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Nucleosides & Nucleotides

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Nucleosides & Nucleotides Nucleosides & Nucleotides Biochemistry Fundamentals > Genetic Information > Genetic Information NUCLEOSIDE AND NUCLEOTIDES SUMMARY NUCLEOSIDES  • Comprise a sugar and a base NUCLEOTIDES  • Phosphorylated nucleosides (at least one phosphorus group) • Link in chains to form polymers called nucleic acids (i.e. DNA and RNA) N-BETA-GLYCOSIDIC BOND  • Links nitrogenous base to sugar in nucleotides and nucleosides • Purines: C1 of sugar bonds with N9 of base • Pyrimidines: C1 of sugar bonds with N1 of base PHOSPHOESTER BOND • Links C3 or C5 hydroxyl group of sugar to phosphate NITROGENOUS BASES  • Adenine • Guanine • Cytosine • Thymine (DNA) 1 / 8 • Uracil (RNA) NUCLEOSIDES • =sugar + base • Adenosine • Guanosine • Cytidine • Thymidine • Uridine NUCLEOTIDE MONOPHOSPHATES – ADD SUFFIX 'SYLATE' • = nucleoside + 1 phosphate group • Adenylate • Guanylate • Cytidylate • Thymidylate • Uridylate Add prefix 'deoxy' when the ribose is a deoxyribose: lacks a hydroxyl group at C2. • Thymine only exists in DNA (deoxy prefix unnecessary for this reason) • Uracil only exists in RNA NUCLEIC ACIDS (DNA AND RNA)  • Phosphodiester bonds: a phosphate group attached to C5 of one sugar bonds with - OH group on C3 of next sugar • Nucleotide monomers of nucleic acids exist as triphosphates • Nucleotide polymers (i.e. nucleic acids) are monophosphates • 5' end is free phosphate group attached to C5 • 3' end is free -OH group attached to C3 2 / 8 FULL-LENGTH TEXT • Here we will learn about learn about nucleoside and nucleotide structure, and how they create the backbones of nucleic acids (DNA and RNA). • Start a table, so we can address key features of nucleosides and nucleotides. • Denote that nucleosides comprise a sugar and a base. • Denote that they are phosphorylated to form nucleotides. • Denote that nucleotides link in chains to form polymers, called nucleic acids (DNA and RNA). - As a helpful mneomonic, denote that "S" comes before "T" which helps us remember that nucleoside is a building block of a nucleotide. Let's begin with a nucleoside. • Show that a nucleoside comprises: - nitrogenous base - sugar • Show that an N-beta-glycosidic bond links them. • Specifically indicate that: - In purines, carbon 1 of the sugar bonds with N9 of the base - In pyrimidines, carbon 1 of the sugar bonds with N1 of the base. Now, let's draw adenosine, as an example of a nucleoside. • Write that it is a ribose nucleoside of adenine (purine). • For the sugar, draw a ribose molecule with its carbon atoms numbered, but omit the OH group on carbon 1. 3 / 8 • For the base, draw adenine and label positions 1 through 9. • Notice that we omit the hydrogen at N9. • Show that carbon 1 of ribose forms the bond to N9 of adenine to represent the glycosidic bond. Let's turn our focus to nucleotides. • Show that they comprise: - nitrogenous base - sugar - at least one phosphate group. • Show that an N-beta-glycosidic bond links the sugar and base (as it does with nucleosides). • Show that a phosphoester bond links the sugar and phosphate. • Write that they can have 1, 2, or 3 phosphate groups, which can be added at either the 3-prime or the 5-prime hydroxyl group. Now, let's draw deoxy-cytidine-5 prime-diphosphate as an example of a nucleotide. • Write that it is a deoxyribose nucleotide of cytosine (pyrimidine); two phosphate groups are bound to deoxyribose at its 5-prime hydroxyl group. • For the sugar, draw deoxyribose (which forms DNA) (we drew ribose before, which forms RNA); number its carbon atoms, but omit the hydroxyl groups at carbon 1 and carbon 5. • For the base, attach cytosine to the deoxyribose; number it 1 through 6, omit the hydrogen atom on N1. • Show the glycosidic bond that forms at carbon 1 on the sugar to N1 on the base. Now let's add two phosphate groups to the sugar. • At carbon 5, add an oxygen atom, and then a phosphorous atom. 4 / 8 • Add three more oxygen atoms to the phosphorous atom. • Then add a second phosphorous atom, and attach three oxygen atoms to that phosphorous atom. • Use dashed lines to show that the free oxygen atoms have double bond character. • Also, add a negative charge to the first phosphorous, and two negative charges to the second phosphorous. Before we turn to nucleic acids, let's address the nomenclature of each base in further detail with a table. • Create three headers: - Nitrogenous bases - Nucleosides - Nucleotide monophosphates • Under the nitrogenous base header, write the names of the five bases: - Adenine - Guanine - Cytosine - Thymine - Uracil • Now write that the names of the nucleosides are: - Adenosine - Guanosine - Cytidine - Thymidine - Uridine • Nucleotide monophosphates have the suffix "–ylate" added to their base names, so they are: 5 / 8 - Adenylate - Guanylate - Cytidylate - Thymidylate - Uridylate • Use a star to indicate the prefix deoxy- for the nucleosides and nucleotides of adenine, guanine, cytosine. • Remind ourselves that: - Thymine only exists in DNA. - Uracil only exists in RNA. • Note that thymidine does not require the "deoxy" prefix since the thymine base is not found in RNA. Now let's turn our attention to the sugar-phosphate backbone of nucleic acids. We learned about base pairing in the formation of the DNA's double helix, elsewhere. • Write that nucleic acids are held together by phosphodiester bonds: a phosphoryl group attached to carbon 5 of one sugar forms a bond with the alcohol group on carbon 3 of the next sugar. - The order of bases in the nucleic acid chain gives each organism its unique DNA sequence and is read from 5-prime to 3-prime. • Nucleotide monomers of nucleic acids exist as triphosphates. • Nucleotide polymers (i.e. nucleic acids) are monophosphates. • Write that when nucleotide monomers link (to form DNA or RNA), they become monophosphates (they lose two of the phosphoryl groups), which forms the sugar phosphate backbone and provides energy. Let's draw this backbone now, starting with DNA. • Draw deoxyribose, omitting the alcohol groups on carbons 3 and 5. • At carbon 1, add the word "base", to show that the base attaches here. 6 / 8 • At carbon five, add an oxygen atom, linked to a phosphorous atom, which itself is linked to another oxygen atom and then a squiggly line, which represents that there is more to this molecule. • Add the other two oxygen atoms to phosphorous to complete the phosphate group. • Now let's attach a second nucleotide to our chain. • At carbon 3, add an oxygen atom. • To this oxygen, attach a phosphorous atom, which itself is attached to another oxygen atom. • To this second oxygen atom, add our second deoxyribose. • Attach the base to carbon 1 of deoxyribose. • Add the other two oxygen atoms to phosphorous to complete the phosphate group. • At carbon 3, attach an oxygen which itself is linked to another squiggly line. Now we have a very short DNA sequence. • Show that because each phosphate group has two ester bonds (one linking it to its sugar, and one linking it to the next nucleotide in the chain), it is called a phosphodiester bond. • The nucleotide monomers are monophosphates. • Indicate on our diagram that the 5-prime end is the free phosphate group attached to carbon 5. • Also indicate on our diagram that the 3-prime end is the free hydroxyl group attached to carbon 3. Now let's do the same for RNA. • To draw a ribose sugar, draw the same sugar as we did for DNA. 7 / 8 • Then, add a hydroxyl group to C2. • Attach the base to carbon 1. • Attach a phosphate to carbon 5 • Attach a second phosphate at carbon 3 • Add its corresponding nucleotide the other end of the phosphate. • Add the squiggly lines at both ends to show that this is only a snippet of RNA. • Show that the 5-prime end is the free phosphate groups attached to carbon 5. • Show that the 3-prime end is the free hydroxyl groups attached to carbon 3. Powered by TCPDF (www.tcpdf.org) 8 / 8.
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