Quiz 3: Enzymes

Enzyme Cofactors and Coenzymes

Some enzymes use other things to help them do their job like cofactors and Coenzymes:

Cofactors: Fe, Mg, Mn, Zn

Coenzymes: Enzymes or metaloorganix molecules that act like carriers

Holoenzymes and Apoenzyme

Holoenzymes: Complete structure of protein and cofactor or coenzyme.

Apoenzyme: Protein part of the holoenzyme

Prosthetic Groups: Cofactor or Coenzyme that is covalently bonded to a protein.

Classes of Enzymes

7 of em. List them off the domepiece or you dont know it

Rate constants and orders

First Order: Depends on one compound

Second order: Depends on 2 with units M^-1s^-1

ENZYMES CAN BE STEREOSPECIFIC

Interactions between enzymes and substrates

Binding of substrate to enzyme makes binding energy which is a source of free energy to use for equation.

Covalent interactions between enzymes and substrate lower Ea

Noncovalent Interactions are introduced in the transition state

Desolvation

When substrate enters active site, it displaces water, increasing randomness

Acid-Base Catalysis

Acid Catalysis

Basic Catalysis

Metal Ion Catalysis

Can orient the substrate, increase acidity through resonance, or stabilize charges

nearly 1/3 of all enzymes require metal ions to work

Covalent Catalysis

A transient covalent bond is formed in active site.

Chymotripsin

Protease where it cleaves aromatic amino acid peptide bonds at the COOH side

Chymotripsin Catalyzed reaction

Broad asf, will tune in closer

Steps:

1: Side chain of amino acid adjacent to bond to be cleaves positions itself inside the hydrophobic enzyme

Chymotripsin reaction step 2

proton transfers allow for covalent opening and bonding to carbonyl carbon

Chymotripsin reaction step 3 and 4

Peptide bond breaks by protonating amine, releasing COOH terminal chain of polypeptide

Step 4: H2O enters the site where the product just left

Chymotripsin step 5

His acts as base to turn water to OH-. Nucleophile comes in and does a textbook nucleophilic substitution of ester

Chymotripsin reaction step 6 and 7

ser197 is protonated and made a better leaving group for the nucleophilic ester substitution

Step 7: Cleaved N terminus side dips and enzyme back to original state

HIV Protease Mechanism

Pretty simple stuff just look at it

HIV Protease Inhibitors

Form interactions with enzyme and can be seen as irreversible inhibitors

Hexokinase Induced Fit

Binding energy when ATP interacts causes conformational change so the enzyme can actually start to catalyze the

Xylose still causes this change even though its different from glucose.

Enolase

Basically just a metal ion catalysis. Replaces some bonds and allows for time in order to replace the lost hydrogen with a double bond

Enolase MEchanism

Kd in enzyme kinetics

Dissociation of enzyme substrate complex Kd=[S][E]/[ES]

K-1/k1

Vo for high vs low concentrations of substrate

At low conc., it increases linearly with increased substrate concentration because there are more enzyme than substrate

At high conc., it is an exponential increase because there are more substrate than enzyme so it reaches a limit

Michaelis mentin theory of enzyme kinetics

Final step of enzymatic catalyzation is slower (Breakdown of enzyme complex to enzyme and product)

Michelis Mentin Constant Km

Kcat= k of limiting step

Et= total enzyme concentration Et= [E]+[ES]

km= (k-1 + k2)/k1

The concentration of substrate that gives half max velocity is Km

Vo both equations and why IMPORTANT

Vm= kcat*Et

allows for different ways of finding initial velocity

Kcat significance

The larger the Kcat, the better because it can do more per time

kcat/km gives a value of the enzymes catalytic efficiency (higher the better)

Double reciprocal or lineweaver plots, what is it and how is it

Used to determine if it is michaelis mentin enzyme. Some weird reciprocal of eqn just look

Types of enzyme inhibition

four reversible, one irreversible

Competitive inhibition (graph as well)

More inhibitor, the steeper the line slope gets, y intercept is always the same

Uncompetitive inhibition graph n stuff

Binds to enzyme substrate complex, stopping release of product

Line steepness stays the same but more inhibitor raises it, changing y and x intercept

Mixed Inhibition

Similar to uncompetitive; binds to enzyme or complex ig stopping it from reacting or slowing it down. The more it increases, the lines get steeper and intercept to the left of the y axis

Competitive inhibitor designs

Can be designed as a substrate analog, meaning its like the substrate and enzyme thinks it is

Can be transition state analog because enzymes want to bind to transition state more

Irriversible inhibition

Suicide Inactivation

Does a few steps of the enzyme catalyst until it reaches a point where it can’;t be disconnected

Regulatory enzymes

Control and regulate metabolism and enzyme activity

Roles of regulatory enzymes and mechanics read in depth

Read in Depth

Think as an analog for hormone secretions and stuff. Feedback loops and stuff

Michelis mentin kinetics with regulatory enzymes?

Regulatory enzymes usually dont follow them, the rest in the pathway might though

Allosteric regulation of enzymes

Allosteric enzymes are enzymes that function through other things modulating them, binding to them noncovalently (allosteric modulators or allosteric effectors)
Allosteric modulators are often cofactors or small metabolites

Aspartate Transcarbamoylase (ATCase) what is it and structure

Catalyzes formation of carbamoyl aspartate

kinetic properties of allosteric enzymes (graph and stuff)

Makes a sigmoid curve which is different from michelis mentin graphs and uses K0.5 which is [s] at half maximal velocity instead of Km

Reversible covalent Modulation

Regulation of muscle glycogen phosphorylase activity by phosphorylation of

Enzyme Precursor cleavage

Zymogen is inactive that is cleaves to form an active PROTEASE enzyme

Blood Coagulation Cascade

Regulatory cascade = a mechanism that allows a

very sensitive response to ‘and amplification of’ a

molecular signal

– example = formation of a blood clot

Catabolic vs anabolic pathways

Group transfer ATP I

This is what drives the effect of atp in endergonic reactions.

A group goes to ATP and releases a phosphorous which is favorable

Group Transfer ATP II