the third portion of notes is about proteins and nucleic acids so um proteins are uh a major constituent of living things they account for more than 50% of the dry mass of most cells which means that most organisms are at least 50% protein there are lots of different kinds of proteins that have all kinds of different uh functions like support and communication movement transport defense against uh disease and foreign substances and so we'll talk and also um enzymes and various things like that so we'll talk about some of these functions along the way there are uh on the next slides there are some descriptions of the different functions that you will be responsible for so enzymatic proteins uh accelerate chemical reactions they are biological catalysts as you learned about before this includes things like digestive enzymes that break down molecules like sucrose into its component parts like uh glucose and fructose there are storage proteins that store amino acids for developing embryos and and young um Offspring um casine which is the milk protein is the source of amino acids for baby mammals um the plants have storage proteins in their seeds ovalbumin is the major component of egg white which is the source of amino acids for the developing embryo inside the egg defensive proteins like antibodies these y-shaped molecules here in purple um protect you against disease by inactivating and destroying viruses and bacteria we'll talk more about how those function when we talk about immune systems later on uh transport proteins like hemoglobin and transport proteins through cell membranes like this one right here for facilitated diffusion um allow for the movement of molecules from one place to another some function like hemoglobin and a cell but like the red blood cell others are for facil Fusion or active transport of some kind like a sodium potassium pump hormonal proteins like insulin coordinate body's activity so insulin is the enzyme is the hormone that allows cells to take up excess sugar and so when you have a high blood sugar concentration like you see here the insulin U enables the cells to take up extra sugar and that reduces the blood sugar to the normal level and it's got a partner uh hormone glucagon which when the blood sugar Falls too low uh causes the liver to release um glycogen which will uh or break down glycogen into into glucose and that'll increase the blood sugar until it reaches the set point contractile proteins and other motor proteins involve for movement examples are in the muscle tissue the stri here in the skeletal muscle tissue are made of alternating fibers of actin and M which enable your muscles to contract and then release there are other kinds of motor proteins for other kinds of movements like the encilia and fella is shown here receptor proteins are um function in the responses of cells to to chemical stimuli so here you see um a neuromuscular Junction so you've got the um the neurotransmitter molecules that are being released here and their receptors on the on the muscle cell or on the other on the cell that the that the um nerve is near and that will uh cause that reaction to be transmitted to the cell structural proteins like keratin which is found in hair and nails and things like that um I function for support we've also got things like Silk fibers made by insects um collagen and elastin that are found in connective tissue in mammals will um provide structure and support for the tissues of mammals enzymes in particular we spend some time talking about enzymes they act as catalysts to speed up chemical reactions and the great thing about enzymes is they can repeat they can do this over and over and over again without being changed themselves and that's really necessary to speed up the reactions that are required for living things so the the unbranched chain of amino acids that makes up the protein are called polypeptides they are just the chain of of amino acids they use the same amino acids the same 20 that that we have available in all living things and then to become a protein rather than a polypeptide the the polypeptide has to be put together in a form that is biologically active sometimes it requires just bending or folding in a certain way other times it requires being associated with other polypeptide chains um so we're going to differentiate between the the polypeptide and the protein by talking about the protein being the functional molecule rather than just just the the um Bare Bones uh link together amino acids amino acids are the monomers of proteins they are molecule organic molecules that have a carboxy group on one side and an amino group on the other side there are 20 different amino acids that vary from this basic structure by having different R groups or side chains that can be added there are some of the amino acids that have two side chains attach to this Alpha carbon here and the presence of those side chains or those R groups are what give the amino acids their different structure their different their different properties and when they go together in in the um polypeptide chain they can affect the shape of the molecule by their interactions with each other the amino acids are linked together by a type of bond called a peptide bond this is similar to the glycosidic linkage except it is um between the carboxy group of one amino acid and the amino group of another the polypeptide remember is the polymer of amino acids and that can range in length from a few amino acids to hundreds or thousands of the amino acids put together the um sequence of bases or the sequence I'm sorry the sequence of amino acids in the polypeptide can make will make the polypeptide chain one end of the polypeptide chain will have a carboxy end that's called the C Terminus and the other end will have an amino on the end and that's the end Terminus and so that's going to be the unique to each polypeptide here we have the formation of a polypeptide we have two here um that are linked together in a peptide bond notice peptide bond is between the carbon with a with a um carbonal group and the nitrogen of an amino group so the carbonal group is what's leftover from the carboxy group and forms a bond this way so you l the hydroxy part of the carboxy group and one of the hydrogens from the amino group those two go together to form a water molecule and that leaves the carbon and nitrogen available to bond together in the special peptide bond so here we have a polypeptide made of three amino acids we have the in Terminus the amino end of the chain and the carboxy end or the C Terminus of the chain and the different side chains attached to the different amino acids for every for every two uh two amino acids that join together there will be one peptide bond three there'll be two four there will be three and so forth so to become a functional protein you have to have one or more polypeptides that are precisely shaped for the specific purpose that they are there to fill sometimes they're twisted or folded or coiled and that depends on the sequence of amino acids that's going to determine that three-dimensional structure and then the structure is going to determine its function proteins are very specific to the and they have to have a specific shape in order to function properly the primary structure of a protein is its sequence of amino acids of course which is coded for by the DNA as we've talked about in your introductory biology class the secondary structure com is composed of coils or folds in the polypep chain and most proteins have at least Prim Ary and secondary structure all they all have primary structure of course the tertiary level of structure is formed by interactions among the side chains or R groups because some of them may be polar some of them may be hydrophobic hydrophobic or hydrophilic and they're going to form various kinds of interactions with each other like vanderwal forces and hydrogen bonds and so so forth the quinary structure uh occurs when you've got a protein that's made dep of multiple polypeptide chains that fit together in a certain way and so we're going to look at each one of these so the primary structure is just like the letters in a word and it's going to be determined by that by the genes that code for the sequence of of amino acids in a protein and then the co the coils and folds of the secondary structure are going to depend on hydrogen bonding that occurs between the poly between the parts of the polypeptide backbone the two kinds of secondary structure are a coiled form called an alpha Helix and a folded structure called a beta pleated sheet the um Alpha Helix forms because there are hydrogen bonding that occur between the um the hydrogens here attached to part of the chain and and um and the oxygens that are also part of the chain and so you end up with those between the backbone parts that those uh hydrogen bonds that occur there cause the coiling to occur in the beta plated sheet you've got interactions in a different way but they're still formed by hydrogen bonding um and so that the beta uh strand is usually shown as a flat Arrow like this that shows the folding with an arrow pointing toward the caroal end and you have interactions between the chains that fold in the same way like that so it's still caused by hydrogen bonding the tertiary structure is caused by interactions between the r groups rather than the backbone and so you can have a lot of different kinds of interactions like hydrogen bonds ionic bonding hydrophobic interactions Vander walls interactions sometimes there are polar parts of these um side groups that repel each other or attracted to each other and all of those things can cause variations in the shape there are also strong calent bonds that can occur called disulfide Bridges and that gives a lot of reinforcement to protein structure so here we have various kinds of bonding hydrogen bonding between a hydroxy group and a and a carbonal group here we have hydrophobic actions all these metal groups here are hydrophobic so they're going to be have a tendency to uh Stay Together away from more hydrophilic parts of the molecule we have ionic bonding that can occur between an amino group with an extra hydrogen and a a carox group that's lost its hydrogen to the amino group there disulfide Bridges and so forth so all of these things can affect the the overall structure the tertiary level of structure of the protein and then finally the quinary structure occurs when you have two or more polypeptide chains that form to together form one Macro Molecule an example of a a quinary structure would be the collagen fiber this is three polypeptides that are kind of coiled together like a rope and as you just as it happens with the smaller fibers in the Rope as you coil them together it gives a lot of strength strength to the fiber hemoglobin is another example of of a protein that you know something about that has a that is a globular protein and it's made of four different polypeptides two alpha chains and two beta chains so here we can see the alpha subunits in the dark blue and the beta subunits in the lighter blue each one has an Associated heem section that has an iron molecule in there and that's what gives the overall hemoglobin um globular h globin molecule its affinity for oxygen is the iron so uh the physical and chemical conditions in which the protein is found can also affect its structure if you change the pH or the salinity or the temperature or other kinds of environmental factors like that you can cause the protein to unravel you know that heat in by itself will uh have a a negative effect on hydrogen bonds and um pH and salinity can also have negative effects on those and so when a protein unfolds or loses its netive structure that's called denaturation and when the protein is denatured it is it becomes inactive it will not work properly an example of a denatured protein is a cooked egg white egg white is almost pure protein it's almost pure alumin and when it's when it's in its liquid form it is it's colorless and viscous and when you cook it it becomes white and opaque and very different you can't take it back again so denatured proteins basically become inactive and are no longer useful now there is protein folding that occurs in the cell and you can't always predict what the structure is from its primary structure because there are several different stages that they go through on their way to becoming stable a lot of these changes occur in the um in the elect in the end reticulum and in the gogia apparatus that's where those proteins are packaged and folded and and formed into their fin but the subunits are put together and so forth some of the molecules involved are called chaperonins and they assist the proper folding of protein of various protein molecules they're proteins themselves and we have a number of conditions like Alzheimer's and Parkinson's that are associated with misfolded proteins and so in the case of in the case of those kind of things something has happened to the shepherd ronins or other proteins that are that are work in the in the folding process that make them malfunction so part of the research that's going on nowadays about some of these conditions has to do with researching what's happening to those um those chaperonins and other molecules that are assisting in the folding nucleic acids the final group of U biomolecules we're discussing are of course involved in the storage transmission and expression of hereditary information um so you know that the amino acid sequence of a polypeptide is programmed by a gene and the genes are made of DNA and the message telling the gene which on which order to put the amino acids is coded for by the nucleotides that are the the monomers of the nucleic acids two types of nucleic acids deoxyribonucleic acid or DNA and ribonucleic or nucleic acid or RNA DNA is a self-replication molecule and it directs the synthesis of the various kinds of RNA including messenger RNA of course and then through messenger RNA it controls the synthesis of proteins which occurs on the ribosomes which are also made of RNA um the components of nucleic acids are called nucleotides and so a polymer would be called a polynucleotide each nucleotide is made of three different things it has a nitrogenous base a pentos sugar five carbon sugar and one or more phosphate groups if you look at the nucleotide without the phosphate group it's called a nucleoside rather than a nucleotide so sometimes so if you see that term that just tells you you're talking about the the part other than the phosphate the sugar in the in the nitrogen base so here we have a polynucleotide or the nucleic acid you can see the the pinto sugar here the phosphates are shown as these little yellow circles and then the nitrogen bases are attached to to the sugars one nucleotide is composed of the phosphate group the nitrogen base and the pintos sugar there are five different nitrogen bases divided into three C two categories the two categories are Pines and purines there are three different peridin cytosine thyine and uracil cytosine is found in all nucleic acids thyine is only found in DNA and uracil is only found in RNA all of these peridin have a single ring structure they're somewhat similar they have slightly different side chains here notice that we've got uh a nit a an amino group on this one and we've got a methyl group on this one and this one doesn't have either one of those the purines are double ring structures and they are adenine and guanine which are found in all RNA and DNA notice that Adine has this amino group here whereas guanine instead of the amino group has a Caro a carbonal group the two different kinds of sugars found in nucleic acids are deoxy ribos which is found in DNA and ribos which is found in RNA the difference is this little uh Hydro hydroxy group right here on the ribos loses an oxygen to become deoxy ribos so you should be able to figure that out from the name deoxy Ros means one less oxygen when the polymer forms it forms between the sugar of one um um nucleotide and the phosphate of the next they're joined in calent bonds between the hydroxy group on the on the on one nucleotide and the phosphate on the next notice the designation three prime and five Prime that talks about the numbers of the carbons we talked about sugars we talked about the fact that in a sugar molecule we've got the oxygen is part of the Ring and we start we start uh numbering the carbons clockwise as we move away from the ring so this is carbon number one 2 3 4 and the fifth one is here on the side chain so the three prime carbon would be number one two three the third carbon here and the five carbon would be the one on the side chain so the these create the backbone of sugar phosphate units and then the nitrogen B are the appendages and of course in the case of DNA those nitrogen bases paired nitrogen bases form the rungs of the last ladder the sequence of bases is unique for each gene and so that's that's the really important thing the gene remember is a sequence of bases that codes for a particular protein the RNA molecules are usually single chains whereas the DNA molecules are double and generally speaking the DNA molecules are spiraling around forming a double Helix in the Helix the backbones run in opposite directions from each other this is called antiparallel so one side goes has the three prime end at the bottom and the five Prime end at the top and the other chain is the opposite with the three prime at the top and the five Prime at the bottom so they're anti- parallel to each other one DNA molecule has thousands of nucleotides and it includes many different genes within the molecule the nitrogen bases in DNA pair up and form hydrogen bonds between the pairs of bases adenine which is a purine always pairs with thiamine which is a perimidine and guanine purine always pairs with cytosine with the perimidine this is called complimentary base pairing it can also occur between two RNA molecules or between parts of the same molec Ule but remember in thyine in RNA thyine is replaced by uracil so a pairs with u in RNA rather than a pairing with T so here we have our DNA double helix notice the two anti-parallel sides 3 to five on one side 5 to three on the other we have our base pairs that are joined by hydrogen bonding and that's what holds together the two sides of the double helix hydrogen bonding really important there Transfer RNA is generally a single strand but parts of it are paired up you can see it's in this kind of Twisted form here and one end is going to have these three unpaired bases that will serve as the codon on the or the anti-codon rather on the transfer RNA but the but when you have the parts that are paired up there you again have hydrogen bonding holding the two chains two sides of the chain together now the linear sequences of nucleotides the the SE quences in a row uh are passed on from parents to offspring and when you look at related species you're going to see more similarities in the DNA than you see in more distantly related species and so we can use that to figure out evolutionary kin kinship and so we'll talk more about that as we look at DNA later on and as we look at um at kinship or relationships between different groups of organisms and that's all we have about proteins and DNA