Lecture 3: Energy and Enzymes Flashcards
importance of enzymes
- speed up rates of chemical reactions
phosphatas
- an enzyme that catalyzes the reaction of PO3 from protein
what is energy and its types
energy: capacity to do work
kinetic: motion
potential: stores energy
other forms: electrical, thermal, mechanical, chemical
- energy has to be converted cant be destroyed
thermodynamics
study of energy and transformations
1) energy can be transformed, but not created nor destroyed: total energy in a system must be constant
2) total disorder of a system and surroundings increases: entropy is a measure of disorder
for example: ice is in order, ice lattice structure VS +heat= water when it has disorder
forms of systems
CLOSED: exchanges energy but not matter with surroundings
OPEN: exchanges energy and matter (OUR CELLS!)
ISOLATED: exchanges no energy and no matter
what is disorder
random motion
what form of energy is most often converted into
thermal:
random motion of molecules
increased heat, increases disorder
to go from order to disorder
ORDER (no input of energy)
DISORDER (requires energy)
ORDER-DISORDER: spontaneous
DISORDER-ORDERL requires energy
room analogy:
disorder(messy room) takes energy to clean up (order), but it seems to get messy again without much effort
Spontaneous reactions
- chemical or physical reactions which occur without an input of energy from the surroundings
- change in enthalpy (change in PE) and entropy (measure of disorder) contributes
When do reactions tend to be more spontaneous
when products have less PE than reactants
measured based on two criteria:
1) PE: putting in energy
2) DISORDER: H2O is more disordered than ice (change in entropy)
endothermic vs exothermic
endo: reactions that absorb energy
- more PE in products, absorb energy
ex. ice melting (energy content of water is greater than ice)
exo: reactions that release energy
- less PE in products, release energy
ex. combustion (release of heat makes it spontaneous)
free energy
portion of energy in system available to do work
Change in free energy (Gibbs free energy) will tell you if its spontaneous or not measured using
1) enthalpy (change in PE)
2) entropy (change in order)
negative delta G= spontaneous reaction
Stable vs unstable energy
UNSTABLE
- more free energy
- less stable (can be harnessed)
- greater work capacity
STABLE
- less free energy
- more stable
- less work capacity
- release of free energy can be used for work
Equilibrium
- maximum stability
- equilibrium point is reached when reactants are converted back to products and converted back to reactants at equal rates
equilibrium in living systems
- living systems are open
- free energy is negative (spontaneous)
- organisms reach equilibrium (free energy=0) when they die
thermodynamics and life
- life is highly ordered suggested that it goes against second law (disorder and spontaneous)
- living things bring in energy and matter to generate order
- organisms release heat and byproducts to increase disorder too, increase in entropy
cells create order but still follow second law of thermodynamics
metabolic pathways and reactions
- exergonic reaction: where G is negative because products contain less free energy than reactants
- endergonic reaction: where G is positive because products contain more free energy than reactants
EXERGONIC IS NOT EXOTHERMIC
ENDERGONIC IS NOT ENDOTHERMIC
exergonic vs endergonic
exergonic: free energy is released, products have less energy so its -G and spontaneous
endergonic: free energy is gained, products have more so +G and its not spontaneous
catabolism vs anabolism
catabolism: exergonic, breaking down
anabolism: endergonic, building up
ATP storage and what process will release free energy
- ATP hydrolysis releases free energy that can be used as a source of energy for the cell
- mostly stored in mitochondria
ATP regeneration
- atp used in coupling reactions must be REPLENISHED
- done by linking atp synthesis to catabolic reactions
- atp cycle: continue breakdown and re-synthesis of atp
what type of reaction is hydrolysis of ATP
- exergonic reaction
- it can be coupled to make endergonic reactions proceed spontaneously
REQUIRES ENZYMES
what can we do with spontaneous internal cellular reactions
- harness that energy to create ATP
ATP/ADP cycle
exergonic-catabolic
- reactions supply energy for endergonic reaction producing ATP
exergonic reaction
- hydrolyzing ATP
- provides energy for endergonic reactions in cell
breaking down atp
spontaneous
building atp
not spontaneous
the role of enzymes in biological reactions
a) activation energy=kinetic barrier
b) enzymes reduce activation energy to accelerate reactions
c) enzymes combine with reactants and are released unchanged
d) enzymes reduce the activation energy by inducing the transition state
relationship between the speed of a reaction and spontaneous reactions
unrelated
activation energy
- initial input of energy required to start rxn (even for spontaneous rxns)
transition state
- molecules that gain necessary activation energy occupy the transition state
problem using heat to speed up reactions
- can damage molecules and cells
biological catalysts
catalyst: chemical agent that speeds up rate of run without being part of the rcn
enzymes=catalysts
- increase rate by lowering activation energy
- don’t supply free energy
induced fit
- once a substrate binds to an enzyme, the enzyme will change its 3D shape
- enzyme is released unchanged
Catalytic cycle of enzymes
- enzymes are recycled
1) substrate binds to enzyme forming an enzyme-substrate complex, transition state is reached
TIGHT BINDING, NOT STABLE
between 1 and 2: hydrolytic reaction, -H2O
2) breakage of bond is catalyzed and products are released
3) enzyme can catalyze another reaction
cofactors
- inorganic ions/nonproteins necessary to help the enzyme catalyze its rxn
cofactors: metallic ions
coenzymes: organic cofactors (vitamins)
enzyme catalysis
during catalysis, the substrate and active site form an INTERMEDIATE TRANSITION STATE
1) brings substrate into close proximity
2) expose reactants to changed environments
3) change the shape of substrate
- charged a.a. can cause the reaction to move faster
what conditions and factors affect enzyme activity
1) influence of enzyme and substrate concentration
2) enzyme inhibitors
3) allosteric control (binding to enzyme not an active site, changing how it works +shape)
4) temperature and pH
enzyme and substrate concentrations
1) low enzyme concentration
- reaction rate slows
- enzymes and substrates collide infrequently
(linear, more proportional)
2) high enzyme concentrations
- enzymes become saturated with reactants
- rate of reaction levels off
(levels off, saturation point, enzyme binding sites are occupied and adding more substrate doesn’t affect rate of reaction)
enzyme inhibition
substances that slow down or stop enzymes from doing their job by either blocking the active site or binding somewhere else on enzyme
COMPETITIVE INHIBITORS
- inhibitor competes with normal substrate for active site
NONCOMPETITIVE INHIBITORS
- inhibitor doesn’t compete with normal substrate for active site, binds somewhere else
can be reversible or irreversible
Example of irreversible competitive inhibitor
penicillin: antibiotic
- inhibits enzyme (NEED SLIDE)
Futile cycle
- futile cycle:
two metabolic pathways run simultaneously in opposite directions
NO overall effect: waste of energy
Allosteric regulation
occurs with reversible binding to the allosteric site (outside of active site on the enzyme)
- high affinity: enzyme binds strongly (INCREASES RCN RATE)
- low affinity: enzyme binds weakly or not at all (LOWERS RCN RATE)
feedback inhibition
- product of enzyme catalyzed pathway acts as a regulator of the reaction
- helps conserve cellular resources
temperature and pH effects
- enzyme has optimal pH and temp effects
- as values fall above and below optimum, reaction rates fall off
pH:
- changes in pH affect the charged groups in a.a. of enzyme
temperature:
- temp increases, rate of rxn increases
- gets too high: denatures proteins, and reduces the rate of rxn by doing so
What is the second law of thermodynamics
- systems naturally progress towards increased entropy (disorder),
- meaning that energy tends to spread out and become less usable over time.
- Spontaneous reactions generally release energy (negative enthalpy) and increase disorder (positive entropy), which lowers Gibbs Free Energy (ΔG).
In simple terms, the universe favors chaos and energy dispersal.
What is the second law of thermodynamics
- systems naturally progress towards increased entropy (disorder),
- meaning that energy tends to spread out and become less usable over time.
- Spontaneous reactions generally release energy (negative enthalpy) and increase disorder (positive entropy), which lowers Gibbs Free Energy (ΔG).
In simple terms, the universe favors chaos and energy dispersal.
Increased disorder means what for the energy
Stable because it has a lesser work capacity
How is enzyme activity related to the futile cycle
We can regulate the speed to ensure 1 pathway is faster than the other so we aren’t losing cell material
cofactor vs coenzyme
coenzyme is a type of cofactor that is vitamins, coenzymes include metals
what is true about noncompetitive inhibition
the process changes the enzyme conformation
what is true about finding the same enzyme in different organisms
- enzymes from different organisms function best at their optimal pH and temperature
Instructors often mention ATP hydrolysis as the source of cellular reactions, why is this false
Water does not enter the active site of enzymes linked to ATP breakdown
what’s energy coupling
energy coupling is when the energy that comes from the breakdown of ATP into ADP that’s released in an exergonic reaction is used to drive an endergonic reaction
The closer G gets to 0, the
further the reaction will move to completion until equilibrium is established
the addition of an enzyme..
allows many more molecules to reach transition state
most inhibitor molecules are
toxic
- I.e. cyanide, penicillin (toxic for bacteria)
