AP Bio Unit 3

Chapter 6 - An Intro to Metabolism

  • Forming bonds between molecules: dehydration synthesis, synthesis, and anabolic reactions. Breaking bonds between molecules: hydrolysis, digestion, catabolic reactions.

  • Some chemical reactions release energy, they are said to be exergonic. Some chemical reactions require an input of energy, they are said to be endergonic.

*If forming bonds releases energy and breaking bonds uses energy, then why do these graphs here present the opposite? This is because when we break one bond (in a polymer, for example), we open up two extra spaces on the two newly formed monomers. These two new spaces would theoretically be filled immediately. Net: 2 new bonds formed, 1 original bond broken, therefore more energy was released than used.

  • Reactions that are “downhill” do not happen spontaneously because covalent bonds are stable bonds, and they have what is called an “Activation energy” which is the “hill” that we see in the graphs above. 

*An initial input of energy is required to kickstart the reaction

*The activation energy needed to start most of these reactions are too high for living cells, so cells must use enzymes to lower these activation energies to survivable levels (catalysts)

  • Enzymes: biological catalysts that can increase the rate of reaction without being consumed, reduce activation energy, and they also do not change the free energy released or required for the reaction. Required for most biological processes

  • Enzymes are made up of protein AND RNA

  • Enzymes are highly reaction specific for what molecules they interact with

  • substrate: reactant which binds to an enzyme (the temporary association of enzyme and substrate bound together is called an enzyme-substrate complex)

  • product: end result of the reaction

  • active site: the enzyme's catalytic site; substrate fits into active site 

  • Enzymes are not consumed in a reaction, can catalyze thousands of reactions per second

  • Like proteins (because they are technically proteins), enzymes can be affected/denatured by temperature, pH, and salinity

  • Lock and key model (wrong theoretical model): substrate fits perfectly into the enzyme’s active site

  • Induced fit model (correct model): “conformational change,” the active site changes shape to better fit the substrate

  • Enzymes affect the substrate in different ways to achieve different things. In synthesis, the active site orients substrates into the correct position for a reaction to occur. In digestion, the active site puts stress on the bonds that must be broken, making it easier to separate them.

  • Factors that affect enzyme function/efficiency: enzyme concentration, substrate concentration, temperature, pH, salinity, activators, inhibitors

*Be able to explain graphs like this (for limited/unlimited substrate, enzyme concentration, and why there are plateaus on the graph)

  • Enzymes have optimum temperatures, pHs, and salinity levels to function best.

*Be able to understand these graphs (pretty much similar style for other environmental factors like pH and stuff)

  • Cofactors: activators; non-protein, small inorganic compounds  that bind with enzyme molecule to activate it (Mg, K, Ca, Zn, Fe (like in hemoglobin), Cu)

  • Coenzymes: activators; non-protein, organic molecules that bind temporarily or permanently near an active site (Many vitamins)

  • Inhibitors: molecules that reduce enzyme activity (competitive, noncompetitive, irreversible, feedback)

  • Competitive inhibition: a competitive inhibitor competes for the active site for the substrate. (Can be overcome by increasing substrate concentration)

  • Noncompetitive inhibition: a noncompetitive inhibitor binds with the allosteric site of an enzyme, changing the shape of the active site and making it so the substrate cannot bind with the enzyme.

*Be able to explain this graph

  • Irreversible inhibition: an inhibitor that permanently binds to the active or allosteric site. Makes it so the enzyme is permanently unusable with its intended substrate. (Cyanide poisoning; will be covered in cellular respiration unit)

  • Allosteric regulation: conformational changes by regulatory molecules. Inhibitors keep enzymes in an inactive form. Activators keep enzymes in an active form.

  • Cooperativity: The substrate acts as an activator. Substrate causes a conformational change in enzyme and activates it, making it more effective and active. (hemoglobin for example)

  • Enzymes can run reactions in a specific pathway. Chemical reactions are divided into small steps, each step is done by a different enzyme.

  • Organized groups of enzymes can create efficient and important biological systems, such as the electron transport chain in mitochondria.

  • Feedback inhibition: regulation and coordination of production. The end product acts as an allosteric inhibitor of a previous enzyme. No unnecessary accumulation of product







Chapter 7 - Cellular Respiration and Fermentation

  • In eukaryotes, cellular respiration harvests energy from food and yields large amounts of ATP. A similar process takes place in many prokaryotic organisms as well.

  • Glucose is broken down to carbon dioxide and water, and the cell captures some of the energy from this process to create ATP. Cellular respiration is an exergonic process that transfers energy from the bonds in glucose to ATP.

  • Cellular respiration takes place in the mitochondria of eukaryotes

  • Breathing (respiration) provides oxygen for aerobic respiration.

  • Cellular respiration can produce a net gain of anywhere from about 28-34 ATP molecules. (This is because the two different electron carriers, FADH2 and NADH, carry different amounts of electrons)

  • The majority of ATP production happens at the electron transport chain, where electrons “fall” to a lower energy state (loses potential energy) to the final electron acceptor, oxygen.

  • The movement of electrons from one molecule to another is called an oxidation-reduction reaction (aka a redox reaction). The loss of electrons from a substance is called oxidation and the addition of electrons to another substance is called reduction.

*We say a molecule is oxidized when it loses electrons, and reduced when it gains electrons

  • In cellular respiration, glucose loses its hydrogen atoms and becomes oxidized to CO2. Oxygen gains hydrogen atoms and becomes reduced to H2O.

*Oxidation and reduction of molecules also applies to gains and losses of hydrogen atoms

  • NAD+ (the more important one to know) and FAD are “electron carrier molecules” that collect and carry electrons to the electron transport chain.

  • Glycolysis is the first stage of cellular respiration. This occurs in the cytoplasm outside the mitochondria. Breakdown of glucose into two molecules of a three carbon based molecule called pyruvate. Glycolysis has an energy investment phase and an energy payoff phase. 2 ATP is used in the energy investment phase and 4 ATP is produced in the energy payoff phase. 

*ATP is formed in glycolysis by substrate-level phosphorylation, during which an enzyme transfers a phosphate group from a substrate molecule to ADP (has two phosphates), forming ATP (has three phosphates).

*Occurs both in aerobic AND anaerobic respiration

*NET PRODUCTION OF 2 ATP AND 2NADH

  • Phosphofructokinase is an allosteric enzyme that controls the rate of glycolysis and citric acid cycle. It is allosterically inhibited by ATP and citrate, however, it is stimulated by AMP.

  • Pyruvate oxidation: Prior to the Krebs cycle, in the mitochondrial matrix, pyruvate undergoes a series of enzymatic reactions that remove CO2 and oxidize the remaining fragment, forming an NADH from NAD+. The product of this is acetyl CoA, a highly reactive 2-carbon compound that will be used in the Krebs cycle.

*Remember, this happens twice because there are TWO pyruvates made in the previous step, glycolysis. 

*NET PRODUCTION OF 2 ACETYL CoA, 2 NADH, and 2 CO2

  • Krebs cycle (Citric acid cycle) is the second stage of cellular respiration. Completes the oxidation of organic molecules and generates the necessary electron carriers to produce lots of ATP in the electron transport chain.. This occurs in the mitochondrial matrix. Here, the acetyl CoA is added to a 4-carbon compound, forming citrate.

*The Krebs acid has a lot of very intricate steps, but the image below summarizes the stuff you need to know/understand. 

*For each “turn” of the Krebs cycle, 1 ATP, 3 NADH, 2 CO2, and 1 FADH2 is produced. But remember, from one glucose molecule we get two turns of the cycle

*NET PRODUCTION OF 2 ATP, 6 NADH, 2 FADH2, and 4 CO2



  • Oxidative phosphorylation (Electron transport chain): involves the electron transport chain and chemiosmosis (diffusion of ions, H+ in this case). Requires an adequate supply of oxygen. Occurs in the inner membrane of the mitochondria. Produces the most ATP (26-28). H+ ions are pumped into the intermembrane space of the mitochondria via help from the electron carriers (NADH and FADH2). Electrons continue to be carried along the chain by the cytochromes (proteins that can accept and donate electrons). H+ then diffuses down the electrochemical gradient through ATP synthase. 

*Remember, O2 is the final electron acceptor, binds with H+ to form water molecules.

*NET PRODUCTION OF 26-28 ATP

Yo okay why does enzyme IV look like amogus tho 😳😳😳

  • Poisons that can disrupt the electron transport chain and production of ATP: *DNP, for example, is an uncoupler protein that makes the inner mitochondrial membrane “leaky” to H+ ions. Proton gradient is disrupted, and H+ no longer can effectively diffuse down ATP synthase, resulting in less ATP production. Worst side effect of DNP is hyperthermia, overheating of the body. This is because since ATP cannot be formed, the energy from the electron transport chain is lost as heat.

*Cyanide, another dangerous poison, inhibits a cytochrome in the electron transport chain. This makes it impossible for the chain to pump H+ into the intermembrane space. The pH of the intermembrane would increase as it received less and less H+, and ATP synthesis would stop, resulting in death.





  • Brown fat: a type of tissue found in hibernating mammals and newborn infants. Cells in brown fat are packed with mitochondria that contain an uncoupling protein (similar to DNP, as discussed above). Allows H+ to flow back through the membrane without producing ATP.

*Produces a lot of heat, but not that much ATP

  • Anaerobic respiration: generate (less) ATP using other electron acceptors besides O2 (for example, obligate anaerobes may use sulfate or nitrate instead, and they cannot survive in an environment with O2). Humans muscle cells are facultative anaerobes, meaning that they can use aerobic respiration AND anaerobic respiration. Fermentation is a way of respiration that does not require oxygen by using glycolysis, however, it only yields two molecules of ATP per molecule of glucose. Fermentation provides an anaerobic path for recycling NADH back to NAD+. 

  • Lactic acid fermentation: human muscle cells, for example, use this to oxidize NADH to NAD+ and to reduce pyruvate into lactate. Lactate is then carried via the bloodstream to the liver where it is converted back to pyruvate. NADH is the electron carrier, and lactate is the final electron acceptor.

  • Alcohol fermentation: single-celled yeasts, for example, use this to oxidize NADH to NAD+ and to reduce pyruvate into ethanol, and release CO2 as a byproduct. Similar to lactic acid fermentation, except for the fact that CO2 is released.

  • Evolutionary connection: glycolysis is the universal energy-harvesting process of life. Glycolysis dates back to life long before oxygen was present in the atmosphere and only prokaryotes inhabited the Earth. 

*Evidence: occurrence within ALL domains of life, and location within the cell (using pathways that DO NOT require any membrane bound organelles.

  • In addition to glucose, cells can use other carbohydrates, fats, and proteins to generate ATP. (Fats for example, can yield twice as much ATP per gram, than a gram of carbohydrate or protein)

Chapter 8 - Photosynthesis

  • Photosynthesis: autotrophs use light energy to convert water and carbon dioxide in carbohydrates.

  • Chloroplasts: organelles that serve as site of photosynthesis in plants

  • Like mitochondria, chloroplasts have a double membrane, ribosomes, and circular DNA (Endosymbiont theory). 

  • The stroma is the fluid that fills the interior

  • The specific sites of photosynthesis occur in the thylakoids, which are disk-like structures that are found stacked upon each other (stacks are called grana)

  • The thylakoids are the sites of the light-dependent reactions, which, similarly to mitochondria, contain an electron transport chain system (Will be discussed more in-depth shortly…) 

  • How plants obtain the necessary raw materials for photosynthesis:

  • Sunlight is obtained by chloroplasts found throughout all the green parts of the plant, specifically mesophyll cells in the plant’s leaves. Chloroplasts contain an important molecule that is necessary for capturing sunlight: chlorophyll, which is a green pigment found in thylakoid membranes of chloroplasts. (Will be discussed in more detail later)

  • CO2 (gas exchange) is obtained/conducted through stomata (pores in the leaf), which uptake carbon dioxide and release oxygen and water vapor

  • H2O (as well as other minerals obtained from the soil) obtained via the extensive roots/vascular system of the plant and is transported through vein-like structures called xylem and phloem

  • The Photosynthesis Reaction Process

  • Redox reaction: water is split and electrons are transferred with H+ to CO2 which combine to create a sugar.

  • A helpful acronym for remembering oxidation and reduction: OILRIG, which stands for - Oxidation Is Loss and Reduction Is Gain.

  • Tracking atoms through photosynthesis: Van Niel used a radioactive tracer (O18) to determine the fate of oxygen in the reaction.

  • Photosynthesis = light reactions (photo) + calvin cycle (synthesis)

  • Light-dependent reactions: convert solar (electromagnetic) energy into chemical energy, which is stored in ATP and NADPH.

*Understand this graph in terms of light absorption and reflection (why does chlorophyll b, the most common one, make plants appear green)

  • Engelmann experiment: used bacteria to measure the rate of photosynthesis in algae; established the “action spectrum”

*As you can see, aerobic bacteria thrived more around the 400-500 nm and 600-680 nm range of the spectrum. This is because the algae produced MORE oxygen at these colors for the aerobic bacteria to use (hence, which allowed them to grow more around these regions). However, around the green-yellow range, we see barely any algae growth (which correlates with the rate of photosynthesis in the algae). This is because green is not absorbed by chlorophyll, and it is instead reflected, which is why plants appear “green.” The other colors are completely absorbed and their photons are utilized by the chloroplasts of the algae.


  • In light-dependent reactions, light energy splits H2O to O2, releasing electrons (e-). The movement of e- is used to generate ATP. The electrons will eventually end up of NADP+, where the electrons reduce it to NADPH.

*Photosystem: reaction center and light-harvesting complex (pigment + protein) embedded in the thylakoid membrane

  • You don’t have to remember specifically how the photosystems and light dependent reactions work, just be familiar with the process and understand how to explain it if you are presented with it.

*Main idea: Light energy used to power electron flow through the photosystems (II and I), which is used to generate ATP and NADPH for the Calvin Cycle

*Image below is pretty much the entire light dependent phase of photosynthesis summed up. If you understand this image you should be good.

  • Calvin cycle: occurs in the stroma and uses ATP and NADPH (generated in the light dependent reactions phase), as well as CO2 from the atmosphere to produce a 3-carbon sugar, G3P.

*The Calvin cycle is divided up into 3 stages: carbon fixation, reduction, and the regeneration of RuBP.

*Stage 1 - Carbon fixation: 3CO2 captured from the atmosphere is combined with RuBP to form an intermediate compound (you don’t need to know the names of all of the intermediate molecules). Catalyzed by a very important enzyme, rubisco.

*Stage 2 - Reduction: 6 ATP and 6 NADPH are used to produce 5 G3Ps, but only 1 is actually output, 1 net G3P output from 1 turn of the cycle. Intermediate compound from earlier is reduced by NADPH.

*Stage 3 - Regeneration of RuBP: 3 ATP is used to convert the other 5 G3Ps produced by the reduction phase back into RuBP.

*This image is a simplification of the Calvin cycle, but it’s all you really need to know

  • Rubisco is an enzyme used to fix CO2 (and even O2 when the conditions are right). The most abundant protein/enzyme on Earth. Is used in the Calvin cycle, BUT it can also be used for a process called photorespiration, which is when plants actually consume O2 and produce CO2. Sugar is not produced during photorespiration, instead rubisco binds O2 and breaks down RuBP.

*Occurs on hot, dry, and bright days when stomata close to conserve H2O

  • C3 plants: Basically do everything that was described above for this unit.

C4, and CAM plants: (We don’t have to know these for the test, but I would recommend just quickly looking it over)