Bio98 Lecture 15: Regulation of PDH and TCA Cycle; Intro to Fatty Acids

The net ATP and electrons calculation

Glycolysis: 5-7 ATP equiv.

PDH + TCA: 25 ATP equiv

-2.5x ATP per NADH & 1.5x ATP per FADH2

-Total ATP formed: 30-32

Irreversible steps are most regulated:

-Prequel: ?, TCA: ?

-Prequel: Pyruvate dehydrogenase (PDH)

-TCA: Citrate synthase (CS), isocitrate dehydrogenase (IDH), alpha-ketoglutarate dehydrogenase (KGDH)

Modes of regulation

1) product inhibition: ATP, NADH, intermediates

2) Energy depletion: activation

3) Ca²+ is a signal for muscle contraction: I need more ATP!

(IRREVERSIBLE rxns are usually the MOST regulated)

The regulation of pyruvate dehydrogenase (PDH)

-2 mains modes of regulation:

1) product inhibition

- E1 = CO2; E2 = Acetyl-CoA; E3 = NADH

- ACETYL-CoA inhibits E2 SUBUNIT

- FATTY ACIDS also inhibit E2 SUBUNIT

- HIGH NADH levels INHIBIT E3 SUBUNIT

- activity is ACTIVATED by HIGH levels of CoA-SH + NAD+

2) phosphorylation

- ATP inhibits E1 and AMP activates it ; phosphorylation disturbs E1 active site

-Ca²+ : activates the phosphatase to give back active E1

- Phosphorylation = direct covalent modification of the E1 subunit

TCA Regulation: Step 1 (irreversible)

Condensation of Acetyl-CoA with oxaloacetate (OAA) through citrate synthase to make citrate

• 1st irreversible step

• ATP inhibits allosterically @ citrate synthase to prevent citrate from being produced

• High ATP = abundant energy, TCA not needed

TCA Regulation: Step 3 (irreversible)

- regulated in lots of ways

- ATP & NADH both bind & inhibit allosterically @ isocitrate dehydrogenase to prevent isocitrate from turning into alpha-ketoglutarate

• phosphorylation also regulates IDH activity

• Activated by ADP (low energy state)

-Net result of turning off isocitrate dehydrogenase: citrate rises bc of the equilibrium of the aconitase rxn ; feeds back towards the production of citrate by econotase

• Citrate transports out of mitochondria back into the cytoplasm, where it feeds into lipid biosynthesis

• It leads into the production of acetyl-CoA → leads into production of fats and the storage of energy.

Phosphorylation (TCA)

Step 3 (cont.):

- KINASE uses ATP —> PHOSPHORYLATES IDH = INACTIVE IDH

- DEPHOSPHORYLATED IDH = ACTIVE IDH

- lots of material to go for TCA —> KINASE INHIBITED so that IDH is ACTIVE

TCA Regulation: Step 4 (irreversible)

α-ketoglutarate transformed into succinyl-CoA
—> 3rd IRREVERSIBLE reaction

- reaction + regulation is SIMILAR to PDH (production inhibition):

- HIGH SUCCINYL-CoA levels (acetyl-CoA) = E2 INHIBITED

- HIGH NADH levels = E3 INHIBITED

Why do we need fat?

Sources of energy, hormones, and cell membranes

-Why fat?

• more energy density than other materials (kJ/g)

• less water → 6Xs more energy than glycogen per gram

What’re Fatty Acids (FAs)?

Carboxylic acid + long hydrophobic tail

-Saturated: no double bonds (packed tightly)

-Unsaturated: double bonds (packed loosely)

-Polyunsaturated: multiple double bonds

-Naming system: X:Y^ΔZ (X= # carbons, Y=number of unsaturated bonds, Z= position of unsaturated bonds)

What are Fats (lipids)?

-Fatty acids: carboxylic acids and amphipathic (contain polar and nonpolar ends).

-can act as a detergent, cells don’t want these floating around

-FAs are stored as neutral lipids by reacting with a “head group” such as glycerol

Different Types of Acylglycerols

A. Monoglycerides and diglycerides

-Monoacylglycerol

-Diacylglycerol

B. Triacylglycerols: the main source of energy storage in the body & can be broken down for energy

-Saturated Fat

-Monounsaturated fat

-Polyunsaturated fat

Other types of lipids

- Phospholipids are the main component of the lipid bilayer and organellar membranes

• Phospholipids are fluid-like

- Cholesterol is rigid, provides important structural support in membranes.

Cholesterol: the good and the bad

Good cholesterol:

• high density lipoprotein (HDL)

• Bring cholesterol back to liver

• High protein:fat ratio

Bad cholesterol:

• low density lipoprotein (LDL)

• Accumulates plagues on arterial walls → heart attack

• Low protein:fat ratio

FATTY ACID OXIDATION:

- the metabolic breakdown of fatty acids (to acetyl-CoA)
—> occurs in the CYTOPLASM of fat cells

- DOWNREGULATED (inhibited) by INSULIN
—> wants to store fat

- UPREGULATED (activated) by GLUCAGON
—> wants to break down fat

- Fatty acids transported by albumin

- Glycerol -> G3P in gluconeogenesis in liver

(more about this in next lecture)

Glycerol Oxidation

- Glycerol kinase: phosphorylates glycerol but requires ATP (costs energy)

- Glycerol-3-phosphate dehydrogenase (NOT the same G3P from glycolysis) generates DHAP (generates NADH!)

- TIM (TPI) regenerates G3P (same one from glycolysis) from DHAP

- Either glycolysis or gluconeogenesis depending on what is needed