1: Readings
- Page ID
- 8226
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)- 1.1: How to succeed in BIS2A
- This is a general discussion of our goals in this course, the resources available, and what we feel are the best strategies for your success.
- 1.2: Biology as a Science
- This section describes the "Scientific Method"- a process for the generation and testing of hypotheses, and the "Design Challenge", which is our BIS2A approach to thinking about Biology as a series of problems to be solved by Life.
- 1.3: Models and Simplifying Assumptions
- "Models" are simplifications/approximations of the real thing. Our view of reality is based on the models we build in our head. Various types of models allow us to investigate how Life works.
- 1.4: A Brief History of Our Planet
- A discussion of Origins requires that we understand what conditions were like on Earth when life first arose. Life is based on the ability to collect energy by tapping into chemical reactions. Scientists studying origins and evolution need to understand how the chemistry of Earth, particularly of the Earth's atmosphere and oceans, has changed during the approx. 4 billion years since the solidification of this planet.
- 1.5: Atoms to Bonds
- In order to solve the problem of "building a cell", we need to understand the physical properties the chemicals that make up a cell. The polarity (or non polarity) of chemical bonds, resulting from differences in electronegativities between atoms, will affect the behavior of these molecules in an aqueous environment.
- 1.6: Potential Energy in Biology
- A living thing, as it grows or reproduces, assembles a very specific structure (itself!) from components found in the environment (sometimes including other forms of life). This requires work- or more formally, energy. This reading covers energy, energy transactions, defines G, and defines ∆G (the change in energy available to do work). It also describes a core concept for this course: the "Energy Story".
- 1.7: Equilibrium vs. Homeostasis
- The direction of a reaction (its bulk flow, aka "net flux") is determined by the relative potential energy (Gibbs free energy, G) of the reactants and products. The net flux will be in the direction from higher potential energy to lower potential energy. In Biology, the energy of the components of the reaction will be determined by both their molecular structure and their concentration.
- 1.9: Functional Groups
- A functional group is a specific group of atoms within a molecule that is responsible for a characteristic of that molecule. Many biologically active molecules contain one or more functional groups. In Bis2a we will discuss the major functional groups found in biological molecules. These include: Hydroxyl, Methyl, Carboxyl, Carbonyl, Amino and Phosphate. This article also discusses polarity of molecules, and how that relates to polarity of bonds.
- 1.11: Glycolysis
- Glycolysis is the first metabolic pathway discussed in BIS2A. Because of its ubiquity in biology, it is hypothesized that glycolysis was probably one of the earliest metabolic pathways to evolve (more on this later). It is a 10-step pathway that is centered on the processing of glucose for both energy extraction from chemical fuel and for the processing of the carbons in glucose into various other biomolecules (some of which are key precursors of many much more complicated biomolecules).
- 1.12: Fermentation
- This section discusses the process of fermentation. Due to the heavy emphasis in this course on central carbon metabolism the discussion of fermentation understandably focuses on the fermentation of pyruvate. Nevertheless, some of the core the principles that we cover in this section apply equally well to the fermentation of many other small molecules.
- 1.13: Pyruvate Oxidation and the TCA Cycle
- Under appropriate conditions pyruvate will be oxidized, leading to a loss of one carbon via decarboxylation, and creating acetyl-CoA. The resulting acetyl-CoA can enter any one of several pathways for the biosynthesis of larger molecules. We will focus on its routing to a central metabolic pathway called the Citric Acid Cycle. Here the remaining two carbons in the acetyl group can either be further oxidized or serve as precursors for the construction of various other molecules.
- 1.15: Respiration
- In respiration, high energy (highly reducing) electrons travel down an electron transport chain and are finally delivered to an externally derived oxidizing agent. In eukaryotes and many prokaryotes the electron donor is NADH, and the terminal electron acceptor in O2. Some of the -∆G of this series of redox reactions is stored as a proton gradient, formed by some of the electron carriers, which are also proton pumps. The energy stored in this gradient can be employed to power many +∆G processe