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21 August, 2008

Comparative Physiology: Biol 543. Fall 2008


INDEX : "Click" on the Colored Link.

  • ANNOUNCEMENTS (Check Regularly)
  • SYLLABUS (with links to all course material, lectures, problem sets, etc.)

  • GENERAL COURSE INFO

  • e-Resources (Journals, etc.)

  • number sheet

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    General Information


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    SYLLABUS


    DATE DAY TOPIC Video Chapter Other
    8/21 Th Introduction & Review: Methods, Molecules, Energy, Biosynthesis, Membranes, Channels
    Medical Biochemistry Site - Very Useful!!!

    INTRO (FAST)  (20:48)
    INTRO (SLOW)
    1-4
  • Introduction TOC

  • 8/26 T Digestion: Transport
    Video-dig1 (fast)  (32:59)
    Video-dig1 (slow)

    15-17
  • (ICQ0) In class Questions: Phylogeny, Thermodynamics in Physiological Processes.
  • Digestion TOC
  • Digestion Highlights

  • 8/28 Th Digestion: Secretion/Absorption
    Video-dig2 (fast)  (36:47)
    Video-dig2 (slow)
    15-17
  • (ICQ1) In class Questions: Digestion, Glandular Secretion.
  • Production of HCl.
  • Gastrin Action
  • Digestion TOC

  • 9/2 T Digestion: Secretion/Absorption Video-dig2 (fast)  (36:47)
    Video-dig2 (slow)
    15-17
  • (ICQ2) In class Questions: Digestion, Transport and Absorption.
  • Fat Transport - 2008
  • Digestion TOC

  • 9/4 Th Digestion: Regulation / Intro to Hormones Video-dig3 (fast) (14:44)
    Video-dig3 (slow)
    and
    Video-endo1 (fast) (23:14)
    Video-endo1 (slow)

    8
  • (ICQ3) In class Questions: Digestion - Regulation / Hormones - Introduction.
  • Digestion TOC
  • Hormone TOC
  • Endocrine Highlights

  • 9/9 T Hormones: Release / Target Action
    Bio102 Hormone notes (Vogt) w/diagrams

    Video-endo2 (fast) (33:30)
    Video-endo2 (slow)
    9
  • (ICQ4) In class Questions: Hormones: Mechanisms of Storage and Release / Receptors and Transduction.
  • Hormone TOC

  • 9/11 Th Hormones: Specific Examples
    w/reference to Endo1 and Endo2 lectures

    Video-endo3 (fast) (1:03:36)
    Video-endo3 (slow)
    9
  • (ICQ5) In class Questions: Hormone Examples - Glucagon, Thyroid Hormone & Digestion (Gastrin, Enteroglucagon, ADH).
  • Hormone TOC

  • 9/16 T Hormones: Specific Examples
    w/reference to Endo1 and Endo2 lectures

    Video-endo3 (fast) (1:03:36)
    Video-endo3 (slow)
    9
  • (ICQ6) In class Questions: Hormone Examples - GnRH, LH/FSH, Testosterone & Estrogen (Hypothalamus, Pituitary, Testes, Ovaries).
  • Hormone TOC

  • 9/18 Th Hormones: Specific Examples
    w/reference to Endo1 and Endo2 lectures

    Video-endo3 (fast) (1:03:36)
    Video-endo3 (slow)
    9
  • (ICQ6) In class Questions: Hormone Examples - GnRH, LH/FSH, Testosterone & Estrogen (Hypothalamus, Pituitary, Testes, Ovaries).
  • Hormone TOC

  • 9/23 T MID-TERM EXAM #1
    ANSWERS: CLICK HERE

    EXAM  
    9/25 Th Excretory Systems: Detoxification & Osmoregulation

    Bio 102 Notes, Kidneys and Excretion
    Video-Kid1   (35:37) 14
  • (ICQ13) In class Questions: Kidneys, Excretion -- Detoxification -- Water/Ion Ballance -- Filtration, Secretion, Reabsorption
  • Acclimation vs. Adaptation
  • Ammonia Toxicity
  • Excretion & Kidneys TOC

  • 9/30 T The Mammalian Kidney: Forming a Concentrated Urine.
    Video-Kid2   (46:49) 14
  • (ICQ14) In class Questions: Kidneys, Nephrons & Collecting Ducts & Urine Formation
  • Counter Current Exchange -- PDF
  • Excretion & Kidneys TOC

  • 10/2 Th Hormonal Regulation of Mammalian Kidney: Osmoregulation and Blood Pressure
    Video-Kid3   (19:59) 14
  • (ICQ15) In class Questions: Kidneys, Hormonal Regulation of Blood Osmolarity and Blood Volume: ADH, JGA/Renin/Angiotensin and ANP
  • Excretion & Kidneys TOC

  • 10/7 T Hormonal Regulation of Mammalian Kidney: Osmoregulation and Blood Pressure
    Video-Kid3   (19:59) 14
  • (ICQ15) In class Questions: Kidneys, Hormonal Regulation of Blood Osmolarity and Blood Volume: ADH, JGA/Renin/Angiotensin and ANP
  • Excretion & Kidneys TOC

  • 10/9 Th FALL BREAK - NO CLASS
    10/14 T Muscles: Overview, Contractile Proteins in Prokaryotes and Eukaryotes
    Video-Mus1   (55:08) 10
  • (ICQ16) In class Questions: Muscles, Movement in Prokaryotes and Eukaryotes; microtubules, dyneines, kinesins, muscle & skeleton.
  • Muscle TOC
  • Notes on Movement (Mus1) and Electrical Properties of Cells (Mus2)

  • 10/16 Th Muscles: Electrical Properties of Cells
    Video-Mus2   (56:47) 10
  • (ICQ17) In class Questions: Muscles, Electrical Properties of Cells, Resting and Action Potentials.
  • Muscle TOC
  • Notes on Movement (Mus1) and Electrical Properties of Cells (Mus2)

  • 10/21 T Vertebrate Skeletal Muscle: Actin and Myosin Interactions
    Video-Mus3   (34:45) 10
  • (ICQ18) In class Questions: Muscles, Actin and Myosin Interactions (troponin, tropomyosin, ATP and Ca++).
  • Muscle TOC

  • 10/23 Th Vertebrate Skeletal Muscle: Control; Excitation-Contraction Coupling
    Web Links to Interesting Muscle sites

    Video-Mus4   (52:04) 10
  • (ICQ19) In class Questions: Muscles, Control of Muscle Contraction: Excitation-Contraction Coupling; Graded Contractions; Slow and Fast Twitch Fibers; Skeletal/Cardic/Smooth Muscle.
  • Muscle TOC

  • 10/28 T Vertebrate Skeletal Muscle: Control; Excitation-Contraction Coupling
    Web Links to Interesting Muscle sites

    Video-Mus4   (52:04) 10
  • (ICQ19) In class Questions: Muscles, Control of Muscle Contraction: Excitation-Contraction Coupling; Graded Contractions; Slow and Fast Twitch Fibers; Skeletal/Cardic/Smooth Muscle.
  • Muscle TOC

  • 10/30 Th MID-TERM EXAM #2
    ANSWERS: CLICK HERE

    EXAM  
    11/4 T ELECTION DAY - NO CLASS
    11/6 Th Circulation: Design & Evolution
    BIO102 notes on Circulation and Gas Exchange
    Video-Circ1 (fast)  (25:56)
    Video-Circ1 (slow)

    12
  • (ICQ7) In class Questions: Circulation Intro - Function, Closed v. Open, Respiration & Surface : Volume Relationships - Evolution.
  • Circulation TOC
  • Circulation & Gas Exchange Highlights

  • 11/11 T Circulation: Mammalian Heart and Vascular System
    Video-Circ2 (fast)  (52:27)
    Video-Circ2 (slow)

    12
  • (ICQ8) In class Questions: Circulation, Mammalian Heart: overview, muscle properties (electrical, contractile), (continued from previous class).
  • Circulation TOC
  • Paper describing Atrial Morphology / Conduction, incl. Brachmann's Bundle

  • 11/13 Th Circulation: Mammalian Heart and Vascular System Video-Circ2 (fast)  (52:27)
    Video-Circ2 (slow)

    12
  • (ICQ9) In class Questions: Circulation, Mammalian Heart: Blood Pressure, Arteries & Veins & Capillaries (movement in and out).
  • Circulation TOC

  • 11/18 T Circulation: Regulation
    Video-Circ3 (fast)  (33:58)
    Video-Circ3 (slow)
    12
  • (ICQ10) In class Questions: Circulation, Regulation of the Mammalian heart and circulatory system
  • Circulation TOC
  • Note 2 errors in lecture re. (1) adrenergic receptors and (2) mechanoreceptors and ADH (see Errata section above).

  • 11/20 Th Circ / Gas Exchange
    Video-Gas1   (21:16) 13
  • (ICQ11) In class Questions: Gas Exchange: Overview of Respiratory Surfaces
  • Gas Exchange TOC

  • 11/25 T Gas Exchange
    Video-Gas2   (50:34) 13
  • (ICQ12) In class Questions: Gas Exchange: Chemistry of O2 & CO2 Exchange
  • Gas Exchange TOC

  • 11/27 Th THANKSGIVING - NO CLASS
    12/2 T MID-TERM EXAM #3
    ANSWERS (12/2): CLICK HERE
    EXAM  
    12/4 Th Return Exams, Evaluations, Final Review.    
       
    12/12 Fri FINAL EXAM (optional, see below) 9 AM, CLS 102


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    NEW ANNOUNCEMENTS

    8/14/08
     
  • WELCOME ANNOUNCEMENTS 2008 Quizzes, videos, PDF Notes, schedule, text, problems sets.


    Course Organization (brief summary, details below):
      NOTE: Please ignore the "Course Rules" discussed/described in the Introductory Video Lectures. Rules for 2008 are listed on this web page. These include... (1) 100% of course grade based on 3 required midterms plus optional final, adjusted by attendance and extra credit (see instructions); (2) there will be no daily quizzes.

      LECTURES, CLASS TIME, EVALUATION...

    • Lectures will generally NOT be presented during class time. Lectures that ARE presented during class time will assume students are already familiar with the video lecture for that day, and will therefore be at a relatively "advanced" level.
    • Video Lectures are required and must be viewed outside class via internet streamed video; view before class; keep up with reading.
    • During Class, students will develop and present answers to specific questions (available from this site).
    • Students will be evaluated via short essay exams (3 midterms, one optional final).
    • Class attendance is required, participation expected.

      TEXT BOOK IS REQUIRED! Why? Because in my classes I assume students are there to learn, not to be taught. Learning requires the use of every resource available to you, which includes the text book. The text books I have suggested for the class are the ones I believe are most consistent with my lectures.

    • THE COURSE GAME -- WHAT HAPPENS IN CLASS (CLICK HERE)

  • NOTE: first video lecture indicates there will be daily quizzes; there will be NO daily quizzes (but there will be frequent surprises!).

  • STRONG SUGGESTION: The course is organized in 6 topics. View all lectures of each topic before first class discussing that topic. Review lectures again as needed (at least once more!). OUTLINE LECTURES!
     I. Lecture Topic
      A. Drawing/Page Topic
        1., 2... Information in Page
    During first viewing, minimize notes to get overview of lecture. Take more detailed notes on second viewing. Identify questions -- seek answers in book, in class, on WWW.

    LECTURE TABLE OF CONTENTS (TOC). The lectures are a series of "panels"; each panel is a module focusing on a specific topic or point. While I do not provide a formal outline of the lectures, I do provide a table of contents (TOC) for each lecture, noting the topic of that panel AND the time mark in the video when that panel starts. This effectively serves as an outline of the lecture and may be helpful as an overview of lecture content and as a reviewing tool. The table of contents are linked to the Sylabus section of the web site, and also on the condensed link to the video lectures.

  • DIGESTION HIGHLIGHTS: What you should know about Digestion. Note: I do not plan on generating such "highlights" for each topic; but this may help you interpret the problem sets. The problem sets are a somewhat more chaotic version of this sheet but go into similar depth.


    Video access... If absolutely necessary, I will put the lectures on a single DVD. Supply me with a blank writable DVD and I will make you a copy. INFORM ME ASAP IF YOU HAVE DIFFICULTY VIEWING THE LECTURES

    Attendance. Close read of the syllabus will remind you I am empowered to deduct points for unexcused / uninformed absences. A final grade of 90 (an A) would now be reduced to 89 (a B+). I will take such attendance any time I feel class size is excessively low. I expect you to be in class when I am in class. If I am not in class, I expect you to be viewing and studying the lectures and course material.


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    ANNOUNCEMENT ARCHIVE

    x/x/x  
     

  • Retired announcments will be placed here for back reference.

    PLEASE NOTE ERRATA SECTION BELOW. As I review the lectures I note inconsistencies. This is normal with any "new publication" though as annoying to me as it probably is to you. I am listing these below for your information as well as for correction the next time I record these.

    Acclimation vs. Adaptation Essay:CLICK HERE


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    Sometimes seeing can help... Below are links to three Histology Web Sites
  • Microscopic Anatomy, Univ. Florida
  • Talking Histology! The images speak! College of Medicine, Univ. Illinois
  • Histosearch: Histology Search Engine
  • Martindale Anatomy and Histology Center"

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    ERRATA: NOTED ERRORS IN LECTURES:

    Error in Introductory lecture (ca. 7:35 min). Not an error so much as science marching forward... When I made this lecture, the independent emergence of plant, fungi and animal lineages was not resolved (and me saying that the three lineages emerged simultaneously). However, currently, a divergence is thought to have occured first between a plant and a fungal/animal lineage, and later between the fungal and animal lineages. Each divergence would have been from a common ancestor. This suggests you are more closely related to a mushroom than you are to an ear of corn, and perhaps explains why one's ancestors might appear somewhat moldy in old pictures....

    Error in Circ3 Lecture (ca. 8 min). Epinephrine (hormone) activates the beta-adrenergic receptor. Nor-epinephrine (neurotransmitter) activates the alpha-adrenergic receptor. At high concentrations, epinephrine also activates the alpha-adrenergic receptor. In my lecture, I reversed alpha and beta; all other aspects of this section (the effects that epinephrine and nor-epinephrine have) are correct. Alpha- and beta-adrenergic receptors are both GPCRs (as is the heart ACh receptor - also called a "metabatrobic ACh receptor" to distinguish it from the "nicotinic ACh receptor" of skeletal muscle which is an ion channel, not a GPCR). (Helpful Web site re. adrenergic receptors: http://www.elmhurst.edu/~chm/vchembook/663adrenergic.html)

    Error in Circ3 Lecture (ca. 13 min). In the discussion of Cardiac Mechanoreceptors. The mechanoreceptor in question INHIBITS ADH release (my lecture says they stimulate release). ADH (anti-diuretic hormone) is also called vasopressin, argenine vasopresssin and AVP; it is a 9 amino acid peptide hormone released from neuroendocrine cells in the posterior pituitary. ADH acts on Kidneys to REDUCE urine production by increasing the recovery of salts and water; this also results in an increase in blood volume and blood pressure. If Type B mechanoreceptors fire if blood volume increases and atria fill too quickly. Body responds by reducing blood volume. This would be accomplished by INHIBITING ADH release, resulting in the kidneys increasing urine production. (I said that Type B mechanoreceptors stimulate ADH release to decrease blood volume, which is incorrect).

    Error in Circ3 Lecture (ca. 18 min). In the discussion of the JGA-Renin-Angiotensin pathway, Renin stimulates the conversion of Angiotensinogen to Angiotensin. I say erroneously say the reverse, but you would recognize that Angiotensinogen (like pepsinogen and trypsinogen), is the precursor and angiotensin (like pepsin and trypsin) is the product. It is all in the name. Angiotensin acts on the kidneys and adrenyl gland to do the things I say angiotensinogen does. This pathway is discussed more fully in Kidney 3, which addresses regulation of the circulatory system. In somewhat more detail, renin is a protease and cleaves Angiotensinogen into two peptides, one of which becomes angiotensin-I; angiotensin-I is converted to angiotensin-II by phosphorylation (via a protein kinase). Angiotensin-II is the active form of the hormone.

    Error in Kid3 Lecture (ca. 12 minutes). Action of ANP. In this slide I say ANP acts on Distal Tubule; should have said Proximal Tubule, as I do in the following slide.

    Error in Kid1 Lecture (ca. 21 minutes). Talking about comparative osmolarities. In lecture I write that SW is 1000 Osm; should be 1000 mOsm (which I say).

    Addition... Getting stronger by exercise? Two things... (1) You increase production of mitochondria and enzymes associated with glycolysis, to increase your ability to produce more ATP. (2) You activate myoblasts which differentiate and fuse to existing muscle fibers, contributing nuclei and producing additional contractile proteins. This is hormonally regulated. Useful web site: The WeighTrainer

    I have linked a short discussion about what you should know re. Muscle Lectures 1 & 2: Notes on Movement (Mus1) and Electrical Properties of Cells (Mus2)




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    E-RESOURCES


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    General Information

      Professor: Richard Vogt, CLS 306; vogt@biol.sc.edu (777-8101)

      Times: Lecture/discussion, Tuesday and Thursday, 11:00 - 12:15, CLS 102

      Required Resources:

        Streamed Video Lectures - REQUIRED!!! (available via Web)

        TEXT: Eckert Animal Physiology, 6th edition (2008) David Randall
        (WH Freeman & Co, (ISBN-10: 0716786303; ISBN-13: 978-0716786306)
        Text info and alternatives: CLICK HERE


      Office Hours: By appointment or e-mail (vogt@biol.sc.edu).

      Course Web Site: http://www.biol.sc.edu/courses/phys/sylb543-08.html (Source of Real Video Streamed Lectures)


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    TEXT BOOK

    NOTE: I DID NOT ASK THE BOOKSTORE TO ORDER A TEXTBOOK FOR THIS COURSE. YOU WILL NEED TO ACQUIRE YOUR TEXT BOOK ON LINE OF FROM AN ALTERNATIVE SOURCE.

      Recommended:
        Eckert Animal Physiology, 6th edition (2008) David Randall
        W H Freeman & Co (Sd)
        (new: $113)
        ISBN-10: 0716786303; ISBN-13: 978-0716786306

      Alternatives:
        Eckert Animal Physiology, 5th edition (2001) David Randall, Warren Burggren, and Kathleen French
        W H Freeman & Co (Sd); (new:$104; used from $55)
        ISBN: 0-7167-3863-5; ISBN-13: 978-0-716-73863-3

        Principles of Animal Physiology (2nd Edition) (2007) Christopher D. Moyes and Patricia M. Schulte
        (new: $108; used from $82)

        Animal Physiology (2nd Edition (2008) Richard W. Hill, Gordon A. Wyse, and Margaret Anderson
        (new: $119; used from $82)

        Environmental Physiology of Animals (2004) Pat Willmer, Graham Stone, and Ian Johnston
        (new: $96; used from $49)

        Animal Physiology: From Genes to Organisms (2004) Lauralee Sherwood, Hillar Klandorf, and Paul Yancey
        (new: $114; used from $75)

      Why a Text Book? To do my job, I have to assume you are in my classes to learn, not to be taught (i.e. active vs. passive in the learning process). In this context, you are empowered by taking advantage of all resources available, including text book, reliable web recourses, scientific literature, in addition to my lectures. Furthermore, text books, by default, define the range of knowledge/information that is assumed to be associated with the subject; this may be much broader than any instructor's lectures. In this context, you have no reason to trust me (or any of your professors), either for my accuracy or for the information I choose to emphasize. By using alternative sources (text books, web) you should get confirmation that I am (or am not) teaching you the things that you need to know / emphasizing the topics that should be emphasized. Read and review the material in your text book!

      Why alternative book choices? Books are shockingly expensive and in my classes used primarily as reference sources. Most text books are quite similar; differences can be made up using other sources such as literature or the internet. And, learning diverse methods of finding useful information is an important accomplishement. If you really cannot get one of the listed books, any general physiology book that is not specific to humans (or to any one species) may serve and feed your specific interests. I will be happy to discuss the merrits of any alternative books with you.

      ONLINE SOURCES FOR BOOKS... You may know others and better...

      Save money... buy/share with a friend or buy used.


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    GENERAL ASSIGNMENT You are responsible to develop an understanding of all material discussed in the lectures and all the questions on the In Class Question sheets. You are responsible to participate in class exercises and to contribute to class discussions. Class discussion is to help all of you become familiar with all of the questions. QUESTION! INQUIRE! LISTEN!

    My goal is to help you develop a fundamental knowledge of physiology that will empower you to continue learning for as long is you need or desire.

    THIS COURSE IS DIFFERENT!!! Formal lectures are on-line videos (Real Stream). Class time will be used to develop and discuss answers to specific questions posed to students. See COURSE GAME below. Exam questions will be selected from among these problem sets; exam questions may be slightly altered.

    Viewing the lectures... Each of you will find your own way. But... I suggest you view the lectures more than once. First viewing - look at all the lectures associated with the topic to gain an overview of material covered re. that topic (there are 6 topics). Take some notes, so that you can track your progress. Subsequent viewing ? take detailed notes. I have provided outlines of the lectures in the form of "Tables of Content". Remember questions that arise, and ask them in class.

    Discussing the material with other students will strengthen you knowledge of the material.

    Attendance is required. Grade penalties will be awarded unexcused absences (see below).


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    ABOUT VIDEOS: The VIDEO LECTURES require a RealONE PLAYER on your computer. The RealONE PLAYER is FREE, and can be obtained by downloading the installation file from www.real.com/ (On 8/3/08 I found the link to the FREE player by clicking "Get RealPlayer11 - Free" button, upper right corner of their home page; the Free player link was clearly noted on the subsequent page: "Free Download". They also sell several upscale versions of the player which you do pay for). Save the file on your computer, click on it to open and the player will self install; or follow instrutions as appropriate.

    VIDEOS BEST VIEWED USING FAST INTERNET CONNECTION (Cable RoadRunner or Telephone DSL) or ON CAMPUS (they do not work well via a regular phone modem) Videos can be viewed on any student computers in Biological Sciences, in the Library, and in most computer labs. You may need to provide your own headphones. IF YOU HAVE PROBLEMS, TELL ME ASAP!

    ADJUST YOUR BANDWIDTH: If the video is not smooth (audio is OK but video seems like a slide show), adjust your Real Player's bandwidth. Do this by opening the Real Player, in the "RealPlayer" dropdown menu choose "Preferences". In "Preferences" choose "Connection". For both "Normal Bandwidth" and "Maximum Bandwidth" choose the highest setting that will work for you. My Suggestion: Connection Speed: DSL/Cable; Maximum Bandwidth: 10Mbps and above. If this does not work, lower the settings until you get the best (continuous movement of video).

    ABOUT PDF FILES: I've included some lecture notes in the form of .pdf files. To read these you will need Adobe Acrobat Reader.
    You can get Adobe Acrobat Reader for free from Adobe's web site and following instructions: Click Here...


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    COURSE GAME - WHAT ACTUALLY HAPPENS IN CLASS
      NOTE: WHEN YOU ARRIVE IN CLASS, IT IS ASSUMED YOU HAVE VIEWED AND ARE FAMILIAR WITH THE LECTURES ASSOCIATED WITH THAT CLASS DATE.

      ou might view this course as a game, where I ask questions and you come up with answers. Resources for these answers are (1) my course videos, (2) text book(s), (3) web info, (4) library/journals, (5) your fellow classmates. The "game" works like this. At the beginning of class I will hand out numbers, 1-8. This will randomly assign each of you to a group and a question (the ICQ or "In Class Question" of the day). You and your group will spend about 5 min developing an answer on the black board; each group will answer each question simultaneously and in order. After about 5 minutes, I will evaluate the answers, pointing out which answers are correct in full or in part and which answers seem miss-directed. Some version of these questions/answers will comprise the exams, so it is really in your interest to play, and to note my comments. All the questions are posted on the course syllabus, so it is assumed you will all come prepared to answer all questions. EASY and FUN!


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    LEARNING OBJECTIVES - COMPARATIVE PHYSIOLOGY
      The purpose of the class is to have students explore, expand, integrate, and assess their knowledge of the biological principals that contribute to the ongoing workings and maintainance of an animal's body, including their own, and to do so in an interdisciplinary manner. Successful studentes will...

      • develop a basic understanding of the major phsyiological problems shared by all animals;
      • develop a basic understanding of the physiological solutions that are present in mammals as other animals;
      • develop a basic understanding of the molecular mechanisms underlying these systems and solutions;
      • be empowered to recognize a common physiological problem and suggest a plausible, testable and detailed mechanism underlying the physiological solution to that problem.


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    EXAMS
      Exams will be in the form of essays and short answers designed to test understanding of the concepts. Students are responsible for knowing and understanding everything from the book, from the video lectures, and from the class discussions; exam questions will be written and evaluated on the assumption students have read the book and are familiar with lectures (video and live) lectures. Knowledge and familiarity of relevant terms, anatomy, etc will be assumed. Knowledge of vocabulary will also be assumed. Mid-term exams will cover the material discussed / presented during the immediately preceding period.

      FINAL EXAM, OPTIONAL: The final will be cumulative over the entire term. Students may accept their grade based on the 3 mid-term exams. The final exam will review previous exams and students wishing to improve their grades are strongly encouraged to take the final exam. [NOTE: If you take the exam and turn it in, your exam score will be factored in to your final grade. If you take the exam (or part of it) and decide NOT to turn it in, your final exam will NOT be factored in to your final grade.]

      Mid-term exams will be 100 points, and the final exam 200 points; thus each mid-term will contribute 20% and the final 40% of your grade (final = powerful points). If you choose the "no-final option", then mid-term exams will each contribute 33% of the FINAL COURSE GRADE. This final total will be lowered by penalty points (unexcused absence - see LACK-OF-ATTENDANCE PENALTY below) or raised by bonus points (acceptable optional reports - see EXTRA CREDIT BELOW)


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    EXTRA CREDIT TOPICS
  • Instructions

    DATE     TOPIC
    Digestion
    8/26
  • 1. Phylogeny and thermodynamic properties of mucus.
  • 2. Regulatory control of salivary gland secretion.
  • 3. Structure and phylogeny of transport proteins.

  • 4. Certain migratory animals (e.g. birds, monarch butterflies) travel incredible distances without feeding. Discuss digestive and metabolic adaptations relating to nutrition (substance and energy demands) that permit this.
  • 5. Animals live in habitats differing considerable in water availability. Discuss digestive (not excretion/kidneys)adaptations that correspond to this environmental extreme.

  • 6. Identify major digestive disease states and discuss their molecular/genetic bases.
  • 7. Structural properties of amino acid and glucose transporters in the intestine.
  • 8. Biochemical mechanism by which mucus is secreted in gastric and/or salivary glands.

  • 9. Phylogenetic comparison of vertebrate, arthropod and cnidarian amino acid transport proteins in digestive (absorptive) epithelia.
  • 10. Nutritional demand feedback on the digestive system - how does your body monitor nutritional needs and mechanistically use that information to regulate uptake of specific nutirents.
  • 11. Do intestinal cells coexpress multiple transport pathways (i.e. for either more than one amino acid class, or for both amino acids and sugars) or are they specific to a specific pathway? How is this regulated (how is the phenotype of a transport cell determined)?

  • 12. Neurobiology of taste receptors; molecular biology of taste.
  • 13. Neurobiology of olfaction; molecular biology of smell.
  • 14. Capsaicins: what are they and why do we detect them (evolution of capsaicin response).
  • 15. Ecology and molecularbiology (mechanism) of bitter taste.

  • Excretion
    9/25
  • 1. Evolutionary study of the use of Urea in Osmoregulation.
  • 2. Influence of PO4 that requires its regulated secretion by the kidneys (why not maintain PO4 pools for ATP production, is PO4 toxic?).
  • 3. Adaptive (comparative) study of the Loop of Henle (excluding the mentioned desert kangaroo rat).
  • 4. Mechanism of action of Urea Transporters or of Aquaporins (most current models based on experimental data).
  • 5. Distribution and function of Aquaporins in non-kindey tissues.
  • 6. Evolutionary analysis of excretory systems ("kindeys") across phyla.
  • 7. Behavioral v. physiological (metabloic) stratagies in water balance - cost / benefit.
  • 8. Physiological changes relating to excretory systems of salmon changing from fresh water life to salt water life, and back again.
  • 9. Comparative study of excretory systems of SW v. FW fish.
  • 10. Endocrine and physiological regulation of aquatic to terrestrial transitions (e,g, land crabs, frogs, mosquitos).

  • Muscles
    10/14
  • 1. Role and action of actin in axon growth.
  • 2. Molecular properties of voltage sensitive Calcium channels.
  • 3. Transport of peptide neurotransmitters (or neurohormones) from cell body to axon terminals (e.g. synapses).
  • 4. Mechanisms of neurotransmitter release (bionchemical interactions between neurotransmitter vesicles and presynaptic membranes - and the action of Calcium).

  • 5. Value of voltage sensitive potassium channels (why do we have and use them)?
  • 6. Properties of neurotransmitter sensitive ("gated") ion channels (e.g. the nicotinic acetylcholine receptor).
  • 7. Differences between neurotransmitter sensitive ion channels and neurotransmitter activated G-protein coupled receptors - focus on temporal and other effects on the post-synaptic neuron.
  • 8. Structural features of actin-troponin-tropomyosin and the action of calcium (more detail than covered in lecture).

  • 9. Actin-myosin-ATP interactions (more detail than covered in lecture).
  • 10. Muscle related diseases that are the consequence of low calcium.
  • 11. Structural / evolutionary relatedness of (a) voltage sensitive Calcium channels, DHP receptors and Ryanodine receptors (why are they all legitimately referred to as calcium channels?).
  • 12. Drug effects (action) on specific biochemical elements in nerve-muscle activation (ion channels, neurotransmitter inactivation, receptors, etc)(focus on one element).

  • 13. Insects have no voltage sensitive sodium channels in muscle, but do have voltage sensitive potassium channels. Given the role of potassium channels in the action potential, why do insect muscles contain voltage sensitive potassium channels?
  • 14. Compare the mechanisms of Ca++ regulation of actin-myosin interactions in (a) skelatal, (b) smooth, and (c) cardiac muscle.

  • Circulation
    11/6
  • 1. Maximum size of organism prior to needing a circulatory system (diffusion distance v time of O2, CO2).
  • 2. How are nutrients or signals (e.g. hormones) moved in a multicellular animal that lacks a circulatory system.
  • 3. Minimal density of capillaries in vertebrate tissue.
  • 4. Organization and/or independent regulation of insect hearts.
  • 5. Describe the physiology of swim bladders.
  • 6. Comparative mechanisms of buoyancy.
  • 7. Current views of lung evolution - derived from swim bladders? Alternative views (scientifically based)?
  • 8. Are bird and mammalian hearts homologous? (both are 4 chamber)
  • 9. Do humans have gills (what became of gill structures)?

  • Gas Exchange
    11/6
  • 1. Biochemical properties of resting Ca++ channels that allow self stimulation of heart cells..
  • 2. Mechanism by which Ach and Epi manipulate the conduction velocity through the AV node.
  • 3. Biochemical mechanism of detecting CO2 in sensory neurons.
  • 4. Biochemical mechanism of detecting blood pressure in sensory neurons.
  • 5. Biochemical mechanism of detecting pH changes in blood.
  • 6. Rational for detecting CO2 rather than O2.
  • 7. Evolution of bicarbonate systems as biological pH buffers.
  • 8. Biochemical mechanism by which Ca++ regulates actin-myosin interactions in cardiac muscle cells.


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    EXTRA CREDIT INSTRUCTIONS.

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    LACK-OF-ATTENDANCE PENALTY (unexcused absence):
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    EVALUATION/GRADES:
    Grades will be determined based on performance on Exams, and adjusted by performance on Extra Credit Essays (and penalties for unexcused absences during presentations), each accorded the following values:
    FINAL GRADES will be: A=90-100; B+=85-89; B=80-84; C+=75-79; C=70-74; D+=65-69; D=60-64; F= less than 60.


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    GRADUATE STUDENTS: As this is a 500 level class, it is available to graduate students as graduate credit. Graduate students will be expected to perpare and be evaluated on an additional specific assignment, developed through discussion with the instructor.
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