Exam 3 Study Guide: Thermodynamics, Photosynthesis, and Cellular Respiration

Comprehensive vocabulary flashcards covering thermodynamics, energy coupling, enzyme function and regulation, redox reactions, photosynthesis (light reactions and Calvin cycle), and cellular respiration pathways.

Metabolism

All anabolic and catabolic reactions in a cell, connected in a network of reaction pathways.

Anabolic reactions

Reactions that synthesize or "build" molecules with more bonds, making higher free energy products; they use or store energy (endergonic), reduce entropy, and are non-spontaneous.

Catabolic reactions

Reactions that degrade or "break" molecules to make lower free energy products with fewer bonds; they increase entropy, release energy (exergonic), and are spontaneous.

First and Second Laws of Thermodynamics

Laws stating that energy is transformed in many ways, but always at the cost of energy lost through entropy that is not available to do work.

Free energy ($G$)

Chemical energy available to do work, expressed as the difference between enthalpy (total energy) and entropy (energy lost)

Change in free energy ($\Delta G$)

The change in free energy between reactants and products; the direction of change determines whether a reaction has a positive or negative $\Delta G$ (anabolic or catabolic).

Enzymes

Proteins that reduce the activation energy of a reaction.

Active site

The specific region of an enzyme where substrates interact to form an enzyme-substrate complex with a close interaction through induced fit.

Allosteric effectors

Molecules that regulate enzymes by binding somewhere other than the active site (the allosteric site) and altering the shape of the protein to either inhibit or activate enzyme function.

Negative feedback (Feedback inhibition)

Regulatory loops that use the product of a pathway to inhibit an enzyme at the beginning of the pathway.

Reaction coupling

The process of combining a positive $\Delta G$ reaction with a negative $\Delta G$ reaction to give a new net negative $\Delta G$ for the combined reactions.

ATP hydrolysis (in reaction coupling)

The most common means of reaction coupling, yielding a $\Delta G = -7.3\,\text{kcal/mole}$ to generate phosphorylated intermediate molecules of higher energy.

Redox reactions

Reactions that transfer electrons between molecules.

Oxidation

The loss of electrons by molecules.

Reduction

The gain of electrons by molecules.

NADH (or NADPH)

A commonly used high energy electron carrier in metabolism that captures high energy electrons from organic molecules and holds on to them for later extraction via an electron transport chain to do work.

Photosynthesis

A process that transforms light energy into chemical energy and forms part of the carbon cycle by synthesizing new carbon backbones from $\text{CO}_2$ released when cellular respiration breaks down carbon backbones.

Chloroplast compartments

The three components in eukaryotic chloroplasts (plants and algae) used in photosynthesis: the stroma, thylakoid membranes, and thylakoid lumen.

Light reactions

Reactions of photosynthesis that use two photosystems to capture light and generate high energy electrons.

Photosystem II (PSII)

A photosystem that donates high energy electrons to an electron transport chain starting with PQ, and obtains replacement low energy electrons from the splitting of water through photolysis.

PQ

A high energy electron carrier that receives electrons from Photosystem II and reduces the cytochrome complex.

Cytochrome complex

A complex reduced by PQ that uses energy from electrons to pump hydrogen ions across the membrane into the thylakoid lumen, generating a $\text{H}^+$ gradient across the thylakoid membrane.

PC

The electron carrier reduced in the last step of the photosynthetic ETC, which transfers low energy electrons to Photosystem I.

Photosystem I (PSI)

A photosystem that accepts low energy electrons from PC and re-excites them back to a high energy level before reducing feridoxin (FD).

Feridoxin (FD)

A carrier reduced by Photosystem I that delivers high energy electrons to the enzyme NADP+ reductase.

NADP+ reductase

The enzyme that reduces the final electron acceptor $\text{NADP}^+$ using high energy electrons delivered by feridoxin (FD) to make NADPH.

Photophosphorylation

The formation of ATP in the stroma powered by the enzyme complex ATP synthase as $\text{H}^+$ flows from high concentration in the thylakoid lumen to low concentration in the stroma.

Photolysis

The splitting of water by PSII to obtain low energy replacement electrons that resupply PSII, producing $\text{H}^+$ and oxygen as by-products.

Calvin Cycle

A metabolic pathway that fixes inorganic carbon from $\text{CO}_2$ into organic carbon chains, storing energy in chemical bonds.

Rubisco

The enzyme that covalently bonds $\text{CO}_2$ to the 5C molecule RuBP during the carbon fixation phase of the Calvin Cycle, generating two 3C organic molecules.

Glyceraldehyde-3-phosphate (G3P)

The 3C organic product of the reduction phase of the Calvin Cycle, exported to make other organic molecules (fatty acids, amino acids, and nucleic acids) or used to regenerate RuBP.

Regeneration phase (Calvin Cycle)

The phase of the Calvin Cycle where five G3P molecules are converted back into three molecules of RuBP.

Cellular respiration

The process of breaking down glucose to make ATP using substrate level and oxidative phosphorylation.

Glycolysis

The first process in cellular respiration, which uses glucose as its preferred substrate to make $2\,\text{ATP}$ (net, via substrate level phosphorylation), $2\,\text{NADH}$, and $2\,\text{pyruvate}$.

Pyruvate oxidation

The process where two pyruvates from glycolysis are imported into the mitochondria and converted into $2\,\text{acetyl-CoA}$, producing $2\,\text{NADH}$ and $2\,\text{CO}_2$.

Citric acid cycle

The metabolic pathway where $2\,\text{acetyl-CoA}$ are oxidized to $\text{CO}_2$, yielding $2\,\text{ATP}$ (via substrate level phosphorylation), $6\,\text{NADH}$, and $2\,\text{FADH}_2$.

Proton motive force (PMF)

The gradient generated across the inner mitochondrial membrane when the mitochondrial ETC uses energy from NADH and $\text{FADH}_2$ to pump $\text{H}^+$ from the matrix into the intermembrane space.

Chemiosmosis

The process wherein the flow of hydrogen ions back across the inner mitochondrial membrane powers ATP production by the enzyme complex ATP synthase.

Oxidative phosphorylation

The function of the mitochondrial ETC coupled to chemiosmosis to produce ATP, so named because of the importance of oxygen as the final electron acceptor.

Fermentation

A process that supports glycolysis when the electron transport chain cannot work (such as when oxygen is limited) by recycling NADH back to $\text{NAD}^+$.

Deamination

The removal of nitrogen from amino acids, enabling them to be converted into glucose, acetyl-CoA, or intermediates of the citric acid cycle for cellular respiration.

Beta-oxidation

The pathway that breaks down fatty acids derived from triglycerides into acetyl-CoA, NADH, and $\text{FADH}_2$.