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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.

Many diseases are caused by malfunctions of cellular molecules. These malfunctions may be caused by environmental dangers, like pathogens or radiation, or may be the result of genetic errors. Our cells contain many defenses to fight these malfunctions, ranging from the detoxification of poisons to the forced suicide of compromised cells.

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

  • ABO Blood Type Glycosyltransferases

    ABO Blood Type Glycosyltransferases

    Researchers have discovered that blood comes in several types, which define groups of people with compatible blood. The ABO system defines one of the major types determining groups of people who can donate blood to each other.

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  • Amyloid-beta Precursor Protein

    Amyloid-beta Precursor Protein

    Like Dr. Jekyll and Mr. Hyde, some seemingly innocent proteins have evil alter egos. The amyloid-beta precursor protein is an important example. It is a large membrane protein that normally plays an essential role in neural growth and repair. However, later in life, a corrupted form can destroy nerve cells, leading to the loss of thought and memory in Alzheimer's disease.

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  • Amyloids


    Proteins have evolved to fold into a functional shape, or in cases where a flexible tether is needed, to remain consistently unfolded. In some cases, however, proteins aggregate to form unwanted structures, which can have dangerous consequences. The amyloid-beta precursor protein is a perfect example. In its normal form, it is a membrane-bound protein with folded regions connected by flexible tethers. But if the protein chain is broken, some of the resulting peptides aggregate into long fibrils, termed "amyloids," that can gum up the proper working of cells.

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  • Apoptosomes


    "To be, or not to be"--that question is continually being asked by each of your cells. Your cells are preprogrammed to die on command. This is essential during development of large organisms like ourselves, where cells work together, growing and dying to shape our complicated bodies. It is also essential throughout our adult lives, to remove damaged or infected or cancerous cells. The machinery for cell death is always silently present in cells, but can be instantly mobilized if the choice is made to die.

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  • Carbonic Anhydrase

    Carbonic Anhydrase

    Breathing is a fundamental function in life - ever wondered what really happens when we breathe? The air we breathe in has precious oxygen that fuels the breakdown of sugars and fat in our cells. In our lungs, oxygen diffuses into the blood, binds to hemoglobin and is transported to all the cells of our body (see the Molecule of the Month feature on hemoglobin). Carbon dioxide is a byproduct of sugar and fat breakdown in cells and needs to be removed from our body. Again, blood acts as a transport medium. Carbon dioxide diffuses out of cells and is transported in blood in a few different ways: less than 10% dissolves in the blood plasma, about 20% binds to hemoglobin, while the majority of it (70%) is converted to carbonic acid to be carried to the lungs. An enzyme present in red blood cells, carbonic anhydrase, aids in the conversion of carbon dioxide to carbonic acid and bicarbonate ions. When red blood cells reach the lungs, the same enzyme helps to convert the bicarbonate ions back to carbon dioxide, which we breathe out. Although these reactions can occur even without the enzyme, carbonic anhydrase can increase the rate of these conversions up to a million fold.

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  • Caspases


    Billions of cells in your body will die in the next hour. This is entirely normal--the human body continually renews itself, removing obsolete or damaged cells and replacing them with healthy new ones. However, your body must do this carefully. If cells are damaged, like when you cut yourself, they may swell and burst, contaminating the surrounding area. The body responds harshly to this type of cell death, inflaming the area by rushing in blood cells to clean up the mess. To avoid this messy problem, your cells are boobytrapped with a method to die cleanly and quickly on demand. When given the signal, the cell will disassemble its own internal structure and fragment itself into small, tidy pieces that are readily consumed by neighboring cells. This process of controlled, antiseptic death is called apoptosis.

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  • Crystallins


    As you read this Molecule of the Month, the light from the page is being focused in your eyes by a concentrated solution of crystallin proteins. The lenses in your eyes are built of long cells that, early in their development, filled themselves with crystallins and then made the major sacrifice, ejecting their nuclei and mitochondria and leaving only a smooth, transparent solution of protein. We then rely on these proteins to see for the rest of our lives.

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  • Ebola Virus Proteins

    Ebola Virus Proteins

    The genome of ebola virus contains instructions for building seven proteins, which assemble with the genomic RNA to form one of the deadliest viruses. Ebola virus is surrounded by a membrane stolen from an infected cell, and studded with ebola glycoproteins. A layer of matrix proteins support the membrane on the inside, and hold a cylindrical nucleocapsid at the center, which stores and delivers the RNA genome.

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  • Glucansucrase


    We brush our teeth twice a day with fluoride toothpaste, use mouthwash, limit sugars in our diet...and we still get cavities. Cavities are caused by bacteria that consume some of the sugar in our diet, ferment it, and then release acids. These acids eat away at the hard minerals in our teeth. It seems like it would be easy to brush these bacteria away, and get rid of them once and for all. However, they have a trick to avoid this.

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  • Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

    Hypoxanthine-guanine phosphoribosyltransferase (HGPRT)

    Cells are great recyclers. They need to be, otherwise we would be faced with an insurmountable need for new molecular building blocks and enough energy to manage them. For instance, new messenger RNA chains are made constantly, transmitting information from the nucleus to build new proteins. Afterwards, these chains are broken down and the components are recycled. A complex set of salvage machinery is used to recycle these components.

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    Discussed Structures
  • Leptin


    The delivery of nutrients to cells throughout the body is controlled by a complex network of signaling molecules. Some of these signals happen without us really noticing, for instance, when insulin and glucagon control the level of glucose that is delivered through the blood after we eat. The signaling protein leptin, however, has a more apparent effect, acting within the system that makes us hungry when we need food.

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  • Prions


    Prions are proteins that can adopt two different forms, a normal form and a misfolded form. This may not seem unusual, since many proteins are flexible and adopt different shapes. However, prions have another unusual characteristic: the misfolded form of the prion can force normal prions to change into the misfolded shape. In this way, a few misfolded prions can corrupt a whole population of normal prions, converting them one-by-one into the misfolded shape. This can have deadly consequences, as the levels of misfolded proteins build up. For instance, misfolding of the PrP prion causes fatal neural diseases in humans and other mammals. To make things worse, misfolded prions are infectious, so a small dose of misfolded prions can infect and corrupt an entire organism.

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  • Proton-Gated Urea Channel

    Proton-Gated Urea Channel

    The acid in your stomach helps to digest food, but it also helps protect you from bacterial infection. However, one type of bacteria, Helicobacter pylori, is able to live in the acidic environment of the stomach. It is one of the most common bacterial infections, found worldwide in half of the population. It causes a continued inflammation of the stomach, which leads in some cases to stomach ulcers and stomach cancer.

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  • Ras Protein

    Ras Protein

    Cells are constantly sending messages, discussing nutrient levels and growth rates with other cells, and also managing the internal needs of the cell. These messages need to be clear and strong, so that they can be heard over the busy bustle inside the crowded cytoplasm. One way to strengthen signals is to link them to a process that is chemically irreversible, like the cleavage of ATP or GTP.

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  • Superoxide Dismutase

    Superoxide Dismutase

    We can't live without oxygen. Our cells rely on oxygen as the final acceptor of electrons in respiration, allowing us to extract far more energy from food than would be possible without oxygen. But oxygen is also a dangerous compound. Reactive forms of oxygen, such as superoxide (oxygen with an extra electron), leak from the respiratory enzymes and wreak havoc on the cell. This superoxide can then cause mutations in DNA or attack enzymes that make amino acids and other essential molecules. This is a significant problem: one study showed that for every 10,000 electrons transferred down the respiratory pathway in Escherichia coli cells, about 3 electrons end up on superoxide instead of the proper place. To combat this potential danger, most cells make superoxide dismutase (SOD, shown here from PDB entry 2sod), an enzyme that detoxifies superoxide.

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  • Tetrahydrobiopterin Biosynthesis

    Tetrahydrobiopterin Biosynthesis

    Enzymes that perform unusual chemical reactions often need some assistance. The twenty natural amino acids have many different chemical properties that may be used to catalyze chemical reactions, but sometimes amino acids just aren't enough. In these cases, cofactors with special chemical properties provide the necessary chemical expertise and enzymes use them as tiny tools to perform their reactions. For instance, tetrahydrobiopterin is a cofactor used by several enzymes that juggle molecular oxygen, attaching it to amino acids and other molecules.

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  • Thymine Dimers

    Thymine Dimers

    Summer is here, and we're all heading outdoors to enjoy the sun. But remember to take your sunscreen, since too much sunlight can damage your cells. Small doses of sunlight are needed to create vitamin D, but larger doses attack your DNA. Ultraviolet light is the major culprit. The most energetic and dangerous wavelengths of UV light, termed UVC, are screened out (at least for now) by the ozone in the upper atmosphere. However, the weaker UV light, termed UVA and UVB, passes through the atmosphere and is powerful enough to cause chemical changes in the DNA.

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  • Vitamin D Receptor

    Vitamin D Receptor

    Vitamins are exotic molecules that are essential for the proper function of cells, but somewhere along the process of evolution, our bodies have lost the ability to make them. So instead, we need to obtain them in our diet, or in a daily multivitamin tablet. These include vitamin A, which is used to build the light sensors in our eyes, a host of B vitamins used to build specialized tools for chemical reactions, and vitamin C, which plays an essential role in construction of collagen. Vitamin D is an exceptional case: our cells can make it, but only if there is enough sunlight.

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  • beta-Secretase


    Many of our proteins need to be shaped, folded and trimmed after they are made, to coax them into their proper functional form. A variety of specialized chaperones and proteases perform these tasks. Occasionally, however, these chaperones and proteases make mistakes that can have life-threatening consequences.

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  • p53 Tumor Suppressor

    p53 Tumor Suppressor

    Our cells face many dangers, including chemicals, viruses, and ionizing radiation. If cells are damaged in sensitive places by these attackers, the effects can be disastrous. For instance, if key regulatory elements are damaged, the normal controls on cell growth may be blocked and the cell will rapidly multiply and grow into a tumor. p53 tumor suppressor is one of our defenses against this type of damage. p53 tumor suppressor is normally found at low levels, but when DNA damage is sensed, p53 levels rise and initiate protective measures. p53 binds to many regulatory sites in the genome and begins production of proteins that halt cell division until the damage is repaired. Or, if the damage is too severe, p53 initiates the process of programmed cell death, or apoptosis, which directs the cell to commit suicide, permanently removing the damage.

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