L1-intro - Lecture notes 1 PDF

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notes on the introductory material for the course...

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Chemistry 558

Fung

Introduction Physical Chemistry Study of principles and methods that explain the properties of molecules, and the reactions of these molecules. Thermodynamics, kinetics, quantum mechanics, statistical thermodynamics, etc. are all based on PRINCIPLES OF ELECTROSTATICS. HOW? Biochemistry Study of the chemical processes and chemical transformations in living organisms. Study of the STRUCTURE AND FUNCTION of cellular components, such as proteins, carbohydrates, lipids, nucleic acids, and other biomolecules.

Biophysical Chemistry/Biophysics Use physical principles and methods to study of the properties of biomolecules and the reactions of these biomolecules. Biophysics is divided into three topic areas: molecular structures, biophysical techniques, biological mechanisms.

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Chemistry 558

Fung

The hierarchical organization of biological structures.

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Chemistry 558

Fung

Systems are very large to handle. Often too many molecules for detailed studies. Physics

Temperature, pressure, mass, force .....

101 parameters

Chemistry Chemical composition, reaction .........

102 parameters

Biology

103 parameters

Biomolecules, metabolic reactions, cells, tissues .....

Sociology 104 parameters ******************************************************************** DIVIDE & CONQUER 1. Use a smaller system as a MODEL first. 2. Observe only one part of the system at a time. 3. Compare differences between two systems that are almost identical. 4. Isolate discrete state of the system. Start with basic electrostatic principles, explain how living systems work. Electrostatic principles allow us to understand molecular interactions quantitatively. 3

Chemistry 558

Fung

What is an interaction? http://cen.acs.org/articles/92/i38/Pushing-Limits-Chemical-Bonding.html

In 2013, researchers used atomic force microscopy

see intricate details of intermolecular interactions to

of 8-hydroxyquinoline on a copper surface; C = gray, H = white, O = red, N = blue. (http://www.sciencemag.org/content/342/6158/611.full)

What do you “see”? Is that interaction?

Where atoms are!

http://en.wikipedia.org/wiki/Interaction

Interaction is a kind of action that occurs as two or more objects have an effect upon one another. The idea of a two-way effect is essential in the concept of interaction, as opposed to a one-way causal effect. A closely related term is interconnectivity, which deals with the interactions of interactions within systems: combinations of many simple interactions can lead to surprising emergent phenomena. Interaction has different tailored meanings in various sciences. All systems are related and interdependent. Every action has a consequence. Fundamental Interactions http://en.wikipedia.org/wiki/Fundamental_interaction

In physics, fundamental interactions (sometimes called interactive forces) are the ways that the simplest particles in the universe interact with one another. An interaction is fundamental when it cannot be described in terms of other interactions. 4

Chemistry 558

Fung

The four known fundamental interactions are electromagnetism, strong interaction, weak interaction & gravitation. Electromagnetism is the force that acts between electrically charged particles. This phenomenon includes the electrostatic force acting between charged particles at rest, and the combined effect of electric & magnetic forces acting between charge particles moving relative to each other. Electromagnetism describes almost all macroscopic phenomena of everyday experience, ranging from the impenetrability of solids, friction, rainbows, lightning, and all human-made devices using electric current, such as television, lasers, and computers. Electromagnetism fundamentally determines all macroscopic, and many atomic level, properties of the chemical elements, including all chemical bonding. Electromagnetic forces are tremendously stronger than gravity but conspire to cancel out so perfectly that for large bodies gravity can dominate. What happen if they are not cancelled? How do they conspire to cancel out? When are they not cancelled? ***************************************

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Chemistry 558

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http://cen.acs.org/articles/88/i33/Reviving-Antibiotic-Target.html

“Novel” binding interaction Novel interaction?! “..X-ray crystallography of DNA gyrase interacting with a substrate fragment (a small DNA double helix) and GSK299423 revealed that the agent binds at a different site than quinolone drugs do...”

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