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Bioenergetics This branch of biophysics studies the physics of energy flow in living systems. Bioenergetics is concerned with all levels and branches of biophysics, from the environment, to the organism, to the cell, and to the molecules within the cell.
At the core of bioenergetics is the study of how organisms and cells obtain the energy they need to carry out biological processes. This includes where the energy comes from, how the energy is stored, how the energy is converted into various forms, and where and how excess or unusable energy is released.
While every branch of biophysics needs to be concerned with energy, some biophysicists specialize in understanding the energetics of any biological process, 19 B i o p h y s i c s D e mys tifie d whether the process is protein folding, DNA unwinding, respiration, or energy flow in the environment.
Thermodynamics Very closely related to bioenergetics is the study of thermodynamics. The laws of thermodynamics describe how energy behaves in physical systems, biological or otherwise.
The first law of thermodynamics states that energy cannot be created or destroyed. The second law of thermodynamics states that in a closed system the orderliness of the system can never increase, but can only decrease over time. At first glance, because living things are so complex and highly organized and because they have the ability to stay organized, it would appear that living things may somehow violate the laws of thermodynamics, particularly the second law.
But living things are not closed systems. They interact with their environment.
Yet as recently as the s many scientists continued to consider the possibility that living things do not behave according to the laws of physics, at least as we know them. The Physical Aspects of the Living Cell, he speculated that we may yet discover new laws of physics at work in living things that are not apparent in the inorganic world. However, decades of exhaustive thermodynamic and physical studies of living things only confirm that organisms follow the same laws of physics found in the nonliving universe.
Statistical Mechanics Statistical mechanics is the application of probability and statistics to large populations of molecules. Although it is impossible to measure the exact energy or state of every one of the trillion billion molecules in a test tube or cell, it is possible to develop models of how those molecules behave mechanically. A model in our case is a mathematical description of how the molecules move, how much energy they have, how they change shape, and so on.
The model is then used to calculate the statistical probability of an event, for example, the probability of a protein molecule undergoing a shape change needed for its function.
Once the probabilities are known, they can be used to calculate statistical averages for the entire sample that is, for the entire population of molecules in the test tube or cell. These statistical averages, in turn, can be associated with Chapter 2 B i o p h y s i c a l T o p i c s specific things that we can measure. For example, the statistical averages can be used to calculate and predict thermodynamic quantities such as temperature, pressure, and amount of energy released or absorbed.
In this way, even though it is impossible to directly measure what each and every molecule is doing, statistical mechanics allows us to interpret the things we can measure in terms of what specific molecules are doing. The interpretation is not direct knowledge, but we can design experiments so that the results either support or disprove our interpretation of what the molecules are doing.
This is an important point in biophysics and in science in general. Obviously we want experiments to agree with our ideas of how the physical universe behaves.
If we design an experiment to disprove our model and it fails to do so, this is a stronger support of the model than an experiment designed to agree with the model. Kinetics This branch of biophysics deals with measuring the rate or speed of biological processes such as biochemical reactions, conformational transitions, and binding or unbinding of biomolecules. Kinetics is closely related to energetics and thermodynamics.
Thermodynamics tells us whether a given process or biochemical reaction will occur. Kinetics tells us how fast it will occur. We learn this about a process by studying its thermodynamics. Think of a ball rolling down a hill. The ball has higher potential energy at the top of the hill and moves to a state of lower potential energy at the bottom of the hill. So the process of a ball rolling down a hill is spontaneous. However, the rate at which a process occurs is related to the energy path of a process.
That is, does the energy decrease gradually or does it drop quickly?
Does the energy only decrease throughout the process, or does it decrease and increase and then decrease perhaps multiple times during the process? How fast a ball rolls down a hill, for example, depends on 1 how steep the hill is, 2 whether there are any increases in steepness or flattening out along the way, 3 the presence, height, and slope of any speed bumps, and 4 any other 21 22 B i o p h y s i c s D emys tifieD obstacles along the way. If a process goes through intermediate steps along the way from its start to its end and one or more intermediate steps are higher in energy for example, rolling up a speed bump , these are called high-energy intermediates.
The presence of high-energy intermediates, like speed bumps, tends to slow a process down. One example of this is DNA replication, discussed in Chapter In order to replicate, the DNA double helix needs to unwind temporarily.
This is a higher energy state for the DNA. Once it is replicated, the DNA goes back to its double helical state, which is a lower energy state. Thus, the unwound double helix is the high-energy intermediate in the process of DNA replication.
Living systems often regulate their biological processes by modulating the rate at which they happen. Then, when the organism needs the process to continue for example, it now needs more of the protein , it simply speeds up the rate at which the process is happening. When an organism needs to modulate the rate at which a process happens, typically this is done in one of two ways: either by providing the energy needed to get over a speed bump high-energy intermediate or by providing an alternative path effectively removing or going around the speed bump.
Sometimes a faster path one without a speed bump is provided by a conformational transition, by ligand binding, or by the binding of proteins acting as catalysts. A protein called helicase binds to the DNA and unwinds the double helix. In part, the binding energy contributes to the energy needed to attain the high-energy intermediate the unwound DNA. The end result is the same, you are on the other side of the hill, but the path is different.
For example, when a cell needs to manufacture a certain protein, it connects together hundreds of smaller molecules to make the protein. In addition to this, the cell typically needs to make hundreds or even thousands of copies of the protein. The time it takes to get all people over the hill can be very slow if only some of the people have enough energy to hike over the hill.
The others are tired and hungry. We have two choices to speed up the process of getting people to the other side of the hill.
We can either provide the energy they need to get over the hill carry them, or feed them , or we can remove the fence a conformational change and provide an alternative path around the hill. Biophysicists studying kinetics also develop models to describe the molecular mechanism of a process. This is similar to the use of models in statistical thermodynamics, we have discussed. The model is a hypothesis as to what the molecular mechanism is that causes some process.
Each possible model implies a particular energy path for the process. The model may also suggest or imply a means for changing the reaction rate, by modifying various conditions of the experiment in a way that would alter some part of the mechanism in a known way.
Experiments measuring the rates of biological processes under various conditions can then either support or refute the model.
If the rate is successfully altered as the model suggests, this lends support to the correctness of the model. If not, then the model is proven wrong, and we need to come up with a better model to explain the process.
In this way we can arrive at a molecular interpretation of a biological process by measuring the rate of that process. A motor is a special type of machine that also has the ability to convert potential energy into mechanical energy, that is, into a mechanical force or motion.
So the difference between an ordinary machine and a motor is that, in the case of a motor, the force being changed does not come from outside the machine, but is generated by the machine the motor itself. The motor can continue to generate mechanical force as long as it has a source of potential energy or fuel needed to do so. Living things are full of machines and motors. For example, our muscles use our bones as levers to redirect and in some cases magnify or decrease the forces they apply.
Muscles themselves are motors; muscle fibers have the ability to convert chemical potential energy from the food we eat into the mechanical force of muscle contraction. These are hairlike projections on the surface of some cells that move, allowing the cell to swim.
For example, cilia on the inner surface cells of the lungs help clean the lungs by moving dust and other particles up and out of the lungs. These are longer, whiplike structures that stick out from the body of some cells and move to propel the cell forward. Some cells move by temporarily pushing out on their mem- brane at one or more locations, changing the shape of the cell and causing the cell to crawl along. Secretory cells have various mechanisms for packaging and moving the substances they make.
When a cell is get- ting ready to divide, it first duplicates its chromosomes. Flagella are whiplike projections that propel the cell forward. Each flagellum is a molecular machine embedded in the cell membrane. Courtesy of Wikimedia Commons. For example, the motion generated by muscle contraction, at the lowest level, results from individual molecules of one protein myosin binding to and pushing against the molecules of another protein actin.
Allosterics Often we find that binding in one part of a molecule affects activity in another part of the same molecule. Allostery allows two things to take place: allosteric regulation and cooperativity.
The control of a biological process by a cell or organism is called regulation. That part is known as the active site of the protein.
Many biological processes involve binding or some other interaction between molecules at the active site. Sometimes regulation of a process is achieved through binding somewhere other than the active site. Stan Gibilisco. Phyllis Dutwin. Annie Heminway. Steve Blake. Rhonda Huettenmueller. Bonita Kramer. Sid Kemp. Andrew Sleeper. Home Contact us Help Free delivery worldwide.
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