fall 2014 lecture 1 notes

8/9/2019 Fall 2014 Lecture 1 Notes

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We’ll do a demo to see what happens as we cool a flask of hot water. If we can’t explain how simplesystems work we won’t be able to explain how a cell works.


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We’re 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. Weneed to review what we know we know, especially about intermolecular forces ingeneral (and H-bonding in particular) so we can understand the demo. Ultimately, weneed to understand more about energy flow so that we can appreciate the physicalprinciples that operate in all systems.


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1. Component parts of the cell (the smallest units of matter that matter in livingsystems)a. Organization of the cellb. Macromolecules in the cellc. Small molecules and metabolitesd. Water: THE molecule of life

2. Understanding chemical structures and bonding (electrons and their arrangementsin atoms and molecules)

3. Understanding intermolecular forces (how the component parts of a cell interactwith each other)


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Part of being able to predict intermolecular interactions is being able to understandwhy these interactions occur, their relative strengths, and which factors affect thestrength of intermolecular interactions.

One component of understanding hydrogen bonds is to know why they occur andwhich molecules can participate in them.


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This course is intended to provide an integrated introduction to the life sciences. In thefirst part of the class, we are going to try to provide a foundation for understanding thethermodynamics and kinetics of living systems. In order to do that, we need to start bylearning about the smallest units of matter that matter in living systems: electrons andtheir arrangements in atoms and molecules. The emphasis will be on understandingaspects of chemistry that will enable you to think about what happens in biologicalsystems. I want you to keep in mind a question throughout this course: What does itmean to be “living”?

It has been known for well over a hundred years that all living systems are made up ofa fundamental unit called the cell. The cell is a finite entity with a definite boundary, theplasma membrane. That means that the essence of the living state must be containedwithin that structure.

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I think it is fair to say that most people are far more interested in understanding humanlife than in understanding any other form of life. The problem is that humans are socomplex -- and they reproduce so slowly -- that they aren’t very good systems to study.If the fundamental unit of life is a cell, and a single cell contains the essence of what itmeans 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 allcells, we can begin to consider how different types of cells combine to create amulticellular organism. That, however, is beyond the scope of this course. Here, ourgoal is to provide a foundation for thinking about what happens in the fundamental unitof life, the cell.

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I told you on the previous slide that you have to understand the structures ofmolecules in order to begin to understand how they function in cells. On this and thenext two slides, I am going to introduce you to some of the most important kinds ofmolecules found in cells. On this slide some of the important molecules of life aredepicted. Many of them are biological polymers , such as DNA, RNA, and proteins.Polymers consist of many repeating units, or m o n o m e r s . Because these polymersare typically made of hundreds or thousands of atoms, they are commonly referredto as macromolecu le s . Biological macromolecules play some of the most importantroles in living systems. Some of them store genetic information to be passed down tofuture generations. Some of them are involved in decoding that genetic information.Others are involved in metabolism -- breaking down molecules to obtain energywhich is then used to build other molecules. These macromolecules and their roleswill be discussed in much greater detail throughout this course. Don’t worry if youaren’t yet be able to understand the structures of the molecules shown in thefollowing figures; their details are not important at this point. These structures areshown simply to give you a sense of the diverse nature of the macromolecules of life.


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In addition to macromolecules, sm a ll m olecu les also play a central role in livingsystems. Although there is no discrete size cut- off that distinguishes “small” moleculesfrom macromolecules, most small molecules relevant to life contain fewer than about100 atoms. Unlike the macromolecules of life, which are polymers comprised ofrepeating subunits, the small molecules used by living systems are extremely diversein their basic chemical structures. Their more diverse structures also imply that smallmolecules are synthesized in the cell by a much more diverse collection of chemicalreactions than those used to make macromolecules. Indeed, as we will learn later inthis course, macromolecules are typically generated by repeating one type of chemicalreaction over and over, while small molecules are synthesized through the use ofthousands of different reactions.


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If I had to pick a single molecule of life that is more important than any other -- whichin some sense is a ridiculous exercise since life results from the integrated functions ofa wide variety of molecules -- I would probably pick water. The reason I would pickwater is that while I can imagine substituting the other molecules of life with differentvariants that somehow accomplish the same types of things, I can’t imagine any otherkind of molecule substituting for water. Water is special. Water is different. Wateraffects 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 formcould have arisen and the search for evidence of life on Mars is justified. If water didnot ever exist there, then there is really no point in searching for evidence of life. Weare 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 firstprinciples but not impossible. Most of us take life for granted in the sense that it is sofamiliar to us that we have no problem telling the difference between something that isalive and something that is not alive. Jacques Monod, a famous scientist of the 20 thcentury, once said that it is perfectly obvious to a child of five that a plant is alive but atable is not. The very familiarity of life makes it hard for us to appreciate -- without aframework, that is -- just how unusual it really is. I can tell you exactly why the waterstarted to boil in the ice water, but I can’t 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 sothat you can begin to think about how the components of a cell are organized to createa state that we call “living.”


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1. Component parts of the cell (the smallest units of matter that matter in livingsystems)

2. Understanding chemical structures and bonding (electrons and their arrangementsin atoms and molecules)a. The periodic table and electronegativityb. Ionic bondingc. Covalent bonding and the “octet” ruled. Geometries of organic moleculese. 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 thatexplain phenomena at the molecular level. By the end of these first two lectures, youwill understand exactly why the water boiled and you will also have a foundation thatallows 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 requiresfirst understanding the nature of atoms and chemical bonds. The molecules of life aremade of a t o m s , which are the units of the elements found in the periodic table. Thereare 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 sixkinds 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 -- H 2O. A few other atoms playroles in biology -- mostly ions such as sodium, potassium, magnesium, calcium, zinc,iron, etc. -- but you don’t have to worry about most of the elements in the periodic tableto understand what happens in a cell.


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As you have probably learned before, the periodic table is a tabulation of the elementsaccording to their proton and electron configurations. Each period (or row) representsan electronic shell; the position of each row down the periodic table is numberedaccording 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 shellelectrons, or valence e lec t ron s . For example, carbon is in period 2, group 4.Therefore, it contains two electronic shells with the electronic configuration 1s 2 2s 2 2p 2.The 2s and 2p subshells constitute the valence shel l ; hence, carbon has 4 valenceelectrons (Group 4).


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In the picture on the bottom left, the two 1s electrons of nitrogen are placed on theinner ring around a set of spheres representing the protons and the neutrons in thenucleus. 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 anover-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 theelectrons are distributed. Different orbitals have different shapes, which reflect theprobability of an electron being found within the region of space circumscribed by theorbital. In this course, we will not talk in detail about orbitals; we will focus simply onthe number of valence electrons and how that number determines how atoms combineto 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, andthese trends allow us to predict the types of interactions each element will have. Forexample, the tendency of the atoms to give up electrons to form ca t ions (positivelycharged atoms) decreases across the period while the tendency to acquire electronsto form an ions (negatively charged atoms) increases. Both tendencies are a functionof the effective nuclear charge. The nucleus is positively charged. The more protons ithas, the greater the charge. The greater the charge, the more strongly it pullselectrons towards it. Atoms in groups 1 and 2 have a smaller nuclear charge thanatoms in group 7. Therefore, they tend to give up electrons to form cations while atomsin group 7 tend to acquire electrons to form anions. We have a special name todescribe the tendency of an atom to pull electrons toward itself: elec t ronegat ivi ty .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 containsthe so- called “noble gases,” which are inert). It also increases from the bottom to thetop of the periodic table. That might not seem intuitive because the nuclear charge islarger for elements at the bottom of the table than at the top. However, the outermostelectrons of these elements don’t experience a lot of the nuclear charge because theinner shell electrons have a shielding effect. Elements in the higher periods have fewerinner shell electrons to shield the nuclear charge felt by the outer shell electrons andso the effective nuclear charge they experience is greater. Fluorine, located in thepenultimate column of the second row, is the most electronegative atom in the periodictable.

fall 2014 lecture 1 notes

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