BMB 462 Lecture 17 Outline of Last Lecture I. Continuation of Hormone Classificationa. Mode of Actionb. Release point/Target tissueII. Hormone SignalingIII. Specialized metabolic function of tissuesa. The liverb. The pancreasIV. Insulina. Control of Secretionb. Effects/function of insulinV. Effects of GlucagonVI. Metabolism under starvation conditionsVII. Effects of EpinephrineVIII. Effects of CortisolOutline of Current Lecture I. Nucleotide structure and nomenclaturea. i.e. dAMPII. Nucleotide propertiesIII. Nucleotide FunctionIV. Nucleotide Metabolisma. Regulation of metabolismCurrent LectureConcepts to remembers from previous courses/lectures:-I. Nucleotide structure and nomenclaturea. Nucleotides are carriers of information in the celli. They store information in the DNA and that is transmitted and translated into RNA from which proteins are madeb. They also serve as energy carriers in the cellThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.c. Nucleosides have a pentose sugar and a base attached. If there is also a phosphate on the 5' atom, they're called nucleotides (can have up to 3 phosphates)d. 5 nitrogenous bases in cells; they are either pyrimidines or purinese. Mnemonic that may help you remember purines vs. pyrimidines:i. Purine - Purina dog chow, which is from an agricultural company (AG, adenine and guanine). You should always buy 2 bags (2 rings)ii. Pyrimidines - Cut a single pyramid. (CUT - Cytosine, thymine, uracil)f. i.e. dAMPi. In Purines, the bases are attached via Nitrogen 9 to the sugar. Base atoms are labeled 1-9, sugar atoms are labeled 1'-5' to distinguish them from base atoms.ii. Base is attached to sugar by N-glycosidic bond. The bond can rotate, so have syn- orientation (both the base and the sugar are on the face of bond). Anti- conformation is base and sugar on opposite sides. Most NMPs in DNA are in the anti-conformationiii. The bond forms on the C1' anomeric carbon of the sugar. The anomeric carbon is in the beta-configuration, which means that the OH that originally helped form the bond is pointing upwards (so you can also call it an N-beta-glycosidic bond.iv. An adenosine has an OH at the 2' position.v. Deoxyadenosine does not have that hydroxyl group.vi. When you add the phosphate group to the 5' of deoxyadenosine, you get deoxyadenosine 5'-monophosphate, aka deoxyadenylate or dAMPg. The base is flat while the sugar is not. The flatness allows the bases to stack in the core of the DNA helix and that makes the DNA very strongh. The faces of the base are hydrophobic, making hydrophobic stacking structure. The edges are polar, which is what allows you to make hydrogen bonds and makebase pairing to other bases. Depending on what base you have, you can make different hydrogen bonds.i. As each component of the nucleotide is added to the base, the nomenclature changesi. See table 8-1, page 3 of the lecture notesII. Nucleotide propertiesa. Absorption Spectrai. All bases absorb light at 260nm; this is due to the conjugated double bond in the bases, which absorb light.ii. Use the absorption at 260nm to determine the concentration of basesiii. This is useful in the lab b/c you know that in double stranded DNA, when the Absorption at 260 = 1, that's about 50ng/uL. You can use theabsorption and that standard to calculate the concentration of DNA in a solution. The concentrations for ssDNA and RNA are different.iv. Proteins absorb at wavelengths of 280 nm. Compare absorption at 260 vs 280 to see how pure sample isb. pH and tautomerizationi. An H bond donor: is when an electronegative atom is bonded to the hydrogen and pulls away the e- from the bond. (O, H are very electronegative)ii. If it has a free electron pair, it can become an H bond acceptoriii. CH is none b/c C has similar electronegativity to Hiv. pH can change the form of uracil. When pH is low, uracil switches from lactam to lactim formation. The Hydrogen moves from the N to the O on atom 2. This changes the hydrogen bonding (In lactam N is the donor and O is the acceptor, in lactim, N becomes the acceptor)c. H-bonding and base pairing in DNAi. Because information is stored in the hydrogen bonding of DNA it is important to have the right pH b/c changing pH changes H bonding and you will lose the information.ii. AT has 2 H bonds, and GC has 3 so GC is slightly more stable. Otherwise they are almost identical structurally.iii. The H bonding neutralizes the charge inside the DNA so the inside of the DNA becomes hydrophobic. Then bases stack on each other and create a hydrophobic core that is very stable.iv. The outside of the DNA, the phosphodiester bonds between the sugar and the phosphate, are hydrophilic.III. Nucleotide Functiona. Building Blocksi. One of the most important roles of nucleotides is that they build DNA andRNA.ii. Central Dogma of biology is that DNA is replicated to make other copies of DNA and transmits information to a dividing cell so both daughter cells get the same DNA and the DNA is transcribed into RNA and RNA is translated into protein.iii. DNA and RNA are central to biology.b. Information storage and transferi. Information is stored in DNA and that is replicated and transferred through transcription into RNA. RNA is then translated into proteins.c. Energy Carriersi. Ribo-nucleotides can also be used as energy carriers. Mostly true for ATP and GTP. So they can be building blocks or energy carriersii. deoxynucleotides are mostly just building blocksiii. They are energy carriers b/c the phosphoanhydride bonds are very high inenergy so they are used by the cell to drive a lot of reactions.d. Coenzyme “handles”i. The coenzymes often come from ATPii. CoA, NAD and FAD all have nucleotides included in them.e. Signaling Moleculesi. Nucleotides can also be used in signaling molecules.ii. I.e. cAMP. The 5' phosphate forms a cyclic bond w/ the 3' OH.iii. It's a signaling molecule inside the cell that acts as a secondary messenger. (Primary signals, i.e. hormones, are usually outside of the cell)iv. ppGpp is a secondary molecule used in bacteriaIV. Nucleotide Metabolisma. Overview of Metabolismi. Purines and pyrimidines are constructed differently de novo but both rely on the central molecule PRPP (it's a central molecule in nucleotide metabolism and comes from the pentose phosphate pathway)ii. Bases are built attached to the ribose. SO you start with PRPP and then add
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