8 – Introduction to Bioenergetics Flashcards

Practice flashcards covering the basics of bioenergetics, metabolic thermodynamics, ATP structure, and key electron carriers from BMS527 Lecture 7.

What is the definition of bioenergetics?

The study of how cells transform energy, often by producing, storing, or consuming adenosine triphosphate (ATP).

In bioenergetics, how do cells often transform energy?

By producing, storing, or consuming adenosine triphosphate (ATP).

What is the biological definition of energy?

The capacity to do work.

How is energy measured as "work" in biological systems?

As a quantitative property carried out based on observable properties such as heat or the production of a product.

Which subject deals with tracking the movement of energy?

Thermodynamics.

What does the 1st Law of Thermodynamics state?

Energy is neither created nor destroyed, only transformed.

What does the 2nd Law of Thermodynamics state?

The universe favors disorder.

Why does "life" require a constant input of energy?

To "fight" the second law of thermodynamics by maintaining order.

What is biological energy specifically required to maintain in living systems?

Order.

In eukaryotes, what metabolic process generates biological energy?

Cellular respiration.

Where is ATP primarily produced in humans?

The Electron Transport Chain (ETC).

What is the definition of metabolism?

The network of biochemical reactions breaking down (catabolism) and building up (anabolism) substances to fulfill biological functions.

How is catabolism defined?

The metabolic process of breaking down substances.

How is anabolism defined?

The metabolic process of building up substances.

What is generally released during catabolic processes?

Energy.

What is required for anabolic processes to occur?

An input of energy.

How are catabolic and anabolic processes often coupled together?

Via ATP-ADP cycling.

What are the series of linked, sequential reactions in metabolism called?

Pathways.

When is a reaction considered to be at equilibrium?

When the rates of the forward and reverse reactions are equal.

What is the net change in concentration of reactants and products at equilibrium?

There is no net change.

Does a reaction stop occurring once it reaches equilibrium?

No, reactions are still occurring, just at equal rates.

Which specific reaction in metabolism converts Acetyl-CoA and Oxaloacetate into Citrate?

Citrate formation (catalyzed by citrate synthase).

Is the reaction converting Oxaloacetate to Citrate endergonic or exergonic?

Highly exergonic.

At equilibrium for the Citrate formation reaction, which is present at higher concentrations?

Citrate.

If the formation of product P is favored in the reaction $S \rightarrow P$, what is the sign of $\Delta G$?

$\Delta G < 0$.

If the formation of product P is favored, what is the $\Delta G$ for the reverse reaction $P \rightarrow S$?

$\Delta G > 0$.

What is the value of $\Delta G$ when a reaction is at equilibrium?

$\Delta G = 0$.

What term describes a reaction that is thermodynamically favorable and moves to a lower energy state?

Spontaneous.

What term describes a reaction where energy is released (negative change)?

Exergonic.

What term describes a reaction that requires an input of energy to proceed?

Non-spontaneous.

What term describes a reaction where energy is an input (positive change)?

Endergonic.

Does thermodynamics tell us how fast a reaction proceeds?

No, that is determined by kinetics.

What is $K_{eq}$ the equilibrium constant for?

A reversible reaction.

How is the equilibrium constant ($K_{eq}$) calculated?

By dividing the concentration of products by the concentration of reactants when the reaction is at equilibrium ($K_{eq} = \frac{[Products]}{[Substrate]}$).

What does it mean if $K_{eq} > 1$?

The concentration of the products is greater than the concentration of the substrate at equilibrium.

What does it mean if $K_{eq} < 1$?

The concentration of the substrate is greater than the products at equilibrium.

What occurs when $K_{eq} = 1$?

Roughly equal amounts of reactants and products are present at equilibrium.

Is the forward reaction favorable when $K_{eq} > 1$?

Yes.

Under what concentration condition is a forward reaction favorable if $K_{eq} < 1$?

Only if there is a large excess of substrate relative to product ($[sub] > [prod]$).

What does Gibbs free energy ($G$) represent?

Useable energy.

What is the formula used to calculate $\Delta G$?

$\Delta G = \Delta H - T\Delta S$.

What factors must be considered to know what direction a reaction may proceed?

Gibbs free energy change and the concentrations of reactants and products.

What are the three standard conditions set for $\Delta G^\circ$?

$1\,M$ concentration of all reactants/products, $1\,atm$ pressure, and a temperature of $25^\circ C$.

Does $\Delta G^\circ$ change over time during a reaction?

No, because the concentrations are set and is not proceeding towards equilibrium.

What is the difference between $\Delta G^\circ$ and $\Delta G^{\circ '}$?

$\Delta G^{\circ '}$ factors in a standard $pH$ of $7.4$.

What is the equation relating $\Delta G^\circ$ to the equilibrium constant?

$\Delta G^\circ = -RT \ln(K_{eq})$.

How is the biological requirement for unfavorable reactions met?

By coupling favorable and unfavorable reactions together.

What does the first step of glycolysis couple ATP hydrolysis to?

Trapping glucose in the cell.

What is the $\Delta G$ for the reaction $Glucose + P_i \rightarrow Glucose-6-phosphate + H_2O$?

$+13.8\,kJ\,mol^{-1}$.

What is the $\Delta G$ for the hydrolysis of ATP ($ATP + H_2O \rightarrow ADP + P_i$)?

$-30.5\,kJ\,mol^{-1}$.

What is the net $\Delta G$ for the coupled reaction of Glucose and ATP to form Glucose-6-phosphate and ADP?

$-16.7\,kJ\,mol^{-1}$.

How is the coupling of reactions most often mediated?

Through the synthesis of "high-energy" intermediates.

What are the three structural components of ATP?

An adenine base, a ribose sugar, and three phosphate groups.

What type of bond connects the adenine base to the ribose sugar in ATP?

A glycosidic bond.

What type of bond connects the ribose sugar to the alpha phosphate in ATP?

A phosphoester bond.

What type of bonds connect the phosphate groups in ATP?

Phosphoanhydride bonds.

Why are phosphoanhydride bonds considered "energy rich"?

Because of the relative stabilities of the reactants and products in the breakdown of ATP.

How does the entropy of hydrolysis products compare to ATP?

The entropy of $ADP + P_i$ is greater than that of ATP.

What competition for electrons destabilizes ATP compared to its hydrolysis products?

Phosphoryl groups compete for the lone pair of electrons of its bridging oxygen atom.

How many negative charges does ATP typically have in the physiological $pH$ range?

Three to four negative charges.

What is the typical ATP:ADP ratio maintained in a healthy cell?

Approximately $10:1$.

What is the range for ATP:ADP ratios in necrotic cells?

It can drop down to $0.1:1$.

What do electron carriers exist as in their oxidized form?

A form with a $+$ charge.

What do electron carriers exist as in their reduced form?

A form with an $H$ added.

What are the three biological roles listed for oxidation and reduction reactions?

Protein structure (disulfide bonds), quenching reactive oxygen species, and reduction of electron carriers for cellular energy.

Which enzyme is responsible for quenching superoxide reactive oxygen species?

Superoxide dismutase.

What is an oxidation state?

A number assigned to an atom in a molecule or ion that indicates its partial gain or loss of electrons.

Is an oxidation number an average value for a molecule?

No, it is an individual value assigned to each atom.

In assigning oxidation numbers, which atom gets the electrons in a bond?

The more electronegative atom.

What is the oxidation number of a pure element?

$0$.

What is the oxidation number of a monatomic ion?

It is equal to its charge.

What is the oxidation number of Fluorine in compounds?

Always $-1$.

What is the usual oxidation number of Oxygen?

$-2$ (except in $OF_2$ and $H_2O_2$).

What is the sum of oxidation numbers in a polyatomic molecule or ion?

The total charge of the molecule or ion.

What does NAD stand for?

Nicotinamide adenine dinucleotide.

What are the oxidized and reduced forms of NAD?

$NAD^+$ (oxidized) and $NADH$ (reduced).

In which type of metabolic reactions is NAD typically involved?

Catabolic reactions, such as the ETC.

What is the typical cytoplasmic ratio of $NAD^+$ to $NADH$ in a healthy cell?

Around $700:1$.

What does NADP stand for?

Nicotinamide adenine dinucleotide phosphate.

Where is the extra phosphate located on the NADP molecule?

On the $2'$ carbon of the ribose sugar of the adenine nucleotide.

In which type of metabolic pathways is NADP often used?

Anabolic pathways.

What is the typical $[NADP^+]/[NADPH]$ ratio maintained by healthy cells?

Near $1:100$, favoring more NADPH.

What are the dietary sources from which humans can synthesize NAD/NADP?

Dietary vitamin B3 (Niacin/Nicatinamide) or tryptophan.

Which pathway synthesizes NAD from nicotinic acid?

The Preiss-Handler pathway.

What is the fully reduced form of Flavin adenine dinucleotide (FAD)?

$FADH_2$.

Which vitamin is the precursor for Flavin Mononucleotide (FMN) and FAD?

Riboflavin (vitamin B2).

What are the constituents of the tripeptide glutathione?

Glutamate ($E$), Cysteine ($C$), and Glycine ($G$).

What specific linkage exists between the glutamate and cysteine in glutathione?

A gamma peptide linkage.

What is the ratio of reduced glutathione to oxidized glutathione in healthy cells?

$50:1$.