BIOC Metabolism

What is metabolism?

The sum of all chemical processes necessary to make possible the characteristics of living cells and organisms

What are the three fundamental requirements all organisms need to maintain themselves grow and reproduce?

Energy; carbon sources; and reducing power

What is reducing power in a biological context?

The supply of electrons (e⁻) needed for biosynthetic reactions — often carried by molecules like NADPH which donate electrons to reduce substrates during anabolism

What is the difference between a phototroph and a chemotroph?

Phototrophs use light as their energy source; chemotrophs use chemical compounds (either inorganic or organic) as their energy source

What is the difference between an autotroph and a heterotroph?

Autotrophs use inorganic carbon (CO₂) as their carbon source; heterotrophs use organic compounds as their carbon source

What are the energy carbon and electron sources of a photoautotroph?

Light for energy; CO₂ as carbon source; inorganic compounds like H₂O or H₂S as electron source

What are the energy carbon and electron sources of a chemoautotroph?

Inorganic compounds like H₂ FeCO₃ or NH₃ for energy; CO₂ as carbon source; same inorganic compounds as electron source

What are the energy carbon and electron sources of a photoheterotroph?

Light for energy; organic compounds like isopropanol or lactate as both carbon and electron source

What are the energy carbon and electron sources of a chemoheterotroph?

Organic compounds like glucose or fats for energy; organic compounds as carbon source; organic compounds as electron source

Why are photoheterotrophs considered very rare?

It is an unusual combination to use light for energy while depending on organic compounds for carbon and electrons — making ecological niches for this metabolism very limited

What metabolic category do humans belong to and why?

Chemoheterotrophs — they obtain energy carbon and electrons from organic compounds such as carbohydrates fats and proteins

What metabolic category do higher plants belong to?

Photoautotrophs

What metabolic category do sulphur bacteria belong to?

Chemoautotrophs (also called chemolithotrophs)

What metabolic category do most microbes belong to?

Chemoheterotrophs (also called chemoorganotrophs)

What metabolic category do blue-green algae belong to?

Photoautotrophs

What metabolic category do non-sulphur purple bacteria belong to?

Photoheterotrophs

What is the scientific name of the giant tubeworm and where does it live?

Riftia pachyptila — lives in hydrothermal vents at ocean depths where sunlight cannot reach

What type of bacteria do giant tubeworms have a symbiotic relationship with?

Chemolithotrophic bacteria

What do giant tubeworms provide to their symbiotic bacteria?

Oxygen

What do the chemolithotrophic bacteria inside giant tubeworms use the oxygen for?

To oxidise hydrogen sulphide releasing energy used to fix CO₂

What do the bacteria provide to the tubeworms in return?

Nutrients

Why is the giant tubeworm an interesting metabolic example?

It demonstrates a symbiotic relationship where a macroorganism supports chemolithotrophic bacteria performing CO₂ fixation without sunlight — illustrating how chemosynthesis can sustain life in extreme environments

What is catabolism?

The breakdown of complex molecules into simpler ones releasing energy overall involving oxidative reactions where electrons and hydrogen are removed or oxygen is added

What is anabolism?

The biosynthesis of complex molecules from simpler ones requiring energy input involving reductive reactions where electrons and hydrogen are added

Give an example of a catabolic pathway.

Respiration of glucose

Give an example of an anabolic pathway.

Protein synthesis

What is the sign of ΔG for a catabolic reaction and what does this mean?

Negative ΔG — the reaction releases energy and can occur spontaneously

What is the sign of ΔG for an anabolic reaction and what does this mean?

Positive ΔG in isolation — the reaction requires energy and cannot occur spontaneously on its own

How do cells drive anabolic reactions that have a positive ΔG?

By coupling them to exothermic reactions via enzymes so the overall ΔG of the combined reactions is negative

What is the Gibbs Free Energy equation relating ΔG° to the equilibrium constant?

ΔG° = −RT ln Keq

What is the full Gibbs Free Energy equation accounting for actual concentrations?

ΔG = ΔG° + RT ln ([C][D] / [A][B])

What does a Keq greater than 1 tell you about ΔG°?

ΔG° is negative — the forward reaction is thermodynamically favourable under standard conditions

What does a Keq less than 1 tell you about ΔG°?

ΔG° is positive — the reverse reaction is favoured under standard conditions

How can the actual ΔG of a reaction differ from ΔG°?

ΔG depends on actual concentrations of reactants and products not just standard conditions — cells can manipulate concentrations to drive reactions that appear unfavourable under standard conditions

What are the three main forms of energy currency in metabolism?

High energy bonds such as ATP; reduced coenzymes such as NADH; concentration gradients such as the proton (H⁺) gradient

What is ATP and what bond stores its energy?

Adenosine triphosphate — energy is stored in its high-energy phosphoanhydride bonds between the phosphate groups

What is the ΔG of ATP hydrolysis?

Approximately −50 kJ/mol

What is the chemical equation for ATP hydrolysis?

ATP + H₂O → ADP + Pi

What is NAD⁺ and what is its role in metabolism?

Nicotinamide adenine dinucleotide in its oxidised form — acts as an oxidising agent in catabolic pathways accepting electrons and hydrogen from substrates

What is NADH?

The reduced form of NAD⁺ formed when NAD⁺ accepts two electrons and one hydrogen ion from a substrate during catabolism

What happens to NADH after it is produced in catabolism?

It is reoxidised back to NAD⁺ at the electron transport chain with the released energy used to generate ATP

What is NADPH and what is its role in metabolism?

Nicotinamide adenine dinucleotide phosphate in its reduced form — acts as a reducing agent in anabolic pathways donating electrons and hydrogen to biosynthetic reactions

How does NADPH differ structurally from NADH?

NADPH has an additional phosphate group on the 2' position of the adenosine ribose compared to NADH

Why is it important that NAD⁺/NADH and NADP⁺/NADPH are kept as separate pools?

NAD⁺ is used mainly in catabolism and NADPH mainly in anabolism — keeping them separate allows the cell to regulate opposing pathways independently and maintain correct redox balance in each

What is FAD and what is its role in metabolism?

Flavin adenine dinucleotide in its oxidised form — acts as an oxidising agent in catabolic pathways accepting electrons and hydrogen to become FADH₂

What is a key physical property of FAD that distinguishes it from NAD⁺?

FAD is not found free in solution — it is always protein bound within flavoproteins

Why does FAD being protein bound matter functionally?

It means FAD acts as a tightly associated prosthetic group of its enzyme rather than a freely diffusible coenzyme — keeping it localised to specific reactions

Where does FADH₂ ultimately donate its electrons?

To the electron transport chain

What are the four key catabolic pathways?

Glycolysis; fatty acid oxidation; the citric acid cycle; the electron transport chain

What is the central hub molecule linking glycolysis fatty acid oxidation and the citric acid cycle?

Acetyl-CoA

What additional waste product is produced when humans catabolise proteins compared to carbohydrates and fats?

Urea — produced from the nitrogen-containing amino groups of amino acids

Why must waste nitrogen be removed as urea rather than ammonia?

Ammonia is highly toxic so the liver converts it to urea via the urea cycle which is less toxic and can be safely excreted in urine

What are the five key needs that metabolic regulation must meet in the human body?

All cells must receive adequate metabolic fuel; fuel must be delivered in the correct form for each tissue; blood glucose must be kept within a set range; excess fuel must be stored rather than wasted; waste products like nitrogen must be safely removed

Why does the brain specifically need glucose as its metabolic fuel?

The brain normally cannot use fatty acids as it is separated from the circulation by the blood-brain barrier and lacks significant capacity for fatty acid oxidation

What alternative fuel can the brain use during starvation?

Ketone bodies

What are ketone bodies and where are they produced?

Acetoacetate; beta-hydroxybutyrate; and acetone — produced by the liver from acetyl-CoA during prolonged fasting when glucose is scarce

What is the metabolic role of the liver in the fed state?

Uses excess fuel to make glycogen and fat storing energy for later use

What is the metabolic role of the liver in the fasting state?

Releases glucose into the blood and produces ketone bodies to fuel other tissues

What is the metabolic role of skeletal muscle in the fed state?

Takes up excess glucose and stores it as glycogen for its own future use

What is the metabolic role of adipose tissue in the fed state?

Takes up fat from the circulation and stores it as triglycerides

What is the metabolic role of adipose tissue in the fasting state?

Releases fatty acids into the bloodstream for other tissues to use as fuel

Why can't muscle glycogen contribute to blood glucose?

Muscle cells lack the enzyme glucose-6-phosphatase which is needed to release free glucose into the bloodstream

What is glycolysis?

The metabolic pathway that breaks down one molecule of glucose into two molecules of pyruvate producing ATP NADH and carbon compounds in the process

What are the three main outputs of glycolysis?

ATP (energy); NADH (reducing power); and pyruvate/carbon intermediates for biosynthesis or further metabolism

Why is glycolysis described as unique?

It is the only metabolic pathway that can produce ATP without requiring mitochondria or oxygen — it occurs entirely in the cytosol

What percentage of glucose's energy is released during anaerobic glycolysis alone?

Only about 10% of glucose's total energy

Where in the cell does glycolysis take place?

The cytosol (cytoplasm)

What is the starting molecule of glycolysis?

Glucose (or glucose-6-phosphate if entering from glycogen)

What is the end product of glycolysis?

Two molecules of pyruvate per glucose

What are four types of cells that rely heavily on glycolysis?

"Red blood cells; ischaemic heart tissue; active white skeletal muscle; fast-growing tumours"

Why do red blood cells rely entirely on glycolysis?

Red blood cells lack mitochondria so they cannot perform aerobic respiration and must rely solely on glycolysis for ATP

Why do fast-growing tumours rely heavily on glycolysis?

Tumours often outgrow their blood supply resulting in poor oxygen delivery and preferentially use glycolysis even in the presence of oxygen — the Warburg effect

What are the three main sources of glucose for glycolysis?

Dietary glucose from digestion (fed state); glycogen breakdown — glycogenolysis (fasting/exercise); gluconeogenesis from lactate amino acids and glycerol (starvation)

What enzyme breaks glycogen down to release glucose for glycolysis?

Glycogen phosphorylase — cleaves glucose units as glucose-1-phosphate

What enzyme converts glucose-1-phosphate to glucose-6-phosphate?

Phosphoglucomutase

What do the 10 enzymes of glycolysis in order?

Hexokinase; glucose phosphate isomerase; phosphofructokinase; aldolase; triose phosphate isomerase; glyceraldehyde-3-phosphate dehydrogenase; phosphoglycerate kinase; phosphoglycerate mutase; enolase; pyruvate kinase

What are the three major enzyme classes present in glycolysis?

Kinases (transfer phosphate groups); isomerases including mutases (rearrange molecules); dehydrogenases (oxidise substrates)

What does hexokinase do and why is it important?

Phosphorylates glucose to glucose-6-phosphate using one ATP — traps glucose inside the cell because glucose-6-phosphate cannot cross the plasma membrane

Why is the hexokinase reaction thermodynamically favourable overall?

ATP hydrolysis has a ΔG of approximately −50 kJ/mol which more than offsets the +17 kJ/mol cost of phosphorylating glucose giving an overall ΔG of approximately −33 kJ/mol

What is the role of glucose phosphate isomerase?

Converts glucose-6-phosphate (an aldose) to fructose-6-phosphate (a ketose) isomerising the molecule

What does phosphofructokinase (PFK) do?

Phosphorylates fructose-6-phosphate to fructose-1,6-bisphosphate using one ATP — the most important regulatory step of glycolysis

Why is PFK the most important regulatory point of glycolysis?

It catalyses the committed step — once fructose-1,6-bisphosphate is made the cell is committed to completing glycolysis; highly regulated by ATP AMP ADP and citrate

What does aldolase do?

Cleaves fructose-1,6-bisphosphate into two three-carbon molecules: glyceraldehyde-3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP)

What does triose phosphate isomerase do?

Converts DHAP into GAP so both three-carbon products can continue through the lower half of glycolysis

What is the energy investment phase of glycolysis?

The first steps up to and including formation of fructose-1,6-bisphosphate during which 2 ATP are consumed to prepare glucose for splitting

What does glyceraldehyde-3-phosphate dehydrogenase (GAPDH) do?

Oxidises GAP and simultaneously phosphorylates it to produce 1,3-bisphosphoglycerate (1,3-BPG) reducing NAD⁺ to NADH in the process

Why does GAPDH use a thioester intermediate?

Phosphorylation of GAP has a high activation energy with a positive ΔG; GAPDH first oxidises GAP (releasing energy) to form a high-energy thioester intermediate via a cysteine residue — this stored energy then drives the otherwise unfavourable phosphorylation step

What is substrate-level phosphorylation?

The direct transfer of a phosphate group from a high-energy substrate to ADP to form ATP without involving the mitochondrial respiratory chain — occurs at phosphoglycerate kinase and pyruvate kinase steps

What does phosphoglycerate kinase do?

Transfers the high-energy phosphate from 1,3-bisphosphoglycerate to ADP producing 3-phosphoglycerate and ATP

What does phosphoglycerate mutase do?

Moves the phosphate group from carbon 3 to carbon 2 converting 3-phosphoglycerate to 2-phosphoglycerate

What does enolase do?

Removes a water molecule from 2-phosphoglycerate to produce phosphoenolpyruvate (PEP) a high-energy compound

What does pyruvate kinase do?

Transfers the phosphate from PEP to ADP producing pyruvate and ATP

Why is the pyruvate kinase reaction essentially irreversible in the cell?

The enol form of pyruvate spontaneously and rapidly converts to the more stable keto form — because enolpyruvate concentration is kept very low there is negligible substrate for the reverse reaction

What is the net ATP yield from glycolysis starting from free glucose?

Net 2 ATP (2 consumed in investment phase, 4 produced in payoff phase)

What is the net ATP yield if glucose enters from glycogen?

Net 3 ATP — because glycogen breakdown by glycogen phosphorylase does not require ATP to phosphorylate the glucose unit (enters as glucose-1-phosphate bypassing the hexokinase step)

What is the net ATP yield from glycolysis of fructose-6-phosphate?

Net 3 ATP — enters after the hexokinase step so only 1 ATP consumed (by PFK)

What is the net ATP yield from glycolysis of fructose-1

6-bisphosphate?,Net 4 ATP — enters after both hexokinase and PFK steps so no ATP consumed in investment phase

What is the net yield from glycolysis of one molecule of glyceraldehyde-3-phosphate?

Net 2 ATP and 1 NADH — enters the lower half of glycolysis directly

How many NADH molecules are produced per glucose during glycolysis?

2 NADH (one from each GAP oxidised by GAPDH)

What happens to NADH produced in the cytosol during aerobic conditions?

Electrons from NADH are shuttled into the mitochondria via the malate-aspartate shuttle and fed into the electron transport chain generating approximately 1.5-2.5 ATP per NADH