anatomy and physiology one chapter to the chemical level of organization now thank goodness this is not a chemistry class so we don't have to go crazy super deep but we do need to have a basic understanding of some chemistry and biochemistry principles in order to really go any further with physiology so we'll start first with what chemistry is all about so this is the science that deals with the structure of matter which is anything that takes up space and has mass and the study of chemistry is also going to include the structure of atoms which are the smallest most stable units of matter basic chemical building blocks and how atoms can combine to form more complex structures so again reiterating what matter is it's anything that takes up space and has mass it's made up of atoms and atoms can join together to form chemicals that have different characteristics again chemicals or what the body is made of so we do need to understand a little bit about this chemistry to really get into the Physiology chemical characteristics can determine physiology at the molecular and cellular levels and we'll be talking about the cell in the next chapter chapter 3 so atoms are made of sub atomic particles protons which have a positive charge neutrons which are neutral and electrons which are negative so when we look at a drawing in a book of an atom you'll find that protons and neutrons are at the center of the atom all so known as the nucleus or hub middle of the atom and the electrons will be found orbiting around the outside of that central nucleus atomic number is the number of protons and atom has the nucleus as we just mentioned is going to contain the protons and neutrons together at the core in the electron cloud in some books we're going to see an electron cloud and I'll show you a difference between that and the electron shell but the electron cloud is the spherical area that's going to contain the electrons and the electron shell is a two-dimensional representation of the electron cloud and most of the figures we're going to use are going to have the electron shell so here you can see the electron cloud on the right which kind of looks like a hazy cloud representing where the electrons are found and then on the Left we have the electron shell which is the two-dimensional representation so we can see the actual atom or excuse me the actual electrons here and here in that shell and then notice at the middle which we call the nucleus we can see the pink colored protons and the gray colored neutrons remember again that protons are positively charged and neutrons are neutral so an atom is made up of protons and neutrons again located in a central nucleus the nucleus is surrounded by the electrons now the electrons hang out with this nucleus because protons are positive and positive plus neutral or nothing equals an overall positive charge in the nucleus the electrons are negative and what happens when negative and positive are near each other attract so the electrons are going to be attracted to the nucleus which will keep them around orbiting an element is a pure substance made up of atoms of the same kind and as we mentioned previously the atomic number or number of protons in an atom is going to help determine its chemical properties there are 92 elements that exist in nature atoms of each element can be distinguished by their specific number of protons so again each atom has a specific proton number and that's part of that atoms identity so it's not going to change carbon for example has six protons and we can see six protons here in our chart for carbon that's never going to change that's what makes carbon carbon but the number of neutrons can vary in the same atom and we call those variant forms of an element isotopes so an isotope is this is a variant form of an atom that differs only by Neutron number because remember we can't change the proton number that's specific for that atom so if we look at the chart down here we can see that there are three forms of carbon or isotopes in this chart carbon-12 carbon-13 and carbon-14 we know carbon has six protons and you will see in these isotopes six six and six that's not going to change if we know the number of protons in the atom we also know the number of electrons because the proton number and electron number will match in the atom so since we know there are six protons in carbon there will also be six electrons in carbon and if we across at these isotopes we see six electrons six electrons and six electrons for all three types of carbon notice where the difference is in the neutrons which again is the definition of isotope same or variant forms of an element differ only by a neutron number so carbon-12 has six neutrons carbon 13 has seven and carbon-14 has eight so these guys have identical chemical properties and are alike except for that Neutron number which is going to change their mass so they're going to be different in mass okay so next we talk a little more about electrons so electrons and the electron cloud can determine the reactivity of the atom the electron cloud contains what are called shells or energy levels and each of those energy levels can hold a limited amount of electrons again thank goodness this isn't chemistry if you take chemistry you'll need to know about all those energy levels and how many electrons go in each one which is super super fun it's not fun at all not at all not even a little but we do need to know for purposes of anatomy we need to understand about bonding and in order to understand about bonding we do care about the outermost shell of the elect of the atom the outermost shell in the atom is called the valence shell and it is going to determine bonding so an atom with an unfilled valence shell is more likely to react with other atoms to try to obtain a full outer shell atoms with full outer shells already are stable and do not readily react with others so in most not all but in most Adams's the outer shell can hold eight electrons so if an ad elects any of those eight electrons in its outermost shell the only one we care about right now is going to be more likely to form bonds with other atoms and in those bonds they will either share gained an electron from another atom or lose an electron to another atom so let's go into bonding now the chemical bonds we're going to look at involve again sharing gaining or losing electrons and there are three major types of chemical bonds whenever we have bonds this is going to help us to form molecules and also compounds so the three major types of bonds we're going to go over our first ionic second covalent and third hydrogen so let's start with ionic ionic bonds are a bond between atoms of opposite charges so let's go through that line by line so first of all we need to know an ion is an ion is an atom that has a charge so either a plus or a minus beside it in a bond like an ionic bond one atom is known as the electron donor so it's going to give one or more electrons away it's going to donate them and when it gives away those electrons remember electrons are negative so if it gives away negativity it's going to become more positive than it used to be so that means it will become a cation a cation is a positively charged atom so remember when we give away some negativity give away an electron that's going to make us more positive than we used to be so we're going to have now a positive charge so that atom is a cation and one little tip help you remember cation the T in cation reminds us of a plus sign so that T should make you think of a plus or positive charge on that atom slash ion another atom in the ionic bond is going to be what's called the electron acceptor this guy is going to take the electrons so when we take electrons we're taking on extra negativity so that's going to make the atom more negative than it used to be so that atom slash ion will be called an anion an anion is a negatively charged atom so what you can remember that is there's an in an anion and in makes us think of the word negative so in negative this atom is going to have a negative charge ionic bonds again are defined as attractions between the cation which is the positive ion and an anion which is our negative ion so let's take a look at a picture or figure from a book on this so this is how an ionic bond forms so in this picture we can see at the top a sodium atom and we can also see at bottom a chlorine atom now let's look at the outer shell of the sodium remember that's the valence shell that likes to have eight in it and you can see represented by the yellow circles the yellow circles are the electrons we have right now there is only one electron in sodium's outer shell so it's it's a it's a ways from being full if we have an outer shell that has eight in it then the atom becomes stable so let's look down at the second shell of sodium second down and in this one there are eight electrons in chlorine the outer shell has seven electrons and this open circle represents where we don't have an electron but we could have one and if we did that would mean that our outer shell would be full and we would be stable so chlorine only needs one one electron to become stable so these guys are actually a perfect pair if sodium gives up or donates this electron to chlorine who will accept it then that means that the second shell down will become sodium's outer shell and it will be full which will make sodium more stable so that would look like this so in this picture sodium has donated that extra electron to chlorine and now the second shell down is its new outer shell and it has eight in it making it more stable sodium is happy since sodium gave away that extra electron gave away some of that negativity sodium became more positive so now we have a positive sign next to sodium which means it's a cation now chlorine accepted that extra electron from sodium as we can see it did right here in this picture and when chlorine accepted that extra electron accepted that negativity chlorine became more negative now we call it chloride so now we have a positive sodium cation and we have a negative chloride anion what happens when positive and negative get near each other they attract so sodium chloride will attract to form an ionic bond again an ionic bond is a bond between two oppositely charged atoms we now call this the compound sodium fluoride okay so next are the covalent bonds and covalent bonds are the strongest of the three so we would rank covalent as one as far as strength we would thin rank ionic in the middle and we drank our last one hydrogen is the weakest so we're going to get to that in just a minute so covalent bonds are strong bonds that involve shared electrons so remember in ionic bonding we didn't share electrons we either donated or we accepted there was no sharing so in covalent we're going to share one electron is donated by each atom to make the pair that is going to be shared sharing one pair of electrons is called a single covalent bond now if you go on and take chemistry or you have taken chemistry you know that there are double and triple covalent bonds which we're not going to go there but single covalent bond is good enough for now so in the covalent bond world we can have nonpolar covalent bond or a polar covalent bond non-color nonpolar covalent bonds are bonds that have an equal sharing of electrons between the atoms these atoms are going to have an equal pull on the electrons so we're going to share equally and fairly we call that nonpolar so this happens for instance between two atoms of the same type so for example two hydrogen atoms may share a pair of electrons equally the electrons are going to spin the same time with one hydrogen as they spend with the other so that's going to mean equal or fair sharing of electrons nonpolar covalent bond polar covalent bond is an unequal sharing of electrons because one atom has a stronger pull on the electrons than the other so we call this a polar molecule that forms in this in this type of bonding and an example of this would be water and I'll show you a picture of that just a second so polar covalent bonds is unequal or unfair sharing in other words somebody's going to hog the electrons and in water molecules we know water is h2o oxygen is big and strong and it's going to have a stronger pull on the electrons than the hydrogen's will so oxygen is going to hog the electrons making it unequal sharing so here's a picture of a water molecule kind of looks a little bit like a Mickey Mouse head we've got a big oxygen atom and then we've got and when I say big we're talking about atoms so you guys know big is not big because the oxygen is stronger or has a stronger pull it's going to spend more time with the electrons than the hydrogen's will get to spend with the electrons because the oxygen will spend more time with the pair of electrons remember electrons are negative this is going to make oxygen slightly negative and we can represent that by this little symbol that kind of looks like a broken eighth and that means slight negative charge so because it's spending time with two electrons it's going to have a slight negative charge because those electrons are hanging around that oxygen so much the hydrogen atoms are not spending as much time with the electron so because they're not spending that much time with a negative charge they're going to be slightly positive as you can see here and here so this makes water a polar molecule positive on one right and negative on the other side so when we put a bunch of water molecules together they're going to form our third type of bond called a hydrogen bond okay so in the hydrogen bond these are weak polar bonds between adjacent molecules based on their electrical attractions these are going to involve attractions between a slight positive charge and a slight negative charge so we see that in water molecules so in this picture there are multiple of our little Mickey Mouse heads or water molecules and remember how we just talked about that oxygen is slightly negative as symbolized here and hydrogen is slightly positive as symbolized here so the slightly negative oxygens are going to be attracted to the slightly positive hydrogen's you see the same thing here slightly positive hydrogen attracted to slightly negative oxygen and those slight weak attractions between the hydrogen's and the oxygen is going to cause what we call hydrogen bonding hydrogen bonding in water can cause what's called surface tension and surface tension acts as a barrier on the surface of water this can allow insects to walk on the surface of water or water to bead up on plants leaves or even on your skin like when you get out of the shower okay so moving on to chemical reactions in a chemical reaction either new bonds are formed or existing bonds are broken down in a reaction we're going to have what are called reactants these are I like to think of them as the ingredients these are the materials we put in or the ingredients we put in to make something and then we've got the products which are the materials coming out of a reaction so materials going in our reactants and products are the materials coming out of the reaction metabolism is defined as all the reactions that are occurring at one time energy is defined as the capacity to do work work is moving an object or changing its physical structure kinetic energy is the energy of motion so walking running swimming flying all kinetic energy energy of movement and potential energy is stored energy and it can be stored based on position so if you imagine a ball at the top of the hill it has not actually started rolling down the hill yet but it could so there's potential for it to move but it hasn't so that ball would be storing potential energy if the ball begins to roll then we call that kinetic energy so back to reactions the types of chemical reactions we're going to look at our decomposition and synthesis decomposition reactions or catabolism is when we break chemical bonds for example this a B would be broken up into a and B separately a be broken up into its components a and B so when we break bonds and we can use a hydrolysis reaction to do that in other words add water and we see this happen when we put sugar in water and stir it up that water can break up that sugar and help it to dissolve and then the water tastes sweet synthesis reaction is when we make something we form chemical bonds and we call that anabolism so decomposition breaking things down anabolism building things up making new things so this would be like a plus B equals a B a plus B two individuals will combine to make a B and we can do this using dehydration synthesis where we take water out and we're able to make something new so we're going to go back to hydrolysis and dehydration synthesis in a little while and go over it again so decomposition breaking things down catabolism synthesis animalism building things up making new things okay so in biochemical reactions in cells they do not occur on their own they do not occur spontaneously activation energy is how much energy we need to get a reaction going so how much do we have to put in to get the reaction started enzymes are protein catalysts that are going to make it easier and quicker to get the reaction going so enzymes are wonderful they're going to speed up reactions by lowering the amount of activation energy we need to get the reaction going for example we can see in this figure in this chart we have energy going up and the progress of the reaction going to the right so in any reaction as we talked about before we need reactants which are the the items going in and again I like to think of these as the ingredients this sharp Hill represents how much energy or activation energy we need to put in to get the reaction going which looks like a lot by the way and then we end up with a stable product or the finished product pay so if we use an enzyme we can actually lower that hill and make it easier which is represented by the red hill here this is how much energy it would take to get to the product using an enzyme now I know it's slightly lame but I have an everyday example I like to think of when looking at this particular concept so if you wanted to make a cake from scratch you would need a lot of ingredients and you need to put in a lot more time and focus to get to that stable cake product so the reactants in in the homemade from scratch cake are going to include a lot of ingredients oil eggs flour sugar baking powder etc lots of ingredients and then this Hill represents the amount of time the amount of ingredients the amount of concentration and measuring to do just right to end up with a beautiful from scratch stable product cake that's great but the human body always wants to conserve energy so we're going to try to do things easier if possible so in our everyday example we could make a cake from a cake mix we're going to end up with a similar stable product but it's going to be a lot easier so our cake mix represents using an enzyme okay so the reactants or ingredients are less the box of cake mix and a few little things we add and it's kind of hard to mess it up so this Hill represents the amount of energy to get to our cake if we use a cake mix so less energy less focus less ingredients and we will arrive at a similar product nutrients are essential molecules we get from our food and metabolites are molecules that we either make or break down in our body these are a byproduct of our metabolism which our metabolism remember is all the chemical reactions going on in the body organic compounds include molecules that contain carbon and hydrogen as their primary components and there are four big organic compounds of life carbohydrates proteins lipids and nucleic acids we're going to come back to those and go into them in a little bit more detail before we do we're going to talk a little bit about water water makes up two-thirds of your total body weight and hydrophilic and hydrophobic compounds are defined as either hydrophilic hydrometer Phillip fellows meaning loving so hydrophilic water loving these are things that interact with water so things that mix with water will glucose sugar mixes with water will hydrophobic is water fearing so these are things that do not interact well with water like oil for example whenever you put oil with water the two separate pH is a measure of the concentration of hydrogen ions in a solution neutral is 7 on the pH scale acidic is 0 to 6 and basic would be 8 to 14 the pH scale has an inverse relationship with hydrogen ion concentration more hydrogen ions means lower pH fewer hydrogen ions means higher pH so an acidic ph is lower than seven as we mentioned before zero to six and it is going to have a high hydrogen ion concentration in a very low hydroxide concentration basic or alkaline pH is higher than seven so eight to fourteen it's going to have a low hydrogen ion concentration and a high hydroxide concentration the pH of human blood ranges from 7.35 to 7.45 that would be considered the homeostatic range like we talked about homeostatic ranges back in chapter 1 so here's the pH scale and you can see from the left leading up to neutral these are the acids and some examples of acid would be hydrochloric acid that's way down there beer vinegar wine pickles grapes Tomatoes things that are a little tart or a little sour are typically going to be found on the acidic side as we move to the middle at neutral 7 we see pure water and blood and as we go from 8 to 14 these are the bases and will include things like ocean water bleach ammonia oven cleaner all household things that are basic so an acid gives off hydrogen ions we call that a proton donor so don't confuse this type of proton with the first type we talked about in the atom that the positively charged proton proton meaning hydrogen ion here so acids are hydrogen ion donors they add hydrogen to a solution strong acids are going to sociate or give off hydrogens completely give off a lot to hydrogen bases our hydrogen ion acceptors and they will remove hydrogen ions from a solution strong bases dissociate completely in solution we cast sand weak bases do not dissociate completely and they will help to balance the pH cells are kept close to pH of 7 by buffers and buffers are things that will resist pH change they will accept hydrogen's when there are too many and they will donate them when there are not enough and this is what's going to help to keep our pH within homeostatic range buffers are not perfect they're not foolproof transitioning to organic molecules these are going to contain hydrogen carbon and usually oxygen they have covalent bonds and are going to include the for carbohydrates lipids proteins and nucleic acids so let's start first with carbs carbohydrates are going to contain carbon hydrogen and oxygen these are delicious you know bread cake cookies or a fine sugar I'm picking all the unhealthy ones because you know they taste so good but there are also other healthier ones like grains like rice and whole wheat monosaccharides are simple sugars these are going to include glucose and fructose so mono meeting one disaccharides are two monosaccharides combined by dehydration synthesis which joins the monosaccharides together some examples of disaccharides include sucrose which is just table sugar what we put in our coffee or tea and maltose polysaccharides are made of many sugars condensed together or connected by dehydration synthesis and this is going to include glycogen starch and cellulose so here's a picture of dehydration synthesis I promised we would come back to it dehydration synthesis is also called a condensation reaction and this is how we form more complex sugars so in this picture we have on the Left a glucose and on the right we have a fructose so these are two monosaccharides and if we want to combine these two monosaccharides to make a die saccharide then we will need to dehydrate them or remove water and if you look between the two you can see the components of water o H and H if we combine those that's h2o so if we remove that water or dehydrate it this will link the two together to create a disaccharide or double sugar called sucrose which is table sugar it's kind of cute it looks like they're holding hands okay and then in hydrolysis hydrolysis is when we add water to break things apart so here we have sucrose or table sugar and if we want to break the sucrose apart back into its two individual monosaccharides then we can just add water so if we take the sucrose and add water which we call hydrolysis that will break the tube back apart into the individual monosaccharides glucose and fructose lipids lipids are mainly hydrophobic molecules such as fats oils and waxes they're made mostly of carbon and hydrogen atoms and are going to include fatty acids eCos anoints glycerides steroids phospholipids and glycolipids phospholipids we're going to hear about again because they are so integral in the cell's membrane if you recall from your biology phospholipids look like so they're made up of a hydrophilic which means water loving head and hydrophobic tails hydrophobic meaning water fearing and so when these guys group up side to side to side they can start to form a membrane but remember cell membranes are a bilayer a double layer of these hydrophilic heads so we're going to revisit that phospholipid bilayer again in chapter 3 just to remind ourselves what the plasma membrane looks like proteins are the most abundant and important organic molecules they contain basic elements and they're made up of individual amino acids joined by peptide bonds to form proteins so proteins are long chains of amino acids again joined by peptide bonds and there are four main protein shapes so proteins can come in different shapes and these shapes are really important to the function of the proteins so primary shape is the simplest primary proteins are a linear straight chain of amino acids so this is an example of a primary protein it's a straight chain of amino acids so each one of these blocks represents an amino acid and in between we have a peptide bond peptide bonds are what joins amino acid to make the chain so the long straight chain is again the primary protein secondary proteins can be either found in an alpha helix which kind of looks like a curly hue or a beta pleated sheet which looks a bit more like a zigzag or a fan so again that's an either/or it's a little bit more complex than the primary structure so here is a secondary protein that looks like the curly Q this is called an alpha helix so it can look like this or it could look like this like a fan zigzag also known as a pleated sheet so a little more complicated tertiary structure is when the protein coils and folds producing a three-dimensional shape so that's even more complicated yet so here's a tertiary protein you can see it has coils in it and they're all folded up so it makes it a little bit more globular a little bit more large that's a tertiary protein and then a quaternary structure is a protein complex produced by interacting polypeptide chains or subunits so first let me say that polypeptides greater than 100 amino acids are called proteins so if you see the word polypeptide we call it a protein when there are a hundred or more amino acids grouped together so these are bigger but the quaternary structure is is a protein complex produced by interacting polypeptide chains so lots of polypeptide or multiple polypeptide subunits grouped together to make a very complex protein so you can see that these individual polypeptide subunits you can see some blue and some purple are interacting to form a larger molecule and an example of this protein would be hemoglobin and hemoglobin is pretty critical this is what carries oxygen in the blood so proteins are huge and when I say huge I don't mean size-wise necessarily but they're huge in importance they're very important in the body they make up a ton of what makes us up proteins are found in the skin and the lens of the eye and the muscle of the heart the skeletal muscle the smooth muscle they make up your hair your nails we could go on and on so proteins are critical in the human body so if a protein gets pushed out of its optimal homeostatic range and then it is either permanently or temporarily going to lose its shape we call that denaturation so again it's a change in shape of the protein that can be temporary or permanent due to an extreme in heat or pH and we're going to add a little bit to that actually so denaturation or loss of protein shape can be caused by extremes in pH now this could mean too acidic or too basic temperature which again could be too hot or too cold UV light and salt levels if any of these are out of normal range it can cause a protein to become permanently or temporarily denature which means that it will lose its shape and if it doesn't have the shape that's so critical that we just went over then it can actually be unable to function and imagine in the human body proteins like hemoglobin how greatly that could affect its ability to carry oxygen if it were to lose its characteristic shape nucleic acids are our final organic molecule they are large they store and process information and there are two types deoxyribonucleic acid or DNA which determines your inherited characteristics helps to direct protein formation controls enzyme production because enzymes or proteins typically and will help control your metabolism RNA or ribonucleic acid will control the intermediate steps in protein synthesis or protein formation and we know now how important proteins are so structure of nucleic acids DNA and RNA consists of long chains of nucleotides which contain a sugar either deoxyribose or ribose a phosphate group and then nitrogenous bases like a G T C and you so let's break that down a little bit okay so we're going to organize this into two sections DNA and RNA so that we can kind of compare and contrast the two okay so DNA is made up of a sugar phosphate backbone and the sugar is deoxyribose now if we were to describe what DNA looked like we would describe it as a double helix and it also is going to have in it nitrogenous bases and the nitrogenous bases are the letters that we often see in diagrams of DNA so that would be a for adenine T 4 thymine G for guanine and C for cytosine okay and remember that a will bind with T and C will bind with G in DNA so then we've got RNA which is also made of a sugar phosphate backbone the sugar is ribose and RNA is a straight chain rather than a double helix it too has nitrogenous bases or those letters and they are mostly the same we have adenine again instead of T we have a you for uracil G guanine and C again cytosine and a will bind with you and C will still bind with G here is a picture of RNA versus DNA RNA on the left single strand DNA is a double helix looks kind of like a ladder that's been twisted around and finally high-energy compounds now this is very important throughout physiology because ATP is the energy currency of the cell ATP at the bottom adenosine triphosphate it's a high-energy compound that contains three phosphate groups which is why tri phosphate is part of its name tri meaning three adenosine diphosphate contains two phosphate groups dye and adenosine monophosphate contains one phosphate group mono meaning one this concludes chapter two review of chemistry and biochemistry see you in Chapter three you