::A
biochemist's view of biology:: Understand... is a word that means different things to different people. Understanding something in
science means verifiable prediction. Hierarchy
among the sciences, one builds upon the other One of the main things we are going to do this semester
is to explain how living things function at the level of chemistry. We
will cover Having put all this emphasis on biochemistry, let me pull back a bit
and reassure you that we will not be going deeply into chemical mechanisms.
This is ::Characteristics of living
things:: Complex structure
In this course we will emphasize a common denominator approach; we will
focus on unifying principles rather than on characteristics that distinguish
one living thing from another. The latter is often used to good effect
in for example,… ecology ... evolution (Darwin examined finches -
he looked for the differences that set each species apart). It turns out
that the common denominator approach works very well because, amazingly,
we living things all do these three things (maintain a complex structure,
chemically interact with the environment, and reproduce), … basically,
… chemically … , the As this unity became apparent,
biologists began gravitating to simpler and simpler living systems to
use as ::Cells:: We can do a similar experiment with a complex living thing, say, a person, and ask for the smallest unit that exhibits the characteristics of living things in our short list: Take a piece of skin of a person, put it in culture (i.e., bathed in a nutrient solution simulating "blood"). It .... grows (reproduces) … has a complex structure (if looked at under a microscope), and interacts with the culture medium chemically (nutrients are consumed, substances are excreted from the skin fragment). The person is alive, the person's arm is alive, and even the arm skin piece is alive by the 3 criteria above.
Shake the skin piece in a salt solution for a few hours; this frees up
spheres (seen easily with a microscope), or cells also are alive: they retain
the 3 characteristics we have defined, and most dramatically, they reproduce:
one cell becomes many. Now put them in a powerful blender, break them into sub-cellular pieces: Some structure still is present (but much less) and some metabolism can be measured (but much less), but there's no reproduction. These subcellualr fragments and molecuels are not living; they're dead, killed actually. All living
things are made up of cells, the basic building
block in biology.
And since a cell is alive, it represents a simple object for study, suitable for learning the most fundamental processes that characterize living things. Let's take a quick look at this skin cell: Some parts: 1) nucleus, 2) cytoplasm, 3) membrane (= "plasma" membrane = cell membrane) Cytoplasmic machinery (organelles): ribosomes, mitochondria, lysosomes, etc. The cell membrane is very important in several senses:
Click here for a better picture of a typical animal eukaryotic cell. [See Ch. 4 of Becker and/or Ch. 4 of Purves to read more about cell structure if you want. Most intro bio courses include this material at this point]
[As an aside, consider some units of size here: 1 millimeter
( Typical animal cells = ~10 µm in diameter The
e.g., water (~0.5 nm), the alcohol ethanol (~1 nm), the sugar glucose (~1.5 nm) [a term less used but that you may run into: The smallest cells are ~ 1 um. What about these
smallest cells, the 1 micron cells? Smaller should be simpler yet, no?
There'd be less room for much stuff. This is true. The They are 1-2 µm in cross-section, so they are about 1/1000 the size of our 10 µm skin cell (comparing a cube of 1 um dimensions vs. a cube of 10 um dimensions). They have a more complicated surface (there is a hard cell wall outside the plasma membrane, to protect them). But there is no true nucleus, and much less complicated machinery inside, no big organelles. Indeed, bacteria are about the size of many animal or plant cell organelles (e.g., a mitochondrion). Click here for a better picture of a prokaryotic cell. The simplest living things are made up of a single cell. A second big simplification (besides size): the That is, most bacteria are Before we go any further considering bacteria, the simplest of all living things, let's see how they fit into a classification of all other living things according to these 2 criteria so far raised: simplicity and unicellularity. Examples:
Click here for a view of an evolutionary classification of all living things The simplest cell is a bacterial
cell. Study of the basic characteristics of life in
simple bacterial cells has facilitated understanding in biology.
E. coli grow by Their ::What are cells made of?::
Notice there is only one organic (= carbon (C)-containing) compound in this medium (glucose). The remaining substances are inorganic salts, providing the elements potassium, phosphorous, magnesium, sulfur, nitrogen, hydrogen and oxygen. There are also a few more metal elements needed in very small amounts. E. coli can be made from
glucose We will be considering how E. coli, and some other kinds of cells, do exactly this (that is, reproduce), over the next 2 months. I found myself explaining some of this to my father-in-law once; he had seen a diagram of the glucose molecule on my computer screen and asked what it was. I explained that it was glucose, and, with this lecture in mind, that glucose was just about all you needed to make an E. coli cell. Figuring me for a biotechnologist, and expecting ever-greater things from biology from his reading of the Tuesday Times, he said, "Are you serious? You mean you can synthesize a living E. coli cell in the laboratory from glucose? How do you do it?" When I explained: "Well, you need to start with one E. coli cell to get the second one …", his face dropped. "Oh. Okay, but that's cheating," was his reaction. He was taking life, cell growth, for granted, because it was so familiar:
children get taller and taller, the grass has to be mowed twice a week,
mold the size of a quarter appears on an old peach overnight. No, we can't
put together a brand new E. coli cell in a test tube; that would be a
truly amazing feat. But is it really any less amazing that E. coli can
do it, without a test tube? In one hour, take 10 million glucose molecules
and transform them into 5000 different things, all organized to fit together
in a cell that can do it all over again, in one more hour. How? How do
these little cells know ::Cell reproduction:: We can break the problem down into several parts, which will give you a preview of where we're headed: To understand the question,
we first must know just what molecules a cell is made of . 2. How do we get those chemicals? 3. Where does the energy for this process
come from? 4. Where does E. coli get the information for doing all this?
------------------------------------------------------------------------- Before we get down to business with question #1 (the chemical definition of the cell), let's consider some mathematical consequences of this reproduction by binary fission, or bacterial cell growth. ::Exponential growth:: Binary
fission leads to exponential growth. 1 cell --> 2 cells in 60 min., or 1 generation; 60
min. = Doubling time = t How can we calculate the time it will take to get a billion cells, so we know when to come back to the lab to collect these cells for analysis? Let g = number of generations. From the binary fission mechanism: after 2 gens. --> 4 cells, after 3 gens. --> 8 cells, etc. So we can see that the number of cells at any given
point, N = 1 x 2 If we started with one million cells, then N = 10 More generally, starting with N Since
we want to know what So now N = N Or, more generally and simpler to write: N = N Exponential growth is mathematically
predictable. N = N and: N = N Note here that the growth constant k is being defined differently for the different bases used to express the exponential nature of the growth. The derivation of these forms is described in the exponential growth handout. Below in italics was not in the live lecture by intention, since it
is more easily followed at your leisure here.
we get log And plugging in the numbers we have: t = log But say your calculator does log base 10 but not log base 2. No problem, convert log base 2 to log base 10 (log) or to the natural log, base e (ln). log or, log Applying this last one (base 10) to our problem, and since you now know that the log2 = 0.3 from the line above: t = log Related exponential transformations are: 2 And useful numbers are: log(2) = 0.30, ln(2) = 0.69 To continue our transmogrification of these exponential growth equations: log So log log(N/N or, converting back to the exponential form:
K=0.3/tas mentioned before._{D
}Since most scientific calculators have natural log functions, similarly, we can write N = N Let's have one more look at the exponential growth equation: We could also have approached this question of rates of change of N with time more directly and naturally using calculus. If you have a million cells, then after one generation time you will have gained 1 million. If you had 200, then you would have gained 200. In general, the rate of increase of N with time is just proportional to the number of cells you have at any moment in time, or: dN/dt = kN Separating variables: dN/N = kdt Integrating between time zero when N = N lnN - ln N
We can now calculate this constant k by considering the time interval
over which N ln2=kt This is probably the last time you will see calculus in this course, so don't be scared off by thoughts of complex math. You will need mostly arithmetic, some algebra, and an ability to work with exponential notation and an occasional logarithm. There are several problems of this type in the problem book, solving
for N, for t, for N Finally,let's look
at the growth of a bacterial culture graphically. But ln(N) vs. t should give a straight line (a semi-log plot): In reality, a growth curve for a bacterial culture looks more like this: Note the 3 phases: a lag (while the cells are getting geared up), log (logarithmic) phase or exponential phase (linear on a semi-log plot such as this), and finally stationary phase (after the nutrients have been exhausted and/or toxic excreted products have built up as the culture becomes dense).So we can treat cell reproduction quantitatively, and that's what growth looks like mathematically. We now start on the problem of how the bacterium E. coli reproduces, how it grows; how we get two E. coli cells from one. First we need to know what are the chemicals that need to be made if we are to create one net E. coli cell. We need to turn to the nature of the chemicals that make up an E. coli cell, so we know what it is that we need to make in an hour. We will start with the most abundant and most important molecule in the
cell, not an organic molecule, but Clickable pictures are from Purves, et. al., Life, 5th Edition, Sinauer-Freeman's
Images of Life 5.0. A production of the Columbia Center for New Media Teaching and Learning |