Exam 2 Review: Thermodynamics, Cellular Respiration, Photosynthesis, and Membrane Transport

Comprehensive vocabulary flashcards covering thermodynamic laws, enzymatic regulation, cellular respiration, photosynthesis pathways, organelle anatomy, and membrane transport mechanisms.

Thermodynamics

The study of energy conversions.

First Law of Thermodynamics

The law of conservation of energy stating that energy cannot be created or destroyed, but can be transformed from one type to another.

Second Law of Thermodynamics

The principle stating that the amount of disorder or entropy ($\Delta S$) increases in an isolated system over time.

Exothermic Reaction

A chemical reaction that releases heat energy.

Endothermic Reaction

A chemical reaction that absorbs heat energy.

Spontaneous Reaction

A reaction that occurs without an input of energy, is exergonic, has a negative $\Delta G$, and proceeds in the direction of lower potential energy and increased disorder.

Nonspontaneous Reaction

An endergonic reaction that requires an input of energy and has a positive $\Delta G$.

Endergonic Reaction

A nonspontaneous chemical reaction requiring energy input with a positive free energy change ($\Delta G > 0$).

Exergonic Reaction

A spontaneous chemical reaction that releases energy, has a negative free energy change ($\Delta G < 0$), and requires activation energy to start.

Energy Coupling

The process of pairing an exergonic reaction (such as ATP hydrolysis) with an endergonic reaction to make the overall process spontaneous.

Entropy ($S$)

A measure of disorder, randomness, or the dispersion of unusable energy within a system.

Gibbs Free Energy ($G$)

The amount of usable energy available to do work in a system, determined by $G_{\text{energy}} = G_{\text{products}} - G_{\text{reactants}}$.

Enthalpy ($H$)

The total energy of a system, represented in the equation $H = G + TS$.

Oxidation

A catabolic process involving the removal of electrons during molecular breakdown.

Reduction

An anabolic process involving the addition of electrons during molecular synthesis.

Catabolic Reaction

An exergonic reaction that breaks down a large molecule into smaller ones, releasing energy in the process.

Anabolic Reaction

An endergonic reaction that combines small molecules into larger ones, requiring energy input and coupling to exergonic reactions.

Enzyme

A catalytic protein (typically three-dimensional) that speeds up chemical reactions without being consumed, functioning via induced fit.

Active Site

The specialized, flexible region on an enzyme where a specific substrate binds and the chemical reaction occurs.

Allosteric Site

A specialized region on an enzyme separate from the active site where a regulatory molecule binds to alter the enzyme's shape and activity.

Feedback Inhibition

A regulation pathway where the final product binds to an allosteric site to induce a conformational change, inactivating an enzyme to conserve energy and prevent toxic buildup.

Competitive Inhibitor

A reversible substance that directly competes with the substrate for binding at the enzyme's active site.

Noncompetitive Inhibitor

A reversible substance that binds to an allosteric site rather than the active site, inducing a conformational change in the active site.

Irreversible Inhibitor

An inhibitor that covalently binds to an enzyme, permanently disabling its function and necessitating the synthesis of a new enzyme.

Chemiosmosis

The movement of ions (specifically hydrogen ions or protons) across a selectively permeable membrane down their electrochemical gradient.

Substrate-Level Phosphorylation

A metabolic reaction that transfers a phosphate group from a reactive intermediate substrate directly to ADP to form ATP.

Glycolysis

A ten-step anaerobic metabolic process in the cytosol consisting of energy investment, cleavage, and energy liberation phases, producing $2$ pyruvate, $2\,\text{NADH}$, and a net of $2\,\text{ATP}$.

Pyruvate Breakdown

The stage in the mitochondrial matrix where ???? dehydrogenase removes carbon dioxide, producing $1\,\text{NADH}$ and attaching the remaining acetyl group to CoA to yield acetyl CoA.

Citric Acid Cycle (Krebs)

A continuous metabolic cycle in the mitochondrial matrix that couples acetyl groups with oxaloacetate to form citrate, producing $2\,CO_2$, $1\,\text{ATP}$, $3\,\text{NADH}$, and $1\,\text{FADH}_2$ per turn while regenerating oxaloacetate.

Oxidative Phosphorylation

The metabolic process occurring in the inner mitochondrial membrane where high-energy electrons from $\text{NADH}$ and $\text{FADH}_2$ traverse the electron transport chain to power the phosphorylation of ADP into ATP.

Mitochondrion

The double-membraned organelle containing an outer membrane, inner membrane, intramembrane space, cristae, matrix, ribosomes, and circular DNA.

Chloroplast

The organelle of photosynthesis containing an outer membrane, inner membrane, stroma, grana, thylakoids, and a thylakoid lumen.

Alcoholic Fermentation

An anaerobic process in yeast where pyruvate is converted to acetaldehyde and then ethanol, producing $CO_2$ and regenerating $\text{NAD}^+$.

Lactic Acid Fermentation

An anaerobic process in animal cells where pyruvate is directly reduced to lactate to regenerate $\text{NAD}^+$ and prevent electron transport chain collapse.

Heterotroph

An organism that must consume organic molecules from its environment to sustain life, such as animals, fungi, protists, and bacteria.

Autotroph

A 'self-feeding' organism that synthesizes organic molecules from inorganic molecules, such as plants, algae, and some bacteria.

Photoautotroph

An autotrophic organism that uses sunlight as its primary energy source to synthesize organic molecules.

Chlorophyll a

The primary photosynthetic pigment that absorbs blue-violet light and reflects blue-green light.

Chlorophyll b

An accessory photosynthetic pigment that absorbs blue and red-orange light and reflects yellow-green light.

Carotenoids

Accessory photosynthetic pigments (carotene and xanthophylls) that absorb blue and blue-green light while reflecting yellow, orange, and red light.

Phycobilins

Accessory photosynthetic pigments (phycoerythrin and phycocyanin) that absorb green and orange/yellow-green light while reflecting red and blue light.

Action Spectrum

A visual profile that measures the rate of photosynthesis across different wavelengths of light.

Absorption Spectrum

A visual profile that measures the amount of light energy absorbed across different wavelengths of light.

Rubisco

The abundant enzyme in the chloroplast stroma that catalyzes carbon fixation by attaching $CO_2$ to ribulose bisphosphate (RuBP).

Photosystem II (PSII)

The initial photosystem in the thylakoid membrane where light excites electrons in P680, water is oxidized to yield $O_2$ and $H^+$, and electrons are transferred to an ETC.

Photosystem I (PSI)

The photosystem where sunlight re-excites electrons removed from P700 to generate $\text{NADPH}$ using electrons and $H^+$.

Calvin Cycle

The light-independent reactions occurring in the chloroplast stroma consisting of carbon fixation, reduction/carbohydrate production, and RuBP regeneration to synthesize G3P and sugars.

Stomata

Microscopic pores on plant leaves that take in $CO_2$ and release $O_2$, closing during high heat to limit water loss.

Glycosylation

The process of attaching carbohydrates covalently to a lipid (forming a glycolipid) or a protein (forming a glycoprotein).

Osmotic Lysis

The swelling and bursting of an animal cell caused by excessive water entry in a hypotonic solution.

Plasmolysis

The shrinking and pulling away of the plant cell membrane and cytoplasm from the cell wall in a hypertonic solution.

Crenation

The shriveling and notched appearance of an animal cell resulting from water leaving in a hypertonic solution.

Turgor Pressure

The outward hydrostatic pressure exerted by water inside a plant cell pushing against the rigid cell wall.

Uniporter

A transport protein that moves a single solute across the membrane in one direction.

Symporter

A transport protein that moves two different solutes across the membrane simultaneously in the same direction.

Antiporter

A transport protein that moves two different solutes across the membrane in opposite directions.

Endocytosis

A bulk transport process by which extracellular substances and nutrients enter the cell.

Exocytosis

A bulk transport process by which cellular materials exit the cell via secretory vesicles into the extracellular medium.

$$\text{ATP}$$

Highest energy state; reduced form.

$$\text{ADP}$$

Lowest energy state; oxidized form.

$$\text{FADH}_2$$

Highest energy state; reduced form.

$$\text{FAD}$$

Lowest energy state; oxidized form.

$$\text{NAD}^+$$

Lowest energy state; oxidized form.

$$\text{NADH}$$

Highest energy state; reduced form.

$$\text{NADPH}$$

Highest energy state; reduced form.

$$\text{NADP}$$

Lowest energy state; oxidized form.

Outer membrane (mitochondrion)

Smooth phospholipid bilayer encasing the entire organelle.

Inner membrane (mitochondrion)

Highly impermeable interior membrane housing respiratory complexes and ATP synthase.

Intramembrane space

The narrow fluid compartment situated between the outer and inner mitochondrial membranes.

Cristae

Extensive invaginations and deep folds of the inner mitochondrial membrane that amplify available surface area for oxidative phosphorylation.

Mitochondrial matrix

Central aqueous compartment enclosed by the inner membrane, containing pyruvate dehydrogenase, citric acid cycle enzymes, ribosomes, and DNA.

Mitochondrial ribosomes

Autonomous ribosomes suspended in the matrix responsible for organellar protein synthesis.

Mitochondrial DNA

The organellar genome consisting of circular DNA molecules located within the matrix.

Glycolysis Location and Oxygen Requirement

Occurs exclusively in the cytosol under strictly anaerobic conditions (requires no oxygen).

Glycolysis Energy Investment Phase

Hydrolysis of $2\,\text{ATP}$ to convert glucose into fructose-1,6-bisphosphate.

Glycolysis Cleavage Phase

The 6-carbon phosphorylated backbone is broken in half into two 3-carbon molecules of glyceraldehyde-3-phosphate (G3P).

Glycolysis Energy Liberation Phase

Two G3P molecules are oxidized and transformed into 2 pyruvate molecules, yielding $2\,\text{NADH}$ and $4\,\text{ATP}$ (net gain of $2\,\text{ATP}$).

Pyruvate Breakdown Location and Enzyme

Occurs in the mitochondrial matrix and is catalyzed by the multienzyme complex pyruvate dehydrogenase.

Decarboxylation in Pyruvate Breakdown

Pyruvate dehydrogenase removes carbon and oxygen atoms from pyruvate, releasing them as carbon dioxide ($CO_2$).

Chemical Conjugation in Pyruvate Breakdown

The remaining 2-carbon acetyl group is linked to Coenzyme A (CoA) to form acetyl-CoA.

Pyruvate Breakdown Yield per Pyruvate

Yields $1\,\text{NADH}$ per pyruvate molecule oxidized ($2\,\text{NADH}$ per glucose).

Citric Acid Cycle Location

Occurs in the mitochondrial matrix of eukaryotic cells and in the cytoplasm of prokaryotic cells.

Citric Acid Cycle Entry Step

The 2-carbon acetyl group is detached from CoA and combined with a 4-carbon oxaloacetate molecule to form 6-carbon citrate (citric acid).

Citric Acid Cycle Yield (per cycle turn)

Releases $2\,CO_2$, $1\,\text{ATP}$, $3\,\text{NADH}$, and $1\,\text{FADH}_2$.

Unique Electron Carrier of the Citric Acid Cycle

$\text{FADH}_2$ (the Citric Acid Cycle is the only stage of cellular respiration where $\text{FADH}_2$ is produced).

Oxaloacetate Regeneration

Oxaloacetate is fully regenerated at the end of the Citric Acid Cycle to accept another acetyl group and start the cycle again.

Oxidative Phosphorylation Mechanism and ATP Output

Generates the vast majority of cellular ATP using high-energy electrons donated by $NADH$ and $FADH_2$ through the protein complexes of the Electron Transport Chain (ETC) to power the phosphorylation of ADP.

Oxidative Phosphorylation Subcellular Site

Localized to the inner mitochondrial membrane in eukaryotes and across the plasma membrane in prokaryotes.

Isotonic solution

A solution where the solute concentration is identical inside and outside the cell, resulting in no net movement of water.

Hypotonic solution

A solution where the surrounding solution has a lower solute concentration than the cellular interior, causing excessive water to flow osmotically into the cell and leading to cellular swelling.

Osmotic lysis

The physical rupture and bursting of an animal cell when placed in a hypotonic medium.

Optimal Temperature for Human Enzymes

The temperature at which human enzymes function at peak catalytic efficiency, specifically $37\,^\circ\text{C}$.

Thermal Denaturation

The loss of an enzyme's native three-dimensional protein conformation occurring when temperatures surpass optimal thresholds.

Effect of pH on Enzyme Function

Deviations from optimal pH alter the ionization states and electrical charges of amino acid R-groups, which compromises substrate binding and catalytic efficiency.

Factors Determining Substrate Specificity

Physical compatibility, size, shape, chemical polarity, and ionic charge between the enzyme active site and the substrate.

Enzyme Operational Range

The narrow range of environmental temperature and pH within which enzymes can maintain proper structure and function optimally

Aerobic Respiration

A metabolic pathway utilizing oxygen ($O_2$) as a terminal electron acceptor.

Anaerobic Respiration

A metabolic pathway that operates in the complete absence of oxygen ($O_2$).

Reversible inhibitors

Molecules that bind non-covalently to temporarily halt enzymatic function.

Competitive inhibitors

Inhibitors that compete directly with the native substrate for occupancy of the active site.