BIOCHEM 501 Unit 3

What molecule provides the most energy when fully oxidized?

the one w/ the most C-H and C-C bonds

How do cells obtain most of their energy?

thru oxidation rxns (not by direct rxn w/ oxygen)

Thermodynamics

how much energy is released as a rxn proceeds towards equilibrium

Does thermodynamics help predict the rate of a reaction?

no

Gibbs free energy (ΔG)

how far a rxn is from equilibrium

-ΔG

exergonic; reactants → products (Keq >1)

+ΔG

endergonic; products → reactants (Keq < 1)

What does it mean if ΔG = 0?

rxn is at equilibrium

ΔG°

change in energy from standard conditions to equilibrium

How do enzymes increase reaction rate?

they lower activation energy, but don’t change Keq

Change in enthalpy (ΔH)

difference in bond energies between reactants and products

-ΔH

exothermic; >stable bonds are formed and heat is released

+ΔH

endothermic; < stable bonds are formed and heat is absorbed

Change in entropy (ΔS)

randomness

If a system’s entropy decreases, what happens to the entropy of its surroundings?

it increases

How does ATP usually provide energy?

thru group transfers (not by direct hydrolysis)

Glycolysis

1 glucose → 2 pyruvate (NADH) and net gain of 2 ATP

Where does glycolysis occur?

in cytosol

What input does the preparatory stage of glycolysis require?

2 ATP

How much ATP does the payoff stage of glycolysis yield (NOT net gain of glycolysis)?

4 ATP

What is the irreversible step of glycolysis?

phosphofructokinase adds a phosphate to fructose-6-P → fructose-1,6-bisP

How does feedback inhibition of phosphofructokinase work?

small molecules bind to non-active site areas → alters conformation of active site

What inhibits phosphofructokinase (and glycolysis)?

ATP, fatty acids, citrate

What stimulates phosphofructokinase (and glycolysis)?

AMP and ADP signal low energy levels

During the set-up glycolysis reaction, what is the 1st byproduct that’s formed?

CO2

Why is the set-up glycolysis reaction not considered an oxidation reaction?

C-C bond of NADH is replaced by a C-H bond (both are reduced bonds)

What enzyme does the set-up glycolysis reaction take place on?

E1

What enzyme does the oxidation glycolysis reaction take place on?

E2

What is the byproduct of the oxidation glycolysis reaction?

acetyl-CoA

Why is glycolysis irreversible and regulated?

to avoid futile cycling (opposing rxns run simultaneously)

Gluconeogenesis

NADH converts to glucose using “bypass” enzymes and reversible glycolysis rxns

Fermentation

anaerobically regenerates NAD+ from NADH to maintain glycolysis; inefficient way to make energy

Type I fermentation

NADH → lactate and NAD+ (for glycolysis)

Type II fermentation

NADH → ethanol  and NAD+ (for glycolysis)

What happens to NADH under anaerobic conditions?

fermentation

What happens to NADH under aerobic conditions?

pyruvate dehydrogenase (PDH) converts NADH into acetyl-CoA

Pyruvate dehydrogenase (PDH)

converts NADH into acetyl-CoA

acetyl-CoA

substrate for citric acid cycle

What are key cofactors of PDH?

NAD+, FAD, TPP, and lipoic acid

Thiamine pyrophosphate (TPP)

acts as an anion involved in the rxn

What compound would be elevated in a thiamine deficient person?

NADH

Lipoic acid

acyl and redox (substrate) carrier

Where does the citric acid cycle occur?

mitochondria

What are inputs of the citric acid cycle?

acetate from acetyl-CoA (2C and 4 reduced bonds)

How many reduced bonds does acetate have? In other words, how many reduced cofactors are formed when acetate is fully oxidized in the citric acid cycle?

4

What are outputs of the citric acid cycle?

3 NADH, FADH2, 2CO2, 1 GTP

Why can the E3 subunit be the same in PDH and α-ketoglutarate dehydrogenase?

the substrates for it are the same in both rxns

When the citric acid cycle is running, the concentration of oxaloacetate must be…

quite low relative to L-malate, so that the actual ΔG is negative

What acts as inhibitors of the citric acid cycle?

high levels of metabolites that indicate there’s plenty of energy in the cell

Lipids

include membrane components, hormones, vitamins, etc.

Triglyceride

type of lipid used for energy storage

Detergent

emulsifies (breaks down) triglycerides

Lipase

responsible for hydrolysis of triglycerides to fatty acids, which can be transported across the plasma membrane

High levels of fatty acids are toxic, so they’re…

continuously being disassembled to cross tissues and reassembled so they don’t reach toxic levels

Once inside the cell, fatty acids are…

activated by acyl-CoA synthetases on the outer membrane of the mitochondria

Why do fatty acids bond w/ carnitine prior to β-oxidation?

fatty-acyl-carnitine can be transported across inner mitochondrial membrane; fatty-acyl-CoA can’t

What happens to fatty acids in the mitochondria?

they’re destined for breakdown (β-oxidation)

What happens to fatty acids in cytosol?

fatty acid (and triglyceride) synthesis occurs when there’s excess carbs

β-oxidation

conversion of fatty acid into 8 acetyl-CoA units in mitochondria

How many acetyl-CoAs are formed from (n - 1) β-oxidations?

n acetyl-CoAs

What type of enzyme typically catalyzes redox rxns?

dehydrogenases

Why is NAD+, FAD, and CoA involved in these rxns?

they have 1 end to carry electrons or chemical units, and another to base-pair at the active site of a ribozyme (RNA enzyme w/ a catalytic binding pocket)

High levels of acetyl-CoA ___ PDH and ___ the citric acid cycle.

inhibits; has no effect on the rate of

What was concluded from the Knoop experiment?

fatty acids are oxidized 2-C units at a time

Urea cycle

transforms toxic ammonia byproduct into urea, which is eliminated thru mammal urine

Ammonia

toxic b/c it crosses the blood/brain barrier and converts to glutamine, which can alter osmotic balance → swelling and coma

Glutamine synthetase

detoxifies ammonia generated by non-liver tissues by converting NH4+ and glutamate to glutamine

Glutamine

won’t diffuse across blood/brain barrier; disassembled to release ammonia

Where does the urea cycle occur?

mitochondria and cytosol

Where is urea produced?

liver

What are the N donors into the urea cycle to produce urea?

glutamate and glutamine

Alanine

carries N from muscle cells to the liver, where it’s converted to glutamate before entering the mitochondria

Carbamoyl phosphate

captures ammonia from glutamine and glutamate

When glutamate donates an amino group to oxaloacetate, what is formed?

aspartate

How does aspartate contribute the 2nd N of the urea cycle?

it combines w/ citrulline → argininosuccinate

How is urea formed?

2 former amino groups are added to CO2

Transamination

generates keto acids for the citric acid cycle and glutamate/aspartate for urea formation in liver

Aminotransferase

catalyzes transamination; always involves glutamate and α-ketoglutarate

If C atoms from breakdown of certain amino acids end up in acetyl-CoA, the amino acids are ___

ketogenic

If C atoms from breakdown of certain amino acids end up as part of citric acid cycle intermediates (NADH, oxaloacetate, α-ketoglutarate, etc.), the amino acids are ___

glucogenic

Oxidative phosphorylation

NADH and FADH2 are oxidized for ATP production (phosphorylation of ADP)

Electron transport chain

transports electrons from NADH and FADH2 to O2 and energy stored in ATP

ΔE

difference in reduction potentials that can describe the energy in a redox rxn

Standard reduction potential (E°)

measures a molecule’s affinity for electrons

• used to predict direction of a rxn (ΔE and Keq) between any pair

The half-rxn w/ the higher E° value will proceed as…

reduction and accepts electrons

The half-rxn w/ the lower E° value will proceed as…

reverse rxn (oxidation) and donates electrons

Complex I

takes electrons from NADH and transfers them to ubiquinone (carrier)

Ubiquinone (Q)

carrier which takes electrons to complex III

Complex I oxidizes ___ and reduces ___

NADH; Q

Complex III

moves electrons to cytochrome C

Cytochrome C

protein that shuttles electrons between complexes III and IV

Complex III oxidizes ___ and reduces ___

QH2; cytochrome C

Complex IV

gives total of 4 electrons to O2 → H2O

Complex IV oxidizes ___ and reduces ___

cytochrome C; O2

Complex II

takes electrons from FADH2, but otherwise follows the same pathway as complex I

• the only membrane-inserted enzyme of the citric cycle

Complex II oxidizes ___ and reduces ___

succinate (FADH2 as bound cofactor); Q

Which complexes pump protons from inside the inner membrane to outside it?

I, III, IV

Overall, electrons flow from…

high energy to low energy (some energy is captured in a proton gradient)

For every 1 NADH molecule oxidized at complex I, how many TOTAL protons are pumped across all complexes from the mitochondrial matrix to the inner membrane space?

10

How many protons are pumped at complex I?

4