Chapter 2 Biology: Chemical Context of Life

So your book likes to utilize real life examples and connections as a way to support the concepts that we go through within a chapter or within a particular module and so here we have wood ends and these wood ants are ejecting formic acid from their venom glands and so we can assume that it\'s likel...

So your book likes to utilize real life examples and connections as a way to support the concepts that we go through within a chapter or within a particular module and so here we have wood ends and these wood ants are ejecting formic acid from their venom glands and so we can assume that it\'s likely directing this acid towards a predator so something like a bird perhaps and So what this is meant to illustrate is how a living Organism can harness the power of chemicals so this is something that we can also do as humans which we\'ll discuss in the context of different types of chemical reactions that take place within our bodies but we also do this outside the context of our bodies when we think about medications that we may take or chemicals that we may utilize to clean the environment or control pests So what you want to start doing as we go through these concepts is think about how these things relate to everyday events events that are personal to you or events that you can easily relate to these scientific concepts making an effort to make those connections early on allows you to start to work your way through more difficult concepts and it\'s important to be able to distill those concepts into something that is manageable for you and something that is easy to understand all life is made-up of matter and matter is anything that has mass and takes up space and matter can exist as a solid as a liquid or as a gas and when it comes to matter it consists of elements and an element is a pure substance that contains only one kind of atom and we\'ll discuss atoms in more detail in module 2 because of the size of atoms there is a requirement for sophisticated technology in order to visualize them and through visualization we can learn more about them we can study them OK what we\'re thinking about here is OK How two different things can come together and what they can make O matter consists of chemical elements in pure form and in combinations and through that we can generate compounds and a compound is a substance that is consisting of two or more elements in a fixed ratio and a compound is going to have properties or characteristics that are different from the elements that generated them and below that title you have an example of this so something to consider about this reaction we have sodium plus chlorine gas yields sodium chloride sodium and the chlorine have properties on their own that are very different from the salt sodium we can see is a solid metal chlorine is a poisonous gas but when the two combine the result is something that we can safely ingest so consider how that is possible what is it about the form that helps to promote the functioning how are these two things coming together to form sodium chloride what type of bond perhaps might join them and how might that contribute towards the essentially stability of that compound OK so within this slide we have opportunities to define things we can define matter define elements defined compounds and then think about how these things can have their own distinct properties and how when they combine to form a compound those properties shift those properties change here we have table 2.1 which goes to the elements in the human body remember that this is a biology focused course and so even when we consider elements we\'re really going to focus on the elements that we find very readily or in abundance within a living Organism we\'ll talk about elements based on their definitions in module 2 here I want to place an emphasis on elements found in living systems so this table from the camel book is highlighting the elements and within them there are 11 elements within the ones that are naturally occurring that are present in levels that are higher than trace amounts and trace amounts will be anything less than oh.01% of body mass this table groups oxygen carbon hydrogen and nitrogen together and they collectively make up 96.3 percent of body mass oxygen is the most abundant element in your body and that\'s supported by the most common molecule that we find within our bodies which is water in addition many of the molecules that you\'ll find within your body are organic molecules which means they are carbon containing so that\'s our next highest value we find nitrogen in high abundance for proteins so we will come across these major elements a lot because when it comes to bio 100 the first portion of the chorus focuses on building blocks OK so large biomolecules that we find within our bodies to help us to achieve different things also keep in mind that even though some of the elements found within a living Organism may be lower it doesn\'t mean that they aren\'t crucial that they aren\'t essential components to events that take place in your body we\'ll see the importance that sodium plays we\'ll talk about sodium potassium pumps in terms of movement of ions across the membrane they are important within discussions for bio 102 as well as 100 and we can think about trace elements even with respect to human Physiology when we discuss bio one on two calcium and phosphorus are important to skeletons and to the shells of animals and all of these things as important components of our body when looking at this table the goal is not to memorize these specific percentages I want you to look for a theme as you continue to expand your understanding of events that take place within organisms makes sense for a lot of our large biological molecules to contain these components when we consider the percentage of body mass in which we find these that\'s going to help to answer that question where do we see these elements in high abundance so that\'s something to take from this particular table so we\'ll never go through the entire periodic table of we\'re going to limit our our discussion on these elements that we find within this table but not again from a memorization perspective but through application where do we start to see these elements repeat themselves within our subsequent discussions chapter 2 the chemical context of life module 2 an element\'s properties depend on the structure of its atoms I want you to think about this title here because this title supports one of our underlying theme how we expect an element to behave or its desire to do a certain event when in proximity to something else depends on the structure of its atoms or the form of its atoms visually we\'ll just walk through the basic definition of atoms in their subatomic particles but I want you to consider how even at this early point we\'re considering how important form is to behavior and how that helps us to predict expected behaviors within a living Organism so each element is composed of a unique organization of atoms and an atom is the smallest unit of matter remember matter takes up space and it has mass and that atom still retains the properties of an element atoms are composed of subatomic particles the two illustrations here so 1 and 2 are depicting one of those subatomic particles a little differently we\'ll start within the nucleus and within the nucleus in both scenarios we are going to find two of those 3 subatomic particles we will find protons which are shown in pink and we will find neutrons shown in brown within the nucleus we see that the protons and neutrons are held in close proximity to one another so there is a force that\'s working across them over a short subatomic distance to keep them together protons carry a positive charge which is why there\'s a + within this pink sphere and the neutrons have no charge which is why nothing is depicted the third subatomic particle is the electron the electron has a negative charge the difference between these two illustrations is that in the left hand image we\'re seeing a cloud of negative charge and that cloud of negative charge is found around the nucleus so it\'s hanging out in close proximity to the nucleus and it\'s depicted in yellow when it comes to this illustration of why it\'s done that way this is because you can predict the probability of finding an electron in a particular area but you can\'t actually say this is the precise location of the electron that\'s based on the physics of subatomic particles and it\'s beyond the scope of our classroom OK but there are principles of physics that suggest that we cannot explicitly so that is why you\'ll see some illustrations that just draw a cloud we know what\'s in this area but we don\'t know with specificity where we find it but these electrons are going to be found in regions called orbitals and they can be found at varying distances around the nucleus now they\'re going to stay near that nucleus because there is an attraction that those electrons have for the nucleus due to the protons so the negative charge of the electrons attracted to the positive charge of the protons and that level of attraction is what allows for the electrons to stay within their respective the right hand side is simplifying it with a yellow circle surrounding the nucleus and then it\'s showing us the amount of electrons so we can see visually within the illustration that there are two electrons rather than being told that there are two electrons when we use the cloud illustration typically an atom has one electron for each proton this example has two electrons and for those two electrons there are two protons this relationship yields an electrically neutral atom since the negative charge and the positive charge of one cancel each other out the negative and positive charge of the other cancel one another out and when it comes to behavior chemical behavior the chemical behavior of the atom is going to be based on the number of and configuration of electrons and their ability or or lack of desire to interact in particular ways is going to give us some information on how large your structures should be expected to behave even on the level of an atom form is going to impart information to us regarding its function each element differs from other elements based on the number of protons found within their nucleus here we have helium which is abbreviated as upper case H lower case E and this is the chemical symbol no other element will utilize this nomenclature as their chemical symbol in looking at the atomic nucleus we see that helium has two protons in there so 1-2 and your protons again have a positive charge this is the elements atomic number and atom of helium will always have two protons so this idea of atomic number and the amount of protons we find within the atomic nucleus is unique it\'s something that we see in each element and it\'s consistent it does not change atomic number is what defines an element and atoms with the same atomic number have the same chemical properties next we have the atomic mass and the elements atomic mass is its total mass and it can be approximated by the mass number and an elements mass number is the sum of protons and neutrons and protons and neutrons for what we find within the atomic nucleus masses in reference to the amount of a substance and should not be confused with weight which would be the force that gravity would be exerting on that substance and atomic mass units are measured in daltons atoms with the same element will have the same number of protons if you change the proton amount you change the element but elements can exist in multiple forms called isotopes isotopes will differ with respect to the number of neutrons that they contain in this example we have the element hydrogen hydrogen has one proton when looking at the hydrogen here the superscript value represents the sum of protons and neutrons so PP plus N notice that there are no neutrons within the nucleus here and so when we add the amount of protons neutrons we have one protons 0 neutrons so our superscript value is 1 and our subscript or our lower value is going to be the atomic number so the number of protons if we look all the way across we see that the value on the bottom which is also shown in red is consistent so these are all forms of the element hydrogen in this particular example they have names for the isotope versions of hydrogen but that may not always be the case so there is deuterium and tritium for deuterium we can see now that there is a neutron there and so that\'s going to bring up our sum to two and then for tritium there are 1-2 neutrons now and so those two neutrons plus the additional proton bring the sum up to three so when we\'re thinking about isotopes these are still going to be the same element but a variation of it and that variation is due to a change in the amount of neutrons that are present within the atomic nucleus isotopes of an atom will have similar chemical properties but they can have different physical properties and some isotopes may be very unstable that behavior can affect how it behaves over a period of time and looking at these two isotopes of hydrogen deuterium is actually stable while tritium is very much unstable and in our upcoming slide we\'ll think about the impact or implications of discovering an unstable variant or an isotope and unstable isotope so the purpose of this slide thinking about how we define an isotope how we could describe it here how they vary from one another and the fact that isotope chemical properties can be similar but physical properties can be very different and even in looking at deuterium and tritium their stability is vastly different as well and then we\'ll expand on instability of isotopes and what that means biologically speaking in the upcoming slide in taking a class such as this one students often have a goal of entering a health related field and when there are opportunities to make those clinical connections with the basic science that takes place in bio 100 I will try to accomplish that and what we have in this slide highlights an integration between biology and medicine through the use of radioactive tracers or radio tracers radios rely on the presence of naturally occurring isotopes isotopes will be atoms of a particular chemical element that have a different number of neutrons in their nucleus that results in a slightly different atomic weight when we shift to the term radio isotope versus isotope we are providing information regarding the stability of that isotope so the term isotope will let us know that the isotope lacks stability and as a result of that instability the radio isotope will spontaneously give off energy through radiation and this release of energy transforms the atom now how high levels of radioactivity can be harmful they can damage our cells it can cause damage to the DNA that can lead to long term issues if we are subjected or surrounded by high amounts of it there are useful applications that can be harnessed in research as well as medicine we can use radioisotopes as a means to label or tag molecules which is what\'s taking place here this labeling can allow for researchers to track or trace events such as chemical reactions or in addition localization so localization just means where do we find it located within a living cell or tissue which is showing us a positron emission tomography scan or a pet scan this is accomplished by using a radioactively labeled glucose molecule this is our radioisotope tracer it\'s called fluorodeoxyglucose or FDG that is not an essential you know testable information just letting you know and it\'s administered through an injection now the breakdown or metabolism of glucose is something that we discuss in more depth when we get to Chapter 9 or when we discuss cellular respiration but for now we want to consider how cancer cells and glucose metabolism are related in general cancer cells have been shown to take up glucose at a significantly higher rate than normal tissues and this distinction can be used to assess the presence of cancerous cells within the body so when we\'re taking a look at this image where we see that bright staining at the throat that is going to indicate high amounts of that flower floral glucose and that\'s going to be an indicator of a potentially cancerous site within the body and I\'ll just add that there are areas of the body that just naturally are going to metabolize glucose more than others the brain being one of them So this does not necessarily mean that wherever you see glucose accumulation is automatically linked to cancer but this is a technique that can be used to kind of harness this knowledge regarding radioactive tracers and glucose metabolism Some radioactive isotopes are more unstable others and with higher instability comes a faster rate of decay whatever that isotope is the rate of decay is constant and it will be expressed as the isotopes half life so this is a measurement of how much time it takes for 1/2 of the atoms in that sample the decay graph book discusses carbon 14 carbon 14 contains 8 neutrons and it\'s often used for carbon dating of fossils inorganic materials it\'s half life is about 5730 years so that\'s how long it would take for half of the atoms in that sample so by determining the ratios of different isotopes of carbon and other elements from biological samples it\'s possible to quantify when materials were formed so this is another application of radial isotopes when it comes to P32 to put that into perspective the half life of P 32 is about 14 days so in terms of handling we know that depending on how long that P32 was housed within our biological fridge we\'d know how safe it was to handle how much radioactivity and we aren\'t just going based on the half life value we would use technical instruments in order to measure how much kind of feedback we were getting on that machine as an indicator of how hot quote UN and we aren\'t just going based on the half life value we would use technical instruments in order to measure how much kind of feedback we were getting on that machine as an indicator of how hot quote UN quote the radioisotope was the behavior of electrons within an atom determines how it will combine or interact with other atoms because biology is focusing on behavior of living organisms the emphasis of a biological discussion hinges upon electron behavior so biologists are primarily concerned with because their behavior electron behavior is associated with the types of chemical reactions that can take place within an Organism electrons are found in that region of space surrounding the atomic nucleus and that space is often referred to as their orbital and orbitals can have specific shapes and orientations and that\'s something that\'s heavily emphasized within chemistry but is something that we are not going to discuss here so I will not be talking about S orbitals or key or D so for our purposes I\'m merely acknowledging that orbitals have an impact on the geometry of an atom but where we will focus will be on the energy level seen in these different regions of space energy is the capacity to cause change and there are different forms of energy potential energy is energy that matter has based on its location and based on its structure and we\'ll focus on potential energy here with respect to location relative to the atomic nucleus the electrons of an atom are going to differ in their amounts of potential energy and that will be based on their location relative to the atomic nucleus so when electrons state of potential energy is called its energy level or its electron shell the amount of energy that an electron has is related to its distance from the nucleus so if an electron is the same distance as another they\'re both found in the same energy level while energy levels do have particular nomenclature we won\'t use them in our discussion so we\'ll use terms such as first shell second shell third shell etc as we progress further away from the atomic nucleus we can see based on these notes here that the energy is increasing so the further away we get from the nucleus the higher the energy level and the higher the potential energy so potential energy rises the further away we get from the atomic nucleus and what we care about as biologists is what we can do with this potential energy in the context of a living Organism we\'ll discuss the role of energy absorption and energy loss a little bit later on in our two semester sequence so I\'m acknowledging that it\'s here in the image but what I would like you to focus on right now how energy changes relative to an electron\'s position with respect to the atomic nucleus so the chemical behavior of an atom is determined by the distribution of electrons within their electron shells what we have here is a partial periodic table and a periodic table is going to show us elements and this particular one is showing us electron distribution for each element we go as far as 18 within this table what we care about in terms of behavior is going to be the valence electrons the valence electrons will be the electrons found in the outermost shell the outermost shell will be the one that\'s the furthest away from the atomic nucleus so it will be the one with the highest energy level and chemical behavior of an atom is primarily determined by those valence electrons now elements that have a complete or a full valence shell are considered chemically inert this would be based on them having 8 electrons within their last shell so here you have neon that contains 8 if we count them up same thing for argon when we work our way downward now when it comes to helium helium is also inert but when it comes to the very first shell maximum occupancy will be two electrons to be inert means to be non reactive now anything that falls outside of this is going to have a desire to complete their outermost shell so that they can reach the same level of stability that\'s seen within these three elements that I have just described and this desire to complete that outermost shell is going to drive their chemical behavior chapter 2 the chemical context of life module 3 so I just want to show this partial periodic table one more time just because it helps to drive home our concept file within module 3 and so this third concept is that atoms with incomplete valence shells that outermost shell can share or transfer valence electrons with certain other atoms and these interactions allow for atoms to stay in close proximity to one another and these attractions are referred to as chemical bonds so the formation and function of molecules depends on chemical bonding between atoms and we have a sense of which elements which atoms will be more reactive than others based on how complete their valence shell is and depending on the valence shell and the amount of electrons we find there that will also play a role in what type of chemical bond it will participate in here we have a hydrogen molecule which by definition is a group of atoms held together in stable association by energy covalent bonds build stable molecules and in this example we have hydrogen and each hydrogen atom has an unpaired electron and needs one more electron in order to fill its valence shell its outermost shell this makes a hydrogen atom reactive so it wants to form this interaction when 2 hydrogen atoms are in close enough proximity to one another each atoms electrons will be attracted to both nuclei so at this point they will begin to share electrons and as a result they are able to produce a diatomic molecule of hydrogen gas the formation of this molecule imparts stability each independent atom had one proton and one electron making it electrically neutral the new molecule contains 2 protons and two electrons and thus maintains that net charge desire to fill the valence shell has been satisfied here with these two electrons that have been shared for Adam\'s with more than one shell filling the valence shell will require a total of 8 electrons and that process of reaching completion is referred to as the octet rule for our hydrogen molecule we were showing a covalent bond but we weren\'t expressing it in quite the same way then this illustration we\'re showing our hydrogen atoms and we\'re showing those lone electrons that need a partner in order to be fulfilled so here we\'re showing it in a slightly different way but the idea is still the same we\'re sharing these electrons so that both of these hydrogen atoms can complete their outermost shell so this is showing us a single covalent bond or a single bond so that\'s the sharing of one pair of valence electrons you can also have a double covalent bond or a double bond which would be the sharing of two valence electrons and so in this example what we have here is if we\'re looking at the oxygen atoms it has 2456 in our outermost shell for each of them OK so 6:00 and 6:00 but in order for them to be complete because we\'re now working outside of that very first shell we need to reach 8 electrons and so in order to accomplish that we\'re going to need to share 2 pairs of electrons so there will be a double covalent bond here and the same thing applies which is that we\'re able to satisfy the octet rule for each of these oxygen atoms and so we\'ve imparted stability here so the strength of a covalent bond really depends on the number of shared electrons so a double bond satisfying this octet rule is going to be stronger than a single bond size flying as octet rule so comparatively speaking double bonds will need more energy to break as compared to a single bond the strongest covalent bond would be a triple bond which is seen in the formation of nitrogen gas and that would be the sharing of three pairs of valence electrons you just be quiet here we have different examples of covalent bonding so some that will produce molecules by their definition so hydrogen gas and oxygen gas which we discussed when we went through single covalent and double covalent bonding others can produce compounds so you have an example of water here you have an example of methane the goal with all of these remains the same which is to complete the outermost shell and confer stability to the individual atoms through the sharing of electrons the degree of sharing can vary between atoms and this can also impart particular behavior which is something that we\'ll discuss later on in this image we\'ll go through ionic bonding and with ionic bonds it can happen that atoms may strip electrons from their bonding partners rather than share them in this example we have the transfer of an electron from the sodium atom to the chlorine atom so if we take a look at the valence shell of sodium it has just one electron in its outermost shell and it would have needed seven more electrons to complete that octet rule and the likelihood of that event taking place is pretty low if we compare that to the chlorine atom this chlorine atom has seven electrons in its outermost shell and justice needs 1 electron in order to be satisfied so this transfer of electrons helps to satisfy both atoms because when we donate the electron from the sodium atom we\'re now reducing it back down to the second so we\'ve gone from having 3 shells and the left hand side here to having 2 shells once we form that ionic bond and then that 2 shell example we have our 8 electrons so both are satisfied one through the loss of an electron one through the gain of an electron and so the sodium ion will which will be a positively charged ion and that will be because of that loss of that electron the loss of that negative charge balanced with the amount of protons found within the atomic nucleus and the chloride ion will be an anion or a negatively charged ion because it has an additional electron so it\'s no longer balanced with respect to its relationship of protons within the nucleus another way to describe this is that sodium has been oxidized so a loss of an electron can be referred to as being oxidized and chlorine has been reduced which means it has gained an electron and this is a concept that we will discuss in later content now compounds formed by this process so removal of electrons rather than an actual sharing can result in ionic compounds or salts so here we\'re looking at table salt again which is sodium chloride and sodium chloride often exists and the crystalline structure so in this image we\'re supposed to be zooming in on a portion of that crystal and when we zoom into the crystal structure we see that the organization of the crystal is based on a level of attraction between sodium and chlorine and because we have these opposite charges so your cat ion and you\'re an ion they\'re going to have a level of electrostatic attraction so opposites attract they will aggregate with a very precise geometry but this interaction is not as strong as a covalent bond this means that certain forces can disrupt these interactions can cause the crystal structure to dissociate and that can result in mixtures that contain free sodium ions and free chlorine ions and this is essentially what can happen when salt is placed in an aqueous solution like a glass of water so a number of compounds can be composed of more than two atoms and the amount that is required to form a compound will be based on what is needed to satisfy that outer energy level here we have water shown as H2O and ammonia NH3 and water and ammonia are individually participating in covalent bonds which are depicted using these solid lines in both of these individual compounds the degree of sharing electrons is unequal the degree of sharing can be defined as the property of electronegativity another term that I often use in relationship to this is affinity or desire for something if you refer back to the periodic table electronegativity will increase as we progress from left to right across a row of the periodic table and it will decrease as we work our way down a particular column so the region of the periodic table that is found in the upper right corner will have the highest electronegativity for the water molecule oxygen is found on that upper right hand side of the table and has a greater electronegativity than the hydrogen atoms so while they are sharing electrons and they are satisfying their outermost shell in doing so the sharing event that occurs is not the same because the affinity or attraction for those electrons are unequal so as a reminder electrons are found within a cloud and there\'s movement that\'s occurring within there so they\'re not locked into a particular location with a stronger electronegativity the electrons that are being shared with the two hydrogen atoms are doing so by spending more time on the oxygen side than on the hydrogen side so while the molecule is still considered electrically neutral meaning that you have equal parts protons and equal parts electrons the unequal time will create regions of partial which is depicted here and partial positive so for regions that are partial negative this is going to be because those electrons are going to spend more time near the electronegative atom so the presence of electrons will create a partial negative overall charge Since the electrons in those moments of hanging out there will no longer be equal to the amount of protons seen in oxygen conversely the electrons are spending less time near the hydrogen atoms so the protons will win out slightly with that positive charge resulting in more protons relative to electrons within a particular point in time so our partial positive and partial negatives are based on electron proximity to each respective atom this is also what\'s seen in ammonia so the nitrogen atom will be the more electronegative 1 compared to the hydrogen atoms so again both water and ammonia are participating in covalent bonds but the sharing is unequal so these will be polar covalent bonds seen within each of these compounds so now that we\'ve established these definitions we can think about how these types of bonds allow for the interactions seen between water and ammonia which is the hydrogen bond the partial negative and partial positive areas seen in each of these compounds allows for a weak chemical association with each other and that\'s expressed usually with dashed or dotted lines so covalent bonds are usually expressed with a solid line hydrogen bonds use dotted or dashed lines and a hydrogen bond forms when a hydrogen atom covalently bonded to an electronegative atom so that would be hydrogen bound to oxygen here OK is Are usually oxygen or nitrogen but they don\'t have to be and while we\'ll describe this bond as a weak one they can have an additive force so when you have a ton of hydrogen bonding that can be strong and this will be essential to the immersion properties of water that are discussed in chapter 3 of our Campbell book vander waals interactions are due to uneven distribution of electrons which can result in accumulation by chance in one part of the molecule so this is different from a polar covalent bond because we know that our very electronegative atom is purposefully pulling electrons towards one side so that is creating this partial positive or partial negative charge for the van der waals these are snapshots in time in which there can be uneven distribution of those electrons so it is a temporary fluctuation in charge and vanderwall interactions are going to be attractions between molecules that are close to one another so they are in close proximity and this will be based on non polar molecules so nonpolar molecule will mean that their electronegativities are pretty much the same and brief variations in electron distribution will yield opposite charge distribution which will result in a level of attraction so again opposites attract Fender walls can also be called vander waals forces vander waals attractions and this is going to be a non directional attractive force so these forces come into play only when the two atoms are close to one another this reaction is the weakest one of the ones that we\'ve discussed and this attraction can disappear if the atoms move too far apart from one another so proximity is playing a really important role here now the significance of vanderwall\'s can increase just in the way that we\'ve discussed for hydrogen bonding if there are numerous atoms in the molecule coming into close proximity with numerous atoms in another molecule and these forces can be used for events like what\'s depicted here which is the movement of a gecko climbing up a wall and if we kind of focus just in on the hand which is allowing this Organism to climb up the wall we can also see that there\'s tons of tiny projections there and so in addition to having vander walls we have tons of surface area that\'s kind of imparted by the overall shape or morphology of this hand and that also helps to drive that movement along a surface ohh you don\'t know sign language so if you gave the cloth to shima so here is just a way for you to connect these earlier concepts with things that might be more pertinent or relevant to everyday discussion and so we\'ve really talked about electrons and a little bit the idea of orbitals and imparting geometry but molecular shape and function is a huge underlying theme when it comes to our topics for the first portion of bio 100 and so molecular shape can determine how biological molecules can be recognized or can recognize something else and how they choose to respond so size and shape is key to function so there is a relationship between form and function that is a huge theme within this book and we explore it in multitude of times and by the end of your time going through this content you should always be asking yourself how is form playing a role in the functional behavior of whatever this biological molecule whatever the behavior of this cell is going to be so when we look at this image we have a discrete region between two different molecules so we have natural endorphins and we have morphine and in the area that\'s shown in this kind of rectangle here we find that there is a high level of similarity with respect to its molecular shape and as a result the natural endorphins and morphine which is an opiate can have similar effects because their shapes are similar and they\'ll be able to bind to the same receptor so we have these endorphin receptors that are found on the cell and it\'s a brain cell and the natural endorphin and morphine are able to bind in that same location and a concept that we talked about later on within cell communication is that this can elicit a pathway and this pathway can have a downstream response which can impart feelings of euphoria if we\'re thinking about the capabilities of endorphins as compared to morphine so molecular shape and function play a really important role in how cells are able to respond and that then means that we can harness our knowledge of molecular shape geometry stability desire to fill these outermost shells in a way to design and construct certain types of chemicals that may be synthetic in nature or may be modified from those that are already existing our final module for this chapter chapter 2 the chemical context of life will be module 4 so our 4th concept is that chemical reactions make and break chemical bonds and so when it comes to a reaction there\'s a starting side so our starting molecules of a chemical reaction are referred to as reactants the final molecules of a chemical reaction are referred to has yes as products and in this scenario this is the end of the process but as we start to discuss things that increase with respect to their complexity we may find that there are multiple steps that allow us to transition from reaction to final product and so we\'ll make that distinction as we cover later material chemical reactions involve some type of shifting of atoms so here we can see if we have our diatomic hydrogen here we have our diatomic oxygen and then we have a chemical reaction that allows us to produce 2 molecules of water and a chemical reaction can shift atoms from 1 molecule to another or from an ionic compound and this can result without any change to number or identity of atoms and chemical reactions can be influenced by different factors and so this will be a large part of chapter 8 and so examples of factors that can influence chemical reactions include environmental conditions so things such as temperature the amount of reactants and products that are available and driving a reaction forward or backwards and if there is some type of substance that\'s being used in order to help increase the rate of the reaction or the rate of product formation so here\'s just a second example of a chemical reaction that\'s a little bit more complex than the formation of water so in this reaction we have carbon dioxide 6 molecules over that and we have our six molecules of water and in the presence of sunlight we can drive the reaction forward and this allows us to ultimately downstream produce the sugar glucose and oxygen gas and so this is a simplified chemical reaction for that of photosynthesis here we can revisit the earlier image of the Ant releasing formic acid and now start to layer our discussion that we\'ve had so far formic acid is composed of carbon 2 regions and two oxygens so atoms whose protons will dictate which element they are are going to be consistent so we know how many protons are present within oxygen carbon and hydrogen and we should not see any deviation if for example we look at this oxygen to see how many protons are there versus this one now for this particular image it zooms in on the oxygen atom and when we are taking a look at that atom within the atomic nucleus there are going to be 8 protons it\'s not visible here as obvious but imagine that this is 3 dimensional and that there are some photons you can\'t see kind of behind the image and when it comes to those protons again that determines the identity right so we know that the number of protons determines the identity there are 8 protons the identity is therefore oxygen let\'s consider the relationship between protons and electrons 8 protons we\'re looking at something that\'s going to be neutral in terms of charge we\'re going to expect to see 8 electrons so that they can cancel each other out there are two electrons in the innermost ring and then you have 1/2 3456 found in the outermost or the valence shell now when we take a look at the electron distribution that\'s going to determine the properties and the desire to form bonds so there are two empty spots in that valence shell so there are two opportunities to share electrons in order to help satisfy the octet rule for this atom and it can do that with hydrogen bond and the carbon that\'s bound so we can satisfy it here so there\'s a sharing of one pair here\'s the sharing of the second chair or when we take a look at the other oxygen it can be accomplished through a double bond and there we are sharing in both sides and so we\'re satisfying the outer most shell by participating in those particular types of thoughts and that same process gets applied to the other atoms and it supports how many bonds we see in order to help satisfy the outermost shell so that everyone is happy through these covalent bonds we generate a compound we know that the atoms subatomic particles in part information on their behavior and that form helps to support function the same can be said for the compound so the compounds properties behaviour function will also be based on the form and their form is based on how the atoms are bonded together in this lower area we can see the compound behaving as an acid it will do this in an aqueous environment and there will be dissociation or dissolving or formic acid in order to yield this H plus to the surrounding environment and this helps support the idea of reactants products and we can think about this relationship as far as chemical reactions go and how we can drive the reactant side towards the product or vice versa depending on the scenario so this particular image really helps to tie in a lot of what we\'ve discussed so far and I think this is a good way to close out this chapter if thinking about all of the connections that can be made so again consider the vocabulary don\'t make that the entire tape full message but it\'s really just more of a refresher because you should have experienced pretty much all of this within chemistry but now think about where we\'re going with this so it\'s not just about defining these things but thinking about real life applications and how they help to support our knowledge of these basic underlying themes within biology