Ch 5: Cell Metabolism — Synthesis and Degradation of Biological Molecules (Vocabulary Flashcards)
Key Concept 5.1: ATP and Reduced Coenzymes Are the Energy Currency for Biosynthesis
Energy in cells is stored in chemical bonds; energy can be released and transformed by metabolic pathways. A metabolic pathway is a coordinated sequence of biochemical reactions converting molecules into other molecules, typically catalyzed by specific enzymes.
Major characteristics of metabolic pathways:
They consist of a series of intermediate reactions.
Each reaction is catalyzed by a specific enzyme.
Most pathways are conserved across organisms (from prokaryotes to eukaryotes).
Many pathways are compartmentalized (cytosol vs. organelles in eukaryotes; cytosol in prokaryotes).
Pathways are controlled by one or a few key enzymes that can be inhibited or activated, thereby tuning the rate of the pathway.
Energy sources for cellular work come from the breakdown of energy-rich organic molecules; some organisms also use energy from the Sun (photosynthesis) or inorganic sources (e.g., H2S at hydrothermal vents).
Endergonic vs. exergonic:
Endergonic reactions require net energy input to proceed.
Exergonic reactions release energy.
In cells, endergonic reactions are coupled to exergonic reactions so that energy is supplied when and where needed.
Energy currencies in cells:
The two most widely used energy currencies are ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).
ATP hydrolysis releases energy that can be used to drive endergonic processes. The hydrolysis reaction is typically written as:
\mathrm{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi} + \text{free energy}
with a standard free energy change of about \Delta G^\circ_{\text{hydrolysis}} \approx -7.3\ \text{kcal/mol} under standard lab conditions, though cellular conditions can differ.The energy stored in ATP is replenished by cellular processes that synthesize ATP from ADP and P_i, often coupling to exergonic reactions elsewhere in metabolism.
ATP can be formed by substrate-level phosphorylation (a direct transfer of a phosphate from a donor molecule to ADP) or by oxidative phosphorylation (the primary source in most cells).
ATP as an energy currency in cells:
ATP hydrolysis to ADP and P_i releases energy used to drive endergonic reactions (e.g., active transport, macromolecule synthesis, motor protein movement).
In many cellular contexts, endergonic reactions are powered by coupling to ATP hydrolysis or to the oxidation of NADH/NADPH and subsequent formation of ATP.
Redox energy transfer and reduced coenzymes:
Redox reactions involve transfer of electrons between molecules; oxidation is loss of electrons, reduction is gain of electrons (OIL RIG).
Redox reactions can be described in terms of electron transfer or, equivalently, hydrogen transfer (H atom transfer).
Oxidizing agents accept electrons; reducing agents donate electrons.
NAD+ and NADH are key electron carriers. NAD+ is the oxidized form; NADH is the reduced form. A typical reduction is:
\mathrm{NAD^+} + \mathrm{H^+} + 2e^- \rightarrow \mathrm{NADH}The oxidation of NADH by oxygen is a major exergonic step in respiration:
\mathrm{NADH} + \mathrm{H^+} + \tfrac{1}{2}\mathrm{O2} \rightarrow \mathrm{NAD^+} + \mathrm{H2O}
with a large free-energy change, \Delta G^\circ \approx -52.4\ \text{kcal/mol} (about -219\ \text{kJ/mol}).
Oxygen as terminal electron acceptor: NADH oxidation by O2 is highly exergonic and drives ATP production through oxidative phosphorylation.
Other redox-active cofactors include FAD/FADH2 and NADP+/NADPH. These participate in glycolysis, the citric acid cycle, and photosynthesis (NADPH is the NADP+ reduced form).
Coupling energy flow: catabolism releases energy from oxidation, the energy is captured mainly in NADH (and other reduced cofactors), and the energy in NADH is ultimately used to generate ATP (via oxidative phosphorylation).
Illustrative energy flow in a cell:
Organic molecules are oxidized (catabolism), releasing energy.
Reduced cofactors (e.g., NADH) are formed, storing energy in chemical bonds.
NADH is oxidized to NAD+ and reduces O2 to H2O, releasing energy that is used to synthesize ATP via oxidative phosphorylation.
Summary points for 5.1:
ATP is the cell’s main energy currency; its hydrolysis provides energy for endergonic processes.
NADH and other reduced cofactors store energy and deliver electrons to drive ATP synthesis.
Redox chemistry (OIL RIG) underpins energy transfer; NAD+/NADH and NADP+/NADPH are central to energy flow in metabolism.
The high-energy phosphate bonds of ATP (P–O–P bonds) are a key feature; hydrolysis of these bonds releases energy that can be captured in ATP synthesis and used for cellular work.
Review & Apply (Key questions to reinforce 5.1):
In Chapter 4 you learned about the sodium-potassium pump and ATP usage. Explain how the high-energy bonds in ATP enable active transport.
For each of the following reactions, determine whether carbon atoms are being oxidized or reduced:
a. ${\mathrm{CH2O6}} + 6\mathrm{O2} \rightarrow 6\mathrm{CO2} + 6\mathrm{H_2O}$
b. $6\mathrm{CO} + 6\mathrm{H2O} \rightarrow \mathrm{CH2O} + 6\mathrm{O_2}$
The energy required to reduce NAD+ to NADH is substantial. Where does this energy come from in cellular metabolism?
Key Concept 5.2: Carbohydrate Catabolism in the Presence of Oxygen Releases a Large Amount of Energy
Aerobic respiration comprises four major stages in glucose catabolism: glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation (electron transport/chemiosmosis).
Overall equation for complete glucose oxidation (in vivo and in the lab) is the same:
\text{Glucose} + 6\mathrm{O2} \rightarrow 6\mathrm{CO2} + 6\mathrm{H_2O} + \text{energy}
with a significant energy release (about 686\ \text{kcal/mol}, 2,872\ \text{kJ/mol} per mole of glucose).Actual energy captured by cells is substantial but not 100% efficient; about 234\ \text{kcal/mol} (34% of total) is captured in the high-energy phosphoanhydride bonds of ATP during aerobic respiration.
Efficiency of energy capture is high, comparable to gasoline-powered cars (~25–50% typical in engines).
Why do many steps occur in small increments? The energy released is captured in small, manageable chunks (e.g., NADH reduction and ATP phosphorylation) rather than a single large release.
Fermentation vs aerobic respiration:
When O2 is scarce, glucose is only partially oxidized; energy yield drops to about 28\ \text{kcal/mol} (≈ 2% efficiency).
Fermentation occurs in the absence of O2 and yields far less ATP than aerobic respiration but allows glycolysis to continue by regenerating NAD+.
Stages in detail:
Glycolysis (cytosol): 10 enzyme-catalyzed steps; converts glucose (6C) to two pyruvate (3C). Net products: 2 ATP (substrate-level phosphorylation) and 2 NADH; two major phases: energy-investment (steps 1–5) and energy-harvesting (steps 6–10).
Pyruvate oxidation (mitochondrial matrix in eukaryotes): each pyruvate is oxidized to acetyl-CoA, producing 1 NADH per pyruvate; overall: 2 pyruvate → 2 acetyl-CoA + 2 CO2 + 2 NADH.
Citric acid cycle (Krebs cycle, mitochondrial matrix): per acetyl-CoA, the cycle yields 3 NADH, 1 FADH2, and 1 GTP (which can be used as ATP). Since glucose yields 2 acetyl-CoA, per glucose: 6 NADH, 2 FADH2, 2 GTP.
Oxidative phosphorylation (inner mitochondrial membrane): NADH and FADH2 donate electrons to the respiratory chain, pumping protons to generate a proton-motive force; ATP synthase uses this proton gradient to synthesize ATP from ADP and P_i.
Electron transport chain (ETC):
NADH oxidation to NAD+ donates electrons to the chain; O2 is the terminal electron acceptor and is reduced to H2O.
FADH2 feeds into the chain later than NADH, delivering fewer protons across the membrane and therefore yielding fewer ATP.
The reduced coenzymes (NADH, FADH2) ultimately transfer their energy to ATP production via oxidative phosphorylation.
Quantitative energy yield per glucose (summary):
Glycolysis: 2 ATP (substrate-level) + 2 NADH (cytosolic) → approximately 3 ATP from cytosolic NADH due to shuttle costs.
Pyruvate oxidation: 2 NADH → about 5 ATP.
Citric acid cycle: 6 NADH (10 ATP per acetyl-CoA turn total of 6 turns) → about 15 ATP; 2 FADH2 → about 3 ATP; 2 GTP → 2 ATP.
Oxidative phosphorylation: NADH (from mitochondrial matrix) ≈ 2.5 ATP each; FADH2 ≈ 1.5 ATP each.
Net yield: about 30 ATP per glucose under typical cellular conditions.
NADH and FADH2 stoichiometries:
Oxidation of NADH in mitochondria yields approximately 2.5 ATP molecules.
Oxidation of FADH2 yields approximately 1.5 ATP molecules.
Practical highlights:
Glycolysis occurs in the cytosol and provides ATP and NADH; some NADH must be shuttled into mitochondria for oxidative phosphorylation.
The complete oxidation of glucose to CO2 involves a highly regulated sequence of enzyme-catalyzed steps, allowing energy capture in manageable increments.
Fermentation recap (contrast with respiration):
In absence of oxygen, the respiratory chain cannot operate; glycolysis continues to produce ATP but must regenerate NAD+ via fermentation (lactic acid fermentation or alcoholic fermentation), yielding only 2 ATP per glucose.
Connections to real-world relevance: fermentation provides a way to regenerate NAD+ under anaerobic conditions (e.g., muscle during intense exercise). However, aerobic respiration is far more energy-efficient.
Key Concept 5.2 REVIEW & APPLY (illustrative prompts):
1) If glucose is fully oxidized under aerobic conditions, which steps generate ATP and how much per step? 2) Compare aerobic respiration and fermentation in terms of products, energy released, and the role of mitochondria. 3) How is carbohydrate catabolism regulated at the enzyme level? 4) When cyanide blocks electron transport, how can cells still generate ATP from glucose? 5) Why is replenishment of NAD+ crucial to metabolism? Would high NAD+ activate or inhibit early glycolysis enzymes?
Key Concept 5.3: Catabolic Pathways for Carbohydrates, Lipids, and Proteins Are Interconnected
The catabolic pathways for carbohydrates (glycolysis, CAC), lipids (β-oxidation), and proteins feed into aerobic respiration or gluconeogenesis and are interconnected.
Lipids: triglycerides are a major energy storage form; hydrolysis yields glycerol and fatty acids. Glycerol feeds into glycolysis as dihydroxyacetone phosphate (DHAP); fatty acids are highly reduced and are converted to acetyl-CoA via β-oxidation, then enter the CAC.
β-oxidation details (conceptual):
Fatty acids are progressively shortened by two-carbon units to yield acetyl-CoA; each cycle yields one FADH2 and one NADH, and the remaining fatty acyl chain shortens by two carbons.
The acetyl-CoA units produced enter the CAC and are fully oxidized to CO2.
Carbohydrates, lipids, and proteins provide substrates that feed into central metabolism; nucleic acids can be hydrolyzed to nucleotides and further catabolized (ribose/deoxyribose enter glycolysis or CAC, bases enter CAC or glycolytic pathways).
Proteins: proteolysis breaks proteins down to amino acids; amino acids feed into glycolysis or CAC at various points after deamination and other transformations.
Interconnections and energy flow:
Anabolic and catabolic pathways are integrated; energy levels regulate pathway direction (high ATP/NADH promote synthesis; low energy shifts metabolism toward energy production).
The metabolic pool (sum of all cellular metabolites) tends to remain relatively constant; regulation occurs at transcriptional and translational levels, as well as via allosteric control of enzymes.
Practical implications and examples:
Glucose can be stored as glycogen or converted to fats for long-term storage; excess citrate from CAC can be diverted to fatty acid synthesis.
The energy status of the cell influences whether substrates are used for energy or stored as macromolecules.
Catalytic reversibility: many steps in anabolic pathways are reverse copies of catabolic steps, but some steps (highly exergonic) require alternative reactions or enzymes because reversing them would be energetically unfavorable.
Key Concept 5.3 REVIEWS & APPLY questions (selected):
Describe where triglyceride entry into aerobic respiration occurs and what happens to their hydrogen and carbon atoms.
Calculate ATP yield from a 16-carbon fatty acid (consider β-oxidation, CAC, and substrate-level phosphorylation, including activation costs).
Explain how an anaerobic bacterium could derive energy if only oxygen-depleted environments are available for respiration.
Key Concept 5.4: Anabolic Pathways Use Large Amounts of ATP
Anabolism involves constructing macromolecules and subunits; these processes require energy, typically supplied by ATP and NADH.
Anabolic pathways often resemble the reverse of catabolic pathways, but reversing some highly exergonic steps would require substantial energy input; thus, alternate enzymes may be used (e.g., gluconeogenesis uses enzymes different from those used in glycolysis for the most exergonic steps).
Energy balance and regulation:
ATP and NADH accumulation promotes anabolic processes (e.g., glycogen and fatty acid synthesis).
Enzyme regulation occurs both at the level of enzyme abundance (gene expression) and enzyme activity (allosteric regulation, feedback inhibition).
Key concept: gluconeogenesis uses many of the same enzymes as glycolysis but employs alternative enzymes for several highly exergonic steps to make the pathway energetically feasible.
Interrelationships:
Accumulated intermediates from glycolysis and CAC can be diverted toward synthesis of glucose, nucleotides, fatty acids, amino acids, and other macromolecules.
The balance between catabolism and anabolism ensures that metabolic pools remain fairly constant despite fluctuating dietary inputs.
Practical points and examples:
A carbon atom from dietary protein can end up in DNA, fat, or CO2, depending on cellular needs and regulatory state.
Gluconeogenesis requires substantial energy input (roughly six ATP equivalents to synthesize one glucose from two pyruvate molecules).
Acetyl-CoA from catabolism can be used for fatty acid synthesis (an anabolic reversal of fatty acid oxidation).
Regulation and integration:
Energy status (ATP/NADH levels) influences whether cells favor synthesis or breakdown.
Nutrient imbalances are mitigated by shifts in enzyme activities and gene expression, maintaining metabolic homeostasis.
Key Concept 5.4 REVIEW & APPLY questions (selected):
Why is gluconeogenesis energetically costly relative to glycolysis? Which steps require different enzymes and why?
Trace how a carbon atom from starch could end up in a muscle protein. Which pathways and intermediates are involved?
How might a high-protein, low-carbohydrate diet influence glycolysis and gluconeogenesis? Do you expect enzyme expression changes?
Key Concept 5.5: Life Is Supported by the Sun: Light Energy Captured during Photosynthesis Converts Carbon Dioxide to Carbohydrates
Photosynthesis comprises two main phases:
Light reactions convert light energy into chemical-bond energy, producing ATP and the reduced carrier NADPH.
The Calvin cycle (carbon fixation, light-independent reactions) uses ATP and NADPH to convert CO₂ into carbohydrates (sugars).
Chloroplast structure and localization:
In plants and algae, light reactions occur in the thylakoid membranes; the Calvin cycle occurs in the stroma.
In photosynthetic prokaryotes, similar processes occur on internal membranes or the cytosol.
Light absorption and pigments:
Pigments such as chlorophyll a and chlorophyll b absorb photons in the blue and red regions of the visible spectrum; accessories (β-carotene, phycobilins) broaden the range of absorbed wavelengths.
Absorption spectra of pigments determine absorption efficiency; action spectra of photosynthesis peaks roughly align with pigment absorption peaks.
Chlorophyll has a porphyrin ring coordinating a central magnesium ion and a hydrophobic tail that anchors it to thylakoid membranes.
Photosystems and energy transfer:
Photosystem II (PSII) contains reaction center chlorophyll a (P680). It absorbs light at 680 nm, splits water, and donates electrons to the electron transport chain (ETC).
Water splitting in PSII releases O₂, protons, and electrons: the overall water-splitting reaction is
2\mathrm{H2O} \rightarrow 4\mathrm{H^+} + 4e^- + \mathrm{O2}.Photosystem I (PSI) contains reaction center chlorophyll a (P700). It absorbs light at 700 nm; excited electrons are transferred to NADP+, forming NADPH (via an ETC).
The two photosystems drive a Z-scheme (noncyclic electron flow) that produces NADPH and ATP; ATP synthase in the thylakoid membrane uses the proton gradient to form ATP from ADP and P_i.
Cyclic photophosphorylation involves electrons cycling around PSI, pumping protons to generate extra ATP without producing NADPH, thereby balancing ATP/NADPH supply for Calvin cycle.
The Calvin cycle (carbon fixation) uses ATP and NADPH to convert CO₂ into carbohydrate:
Stage 1: Fixation – CO₂ is fixed to RuBP by Rubisco to form 3-phosphoglycerate (3-PGA).
Stage 2: Reduction – 3-PGA is phosphorylated by ATP and reduced by NADPH to glyceraldehyde-3-phosphate (G3P).
Stage 3: Regeneration – The majority of G3P is recycled to regenerate RuBP (to accept more CO₂); some G3P is exported to form sugars (glucose, fructose) and other carbon compounds.
Overall for one glucose (two G3P): the Calvin cycle requires 12 NADPH and 18 ATP.
Key reactions and stoichiometry (Calvin cycle):
Fixation: CO₂ + RuBP → 2 × 3-phosphoglycerate (3-PGA).
Reduction: 3-PGA → G3P with ATP and NADPH.
Regeneration: Most G3P is converted back to RuBP using ATP to continue CO₂ fixation.
Export and starch synthesis: G3P can be exported to the cytosol to form hexoses (glucose, fructose) or exported for sucrose formation and plant transport; glucose units can be polymerized into starch for storage.
Practical details and plant biology:
Rubisco can fix CO₂ but also reacts with O₂ (photorespiration), which reduces photosynthetic efficiency and releases CO₂. The relative O₂/CO₂ concentrations and temperature influence Rubisco's selectivity; higher O₂ or higher temperature increases photorespiration.
C₄ and CAM plants evolved mechanisms to reduce photorespiration by concentrating CO₂ around Rubisco. In C₄ plants, CO₂ is fixed in mesophyll cells to form a 4-carbon compound that delivers CO₂ to bundle-sheath cells for fixation; in CAM plants, CO₂ is fixed at night into a 4-carbon compound stored until daytime.
The broader significance of photosynthesis:
Photosynthesis is the primary source of chemical-bond energy for life on Earth; most energy captured ultimately enters cellular respiration in heterotrophs.
Photosynthetic organisms form the base of food webs and influence atmospheric O₂ and CO₂ balance.
Formula and energy accounting highlights:
Overall photosynthesis equation (simplified):
6\mathrm{CO2} + 12\mathrm{H2O} \rightarrow \mathrm{C}6\mathrm{H}{12}\mathrm{O}6 + 6\mathrm{O2} + 6\mathrm{H_2O}The oxygen produced by photosynthesis originates from water, not from CO₂, which is a crucial distinction.
To produce one glucose, the Calvin cycle consumes 12 NADPH and 18 ATP, generated by the light reactions.
Visual & cellular context:
The chloroplast structure includes the thylakoid membranes (where light reactions occur) and the stroma (where the Calvin cycle occurs).
Light-harvesting complexes collect photons and funnel energy to reaction centers; pigments are organized in antenna complexes around reaction centers to optimize energy capture.
Investigative and real-world connections:
Brown adipose tissue and UCP1 (uncoupling protein 1) can dissipate the proton gradient as heat rather than making ATP, a mechanism exploited by brown fat to generate heat in mammals.
The energy economy of photosynthesis has implications for bioenergetics, ecology, and even medical or industrial strategies (e.g., uncouplers and metabolic regulation).
Key Concept 5.5 REVIEW & APPLY prompts (selected):
What are the reactants and products of the light-dependent reactions? Where do these reactions occur in the chloroplast?
How is energy from photons used in the light reactions to drive ATP and NADPH production?
Why does carbon fixation rate drop on hot, dry days in C₃ plants, and how do C₄ and CAM plants mitigate this?
Write the equations for the production of Chl, O₂, ATP, and NADPH in photosynthesis, and indicate whether each is an oxidation, reduction, or neither.
If radioactive CO₂ was provided to a plant, trace which molecules would become labeled first and the sequential incorporation into sugars over time (as described in the exercise).
The overall perspective of sunlight-driven energy capture and usage:
Light energy captured by photosystems is converted to chemical-bond energy in ATP and NADPH, which are then used by the Calvin cycle to fix CO₂ into carbohydrates.
The energy stored in CHO bonds supports nearly all life on Earth, directly or indirectly, via the flow of energy from the Sun through photosynthesis and cellular respiration.
Quick reference equations and numeric highlights
Glucose oxidation (aerobic respiration):
\text{Glucose} + 6\,\mathrm{O2} \rightarrow 6\,\mathrm{CO2} + 6\,\mathrm{H_2O} + \text{energy}
with a standard free energy release around \Delta G^\circ \approx -686\ \text{kcal/mol} (-2872\ \text{kJ/mol}).ATP hydrolysis (high-energy phosphate bond):
\mathrm{ATP} + \mathrm{H2O} \rightarrow \mathrm{ADP} + \mathrm{Pi}
\Delta G^\circ_{\text{hydrolysis}} \approx -7.3\ \text{kcal/mol}.NADH oxidation in respiration (to NAD+):
\mathrm{NADH} + \mathrm{H^+} + \tfrac{1}{2}\mathrm{O2} \rightarrow \mathrm{NAD^+} + \mathrm{H2O}
\Delta G^\circ \approx -52.4\ \text{kcal/mol}.ATP yield per glucose (typical cellular accounting): ≈ 30\text{ ATP} per glucose in aerobic respiration, with the breakdown roughly as follows:
Glycolysis: 2 ATP (substrate-level) + 2 NADH (cytosolic) → about 3 ATP from cytosolic NADH
Pyruvate oxidation: 2 NADH → about 5 ATP
Citric acid cycle: 6 NADH (10 ATP per acetyl-CoA turn) + 2 FADH2 (1.5 ATP each) + 2 GTP (2 ATP) → about 20 ATP
Oxidative phosphorylation: NADH (2.5 ATP each) and FADH2 (1.5 ATP each) drive additional ATP synthesis
Calvin cycle energy requirements for one glucose:
12\,\text{NADPH} + 18\,\text{ATP} \rightarrow \text{G3P (two molecules)} \, (\text{glucose precursors})Photosystem II water splitting (stoichiometry):
2\mathrm{H2O} \rightarrow 4\mathrm{H^+} + 4e^- + \mathrm{O2}Noncyclic (Z-scheme) vs cyclic photophosphorylation:
Noncyclic: produces both ATP and NADPH
Cyclic: produces ATP without NADPH, to balance energy needs for CO₂ fixation
Rubisco and photorespiration:
Rubisco fixes CO₂ but can also react with O₂; this leads to photorespiration, reducing efficiency and releasing CO₂ back to the atmosphere.
Photosynthetic plant strategies:
C₃ plants fix CO₂ directly via Rubisco in the Calvin cycle.
C₄ plants concentrate CO₂ around Rubisco in specialized cells (bundle-sheath) to reduce photorespiration.
CAM plants fix CO₂ at night, storing it as a four-carbon compound for use during the day.
Notes:
All numeric values are taken from the included transcript (book-like content) and are used here to aid study and exam preparation. In practice, metabolic yields can vary with organism, tissue type, and cellular conditions; the numbers above reflect the standard teaching figures presented in the source content.