The big surprise was not only that almost all of the DNA is used but also that a large proportion of it is gene switches. Before Encode, said Dr. John Stamatoyannopoulos, a University of Washington scientist who was part of the project, “if you had said half of the genome and probably more has instructions for turning genes on and off, I don’t think people would have believed you.”By the time the National Human Genome Research Institute, part of the National Institutes of Health, embarked on Encode, major advances in DNA sequencing and computational biology had made it conceivable to try to understand the dark matter of human DNA. Even so, the analysis was daunting — the researchers generated 15 trillion bytes of raw data. Analyzing the data required the equivalent of more than 300 years of computer time.Just organizing the researchers and coordinating the work was a huge undertaking. Dr. Gerstein, one of the project’s leaders, has produced a diagram of the authors with their connections to one another. It looks nearly as complicated as the wiring diagram for the human DNA switches. Now that part of the work is done, and the hundreds of authors have written their papers.“There is literally a flotilla of papers,” Dr. Gerstein said. But, he added, more work has yet to be done — there are still parts of the genome that have not been figured out.That, though, is for the next stage of Encode.
Chapter 3 - Cell Metabolism (includes guide to Chapter material and Discussion
article)
The chapter begins with a brief introduction to the different types of reactions that commonly occur
inside of cells, including hydrolysis, condensation, phosphorylation, dephosphorylation, and oxidation-
Required Text Reading (section title and start page):
- Types of Metabolic Reactions,
3.1
page 57
Hydrolysis and Condensation Reactions
Phosphorylation and Dephosphorylation Reactions
Oxidation-Reduction Reactions
- Metabolic Reactions and Energy,
3.2
page 59
Energy and the Laws of Thermodynamics
Energy Changes in Reactions
How the Energy Change of a Reaction Determines its Direction
Chemical Equilibrium
The Law of Mass Action
Activation Energy
- Reaction Rates,
3.3
page 63
Factors Affecting the Rates of Chemical Reactions
Reactant and Product Concentrations
Temperatures
The Height of the Activation Energy Barrier
The Role of Enzymes in Chemical Reactions
Mechanisms of Enzyme Action
Substrate Specificity
Cofactors and Coenzymes
Factors Affecting the Rates of Enzyme-Catalyzed Reactions
Regulation of Enzyme Activity
- ATP: The Medium of Energy Exchange,
3.4
page 72
- Glucose Oxidation: The Central Reaction of Energy Metabolism, page 73
Coupling Glucose Oxidation to ATP Synthesis
Level
Teacher
