The following informal questions will guide your studying efforts towards the key conceptional ideas we have covered and will strenghen your knowledge for the upcoming exam. GOOD LUCK STUDYING AND PLEASE PHONE OR MAIL ME AS QUESTIONS ARISE DURING YOUR REVIEW FOR THE EXAM! For all exams: NOTE: You should know specific vocabulary words and conventions we have defined and not be afraid to use them! YOU WILL BE REQUIRED TO PROVIDE DETAILED INFORMATION AS WELL AS TO APPLY PRACTICAL LOGIC FROM CONCEPTS STUDIED.... MAKE SURE YOU PREPARE YOURSELF FOR MULTIPLE TESTING FORMATS AND STUDY YOUR MATERIAL KNOWING THAT THERE WILL BE t/f, FILL IN THE BLANKS, SHORT ANSWER, AS WELL AS MULTIPLE CHOICE. I WANT TO TEST YOU FOR YOUR KNOWLEDGE, NOT YOUR ABILITY TO EXAMINE, THEREFORE THE FORMAT IS DIVERSE AND UNBIASED. GOOD LUCK!!!! First Exam Study Questions: Omit the red questions for examination purposes 1. What are the 10 themes of the Study of Life? What is the hierachy of organization from the atom to the community? 2. What is the smallest unit of life? of matter? What two men were instrumental in developing the Cell Theory? How did they contribute? 3. What are the two major classes of cells? Name four characteristics of ALL cells? Compare and contrast the prokaryotic from the eukaryotic cell? 4. Who discovered DNA? What is a nucleotide? A genome? The double helix? Complementary h-bonding? Know the structural differences between purines and pyrimidines? 5. What is the taxonomy of living organisms? How is it arranged? What are the 3 domains? What are the 2 major theories upheld today and established by Charles Darwin? 6. What are the two major forms of inquiry practiced by scientists today? Be familiar with the scientific method and know the difference between a theory and a hypothesis. How is science a social process? 7. Define the differences between matter, weight, mass, element, compound, molecules, subatomic particles, atomic number, atomic weight, and mass number. 8. Which elements are life essential? Which comprise most of our body composition? Which comprise only a few percentages? Which are termed trace elements? Know the symbols, atomic weight, valence, and bonding capacity of these 25 of 92 elements. 9. What is a dalton? How much does a neutron weigh? If you know the weight and charge of an element, can you calculate the number of protons, neutrons, or electrons it contains? 10. What's the difference between an isotope and an isomer? 11. How are radioactive isotopes harmful and useful in society? 12. What does potential energy have to do with electron shells or orbitals? How is this information portrayed in the periodic table? What is the difference between the number of unpaired electrons, valence, reactivity, and inert chemicals? 13. What is this element? 1s2 2S2 Sp6 3S2 3p5 (HTML doesn't allow superscript!) 14. Describe the differences between ionic bonds, covalent bonds, and hydrogen bonds. Give some good examples. What is the difference between a molecular formula and a structural formula? Can a molecule have the same molecular formula but a different structural formula? Would this make it a different chemical, why or why not? 15. What is polarity? How can this be explained in terms of a dipole moment? 16. Why is water more structured than other liquids? 17. What are Van der Waals Interactions? 18. How does water provide stabilization of temperature? Define the difference between heat and temperature? What is kinetic energy? Be able to perform calculations with the units of temperature and heat. What is the heat of vaporization and the process of evaporative cooling? What does H-bonding have to do with these processes? 19. How does water expand when it freezes, but other liquids do not? Why is this biologically fortunate? 20. Define solution, solvent, solutes, aqueous solution, hydrophillic, hydrophobic, and Avogadro's number. Make up a solution 0.25 M glucose (add up all the atomic weights from the structure you now know) - if our experiment only calls for one-half milliliter of this molarity of glucose, how much will we need in g? 21. If MgSO4 has a FW of 120g and we add 60g into a Liter flask, how many molecules will we have in our flask? 22. If our solution of MgSO4 has a hydroxide ion concentration of 0.01 what will be the pH of the solution? What if the hydrogen concentration how changes by 1000 fold.....what will be the new pH of the solution? 23. What are some examples of weak acids and weak bases? What makes an acid or base a strong one? What is a buffer? How does acid precipitation occur in our environment and what damage can it encure? 24. Who were some of the early scientist that defined the field of organic chemistry? What were some of their experiments? How does the definition of organic chemistry differ from that of say the early 19th century? 25. Name 6 ways in which C atoms demonstrate versatility? 26. Given two structures, be able to identify whether the compounds are structural, geometric, or enatiomer types of isomers. What is the definition of a functional group? Know all 6 functional groups and be able to build or take apart compounds if asked to add or subtract a certain functional group. Know what type of compounds contain these functional groups. 27. What is a monosaccharide? What are two classes of monosaccharides? What type of reactions are used to build or disassemble disaccharides? How do you make maltose, lactose, or sucrose? 28. What is a polysaccharide? Which of the following are used as fuel - starch, cellulose, chitin, glycogen? What is a 1-4 linkage? Where would you find 1-6 linkages? What is the difference between alpha and beta glucose? Are microfibrils made out of which form? 29. Describe why fats, phospholipids, and steroids are hydrophobic? How are triglycerides similar in structure to a phospholipid? What are triglycerides used for biologically? Phospholipids (PLs)? Steroids? 30. Define saturated versus unsaturated fat? What is amphipathic? What are two types of arrangements commonly found for PLs? 31. How do the four levels of proteins differ? What is the structure of an amino acid, the building block of all proteins? Which amino acids are classified into the following groups based upon side chain (R)? - acidic, basic, nonpolar, polar? Which two functional groups form a peptide bond? What is a glycosidic bond? What is a ester linkage? 32. What's the difference between the double helix and an alpha helix? 33. Define chaperone proteins, denaturation (and common causes), and how scientists today discover protein structure? 34. Be able to model (draw) the Fluid Mosaic Model of the membrane phospholipid bilayer and discuss properties such as its selective permeability, its fluidity, its mosaicism, and its sidedness. How was the model advanced from Gorter and Grendel to Davson and Danielli to finally Singer and Nicolson? 35. What are six important functions (and give examples) of the PM? Second Exam Study Questions: 1. Define metabolism. What is the difference between catabolic and anabolic pathways? Why are these two types of pathways favorably coupled? 2. Define energy. What are the 3 types of energy important to organisms? How are chemical reactions related to potential energy and finally kinetic energy? 3. What are the first and second law of thermodynamics governing energy transformations? 4. Define free energy in vocabulary terms and in equation form. What does it mean for a reaction to be spontaneous? Are enzymes required for spontaneous reactions? If you want to have a reaction proceed, how does a change in total enthalpy, temperature, entropy, or enzyme affect the reaction? 5. Know the delta G values for respiration, hydrolysis of ATP, photosynthesis, and a reaction at equilibrium. 6. Discuss what is meant by life being "Metabolic Disequilibrium". 7. What 3 types of work require the energy coupling by ATP? What is the chemical structure of ATP (functional "groups")? What is the formula for hydrolysis of ATP? How does ATP phosphorylate substrates and couple to endergonic reactions? What is it called when a phosphate is removed from a substrate? 8. What are 5 characteristics of the catalytic proteins, enzymes? 9. What are the 3 basic steps of ALL chemical reactions? Think about this in terms of the energy profile. Be able to draw or interprete an energy profile of a reaction. What part of the energy profile does an enzyme modify? What part of the profile is unaffected by an enzyme? 10. What is the active site of an enzyme? How is this related to the Induced Fit Model? How is this related to substrate specificity? To saturation? What is the enzyme-substrate complex? How does the active site promote the proper orientation of reactants? 11. How do you think temperature, pH, and co-factors influence the enzyme-substrate complex? 12. Distinguish between competitive inhibition, noncompetitive inhibition, and allosteric regulation? Is allosteric regulation inhibitory or excitatory? Would you think that Feedback Inhibition acts at the active site? Why or why not? What about Cooperativity? 13. Which substances are permeant across the PM? Which ones are highly impermeant across the PM? 14. Specificity of transport of impermeant substances is determined by the type of protein, but what determines the rate and direction of how the substance will move? 15. What is simple diffusion? Does it require an input of energy? 16. How is passive transport different and similar to active transport? 17. If given an osmotic condition, be able to determine which way water will flow across a semi-permeable membrane. If given a concentration gradient, be able to determine which way a solute will flow. Understand the terms isotonic, hypertonic, and hypotonic. Know how animal versus plants cells would respond in each of the above external environments. 18. How does facilitated diffusion compare with simple diffusion? 19. Understand the cellular workings of the 3Na/2K ATPase pump. Understand how the gradient built up through the expenditure of energy is created by conformational changes induced by phosphorylation and dephosphorylation. Why do all cells have an unequal distribution of charge? What is this voltage difference called? What is an electrochemical gradient? When do cells follow an electrochemical gradient...when at rest, or when activated? Why? 20. Why do you think co-transport is often called secondary active transport? What is the advantage of such a type of transport? 21. Define the following: exocytosis, endocytosis, phagocytosis, pinocytosis, and receptor-mediated endocytosis. 22. Know how many molecules of ATP, NADH, and FADH are generated (and which steps) during cellular respiration in the presence and absence of oxygen. 23. What are redox reactions and what do they have to do with cellular respiration or photosynthesis? Define oxidation, reduction, a reducting agent, an oxidizing agent, an electron acceptor, and an electron donor. 24. Understand how the electron transport chain represent a controled release of energy as 2H combines with 1/2 O2. 25. What are the two primary ways to synthesize ATP? Which is our predominant source of ATP? If we accentuate or block on of these two ways of synthesis, be able to calculate how many ATP could then be generated in X number of glucose molecules. 26. Know the component electron acceptors of the mitochondrial electron transport chain. Compare the chloroplast electron transport chain with that of the mitochondrial one? How are they similar but how are they distinct? 27. Why does FADH provide less energy than NADH? 28. Explain and fully comprehend Peter Mitchell's Chemiosmotic Hypothesis. How does it operate in both animals and plants? 29. How are fats and proteins (in a general, global sense) catabolized? 30. What molecules act to upregulate or inhibit phosphofructokinase? Why is this important? What is this principle called? 31. Define autotroph, heterotroph, consumer, producer, decomposer. What are the 2 subdivisions of autotrophs? 32. Compare the net result of photosynthesis versus that of cellular respiration in terms of chemical reactions as well as verbally. 33. Know where the atoms of the reactants of photosynthesis are incorporated into the products. 34. What are the 2 stages of photosynthesis? Which is dependent upon light? Which is dependent upon energy molecules. In which one is glucose actually synthesized? What is the subcellular site of each of these two stages? 35. What is EMR and what portion of the light spectrum drives photosynthesis? 36. Explain using the absorption spectrum why plants are green? Of the three pigments of photosynthesis, which do you suppose is of greatest concentration in red algae? Why? 37. Understand the basis of Thomas Engelmann's algal-bacteria experiments. 38. Model the structure of a photosystem including, porphyrin ring, hydrocarbon tail, the thylakoid membrane, the reaction center, the ground state, and the exctied state. Where does the redox reaction occur? What replaces the lost electron in chlorophyll a that is trapped in the primary electron acceptor? 39. Why are there two different routes of electron flow during the Light Reaction? What are the component of these routes? What is produced and how much during each of these routes? 40. Name three ways in which ATP synthesis in plants is different than that of cellular respiration in mitochondria? 41. What are the 3 stages of the Calvin Reactions? How many molecules of CO2, ATP, and NADPH must be consumed to generate 3 molecules of glucose? Third Exam Study Questions: 1. Know what the major important contributions were by the following scientists: Thomas Hunt Morgan, Gregor Mendel, Frederick Griffin, Oswald Avery, Alfred Hershey & Martha Chase, Maurice Wilkins & Rosalind Franklin, Erwin Chargaff, James Watson & Francis Crick, and Matthew Meselson & Franklin Stahl. Be able to describe the experiments they set up, what the important equipment or tools were, what the results of their experiment were, and how this information/data contributed to the knowledge of the structure of dna or the method of genetic inheritance. For example, describe two different experiments that were performed that made advantageous use of radioactivity and what was discovered? 2. What is the difference between phenotype, genotype, allele, dominant trait, recessive trait? 3. How do we transform bacteria (e. coli) today differently than Griffin did in 1928? What would be some typical goals of why we would want to transform e. coli? 4. Concerning the structure of DNA: how long is one helix turn? how far apart are the nucleotide bases? how many layers of bases per helical turn? how wide is the helix? why is this important for the arrangment of hydrogen bonding? how were all these spacing/alignments discerned? 5. What does it mean that DNA has a 5' to 3' orientation? Be able to draw this out and describe the phosphate versus hydroxyl end of the phosphate sugar backbone and why we say the orientation is anti-parallel. What does it mean that replication is semiconservative? What were two other theories of the day that were rejected concerning DNA replication? How were they disproved? 6. How many base pairs are there in every individual cell and what is the error rate during replication? How are errors corrected? What is a frame shift? What is a single point mutation? What is a deletion? What is an insertion? 7. What is the difference between the replication fork, the replication bubble, and the origin of repliction? Do the origin of replication exist on the parent or the daughter strand? Are nucleotide bases added at the fork or the origin? Does replication proceed at multiple sites or just one site? Is replication taking place in one direction or does it move in both directions? How many nucleotide can be added per second? 8. What is the name of the enzyme that adds nucleotide bases? How does it do so? What is the leading strand versus the lagging strand? Why does one of these strands produce Okazaki Fragments? What enzyme joins the fragments? 9. What is the role for the RNA primase and RNA primer for DNA replication? What enzyme fills in the RNA from the primer with DNA bases? What is the function of helicase and single-stranded binding protein? 10. What is meant by the statement: "Proteins are the link between the genotype and the phenotype"? What is meant by the statement: "One gene-one polypeptide"? 11. How does transcription differ between prokaryotes and eukaryotes? 12. Define transcription versus translation? What are the three stages of each of these and how do the events differ? 13. How is the primary transcript (pre-mRNA) altered through RNA processing to become true mRNA (two ways)? How does this assist in the process of translation? What is the evolutionary advantage of alternative RNA slicing? Where does RNA slicing take place? What is exon shuffling? What is the difference between an exon and an intron? 14. Why must the genetic code be comprised of at least 3 nucleotides to create a code for an amino acid? Define the following terms: codon, redundant code, anticodon, stop codon, start codon. 15. If given a sequence of DNA and a mRNA codon table, be able to determine the order of the resulting peptide. If given a peptide sequence and a mRNA codon table, be able to provide a plausible sequence or sequences of DNA (remember redundancy) for that peptide sequence. If told that there has been a particular mutation (an example would be: insertion of a nucleotide at position X), be able to determine how this will affect the production of the peptide. 16. What composes the transcription initiation complex? What are the individual roles of the components of this complex? How does the template affect which way the complex will move? Describe the steps of initiation, elongation, and termination during transcription. 17. Know the functions of the following types of RNA: mRNA, tRNA, rRNA, pre mRNA (primary transcript), snRNA, and SRP RNA. 18. What is the structure of a tRNA, naming two major structural motifs? What enzyme catalyzes the phosphorylation of an amino acid to attach a particular amino acid to the aa attachment site? What does the active site of the enzyme have to do with the specificity of the anticodon? 19. What are the steps that occur during intiation of translation to assemble the translation initiation complex? What are the roles of the mRNA, small subunit of the ribosome, large subunit of the ribosome, initiation factor, GTP expenditure? 20. What are the formal names and functions of the E, P, and A sites? How many GTP are expended to bind an incoming tRNA to the A site? What catalyzes the formation of the peptide bond between the growing peptide chain and the new incoming aa? What allows the tRNA to slide from positions P and A to positions E and P? 21. What type of chemical reaction occurs when the release factor is bound at the A site for the tRNA that has the anticodon for uga (stop codon)? 22. What is a chaperon protein and how does it assist protein function? How does the polyribosome permit the synthesis of many copies of the same protein? Click here for additional Third Hour Examination Questions and Guide to Study for the Final Examination
Click here for additional Third Hour Examination Questions and Guide to Study for the Final Examination