Membrane Biophysics BSC5786

Final Examination Study Guide

Fall 2024

As a reminder, your course grade will be divided equally across four evaluations: (1) 25% Ion Channel Lecture Presentation, (2) 25% Biophysical Technique Lecture Presentation, (3) 25% Class Preparedness, Annotated Bibliography, and Course Participation, (4) 25% Final Examination. On the afternoon of your final, I will print out your bibliographies and the first page of your powerpoint presentations to provide feedback on your current progress.

Your final examination will have two components, (1) computational membrane biophysics and (2) standard comprehensive examination comprised of material drawn from my lectures, the presentations of your colleagues, your textbook assigned readings, and concepts garnished from our primary literature readings. The examination will take place in KIN 1056 from 8 to 11 am, Tuesday, 10 December 2024. It is my intention to gauge the examination to fit this time block but I do not have any problem with students staying past this interval if they would like to work more slowly.

(1) __computational membrane
biophysics component__ -

To best prepare for this component, you should have completed all assigned homework calculations. Review your calculations and organize your notebook / lecture notes for ready access to equations needed to complete all assigned homework You may also be asked to perform some simple calculations presented in lecture but not fully practiced in the homework (minor emphasis). You may also wish to organize major formulas from your Hille Text with those provided during lecture in a quick reference sheet. For this component you will have access to all materials you wish to utilize (open book/note style). Be sure to bring your calculator and your laptop. You may email me any graphics components of your answers.

(2) __tradition comprehensive
component __-

Upon completion of the first computational component, I will provide you a copy of the comprehensive examination to be taken closed notes/book. The format will be multiple choice, fill in the blank, t/f, and short answer. You will also be asked to apply one or more of the six biophysical techniques studied in the course to one or more practical problems. Here you will be asked to apply what you have learned (outside your own assigned presentation) to prove a given hypothesis.

Review all the powerpoint visual information posted from your colleagues’ presentations.

Reread all the abstracts of the articles we read for a refresher.

__Please review the following
questions to direct the tuning of your review/preparation for my general
lecture material:__

1. What are the two major classes of transport mechanisms to go across the “bimolecular diffusion barrier”?

2. Know the historical perspective of ion channels in the biological membrane starting from Sidney Ringer through Singer and Nicholson’s Fluid Mosaic Model. What are the properties associated with this model? Which components govern fluidity and which govern selectivity?

3. Review the working laws and definitions of electricity: ionization, electrical prefixes, physical constants, law of charges, electrostatics, resistance, conventional current flow vs. electron flow theory, Kirchoff’s Laws, the difference between current and voltage.

4. The size of current is determined by what two factors? What is Ohm’s Law and how is it related to Resistivity? Discuss why Ohm’s Law plays a central law in membrane biophysics?

5. Discuss how the membrane is a capacitor? Define capacitance in terms of charge? In terms of dielectric constant and thickness? How does capacitance slow down a voltage response? How is this related to a discharge of an RC circuit?

6. What is simple diffusion and how is it related to Brownian Movement? What is Fick’s First Law of diffusion and how does this get altered when incorporating the bilayer? What is Van’t Hoff’s Law and how does it describe the process of osmosis?

7. What are some common properties of protein-mediated transport collectively? What are three types of protein-mediated transport - compare these in terms of gradients and energy requirements?

8. Describe fully the process of Molecular Peristalsis of the Na/K ATPase pump?

9. Describe fully the mechanisms underlying the resting membrane potential?

10. How is the equilibrium potential related to the shape of an action potential? Know the underlying ionic basis of the action potential and physiological terms such as spiking, oscillation, refractory period (relative and absolute), depolarization, repolarization, hyperpolarization.

11. How are the Boltzman and Nernst Equation Related? What additional components does the Nernst incorporate? What are the five assumptions of the Nernst Equation?

12. What is a Reversal Potential? When would it be more appropriate to use the Goldman Equation over that of the Nernst Potential for defining the Reversal Potential? What is the utility of calculating and experimentally discovering the “Zero-current”? What two properties is ion transport across the bilayer dependent upon and is incorporated into the Goldman Equation? What do bionic substitution experiments contribute to permeability knowledge?

13. Which ion has the greatest influence on the Membrane Potential? Explain both verbally and in terms of computations.

14. If an ion is not passive distributed, what does this infer?

15. Review current-voltage relationships: What does the slope indicate? How do you determine ion selectivity from electrical measurements? How does the shape of the curve infer electrodiffusion? How is voltage-dependence noted? How do you convert the I-V to gV curves?

16. Review the Ionic Theory of the Membrane as revealed by combined classical biophysicists Hodgkin, Huxley, Cole, Curtis, and Katz including the overview of the action potential, cable theory, local circuits, idea of propagation, and passive spread of current. Describe H-H first experiment with the squid giant axon and its implications.

17. Describe the basic theory of voltage-clamp recording - what electrical property does it artificially eliminate? What is the difference between patch and voltage-clamp? Who discovered which?

18. What is the H-H Independence Relation?

19. What is activation and inactivation and how are they graphically computed? What about recovery from inactivation?

20. How can we mathematically define the rise and fall of Na, K, and leak current across the membrane? Discuss this in terms of the H-H Model in words and equations? What are the modern day limitations of this model?

21. What are three hypotheses behind gating currents? How would you globally define a gating current? How can one apply the Boltzman Theory to comprehend the degree of voltage dependence to gating currents? What is the “equivalent” or “partial charge movement”?

22. Know basic pharmacology of classic ion channel blockers in the Superfamily of Voltage-gated Ion channels. What are some traditional properties of blockers and how is Kd determined?

How can we determine Bmax to estimate the number of ion channels in a membrane based upon a bound blocker? What does it mean if a blocker has state dependency?

23. How did invertebrates versus vertebrates increase cv by differentially altering the length constant?

24. What is the subunit composition of each of the major ion channels we have studied?

25. What is stochastic behavior in relationship to ion channel activity? How can an ensemble average approximate the macroscopic I?

26. Review each of the major Voltage-gated Ion Channel Families: What are the general functions? Are there special signature sequences or particular defining structural characteristics? What are the types of architectures for each family? What are the functional domains discovered primarily by mutagenesis or crystal structures? What are the gene subfamilies?

27. Be particularly fluent in the characteristics of the following families: Shaker, KCa, KIR, Ih, Cl, Vca since we spent lecture time defining each of these in detail.

28. What are the classical components for data acquisition for patch-clamp electrophysiology? Be very familiar with the considerations for cell-type, patch seal formation, electrode glass, AgAg/Cl electrode, sources of electrical and mechanical noise. What is the basic principle behind the voltage-clamp method? Why is the configuration useful and in what respects is it artificial?

29. What are nine types of biological preparations that are useful for patch-clamp electrophysiology (i.e. cultured cells, bilayer.....etc.)? What are the various experimental advantages for each of these preparations?

30. Describe parallel tools to electrophysiology such as the use of heterologous expression systems, site-directed mutagenesis, advanced types of mutations, and RT PCR?

31. Much of your examination containing single ion channel behaviors will be evaluated computationally but review global principles we have additionally covered for this section including: randomness but not chaotic behavior, conservation equation, factors that affect gating, macroscopic versus unitary currents, types of pipette configurations to match experimental questions, point by point versus event amplitude histograms, dwell time distributions, stationary versus non-stationary kinetics, dealing with the detection of multiple channels and multiple states, the eight types of advanced channel behaviors that we covered in lecture (bursting, first latency, etc.).

32. What are the functional benefits of electrical versus chemical synapses? What are the primary chemical transmission events? What is the theory of integration?

33. Describe in depth the Quantum Hypothesis; Its discovery in the 1950s by Castillo and Katz, Its statistic treatment, and how it is similar but distinct from single channel behaviors?

34. What is use dependent plasticity? Describe in full four types that we studied?

35. The formulation of the Calcium Hypothesis was generated over a thirty year period of exploration. Be prepared to understand the significance and important features of each of these investigations that we explored in lecture during this time period.

36. What is the distinction between orthodromic and antidromic current? How are IV relationships for synaptic currents different from those of somatic IV relationships?

How does the lack of space clamp affect the calculations and recordings of true synaptic currents? How can we apply the physics of cable properties to estimate synaptic currents? How do synaptic kinetics influence the shape of the synaptic currents?

37. Discuss spatial and temporal summation of synaptic input?