AP Biology Unit 6: Cell Energetics Notes Pt. 1

Absorption of Light: 

• Plant pigment molecules absorb only light in the wavelength range of 700 nm to 400 nm; this range is referred to as photosynthetically-active radiation.

• Violet and blue have the shortest wavelengths and the most energy, whereas red has the longest wavelengths and carries the least amount of energy.

• Pigments reflect or transmit the wavelengths they cannot absorb, making them appear in the corresponding color.

• Chlorophylls and carotenoids are the major pigments in plants; while there are dozens of carotenoids, there are only five important chlorophylls: a, b, c, d, and bacteriochlorophyll.

• Chlorophyll a absorbs light in the blue-violet region, chlorophyll b absorbs red-blue light, and both a and b reflect green light (which is why chlorophyll appears green).

• Carotenoids absorb light in the blue-green and violet region and reflect the longer yellow, red, and orange wavelengths; these pigments also dispose excess energy out of the cell.

Vocabulary

• chlorophyll: Any of a group of green pigments that are found in the chloroplasts of plants and in other photosynthetic organisms such as cyanobacteria.

• carotenoid: Any of a class of yellow to red plant pigments including the carotenes and xanthophylls.

• spectrophotometer: An instrument used to measure the intensity of electromagnetic radiation at different wavelengths.

1- What are two major classes of photosynthetic pigments found in plants and algae? Name five major chlorophylls.

The two major classes of photosynthetic pigments found in plants and algae are chlorophylls and carotenoids. The five major chlorophylls are a, b, c and d, and bacteriochlorophyll. 

2- How do carotenoids help in disposal of excess energy, for example when the plant is exposed to full sunlight? 

Carotenoids help in the disposal of excess energy by absorbing the excess energy and safely release the energy as heat. This is done so the leaf is not harmed by the energy. 

3- Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light, which is the absorption spectrum.

4- Approximately in what wavelength chlorophyll a and b have their peak of light absorption? 

Chlorophyll a peak wavelength- 435nm Range: 375 - 440 (darker green)

Chlorophyll b peak wavelength- 455nm Range: 400 - 475 (green)

What is the photosystem and where can you find it?

• The photosystem is in the thylakoid membrane and they are used to absorb photons. These photons excite electrons and cause the electrons to travel down the electron transport chain. This results in the production of ATP and NADPH. 

Q:  How do cyclic and noncyclic electron flow generate material for the Calvin Cycle? 

• Only photosystem I is used in cyclic photophosphorylation where the electrons are passed back to the same photosystem, while non-cyclic phosphorylation uses both photosystems.

1. What color of light is least effective in driving photosynthesis?

• Green light is least effective in driving photosynthesis since it is reflected and not absorbed by the chlorophyll. 

2. In the light reactions, what is the initial electron donor? Where do the electrons end?

• In the light reactions, water is the initial electron donor. They are used as replacement electrons in PSII. NADP+ accepts these electrons at the end of the ETC, becoming reduced to NADPH. 

3. Compare cyclic and noncyclic electron flow. 

• Cyclic electron flow (temporary excess light, NADP+ shortage) generates ATP that is highly necessary for the functioning of the Calvin cycle. When there are days with long hours of sunlight, there are times when NADP+ runs out. As the electrons are passed down the chain from PSI, the energy level drops. When the energy level drops, energy is used to change ADP and P(i) into ATP. Once the electrons are passed down the chain from PSI, they are fed back into the system to create more ATP. They can’t do photosynthesis but it is a temporary solution until more NADP+ is produced.  

• Noncyclic electron flow (normal situation) generates ATP and NADPH which are both necessary for the functioning of the Calvin cycle. As the electrons are passed down the chain from PSII, the energy level drops. When the energy level drops, energy is used to change ADP and P(i) into ATP. As the electrons are passed down the chain from PSI, the energy level drops. When the energy level drops, energy is used to change NADP+ 2e- and H+ into NADPH. 

What are the main steps in Calvin Cycle?

• The main steps in the Calvin cycle are carbon fixation, reduction phase and regeneration phase.

1. To synthesize one glucose molecule, the Calvin cycle uses three molecules of CO2, nine molecules of ATP, and six molecules of NADPH.

2. Explain why a poison that inhibits an enzyme of the Calvin cycle will also inhibit the light reactions. 

• The light reactions require ADP and NADP+, which are not recycled from ATP and NADPH when the Calvin cycle stops. If there is a poison that inhibits an enzyme of the Calvin cycle, it will surely slow down of stop the light reaction. 

1. Explain why photorespiration lowers photosynthetic output for plants. 

• Photorespiration decreases photosynthetic output by adding oxygen (O2), instead of carbon dioxide (CO2), to the Calvin cycle.

2. How would you expect the relative abundance of C3 versus C4 and CAM species to change in a geographic region whose climate becomes hotter and drier?

• The relative of C3 would decrease from 85% as the abundance of C4 and CAM would increase in a geographic region whose climate becomes hotter and drier. This is because the only species that would survive in the hot and dry conditions are the C4 and CAM species. They are adapted to survive in these conditions.

1) Photorespiration was called a wasteful pathway. Why is the reason for that?

Photorespiration is called a wasteful pathway since rubisco uses O2 instead of CO2. When plants' stomata are closed, there is no way to dispose of the O2 and take in CO2. Though there is a lack of the necessary CO2, the Calvin cycle continues. Since O2 is the only available molecule, it is used to substitute the CO2. This results in a waste of energy as well as fixed carbons. In addition to this, the product of O2 being the reactant in the Calvin cycle is a harmful molecule that is poisonous to the plant. 

2) Explain the energetic price for C4 and CAM pathways?

In C4, the light reaction and the Calvin cycle are physically separated from each other. ATP is used to move the 3C molecule from the bundle-sheath cells and to have it picked up by CO2 molecules. CAM photosynthesis uses ATP multiple times. Similar to C4, energy is necessary to drive the movement of carbon around the cell. 

3) The C4 pathway is separated by space and CAM pathway by time. Explain.

- In C4, the light reaction occurs in the mesophyll cells while the Calvin cycle occurs in the bundle-sheath cells. CO2 is fixed in the mesophyll cell into 4 carbon organic acid by RER carboxylase. The oxaloacetate (4 carbon organic acid) is converted into malate which is moved into the bundle-sheath cells, where the malate breaks down into CO2. The CO2 is fixed by rubisco and becomes sugars using the Calvin cycle. Since the mesophyll cells constantly pump CO2 into other bundle-sheath cells as malate, there is a high concentration of CO2 relative to O2 near rubisco. 

- In CAM plants, the light-dependent reaction and Calvin cycle are separated by time. The stomata open at night and allow for CO2 to diffuse in. The CO2 is fixed into oxaloacetate by PEP carboxylase and becomes malate. Then the malate is transported out of the vacuole at daylight, and is broken down to release CO2 which enters the Calvin cycle, all while the stomata are closed. This timed stomata opening maintains a high concentration of CO2 around rubisco.

Glycolysis

Glycolysis is the first step in cellular respiration, and it is anaerobic. It occurs in the cytoplasm, so it not only happens in eukaryotic cells, but also in prokaryotic cells. This process when simplified, breaks one glucose molecule down into two pyruvate molecules, which is an exergonic process. The reactants for glycolysis are glucose, 2 NAD+, 2 ATP, 4 ADP, and 4 P(i). The products are 2 pyruvates, 2 NADH, 2 ADP and 4 ATP. The glucose molecule is oxidized to create the two pyruvate molecules. The two ATP molecules are considered investments, since there are four ATP molecules produced. There is a net increase of 2 ATP molecules, which are produced using substrate level phosphorylation. Substrate level phosphorylation uses a kinase enzyme to transfer a phosphate group from a substrate to an ADP molecule to make ATP. 

The first step is using hexokinase to attach a phosphate group to the glucose, making the molecule a glucose 6-phosphate using one ATP molecule. This glucose 6-phosphate molecule is then changed to an isomer, which means the chemical formula is the same but the location and structure is changed, using a phosphoglucose isomerase to make a fructose 6-phosphate. The fructose 6-phosphate is synthesized using phosphofructokinase-1 and an ATP molecule to attach another phosphate group to make it fructose 1,6-bisphosphate. This is then separated into dihydroxyacetone phosphate to then become two glyceraldehyde 3-phosphate, or directly into two glyceraldehyde 3-phosphate. The glyceraldehyde 3-phosphate dehydrogenase uses 2 NAD+ and reduces it to 2 NADH molecules to take away hydrogen and add a phosphate instead to make two molecules of 1,3-bisphosphoglycerate. Phosphoglycerate kinase uses 2 ADP and attaches a phosphate that is taken from the two molecules of 1,3-bisphosphoglycerate to form two molecules of 3-phosphoglycerate. The phosphoglyceromutase synthesizes the two molecules of 3-phosphoglycerate into two molecules of 2-phosphoglycerate which is an isomer. Enolase takes 2H2O molecules and forms two molecules of phosphoenolpyruvate which has a 2,3 double carbon bond. Pyruvate kinase uses 2 ADP molecules to synthesize 2 molecules of pyruvate from the two molecules of phosphoenolpyruvate. 

1.  In which molecules is most of the energy from the citric acid cycle’s redox reactions conserved? Where will these molecules go to next?

   1. The molecules that conserve the most energy from the citric acid cycle are the NADH molecules. They are formed when the NAD+ molecules are reduced. These molecules are transported using the electron transport chain and become hydrogen donors. These hydrogens are saved to make ATP after being transported to the intermembrane of the mitochondria and through oxidative phosphorylation create ATP molecules from preexisting ADP molecules. The NADH molecule is able to produce 3 individual ATP molecules during oxidative phosphorylation. 

2. What are the TOTAL products of the Krebs cycle?(ONE ROUND)

   1. From one round of the Krebs cycle, 3 molecules of NADH and 1 molecule of FADH2 are generated along with 2 CO2 molecules and 1 ATP or GTP molecule. The molecule left over to repeat the process is 1 oxaloacetate. 

3. How many NADH and FADH2 molecules are produced per one molecule of glucose in the Krebs cycle?

   1. Per one molecule of glucose, the Krebs cycle is repeated twice. This means that 6 molecules of NADH and 2 molecules of FADH2 are generated along with 4 CO2 molecules and 2 ATP or GTP molecules. 2 oxaloacetates are left over to repeat the process.