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ENZYMES
ENZYMES

... - the substrates A-F are not limited to one pathway, they may participate in multiple reaction mechanisms in the cell. Simple Collision Theory - in a chemical reaction, what actually occurs in order for reactants to make products? The answers can be found using collision theory. - molecules are alwa ...
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Computers_in_chemistry - University of St Andrews
Computers_in_chemistry - University of St Andrews

... mechanics needed to simulate a chemical reaction. Nonetheless, molecular dynamics is very important for understanding shape changes, interactions and energetics of large molecules. ...
Unit 7 Packet
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... Just as there are patterns in the way elements bond and the types of compounds they make, there are patterns in the way chemical bonds are rearranged in a reaction. These patterns make it easier to predict the outcome of a chemical reaction. Below are 5 useful reaction patterns. Look at the examples ...
CAD_issue_#3 - University of Illinois Archives
CAD_issue_#3 - University of Illinois Archives

... dynamic of the mechanism's evolution; beyond that into the evolution of (all or most) biological macromolecules; then to the evolution of biological entities (and processes?) at all its organizational levels; and (see CAD issue #2) finally into the evolutionary nature of the Universe itself (not to ...
Mass-Action Ratios!
Mass-Action Ratios!

... above its "resting" or Keq state, equilibrium can be regained by shifting the reactions to the right (glucose is shipped out, or glycolysis is continued). Similarly, if Glu-1-P builds up, it is too restrictive to simply say the phosphoglucomutase reaction will shift right, when equilibrium can be re ...
Citric acid Cycle Remake - Study in Universal Science College
Citric acid Cycle Remake - Study in Universal Science College

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Single Replacement Reactions - Tri
Single Replacement Reactions - Tri

... • The obituary stated "The merchant of death is dead" and went on to say, "Dr. Alfred Nobel, who became rich by finding ways to kill more people faster than ever before, died yesterday.” • In reality the newspaper had instead confused Alfred for his brother who had passed away. ...
Ministry Strand: Quantities in Chemical Reactions Teacher
Ministry Strand: Quantities in Chemical Reactions Teacher

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... Making and testing theoretical models The German scientist Emil Fisher introduced the lock and key model in 1890. Daniel Koshland suggested the induced-fit model in 1959 in the US. The conformational changes predicted by Koshland’s model were subsequently observed using high-resolution X-rays analy ...
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Chapter 7 - Chemical Quantities

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I can - Net Start Class

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Template for calculating the ΔH° in a multiple step chemical reaction
Template for calculating the ΔH° in a multiple step chemical reaction

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Circuit Engineers Doing Biology

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Enzymes A simulation of Invertase Activity

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3-D STRUCTURE PREDICTION OF AQUAPORIN-2, VIRTUAL SCREENING AND IN-SILICO
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... vasopressin binds to the cell surface vasopressin receptor which activates a signalling pathway that causes the aquaporin 2 containing vesicles to fuse with the plasma membrane so that aquaporin 2 can be used by the cell 2. Water flows through the membranes of all living cells by two distinct mechan ...
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Glycolysis: Derived from Greek words

... ATP is the end product of glycolysis as well as it is substrate for PFK-1. In presence of high concentration of ATP, ATP binds to inhibition site of PFK, and thereby decreases the activity of enzyme. AMP, ADP and Fructose 2, 6 biphosphate act as allosteric activators of this enzyme. Activation of en ...
Thermochemistry Questions
Thermochemistry Questions

... • The specific heat of octane, C8H18(l), is 2.22 J/g⋅K. a) How many J of heat are needed to raise the temperature of 70.0g of octane from 11.2∘C to 26.0∘C? b) Which will require more heat, increasing the temperature of 1 mol of C8H18(l) by a certain amount or increasing the temperature of 1 mol of H ...
Non-covalent binding of fullerenes and biomolecules at surface
Non-covalent binding of fullerenes and biomolecules at surface

... interactions, such as electrostatics forces, hydrogen bonds, van der Waals forces, or metal coordination. Recently several examples have shown that supramolecular systems with open voids can be fabricated from self-assembly of simple molecular components at liquid–solid or vacuum–solid interfaces, w ...
Slide 1
Slide 1

... ATP is the end product of glycolysis as well as it is substrate for PFK-1. In presence of high concentration of ATP, ATP binds to inhibition site of PFK, and thereby decreases the activity of enzyme. AMP, ADP and Fructose 2, 6 biphosphate act as allosteric activators of this enzyme. Activation of en ...
Can we model DNA at the mesoscale - HAL
Can we model DNA at the mesoscale - HAL

... This review includes a discussion on the theoretical approaches intending to provide a quantitative analysis of DNA fluctuations, but, as this topic is very broad, it concentrates on two particular cases: the two-state Poland-Scheraga model [3] and the Peyrard-Bishop-Dauxois (PBD) mesoscopic approac ...
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A New Qualitative Simulation Environment for Molecular Biology
A New Qualitative Simulation Environment for Molecular Biology

... using kinetics and differential equationsin a quantitative simulator. However,for manybiological processes detailed quantitative information is not available, only qualitative or fuzzy statements about the nature of interactions. In a previous paper we have shownthe applicability of qualitative reas ...
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Multi-state modeling of biomolecules

Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour of biological molecules or complexes that can adopt a large number of possible functional states.Biological signaling systems often rely on complexes of biological macromolecules that can undergo several functionally significant modifications that are mutually compatible. Thus, they can exist in a very large number of functionally different states. Modeling such multi-state systems poses two problems: The problem of how to describe and specify a multi-state system (the ""specification problem"") and the problem of how to use a computer to simulate the progress of the system over time (the ""computation problem""). To address the specification problem, modelers have in recent years moved away from explicit specification of all possible states, and towards rule-based formalisms that allow for implicit model specification, including the κ-calculus, BioNetGen, the Allosteric Network Compiler and others. To tackle the computation problem, they have turned to particle-based methods that have in many cases proved more computationally efficient than population-based methods based on ordinary differential equations, partial differential equations, or the Gillespie stochastic simulation algorithm. Given current computing technology, particle-based methods are sometimes the only possible option. Particle-based simulators further fall into two categories: Non-spatial simulators such as StochSim, DYNSTOC, RuleMonkey, and NFSim and spatial simulators, including Meredys, SRSim and MCell. Modelers can thus choose from a variety of tools; the best choice depending on the particular problem. Development of faster and more powerful methods is ongoing, promising the ability to simulate ever more complex signaling processes in the future.
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