2.1 Enzymes

Question 1

______ are the work horse of chemical/biological systems that catalyze biological reactions

Answer 1

Enzymes

Question 2

Enzyme characteristics

Answer 2

• highly specific for catalyzed reactions
• encoded by majority of protein coding genes
• end in “ase”: kinase, phosphatase, dehydrogenase (exceptions: trypsin, chymotrypsin)

Question 3

how do enzymes act as catalysts? (what do they do to chemical reactions?

Answer 3

increase reaction rate, but do NOT change equilibrium

Question 4

2 types of macromolecules with enzymatic functions?

Answer 4

1. proteins (almost all enzymes = proteins)

2. RNA (ribozymes = catalytic RNA = RNA w enzymatic fxn)

Question 5

how many proteinogenic AAs? and in eukaryotes?

Answer 5

22 total (pyrrolysine only found in archaea and bacteria), 21 in eukaryotes

Question 6

How many essential AA? How to remember them?

Answer 6

9, Private Tim Hall
P V T T I M H A L L
phenylalanine, valine, threonine, tryptophan, isoleucine, methionine, histdine, arginine, leucine, lycine
(recognize structures in red on pic)

Question 7

Differences in bonds for secondary structures?

Answer 7

• both have H-bonds
• a-helix: bond for every fourth base
• B-sheet: bond with adjacent bases

Question 8

what are the strong bonds in tertiary structures?

Answer 8

Di-sulfide

Question 9

what is a basic enzymatic reaction? what are the transient complexes?

Answer 9

E + S <–> ES <–> EP <–> E + P

transient = ES, EP

Question 10

enzymes affect _____ not ____, so they make reactions go faster

Answer 10

reaction rates, equilibria

Question 11

Oxioreductases

Answer 11

do oxidation/reduction of molecules (e- transfer)

Question 12

dehyderogenases

Answer 12

transfers e- to NAD+, NADP+, FMN, FAD

Question 13

oxidases

Answer 13

transfer e- to Oxy

Question 14

transferases

Answer 14

transfer groups (CH3, C2H3O, etc)

Question 15

hydrolases

Answer 15

transfer functional groups to water; water to break chemical bonds

Question 16

lysases

Answer 16

addition/removal of groups to form double bonds

Question 17

isomerases

Answer 17

intramolecular group transfer (makes isomers)

Question 18

ligases

Answer 18

ligation of 2 substances (joining)

Question 19

what are tertiary and quaternary structures governed by?

Answer 19

weak non-covalent bonds

Question 20

enzymes accelerate the reaction by ___________

Answer 20

lowering the activation energy of the reaction

Question 21

The interaction of E and S release binding energy that contributes to _____

Answer 21

lowering the EA

Question 22

Enzyme binds substrate in a way that makes it easier to _____

Answer 22

manipulate the substrate and break/form bonds

Question 23

S binds to E initially with weak actions and the bond is strengthened by _____

Answer 23

formation of more interactions at the site

Question 24

What is wrong with the lock and key model?

Answer 24

it does not produce enough energy

Question 25

What is the induced fit model? why is it favored?

Answer 25

- Initial ES formation =weak interactions, but full interactions in transition state - explains where extra energy to lower activation energy is derived from

Question 26

4 strategies for catalysis

Answer 26

1. general acid-base (donate/accept protons) 2. covalent catalysis (covalent bond forms bw SE) 3. Metal ion catalysis (1/3 of all enzymes need metal for catalysis) 4. catalysis by approximation (molecules so close that it is spontaneous)

Question 27

examples of AA commonly involved in acid-base catalysis? (dont have to memorize, but recognize them)

Answer 27

Glu, Asp, Lys, Arg, Cys, His, Ser, Tyr

Question 28

pKa definition

Answer 28

strength of acid, how likely to accept/lose H+

Question 29

pattern between pH and pKa

Answer 29

if pH > pkA, use acidic form (>i think, check this?)

Question 30

EX of enzyme using acid-base and covalent catalysis

Answer 30

Chymotrypsin= protease in pancreatic juice | - enzyme can use multiple strategies!

Question 31

Ex of metal-ion catalysis?

Answer 31

- carbonic anhydrase (buffering system for pH) - Zn2+ = prosthetic group - Zn facilitates deprotonation of H2O and making OH a nucleophile

Question 32

10 factors effecting enzyme function

Answer 32

1. substrate concentration 2. Inhibitors 3. Allosteric effectors (modulators) 4. Cofactors 5. reversible covalent modifications 6. pH and temperature 7. Proteolytic cleavage 8. protein-protein interactions 9. enzyme concentration 10. isozymes

Question 33

At low Vo, [S] increases _______ and at high Vo, [S] increases ______

Answer 33

1. linearly | 2. slowly until approaches Vmax

Question 34

what does Michaelis Mentin curve describe?

Answer 34

the rate of catalysis of the enzyme at some particular substrate concentration.

Question 35

what is Km?

Answer 35

[S] at which half of E active sites are occupied

Question 36

Km = Michaelis constant = ______

Answer 36

1/2 Vmax | Vmax = when all enzymes are saturated with substrate

Question 37

High Km suggests ___________ | Low Km suggests ____________

Answer 37

1. weak binding of S to E (lower reaction rate) 2. strong binding of S to E (higher reaction rate) 0.05 kM = stronger bond than 5 kM

Question 38

do hexokinase or glucokinase have a stronger binding?

Answer 38

hexokinase (lower kM)

Question 39

Inhibitors

Answer 39

therapeutic agents to control pathways (reversible, nonreversible)

Question 40

Reversible competitive inhibitor

Answer 40

- Inhibitor binds to active site - you can overcome inhibitor by adding more S - binding is reversible`

Question 41

Non-Reversible competitive inhibitor

Answer 41

- binds to a dif site than the catalytic site to alter proteins conformation - binding of NI alters conformation of E so S cant bind

Question 42

_______ are irreversible inhibitors that resemble the substrate and covalently modify the enzyme

Answer 42

Substrate analogs

Question 43

what do suicide inhibitors do?

Answer 43

Enzyme modifies and inactivates the substrate by forming a stable complex (enzyme modifies it and it can't leave now)

Question 44

do Allosteric enzymes follow michaelis-mentin?

Answer 44

no because they have more than 1 binding site

Question 45

Allosteric enzymes

Answer 45

enzymes whose conformations are altered when an allosteric effector binds - allosteric effectors can bind to the allosteric site and change the conformation of E to be more or less active

Question 46

how is ATCase a good example of how different allosteric effectors can effect a particular enzyme?

Answer 46

- It has homo and hetero-regulation - homo: Substrate is also the effector; it binds and activates enzyme function (aspartate) - hetero: CTP netgatvely regulates and ATP positively regulates

Question 47

cooperative binding example

Answer 47

- Hemoglobin has 4 spots for O2 | - each time an O2 binds, there is a conformational change that makes it easier for the next to bind

Question 48

_____ are non-proteinaceous molecules for Enzyme activity

Answer 48

Cofactors | - can be organic or inorganic

Question 49

Inorganic co-factors

Answer 49

Zn, Mg, Mn, Fe, etc (remember, metal cofactors play a role in 1/3 of enzyme processes)

Question 50

What are coenzymes?

Answer 50

organic cofactors that act as transient carriers of moieties like e-, methyl-,acyl- etc

Question 51

Many enzymes need ______ for activity

Answer 51

cofactors

Question 52

Enzyme without cofactor = ______ = inactive

Answer 52

apoenzyme

Question 53

Enzyme with cofactor = ______ = active

Answer 53

holoenzyme

Question 54

covalent modifications can effect enzyme function by modifying groups such as ______

Answer 54

phosphoryl, acetyl, methyl, carboxyl, etc | ex: phosphorylation/dephos

Question 55

each enzyme has an optimal ______ and _____ range

Answer 55

pH, temperature

Question 56

What is Tm

Answer 56

melting point

Question 57

thermal denaturation

Answer 57

unfolding of protein due to heat

Question 58

______ are inactive precursors of enzymes that must be cleaved to becomes active

Answer 58

Zymogens

Question 59

Some proteins are inactive until _____

Answer 59

binding of a modulator protein causes a conformational change at the active site to activate or inhibit the enzyme - Enzyme: GTP complex binds and regulates fxn of target protein

Question 60

______ catalyze the same reaction but have different primary structures (EX?)

Answer 60

isozymes | EX: hexokinase/glucokinase