Well do a demo to see what happens as we cool a flask of hot water.

If we cant explain how simple

systems work we wont be able to explain how a cell works.

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Were going to begin this course by reintroducing concepts many of you have seen
but in a way that allows us to think about them in the context of living systems. We
need to review what we know we know, especially about intermolecular forces in
general (and H-bonding in particular) so we can understand the demo. Ultimately, we
need to understand more about energy flow so that we can appreciate the physical
principles that operate in all systems.

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1. Component parts of the cell (the smallest units of matter that matter in living
systems)
a. Organization of the cell
b. Macromolecules in the cell
c. Small molecules and metabolites
d. Water: THE molecule of life

2. Understanding chemical structures and bonding (electrons and their arrangements

in atoms and molecules)
3. Understanding intermolecular forces (how the component parts of a cell interact
with each other)

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Part of being able to predict intermolecular interactions is being able to understand

why these interactions occur, their relative strengths, and which factors affect the
strength of intermolecular interactions.
One component of understanding hydrogen bonds is to know why they occur and
which molecules can participate in them.

This course is intended to provide an integrated introduction to the life sciences. In the
first part of the class, we are going to try to provide a foundation for understanding the
thermodynamics and kinetics of living systems. In order to do that, we need to start by
learning about the smallest units of matter that matter in living systems: electrons and
their arrangements in atoms and molecules. The emphasis will be on understanding
aspects of chemistry that will enable you to think about what happens in biological
systems. I want you to keep in mind a question throughout this course: What does it
mean to be living?
It has been known for well over a hundred years that all living systems are made up of
a fundamental unit called the cell. The cell is a finite entity with a definite boundary, the
plasma membrane. That means that the essence of the living state must be contained
within that structure.
(Continued on next page).

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I think it is fair to say that most people are far more interested in understanding human
life than in understanding any other form of life. The problem is that humans are so
complex -- and they reproduce so slowly -- that they arent very good systems to study.
If the fundamental unit of life is a cell, and a single cell contains the essence of what it
means to be alive (if not intelligent), then we should start by considering single cells.
After we understand the essential functions and characteristics that are shared by all
cells, we can begin to consider how different types of cells combine to create a
multicellular organism. That, however, is beyond the scope of this course. Here, our
goal is to provide a foundation for thinking about what happens in the fundamental unit
of life, the cell.
(Continued on next page).

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I told you on the previous slide that you have to understand the structures of
molecules in order to begin to understand how they function in cells. On this and the
next two slides, I am going to introduce you to some of the most important kinds of
molecules found in cells. On this slide some of the important molecules of life are
depicted. Many of them are biological polymers, such as DNA, RNA, and proteins.
Polymers consist of many repeating units, or monomers. Because these polymers
are typically made of hundreds or thousands of atoms, they are commonly referred
to as macromolecules. Biological macromolecules play some of the most important
roles in living systems. Some of them store genetic information to be passed down to
future generations. Some of them are involved in decoding that genetic information.
Others are involved in metabolism -- breaking down molecules to obtain energy
which is then used to build other molecules. These macromolecules and their roles
will be discussed in much greater detail throughout this course. Dont worry if you
arent yet be able to understand the structures of the molecules shown in the
following figures; their details are not important at this point. These structures are
shown simply to give you a sense of the diverse nature of the macromolecules of life.

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In addition to macromolecules, small molecules also play a central role in living

systems. Although there is no discrete size cut-off that distinguishes small molecules
from macromolecules, most small molecules relevant to life contain fewer than about
100 atoms. Unlike the macromolecules of life, which are polymers comprised of
repeating subunits, the small molecules used by living systems are extremely diverse
in their basic chemical structures. Their more diverse structures also imply that small
molecules are synthesized in the cell by a much more diverse collection of chemical
reactions than those used to make macromolecules. Indeed, as we will learn later in
this course, macromolecules are typically generated by repeating one type of chemical
reaction over and over, while small molecules are synthesized through the use of
thousands of different reactions.

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If I had to pick a single molecule of life that is more important than any other -- which
in some sense is a ridiculous exercise since life results from the integrated functions of
a wide variety of molecules -- I would probably pick water. The reason I would pick
water is that while I can imagine substituting the other molecules of life with different
variants that somehow accomplish the same types of things, I cant imagine any other
kind of molecule substituting for water. Water is special. Water is different. Water
affects the way in which all other molecules function, and there is no substitute for it.
Without water, life could not exist. That is why the issue of whether there is -- or was -water on Mars is so important. If water ever existed on Mars, then life in some form
could have arisen and the search for evidence of life on Mars is justified. If water did
not ever exist there, then there is really no point in searching for evidence of life. We
are going to talk a lot about water and its role in this course.

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I want you to realize that life itself is an unexpected phenomenon: implausible from first
principles but not impossible. Most of us take life for granted in the sense that it is so
familiar to us that we have no problem telling the difference between something that is
alive and something that is not alive. Jacques Monod, a famous scientist of the 20 th
century, once said that it is perfectly obvious to a child of five that a plant is alive but a
table is not. The very familiarity of life makes it hard for us to appreciate -- without a
framework, that is -- just how unusual it really is. I can tell you exactly why the water
started to boil in the ice water, but I cant tell you exactly what makes something alive.
Our goal in this course is to give all of you the same information that all of us have so
that you can begin to think about how the components of a cell are organized to create
a state that we call living.

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1. Component parts of the cell (the smallest units of matter that matter in living
systems)
2. Understanding chemical structures and bonding (electrons and their arrangements
in atoms and molecules)
a. The periodic table and electronegativity
b. Ionic bonding
c. Covalent bonding and the octet rule
d. Geometries of organic molecules
e. Covalent bond energy
3. Understanding intermolecular forces (how the component parts of a cell interact
with each other)

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In order to begin to understand life, we need to start by reducing it to principles that

explain phenomena at the molecular level. By the end of these first two lectures, you
will understand exactly why the water boiled and you will also have a foundation that
allows us to begin to talk in more detail about the molecules of life.
To understand the structures of the molecules that make up living systems requires
first understanding the nature of atoms and chemical bonds. The molecules of life are
made of atoms, which are the units of the elements found in the periodic table. There
are a lot of elements in the periodic table, but only a few of them are abundant in cells.
In fact, the vast majority of biological matter about 99% in fact is made of just six
kinds of these atoms: carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus
(conveniently remembered as SPONCH). Water, as you all know, is made of two
atoms of hydrogen connected to an atom of oxygen -- H2O. A few other atoms play
roles in biology -- mostly ions such as sodium, potassium, magnesium, calcium, zinc,
iron, etc. -- but you dont have to worry about most of the elements in the periodic table
to understand what happens in a cell.

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As you have probably learned before, the periodic table is a tabulation of the elements
according to their proton and electron configurations. Each period (or row) represents
an electronic shell; the position of each row down the periodic table is numbered
according to how many electronic shells the atoms in that row have.

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The groups (or columns) represent atoms having the same number of outermost shell
electrons, or valence electrons. For example, carbon is in period 2, group 4.
Therefore, it contains two electronic shells with the electronic configuration 1s 2 2s2 2p2.
The 2s and 2p subshells constitute the valence shell; hence, carbon has 4 valence
electrons (Group 4).

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In the picture on the bottom left, the two 1s electrons of nitrogen are placed on the
inner ring around a set of spheres representing the protons and the neutrons in the
nucleus. The four valence electrons (2s and 2p electrons) are placed on the outer ring.
The rings denote the inner and outer electronic shells, but the representation is an
over-simplification because it implies that all electrons in a given shell are equivalent.
In fact, the s and p notations refer to different types of orbitals in which the
electrons are distributed. Different orbitals have different shapes, which reflect the
probability of an electron being found within the region of space circumscribed by the
orbital. In this course, we will not talk in detail about orbitals; we will focus simply on
the number of valence electrons and how that number determines how atoms combine
to form molecules (i.e., how many bonds they make).

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There are trends in the properties of elements as we go across the periodic table, and
these trends allow us to predict the types of interactions each element will have. For
example, the tendency of the atoms to give up electrons to form cations (positively
charged atoms) decreases across the period while the tendency to acquire electrons
to form anions (negatively charged atoms) increases. Both tendencies are a function
of the effective nuclear charge. The nucleus is positively charged. The more protons it
has, the greater the charge. The greater the charge, the more strongly it pulls
electrons towards it. Atoms in groups 1 and 2 have a smaller nuclear charge than
atoms in group 7. Therefore, they tend to give up electrons to form cations while atoms
in group 7 tend to acquire electrons to form anions. We have a special name to
describe the tendency of an atom to pull electrons toward itself: electronegativity.
As we have noted, electronegativity increases from left to right of the periodic table as
the effective nuclear charge increases (until you get to the last column, which contains
the so-called noble gases, which are inert). It also increases from the bottom to the
top of the periodic table. That might not seem intuitive because the nuclear charge is
larger for elements at the bottom of the table than at the top. However, the outermost
electrons of these elements dont experience a lot of the nuclear charge because the
inner shell electrons have a shielding effect. Elements in the higher periods have fewer
inner shell electrons to shield the nuclear charge felt by the outer shell electrons and
so the effective nuclear charge they experience is greater. Fluorine, located in the
penultimate column of the second row, is the most electronegative atom in the periodic
table.
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