Kine 324 exam 1
enzyme synthesis
(copy) transcriptional control: gene expression limiting pretransitional control: limitation at ribosome amino acid-->enzyme protein
redox potential
-a measure of electrical driving force -the tendency for electrons to move in a particular direction -oxidation-reduction potential (redox potential) is analogous to chemical Keq values -a driving force exists between the fuel electrons and oxygen -carbohydrate and fat are highly reduced (electron rich) -oxygen is electron poor -oxygen readily accepts the electrons from fuels -energy released as the electrons go down the electrical (redox) prudent is used to synthesize ATP -redox potential can be quantified in the lab
laws of thermodynamics
E in=E out (work) + E (heat) +/- E stored (fat)
equilibrium constant (Keq)
Keq is a measure of the tendency of a rxn to proceed. the greater the Keq, the greater the "chemical pressure" of the rxn Keq=products/reactants more negative Keq, more likely rxn to occur
enzyme regulation
catalytic does the work. cant work closed, add phosphate through kinase to open up catalytic to do work. phosphotase takes phosphate. -hexokinase: muscle -glucokinase: liver
2 basic mechanisms to regulate enzyme activity
chronic- enzyme amount: train to get more enzyme to work more quickly acute-catalytic efficiency Q10 of an enzyme=factor by which the Vmax of an enzyme changes for every 10*C change in temp ex: Q10= 20 when increasing T from 25-35*C will double Vmax
enzyme inhibition
competing for same binding site. more ethanol competing that methanol
regulation of enzyme amount
constitutive enzymes inducible enzymes
strong bonds
covalent bonds- shared electrons -peptide- responsible for 1 structure -disulfide- formed by 2 residues, 2 structure
first order rxn are
dependent on substrate concentration
ATP supply vs ATP demand
dependent upon -coordination of fuel type -utilization -fiber type recruitment -regulation of ATP demand: cell will not let itself run out of ATP
^Eh
driving force for electrons to move down the electron transport chain -NADH releases 2 electrons to become NAD+ and the 2 electrons turn 1/2 O2 into H2O
thermodynamics
energy change: ^E entropy change: T^S (disorder) enthalpy: ^H (heat) free energy: ^G (energy free to do work)
^G= -nF^Eh
energy made available when electrons go down an electrical gradient is given by the product of: the size of the electrical gradient(^Eh) the number of electrons going down the gradient(n) and a proportionality constant (F) to express the energy made available in calories
exergonic rxns liberate
energy while endergonic rxns require energy input
heat and temp mechanical application
engines use the heat to convert to mechanical energy
enzyme activity depends on
enzyme amount catalytic efficiency
enzymes reduce activation energy
enzyme catalysis reduces the activation energy of a rxn ^G of rxn is not affected by catalysis path of rxn is changed by catalysis, but not initial and final states
open thermodynamic system
exchange both matter and energy equilibrium thermodynamics do not apply -flow of matter and energy across boundaries precludes attainment to true equilibrium
structural protein
fibrous proteins. operates like the structural element of cells instead of acting like and enzyme
disulfide bond
formed when 2 polypeptide chains are covalently linked by cystine side chains (R groups)
reversible rxn
forward rate v=k1[A] backward rate v=k-1[B]
enzyme degradation
gene-->protein enzyme protein-->amino acids a specific enzyme changes the structure of the neurotransmitter so it is not recognized by the receptor. For example, acetylcholinesterase is the enzyme that breaks acetylcholine into choline and acetate.
exergonic rxns
gives up energy activation energy
energetic equivalent per L O2
glucose has more energy per L of O2
heat and temp biological application
heat is a useless byproduct
modulation by effectors
hexokinase by glucophosphate short term, positive or negative regulation w/n given metabolic pathway between 2 pathways product inhibition: citrate inhibits citrus kinase freeforward regulation
weak bonds
hydrogen-responsible for 2, 3, and 4 structure hydrophobic- formed by nonpolar side chains, assist in 3 structure electrostatic- salt bonds formed by ionized R group, 4 structure
energy systems contribution over time
immediate: immediate high contribution lasting very little time nonoxidative: high contribution lasting fair amount of time oxidative:beginning low contribution works to high and stays high overtime
^Eh is
index of electron affinity
Q10 effect
is a measure of the temperature dependence of enzyme activity
Gibbs free energy
isolated system: driving force for a rxn is an increase in S magnitude of driving force for rxn is given by: ^G=-T^S
enzymes
large biological molecules responsible for thousands of metabolic processes sustaining life. highly selective catalysts. greatly accelerate rate and specificity of metabolic reactions
inducible enzyme
levels fluctuate according to environmental demand, i.e. alcohol dehydrogenase as you ingest alcohol, enzymes are built high energy expense for body to maintain high levels of enzymes training: mitochondria, don't use it ya lose it, same for enzymes
catalytic site
location on enzyme where substrates bind and chemical transformation occurs
^G=^H-T^S
magnitude of ^G is a measure of the 'push' of the rxn
constitutive enzyme
maintained at relatively stable levels not responsive to environmental stimuli, i.e. exercise training
ATP utilization end
mechanisms to protect against degradation of energy homeostasis
ATP production end
metabolic source muscle fiber recruitment (small-large) nonoxidative vs oxidative muscle fiber recruitment small=oxidative 1st recruited don't want to break down fat w/o being able to use it fuel must be appropriately integrated
catalyst
molecule that participates in and undergoes physical change then reverts to original form when rxn is complete -organic molecules are highly unreactive
lipid stores
more energy per unit mass while carbohydrate yields more energy per L O2 consumed
energy metabolism
must be matched
isolated thermodynamic system
no exchange of either matter or energy with surroundings thermodynamically represent a micro universe ex: ideally insulated thermos bottle
closed thermodynamic system
no exchange of matter energy is exchanged ex: hot water bottle
rxn rate depends
on frequency and energy collisions
kinase
phosphorolates adds phosphate
covalent modification
phosphrylation long term, positive or negative
modulators
positive or negative internal -often products of the pathways, typically negative external -often products f the pathways or hormones
catalytic efficiency is
positively and negatively affected -covalent modificatin, product inhibition -modulated rxnz/steps are early in metabolic pathways
protein structure
primary structure(1) -amino acid sequence secondary structure (2) -shape of the amino acid sequence tertiary structure(3) -folding of single polypeptide chain quaternary structure (4) -2 or more polypeptide chains united by weak bonds
free energy related to Keq
products/reactants
complex protein
protein containing a simple protein and at least one molecule of another substance
first order rxn
rate is linerly dependent on S -rate= k[A] k is rate constant
critical importance to energy metabolism
rate of ATP production must precisely match ATP utilization
rxn rate of enzyme-catalyzed rxn
rate of product formation (rate of run) given by: v=k2[ES] problem: we can't know k2 of [ES] solution:Km=(k-1+k2)/k1 v=velocity result:mechaelis-menton equation v=(Vmax[S])/(Km+S)
kinetic theory of rxn
rate of rxn depends on: frequency of collisions energy of collusions (to overcome energy of activation)
phosphotase
removes phosphate
endergonic rxn
requires energy
lohmann reaction
reversible rxn, catalysed by creatin kinase, in which ATP and creatine are formed from ADP and phosphocreatine
^G=0
rxn is at equilibrium
zero order rxn
rxn rate is independent of substrate independent of A
^G>0
rxn will not proceed spontaneously
^G<0
rxn will proceed spontaneously
transport protein
serves function of moving other materials within an organism
allosteric sites
sites on the enzyme where specific molecules may bind resulting in a modification of the change in the catalytic efficiency
properties of enzymes
specificity: an enzyme catalyzes only one reaction coenzymes -nonprotein organic molecules -holoenzyme= apoenzyme + coenzyme -bound covalently or noncovalently -NAD, FAD, TPP, Pyridoxal phosphate -are co-substrates
bioenergetics
study of energy transfer in biology energetics=thermodynamics
michaelis-menton kinetics demonstrate
substrate dependence, as well as saturation -Vmax is the maximum velocity of a run -Km indicates the affinity of an enzyme for a substrate
flux generating step
substrate saturated ([S]>>Km) origin of carbon flow, but not necessarily rate-controlling can be glycogen or glucose
enzyme amount depends on
synthesis and degradation (turnover of proteins) -transcriptional control
basic structure of thermodynamics
system= compartment under consideration surroundings=everything outside of system system+surroundings=universe only concerned with energy change(^E or ^H)
reduction
the addition of electrons
oxidation
the removal of an electron
hydrogen bonds
the sharing of an H atom between N and carbonyl oxygen of different peptide bonds in the same or different peptide chains
Actual redox potential, ^Eh, of a redox couple
-actual redox potential must take into account the concentrations of reduced and oxidized species -actual redox potential at pH 7: Eh= Em + (2.3RT/nF) log(ox/red) Em:midpoint F: faraday constant= 23.062 n= # e- transferred
usefulness of bioenergetics
-calculation of the energy change allows quantification of useful work that can be done -calculation of thermodynamics efficiency -id of allowable vs impossible rxnx/mechs/stoichiometries -gluconeogenesis via the reversal of the pyruvate kinase reaction -stoichiometry of ATP production/fuel utilization -nonequilibrium (irreversible) thermodynamics -allow calcs of rate of energy flow
1st law of thermodynamics
-conservation of energy in the universe -forms of energy can be transducer -chemical=ATP, food -electrical=neurons -mechanical=muscle -thermal=heat generation -energy transduction has quantitative correspondence -mechanical eqivalent of heat is 4.18 J/cal -heat changes and chemical runs -heat evolved in run establishes upper limit to the amount of work the rxn can perform -heat is easily measured -standard conditions -25*C -1 atm -pH 7.0
remember 1st law of thermodynamics
-energy is neither created nor destroyed -energy may be transduced
catalytic and allosteric sites of enzymes
-formed by tertiary and or quaternary structure
^G
-probability of a rxn to occur -different forms of ^G -can be calculated from the ratios of products and reactants -^G can be calculated from ^Eh -differnet forms of ^G inter-related -change in one form affects value in other form
general order of rxn
A--->B
^Eh is potential diff between 2 redox couples
^Eh= Eh(e- acceptor) - Eh(e-donor)
different forms of ^G
^G itself: -available energy change in chem runs -ex: energy changes in -rxns of glycolytic pathway -hydrolysis/synthesis of ATP (^G ATP) ^E-redox potential change -available energy changes in runs involving the transfer of electrons -ex: energy changes in -electron transfer rxns of electron transport chain ^u- electrochemical potential of an ion across a gradient -available energy change in the flux of an ion across a gradient -ex: energy changes in -Ca2+ flux across the SR membrane -proton flux across the inner mitochondrial membrane
calculating actual ^G'
^G'=^G*'+2.3RT log r
standard free energy (^G*') and Keq
^G*'= -RT ln Keq ^G*'= -(2.3)RT log Keq R=1.987 cal/deg mol
each energy system has
a different capacity and rate of ATP production fastest is creatine phosphate
simple protein
a protein that only yields amino acids when hydrolyzed
catalysis
acceleration of chemical reactions
enzymes reduce
activation energy
Michaelis constant
affinity enzyme has for a substrate Km Km is concentration of S at 1/2 the max enzyme velocity STUDY SLIDE
catalytic efficiency
amount of substrate