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Structural View of Biology >> Biological Energy >> Capturing the Energy in Food

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.

Food is digested and broken down in many controlled chemical steps, capturing chemical energy along the way. Much of the machinery of the cell is involved in this process in one way or another, including the digestion of proteins and nucleic acids into their components, breakage of these molecules into carbon dioxide, water and other small molecules, and the linkage of this breakdown with the formation of energy-storing molecules like ATP.

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

  • ATP Synthase

    ATP Synthase

    ATP synthase is one of the wonders of the molecular world. ATP synthase is an enzyme, a molecular motor, an ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine. It plays an indispensable role in our cells, building most of the ATP that powers our cellular processes. The mechanism by which it performs this task is a real surprise.

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    Discussed Structures
    ATP synthase F0 motor domain
    ATP synthase F0 motor domain
    ATP synthase F1 motor domain
    ATP synthase F1 motor domain
  • Aconitase and Iron Regulatory Protein 1

    Aconitase and Iron Regulatory Protein 1

    Aconitase is an essential enzyme in the tricarboxylic acid cycle and iron regulatory protein 1 interacts with messenger RNA to control the levels of iron inside cells. You might ask: what do these two proteins have in common? They were discovered and studied by different researchers, who gave them names that described their two very different functions. But surprisingly, when they looked at the amino acid sequence of these proteins, they turned out to be identical. The same protein is performing two very different jobs.

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    Discussed Structures
    aconitase
    aconitase
    aconitase
    aconitase
    iron regulatory protein (aconitase)
    iron regulatory protein (aconitase)
  • Alcohol Dehydrogenase

    Alcohol Dehydrogenase

    Here's a toast to alcohol dehydrogenase. While recovering from the excesses of New Year's Eve, we might ponder the enzyme that ceaselessly battles the champagne that we consume. Alcohol dehydrogenase is our primary defense against alcohol, a toxic molecule that compromises the function of our nervous system. The high levels of alcohol dehydrogenase in our liver and stomach detoxify about one stiff drink each hour. The alcohol is converted to acetaldehyde, an even more toxic molecule, which is then quickly converted into acetate and other molecules that are easily utilized by our cells. Thus, a potentially dangerous molecule is converted, through alcohol dehydrogenase, into a mere foodstuff.

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    Discussed Structures
    alcohol dehydrogenase with NAD
    alcohol dehydrogenase with NAD
    alcohol dehydrogenase with ethanol
    alcohol dehydrogenase with ethanol
    bacterial alcohol dehydrogenase
    bacterial alcohol dehydrogenase
  • Alpha-amylase

    Alpha-amylase

    Glucose is a major source of energy in your body, but unfortunately, free glucose is relatively rare in our typical diet. Instead, glucose is locked up in many larger forms, including lactose and sucrose, where two small sugars are connected together, and long chains of glucose like starches and glycogen. One of the major jobs of digestion is to break these chains into their individual glucose units, which are then delivered by the blood to hungry cells throughout your body.

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    Discussed Structures
    Alpha-amylase
    Alpha-amylase
  • Citrate Synthase

    Citrate Synthase

    Your body burns up a lot of food every day. However, cells don't burn food like a fireplace. Instead, food molecules are combined with oxygen molecules one-by-one, in many carefully controlled steps. In this way, the energy that is released can be captured in convenient forms, like ATP or NADH, which are then used elsewhere to power essential cellular functions. Our cells get most of their energy from a long series of reactions that combine oxygen and glucose, forming carbon dioxide and water, and creating lots of ATP and NADH in the process.

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    Discussed Structures
    citrate synthase open form
    citrate synthase open form
    citrate synthase closed form
    citrate synthase closed form
    bacterial citrate synthase
    bacterial citrate synthase
  • Citric Acid Cycle

    Citric Acid Cycle

    The citric acid cycle, also known as the Krebs cycle or the tricarboxylic acid cycle, is at the center of cellular metabolism, playing a starring role in both the process of energy production and biosynthesis. It finishes the sugar-breaking job started in glycolysis and fuels the production of ATP in the process. It is also a central hub in biosynthetic reactions, providing intermediates that are used to build amino acids and other molecules.

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    Discussed Structures
    Aconitase
    Aconitase
    2-Oxoglutarate dehydrogenase complex
    2-Oxoglutarate dehydrogenase complex
    Succinyl-CoA synthetase
    Succinyl-CoA synthetase
    Succinate dehydrogenase
    Succinate dehydrogenase
    Fumarase
    Fumarase
    Malate dehydrogenase
    Malate dehydrogenase
    citrate synthase open form
    citrate synthase open form
    isocitrate dehydrogenase
    isocitrate dehydrogenase
  • Complex I

    Complex I

    Complex I, also known as NADH:quinone oxidoreductase, performs the first step in respiratory electron transport, the process that creates much of the energy that powers our cells. Complex I is a huge membrane-bound molecular machine that links two different reactions: the transport of electrons from NADH to ubiquinone, and the transport of protons across a membrane.

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    Discussed Structures
    Complex I
    Complex I
    Complex I hydrophilic domain
    Complex I hydrophilic domain
    Complex I membrane-bound domain
    Complex I membrane-bound domain
  • 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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  • Cytochrome c

    Cytochrome c

    Cytochrome c, shown here from PDB entry 3cyt, is a carrier of electrons. Like many proteins that carry electrons, it contains a special prosthetic group that handles the slippery electrons. Cytochrome c contains a heme group with an iron ion gripped tightly inside, colored red here. The iron ion readily accepts and releases an electron. The surrounding protein creates the perfect environment for the electron, tuning how tightly it is held. As shown on the next page, the protein also determines where cytochrome c fits into the overall cellular electronic circuit.

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    Discussed Structures
    cytochrome c
    cytochrome c
    cytochrome c bound to cytochrome bc1
    cytochrome c bound to cytochrome bc1
  • Cytochrome c Oxidase

    Cytochrome c Oxidase

    Oxygen is an unstable molecule. If given a chance, it will break apart and combine with other molecules. This is the process of oxidation, seen in our familiar world as the rusting of iron in cars and nails. But, surprisingly, the unusual electronic properties of oxygen molecules make this reaction very slow. So, paper doesn't spontaneously burn up--flames must be kindled. All animals and plants, and many microorganisms, use the instability of oxygen to power the processes of life. The molecules in food are oxidized and the energy is used to build new molecules, to swim or crawl, and to reproduce. Food is not oxidized in a fiery flame, however. It is oxidized in many slow steps, each carefully controlled and designed to capture as much useable energy as possible. Cytochrome c oxidase controls the last step of food oxidation. At this point, the atoms themselves have all been removed and all that is left are a few of the electrons from the food molecules. Cytochrome c oxidase, shown here, takes these electrons and attaches them to an oxygen molecule. Then, a few hydrogen ions are added as well, forming two water molecules.

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    Discussed Structures
    cow cytochrome c oxidase
    cow cytochrome c oxidase
    bacterial cytochrome c oxidase
    bacterial cytochrome c oxidase
  • Erythrocruorin

    Erythrocruorin

    Hemoglobin comes in many shapes and sizes. In our blood, a hemoglobin with four chains carries oxygen from the lungs to cells throughout the body. Some plants build a single-chain hemoglobin to help protect sensitive nitrogen-fixing bacteria from oxygen, similar to the single chain myoglobin that stores oxygen in our muscle cells. Some bacteria also make simple forms of hemoglobin to help manage oxygen and other small molecules. Earthworms, however, are the champions when it comes to building huge hemoglobins. They, and a few other types of invertebrate animals, build enormous complexes of hemoglobin to carry their oxygen, termed erythrocruorins.

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    Discussed Structures
    Erythrocruorin
    Erythrocruorin
  • Fatty Acid Synthase

    Fatty Acid Synthase

    Fat, these days, is a bad word. But we can't survive without fats, and more particularly, without fatty acids. Fatty acids are small molecules composed of a long string of carbon and hydrogen atoms, with an acidic group at one end. They are used for two essential things in your body. First, they are used to build the lipids that make up all of the membranes around and inside your cells. Second, fatty acids are a concentrated source of energy, so they are often connected to glycerol to form fats, which is a compact way to store energy until it is needed. But as we all know, if we eat too much, this extra fat can build up!

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    Discussed Structures
    fatty acid synthase
    fatty acid synthase
    fatty acid synthase
    fatty acid synthase
    acyl carrier protein
    acyl carrier protein
  • Glycogen Phosphorylase

    Glycogen Phosphorylase

    Although it may not seem so during the holiday season, we do not have to eat continually throughout the day. Our cells do require a constant supply of sugars and other nourishment, but fortunately our bodies contain a mechanism for storing sugar during meals and then metering it out for the rest of the day. The sugars are stored in glycogen, a large molecule that contains up to 10,000 glucose molecules connected in a dense ball of branching chains. Your muscles store enough glycogen to power your daily activities, and your liver stores enough to feed your nervous system and other tissues all through the day and on through the night.

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    Discussed Structures
    glycogen phosphorylase
    glycogen phosphorylase
    glycogen phosphorylase
    glycogen phosphorylase
  • Glycolytic Enzymes

    Glycolytic Enzymes

    Glucose powers cells throughout your body. Glucose is a convenient fuel molecule because it is stable and soluble, so it is easy to transport through the blood from places where it is stored to places where it is needed. Glucose is packed with chemical energy, ready for the taking. In a test tube, you can burn glucose, forming carbon dioxide and water and a lot of light and heat. Our cells also burn glucose, but they do it in many small, well-controlled steps, so that they can capture the energy in more useable forms, such as ATP (adenosine triphosphate). Glycolysis (sugar-breaking) is the first process in the cellular combustion of glucose.

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    Discussed Structures
    hexokinase open form
    hexokinase open form
    hexokinase closed form
    hexokinase closed form
    phosphoglucose isomerase
    phosphoglucose isomerase
    phosphofructokinase active form
    phosphofructokinase active form
    phosphofructokinase inactive form
    phosphofructokinase inactive form
    fructose 1,6-bisphosphate aldolase
    fructose 1,6-bisphosphate aldolase
    triose phosphate isomerase
    triose phosphate isomerase
    glyceraldehyde-3-phosphate dehydrogenase
    glyceraldehyde-3-phosphate dehydrogenase
    phosphoglycerate kinase open form
    phosphoglycerate kinase open form
    phosphoglycerate kinase closed form
    phosphoglycerate kinase closed form
    phosphoglycerate mutase
    phosphoglycerate mutase
    enolase
    enolase
    pyruvate kinase active form
    pyruvate kinase active form
    pyruvate kinase inactive form
    pyruvate kinase inactive form
  • Hemoglobin

    Hemoglobin

    Ever wondered why blood vessels appear blue? Oxygenated blood is bright red: when you are cut, the blood you see is brilliant red oxygenated blood. Deoxygenated blood is deep purple: when you donate blood or give a blood sample at the doctor's office, it is drawn into a storage tube away from oxygen, so you can see this dark purple color. However, deep purple deoxygenated blood appears blue as it flows through our veins, especially in people with fair skin. This is due to the way that different colors of light travel through skin: blue light is reflected in the surface layers of the skin, whereas red light penetrates more deeply. The dark blood in the vein absorbs most of this red light (as well as any blue light that makes it in that far), so what we see is the blue light that is reflected at the skin's surface. Some organisms like snails and crabs, on the other hand, use copper to transport oxygen, so they truly have blue blood.

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    Discussed Structures
    human oxyhemoglobin
    human oxyhemoglobin
    human deoxyhemoglobin
    human deoxyhemoglobin
    horse deoxyhemoglobin
    horse deoxyhemoglobin
    sickle cell hemoglobin
    sickle cell hemoglobin
  • Isocitrate Dehydrogenase

    Isocitrate Dehydrogenase

    Sugar tastes great. This should be no surprise, though, since glucose is the central fuel used by oxygen-breathing organisms. Sugar is broken down in the central catabolic pathways of glycolysis and the citric acid cycle, and ultimately used to construct ATP. The enzymes in these pathways systematically break down glucose molecules into their component parts, capturing the energy of disassembly at each step. Isocitrate dehydrogenase performs the third reaction in the citric acid cycle, which releases one of the carbon atoms as carbon dioxide. In the process, two hydrogens are also removed. One of these, in the form of a hydride, is transferred to the carrier NAD (or NADP), and will be used later to power the rotation of ATP synthase.

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    Discussed Structures
    isocitrate dehydrogenase
    isocitrate dehydrogenase
    isocitrate dehydrogenase
    isocitrate dehydrogenase
    isocitrate dehydrogenase and IDH kinase/phosphatase
    isocitrate dehydrogenase and IDH kinase/phosphatase
  • Lactate Dehydrogenase

    Lactate Dehydrogenase

    Lactate dehydrogenase is a safety valve in our pipeline of energy production. Most of the time, our cells break down glucose completely, releasing the carbon atoms as carbon dioxide and the hydrogen atoms as water. This requires a lot of oxygen. If the flow of oxygen is not sufficient, however, the pipeline of energy production gets stopped up at the end of glycolysis. Lactate dehydrogenase is the way that cells solve this problem, at least temporarily.

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    Discussed Structures
    lactate dehydrogenase
    lactate dehydrogenase
    lactate dehydrogenase (LDH)
    lactate dehydrogenase (LDH)
  • Myoglobin

    Myoglobin

    Any discussion of protein structure must necessarily begin with myoglobin, because myoglobin is where the science of protein structure really began. After years of arduous work, John Kendrew and his coworkers determined the atomic structure of myoglobin, laying the foundation for an era of biological understanding. That first glimpse at protein structure is available at the PDB, under the accession code 1mbn. Take a closer look at this molecule, or look directly at the PDB information for 1mbn. You will be amazed, just like the world was in 1960, at the beautiful intricacy of this protein.

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    Discussed Structures
    sperm whale myoglobin
    sperm whale myoglobin
    oxymyoglobin
    oxymyoglobin
  • PDB Pioneers

    PDB Pioneers

    Structural biology was born in 1958 with John Kendrew's atomic structure of myoglobin, and in the following decade, the field grew rapidly. By the early 1970's, there were a dozen atomic structures of proteins, and researchers were discovering that they had a goldmine of information.

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    Discussed Structures
    sperm whale myoglobin
    sperm whale myoglobin
    lysozyme
    lysozyme
    horse deoxyhemoglobin
    horse deoxyhemoglobin
  • Pepsin

    Pepsin

    During the holiday season, we often place greater demands on our digestive enzymes than at other times of the year. Our digestive system contains a host of tough, stable enzymes designed to seek out those rich holiday treats and break them into small pieces. Pepsin is the first in a series of enzymes that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.

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    Discussed Structures
    pepsin
    pepsin
    pepsinogen
    pepsinogen
  • Pyruvate Dehydrogenase Complex

    Pyruvate Dehydrogenase Complex

    A combination of crystallography, NMR spectroscopy and electron microscopy is revealing the secrets of pyruvate dehydrogenase complex. The complex performs a central step in energy production, catalyzing the reaction that links glycolysis with the tricarboxylic acid cycle. The reaction is performed in three separate steps by three separate enzymes, but all three enzymes are linked efficiently together into one large multienzyme complex.

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    Discussed Structures
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
    pyruvate dehydrogenase complex
  • Serum Albumin

    Serum Albumin

    Think about how convenient it is to be able to eat. Each one of your ten trillion cells requires a constant supply of nourishment. But we don't have to worry about this--we merely eat our dinner and our body does the rest. The food is digested and the useful pieces are delivered to cells throughout the body, using the bloodstream as the delivery system. Delivery of water-soluble molecules, like sugar, is easy. They float in the watery bloodstream and are picked up by cells along the way. Other important nutrients, however, are not soluble in water, so special carriers must be made to chaperone them to hungry cells.

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    Discussed Structures
    serum albumin
    serum albumin
  • Trypsin

    Trypsin

    Proteins are tough, so we use an arsenal of enzymes to digest them into their component amino acids. Digestion of proteins begins in the stomach, where hydrochloric acid unfolds proteins and the enzyme pepsin begins a rough disassembly. The real work then starts in the intestines. The pancreas adds a collection of protein-cutting enzymes, with trypsin playing the central role, that chop the protein chains into pieces just a few amino acids long. Then, enzymes on the surfaces of intestinal cells and inside the cells chop them into amino acids, ready for use throughout the body.

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    Discussed Structures
    trypsin
    trypsin
    trypsinogen
    trypsinogen
    trypsin and trypsin inhibitor
    trypsin and trypsin inhibitor

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