Structure & function — Science Leadership Academy @ Center City
in function, structural biology is between two different chains. Mary Poffenroth looks at the biological classification system in a video from Mahalo The beginning teacher analyzes how structure complements function in cells. . Competency Relationships Between Organisms and the Environment. Shmoop Biology theme of Structure and Function in Cells. Are you ready to acknowledge the vital relationship between structure and function yet, or what?.
Such inhibitors would prevent infection by binding to a virus, interfering with its ability to attach itself to and to infect a human cell.
Dihydrofolate reductase is an essential enzyme for cell growth. It is the target both for antibacterial drug design and for chemotherapeutic agents that arrest human cancers.
So far, studies of the three-dimensional structure of the enzyme complexed with various inhibitors have resulted in the development of the new antibacterial drug trimethoprim. The antihypertensive drug captopril lowers blood pressure by inhibiting angiotensin-converting enzyme that normally produces a substance that constricts blood vessels and raises blood pressure.
Captopril was designed by studying the three-dimensional structure of a digestive enzyme related in its chemical activity to the angiotensin-converting enzyme and by synthesizing a compound that would fit tightly to and block the active site of a converting enzyme. Drugs that bind to the blood protein hemoglobin, preventing it from aggregating in individuals with the hereditary sickle-cell trait, are also being studied. Designing drugs by understanding the atomic details of how inhibitors fit onto the surfaces of proteins and block normal activities is just beginning.
Many believe we are entering a new era of drug discovery based on designing molecules for stereochemical fit to their targets by actually seeing the target molecules with substrates and the drugs that are bound to them. It represented a neat solution to a number of chemical and biological problems, and it was easy to describe and to remember. The importance of pairing between bases on the two DNA strands and stacking of adjacent bases along each individual DNA strand is overwhelming in nucleic acid structures.
In terms of relative importance to the overall structure, there are no counterparts in proteins. However, with time, the structure of DNA has been found to be much more complex than was originally thought, since there are a variety of different double helical structures.
The diversity of such structures has dramatically altered our thinking about the DNA molecule. To date, the folding of DNA has been largely thought of as the assembly of the double helix through formation of successive base pairs.
The insertion and deletion of extra helical twists in circular DNA molecules has forced attention on the topology of these complex systems and has presented a massive mechanistic problem at the enzyme level.
The bending of the double helix and its control by sequence variation is also under intensive investigation. The double helix was initially thought to be rigid.
In view of the compact packing required in the nucleus of the cell, bending was obviously essential. However, the structural details of the contortions that the double helix can actually undergo have only recently been recognized. The structure of the nucleosome, now known at high resolution with its coiled double helix and protein core, is a beautiful example of the biological importance of bending. Other proteins that interact with DNA can also induce bending.
The dynamic aspects of the equilibrium structures of DNA have become clear with direct experimental measurement of the swinging in and out of individual bases to and from the axis of the helix. Larger scale motions on a much longer time scale are revealed by pulsed field gel electrophoresis, which separates molecules of enormous molecular weight.
Only the smallest class, transfer RNA, has yielded any solved crystal structures. All the transfer RNAs turn out to be similar L-shaped molecules. This similarity is reflected in the cloverleaf model for secondary structure, originally derived by searching for similar base pairing possibilities within the single chains.
Although no other RNA structures are yet available through diffraction procedures, the extensive use of sequence data and sequence homology has led to a large array of secondary structure predictions that will almost certainly be retained in the three-dimensional structures eventually determined.
Nuclear magnetic resonance NMR is starting to provide a substantial amount of structural information on RNAs, but diffraction-quality crystals would be enormously useful. These introns are precisely cut out of the transcript and the functional structures exons are rejoined to yield the mature RNA in what is called an RNA splicing reaction. In some cases, this reaction can be carried out by the intron RNA itself without the help of any proteins.
These RNA molecules are the first known examples of true, nonprotein biological catalysts.
The details of the highly organized three-dimensional structures of these catalytic RNA molecules have not yet been unraveled. Much Remains to Be Learned About the Structures of Carbohydrates Significant by its absence in the above discussion is any mention of the three-dimensional structure of polysaccharides a carbohydrate made up of a large number of sugar molecules. As mentioned earlier, these substances have been particularly intransigent in yielding high-resolution structural data.
Only the smallest compounds have provided truly crystalline material. Most studies have been chemical or spectroscopic. In view of their unquestioned biological importance, much greater effort on the three-dimensional structure of this class of polymers is indicated.
We do not even know whether such molecules have unique three-dimensional structures. A Technical Breakthrough Promises Information About Dynamic Processes in the Function of Proteins The massive electron-storage rings that physicists use to probe the fundamental components of matter also emit x-ray beams high in power. These synchrotron x-ray sources have recently been used to study large biological molecules. The beams of x-rays are thousands of times as strong as those from conventional laboratory x-ray sources, reducing x-ray data-collection time from months to hours.
An experimental breakthrough in the application of multiple-wavelength x-ray diffraction now provides exposure times of milliseconds. The biochemical events on the surface of a protein can therefore be studied by a series of snapshots of the structure every few milliseconds. This should allow the sequence of events that constitute a chemical reaction or protein conformational change to be understood in atomic detail.
Examining the dynamics of fundamental biological reactions will deepen our understanding of how proteins work, provide insight into normal functions, and raise the possibility of understanding abnormal functioning in disease.
Crystallography Will Continue to Increase in Importance The future for structural biology is particularly bright at present because two factors have coincided. First, the recent explosive growth in the power of molecular biology, as a result of gene cloning and recombinant DNA technology, suddenly provides a large amount of any given macromolecule and the ability to modify these at will, to test or alter their functions.
This brings the fundamental molecules at the basis of almost every process in living systems into the range of structural study. Second, as the discovery of new molecules has accelerated, the technology by which x-ray structures are determined has undergone a rapid evolution.
New methods and algorithms have made determining x-ray structures easier, but most important, because x-ray crystallography is highly technical, it has benefited enormously from the recent leap in computational power and computer-controlled instrumentation. Nuclear Magnetic Resonance is the Technique of Choice for Studying Molecular Structures in Solution Recently, NMR, a structural and analytical tool used by chemists for many years Chapter 2has made rapid progress in providing information in structural biology.
NMR is a spectroscopic technique in which the absorption of radio-frequency energy is measured for the nuclei of molecules placed in highly magnetic fields. Because the absorption frequency is related to the chemical environment of a nucleus, NMR measurements provide structural details such as inter-atomic distances and conformational angles from samples in aqueous solution.
The spectra are very complex. The recently developed procedures for spreading out the absorption peaks in two dimensions have dramatically improved both resolution and the ability to assign each peak to specific atoms in the macromolecule.
Intricate patterns of radio-frequency pulses can be used to collect information on which atoms are close to which others. As with all spectroscopic techniques, each absorption process occurs on a different, characteristic, time scale, and it is sensitive to events that occur on that same time scale.
Thus, the dynamic behavior of many parts of the molecule can be directly measured over a broad frequency range. Recently, the chain-folding of a small protein was determined from an analysis of interatomic distances provided by NMR. X-ray diffraction simultaneously verified the structure, confirming as a side benefit that the structure of a protein in solution as seen by NMR is the same as that in a crystal as seen by x-ray diffraction.
We can now confidently predict that NMR will make it possible to determine a series of structures of small proteins in solution. The two techniques are complementary in the nature of the information that they can best supply. X-ray crystallography can provide precise atomic positions for almost all the atoms in a macromolecule, and it can be applied to very large molecules with no size limit yet found.
However, it requires crystals of excellent quality, poorly ordered regions cannot be defined, and no estimates of the rates of certain types of molecular motion can be inferred. NMR can provide structural information, but not yet with the precision obtainable from x-ray structures. So far, NMR studies have produced atomic level data for only very small proteins.
However, the procedure uses solutions rather than crystals, it can provide information on flexible regions, and it can reveal the times required for many dynamic processes. Both techniques are rapidly improving their capabilities and are likely to continue to dominate structural biology in the near future. Molecular Assemblies The past decade has seen major advances in our ability to study the structure of molecular assemblies.
These are aggregates of individual macromolecules, most frequently complexes between proteins or proteins and nucleic acids.
Among the major triumphs have been solution by x-ray methods of large structures such as the nucleosome, the photosynthetic reaction center, an antibody-antigen complex, and spherical viruses. Another highlight was the solution of the structure of a protein within its native membrane by electron microscopy; this structure is still at relatively low resolution, but it should be possible to extend it to 3 angstroms. Understanding of the molecular architecture and function of some key filamentous complexes and organelles—such as actin filaments decorated with the myosin head, the ribosome, and clathrin-coated vesicles—has significantly advanced through the use of three-dimensional electron image reconstruction combined with in vitro reassembly.
Also important has been the use of deuterium labeling and neutron scattering to derive three-dimensional maps specifying the relative locations of macromolecular components in large complexes such as RNA polymerase and the E.
Crucial insight, paralleling physiological and biochemical data, has been gained into dynamic processes such as muscle contraction and microtubule assembly through the use of time-resolved synchrotron x-radiation. In x-ray crystallography, particularly of viruses, the progress can be traced to four advances: An additional major breakthrough was learning to crystallize membrane protein assemblies in the form of protein-detergent micelles.
Crystallization has been achieved now for several such membrane proteins, including the photosynthetic reaction center, E. Also of particular significance for membrane structure has been the progress made in electron microscopy.
Preparative methods that preserve specimens have been developed as have mathematical analyses of the image that can provide three-dimensional details. The advent of cryo-electron microscopy, in which wet specimens are prepared by being frozen so rapidly that the water remains amorphous rather than crystalline, has made it possible to see functional molecules in action for the first time.
The nucleosome is the fundamental repeating structural unit that makes up the chromosomes of all eukaryotic cells. The elucidation of the molecular details of the nucleosome necessitated the use of a wide range of newly developed physical and biochemical approaches. The existence of nucleosomes was first recognized by electron microscopy and from the finding of a unit of histone organization that could explain the nuclease cutting pattern of chromosomal DNA.
The nucleosome was perceived and eventually proven to consist of a histone octamer about which is wrapped approximately base pairs of DNA, with a single molecule of an additional histone bound on the outside. Electron and x-ray crystallographic analyses showed that the DNA is coiled in two left-handed turns around the central histone octamer.
With the methods used to analyze nucleosome digestion, and with the use of cloned DNAs, the chromatin organization of many genes has been studied.
It is now understood that transcriptionally inactive genes are packaged in nucleosomes, but the active genes are organized differently, with regulatory sequences in special exposed regions and with gene and flanking sequences in altered nucleosomes or in novel particulate structures.
Challenges for the future are to determine how chains of nucleosomes are further coiled or folded in condensed states of chromosomes, to elucidate the mechanism of unfolding that accompanies gene activation, and to solve the structure of transcriptionally active genes.
Major insights into the three-dimensional structure of membranes came from the electron microscopic analysis of bacteriorhodopsin—a light-driven proton pump—in the purple membranes isolated from the cell membrane of the bacterium Halobacterium halobium.
The structural maps provided the first case in which a membrane protein was shown to be composed of a bundle of alpha-helical segments.
There were seven such segments, closely packed in a left-handed configuration extending roughly perpendicular to the plane of the membrane bilayer for most of its width Figure The amino acid sequence for a number of cell-surface receptors such as rhodopsin, the beta-adrenergic receptor, and the muscarinic acetylcholine receptor have recently been determined. Analysis of the patterns of secondary structure and distribution of hydrophobic residues predicted from these sequences indicate that the 7-alpha-helical bundle is a recurring motif among cell-surface receptors.
The quaternary structures of protein oligomers that form membrane channels, such as the nicotinic acetylcholine receptor and the gap-junction connection, have become better understood through the same approach. Figure Bacteriorhodopsin as it sits in a bilayer [R. The three-dimensional structures of a number of plant and animal viruses have been determined by x-ray diffraction; they show assemblies of as many as proteins forming icosahedral shells that package the virus's genetic information Figure Each determination of a vital structure has been a triumph of both persistence and innovation, and we have learned much from every new step.
Determining the structures of the simple plant viruses was a major advance. These structures were far larger than any previously determined by crystallography; they provided our first real insights into vital architecture at the molecular level.
The viral images also led to insights into how viruses assemble themselves. One day we may learn to use this insight to design strategies to prevent viruses from assembling as part of an effort to control the infections they cause. Recently, the structures of two animal viruses rhinovirus and poliovirus and the structure of the adenovirus hexon have revealed that the molecular topology of their coat proteins is essentially the same as that of the simple plant viruses.
Thus all such viruses may have a common evolutionary ancestor. Figure A schematic diagram of the location of the protein subunits on the surface of the tomato bushy stunt virus, as determined by x-ray diffraction.
From these structures it has been possible to ascertain the sites of attachment of various types of neutralizing antibodies and the sites of binding for a series of experimental antiviral drugs that are suspected of inhibiting virus replication by preventing the low pH-mediated uncoating of the vital RNA. The structural results show that these antiviral compounds insert themselves into the hydrophobic interior of one subunit of the protein coat, suggesting how the drugs may inhibit the disassembly of the virus.
In the near future, this newly developed technology should allow a fairly rapid survey of the structures of numerous vital pathogens or their components and thereby provide a good deal of information about how they work. We should come to understand the mechanism of neutralization of viruses by antibodies by looking at the structure of neutralizing monoclonal antibodies and their complexes with the virus.
Moreover, it should become possible to design more powerful antiviral drugs that interfere with attachment, penetration, uncoating, or assembly. In the past five years, the determinations of the crystal structures of poliovirus, rhinovirus, and both of the surface proteins of influenza virus have allowed us to visualize those parts of the viruses recognized by the human immune system.
Monoclonal antibodies and the amino acid sequences of many strains of viruses have made it possible to map the regions of each virus that are attacked by human antibodies. Plate 3for example, shows five sites A-E on an influenza virus that bind antibodies. How these antigenic sites vary in structure every few years, resulting in new epidemics of ''the flu," is now under study. Plate 3 Sites A-E on the surface protein of the flu virus are recognized by our immune system.
Variation in the structure of these sites results in the recurrence of epidemics in the human population. Wiley, Harvard University, and J. Even Larger Structures Will Be Solved During the Next Decade Research on molecular assemblies over the next decades is likely to involve extending x-ray analytical methods to still larger aggregates, such as ribosomal subunits, and to more difficult materials, such as membrane complexes and networks of peptides and sugars called proteoglycans, which are materials that play important roles in the interactions between cells.
There will be greater use of clusters of heavy atoms rather than simply individual atoms to determine the structures. Area detectors and synchrotron radiation will be used to collect x-ray data. The increase in power and accessibility of computing resources will greatly benefit the data processing.
With symmetrical assemblies, new methods may eventually allow the determination of new high-resolution structures without the need to resort to heavy-atom methods.
Since progress on each of these points is already being made, one can anticipate that early in the next decade determining the structure of small viruses will be routine and that a number of larger viruses will also be solved. Electron microscopy of rapidly frozen specimens, in the form of two-dimensional crystals or isolated molecules and in conjunction with heavy-atom cluster labels, should provide a wealth of new information on molecular assemblies trapped in different conformational states in nearly physiological conditions.
Methods of three-dimensional image reconstruction from crystalline specimens will be further refined by computational procedures. Averaging methods to extract details from isolated molecules will become more powerful.
With further improvements in methods for electron microscopy at very low temperatures, we can expect images of two-dimensional crystals in some instances to yield atomic resolution and, more generally, resolution at the secondary structure level.
These images, when combined to derive three-dimensional maps, will provide essential frameworks upon which other diverse information can be added to build up detailed pictures of molecular structure and action. Oligomeric membrane proteins may become fairly well understood by such an approach, since the lipid bilayer imposes stringent constraints on possible transmembrane structures.
The identification of residues exposed at one or the other surface of the bilayer can readily be accomplished by labeling, for example, with antibodies to specific strings of amino acids. The ability to capture a particular conformation by rapid freezing should soon make it possible to visualize the configuration of the myosin head attached to actin at different stages in the contraction-relaxation cycle and to visualize membrane channels in their closed, open, and inactivated states.
Closer ties with physiology can also be expected to emerge as a result of further development of microscopic and time-resolved techniques. Computer-aided light microscopy, for example, has facilitated the discovery of the mechanisms of microtubule-based motility and is beginning to reveal the fate of very small populations of molecules in cells. Similarly, time-resolved x-ray diffraction has been developed on the basis of very few model systems muscle contraction, microtubule assemblybut the applicability of these methods goes far beyond the original aims.
Crystallization of the Sample Is Still an Major Hurdle The major obstacle to the structural analysis of molecular assemblies has been and will continue to be in preparing suitable crystals. The growth of two-dimensional crystals has become a key aspect of electron microscopic structure determination, and new general approaches are urgently needed.
Thus, the lipid-layer crystallization technique in which macromolecules are bound to a lipid ligand in mono- or multilayers in order to facilitate high lateral concentration and oriented bindingif successfully developed, would play a critical role.
The difficulties encountered in three-dimensional crystallization, as needed for highresolution x-ray analysis, will depend on the type of assembly in question. With membrane complexes, the crystals must be grown from precise mixtures of detergents, amphiphiles polar molecules that have an affinity to both aqueous and nonaqueous areasprotein, and lipid; the process of crystallization has an additional dimension compared with that of soluble proteins.
A major difficulty at present, therefore, is in obtaining sufficient commitments of financing and time to support such crystallization efforts. The first such crystallizations were carried out only after many years of trials in Europe, where the support of science can maintain a constant effort in a high-risk, long-term endeavor. Because risks have been demonstrably reduced, considerable weight must be given to early successes in growing crystals of sufficient quality for high-resolution analyses.
The crystallization of viruses is often made difficult by the small supplies available for systematic experimentation. Thus, large cell-culture laboratories with suitable biohazard containment are required. New methods of crystallization may also be needed, particularly for lipid-enveloped viruses such as rubella or measles.
The forming of homogeneous complexes of viruses with antibodies, drugs, and receptors will call for considerable effort. An alternative approach, which has proven successful in the past, consists of crystallization of components of the assembled structure, determining the three-dimensional structures of each of the components, and then using electron microscopy studies to provide the architectural details of how the components are arranged in the assembly.
Complementary analyses of this nature will also, in many instances, provide the most appropriate pathway toward understanding the details and action of the large intracellular organelles, such as the nuclear pore and the various types of cytoskeletal filaments. An exciting result to be expected along these lines over the next 10 years is the merging of the available low-resolution picture of myosin-actin filament interaction with that of the high-resolution structures currently being determined for the actin monomer and the myosin head.
Complex Biological Structures Can Assemble Themselves Researchers have begun to unravel how molecular assemblies are formed. In living cells, the production of the components destined to be assembled is often coordinated tightly both spatially and temporally. This coordination is revealed by studies with mutants, in which individual components are defective or are not synthesized in the proper amounts.
Sometimes assembly occurs just by spontaneous association of individual proteins and nucleic acids, but steps in assembly are frequently accompanied by the covalent modification of key proteins and nucleic acids. Such modification can make the assembly irreversible—in essence, to lock the pieces into place. Other assembly mechanisms have been found to make use of scaffolding molecules. These molecules are present at intermediate stages in the assembly to help align critical components, but they disappear before the final structure is formed, just as a scaffold is taken down as a building is finished.
Studies that attempt to assemble biological structures in vitro have been particularly fruitful. These allow the timing of particular steps to be controlled at will, and particular components can be added sequentially or simultaneously, which in turn allows detailed study of assembly pathways and direct tests of the function of specific components of the assembly by single-component-omission experiments.
Such studies are not always possible in vivo. For example, if a protein has functions critical to the cell, it will be difficult to see its effect on the structure or function of an assembly by simply preventing its being synthesized. In vitro assembly is also useful for many structural studies. For example, neutron-scattering measurements usually require the creation of an assembly in which some components contain the normal isotope of hydrogen whereas in others the hydrogen is substituted with deuterium.
Such manipulations can be carried out only by starting with isolated components in vitro. Complex biological structures successfully assembled in vitro include ribosomes, microtubules, nucleosomes, and even many viruses. Directed Modification of Proteins We Can Now Design and Construct New Molecular Machines Until recently, the experimental strategies available to structural biology were largely limited to examining naturally occurring biological structures.
Testing specific hypotheses by altering structures was limited to observing naturally occurring biological variants when they could be identified, as in the numerous mutant hemoglobins.
This approach is limited in having no systematic way to search for a particular desired variant. Furthermore, one was restricted to those variants that had no lethal consequences for the organism and variants that had a significant chance of arising by natural biological mutation or evolution.
The development of recombinant DNA technology has dramatically altered our study of the structure and function of proteins. The major breakthrough lies in our new ability to modify or synthesize de novo genes DNA that, when introduced into cells, direct the synthesis of modified or new protein molecules.
What was only a fantasy a few years ago is today a routine procedure: We can produce protein molecules of any desired sequence. We can produce altered proteins in bacteria, yeast, or plant or animal tissue-culture cells, which makes it possible to isolate large enough quantities for structural and functional studies.
In addition we can produce the altered proteins in vivo in transgenic animals to gauge the effect of the altered protein on complex biological processes.
Such integrated approaches will allow more rapid and informative studies of the structures of proteins and how these structures determine function. The future will see ever-closer working relations among scientists expert in these different disciplines. Whereas anatomy is about structure, physiology is about function. Human physiology is the scientific study of the chemistry and physics of the structures of the body and the ways in which they work together to support the functions of life.
Homeostasis is the state of steady internal conditions maintained by living things. The study of physiology certainly includes observation, both with the naked eye and with microscopes, as well as manipulations and measurements.
Current advances in physiology usually depend on carefully designed laboratory experiments that reveal the functions of the many structures and chemical compounds that make up the human body. Like anatomists, physiologists typically specialize in a particular branch of physiology. For example, neurophysiology is the study of the brain, spinal cord, and nerves and how these work together to perform functions as complex and diverse as vision, movement, and thinking.
Physiologists may work from the organ level exploring, for example, what different parts of the brain does to the molecular level such as exploring how an electrochemical signal travels along nerves. Form is closely related to function in all living things. For example, the thin flap of your eyelid can snap down to clear away dust particles and almost instantaneously slide back up to allow you to see again.
At the microscopic level, the arrangement and function of the nerves and muscles that serve the eyelid allow for its quick action and retreat. At a smaller level of analysis, the function of these nerves and muscles likewise relies on the interactions of specific molecules and ions. Even the three-dimensional structure of certain molecules is essential to their function. Your study of anatomy and physiology will make more sense if you continually relate the form of the structures you are studying to their function.
In fact, it can be somewhat frustrating to attempt to study anatomy without an understanding of the physiology that a body structure supports.
Click on the Animal Systems menu to learn about each body system. Human Body Systems and their Functions The beginning teacher identifies human body systems and describes their functions.6.2.5 Relationship between structure and function of arteries, veins and capillaries
The human body has several organ systems. Read this web page for a quick overview of the body systems, including organs, and the major role of each. Animal Tissues and Organs. To review organ systems and their functions, select the appropriate links on this site to watch a short video.
These slides and notes provide an overview of tissues in the human body. How Organisms Obtain and Use Energy and Matter The beginning teacher describes how organisms obtain and use energy and matter.
All living organisms depend on a source of energy to survive. Energy is the ability to perform work. Adenine triphosphate ATP is the chemical that stores and releases energy to drive reactions in each cell. Producing chemical energy from the light energy electromagnetic radiation is called photosynthesis. The chemical energy and molecular building blocks nutrients obtained from these food sources are used by heterotrophs for new body structures or are converted to energy for work.
Metabolism is all of the chemical reactions in an organism that occur in order to manage its material and energy resources. Watch this video to learn about autotrophs and heterotrophs. Energy, Ecosystems and the Atmosphere. Nancy Moreno discusses the flow of energy from the sun through producers and consumers.
Cycling through the Food Web. Scientists from the Bigelow Laboratory for Ocean Scientists explain the cycling of matter and energy flow. ATP and Energy Storage. Interactive animation of how ATP stores energy from Dr. Structure and Function of Basic Chemical Components of Living Things The beginning teacher applies chemical principles to describe the structure and function of the basic chemical components e.
All living organisms on earth are made up of chemicals based mostly on the element carbon. Carbon can form covalent bonds with up to four atoms. This characteristic allows carbon to form many diverse molecules.
Most biological molecules consist of carbon atoms bonded to other carbon atoms or to atoms of oxygen, nitrogen, sulfur or hydrogen. Molecules containing carbon can form chains, branches or rings. Some biological molecules, such as sugars, are relatively small. Other biological molecules are large and complex, and are referred to as macromolecules.
In many cases, the macromolecules are polymers, which are long chains of similar, linked subunits.