55 Matching Annotations
  1. Last 7 days
  2. Sep 2023
  3. Oct 2022
    1. Again, Dr. Britt will only quiz you on what goes into the Calvin cycle, its first step, and what comes out.

      What will be the focus in the Calvin cycle?

    2. Six molecules of both ATP and NADPH are used up in the process, helping to drive the reactions and produce the electrons required to reduce the incoming CO2. The "spent" molecules (ADP and NADP+) return to the nearby thylakoids to be recycled back into ATP and NADPH.

      What is used up during the Calvin cycle? Do they regenerate?

    3. Ribulose-1,5-bisphosphate (RuBP) is composed of five carbon atoms and includes two phosphates.

      What is RuBP? What is it composed of?

    4. In the stroma of plant chloroplasts, in addition to CO2, two other components are present to initiate the light-independent reactions:

      What three components are required for carbon fixation?

    5. The biological pathway that leads to carbon fixation in green plants and cyanobacteria is called the Calvin Cycle and is a reductive pathway (consumes energy and electrons) which leads to the reduction of CO2 to G3P.

      What is the Calvin cycle? What is it used for?

    6. "Carbon Fixation", the incorporation of inorganic carbon (CO2) into organic molecules

      What is carbon Fixation? What is it used for?

    7. while those organisms that require organic sources of carbon, such as glucose or amino acids, are referred to as heterotrophs

      What is a heterotroph how are they different from autotrophs?

    8. Organisms that can obtain all of their required carbon from an inorganic source (CO2) are referred to as autotrophs,

      What is an Autotroph?

    9. It is at this step that light energy is transformed into the more stable form of chemical energy. All of the subsequent redox reactions are involved in pumping protons or in delivering that e- to NADP.

      When does the photon energy go from being unstable to stable?

    10. The Calvin cycle takes place in the stroma, conveniently located vis a vis the ATP- and NADPH-producing thylakoids

      Where does the Calvin Cycle take place?

    11. The captured energy is transferred from chlorophyll to chlorophyll until ...eventually... (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons. In other words, no new bonds have formed.

      How does energy captured from a photon make it to the reaction center?

    12. Both photosystems have the same basic structure; a number of antenna proteins to which chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by this light-harvesting complex, which passes energy from sunlight to the reaction center;

      What is the structure of the photo systems 1 & 2 Where does the photochemistry take place?

    13. These two types are simply called photosystem II (PSII, carrying P680) and photosystem I (PSI, carrying P700), and were named (confusingly) in the order of their discovery. The two complexes differ on the basis of what they oxidize (that is, their source of electrons) and what they reduce (the place to which they deliver their energized electrons). Working in tandem, these two photosystems can power the production of both NADPH and ATP.

      What are the two pigments used in Oxygenic Photosynthesis? What do they do?

    14. In oxygenic photosynthesis, two types of pigment are found embedded in the thylakoid membrane (in plants) or the bacterial inner membrane (in cyanobacteria).

      Where are the two types of pigments used in oxygenic Photosynthesis stored?

    15. oxygenic photosynthesis is more complex than the "sulfur-genic" photosynthesis described above, requiring two different reaction centers, with different reduction potentials.

      How is oxygenic photosynthesis different from sulfur-genic photosythesis?

    16. The overall function of "light-dependent" reactions of photosynthesis is to transform solar energy into chemical compounds, in the form of NADPH and ATP. This energy supports the "light-independent" reactions and fuels the assembly of sugar molecules.

      What are the functions of the “light dependent” rxns and what do they support?

    17. In non-cyclic photophosphorylation electrons are removed from the photosystem, as they end up in NADPH after moving through an electron transport chain

      How is cyclic Photophosphorylation different from Non-cyclic?

    18. As in the green sulfur bacteria example above, the step that transfers light energy into the biomolecule takes place in a multiprotein, multipigment complex called a photosystem

      What is a photosystem?

    19. This NADPH will be used for carbon fixation. Thus in order to keep generating NADPH there's needs to be a source of electrons to refill the "electron hole" in bacteriochlorophyll

      What is needed to keep a steady state for the production of NADPH?

    20. In an electron transport chain analogous to that of respiration, the electron is passed exergonically from carrier to carrier. The redox reaction at one of the carriers powers a proton pump, pushing protons into a higher concentration compartment. Eventually the electron is used to reduce bacteriochlorophyllox (making a complete loop) and the whole process can start again.

      How is the reduction of bacteriochlorophyll(ox) seem similar to glycolysis?

    21. This electron must come from an external source with a lower reduction potential than the (ground state) pigment and depending on the reduction potential of that pigment there are different possible sources that might be employed, including H2O, reduced sulfur compounds such as SH2, and even elemental S0

      Since pigments don’t get regenerated by the plant, how can the pigment attain another e-? What conditions does the e- donor need to fulfill in order to donate the e-?

    22. The visible light seen by humans as white light is composed of a rainbow of colors, each with a characteristic wavelength.

      What is visible light?

    23. However, the electron energized by light might have an alternative fate: it might descend through a different series of carriers (without pumping protons) and instead be deposited onto a close relative of NAD+ called NADP. Addition of 2 e- generates NADPH, which is going to be used to build sugars from CO2

      What is the plant version of NAD+ How is it used?

    24. This electrochemical gradient generates a proton motive force whose concentration gradient can then be coupled to the endergonic production of ATP, via ATP synthase (again, just as in respiration).

      Does Photosynthesis use ATP synthase? How?

    25. For example, as you can see in the Table below, the ground state pigment at the reaction center of PSII (the "chlorophyll a" in P680) cannot reduce anything listed in the table- it is the weakest reducing agent described there (even weaker than H2O!).

      Where is Chlorophyll on the redox tower?

    26. While in the excited state, the pigment has a much lower reduction potential (E˚', it moves upward on our electron tower, it becomes a stronger reducing agent) and can donate these unstable, high potential energy electrons to carriers with greater E˚'

      How does a higher orbital state change the electron’s reduction potential?

    27. "unexcited", or "ground state"

      What is “ground state” for electrons

    28. The first step of the process involves the absorption of a photon by a pigment molecule. Light energy is transferred to the pigment and promotes electrons into an excited state.

      What is the first step of Photophosphorylation?

    29. Photophosphorylation probably evolved relatively shortly after electron transport chains and anaerobic respiration.

      When is it hypothesized that Photophosphorylation evolved?

    30. Photophosphorylation is the process of transferring the energy from light into ATP.

      What is photophosphorylation?

    31. Because the energy changed the reduction potential such that the molecule is now a stronger e- donor, this high-energy e- can be transferred exergonically to an appropriate e- acceptor. In other words, the excited state can be involved in a redox reactions. This is a photochemical reaction

      What is a photochemical reaction?

    32. When an atom absorbs a photon of light, an electron acquires that energy, leaving its ground (lowest potential energy) orbital and moving up to a higher energy orbital. This is an unstable situation.

      What happens when an atom absorbs a photon?

    33. Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light. This characteristic is known as the pigment's absorption spectrum.

      What is the absorption spectrum?

    34. Carotenoids are the red/orange/yellow pigments found in nature. They are found in fruit

      What are carotenoids and where are they typically found?

    35. This ring structure is chemically related to the structure of heme compounds that also coordinate a metal and are involved in oxygen binding and/or transport in many organisms. Different chlorophylls are distinguished from one another by different "decorations"/chemical groups on the porphyrin ring

      Where does chlorophylls ring structure come from? How can different types of Chlorophyll be identified through its structure? How does Heme relate to this?

    36. There are five major chlorophyll pigments named: a, b, c, d, and f. Chlorophyll a is related to a class of more ancient molecules found in bacteria called bacteriochlorophylls. Chlorophylls are structurally characterized by ring-like porphyrin group that coordinates a metal ion.

      How many major chlorophyll pigments are there? What is Chlorophyll’s structure?

    37. If a plant were able to absorb 100% of incident photons, what color would it be? What if a variant of the same species of plant lacked a pigment required to absorb red light?

      If the plant were able to absorb all the light photons, then it would look pure white. If it was a variant that couldn’t absorb red light then it would look red.

    38. green plants appear green because they reflect, rather than absorb, most of the photons at a combination of wavelengths that we perceive as green

      How does light work? What are we actually seeing?

    39. At the center of the biological interactions with light are groups of molecules we call organic pigments.

      What are organic pigments?

    40. Signaling interactions are largely responsible for perceiving changes in the environment

      What are signaling interactions?

    41. A specific "color" of light has a characteristic wavelength.

      How are different colors differentiated?

    42. The distance between peaks in a wave is referred to as the wavelength and is abbreviated with the Greek letter lambda (Ⲗ

      What is lambda and what does it refer to?

  4. May 2022
    1. Like all plants, the bulrush requires oxygen to produce energy. One solution is obvious: Send shoots skyward like straws to suck down oxygen to the roots.

      Plants don't require oxygen to produce energy (photosynthesis), they require CO2.


      Oxygen is generated as a byproduct of this, not a requirement.

  5. Oct 2020
    1. Plants store starch in the form of sugars.

      The plant stores the starch inside of its cell organelles known better as the amyloplasts. The starch is created on a bright sunny day when the plant retrieves and creates an over abundance of sugar for energy. Making the excess into starch allows for the plant to retrieve it later on when it's harder to get the energy it needs on the gloomier days.

  6. Aug 2018
    1. . The dynamic response of stomata or gs to fluctuations in light intensity has been studied in several understorey forest-dwelling species, but relatively few reports have studied crop species (Chazdon and Pearcy, 1986; Chazdon, 1991; Tinoco-Ojanguren and Pearcy, 1993; Leakey et al., 2005; McAusland et al., 2016).
    2. Efforts to develop a big data approach to photosynthetic phenomics by recruiting many researchers into online cloud-based initiatives (Kuhlgert et al., 2016) may be promising because not only can they assay many genotypes but they can also do so under the diverse conditions which plants experience in nature.
    3. However, the importance of the dynamic responses of photosynthesis raises a key problem that has not been adequately addressed: it is difficult to capture photosynthetic responses within (rapidly) fluctuating environments, especially in the field.

      The Challenge

    4. Whilst morphological adaptations to such extreme temperature fluctuations are well documented, the physiological adjustments are not (Hedberg, 1970).

      Gap in knowledge

    5. Indeed, it is particularly important that light is accurately tracked by the plant for optimal photosynthetic performance

      This would suggest that chloroplast movement, which is relatively slow, could be a limiting factor of photosynthesis.

    6. ‘photosynthome’

      Phenome of photosynthesis

    7. Indeed, we are beginning to understand that the way in which photosynthesis is regulated in response to fluctuations in the environment is perhaps a more important determinant of plant productivity than its performance under steady-state or temporarily steady-state conditions

      Other ways of measuring photosynthesis are needed.

  7. Dec 2016
    1. Inference: Leaves show great variations to spread chloroplast over a large surface area to maximize light absorption. At the same time, internal leaf structure needs to optimize carbon exchange. Especially since carbon fixation is rate limiting. Therefore, there should be a relationship between leaf area and leaf structure. How strong is this relationship?

    2. How then can leaves cope?
      1. Chloroplast arrangement
      2. Biochemistry
      3. Leaf orientation