LS1a Fall 2008 9-16 lecture notes

LS1a Fall 2008 9-16 lecture notes - The flask vs the cell...

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Unformatted text preview: The flask vs the cell The cell The flask What does it mean to be alive? page 1 Life Sciences 1a An Integrated Introduction to the Life Sciences Lecture Slides Set 1 Fall 2008 Prof. Daniel Kahne page 2 Lectures 1 & 2: The Chemical Foundations of Life I 1. Component parts of the cell a. Organization of the cell b. Macromolecules in the cell c. Small molecules and metabolites d. Water: THE molecule of life 2. Understanding the molecules of life: chemical structures and bonding 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 a. Ionic interactions b. Hydrogen bonding c. Partial-partial charge interactions d. Van der Waals forces e. The continuum of intermolecular forces f. Understanding phase changes in water page 3 The flask vs the cell The cell The flask What does it mean to be alive? 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. We can't understand what happens in living cells without understanding what the component parts of a cell are and how they interact, so we will spend time learning about those component parts. After a description of the component parts, we will move on to examine how scientists try to understand the complexity of the cell because a cell is much more than the sum of its component parts. After all, we can't simply reconstitute a cell by mixing its component parts together in a flask. There is a level of organization and regulation in the way the component parts of a cell function together that leads to what we call "life". How much do we really understand about "life" in the scientific sense? How much further do we have to go and how can we get there? At the end of the course, we hope that you have a foundation for thinking about what happens in biological systems -- both from the chemical and the biological perspectives -- and that you have a better appreciation of the complexity of cells. page 4 Cell structure The cell The human body 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 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 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. page 5 Cell structure The cell The human body The cell can be viewed as a semi-permeable bag (the cell membrane) containing lots of different molecules. The molecules are not randomly distributed, but are organized within the interior of the cell. This is true whether the cell is a prokaryotic cell (which doesn't have a nucleus) like a bacterium or a eukaryotic cell (which has a nucleus), like a yeast or human cell. The manner in which organization is achieved is different in prokaryotic and eukaryotic cells. Although eukaryotic cells are widely considered to be more complex -- they are much bigger and have many more genes -- we understand some aspects of how the molecules are localized to particular regions of eukaryotic cells better than we do for prokaryotic cells. That is because eukaryotic cells contain within them a series of smaller, semi-permeable bags, each of which contain sets of different molecules dedicated to specific functions. These smaller bags are called organelles. We are going to talk about what happens in some of the organelles later in the course, but we aren't going to talk about the organelles in detail. That's because you don't need to have organelles to have life -- as we know from studying bacteria. What you need is organization and regulation of a set of processes that enable the cell to grow and divide. To understand organization and regulation, you need first to know the basics of molecular structure as well as thermodynamics and kinetics. In other words, in order to understand the complexity of a cell, we are first going to reduce that complexity to a set of phenomena we think we understand pretty well. page 6 Macromolecules NH2 O P O HO OH HO N O N N N nucleic acid polymer nucleotide monomer HO The nucleus protein polymer H2N O OH amino acid monomer 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. Don't worry if you aren't 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. page 7 Small molecules and metabolites OH HO HO HO O OH OH HO N H OH H3C H3C H3C H H HO H H3C CH3 CH3 Glucose (Sugar) NH2 HO N H Pyridoxine (Vitamin B6) S Cholesterol (Steroid) NH2 O O O P P P O HO O O HO OH OH HO N O N N N H2N O OH OH Serotonin (Neurotransmitter) Methionine (Amino Acid) Adenosine Triphosphate (Nucleotide) 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. page 8 Water and electrolytes (salt) The cell Ions and water molecules 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 can't 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 searching for evidence of life. We are going to talk a lot about water and its role in this course. page 9 A demonstration Water boils upon heating Water stops boiling when taken off the heat The demonstration involves the simplest system I can think of that involves a cellular component. The cellular component is water, something I just told you is essential for all life and that makes up most of the mass of a cell. I have here two containers of water: one is a four liter beaker containing two forms of water -one in the solid state (ice) and one in the liquid state; the other is a one liter round bottom flask that also contains two forms of water -- one in the liquid state and one in the gaseous state (water vapor). In other words, the water in the round bottom flask is boiling. I am going to take the flask of boiling water off the heat source, but first, I'm going to stopper the flask so that I don't lose the gaseous water vapor into the auditorium. What do you think will happen to the boiling water in the flask if I take it off the heat source? page 10 A demonstration Water boils upon heating Water stops boiling when taken off the heat Water boils again when placed in ice water (see surface disturbance in flask) I'm guessing that at least some of you will say that the water will stop boiling now that we have removed it from the heat source. And you would be right!! How exciting is that? Okay, it's not exciting yet: at this point my nine year old son told me this demo was boring because any idiot knows that water stops boiling when you take it off the heat. Next question: suppose I take the flask, which I have removed from the heating mantle so that it has stopped boiling, and I plunge it into the beaker of ice water? How many of you think nothing exciting is going to happen? Well, let's see. Look! It has started to boil again! Why does that happen? How can cooling a flask of hot water down quickly cause it to boil? I wanted to show you this demonstration to make a point, which is that the behavior of even simple molecules can be unexpected. The first step towards understanding a cell involves understanding some very basic principles of how molecules interact -- because if you can't understand a simple system, you can't possibly understand a complex one. Very few things are simpler than a flask of boiling water, and yet most people are surprised by the demonstration I just showed you. Most people can't explain why the water starts to boil again when we put it in the ice bath because they have no framework for explaining the behavior and they have never seen anything to prepare them for it. I will explain more about the demonstration as we get to the end of the second lecture. page 11 Complexity in life A table A plant Life is obvious.... but unexpected. 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. Jaques Monod, a scientist we will encounter later in the course, 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 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 so that you can begin to think about how the components of a cell are organized to create a state that we call "living." page 12 The periodic table of the elements H, C, N, O, P, S (aka SPONCH) = 99% of living matter 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 don't have to worry about most of the elements in the periodic table to understand what happens in a cell. page 13 Basic structure of atoms Group (column) Period (row) Electron shell being filled shell 1 shell 2 shell 3 # of valence electrons 1 2 3 4 5 6 7 0 (8) A nitrogen atom (nucleus greatly enlarged for clarity) 7 electrons total 5 valence electrons (in the "outer shell") 7 protons 7 neutrons electron clouds ("orbitals") 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. The groups (or columns) represent atoms having the same number of outermost shell, or valence electrons. For example, nitrogen is in period 2 group 5. Therefore, it contains two electronic shells with the electronic configuration 1s2 2s2 2p3 . The 2s and 2p subshells constitute the valence shell; hence, nitrogen has 5 valence electrons (Group 5). 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 five 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 oversimplification 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). page 14 Electronegativity Electronegativity describes the tendency of an atom to pull electrons towards itself... Atoms with very different electronegativities come together to form ionic compounds while atoms with similar electronegativities form covalent molecules 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 decreases across the period while the tendency to acquire electrons to form anions 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 don't 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. page 15 Ionic bonding Electronegativities of selected elements A molecule that has lost an electron bonds to a molecule that has gained one. These charged molecules are called ions. Na Cl Na + Cl - There are a variety of ways to connect the atoms represented on the periodic table to form molecules; these connections are called chemical bonds. Electronegativity is a property that strongly influences the way atoms interact with each other and how they combine to form molecules. In fact, the electronegativity difference between interacting atoms allows us to predict the nature of the chemical bond that forms between them. If the electronegativity difference between the interacting atoms is very large, as it is for Na and Cl, the resulting bond that forms between the atoms is an "ionic" bond in which Na has given up its single valence electron to Cl. As a result, the Na is positively charged (Na+), the Cl is negatively charged (Cl-), and the two have a strongly favorable electrostatic interaction like the opposite poles of two magnets. Compounds connected by ionic bonds are often referred to as salts. page 16 ...
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This note was uploaded on 09/23/2008 for the course LIFESCI 1a taught by Professor Kahne during the Fall '08 term at Harvard.

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