module 6: enzymes Flashcards
what is the most important feature about enzymes?
their catalytic power & specificity
what is vitalism?
the belief that things are fundamentally different from non-living things
who developed vitalism?
Edward Buchner
what are co-factors?
non-protein factor & activator
what are examples of co-factors?
inorganic ions (Mg, Fe)
what are co-enzymes?
complex organic molecules for activity
what is an example of a co-enzyme?
vitamins- required by the body but cannot be produced
what is a holoenzyme made of?
apoenzyme + co-factor/co-enzyme
what is a holoenzyme?
whole enzyme that represents a biologically active form
what is an apoenzyme?
inactive protein portion
what is a prosthetic group?
co-enzyme or co-factor that is highly associated with the enzyme
what is the difference between a co-enzyme / co-factor and a prosthetic group?
the degree of association
what are 2 functions of catalysts?
- lower amount of energy required for a reaction to occur
- speed up attainment of equilibrium but do not change it
are enzymes or catalysts faster?
enzymes
enzymes or catalysts: which functions under physiological conditions & which requires complex extreme conditions?
enzymes: physiological conditions
catalysts: complex & extreme conditions
enzymes or catalysts: which has a higher degree of specificity?
enzymes
enzymes or catalysts: which are responsive to changing conditons?
enzymes
what are catabolic reactions?
breaks stuff down & are less specific
what are anabolic reactions?
builds stuff up
what is the Circe effect?
ability of some enzymes to catalyze reactions faster than diffusion-controlled rate limits through electrostatic interactions
what is a substrate?
the molecule acted upon by the enzyme
what is the product?
the molecule produced by the enzyme
what is the active site?
the portion of the enzyme responsible for binding the substrate to ES complex
what is the ES complex equilibrium equation?
E + S <–> ES <–> E + P (goes both ways)
what kind of environments are active sites?
micro-environments
what can substrate binding cause?
induced fit
what is a lock & key enzyme?
the substrate fits into enzyme without changing its confirmation
what is a hand in glove enzyme?
substrate changes its confirmation to fit into the enzyme (induced fit)
what will be favoured in free energy graphs?
substrate/product using lower energy
what causes a more skewed equilibrium in free energy graphs?
greater difference between free energies
what does the difference between free energies in substrate & product mean?
shows where equilibrium lies but not the rate it is reached
what does a higher barrier tell us on a free energy graph?
slower rate of equilibrium
what does a lower energy path do on a free energy graph?
increases the rate of reaction but equilibrium remains the same
the reaction is spontaneous only if G is…
negative
does G provide information about the rate of a reaction?
no
what does G depend on?
free energy of the product - free energy of the reactants
what do enzymes do in free energy graphs?
provide a lower energy pathway which increases rate of reaction & decreasing activation energy
what does the binding of a substrate do?
provides specificity & catalytic power
how much can catalytic mechanisms increase reaction rates?
by a 10,000 fold
what is the most difficult moment to achieve?
transition state stabilization
what is transition state stabilization?
an increased interaction of the enzyme substrate occurs in the transition state
the active site is ( ) to the transition state in shape & chemical character
complementary
enzymes bind to their transition states ( ) more tightly than their substrates
10^10 - 10^15
what are transition state analogs?
stable compounds that resemble unstable transition states
what are competitive inhibitors?
molecules that bind to the active state of an enzyme (tend to resemble the substrate molecule)
what is prevented when transition state analogs bind with high affinity?
substrate binding
what does the active site often contain?
polar, ionizable side chains
what is acid-base catalysis?
enzyme donates or accepts proton & changes protonation state of substrate
what amino acid is often involved in acid-base catalysis?
histidine
what is the pKa of a functional group is influenced by?
chemical microenvironment
what is covalent catalysis?
covalent intermediate is formed between the enzyme & the substrate molecule
what does a steep drop off mean on a graph?
all enzyme is unfolded at max temp & there is no more activity
what do K1 & K-1 represent?
rapid, non-covalent interactions between enzyme & substrate
what does K2 represent?
rate constant of formation of product from ES
how to calculate initial velocity?
Vo= [ES] K2
how to calculate velocity?
V= delta P / delta t
steady state assumption equation?
[E] [S] K1 = [ES]K-1 + [ES]K2
what is the michaelis-menten graph?
relationship between substrate concentration & initial velocity
what is the michaelis-menten equation?
Vo= Vmax [S] / Km + [S]
what is Km?
the concentration of substrate required to reach 1/2 Vmax
[S] < Km
enzymes are highly sensitive to changes, but have little activity
[S] > Km
enzymes have high activity but are insensitive to changes
[S]=Km
enzyme has significant activity & is responsive to changes
Thrombin cleaves…
Arg-Gly bonds
Trypsin cleaves by…
Lys & Arg
Chymotrypsin cleaves by…
Phe, Tyr & Met
Elastase cleaves by…
Gly & Ala
what does Papain do?
cuts all peptide bonds
what is the catalytic triad made of?
Asp, His & Ser
what does His do in the catalytic triad?
accepts & donates a proton at each stage of acid-base catalysis
what does Asp do in the catalytic triad?
stabilizes positively charged His to facilitate serine ionzation
what does Ser do in the catalytic triad?
attacks carbonyl group of peptide bond to be cleaved
what function does Ser cause in the catalytic triad?
covalent catalysis
is changing amount of enzyme long term or short term?
long
3 factors of covalent modifcation
- phosphorylation
- methylation
- glyosylation
what is the mechanism used for non-covalent modification?
allosteric regulation
what type of feedback are enzymatic pathways controlled by?
negative feedback
what are allosteric enzymes?
slow, information sensors that coordinate cellular metabolism
what shape of data are allosteric enzymes represented by?
sigmoidal curve
what structure level do allosteric enzymes have?
quaternary
how are allosteric enzymes regulated?
by allosteric modulators that bond non-covalently at sites that are NOT active sites
allosteric enzymes transition from an ( ) active state to a ( ) active state within a ( ) range of concentration
less active –> more active in narrow range
what is the threshold effect?
below a certain substrate concentration there is little activity & after threshold has been reached, activity increases rapidly
what does Phosphopfructokinase 1 (PFK1) do?
catalyzes an early step of glycolysis
what is Phosphoenolpyruvate (PEP)?
an intermediate near the end of the pathway & is an allosteric inhibitor of PK1
ADP is a ( ) of PK1
allosteric activator
When the ratio [PEP] / [ADP] is high, what is inhibited?
PFK1 is inhibited
When the ratio [PEP] / [ADP] is low, what happens?
PFK1 is activated & glycolysis produces more ATP from ADP
what do concentrations of PEP & ADP do?
act allosterically through PKF1 to regulate activity
how are enzymes regulated?
covalent linkage of a modifying group to change protein behaviour
what is the most common post-translational covalent modification?
through phosphorylation
are modifications reversible?
yes
what is glycogen synthase?
anabolic production of glycogen from glucose
(Glucose -> Glycogen)
what is glycogen phosphorylase?
catabolic breakdown of glycogen into glucose
(glycogen -> glucose)
what hormone is regulated when you are hungry?
glucagon
what is phosphorylation?
activates the catabolic enzyme & inactivates the anabolic enzyme
what does phosphorylation favour?
breakdown of glycogen into glucose
when is the breakdown of glycogen into glucose favoured?
when both are un-phosphorylated
where do un-competitive inhibitors bind to?
only ES complex
where do non-competitive inhibitors bind to?
either ES or E
what are zymogens activated by?
activated by selective proteolysis
