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Structural View of Biology


Biomolecular structures allow us to understand the molecular nature of healthy cells and treat the underlying molecular causes of disease. Our cells contain thousands of molecules that must all work in concert to keep us healthy. When any of these molecules fails, or when a poison or pathogenic organism attacks these molecules, it may cause disease. Our bodies have many defenses against disease, and medical science has developed powerful drugs to assist these defenses.

Drugs are artificial molecules that we use to modify the function of molecules in cells. Antibiotic drugs specifically attack molecules in pathogens, killing them and stopping infection. Other drugs bind to our own molecules, stopping pain, lowering blood pressure, or making other useful medical changes.

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

  • Actinomycin

    Actinomycin

    Cells are master chemists, and many times the search for medical compounds begins by looking to nature. Many antibiotics have been found by studying the constant warfare between bacteria and fungi, and isolating the toxic molecules that they build to protect themselves. Actinomycin is the first natural antibiotic discovered that has anti-cancer activity. It was discovered in the bacterium Streptomyces antibioticus in 1940. Unfortunately, it is too toxic for general use, killing cancer cells but also poisoning the patient, but related molecules have subsequently been discovered, and are now widely used for cancer chemotherapy.

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    Discussed Structures
    Actinomycin and DNA
    Actinomycin and DNA
    Topoisomerase I with DNA and Topotecan
    Topoisomerase I with DNA and Topotecan
  • Aminoglycoside Antibiotics

    Aminoglycoside Antibiotics

    The discovery of streptomycin in 1944 provided the first effective treatment for tuberculosis. Ever since then, we have fought an escalating battle with bacteria using streptomycin and other aminoglycoside antibiotics. Researchers have discovered many natural aminoglycosides made by bacteria, and chemists have created entirely new antibiotics based on these effective natural defenses.

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    Discussed Structures
    16S rRNA methylase
    16S rRNA methylase
    16S rRNA methylase
    16S rRNA methylase
    aminoglycoside 3'-phosphotransferase
    aminoglycoside 3'-phosphotransferase
    aminoglycoside 3-N-acetyltransferase
    aminoglycoside 3-N-acetyltransferase
    kanamycin nucleotidyltransferase
    kanamycin nucleotidyltransferase
    30S ribosome with paromomycin
    30S ribosome with paromomycin
  • Circadian Clock Proteins

    Circadian Clock Proteins

    Our cells contain tiny molecular clocks that measure out a 24-hour circadian rhythm. This clock decides when we get hungry and when we get sleepy. This clock can sense when the days are getting longer and shorter, and then trigger seasonal changes. Our major clock is housed in a small region of the brain, called the suprachiasmic nuclei. It acts as our central pacemaker, checking the cycles of light and dark outside, and then sending signals to synchronize clocks throughout the rest of the body.

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    Discussed Structures
    circadian clock protein KaiA
    circadian clock protein KaiA
    circadian clock protein KaiB
    circadian clock protein KaiB
    circadian clock protein KaiC
    circadian clock protein KaiC
  • Cyclooxygenase

    Cyclooxygenase

    What is the most commonly-taken drug today? It is an effective painkiller. It reduces fever and inflammation when the body gets overzealous in its defenses against infection and damage. It slows blood clotting, reducing the chance of stroke and heart attack in susceptible individuals. And, there is growing evidence that it is an effective addition to the fight against cancer. This wonder drug, with manifold uses in medicine, is aspirin. Aspirin has been used professionally for a century, and traditionally since ancient times. A similar compound found in willow bark, salicylic acid, has a long history of use in herbal treatment. But only in the last few decades have we understood how aspirin works, and how it might be improved.

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    Discussed Structures
    prostaglandin H2 synthase
    prostaglandin H2 synthase
  • Cytochrome p450

    Cytochrome p450

    If you have a headache and take a drug to block the pain, you'll notice that the effects of the drug wear off in a few hours. This happens because you have a powerful detoxification system that finds unusual chemicals, like drugs, and flushes them out of your body. This system fights all sorts of unpleasant chemicals that we eat and breathe, including drugs, poisonous compounds in plants, carcinogens formed during cooking, and environmental pollutants. The cytochrome p450 enzymes are our first line of defense in this chemical battle.

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    Discussed Structures
    cytochrome p450 3A4
    cytochrome p450 3A4
    cytochrome p450 14alpha-sterol demethylase
    cytochrome p450 14alpha-sterol demethylase
    cytochrome p450cam
    cytochrome p450cam
    cytochrome p450cam
    cytochrome p450cam
  • Dihydrofolate Reductase

    Dihydrofolate Reductase

    Dihydrofolate reductase is a small enzyme that plays a supporting role, but an essential role, in the building of DNA and other processes. It manages the state of folate, a snaky organic molecule that shuttles carbon atoms to enzymes that need them in their reactions. Of particular importance, the enzyme thymidylate synthase uses these carbon atoms to build thymine bases, an essential component of DNA. After folate has released its carbon atoms, it has to be recycled. This is the job performed by dihydrofolate reductase.

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  • Estrogen Receptor

    Estrogen Receptor

    Estrogens are small, carbon-rich molecules built from cholesterol. This is quite different than larger hormones, such as insulin and growth hormone, which are sensed by receptors on the cell surface. Estrogens pass directly into cells throughout the body, so the cell can use receptors that are in the nucleus, right at the site of action on the DNA. When estrogen enters the nucleus, it binds to the estrogen receptor, causing it to pair up and form a dimer. This dimer then binds to several dozen specific sites in the DNA, strategically placed next to the genes that need to be activated. Then, the DNA-bound receptor activates the DNA-reading machinery and starts the production of messenger RNA.

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    Discussed Structures
    estrogen receptor hormone-binding domain
    estrogen receptor hormone-binding domain
    estrogen receptor DNA-binding domain
    estrogen receptor DNA-binding domain
    estrogen receptor and tamoxifen
    estrogen receptor and tamoxifen
  • HIV-1 Protease

    HIV-1 Protease

    Drugs that attack HIV-1 protease are one of the triumphs of modern medicine. The AIDS epidemic started a few short decades ago-- before that, HIV was unknown. These drugs demonstrate the powerful tools that medical science has to combat a new disease. Already, researchers have discovered a panel of effective drugs which slow the growth of the virus to a standstill. Important problems still remain, however. In particular, an effective vaccine against HIV is not available. But today, HIV-infected individuals have potent options for treatment.

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    Discussed Structures
    HIV protease with a peptide-like inhibitor
    HIV protease with a peptide-like inhibitor
    HIV protease with saquinavir
    HIV protease with saquinavir
  • Integrase

    Integrase

    Retroviruses, such as HIV, are particularly insidious. Most viruses infect a cell, force it make many new copies of the virus, and then leave when the cell is used up. Retroviruses, however, take a long-term approach to infection. They enter cells and build a DNA copy of their genome.

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    Discussed Structures
    integrase target capture complex
    integrase target capture complex
    integrase strand transfer complex
    integrase strand transfer complex
  • Interferons

    Interferons

    Our cells have many defenses against viruses. When cells are infected, they build enzymes t hat slow protein synthesis, and thus also slow down viral growth, and they build enzymes to chop up double-stranded RNA, which is made primarily by viruses. Infected cells also alert the immune system by displaying pieces of the virus on their surfaces. In the worst cases, infected cells make the ultimate sacrifice and destroy themselves by apoptosis.

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    Discussed Structures
    interferon alpha
    interferon alpha
    interferon beta
    interferon beta
    interferon gamma
    interferon gamma
    interferon-gamma and receptor
    interferon-gamma and receptor
  • Multidrug Resistance Transporters

    Multidrug Resistance Transporters

    Ever since the discovery of penicillin, we have lived our lives with far less fear of infectious disease. In the decades since then, a wide variety of drugs have been isolated from natural sources or synthesized by chemists, giving our doctors a large arsenal of antibiotics to fight infection. Bacteria, however, are dynamic evolving organisms, and they have developed many methods to fight back. In some cases, they develop ways to destroy antibiotic drugs directly, for instance, some bacteria make beta-lactamase enzymes that break down penicillin. In other cases, the bacteria change their own molecular machinery, making it invulnerable to the drugs. For instance, methicillin-resistant Staphylococcus bacteria use new, resistant enzymes to build their cell walls. If these methods don't work, bacteria also have a more general method. They build special pumps that transport many different antibiotics out of the cell before they can do their job.

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    Discussed Structures
    Sav1866 multidrug resistance transporter
    Sav1866 multidrug resistance transporter
    EmrD multidrug resistance transporter
    EmrD multidrug resistance transporter
    AcrB multidrug resistance transporter
    AcrB multidrug resistance transporter
    P-glycoprotein
    P-glycoprotein
  • Nitric Oxide Synthase

    Nitric Oxide Synthase

    Nitroglycerin is a powerful explosive, detonating when exposed to heat or pressure. The same molecule, however, can save your life if you're experiencing a heart attack. A small dose of nitroglycerin will slowly break down and release nitric oxide (NO), which then spreads to the muscle cells surrounding blood vessels, telling them to relax. The curative properties of nitroglycerin have been used in this way for over a century, but scientists have only recently revealed how NO performs its job.

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    Discussed Structures
    inducible nitric oxide synthase, catalytic domain
    inducible nitric oxide synthase, catalytic domain
    neuronal nitric oxide synthase, reductase domain
    neuronal nitric oxide synthase, reductase domain
  • P-glycoprotein

    P-glycoprotein

    Our environment is filled with toxic substances that attack our molecular machinery. Our cells protect themselves from these dangers in many ways. In some cases, they use enzymes to convert them into harmless compounds. In other cases, they sequester them safely out of the way. For others, cells build specialized pumps that find toxins and eject them outside, for safe disposal.

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    Discussed Structures
    P-glycoprotein
    P-glycoprotein
  • Penicillin-binding Proteins

    Penicillin-binding Proteins

    Bacteria pose a continual threat of infection, both to humans and to other higher organisms. Thus, when looking for new ways to fight infection, it is often productive to look at how other plants, animals and fungi protect themselves. This is how penicillin was discovered. Through a chance observation in 1928, Alexander Fleming discovered that colonies of Penicillium mold growing in his bacterial cultures were able to stave off infection. With more study, he found that the mold was flooding the culture with a molecule that killed the bacteria, penicillin.

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    Discussed Structures
    D-alanyl-D-alanine carboxypeptidase/transpeptidase
    D-alanyl-D-alanine carboxypeptidase/transpeptidase
    beta-lactamase
    beta-lactamase
  • Serotonin Receptor

    Serotonin Receptor

    Are you feeling happy today? Are you feeling hungry? Do you get migraines? All of these behaviors, and many more, are controlled in part by the neurotransmitter serotonin. Serotonin, a small molecule made from the amino acid tryptophan, was discovered for its role in the constriction of blood vessels. Most of the serotonin in your body is found in the digestive system where it helps to control the motions needed for digestion. However, the most dramatic effects of serotonin are in the brain. Less than one in a million neurons uses serotonin for communication, but these neurons help to control our emotions, moods and thoughts.

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    Discussed Structures
    Serotonin Receptor
    Serotonin Receptor

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