Enzymes and Bioenergetics Flashcards
enzymes
catalysts that facilitate reactions in biological settings
consist of amino acids primarily
cofactors
non amino acid component often in conjunction with enzymes
inorganic product
coenzyme
non-amino acid component used with enzymes
organic
often derived from vital organic compounds obtained from vitamins
rate laws
experimentally determined, express reaction rate in terms of reactants concentration
rate =k[A]^m[B]^n
where m and n are reaction order
1st order reaction rate
rate = k[S]
depends on substrate concentration
occurs when km»[S]
zero order reaction rate
rate = k
does not depend on substrate concentration
occurs when excess substrate and limited enzymes
km<
noncompetitive inhibition
binds to allosteric sites, so doesn’t affect Km
however, less product will be made so decreases Vmax
will show on Lineweaver-Burk Plot as increased Y axis and no change in x axis
competitive inhibition
will competitively take over binding sites, so Km will increase (takes more to reach same level) = right shift
vmax not effected because Km can still overcome
uncompetitive inhibition
only binds to the enzyme-substrate complex
Km decreases at same rate as Vmax decreases
locks the enzyme in place so that the substrate can bind (decreasing Km) but won’t be able to make a product (decreasing Vmax)
Km and Vmax must decrease at the EXACT SAME rate -> will have same slope as uninhibited slope
left shift, upward shift
mixed inhibition
can bind to both enzyme or enzyme-substrate complex
Vmax decreases for both
binds allosterically
when binding to enzyme, will increase Km, when binding to enzyme-substrate complex, will decrease Km
catalytic efficiency
proportional to 1/slope of Lineweaver-Burk Plot
how effective an enzyme is at converting substrate to product. higher Kcat means increase turnover rate and lower km means higher binding affinity.
kcat/km
Mixed inhibitor binding to free enzyme
Km will increase because will take more to reach same level
Mixed inhibitor binding to ES complex
Km will decrease because inhibitor will hold enzyme in place for easier access of substrate
enzyme activity can be increased by
increasing Kcat which will increase Vmax
decreasing Km to reach rate more quickly
increase catalytic efficiency (kcat/km)
Kcat
turnover number = the number of times each enzyme site converts substrate to product per unit time
Vmax/[E]
calculating Vmax
Kcat[E]
concentration of enzymes x how fast enzymes are converting substrates to product / unit of time
Michaelis-Menten Equation
V0 = Vmax[S]/Km+[S]
Vmax = Kcat[E]
zymogens
enzyme in inactive form; must be altered by covalent modifications to become activated
hill coefficient
quantitative measurement of cooperativity
n>1 cooperative -> sigmoidal shape
n=1 not cooperative -> hyperbolic shape
n<1 negative cooperativity
protease
type of hydrolase that uses water to break peptide bond
R-state binding
relaxed state has higher affinity for binding
high cooperativity
T-state binding
tense state has low affinity for binding
low cooperativity
effects on reaction of a deleterious mutation in an ezyme
increase activation energy
decrease reduction rate
no change to gibbs free energy or equilibrium constant
increase K and Kcat
decrease catalystic efficiency (kcat/Km) and decrease Vmax
lock and key theory
proposes the enzyme’s active site is already in the proper structural conformation to allow a substrate to bind readily and form an ES complex
no conformation changes are necessary for catalysis to occur
induced fit model
conformation change is induced when the substrate binds the active site, resulting in a formation of a functional ES complex that is said to be in the induced form
binding is highly specific and the conformational change requires energy input
apoenzyme
enzymes that require a cofactor and the cofactor is absent
holoenzymes
enzymes that require a cofactor and the cofactor is present
entropy
the measure of disorder within a system
+ delta S = increased disorder
hydrophobic molecules interacting with water
they cannot hydrogen bond with water so water molecules will hydrogen bond with themselves and so they form a rigid, highly ordered network called the solvation layer aroud hydrophobic molecules
this decreases entropy - which is why hydrophobic molecules fold to decrease surface area and hide hydrophobic residues, increasing entropy (disorder)
hydrophilic molecules interacting with water
they can hydrogen bond with water and will do so
formation of solvation layers is unnecessary
entropy is increased
what amino acids can act as nucleophiles?
amino acids containing thiol (-SH) or hydroxyl (-OH) groups
most common are cysteine and serine
nucleophiles want to give up electrons so are very attracted to positive charge of atomic nuclei
the greater the negativity, the stronger the nucleophile
What will increase the nucleophilicity of cysteine?
deprotonation of cysteine results in a negatively charged sulfur which enhances its nucleophilicity
transmembrane domain
contains phopholipid bilayers with hydrophilic head groups facing aqueous environment and hydrophobic tails facing inward
only membrane spanning protein domains containing hydrophobic residues are thermodynamically stable because hydrophilic amino acid residues will interact unfavorably with hydrophobic phospholipid tails
transmembrane protein
contains hydrophobic transmembrane domains composed of largely non-polar amino acids. They interact favorably with hydrophobic tails of phospholipids in cellular membranes
Specific binding
some enzymes are highly specific for a particular substrate
demonstrate high reaction rates with substrate of interest but not with any other molecules
Equation for Vo
Vo = Kcat[E][S]/Km+[S]
Kcat[E] = Vmax so
Vo = Vmax[S]/Km+[S]
fructose 2,6 biphosphate
activated by insulin, can activate phosphofructokinase 1 which turns fructose 6 phosphate into fructose 1,6 phosphate even there is enough ATP that the forward reaction is inhibited
