Chapter 6

Question 1

What are enzymes?

Answer 1

They provide a mechanism for the acceleration, regulation, and coordination of chemical reactions

All enzymes are proteins

Catalyze the interconversion of substrate and product

Increase the rate of a reaction, but do not affect equilibrium

Question 2

What is vitalism?

Answer 2

Belief that living things are fundamentally different from non-living things

Question 3

What is a co-enzyme or co-factor?

Answer 3

For enzymes where the protein component alone isn’t fully active, they require co-factors which are tightly associated with the enzyme and called prosthetic groups
Co factors- inorganic ions (Mg Fe)
Co enzymes- complex organic molecules (vitamins)

Question 4

What are the three things catalysts do?

Answer 4

1. Lower the amount of energy required for a reaction to proceed
2. Speed up attainment of equilibrium but do not change equilibrium
3. Are unchanged by the reaction; recycled to participate in another reaction

Question 5

What are the four areas where enzymes differ from chemical catalysts?

Answer 5

Speed- enzymes have remarkable catalytic power (some catalytic perfection)
Conditions- many catalysts require extreme temp pH and pressure, while enzymes function at physiological conditions
Specificity- enzymes have higher degree of specificity
Regulation- many enzymes are responsive to dynamic needs of cell and organism

Question 6

What is the Circe effect?

Answer 6

Where enzymes are able to catalyze reactions faster than predicted by diffusion control limits

Question 7

What are the five points on how enzymes work? (Active site)

Answer 7

1. The Active site is a 3D cleft formed from groups that come from the polypeptide chain
2. The Active site represents a small part of the enzyme
3. Active sites are unique microenvironments
4. Substrates are bound to enzymes by multiple weak interactions
5. The specificity of substrate bonding depends on the precisely defined arrangement of atoms in the Active site

Question 8

What are the two types of enzyme specificity?

Which replaced which?

Answer 8

Lock and key- everything fits perfect
Hand in glove- the enzyme has a rough shape of the substrate then when the substrate touches the enzyme it forms the perfect connection

Lock and key got replaced by hand in glove!

Question 9

What is the relationship between the rate of a reaction and the activation energy?

Answer 9

Inverse and exponential

Study graph of transition state, activation energy etc about 1/3 down

Question 10

When can a reaction take place spontaneously?

What is ΔG at equilibrium?

Answer 10

When ΔG is negative

At equilibrium, ΔG is zero

ΔG provides no info on the rate of a reaction

Question 11

What two things result in catalytic capabilities?

Answer 11

1. Binding effects
   - substrate binding (E+S->ES)
   transition state stabilization
   (ES->ETS)
2. Chemical Effects
   - acid/base catalysis, covalent catalysis

Question 12

What are the five things substrate binding promotes reactions by?

Answer 12

1. Reducing entropy
2. Alignment of reactive functional groups of enzyme with substrate
3. Desolvation of the substrate (removal of water molecules)
4. Distortion of substrates
5. Induced fit of the enzyme

Question 13

Would you rather have an enzyme complementary to the substrate or the transition state?

Answer 13

The transition state so then the substrate can go in, be bent and snapped into two products, and the products can leave

Question 14

What are transition-state analogs (TSAs)?

Answer 14

Stable compounds that resemble unstable transition states
Have potential therapeutic applications as competitive inhibitors

Look at picture near middle of lecture notes

Question 15

What are competitive inhibitors?

Answer 15

Where TSAs can bind to the active sire of a target enzyme active site with high affinity, preventing substrate binding

Question 16

What is acid-base catalysis?

Answer 16

Reaction acceleration by catalytic transfer of a proton

Side chains of amino acids can act as either a base (proton acceptor) or an acid (proton donor)

Question 17

What is covalent catalysis?

Answer 17

Where all or part of the substrate undergoes a state where it is bound covalently to the enzyme to form a reactive intermediate
Involves two steps, one to form covalent linkage to the enzyme, second to regenerate the free enzyme
Picture just before half way on lecture notes

Question 18

What is the equation for the rate of a reaction?

Answer 18

V= Δ[P] / Δt
[P] = concentration of product

Question 19

What are the 4 variables that affect the reaction rate?

Answer 19

pH- graph is an upside down u
temp- graph is an upside down u
[E] (enz. Conc.)- graph is straight line from 0,0 out
[S] (sub. Conc.)- graph goes up then flatlines eventually

Pictures around halfway in lecture notes

Question 20

What is the equation for the initial velocity?

Answer 20

V0= [ES]k2

Look at slide around half way

Question 21

What is the formula for the steady state assumption?

What does this equation result in using vmax and Km?

Answer 21

[E][S]k1 = [ES]k-1 + [ES]k2

Results in:
V0= Vmax[S] / Km + [S]
Km- conc. Of substrate required to reach 1/2 Vmax
Vmax- max velocity of the enzyme

Graph at half way point of slide notes

Question 22

How are enzymes affected when [S] < Km?
[S] > Km?
[S] = Km?

Answer 22

[S] < Km- enzymes highly sensitive, very little activity
[S] > Km- enzymes insensitive, high activity
[S] = Km- enzymes neutral sensitive to change in substrate conc. , significant activity

Question 23

What is a lineweaver-Burke plot?

Answer 23

Describes the relationship between [S] and V0 but instead it’s 1/V0 and 1/[S]
Graph is all above y axis but like starts in negative x area and moves up into positive x area
(Look at graph just over half lecture notes)

Question 24

What is the enzyme turnover number (kcat)?

Answer 24

Equals number of molecules of substrate converted to product per unit time
kcat= Vmax/ [Et]

[Et]- total concentration of enzyme

Question 25

What is a competitive inhibitor compared to an uncompetitive inhibitor?
(How do their lineweaver plots compare)

Answer 25

Competitive- resemble the substrate, bind sonly to free enzyme (the linweaver plot is the same but slightly rotated upwards at the y intercept)
Uncompetitive- binds only to ES complex, Vmax decreased (the lineweaver plot is the exact same slope just moved back a few x values)

Question 26

What is non competitive inhibition?

How does it’s lineweaver plot compare

Answer 26

Binds both to E and ES
Vmax decreased

Lineweaver plot is tilted slightly upwards at the x intercept this time

Question 27

What are serine proteases?

Answer 27

Digestive enzymes
Mediates the turnover of self proteins
Stored in pancreas
Contains both covalent and acid-base catalysis
Have a conserved catalytic mechanism based on a catalytic triad of residues (Asp, His, Ser)

Question 28

What are the functions of histidine, aspartate, and serine in serine protease?

Answer 28

His- removes H from Ser hydroxyl
Asp- stabilizes the positively-charged His to facilitate serine ionization
Ser- acts as a nucleophile attacking the carbonyl group of the polypeptide substrate

Question 29

What is phase 1 of chymotrypsin mechanism?

Answer 29

Step 1 (acid base)- his acts as base, extracts proton from hydroxyl of Ser
Step 2 (covalent)- forms covalent linkage of hydroxyl group to carbonyl carbon
Step 3 (acid base)- his acts as an acid, donates proton to amine group of peptide bond, cuts peptide into two pieces

Question 30

What is phase 2 of chymotrypsin?

Answer 30

Step 1 (acid base)- his acts as base and extracts proton form water
Step 2 (covalent)- activated water molecule attacks point of covalent linkage between enzyme and substrate
Step 3 (acid base)- his acts as an acid, donates proton to reform hydroxyl of Ser

Question 31

What are the two ways regulation of enzyme activity can be regulated?

Answer 31

1. Regulation of enzyme availability
   - location, rates of synthesis and degradation
2. Regulation of enzyme activity
   a) covalent modification (phosphorylation)
   b) non-covalent modification (allosteric regulation)

Question 32

What is the logical point to regulate a reaction pathway?

Answer 32

Enzymatic pathways often controlled through negative feedback regulation by the final product of the pathway

Picture 3/4 through slides

Question 33

What are allosteric enzymes?

Answer 33

• Have activities that are regulated by interaction with metabolic intermediates
• Are regulated by allosteric modulators that bind non-covalently to the enzyme
• Quaternary structure
• Catalyze rate limiting step (slow)
• Rapid switch between T and R state
• Sigmoidal curve

Question 34

What is the threshold effect?

Answer 34

Below a certain substrate concentration, there is little enzyme activity then after the threshold the enzyme activity increases rapidly

Question 35

What is phosphofructokinase 1?

Answer 35

• Catalyze early step of glycolysis
• Phosphoenolpyruvate (PEP) is the allosteric inhibitor of this
• ADP is the allosteric activator

Question 36

What is enzyme regulation by covalent modification?

Answer 36

Regulation through the covalent linkage of a modifying group to change some aspect of the proteins behaviour
(Phosphorylation)

Question 37

What are the two enzymes that are in charge of production and utilization of glycogen?

Answer 37

Glycogen synthase (anabolic) catalyzes production of glycogen from glucose
Glycogen phosphorylase (catabolic) catalyzes the breakdown of glycogen into glucose

Both enzymes are phosphorylated when hungry or scared
Both enzymes are unphosphorylated when in fed state (insulin)