Metabolism

chemical energy

A form of potential energy involving energy stored in chemical bonds.

Define "enzyme" and "catalyst."

Catalysts are chemical agents that speed up reactions, but aren't consumed by them. Enzymes are just organic macromolecule catalysts, used by the body to speed up reactions so they happen within your life time.

Contrast endergonic reactions with exergonic reactions

Endergonic reactions require more energy than they release. Exergonic reactions release more energies than they require.

How is ATP regenerated from ADP + Pi?

Energy is added to the two products to combine them back into ATP.

What happens when ATP is converted into ADP + Pi

Free energy is released.

Figure out a way to remember this often misunderstood fact about chemistry: FORMING BONDS RELEASES ENERGY. BREAKING BONDS REQUIRES/ABSORBS ENERGY

How do you light a candle, without a match?

Why is disequilibrium one of the defining features of life

In order to continue having a metabolism the cell can't be at equilibrium. If the cell is totally at equilibrium, then it can do no work, because it has no free energy and the only way to get out of equilibrium is to spend free energy.

Anabolic pathway

Metabolic pathways that involve converting molecules into more complex forms by using energy, a building up.

Catabolic pathway

Metabolic pathways that involve converting molecules into simpler forms to gain energy, a breaking down.

potential energy

Stored energy

Explain the importance of the active site of an enzyme, and describe how the specificity of an enzyme depends on its structure

The active site is where the enzyme binds to the substrate, and thus the shape of the site, and following that the shape of the enzyme as a whole, controls what molecules the enzyme will effect.

What is free energy

The amount of a system's energy that can do work if pressure and temperature are uniform, which is very important in the consistent internal environment of the cell.

kinetic energy

The energy of motion.

Bioenergetics

The study of how energy flows through living organisms.

Metabolism

The sum total of all chemical reactions that occur in the human body.

What's the relationship between the sponaneity of a process or reaction, and its speed

There isn't any relationship.

Describe the catalytic cycle of an enzyme (see figure 6.15)

This is simple. You have an enzyme, reactants go in, they are held to the active site and the active site changes shape, the substrates turn into products, the products are released, and the active site goes back to its normal shape.

Describe competitive and non-competitive inhibition of enzymes.

Competitive inhibiters place themselves into the active site, and thereby prevent the substrate from entering the enzyme. Noncompetitive inhibitors bind to other parts of the enzyme, thus changing the enzyme's shape, and the shape of the active site, so that the active site is less effective at catalyzing.

How is cell structure related to control of enzymes?

Enzymes are often found in different locations in the cell, or even within organelles, depending on where the reactions they catalyze are needed most.

What's the relationship between spontaneity and equilibrium

Equilibrium is a state where the reaction has the lowest G possible, that is to say, the decrease in free energy is at its highest magnitude. In equilibrium the rate of transformation between the reactants and product is the same, with both switching back and forth constantly. This relationship is perfectly stable, as it's free energy is basically nil. In order to take a reaction out of equilibrium, free energy must be added, and any spontaneous reaction must be moving towards equilibrium. If they are already at equilibrium they can't spontaneously react.

Using figure 6.9, describe how ATP is used to drive the conversion of glutamic acid and ammonia into glutamine (an endergonic process)

Glutamic acid becomes phosphorylated, which makes it more reactive, such that Ammonia ends up connecting to the glutamic acid while displacing the phosphate group. Glutamic acid and ammonia combined together is glutamine.

heat

Heat is thermal energy being transferred from one object to another, thermal energy being energy from the random motion of atoms and molecules.

Read the section on "equilibrium and metabolism." Why, in figure 6.7, is diagram "c" the best metaphor for the metabolism of cells, as opposed to "b" or "a?

In the cell reactions occur in exergonic series, where the products and energy are used to enable the next reaction, so equilibrium is prevented.

What is energy coupling

It's the use of an exergonic reaction to fuel an endergonic reaction.

What is feedback inhibition?

It's when the product catalyzed by an enzyme also inhibits that same enzyme, so if there's a lot of it, it won't be produced as much, and when there isn't much of it the enzyme will produce more.

What is a phosphorylated intermediate

Its a molecule that has an added phosphate group, which is the free phosphate group created when ATP is broken down, and having that phosphate group makes the molecule its attached to less stable and thus able to change to a new form. This is how ATP gets things done.

What are the three kinds of cellular work? Describe a specific example of each one that is occurring in your body

1. Chemical Work: Forcing endergonic reactions to happen, like turning glucose into starch. 2. Transport Work: Moving substances against concentration gradients, such as sodium pumps. 3. Mechanical Work: Physical motion like muscles contracting.

What's the relationship between the spontaneity of a process and a system's stability

A process can only be spontaneous if the system loses free energy in the process. The higher the free energy, the less stable a system is, the lower the free energy, the more stable a system is.

metabolic pathway

A series of specific steps where a starting molecule undergoes reactions catalyzed by enzymes several times until it reaches its final form, called the product.

What are cofactors? Coenzymes?

Cofactors are non-protein molecules that help an enzyme perform catalysis. They may be bound permanently to the enzyme, or only bind reversibly when the substrate come along. Coenzymes are cofactors that are organic, since some cofactors are actually inorganic molecules like various metals.

Define activation energy, and explain the relationship between enzymes and activation energy. Note that you should be able to draw, from memory, figure 6.12, which does this in graphic form

Activation energy is the start up energy you need to transform a molecule into a more unstable state, then the bonds are broken and reformed creating a new molecule and releasing more free energy than was used. Enzymes lower the amount of needed activation energy.

How do cells regulate enzymes? Describe allosteric regulation and inhibition of enzymes

Cells can turn on or off the genes that code for the creation of certain enzymes, or they can inhabit enzymes that already exist. Allostatic regulation is any case where a protein's function in one area is changed by a regulatory molecule binding to a different area of the protein. This includes both inhibiting and stimulating the enzyme.

When can reactions happen spontaneously

Spontaneous reactions are reactions that don't require an input of energy, and they only happen when the entropy of the universe is increased.

Summarize the passage about how enzymes speed up reactions.

Spontaneous reactions in the body won't get anywhere until they receive their activation energy, which would normally take ages. Enzymes lower the amount of needed activation energy, allowing these reactions to happen much faster.

Explain the effects of temperature and pH affect on enzyme activity.

Temperature and pH can denature enzymes, because they are just another type of proteins, thus preventing them from carrying out their functions.

Energy

The capacity to cause change.

What are exergonic reactions? In your answer, include how exergonic relates to 𝝙G and spontaneity.

They are reactions where the end result is a net release of free energy. These are always spontaneous reactions with a negative G. The cell loses total free energy, as it is being released in the reaction to perform work.

Explain the "induced fit" model of enzyme action, and list three ways in which enzymes catalyze reactions.

When an enzyme binds to a substrate the shape of the active site changes a bit to allow it to connect with the substrate. When the substrate leaves the site changes back to its regular shape. 1. The enzyme may change the position of substrate molecules so that their bonds are weaker and easier to break. 2. The active site may provide an environment more suitable for the substrate to turn into its transition state, through things like ph. 3. Sometimes the side chains of an amino acid in the active site may covalently bond to parts of the substrate to help them react.