Chapter 13 - Bioenergenics and Biochemical Reaction Types

What is metabolism?

The study of synthesis and use of energy

What is the difference between catabolism and anabolism? Which one requires energy and which produces energy?

Catabolism: breaking down macromolecules into building blocks and is energy producing

Anabolism: building macromolecules from building blocks and requires energy

Where does catabolism take place?

Cytosol or mitochondria

What are the key features of metabolic pathways? (2)

1. 1st committed step with a large -ΔG’ and makes the pathway irreversible

2. Catabolic and anabolic pathways are different

Do irreversible reactions have ΔG’s closer to or further from equilibrium?

Further from

What is an exergonic reaction? What is an endergonic reaction?

Exergonic: ΔG < 0 spontaneous, forward reaction favored

Endergonic: ΔG > 0 nonspontaneous, reverse reaction favored

What is dynamic equilibrium?

The rate of the forward reaction equals the rate of the reverse

What is steady state?

Input of reactants = removal of products

Observe no net change

What is flux?

The direction of flow through metabolic pathways, also known as flow

In what ways can metabolic flux be regulated? (4)

1. Change the concentration of substrate

2. Allostery control: binding of a molecule at site other than active site to induce a conformational change

3. Covalent modification (e.g. phosphorylation, ubiquiniation)

4. Making more/degrading enzyme (e.g. transcription/translation)

What is the difference between a kinase vs a phosphatase?

Kinase = +P

Phosphatase = -P

What are the high energy intermediates? (3) What are examples?

1. Phosphorylated intermediates: ATP

2. Thioester compounds: Acetyl-CoA

3. Reduced coenzymes: NADH, NADPH, FADH₂, FMNH₂

How to recognize a thioester compound

What is Acetyl-CoA?

A high energy thioester intermediate compound that contains a thioester group and an adenosine

Why is ATP a high energy compound? (4)

1. The hydrolysis of ATP releases energy and makes ΔG more negative.

2. It has resonance destabilization where electrons can move between two phosphates

3. It has electrostatic repulsion between O^- and O^- making electron density high with phosphate group

4. Phosphate is able to adapt stable resonance

Why are thioester compounds high energy? (2)

1. They have resonance stabilization with the acetyl group → acetate

2. S and C can pull electron density

What is an acetyl group?

CH₃CO-

What is CoASH?

CoA in its free thiol form (HS^-)

What is a redox reaction?

Oxidation and reduction that involves the transfer of electrons

What is reduction?

A reduction of charge such as Fe³⁺ → Fe²⁺

What is oxidation?

An increase in charge such as Cu⁺ → Cu²⁺

In what ways can oxidation and reduction occur? (4)

1. Direct transfer of electrons

2. Transfer of H (1 proton/1 electron)

   1. Gaining H = reduction

3. Transfer of hydride (H^-)

   1. 2 electrons transferred

4. Adding oxygen

   1. Losing H = oxidation

How do NAD⁺ and NADH differ in structure?

NAD⁺ is the oxidized form with the nicotinamide containing 3 double bonds.

NADH is the reduced from with the nicotinamide containing 2 double bonds.

How does the reduction of NAD⁺ to NADH occur?

Hydride transfer

NAD⁺ + 2e^- → NADH + H⁺

How do NAD⁺ and NADH differ in their absorbance at 340nm?

Only the reduced NADH has absorbance at 340nm

What is the difference between NAD⁺ and NADP⁺?

In NAD⁺, the ribose sugar has a 2’ OH

In NADPH⁺, the ribose sugar has a phosphate on 2’ C

How do FAD and FMN differ?

FAD: Flavin adenine dinucleotide contains isoalloxazine ring (flavin)

FMN: Missing ribose sugar ring with adenine, contains modified sugar + flavin

What is special about FAD and FMN?

they can only accept 1 H at a time, making radical intermediates until getting to their fully reduce form

What is the standard reduction potential? Why is it useful?

E = measure of affinity for electrons, energy associated with reduction.

It is important to predict whether or not redox will occur

How to determine E’?

Write the E of reduction reaction and flip the sign of E for oxidation and add them together

What is E telling you?

How easy it is to reduce a reaction

How to recognize a redox reaction

Look for elements that are uncombined (oxidation state equals 0) on one side of the equation but part of a compound (oxidation state does not equal 0) on the other side of the equation.

How to identify a more oxidized vs more reduced molecule?

More oxidized = more oxygens

More reduced = more hydrogens