Biochem - Enzymes

Front 1

What can enzymes be made out of?

Back 1

Protein or RNA

Front 2

Scissile bond-

Back 2

a bond of a substrate that is subject to enzymatic cleavage

Front 3

Cofactors-

Back 3

small molecules bound to the enzyme

Front 4

apoenzymes-

Back 4

enzymes without their associated cofactors

Front 5

holoenzymes-

Back 5

enzymes with their cofactors

Front 6

coenzymes-

Back 6

small organic cofactors

Front 7

What are the 4 reaction groups in organic chem? biochem?

Back 7

Organic - rearrangement, elimination, addition, substitution

Biochem Isomerase, Lyase, Ligase, Oxidoreductase, Transferase, Hydrolase

Front 8

What enzyme group does proteases belong?

Back 8

hydrolases

Front 9

How do enzymes work?

Back 9

Make it easier for the substrate to turn into the transition state

Front 10

What does the velocity of the reaction depend on?

Back 10

on the energy of activation

Front 11

Through what interactions are substrates bound to the enzyme?

Back 11

Through multiple weak interactions- H bonds, van der waals, ect

Front 12

What are the 2 different models for substrates binding? which is more correct?

Back 12

Lock and key and induced fit

induced fit

Front 13

K_m-

Back 13

concentration of S at which the reaction rate is half the maximal rate (V_max)
- the concentation of S at which half of all active sites are occupied
-the dissociation constant for the breakdown of the ES complex

Front 14

What does michaelis -menten model assume?

Back 14

-no P reverts back to S

Front 15

What is constant in steady-state? What changes

Back 15

constant- ES
changed - S and P

Front 16

What is the rate of breakdown

Back 16

breakdown of the ES - can go either way forward or backwards

Front 17

E_T

Back 17

enzyme total - made of both the bound and unbound enzymes

Front 18

What is the X and Y axis in a Lineweaver-Burk plot?

Back 18

X axis- 1/S concentration

Y axis- 1/V

Front 19

What is the slope?
X intercept
Y intercept on a Lineweaver-Burk plot

Back 19

Slope- K_m/V_max
X intercept - -1/K_m
Y intercept- 1/V_max

Front 20

What does a small Km mean?

Back 20

the smaller the number the tighter the binding of ES

Front 21

Turnover number-

Back 21

the number of substrate molecules converted to product per second when enzyme is fully saturated with substrate K_2

Front 22

Kinetic perfection-

Back 22

every single times a substrate hits the enzyme a reaction takes place - Or - the diffusion-controlled encounter of enzyme and substrate

Front 23

What does K-cat include?

Back 23

all the catabolic steps of an enzyme - K1, K2 ect

Front 24

What does Kcat/Km measure?

Back 24

the effectiveness of the enzyme - the bigger the number the more effective the enzyme

Front 25

What are the 2 classes of multiple substrate reactions?

Back 25

sequential displacement and double displacement

Front 26

What are the 2 subclasses of a bisubstrate reaction?

Back 26

sequential ordered and random sequential

Front 27

sequential ordered mechanism for multiple substrates-

Back 27

the order of the binding of the substrates and the release order of the products matter

Front 28

Multiple substrates - random sequential mechanism

Back 28

the order of the substrate binding and product release doesnt matter

Front 29

Multiple substrates -double displacement-

Back 29

one the of products is released before all the substrates are bound -- has a substituted enzume intermediate

Front 30

What are the 2 types of reversible inhibition?

Back 30

competitive and noncompetitve

Front 31

What is the results of the Vmax and Km in competitive inhibition?

Back 31

Vmax- is unchanged

Km- increases

Front 32

How can competitive be overcome?

Back 32

by increasing substrate concentration

Front 33

What is the results of the Vmax and Km in non-competitive inhibition?

Back 33

Vmax decreases

Km unchanged
Can be overcome by increasing enzyme not substrate

Front 34

What does a competitive inhibitor look like on a lineweaver burk plot?

Back 34

Competitive - still crosses at the same Y intercept (1/Vmax)

Front 35

What does a noncompetitive inhibitor look like on a lineweaver burk plot?

Back 35

Still keeps the same Xaxis (-1/Km)

Front 36

IC_50 value-

Back 36

the effectiveness of drugs as inhibitors
- the concentration of inhibitor at which half of max enzyme activity is inhibited - very dependent upon the conditions under which they are measured

Front 37

Where do irreversible inhibitors often bind?

Back 37

to the catalytic site residues

Front 38

What are the 3 types of irreversible inhibition and how do they work?

Back 38

group specific - bind to specific side chains

affinity labels-structurally similar to substrate molecules, and covalently modify the active site

suicide inhibitors- modified substrates and are the most specific for labeling an active site

Front 39

Besides looking like substrate what is something else to look like and inhibit?

Back 39

The substrate transition state

Front 40

How does penicillin inhibit bacterial growth? through what type of inhibition?

Back 40

interfers with bacterial cell wall growth through irreversible inhibition

Front 41

What is bacterial cell wall made out of? what does that consist of?

Back 41

peptidoglycan - polysaccharide chains cross linked by short peptides and sugars

Front 42

What specific part of the bacterial wall does penicillin interfere with? what enzyme catalyzes this and that penicillin bindsto?

Back 42

blocks the cross links of the polysaccharide chains - glycopeptide transpeptidase

Front 43

What are vitamins often precursors to?

Back 43

essential coenzymes (small organic cofactors)

Front 44

enzyme strategy - Binding energy-

Back 44

the free energy released in the formation of numerous weak interactions between an enzyme and its substrate

Front 45

enzyme strategy covalent catalysis-

Back 45

active site contains a reactive group that is temporarily covalently modified

Front 46

enzyme strategy General acid-base catalysis-

Back 46

a molecule/residue (not water) plays the role of proton donor/acceptor

Front 47

enzyme strategy Metal-ion catalysis

Back 47

uses a bound metal ion

Front 48

enzyme strategy - catalysis by approximation-

Back 48

involves 2 substrates that are brought together on a single binding surface to enhance the rate of the reaction

Front 49

What is the delta G of peptide bond breaking?

Back 49

negative -happens spontaneous -has to if enzymes speed it up- but very slow

Front 50

Where does chymotrypsin cleave? What protease family is it apart of/

Back 50

on the carboxyl side of aromatic or large hydrophobic groups -(trp, tpr, phe, met, leu) - the serine protease family

Front 51

What enzyme strategy does chymotrypsin use?

Back 51

covalent modification - the substrate has to be bound

Front 52

How many steps does chymotrypsin use? What are the phases called?

Back 52

2 - burst phase (acylation) and steady state phase (deacylation)

Front 53

What is the active site of made of in chymotrypsin?

Back 53

catalytic triad - his, asp, and the reactive ser

Front 54

What does the catalytic triad do the ser?

Back 54

Help pull proton away from the ser - creating a reactive alkoxide ion - a powerful nucleophile

Front 55

What does the oxyanion hole stabilize?

Back 55

the very unstable tetrahedral intermediate in the chymotrypsin catalytic mechanism

Front 56

What are the 3 main other classes of proteases besides serine?

Back 56

1. Cystein proteases
2. Aspartyl proteases - no catalytic triad
3. Metalloproteases- use a bound metal ion to activate water

Front 57

Why is the aspartyl proteases asp so reactive?

Back 57

2 asp share a proton - a 1/2 charge on each = very reactive