[SOUND]. This is the second lecture in the Introduction to Systems Biology. And in this lecture, I will provide some sort of background with respect to the eh how bout chemistry and cell biology have contributed to the development of systems biology using the cyclic amp pathway. Do we, biochemists and cell biologists and cell physiologists in this course might recognize this lecture as relatively standard biochemistry, cell regulatory systems. But the goal is to provide the engineers and the computer scientists and others, how discovery of individual components and putting them together into sort of smaller systems, and the use of mathematical representations of the system, has enabled to understand system characteristics. So let's get started. The bottom, the bottom-up approaches will use the cyclic AMP pathway as our major example. This is the prototypic cell signaling pathway. In this path, we go over the last two I know between 50 years and 50 or 60 years. Each component was discovered individually connected to an upstream and downstream component and the path we just surmised from these sort of binary connections. The cyclic AMP pathway has been the prototypic signaling pathway. And because of of this and because of the fact that many of the concepts, the general concepts in cell signaling come from this pathway. This has been a particularly rich pathway with this [INAUDIBLE] Nobel Prizes for discovery of psychic amp to a [UNKNOWN] I think back in 1971, Carl going all the way to last year when Bob Lefkowitz and Brian Kobilka won the Nobel Prize in chemistry for the studies for their studies sort of describing the structure and functions of beta adrenergic receptors. In between there was a prize for it [UNKNOWN] and for G proteins and for [UNKNOWN] and Marty [UNKNOWN]. So here is the cyclic cAMP pathway as we know it today. The cyclic AMP pathway consists of beta-adrenergic receptors, activating the G protein GS. This allows a signal G is to activate anocycles, it produces cyclic AMP, and cyclic AMP classically was thought to activate protein kines A, to signal down to like CREB, or, or to metabolic enzymes, for instance to control glucose metabolism. Over the past I guess twenty, thirty years or so, other directive actors of cyclic AMP have been discovered including a cyclic AMP gated channel as well as an exchange factor and I'll tell you what exchange factors are in the latter part of this lecture actually in the second part but suffices to say that exchange factors regulate small G proteins, and cyclic AMP activates this exchange factor [UNKNOWN] to activate the small G protein that can lead to [UNKNOWN] signal. So you can see that even with a simple signalling pathway such as cyclic AMP, you can get a signal [UNKNOWN] or through multiple pathways leading to a network there's already cyclic AMP activates the enzyme that degrades the protein kinates activates the enzyme that degrades cyclic AMP so there's a feedback loop and other things, so even simple pathways become very complicated reasonably complicated. Starting at the receptor, signal can flow to the cyclic AMP pathway to metabolic enzymes, to channels, or to transcription factors to regulate gene expression. So this kind of signal flow allows for a very rich, sort of interconnectivity between the various pathways, to various cellular functions, to various organismal level functions. And here is an example of what I told you in the last lecture with respect to multi skill. So in this particular cartoon taken from a paper that I published back in 2002, a review paper, one can see a whole range of a whole range of neurohormones, neurotransmitters, etc binding to different classes of receptors. These classes of receptors are characterized by the G proteins they use for signaling, so there's the GS that I just mentioned that go, goes to into the cyclic AMP pathways. The GI GO, the GQ that goes to the forceful IPC pathway, and G12 and 11. And these G protein pathways in turn, activate a range of bio chemical functions, including metabolic enzymes, iron channels, transcriptional machinery, mutability in contracting contractility machinery, secretory machineries and so on. And all of these sort of biochemical to same electrical and mechanical properties lead to sort of cell level functions such as glucose metabolism or [UNKNOWN] in hormone production. Or regulation of [UNKNOWN] activity in the heart or chemotaxis and so on and this in turn lead to a variety of organismal functions such as homeostasis at the level of organism, embryonic development, and learning, and memory. So you can see that there are multiple scales of organization from the signaling pathways to biochemical functions, biochemical functions to, sort of cell level, cell tissue level functions, to sort of organism functions, to produce various effects. So, given the importance of hormones, neurotransmitters, and other agents to to evoke these various kind of physiological responses, it has been very sort of useful to study the quantitative aspects of how a certain amount of ligand, such as hormone or neurotransmitters regulate the activity of the receptors. Typically, for this, we use ordinary differential equations. For the biologists who are thinking, so what are ordinary differential equations? You can look up sort of an elementary textbook on differential equations. But basically this allows one to sort of calculate the rate of change of an entity with respect to time depending on the concentrations of the entities of interest and relative rates and affinities with which they, they interact. So, in the case of ligand plus receptor binding, one is interested in calculating the rate of ligand receptor complex formation, and this is a function of the ligand concentration, the receptor concentration, and the forward and backward reaction rates. And this can give you the overall affinity of this receptors. These models are called deterministic models using ordinary differential equations. And the word deterministic re a sort of im characterizes the fact that once you know the initial rates and initial concentra, the rates and the initial concentrations of the reactants, you can specify their time dependent evolution of the product formation which in this case is like interceptor complex. So when the ligand binds to the receptor we typically use the word transduced. So exactly what is transduced? What is transduced is, the information from a form transduced. Kind of meaning converted from from form that is recognizable outside the cell. The information is converted to a chemical form that is recognized inside the cell. So for instances when a ligand, such as epinephrine or the other name for it is adrenaline it binds to the receptor, it activates the G protein to produce cyclic AMP that can produce various effects. But imagine if the cell could just take cyclic AMP into the cell. The cell would not recognize I'm sorry imagine the cell could take epinephrine into the cell the cell would not recognize epinephrine as a signaling molecule that it carries an information. It will just be a foreign chemical that got into the cell that needs to be degraded. So to extract the information that is contained in epinephrine or the levels of epinephrine the the molecule needs to bind to its receptor that then activates the G protein that in turn activates adinocyclist to produce cyclic AMP. And the conversion of the epinephrine signal into cyclic AMP signal in the, cell at the level of the cell membrane is, is the process of transduction. This process the beta [INAUDIBLE] receptor to say protein cyclic AMP and protein [INAUDIBLE] A transaction process can be written as a series of ordinary differential equations to represent enzyme action. At this stage, I should introduce everybody to Michaelis-Menten Kinetics because this is kind of the standard way in which these reactions, enzymatic reactions, are written. For each reaction, the signal transduction process pathway such as ligand receptor activation of the G protein, G protein activation of adenylyl cyclase, and adenyly cyclase activation and cyclic AMP production and, and activation of port, protein kinase A. We can write a set of ordinary differential equations and calculate the products. And I show you here there is a lecture handout that kind of very simply eh, summarizes this. You can look at it along with other materials for lecture two, but here I, I summarize just the product formation of the enzyme-substrate complex as a function of time, this is, when one knows the enzyme velocity for product formation is sort of seregate for the product, formation of the product. And it's given by the equation shown here and from this we can calculate velocity at any given time as a function of both the KM or the MichaelisâMenten constant, as well as the concentration of the substrate. KM is defined as the K inverse for the binding reaction, plus the K forward for the enzyme substrate to product conversion, divided by the K forward for the binding reaction. So KM is an important number to remember because it gives you a value that is indicative of the overall ability of the enzyme to catalyze the reaction. There are two other numbers with respect to the to the enzyme kinetics that is very useful and one is called the turnover number, which is the reaction velocity as a function of enzyme concentration. So here one looks at conversion of ES to E plus P and the operative reaction here is the key to reaction and if you take this number and divide it by the concentration of enzymes you get the turnover number, which is the moles of product form per mole of enzyme. Yeah that is of course the maximum velocity which is typically the K2 value. And these numbers are really useful because they tell you, quantitatively tell you what the reaction capabilities of the system are. So what I described to you is sort of a very simple case where there is a, a, logging binding side and which leads to sort of some time of enzymatic activity that of course more complex situations and this process called, allostery, where binding to one side results in changing affinity of another side, leaning to altered enzyme kinetics, or altered kinetics of the system. And the term most often used to understand Allostery is called the Hill coefficient. And the Hill coefficient, the equation that describes the Hill coefficient is sort of shown here where you can see that the actually the velocity the observed velocity is a function of remax is some is dependent on the substrate concentration raised to a factor and that reflects interaction between the substrate binding sides. And a net affinity K prime which again represents the overall affinity of the different sides with the, the sort of interaction at multiple sides. So the Hill coefficient N is sort of very often used as a number that indicates a deviation from sort of proportionality that we observe when in the Michaelis-Minton kinetics, and so this is a number that we, we will keep referring to and we should sort of keep this in mind. So when one has a set of reactions what, what really happens? In the case of information flow, the protein kinase A, the example that I've used protein kinase A upon activation is an actuated enzyme that first phorylates that is transfers the gamma phosphate from ATP to substrates like enzymes, metabolical enzymes like I just showed you. Channels, transcription factors, to change their activity, thus biochemical information gets converted to cell biology or cell physiological information. This leads to the fact that overall binding of the receptor binding of adrenaline, the ligand to the receptor, to a series of coupled enzymatic [INAUDIBLE] can result, for instance, glucose production in the liver. And with the muscle, the glucose that's produced in the liver is relayed to the bloodstream, and provides energy for the flight or flight response. And so thus you can see how physiolo information can be convert eh, in terms of chemical molecule, of chemistry, of chemical molecules can be converted to physiological responses. [SOUND]
