Bioenergetics & Oxidative Metabolism (14&17)

Catabolic vs. Anabolic Pathways

catabolic pathways convert large/complex biomolecules to smaller molecules for energy generation (often requires oxygen)

anabolic pathways involve the biosynthesis of large/complex biomolecules (requires energy)

First law of thermodynamics

energy is conserved (can neither be created or destroyed)

Second law of thermodynamics

all processes progress towards the maximum entropy (increases in disorder)

ΔG values and their meanings

ΔG=zero: system is at equilibrium

ΔG= (+): reaction is non-spontaneous and requires energy

ΔG= (-): reaction is spontaneous

Gibbs free energy

the portion of the total energy in a system that is available for useful work

Equations:

• ΔG= ΔH - TΔS

• ΔG= ΔG* + RTlnQ (Q=concentration of products over reactants)

If ΔG is larger than 15 kJ/mol…

then it is hard to reverse

reversible vs. irreversible enzymes

reversible: enzymes with small ΔG* values (can be positive or negative)

• Never used for regulation of a pathway

irreversible: enzymes with large, negative ΔG values

• these are going to be used for regulation of pathways

• often found at beginning to lock in substrate and at the end to ensure the pathway goes to completion

What does producing a CO₂ molecule do to an equilibrium reaction?

it drives the reaction towards the product(s) because CO₂ is free to diffuse across membranes and exit the cell (resulting in an irreversible enzyme with a large, negative ΔG*)

Can ΔG* be added with other ΔG* values?

Yes, you add them together and as long as the total ΔG* is negative, then the pathway will proceed to the end

Regulation of Enzymes

-change in the de novo synthesis of the enzyme to either make more or increase the degradation rate

-allosteric activators, inhibitors, and through covalent modifications

• allosteric is fast but concentration driven (i.e. product inhibition)

• covalent modification could include the phosphorylation of an S, T, or Y residue with a kinase (reversible when a phosphatase removes the phosphate group)

What makes a bond “high energy”?

-resonance forms: more resonance=more stable so it lowers its energy (inorganic phosphate has 4 res. structures while it only has 3 when on ATP which is why it breaks off releasing that energy to become more stable)

-have groups of similar charges near each other

-hydrolysis leads to products that can isomerize to a more stable compound (cis → trans)

-hydrolysis of bond leads to an acid (acid dissociation)

Oxidoreductases

-catalyze oxidation-reduction reactions

-require NAD+ (NADH) or FAD (FADH₂) cofactors

-name is the substrate + “dehydrogenase”

Transferases

-transfers functional groups between donors and acceptors

-kinases that transfer phosphate groups (requires ATP as phosphate donor)

-name is the substrate + “kinase”

Hydrolyases

-special class of transferases in which the donor is water

-proteolytic enzymes are a special class of hydrolyases called peptidases

-ex. serine protease

Lyases

-add or remove elements of H₂O, NH₃, CO₂

• decarboxylase: removes CO₂ from amino acids

• dehydratase: remove H₂O in a dehydration reaction

• aminase: NH₃

Isomerases

-catalyze isomerization of several types: cis/trans, aldose/ketose, etc.

-ex. mutase: there is an intramolecular transfer of a group (L-Glu → D-Glu)

Ligases

-involved in synthetic reaction where 2 molecules are joined together in an endothermic reaction

-requires energy

• if energy source is ATP: name is product + “synthetase”

• any other energy source: name is product + “synthase”

What are the three possible fates of Acetyl CoA?

-oxidate acetyl groups in the TCA cycle for energy generation **

-convert to ketone bodies in the liver

-transfer of acetyl units into cytosol in biosynthesis of sterols and long chain fatty acids

Where in the body is there no mitochondria?

red blood cells, lens, cornea, testes

What is the primary function of the TCA cycle?

to generate reducing equivalents (NADH & FADH₂) that are used to generate energy in the electron transport-oxidative phosphorylation sequence

-secondary function is to generate intermediates used in other biosynthetic pathways

What type of cleavage is done to accomplish the process of oxidizing acetyl units to 2 CO₂ molecules and capturing the liberating energy in NADH, FADH₂, and GTP?

beta-cleavage

-acetyl does not have a beta carbon so the body adapts by adding the acetyl group to oxaloacetate (4C) in the first step of the TCA cycle

In electron transport and oxidative phosphorylation, how many ATP do NADH and FADH₂ produce?

NADH: 2.5 ATP

FADH₂: 1.5 ATP

Step 1 TCA Cycle

Acetyl CoA + oxaloacetate + H₂O→citrate + CoA

enzyme=citrate synthase

-condensation reaction to form 6C molecule

-large, negative ΔG (-31.4kJ/mol) so is highly regulated

Step 2 TCA Cycle

citrate → isocitrate

enzyme=aconitase

-mutase reaction in which the OH group is moved from one carbon to another to make a secondary alcohol that can be oxidized (tertiary alcohols cannot be oxidized)

-small, positive ΔG

Step 3 TCA Cycle

isocitrate+NAD⁺→alpha-ketoglutarate +NADH+H⁺+CO₂

enzyme= isocitrate dehydrogenase

-redox reaction

-irreversible so enzyme is inhibited by high levels of ATP/NADH levels

Step 4 TCA Cycle

alpha-ketoglutarate + NAD⁺+ CoA→ succinyl-CoA +NADH+H⁺+ CO₂

enzyme=alpha-ketogutarate dehydrogenase

-irreversible with a large, negative ΔG (-30kJ/mol)

Step 5 TCA Cycle

succinyl-CoA + P_i + GDP→succinate+ GTP + CoA

enzyme= succinyl-CoA synthetase

-small, positive ΔG and reversible so this is a good point for molecules to enter/leave the cycle

-GTP is equivalent to an ATP

Step 6 TCA Cycle

succinate + FAD→fumarate + FADH₂

enzyme: succinate dehydrogenase

-enzyme is reversible but inhibited by oxaloacetate and malonate

-redox reaction

Step 7 TCA Cycle

fumarate + H₂O → malate

enzyme=fumerase

-trans addition of H₂O across double bond to introduce the oxygen needed in oxaloacetate and set up one more redox reaction

Step 8 TCA Cycle

malate + NAD⁺ → oxaloacetate + NADH + H⁺

enzyme=malate dehydrogenase

-very endergonic reaction (ΔG=+30kJ/mol) but is pulled forward by the favorable citrate reaction

Places for regulation in the TCA cycle

-citrate synthase: main regulatory enzyme that is inhibited by ATP (also NADH and succinyl-CoA) via negative feedback

-isocitrate dehydrogenase: allosteric activation by ADP and NAD⁺ and inhibition by ATP and NADH

-alpha-ketoglutarate dehydrogenase: inhibited by NADH and succinyl-CoA and activated by AMP