A Tour of the Cell

Important words and concepts from Chapter 7, Campbell & Reece, 2002 (1/14/2005):

by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University

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(1) Chapter title: A Tour of the Cell

(a) “…any one cell embodying as it does the record of a billion years of evolution, represents more an historical than a physical event…. You cannot expect to explain so wise an old bird in a few simple words.” Max Delbrück (as quoted by Stent, in Max Delbrück, 1906-1981, 1982, Genetics 101:1-16)

(b) “In an ideal world, biological processes would be understood at the molecular level by first identifying all the participating components and then by deducing their roles in the system through experiment. In reality, knowledge of each component is hard-won, and the temptation to assume that the key players are those that are currently known, ever-present.” (Adrian Bird, DNA methylation de novo, 1999, Science 286:2287-2288)

How to do Biology 113, Phase II

Now that we are just past the first exam and you are wondering what happened/how to improve…

1. The questions come from the notes that I hand out; study anything else (for the exam) and you are not being efficient. Reading the text is a great way to become familiar with and otherwise come to understand the concepts. That’s great, and should be the first thing you do as we move along in the course. However, I make no effort to pull exam questions directly from your text (except for assigned problems or for bonus questions on exams). Therefore you are not working efficiently if you are studying from your text, except to the degree that going back to your text aids in your understanding of the material. Similarly, while in the lectures I try to highlight the material, particularly that which is more difficult to understand, I do not write exam questions directly from what I present in the classroom (again, except for bonus questions on exams). Your text and lectures are a great way of repetitively increasing your familiarity and understanding of the material, but your lecture notes—the third in this triad of repetition—are where the exam questions come from.

2. Reading is not necessarily equivalent to studying. That doesn’t mean that you shouldn’t read, but studying involves trying to understand concepts and forcing information into your brain, and often those processes can be quite strenuous. If are not straining to some degree (other than fighting the studying process) then you likely are not so much studying as reviewing. The latter is a poor substitute for the former.

3. Putting in more time is not necessarily as important as studying well, efficiently, or effectively. Clearly if you studied for 20 hours for the first exam in this course and did not earn at least a B (and preferably a much higher grade) then you really need to reexamine how it is that you study to make much better use of your time.

4. You are not putting in a lot of time in until you are putting in excess of ~20 hours/week to studying biology/attending class and lab. But remember that seven hours of that 20 is spent in class or in lab and even just one hour spent per period per week works out to another five hours committed to biology.

5. If you don't learn/understand the material before going on to the next topic/material, when will you learn the old material? You won’t have enough time to learn material for the first time while you are studying for an exam. Furthermore, for most people learning thrives on repetition over relatively long spans of time. Such long-term repetition is not possible if you put off studying until exam time. Instead, you have to pause at difficult concepts when we first encounter them and at least make a cursory effort towards gaining some understanding.

6. Organizing the material is not equivalent to studying for exams (though certainly it helps you prepare for studying). If you are copying down material or even triaging while you are preparing for an exam, just keep in mind that while you may feel very productive while you are doing this, you aren’t actually studying (or at least not studying very intensively) for that exam. Organizing is great, can be very time consuming, but, like reading, it isn’t really studying.

7. If you want to do well, you must learn the majority of the material really, really well. You need to go for both breadth and depth. I will be testing you on both. If you blow off learning material, or otherwise don’t have time to get to it, you are simply taking a chance that this material will not be found on the exam. Typically it is very easy for me to tell when the breadth or depth of a student’s grasp of the material is not great. Often I may be accused of being picayune or of not adequately testing a student on what they do know—but my goal is to get you to a point where you both really know biology and really know how to study biology, and I think my exams do a wonderful job of determining the degree to which you have addressed both goals.

8. Try triaging, i.e., concentrate on learning and memorizing that material that (a) you don't know/have memorized and (b) have some reasonable probability of learning. But don’t fall into the trap of triaging away a large chunk of material simply because you haven’t given yourself sufficient time to study for an exam. Your triaging should be done days before the actual exam. And then, if you have time, you can go back to that material you discarded as being hopeless. But don’t, in the process, stress yourself out. That can sometimes be worse than just ignoring some material since stress can make you under perform even on material you do know well.

9. Part of studying for the exam should involved IDing that material to concentrate your studying on. Part of your college education is going to involve learning how to predict what an individual (your professor) cares about versus what serves simply as extraneous fluff. One of the secrets of college-level success is being able to focus on the material that is most important or most likely to end up as an exam question.

10. If you can't at least make a reasonable attempt at knowing the material to the point where you can recite it from memory, then you are not doing an adequate job of studying for an exam. One can similarly say that if you don’t reach a certain level of understanding of the material over the course of your studying then similarly you are not doing an adequate job studying, and it should be stressed that it is a whole lot easier to memorize material you understand (and, of course, that you care about) than it is to memorize material that you do not understand. Understanding allows derivation, and derivation (deductive along with inductive reasoning) is basically what much of biology is all about.

11. Don't put off learning the material until the night before the exam. And don’t forget to get a good night’s sleep prior to the exam. Take care of yourself. Treat yourself well and your self will respond by performing at a high level when that becomes necessary. An exam is like an athletic event. It takes training to do well, and it also takes peaking on the day of the event. Nobody I’ve ever met prepares to run a marathon by pulling an all nighter the night before nor spends that time running, running, and then running some more. The night before the event is a time to take care of yourself so that you will be in peak form when it comes time to prove yourself. Similarly, stressing yourself out by studying the day of the exam may allow you to learn material you really should have had down pat the night before (if not days prior), but at what cost in your ability to calmly and effectively understand and then correctly answer exam questions?

12. Studying is not easy, no way, no how (and that's why you get summers off). Indeed, studying towards a science degree can be so difficult that you might consider the pros and cons of prioritizing much more into your life except studying. But don’t forget that you need to have a life, too. If you aren’t enjoying yourself, then you may end up considering your classes to be a burden, but it is far easier to do something within the context of pleasure than to persevere in the face of pain. Do yourself a favor, do what it takes to live a long, kind, and enjoyable life.

BASIC PROPERTIES OF CELLS

(2) Cells

(a) Cells are the fundamental units distinguishing living from non-living entities

(b) Cells are membrane-enclosed, DNA-containing, metabolizing, and self-replicating

(3) Organelle

(a) Organelles are sub-cellular, multimolecular, organic machines

(b) Some organelles are surrounded by membranes (membrane-bound organelle)

(d) [organelle (Google Search)] [organelles (Caduceus MCAT Review)] [index]

(4) Prokaryote

(a) Prokaryotes are organisms whose cells lack nuclei

(b) Prokaryotic cells generally lack membrane-bound organelles

(d) Bacteria are an example of prokaryotic organisms (in addition to the previous link, see also the chapters 18 and 27 of your text)

(e) See Figure 7.4, A prokaryotic cell

(f) [prokaryote (Google Search)] [index]

(5) Eukaryote

(a) Eukaryotes have cells that contain nuclei

(b) Generally, eukaryotic cells contain membrane-bound organelles in addition to the membrane-bound nuclei

(c) Individual eukaryotic cells also tend to be quite a bit larger than individual prokaryotic cells (e.g, prokaryotic cells are about the size of the mitochondria or chloroplasts in Figures 7.7 and 7.8)

(d) Eukaryotes are typically unicellular (i.e., protozoa ) but there are many (and you are more familiar with) multicellular eukaryotes (i.e., plants, fungi, animals)

(e) See Figures 7.7 and 7.8 (for comparison to Figure 7.4): Overview of an animal cell, Overview of a plant cell, and A prokaryotic cells (respectively)

(f) Note in Figures 7.7 and 7.8 the various organelles, both membrane-bound and not membrane bound

(g) [eukaryote (Google Search)] [virtual plant cell (Matej Lexa)] [index]

(6) Plasma membrane

(a) The plasma membrane is the membrane surrounding and defining the limits of individual cells

(b) Not all membranes associated with a cell are the plasma membrane

(d) Note that the rate of nutrient acquisition and waste removal by a cell is proportional to area of plasma membrane (see "cells are small" below)

(e) See Figure 7.7, Overview of an animal cell

(f) [plasma membrane (Google Search)] [the cell membrane (Online Biology Book)] [plasma membrane (Caduceus MCAT Review)] [index]

(g) For more on membranes and membrane function, see the chapter 8

(7) Cytoplasm

(a) The cytoplasm is the stuff contained by the plasma membrane

(b) The cytoplasm consists of water solution, macromolecules, salts, various non-membrane-bound organelles, and a number of structural components

(d) See Figure 7.7, Overview of an animal cell

(e) [cytoplasm (Google Search)] [cytoplasmic constituents (Timothy Paustian’s Microbiology Textbook)] [index]

(8) Cytosol

(a) The cytosol is the water solution that makes up the cytoplasm (that is, the cytoplasm is the swimming pool while the cytosol is the water, you are an organelle… ha, ha)

(b) See Figure 7.7, Overview of an animal cell

(d) [cytosol (Google Search)] [index]

(9) Cells are small

(a) The size of cells is limited by the plasma-membrane-area-to-cytoplasmic-volume ratio

(b) The more cytoplasm a cell has, the more plasma membrane it needs to carry off wastes and obtain nutrients through

(c) As cell volumes increase in size, the ratio of surface area to interior volume decreases (these arguments are based simply on geometry, i.e., the formula for the volume of a solid versus the formula for the surface-area of a solid; the former increases as a cube function while the latter increases only as a square function)

(d) Consequently, bigger and bigger cells have greater and greater problems feeding themselves, ultimately limiting the useful size that cells may obtain

(e) One way around this surface-area constraint on cell size is the formation of various structures that serve either to increase the area of the plasma membrane without significantly increasing cytoplasmic volume (e.g., infolding of the plasma membrane) or to develop specialized cellular components that serve to increase membrane area without actually increasing the surface area of a cell’s plasma membrane (e.g., the endomembrane system of eukaryotic cells)

(f) See Figure 7.5, Geometric relationships explain why most cells microscopic?

(10) Compartmentalization

(a) In procaryotes the plasma membrane is additionally employed as an anchor for enzymes

(b) Since procaryotes typically lack internal membranes (i.e., no membrane-bound organelles) they have only limited membrane in which to anchor these enzymes

(d) Together these limitations circumscribe (i.e., restrict) the structural/morphological/even biochemical complexity individual procaryotes can attain

(e) By contrast, eucaryotic cells have numerous membranes in addition to the plasma membrane

(f) See Figure 7.7, Overview of an animal cell

(g) FAQ: What exactly is compartmentalization? The idea is that two otherwise incompatible chemical reactions can go on within the same cell so long as they don't (can't) come into contact with each other. How to keep them apart? By placing a membrane between the two reactions. Thus, within eukaryotic cells there exist numerous membrane-enclosed compartments such as lysosomes (and the rest of the endomembrane system), mitochondria, etc. This allows eucaryotes to perform more sophisticated intracellular chemistry than can procaryotes.

(h) [cell compartmentalization (Google Search)] [index]

(11) Membrane-bound organelle

(a) An important distinction between prokaryotic and eukaryotic cells is for the most part the absence in the former and the ubiquitous presence in the latter of membrane-bound organelles

(b) A membrane-bound organelle is an organelle that is bounded, i.e., surrounded, by a lipid bilayer

(c) A major component of the membrane-bound organelles found in eukaryotic cells are members of what is known as the endomembrane system plus the various endosymbionts (e.g., mitochondria and chloroplasts)

(d) [membrane-bound organelle (Google Search)] [index]

ENDOMEMBRANE

(12) Endomembrane system

(a) Many of the eukaryotic membranes form an interconnected or otherwise related network called the endomembrane system

(b) Via the endomembrane system, the membranes associated with different organelle members have different jobs

(c) Members of the endomembrane system may be either physically continuous with other members or not continuous but still communicating with other members of the endomembrane system via the release and fusion of transport vesicles

(d) See Figure 7.7, Overview of an animal cell

(e) Included in the endomembrane system are:

(i) the nuclear membrane

(ii) the endoplasmic reticulum (both rough and smooth)

(iii) the golgi apparatus

(iv) lysosomes

(v) vacuoles

(vi) the plasma membrane

(vii) transport vesicles

(f) [endomembrane system (Google Search)] [index]

(13) Nucleus

(a) In eukaryotic cells the cell DNA is separated from the cytoplasm