Nucleosides & Nucleotides

Nucleosides & Nucleotides

Sections

Overview
Introduction
Nucleosides
Nucleotides
Sugar-phosphate backbone

nucleoside and nucleotides

Overview

Summary

NUCLEOSIDES & NUCLEOTIDES

Nucleosides

Nucleosides comprise a sugar + a base

• nucleosides = sugar + base
  • Adenosine
  • Guanosine
  • Cytidine
  • Thymidine
  • Uridine

Nucleotides

Nucleotides comprise a sugar + base + a phosphate
Nucleotides are phosphorylated nucleosides (at least one phosphorus group). They link in chains to form polymers called nucleic acids (i.e. DNA and RNA, see below)

• The 5' end of the incoming nucleotide contains the triphosphate, which is the key energy source.
• Nucleotide monophosphates – add suffix 'sylate' = nucleoside + 1 phosphate group
  • Adenylate
  • Guanylate
  • Cytidylate
  • Thymidylate
  • Uridylate

"S" comes before "T" which helps us remember that a nucleoside is a building block of a nucleotide.

N-beta-glycosidic bond

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

Phoshpodiester bond

Phoshpodiester bond links the C3 or C5 hydroxyl group of sugar to phosphate. 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.

Nitrogenous bases

Nitrogenous bases combine with a sugar to form a nucleoside.

• Nitrogenous bases are:
  • Adenine
  • Guanine
  • Cytosine
  • Thymine (DNA)
  • Uracil (RNA)

• 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

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

Introduction

Here we will learn about learn about nucleoside and nucleotide structure, and how they create the backbones of nucleic acids (DNA and RNA).

Overview

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.

Nucleosides

Components

Show that a nucleoside comprises:

• nitrogenous base
• sugar

N-beta-glycosidic bond

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.

Adenosine (Nucleoside Example)

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.
• 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.

Nucleotides

Let's turn our focus to nucleotides.

Nucleotide Components

• 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.

Deoxy-cytidine-5 prime-diphosphate (Nucleotide example)

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.

Phosphates

Now let's add two phosphate groups to the sugar.

• At carbon 5, add an oxygen atom, and then a phosphorous atom.
• 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.

Nomenclature

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

Nitrogenous Bases

Under the nitrogenous base header, write the names of the five bases:

• Adenine
• Guanine
• Cytosine
• Thymine
• Uracil

Nucleosides

Now write that the names of the nucleosides are:

• Adenosine
• Guanosine
• Cytidine
• Thymidine
• Uridine

Nucleotide monophosphates

Nucleotide monophosphates have the suffix "–ylate" added to their base names, so they are:

• Adenylate
• Guanylate
• Cytidylate
• Thymidylate
• Uridylate

Deoxy-

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.

Sugar-phosphate backbone

Introduction

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.

Triphosphates

Nucleotide monomers of nucleic acids exist as triphosphates.

Monosphates

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.

DNA Backbone

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.
• 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.

RNA Backone

Now let's do the same for RNA.

• To draw a ribose sugar, draw the same sugar as we did for DNA.
• 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.