Energy and Enzymes, E1 Flashcards
Energy definition; Biologically, Different forms
Ability to do work; (biology) ability to cause some kind of change. Different forms, for example: light, heat, and electrical energy
Kinetic energy; Thermal energy…relation to Kinetic E; Average thermal energy of a group of molecules is called…; Thermal energy transferred between 2 objects is known as…
KE: energy from an object’s motion.
Thermal E: type of kinetic E where the energy is associated with constant, random bouncing of atoms or molecules.
The greater the thermal energy, the greater the kinetic energy of atomic motion, and vice versa.
The average thermal energy of a group of molecules is called TEMPERATURE, and when thermal energy is being transferred between two objects, it’s known as HEAT.
Potential energy; Chemical energy
Energy conversions
Energy is never lost, and an object’s energy can be converted from one form to another
PE: object has the potential to move and to have kinetic energy; the energy associated with an object because of its position or structure.
CE: a type of potential energy and is the energy stored in chemical bonds
Energy conversions: An object’s E can be converted from one form to another. Energy can change forms in a similar way in living organisms. For instance, energy stored in bonds of the small molecule ATP (potential energy) can power the movement of a motor protein and its cargo along a microtubule track, or the contraction of muscle cells to move a limb (kinetic energy).
Gibbs free energy (G); ΔG simple equation; What does the ΔG tell us?; ΔG equation with enthalpy, temperature, and entropy???
Must make assumptions (constant temperature and pressure)
Gibbs free energy (G) of a system is a measure of amount of usable energy that can do work (in that system).
The change in Gibbs free energy:
ΔG=Gfinal–Ginitial
ΔG tells us maximum usable energy released (or absorbed) in going from the initial to the final state and its sign (positive or negative) tells us whether a reaction will occur spontaneously ( without added energy)
ΔG with enthalpy (H) and entropy (S)
ΔG=ΔH−TΔS
Enthalpy; What is it?; Negative sign means…-; Positive sign means…+
∆H is the enthalpy change.
Enthalpy in biology refers to energy stored in bonds, and the change in enthalpy is the difference in bond energies between products and reactants.
A negative ∆H means heat is released in going from reactants to products, while a positive ∆H means heat is absorbed. (This interpretation of ∆H assumes constant pressure, which is a reasonable assumption inside a living cell).
Entropy; what is it?; Positive sign means…; Example for positive; Negative sign means…
∆S is the entropy change of the system during the reaction.
If ∆S is positive, the system becomes more disordered during the reaction (for instance, when one large molecule splits into several smaller ones).
If ∆S is negative, it means the system becomes more ordered.
Temperature (K) determines the relative impacts of the…; The higher the temperature, the greater the impact of the…
Temperature (T) determines the relative impacts of the ∆S and ∆H terms on the overall free energy change of the reaction.
(The higher the temperature, the greater the impact of the ∆S term relative to the ∆H term.)
Negative deltaG means and relation to energy; Positive deltaG means and relation to energy
Reactions with a negative ∆G release energy, which means that they can proceed without an energy input (are spontaneous).
Reactions with a positive ∆G need an input of energy in order to take place (are non-spontaneous).
not super pertinent…..When a reaction releases heat (negative ∆H) or increases entropy of system, these factors make ∆G more negative. On the other hand, when a reaction absorbs heat or decreases the entropy of the system, these factors make ∆G more positive.
Exergonic reactions; Relation to deltaG; Relationship between reactants and products involving free energy; Called spontaneous reactions, why?
Reactions that have a negative ∆G release free energy and are called exergonic reactions.
A negative ∆G means that the reactants, or initial state, have more free energy than the products.
Exergonic reactions are called spontaneous reactions because they can occur without addition of energy.
Endergonic reactions; Relation to deltaG; Relationship between reactants and products; involving free energy; Called non-spontaneous reactions, why?
Reactions with a positive ∆G (∆G > 0) require an input of energy and are called endergonic reactions.
The products, or final state, have more free energy than the reactants, or initial state.
Endergonic reactions are non-spontaneous and need added energy before they can proceed.
not supes important but…You can think of endergonic reactions as storing some added energy in higher-energy products they form.
What does the rate of reaction depend on?
What does spontaneity depend on?
The rate of a reaction depends on the path it takes between starting and final states, while spontaneity is only dependent on the starting and final states themselves.
standard free energy change (∆Gº’) definition;
What are the standard conditions for biochemical reactions?
Compare conditions inside a cell or organism with standard conditions
The standard free energy change (∆Gº’) of a chemical reaction is the amount of energy released in the conversion of reactants to products under standard conditions.
For biochemical reactions, standard conditions are generally defined as 25°C (298K), 1 M concentrations of all reactants and products, 1 atm, and 7.0 pH.
The conditions inside a cell or organism can be very different from these standard conditions, so ∆G values for biological reactions in vivo may vary widely from their standard free energy change (∆Gº’) values. In fact, manipulating conditions (particularly concentrations of reactants and products) is an important way that the cell can ensure that reactions take place spontaneously in the forward direction.
Chemical equilibrium; Relationship between forward and reverse reactions; At equilibrium, what type of energy state is an reaction system in?; What happens if a reaction is not at equilibrium? And why does this happen?
A chemical equilibrium is when forward and reverse reactions take place at the same rate. Both reactions occur but the overall concentrations of products and reactants no longer change.
At equilibrium, the reaction system is in its lowest-energy state possible (has the least possible free energy).
If a reaction is not at equilibrium, it will move spontaneously towards equilibrium, because this allows it to reach a lower-energy, more stable state. This may mean a net movement in the forward direction, converting reactants to products, or in the reverse direction, turning products back into reactants.
What happens to the free energy of the system as the reaction moves towards equilibrium?
What happens when the reactions moves away from equilibrium?
As the reaction moves towards equilibrium (as the concentrations of products and reactants get closer to equilibrium ratio), the system’s free energy gets increasingly lower. A reaction at equilibrium can no longer do any work because the free energy of the system is as low as possible.
Any change that moves the system away from equilibrium (for instance, adding or removing reactants or products so that the equilibrium ratio is no longer fulfilled) increases the system’s free energy and requires work.
Cells in isolated systems…relation to equilibrium; Good or bad?; Free energy and work?
If a cell were an isolated system, its chemical reactions would reach equilibrium, which would not be a good thing.
The cell would die because there would be no free energy to perform work needed to keep it alive.
How do cells stay out of equilibrium?
- Importing reactants
- Exporting products
- Chemical reactions into metabolic pathways…
What happens in cases where there are high concentrations of reactants and/or products?
Cells stay out of equilibrium by manipulating concentrations of reactants and products to keep their metabolic reactions running in the right direction.
For instance:
- They may use energy to import reactant molecules (keeping them at a high concentration).
- They may use energy to export product molecules (keeping them at a low concentration).
- They may organize chemical reactions into metabolic pathways, in which one reaction “feeds” the next.
Providing a high concentration of a reactant can “push” a chemical reaction in the direction of products (that is, make it run in the forward direction to reach equilibrium). The same is true of rapidly removing a product, but with the low product concentration “pulling” the reaction forward. In a metabolic pathway, reactions can “push” and “pull” each other because they are linked by shared intermediates: the product of one step is the reactant for the next
What is ATP? What can it be thought of? What does hydrolysis do?
ATP’s structure?; Labelling of three phosphate groups
Why is ATP unstable because of the phosphate groups?
Phosphoanhydride bonds
ATP is a small and relatively simple molecule. Can be thought of as the main currency of cells (like MONEYYY). Hydrolysis breaks down ATP and ATP is then used to power many energy-requiring cellular reactions.
Structurally, ATP is an RNA nucleotide with a chain of 3 phosphates. At the center of the molecule lies a five-carbon sugar ribose, which is attached to the nitrogenous base adenine (of RNA) and to the chain of three phosphates.
The three P groups, in order of closest to furthest from the ribose sugar, are labeled alpha, beta, and gamma.
ATP is made unstable by the 3 adjacent “-“ charges in its phosphate tail because they “want” to get away from each other. The bonds between phosphate groups are called phosphoanhydride bonds and may be referred to as “high-energy” bonds.
Why are phosphoanhydride bonds considered _-energy?
What is Hydrolysis?; Equation
Why is the regeneration of ATP necessary?; Equation
Free energy release
-Standard versus non-standard conditions
Because they have an appreciable amount of energy released when one of the phosphoanhydride bonds is broken through hydrolysis. Like when ATP is hydrolyzed to ADP.
Hydrolysis is a water-mediated breakdown.
ATP+H2 O↔ADP+Pi+energy
Regeneration of ATP necessary because ATP is quickly hydrolyzed=used up
energy+ADP+Pi↔ATP+H2O
Under standard conditions: -7.3kcal/mol or -30.5kJ/mol buut 1M, 25 celsius, 7pH
Nonstandard conditions: hydrolysis of 1 mole of ATP in a living cell is almost double the value at standard conditions (ex. ~14kcal/mol or -57kJ/mol)
Reaction coupling; Shared intermediate
Under what condition can two reactions be coupled?!
What happens to the intermediate during reactions?
Reaction coupling is a strategy that cells use to directly link an energetically unfavorable reaction with an energetically favorable reaction (like ATP hydrolysis). This linking is often through a shared intermediate, where the product of one reaction is “picked up” and used as a reactant in the second reaction.
Reactions can be coupled as long as the overall deltaG value is NEGATIVE!
The intermediate does NOT appear in the overall coupled reaction because it appears as both a product and react so they cancel out.
ATP in reaction coupling; Shared intermediate
Does the addition of a phosphate group from an ATP make a molecule more energetically favorable or unfavorable and relatively stable or unstable? WHY?
When reaction coupling involves ATP, the shared intermediate is often a phosphorylated molecule (a molecule to which one of the phosphate groups of ATP has been attached).
When a phosphate group is transferred from ATP to glucose, forming a phosphorylated glucose intermediate (glucose-P), this is an energetically FAVORABLE (energy-releasing) reaction because ATP is so unstable, i.e., really “wants” to lose its phosphate group.
Different types of reaction coupling in the cell:
ATP hydrolysis coupled to a biosynthetic reaction. Sodium-potassium pump
It’s energetically unfavorable to move Na+ out of, or K+, into, a typical cell, because this movement is against the concentration gradients of the ions.
ATP provides energy for the transport of sodium and potassium by way of a membrane-embedded protein called the sodium-potassium pump (Na+/K+ pump).
In this process, ATP transfers one its P groups to the pump protein, forming ADP and a phosphorylated “intermediate” form of the pump. The phosphorylated pump is unstable in its original conformation, so it changes shape, opening towards the outside of the cell and releasing Na+ outside. When extracellular K+ bind to phosphorylated pump, they trigger the removal of the P group, making the protein unstable in its outward-facing form. The protein will then become more stable by returning to its original shape, releasing the K+ inside the cell.
Activation energy definition;
Activation energy (EA): is kind of like that “hump” you have to get over to get yourself out of bed. E-releasing (exergonic) reactions require some amount of E input to get going, before they can proceed with their E-releasing steps. This initial energy input, which is later paid back as the reaction proceeds, is called the activation energy and is abbreviated EA.
Transition state;
Is EA always positive or negative here?
Transition state is an unstable state that a molecule is contorted/deformed/bent into in order to get the bonds into a state that allows them to break, so that the new bonds from products can form to allow reactions to take place.
EA is always POSITIVE; it does not matter whether a reaction is endergonic or exergonic overall.
Typical activation energy source?
-What does this cause?
The source of activation energy is typically heat, with reactant molecules absorbing thermal energy from their surroundings.
This thermal energy speeds up the motion of reactant molecules, increasing frequency and force of their collisions, and also jostles the atoms and bonds within the individual molecules, making it more likely that bonds will break. Once a reactant molecule absorbs enough energy to reach the transition state, it can proceed through the remainder of the reaction.
