class 12 - capturing + using energy 2

system

object of study (ex: a cell, body, ecosystem)

• note: bio always has open systems- exchange of matter and energy with their surroundings

first law of thermodynamics

law of conservation energy

• energy can’t be created nor destroyed

• can be transferred

• total amount of energy is always the same

second law of thermodynamics

• total disorder/entropy of a reacting system increases with every reaction

• energy available to do work decreases every time energy changes form (because energy transformations are never 100% efficient)

  • ex: during a reaction, you lose thermal energy, increasing entropy due to increased random molecular movement

spontaneous

if you left the reactants alone for long enough, you would eventually get the product

non-spontaneous

you can leave the reactants together for an infinite amount of time, but they will not turn into product

Gibbs free energy equation

ΔG = ΔH - TΔS

• ΔG = Gibbs free energy = energy available to do work

• ΔH = enthalpy

• T = temperature (because temperature influences reaction spontaneity)

• S = entropy

enthalpy

• total amount of energy in the system

which is more likely to be spontaneous: -ΔH or +ΔH?

-ΔH is more likely to be spontaneous as it indicates a release of energy from the system, favoring reaction spontaneity.

-ΔH = reactants have more potential energy than products, releases energy

+ΔH = products have more potential energy than reactants, gains energy

• -ΔH is more likely to be spontaneous as a release of energy is favored, as the system would be moving toward a lower-energy, more stable state

entropy

measure of disorder or randomness in a system

which is more likely to be spontaneous: -ΔS or +ΔS?

-ΔS = reactants are more disordered

+ΔS = products are more disordered

• +ΔS is more likely to be spontaneous, as system will favor becoming more disordered

+ΔG: is it ender/exergonic? is it spontaneous or not spontaneous? what would the graph look like?

+ΔG = endergonic, not spontanous

• products have more free energy than reactants

• not spontaneous as reaction requires a sustained input of energy

  • think about it as you can’t go up a hill without adding energy

-ΔG: is it ender/exergonic? is it spontaneous or not spontaneous? what would the graph look like?

-ΔG = exergonic, spontaneous

• reactants have more free energy than products

• reaction releases energy (think of exo = exit)

relationship between spontaneity and speed of reaction

spontaneous does not mean fast reaction! they are unrelated.

what would happen if you didn’t have enough ATP for an endergonic reaction?

the reaction wouldn’t get to the final product, because there isn’t enough accessible energy to power the reaction

what would happen if you didn’t have enough ATP for an exergonic reaction?

the reaction could still proceed, but it may not be as efficient or may occur at a slower rate

-ΔH

negative enthalpy change

• reactants → products release energy

• reactants have more potential energy, products have less potential energy

• favors spontaneity 

+ΔH

positive enthalpy change

• products have more potential energy

• reactants → products gains energy

• does not favor spontaneity

-ΔS

negative entropy change

• reactants are more disordered

• reactants → products, system becomes more ordered

• does not favor spontaneity 

+ΔS

positive entropy change

• products are more disordered

• reactants → products, system becomes more disordered

• favors spontaneity

-ΔH, -ΔS

• spontaneous at low temperatures

• non spontaneous at high temperatures

• enthalpy and entropy changes

+ΔH, -ΔS

nonspontaneous at all temperatures

-ΔH, +ΔS

spontaneous at all temperatures

+ΔH, +ΔS

• spontaneous at high temperatures

• nonspontaneous at low temperatures

exergonic

requires energy to form bonds (ex: dehydration synthesis), proceeds spontaneously (-ΔG)

endergonic

releases energy when breaking bonds (ex: ATP hydrolysis), not spontaneous (+ΔG)

energetic coupling

• the driving of a non spontaneous reaction (-ΔG) by a spontaneous reaction (+ΔG)

• pairs ATP hydrolysis (spontaneous exergonic) with nonspontaneous endergonic reaction

coupled reaction

a +ΔG reaction (endergonic) is paired with a -ΔG reaction (exergonic). If the total ΔG is negative (exergonic, spontaneous), then the coupled reaction will occur together spontaneously

ATP hydrolysis

ATP + H2O → ADP + Pi + energy

• goes from less stable ATP to more stable ADP

• exergonic process

enzyme

protein based, made of amino acids

acts as a catalyst to accelerate the rate of a chemical reaction by lowering the activation energy (E_A) of a reacting system and stabilizing the transition state of reactants

activation energy (E_A)

energy input necessary to reach transition state

transition state

the hump that reactants have to get over to make the product

• the brief time in a chemical reaction where the reactant’s bonds are broken and product’s bonds are formed

when are enzymes good?

enzymes are useful because they are able to speed up reactions under mild conditions, so you don’t have to add heat and accidentally denature a molecule.

additionally, they don’t get consumed in the process

substrate

the reactant in an enzyme-catalyzed reaction

process of a substrate being catalyzed by an enzyme

1. enzyme is separate from substrate

2. enzyme-substrate complex - substrate binds to enzyme

3. enzyme-product complex - enzyme sonverts substrate

4. product is released, enzyme remains unchanged

catabolism

breaks down molecules into smaller units

• released energy is used to product ATP from ADP and Pi

anabolism

builds molecules from smaller units

• requires energy input

chemical equilibrium

rate of forward reaction = rate of reverse reaction

• the concentration of reactants and products don’t change 

describe how enzyme structure is related to function

enzyme’s tertiary structure determines shape of active site

• altering tertiary structure (ex: by pH, heat, denaturation) → active site may change shape, so substrate may no longer be able to bind properly, blocking reaction

enzyme’s relationship with spontaneity

enzyme’s don’t change the ΔG of the reaction

cofactor

enzymes don’t always work alone, they sometimes use a cofactor

• cofactor- non-protein, non substrate molecule helps enzyme activity

active site

location on enzyme where substrate binds

allosteric site

the place on an enzyme that a molecule (not a substrate) binds to inhibit or stimulate enzyme activity

competitive inhibition

• inhibitor binds to active site

• blocks substrate from binding

• direct competition with substrate

non-competitive inhibition

• inhibitor binds elsewhere on enzyme (not active site), such as allosteric site

• changes enzyme shape → prevents substrate binding or conversion

• substrate may still bind, but cannot be converted into product

what factors speeds up a reaction?

• increasing presence of enzyme activity/number of enzymes

• lower E_A

• increasing temperature to a certain point (avoiding denaturing)

• increasing substrate concentration until Vmax

• adding cofactors

what factors slows down a reaction?

• decreasing heat = decreased rate

• extreme temperatures (too high temperature → denaturation)

• competitive / non-competitive inhibition (reversible vs irreversible)

• pH out of enzymes range

• mutation (impacts primary structure)

impact of enzyme denaturation

changing enzyme structure changes enzyme function - enzyme may no longer bind

Michaelis-Menten plot

• shows enzyme kinetics

• as substrate increases, reaction rate reaches Vmax (maximum velocity)

on a Michaelis-Menten plot, how do you increase the rate beyond Vmax?

• you must increase the enzyme concentration

Vmax

maximum reaction rate (all active sites developed) possible with given amount of enzymes

• you know when you are at Vmax because the line flattens out

Km

substrate concentration at ½ Vmax

• indicator of enzyme-substrate affinity

what does a low Km mean?

• the substrate saturates quickly, since a low Km means that the enzyme reaches half of its Vmax at a lower substrate concentration

• Therefore, it doesn't need much substrate to saturate, indicating high enzyme and substrate affinity

what does a high Km mean?

• the substrate doesn't saturate quickly, indicating that a higher concentration of substrate is required to reach half of its Vmax

• This suggests a lower affinity between enzyme and substrate, and that it would take longer to saturate

what does competitive inhibition do on a Michaelis Menten plot:

competitive inihibition - increases Km (needs more substrate), Vmax changed

• Km is increased because you can’t outcompete a competitive inhibitor

what does noncompetitive inhibition do on a Michaelis Menten plot:

decreases Vmax (less overall activity), Km unchanged

• Km is unchanged because substrate can still bind, but inhibitor prevents reaction from flowing