Exploring the Molecules of Life:  Nucleotides

Suppose that there were only four amino acids available to form peptides (A, B, C, and D).  If you were going to make all the possible dipeptides from the four possible amino acids above, how many possible dipeptides could you make?

How do cells know which proteins to make out of the near infinite number of amino acid sequences?

The nucleus of a cell is made up of basic proteins and compounds known as nucleic acids.  There are two kinds of nucleic acids.  They are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).  DNA is found in the chromosomes of the nucleus in a cell and it carries hereditary information.  RNA is located in the cell but not in the nucleus.  Just as proteins consist of long chains of amino acids, DNA and RNA consists of nucleic acid chains called nucleotides.

Nucleotides are composed of three units: base, sugar (monosaccharide) and phosphate.  Bases are found in both DNA and RNA.  As seen below, they are adenine, cytosine, guanine, thymine, and uracil.  They are abbreviated (A, C, G, T, U).  Three of the bases (A, G, C) are found in both DNA and RNA.  However, uracil (U) is found only in RNA and thymine (T) is found only in DNA.

The building blocks for DNA and RNA are given below.

The five bases needed:

adenine (A)          cytosine (C)             guanine (G)             thymine (T)              uracil  (U) 

The sugar component in RNA is ribose and in DNA is deoxyribose (hence the name ribonucleic acid and deoxyribonucleic acid).  The third component of nucleotides is the phosphate ion. 

The two sugars needed:

deoxyribose                ribose

The phosphate ion needed:

 

Below is a simplified chart that summarizes what was talked about above:

Nucleic Acids Phosphate Sugar Bases
DNA yes deoxyribose A, C, G, T
RNA yes ribose A, C, G, U

Here is a structure of DNA below.  Be sure to move the structure around.

Can you find the backbone, or the continuous chain?  How many chains in the DNA molecule? (right click go to color and click on chains, to reset select CPK under color) 

Can you see where the sugar and phosphate are bonded together?  How are the base pairs positioned in DNA?

If you right click, go to select, and choose nucleic, you can click on the part of the DNA molecule you want to stand out when you change the display.  To get out of this option select nucleic or DNA or press refresh or reload on your browser.

If you had to describe the structure of DNA to a friend who never had any biology, how would you describe it?

The primary structure of DNA can be broken in two parts: 1) the backbone of the molecule and 2) the bases, which are the side chains.

The backbone of DNA is made up of alternating sugar (deoxyribose) and phosphate groups as seen below:

              sugar-phosphate-sugar-phosphate-sugar-phosphate...

Then the bases (side chains) are attached to the sugar in a sequence order as seen below:

              (A)sugar-phosphate/(G)sugar-phosphate/(T)sugar-phosphate/(C)sugar-phosphate...

The primary structure of RNA is similar except that the sugar is ribose and uracil is present instead of thymine.

             (A)sugar-phosphate/(G)sugar-phosphate/(U)sugar-phosphate/(C)sugar-phosphate...

If you are having trouble seeing the items discussed above, click here to check out a great site at the University of Massachusetts.  For a colorful version of the same- click here

Just as the order of amino acid of a protein side chain determines primary structure, the order of bases also provides the primary structure for DNA.    For example the sequence of (-ATG) is not the same as (-GTA).  The primary structure of DNA is one polynucleotide chain.

The secondary structure of DNA is in the form of a double helix (a twisted ladder).  This secondary structure is not the same as that of proteins.   Two polynucleotide chains come together to form this double helix.  The sugar-phosphate backbone is on the outside and the bases point inward toward each other. 

The bases are paired in a specific manner in the double helix.  For each adenine on one side of the chain, a thymine is opposite; each guanine on one side of the chain has a cystosine as its opposite.  The paired bases form hydrogen bonds with each other and this stabilizes the double helix structure.  The bases are paired in what is known as complementary base pairs.

The same sequence works for RNA except instead of thymine there is uracil.  Therefore each adenine in RNA is paired with a uracil; each guanine is still paired with cytosine.

Below is a chart that summarizes what you have seen above.

  DNA

  RNA
  adenine-thymine (A-T) adenine-uracil (A-U)
guanine-cytosine (G-C) guanine-cytosine (G-C)

Below you can see adenine-thymine pair and guanine-cytosine pair of DNA.  Can you see where hydrogen bonding will take place? (Right click on the image, go to options, select show hydrogen bonds.)

    

adenine-thymine                                 guanine-cytosine

Why does the A-T pair not have a third hydrogen bond in it?

The bases can be paired in any order in the secondary structure of the double helix as long as adenine and thymine are together; guanine and cytosine are together, etc.  For example, (T-A) is the same as (A-T) only in the helix structure not the primary structure as we saw before.

By now you must have realized how important hydrogen bonding is in proteins and the nucleotides.

DNA is vital in protein synthesis and critical for replicating its instructions for protein synthesis.  Click here to go to an inactive DNA workshop done by PBS (need Shockwave installed on your computer).  

In the table below finish the second strand of nucleotides by completing the base pairs for the DNA molecule.

A T G G C A A C T A T G G
                         

If the strand above was RNA, what would be different?

Vasopressin is a nonapeptide, 9 amino acids in the primary structure.  They are given below:

cys-tyr-phe-glu-asp-cys-pro-arg-gly

The number of possible arrangements of this polypeptide can be calculated by a counting technique in statistics called arrangements with repetition.  The formula is given by N = nr where N is the possible number of arrangements, n is the number of different amino acids used, and r is the total number of amino acids in the chain.  Calculate the number of possibilities.

Try calculating the number of possible arrangements for insulin, which has 51 amino acids in the chain made using 17 different amino acids.  Protein synthesis is obviously a very well directed biochemical process.

Hydrogen bonding is a critical attractive force in the alpha-helix structure of proteins and the double helical structure of DNA; however, the arrangement of hydrogen bonds is very different in the two molecules.  Describe the arrangement of hydrogen bonds in each.

Many of the structures on this page are from the molecules collection available at the NSF-funded C4 Project at Cabrillo Community College.

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