Anabolic and Catabolic Reactions & Metabolism - Vocabulary Flashcards
Anabolic and Catabolic Reactions
Two major types of body reactions important for homeostasis: anabolic (constructive) and catabolic (degradative).
Anabolic reactions produce something larger or more complex than the starting materials; they are also called synthesis reactions.
Catabolic reactions break large molecules into smaller parts; they are also called decomposition reactions.
Illustration: growth and repair (e.g., muscle and bone growth) depend on anabolic processes; digestion and energy extraction depend on catabolic processes.
Water involvement in many reactions:
Anabolic (synthesis) reactions often involve dehydration synthesis, where water is removed to join two molecules.
Catabolic (decomposition) reactions often involve hydrolysis, where water is used to split larger molecules.
Key definitions:
Dehydration synthesis: water removal to join two molecules into a larger one.
Hydrolysis: water addition to break a molecule into smaller parts.
Hydration between molecules during synthesis commonly removes a hydroxyl group (OH) from one molecule and a hydrogen (H) from another, forming water and linking the molecules.
Example of an anabolic reaction: linking relatively small amino acids into a larger protein.
When water is released in anabolic synthesis, the process is dehydration synthesis; when water is added to break bonds, the process is hydrolysis.
Hydrolysis plays a central role in digestion, breaking down large food molecules into smaller units that can be absorbed and reused in dehydration synthesis to build larger macromolecules.
The same concepts apply to nutrient processing and tissue maintenance: digestion (catabolic) provides monomers that can be rebuilt (anabolic) into cellular components.
In summary:
Anabolic = synthesis, build up (dehydration synthesis when water leaves).
Catabolic = decomposition, break down (hydrolysis when water is added).
Metabolism, Metabolic Pathways, and Enzymes
Metabolism: all the chemical activities of a living organism; encompasses all chemical reactions.
Metabolism is often organized into metabolic pathways: linked sequences of reactions that convert a starting material (substrate) through intermediates to a final product.
Example of a simple three-step pathway: Reaction 1 produces substance 3; substance 3 becomes the substrate for Reaction 2, which produces substance 5; substance 5 becomes the substrate for Reaction 3, leading to the final product.
Important idea: for a reaction to occur, all reactants must be present; missing any reactant prevents the pathway from proceeding to the final product.
Enzymes: proteins that act as catalysts to increase the likelihood a reaction will occur (they speed up reactions).
Enzyme specificity: each enzyme typically catalyzes a single reaction and binds to a substrate at the enzyme’s active site.
Enzyme example: an enzyme helps assemble sugar units into glycogen; a different enzyme is needed to break glycogen back down into glucose.
In a metabolic pathway, each step is catalyzed by a different enzyme; the pathway diagram often shows the enzyme name above the reaction arrow.
Regulation of pathways: cells regulate pathways by varying the amount or activity of enzymes; increasing enzyme levels can increase final product output and decreasing enzyme levels reduces output.
When a required enzyme is absent or defective, the corresponding reaction slows dramatically or cannot occur, which limits the final product of the pathway in a domino-like chain reaction.
Important analogy: a chain of dominoes; if any domino is missing or a reaction lacks its enzyme, the entire chain stops and the final product is limited.
Enzymes as catalysts do not change themselves; they are reused after the reaction.
Summary: metabolism = cellular reactions; metabolic pathways = linked reactions; enzymes = catalysts that enable these pathways; regulation adjusts output.
Enzyme Inhibitors and Regulation
Enzyme inhibitors are molecules that bind to enzymes and prevent them from working at maximum efficiency.
Key terms:
Active site: region of the enzyme where the substrate binds.
Substrate: the target molecule that binds to the enzyme’s active site.
Inhibitor: molecule that binds to the enzyme and reduces its activity.
Allosteric site: regulatory site other than the active site; binding here changes enzyme shape and activity.
Competitive inhibition: inhibitor competes with the substrate for the active site; effectiveness depends on the substrate-to-inhibitor ratio; inhibition is reversible.
Noncompetitive (allosteric) inhibition: inhibitor binds to an allosteric site, changing the enzyme’s shape so the active site is no longer functional; this cannot be overcome by simply increasing substrate concentration.
Feedback inhibition: end product of a pathway inhibits an earlier enzyme to regulate the pathway’s activity, conserving cellular resources.
Practical examples:
Penicillin inhibits bacterial cell wall synthesis by targeting enzymes critical to cross-link formation, weakening the cell wall and leading to lysis.
Conceptual flow: inhibitors modulate enzyme activity, affecting metabolic flux through pathways; feedback inhibition helps cells maintain homeostasis by aligning production with demand.
Redox Reactions and Electron Carriers
Redox reactions involve oxidation (loss of electrons) and reduction (gain of electrons); they occur together (coupled) in redox couples.
Oxidation state changes are tracked by hydrogen transfer in biology; oxidation of a molecule typically releases energy that can be captured by electron carriers.
Electron carriers commonly used in cellular respiration: NADH, FADH2, NADPH.
Basic idea: electrons (and associated energy) are transferred through carriers to power energy-harvesting processes.
Redox reactions are central to cellular respiration, enabling energy extraction from carbohydrates, lipids, and proteins.
Note: fructose, glucose, and other substrates can be oxidized stepwise, with electrons handed off to carriers that shuttle them to the electron transport chain (ETC).
Carbohydrate Catabolism: Glycolysis
Location: cytoplasm (in both prokaryotes and eukaryotes).
Overall goal: convert glucose to pyruvate while capturing energy as ATP and reducing equivalents (NADH).
Phases of glycolysis (three major phases):
Energy investment (activation) phase: invest 2 ATP to phosphorylate glucose, forming fructose-1,6-bisphosphate; this destabilizes the glucose for cleavage.
Cleavage (lysis) phase: fructose-1,6-bisphosphate is split into two three-carbon molecules: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P).
Energy payoff phase: DHAP isomerized to a second G3P; each G3P proceeds through oxidation and substrate-level phosphorylation to yield ATP and NADH, ultimately forming pyruvate.
Key carbons and intermediates:
Start: C6H{12}O_6 (glucose).
After phosphorylation: fructose-1,6-bisphosphate (C6 with two phosphates).
Cleavage products: dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P).
DHAP isomerizes to a second molecule of G3P, so two G3P enter payoff phase.
Energy accounting (per glucose):
Energy investment: -2 ATP (two ATP consumed).
Energy generation: from each G3P, the steps yield ATP and NADH; overall for two G3P molecules, net yield is +4 ATP from substrate-level phosphorylation, yielding a total of +4 - 2 = +2 ATP per glucose.
Reducing power: two NADH produced during glycolysis.
Overall products of glycolysis per glucose: 2 pyruvate, 2 NADH, and net 2 ATP.
Important notes:
NADH produced in glycolysis can be shuttled into mitochondria in eukaryotes (costing ATP to move across membranes) or used directly in prokaryotes.
The pyruvate molecules produced are substrate for the next steps of cellular respiration (intermediate step), not directly used in glycolysis again.
Practical analogy: how a recipe requires all ingredients to be present; glycolysis requires glucose and cofactors; enzymes drive each step like specialized cooks; the “domino” concept emphasizes that removing a step impedes downstream production.
Intermediate Step (Pyruvate Oxidation to Acetyl-CoA)
Purpose: connect glycolysis to the citric acid cycle by preparing pyruvate for entry into the cycle.
For each glucose, two pyruvate molecules are produced; this step must occur twice.
Key events per pyruvate:
Decarboxylation: release of CO_2, reducing the carbon skeleton from three carbons to two carbons (acetyl group).
Oxidation: electrons removed are transferred to the electron carrier NAD+, forming NADH.
Coenzyme A binds to the acetyl group to form acetyl-CoA.
Net products per glucose (two pyruvate):
2 ext{ NADH} produced.
2 ext{ acetyl-CoA} produced.
2 ext{ CO}_2 released (waste product).
Why acetyl-CoA is used: two-carbon acetyl-CoA is the substrate that enters the citric acid cycle with oxaloacetate to form citric acid.
Carbon accounting reminder: pyruvate has 3 carbons; acetyl-CoA has 2 carbons; a decarboxylation step reduces carbon count by 1 per pyruvate.
Citric Acid Cycle (Krebs Cycle, TCA)
Location: mitochondrial matrix in eukaryotes; cytoplasm in many bacteria.
Overall purpose: fully oxidize acetyl-CoA and generate reduced electron carriers (NADH, FADH2) and a substrate-level phosphate (GTP) while releasing CO2.
Start and key intermediates:
Start with acetyl-CoA (two carbons) and oxaloacetate (four carbons) to form citric acid (six carbons).
Isomerization converts citric acid to a form amenable to oxidation (isocitric acid).
Sequence and outputs per turn (per acetyl-CoA):
2 CO2 released (during decarboxylation steps).
NADH produced in multiple steps: total per turn = 3 ext{ NADH}.
A second redox step produces another 1 ext{ NADH} and a covalently bound acetyl-CoA-derived fragment becomes succinyl-CoA; in this step, NADH is produced and CoA is released.
FADH2 produced in one step (succinate to fumarate).
GDP (or ADP) // substrate-level phosphorylation yields GTP (or ATP).
Regeneration of oxaloacetate completes the cycle, allowing another turn with a fresh acetyl-CoA.
Per glucose (two turns of the cycle):
6 ext{ NADH}, 2 ext{ FADH}2, 2 ext{ GTP} (equivalently 2 ext{ ATP} via substrate-level phosphorylation), and 6 ext{ CO}2 released.
Oxaloacetate is regenerated to continue the cycle.
Carbon dioxide production significance:
The CO_2 produced is the same gas exhaled by lungs; its management relates to acid-base balance in the body via carbonic acid buffering.
Conceptual big-picture: energy stored as reduced electron carriers (NADH, FADH2) will be cashed in later via the electron transport chain to generate ATP.
Electron Transport Chain (ETC) and Aerobic Respiration in Eukaryotes
Location: embedded in the inner mitochondrial membrane (eukaryotes) with a separate cytosolic environment; in prokaryotes, the chain resides in the cell membrane.
Components: three complexes (I, II, III) plus IV, plus ATP synthase; electrons flow through these complexes, driving proton pumping across the membrane to create a proton gradient.
Electron donors and final acceptor:
Reduced carriers NADH and FADH2 donate electrons to the chain.
Final electron acceptor is molecular oxygen (O2), which becomes water after accepting electrons and protons.
Proton pumping and the proton gradient:
NADH oxidation drives pumping of protons across the membrane at multiple complexes, creating a proton motive force.
In the classic view, a single NADH can drive pumping of about 10 protons (4 at Complex I, 4 at Complex III, 2 at Complex IV).
A single FADH2, which donates electrons at Complex II, contributes fewer pumped protons (typically about 6 total: 4 at Complex III and 2 at Complex IV).
Chemiosmosis and ATP synthesis:
Protons flow back through ATP synthase, driving the rotary mechanism which catalyzes the formation of ATP from ADP and inorganic phosphate (Pi).
A general rule: about 3 protons flowing back yields 1 ATP; thus, NADH-derived flow yields about 3 ext{ ATP} and FADH2-derived flow yields about 2 ext{ ATP}.
ATP yield per glucose (a common summary):
NADH contribution: about 3 ext{ ATP} per NADH.
FADH2 contribution: about 2 ext{ ATP} per FADH2.
Per glucose, total ATP yield in eukaryotes is typically around 36-36/38 ATP, commonly cited as 36 ATP, because transporting cytosolic NADH into the mitochondrion costs energy.
In prokaryotes, ETC can occur at the cell membrane with no transport cost across organelle membranes, yielding up to about 38 ext{ ATP} per glucose.
Important distinctions:
Eukaryotic mitochondria require transport of cytosolic NADH into the mitochondrion, which consumes energy and reduces net yield.
Prokaryotes lack mitochondria; their ETC is located in the plasma membrane and can maximize ATP yield to about 38 per glucose.
Key takeaway: the ETC and chemiosmosis are the main source of ATP in aerobic respiration, with most ATP produced here rather than in glycolysis or the citric acid cycle alone.
Electron Transport Chain: Prokaryotes vs Eukaryotes; Aerobic vs Anaerobic Chains
Similar phases across organisms: glycolysis, intermediate step, citric acid cycle, and ETC (in many organisms).
Differences lie in final electron acceptors and cellular location. Some bacteria use alternatives to O2 as the final electron acceptor (examples: nitrate, nitrite, sulfate, carbonate, etc.), enabling anaerobic respiration.
If the final electron acceptor is carbonate (CO3^2-), the outcome can be methane production in certain archaea, illustrating how the ETC can be adapted to different chemical environments.
Fermentation as an alternative to respiration occurs when no suitable final electron acceptor is available; NAD+ regeneration is achieved by transferring electrons to organic molecules during glycolysis, allowing glycolysis to continue without an ETC.
Chemiosmosis and Proton Motive Force
Chemiosmosis: generation of a proton gradient (proton motive force) across a membrane by pumping protons (H+) during electron transport.
Proton motive force drives ATP synthase to synthesize ATP from ADP and Pi, using the energy stored in the gradient.
The gradient is a form of potential energy that can be harnessed to do cellular work, including ATP production.
Analogy: water dam powering a turbine; in cells, protons flow through ATP synthase to drive ATP production.
Most ATP production in aerobic respiration comes from chemiosmosis via ATP synthase and proton motive force.
Fermentation (Anaerobic or Oxygen-Limited Conditions)
When oxygen or other terminal electron acceptors are unavailable, cells regenerate NAD+ by transferring electrons to organic molecules via fermentation.
Glycolysis continues to operate to produce a net 2 ATP per glucose, but fermentation avoids a block by regenerating NAD+.
Common fermentation endpoints:
Lactic acid fermentation: pyruvate accepts electrons to form lactate.
Ethanol fermentation: pyruvate is converted to acetaldehyde, which accepts electrons to form ethanol (via NADH and natural intermediate steps).
Fermentation yields various byproducts depending on the organism and conditions; it allows glycolysis to continue in the absence of a functional ETC.
Lipid Catabolism
Lipids and proteins serve as alternate energy sources when carbohydrates are scarce.
Lipids are primarily broken down from triglycerides into glycerol and fatty acids via hydrolysis, catalyzed by lipase.
Glycerol pathway: glycerol is converted to dihydroxyacetone phosphate (DHAP) by phosphorylation, then enters glycolysis as G3P and proceeds to pyruvate, yielding ATP and NADH.
Fatty acid beta-oxidation: fatty acids are cleaved two carbons at a time as acetyl-CoA units; each round yields NADH and FADH2 and acetyl-CoA for the citric acid cycle.
Net energy carriers produced by beta-oxidation contribute to the ETC and ATP generation.
Protein Catabolism
Proteins can be used for energy and precursor metabolites when carbohydrates or lipids are limited.
Proteins are first broken down by exoenzymes (proteases) outside the cell into amino acids.
Amino acids are then transported into the cell and deaminated (amine group removed) to form carbon skeletons that feed into glycolysis or the citric acid cycle.
Some amino acids can be converted directly to intermediates that enter the TCA cycle or glycolysis for energy production.
Essential amino acids are those that cannot be synthesized by the organism and must be obtained from the diet.
Anabolic Pathways and Biosynthesis
Anabolic pathways build macromolecules from precursor metabolites and require energy input.
Many biosynthetic reactions are reversible and can proceed in either direction depending on cellular needs and regulation.
Carbohydrate biosynthesis:
Calvin-Benson cycle in photosynthetic organisms converts CO₂ into glyceraldehyde-3-phosphate; glyceraldehyde-3-phosphate serves as a starting point to synthesize sugars such as starch, glycogen, peptidoglycan, and cellulose.
Gluconeogenesis: synthesis of glucose from non-carbohydrate precursors (e.g., glycerol, fatty acids, amino acids); requires substantial energy input.
Lipid biosynthesis (reverse of lipid catabolism):
Glycerol component can be formed from DHAP; fatty acids are synthesized by extending acetyl-CoA units and used to form triglycerides via dehydration synthesis.
Amino acid biosynthesis:
Some cells can synthesize all amino acids; others rely on essential amino acids from the diet.
Precursor metabolites such as oxaloacetate can be converted into amino acids via amination (adding an amino group) or transamination (transferring an amino group from one amino acid to another precursor).
Nucleotide biosynthesis:
Nucleotides consist of a five-carbon sugar, nitrogenous base, and phosphate.
Bases are built from amino acids (e.g., aspartic acid, glutamine, glycine) with ATP involvement in conversion steps.
Purines and pyrimidines are synthesized through pathways that rely on amino acid-derived precursors; nucleotides are later polymerized into DNA and RNA (details in later lectures).
Overall, biosynthesis relies on precursor metabolites from catabolic pathways and cellular energy to build cellular components and macromolecules.
Connections, Implications, and Big Picture
The entire metabolic system is tightly integrated: catabolic pathways feed energy and precursors into anabolic pathways, while anabolic pathways consume energy and precursors to build macromolecules.
Energy currency: ATP and reduced electron carriers (NADH, FADH2) link catabolism to anabolism and drive biosynthetic reactions.
Homeostasis and regulation: cells regulate metabolic flux through enzyme levels and allosteric control, enabling adaptation to changing energy demands and nutrient availability.
Real-world relevance: metabolic processes underpin growth, maintenance, exercise adaptation, digestion, energy production, and responses to nutrient availability; disruptions can affect pH balance, energy production, and overall health.
Key numerical concepts to memorize (per glucose) for aerobic respiration:
Glycolysis: net 2 ATP, 2 NADH.
Intermediate step (pyruvate to acetyl-CoA): 2 ext{ NADH}, 2 ext{ CO}_2.
Citric acid cycle (per glucose, two turns): 6 ext{ NADH}, 2 ext{ FADH}2, 2 ext{ GTP}, 6 ext{ CO}2.
Electron transport chain: NADH yields about 3 ext{ ATP} each; FADH2 yields about 2 ext{ ATP} each.
Typical total ATP yield for aerobic respiration in eukaryotes: about 36-36/38 ATP per glucose (commonly cited as 36) due to ATP cost of NADH transport into mitochondria; prokaryotes can yield about 38 ATP per glucose since they lack mitochondrial compartments.
The carbon balance and gas exchange: CO₂ is produced in intermediate and citric acid cycle steps and is the same CO₂ exhaled by the respiratory system; this links cellular metabolism to respiratory and cardiovascular system function to maintain pH and gas balance.
The interplay of respiration and fermentation allows cells to adapt to oxygen availability: respiration yields more ATP, whereas fermentation preserves glycolytic flux when respiration is not possible.
Ethical, philosophical, and practical implications: understanding metabolism informs medical treatment, nutrition science, and interventions in metabolic disorders, athletic performance, and infectious disease management (e.g., how pathogens metabolize host resources).
Quick Reference: Key Formulas and Facts (LaTeX)
Glucose formula: C6H{12}O_6
Net ATP glycolysis: 2 ATP
NADH produced in glycolysis: 2 NADH
Pyruvate produced per glucose: 2 pyruvate
Intermediate step products per glucose (two pyruvate): 2\ NADH, 2\ CO_2, 2\ acetyl\text{-}CoA
Citric Acid Cycle (per glucose, two turns): 6\ NADH,\ 2\ FADH2,\ 2\ GTP,\ 6\ CO2
NADH energy yield: ext{NADH} \rightarrow \approx 3\ \text{ATP}
FADH2 energy yield: \approx 2\ \text{ATP}
Total ATP yield (eukaryotic): \approx 36\text{ ATP} per glucose; prokaryotic yield can be about 38\ \text{ATP} per glucose
Proton pumping (per NADH): Complex I (4 H+), Complex III (4 H+), Complex IV (2 H+) → total 10\ H^+ per NADH
Proton pumping (per FADH2): entry at Complex II; Complex III (4 H+), Complex IV (2 H+) → total 6\ H^+ per FADH2
Final electron acceptor in aerobic respiration: O2 → H2O
Main energy carriers: NADH,\ FADH_2,\ NADPH
Dehydration synthesis: water removal to join two molecules
Hydrolysis: water addition to split molecules
Major byproducts: CO2 (carbon dioxide) and H2O (water) as dictated by oxidation states and electron flow