Ap biology Unit 3
Enzymes:
Enzymes are biological catalysts that speed up reactions by lowering the activation energy(initial energy needed to start a reaction), and they were mainly proteins which have tertiary structures and these structures must be maintained for proper function. Enzymes have active sites, these active sites bind to substrates to produce a reaction. The active sites have unique shapes and sizes specific to a substrate, and may have chemical charges. There may be slight changes in the active site to better fit the substrate. The substrate’s physical and chemical properties must be compatible with the active site. Enzymes are reusable because they are not changed/consumed in reactions. Each enzyme only catalyzes one type of reaction! They facilitate digestion reactions and synthesis. Enzymes help facilitate biological processes by: being reusable, only targeting specific molecules, and only starting a reaction when it’s needed.
Structures
Enzymes have tertiary structures, and if these structures are affected, then the function of the enzyme is also affected. Structural changes can be caused by: extreme pH, temperature, and salt concentration. Enzymes work best at an optimal pH and temperature. At low temperatures, the reaction will slow due to the slow movement of particles/kinetic energy. At high temperatures, the reaction will initially increase but if too high the enzyme will denature, causing reaction to slow/stop completely. Enzymes work best at pH of 6-7. Too acidic or too basic pH(hydrogen ions) cause disruption of the hydrogen bonds, and this causes the enzyme to denature. Too little or too much salt concentration(ions) can disrupt the hydrogen bonds as well and affect the structure of the enzyme, causing it to denature.
Denaturization is irreversible if caused by high temperature or pH. The active site’s shape is changed, meaning the substrate cannot bind to it properly and therefore a reaction won’t happen properly or even at all. This can be irreversible if there were slight changes in pH and temperature and temporary chemical stress.
Environmental impacts
The substrate concentration and product buildup determine how well an enzyme can catalyze a reaction. The higher the substrate concentration, the faster the reaction is due to more substrates binding to the active sites. This will eventually reach to vmax, where the active sites are all full(saturation), and the reaction rate will remain constant. If there are low substrates, there is a slower reaction rate. The more product buildup there is, the slower the reaction will be. This is because sometimes product can get stuck to an enzyme, which causes slower reactions.
There are inhibitors(things that slow down/stop enzyme activity) and activators(speed up enzyme activity). The two types of inhibitors are competitive and noncompetitive. Competitive inhibitors bind directly to the active site and compete with other substrates for the spot in the active site. They can be reversable, meaning after they’re done, they leave the active site and another substrate can take its place. Adding more substrates can out compete this! For noncompetitive inhibitors, they bind to the allosteric active site. These are irreversible, and change the shape of the active site. Due to the changed shape, substrates cannot bind properly to the active site therefore a reaction won’t occur.
Photosynthesis
Photosynthesis is the process that converts solar energy(sun) into chemical energy(food), and this occurs in the chloroplast. Photosynthesis is a redox reaction, meaning electrons are taken from water(oxidation) and given to carbon dioxide(reduction). Oxidation then forms oxygen gas, and the reduction forms sugar(carb).
Light energy is absorbed by the chlorophyll and drives the synthesis of organic molecules in the chloroplast. Water is in the stomata, and through the stomata, co2 enters the leaf and O2 exits. Chloroplasts are found in the cells of mesophyll, and each mesophyll has 30 to 40 chloroplasts. Chloroplasts are in the membranes of thylakoids, and stacked thylakoids are called granas. The stroma is a fluid outside the thylakoid.
Light reactions(photo part) and the Calvin Cycle(synthesis past):
The two phases of photosynthesis are light reactions and the calvin cycle. Light reactions occur in the thylakoid, and they split water, release O2, produce ATP, and form NADPH(electron carrier). The Calvin Cycle occurs in the stroma and forms sugar from CO2 using ATP and NADPH. Light is a form of electromagnetic energy, and consists of photons and travels in waves. Pigments absorb wavelengths, and the wavelengths that aren’t absorbed are reflected or transmitted. CHLOROPLASTS ABSORB RED AND BLUE PIGMENTS AND REFLECT GREEN LIGHT
Light reactions
Photosystem is protein complex located in the thylakoid membrane that converts light energy into chemical energy. Photosystems are embedded with pigment molecules that capture solar energy and transfer that energy to two special chlorophyll a molecules. The energy transferred to the chlorophyll a molecules is used to boost an electron to a high energy level. A primary electron acceptor captures the high energy electrons and transfers them out of the photosystem.
Light reactions capture light energy and use that energy to synthesize ATP and NADPH. This process involves the movement of electrons from water to NADP+(becomes NADPH+ once reduced).
Light reactions consist of:
Photosystems ll
ETC
Photosystem l
NADP+ Reductase
Atp synthase
Photosytems ll: Light energy excites electrons from special chlorophyll molecules, and these electrons are captured by an electron acceptor that then transports them through the electron transport chain. The light energy absorbed by photosystem II is also used to split a water molecule into an oxygen atom, two H+ ions, and two electrons. The electrons from water are used to replace the electrons lost by the chlorophyll a molecules (P680). This allows the process to continue.
Electron transport chain: The electrons from photosystem II are then transported through an electron transport chain. ○ The electrons lose energy as they are being transported. A protein complex in the chain uses the energy from the electrons to pump H+ ions from the stroma into the thylakoid space. This creates a hydrogen ion concentration gradient across the thylakoid membrane: a high H+ concentration inside the thylakoid space and a low H+ concentration in the stroma.
Photosystem l: Photosystem I and II are almost identical, with a few important exceptions: In photosystem I, light energy excites electrons from two special chlorophyll a molecules, called P700 (because the pigment is best at absorbing light with a wavelength of 700nm). The high energy electrons are captured by an electron acceptor that transports the electrons to a protein complex called, NADP+ Reductase. The electron pair from photosystem II that traveled through the electron transport chain replaces the electrons lost by P700. ○ This allows the process to continue.
NADP+ Reductase: The pair of high energy electrons from photosystem I are transported to NADP+ reductase, an enzyme complex that gives the electron pair to NADP+ (reduction). NADP+ is an electron carrier molecule used in photosynthesis. It is the final electron acceptor for the light reactions. In cell respiration, the final electron acceptor of the ETC is oxygen. The reduction of NADP+ creates NADPH. NADPH will carry the high energy electrons to the Calvin cycle.
Chemiosmosis: The proton (H+) gradient created by the electron transport chain is used to drive ATP synthesis via ATP synthase. H+ diffuses across the thylakoid membrane from the thylakoid space (high conc.) to the stroma (low conc.). ATP synthase uses the kinetic energy from the protons to power the production of ATP. The ATP created via chemiosmosis is used in the Calvin cycle.
Calvin Cycle
The Calvin cycle regenerates its starting material after molecules enter and leave the cycle, like oxaloacetate in the Krebs cycle. ○ In the Calvin cycle, the starting material is a 5-carbon molecule called ribulose bisphosphate (RuBP). The cycle builds sugar from smaller molecules by using ATP and the reducing power of electrons carried by NADPH. Carbon atoms enter the cycle as CO2 and leave as a sugar named glyceraldehyde-3-phosphate (G3P). For net synthesis of one G3P (a 3-carbon compound), the cycle must take place three times, fixing three molecules of CO2.
The Three Phases of the Calvin Cycle are Carbon Fixation, Reduction, Regeneration of RuBD
Carbon Fixation: In the first phase, three carbon dioxide molecules are connected (fixed) to three RuBP to form three 6-carbon compounds, which immediately break down into six 3-carbon compounds called 3-PGA. The fixation of carbon dioxide to RuBP is controlled by a very important enzyme called rubisco.
Reduction: In the second phase, NADPH reduces the six 3-PGA molecules into another 3-carbon compound called G3P. This process requires ATP. A total of six G3P molecules are created during three turns of the cycle. One of the six will leave the cycle.
Regeneration: The remaining five G3P molecules are turned back into three molecules of RuBP, so that the cycle can continue. This phase requires ATP.
One G3P is produced and released from the Calvin cycle every three turns of the cycle. G3P can be used by the cell to build glucose or other organic compounds such as: Fatty acids and glycerol to make plant oil ○ Fructose, starch, cellulose, amino acids used to make proteins. Two G3P can be joined together to make one molecule of glucose. This would require the cycle to occur a total of six times.