Energy and Enzymes, E1

Question 1

Energy definition; Biologically, Different forms

Answer 1

Ability to do work; (biology) ability to cause some kind of change. Different forms, for example: light, heat, and electrical energy

Question 2

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…

Answer 2

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.

Question 3

Potential energy; Chemical energy

Energy conversions

Energy is never lost, and an object’s energy can be converted from one form to another

Answer 3

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).

Question 4

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)

Answer 4

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

Question 5

Enthalpy; What is it?; Negative sign means…-; Positive sign means…+

Answer 5

∆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).

Question 6

Entropy; what is it?; Positive sign means…; Example for positive; Negative sign means…

Answer 6

∆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.

Question 7

Temperature (K) determines the relative impacts of the…; The higher the temperature, the greater the impact of the…

Answer 7

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.)

Question 8

Negative deltaG means and relation to energy; Positive deltaG means and relation to energy

Answer 8

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.

Question 9

Exergonic reactions; Relation to deltaG; Relationship between reactants and products involving free energy; Called spontaneous reactions, why?

Answer 9

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.

Question 10

Endergonic reactions; Relation to deltaG; Relationship between reactants and products; involving free energy; Called non-spontaneous reactions, why?

Answer 10

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.

Question 11

What does the rate of reaction depend on?

What does spontaneity depend on?

Answer 11

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.

Question 12

standard free energy change (∆Gº’) definition;

What are the standard conditions for biochemical reactions?

Compare conditions inside a cell or organism with standard conditions

Answer 12

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.

Question 13

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?

Answer 13

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.

Question 14

What happens to the free energy of the system as the reaction moves towards equilibrium?

What happens when the reactions moves away from equilibrium?

Answer 14

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.

Question 15

Cells in isolated systems…relation to equilibrium; Good or bad?; Free energy and work?

Answer 15

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.

Question 16

How do cells stay out of equilibrium?

1. Importing reactants
2. Exporting products
3. Chemical reactions into metabolic pathways…

What happens in cases where there are high concentrations of reactants and/or products?

Answer 16

Cells stay out of equilibrium by manipulating concentrations of reactants and products to keep their metabolic reactions running in the right direction.

For instance:

1. They may use energy to import reactant molecules (keeping them at a high concentration).
2. They may use energy to export product molecules (keeping them at a low concentration).
3. 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

Question 17

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

Answer 17

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.

Question 18

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

Answer 18

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+H​2​ O↔ADP+P​i+energy

Regeneration of ATP necessary because ATP is quickly hydrolyzed=used up
energy+ADP+Pi↔ATP+H​2O

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)

Question 19

Reaction coupling; Shared intermediate

Under what condition can two reactions be coupled?!

What happens to the intermediate during reactions?

Answer 19

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.

Question 20

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?

Answer 20

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.

Question 21

Different types of reaction coupling in the cell:

ATP hydrolysis coupled to a biosynthetic reaction. Sodium-potassium pump

Answer 21

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.

Question 22

Activation energy definition;

Answer 22

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.

Question 23

Transition state;

Is EA always positive or negative here?

Answer 23

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.

Question 24

Typical activation energy source?

-What does this cause?

Answer 24

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.

Question 25

Relationship between activation energy and its rate?; Higher the EA….Why?

Answer 25

The EA of a chemical reaction is closely related to its rate. The higher the activation energy, the slower the chemical reaction will be. This is because molecules can only complete the reaction once they have reached the top of the activation energy barrier. The higher the barrier is, the fewer molecules that will have enough energy to make it over at any given moment

Question 26

Catalysis; Catalyst; Enzymes

Answer 26

The process of speeding up a reaction by reducing its activation energy is known as CATALYSIS, and the factor that’s added to lower the activation energy is called a CATALYST. Biological catalysts are known as ENZYMES.

Question 27

Catalyst; Enzymes; RNA

How do enzymes lower the activation energy?

Enzyme relationship with free energy

Enzyme relationship with transition state

Where is the transition state on a diagram?

Answer 27

A substance that speeds up a chemical reaction—without being a reactant—is called a catalyst.

The catalysts for biochemical reactions that happen in living organisms are called enzymes. Enzymes are usually proteins, though some ribonucleic acid (RNA) molecules act as enzymes too.

Enzymes perform the critical task of lowering a reaction’s activation energy—that is, the amount of energy that must be put in for the reaction to begin. Enzymes work by binding to reactant molecules and holding them in such a way that the chemical bond-breaking and bond-forming processes take place more readily.

Enzymes don’t change a reaction’s ∆G value. They don’t change whether a reaction is energy-releasing or energy-absorbing overall, because enzymes don’t affect the free energy of the reactants or products.
Instead, enzymes lower the energy of the transition state, an unstable state that products must pass through to become reactants. The transition state is at the top of the energy “hill” in diagrams.

Question 28

Substrates

Active site of enzyme…What happens here?

AMINO ACIDS; have a very specific size, shape, and chemical behavior.

Answer 28

To catalyze a reaction, an enzyme will bind to one or more reactant molecules. These molecules are the enzyme’s substrates.

The part of the enzyme where the substrate binds is called the active site and is where catalytic “action” happens.

The set of amino acids found in the active site, along with their positions in 3D space, give the active site a very specific size, shape, and chemical behavior. Thanks to these amino acids, an enzyme’s active site is uniquely suited to bind to a particular target—the enzyme’s substrate or substrates—and help them undergo a chemical reaction.

Question 29

Temperature; Higher temperature generally; Chemical bonds; Denaturation

Answer 29

Because active sites are finely tuned to help a chemical reaction happen, they can be very sensitive to changes in the enzyme’s environment.

Temperature may affect the active site and enzyme function:

A higher temperature generally makes for higher rates of reaction, enzyme-catalyzed or otherwise.

However, increasing or decreasing temperature OUTSIDE of a TOLERABLE range can affect chemical bonds in the active site, making them less-suited to bind substrates.

Very high temperatures (for animal enzymes >40 degrees celsius or 104 degrees Fahrenheit) may cause an enzyme to DENATURE and lose its shape and activity)

Question 30

pH; Active site amino acid residues often have WHAT properties important for catalysis?; what might changes in pH cause?

Answer 30

Because active sites are finely tuned to help a chemical reaction happen, they can be very sensitive to changes in the enzyme’s environment.

pH may affect the active site and enzyme function:

Active site AMINO ACID RESIDUES often have acidic or basic properties that are important for catalysis. Changes in pH can AFFECT these residues and make it HARD for substrates to BIND. Enzymes work best within a CERTAIN pH RANGE, and, as with temperature, EXTREME pH values (acidic or basic) can make enzymes DENATURE.

Question 31

Induced fit

Answer 31

The matching between an enzyme’s active site and substrate is NOT just like two puzzle pieces fitting together (it should NOT be called the “lock-and-key” model).

INSTEAD, an enzyme changes shape SLIGHTLY when it binds its substrate, resulting in an even tighter fit. This adjustment of the enzyme to SNUGLY FIT the substrate is called INDUCED FIT.

Question 32

How does an enzyme actually lower activation energies of reactions?

1. 2 substrates together
2. Environment inside active
   site
3. Bending substrate molecules
4. Covalent bonds

Answer 32

The answer depends on the enzyme. Some enzymes speed up chemical reactions by bringing two substrates together in the right orientation.

Others create an environment inside the active site that’s favorable to the reaction (for instance, one that’s slightly acidic or non-polar).

The enzyme-substrate complex can also lower activation energy by bending substrate molecules in a way that facilitates bond-breaking, helping to reach the transition state.

Some enzymes lower activation energies by taking part in the chemical reaction themselves. That is, active site RESIDUES may form temporary COVALENT BONDS with substrate molecules as part of the reaction process.

Question 33

What happens to enzymes after substrate binding?

Answer 33

After substrate binding, enzymes return to their original states. They are not altered by the reactions they catalyze, and when an enzyme is done catalyzing a reaction, it releases product/products and is ready for the next cycle of catalysis.

Question 34

Because enzymes guide and regulate the metabolism of a cell, they tend to be carefully controlled.
Regulatory molecules
Activators
Inhibitors

Answer 34

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Question 35

Competitive vs. noncompetitive
Reversible binding
Competitive inhibition
Can be elsewhere than active site?
How does this impact reaction rate?
Not a lot of substrate
Lots of substrate

Answer 35

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Question 36

Competitive vs. noncompetitive
Reversible binding

Noncompetitive inhibition
Both the inhibitor and substrate can be bound at the same time…so…if the substrate binds first, will the reaction proceed/not proceed?
Will this reach its normal maximum rate with a lot of substrate?

Answer 36

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