Chapter 6 Flashcards
What are enzymes?
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
What is vitalism?
Belief that living things are fundamentally different from non-living things
What is a co-enzyme or co-factor?
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)
What are the three things catalysts do?
- Lower the amount of energy required for a reaction to proceed
- Speed up attainment of equilibrium but do not change equilibrium
- Are unchanged by the reaction; recycled to participate in another reaction
What are the four areas where enzymes differ from chemical catalysts?
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
What is the Circe effect?
Where enzymes are able to catalyze reactions faster than predicted by diffusion control limits
What are the five points on how enzymes work? (Active site)
- The Active site is a 3D cleft formed from groups that come from the polypeptide chain
- The Active site represents a small part of the enzyme
- Active sites are unique microenvironments
- Substrates are bound to enzymes by multiple weak interactions
- The specificity of substrate bonding depends on the precisely defined arrangement of atoms in the Active site
What are the two types of enzyme specificity?
Which replaced which?
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!
What is the relationship between the rate of a reaction and the activation energy?
Inverse and exponential
Study graph of transition state, activation energy etc about 1/3 down
When can a reaction take place spontaneously?
What is ΔG at equilibrium?
When ΔG is negative
At equilibrium, ΔG is zero
ΔG provides no info on the rate of a reaction
What two things result in catalytic capabilities?
- Binding effects
- substrate binding (E+S->ES)
transition state stabilization
(ES->ETS) - Chemical Effects
- acid/base catalysis, covalent catalysis
What are the five things substrate binding promotes reactions by?
- Reducing entropy
- Alignment of reactive functional groups of enzyme with substrate
- Desolvation of the substrate (removal of water molecules)
- Distortion of substrates
- Induced fit of the enzyme
Would you rather have an enzyme complementary to the substrate or the transition state?
The transition state so then the substrate can go in, be bent and snapped into two products, and the products can leave
What are transition-state analogs (TSAs)?
Stable compounds that resemble unstable transition states
Have potential therapeutic applications as competitive inhibitors
Look at picture near middle of lecture notes
What are competitive inhibitors?
Where TSAs can bind to the active sire of a target enzyme active site with high affinity, preventing substrate binding
What is acid-base catalysis?
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)
What is covalent catalysis?
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
What is the equation for the rate of a reaction?
V= Δ[P] / Δt [P] = concentration of product
What are the 4 variables that affect the reaction rate?
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
What is the equation for the initial velocity?
V0= [ES]k2
Look at slide around half way
What is the formula for the steady state assumption?
What does this equation result in using vmax and Km?
[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
How are enzymes affected when [S] < Km?
[S] > Km?
[S] = Km?
[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
What is a lineweaver-Burke plot?
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)
What is the enzyme turnover number (kcat)?
Equals number of molecules of substrate converted to product per unit time
kcat= Vmax/ [Et]
[Et]- total concentration of enzyme
What is a competitive inhibitor compared to an uncompetitive inhibitor?
(How do their lineweaver plots compare)
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)
What is non competitive inhibition?
How does it’s lineweaver plot compare
Binds both to E and ES
Vmax decreased
Lineweaver plot is tilted slightly upwards at the x intercept this time
What are serine proteases?
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)
What are the functions of histidine, aspartate, and serine in serine protease?
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
What is phase 1 of chymotrypsin mechanism?
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
What is phase 2 of chymotrypsin?
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
What are the two ways regulation of enzyme activity can be regulated?
- Regulation of enzyme availability
- location, rates of synthesis and degradation - Regulation of enzyme activity
a) covalent modification (phosphorylation)
b) non-covalent modification (allosteric regulation)
What is the logical point to regulate a reaction pathway?
Enzymatic pathways often controlled through negative feedback regulation by the final product of the pathway
Picture 3/4 through slides
What are allosteric enzymes?
- 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
What is the threshold effect?
Below a certain substrate concentration, there is little enzyme activity then after the threshold the enzyme activity increases rapidly
What is phosphofructokinase 1?
- Catalyze early step of glycolysis
- Phosphoenolpyruvate (PEP) is the allosteric inhibitor of this
- ADP is the allosteric activator
What is enzyme regulation by covalent modification?
Regulation through the covalent linkage of a modifying group to change some aspect of the proteins behaviour
(Phosphorylation)
What are the two enzymes that are in charge of production and utilization of glycogen?
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)
