Kinetics and Regulation Flashcards

Question

What is Kcat? How does it relate to k2?

Answer 1

Kcat- is the turnover number of enzyme, or number of substrate molecules that an enzyme can convert into products per second. Kcat is also the same as k2, as the turnover rate is = to constant (k2).

Answer 2

The higher the kcat value, the more substrates are turned over (converted into product)

Answer 3

highest turnover numbers- carbonic anhydrase. lowest turnover numbers- lysozyme hence enzymes with higher binding affinities (low km), have lower turnover numbers.

Answer 4

can provide info about the preferences enzymes have for different substances based on kcat/km value. Ex: Chymotrypsin has a preference for bulky hydrophobic side chains (phenylalanine, norvaline/norleucine.

Answer 5

1. Sequential reactions- form ternary complex consisting of two substrates and enzyme. Mech: the first substrate(NADH) will bind to enzyme, followed by second substrate (Pyruvate)to form complex. all substrates must first bind to the enzyme, before being catalyzed and released as products (lactate and NAD+) 2. Double-displacement reactions (ping pong)- characterized by formation of substituted enzyme intermediate. Mech: first substrate (aspartate) will bind to enzyme, then catalytic step occurs, which creates substituted enzyme (E-NH3), and substrate is released as product (oxaloacetate); then second substrate(alpha ketoglutarate) will bind to substituted enzyme, creating catalytic step and NH3 transfers to substrate form last product (glutamate). Hence this is like ping-pong where substrates and products bounce on and off.

Answer 6

Michaelis menten- hyperbolic curve allosteric enzymes- sigmoidal curve (due to sharp increase in Vo at middle of graph) significance of sigmoidal curve for allosteric enzymes: they can transition from a less active state to a more active state with a narrower range of substrate concentration (change rate quicker with smaller substrate [} ) Micahelis (requires 27 fold increase in [ S] ), while Allosteric needs 4 fold increase in [ S]

Answer 7

``` R (relaxed is the more stable state, as it is easier for substrate to bind to enzyme, and requires less [S} T state (Tense) is less stable, more difficult for substrate binding to enzyme. Requires more [S] ```

Answer 8

T- Tense state ; square shape | R- Relaxed state: circle shape

Answer 9

describes the sensitivity of allosteric enzymes, and how they are more sensitive to changes in substrate concentration near Km than Michaelis Menten. below a certain substrate [ ], there is little enzyme activity. After threshold is reached, enzyme activity increases rapidly.

Answer 10

behavior in which the initial binding of substrate to one active site in R form or any form will lead to other active sites being trapped in R (or other state). binding of substrate will disrupt T to R equilibrium in favor of R (make it easier for substrate to bind R) cooperativity is what causes sharp increase in Vo for Velocity vs substrate concentration. It works like an on/off switch: either the majority of enzyme is ON state (R state) or OFF state (T state)

Answer 11

The committed step is the conversion of A to B, and after this step occurs, B will be committed to being converted to F (all of the remaining steps will continue). Allosteric enzymes catalyze committed step of metabolic pathways Michaelis- Menten enzymes facilitate the remaining steps.

Answer 12

Michaelis menten- enzyme velocity only depends on substrate concentration and S forming products; only catalysis role. Allosteric enzymes- regulate metabolic pathways, series of roles including regulating inhibitory and stimulatory molecules, receiving and transducing chemical signals

Answer 13

way of regulating biochemical reactions by preventing the production of too much product. Feedback inhibition helps regulate the amount of F synthesized (prevent it from making too much of F). Mech: When enough F is present, F will bind reversibly to e1 which is enzyme used for committed step of reaction (A to B) and will inhibit reaction. The pathway product F inhibits enzyme e1 by binding to regulatory site of enzyme distinct from active site.

Answer 14

because allosteric enzymes may be inhibited or stimulated by several regulatory molecules.

Answer 15

They DO NOT conform to Michaelis Menten kinetics; They have unique features of how they respond to changes in substrate concentration and also use sigmoidal kinetics. Structure- 4 subunits on 4 active sites.

Answer 16

Allosteric enzymes depend on alterations in quaternary structure that has multiple active sites, regulatory sites. binding of one substrate to one active site, will trap the other active sites in R state and remove substrate bound enzyme from T to R equilibrium. Disruption of T- R equilibrium by binding of substrate favors conversion of more enzymes to R state.

Answer 17

1. The enzyme exists in 2 different quaternary structures designated T (tense state) or R (relaxed state). 2. If T and R are in equilibrium (no signals or substrate), T will be more stable state. 3. The R state is enzymatically more active (will catalyze reactions) than T state 4. all active states must be in same state (ALL or NONE; either all R or all T) (aka symmetry rule) also substrate binds more readily to R form of enzyme than T form.

Answer 18

the allosteric constant, where L0= T/R ratio

Answer 19

allosteric regulators disrupt the R to T equilibrium when they bind the enzyme. Activators, or positive effectors bind to R form at regulatory site of enzyme to stabilize R form( thus increasing concentration of R, make R and S interaction more likely). Inhibitors or negative effectors, binds to T to stabilize T form (thus increasing T [ ] and reducing likelihood of R and S interaction). Activators will lower threshold [ ] needed for enzyme activity; inhibitors raise threshold [ ]

Answer 20

Hetertropic effect: the effect of REGULATORY molecules on allosteric enzymes; for Hetero effect, the sigmoidal curve will shift left ( activators, ATP) and right( inhibitors, CTP) Homotropic effect; the effect of SUBSTRATES on allosteric enzymes. This homotropic effect is used mainly for sigmoidal nature of the kinetics curve (black curve)