Important words and concepts from Chapter 7, Campbell & Reece, 2002 (1/14/2005):
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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
(a) Cells are the fundamental units distinguishing living from non-living entities
(a) Organelles are sub-cellular, multimolecular, organic machines
(b) Some organelles are surrounded by membranes (membrane-bound organelle)
(c) Others organelles lack membranes
(4) Prokaryote (see also prokaryote)
(a) Prokaryotes are organisms whose cells lack nuclei
(b) Prokaryotic cells generally lack membrane-bound organelles
(c) Prokaryotic organisms are typically unicellular
(e) See Figure, A prokaryotic cell
(5) Eukaryote (see also eukaryote)
(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)
(e) See Figures: Overview of an animal cell, Overview of a plant cell, and A prokaryotic cells (respectively)
(f) Note in Figures the various organelles, both membrane-bound and not membrane bound
(6) Plasma membrane (see also plasma membrane)
(b) Not all membranes associated with a cell are the plasma membrane
(c) Like all membranes associated with a cell, the plasma membrane forms a selective barrier
(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, Overview of an animal cell
(g) For more on membranes and membrane function, see the chapter 8
(7) Cytoplasm (see also cytoplasm)
(a) The cytoplasm is the stuff contained by the plasma membrane
(c) The cytoplasm is the stuff that is external to membrane-bound organelles
(b) See Figure, Overview of an animal cell
(c) Note that many consider the terms cytoplasm and cytosol to be synonymous
(9) Cells are small (see also surface-to-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, Geometric relationships explain why most cells microscopic?
(10) Compartmentalization (see also compartmentalization)
(b) Since prokaryotes typically lack internal membranes (i.e., no membrane-bound organelles) they have only limited membrane in which to anchor these enzymes
(c) In addition, prokaryotes have only a limited potential to separate mutually-incompatible metabolic processes
(d) Together these limitations circumscribe (i.e., restrict) the structural/morphological/even biochemical complexity individual prokaryotes can attain
(e) By contrast, eucaryotic cells have numerous membranes in addition to the plasma membrane
(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 eukaryotes to perform more sophisticated intracellular chemistry than can prokaryotes.
(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)
(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, Overview of an animal cell
(e) Included in the endomembrane system are:
(i) the nuclear membrane
(iii) the Golgi apparatus
(vi) the plasma membrane
(vii) transport vesicles
(13) Nucleus (see also cell nucleus)
(b) Most of this DNA is contained within the cell's nucleus
(c) The DNA within the nucleus is found as DNA-protein structures called chromatin
(f) Prokaryotic cells, by definition, lack nuclei (which is the plural of nucleus)
(14) Nuclear membrane (see also nuclear membrane)
(a) The nuclear membrane is a double membrane
(e) Connecting the interior volume of a nucleus with the external cytoplasm are numerous pores that form a fluid-filled bridge that crosses the nuclear membrane
(f) See Figure, The nucleus and its envelope
(b) Ribosomes come in two types differing only in their cellular location
(c) Free ribosomes are suspended in the cytosol
(e) See Figure, Ribosomes
(16) Nucleolus (see also nucleolus)
(b) Ribosomes are assembled in a region called the nucleolus
(c) After assembly, ribosomes are transported to the cytoplasm, exiting the nucleus via the nuclear pores
(d) See Figure, Ribosomes
(b) The endoplasmic reticulum is a network of membranous tubules and sacs called cisternae
(c) See Figure, Endoplasmic reticulum
(d) The space within the ER (lumen) is continuous with the space between the two membranes of the nucleus
(a) Rough endoplasmic reticulum derives its name from its rough appearance in electron micrographs
(c) The rough ER is responsible for:
(ii) synthesis of integral-membrane-protein synthesis
(iii) some protein modification
(iv) membrane assembly
(19) Smooth endoplasmic reticulum (smooth ER) (see also smooth endoplasmic reticulum)
(b) See Figure, Endoplasmic reticulum (ER)
(c) Responsible for:
(i) lipid synthesis (particularly steroids)
(ii) carbohydrate metabolism (e.g., glycogen metabolism)
(iii) poison and drug detoxification
(20) Transport vesicles (see also vesicle)
(b) The rest of the endomembrane-system members communicate via transport vesicles
(c) See Figure, Review: relationships among endomembranes, respectively
(d) See Figure, Overview of an animal cell
(e) Transport vesicles are membrane-enclosed, more-or-less spherical objects whose interior (lumen) is equivalent to the interior (lumen) of the ER
(f) Transport vesicles arise from various endomembrane-system members
(g) Transport vesicles transport their contents and membranes to endomembrane-system members by fusing their membranes with target members
(h) Targets can be many or all of the various endomembrane-system members
(a) Central to the transport of vesicles is the golgi apparatus
(c) The Golgi is also involved in protein modification and storage
(d) The golgi is also a site of manufacturing of certain materials
(e) FAQ: Golgi apparatus- a little more info dealing with the transport vesicles? The Golgi isn't directly connected to either the ER or any of its various targets (e.g., the plasma membrane). Movement of membrane-enclosed "compartments" (i.e., vesicles) to and from the Golgi allows the movement of membrane as well as endomembrane luminal contents (e.g., proteins) to and from the Golgi. These vesicles form by pinching off from existing endomembrane system components and deliver by fusing with endomembrane components. They allow a communication between endomembrane components without (drastically) disrupting compartmentalization. Vesicles differ according to their contents and targets. One job of the Golgi is to properly match targets with contents.
(a) See Figure, The Golgi Apparatus
(c) The side of the golgi closest to the ER is called the cis face
(d) The side of the golgi farthest from the ER is called the trans face
(h) It is the Golgi apparatus's job to make sure that substances, including membrane components, are shipped to the correct locations
(23) Lumen protein, secreted protein, and membrane-protein synthesis (see also secreted protein)
(e) Some proteins are only partially extruded through the membrane; these remain in the membrane and most of a cell's integral membrane proteins (all?) are produced in this manner
(f) See Figure, Review: relationship among endomembranes
(k) The proteins within secretory vesicles represent proteins to-be secreted by a cell
(24) Lysosomes (see also lysosome)
(b) Lysosomes are created by the Golgi apparatus
(d) The job of lysosomes is to provide a region that is separate from the cytoplasm in which cellular components may be digested back to their component parts
(e) This separation (compartmentalization) protects the cell from uncontrolled auto-digestion
(25) Vacuoles (see also vacuole)
(a) Various other components of the endomembrane system are termed vacuoles
(d) See Figure, The plant cell vacuole
(e) See Figure, Overview of a plant cell
(g) FAQ: What is a vacuole, other than a component of the endomembrane system that are connected to the Golgi? Vacuoles aren't physically connected to the Golgi. A vacuole is just a big vesicle. That is, vacuoles are yet another part of the endomembrane system that is not physically continuous with the ER, the Golgi, the plasma membrane, etc. There are a number of different, specialized endomembrane components that are called vacuoles including food vacuoles (where stuff engulfed during endocytosis ends up), contractile vacuoles (which pump water out of the highly hypertonic cytoplasm of protozoa), and, of course, the central vacuole in plant cells which is a storage area that serves, in part, to take up space within the plant cell. Cytoplasmic components are expensive (mitochondria, chloroplasts, ribosomes, proteins, etc.). Central vacuoles allow plant cells to have a relatively large volume while simultaneously having a relatively small cytoplasmic volume. Other functions are listed in your text.
(b) Enclosed within these food vacuoles may be trapped extra-cellular material
(d) See Figure, The formation and functions of lysosome
(a) Gram-negative bacteria are a type of bacteria that includes many pathogenic bacterial types, such as Escherichia coli (though, in fact, many more are not pathogenic than are pathogenic)
(b) The typical cellular anatomy of a Gram-negative bacterium includes, outside going in:
(i) outer membrane
(ii) cell wall
(iii) periplasmic space
(iv) inner membrane
(c) (Gram-positive bacteria, another type of bacteria, are similar in their cellular anatomy to Gram-negative bacteria but lack the outer membrane and also lack the periplasmic space)
(d) Gram-negative bacteria, like most bacteria, divide by binary fission
(e) Many Gram-negative bacteria, as well as Gram-positive bacteria generate their ATP via cellular respiration, by mechanisms very similar to how the mitochondria of eukaryotic cells generate ATP, also via cellular respiration
(28) Mitochondria (see also mitochondria)
(c) See Figure, The mitochondrion, site of cellular respiration
(d) Mitochondrial structures, analogous to those found in Gram-negative bacteria, include going from the outside in:
(i) outer membrane
(ii) intermembrane space (periplasmic-space equivalent)
(iii) inner membrane
(iv) mitochondrial matrix (cytoplasm equivalent)
(e) Mitochondria divide by binary fission
(f) Notably absent from the above list is the Gram-negative cell wall but, nevertheless, mitochondria are essentially gram-negative bacterium in terms of structure as well as their genetics and biochemistry
(g) Though membranous, note that mitochondria are not a part of endomembrane system
(h) We will consider the origin of mitochondria in greater detail in chapter 28 of your text; suffice for now with our simply noting that mitochondria in fact are Gram-negative bacteria that live within the cytoplasm of most eukaryotic cells and which are responsible for carrying out the cellular respiration from which eukaryotic cells derive most of their ATP
(i) See Figure, Overview of a animal cell
(29) Cristae (see also cristae)
(b) The existence of these folds, called cristae, serves to increase the amount cellular-respiration enzymes found only in the mitochondria inner membrane, and therefore to increase the cellular-respiration capacity of a given mitochondrion
(c) See Figure, The mitochondrion, site of cellular respiration
(30) Cyanobacteria (see also cyanobacteria)
(a) Cyanobacteria are Gram-negative-like bacteria that live particularly in water (they are a constituent of pond scum)
(31) Chloroplast (see also chloroplast)
(b) See Figure, The chloroplast, site of photosynthesis
(c) Chloroplast structures, analogous to those also found in cyanobacteria, include going from the outside in:
(i) outer membrane
(ii) intermembrane space
(iii) inner membrane
(iv) stroma (the cytoplasm equivalent, liquid found external to the thylakoids)
(e) Chloroplasts are not a part of endomembrane system
(f) Yes, chloroplasts, like mitochondria, are essentially gram-negative bacteria, though chloroplasts particularly are not-free-living cyanobacteria
(g) Other, non-photosynthesizing bacteria-like plastids also exist in plants
(h) See Figure, Overview of a plant cell
(b) These organelles look like flattened disks (they have a large surface they expose to sun)
(c) These disks arrayed in stacks called grana (singular: granum)
(d) The thylakoids are derived from the inner membrane of chloroplasts
(f) The interior of thylakoids is called the thylakoid space
(g) See Figure, The chloroplast, site of photosynthesis
(33) Cytoskeleton (see also cytoskeleton)
(b) There are three classes of fibers:
(iii) intermediate filaments
(c) See Table, The structure and function of the cytoskeleton
(d) The cytoskeleton members perform various functions as discussed below
(a) Microtubules are the largest-diameter cytoskeleton components
(b) Microtubules can be very long (e.g., on the order of cell dimensions)
(d) Microtubules serve to shape and support the cell
(e) Microtubules are easily dismantled by removing tubulin subunits; they are also easily lengthened by adding tubulin subunits
(f) Microtubules serve as tracks along which organelles can move
(g) See Figure, Motor molecules and the cytoskeleton
(a) The centrosome is essentially the central microtubule-supporting member
(b) Microtubules radiate out from a single centrosome, rigidly supporting cell structure
(c) Within the centrosome are a pair of centrioles
(d) See Figure, Centrosome containing a pair of centrioles
(e) The centrioles are replicated during cell division so that each daughter cell receives one centrosome
(a) Microtubules also make up cilia and flagella
(c) Flagella are long, whip-like structures that are typically few in number per cell
(d) Cilia are shorter, oar-like structures that are typically many in number per cell
(f) See Figure, A comparison of the beating of flagella and cilia
(g) Cilia are also involved in movement of material over surfaces of cell (e.g., ciliated cells line the respiratory system and push foreign material out of the lungs, but are paralyzed by cigarette smoke, hence the smoker's hack)
(h) See Figure, Ultrastructure of a eukaryotic flagellum or cilium
(i) The microtubules internally support the shape of cilia and flagella
(j) The microtubules also interact, partially sliding past one-another to allow cilia and flagella to bend (mechanism analogous to what makes muscles contract; also ATP-powered)
(k) See Figure, How dynein "walking" moves cilia and flagella
(a) Microfilaments consist of two twisted-together chains of actin-protein subunits
(b) Microfilaments are the smallest in diameter of the cytoskeleton components
(c) Together with the protein myosin, microfilaments make up the contractile organelles within muscle cells
(d) See Figure, Microfilaments and motility
(e) ATP powers movement of actin filaments relative to myosin filaments
(g) Microfilaments are also involved in projection of pseudopodia (amoeboid movement)
(h) See Figure, Microfilaments and motility
(j) See Figure, Microfilaments and motility
(k) Microfilaments also support microvilli (non-movable finger-like projections superficially resembling cilia)
(l) See Figure, A structural role of microfilaments
(38) Intermediate filaments (see also intermediate filament)
(a) Intermediate filaments are a more-structurally diverse array of cytoskeleton components
(b) The extracellular matrix glues animal cells together
(d) These are the fibers and the gluey matrix in which these fibers are embedded, respectively
(e) See Figure, Extracellular matrix of an animal cell
CONNECTIONS BETWEEN CELLS
(a) Various molecules and structures attach to the outside (as well as inside) of the plasma membrane
(b) On the inside is the cytoskeleton
(c) On the outside is the extracellular matrix
(d) Desmosomes: Plasma membranes can attach to adjacent cells for increased structural support of tissue
(e) Gap Junctions: Protein tubes between adjacent cells form, for relatively small molecules (up to about 1000 dalton) a continuous cytoplasm between cells
(f) Tight junctions: Plasma membranes form junctions between them that are water tight
(g) See Figure, Intercellular junctions in animal tissues
(c) Bound ribosomes
(e) Cells are small
(x) Free ribosomes
(y) Gap junctions
(z) Golgi apparatus
(kk) Nuclear membrane
(pp) Plasma membrane
(uu) Smooth ER
(ww) Thylakoid space
(xx) Tight junctions
(yy) Transport vesicles
(42) Practice questions [index]
(a) Name five membrane-bound organelles that are members of the endomembrane system.
(b) In terms of function, distinguish the cis from the trans faces of the Golgi apparatus.
(c) In terms of function, distinguish bound from free ribosomes.
(d) Neatly sketch a mitochondrion, labeling four components (but don't show or label enzymes or pathways involved in cellular respiration, i.e., don't include these as one or more of the four components shown).
(e) Matching: (a) microtubule, (b) microfilament, (c) intermediate filament. Each may be used more than once.
(i) flagella __________
(ii) muscles __________
(iii) structurally diverse _________
(iv) centrosome __________
(v) tubulin subunits __________
(f) Collagen fibers are found inside/outside (circle one of previous) of cells as supporting components of the __________.
(g) Within which specific structure of eucaryotic cells do to-be-secreted proteins do the majority of their folding? (neither cytoplasm nor Golgi are correct answers)
(i) inner membrane __________
(ii) grana __________
(iii) golgi _________
(iv) matrix __________
(v) outer membrane __________
(i) Define Cristae and Cisternae.
(j) Complete the table:
Protein consists of
(k) Name five organelles that may be found in unicellular eukaryotes that are not found in unicellular prokaryotes.
(l) What water-solution-filled space is physically continuous (i.e., not just connected via transport vesicles) with the water solution-filled space found between the two membranes of the nucleus? Be specific.
(m) What specific structure/region is associated with ribosome assembly. (hint: nucleus is not the answer)
(n) The smooth endoplasmic reticulum is associated with the synthesis (i.e., anabolism) of what?
(o) Distinguish the cis and trans faces of the Golgi apparatus.
(p) In terms of their synthesis via ribosomes, how are membrane proteins (found in the endomembrane system) and secreted proteins similar?
(q) Name three types of things that divide by binary fission. These things may be free living or can take the form of organelles. Include at least two organelles in your list.
(r) What category of members-of-the-cytoskeleton serve as tracks along which organelles can move within the cytoplasm?
(s) Define cytosol.
(t) Complete the table:
(u) It is the job of what eukaryotic organelle to make sure that to-be-secreted proteins as well as membrane proteins are both shipped to the correct locations?
(v) What kind of a cytoskeleton component is associated with a centriole?
(w) The defining difference between smooth and rough endoplasmic reticulum is __________ (short answer).
(x) The plasma membranes of adjacent cells can interact in a number of ways, employing a more-or-less equal number of specialized structures. Name two ways in which plasma membranes can interact.
(y) What is a proteoglycan?
(z) __________ are more structurally diverse and more permanently assembled.
(i) Actin filaments
(ii) Intermediate filaments
(aa) Microtubules radiate out from a single __________, supporting the interphase cell structure.
(bb) What are thylakoids?
(cc) Another name for free-living Gram-negative-like bacteria that photosynthesize in a manner that is very similar to that of the chloroplasts of green plants is __________.
(dd) Name an organelle that is found within the matrix of mitochondria (matrix, cytoplasm, inner membrane, and cristae are all not correct answers).
(ee) Following phagocytosis, what kind of endomembrane member is the engulfed material now found in?
(ff) Another name for an intracellular compartment that contains hydrolytic enzymes is _________.
(gg) Other than location, what do secreted proteins and membrane proteins have in common that distinguishes them from the soluble proteins that are found in the cytoplasm.
(hh) What are cisternae?
(ii) What portion of the endomembrane system is involved in the detoxification of many especially hydrophobic drugs? Be reasonably specific.
(jj) Name two members of the endomembrane system that are continuously physically connected. Vesicles are not one of the two answers.
(kk) What kind of cells lack a nucleus?
(ll) Which kind of cell has the least compartmentalization?
(i) Animal cells
(iii) Gram-negative bacteria
(iv) Plant cells
(mm) What limits the size of cells? For example, why can't most cells be the size of a baseball? ("not enough room" is definitely not the answer I am looking for)
(nn) Cells may be described fundamentally as entities that are DNA-containing, self-replicating, metabolizing, and ________ enclosed.
(oo) Another name for subcellular machines that are much larger than individual proteins but (of course) much smaller than the cell itself is __________.
(pp) Cells that contain nuclei are called __________ cells to distinguish them in terms of basic cellular structure from the morphologically distinct bacteria cells (which lack nuclei).
(qq) The selectively permeable barrier surrounding/defining the limits of a cell is called a(n) __________.
(rr) The rate of nutrient acquisition and carrying off of wastes limits what aspect of cellular anatomy?
(ss) Most of the membrane-bound organelles found in, for example, animal cells are members of the __________ system.
(tt) Draw a nucleus indicating all relevant features shown in Figure of your text ("The nucleus and its envelope"). Please draw all lipid bilayers as two-layered structures (e.g., ===== rather than -----) and with the nucleus as it appears in interphase I of the cell cycle.
(uu) In addition to the nuclear membrane, rough endoplasmic reticulum is physically connected (attached) to what otherwise not membrane-bound organelle?
(vv) Most endomembrane-system membranes are targets for fusion with the relatively small-sized members of the endomembrane system called __________.
(ww) Disintegration of the membrane-enclosed organelles called __________ can lead to cellular auto-digestion.
(xx) By what process does food come to appear in food vacuoles?
(yy) Cristae increase the __________ capacity of individual mitochondria.
(zz) The interior of a thylakoid is called a(n) __________.
(aaa) Which is more-intimately involved in the movement of material over cell surfaces such as the movement of material up and out of the lungs via what is known as the mucociliary escalator?
(i) Intermediate filaments
(bbb) Which cytoskeleton member is associated with the protein myosin, effecting muscle contraction?
(i) Intermediate filaments
(ccc) Proteoglycan and collagen together make up a substantial portion of the __________ that surrounds many animal cells.
(ddd) A category of cellular life forms that are typically unicellular and also typically lacking in membrane-bound organelles are the __________.
(eee) A category of cellular life forms that are typically unicellular (though there also are abundant and wondrous exceptions) and also typically contain membrane-bound organelles are the __________.
(fff) All cells possess a lipid bilayer commonly called the/a/an __________ membrane (I'm looking for an answer other than "cell" or "cytoplasmic").
(ggg) Most membrane-bound organelles in turn have their lipid bilayers surrounded by the relatively fluid __________ contained by the plasma membrane.
(hhh) To deal with the need to carry off wastes plus to obtain nutrients, bigger cells require proportionately more __________, which can be challenging to attain as a consequence of simple laws of geometry.
(iii) Due to their relative lack of membrane-bound organelles, prokaryotes must employ their plasma membrane as an anchor for membrane-associated enzymes plus most prokaryotes lack the ability to __________ (a.k.a., separate) incompatible metabolic processes. Together these limitations circumscribe the morphological, structural, and biochemical complexity individual prokaryotes can attain.
(jjj) Membrane-bound organelles are bounded by __________ ("membrane" not the answer).
(kkk) The endomembrane system of eukaryotic cells includes the nuclear membrane, the endoplasmic reticulum (both rough and smooth), the Golgi apparatus, lysosomes, the plasma membrane, vacuoles, and __________.
(lll) Bound ribosomes are bound to what? Be specific.
(mmm) Found associated with the nucleus of eukaryotic cells are the inner and outer nuclear membranes and, bounded within the space created by the inner nuclear membrane, are the chromatin/chromosomes and the ________.
(nnn) The tubular network known as the __________ consists of membrane, a lumen, and cisternae.
(ooo) Describe two functions of the rough endoplasmic reticulum.
(ppp) Though not physically continuous with the other members of the endomembrane system, the Golgi apparatus nevertheless "communicates" with these other structures via movement of __________, which are important additional members of the endomembrane system.
(qqq) The trans face of the Golgi apparatus receives vesicles from where?
(rrr) Explain why it is that in eukaryotes soluble proteins found in the cytosol do not typically have oligosaccharides attached to them, but secreted and membrane proteins often do.
(sss) The membrane of what membrane-bound organelle helps protect cells from auto-digestion?
(ttt) From what endo-membrane member do food vacuoles originate?
(uuu) Draw and label a mitochondrion indicating the outer membrane, inner membrane, and matrix.
(vvv) Which of the following is not a member of the endomembrane system?
(i) Golgi apparatus
(ii) Inner nuclear membrane
(iv) Smooth endoplasmic reticulum
(www) What purpose do cristae serve?
(xxx) Which membrane-bound organelle is indeed found within at least some prokaryotic cells?
(ii) Endoplasmic reticulum
(iii) Nuclear membrane
(iv) Outer membrane
(yyy) The portion of a chloroplast that surrounded by but nevertheless is not continuous with the stroma is called the __________ space.
(zzz) Name three distinct types or categories of proteinaceous fibers found within eukaryotic cells.
(aaaa) Cilia and flagella are internally supported by __________.
(ii) Intermediate filaments
(bbbb) The cytoplasmic streaming seen in plants and the projection of pseudopods by amoebas are both powered by ATP and involve the cytoskeleton member known as __________.
(cccc) Where relative to eukaryotic cells such as animal cells is proteoglycan located?
(dddd) What is a desmosome?
(eeee) What is a cell?
(ffff) What do prokaryotes lack that eukaryotes possess?
(gggg) The rate of nutrient acquisition and waste removal of a cell is proportional to the area of what?
(hhhh) What is the general term for the "stuff" that is external to the membrane-bound organelles found within eukaryotic cells?
(iiii) Most of the membrane-bound organelles found within a eukaryotic cell are components of the __________ system.
(jjjj) A typical eukaryote's cell nucleus is separated from the cytoplasm by __________.
(i) A plasma membrane
(ii) A protein sheath
(iv) The rough endoplasmic reticulum
(v) Two membranes
(kkkk) To the cytoplasmic side of what membrane-bound organelle within eukaryotic cells are ribosomes attached?
(llll) What is found external to the nucleus but is physically continuous with the nuclear membranes?
(mmmm) In eukaryotic cells, what organelle is the site of integral-membrane-protein synthesis (looking for term(s) other than ribosome).
(nnnn) In eukaryotic cells the detoxification of certain poisons and the synthesis of certain lipids (such as steroids) occurs where?
(oooo) Central to the transport of vesicles within the cytoplasm of eukaryotic cells is the __________ __________, an membrane-enclosed organelle also associated with some protein modification though not with protein synthesis itself.
(pppp) Distinguish cis and trans with regard to the Golgi apparatus.
(qqqq) What is a lysosome?
(rrrr) Phagocytosis gives rise to __________ vacuoles.
(ssss) By what mechanism do cells give rise to new mitochondria?
(tttt) With what membrane-bound organelle are cristae associated?
(uuuu) What contains an outer membrane, an inner membrane, ribosomes, and stroma?
(vvvv) From what structure are the thylakoids of chloroplasts derived?
(iii) Inner membrane
(v) The intermembrane space
(wwww) Which has the greatest diameter, microtubules, microfilaments, or intermediate filaments?
(xxxx) True or False, centrioles are constructed predominantly of intermediate filament material.
(yyyy) __________ consist(s) of two twisted-together chains of the protein actin.
(i) Intermediate filaments
(zzzz) What is the stuff that glues animal cells together?
(aaaaa) What are gap junctions?
(bbbbb) Another word for "sub-cellular, multimolecular, organic machine" is __________. (looking for general term)
(ccccc) True or False, Eukaryotes are typically unicellular.
(ddddd) The membrane that surrounds the cell, defining the distinction between intracellular and extracellular in the past had been described as the cytoplasmic membrane but today is usually described as the " __________ membrane" instead.
(eeeee) What is cytosol?
(fffff) The endoplasmic reticulum is an organelle that is bound by what?
(ggggg) Included in the endomembrane system are all of the following. What endomembrane-system member is missing from this list?
(i) the nuclear membrane
(ii) the endoplasmic reticulum (both rough and smooth)
(iii) the Golgi apparatus
(vi) transport vesicles
(hhhhh) The nuclear membrane consists of how many layers of lipid bilayer? (please, if you are confused about what might serve as a layer and what might not, then by all means draw a cross section of the membrane indicating what you consider to be a layer).
(iiiii) Ribosome assembly as it occurs in the nucleus takes place in a region called the __________.
(jjjjj) What are cisternae?
(kkkkk) Matching: (a) Rough ER, (b) Smooth ER, (c) neither rough nor smooth.
(i) Drug detoxification: __________
(ii) Membrane assembly: __________
(iii) Steroid (lipid) synthesis: __________
(iv) Synthesis of secreted proteins: __________
(lllll) What is the endomembrane-system intermediate that connects the rough ER with the cis face of the Golgi apparatus?
(mmmmm) Lysosomes are created by what?
(nnnnn) Phagocytosis is the primary process involved in the formation of __________ vacuoles.
(ooooo) The mitochondrial matrix is equivalent to what in Gram-negative bacteria?
(ppppp) What is a thylakoid?
(qqqqq) The cytoskeleton of the Eukaryotic cell consists of three proteinaceous components: Microtubules, Microfilaments, and __________.
(rrrrr) Centrosomes consist mainly of what cytoskeleton member?
(sssss) Distinguish "cilia" from "flagella" of eukaryotes.
(ttttt) Intermediate __________ serve to reinforce the shape of a cell as well as anchor various organelles.
(43) Practice question answers [index]
(a) (i) nucleus, (ii) rough endoplasmic reticulum, (iii) smooth ER, (iv) transport vesicle, (v) Golgi apparatus, (vi) lysosome, (vii) plasma membrane, (viii) various vacuoles.
(b) the cis face of the Golgi apparatus communicates with the endoplasmic reticulum via transport vesicles; the trans face of the Golgi apparatus communicates with non-ER and nuclear membrane aspects of the endomembrane system via transport vesicles.
(c) bound ribosomes produce proteins that are either found in membranes or are found in the lumen of the endomembrane system; free ribosomes produce proteins that are found in the cytoplasm.
(d) Components which may be labeled include: inner membrane, outer membrane, intermembrane space, cristae, matrix, DNA, or ribosomes. The outer and inner membranes must be present.
(e) (i) microtubule, (ii) microfilment, (iii) intermediate filament, (iv) microtubule, (v) microtubule.
(f) outside, extracellular matrix
(g) rough endoplasmic reticulum.
(h) (i) chloroplasts and mitochondria, (ii) chloroplasts, (iii) endomembrane system, (iv) mitochondria, (v) chloroplasts and mitochondria.
(i) Cristae are the folds in the inner membrane of the mitochondria. Cisternae are the tubules and sacs making up the endoplasmic reticulum.
Protein consists of
(k) nucleus, smooth endoplasmic reticulum, rough endoplasmic reticulum, lysosome, mitochondria, vacuole, etc. Not plasma membrane or ribosomes
(l) The lumen of the endoplasmic reticulum
(o) The cis face is that face closest to the endoplasmic reticulum while the trans face is that face farthest from the endoplasmic reticulum
(p) Both are synthesized by bound ribosomes, not by free ribosomes
(q) bacteria, cyanobacteria, mitochondria, chloroplasts
(s) The water solution making up the cytoplasm
(u) the Golgi apparatus
(w) the presence of ribosomes on rough endoplasmic reticulum
(x) Water-tight (tight) junctions, structural support between cells (desmosomes), direct-communication of cytoplasm (gap junctions), and also mutual connection to the extracellular matrix
(y) A proteoglycan is a glycoprotein to which a very large amount of carbohydrate is attached; proteoglycans make up the gluey matrix of the extracellular matrix found between cells (collagen fibers are found within this proteoglycan matrix)
(z) (ii) intermediate filaments
(bb) thylakoids are membrane-bound, inner-membrane-derived, chloroplast organelles that are the actual site of photosynthesis (the light reaction in particular)
(cc) cyanobacterial (blue-green algae)
(dd) ribosome as well as chromosome are correct answers
(ee) a vacuole, specifically a food vacuole
(gg) secreted and membrane proteins are both synthesized by bound ribosomes whereas soluble proteins found in the cytoplasm are synthesized by free ribosomes)
(hh) the cisternae are networks of ER sacs and tubules
(ii) smooth endoplasmic reticulum
(jj) endoplasmic reticulum and the nuclear membrane
(kk) particularly prokaryotic cells lack a nucleus
(ll) (iii) Gram-negative bacteria (cyanobacteria can have thylakoids)
(mm) surface-to-volume (particularly nutrient-transport) problems become worse (more difficult to overcome) the larger a cell is
(qq) plasma membrane
(rr) volume (size)
(tt) should show double-membraned nuclear envelope, chromatin, nucleolus, and pores
(vv) transport vesicles
(xx) it is obtained via phagocytosis
(yy) reparative (cellular respiration)
(zz) thylakoid space
(aaa) (v) Microtubules, because they are a major component of the structure of cilia and flagella
(bbb) (iii) Microfilaments
(ccc) extracellular matrix
(fff) plasma membrane
(jjj) lipid bilayers
(kkk) transport vesicles
(lll) endoplasmic reticulum
(nnn) endoplasmic reticulum
(ooo) membrane and secreted protein synthesis, protein modification, membrane assembly
(ppp) transport vesicles
(qqq) vacuoles and the plasma membrane
(rrr) because oligosaccharide attachment occurs within the lumen of the endomembrane system
(ttt) the plasma membrane
(uuu) going from the outside in: outer membrane, intermembrane space, inner membrane, matrix
(vvv) (iii) Mitochondria
(www) cristae increase the surface area of the mitochondria inner membrane (thereby increasing the amount of respiratory components present within individual mitochondria)
(xxx) (v) Thylakoid (chloroplasts)
(yyy) thylakoid space
(zzz) microtubules (tubulin), intermediate filaments, microfilaments (actin)
(aaaa) microtubules (tubulin)
(cccc) the extracellular matrix
(dddd) a desmosome is a strong coupling between adjacent plasma membranes (between two animal cells)
(eeee) Cells are the fundamental units distinguishing living from non-living entities; they are membrane-enclosed, DNA-containing, metabolizing, and self-replicating
(ffff) A nucleus; to a lesser extent, membrane-bound organelles
(gggg) Plasma membrane
(jjjj) (v) Two membranes
(kkkk) Rough endoplasmic reticulum; nucleus
(llll) Endoplasmic reticulum
(mmmm) Rough endoplasmic reticulum
(nnnn) Smooth endoplasmic reticulum
(oooo) Golgi apparatus
(pppp) The cis face of the Golgi faces the endoplasmic reticulum while the trans face faces away from the ER
(qqqq) A lysozyme is a membrane-enclosed bag (vesicle) of hydrolytic enzymes
(ssss) Binary fission --> "cell" division of mitochondria
(vvvv) (iii) Inner membrane
(xxxx) False, they are constructed of microtubules
(yyyy) (iii) Microfilaments
(zzzz) Extracellular matrix; proteoglycan, etc.
(aaaaa) Gap junctions are connections between adjacent animal cells in which connect cytoplasms by creating a continuous tube.
(eeeee) Cytosol is the aqueous portion of the cytoplasm, water place various molecules and ions dissolved and suspended in it
(fffff) A membrane; it is a membrane-bound organelle
(ggggg) The plasma membrane
(hhhhh) Two (i.e., two membranes--or four lipid layers)
(jjjjj) Cisternae are the meandering tubules making up the endoplasmic reticulum
(kkkkk) (i) (b), (ii) (a), (iii) (b), (iv) (a)
(lllll) Transport vesicles
(mmmmm) The Golgi apparatus
(ooooo) The bacterial cytoplasm
(ppppp) A thylakoid is a membrane-bound organelle found in chloroplasts
(qqqqq) Intermediate filaments
(sssss) Cilia are shorter and typically more numerous than flagella, plus act more like oars than like whips
Chapter 7, Bio 113 questions:
(#) Matching: (a) continuous cytoplasm, (b) proteoglycans, (c) structural support, (d) water-tight junctions. Use each only once.
(i) Desmosomes: __________
(ii) Extracellular matrix: __________
(iii) Gap junctions: __________
(iv) Tight junctions: __________
A: (i) (c) structural support, (ii) (b) proteoglycans, (iii) (a) continuous cytoplasm, (iv) (d) water-tight junction.
(#) Other than being intermediate in terms of diameter, name at least one way in which Intermediate Filaments differ from microtubules and microfilaments.
A: They are more permanently assembled; they serve to anchor various organelles; they are more structurally diverse; they consist of neither actin nor tubulin.
(#) What cytoskeleton member serves as the internal support for cilia and flagella?
(bonus) Though not members of the endomembrane system, nevertheless thylakoids are reminiscent of endomembrane members. In what way is this so?
A: they are derived from the plasma-membrane equivalent of the chloroplast.
(#) What is a cyanobacterium?
A: blue-green algae; free-living chloroplasts; the ancestors of chloroplasts; photosynthesizing bacteria; a constituent of pond scum; bacteria able to photosynthesize using the same mechanism as employed by green plants
(#) What is the importance of cristae? One way to consider this question is to ask yourself what would change if there were no cristae.
A: cristae increase the total amount of inner membrane in mitochondria and in so doing they increase the amount of respiratory enzymes found within a given mitochondria.
(#) Arrange in correct order, outside going in (to avoid ambiguity, please indicate which is on the outside and which is found on the inside):
(i) Cell wall
(iii) Inner membrane
(iv) Outer membrane
(v) Periplasmic space
A: (iv) Outer membrane, (i)/(v) Cell wall/Periplasmic space, (iii) Inner membrane, (ii) Cytoplasm.
(#) Food vacuoles are formed by (please circle the most-correct term):
(v) Receptor-mediate endocytosis
A: (iii) Phagocytosis
(#) Lysozymes are created by what endomembrane organelle?
A: the Golgi apparatus
(#) Both rough endoplasmic reticulum lumen proteins and membrane proteins are transported from the ER by transport vesicles to the __________ face of the Golgi apparatus.
(#) What in the cell is associated with lipid synthesis, carbohydrate metabolism, and poison detoxification? Please be specific.
A: the smooth endoplasmic reticulum
(#) Name a portion of the endomembrane system other than the endoplasmic reticulum that is involved in the ribosome-mediated synthesis of integral-membrane proteins.
A: the nuclear envelope
(#) True or False, Prokaryotic cells have numerous membranes in addition to the plasma membrane.
A: False, that statement would be true only for eukaryotes, not prokaryotes.
(#) What is cytosol?
A: cytosol is the water solution that makes up the cytoplasm