AP Bio - Unit 3

Positive Control

Used to confirm that the system being used in an experiment (that is checking the dependant variable) is working correctly. Critical, give a point of comparison 

Enzyme

A biological catalyst that speeds up chemical reactions necessary for life by lowering their activation energy. Bind to a reactant (substrate) at an active site to release a product (completing the reaction).

Active site

The specific region on an enzyme where a substrate molecule binds with the enzyme to start a chemical reaction.

Substrate

The specific reactant molecule that binds to an enzyme at the active site, undergoing a chemical reaction to form the product. 

Denaturation

The process by which a protein (e.g. enzymes) loses its 3D shape as weak interactions within the molecule are interrupted. Losing its shape often results in a decrease or loss of function. Denaturation occurs due to heat, extreme pH, or certain chemicals.

Competitive inhibition

When a molecule (inhibitor) competes with a substrate over an enzyme’s active site, which slows down the rate of a reaction. The inhibitor is structured similarly to the substrate and competitive inhibition is often reversible.

Noncompetitive inhibition

A type of inhibition where the inhibitor binds to the enzyme’s allosteric site (site other than active site) and changes the active site so it can’t bind substrates. The enzyme’s activity towards catalyzing a reaction is worsened. Can be reversible if no covalent bonds are formed. 

Allosteric site

A specific region on the enzyme separate from the active site. It allows molecules to either activate or inhibit enzyme activity (not reaction). 

Free energy

The amount of energy available to do work in a cell. This changes due to energy transfers (like chemical reactions). 

Cellular respiration

The metabolic process that cells use to convert chemical energy (like glucose) into ATP.

Fermentation

The anaerobic process that converts sugar into acids (like lactic acid), gases, or alcohol (like ethanol). It begins with glycolysis, producing some ATP, then uses pyruvate to regenerate NAD+ so that glycolysis continues. 

Alcohol

Produced by alcoholic fermentation. Converts pyruvate into ethanol and carbon dioxide. Happens in yeast.

Lactic acid

Produced by lactic acid fermentation. Converts pyruvate into lactate (lactic acid). Happens during intense exercise. 

Aerobic

Aerobic respiration is the most efficient form of cellular respiration. The process occurs in eukaryotic cells where glucose and oxygen is converted to carbon dioxide, water, and ATP. Includes glycolysis, the link reaction, the Krebs cycle, and ETC. Produces 36-38 ATP. 

Anaerobic

Anaerobic respiration is the less efficient form of cellular respiration that happens quicker to meet demands in low-oxygen environments. It consists of glycolysis and fermentation to generate ATP faster with a lower yield (2).

Glycolysis

A set of reactions that breaks down one molecule of glucose to two pyruvate molecules, producing two ATP and two NADPH. It’s the first step in both types of respiration and occurs in the cytoplasm (doesn’t need oxygen). 

Glucose

A simple sugar (monosaccharide) that’s the primary energy source for living organisms. It’s produced during photosynthesis and is broken down in cellular respiration to produce ATP. 

Pyruvate

A three-carbon that is produced by glycolysis. Where pyruvate goes depends on the amount of oxygen: If there’s enough, it goes into the mitochondria for the next part of aerobic respiration. If there isn’t, it undergoes fermentation in anaerobic conditions.

Oxidation

A chemical process where a molecule loses its electrons (loss of hydrogen atoms, gain of oxygen atoms). More positive charge.

Reduction

A chemical process where a molecule gains electrons, becoming reduced (gain of hydrogen atoms, loss of oxygen atoms). More negative charge.

ADP

Adenosine diphosphate

A nucleotide that serves as a depleted battery that can become ATP with the addition of an inorganic phosphate (a process called phosphorylation). It is formed when ATP loses a phosphate to release energy.

ATP

Adenosine triphosphate

A nucleotide that stores (in the bonds that connect the phosphate groups) and transfers (by being broken down into ADP) energy for cellular processes like apoptosis, binary fission, and active transport.

NAD+

Nicotinamide adenine dinucleotide

An essential coenzyme that is highly oxidized, accepting electrons and protons in cellular respiration and becoming reduced to NADH.

NADH

Oxidized form of nicotinamide adenine dinucleotide

A coenzyme and high-energy electron carrier that’s critical to cellular respiration, produced during glycolysis and the Krebs cycle. NADH moves electrons to the ETC where they generate large amounts of ATP through oxidative phosphorylation. 

FAD

Flavin adenine dinucleotide

A coenzyme/high-energy electron carrier that is essential for for cellular respiration. FAD accepts electrons and protons during the Krebs cycle and link reaction, becoming FADH₂. 

FADH₂

Reduced form of flavin adenine dinucleotide

A coenzyme and high-energy electron carrier made from FAD in the Krebs cycle by accepting electrons, which it releases to the ETC, providing the energy to create a proton gradient across the inner mitochondrial membrane (powering the ETC). After donating the electrons, FADH2 becomes FAD again.

Krebs cycle

A metabolic pathway in the mitochondrial matrix that generates energy for the cell by oxidizing acetyl-CoA (it combines with oxaloacetate) to make citrate. The cycle turns twice per one glucose molecule, releasing 4 CO2, 6 NADH, 2 FADH2, and 2 ATP.

Oxidative phosphorylation

The final stage of cellular respiration where most ATP is generated, which uses the energy from electrons (passed down from the ETC) to pump protons and create a gradient that drives the creation of ATP from ADP (chemiosmosis). 

Electron transport chain

A series of protein complexes that receives electrons from electron carriers (like NADH and FADH2 from glycolysis/Krebs cycle). As they move from the chain, the released energy is used to pump protons (H+) from the mitochondrial matrix to the intermembrane space, creating a proton gradient. The potential energy stored in the proton gradient is used by the ATP synthase to produce a lot of ATP. Oxygen is the final acceptor that combines with the electrons/protons to form water. 

ATP synthase 

An enzyme that catalyzes the synthesis of ATP, acting like a motor (driven by the flow of protons) to push together ADP and P_i by using the energy from the proton gradient across the membrane (that was formed by the ETC).

Inner mitochondrial membrane

A highly folded, selectively permeable membrane in eukaryotes that surrounds the mitochondrial matrix (critical for cellular respiration) and houses the ATP synthase and ETC. The folding in the cristae maximizes the surface area for these reactions. 

Photosynthesis

The process that plants, algae, and some bacteria use to convert light energy into usable chemical energy. Water and carbon dioxide are turned into glucose and oxygen through a series of reactions that occur in the chloroplasts’ thylakoid membranes and stromas (light-dependant and light-independant). 

Cyanobacteria

Photosynthetic prokaryotes that perform oxygenic photosynthesis, notable for being the first organisms to produce oxygen. They do this by using chlorophyll and phycobilisomes, with many having the ability to turn nitrogen into ammonia.

Light-dependant reactions

First stage of photosynthesis, occuring in the thylakoid membranes of chloroplasts. Chlorophylls absorb light in photosystems (PSII and PSI).

Photosystems I and II (PSI and PSII)

Photosystems I and II are protein-pigment complexes in the thylakoid membrane that capture light energy for photosynthesis. Photosystem II (PSII) is the first to act, using energy from light to split water (photolysis) into protons and electrons (with oxygen as a byproduct). Photosystem I (PSI) then uses its light energy to re-energize the electrons and transfer them to NADP+, which makes NADPH. 

NADPH

Coenzyme electron carrier that is generated in the photosystems of photosynthesis. It provides electrons to the Calvin cycle. The oxidized form after donating electrons (NADP+) is recycled back to the light-dependant reactions to be reduced to more NADPH.

Thylakoid (internal) membrane of chloroplasts

An internal chloroplast membrane where the light-dependant reactions of photosynthesis occur. It contains chlorophyll and other pigments (to catch energy) while housing protein complexes like photosystems and ATP synthase. It is a lipid bilayer.

Calvin cycle (Light-independent reactions) 

Second stage of photosynthesis that occurs in the stroma, converting carbon dioxide into glucose. It uses the energy from ATP and NADPH instead of light energy to fix carbon (attached to RuBP/RuBisCO, a five-carbon enzyme) and create a three-carbon sugar called glyceraldehyde-3-phosphate (G3P) used to build glucose.

G3P

Glyceraldehyde-3-phosphate

A 3-carbon sugar produced directly by the Calvin cycle. Its synthesized using the energy from ATP and NADPH. Some of its molecules are used to build glucose while others are used to regenerate the CO2 acceptor molecule (keeping the cycle going).

Exergonic

A chemical reaction that release energy into the surroundings.

Endergonic

A chemical reaction that needs an input of energy to work.

Metabolic

Metabolic is the sum (catabolic + anabolic) of all chemical reactions that occur in a living organism.

Catabolic

Process of breaking down complex molecules to release energy (e.g. cellular respiration). 

Anabolic

Process of building complex molecules from simple ones that requires energy (e.g. photosynthesis).

Substrate-level phosphorylation

Some ATP is made by directly transferring a phosphate group from an organic substrate to ADP using an enzyme.

Why is ATP not synthesized with the insertion of channel proteins into the thylakoid membrane? (plant respiration)

Because channel proteins allow protons to enter the membrane (dissipating the proton concentration difference), while they would normally go through ATP synthase molecules, making ATP.