The specific region of an enzyme where the substrate binds. Formed by amino acid R-groups that create a 3D pocket. The active site has a specific shape and chemical environment complementary to its substrate (lock-and-key or induced fit). Catalytic residues lower activation energy
Enzymes bind specific substrates because of the precise 3D shape and charge distribution of the active site. Determined by the enzyme's primary structure (amino acid sequence). Cofactors (metal ions, vitamins) may assist substrate binding. Different enzymes can act on similar substrates (e.g., digestive proteases)
The enzyme changes shape slightly upon substrate binding, improving the fit. The "induced fit" strengthens the enzyme-substrate interaction and brings catalytic residues into optimal positions. Substrate binding causes the enzyme to close around it - like a glove closing on a hand
The minimum energy required for a chemical reaction to occur. Enzymes lower the activation energy (Ea) without changing the free energy change (DeltaG) of the reaction. They stabilize the transition state, making it easier to reach. Lower Ea -> faster reaction rate at a given temperature
The speed at which reactants are converted to products. Enzyme reaction rate is affected by: substrate concentration ([S] -> increases until Vmax), temperature (optimal ~37 degrees C for human enzymes), pH (each enzyme has optimal pH), inhibitor presence. Michaelis-Menten kinetics: V = (Vmax[S])/(Km + [S])
The loss of tertiary and secondary protein structure, destroying enzyme function. Causes: heat ( up temperature), extreme pH, organic solvents, heavy metals, chaotropic agents. Often irreversible. The primary (amino acid sequence) remains intact - renaturation may be possible if conditions are restored quickly
Enzyme activity increases with temperature (up to a point) because more molecules have sufficient kinetic energy to overcome Ea. Above optimal temperature, the enzyme denatures - hydrogen bonds break -> 3D structure lost -> active site destroyed -> activity drops to zero. Cold temperatures slow reactions but do not denature enzymes
Each enzyme has an optimal pH range where its active site and catalytic residues are in the correct ionization state. Extreme pH disrupts hydrogen bonds and ionic bonds -> denaturation. Examples: pepsin (stomach, pH ~2), trypsin (small intestine, pH ~8), most human enzymes (pH ~7.4)
A reversible inhibitor that binds to the active site, directly blocking substrate binding. The inhibitor resembles the substrate in structure. Inhibition can be overcome by increasing substrate concentration (more substrate outcompetes inhibitor). Example: methotrexate inhibits dihydrofolate reductase
A reversible inhibitor that binds to an allosteric site (not the active site), changing the enzyme's shape and reducing its activity. The inhibitor does not resemble the substrate. Inhibition cannot be overcome by adding more substrate. Example: heavy metals (Pb2+, Hg2+) inhibit many enzymes
The use of an exergonic (energy-releasing) reaction to drive an endergonic (energy-requiring) reaction. Usually involves ATP as the energy currency: ATP -> ADP + Pi (exergonic) provides energy for cellular work. Allows unfavorable reactions to proceed in cells. Example: ATP-powered active transport
Chemical reactions that release energy (DeltaG < 0). The products have less free energy than the reactants. Spontaneous in the thermodynamic sense (but may still be slow). Examples: cellular respiration, catabolism, ATP hydrolysis. They can be coupled to endergonic reactions via ATP
Chemical reactions that require energy input (DeltaG > 0). The products have more free energy than the reactants. Non-spontaneous; require coupling to an exergonic reaction. Examples: photosynthesis, protein synthesis, active transport, anabolic pathways
Adenosine triphosphate: adenine + ribose sugar + three phosphate groups. The bond between the 2nd and 3rd phosphate is a high-energy bond (~7.3 kcal/mol). Hydrolysis: ATP + H2O -> ADP + Pi + energy (exergonic). ATP is continuously regenerated via cellular respiration (ADP + Pi -> ATP). Functions: active transport, mechanical work, chemical work (biosynthesis)
The primary photosynthetic pigments in plants. Chlorophyll a: main pigment, absorbs red (~660-670 nm) and violet-blue light (~430 nm); appears green. Chlorophyll b: accessory pigment, absorbs blue (~450 nm) and orange light (~640 nm); extends light range absorbed. Other accessory pigments (carotenoids) absorb blue-green light
Occur in the thylakoid membrane. Inputs: H2O, light. Outputs: ATP, NADPH, O2. Process: light -> chlorophyll excited -> electrons -> ETC -> H+ gradient -> ATP synthase (photophosphorylation) -> NADP+ -> NADPH. Photolysis of water releases O2 as a byproduct. Uses photosystem II -> cytochrome b6f -> photosystem I
Produced at the end of the light-dependent reactions when NADP+ accepts electrons from the electron transport chain (driven by photosystem I). NADPH is a reducing agent (carries high-energy electrons). Used in the Calvin cycle to reduce 3-PGA to G3P
Two protein-pigment complexes in the thylakoid membrane. PS II: contains P680 reaction center; splits water (photolysis: 2H2O -> 4H+ + 4e- + O2); generates ATP via photophosphorylation. PS I: contains P700 reaction center; generates NADPH. Electrons flow from PS II -> electron transport chain -> PS I
(Dark Reactions)**: Occurs in the stroma. Does NOT require light directly (but requires products of light reactions: ATP, NADPH). Also called carbon fixation: CO2 is "fixed" into organic molecules. Key steps: CO2 + RuBP -> 2× 3-PGA (catalyzed by RuBisCO) -> G3P (glyceraldehyde-3-phosphate) -> glucose, sucrose, starch. RuBP regeneration requires ATP. 3 turns = 1 net G3P ( -> glucose)
Anaerobic pathway that regenerates NAD+ from NADH, allowing glycolysis to continue. Two types: Alcoholic fermentation: pyruvate -> ethanol + CO2 (yeast, some bacteria). Lactic acid fermentation: pyruvate -> lactate (muscle cells, lactic acid bacteria). Produces only 2 ATP per glucose (from glycolysis). Not sustainable - lactate/ethanol buildup eventually inhibits the cell
Occurs in the mitochondrial matrix (eukaryotes) or cytoplasm (prokaryotes). Each pyruvate -> acetyl-CoA + CO2 + NADH (1 per pyruvate; 2 per glucose). Acetyl-CoA enters the Krebs cycle. This step links glycolysis to the Krebs cycle and produces the first CO2 of aerobic respiration
Occurs in the inner mitochondrial membrane ( eukaryotes). A series of protein complexes and electron carriers. Electrons from NADH and FADH2 pass through, releasing energy. This energy pumps H+ from the matrix -> intermembrane space, creating an H+ gradient. O2 is the final electron acceptor -> forms H2O. If O2 absent -> ETC stops -> no ATP via oxidative phosphorylation
The production of ATP using the energy from the electron transport chain. The H+ gradient drives ATP synthase (chemiosmosis). Each H+ flowing through ATP synthase phosphorylates ADP -> ATP. Produces ~32-34 ATP per glucose (much more than glycolysis alone). Total ATP from one glucose: ~36-38 ATP (aerobic) vs 2 ATP (anaerobic)
Occurs in the cytoplasm; anaerobic; does not require oxygen. Input: 1 glucose -> 2 pyruvate. Net output: 2 ATP, 2 NADH. Steps: glucose is phosphorylated twice (uses 2 ATP) -> split into 2× 3-carbon molecules -> substrate-level phosphorylation produces 4 ATP (net 2 ATP) -> NAD+ reduced to 2 NADH. Occurs in all organisms
Occurs in the mitochondrial matrix. Acetyl-CoA enters; 2 carbons are released as 2× CO2 per acetyl-CoA. Per turn: 3 NADH, 1 FADH2, 1 GTP (ATP). The cycle runs twice per glucose molecule. All six carbons of glucose are released as CO2 across glycolysis + Krebs cycle
The H+ concentration difference between the intermembrane space (high [H+]) and the matrix (low [H+]). Created by ETC pumping H+ against gradient using electron energy. The gradient stores potential energy (proton-motive force). Flows back through ATP synthase, driving ATP synthesis. Dissipated when O2 combines with electrons and H+ at the end of the ETC
Genetic variation at the molecular level (DNA, protein sequences) underlies phenotypic variation. Neutral mutations cause molecular variation without affecting function. This variation is the raw material for natural selection. Examples: different hemoglobin alleles, enzyme variants, membrane lipid composition
The maintenance of internal body temperature. Mechanisms: vasodilation/vasoconstriction (blood flow), sweating/piloerection (evaporative cooling), shivering (muscle-generated heat), brown fat thermogenesis. At the molecular level: enzyme adaptations, membrane lipid composition (more unsaturated in cold climates). Ectotherms vs endotherms
The specific region of an enzyme where the substrate binds. Formed by amino acid R-groups that create a 3D pocket. The active site has a specific shape and chemical environment complementary to its substrate (lock-and-key or induced fit). Catalytic residues lower activation energy
Enzymes bind specific substrates because of the precise 3D shape and charge distribution of the active site. Determined by the enzyme's primary structure (amino acid sequence). Cofactors (metal ions, vitamins) may assist substrate binding. Different enzymes can act on similar substrates (e.g., digestive proteases)
The enzyme changes shape slightly upon substrate binding, improving the fit. The "induced fit" strengthens the enzyme-substrate interaction and brings catalytic residues into optimal positions. Substrate binding causes the enzyme to close around it - like a glove closing on a hand
The minimum energy required for a chemical reaction to occur. Enzymes lower the activation energy (Ea) without changing the free energy change (DeltaG) of the reaction. They stabilize the transition state, making it easier to reach. Lower Ea -> faster reaction rate at a given temperature
The speed at which reactants are converted to products. Enzyme reaction rate is affected by: substrate concentration ([S] -> increases until Vmax), temperature (optimal ~37 degrees C for human enzymes), pH (each enzyme has optimal pH), inhibitor presence. Michaelis-Menten kinetics: V = (Vmax[S])/(Km + [S])
The loss of tertiary and secondary protein structure, destroying enzyme function. Causes: heat ( up temperature), extreme pH, organic solvents, heavy metals, chaotropic agents. Often irreversible. The primary (amino acid sequence) remains intact - renaturation may be possible if conditions are restored quickly
Enzyme activity increases with temperature (up to a point) because more molecules have sufficient kinetic energy to overcome Ea. Above optimal temperature, the enzyme denatures - hydrogen bonds break -> 3D structure lost -> active site destroyed -> activity drops to zero. Cold temperatures slow reactions but do not denature enzymes
Each enzyme has an optimal pH range where its active site and catalytic residues are in the correct ionization state. Extreme pH disrupts hydrogen bonds and ionic bonds -> denaturation. Examples: pepsin (stomach, pH ~2), trypsin (small intestine, pH ~8), most human enzymes (pH ~7.4)
A reversible inhibitor that binds to the active site, directly blocking substrate binding. The inhibitor resembles the substrate in structure. Inhibition can be overcome by increasing substrate concentration (more substrate outcompetes inhibitor). Example: methotrexate inhibits dihydrofolate reductase
A reversible inhibitor that binds to an allosteric site (not the active site), changing the enzyme's shape and reducing its activity. The inhibitor does not resemble the substrate. Inhibition cannot be overcome by adding more substrate. Example: heavy metals (Pb2+, Hg2+) inhibit many enzymes
The use of an exergonic (energy-releasing) reaction to drive an endergonic (energy-requiring) reaction. Usually involves ATP as the energy currency: ATP -> ADP + Pi (exergonic) provides energy for cellular work. Allows unfavorable reactions to proceed in cells. Example: ATP-powered active transport
Chemical reactions that release energy (DeltaG < 0). The products have less free energy than the reactants. Spontaneous in the thermodynamic sense (but may still be slow). Examples: cellular respiration, catabolism, ATP hydrolysis. They can be coupled to endergonic reactions via ATP
Chemical reactions that require energy input (DeltaG > 0). The products have more free energy than the reactants. Non-spontaneous; require coupling to an exergonic reaction. Examples: photosynthesis, protein synthesis, active transport, anabolic pathways
Adenosine triphosphate: adenine + ribose sugar + three phosphate groups. The bond between the 2nd and 3rd phosphate is a high-energy bond (~7.3 kcal/mol). Hydrolysis: ATP + H2O -> ADP + Pi + energy (exergonic). ATP is continuously regenerated via cellular respiration (ADP + Pi -> ATP). Functions: active transport, mechanical work, chemical work (biosynthesis)
The primary photosynthetic pigments in plants. Chlorophyll a: main pigment, absorbs red (~660-670 nm) and violet-blue light (~430 nm); appears green. Chlorophyll b: accessory pigment, absorbs blue (~450 nm) and orange light (~640 nm); extends light range absorbed. Other accessory pigments (carotenoids) absorb blue-green light
Occur in the thylakoid membrane. Inputs: H2O, light. Outputs: ATP, NADPH, O2. Process: light -> chlorophyll excited -> electrons -> ETC -> H+ gradient -> ATP synthase (photophosphorylation) -> NADP+ -> NADPH. Photolysis of water releases O2 as a byproduct. Uses photosystem II -> cytochrome b6f -> photosystem I
Produced at the end of the light-dependent reactions when NADP+ accepts electrons from the electron transport chain (driven by photosystem I). NADPH is a reducing agent (carries high-energy electrons). Used in the Calvin cycle to reduce 3-PGA to G3P
Two protein-pigment complexes in the thylakoid membrane. PS II: contains P680 reaction center; splits water (photolysis: 2H2O -> 4H+ + 4e- + O2); generates ATP via photophosphorylation. PS I: contains P700 reaction center; generates NADPH. Electrons flow from PS II -> electron transport chain -> PS I
(Dark Reactions)**: Occurs in the stroma. Does NOT require light directly (but requires products of light reactions: ATP, NADPH). Also called carbon fixation: CO2 is "fixed" into organic molecules. Key steps: CO2 + RuBP -> 2× 3-PGA (catalyzed by RuBisCO) -> G3P (glyceraldehyde-3-phosphate) -> glucose, sucrose, starch. RuBP regeneration requires ATP. 3 turns = 1 net G3P ( -> glucose)
Anaerobic pathway that regenerates NAD+ from NADH, allowing glycolysis to continue. Two types: Alcoholic fermentation: pyruvate -> ethanol + CO2 (yeast, some bacteria). Lactic acid fermentation: pyruvate -> lactate (muscle cells, lactic acid bacteria). Produces only 2 ATP per glucose (from glycolysis). Not sustainable - lactate/ethanol buildup eventually inhibits the cell
Occurs in the mitochondrial matrix (eukaryotes) or cytoplasm (prokaryotes). Each pyruvate -> acetyl-CoA + CO2 + NADH (1 per pyruvate; 2 per glucose). Acetyl-CoA enters the Krebs cycle. This step links glycolysis to the Krebs cycle and produces the first CO2 of aerobic respiration
Occurs in the inner mitochondrial membrane ( eukaryotes). A series of protein complexes and electron carriers. Electrons from NADH and FADH2 pass through, releasing energy. This energy pumps H+ from the matrix -> intermembrane space, creating an H+ gradient. O2 is the final electron acceptor -> forms H2O. If O2 absent -> ETC stops -> no ATP via oxidative phosphorylation
The production of ATP using the energy from the electron transport chain. The H+ gradient drives ATP synthase (chemiosmosis). Each H+ flowing through ATP synthase phosphorylates ADP -> ATP. Produces ~32-34 ATP per glucose (much more than glycolysis alone). Total ATP from one glucose: ~36-38 ATP (aerobic) vs 2 ATP (anaerobic)
Occurs in the cytoplasm; anaerobic; does not require oxygen. Input: 1 glucose -> 2 pyruvate. Net output: 2 ATP, 2 NADH. Steps: glucose is phosphorylated twice (uses 2 ATP) -> split into 2× 3-carbon molecules -> substrate-level phosphorylation produces 4 ATP (net 2 ATP) -> NAD+ reduced to 2 NADH. Occurs in all organisms
Occurs in the mitochondrial matrix. Acetyl-CoA enters; 2 carbons are released as 2× CO2 per acetyl-CoA. Per turn: 3 NADH, 1 FADH2, 1 GTP (ATP). The cycle runs twice per glucose molecule. All six carbons of glucose are released as CO2 across glycolysis + Krebs cycle
The H+ concentration difference between the intermembrane space (high [H+]) and the matrix (low [H+]). Created by ETC pumping H+ against gradient using electron energy. The gradient stores potential energy (proton-motive force). Flows back through ATP synthase, driving ATP synthesis. Dissipated when O2 combines with electrons and H+ at the end of the ETC
Genetic variation at the molecular level (DNA, protein sequences) underlies phenotypic variation. Neutral mutations cause molecular variation without affecting function. This variation is the raw material for natural selection. Examples: different hemoglobin alleles, enzyme variants, membrane lipid composition
The maintenance of internal body temperature. Mechanisms: vasodilation/vasoconstriction (blood flow), sweating/piloerection (evaporative cooling), shivering (muscle-generated heat), brown fat thermogenesis. At the molecular level: enzyme adaptations, membrane lipid composition (more unsaturated in cold climates). Ectotherms vs endotherms