weber uiuc edu 07 September 2007 MCB150 Lecture 07 Lecture 07 07 September 2007 Announcements Crap I broke my thumb yesterday First of 10 weekly review questions are due today at 5pm First exam is in two weeks The homework should be an indicator of what we will have on our exam We should challenge ourselves against the material WebCrossing is now active Reversible Non competitive Inhibition Some inhibitor molecule is in the allosteric site usually changing the conformation of the active site No substrate can get in there With competitive inhibition whoever gets there first wins Thus an increase in substrate will result in the flooding out of the competitive inhibitor This does not work with non competitive inhibitors o Why Because increasing the substrate has no effect if it cannot get into the active site Once the active site is closed it stays closed o It is a reversible reaction the allosteric inhibitor can come free restoring the shape of the active state It can finish what it started but it won t be able to take on new substrate Macromolecule 3 Nucleic Acids There are two different flavors of nucleic acids DNA RNA DNA RNA are information storage molecules o DNA is exclusively an information storage molecule o It is the blueprint for making other molecules o There are some catalytic RNA molecules RNA can act as ribozymes The monomers of the nucleic acids are nucleotides The structure is made up of three components o The base is also called a nitrogenous base or a nitrogen containing base o The sugar component is a pentose sugar o The phosphate group is attached to the 5th carbon There are different species of nucleotides one two or three phosphate groups Naming and Number Conventions Number the members of the ring in the base group o Start with N in the right hand corner o Number only the members of the ring In the sugar use prime notation to distinguish them from those in the base o 1 is the first carbon o 2 may or may not have a hydroxyl group ribose vs deoxyribose o The phosphate is added to the 5 end Because the number of phosphates is variable we will want to standardize the name of the sugar and nitrogenous base We call this a nucleoside o It does not include any phosphates o The whole thing with phosphates is nucleotide Page 1 of 4 weber uiuc edu 07 September 2007 MCB150 Lecture 07 o We can then specify how many phosphates are on the molecule 1 phosphate nucleoside monophospate 2 phosphates nucleoside diphosphate 3 phosphates nucleoside triphosphate o These names are the most specific of the names It tells how many phosphates are available DNA vs RNA The bases differ in DNA vs RNA Single ring structures pyrimidines pyrimidine single ring o Uracil RNA o Cytosine RNA DNA o Thymine DNA Double ring structures purines o Adenine RNA DNA o Guanine RNA DNA Each type of NA takes four Both use the purines Will not find uracil in DNA nor will you find thymine in RNA At least not in normal circumstances Nomenclature What is common What differs o In DNA nucleotides every monomer has the same 5 carbon sugar and a single monophosphate group except for the last one o In RNA nucleotides every monomer has the same 5 carbon sugar and a single monophosphate group Because of this you can refer to the base by its one letter name The base is all that differs in the string Thus GATTACA Can immediately tell RNA if there is a U or DNA if there is a T Differences in Nucleotides What is the identity of the five carbon sugar o In RNA ribose is the five carbon sugar pentose It has hydroxyl groups on the 2 3 and 5 carbon o In DNA deoxyribose is the five carbon sugar pentose It is missing a hydroxyl group in the 2 position Summary DNA o o o o Deoxyribose sugar H at 2 carbon Pyrimidine bases are cytosine C and thymine T Purine bases are adenine A and guanine G The monomers are triphosphate species of deoxyribonucleotides This is most specifically called deoxyribonucleoside triphosphate The abbreviations are dNTP dCTP dTTP dATP dGTP o DNA is usually double stranded associated in a double helix RNA Page 2 of 4 weber uiuc edu 07 September 2007 MCB150 Lecture 07 Ribose sugar OH at 2 carbon Pyrimidine bases are cytosine C and uracil U Purine bases are adenine A and guanine G Therefore the monomers are triphosphate species of ribonucleotides This is most specifically called ribonucleoside triphosphates The abbreviations are NTP CTP UTP ATP GTP Note that there is no r in front of the NTPs o They are usually single stranded for the purposes of this course o o o o How are Monomers Added How are the nuclei acids synthesized The triphosphate species is always used o Two of the phosphates are immediately broken off as a unit o Pyrophosphate group two broken off hydrolyzed together The remaining phosphate is covalently linked to the hydroxyl group at the 3 carbon It doesn t matter if it is DNA or RNA Can create strands of both using the same mechanism The single phosphate group is called a phosphodiester bond linkage Recall our previous special linkages o E g Peptide bonds glycosidic linkages in carbos etc There is a family of enzymes which will polymerize this reaction o These are called polymerases o It is an endergonic reaction Macromolecule 4 Lipids This is our final macromolecule for this class Previous macromolecules are defined by their chemical structure Lipids are defined by their physical properties insolubility in water There are many water insoluble molecules so the structure of the lipids will differ Major categories of lipids o Triglycerides energy storage for the most part o Phospholipids components of biological membranes for the most part o Steroids signaling molecules for the most part There are important exceptions to this classification for example sterols like cholesterol appear in membranes Fatty Acids The Monomers of Lipids They all have a hydrocarbon tail Hydrophobic They have an acidic group at the other end Hydrophilic Saturated versus Unsaturated o 16 0 16 carbons 0 double bonds saturated o 18 0 18 carbons 0 double bonds saturated Page 3 of 4 weber uiuc edu 07 September 2007 MCB150 Lecture 07 o 18 1 18 carbons 1 double bond unsaturated o 20 2 20 carbons 2 double bonds polyunsaturated o Saturated means that each carbon contains as many hydrocarbons as possible Of course there are no double bonds o The numbering convention above carbons double bonds Fatty Acids Glycerol Triglyceride Components three fatty acids glycerol Glycerol provides a three carbon backbone for a large variety of