Lectures 7-8

Question 1

What kind of energy do cells use to do work?

Answer 1

Energy stored in chemical bonds.

Question 2

What are reactions that release free energy called?

Answer 2

Exergonic.

Question 3

What are reactions that require free energy called? Where is that free energy harvested?

Answer 3

They are called endergonic. They use energy that has been freed by exergonic reactions.

Question 4

Which of exergonic or endergonic reactions happen spontaneously? Why?

Answer 4

Exergonic reactions happen spontaneously, this is because they result in increased disorder.

Question 5

Explain activation energy, endergonic and exergonic reactions.

Answer 5

When a reaction takes place, bonds are first broken, and then new bonds are formed. Activation energy is the energy required to break the bonds and “start the reaction.”

In an exergonic reaction, the formation of the new bonds creates more energy than was required to activate the reaction. In an endergonic reaction, the opposite is true.

Question 6

What are the two ways in which the rate of reaction can be sped up?

Answer 6

By adding energy to the system, or by lowering the activation energy of the reaction.

Question 7

How do catalysts function?

Answer 7

They stabilize the intermediate products or transition states of the reaction, speeding it up.

Question 8

Is the hydrolysis of ATP exergonic or endergonic?

Answer 8

It is exergonic, it releases energy.

Question 9

What are enzymes and how do they function?

Answer 9

Enzymes are biological catalysts. They are usually proteins but they can also be RNA.

They speed up reactions by orienting substrates, bringing reactants together, or by stressing particular bonds in the molecules.

Question 10

What is induced fit?

Answer 10

When the substrate bind to the active site of the enzyme, the enzyme slightly shifts its tertiary structure in order to clamp the substrate down.

Question 11

What are multienzyme complexes?

Answer 11

When multiple enzymes are stuck together to facilitate the movement of the substrate from one enzyme to the next in a reaction that uses multiple enzymes.

Question 12

How does the concentration of substrate affect the rate of the reaction?

Answer 12

As enzymes are reused over and over again, their concentration does not fluctuate. This means that unless all molecules of an enzyme are actively catalyzing the reaction, when the concentration of the substrate increases, the rate of the reaction will also increase (more collisions).

Question 13

What is Km?

Answer 13

The concentration of substrate required for the reaction speed to reach 1/2 of its maximum value.

The maximum velocity of a reaction only occurs when all enzyme molecules are busy (excess of substrate).

Question 14

What is binding affinity?

Answer 14

A measure of how strong their non-covalent interaction is. In other words, it measures how well the enzyme will bind to the substrate.

Question 15

What does a high binding affinity mean? How does this affect the Km value?

Answer 15

That there is less substrate required to saturate the enzyme. The Km value will be lower.

Question 16

What are the three ways in which the environment affects binding affinity?

Answer 16

1. Temperature.
2. PH.
3. Specific molecules (activators and inhibitors).

Question 17

How does temperature affect binding affinity?

Answer 17

When temperature increases, the molecules move more, so collisions are more effective. For humans, the optimal temperature for our enzymes is 37 degrees C.

Beyond a certain temperature, proteins will denature, and so the enzymes will no longer work.

Question 18

How does pH affect binding affinity?

Answer 18

Charges present in solution affect the tertiary structure of the protein. Some proteins work better in acidic or basic conditions. (Think of stomach pepsin).

Question 19

What are the two types of inhibitors?

Answer 19

Competitive inhibitors bind at the active sites of enzymes to block substrates.

Non-competitive inhibitors bind to the enzyme to change its tertiary structure, making it non-suitable to binding its substrate.

Question 20

What is the main difference between competitive inhibition and non-competitive inhibition?

Answer 20

In competitive inhibition, the inhibitor can be outcompeted if the substrate concentration is high enough.

Non-competitive inhibition completely disables the enzyme, no matter the concentration of substrate.

Question 21

What is feedback inhibition?

Answer 21

When a product of a chain of reaction inhibits above stages of the reaction. In other words, when enough product is made, that product will inhibit and stop the reaction. It is self-regulating.

Question 22

What do cofactors and coenzymes do?

Answer 22

They increase enzymatic function.

Question 23

What are rybozymes?

Answer 23

Catalytically active segments of RNA. (Remember how RNA can self catalyze).

Question 24

What is the metabolism?

Answer 24

The totality of the reactions taking place in the organism.

Question 25

What are endergonic reactions in terms of metabolism?

Answer 25

Reactions that require energy, they are referred to as the anabolism.

Question 26

What are exergonic reactions in terms of metabolism?

Answer 26

Reactions that release energy, they are referred to as the carabolism.

Question 27

What is a biological pathway?

Answer 27

When the product of one reaction becomes the substrate of the next.

Question 28

What are the two ways in which organisms harvest energy for anabolism?

Answer 28

Autotroph and heterotroph.

Question 29

What is the main task of the catabolism?

Answer 29

To generate ATP.

Question 30

What is the main metabolite used by organisms to generate ATP?

Answer 30

Glucose.

Question 31

What are the two ways in which glucose can be transformed into ATP? Which one is the most used?

Answer 31

1. Substrate level phosphorylation.
2. Oxidative phosphorylation.

The second method is the most common.

Question 32

What is substrate level phosphorylation?

Answer 32

When kinases transfer a phosphate group to ADP to form ATP. This happens during glycolysis, the cellular breakdown of glucose.

Question 33

What is oxidative phosphorylation?

Answer 33

When the ATP synthase multi-enzyme complex located in the mitochondria uses energy from a proton gradient to catalyze the formation of ATP.

Question 34

What process is oxidative phosphorylation part of? How?

Answer 34

Cellular respiration.
During cellular respiration, electrons from high-energy molecules, (such as glucose) are transferred to electron acceptors (such as NaD+). The energy released during this transfer is used to make ATP.

Question 35

What is aerobic respiration? Where does it occur?

Answer 35

The breakdown of glucose using oxygen and yielding ATP, H2O, and CO2.

It occurs in the cytoplasm and in the mitochondria.

Question 36

What is the net yield of glycolysis?

Answer 36

2 ATP, 2 pyruvates, 2 NADH molecules.

Question 37

What are the three series of reactions for glycolysis?

Answer 37

1. Priming reactions.
2. Cleavage reactions.
3. Energy generation reactions.

Question 38

What are priming reactions?

Answer 38

They are reactions that require ATP and prepare glucose so that it can be split into two molecules of pyruvate in later steps.

Question 39

What are cleavage reactions?

Answer 39

This is when the primed glucose is split into two molecules of G 3-P or glyceraldehyde 3-phosphate. These two molecules each contain 3 carbons.

Question 40

What are energy generation reactions?

Answer 40

They are a series of reactions where where 2 NADH are produced from the oxidation of the 3-carbon sugars, and 2 ATPs are produced using substrate-level phosphorilation.

Question 41

Briefly describe the detailed steps of glycolysis.

Answer 41

1. Add a phosphate to glucose (requires 1 ATP)
2. Isomerize (becomes fructose)
3. Add another phosphate (requires another ATP)
   4-5. Cleavage creating 2 Glyceraldehyde 3-phosphates (technically the second G 3-P comes from the isomerization of another molecule)
4. Addition of 1 additional phosphate to each G 3-P (also oxidizes 2 NADH molecules in the process)
5. Enzyme takes one phosphate from G 3-P (no longer called G 3-P but wtv) and puts it on ADP to create 2 ATP.
   8-10. Isomerization of what’s left of G 3-P, dehydration to make it into pyruvate, last phosphate removed, creating an additional 2 ATPs.