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It seems safe to assume that the above-quoted pitch of the double helix of DNA corresponds to the free-energy minimum for that molecule. Within a cell, however, the scarcity of room forces the DNA into a strained condition. If the DNA in a bacterium such as *Escherichia coli* was stretched out into a line, it would mea... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.2 Nucleic Acid Conformation: DNA**",
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This leaves an expression for the supercoiling energy that contains only parameters that can be determined by experiment. Indeed, it is possible in principle to derive them by computer simulation, using analytical forms of the various interatomic interactions given in Chapter 3. In practice, such calculations are still... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.2 Nucleic Acid Conformation: DNA**",
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$$\begin{array}{cccccccccccccccccccccccccccccccccccc$$
**Figure 7.3** An amino acid molecule has amine ( NH2) and organic acid (COOH) terminals. The centrally located alpha-carbon provides the point of attachment for a lone hydrogen atom and the side group (R). There are twenty different forms of the latter, and th... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.2 Nucleic Acid Conformation: DNA**",
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At medium pH, both processes occur with high probability, and the resulting zwitterionic form does not favour spontaneous amino acid polymerisation (which thus requires a suitable enzyme)
**Table 7.3** Values for pK for some of the more common amino-acid side groups
| Amino acid | pK (25ºC) |
|------------|--------... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.2 Nucleic Acid Conformation: DNA**",
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The most common of these are the alpha-helix (a-helix) and the beta-sheet (b-sheet). The alpha-helix, as its name implies, is a helical arrangement in which there are 3.6 amino-acid residues per turn (that is to say, per helical pitch). This gives a translation displacement of 0.15 nm along the axis of the helix for ea... | {
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"Header 2": "**7.2 Nucleic Acid Conformation: DNA**",
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It should be noted, in passing, that because
**Figure 7.14** Some restriction enzymes cleave a few of the hydrogen bonds between the bases joining the two strands of DNA, as well as two of the covalent bonds in the backbones. The enzyme of this class known as *Bam H1*, found in *Bacill... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.2 Nucleic Acid Conformation: DNA**",
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In 1940, Max Perutz intrigued his head of department, Lawrence Bragg, by inspired by certain experimental results obtained by Mortimer Anson and Alfred Mirsky, which indicated that the denaturing of a protein could be reversed, under favourable circumstances. As was discussed above, proteins are produced as strings of ... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.5 Protein Folding**",
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We should note the very small magnitudes of these differences, compared with the individual free-energy contributions discussed above.
The melting temperatures referred to above should more strictly be described as the temperatures at which the degree of denaturation is 50%. Recalling our discussion of equilibrium co... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.5 Protein Folding**",
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The restriction enzyme *Hind* III, which is used in genetic engineering, is able to cut the DNA molecule as indicated in the following diagram:
From your knowledge of the strengths of hydrogen and covalent bonds, and from the fact that an enzyme can cu... | {
"Header 1": "**7 Biological Polymers**",
"Header 2": "**7.5 Protein Folding**",
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What is the largest organ in the human body?There are not many people who, if asked that question, would correctly reply: the *skin*. To many, the skin appears to provide a conveniently flexible and watertight, but otherwise inert, container. On the contrary, the skin is a dynamic structure, which supports a variety of... | {
"Header 1": "**8 Biological Membranes**",
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In 1855, Carl Na¨geli noted differences in the rates of penetration of pigments into damaged and undamaged plant cells and concluded that there must be an outer layer with its own special properties. He called it the plasma membrane. In 1897, Wilhelm Pfeffer demonstrated that the membrane is a universal barrier to the ... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
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As we would expect, the mobility of such proteins in the plane of the membrane is low when the lipid molecules are in the ordered state, and considerably higher when the lipid is disordered. Since function might in some cases depend on the mobility of the proteins, it can be important for an organ's function that the d... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
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These two parts, the positions of which are indicated schematically in Figure 8.6, are also referred to as the hydrophobic
$$HO - CH_2 - CH_2 - CH_2 - N^+(CH_2)_3$$
**Figure 8.4** When the X in Figure 8.1 stands for choline the terminal group is related to the molecule shown here
$$CH_{3}-(CH_{2})_{12}-C = C - C ... | {
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"Header 2": "**8.1 Historical Background**",
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At the other extreme, the myelin membranes in the nervous system have a very low protein content (with a 1:10 protein:lipid ratio), and they have the high flexibility consistent with their role as – to put it simply – electrical insulators.
The structure of a membrane is also determined by the surrounding medium, of ... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
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Moreover, because the solubility of the typical hydrocarbon in water is very low, the mutual interaction between hydrocarbon molecules, when they are thus deployed, is negligible, so the activity coefficient is essentially unity (and its logarithm is thus zero). In a solubility experiment, with the pure hydrocarbon in ... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
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The flux from side 1 to side 2 is then given by
$$J_{1\to 2} = PC_1 \exp\left[\frac{-nF(V_{\text{max}} - V_1)}{RT}\right]$$
(8.11)
where F is the Faraday constant and n is the number of unit charges on each solute particle. Once again, we find a rate that is governed by a Boltzmann factor.
As we shall discuss in ... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
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(It is for this reason that the term mesogen is favoured for the substance forming the bilayer, because one might otherwise erroneously assume that a melted liquid crystal is no longer a liquid crystal.) Differential scanning calorimetry is used to study such a bilayer transition, because this is accompanied by a heat ... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
"token_count": 2045,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Medicine* **41**, 439–443.
- Hames, B. D. and Hooper, N. M., (2000). *Biochemistry*, *Second Edition*. BIOS Scientific, Oxford.
- Israelachvili, J. N., (1977). Refinements of the fluid-mosaic model of membrane structure. *Biochim. Biophys. Acta* **469**, 221–225.
- Merz, K. M. and Roux, B., eds., (1996). *Biological Me... | {
"Header 1": "**8 Biological Membranes**",
"Header 2": "**8.1 Historical Background**",
"token_count": 516,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The goal of this chapter is to account for the energy changes in organisms, across the range of sizes from the macroscopic right down to the atomic. We wish to see how energy is gained from the environment, and how it is then utilized by the organism in order to provide the driving force for the various cellular and su... | {
"Header 1": "**9 Biological Energy**",
"token_count": 243,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The unit of energy usually employed in the dietary domain is the calorie (symbol: cal), or the dietician's capitalized Calorie (symbol: Cal), which is equal to one kilo-calorie (i.e. 1Cal = 1000 cal = 1 kilo-calorie = 1 kcal). In 1798, Count Rumford demonstrated the equivalence between thermal and mechanical energy, th... | {
"Header 1": "**9.1 Energy Consumption**",
"token_count": 361,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Our first major task is to get an overall view of how these energy-gaining and energy-consuming processes take place. In Chapter 4, we learned that the energy of vibration that is present in all matter above the absolute zero of temperature is not generally available for bond-rearranging tasks because it is too diffuse... | {
"Header 1": "**9.2 Respiration**",
"token_count": 2035,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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These are produced when there is resonance between different, but equivalent, arrangements of double bonds, the important examples being those found in the chromophores of cytochrome, myoglobin and haemoglobin, and chlorophyll. In the latter (see Figure 9.3), the prosthetic group contains a pyrrole ring of nitrogen ato... | {
"Header 1": "**9.2 Respiration**",
"token_count": 2024,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Indeed, and as we will shortly discover, photosynthesis (and also respiration) involves a series of such intermolecular electron transfers.
Whether or not electron transfer will take place depends upon a quantity known as the redox potential (see Chapter 4), and its entry into the story means that we should pause for... | {
"Header 1": "**9.2 Respiration**",
"token_count": 2011,
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(The chemical details of an analogous cycle which operates during glucose-consuming respiration were elucidated by Hans Krebs.) In contrast to the reactions we have considered thus far, it does not require the contribution of light energy, and it is consequently known as the dark stage. It involves the fixation of CO2 ... | {
"Header 1": "**9.2 Respiration**",
"token_count": 398,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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So much for the Calvin cycle, and indeed for photosynthesis itself. We must now move on to the fascinating mechanism whereby molecules of ATP are produced from molecules of ADP and inorganic phosphate, Pi. This very important reaction is catalysed by ATP synthase, and in 1964 Paul Boyer postulated that the process invo... | {
"Header 1": "**9.2 Respiration**",
"Header 2": "**9.4 ATP Synthesis**",
"token_count": 1994,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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However, the overwhelmingly
**Figure 9.14** Schematic diagram of the electron probability lobes in the water molecule, with no attempt to illustrate their tetrahedral arrangement
**Figure 9.15** A resonance effect causes the double bond in the terminal ... | {
"Header 1": "**9.2 Respiration**",
"Header 2": "**9.4 ATP Synthesis**",
"token_count": 2021,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Structureof the protein subunits in the photosynthetic reaction center of *Rhodopseudomonas viridis* at 3A˚ resolution. *Nature* **318**, 618–624.
- Dyson, R. D., (1974). *Cell Biology: A M olecular Approach* Allyn and Bacon, Boston.
- Elston, T., Wang, H. and Oster, G., (1998). Energy transduction in ATP synthase. *Na... | {
"Header 1": "**9.2 Respiration**",
"Header 2": "**9.4 ATP Synthesis**",
"token_count": 593,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The small sizes of single-cellular organisms such as bacteria make for difficulties of movement. In contrast to the cases of swimming fish and humans, for example, viscosity plays a dominant role. Conversely, inertia is irrelevant; the typical bacterium cannot coast. The situation is governed by what is known as the Re... | {
"Header 1": "**10 Movement of Organisms**",
"Header 2": "**10.1 Bacterial Motion**",
"token_count": 2027,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The actual bending movement of a cilium is caused by the mutual sliding of adjacent microtubule doublets, and by the fact that these are nevertheless
**Figure 10.3** (a) Cross-section of a cilary axoneme, observed by transmission electron microscopy, showing the 9 á 2 arrangement of ... | {
"Header 1": "**10 Movement of Organisms**",
"Header 2": "**10.1 Bacterial Motion**",
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Although the necessary structure determinations have still to be carried out, one could speculate that the flagellum's so-called M ring (see Figure 10.7) is caused to rotate by the local passage of a proton, as would the out-of-gear propeller of an aeroplane by the passing air molecules, during a sufficiently strong wi... | {
"Header 1": "**10 Movement of Organisms**",
"Header 2": "**10.1 Bacterial Motion**",
"token_count": 303,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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A bacterium like *E. coli* is unable to gauge the spatial variation of nutrients in its environment, at any instant, so it procures information by probing its surroundings, through the propulsion provided by its flagellum. In effect, this creature integrates incoming chemical signals during a few-second period of its t... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"token_count": 1013,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The movement of large multicellular organisms, such as ourselves, is achieved through the contraction of muscles, which are themselves composed of numerous specialized cells. These are eucaryotes, of course, so the ultimate control is by ions, just as for the simpler eucaryotic cilia and flagella discussed earlier. How... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"Header 2": "**10.3 Muscular Movement**",
"token_count": 2001,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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An ATP molecule binds to the groove in the myosin head, causing it to separate from the actin filament, and the ATP molecule then breaks down into ADP and inorganic
**Figure 10.12** Structure of the myosin S1 fragment (Protein Data Bank ID: 2MYS; Rayment *et al*., 1993
phosphate, Pi.... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"Header 2": "**10.3 Muscular Movement**",
"token_count": 1942,
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Hill found that his experimental data could be optimally fitted when the following conditions were fulfilled
$$\frac{-a}{\mathcal{F}_0} = \frac{b}{v_{\text{max}}} = \frac{1}{4}$$
(10.13)
Using these relationships, Equation (10.12) can be reduced to what has naturally come to be known as the Hill equation, namely
... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"Header 2": "**10.3 Muscular Movement**",
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As a final point in this discussion of the sliding-filament model, we ought to take a closer look at the diffusion of $Ca^{2+}$ ions invoked to explain the triggering of the molecular movements. The typical skeletal muscle cell has a diameter of about $200\,\mu\text{m}$ (i.e. a radius of about $10^{-2}\,\text{cm... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"Header 2": "**10.3 Muscular Movement**",
"token_count": 534,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Let us close this chapter with an example drawn from life – the present author's life, indeed. He somewhat rashly estimated that he would be able to run up the 50 m high Monument to the fire of London in less than 1 min. This resulted in a wager, which the 75 kg author won, by scaling the tower in just 53 s (and then a... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"Header 2": "**10.4 Human Performance**",
"token_count": 2025,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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*Science* **288**, 95–99.
- Marko, J. F. and Siggia, E. D., (1995). Stretching DNA. *M acromolecules* **28**, 8759–8770.
- Marszalek, P. E., (1999). Mechanical unfolding intermediates in titin molecules. *Nature* **402**, 100–103.
- Nielsen, B. G., (2001). *Computational Issues of Voluntary M ovement: From Neurons to N... | {
"Header 1": "**10.2 Chemical Memory in Primitive Organisms**",
"Header 2": "**10.4 Human Performance**",
"token_count": 576,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The signal-mediating cells of the nervous system are referred to by the name neurons (or sometimes, neurones). They are special, in that they are able to send signals to one another with velocities that greatly exceed those displayed by mere diffusion. Neurons have shapes that differ markedly from those of the body's o... | {
"Header 1": "**11 Excitable Membranes**",
"token_count": 357,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The analytical development of an expression for the resting potential requires several preliminaries, of which the first is a relationship derived by Albert Einstein. We have earlier developed expressions which describe the motion of particles under the influence of concentration gradients, that is to say purely
![](... | {
"Header 1": "**11 Excitable Membranes**",
"Header 2": "**11.1 Diffusion and Mobility of Ions**",
"token_count": 1099,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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We now proceed toward deriving an expression for the resting potential, $V_{\rm rest}$ , and begin by considering the situation in which two different species of ions, positive and negative, denoted by the subscripts + and -, are present. As before, we consider the general situation in which motion is induced by both ... | {
"Header 1": "11.2 Resting Potential",
"token_count": 1873,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The total membrane conductance is simply the sum of the individual conductances (which are, of course, inverse resistances):
$$g_{\text{total}} = \sum_{j} g_{j} \tag{11.21}$$
Figure 11.3 The chemical gradients across the nerve membre of the various ions can be thought of as being equ... | {
"Header 1": "11.2 Resting Potential",
"token_count": 2030,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Journal of Physiology (London)* **128**, 28–60.
- Hodgkin, A. L. and Rushton, W. A. H., (1946). The electrical constants of a crustacian nerve fibre. *Proceedings of the Royal Society ( London)* **B 133**, 444–479.
- Hodgkin, A. L., Huxley, A. F. and Katz, B., (1952). Measurement of current-voltage relations in the m... | {
"Header 1": "11.2 Resting Potential",
"token_count": 394,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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It is frequently justifiable to consider only the axon of a neuron, and perhaps that part of the soma adjacent to the axon (i.e. the axon hillock), as having (protein) ion channels in its membrane. It is these channels which give rise to the resting potential that was discussed in the preceding chapter. It is a reasona... | {
"Header 1": "**12 Nerve Signals**",
"token_count": 221,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The general situation regarding a nerve process will be as shown in Figure 12.1, its length being imagined as being divided up into segments, each having unit magnitude. The conducting medium located inside the process, that is to say the axoplasm, offers a resistance *R*<sup>i</sup> per unit length, while the correspo... | {
"Header 1": "**12 Nerve Signals**",
"Header 2": "**12.1 Passive Response**",
"token_count": 2033,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Indeed, passive cable response underlies what could be called the arithmetic processing that takes place in that region of every neuron.
We must now move on to consider what happens when things are changing as a function of time. In such a case, and despite the fact that the response is still a passive one, we can no... | {
"Header 1": "**12 Nerve Signals**",
"Header 2": "**12.1 Passive Response**",
"token_count": 1696,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Figure 12.4 shows what happens if the depolarization exceeds a certain threshold value. We see that there is a gradual and systematic departure from the asymptotically exponential behaviour observed in Figure 12.3(d), the reaction ultimately being so pronounced that it actually reverses the membrane's polarity. (Indeed... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"token_count": 1974,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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For the potassium conductance, similarly, it was found that
$$g_{K} = n^{4} g_{K, \text{max}}$$
$$\frac{dn}{dt} = \alpha_{n} (1 - n) - \beta_{n} n$$
$$\alpha_{n} = 0.01(V' + 10) / \left( \exp\left(\frac{V' + 10}{10}\right) - 1 \right)$$
$$\beta_{n} = 0.125 \exp\left(\frac{V'}{80}\right)$$
(12.18)
During the p... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"token_count": 1655,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The number of potassium ions transported in the other direction, per square centimetre per action potential, will naturally be the same, because the two types of ion bear the same charge, and because the magnitude
Th
| Fibre | Fibre<br>diameter, μm | ... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"token_count": 2022,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Such a dipole will experience a torque, just as does a magnetic dipole when it is under the influence of a magnetic field. A possible channel-opening mechanism might thus be as follows. The torque acting on the alpha helices when the voltage across the membrane is at its resting value is sufficient to keep the holes cl... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"token_count": 814,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The job of the nervous system is, of course, to mediate the passing of nerve signals from one part of the body to another. The task of an individual neuron is to receive signals via its dendrites and, if the resulting depolarization at the axon hillock is sufficient to exceed the threshold, to pass signals out along it... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"Header 2": "**12.3 The Nervous System**",
"token_count": 2044,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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As mentioned earlier, the post-synaptic membrane possesses chemoreceptors. The highly schematic arrangement shown in Figure 12.10 is composed of four copies of the neuron from Figure 12.9, one of these now being the receiving neuron while the remaining three copies are positioned so as to be able to dispatch neurotrans... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"Header 2": "**12.3 The Nervous System**",
"token_count": 2027,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The structure of the potassium channel: molecular basis of Ká conduction and selectivity. *Science* **280**, 69–77.
Eccles, J. C., (1964). *The Physiology of Synapses*. Springer-Verlag, Berlin.
Fatt, P. and Katz, B., (1951). An analysis of the end-plate potential recorded with an intercellular electrode. *Journal o... | {
"Header 1": "**12.2 Nerve Impulses (Action Potentials)**",
"Header 2": "**12.3 The Nervous System**",
"token_count": 745,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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In 1949, Donald Hebb published a book entitled *The Organization of Behaviour*. It has become one of the pillars of neuroscience, because of the seminal ideas that it contained. One of these was a surprisingly simple theory for the changes that provide the nervous system with the possibility of storing memories. Hebb s... | {
"Header 1": "**13.1 Hebbian Learning**",
"token_count": 2041,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The opposite happens in the case of sensitization, namely an enhancement in the membrane's capacity for allowing the passage of calcium. An additional type of neuron is required, however, to make this feasible. It is called an interneuron. The dendrites of a second sensory neuron are located in the tail, while its ax... | {
"Header 1": "**13.1 Hebbian Learning**",
"token_count": 274,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The feasibility of synaptic modification having thus been established, let us turn to the question of how memories are stored in a network of mutually interacting neurons. In 1961, Karl Steinbuch put forward the idea for a neural network that would display association. His main interest was the possibility of capturing... | {
"Header 1": "**13.2 Neural Networks**",
"token_count": 2027,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Another deficiency is that the network is always being forced to make a choice between alternative stable memories. It cannot merely relax to a condition in which all activity dies away to zero, as is frequently the case in a real neural network. The insights into the basic manner in which a neural network functions ... | {
"Header 1": "**13.2 Neural Networks**",
"token_count": 826,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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A feature of Figure 11.1 which has not been properly touched upon, so far, is the axon collateral. A relatively short distance from the place where the axon leaves the soma (that is to say, the axon hillock), the single axon is frequently observed to branch into two or more strands. When this happens, the main route is... | {
"Header 1": "**13.2 Neural Networks**",
"Header 2": "**13.3 Auto-association**",
"token_count": 2047,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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If we then add the recurrent collaterals, the expression for the output vector acquires an extra term
$$V_{\text{out}}(t + \Delta t) = V_{\text{in}}^*(t)$$
$$V_{\text{out}}(t + 2\Delta t) = [S] V_{\text{out}}^*(t + \Delta t)$$
(13.4)
As noted earlier, the merit of such an auto-associative circuit is that it can r... | {
"Header 1": "**13.2 Neural Networks**",
"Header 2": "**13.3 Auto-association**",
"token_count": 1676,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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One of the present author's favourite cartoons shows two people looking at the elephants in a zoo. One asks the other, rhetorically: 'Did you know that elephants never forget?' After contemplating this for a few moments, the other person retorts: 'Ah, but what would an elephant actually have to remember?' The implicati... | {
"Header 1": "**14 Control of Movement**",
"token_count": 303,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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In Chapter 10, we learned that the smallest creatures, that is to say unicellular animals, move about through the agencies of their cilia and flagella, whereas the larger examples, such as ourselves, move through the flexing of muscles. Indeed, as Charles Sherrington noted: *To move is all mankind can do, and for such,... | {
"Header 1": "**14.1 The Primacy of Movement**",
"token_count": 795,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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By way of illustrating ballistic control, let us consider a grossly simplified situation in which a visually observed obstacle is to be avoided. This example is shown in Figure 14.2, and although the rudimentary visual system depicted does not faithfully reproduce all the biological details, we will find that the figur... | {
"Header 1": "**14.2 Ballistic Control in a Simplified Visual System**",
"token_count": 1975,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The rod receptors (R), which are sensitive to brightness, and the cone receptors (C),
**Figure 14.4** The mammalian retina has a complicated structure that comprises neurons of six different types as indicated in this highly schematic diagram
which monitor contrast, motion, size and ... | {
"Header 1": "**14.2 Ballistic Control in a Simplified Visual System**",
"token_count": 307,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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The strengths of the synapses which connect neurons in the later parts of the animal's nervous system can be modified as the result of experience. In the situation we have been considering here, for example, the occasional bumping into the obstacle by the moving animal would be expected to cause at least mild pain, and... | {
"Header 1": "**14.2 Ballistic Control in a Simplified Visual System**",
"Header 2": "**14.3 More Sophisticated Modes of Control**",
"token_count": 536,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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Nature's way of allowing for this need has been to produce muscle structures which are more complicated than one might have guessed. Figure 10.9 shows the activation of a muscle by a nerve cell, but it is not always the case that the effector cell is directly activated by what could be called a higher centre. In suffic... | {
"Header 1": "**14.2 Ballistic Control in a Simplified Visual System**",
"Header 2": "**14.4 The Heterogeneous Structure of Muscle Fibres**",
"token_count": 848,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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When a sequence of muscular movements is routinely required to be brought into action, as in the case of the rhythmic motion of the legs when a mammal walks, or the rhythmic undulation of the fins when a fish swims, such functions can be delegated to self-contained units known as central pattern generators. Nerve signa... | {
"Header 1": "**14.2 Ballistic Control in a Simplified Visual System**",
"Header 2": "**14.5 Central Pattern Generators**",
"token_count": 1679,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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So far in this chapter, we have invoked only circuits of the feed-forward type. Moreover, nothing has been said about the manner in which the neural networks that control movement become adapted as a result of experience. An animal has to learn which environmental stimuli, and which of its movements, lead to significan... | {
"Header 1": "**14.6 Conditioned Reflexes**",
"token_count": 1696,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
It is usually assumed that sufficiently advanced species possess something more than has yet been discussed in this chapter, namely volition – what is commonly referred to as free will. The vehicle through which free will is exercised is just as commonly taken to be consciousness. And the degree of success with which t... | {
"Header 1": "**14.6 Conditioned Reflexes**",
"Header 2": "**14.7 Volition and Free Will**",
"token_count": 2040,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
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As one can see from the Carpenter-Williams results reproduced in Figure 14.12, which shows how the cumulative probability varies with saccadic latency, that is precisely what is observed, and this provides strong evidence that their model is a good one.
As one can see from Figure 14.12, about 5% of the experimental d... | {
"Header 1": "**14.6 Conditioned Reflexes**",
"Header 2": "**14.7 Volition and Free Will**",
"token_count": 501,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
If we are apprised too late of our intentions to act – as the observations of Benjamin Libet and his colleagues appear to suggest – and if we are not party to the processes underlying our decisions, what use could consciousness possibly serve? It might seem that one promising strategy would be to focus on the issues of... | {
"Header 1": "**14.6 Conditioned Reflexes**",
"Header 2": "**14.8 What Purpose Does Consciousness Serve?**",
"token_count": 2046,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
In the bacterium, therefore, we see a behavioural repertoire that has been telescoped down to a single binary choice: clockwise or anti-clockwise. However, that (unconscious) choice could still be used, logically, as the basis of cognition. The reversal of direction of rotation of the bacterium's flagellum can be regar... | {
"Header 1": "**14.6 Conditioned Reflexes**",
"Header 2": "**14.8 What Purpose Does Consciousness Serve?**",
"token_count": 423,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
The honeybee and the lamprey, which we discussed earlier, do not possess consciousness because their nervous systems lack certain vital components and connections. When a child attempts its first step, prior attainment of the balanced upright position will have involved failed attempts, with attendant pain. What leads ... | {
"Header 1": "**14.9 Passive versus Activein Mental Processing**",
"token_count": 1996,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
The present author knows of no mirror neuron work extended to human observation of birds taking off to fly, but his assumption would be that this activates the same premotor neurons as those galvanized when the person flaps his arms, such action being the closest we come to imitating a bird. However, it cannot be emp... | {
"Header 1": "**14.9 Passive versus Activein Mental Processing**",
"token_count": 228,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
From the above definition of a schema, we see why the motor-planning area and the sensory processing area have to be implicated, but why also the thalamic intralaminar nuclei? They enter into suggestive interactions with several other brain components, including the anterior cingulate (see Figure 14.15), intimately
*... | {
"Header 1": "**14.9 Passive versus Activein Mental Processing**",
"Header 2": "**14.10 The Relevant Anatomy and Physiology**",
"token_count": 2035,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
It captures correlations between all motor patterns and the resulting sensory feedback; and the captured contexts are thereafter available for generalized muscular *navigation*, this naturally including the version employed by the articulatory system in speech.
When is the system updated, so as to incorporate the new... | {
"Header 1": "**14.9 Passive versus Activein Mental Processing**",
"Header 2": "**14.10 The Relevant Anatomy and Physiology**",
"token_count": 1947,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
The premotor and supplementary motor cortices are essentially the higher counterparts of the pattern generators located in the spinal cord, the classic example of which are those found in the lamprey, which we discussed above. The difference is that although a variety of motor patterns can be generated by the latter, t... | {
"Header 1": "**14.11 Intelligence and Creativity**",
"token_count": 1581,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
To the best of the present author's knowledge, this is the first book on biophysics to include discussions of consciousness and biological intelligence.This is reflected in the relatively large number of citations to the writings of other authors, at the end of this chapter. The relevant literature is probably not so a... | {
"Header 1": "**14.11 Intelligence and Creativity**",
"Header 2": "**14.12 A Final Word**",
"token_count": 2043,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
Information processing in dendritic trees. *Neural Computation* **6**, 1031–1085.
- Middleton, F. A. and Strick, P. L., (1994). Anatomical evidence for cerebellar and basal ganglia involvement in higher cognitive function. *Science* **266**, 458–461.
- Milner, B., Petrides, M. andSmith, M. L., (1985). Frontal Lobes and... | {
"Header 1": "**14.11 Intelligence and Creativity**",
"Header 2": "**14.12 A Final Word**",
"token_count": 1089,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
Toward the end of the 19th century, it appeared that most physical phenomena had received reasonably satisfactory explanations, but there were three issues which continued to defy the theoreticians. The first of these stemmed from the failure by Albert Michelson and Edward Morley to detect what was known as the ether d... | {
"Header 1": "**A.1 Quantization of Energy**",
"token_count": 1158,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
Niels Bohr invoked the quantum ideas of Planck and Einstein in his strikingly simple model for the structure of atoms, which explained the above-cited puzzle of the sharp spectral lines. Ernest Rutherford had discovered that almost all the mass of an atom is concentrated in a small region at its centre, the positively-... | {
"Header 1": "**A.1 Quantization of Energy**",
"Header 2": "**A.2 Atomic Structure**",
"token_count": 1341,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
In classical mechanics, as was demonstrated by Isaac Newton, the motion of a particle can be described through an equation linking its mass and acceleration to the force acting on the particle. In 1927, Erwin Schrödinger had been speculating upon the changes to Newton's equation that would be required in view of wave-p... | {
"Header 1": "A.3 The Wave Equation",
"token_count": 1767,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
In classical mechanics, an object travelling with insufficient energy to surmount a barrier will merely be reflected by it. In quantum mechanics, the amplitude of a particle-wave is non-zero everywhere except at a node, and this implies the possibility of simultaneous transmission and reflection. This gives rise to the... | {
"Header 1": "A.4 Quantum Mechanical Tunnelling",
"token_count": 1192,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
#### **B.1** The Hamiltonian
A useful shorthand manner of writing the Schrödinger wave equation employs an operator known as the Hamiltonian, $\mathcal{H}$ (named after William Hamilton), an operator being a prescription for a set of mathematical operations. In Appendix A, we encountered several expressions in whic... | {
"Header 1": "**Appendix B: The Hydrogen Atom**",
"token_count": 415,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
The question of the nature of the allowed quantum states of the hydrogen atom is the most important problem in the field of atomic and molecular structure,
not only because the theoretical treatment of this atom is simpler than that of all other atoms and molecules but also because it forms the basis for the discussi... | {
"Header 1": "**B.2** The Hydrogen Atom",
"token_count": 1902,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
Equation (B.8) has acceptable solutions
$$\Phi_m(\phi) = \frac{1}{\sqrt{2\pi}} \exp(im\phi)$$
(B.13)
if, and only if, the m are positive or negative integers, or zero. The wave function is then single-valued at $\phi = 0$ (which is of course identical with $\phi = 2\pi$ ). The denominator is a normalization cons... | {
"Header 1": "**B.3** Solution of the $\\Phi$ Equation",
"token_count": 2031,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
#### **B.7** Wave Functions
The universally accepted nomenclature uses the numerals 1, 2, 3, and so on to designate the value of the total quantum number, and the letters s, p, d and f for l values of 0, 1, 2, and 3, respectively. These letters are of historical origin, and they refer to the various sets of observe... | {
"Header 1": "**B.3** Solution of the $\\Phi$ Equation",
"token_count": 1170,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
The classical treatment of an ideal gas seeks to relate macroscopically observable properties, such as the volume, temperature and pressure to the microscopic parameters that characterize the individual atomic or molecular motions. Empirical relationships between macroscopic properties had been established, examples be... | {
"Header 1": "**Appendix C: Thermal Motion**",
"Header 2": "**C.1 Ideal Gases**",
"token_count": 1963,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
We thus see that the number N(v) of these molecules, in the above-identified interval will be
$$N(v) = 4\pi v^2 f(v) = 4\pi v^2 A \exp(-\beta v^2)$$
(C.13)
We can determine the unknown constants through consideration of the total number N of molecules and the total kinetic energy $\mathcal{E}_{kin, total}$ . We ha... | {
"Header 1": "**Appendix C: Thermal Motion**",
"Header 2": "**C.1 Ideal Gases**",
"token_count": 2014,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
#### D.1 Bernoulli Trials and the Binomial Distribution
Repeated independent trials (or elements) in which there are only two possible outcomes are known as Bernoulli trials (after Jacob Bernoulli) if the probabilities of the outcomes remain constant. Let those probabilities be p for success and q for failure, which ... | {
"Header 1": "**Appendix D: Probability Distributions**",
"token_count": 871,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
Let us now generalize to the situation in which each element (or trial) in a probability aggregate can have any of *s* distinguishable properties (as in the throwing of dice, for which *s* = 6), rather than just two (as in the tossing of a coin). In the measurement of a property that is continuous (such as macroscopic ... | {
"Header 1": "**Appendix D: Probability Distributions**",
"Header 2": "**D.3 The Normal, or Gaussian, Distribution**",
"token_count": 1125,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
A differential equation is one in which differential coefficients of various orders occur, together with functions of both the independent and dependent variables, but no arbitrary constants. The order of a differential equation is the highest order of derivative that is present, while the degree of a differential equa... | {
"Header 1": "**Appendix E: Differential Equations**",
"token_count": 1170,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
| Adrian, Edgar 3<br>Alder, Berni 115 | Bragg, William 2, 59<br>Bravais, Auguste 84, 85 |
|-----------------------------------------------|----------------------------------------------------|
| Altman, Sidney 134 | Bray, Dennis 214 |
| Andersen,... | {
"Header 1": "Name Index",
"token_count": 1928,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
165 Jaenicke, Rainer 151 Jeannerod, Marc 330 Jeans, James 344 Josephson, Brian 3 Joule, James 80 Kandel, Eric 278, 281, 294 Karle, Jerome 93 Karplus, Martin 115, 153 Katz, Bernard 273, 274 Kellermayer, Miklos 231 Kelvin, Lord 48, 365 Kendrew, John 2, 146 Keynes, Richard 245, 262 Kinnunen, Paavo 182 Kinomura, Shigeo 323... | {
"Header 1": "Name Index",
"token_count": 1889,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
J.) 3, 7, 86, 345 Thomson, William 48 Tilney, Lewis 213 Tiselius, Arne 2, 131
van der Waals, Johannes 21, 29, 30, 181, 184, 369 van't Hoff, Jacobus 57, 154 Velmans, Max 315, 326 Verlet, Loup 114 Vineyard, George 115 Volta, Alessandro 64 von Frisch, Karl 322
Wagner, Allan 312 Wainwright, Thomas 115 Wald, George 271 ... | {
"Header 1": "Name Index",
"token_count": 302,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
| A-bands | amygdala |
|--------------------------------|--------------------------------------|
| 221 | 330 |
| absolute temperature | anabolic processes |
| 365 ... | {
"Header 1": "**Subject Index**",
"token_count": 11714,
"source_pdf": "datasets/websources/biochem/Introduction_of_Biophysics.pdf"
} |
**NINA PARKER, SHENANDOAH UNIVERSITY MARK SCHNEEGURT, WICHITA STATE UNIVERSITY ANH-HUE THI TU, GEORGIA SOUTHWESTERN STATE UNIVERSITY BRIAN M. FORSTER, SAINT JOSEPH'S UNIVERSITY PHILIP LISTER, CENTRAL NEW MEXICO COMMUNITY COLLEGE**
#### **OpenStax**
Rice University 6100 Main Street MS-3... | {
"Header 1": "**Microbiology**",
"Header 3": "SENIOR CONTRIBUTING AUTHORS",
"token_count": 1429,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
| Preface 1 | |
|----------------------------------------------------------------------------|----|
| Chapter 1: An Invisible World<br> | 15 |
| 1.1 What Our Ancestors Knew ... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Table of Contents**",
"token_count": 3316,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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*Microbiology* is licensed under a Creative Commons Attribution 4.0 International (CC BY) license, which means that you can distribute, remix, and build upon the content, as long as you provide attribution to OpenStax and its content contributors.
Because our books are openly licensed, you are free to use the entire ... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Preface**",
"Header 3": "**About OpenStax Resources Customization**",
"token_count": 433,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
The scope and sequence of *Microbiology* has been developed and vetted with input from numerous instructors at institutions across the US. It is designed to meet the needs of most microbiology courses for non-majors and allied health students. In addition, we have also considered the needs of institutions that offer mi... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Preface**",
"Header 3": "**Coverage and Scope**",
"token_count": 661,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
Microbiology is produced through a collaborative publishing agreement between OpenStax and the American Society for Microbiology Press. The book has been developed to align to the curriculum guidelines of the American Society for Microbiology.
#### **About ASM**
The American Society for Microbiology is the largest ... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Preface**",
"Header 3": "**American Society of Microbiology (ASM) Partnership**",
"token_count": 1295,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
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#### **OpenStax** *Microbiology* **Correlation to ASM Recommended Curriculum Guidelines for Undergraduate Microbiology Education**
#### **OpenStax** *Microbiology* **Correlation to ASM Curriculum Guidelines**
| Chapter | ASM Curriculum Guidelines | |
|-------------... | {
"Header 1": "WOULDN'T THIS LOOK BETTER ON A BRAND NEW IPAD MINI?",
"Header 2": "**Preface**",
"Header 3": "**American Society of Microbiology (ASM) Partnership**",
"token_count": 1107,
"source_pdf": "datasets/websources/biochem/Microbiology-LR.pdf"
} |
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