Bioenergetics and Enzymes Flashcards
what is keq that is at equilibrium?
1
Forms of kinetic energy
radiant energy from sun thermal (at certain temp to function optimally) Mechanical (mvmt of cells) Electrical (mvmt of charged particles down gradients)
Kcat
turnover number measures the number of substrate molecules turn over into product per enzyme molecule per second at saturation dictated by rate limiting step Vo=Kcat [Et][S]/([S]+ Km)
what is keq that favors reverse reaction
less than one
Catalyst
increase the rate of a reaction (making or breaking bonds) without changing in the process
when k’eq is >1
delta G is negative and favors forward reaction
Km
(reaction of ES–> E+S * reaction of ES –> E+P)/(reaction of E+S–> ES) breakdown of reactants and products/ formation of ES not a binding constnat describes amount of substrate needed to reach 1/2 V Max
Comparing Km to Kcat
Kcat/Km is the specificity contact ( rate constant for conversion of E+S to E+P) Comparison for efficiency of enzyme Enzymes with greater number have reached a higher catalytic proficiency.
what are the rearrangements of covalent bonds made in the active site?
general acid base catalysis covalent catalysis Metal ion catalysis
Uncompetitive inhibition
binding to ES in site other than active site reversible changes all parameters: lowers Vmax, Km and Kcat V = Vmax [S]/(Km +alpha’ [S]) alpha’ = 1+[inhibitor]/Ki (dissociation constant)
proteolytic cleavage
enzyme is inactive when it is made, but once cleaved into small fragment to become activated trypsinogen –> trypsin Chymotrypsinogen pepsingon most enzymes in stomach and pancrease
apoenzyme or apoprotein
protein part of the enzyme, inactive enzyme
Change in reduction potential
E of electron acceptors (reduced) - E of electron donor
Enthalpy
(H) heat content for reaction system, energy in chemical bonds Negative is exothermic and favorable, positive is endothermic and unfavorable.
Covalent modification of enzymes
Phosphorylation, acetyl, adenylyl, methyl, amid, carboxyl, ubiquitation, ect. to change the conformation to change the function of the protein. due to intra or extra cellular signals
what is keq that favors a forward reaction
greater than one
Competitive Inhibition
competes with substrate to active site reversible Kcat is unaffected Km increases as concentration of inhibitor increases V = Vmax [S]/(alphaKm + [S]) alpha = 1+[inhibitor]/Ki (dissociation constant)
Linweaver-Burk Plot
rearranged so that slope is Km/Vmax Competitive and mixed inhibition increases slope with increasing [I] non-competitive keeps slow the same with increasing [I]
prosthetic group
a coenzyme and cofactor that is tightly bound to enzyme
Gibbs Free Energy
amount of energy capable of doing work during a reaction at contact temp and pressure. Not an indication of time dG = dH - TdS
Thermodynamically favorable reactions have a _____ delta G.
negative
how is ATP synthesized?
harnessing energy in gradient of H+ and electric potential across in cell membrane in mito provides energy for ATP synthase rotation
Ground state
starting point for either forward or reverse reaction
Coenzyme
complex of organic or metalloorganic molecules provide chemical groups for reaction and are used up ex. Pyruvate decarboxylase
when k’eq is 1
delta G is zero and is in equilibrium
Redox
oxidation is loss of e- reduction is gain of e-
Rank in order of how much energy can be made from oxidation of carbon? Co2, lipid, carbohydrate
Lipid>carb> CO2
General acid base catalysis
amino acid side chains donate or accept protons to stabilize TS. with this, unstable intermediates break down rapidly to form reactants when proton transfer is show, only a small portion of intermediates are made, adding more proton donors and acceptors increase reaction rate.
Mixed inhibition where it is non-competative
rare only when alpha = alpha’ Kcat and vmax are affect Km remains the same
what does lyase do?
addition of groups to double bond, formation of double bonds by removal of groups
how does ES complex form?
multiple weak non-covalent interacts provide specificity as well as catalysis enzymes are optimized to bind the transition state
Keq
Kf/kr = [c][d]/[a][b]
what bonds make the high energy bonds in ATP
phosphoanhydride where ADP and AMP are more stable than ATP nucleophilic attach can occur at 3 positions where they transfer a phosphoryl transfer
Entropy
S - qualitative exp for disorder Positive: disorder increases (favorable) negative : disorder degreses (unfavorable)
what do oxidoreductase enzymes do?
transer electrons
Cofactor
either one or more inorganic ions such as Fe2+, Mg2+, Mn2_ and Zn2+ provide chemical groups and are not used up alcohol dehydrogenase
Velocity of enzymatic reaction is dependent on..
concentration of substrate low [sub] low velocity at saturation v = vmax
Log of a number less than one.
create a negative number!
Michaelis-Menton Equation
Vo = Vmax [Substrate]/([Substrate]+Km)
Forms of potential energy
Chemical bonds concentration gradients, electric fields redox pairs
Irreversible Inhibtion
combine with or destroy a functional group on enzyme that is essential for their activity Penicillin cymotrypsin
Allosteric Regulation of enzyme
Binding of another molecule, a regulator, to change conformation of enzyme to alter its function. Most feedback loops are regulated this way
Reduction potential
E readiness to accept electron positive value is ready to gain electrons; negative is ready to loose electrons
transition state theory
there is a single path for ground state to convert to the ground state of product and the TS is the highest energy state along this path. At TS, the reaction is equally likely to go forward or reverse
How do enzymes work?
provide a specific environment within with a given reaction can occur more frequently. Decreases the rate of a reaction and does not affect reaction equilibria. lowers the activation energy (transition state)
Mixed Inhibition
bind to both E and ES complex reversible Km, Vmax, and Kcat are affected. V = Vmax [S]/(alphaKm +alpha’ [S])
Velocity of reaction
k{substrates]
where is Km on a graph of [s] vs veloicy
km is the x coordinate in which 1/2 vmax is reached
Delta G at equilibrium
-2.3RT log Keq or -1362 log Keq
Characteristics of an enzyme
1) make primarily of proteins with specific structures and active sites 2) some use cofactors or coenzymes 3) they are classified and named by what they do
how are unfavorable reactions cone
by coupling!
Electrical field in bioenergetics
increasing different in electrical potential increases delta G.
Bioenergetics of REDOX reaction
deltag = -nFdeltaE. n = number of electrons transfered F is faraday constant DeltaE is change in reduction potential in volts
holoenzyme
intact and activated complex of enzyme with coenzyme
High energy bonds
1)thioester bonds 2) phosphate bonds 2a) phsophoanhydride 2b) phosphoenolpyruvate 2c) phosphocreatine
how is gradient concentration related to bioenergetics
delta G is a function of the lob of [prod]/[reactants], generate more work by large gradient If you have more products than reactants, dG is positive If you have more reactants than products, dG is negative
how do enzymes lower activation energy?
Lock and key model is not a suitable model because TS has equally high energy Induced Fit: where enzyme is complimentary transition state to lower activation energy
Covalent catalysis
transient covalent bond forms between enzyme and substrate
Metal Ion Catalysis
bound metal ions help position substrate and can be driving force in REDOX reaction
when k’eq is <1
delta G is positive and favors reverse reaction
what do hydrolases do?
hydrolysis
Ligase
formation of bonds with ATP cleavage
