1-8 BIO

Photoautotrophs

Organisms that use sunlight to make food, including plants, algae, and cyanobacteria.

Chemoautotrophs

Organisms, such as thermophilic bacteria, that capture energy from inorganic compounds to make food.

Heterotrophs

Organisms, including animals, fungi, and most bacteria, that rely on organic carbon produced by autotrophs for their energy needs.

Anoxygenic Photosynthesis

A form of photosynthesis that does not generate oxygen, performed by some bacteria.

Stomata

Small pores on the leaf underside through which gas exchange occurs ($CO_2$ enters and $O_2$ exits).

Guard Cells

The specialized cells that surround a stoma (singular) to regulate the opening and closing of the pore.

Thylakoid

Disc-shaped structures within the chloroplast where the light reaction occurs; the membranes contain chlorophyll and other pigments.

Grana

The name given to stacks of thylakoids within the chloroplast.

Stroma

The fluid-filled space within the chloroplast (outside the thylakoids) where the Calvin cycle occurs.

Lumen

The internal space located inside the thylakoid membrane.

Mesophyll

The specialized "middle leaf" cells where high densities of chloroplasts are found.

Electromagnetic Energy

Light energy composed of photon particles that travel as waves; shorter wavelengths carry more energy than longer wavelengths.

Visible Range

The fraction of electromagnetic energy seen by humans and used by plants, ranging from $700-400\,nm$.

Chlorophyll a

A primary pigment consisting of a phytol chain embedded in the membrane and a tetraporhyrin ring that lies flat on the thylakoid surface.

Chlorophyll b

An accessory pigment similar to chlorophyll a, but containing a $-CHO$ group instead of a $-CH_3$ group in a specific position.

$\beta$-carotene

A type of carotenoid pigment that protects photosystems by dissipating excess energy, also responsible for the color of carrots and oranges.

Photosystem II (PSII)

The site of light absorption where electrons are excited and water is split to release oxygen ($O_2$) as a by-product.

Photosystem I (PSI)

The site where light excites an electron from the chlorophyll a pair, which is then passed to the second part of the ETC leading to NADP reductase.

ATP Synthase (ATPase)

An enzyme complex in the thylakoid membrane that uses a $H^+$ gradient (chemiosmosis) to generate ATP from ADP and $P_i$.

Plastocyanin (Pc)

A component of the first electron transport chain that helps transport electrons between the Cytochrome $b_6f$ complex and PSI.

Ferredoxin (Fd)

A molecule that transports electrons from Photosystem I to NADP reductase in the second part of the ETC.

NADP Reductase

The enzyme complex that uses electrons from the second ETC to reduce $NADP^+$ into NADPH.

RuBisCO

Ribulose bis-phosphate carboxylase-oxidase; the enzyme that catalyzes the addition of $CO_2$ to RuBP in the Calvin cycle.

Carbon Fixation

The first stage of the Calvin cycle where $CO_2$ is added to RuBP by RuBisCO to generate two $3$-PGA molecules.

Reduction (Calvin Cycle)

The second stage of the Calvin cycle where ATP and NADPH are used to add electrons to molecules, producing sugar in the form of GA3P.

GA3P (Glyceraldehyde-3-phosphate)

The organic carbon product of the Calvin cycle; three cycles are required to create one molecule, and $2\,GA3P$ molecules are needed to make one glucose.

Photorespiration

The process that occurs when RuBisCO functions as an oxygenase instead of a carboxylase, resulting in no sugar production.

Primary Production Proxies

Methods used to quantify photosynthesis, such as measuring $[^{14}C]\text{-}HCO_3$ uptake, dissolved $O_2$ production, or $[^{18}O]\text{-}H_2O$ water splitting.

Cellular Respiration

The process by which cells extract energy from food to generate $ATP$ through glucose catabolism.

Redox Reactions

Chemical reactions characterized by the transfer of electrons from one molecule to another.

Reducing Agent

A molecule that can donate electrons in a redox reaction.

Oxidizing Agent

A molecule that can accept electrons in a redox reaction.

Reduction

gain of electron

Oxidation

The process by which a molecule loses one or more electrons during a chemical reaction.

Electron Carrier

Molecules like $NAD^+$ or $FAD^+$ that shuttle high-energy electrons to electron transport chains where $ATP$ is produced.

Dephosphorylation

The chemical process involving the loss of a phosphate group from a molecule.

Phosphorylation

The process of adding a phosphate group to a molecule, which often makes the molecule less stable and more reactive.

Substrate-Level Phosphorylation

A method of generating $ATP$ via a coupled exergonic reaction that does not require a membrane.

Chemiosmosis

A process for making $ATP$ that requires the enzyme $ATP\text{ synthase}$ and a $H^+$ concentration gradient; it produces $90$% of $ATP$ during glucose catabolism.

Glycolysis

The first metabolic pathway of glucose metabolism, occurring in the cytoplasm, which breaks down one glucose into two pyruvate molecules.

Glyceraldehyde-3-phosphate (G3P)

The two three-carbon molecules formed when glucose is phosphorylated and split during the first half of glycolysis.

Acetyl CoA

The molecule formed in the mitochondria when pyruvate is oxidized and coenzyme A is attached before entering the Citric Acid Cycle.

Citric Acid Cycle (CAC)

A series of reactions in the mitochondrial matrix where citrate is oxidized to produce $NADH$, $FADH_2$, and $ATP$ or $GTP$.

Oxaloacetate

The four-carbon molecule that is the final product of the Citric Acid Cycle and combines with the acetyl group to start the cycle again.

Oxidative Phosphorylation

The final stage of cellular respiration consisting of the electron transport chain and chemiosmosis.

Electron Transport Chain (ETC)

A series of transporters embedded in the inner mitochondrial membrane that shuttle electrons from $NADH$ and $FADH_2$ to $O_2$.

Ubiquinone (Q)

A mobile electron carrier that shuttles electrons from complexes I and II to complex III in the electron transport chain.

Cytochrome C

A peripheral protein that carries individual electrons to complex IV of the electron transport chain.

ATP synthase

A complex integral protein that uses the kinetic energy from protons falling down a gradient to form $ATP$ from $ADP$ and $P_i$.

Lactic Acid Fermentation

An anaerobic process occurring in muscle cells and some bacteria where pyruvate is converted to lactate to regenerate $NAD^+$.

Alcohol Fermentation

An anaerobic process used by yeast where pyruvate is converted into $CO_2$, acetaldehyde, and finally ethanol.

Glut4

Vesicles that fuse with the plasma membrane in the presence of insulin to allow glucose to enter the cell.

Hexokinase

The glycolysis enzyme affected by feedback inhibition from elevated levels of glucose-6-phosphate.

Cellular Respiration

The process by which cells extract energy from food to generate ATP, also known as glucose catabolism.

Redox Reactions

Chemical reactions where electrons are transferred from one molecule to another.

Reducing Agents

Molecules that can donate electron(s) in a redox reaction.

Oxidizing Agents

Molecules that can accept electrons in a redox reaction.

Reduced

The state of a molecule that has gained electron(s) after a chemical reaction.

Oxidized

The state of a molecule that has lost electron(s) after a chemical reaction.

NAD+

The oxidized state of nicotinamide adenine dinucleotide, which acts as an electron carrier by accepting electrons.

NADH

The reduced state of nicotinamide adenine dinucleotide, which carries $2\,e^-$ and $1\,H^+$ more than its oxidized form.

Dephosphorylation

The loss of a phosphate group from a molecule.

Phosphorylation

The process of adding a phosphate group to a molecule; phosphorylated molecules tend to be less stable and more likely to react.

Chemiosmosis

A process that generates $90\%$ of ATP using the enzyme ATP synthase and a $H^+$ concentration gradient; it occurs in mitochondria, chloroplasts, and plasma membranes of aerobic prokaryotes.

ATP Synthase

An integral membrane protein and enzyme that mediates the reaction $ADP + Pi \rightarrow ATP$ using kinetic energy from protons.

Glycolysis

The first metabolic pathway of glucose metabolism, occurring in the cytoplasm, involving 10 enzymatic reactions and not requiring $O_2$.

Glyceraldehyde-3-phosphate (G3P)

The two three-carbon molecules formed when glucose is phosphorylated and split during the first half of glycolysis.

Net ATP production of glycolysis

$2\,ATP$ ($4\,ATP$ produced minus $2\,ATP$ invested).

Oxidation of Pyruvate

The process in eukaryotic cells where, if oxygen is present, two pyruvate molecules enter the mitochondria and are converted to acetyl CoA.

Citric Acid Cycle (CAC)

A continuous cycle occurring in the mitochondrial matrix where acetyl CoA and oxaloacetate form citrate, which is then oxidized to produce NADH, $FADH_2$, and ATP/GTP.

Oxaloacetate

The final product of the citric acid cycle that also combines with the acetyl group in the first step.

Oxidative Phosphorylation

The last pathway of cellular respiration consisting of the electron transport chain and chemiosmosis; it is the only pathway where $O_2$ is an input.

Electron Transport Chain (ETC)

A series of electron transporters embedded in the inner mitochondrial membrane that shuttle electrons from NADH and $FADH_2$ to $O_2$, pumping protons in the process.

Ubiquinone (Q)

A component of the ETC that carries electrons from complexes I and II to complex III.

Cytochrome C

A peripheral protein that carries each individual electron from complex III to complex IV.

Final Electron Acceptor

Oxygen ($O_2$), which is reduced at complex IV to form $H_2O$.

ATP Yield per Glucose

$30$-$36$ ATP per glucose molecule, storing ~$34\%$ of the energy from glucose.

Fermentation

A metabolic process that regenerates NAD+ from NADH when $O_2$ is lacking, allowing glycolysis to continue.

Lactic Acid Fermentation

A type of substrate-level phosphorylation occurring when $O_2$ is limited in muscle cells, red blood cells, and some bacteria; catalyzed by lactate dehydrogenase.

Alcohol Fermentation

A two-reaction process in anaerobic yeast involving pyruvate decarboxylase and alcohol dehydrogenase to produce ethanol and $CO_2$.

Glut4

A protein residing in vesicles that fuses with the plasma membrane in the presence of insulin to allow glucose into the cell.

Hexokinase

An enzyme in glycolysis that is inhibited by elevated levels of glucose-6-phosphate.

Phosphofructokinase

The glycolysis enzyme whose activity is increased by fructose-6-phosphate and decreased by citrate or acidic pH.

Bioenergetics

The study of energy flow through a living system.

Chemotrophs

Organisms that use chemical compounds as their primary energy source.

Phototrophs

Organisms that use light as their primary energy source.

Chemolithotrophs

Organisms that use inorganic chemicals as an energy source.

Chemoorganotrophs

Organisms that use organic chemicals as an energy source.

Metabolism

All chemical reactions of a cell or organism.

Metabolic pathway

A series of biochemical reactions that converts one or more substrates into a final product.

Anabolic

Metabolic pathways that require energy and synthesize large molecules.

Catabolic

Metabolic pathways that release energy and break down large molecules into smaller molecules.

First law of thermodynamics

States that the total amount of energy in the universe is constant; energy cannot be created or destroyed.

Second law of thermodynamics

States that the transfer of energy is not completely efficient, resulting in some energy being lost as unusable heat and increased entropy (disorder).

Kinetic energy

The energy possessed by objects in motion.

Potential energy

The energy possessed by objects that have the potential to move, including chemical energy stored in bonds.

Activation energy

The energy required for a reaction to proceed, which causes reactants to become contorted and unstable.

Transition state

An unstable state during a chemical reaction that allows bond(s) to be broken or made.

Exergonic

A chemical reaction that releases energy, characterized by $\Delta G < 0$ and being spontaneous.

Endergonic

A chemical reaction that requires an input of energy, characterized by $\Delta G > 0$.