Symbiotic bacteria can fixate N2 from the atmosphere but what is the problem with this?

It require a huge amount of energy. 16 ATP.

Nitrogenase is used to accelerate the reaction.

The greater the Ea the...

Slower reaction rate

Are enzymes lock and key?

No. Induced fit. Full complimentarity is achieved after the substrate binds to the active site.

What is the active site most complimentary to?

The transition state. The transition state is therefore stabilised and the energy barrier is lowered.

What are the residues at the active site involved in?

Catalysis as well as binding energy

WHat do the residues at the active site do in catalysis?

1. Be proton donors/acceptors

2. Form temporal covalent bonds to substrate

3. Hold metal cofactors

(Asp and Glu for most, Cys and His for heavy ones)

Extra functional groups are provided by small molecules that may bind near the active site. What are they called and what can tehy be classified into?

Cofactors.

1. Essential ions- loosely or tightly bound in metalloenzymes

2. Coenzymes- carriers of functional groups or atoms.

-loosely bound=cosubstrates

-covalently bound = prosthetic groups e.g. haem

What does the graph look like in a reaction, time against total amount of product?

The first part of the curve is linear, and corresponds to the inital rate of reaction. Over time the curve levels off because substrate is being used up.

If we plot initial rate of reaction versus the substrate concentration, what do we get?

We obtain a straight line. Its slope is k1.

If we plot initial rate versus the substrate concentration for a catalyzed reaction what do we get?

First order at first then zero order

What's the formula for velocity?

V= d[P]/dt = Vmax[S]/ Km+[S]

How many steps to enzymatic reactions have and which is usually the time-limiting step?

-Enzymatic reactions have at least 2 steps

-The second is usually the time-limiting step

E+S ES -> E + P

What is the Michaelis constant (Km) defined as?

K-1 +K2/ K1.

K2 is negligable because it's so slow. K-1/K1.

K1 is the first reaction from E+S to ES. K-1 is the backwards one to this. K2 is the second reaction from ES to E + P.

What is Km a measure of?

Km is a measure of the affinity of an enzyme for its substrate. The lower the Km, the higher the affinity and the tighter the substrance is bound.

What is the formula for kcat?

Kcat = Vmax / [Et]

[Et] = total enzyme concentration i.e. number of active sites.

What is Kcat a measure of?

The number of molecules of substrate converted to product per second per active site.

The higher the Kcat/Km the ....?

Better the enzyme

Means it has higher affinity and the more substrate converted to product

What are the 6 classes of enzymes?

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- Oxidoreductases (dehydrogenases)- catalyze oxidation- reduction reactions
- Transferases- catalyzes group transfer reactions
- Hydrolases- hydrolysis rxns
- Lyases- lysis
- Isomerases- isomerism reactions
- Ligases- ligation (joining) of 2 substrates

What is the michaelis menten equation?

V= vmax[S]/Km+[S]

V= reaction rate

Vmax= max. rate of rxn

Km= conc. at which 1/2 vmax

[S]= conc. substrate

What does the michaelis menten equation relate?

Reaction rate to concentration of substrate

What is Vmax?

The max initial velocity when the enzyme is saturated with substrate. It's proportional to [E]. (conc of enzymes)

What is vmax relation to kcat?

vmax= Kcat[E]t

Kcat= catalytic constant or turnover number

Kcat= k2 for simple reactions and represents the number of substrate molecules converted into products

What do we plot the lineweaver- burk plot?

1/Vo versus 1/[S]

What can we find from a lineweaver-burk plot?

Km and Vmax

Where the line meets the X-axis or the 1/[S] axis the value is -1/Km

Where the line meets the Y axis or the 1/Vi axis, the value is 1/Vmax

What is 1/V??

Flip over the michaelis menten equation

(1/v) = Km+[S] / Vmax[S]

= (Km/ vmax)(1/[S]) + 1/vmax

gives a lineweaver burk graph equation

In the lineweaver-Burk plot. What is the equation of the line in the form y=ax+b?

1/V= (km/vmax) x (1/[s]) + (1/vmax)

y= 1/v

x = 1/[S]

a= km/vmax

b= 1/vmax

which can be derived from turning the michaeles menten equation upside down