Structural View of Biology
Infrastructure and Communication
Infrastructure and Communication Cells require a complex infrastructure of molecules for support and communication. Our bodies contain about 10 trillion cells, which must cooperate for the good of the entire body. This requires a complex infrastructure to organize them into tissues and organs, and a complex network of signals to coordinate their action.
Signaling and Transport Across Cell Membranes
Receptors and transporters are used to manage traffic of molecules and information across the waterproof cell membrane. Receptors capture signaling molecules on the surface of cells, and transmit the information inside, often starting a cascade of responses. Transporters oversee the traffic of molecules into and out of the cell, bringing in nutrients and expelling wastes.
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Acetylcholine Receptor
Nerve cells need to be able to send messages to each other quickly and clearly. One way that nerve cells communicate with their neighbors is by sending a burst of small neurotransmitter molecules. These molecules diffuse to the neighboring cell and bind to special receptor proteins in the cell surface. These receptors then open, allowing ions to flow inside. The process is fast because the small neurotransmitters, such as acetylcholine or serotonin, diffuse rapidly across the narrow synapse between the cells. The channels open in milliseconds, allowing ions to flood into the cell. Then, they close up just as fast, quickly terminating the message as the neurotransmitters separate and are removed from the synapse.
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acetylcholine receptor -
Acetylcholinesterase
Every time you move a muscle and every time you think a thought, your nerve cells are hard at work. They are processing information: receiving signals, deciding what to do with them, and dispatching new messages off to their neighbors. Some nerve cells communicate directly with muscle cells, sending them the signal to contract. Other nerve cells are involved solely in the bureaucracy of information, spending their lives communicating only with other nerve cells. But unlike our human bureaucracies, this processing of information must be fast in order to keep up with the ever-changing demands of life.
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acetylcholinesterase -
Adrenergic Receptors
Our bodies have many built-in defenses. Our immune system prowls through the body looking for infections by viruses and bacteria. Our blood is filled with molecules that form clots at the first sign of damage. Our nervous system is also hard-wired with instinctive defenses that stand ready to protect us in times of danger. You have probably experienced one of these defenses yourself--when you are startled or scared by an impending danger, you will feel a rush of energy flowing through your body. This has been termed the "flight or fight" response--your body is mobilizing its many resources to make you ready either to run away from danger, or stay and fight.
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adrenergic receptor
adrenergic receptor -
Auxin and TIR1 Ubiquitin Ligase
Plants, like animals, have hormones that deliver chemical messages between distant cells. Charles Darwin and his son discovered this over a century ago--they noticed that if they shined a light on the tips of grass shoots, the stems bend to bring the entire shoot towards the light. Somehow, a message was being sent from the tip down to the stem. You might also have observed the action of hormonal signals in plants: when you prune a tree to make it more bushy, you are modifying the traffic of plant hormones. Both of these effects are caused by the phytohormone auxin.
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TIR1 ubiquitin ligase
IAA-aminoacid hydrolase -
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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bacteriorhodopsin ground state
bacteriorhodopsin light-activated state -
Calcium Pump
Every time we move a muscle, it requires the combined action of trillions of myosin motors. Our muscle cells use calcium ions to coordinate this massive molecular effort. When a muscle cell is given the signal to contract from its associated nerves, it releases a flood of calcium ions from a special intracellular container, the sarcoplasmic reticulum, that surrounds the bundles of actin and myosin filaments. The calcium ions rapidly spread and bind to tropomyosins on the actin filaments. They shift shape slightly and allow myosin to bind and begin climbing up the filament. These trillions of myosin motors will continue climbing, contracting the muscle, until the calcium is removed.
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calcium pump with no calcium
calcium pump with calcium -
Calmodulin
Calcium is the most plentiful mineral element found in your body, with phosphorous coming in second. This probably doesn't come as a surprise, since your bones are strengthened and supported by about two kilograms of calcium and phosphorous. Your body also uses a small amount of calcium, in the form of calcium ions, to perform more active duties. Calcium ions play essential roles in cell signaling, helping to control processes such as muscle contraction, nerve signaling, fertilization and cell division. Through the action of calcium pumps and several kinds of calcium binding proteins, cells keep their internal calcium levels 1000-10,000 times lower than the calcium levels in the blood. Thus when calcium is released into cells, it can interact with calcium sensing proteins and trigger different biological effects, causing a muscle to contract, releasing insulin from the pancreas, or blocking the entry of additional sperm cells once an egg has been fertilized.
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calmodulin
calmodulin
calmodulin and target peptide -
Epidermal Growth Factor
The cells in your body constantly communicate with each other, negotiating the transport and use of resources and deciding when to grow, when to rest, and when to die. Often, these messages are carried by small proteins, such as epidermal growth factor (EGF), shown here in red from PDB entry 1egf. EGF is a message telling cells that they have permission to grow. It is released by cells in areas of active growth, then is either picked up by the cell itself or by neighboring cells, stimulating their ability to divide. The message is received by a receptor on the cell surface, which binds to EGF and relays the message to signaling proteins inside the cell, ultimately mobilizing the processes needed for growth.
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epidermal growth factor
EGF receptor extracellular domain
EGF receptor extracellular domain and EGF
EGF receptor transmembrane domain
EGF receptor tyrosine kinase domain
EGF receptor tyrosine kinase domain -
G Proteins
Cells communicate by passing small, disposable messages to one another. Some of these messengers travel to distant parts of the body through the blood, others simply diffuse over to a neighboring cell. Then, another cell picks the message up and reads it. Thousands of these messages are used in the human body. Some familiar examples include adrenaline, which controls the level of excitement, glucagon, which carries messages about blood sugar levels, histamine, which signals tissue damage, and dopamine, which relays messages in the nervous system.
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G-protein heterotrimer
G-protein alpha subunit and adenylyl cyclase
G-protein beta and gamma subunits -
Importins
Inside your cells, the process of protein synthesis is separated into two compartments. The first half of the job, when DNA is transcribed into RNA, is performed in the nucleus. The second half is then performed outside the nucleus, when ribosomes translate the RNA to construct proteins in the cytoplasm. This separation requires a continuous traffic of molecules: new RNA molecules must be transported out of the nucleus and nuclear proteins, such as newly-synthesized histones or polymerases, must be transported back into the nucleus. Huge tube-shaped nuclear pores act as the highway connecting the nucleus and the cytoplasm, and importins and exportins (collectively known as karyopherins) ferry molecules back and forth through the pore.
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importin-alpha
importin-alpha
importin-alpha, Ran, and CAS
importin-alpha, Ran, and CAS -
Mechanosensitive Channels
We are remarkably resistant to changes in our surrounding environment. Our bulky bodies allow us to weather extremes of heat and cold, and our skin protects us if we go for a swim in fresh water or salty water. If things get too uncomfortable, we can always get up and walk away, finding a warmer or cooler or drier place. Bacteria don't have as many options. They are tiny and they are immersed in water, so changes in the environment can pose life-threatening challenges. For instance, if it rains they may be suddenly surrounded by fresh water. This is dangerous because the water seeps into the cell through osmosis and increases the pressure inside. At other times, the bacterium may be shifted suddenly to salty conditions, which pulls water out and dehydrates the cell. Bacteria have methods for resisting these changes, so they can keep a steady, comfortable osmotic pressure inside.
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mechanosensitive channel MscS
mechanosensitive channel MscS
mechanosensitive channel MscL -
Neurotrophins
Your brain is composed of 85 billion interconnected neurons. Individually, each neuron receives signals from its many neighbors, and based on these signals, decides whether to dispatch its own signal to other nerve cells. Together, the combined action of all of these neurons allows us to sense the surrounding world, think about what we see, and make appropriate actions. Remarkably, this complicated structure is formed in nine short months as an embryo grows into a baby. Nerve cells start as typical, compact cells, but then they send out long axons and dendrites, connecting to other cells in the brain or even to entirely different parts of the body. Neurons in the growing brain test the connections with their neighbors, looking for the proper wiring. Half of the neurons are discarded during this process, in areas that get too crowded. The half that remain become the nervous system. Throughout the rest of life, these neurons typically do not reproduce, although they do send out more dendrites to neighboring cells as the nervous system grows or repairs damaged areas.
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nerve growth factor
nerve growth factor and receptor
nerve growth factor and receptor p75 -
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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inducible nitric oxide synthase, catalytic domain
neuronal nitric oxide synthase, reductase domain -
Potassium Channels
All living cells are surrounded by a membrane that separates the watery world inside from the environment outside. Membranes are effective barriers for small ions (as well as for large molecules like proteins and DNA), providing a novel opportunity: differences in ion levels may be used for rapid signaling. For instance, a cell can raise the level of potassium ions inside it. Then, at a moment's notice, potassium can be released through channels in the membrane, creating a large change in the potassium level that will be felt throughout the cell. This process is used in all types of cells - bacteria, plants and animals. Two common examples of ion channels at work are seen in muscle contraction (which is started by the release of calcium ions), and nerve signaling (which involves a complex flow of sodium and potassium ions).
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potassium channel selectivity filter
potassium channel -
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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Ras with GTP analog
Ras with GDP -
Sodium-Potassium Pump
Our bodies use a lot of energy. ATP (adenosine triphosphate) is one of the major currencies of energy in our cells; it is continually used and rebuilt throughout the day. Amazingly, if you add up the amount of ATP that is built each day, it would roughly equal the weight of your entire body. This ATP is spent in many ways: to power muscles, to make sure that enzymes perform the proper reactions, to heat your body. The lion's share, however, goes to the protein pictured here: roughly a third of the ATP made by our cells is spent to power the sodium-potassium pump.
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sodium-potassium pump -
Src Tyrosine Kinase
Your body is a democratic nation of cells. Each cell is an individual with its own needs, but all of your cells work together to keep you alive. As you might imagine, this requires an incredible amount of cooperation. Cells are in constant communication to inform their neighbors of their needs and future plans. They send messages to each other, passing hormones and chemokines and other molecular messages from cell to cell. These messages are received by proteins in the cell membrane, which transmit the signal inside. There, a bewilderingly complex collection of proteins relays the message to all of the appropriate places inside the cell.
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Src tyrosine kinase
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