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.
Genetically Engineered Proteins Reveal Much About How Proteins Function
The use of site-directed protein modification offers great promise for answering some of the fundamental questions in contemporary biology. For example cell-surface receptors must migrate throughout the cell from one organelle to another, moving from the endoplasmic reticulum to the Golgi complex to the plasma membrane . Once inside a coated pit, these proteins are taken inside the cell in a coated vesicle and then recycled back to the cell surface in a recycling vesicle. All of these movements seem to be dictated by signals contained within the structure of the protein itself. What are these targeting signals? Are they simply short, continuous stretches of amino acids or are they determined by the three-dimensional structure of the protein? Are protein modifications, such as phosphorylation or fatty acylation of the protein, required for any of these targeting signals?
The use of chimeric proteins has made it possible to define the functions of linear sequences responsible for protein translocation into the endoplasmic reticulum, mitochondria, and nucleus. However, signals that are defined by noncontinuous amino acid sequences are more difficult to define functionally with chimeric proteins. Incorrect protein folding becomes a major obstacle when the function of an internal sequence or domain is examined by this approach.
Mitochondrial Membranes And Membrane Compartments
As ubiquitous, semi-autonomous cellular organelles, mitochondria are separated from the cytoplasm by the outer and inner mitochondrial membrane . The outer membrane is porous and freely traversed by ions and small, uncharged molecules through pore-forming membrane proteins , such as the voltage-dependent anion channel VDAC . Any larger molecules, especially proteins, have to be imported by special translocases. Because of its porosity, there is no membrane potential across the outer membrane. By contrast, the inner membrane is a tight diffusion barrier to all ions and molecules. These can only get across with the aid of specific membrane transport proteins, each of which is selective for a particular ion or molecule. As a result of its ion selectivity, an electrochemical membrane potential of about 180 mV builds up across the inner mitochondrial membrane. The inner membrane is where oxidative phosphorylation takes place in a suite of membrane protein complexes that create the electrochemical gradient across the inner membrane, or use it for ATP synthesis.
The biosynthetic reactions that happen in the matrix include those of the citric acid cycle. As each reaction is catalyzed by its specific enzyme, the mitochondrial matrix has a high protein density of up to 500 mg/ml, close to that in a protein crystal. For cryo-ET of intact organelles, the high matrix density has the disadvantage of obscuring internal detail.
Levels Of Organization Of Living Things
Living things are highly organized and structured, following a hierarchy on a scale from small to large. The atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules. A molecule is a chemical structure consisting of at least two atoms held together by a chemical bond. Many molecules that are biologically important are macromolecules, large molecules that are typically formed by combining smaller units called monomers. An example of a macromolecule is deoxyribonucleic acid , which contains the instructions for the functioning of the organism that contains it.
Cell Structure And Function
The basic parts of a cell are cell membrane, cytoplasm, and nucleus.
Cell membrane is also known as the plasma membrane.
The plasma membrane is porous and allows certain substances or materials move both inward and outward.
The central dense round structure in the center is known as nucleus.
The jelly-like substance between the nucleus and the cell membrane is known as cytoplasm.
Different organelles of cells are also present in the cytoplasm such as Mitochondria, Golgi bodies, Ribosomes, etc.
Located in central part, nucleus is almost in spherical shape.
Nucleus is separated from the cytoplasm by a porous membrane known as the nuclear membrane.
The smaller and spherical structure, found inside the nucleus, is known as nucleolus.
Nucleus contains thread-like structures known as chromosomes.
Chromosomes carry genes and help in inheriting the characteristics of the parents to the offspring.
Gene is a fundamental unit of inheritance in living organisms.
The entire constituents of a living cell are known as protoplasm, which include nucleus and cytoplasm.
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What Makes A Function A Function
A function is a relation in which each input has only one output. In the relation , y is a function of x, because for each input x , there is only one output y. x is not a function of y, because the input y = 3 has multiple outputs: x = 1 and x = 2.
Is any function which can be defined?
In mathematics, a rational function is any function that can be defined by a rational fraction, which is an algebraic fraction such that both the numerator and the denominator are polynomials. The coefficients of the polynomials need not be rational numbers they may be taken in any field K.
What is cell function?
The essential functions of the cell include: The cell provides support and structure to the body. It facilitates growth by mitosis. It helps in reproduction. Provides energy and allows the transport of substances.
Examples Of Disorders Related To Mrna Processing
Over 200 diseases are associated with defects in the processing of pre-mRNA to mRNA. Mutations in DNA or splicing machinery majorly affect pre-mRNA splicing accuracy. For example, an abnormal DNA sequence can eliminate, weaken or activate hidden splice sites in pre-mRNA. Likewise if the splicing machinery is not working properly, the spliceosome may cut the pre-mRNA incorrectly regardless of the sequence. These mutations result in the processing of pre-mMRA to mRNAs that will go on to encode malfunctioning proteins. The abnormal mRNAs themselves are also sometimes the targets for nonsense-mediated mRNA decay as well as co-transcriptional degradation of nascent pre-mRNAs. Cells derived from patients with a variety of diseases including progeria, breast cancer and cystic fibrosis display RNA splicing defects, with cancer and neuropathological diseases being the most common.
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Nucleic Acid And Protein Sequence Data Are Accumulating Rapidly
The amount of available information on the primary structure of biological polymers is increasing at an astounding rate. Two decades ago we knew the nucleotide sequence of only a single small nucleic acid, the yeast alanine transfer RNA. We knew the amino acid sequence of fewer than 100 different types of proteins.
Today more than 18 million base pairs of DNA have been sequenced, and the data are accumulating at more than several million bases a year. The first completed sequences were research landmarks. Now sequences are appearing so rapidly that many research journals refuse to publish such information unless it has some particular novel or utilitarian aspects. Indeed, sequence data are currently accumulating faster than we can analyze them, and even faster than we can enter them into the data bases by existing methods.
Dna Is An Dynamic Molecule That Can Switch Between Different Structural States
When the double helix structure for DNA was first announced, it was an instant public success. 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.
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.
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The Folding Problem Now Seems Ripe For Major Advances
The immediate future for the folding problem looks remarkably bright. The development of both fundamental and ad hoc theoretical approaches is advancing rapidly. The correlation and interactions between theory and experiment will be much closer than has generally been true in the past. Combined approaches, with various levels of theory or theory and experiment, seem likely to be the most fruitful. The ability to easily synthesize specific polymers, themselves specifically designed to test theoretical predictions or to provide missing values for parameters, seems particularly promising.
Instrumentation. The solution of the structures of new proteins, and of mutant versions of older proteins, will continue to be of major importance. Thus the development and implementation of new and improved x-ray and neutron diffraction procedures is as important to the folding problem it is as to other areas in structural biology. Improvements in both solid-state and high-resolution NMR will be central to the specification of the unfolded state and the search for definable folding intermediates. Proteins that are isotopically labeled at specific sites will be essential in this process, and they will also permit the study by NMR of substantially larger proteins than can currently be tackled.
Criteria For Life In Cells And Organisms
Order: Cells and parts of cells have a specific order every time. The organelles in a cell are always organised in a similar way. For instance, skin cells are organised in rows.
Reproduction: Cells can produce offspring or new cells, sexually or asexually. In eukaryotes, new cells are formed through mitosis. Prokaryotes usually reproduce through binary fission. On a larger scale, animals reproduce and produce young.
Growth: For example, the growth of a plant from a seed to a tree.
Use of energy: An organism produces energy sources such as ATP, which is needed for various reactions, for example, muscle movement.
Homeostasis: Maintaining stable conditions within a body or cell. The inside of a cell always has a specific pH so that reactions can take place at optimal conditions.
Response to stimuli: Movement and enzyme production. For example, when plants grow in the direction of sunlight, the plant responds to sunlights stimuli. The same happens with unicellular organisms. When a prokaryote encounters a different environment, it responds to those environmental changes by, for example, producing enzymes.
Ability to adapt: Bacteria have not always been resistant to antibiotics this has come through their ability to adapt through genetic mutation.
Cells are considered the building blocks of life because they are the smallest unit to meet these criteria. Even a single-celled prokaryote is considered a living organism.
What Do You Mean Function
function, in mathematics, an expression, rule, or law that defines a relationship between one variable and another variable . Functions are ubiquitous in mathematics and are essential for formulating physical relationships in the sciences.
What is a function easy definition?
Where is function defined?
Explanation: functions can be defined inside a module, a class or another function.
The Major Goal Of Protein Crystallography Is To Show How Proteins Function
The majority of the proteins of known structure are enzymes. When the unique three-dimensional spatial information from the structure is combined with a vast array of observations on the properties of the protein, many of the secrets of how enzymes catalyze chemical reactions are revealed. For example, we know how enzymes can bind certain substrate molecules specifically, how certain amino acid side chains are positioned to act as catalysts, and how the enzyme can change its shape in response to binding the substrate or regulatory molecules. We know that sometimes these shape changes can be transmitted through the structure. We also know how the same structural motifs can be varied in different proteins to produce a series of enzymes with similar mechanism but different substrate specificities. For example, a whole set of proteases have extremely similar active sites, all of which contain an activated serine residue.
. In 1987, the structure of the first membrane assembly involved in photosynthesis, the photoreaction center, was determined. This complex of four proteins converts light energy into an electrical gradient across a membrane . The structure immediately showed the path through the protein that electrons traverse to cross photosynthetic membranes, a key initial step in the conversion of light into chemical energy.
Cartoon of the three-dimensional structure of photoreaction center.
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What Do I Mean When I Use The Structure/function Core Concept
The structure/function core concept is one of five core concepts that Michael and McFarland have described as being ways of looking at the world. They serve as thinking tools used by physiologists when they confront any problem or question about a living organism. These concepts often represent a kind of tacit knowledge knowledge that usually is not openly expressed or taught but is used in practice . This seems an apt description for structure/function for most physiology teachers.
I have used the structure/function core concept in at least five different ways in helping students make sense of physiology. The physiology textbooks referred to above contain descriptions of most of the phenomena I discuss below.
Like the textbook authors cited above, I have used the phrase structure/function in the classroom simply to refer to the fact that to understand the function of a system you must understand structure of that system. It is a signal to the students that both the anatomy and the physiology will be considered as they seek to understand physiology. This is the usual admonition used by physiology teachers and physiology textbook authors. Whether this core concept is of any use to students when left as an admonition is open to question.
However, I have also used structure/function concept in four quite specific ways to assist students in their attempt to master physiology.
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Structure And Function In Biology
Biological structures come about as a species adapts to its environment. The result is an adaptation: a trait that helps the members of a species to survive and reproduce. Adaptation comes about through evolution, which weve looked at briefly in the opening tutorials in this module, and which well study later in this course. But for now, lets look at some structure-function relationships in living things.
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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 . 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.
The Four Types Of Tissues
Epithelial tissue, also referred to as epithelium, refers to the sheets of cells that cover exterior surfaces of the body, line internal cavities and passageways, and form certain glands. Examples of epithelial tissue include skin, mucous membranes, endocrine glands, and sweat glands. Connective tissue, as its name implies, binds the cells and organs of the body together and functions in the protection, support, and integration of all parts of the body. Connective tissue is diverse and includes bone, tendons, ligaments, cartilage, fat, and blood. Muscle tissue is excitable, responding to stimulation and contracting to provide movement, and occurs as three major types: skeletal muscle, smooth muscle, and cardiac muscle in the heart. Nervous tissue is also excitable, allowing the propagation of electrochemical signals in the form of nerve impulses that communicate between different regions of the body .
The next level of organization is the organ, where two or more types of tissues come together to perform specific functions. Just as knowing the structure and function of cells helps you in your study of tissues, knowledge of tissues will help you understand how organs function.
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Structural Motifs Are Repeatedly Used To Carry Out Similar Functions
A structural motif composed of three extended strands and two helical coils of protein, named the nucleotide-binding domain, is found as part of many enzymes that bind nucleotides, such as adenosine triphosphate . Recently, from the nucleotide sequence of the gene encoding a protein associated with bladder cancer in humans, the nucleotide-binding domain was correctly predicted to be part of this protein’s three-dimensional structure.
Another structural motif has been seen in some of the proteins that recognize specific sequences of DNA and consequently regulate genes by turning them off or on. In this instance, two helical coils of protein connected by a short bend form a module that can plug into the major groove of a DNA double helix. The atomic surface of this recognition-helix motif is different in different proteins, imparting to them the ability to recognize and bind tightly to different specific sequences of DNA. As a result, one protein turns on one specific gene, whereas another might turn off another gene. Understanding how this structure functions has allowed scientists to synthesize novel regulators of genetic information.