Enzymes

Question 1

What are the functions of enzymes?

Answer 1

Digestion
Blood clotting: fibrin clot catalysed by thrombin
Defence: immune system activation of complement
Movement: actomyosin is an ATPase
Nerve conduction: Membrane ion pumps for Na+, Ca2+

Question 2

What are the key properties of enzymes?

Answer 2

↑ reaction rate 
Specificity
Unchanged at end of reaction
Don't alter eq
↓ free energy of activation of reaction

Question 3

What’s free energy of activation?

Answer 3

If there’s drop in free energy from R->P

reaction is favourable but must put free energy in first

Question 4

Define transition state

Answer 4

highest point of the free energy of activation

Question 5

How do enzymes speed up reactions?

Answer 5

↓free energy of activation enzyme uses binding energy of its substrate to ↓ activation energy

Question 6

What are the kinetic parameters of enzymes?

Answer 6

Vmax = max rate of enzyme reaction
Km = how tightly substrate can bind to active site

Question 7

Describe Michaelis-Menten curve

Answer 7

plot diff substrate conc against reaction velocity, develops asymptote
Vmax: all active site occupied so measure of E-S-> E+P
Km: substrate conc when Vmax is half so how sticky substrate is for enzyme (affinity)

Question 8

What can the E-S do?

Answer 8

E + S —k1—> E-S —–k3—-> E + P

• break up so E-S —-k2—–> E + S
• chemistry! E-S —-k3—-> E + P

Question 9

What limits enzyme binding to substrate?

Answer 9

diffusion

Question 10

What makes a perfect enzyme + eg?

Answer 10

not limited by chemical activity only by diffusion

carbonic anhydrase so K3/Km = 10⁸M⁻¹s⁻¹

Question 11

How do you calculate diffusion limited rate?

Answer 11

K3/Km = 10⁸M⁻¹s⁻¹
K3 is chemical rate constant (Vmax/[enzyme]total) then divide by Km, measures from E+S to E+P. If ratio’s 10⁸M⁻¹s⁻¹=diffusion limited reaction

Question 12

Why aren’t all enzymes working to their max (perfect)?

Answer 12

all available nutrients will be degraded

Question 13

What’s Triosephosphate Isomerase (TIM) + role?

Answer 13

perfect glycolysis enzyme
interconverts 2 products
catalyses breakdown of fructose 1, 6-bisphosphate to get 2 products: glyceraldehyde-3-phosphate (USEFUL) + useless converted to G3P

Question 14

Define proteases + eg of various classes?

Answer 14

hydrolyses peptide bonds used as therapeutic targets

serine, cysteine, aspartyl, metallo proteinases

Question 15

Why are serine proteases so reactive?

Answer 15

• has catalytic triad
• other residues that H bond w serine
• aspartate + histidine move proton making serine -ve

Question 16

Why isn’t every peptide bond hydrolysed by every protease?

Answer 16

specificity - only hydrolyse certain peptide bonds

Question 17

How does trypsin hydrolyse peptide bonds?

Answer 17

only if side chain +ve side chain (lys or arg) because binding pocket is -ve

Question 18

How does chymotrypsin hydrolyse peptide bonds?

Answer 18

side chain to be Phe, Trpor Tyr because binding pocket
is hydrophobic
forming acyl-enzyme intermediate

Question 19

How does elastin hydrolyse peptide bonds?

Answer 19

small residue because binding pocket is small

Question 20

What does the catalytic triad of a protease do?

Answer 20

Changing the chemistry
Making steps easier than uncatalyzed reaction
↓ free energy of activation

Question 21

What are serine proteases?

Answer 21

have conserved 3D structure w charge relay system

diff proteases accommodates to diff side chains

Question 22

How mitochondrial enzymes act as nano machines?

Answer 22

• In oxidative phosphorylation, H+ pumped into space
• inner impermeable to H+
• H+ gradient
• storing energy + pd across membrane
• ATP synthase on inner acts as a motor
• activated by rotating spindle w 3 active sites
• H+ drives motor producing ATP

Question 23

How’s Topoisomerase II a nananomachine?

Answer 23

molecular clamp that unlinks tangled chromosomes using ATP to work clamp