

1. Oxidoreductases 2. Transferases 3. Hydrolases 4. Lyases 5. Isomerases 6. Ligases

Question 33

Oxidoreductases

Answer 33

Enzyme class Oxidation - reduction Ex. Lactate dehydrogenase

Question 34

Transferases

Answer 34

Enzyme class Group transfer Ex. Nucleoside monophosphate kinase (NMP kinase)

Question 35

Hydrolases

Answer 35

``` Enzyme class Hydrolysis reactions (transfer of functional groups to water) Ex. Chymotrypsin ```

Question 36

Lyases

Answer 36

``` Enzyme class Addition or removal of groups to form double bonds Ex. Fumarase ```

Question 37

Isomerases

Answer 37

``` Enzyme class Isomerization (intramolecular group transfer) Ex. Triose phosphate isomerase ```

Question 38

Ligases

Answer 38

Enzyme class Ligation of two substrates at the expense of ATP hydrolysis Ex. Aminoacyl-tRNA synthetase

Question 39

Oxidoreductases

Answer 39

Enzyme that catalyzes the transfer of electrons from one molecule to another - Reductant - Oxidant

Question 40

Reductant

Answer 40

Hydrogen or electron donor

Question 41

Oxidant

Answer 41

Hydrogen or electron acceptor

Question 42

ADH

Answer 42

Alcohol dehydrogenases

Question 43

Alcohol dehydrogenases

Answer 43

Converts alcohols to aldyhydes or ketones with the reduction of NAD+ (cofactor) to NADH - Alcohol = oxidized - NAD+ = reduced

Question 44

Opposite of alcohol dehydrogenase

Answer 44

Fermentation

Question 45

Transferases

Answer 45

Enzyme that catalyzes the transfer of a functional group from one molecule to another - donor molecules required - --Source of methyl groups or phosphates (ATP) as examples

Question 46

Kinase Receptors

Answer 46

Phosphorylate proteins and themselves | -usually at tyrosine (TKRs), serine and threonine residues

Question 47

Hyrolases

Answer 47

Enzyme that catalyzes the hydrolysis of covalent bonds - cleave covalent bonds using water in the process - transfer function groups to water

Question 48

Disaccharidases

Answer 48

Hydrolases - Cleave double sugars to single sugars - Defects in lactase = lactose intolerance

Question 49

Lyases

Answer 49

Enzyme that catalyzes the addition or removal of groups to form double bonds

Question 50

Aldolase

Answer 50

Lyases | -catalyzes second step of glycolysis

Question 51

Isomerases

Answer 51

Enzyme that catalyzes isomerization - intramolecular group transfer - product is an isomer of the substrate * *bonds are just moved around

Question 52

Triose phosphate isomerase

Answer 52

Isomerases example | -Intramolecular oxidation-reduction reaction

Question 53

Ligases

Answer 53

Enzyme that catalyzes the covalent linkage of two substrates - usually at the expense of ATP hydrolysis * *glue things together, uses ATP

Question 54

DNA Ligase

Answer 54

Forms two covalent phophodiester bonds between 3' hydroxy ends of one nucleotide with the 5' phosphate end of another *uses ATP