BIOLOGY 207 1st EditionExam # 1 Study GuideIntroductory Material- Be aware of global impacts and history of microbes and their contributions to biology o How long have microbes existed on Earth?o What are microbes’ contributions to animal and plant life?o What bodily functions are permissible due to microbe presence?o How have microbes evolved from their first common cell ancestor?o What are the three major splits from the common cell ancestor?- What are some of the first revolutionary scientific discoveries involving bacteria?o Who reported the first microbes in the mid-1600s?o How did Sir Alexander Fleming discover the first antibiotics in 1928? Phylogeny of Life- What is phylogeny?o How does one read a phylogenetic tree?o What are the pros of being able to read a phylogenetic tree?o How did Carl Woese create his unified view of molecular phylogeny? How did he affect taxonomy?o Why is rRNA gene sequencing useful for organismal phylogeny?o What is the significance of the 16s rRNA in terms of gene sequencing?- What are some shared characteristics of the three primary lines of evolutionary descent (bacteria, archaea, eukarya)o How do they differ?o What does Norman Pace argue about the term “prokaryote”o How can we suggest that the origin of chloroplasts and mitochondria isendosymbiotic?Energetics- Understand the thermodynamics of redox reactionso How do you determine the reduction potential of an element?o How do you calculate the free energy of a redox reaction?o What common practices exist in microbes allowing them to conserve energy from redox reactions?o How does the proton motive force (PMF) originate in different cell types?o How is ATP synthesized in different cells?o What are the uses of the PMF?o Do electrons flow from the more electronegative to the more electropositive or vice versa?o What is the relationship between Gibbs’ Free Energy and the differencein redox potentials (what is the equation and how is it used)?o How do you determine the oxidation state of an element?o How do we get ATP out of aerobic respiration?o What are some of the main points in glycolysis?o How do you characterize organisms by mode of energy metabolism? What are the two basic energy sources and how do we categorize organisms into them? What is the difference between a heterotroph and an autotroph?o What is fermentation and why does it occur?Cell Structure and Function- Know the difference between chemoorganotrophic respiration, chemolithotriphic respiration and fermentationo How do each of them use the PMF?o What is the source of NADH?o Which forms use the electron transport chain? For what purpose?o How is ATP made?o What are the different sources of energy, electrons and carbon for these three processes?o Why is reducing energy necessary during respiration?- Cytoplasmic membrane functionso What are the three main functions of the CM?o What is the basic structure of the bacterial CM?o Name some differences between bacterial/eukarya membranes and archaea membraneso What are some functions of proteins in the CM? Name three features of transporter proteins How is energy used during transport in and out of the cell through the proteins? What are some types of simple transporters?- Gram + vs. Gram –o Know the differences between gram + and gram – cell walls, in terms of peptidoglycan levelso What is LPS? Where is it found? Why is it dangerous? o How can you tell the differences between gram + and gram – in a laboratory?- Transition metalso Where are they found on the periodic table?o What is their use and why are they important to cell function?- Transportationo What are the 6 basic elements found in all macromolecules and cells?o Why is cell size so important in terms of attaining nutrients and excreting waste? How is cell size so valuable to cell growth, evolution and health?o How do cells move around?  What powers this? How fast can they move? How do they know where to go (areas of higher gradient)? What is the general pattern of movement in cells?Information Flow- Know the central dogma of information flow o What is the common framework associated with flow of information?o How are double stranded DNA strains organized in terms of 3’/5’?o What are the main purine/pyrimidine bases and base pairs?o Since DNA can be 1,645µm long, and cells are only about 1µ long, how are DNA packed into cells?o What is the DNA replication process? Which is the leading strand? Which is the lagging strand? Which enzymes are used and why? What are Okazaki fragments? What does it mean that DNA replication is semiconservative?o What is the process of transcription? Which enzymes are used and why? What is the purpose of transcription? Where does transcription begin and end?o What is the process of translation? How does initiation occur? What is the purpose of it?o How does termination occur? What are some stop codons? What happens during termination?Microbial Growth- What are the functions of some of the main nutrients required by cells? How are they utilized in the cells? Where do they come from?o Carbon? Nitrogen? Phosphorus? Sulfur? - How does the biosynthesis of amino acids occur?o What are some key features?o What is the purpose of NADPH in these processes?o What is the purpose of biosynthesis for cells?- What process occurs if there is not enough carbon for growth in bacteria and archaea?o How is glucose made in these instances?o Why is this glucose needed?- How do bacterial cells divide?o What is the general process of binary fission?o How long on average does it take for a cell to replicate? What about forthe genome to replicate? Why is this different? o Explain why there is an exponential growth of microbes (µ = growth constant) What is the lag period? Why does the cell stop growing after an exponential growth period? How are growth rates used to characterize microbes?o What are different responses of microbes to oxygen and what do they imply about the microbes growth preferences? Aerobic? Anaerobic? Facultative anaerobic? Microaerophilic? - Bacterial evolutiono How has Richard Lenski been able to track the evolution of e. coli over the past 25 years?o What questions is he able to ask and test with the data that he has