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In eukaryotic cells, replication, or synthesis of new DNA, is intimately linked to the cell cycle, which serves to prepare the cell for division. The cell cycle is a series of stages that is stringently regulated to ensure that cell division occurs only when appropriate.
The cell cycle can be represented as a circle.... | {
"Header 1": "The Eukaryotic Cell Cycle",
"token_count": 1887,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
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But if there is an enzyme that maintains chromosomes at the same length, why do they get shorter? That's because the magic of telomerase is active primarily in our egg and sperm cells and in stem cells, which are a stock of undifferentiated cells. Our somatic cells, with few exceptions, make little to no telomerase, ev... | {
"Header 1": "**Aging**",
"token_count": 843,
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Information can be degraded through mutation—that is, changes in the DNA sequence—or by damage to the DNA molecule.
One way that DNA sequence can be changed is if mistakes are made while replicating DNA. And while proofreading by DNA polymerases reduces the incidence of such errors greatly, not all mistakes that are ... | {
"Header 1": "DNA MISMATCH AND EXCISION REPAIR",
"Header 2": "**Sources of Mutation and Damage to DNA**",
"token_count": 313,
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The integrity of information in DNA is compromised when DNA polymerases incorporate the wrong nucleotide into the new strand and the proofreading system does not detect it. One way this might happen is by the transient formation of isomers of the bases, in which some of the atoms mediating hydrogen bonding temporarily ... | {
"Header 1": "**Mismatch Repair**",
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Cells have a set of proteins that deals with UV-damaged DNA. This system, called the nucleotide excision repair (NER) system, also fixes damage from environmental chemicals, such as those found in tobacco smoke and automobile exhaust.
These carcinogenic chemicals include molecules that can attach themselves to bases.... | {
"Header 1": "**Excision Repair**",
"token_count": 942,
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Each individual has 2 sets of chromosomes, one inherited from each parent—23 chromosomes from the mother and 23 from the father. In both sexes, the cells that make the eggs or sperm undergo a special kind of cell division called meiosis. This reduces 2 sets of 23 chromosomes to one set of 23, resulting in what is calle... | {
"Header 1": "Cell Division",
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All the swaps and recombination take place within some very clear rules about what's permitted and what's not. The genes on each chromosome are all organized the same way, and that organization doesn't change. Chromosome 1 from your grandfather carries the same genes, in the same places, as chromosome 1 from your grand... | {
"Header 1": "**Swapping and Recombination**",
"token_count": 352,
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Many of the same proteins that are responsible for recombination are used for another crucial cellular function: the repair of double-strand breaks in DNA.
Double-strand breaks are among the most dangerous forms of damage that happen to DNA. When a DNA molecule is broken on both strands, the 2 pieces of double-strand... | {
"Header 1": "**DNA Repair**",
"token_count": 450,
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Recombination also helps generate the enormous variety of antibodies we need to fight off invaders like bacteria and viruses. Antibodies are defense proteins made in vertebrates that bind tightly and very specifically to targets like microorganisms or foreign molecules. The binding of antibodies to the intruders direct... | {
"Header 1": "**Antibody Creation**",
"token_count": 267,
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For both recombination and repair, the similarity of sequences is what allows the initial base pairing of the broken strand with one of the strands of the intact DNA. Homologous recombination, then, is based on sequence similarity.
On the other hand, the cell's crude repair of double-strand breaks in DNA using nonhom... | {
"Header 1": "**Antibody Creation**",
"Header 2": "**Gene Inactivation and Editing**",
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The copying of RNA is catalyzed by an enzyme called RNA polymerase. Unlike DNA polymerases, cells don't have so many different kinds of RNA polymerases. Prokaryotes have only one; humans have 3.
Transcription, like DNA replication, involves building a string of nucleotides across from a DNA template using the base-pa... | {
"Header 1": "Copying RNA",
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The synthesis process is essentially the same for all types of RNA. It is also the same as the addition of nucleotides for making DNA. As with DNA replication, RNA synthesis only advances in the 5ʹ to 3ʹ direction.
One important difference between DNA polymerases and RNA polymerases is ... | {
"Header 1": "**Making RNA**",
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The process of making RNA is essentially the same in eukaryotes as it is in prokaryotes. The differences are external to the synthesis process. Eukaryotic DNA exists as chromatin, where the DNA is tightly associated with histones and other proteins, increasing the complication of the process. Such packaging of DNA must... | {
"Header 1": "**Transcription in Eukaryotes**",
"token_count": 1217,
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The first thing that's needed for protein production is the instructions in mRNA. Bacterial mRNAs come off the DNA template ready to use. In eukaryotic mRNAs, the 5ʹ end has a special nucleotide cap and the 3ʹ end has a polyA tail, both of which signal to the ribosome that this is an mRNA.
The part of the mRNA coding... | {
"Header 1": "TRANSLATING RNA",
"Header 2": "**Inventory for Protein Production**",
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The main steps of protein synthesis are very similar
In bacteria, a modified methionine called formyl methionine is the first amino acid, but that makes no significant difference to the process.
The ribosome has 2 subunits, a small and a large. When assembled, the ribosome has 3 spots for a tRNA: the amino acyl (... | {
"Header 1": "TRANSLATING RNA",
"Header 2": "**Inventory for Protein Production**",
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That's it for joining amino acids together. But functional proteins are more than strings of amino acids. The process of folding as well as covalent modifications may help them take on various 3-dimensional shapes. Covalent modifications can include the addition of phosphates or molecules like sugars or lipids before p... | {
"Header 1": "**Protein Delivery**",
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Bacteria are marvels of efficiency from a biochemical standpoint. Their genomes are compact. Genes are often clustered in convenient groups such that genes that need to be expressed at the same time are next to each other. This physical proximity allows them to be controlled as a single unit through a single promoter. ... | {
"Header 1": "**Prokaryotic Gene Expression**",
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In addition to regulating transcription in eukaryotes by opening or tightly packing chromatin, there are enzymes that can modify the DNA itself, adding methyl groups at specific places.
In our DNA, for example, enzymes called DNA methyl transferases can add methyl groups onto cytosines that are next to guanines in a ... | {
"Header 1": "**Prokaryotic Gene Expression**",
"Header 2": "**Epigenetic Control**",
"token_count": 395,
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In addition to transcription, there are other steps in gene expression at which cells can regulate which proteins get made in cells.
Eukaryotic mRNAs must be spliced to remove introns, noncoding regions within the protein-coding information in the transcript, and join the exons to make a continuous coding sequence. B... | {
"Header 1": "**Gene Expression after Transcription**",
"token_count": 752,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
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**33**
enetic diseases arise from mutations in our DNA. Sometimes, they affect a single gene, as in sickle cell anemia. Other times, a combination of mutations in different genes may be the cause, as in familial tendencies to develop heart disease or mood disorders. In other cases, because mitochondrial DNA is differ... | {
"Header 1": "HUMAN GENETIC DISEASE ` AND GENE THERAPY",
"token_count": 387,
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Hemophilia is a sex-linked bleeding disorder that affects males disproportionately. Some people with hemophilia bleed internally even without any injury.
Queen Victoria of England famously passed hemophilia to one son and through 2 daughters to no fewer than 9 additional male descendants.
Hemophilia comes mostly in... | {
"Header 1": "HUMAN GENETIC DISEASE ` AND GENE THERAPY",
"Header 2": "**Hemophilia**",
"token_count": 639,
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People with cystic fibrosis (CF) suffer from a buildup of thick mucus in various parts of the body. Mucus is normally produced by the body to protect and lubricate airways and the lining of the digestive system. But in cystic fibrosis, the mucus becomes so thick that cysts and fibrous material form in the body, giving ... | {
"Header 1": "**Cystic Fibrosis**",
"token_count": 711,
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In 2018, Alzheimer's disease affected 5.7 million people in the US. Of these, 5.5 million had the more common late-onset Alzheimer's, which is seen in people past the age of 65, while the remaining 200,000 had the early-onset form, which strikes before then. Early-onset Alzheimer's is associated with mutations in genes... | {
"Header 1": "**Alzheimer's Disease**",
"token_count": 659,
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You get all of your mitochondrial DNA from your mother, which was passed down from her mother, etc.—all the way back up the maternal lineage, with the only changes due to mutation.
Most people don't think of mitochondria in connection with genetic disease, but mitochondria have their own genomes. In humans, it's a do... | {
"Header 1": "**Alzheimer's Disease**",
"Header 2": "**Leber Hereditary Optic Neuropathy**",
"token_count": 778,
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There are many different kinds of cancer, but one thing all types of cancer have in common is unregulated cell division. That contrasts with regulated cell division, which converted us from a single-cell fertilized egg to adulthood. Regulated cell division also helps replace worn-out cells and is essential to healing f... | {
"Header 1": "**Unregulated Cell Division**",
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More than one kind of gene encodes green-light proteins for cell division. The green lights include
- w genes for growth factors that signal cells to divide,
- w genes for receptors of the growth factors, and
- w genes for signaling proteins that pass on the directive to divide.
Any of these genes that encode green... | {
"Header 1": "**Proto-Oncogenes**",
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One way to treat cancer is to use agents that target rapidly dividing cells. Dividing cells need large amounts of DNA nucleotides to replicate their DNA, so drugs that interfere with nucleotide biosynthesis can starve these cells of the building blocks they need.
The downside of such treatments is that cancer cells a... | {
"Header 1": "**Proto-Oncogenes**",
"Header 2": "**Approaches to Treating Cancer**",
"token_count": 771,
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he term *biotechnology* loosely refers to any combination of biology and technology, but modern biotechnology usually refers to the more specific application of biomolecular knowledge about the underpinnings of life. Molecular biology has given scientists and engineers the ability to manipulate the recipes written in o... | {
"Header 1": "BIOTECHNOLOGY, STEM CELLS, SYNTHETIC BIOLOGY",
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There are 2 things that are special about stem cells: They are capable of dividing indefinitely (that is, as long as the organism is alive), and they are undifferentiated.
When a stem cell divides, the new cells may differentiate, or they may remain as part of the stock of stem cells.
In the earliest stages of embr... | {
"Header 1": "**Stem Cells**",
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In a related technique, somatic cell nuclear transfer, sometimes called therapeutic cloning, the aim is not just producing undifferentiated stem cells, but an entire organism. As the name suggests, this method uses the nucleus from a somatic cell.
The nucleus of the somatic cell is extracted for placement inside an u... | {
"Header 1": "**Therapeutic Cloning**",
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Let's say that instead of moving a single gene, we want the output of an entire metabolic pathway. DNA and the genetic code happily supply us with a single protein, but when the desired output is not a single protein, we are likely to need an entire metabolic pathway of enzymes to make molecules so that we can collect ... | {
"Header 1": "**Therapeutic Cloning**",
"Header 2": "**Designer Genomes**",
"token_count": 983,
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The arrival of omics started with genomics, which was itself spawned by the completion of the Human Genome Project in 2003. That massive undertaking determined the order, or sequence, of every base in the human genome.
One of the benefits of this project was the development of ways to sequence DNA that are a million ... | {
"Header 1": "**Genome Sequencing**",
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Scientists are also cataloging single-nucleotide polymorphisms (SNPs), which are specific places in genome sequences where a single nucleotide differs between groups of people—for example, an A is replaced by a C. An SNP is a point mutation, but one that is found in many individuals, not just one person. SNPs are dotte... | {
"Header 1": "**Genome Sequencing**",
"Header 2": "**Cataloging Variations in Genomes**",
"token_count": 1078,
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Transcriptomics analyzes transcripts—that is, RNAs—on a genome-wide level. This allows us to know exactly which genes are being copied into RNA under different conditions. For example, it is possible to identify all the genes transcribed in response to treatment of cells with a hormone or to compare the global transcri... | {
"Header 1": "**Transcriptomics**",
"token_count": 292,
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Besides studying genomes and transcriptomes, researchers also analyze complete collections of proteins with proteomics. All of the proteins that are in a particular cell type or tissue can be extracted, separated, and identified.
Differences in protein profiles between normal and cancerous cells may provide clues to ... | {
"Header 1": "**Other Omics**",
"token_count": 499,
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#### [LECTURE 1](#page-21-0)
- 1 Elements needed for making biomolecules must be able to make multiple bonds and/or share electrons to make covalent bonds. The 6 most abundant ones—carbon, hydrogen, oxygen, phosphorus, sulfur, and nitrogen—meet at least one of these criteria. Other abundant elements on Earth, such as... | {
"Header 1": "**Answers**",
"token_count": 2040,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
That, in fact, is why you kill germs by washing your hands with soaps: You denature proteins they need to survive.
- 2 The inaccuracies are that they often do not show the unsaturated fatty acids, which have bends in them that break up the regular structures often depicted.
3 Skin color is a factor. People with darke... | {
"Header 1": "**Answers**",
"token_count": 2018,
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When enzymes that break down LDL receptors are active, they decrease the number of receptors and thus decrease the number of LDLs removed from the blood, allowing LDL levels to be higher. If the enzymes that break down the receptors are blocked, then there are more receptors to take in LDLs, so LDL levels in the blood ... | {
"Header 1": "**Answers**",
"token_count": 2025,
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If there were a limit on the capacities of these pathways, then mixtures of fructose and glucose, such as high-fructose corn syrup or sucrose, would be better than either pure fructose or pure glucose, depending on which pathway had the capacity limit.
- 1 Although catalytic RNAs can catalyze some reactions, they pro... | {
"Header 1": "**Answers**",
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For example, consider the following sequence:
| AAG | ACA | GCC | UGG | UAC | GUG | CAU | (no deletion) |
|-----|-----|------------------------------------|-----|-----|-----|-----|-------------------|
| LYS | THR | ALA | TRP | TYR | VAL | HIS | ... | {
"Header 1": "**Answers**",
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Ahern, K., and I, Rajagopal. *Biochemistry Free and Easy*. DaVinci Press, 2012. [http://www.davincipress.com/freeforall.html.](http://www.davincipress.com/freeforall.html)
Ahern, K., I. Rajagopal, and T. Tan. *Biochemistry Free for All*. DaVinci Press, 2016.<http://www.davincipress.com/freeforall.html>.
Al-Karadagh... | {
"Header 1": "**Bibliography**",
"token_count": 2021,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Pross, A. *What Is Life? How Chemistry becomes Biology*. Oxford University Press, 2012.
Quackenbush, J. *The Human Genome: Book of Essential Knowledge*. Random House, 2011.
Ralston, A. "Environmental Mutagens, Cell Signaling and DNA Repair." *Nature Education* 1, no. 1 (2008): 114.
Robinson, P. K. "Enzymes: Pri... | {
"Header 1": "**Bibliography**",
"token_count": 841,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
26: [Muffet/Flickr/CC BY 2.0;](#page-31-0) 48: [Ramin Herati/Wikimedia Commons/Public Domain;](#page-53-0) 101: [karandaev/Getty Images](#page-106-0); 193: [luza studios/iStock / Getty Images Plus](#page-198-0); 218: [ooyoo/E+/Getty](#page-223-0) [Images;](#page-223-0) 242: [FredFroese/iStock/Getty Images Plus](#page-... | {
"Header 1": "**Image Credits**",
"token_count": 411,
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Meyer B. Jackson University of Wisconsin Medical School
#### CAMBRIDGE UNIVERSITY PRESS
Cambridge, New York, Melbourne, Madrid, Cape Town, Singapore, São Paulo
Cambridge University Press
The Edinburgh Building, Cambridge CB2 8RU, UK
Published in the United States of America by Ca... | {
"Header 1": "Molecular and Cellular Biophysics",
"token_count": 366,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
| Preface | | page xii |
|---------|-----------------------------------------------------------------------|----------|
| | Acknowledgements | xiv |
| | Chapter<br>1<br>Global<... | {
"Header 1": "Molecular and Cellular Biophysics",
"Header 2": "Contents",
"token_count": 3470,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Debye–Hu¨ ckel screening | 297 |
| | 11.10 Polyelectrolyte solutions II. Counterion-condensation | 300 |
| | 11.11 DNA melting | 302 |
| Chapter | 12<br>Fluctuations | 307 |
| 12.1 | Deviations from the mean ... | {
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"Header 2": "Contents",
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I have tried to present the subject of biophysics from a conceptual perspective. This needs to be stated because biophysics is too often defined as a collection of physical methods that can be used to study molecular and cellular biology. This technical emphasis often fosters narrowness, and in the worst cases leads to... | {
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"Header 2": "Preface",
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The relation between structure and function is central to molecular biology. But molecular structure can mean different things, especially when dealing with complex biological molecules. One can know the chemical structure of a molecule, how the atoms are connected by covalent bonds, but have no idea of the conformatio... | {
"Header 1": "Global transitions in proteins",
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"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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One often has to switch between molecular and molar energy units, and this is usually easy if we keep track of whether we are using k or R. To have some sense for energy magnitudes on the molecular versus the molar scale, consider the value of kT and RT for a physiological temperature of 300 K: $kT = 4.11 \times 10^{-... | {
"Header 1": "Global transitions in proteins",
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Thermal denaturation has been studied extensively in an effort to determine how different forces contribute to the stability of the native, folded state of a protein. These forces will be discussed in more detail in Chapter 2, but for the present purposes, these kinds of experiments provide a good illustration of how g... | {
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"Header 2": "1.4 Lysozyme unfolding",
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(1.9) gives
$$\Delta G^{o} = \Delta H^{o} + T \frac{\partial \Delta G^{o}}{\partial T}$$
(1.16)
Rearranging and dividing by $T^2$ leads to
$$\frac{1}{T}\frac{\partial \Delta G^{o}}{\partial T} - \frac{\Delta G^{o}}{T^{2}} = -\frac{\Delta H^{o}}{T^{2}} \tag{1.17}$$
from which we obtain what is known as the Gib... | {
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"Header 2": "1.4 Lysozyme unfolding",
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The steepness is then related to $\Delta V^{\mathrm{o}}$ , just as the steepness of a thermal transition is related to $\Delta H^{\mathrm{o}}$ . Continuing the analogy with thermal transitions, in a multisubunit protein, $\Delta V^{\mathrm{o}}$ will be multiplied by a cooperative unit reflecting the degree to which... | {
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"Header 2": "1.4 Lysozyme unfolding",
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A more convenient form for this expression can be obtained by replacing $RT/\alpha$ by a new parameter, $V_s$ , and $\Delta G_{vi}{}^o/RT$ by $-V_0/V_s$
$$P_{o} = \frac{1}{1 + e^{(V - V_{o})/V_{s}}} \tag{1.28}$$
These new parameters are very useful in that they represent well defined properties of a voltage... | {
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"Header 2": "1.4 Lysozyme unfolding",
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The voltage-gated channels are a very large superfamily of proteins. They form channels that are closed at negative voltages and open at positive voltages. This superfamily includes channels that are selective for Na $^+$ , K $^+$ , and Ca $^{2+}$ , and they all have some common structural features. One of these is a ... | {
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"Header 2": "1.9 The voltage sensor of voltage-gated channels",
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(1.30) gives
$$P_{o} = 1 / \left( \frac{[AA]}{[BB]} + \frac{[AB]}{[BB]} + \frac{[BA]}{[BB]} + 1 \right)$$
$$= \frac{1}{1 + 2e^{(\Delta G_{vi}^{o} + \alpha V)/RT} + e^{2(\Delta G_{vi}^{o} + \alpha V)/RT}}$$
(1.32)
Note that [BB]/[AA] = [AB]/[AA] times [BB]/[AB] from Eq. (1.30). The denominator of Eq. (1.32) is a c... | {
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Let's take an extreme case so that we have the best chance of observing an effect. We take one of the force constants as very high, so $1/\phi_a$ will be near zero. If the other force constant, $\phi_b$ , is small, then the factor multiplying $V^2$ will be large.
To estimate a reasonable value for $\phi_b$ , we... | {
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In Chapter 1 the global conformation of a protein was treated like a black box, without worrying about the internal machinations. This approach is useful in interpreting many kinds of experiments, but if we want to make use of detailed structural information about a macromolecule, we have to open up the black box and l... | {
"Header 1": "Molecular forces in biological structures",
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One of the fundamental tenets of electricity is that point charges interact with a potential energy that is inversely proportional to the distance of separation, r, and directly proportional to the product of the two charges, q<sup>1</sup> and q2. This is Coulomb's law:
$$U = \frac{q_1 q_2}{\varepsilon r} \tag{2.1}$$... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.1 The Coulomb potential",
"token_count": 1996,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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For transfer of a sodium ion with r ¼ 0.95 ¯ from water, where " ¼ 80, to a hydrocarbon medium where " ¼ 2, the potential energy difference is 0.15 10-<sup>12</sup> erg. This works out to a very large energy of 85 kcal mole-1 . This is a reasonable result because inorganic ions
Fig: 2:1: Hydration enthalpy for differ... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.1 The Coulomb potential",
"token_count": 2049,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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#### 2.4 | Charge-dipole interactions
Charge is generally not distributed uniformly within a molecule, and this enables uncharged molecules to interact by electrical forces. One way to deal with these interactions is to introduce the idea of the electrical dipole, defined as two equal and opposite charges set a fix... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.1 The Coulomb potential",
"token_count": 2050,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The origin is rather complex, so this force is referred to as a cation- $\pi$ interaction rather than with a specific electrostatic term such as quadrupole or induced dipole.
The amino acids phenylalanine, tyrosine, and tryptophan have aromatic side chains with the capacity for cation– $\pi$ interactions. These ami... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.1 The Coulomb potential",
"token_count": 2031,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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This ordering of vicinal water can be explained by noting that water cannot form strong hydrogen bonds (Section 2.10) with hydrocarbon. To maintain energetically favorable hydrogen bonding, water must straddle a hydrophobic surface (Fig. 2.7). This restricts the orientations of water molecules and lowers the entropy (S... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.1 The Coulomb potential",
"token_count": 1297,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Hydrogen atoms have a unique chemical property of being able to form bridges between pairs of electronegative atoms (typically oxygen or nitrogen). The standard theory of chemical bonding allows the hydrogen atom to form only a single covalent bond, but in a hydrogen bond a hydrogen atom shares its electron with two bo... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.10 Hydrogen bonds",
"token_count": 2028,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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#### 2.11 Steric repulsions
Two objects cannot occupy the same space at the same time, and the result is steric repulsions. The origin of this force is the Pauli exclusion principle, which states that two electrons cannot have the same quantum state. This leads to a very steep rise in energy when the electron shell... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.10 Hydrogen bonds",
"token_count": 2044,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Since **x** in Eq. (2.19) is composed of the x, y, and z coordinates for each atom, a molecule with N atoms is represented by a vector with 3N dimensions. The matrix **A** must therefore have 3N eigenvalues (Section A2.3). However, not all of these eigenvalues will reflect deformations of the molecule. There are thre... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.10 Hydrogen bonds",
"token_count": 2045,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Thus, the variable strengths of hydrogen bonds between different atoms, in different geometries, and in different environments can produce a significant drive for protein folding in some but not all proteins. Water-water hydrogen bonds appear to be stronger than water-protein and intramolecular protein hydrogen bonds. ... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.10 Hydrogen bonds",
"token_count": 1814,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Molecular forces determine the conformation and behavior of oligonucleotides, single-stranded polynucleotides (e.g. RNA), and doublestranded polynucleotides (e.g. DNA) (Bloomfield et al., 1974; Record et al., 1981). The three most important interactions in nucleic acids are (1) stacking interactions between the aromati... | {
"Header 1": "Molecular forces in biological structures",
"Header 2": "2.15 Stabilizing forces in nucleic acids",
"token_count": 2031,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The idea of a global state was introduced in Chapter 1 as a way of looking at the behavior of a large molecule without getting bogged down in details. Here we will face the details head on, examining the vast variations of microstates, and in the process gaining some insight into the nature of certain types of global s... | {
"Header 1": "Conformations of macromolecules",
"token_count": 1586,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The denominator in Eqs. (3.4a) and (3.4b) is the sum of the Boltzmann weights of all the configurations of n-butane. Recall that this is how the partition function is defined in statistical mechanics (Section 1.1). More generally, for a molecule with n states the partition function is
$$Q = \sum_{i=1}^{n} e^{-E_i/RT}... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2035,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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(3.17) of the form $\mathbf{r}_n \cdot \mathbf{r}_{n+1}$ are now $l^2 \cos \theta$ . This is a straightforward trigonometric result. The angle between adjacent segments is always $\theta$ , so averaging over $\theta$ is not necessary. To evaluate $\overline{\mathbf{r}_n \cdot \mathbf{r}_{n+2}}$ , we divide $\ma... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2035,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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models are referred to as *ideal chains*, and the more realistic but approximate models that incorporate attractive and excluded volume interactions are referred to as *nonideal chains*.
For the excluded volume effect a number of approximate treatments indicate that the rms end-to-end distance is proportional to a ... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 1984,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The molecule will form a loop when the end has a position near x = y = z = 0 as
$$P_N(0)dxdydz = (2\pi Nl^2)^{-3/2}dxdydz$$
(3.33)
Of course, the actual probability of two ends being within a certain distance will depend on the size of an arbitrary volume element, $\delta x \delta y \delta z$ . But for a given val... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2018,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
Such plots are referred to as Ramachandran plots, after the originator of this approach (Ramachandran and Sasisekharan, 1968). An example is shown in Fig. 3.4 for a peptide containing alanine. The contours enclose regions where $\psi$ and $\phi$ are allowed, i.e. not excluded by steric repulsions.
In the case of ... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2006,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
Thus, using eight rotational states per residue is probably an overestimate, and computer modeling studies of unfolded proteins gave estimates of 1.5 to 3 (Dinner and Karplus, 2001).
The large entropy decrease that occurs when a protein folds into its native state raises an interesting question about how much time fo... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 1998,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Similarly, the mean number of helical residues is the average of i
$$\bar{i} = \frac{\sum_{i,j} i\omega_{i,j} s^i \sigma^j}{\sum_{i,j} \omega_{i,j} s^i \sigma^j}$$
(3.39)
Differentiating Eq. (3.38), dividing, and comparison with Eq. (3.39) (in the same manner used to obtain Eq. (3.11)) provides a useful expression ... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2023,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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(3.40) to obtain the average fraction of helix as
$$\frac{\overline{i}}{N} = \frac{s}{N} \frac{\partial \ln Q}{\partial s} = s \left( \frac{1 + \frac{s - 1 + 2\sigma}{\sqrt{(1 - s)^2 + 4\sigma s}}}{1 + s + \sqrt{(1 - s)^2 + 4\sigma s}} \right)$$
(3.52)
This gives us an expression for the extent of the transition as... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2050,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Side chains are tightly packed in an *a*-helix, which means that large flexible side chains will lose rotational freedom. This explains why, for example, alanine has a higher helical propensity than valine (Aurora et al., 1997). The alanine side chain has no conformational entropy to lose, but the valine side chain doe... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2038,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Higher ratios of H-residues favor collapse into compact structures, but there are then many such compact states with the same minimum energy. On the other hand, at high ratios of P-residues sequences will not fold into a compact configuration, but will assume extended configurations to solvate the P-residues. The optim... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 2024,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Evaluate this quantity at T ¼ 0 K, T ¼ 298 K, and in the limit T! 1.
- 3. Calculate the probability of finding a chain of n-pentane with no gauche bonds, and with only one gauche bond.
- 4. Use Eq. (3.19) to determine an explicit value for leff of polyethylene assuming that it is a freely rotating chain.
- 5. Use Eq.... | {
"Header 1": "3.2 Configurational partition functions and polymer chains",
"token_count": 418,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The preceding chapters treated molecules as isolated entities. Now we will look at how molecules interact with one another. In biological systems molecules are continually binding together and coming apart. Molecular associations are the first step in most forms of biological signaling, as well as in enzyme catalysis. ... | {
"Header 1": "Molecular associations",
"token_count": 2027,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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One of the most important examples of a cooperative association is $O_2$ binding to hemoglobin. Each of the four subunits of hemoglobin binds $O_2$ at an iron-heme binding site. Plots of binding site occupancy versus oxygen tension are sigmoidal; Hill plots give a value of n = 2.7. However, hemoglobin has four su... | {
"Header 1": "Molecular associations",
"token_count": 1987,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
If the ith contact contributes an energy "i, then the contribution of contacts to the binding free energy could be approximated by the sum
$$\Delta G_{\rm ct}^{\ o} = \sum_{i} \varepsilon_{i} \tag{4.15}$$
For hydrogen bonds, " might be taken from Tables 2.1 and 2.2. If the contacts obeyed the Lennard–Jones potentia... | {
"Header 1": "Molecular associations",
"token_count": 454,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
We take the partition function of a molecule, denoted by Q (Section 1.1), and break it down into various terms
$$Q = q_{ct}q_tq_rq_vq_{cf}q_s \tag{4.16}$$
where qct denotes the contributions of intermolecular contacts just discussed, q<sup>t</sup> denotes the translational contribution, q<sup>r</sup> denotes the ro... | {
"Header 1": "Molecular associations",
"Header 2": "4.5 Statistical mechanics of association",
"token_count": 2032,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The result is $(h^2/(2\pi mkT))^{3/2}$ (McQuarrie, 1976; Hill, 1960; Moore, 1972), where m is mass and h is Planck's constant. This gives us the translational partition function for a molecule in a volume V, as
$$q_{\rm t} = V \left(\frac{2\pi mkT}{h^2}\right)^{3/2} = \frac{V}{\Lambda^3} \tag{4.23}$$
Denoting the... | {
"Header 1": "Molecular associations",
"Header 2": "4.5 Statistical mechanics of association",
"token_count": 2032,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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This follows the same strategy used for the translational contribution, and gives an expression for the rotational factor in Eq. (4.16) (McQuarrie, 1976; Hill, 1960; Moore, 1972)
$$q_{\rm r} = \pi^{1/2} \left( \frac{8\pi I_x kT}{h^2} \right)^{1/2} \left( \frac{8\pi I_y kT}{h^2} \right)^{1/2} \left( \frac{8\pi I_z kT}... | {
"Header 1": "Molecular associations",
"Header 2": "4.5 Statistical mechanics of association",
"token_count": 2039,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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We take the molecular weight of a typical ligand as 100 Da and use this value for $\mu$ . Inserting these values for $\mu$ and $\phi$ into Eq. (4.32) tells us that $q_v$ for a single mode can range from 3.7 to 6.3. For six such modes we have
$$\Delta G_{\rm v}^{\ 0} = -RT \ln (q_{\rm v}^{\prime 6}) = -4.6 \tex... | {
"Header 1": "Molecular associations",
"Header 2": "4.5 Statistical mechanics of association",
"token_count": 2022,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Thermodynamic and structural data have been examined in an effort to test these ideas (Spolar and Record, 1994). The translational and rotational contributions were each estimated with the aid of formulas similar to Eqs. (4.25) and (4.30). A hydrophobic entropy term was estimated from the hydrocarbon areas coming int... | {
"Header 1": "Molecular associations",
"Header 2": "4.5 Statistical mechanics of association",
"token_count": 1972,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
The importance of molecular associations in biological signaling processes was mentioned in the preceding chapter. That chapter concentrated on the physical aspects of the association process and paid little attention to the signaling events that are initiated by ligand binding. This chapter will accept the binding eve... | {
"Header 1": "Allosteric interactions",
"token_count": 2016,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
This means that we can assume $Y_0$ is very small, so the value of A at [L] = 0 will be close to zero; $Y_1$ is very large, so the value of A at high [L] approaches one. These points lead to a useful simplification of Eq. (5.4). First, multiply the numerator and denominator by $Y_0$
$$A = \frac{Y_0 + [L]K_R Y_0}... | {
"Header 1": "Allosteric interactions",
"token_count": 2027,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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We can pursue this point a bit further and try to visualize the process in more detail with a simple sketch (Fig. 5.2). Here we see that in the T state there are more contacts within the protein, and fewer contacts between the protein and ligand. In the R state the situation is reversed. There are more protein–ligand... | {
"Header 1": "Allosteric interactions",
"token_count": 2044,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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In these cases models with a third allosteric state have been proposed (Tucek, 1997).
#### 5.6 Binding site interactions
A major goal of allosteric theory is to provide a mechanism for how the occupation of a protein binding site can influence distant parts of the protein. To illustrate this, consider a single-subu... | {
"Header 1": "Allosteric interactions",
"token_count": 1314,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The focus until now has been on proteins with a single subunit. However, the early efforts in allosteric theory were motivated by a desire to understand cooperative processes in multisubunit proteins. The idea that an allosteric transition in a multisubunit protein can lead to cooperativity was introduced by Monod et a... | {
"Header 1": "Allosteric interactions",
"Header 2": "5.7 The Monod–Wyman–Changeux (MWC) model",
"token_count": 2043,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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Because the assumption of concerted binding is unrealistic, the Hill coefficient cannot be equated with the actual number of binding sites. The MWC model is more realistic because it allows different numbers of binding sites to be occupied. Thus n in this model is a real estimate of the number of subunits. It should th... | {
"Header 1": "Allosteric interactions",
"Header 2": "5.7 The Monod–Wyman–Changeux (MWC) model",
"token_count": 1494,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
The preceding section made the point that the MWC model depends on the assumption that the G<sup>b</sup> <sup>o</sup> of binding and the G<sup>o</sup> of the allosteric transition are additive. We can refer to this form of additivity as macroscopic, because the microscopic details are ignored. Now we will consider the ... | {
"Header 1": "Allosteric interactions",
"Header 2": "\\*5.10 Macroscopic and microscopic additivity",
"token_count": 2037,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
The enzyme shows a steep cooperativity in the absence of a regulatory molecule. As an effector is added, $Y_0$ ' decreases or increases. The allosteric transition then becomes easier or harder for ligand binding to induce, and the concentration of substrate needed to induce the transition changes accordingly. The enzy... | {
"Header 1": "Allosteric interactions",
"Header 2": "\\*5.10 Macroscopic and microscopic additivity",
"token_count": 2034,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
5.12), and both $P_1$ and $P_2$ have the same multiplicity, so
$$\frac{[P_2]}{[P_1][L]} = K_s \tag{5.30}$$
Finally, for the third step there is a removal of two unfavorable contacts, so j is reduced by two. There are three sites that can lose ligand so the multiplicity factor is 1/3.
$$\frac{[P_3]}{[P_2][L]} ... | {
"Header 1": "Allosteric interactions",
"Header 2": "\\*5.10 Macroscopic and microscopic additivity",
"token_count": 1348,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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X-ray crystallography has produced structures of hemoglobin crystallized in the presence and absence of oxygen (reviewed by Perutz et al., 1998). This work indicates that the allosteric transition disrupts contacts, mostly salt bridges, between the subunits. Breaking these contacts allows the subunits to shift their po... | {
"Header 1": "\\*5.14 The Szabo–Karplus (SK) model",
"token_count": 2045,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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The SK model provides a natural way to deal with this property. The original SK model could describe most of the results available at that time. Subsequent studies indicated that the *a* and *b* subunits had somewhat different affinities. Further, as noted above, the intrinsic component of the binding affinity, reflect... | {
"Header 1": "\\*5.14 The Szabo–Karplus (SK) model",
"token_count": 565,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
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In the fluid world of biology, molecules are often free to move at random. We will now study the nature of this random motion. This will provide insight into the rates of change in many processes. In this chapter we take our first look at kinetics. The previous chapters all dealt with systems at equilibrium. We asked h... | {
"Header 1": "Diffusion and Brownian motion",
"token_count": 2040,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
Figure 6.1 shows how C(x, t) evolves through time. As expected, the diffusing material spreads out as time passes. The curves remain centered at x = 0 for all time, with C(0, t) going down as diffusion progresses. The curve at t = 0.01 illustrates how the function approaches a delta function as $t \to 0$ .
An impo... | {
"Header 1": "Diffusion and Brownian motion",
"token_count": 2021,
"source_pdf": "datasets/websources/biochem/Cambridge_University_Press_Molecular_and_Cellular_Biophysics.pdf"
} |
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