Enzyme Kinetics

Question 1

How do enzymes accelerate rxns?

Answer 1

By forming a specific 3-dimensional structure within an active site.
They are primarily proteins with specific structures and active sites where catalysis happens. Have specific cofactors (NOT used up) and coenzymes that help in the catalysis.
They decrease the activation energy.

Question 2

HOw do they work

Answer 2

They bind and stabilize the substrate in its transitional state, where induced fit --> change conformation of the substrate and/or enzyme putting more pressure on the substrate to become product. 
This decreases energy activation. 
INCREASED RATE (no change in equil)

Question 3

How do enzymes decrease the activation energy?

Answer 3

1.) Binding energy b/w enzyme and substrate: form ES cmplx, multiple weak noncovalent interactions that provide specificity as well as catalysis
Enzymes are optimized to bind transition site
2.) Increased local concentration of substrates (increase effective concentration, better chance of lining up)
3.) Rearrangement of covalent bonds in specific active site chemistry

Question 4

How to rearrange covalent bonds

Answer 4

1. ) Covalent catalysis: transient covalent bond b/w E and S
2. ) Metal ion chemistry: bound metal ions can help position the substrate or be powerful driver to help form S in redox rxs (almost 1/3 of enzymes use metal ion)
3. ) GEneral acid base catalysis: amino acid side chains can donate or accept protons to stabilize the transition states

Question 5

Cofactor

Answer 5

Often metal ions. NEeds to present with enzyme for a rxn to be catalyzed. Adds catalytic power, no chemical group donation. NOT USED UP.

Question 6

Coenzyme

Answer 6

Organic ligand that works w/ enzyme to provide chemical group that will be used in the rxn. Used up, donates chemical group

Question 7

Prosthetic gorup

Answer 7

coenzyme or cofactor tightly bound to the enzyme

Question 8

Holoenzyme

Answer 8

Cofactor or coenzyme + enzyme

Question 9

Apoenzyme

Answer 9

Enzyme dissociated from cofactor/coenzyme

Question 10

Km

Answer 10

Amount of substrate needed for enzyme velocity to be at 1/2 Vmax (not a binding constant), generally enzymes in cell operate around 1/2 Vmax

Lower Km than another: it needs less susbtrate to operate at Vmax

Question 11

Kcat

Answer 11

more general rate constant that describes rate limiting step of any enzyme catalyzed rxn.
BIGGER KcAT = FASTER

Turnover number

USED TO COMPARE diff enzymes. Doesn’t change with competitive inhibitor.

Question 12

Large kcat/km means?

Answer 12

an efficient enzyme.

Question 13

Allosteric regulation

Answer 13

Often binding of another molecule, regulator. Changes the conformation of enzymes and hence alters fx.

Regulation of a protein by binding an effector mlc somewhere besides active site

Question 14

Covalent modification

Answer 14

Many enzymes can be phosphorylated can be phosphorylated to affect fx.
The enzymes that modify enzymes to them on/off are often kinases.
Other modificaitons: adenylations, methylations etc.

Question 15

Regulatory protein binding

Answer 15

some enzymes are bound by proteins to activate/inactivate

Question 16

Proteolytic activaiton

Answer 16

Some enzymes are inactive until cleaved by an enzyme

Question 17

Competitive

Answer 17

binds only to teh E and competes with or prevents substrate binding.
Increases Km

Question 18

Uncompetitive

Answer 18

Binds to enzyme in a place other than the active site (it doens’t have to compete w/ substrate for binding)

Only binds to ES complex

LOWERs Vmax and changes apparent Km

Question 19

Mixed

Answer 19

Binds outside active site, can bind to either E or ES. affects Km and Vmax. and kcat.

Question 20

Irreversible

Answer 20

Bind with enzyme and cause a permanent change.