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Structural View of Biology


Structures in the PDB reveal how cells use chemical energy, light energy, electrical energy and mechanical energy to power the processes of life. Cells must continually interconvert different forms of energy. Energy is obtained from many sources, including light and food. Molecular machines then use this energy to build new molecules, to power motion, to transport molecules to the proper place, to generate heat and light, and to regulate all of the processes occurring in the cell.

Life on Earth is ultimately powered by sunlight, which is used to build sugars through he process of photosynthesis. Researchers have revealed the way that light is captured by plants and bacteria, and used to create energetic molecules, which may then be used to perform transport and synthetic tasks.

Scroll to a Molecule of the Month Feature in this subcategory:

  • Bacteriorhodopsin

    Bacteriorhodopsin

    Sunlight powers the biological world. Through photosynthesis, plants capture sunlight and build sugars. These sugars then provide all of the starting materials for our growth and energy needs. As seen in the Molecule of Month last October, photosynthesis requires a complex collection of molecular antennas and photosystems. However, some archaebacteria have found a simpler solution to capturing sunlight.

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    Discussed Structures
    bacteriorhodopsin ground state
    bacteriorhodopsin ground state
    bacteriorhodopsin light-activated state
    bacteriorhodopsin light-activated state
  • Cytochrome bc1

    Cytochrome bc1

    Cells are masters at squeezing every drop of energy out of their food. They disassemble the molecules in food atom by atom, driving a variety of unusual energy transformations in the process. At the end, all of the hydrogen atoms have been separated from the food molecules and are used to turn the rotary motor of ATP synthase. To do this, the electrons are stripped from these hydrogen atoms and used to power huge protein pumps that transport protons across a membrane. These protons then power the rotation of ATP synthase as they return to their original positions.

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  • Photosystem I

    Photosystem I

    Look around. Just about everywhere that you go, you will see something green. Plants cover the Earth, and their smaller cousins, algae and photosynthetic bacteria, can be found in nearly every corner. Everywhere, they are busy converting carbon dioxide into sugar, creating living organic molecules out of air using the energy of sunlight as power. This process, termed photosynthesis, provides the material foundation on which all life rests.

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    Discussed Structures
    photosystem I
    photosystem I
    photosynthetic reaction center
    photosynthetic reaction center
  • Photosystem II

    Photosystem II

    Three billion years ago, our world changed completely. Before then, life on Earth relied on the limited natural resources found in the local environment, such as the organic molecules made by lightning, hot springs, and other geochemical sources. However, these resources were rapidly being used up. Everything changed when these tiny cells discovered a way to capture light and use it to power their internal processes. The discovery of photosynthesis opened up vast new possibilities for growth and expansion, and life on the earth boomed. With this new discovery, cells could take carbon dioxide out of the air and combine it with water to create the raw materials and energy needed for growth. Today, photosynthesis is the foundation of life on Earth, providing (with a few exotic exceptions) the food and energy that keeps every organism alive.

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    Discussed Structures
    Photosystem II
    Photosystem II
    light-harvesting protein
    light-harvesting protein
  • Rubisco

    Rubisco

    Carbon is essential to life. All of our molecular machines are built around a central scaffolding of organic carbon. Unfortunately, carbon in the earth and atmosphere is locked in highly oxidized forms, such as carbonate minerals and carbon dioxide gas. In order to be useful, this oxidized carbon must be "fixed" into more organic forms, rich in carbon-carbon bonds and decorated with hydrogen atoms. Powered by the energy of sunlight, plants perform this central task of carbon fixation. Inside plant cells, the enzyme ribulose bisphosphate carboxylase/oxygenase (rubisco) forms the bridge between life and the lifeless, creating organic carbon from the inorganic carbon dioxide in the air. Rubisco takes carbon dioxide and attaches it to ribulose bisphosphate, a short sugar chain with five carbon atoms. Rubisco then clips the lengthened chain into two identical phosphoglycerate pieces, each with three carbon atoms. Phosphoglycerates are familiar molecules in the cell, and many pathways are available to use it. Most of the phosphoglycerate made by rubisco is recycled to build more ribulose bisphosphate, which is needed to feed the carbon-fixing cycle. But one out of every six molecules is skimmed off and used to make sucrose (table sugar) to feed the rest of the plant, or stored away in the form of starch for later use.

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    Discussed Structures
    rubisco from tobacco
    rubisco from tobacco
    rubisco from spinach
    rubisco from spinach
    bacterial rubisco
    bacterial rubisco

Please see our usage polices for citation and reprint information. Copies of the illustrations used in these features are available for download as high resolution TIFF images. Please note that the structures used to illustrate each installment are chosen at the discretion of the authors; the features are not intended to represent a historical record. The process behind the creation of this feature is described by the author.