Bio 93 Midterm 1 Study Guide PDF

Bio 93 Study Guide for Students A student who is ready for the exam will be able to answer basic questions from memory out loud, draw simple explanatory diagrams from memory, and answer clarifying questions about each. All material in the basics lectures is fair game and may be tested on, but these...

Bio 93 Study Guide for Students A student who is ready for the exam will be able to answer basic questions from memory out loud, draw simple explanatory diagrams from memory, and answer clarifying questions about each. All material in the basics lectures is fair game and may be tested on, but these questions below should cover the most likely exam questions. When to study: During non-exam weeks, read over video notes and class notes after class and mark topics that are confusing. Get help understanding these topics immediately - look up videos, read your textbook, visit an instructor office hour, attend peer tutoring. Seven days before the exam (EXAM WEEK), schedule about 2 hours to study every day for the next 7 days. Add these times to your calendar. You can also start work on these questions before the exam week. How to use these questions: When it is time for a study session, sit with your notes and your computer nearby but not open. Have blank paper or a whiteboard or a drawing tablet ready. Make a copy of this study guide. Randomly choose a question from the first lecture and do your best to answer it out loud without any notes. Talk and draw your answer. If you get stuck, make a note where and try to finish up the answer as best as you can. Answers should be succinct and to the point, not full essays. After you’ve done your best to answer the entire question from memory, open your notes and fill in the rest of the answer as completely as possible. Talk and draw. If you realize you still don’t understand something, immediately research the topic online or in the book, post a question on EdDiscussion, or write out the question to ask a TA or friend. Pursue help until you can confidently explain the full answer with correct vocabulary without notes. Mark the question answered. After you are finished with that question, pick a random question from a different lecture. Repeat the steps: explain and draw from memory, add more from notes, research until your answer is complete and you fully understand it. Then pick another random question from a different lecture. Repeat until you have answered all the questions in all the lectures in random order. If you have time, go through all the questions again. This plan uses these evidence-based methods of effective studying: A. Planning your study time B. Judging your understanding C. Spacing studying over many days D. Self-testing / explaining from memory E. Drawing / diagraming (cartoon drawings, not realistic ones) F. Interleaving (studying topics out of order instead of chunking topics) Many students are tempted to study using “easier” methods: rereading or recopying or summarizing notes, rewatching lecture videos, making vocabulary flashcards, and having friends or tutors explain topics. We do NOT recommend you use these techniques during Exam Week. Good luck! You can do this! Professors Thompson-Peer and Williams 1. Chemistry of Elements 1.1. What is the difference between an atom and an element? Give a new example of each not found in the basics video. 1.2. From memory, list the elements most common in biological organisms. Find two examples of molecules that contain a rare element and draw them. 1.3. Which of the six most common biological elements has the most electrons? Explain how you know. 1.4. What is a valence electron? For the list of common biological elements, find each in the periodic table and list another element with the same number of valence electrons. 1.5. Find a list of common ions in biology. Which of these have gained an extra electron? Have any gained or lost more than one electron? 1.6. Find a list of common ions in biology. Find these elements in the periodic table. What groups contain most biological ions? Which ions are similar to each other? 1.7. After you have learned about biomolecules, list the elements commonly found in each type of biomolecule. 2. Bonds and Polarity 2.1. List the types of chemical bonds and give examples of each. 2.2. Compare and contrast the types of chemical bonds 2.3. Explain why biological ionic compounds dissolve in water 2.4. Write out the six most common biological elements. Be able to rank them in order of low to high electronegativity, and draw connections between the elements with similar electronegativities. 2.5. Define bonding capacity and list from memory the bonding capacity of the most common biological elements. 2.6. Explain how bonding capacity and electronegativity affect covalent bonding 2.7. From the table of biological elements in Lecture 01, choose three that are rare. How many bonds will an atom of each element be able to form? Draw these atoms and indicate the locations of the bonds. 2.8. Explain what determines whether a covalent bond will be polar or nonpolar. Find five examples of simple molecules NOT in the video and determine whether each has a polar covalent bond. Draw each molecule and be able to explain why it is polar. 2.9. Define hydrogen bonding. Describe two properties of water that demonstrate hydrogen bonding. Draw these relationships. 2.10. Describe what makes a molecule hydrophilic. Find an example of a hydrophilic molecule NOT in the lecture video, draw it out, and circle the parts that make it hydrophilic. 2.11. Describe what makes a molecule hydrophobic. Find an example of a hydrophobic molecule NOT in the lecture video, draw it out, and circle the parts that make it hydrophobic. 2.12. Define a biological acid or base 2.13. In biological systems, what determines whether a solution is acidic or basic? Use the definition given in this class, not one that uses OH- concentration.  2.14. Describe what happens to protons when a biological acid or base is added to water. How does this affect pH? 3. Biomolecules (Overview, Carbohydrates, Lipids, Proteins, Nucleic Acids) 3.1. List from memory all seven functional group structures and names, and know which are polar, and which might be charged. 3.2. Describe from memory the characteristics of all four types of biological macromolecules. Which are polymers? 3.3. List the names of the dehydration reaction associated with each type of biomolecule. Describe what happens in a dehydration reaction. 3.4. Lookup the carbohydrate starch, and find two different ways of drawing it. Circle the carbons in both drawings. 3.5. Lookup the lipid sphingomyelin, and find two different ways of drawing it. Circle the hydrophobic and hydrophilic regions. 3.6. Describe similarities and differences between carbohydrates and lipids. 3.7. Relate functional groups and carbohydrates to polarity and interactions with water 3.8. Draw three amino acids as individual molecules, then draw how they would look when linked as a peptide. Mark the N and C terminus of the peptide. 3.9. Pick a random amino acid and find three different ways of drawing the structure. Find the alpha carbon and R group in each of these drawings. 3.10. Predict what will happen when proteins are denatured in a cell. What mechanisms cause denaturation? 3.11. What is the difference between secondary and tertiary structure in proteins? Draw simple pictures of each. 3.12. List the similarities and differences of the different nucleic acids. 4. Membrane Structure 4.1. From memory, describe the types of biological molecules found in the cell membrane. Draw a simple picture showing these molecules in a membrane. 4.2. Describe why amphipathic phospholipids are important in cell membrane structure. 4.3. Describe what parts of biological molecules would be found inside the lipid bilayer of a cell membrane, and what parts of biological molecules would be on the outer or inner surface of the lipid bilayer. Draw an explanatory diagram. 4.4. Find the molecular structure of two membrane phospholipids online. Circle the polar region of each. 4.5. Explain what the “fluid” and “mosaic” components of the fluid mosaic model are 4.6. List three functions of proteins in a cell membrane. Draw simple pictures to demonstrate these. 4.7. Predict how temperature, fatty acid saturation, and cholesterol affect cell membrane fluidity 4.8. Describe how membranes in a cell may have different properties because of different components. 4.9. Interpret a graph measuring how cholesterol or membrane thickness affect permeability 4.10. Every time you learn about a protein in future lectures, decide whether this protein is in the cell, in the plasma membrane, or extracellular. 5. Membrane Transport and Osmosis 5.1. Describe how molecule size, charge and concentration affect transport across the cell membrane. Draw an example of each. 5.2. Compare passive and active transport. Provide two examples of each. 5.3. Two solutions are separated by a membrane that is only permeable to water. If Side A has more solutes than Side B, describe which direction water will move overall. How can you predict which direction water will move across a membrane? 5.4. Define a hypertonic and hypotonic solution using only the amount of solute, not by the behavior of a cell in the solution. 5.5. What type of transport is cotransport - passive or active? Why? 5.6. What type of transport is endocytosis and pinocytosis - passive or active? Why? 5.7. Why would exocytosis be used by the cell? 5.8. Write out the steps of the sodium potassium pump with a simple diagram from memory. 5.9. Where is sodium concentration higher in living organisms, extracellular or intracellular fluids? Why? 5.10. How do most water molecules cross the plasma membrane? Why is this method the most effective? 5.11. Can a cell pump water from low to high concentration? How is water moved from one compartment to another? 5.12. As you learn about how proteins are made in the organelle lecture, be able to connect how transport proteins are made with where in the cell they are active. 6. Cytoskeleton 6.1. What are the types of fibers of the cytoskeleton, and what is the function of each? 6.2. How do actin and microtubules grow and shrink differently? 6.3. Find examples of cellular functions that use different cytoskeletal elements, and relate this to the location in the cell where the function occurs. 6.4. What is the general structure of a motor protein? 6.5. What are the three main types of motor proteins, and how are they different from each other? 6.6. How is the shape of motor proteins different if they are transport proteins vs force-generating proteins? Use kinesin on microtubules vs myosin with actin as your comparison. 6.7. How does the cytoskeleton act with motor proteins to produce movement in muscle cells? 6.8. Given that kinesin and dynein move in different directions on microtubules, predict which would be used in endocytosis and exocytosis. 6.9. Imagine a drug that inactivates a cytoskeletal element (like microtubules) or motor protein (like dynein). What cell functions would be affected by this? 6.10. Give two examples (other than those from the video) that would use different microscopy techniques to view correctly. 7. Organelles 7.1. Draw a simple cell with all the major organelles and label them 7.2. Draw a nucleus and label the structures and contents  7.3. Explain from memory the functions of each of the organelles of the cell 7.4. Create a list of five molecules that must transport into or out of the nucleus and therefore have import or export sequences 7.5. Describe the difference between rough and smooth endoplasmic reticulum 7.6. Describe the components of a ribosome and explain from memory how one is manufactured and assembled 7.7. Describe the difference between a free and a bound ribosome 7.8. Describe how a protein that is exported out of the cell moves through the endomembrane system 7.9. How does a cell make a lysosome? How is this similar and different to how a cell exports a protein hormone like insulin? 7.10. Pick a protein from each of these lectures: membrane transport, cell communication, cytoskeleton. Draw a cartoon that shows the organelles involved in making each protein and locating it in the correct position in the cell. 7.11. Describe what cellular functions would be affected if there was a malfunction with each cell organelle 8. Cell Communication 8.1. Describe and give examples of intracellular signaling, cell surface signaling, local signaling, and hormone signaling 8.2. Name and describe the three steps of signaling 8.3. Be able to describe the steps of the epinephrine-GPCR pathway from memory and by drawing a simple diagram. 8.4. Describe and give examples of G protein linked receptors, tyrosine kinase receptors, ligand gated ion channels, and intracellular receptors 8.5. Find all examples of GTP and ATP used by this lecture’s receptors. Which uses each energy source? 8.6. Search for a receptor type online (such as tyrosine kinase receptors) and find a new example with an image or description. Describe how the RTK acts in this pathway as best you can (the system will probably be very complicated but you should be able to find the receptor and something it activates). 8.7. What receptor type binds to DNA? What characteristics of this molecule would allow it to cross the cell membrane and nuclear membrane? 8.8. Using the epinephrine-GPCR pathway as an example, block different parts of the pathway and be able to describe what cell molecules will increase and decrease in concentration. Similarly, if a response molecule is increasing or decreasing, be able to describe what part of the pathway has likely been blocked or activated. 9. Experimental Design Almost every class time includes an experiment and at least one figure. Go back to the first class notes that contain a figure, and be able to answer these questions. Repeat for each lecture. 9.1. Explain which data points are the control(s), and what the researchers likely did to that group of cells or subjects to get that control group 9.2. Describe the most likely hypothesis for that figure 9.3. Label all the parts of the figure 9.4. Explain which variables are discrete and which are continuous  9.5. Explain what type of figure it is (bar, line, scatter, other) In order to answer experimental questions on exams, you should also be able to answer questions like these. Practice using the figures with PollEverywhere questions in class and using old exam questions. 9.6. What are the familiar biology words in this question? What lecture do these words come from? 9.7. The figure may show a new protein or cell type or gene or organism with a strange name. Describe what makes this new protein or cell type or gene or organism most interesting. Connect the new thing to something you already know. 9.8. Read through the stem of the question and the answer options. What do you need to figure out in order to choose the correct answer? 9.9. Explain how information from lecture or information from this figure will help you determine the correct answer(s). Explain why the other answer options are incorrect. 9.10. Try to create a new multiple choice question using the same figure. Quiz a friend, then explain the correct answer.