Exam 3

Kinetic energy

Energy of motion.

Potential energy

Stored energy resulting from position or structure.

Main energy source for the biosphere

The Sun.

Oxidation

The loss of electrons.

Reduction

The gain of electrons.

First law of thermodynamics

Energy cannot be created or destroyed, only transferred or transformed.

Second law of thermodynamics

Energy transfers increase universal entropy, and some energy is lost as unusable thermal energy.

Free energy change formula

$$\Delta G = \Delta H - T\Delta S$$

Exergonic reaction

A reaction characterized by $\Delta G < 0$ that proceeds spontaneously and releases free energy.

Endergonic reaction

A non-spontaneous reaction characterized by $\Delta G > 0$ that requires free energy input.

Activation energy

The minimum energy required to initiate a chemical reaction.

Catalyst

A substance that accelerates a reaction by lowering activation energy without altering $\Delta G$.

ATP chemical structure

Adenine attached to ribose and a chain of three phosphate groups.

ATP hydrolysis

Exergonic reaction releasing inorganic phosphate and free energy that powers endergonic cellular processes.

Thermodynamics memory tip

Negative $\Delta G$ releases energy; ATP helps power work.

Enzyme

A biological macromolecular catalyst that speeds up chemical reactions without being consumed.

Ribozyme

An RNA molecule capable of catalyzing specific biochemical reactions.

Active site

The specific catalytic pocket of an enzyme where the substrate binds.

Enzyme-substrate complex

The intermediate structure formed upon substrate binding to an enzyme active site.

Factors affecting enzyme activity

Substrate and enzyme concentrations, temperature, pH, and environmental factors altering protein conformation.

Competitive inhibitor

An inhibitor that binds directly to the active site, competing with the substrate.

Noncompetitive inhibitor

An inhibitor that binds an allosteric site away from the active site, inducing a conformational change that alters enzyme function.

Allosteric activator

A regulatory molecule that binds to an allosteric site to stabilize the active enzyme conformation and increase activity.

Allosteric inhibitor

A regulatory molecule that binds to an allosteric site to stabilize an inactive enzyme conformation and decrease activity.

Enzyme inhibition memory tip

Competitive inhibitors block the active site; noncompetitive inhibitors act from another site.

Metabolism

The totality of an organism's chemical reactions.

Anabolism

Metabolic pathways that construct complex molecules from simpler units, consuming energy.

Catabolism

Metabolic pathways that break down complex molecules into simpler units, releasing energy.

Biochemical pathway

A sequential series of enzymatic reactions where the product of one serves as the substrate for the next.

Feedback inhibition

A regulatory mechanism in which the final product of a pathway inhibits an earlier enzyme to prevent overaccumulation.

Metabolic pathways memory tip

Anabolism builds; catabolism breaks down.

Autotroph

An organism that produces organic compounds from inorganic substances using light or chemical energy.

Heterotroph

An organism that obtains carbon and energy by consuming organic compounds produced by other organisms.

Dehydrogenation

The loss of hydrogen atoms, each consisting of an electron and a proton.

Cellular respiration balanced equation

$$C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O + \text{energy}$$

Molecule oxidized in cellular respiration

Glucose is oxidized to carbon dioxide ($CO_2$).

Molecule reduced in cellular respiration

Oxygen ($O_2$) is reduced to water ($H_2O$).

Aerobic respiration

Catabolic respiration pathway utilizing molecular oxygen ($O_2$) as the final electron acceptor.

Anaerobic respiration

Respiration that employs an inorganic molecule other than oxygen as the terminal electron acceptor.

Role of $NAD^+$ in respiration

Acts as an electron carrier, accepting electrons and a proton to become NADH which delivers electrons to the ETC.

Components accepted by $NAD^+$ to become NADH

Two electrons and one proton ($2e^-$ and $1H^+$).

Substrate-level phosphorylation

The direct enzymatic transfer of a phosphate group from a phosphorylated substrate directly to ADP.

Oxidative phosphorylation

ATP production coupled to the transfer of electrons down the electron transport chain and driven by a proton gradient.

Four stages of cellular respiration

Glycolysis, pyruvate oxidation, citric acid cycle, and oxidative phosphorylation (ETC with chemiosmosis).

Cellular location of glycolysis

Cytoplasm (cytosol).

Glycolysis inputs (per glucose)

$1\text{ glucose}$, $2\,NAD^+$, and $2\text{ ADP} + 2\,P_i$.

Glycolysis net outputs (per glucose)

$2\text{ pyruvate}$, net $2\text{ ATP}$, and $2\text{ NADH}$.

Three phases of glycolysis

Energy investment, cleavage (sugar splitting), and energy payoff.

Oxygen requirement of glycolysis

No; it occurs independently of the presence or absence of oxygen.

Pyruvate oxidation location (eukaryotes)

Mitochondrial matrix.

Enzyme complex catalyzing pyruvate oxidation

Pyruvate dehydrogenase complex.

Pyruvate oxidation inputs (per pyruvate)

$1\text{ pyruvate}$, $1\,NAD^+$, and $1\text{ coenzyme A (CoA)}$.

Pyruvate oxidation outputs (per pyruvate)

$1\,CO_2$, $1\text{ NADH}$, and $1\text{ acetyl-CoA}$.

Pyruvate oxidation outputs (per glucose)

$2\,CO_2$, $2\text{ NADH}$, and $2\text{ acetyl-CoA}$.

Fate of pyruvate when oxygen is available

Transported into the mitochondrion, oxidized to acetyl-CoA, and fed into the citric acid cycle.

Cellular respiration stages 1-2 memory tip

Glycolysis splits glucose; pyruvate oxidation makes acetyl-CoA.

Citric acid cycle cellular location

Mitochondrial matrix.

Citric acid cycle inputs (per acetyl-CoA)

$1\text{ acetyl-CoA}$, $3\,NAD^+$, $1\text{ FAD}$, and $1\text{ ADP} + P_i$.

Citric acid cycle outputs (per acetyl-CoA)

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

Citric acid cycle outputs (per glucose)

$4\,CO_2$, $6\text{ NADH}$, $2\text{ FADH}_2$, and $2\text{ ATP}$.

Three segments of the citric acid cycle

Citrate synthesis; citrate isomerization and decarboxylation; oxaloacetate regeneration.

Molecules that condense to form citrate

Acetyl-CoA and oxaloacetate.

Cumulative running yield after the citric acid cycle (per glucose)

$6\,CO_2$, $4\text{ ATP}$, $10\text{ NADH}$, and $2\text{ FADH}_2$.

Mitochondrial ETC location

Inner mitochondrial membrane (cristae).

Electron donors to the mitochondrial ETC

NADH and $\text{FADH}_2$.

Ions pumped across the inner mitochondrial membrane by ETC complexes

Protons ($H^+$), pumped into the intermembrane space.

Proton-motive force

The electrochemical gradient generated by proton accumulation across a biological membrane.

Chemiosmosis

The flow of protons down an electrochemical gradient through ATP synthase to power the phosphorylation of ADP.

Function of ATP synthase

Harnesses the downhill flow of protons to synthesize ATP from ADP and inorganic phosphate.

Direction of mitochondrial proton flow through ATP synthase

From the intermembrane space back into the mitochondrial matrix.

Approximate net ATP yield per glucose in eukaryotes

Approximately $30\text{ ATP}$.

Approximate net ATP yield per glucose in bacteria

Approximately $32\text{ ATP}$.

Oxidative phosphorylation memory tip

Electrons power proton pumping; proton flow powers ATP synthase.

Regulatory effectors of phosphofructokinase

Allosterically inhibited by elevated levels of ATP and citrate.

Regulatory effector of pyruvate dehydrogenase

Allosterically inhibited by elevated levels of NADH.

Terminal electron acceptor in fermentation

An organic molecule (such as pyruvate or acetaldehyde).

Primary biological role of fermentation

Regenerates $NAD^+$ from NADH to enable continuous ATP generation through glycolysis in anaerobic conditions.

Ethanol fermentation pathway

Conversion of pyruvate into ethanol and $CO_2$ by yeast and some bacteria.

Practical applications of ethanol fermentation

Brewing, winemaking, and baking.

Lactic acid fermentation pathway

Direct reduction of pyruvate into lactate without releasing $CO_2$.

Sites of lactic acid fermentation

Certain bacterial species and oxygen-deprived vertebrate skeletal muscle cells.

ATP yield per glucose from fermentation

$2\text{ ATP}$ (generated strictly via substrate-level phosphorylation in glycolysis).

ATP yield per glucose from aerobic respiration

Approximately $30\text{--}32\text{ ATP}$.

Components of the fermentation pathway

Glycolysis coupled with downstream reactions that reoxidize NADH to $NAD^+$.

Component pathways of aerobic respiration

Glycolysis, pyruvate oxidation, the citric acid cycle, and oxidative phosphorylation.

Point of entry for glycerol into cellular respiration

Converted into glyceraldehyde 3-phosphate (G3P) and enters glycolysis.

Point of entry for fatty acids into cellular respiration

Cleaved via beta-oxidation into two-carbon units that enter as acetyl-CoA.

Point of entry for amino acids into cellular respiration

Deaminated carbon skeletons enter as intermediates in glycolysis or the citric acid cycle.

Fermentation pathway memory tip

Fermentation regenerates $NAD^+$; it does not replace the ETC.

Photosynthesis site in plant cells

Chloroplasts.

Thylakoids

Internal flattened membranous sacs within chloroplasts hosting the light reactions.

Grana

Dense stacks of thylakoids.

Stroma

The dense fluid matrix surrounding thylakoids where the Calvin cycle takes place.

Stomata

Microscopic pores on leaf surfaces that mediate gas exchange ($CO_2$ uptake and $O_2$ release).

Photosynthesis balanced chemical equation

$$6CO_2 + 12H_2O + \text{light} \rightarrow C_6H_{12}O_6 + 6H_2O + 6O_2$$

Molecule oxidized during photosynthesis

Water ($H_2O$ is oxidized, producing molecular oxygen $O_2$).

Molecule reduced during photosynthesis

Carbon dioxide ($CO_2$ is reduced to form carbohydrate molecules).

Two primary stages of photosynthesis

Light-dependent reactions and the light-independent Calvin cycle.

Pigment

A chemical compound that absorbs specific wavelengths of visible light.

Reason plant foliage appears green

Chlorophyll absorbs blue and red wavelengths while transmitting or reflecting green light.