Metabolism, Enzymes, and Biochemical Pathways: Key Concepts for Biology

What is metabolism?

The process through which living systems acquire and utilize free energy to carry out functions.

What is catabolism?

Degradative process where nutrients are broken down to salvage components or generate energy.

What is anabolism?

Biosynthetic process where biomolecules are synthesized from simpler components.

Is catabolism exergonic or endergonic?

Exergonic (spontaneous oxidation).

Is anabolism exergonic or endergonic?

Endergonic (nonspontaneous).

How are endergonic and exergonic reactions often coupled?

Through high-energy intermediate compounds like ATP.

Why are living organisms considered open systems?

They take up nutrients, release waste, and generate work/heat, meaning they are never at equilibrium.

What is homeostasis in a metabolic context?

Maintaining a non-equilibrium steady state.

What defines an autotroph?

An organism that synthesizes cellular constituents from simple molecules (H2O, CO2, NH3).

What defines a chemolithotroph?

An autotroph that obtains energy through the oxidation of inorganic compounds like NH3 or Fe2+.

What defines a photoautotroph?

An organism that uses light energy to power electron transfer for carbohydrate production.

What defines a heterotroph?

An organism that obtains free energy through the oxidation of organic compounds (carbs, lipids, proteins).

What is an obligate anaerobe?

An organism poisoned by the presence of O2.

What is a facultative anaerobe?

An organism that can grow in the presence or absence of O2.

What is an obligate aerobe?

An organism (like animals) that must use O2 as the oxidizing agent for nutrient breakdown.

What is a metabolite?

Reactants, intermediates, and products of enzymatic reactions in metabolic pathways.

What is a cofactor?

A molecular module enabling enzymes to expand their chemical repertoire.

Distinguish between a coenzyme and a metal ion.

Coenzymes are organic/biological cofactors; metal ions are essential non-protein elements.

What is a cosubstrate?

A transiently enzyme-associated coenzyme (e.g., NAD+).

What is a prosthetic group?

A permanently enzyme-associated coenzyme (e.g., heme).

What is the coenzyme form of thiamine (B1)?

Thiamine pyrophosphate (TPP).

What is the deficiency disease associated with thiamine?

Beriberi or Wernicke-Korsakoff syndrome.

What are the coenzyme forms of riboflavin (B2)?

FMN and FAD.

What are the coenzyme forms of niacin (B3)?

NAD+ and NADP+.

What is the deficiency disease associated with niacin?

Pellagra.

What is the coenzyme form of pantothenic acid (B5)?

Coenzyme A (CoA).

What is the coenzyme form of pyridoxine (B6)?

Pyridoxal phosphate (PLP).

What is the function of biotin (B7)?

Direct coenzyme for carboxylation reactions.

What is the coenzyme form of folate (B9)?

Tetrahydrofolate (THF).

What is the deficiency disease associated with cobalamin (B12)?

Pernicious anemia.

What is the deficiency disease associated with ascorbic acid (C)?

Scurvy.

What role does vitamin K play?

Cofactor for vitamin K-dependent carboxylase.

What is nixtamalization?

Soaking corn in alkaline solution (limewater) to release niacin and prevent Pellagra.

What is the function of lipoic acid?

Mediates acyl transfers.

What type of reaction does biocytin participate in?

Carboxylation.

Why are metabolic pathways irreversible?

They have large negative free energy changes that prevent equilibrium.

What is the 'first committed step'?

An irreversible step early in a pathway that commits the metabolite to that pathway.

How must catabolic and anabolic pathways differ?

They must have at least one different enzymatic step to allow separate regulation.

What are isozymes?

Enzymes catalyzing the same reaction but encoded by different genes with different regulatory properties.

What is the role of LDH Type M?

Reduction of pyruvate to lactate in muscle/liver.

What is the role of LDH Type H?

Catalyzes the reverse reaction (lactate to pyruvate) in heart muscle.

Where does glycolysis occur?

Cytosol.

Where does the citric acid cycle occur?

Mitochondria.

Where does oxidative phosphorylation occur?

Mitochondria.

Where does gluconeogenesis primarily occur?

Liver.

What is the common intermediate for catabolism of many nutrients?

Acetyl-CoA.

What are the 4 major categories of biochemical reactions?

Redox, Group-transfer, Eliminations/Isomerizations, Making/Breaking C-C bonds.

What is the standard free energy equation for a reaction?

ΔG = ΔG°' + RT ln([C][D]/[A][B]).

What is the condition for a 'near-equilibrium' reaction?

ΔG ≈ 0.

How do enzymes control flow far from equilibrium?

By varying activity like a dam in a river.

What is Allosteric Control?

Regulation by substrates, products, or coenzymes of the pathway.

What is an example of Covalent Modification?

Phosphorylation or dephosphorylation by kinases/phosphatases.

What are Substrate Cycles?

Separate regulation of forward and reverse fluxes.

What is Genetic Control?

Up or down regulation of enzyme production.

What characterizes a high-energy phosphate bond?

Often designated by a 'squiggle' (∼).

What is the typical ΔG of ATP hydrolysis in a cell?

Approximately -50 kJ/mol.

Why is ATP hydrolysis so energetic? (Reason 1)

Less resonance stabilization in phosphoanhydride bonds vs. hydrolysis products.

Why is ATP hydrolysis so energetic? (Reason 2)

Electrostatic repulsion between negative charges at neutral pH.

Why is ATP hydrolysis so energetic? (Reason 3)

Higher solvation energy of hydrolysis products.

What is a Thioester?

A high-energy compound where a sulfur atom replaces oxygen in an ester (e.g., Acetyl-CoA).

What is the ΔG°' for thioester hydrolysis?

-31.5 kJ/mol.

What is Substrate-level Phosphorylation?

Direct transfer of phosphate from a high-energy compound to ADP.

What is Oxidative Phosphorylation?

Generating ATP using an ion gradient created by electron transfer.

What is the Adenylate Kinase reaction?

AMP + ATP ⇌ 2ADP.

What is the role of Phosphocreatine?

ATP storage/buffer in muscle and nerve cells.

What is the average ATP turnover rate for a human?

~1.5 kg per hour.

What is the use of Inhibitors in metabolism studies?

Identify pathway blocks; metabolites before increase, after decrease.

What is the purpose of Radioactive Tracers?

Identify metabolites by tracking radioactivity from precursors.

What is the advantage of NMR in metabolism?

Non-invasive monitoring of specifically labeled atoms (e.g., 13C).

What is Transcriptomics?

Study of mRNA expression patterns using bulk-RNAseq or DNA microarrays.

What is Metabolomics?

Global study of metabolites, often using mass spectrometry.

What is Oxidation in terms of electrons?

Loss of electrons ('L.E.O.').

What is Reduction in terms of electrons?

Gain of electrons ('G.E.R.').

What is a Reductant?

A reducing agent (the one being oxidized/losing electrons).

What is an Oxidant?

An oxidizing agent (the one being reduced/gaining electrons).

What is the Nernst Equation form relating ΔG and ΔE?

ΔG = -nFΔE.

What is 'n' in the Nernst equation?

The number of electrons transferred.

What is 'F' (Faraday Constant)?

96,485 J/mol V.

Does a spontaneous reaction have a positive or negative ΔE?

Positive ΔE (corresponds to negative ΔG).

How many electrons are transferred when NAD+ is reduced to NADH?

2 electrons.

What chemical species attacks NAD+ during reduction?

A hydride ion (H-).

How many hydrogen atoms does FAD accept to become FADH2?

Two hydrogen radicals (H·), one at a time.

Why can FAD participate in 1-electron transfers while NAD+ cannot?

FAD can form a stable radical intermediate (FADH·).

What is the standard reduction potential of the NAD+/NADH couple?

-0.315 V.

What is the terminal electron acceptor in the aerobic ETC?

O2.

How many ATPs are generated per oxidation of one NADH?

Approximately 3 ATPs.

What is the function of ATP Synthase?

Transforms electrochemical gradient energy into mechanical energy to power ATP production.

What is the strongest oxidizing agent in the common biochemical table?

O2.

What is the weakest reducing agent in the common biochemical table?

H2O.

Why is metabolic compartmentalization important?

Allows control of opposing pathways and intermediate concentrations across membranes.

Where is Fatty Acid Biosynthesis located?

Cytosol.

Where is Acetyl-CoA synthesized?

Mitochondria.

What is the primary role of the Liver in glucose metabolism?

Gluconeogenesis to maintain blood glucose levels.

What is the primary role of Adipose tissue?

Storage of triacylglycerols.

How does Myosin perform work?

Coupling ATP hydrolysis to the mechanical cocking of the myosin head.

What is a Coupled Reaction?

Linking an exergonic reaction to an endergonic one to drive the latter forward.

What is the key enzyme for Glucose phosphorylation?

Hexokinase.

What is the product of Glucose phosphorylation?

Glucose-6-phosphate (G6P).

What is a 'Metabolic Network'?

The graph-like study of the over 2,000 connected metabolic reactions.

How do we measure ΔG when reactants can't be separated?

By using electrochemical cells/half-reactions to measure voltage directly.