C2006/F2402 '11 -- Lecture 1 -- Updated 01/17/11

© 2011  Deborah Mowshowitz, Department of Biological Sciences, Columbia University, New York NY

Handouts: 1A -- Eukaryotic Cell Structure ; 1B  -- Overview of Course (Brief Description) ; Also selections from Scientific American Dec. 2010 'World Changing Ideas.' This handout is on Courseworks; see the Sci. Am website for the entire Innovation section. (You have to be a subscriber, or go through the CU libraries or a CU computer.)

Copies of all class handouts and returned exams will be available on the 7th floor of Mudd, outside Dr. M's office (after class).

Class handout titled 'Overview' is not comprehensive. Be sure to check out 'About C2006' or 'About F2402.'

References to Texts:  References in Becker are to 7th ed. (When fig. numbers or pages in 6th edition are different, refs. to 6th ed. follow in parentheses.) Refs to Sadava are to 9th ed of Life (8th in parentheses).

Current Notes, Audios Etc: The online notes for this term will be extensive outlines, not word-for-word. This is partially for practical reasons and partially for educational reasons -- I think it encourages better student note taking and understanding. The outlines will be provided the night before (if not earlier) so you can print them out in advance and annotate them in class (if you wish). Audio recordings of the lectures will be provided after each lecture on the lecture-links page.

Old Lectures: If you like to read ahead, the outlines & audios from last year (2010) are linked to  the lecture-links10 page. The outlines are also linked to the '10 schedule.  Older schedules, with references to readings in older editions of the texts, are available too, on the old schedules page.

I. The Story So Far -- Summary of last Term

    A. The Major Question: How do Living Things Work? Or how does 1 cell make two?

    B. Answer so far has concentrated on

        1. Prokaryotes (mostly) -- 1 intracellular compartment, unicellular

        2. Macromolecular level -- emphasis on macromolecules, not on larger structures such as organelles, chromosomes, etc.

        3. The "big 5" issues  --  structure, function, manufacture (including energy requirements), regulation, and (evolutionary) origin.

        4. Methods -- the ones used to figure out how living things work, especially the methods used to get at the "big 5."

    C. Bottom Line: DNA → RNA (& more DNA); RNA → protein → job, say catalyzing X → Y. Protein production & activity are regulated.

We emphasized roles of  mRNA, tRNA & rRNA in translation, which are well known. Roles of short regulatory RNAs (micro RNA's, RNAi, etc.) in regulation of translation & transcription were mentioned only briefly, as details are just now being uncovered. 

II. Overview of this Term

    A. Similarities: Same Major Question; Same "big-5" issues; same stress on methods.

    B. Differences:

        1. Organisms: This term will concentrate on Eukaryotes (mostly) as vs prokaryotes.  See Becker table 4-1 for comparison of Eukaryotic and Prokaryotic cells. For pictures, compare Sadava fig. ( 5.4 & 5.7) 4.4 & 4.7.

        2. Structures: This term will consider many things bigger than macromolecules -- intracellular structures (organelles, etc.) and assemblies of cells (organs, tissues, systems).

	Last Term	This Term
Organisms	Prokaryotes	Eukaryotes
Structures	Macromolecules	Bigger

        3. New Issues: Two big innovations of eukaryotic cells are:

            a. Intracellular Compartmentalization  -- multiple membrane-bound compartments per cell

            b. Multicellularity -- multiple cells per organisms

        4. Topics:  Most of the topics this term will deal with the consequences of the two big innovations.

Last Term		This Term
Biochemistry		Cell Biology
Genetics		Signaling
Molecular Biology		Development
		Physiology

    C. Major Subjects of Term

        1. Cell Bio -- study of consequences/implications of compartmentalization within cells (Lectures 1-9 & 12-13)

            a. Macromolecules and bigger things (membranes and organelles) Lectures 1-3.

            b. Co-ordination (between different parts of cell)

                (1). How do molecules cross membranes?  Lectures 4-6.

                (2). How do newly made proteins get to the right place? (Lecture 7) More details on this after development.

            c. Regulation of eukaryotic gene expression  -- chromosome/euk. gene structure & function -- how is DNA arranged (lect. 7 & 8) and how is its transcription regulated?  (Lecture 9 by Dr. Alice Heicklen).

             d. Note: in this part, we will emphasize generalized features of all eukaryotic cells but discuss some specialized cell types.

       2. Development  -- How do you build a multicellular organism? How do cells get specialized and how they stay that way? Lectures 10 & 11 by Dr. Alice Heicklen.

For a taste of what's to come, see what Science magazine describes as the #1 'Breakthrough of the Year' for '08 -- IPS cells.   For an expanded version of the print magazine special section of 2008, that describes IPS cells, go to http://www.sciencemag.org/btoy2008/  For an expanded version of the print magazine 'breakthrough of the year' special for 2009, go to http://www.sciencemag.org/btoy2009/ (There was no equivalent section for 2010.)

         3.  Cell Bio, Cont: Sorting & Function of Organelles -- once cells have specialized, and the 'right' proteins are made in the right cell type, how to do the macro-molecules get to the right place in the cell? What is the role of each organelle? lectures 12 & 13.

        4. Signaling between cells & some of the consequences -- the need for co-ordination between different cells in multicellular organisms (as vs co-ordination between the different parts of a single cell). Some examples of how specialized cells carry out specialized functions.

            a. How cells communicate chemically.   How chemical signals work & how they are used will be discussed in lectures 14-16; see also physiology below.

            b. How cell communicate electrically.  ( Lectures 17 & 18 by Dr. Stuart Firestein); structure and function of nerve cells.    

            c. Wrap up of nerves and integration with Muscle (Lectures 19-21).

        5. Physiology --  Study of selected consequences/implications of multicellularity for maintenance of organism as a whole. How do you run a multicellular organism, once you've built it? How organisms make use of communication, specialization, etc. to maintain a relatively constant internal environment and how all the various functions are coordinated. This subject will be divided as follows:

            a. Homeostasis & Hormones: How the various systems (nervous, hormonal, muscular, respiratory, etc.) work to maintain a constant internal environment of temperature, gas, fluid, salt & water (Primarily lectures 15-16 & 22-23) and respond appropriately to changes in external environment.

            b. Immunology -- The most specialized system; how a multicellular organism fends off invaders (Lecture 24).

        6. Optional Lecture -- Regulation of Cell Cycle & Cancer -- How aberrations in cell-cell communication and/or the cell cycle may cause cancer. (Lect. 25, optional)

III. Eukaryotes -- a  closer look.

    A. What can you see in the light microscope? Suppose we draw a standard light microscope view of eukaryotic cell in interphase -- what can you see?  Can't actually see membranes or details of many organelles. Can see nucleus, nucleolus, chloroplasts and/or mitochondria, Golgi (maybe).

    B. Issues of size -- What you can see is limited by by the size of the object and the amount of magnification you can get using any particular method. For pictures using the different methods of microscopy, see Becker table 1-1 or Sadava  fig. 5.3 (4.3.)

• Limit of Resolution. Useful magnification is limited by the resolution, which depends on the wavelength of the electromagnetic radiation you are using. Limit of resolution = λ/2 = smallest distance you can resolve using electromagnetic radiation of wavelength λ. Items closer than  λ/2 appear as one object, not two. For more details on microscopy, see Becker appendix.

* For a nice SEM picture see Becker fig. 1-3 (1-3). For more SEM pictures of biological specimens see http://www.le.ac.uk/bs/em/sem.htm.
 

• Sizes of things commonly encountered in biology

mm = millimeter = 10^-3 meter
micron (μ) = micrometer or 'mu' = 10^-6 meter
nm = nanometer = 10^-9 meter
Angstrom (Å) = 10^-10 meter

• Sizes of some cells,  structures and very small things (for reference): 

** The idea of  tiny organisms ('Nanobacteria' or nanobes) caused a lot of excitement, but they are probably NOT living. See Scientific American, Jan 2010, article by Young & Martel, for details. You can get the whole article online from a CU computer, or through the CU libraries (or if you are a personal subscriber).

For more examples and tables of relative sizes see Becker fig.1-3 (1-2) & box 1A,  or Sadava fig. 5.1 (4.1) . 

    C. What you can see in the EM? See handout 1A and Becker fig. 4-5 or Sadava  fig. 5.7 (4.7) for pictures of whole euk. cells. Some specific references to pictures of organelles are given below, but all pictures in Ch. 4 of Becker & Ch. 5 (4) of Sadava are well worth it. Methods used to characterize the various parts are described below in IV, but will be discussed as they come up.

        1. Membranes. In the EM you can actually see membranes. 

• Membrane = bilayer of lipid plus associated proteins. Entire structure is 6-9 nm across. 

• In the EM, after staining, bilayer appears as a double line. Can also be described as a three layered structure, with two dark layers sandwiching a lighter layer between them. Only the top and bottom layers are visible in the EM = double line.

• Bilayer (& assoc. proteins) = a single membrane. A 'double membrane' = two complete bilayers. (See nucleus, below.) 

• Detailed structure of membranes (how lipid & proteins are arranged) will be covered next time.

      2. Nuclear details  -- See figs. 4-4 & 4-10 of Becker or fig. 5.8 (4.8) of Sadava or go to Google images and search.

• Nucleolus -- not membrane bounded; staging area for ribosome subunit assembly

• Nuclear Pores & Nuclear Envelope (Double membrane = 2 bilayers, with holes punched across both layers)

•  Space between two layers of nuclear envelope = Perinuclear Space

• No whole ribosomes in the nucleus. (Does contain newly made subunits on their way 'out' to the cytoplasm.)

        3. Endomembrane System (EMS) -- See Sadava figs. 5.10-5.11 (4.10 to 4.12) or Becker fig. 4-15 to 4-18. For a more detailed picture, see fig. 12-1 of Becker.

     a. Components

• ER (smooth & rough) -- continuous, but only rough (RER) has attached ribosomes. Membranes of ER are continuous with outer layer of nuclear envelope. 

• Golgi

• Many types of vesicles. (Some examples: lysosomes, transport vesicles, secretory vesicles, & endosomes.)  Name, structure & function of each type will be discussed later -- features of each type depend on role in processing, packaging, transport, etc. 

• Why it's considered one system: Material can be transferred from one lumen to another -- therefore all lumens effectively (but not physically) connected -- see below for how it works.

    b. Major function = processing, sorting, packaging and transport of proteins to/from outside of cell or proper part of EMS.

    c. Structure of Components

• All parts are made of vesicles and flattened sacs (cisternae). Shapes vary. 

• Each vesicle or sac surrounded by a single membrane (one bilayer)

• Inside of each vesicle/sac = lumen = space inside a hollow organelle, organ, or tube.

• Important: Not all vesicles are part of the EMS.

            d. Isolation: See methods section below for how the various components are isolated and/or distinguished from each other.

            e. Exocytosis and endocytosis-- Unique to eukaryotic cells. See handout 1A for steps

• All internal spaces of endomembrane system (lumens & perinuclear space, but not inside of nucleus) and the outside of the cell are effectively connected -- material can be passed between any of these spaces and the outside of the cell.

• How are these spaces & outside of cell (effectively) connected? Through formation and fusion of vesicles.

• Vesicular traffic (budding off and fusion of vesicles) moves and carries both "cargo" (vesicle contents) and membranes.

• Vesicle traffic can transport cargo two ways (see handout 1A).
  (a) between one membrane-bound compartment inside the cell to another or
  (b) between inside and outside of cell (by exo- & endocytosis).

• You need labeling of cargo to determine direction.

        4. Peroxisomes  (See Becker fig. 4-19 & 4-20 or Sadava 4.17 (8th ed only)

    a. Peroxisomes & lysosomes have some common features:

• Are surrounded by a single membrane (unlike nucleus or endosymbionts).

• Contains enzymes in lumen

• Can be about the same size

• Contain reactive materials that can destroy cytoplasmic molecules

    b. Are peroxisomes & lysosomes 2 different organelles? How do we know? See methods below.

    c. A critical difference: Different enzymes are found inside the 2 organelles

• Lysosomes contain acid hydrolases

• Peroxisomes contain oxidases

• Note: The two organelles arise from different structures as will be explained later. Only lysosomes are part of the EMS.

5.  Mitochondria and chloroplasts

            a. Structures -- see texts (Becker fig. 4-11 & 4-14; Sadava fig. 5-12 & 5-13 (4-13 & 4-14.) Note double membranes (2 bilayers), prokaryotic style ribosomes, circular DNA, overall size similar to that of bacteria.

            b. Have own genetic systems (DNA, ribosomes etc. -- everything needed for DNA replication, transcription & translation.) Mitochondrial DNA is often used for identifications (when nuclear DNA is not available) or for tracing inheritance of the female line. Peroxisomes, lysosomes etc. do NOT contain DNA, ribosomes, etc.

            c. Most proteins of mito and chloro are NOT made inside the organelle -- most are encoded in the nucleus, made in the cytoplasm, and transported into the organelle after synthesis.

            d. Major similarities in function between  mito &. chloro

• Electron transport in membrane used to pump protons

• H⁺ gradient used to make ATP;

• Carbon rearrangements carried out in matrix or equivalent

            e. Major Differences in function/location

• Exergonic process that drives electron transport is different -- light absorption (in chloro) vs oxidation of reduced carbon compounds (in mito).

• Plants have both chloroplasts and mitochondria. Animals have mitochondria only.

            f. Origins -- probably endosymbionts.  Mito. and chloro. were once probably free living bacteria. See Sadava fig. 27.2 & 27.3 (27.7 & 27.8) or Becker Box  11A.

Q's to keep in mind: (1) What are the major similarities and differences between peroxisomes, lysosomes and mitochondria? How can you tell them apart? It is a good idea to make a table that compares and contrasts the three organelles. (2) How are new organelles made? The answers are different for the 3 types of organelles and will be discussed in detail in lectures 12 & 13.

        6. Location/function of ribosomes.

            a. Cytoplasmic ribosomes: Two types of ribosomes are making protein in cytoplasm (cytosol) --  "free" ribosomes or ribosomes attached to membranes of ER.

• Free cytoplasmic ribosomes (attached to mRNA, but not to ER) make proteins for nucleus, cytoplasm, peroxisomes etc. -- all parts of cell except EMS.

• Bound ribosomes on RER make proteins for EMS or outside the cell.

            b. Organellar ribosomes: Additional ribosomes (prokaryotic in size and function) are found inside mitochondria and chloroplasts. (No ribosomes in other organelles.)

            c. Location: How the "right" cytoplasmic ribosomes attach to the ER & how the various proteins reach their correct destinations will be discussed at length later.

        7. Cytoskeleton (see Becker figs. 4-23 & 4-24 or Sadava fig. 5.17 (4.20) -- we will discuss this in more detail next time. How do you locate proteins that have no enzymatic activity?

            a. Three components made of protein

             b. How discovered? By immunofluorescence (see below) using antibodies to tubulin and/or actin.

            c. Functions -- more on structure & function next time

(1). Support/strength -- weight bearing, shape determining.

(2). Movement (MF & MT) -- can change shape of cell (as in muscle or amoeba) and/or  help move organelles within cells.

(3). Localization of other factors -- act as peg board or framework for attachment of organelles, enzymes, etc. (Cytoplasm is not simply a "bag of enzymes.")

IV. Methods -- How do you find out which components are in each cell part? A & B will be discussed in Lecture #1 as we get to them. C will be discussed next time.

Reminder: Becker has a guide to all techniques and methods described in the book -- see  inside front cover.

    A. "Grind and Find" (Biochemical separations and assays). See Becker Box 4B and Box12A or Sadava fig. 5.6 (4.6).

1. Grind: Break up cell into parts, and separate (fractionate) parts by ultracentrifugation.

2. Find: Find the cell part associated with each particular enzyme. How? Assay (test) each cell fraction for enzymes of interest. (Provide substrate for enzyme; look for disappearance of substrate or formation of product.)

    B. In situ labeling (Localization of enzymes "in situ" = in place).

1. Substrate: Provide solution of substrate. Enzyme substrate is soluble, so it diffuses to site of enzyme.

2. Product: Product of enzyme catalyzed reaction is insoluble, so it stays in the place where it is made. If cells are washed, unused substrate will be removed, but product will stay put.

3. Localization: Insoluble product is produced and precipitates only at location of enzyme -- pin points position of enzyme.

4. Detection of product: Can be colored (for detection in light microscope) or electron dense (for detection in EM). For an example, see Becker fig. 12-20.

    C. Immunofluorescence -- Localization of proteins with no enzymatic activity. Use of labeled antibodies as tags -- direct (one step) and indirect (two step). Details & Handout next time. See Becker table 15-2. For more details, see Appendix, A-8  to A-11. For a picture of a typical result, see Becker table 15-1 or Sadava fig. 5.3 (4.3).  Allows you to visualize location(s) of particular proteins.

Next time: More on the cytoskeleton, and the structure of cell membranes.