Lecture 9 DA Flashcards by Rodwan Halimi

Why does metabolism have so many steps?

Energy changes involved need to be kept small, manageable, and controlled.

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What is a benefit of metabolism having so many steps?

Chemically resistant bonds can be manoeuvred.

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What is catabolism? What form of gibbs free energy does it have? Is it oxidation or reduction?

Catabolism releases energy, and is exergonic or oxidative. Has negative gibbs free energy.

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What is anabolism? What form of gibbs free energy does it have? Is it oxidation or reduction?

Anabolism requires energy, and is endergonic or reductive. Has positive gibbs free energy.

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Are cells isothermal?

Yes.

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What is gibbs free energy?

Energy derived from oxidation of dietary fuels.

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What becomes of gibbs free energy?

Transduced into useful work (anabolism) or stored as ATP.

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Can absolute free energy (G) be measured?

No, but the difference of substrates vs products can be known - ΔG.

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What is ΔG°?

Standard free energy change when pH=0, at [1M] and 25°C.

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What is ΔG°’?

Standard biologcal free energy change, pH=7, at [1M], and 25°C.

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What is ΔG?

Change in free energy, the actual change in the cell.

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What does it mean when a reaction has negative free energy, in terms of products and reactants?

Products contain less free energy than the reactants.

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Are reactions with negative gibbs free energy sponatneous or not? Why?

Yes, because the products have less energy, and are more stable than the reactants.

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What does it mean when a reaction has positive free energy, in terms of products and reactants?

Products have more energy than the reactants.

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Are reactions with positive gibbs free energy sponatneous or not? Why?

No, because the products have more energy, and energy input is needed.

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Why is reaction coupling so important?

If reactions are coupled properly, it can be such that an endergonic reaction is driven by the gibbs free energy of an exergonic one.

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Give an example of reaction coupling.

A -> B, ΔG°’ = 20kj/mol
X -> Y, ΔG°’ = -33kj/mol
Therefore, A + X -> B + Y
ΔG°’ = 20 + -33, so -13kj/mol when coupled, and is spontaneous.

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What is needed for reaction coupling?

Enzymes are needed.

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What is the most commonly used reaction for coupling?

ATP -> ADP

What forms of NTPs are used for protein, lipid, and glycogen synthesis respectively? How is this useful?

GTP - protein
CTP - lipid
UTP - glycogen
This allows for compartmentalisation.

In ATP (and other NTPs), is the bond energy between the phosphates high? Why are they called a high energy bond?

High energy bond for the phosphate bonds is a misnomer, the bonds themselves are not high energy, but have a high free energy. They are in fact, very weak, given all the negative elctrostatic stresses.

Why do phosphate bonds in ATP (and other NTPs) have so much free energy?

The negative charges between the phosphates contribute to a high tension, is unstable and strained, wanting to break apart, given its a weak bond. Hence the high free energy.

Why is ATP so popular as an energy donor?

It is stable (despite the high phosphate tension) and enzymes recognise the adenosine for handling.

How much ATP is needed per day by the body? How much is there found at any given time? What is the reason for this disparity?

ATP needed - 45kg
ATP found - 1g
Constant resynthesis of ADP to ATP required to meet demand.

Give an example of coupling using glutamine to glutamate.

Glutamine synthase required. Starts by first phosphorylating the glutamine using ATP. The phosphate is replaced by an amine group, resulting in glutamate. Enzyme integrates energy from ATP -> ADP to substitute the phosphate group with an amine, finishing the reaction.

What does pure ATP hydrolysis release (aside from ADP and Pi)? Are there any exceptions?

Heat only. Exceptions when bound non-covalently to a protein. Hydolysis allows protein to switch between two conformations (myosin heads).

What kind of reaction is ATP synthesis?

Strongly endergonic ~30kj/mol.

What is substrate level phosphorylation? How much ATP is produced this way?

When ATP synthesis is coupled to a metabolic exergonic reation. Largely anaerobic. 5-10% of cellular energy produced this way.

Where does a cell obtain most of its ATP synthesis?

Oxidative phosphorylation.

Do other forms of energy currencies exist aside from ATP?

Yes, there are many for different situations. They just arent as universal.

How does substrate level phosphorylation work?

Works by making intermediates that have a higher free energy for phosphate hydrolysis than ATP, and use that energy to make ATP from ADP.

What cofactor is necessary for ATP synthesis?

NADH.

What are NAD+, NADH and NADPH used for?

NADH - ATP synthesis NAD+ - catabolic reactions NADPH - reductive biosynthesis (anabolism/photosynthesis)

What is NAD?

Specialised e- carrier, and a cofactor of some enzymes.

What does NADP accept?

Hydride ion, H-

What does NADP act as?

Water soluble carrier of electrons, from one metabolite to another.

What is FMN composed of? What about FAD? What are they both known as?

FMN has a base, ribitol and phosphate. FAD has an extra ribose adenine on the end. They are flavoproteins.

What is the function of a flavoprotein?

Can accept 2 electrons and 2 protons, acting asa temporary store of electrons.

Is FAD reduced or oxidised? what about FADH2?

FAD is oxidised, FADH2 is reduced.

What are the major redox coenzymes involved in energy transduction from food to ATP synthesis?

NAD+, FAD, FMN.

How many electrons/protons do NAD+, FAD, and FMN carry?

NAD+ takes one hydride ion, H- (2 electrons, 1 proton), the other proton is released to solution. FMN and FAD take 2 electrons and 2 protons.

What is a source of molecular hydrogen?

Reduced NASH.

What is the ATP produced per mol of NADH oxidised? How much does the body make, and why?

7.3mol of ATP per mol of NADH oxidised. Body makes closer to 2.5mol. Actual in vivo rate doesn't match up with standardised calculations.

What state are most glycolytic intermediates in? Why?

Phosphorylated. It isnt recognised by receptors in this form, and are trapped in. Allows easier identification by enzymes as well.

How are irreversible reactions used?

They can be used to regulate the pathway.

Why are the start or end of a pathway not used for pathway control using irreversible reactions?

Are too drastic, better at more than one point throughout the pathway, as intermediates act as precursors.

What can glycolysis intermediates be used for aside from glycolysis?

Biosynthesis.