Molecular reaction dynamics
This package, written in 1998, includes interactive questions and demonstrations on the dynamics of chemical reactions. The aim is to show the effect of the potential energy surface, on reaction rates.
It is intended for third or fourth year undergraduates in Chemistry.
To download, click on View Download and follow the instructions. To uninstall, use the standard Windows option of “Add or Remove Programs”.
The Hill Reaction: In Vitro and In Vivo Studies
For many students, light-driven electron-transport can be abstract and with little utility. To provide additional ways of visualizing this process, this series of exercises is designed (1) to show that the light-reactions of photosynthesis are proportional to light intensity and can be monitored in isolated chloroplast-particles, (2) to demonstrate that chlorophyll, in solution, traps and re-emits light by fluorescence, and (3) to observe increases in chlorophyll fluorescence in intact green-alg
Teaching Reaction Equilibrium Using Stella Modeling Software
Equilibrium of biochemical reactions is seldom taught in introductory biology labs. However, equilibrium is an excellent topic for the introduction of simple mathematical modeling into the lab curriculum. When properly done, modeling can allow an exploratory, hands-on approach to equilibrium, as well as teach a valuable application of mathematics. Stella modeling software facilitates the exercise by allowing students to construct sound models without dwelling on mathematical details. This exerci
Atomic Structure, Molecular Formulae from the course Introduction to Chemistry
Introduction to Chemistry - Fall 2006. This course covers topics such as stoichiometry, ideal and real gases, acid-base and solubility equilibrium, oxidation-reduction reactions, thermochemistry, introduction to thermodynamics, the atoms and elements, and the periodic table.Streaming video of this course available at webcast.berkeley.edu/courses.
Atomic Structure/Molecular Formulae
Chem 1A: Introduction to Chemistry - Fall 2006. Stoichiometry, ideal and real gases, acid-base and solubility equilibrium, oxidation-reduction reactions, thermochemistry, introduction to thermodynamics, the atoms and elements, and the periodic table. Streaming video of this course available at webcast.berkeley.edu/courses.
Assembly of Proteins in Membranes II from the course General Biochemistry and Molecular Biology
General Biochemistry and Molecular Biology - Fall 2006. This course covers molecular biology of prokaryotic and eukaryotic cells and their viruses. Mechanisms of DNA replication, transcription, translation. Structure of genes and chromosomes. Regulation of gene expression. Biochemical processes and principles in membrane structure and function, intracellular trafficking and subcellular compartmentation, cytoskeletal architecture, nucleocytoplasmic transport, signal transduction mechanisms, and c
Assembly of Proteins in Membranes I from the course General Biochemistry and Molecular Biology
General Biochemistry and Molecular Biology - Fall 2006. This course covers molecular biology of prokaryotic and eukaryotic cells and their viruses. Mechanisms of DNA replication, transcription, translation. Structure of genes and chromosomes. Regulation of gene expression. Biochemical processes and principles in membrane structure and function, intracellular trafficking and subcellular compartmentation, cytoskeletal architecture, nucleocytoplasmic transport, signal transduction mechanisms, and c
A Manual of Online Molecular Biology Techniques
This is a collection of tried-and-true technique descriptions used in teaching postgraduate students in the Department of Molecular & Cell Biology at UCT.
602 Sextillion: Reaction Stoichiometry
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Action-Reaction! Rocket
Students construct a rocket from a balloon propelled along a guide string. They use this model to learn about Newton's three laws of motion, examining the effect of different forces on the motion of the rocket.
Using Molecular Weight
A previous tutorial shows how to calculate the molecular weight of a substance from the atomic weights given. On this page, we use the molecular weight to convert between the macroscopic scale (grams of a substance) and the microscopic scale (number of molecules of that substance).
Molecular Genetics Explorer
With the Genetics Tool, you can:
* Cross two organisms
* Self-cross one organism
* Create mutant versions of one organism
With the Biochemistry Tool, you can:
* Look at the structures and colors of the pigment proteins found in one organism
* Design proteins and observe their shapes and colors
* Compare the amino acid sequences of different pigment proteins
With the Molecular Biology Tool, you can:
* Look at the DNA, mRNA and protein sequences of pigment protein gen
Using Molecular Weight
A previous tutorial shows how to calculate the molecular weight of a substance from the atomic weights given. On this page, we use the molecular weight to convert between the macroscopic scale (grams of a substance) and the microscopic scale (number of molecules of that substance).
Reaction Stoichiometry
Reaction stoichiometry allows us to determine the amount of substance that is consumed or produced by a reaction. The following video considers the first part of this: how much of a reactant is consumed in a chemical reaction. Product formation is discussed elsewhere.
Finding the Empirical Formula from a Molecular Formula
Elemental analysis is a useful qualitative analysis technique since it allows us to check if a sample is consistent with a given molecular formula. For instance, suppose we believe our sample is benzene (C6H6). We can compare the following:The empirical formula (CH) obtained from the molecular formula of benzene (C6H6); The empirical formula obtained from a elemental analysis of the sample. If the two empirical formulae do not agree, then the sample is not benzene. If the formulae agree, then ou
Calculating Molecular Weight
The molecular weight is the mass of one mole of a substance. Usually, the units used for this are grams per mole. In this movie, we show how to calculate the molecular weight of a substance from the atomic weights given on the periodic table. On another page, we use the molecular weight to convert between the macroscopic scale (grams of a substance) and the microscopic scale (number of molecules of that substance).
The Scientific Method: An Introduction Using Reaction Time
Reaction time has many advantages for the introduction of the scientific method--the subject is familiar, many experiments are possible, and students enjoy competition. In our Introductory Biology courses, our students formulate and test a hypothesis about reaction time. We use Kosinski's Reaction Time software, that records reaction times and then analyzes them statistically using the chi-square median test. Students then write a paper that either rejects or fails to reject their null hypothesi
Computational Chemistry: An Introduction to Molecular Dynamic Simulations
This module gives a brief overview of computational chemistry, a branch of chemistry concerned with theoretically determining properties of molecules. The fundamentals of how to conduct a computational project are discussed as well as the variety of different models that can be used. Because of the difficulty of dealing with nanosized materials, computational modeling has become an important characterization tool in nanotechnology.
DNA-a Molecular Identity
In Lesson 1, students learn about what DNA is and several different DNA typing techniques. In Lesson 2, students examine three different situations where DNA typing was used to carry out justice. Students also identify and evaluate different uses of DNA typing techniques and its possible benefits and misuses.
Molecular Stepping Stones
A molecular approach to biology must develop in students an understanding of molecules, their interactions and the consequences of these interactions. Biological phenomenon now more than ever rely on chemical and physical principles for molecular explanations of the phenomenon. We have selected 10 physical-chemical principles that underlie many biological processes: we call them "Molecular Stepping Stones." Below are links to entry level model-based activities for the Stepping Stones.
