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Biology LibreTexts


  • Page ID
    • 2: Biology as a Science
    • 3: Models and Simplifying Assumptions
    • 4: 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.
    • 5: Potential Energy in Biology
    • 6: 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.
    • 7: Activation Energy
    • 8: 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.
    • 9: ATP
    • 10: 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).
    • 11: 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.
    • 12: 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.
    • 13: Cashing in on Redox
    • 14: 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
    • 15: Photosynthesis
    • 16: Protein Structure
    • 17: Enzymes and Allosteric Regulation
    • 18. Prokaryotes
    • 19: Membranes and Transporters
    • 20: Eukaryotes
    • 21: The Mitotic Cell Cycle
    • 22: Meiosis
      The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. In mitosis, both the parent and the daughter nuclei are at the same ploidy level—diploid for most plants and animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei that result at the end of a meiotic cell division are haploid.
    • 23: Mendel's Inheritance
      Gregor Mendel is (now) famous for having discovered the concept of genes (though he simply called them “factors”).
    • 24: DNA Replication
    • 25: Transcription
    • 26: Translation
      The process of translation in biology is the decoding an mRNA message into a polypeptide product. Put another way, a message written in the chemical language of nucleotides is "translated" into the chemical language of amino acids. Amino acids are linearly strung together via covalent bonds (called peptide bonds) between amino and carboxyl termini of adjacent amino acids.
    • 27: Protein Localization
      In this section we will discuss two major modes of protein localization. We will begin with the components of the endomembrane system. This system involves co-translational translocation across membranes, and later delivery and processing through various organelles via vesicles and motor protein-mediated transport. It is employed for proteins that function within the compartments of the endomembrane system, for proteins embedded in the plasma membrane, and for secreted proteins.
    • 28: Mutations
      Here we describe the origin of mutations, their effects on gene expression, and their ultimate role in evolution.
    • 29: Regulation of Gene Expression
      Regulation is all about decision making. Gene regulation is, therefore, all about understanding how cells make decisions about which genes to turn on, turn off or to tune up or tune down. In the following section we discuss some of the fundamental mechanisms and principles used by cells to regulate gene expression in response to changes in cellular or external factors. This biology is important for understanding how cells adjust changing environments.
    • How to succeed in BIS2A- online
      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.