welcome back everybody Uh we're going to cover chapter 2 Uh and right now a little background on what's going on with chapter 2 Uh this is just going to be some basic chemistry um to make sure that we're all at the same starting point as we go further into our discussion of uh the biology of microbes and microorganisms We're going to be talking a lot about uh the uh molecular components of the proarotic and ukareotic cells and then the microbes like uh viruses vyroids prons We're going to often refer to things like lipids and proteins and carbohydrates and of course then the nucleic acids DNA and RNA So we're going to want to make sure that uh we've got a foundation uh before we move on So hopefully this material uh will be um all review material that you've covered in uh previous biology courses uh particularly things like anatomy and physiology Um so hopefully uh really none of this should be new uh and if it is please make sure you get a good understanding of it as uh this is the material that we are going to build on as we learn more about microbiology So we're going to start all the way at the most basic uh level of matter Uh we see that uh atoms are the building block of uh the the all the matter in our universe And uh we see that atoms are made up of by these three components the protons neutrons and electrons Uh protons are positively charged Neutrons have uh no charge to them The protons and the neutrons are both found in the nucleus the inner part of the atom structure Then orbiting the nucleus we have the electrons Electrons are the negatively charged uh portion uh subunit that is orbiting around the nucleus Um uh the term element uh refers to a substance that's made up of only a single type of atom Uh so for example when we're talking about let's say um uh you know nitrogen uh you know we're saying oh bacteria are going to help uh you know put nitrogen into soil We're referring to um the particular um uh atom of nitrogen um being built into molecules that will incorporate it Um so um the molecule is the next uh step up from atoms Uh atoms are going to connect to one another in different ways We'll see different bonding involved in making molecules Uh but as atoms connect to one another they form molecules Um and then we see another term that relates to molecules is compound Uh a compound is a molecule but it's a molecule that consists of at least two different elements Okay so um a molecule doesn't necessarily have to have different elements For example a molecule of oxygen O2 is just two of the same atoms of the same element Uh whereas a compound molecule uh we see in the case of water or anything else that we're going to be talking about in this course for the most part um we're going to be talking about uh compound molecules that are going to be organic compounds made with carbon hydrogen oxygen and other u elements as well Um looking at how um bonds are going to form between atoms uh to create these molecules uh we see the first type of bonding uh is the ionic bonding in which um atoms are going to connect to one another uh because uh they uh assume um ionic forms So uh we see the two ion forms are the positively charged ions which are called cations ions We see the example of a cation here would be uh sodium with the uh positive charge This occurs when the uh atom loses at least one electron and so when it loses an electron it loses that negative subunit and therefore gets an overall positive charge Then annions are going to be ions that gain electrons and therefore take on negative overall charge So we see the uh chloride here has a negative charge as it has gained an electron So cations ions have an overall positive charge Ann ions have an overall negative charge When the two of them interact with one another they attract due to their opposite charges And what links them together is the ionic bond So we see in this case um your salt is linked together with an ionic bond Okay Covealent bonds on the other hand involve atoms sharing electrons with one another Uh so in this case um the electrons that are orbiting uh around one of the atoms will also then orbit around the other atom They'll be shared between the two atoms Um we see here that um if there is a carbon covealently bound to a hydrogen in a molecule structure we call that molecule organic and if there is not a carbon bound to a hydrogen then we consider that molecule to be inorganic Um so we're going to talk a lot about organic compounds especially since we're in biology Um and uh organic compounds will include uh proteins lipids carbohydrates nucleic acids And what they all have in common is that somewhere in their structure they have carbon bound to hydrogen But it is important that you understand carbon and hydrogen need to be um in the structure Um take for example carbon dioxide Carbon dioxide is CO2 There is no hydrogen in carbon dioxide Therefore carbon dioxide is a molecule that is inorganic since it does not include hydrogen uh coalently bound to hydrogen in its structure So we will use the terms organic and inorganic along the way And uh just because a molecule has carbon in it doesn't mean that it is an organic molecule Not all uh carbon based molecules will be organic So coalent bonds um will either involve uh the sharing of electrons evenly Uh so take for example oxygen gas again two oxygen uh atoms Um they're going to uh have the same attraction for the electrons that they're sharing since they're the same atom And so the sharing is even and the result is that we get a uh type of bond called a nonpolar covealent bond Okay And this is going to be different from the uneven sharing that results in a polar covealent bond forming Uh so we we uh can uh visualize this uh with little drawing here So uh going back to um oxygens uh sharing their electrons um we have this blue oxygen that is going to be uh forming a covealent bond with this red oxygen They're both oxygens and so they're going to share these electrons right here in the middle They're going to share these two evenly So the way that this is going to work is that these electrons will orbit this oxygen here and then they will orbit this oxygen here and once again just work their way around evenly between the two oxygens This is the nonpolar covealent bond Uh we'll see why it's called non-polar when we look at a polar covealent bond If we take an oxygen and we have it share its electrons with hydrogens instead The hydrogens are just a single proton So they're atomic number one just a single proton And so they don't have much of a pole on this electron pair So the way that the orbiting of these electrons is going to look this electron pair is going to orbit around the oxygen and then around the oxygen again and then around the oxygen again and then around the oxygen again because the oxygen is attracting them more strongly than the hydrogen but on occasion they'll find their way around the hydrogen So they are shared but they are not shared evenly The effect here is that it's seems like there is more electrons So I'm doing a plus here plus electrons more electrons over in this area than there are in this area And the charge of the electron is negative So this area becomes slightly negative Whereas this area is acting basically like the proton sitting by itself A proton sitting by itself ends up behaving like an area that is positively charged And so ultimately what we see here is um a form of sharing once again that is uneven and creates two ends to this molecule This end of the molecule being more negative This end to the molecule being more positive And so two opposite ends we call polar Two opposite ends polar So this is a polar covealent molecule a co polar covealent bond And now we see why we call this one non-polar because the polar has two opposite ends two different uh charges going on whereas this one has no opposite ends Everything is nice and even So polar non-polar evenly shared non-polar unevenly shared electrons polar but they're both shared so they are both covealent bonds they're both covealent bonds okay now the effect of having polarity is that molecules like uh water uh that we see in this picture here But then other molecules that we'll talk about like uh proteins and uh nucleic acids um they will be able to uh form a type of uh molecular bonding So bonding between molecules called hydrogen bonds Hydrogen bonds form between molecules So what we see here is this is a water molecule This is a water molecule They're going to hold on to each other but they're not going to form a covealent or ionic bond They're not going to um become in this case two H2O's are not going to become H42 They're not going to become one whole molecule but instead they're going to be two water molecules that simply hold on to each other with this hydrogen bond So hydrogen bonds allow for molecules to hold on to each other uh without being covealently bound to each other and the attraction forms because as we saw with water the oxygens are slightly negative in charge the hydrogens's are slightly positive in charge and so the negative uh oxygens are going to be attracted to the positive hydrogens on the neighboring water molecules So we see the effect here is that water molecules will actually connect to one another They'll hold on to each other and similarly we'll see things like the nitrogenous bases in DNA are going to hold on to one another with these hydrogen bonds Um but since these are not covealent they can be pulled apart So these water molecules can pull away from each other It's just when they're next to each other they connect a little bit They attract to each other So it's a breakable connection Now another property relating to uh water in addition to that uh hydrogen bonding that gives water a lot of unique properties like surface tension and um uh high um specific heat and things like that that we learned about back in uh um one of the other properties of water is that um it it serves as a solvent as a fluid that other molecules will float around inside of And one of the um atoms that's going to float around inside of water is the hydrogen ion Okay So hydrogen ions are going to form um in water naturally Um what we see is that um in a glass of pure water uh it's going to naturally uh break up a little bit and form a little bit of H+ and O minus So hydrogen ion also known as a proton because a hydrogen ion is just a proton that has lost its electron So it's just a proton the hydrogen ion or proton And then this is um hydroxide Um so a glass of pure water is is not actually 100% water it has a little bit of um hydrogen ion and hydroxide as this molecule naturally breaks apart Uh now and again the measurement of the amount of hydrogen ion is what's known as pH Oops let me keep that I meant to do this So pH in this example here this pure water has a pH of uh of 7 and this is a neutral pH So pure water pH of 7 neutral pH But if we add more hydrogen to it So if let's say we add the molecule hydrochloric acid If we add hydrochloric acid to this what's going to happen is the hydrochloric acid is going to add more hydrogen to the solution When more hydrogen is added to the solution extra hydrogen So I'm going to write here increased hydrogen creates a lower pH Uh so we'll go 0 to 7 and that is acidic Okay So adding uh an acid to a watery solution is going to add more hydrogen ions By adding more hydrogen ions we're increasing the amount of hydrogen ions This lowers the pH So the um larger the concentration of hydrogen the lower the pH gets So uh if I told you guys that I had a solution with a pH of one your response to that should be "Oh my god one that's a huge number." Even though one sounds like a small number one means the highest concentration of hydrogen ions uh when compared to larger numbers like 2 three four five all the way up So um so the smaller the number gets for pH the more acidic the more hydrogen ions there are Going the other direction if you add a molecule that is basic or alkaline to the solution So if you add something like NH3 to the solution So I'll note that this is an acid And so this right here is going to be a base You add a base to the solution What's going to happen when you add this is it's going to combine with hydrogen ions that are in the watery solution and it's going to remove those hydrogen ions So it's going to become this molecule NH4 plus it's taken hydrogen away from the watery solution And so in this case what we have is a decreased hydrogen ions concentration leads to a higher pH Uh so anything above 7 so 714 and this is basic or alkaline Okay So these are the directions um that the concentration of hydrogen ions in a watery solution can go Either pure water you have the small amount of hydrogen ions that that is natural to pure water You can add to it by adding acids You can take away from it by adding base Um and uh ultimately pH then is the measurement for the amount of hydrogen ions in a solution A solution Okay So pH is a property of aquous solution Aquous means a waterbased solution um and is defined as the concentration of hydrogen ions in the uh solution We see that pH ranges from 0 to 14 where 7 is neutral 0 to 7 is acidic and 7 to 14 is basic So seven is neutral and then by zero to seven we mean you know seven itself is neutral but um up to seven anything else is acidic and then same thing for basic anything up from seven is basic Okay another property of water for us here It's got a it's a that's a very well thoughtout answer there for us Anyway so um so now what we're going to um finish up this chapter with is uh a crash course in the uh biologically significant organic compounds uh that we're going to just keep talking about all throughout the semester Um so cells are going to um uh be made from in addition to water um proteins carbohydrates lipids and nucleic acids All of these molecules are organic compounds Okay Proteins we see uh make up more than half of the cell's overall dry weight which is to say that when water is removed more than half of what's left in the cell is protein Uh protein is um a really special class of molecules because it's incredibly diverse And proteins can be hydrophilic meaning that they dissolve in water They can be hydrophobic meaning that they repel water or do not uh uh um dissolve in water Or they can have regions that do both So one part of them interacts well with water and the other part does not So they they're very diverse in how they interact with uh molecules throughout the cell Proteins are extremely important because uh enzymes are proteins and enzymes uh we learned about through&p especially are just absolutely essential for uh for uh the field of biology for life to exist Enzymes drive our chemical reactions and uh without enzymes we would never be able to survive we'd never be able to maintain homeostasis We need enzymes to drive chemical reactions to happen faster In addition to working as enzymes proteins uh also function uh structurally Uh so they they create many of the um structural parts of a cell Uh they're involved in cell movement We'll see the fugella and pill They're going to be structures that propel um proarotic cells Um they are needed for the uh cell membrane function Um so they u work as channels to allow for molecules to go into and out of the cell And then uh they are needed for uh gene expression which is also the process of making proteins So proteins are needed to make proteins and we said that proteins are also needed to do all these important things within a cell So proteins are just absolutely the most essential molecule class We see that proteins are made by linking amino acids together uh by creating what's called a peptide bond and that proteins are organic compounds that consist of carbon hydrogen oxygen and then nitrogen Um nitrogen uh is um uh not something that we find in the carbohydrates and lipids but is uh critical in creating proteins uh we see the peptide bond here uh where we are linking two amino acids together creating a chain of amino acids and uh as we learned about in uh and p that chain of amino acids is what's called the primary structure and um then what's going to happen is that chain is going to fold on itself and create a three-dimensional structure called uh the the tertiary structure and it's going to be that three-dimensional structure that gives the protein its function Okay carbohydrates are a group of molecules that are once again organic They use carbon hydrogen and oxygen They're generally hydrophilic That's not going to be true for all carbohydrates Uh but many carbohydrates are uh hydrophilic and therefore dissolve in or interact with water They exist as monossaccharides which are the small building blocks The monossaccharides are glucose uh galactose and uh fructose And those are the building blocks the monossaccharide the single saccharide the single molecules that we then link together to form the bigger molecules the disaccharides which are two linked together So uh two monossaccharides put together creates a disaccharide If you put two glucose together you get uh the moltos If you put a glucose and fructose together you get uh sucrose which is your table sugar If you put a glucose and glactose together you get lactose which is milk sugar So disaccharide is two monossaccharides put together And then polysaccharides are long chains of carbohydrates Uh so long chains of monossaccharides So if you link uh hundreds or thousands of glucose molecules together you're going to create polysaccharides including uh glycogen which we use as an energy source in our uh muscles and liver Uh you can create uh starch which is the energy source in plants and then you can create um cellulose which is uh the building block for the the cell wall of uh plant and algae um cells The carbohydrates um main function we see here energy storage Um we'll learn about photosynthesis in this course and we'll see that the importance of carbohydrates is that they are a primary energy source In addition uh they are part of the nucleic acid um structure So they're part of the backbone of the DNA and RNA And as I mentioned uh a moment ago they also are used to build structures like uh the cell wall of uh plants and algae Lipids are um organic compounds Once again they use carbon hydrogen and oxygen They incorporate other uh molecules like phosphorus in order to give an overall um uh uh uh variety to their function We see that they're generally hydrophobic Uh so they uh generally repel water So things that fall in the category of lipids include oils fats waxes Uh so these things generally um do not dissolve in water but they can have hydrophilic groups attached to them like the phosphate group creating uh molecules that are more complex uh such as phospholipids Lipids are extremely good at storing energy Why we store our energy as body fat because lipids are uh much more efficient at storing energy than carbohydrates are they store nine calories per gram compared to carbohydrates and proteins that store only five And with in the case of phospholipids um we're going to be able to use lipids to create the selectively permeable membrane that is the cell membrane So hopefully this is very familiar to you the fluid mosaic model of the cell membrane The cell uh membrane the u the structure that defines a cell um is made from a phospholipid billayer So two layers of phospholipids where the phosphate groups are on the uh outer edges because the phosphate groups are hydrophilic and interact with water And then on the inside we have the uh hydrophobic uh fatty acid chains And so what we create here then is an area that is hydrophobic on the inside Does not like water on the inside and then hydrophilic on the outside where it's going to interact with water both inside and outside of the cell But that's not all there is to a cell's membrane because we see that in addition to the phospholipid billayer we also have proteins that are needed to create channels and uh work as receptors uh both inside and outside of the cell um and also work as enzymes So there's lots of functions to the proteins And then carbohydrate chains will also be found on the surface as well The carbohydrate chains um often work um as identifiers of cells So it allows for um cells to um recognize and interact with one another Our last category of organic compound is the nucleic acid Nucleic acid is uh what's used for um carrying genetic information Our examples of nucleic acids are DNA and RNA And they are both made from nucleotides Nucleotides are the building block that we're going to link together to create the DNA and RNA molecules DNA is a doublestranded molecule Uses the nitrogenous bases AC C G and T And we see the complimentary base pairing between the two strands So one strand will have an A and opposite it the other strand will have a T One strand will have a C opposite it the other strand will have a G So we see the complimentary base pairing of DNA shown there So here's our DNA molecule Two strands of nucleotides and on the inside we have the bases AC G and T For every A it is bound to a T So everywhere we see an A it's bound to a T Complimentary base pairing For every C it is bound to a G Every C it is bound to a G Once again complimentary base pairing And we'll learn a lot more about DNA in this course RNA is the other nucleic acid Once again a chain of nucleotides but this time instead of being a doublestranded molecule RNA is oftentimes singlestranded So we just see one continuous chain of nucleotides instead of uh two pairing up And instead of using ACG and T as the four nitrogenous bases we see it using ACG and U U is uricil So uricil instead of thymine Okay So um hopefully uh this just uh served as a refresher like the goal of this lecture was uh not to uh be overwhelming with a bunch of new material it was to kind of keep it simple to to remind you of the information that hopefully you've learned along the way and bring that back So as we go into our deeper discussions on uh these uh topics of uh the genetics that'll talk about nucleic acids and their functions or the cell structures and functions and metabolism that will talk about proteins and enzymes Um hopefully uh you know this uh this lecture kind of brought all that back to your memory so we're ready to build on it um while also kind of keeping it uh short and sweet and simple right