Tutorial: DNA Structure
Index
DNA Composition | Discovery of DNA | Polymer | Nucleotide Structure | Bacterial Transformation | Transforming Principle | Phages and DNA | The 4 Nucleotides | DNA monopolymer | Nitrogen Base Content | X-Ray Crystallography | Ladder Model | DNA Polymer | Base Pairing | Nucleotide Experiment | Complementary | Quiz


Copyright © Steve Kuensting, 2004, All Rights Reserved.
This web tutorial may not be distributed by any means
without the expressed permission of the author!




DNA Composition

DNA is one type of nucleic acid (the other is RNA), a biochemical composed of carbon, hydrogen, and oxygen, nitrogen, and phosphorus.
This tutorial is an explanation of DNA's structure.

DNA structure



DNA Size

DNA is the largest molecule in the cell and the most complex. Its primary function is to control all cell activities. It is usually found only in the nucleus of a cell.


DNA structure



DNA Research: The Discovery of DNA

DNA was first discovered by Friedrich Miescher in 1871. He extracted the nuclear contents of white blood cells and named the extracted substance "nuclein". Nuclein was made of DNA and protein.

Miescher
Friedrich Miescher

See page for author [Public domain], via Wikimedia Commons
Lymphocyte
White blood cell

By Mgiganteus [Creative Commons Attribution-Share Alike 3.0 Unported or GNU] via Wikimedia Commons.




The Transforming Principle

In 1928, Fred Griffith, while working in vaccine research with Streptococcus pneumonia, discovered the common phenomenon of bacterial transformation. Griffith was culturing different strains of Strep. pneumonia and injecting them into mice to check mortality. He had a virulent (smooth) strain, one that killed mice, and another nonvirulent (rough) strain, that did not kill mice. In one particular experiment, Griffith had injected the remains of dead virulent (smooth) Strep. pneumonia along with living nonvirulent (rough) Strep. pneumonia into living mice. The mice died, and when he cultured the bacteria in the dead mice, he was surprised to find living Strep. pneumonia! The dead virulent bacteria had contributed something to the living nonvirulent bacteria and transformed them. Griffith named the substance the "transforming principle" but died before he could actually identify it.

Griffith



The Transforming Principle Identified

Oswald Avery, Colin MaCleod, and Maclyn McCarty continued with Griffith's experiment. They systematically purified extracts from virulent Strep. pneumonia consisting of either carbohydrate, lipid, protein, and nucleic acid. The only extract that was capable of transforming nonvirulent (rough) bacteria into virulent (smooth) bacteria was the DNA extract. In 1944, their conclusion was that DNA was the hereditary substance that caused bacterial transformation.

Transforming principle



Phage Heredity

Alfred Hershey and Martha Chase furthered DNA research in 1952 when they showed that DNA was the substance of phage (viral) heredity. They cultured viruses on radioactive media to label the viral protein with sulfur-35 and viral DNA with phosphorus-32. When they allowed these radioactive viruses to attack normal bacteria, they found that the viruses had injected the phosphorus-32 into the bacteria. The viruses were putting their DNA into the bacteria to force the bacteria to make more viruses. Viral DNA, not protein, was their hereditary material.

Bacteriophage
Bacteriophage

By Mostafa Fatehi (Own work) [CC-BY-3.0], via Wikimedia Commons
Phage
Phages



Polymer

DNA is a polymer molecule. Polymer molecules are molecules that are actually "chains" or "strings" of smaller molecules called monomers. The string of circles below could represent a polymer molecule, the circles would represent monomer molecules and the dashes between them would represent bonds holding the molecules together.

DNA polymer



DNA and Nucleotides

DNA polymer molecules are made up of strings of smaller monomer molecules called nucleotides. A nucleotide is shown below, with its actual structural formula and an abbreviated form. Symbols are often used below to represent the nucleotide. Notice that the nucleotide is made up of 3 smaller shapes, each representing a molecule.

Monomers in DNA



Nucleotide Structure


Nucleotide structure



Nucleotide Structure

A nucleotide is made up of a nitrogen base, deoxyribose (a sugar), and a phosphate group. There are actually four different types of nucleotides because there are four different types of nitrogen bases. There is only one type of sugar (deoxyribose) and only one phosphate group. The 4 nucleotides are represented below conveniently as shapes:

Nucleotide structure



Purines vs Pyrimidines

Below are drawn the actual structural formulas of the nitrogen bases within DNA. Notice that some of them consist of 2 rings while others consist of 1 ring. The single ring nitrogen bases are called pyrimidines while the double ring bases are called purines. Their abbreviations are shown below.

N base formulas



Structural Formulas

Structural formulas for the 4 DNA nucleotides are shown below. Can you find their differences?

4 nucleotides



Nucleotide Abbreviations

We will be using the abbreviated forms of the nucleotides in most of this program. Notice that the four nucleotides shown below only differ from one another by the shape of their nitrogen bases. Their sugars and phosphates are all identical.

4 nucleotides



The 4 Nucleotides

A nucleotide is named after the nitrogen base it contains. Each nucleotide is abbreviated with its first letter in upper case. Thus, guanine nucleotide = G, cytosine nucleotide = C, thymine nucleotide = T, and adenine nucleotide = A.

Nucleotide abbreviations



DNA Monopolymer

In a DNA polymer molecule, nucleotides bond together to form strings of nucleotides, sometimes thousands of nucleotides long. Below is shown a single chain of nucleotides, 12 nucleotides long. Note how each nucleotide is connected with the nucleotides around it.

Chain of nucleotides



DNA Double Helix

Yet, DNA is much more complex than just a single string of nucleotides. It is actually a double strand of nucleotides, one woven around one another like two strings wound together. We use the Watson & Crick model to understand the DNA molecule more easily.



DNA Research

In the late 1940's, Erwin Chargaff discovered that, within a species, the quantity of thymine nucleotide equalled the quantity of adenine nucleotide, and the same was true for cytosine and guanine. In different species, the proportions of each nucleotide occurred in different levels, but the same rule held true: adenine and thymine were in equal quantities while cytosine and guanine were in equal quantities.

Nitrogen Base Content in Different Species
% A% T% G% C
Human30.929.419.919.8
Chicken28.829.220.521.5
Locust29.329.320.520.7
Wheat27.327.122.722.8
Yeast31.332.918.717.1
E. coli24.723.626.025.7



X-Ray Evidence

In the early 1950's, British researcher Rosalind Franklin was producing X-Ray crystallographs of DNA. She passed x-rays through small frozen samples of purified DNA. Her crystallographs indicated that DNA was made of 2 twisted strands with the nitrogen bases at the middle. She was near the discovery of the structure of DNA.

X-ray crystallograph
DNA X-ray crystallograph produced by Rosalind Franklin
Image from Wikipedia:
Nitrogenous base
Author: Rosalind Franklin, published in the Journal: Nature


Ladder Model

In 1953, James Watson and Francis Crick were given a clear crystallograph from Franklin's lab. James Watson immediately saw the pattern revealed in the x-ray photo and the two hastily constructed models of DNA until they fabricated one that matched everything they knew about DNA. Their model revealed that the DNA molecule is structured much like a ladder, with the sugars and phosphates on the "uprights" of the ladder and the nitrogen bases on the "rungs".

DNA model Mccarty, Watson, and Crick
McCarty, Watson, Crick

By Marjorie McCarty [CC-BY-2.5 or CC-BY-3.0], via Wikimedia Commons




DNA Polymer

If the nucleotide shapes are used to represent the DNA molecule, then the molecule would look much more like this:
(scroll up to compare to a ladder)

DNA ladder model



Base-Pairing

Within the ladder structure of the DNA molecule, the nitrogen bases that face each other only bond in a specific way through hydrogen bonding. Adenine will hydrogen bond only with thymine, and cytosine will hydrogen bond only with guanine. Shown below is a representation of this bonding:

Hydrogen bonding



Base Pairing

A bonds only with T, and C only with G because adenine matches the shape of thymine, and the shape of cytosine matches the shape of guanine. Therefore A or T can't bond with C or G, the shapes won't match.

Complementerity



Nucleotide Experiment

Shown below is a representation of how 4 nucleotides would bond together forming a very short piece of DNA. The numbers show the different nucleotides.

DNA construction



24 Nucleotides in a DNA Strand

Finally, a larger piece of DNA would look like this piece, containing 24 nucleotides, but only 12 nucleotides long.

DNA 12 nucleotides long



One Side of DNA Determines the Other Side

Since adenine only bonds with thymine and cytosine only bonds with guanine, the sequential arrangement of N-bases on one side of a DNA molecule determines the sequential arrangement on the other side.

DNA structure



Complementary

Two opposing strands of a DNA molecule are said to be COMPLEMENTARY. The upper nucleotide strand has an N-base sequence of TGCAAGTCCGAT. It is complementary to the nucleotide strand opposite to it with the sequence ACGTTCAGGCTA.

DNA code



Genetic Code

The sequence of the N-bases contains the genetic code which controls all cell functions and all hereditary characteristics of a cell. The actual code will be explored in a later program.

DNA code



Quiz

  1. What molecule matches the shape of thymine nucleotide?

  2. What molecule matches the shape of cytosine nucleotide?

  3. What molecule matches the shape of adenine nucleotide?

  4. What molecule matches the shape of guanine nucleotide?

  5. What word is used to describe two opposing strands of DNA?

  6. How many different types of nitrogen bases are there in DNA?

  7. How many different types of sugars are there in DNA?

  8. How many different types of phosphates are there in DNA?

  9. What two molecules are found in the uprights of the DNA molecule?

  10. What types of molecules are found in the rungs of the DNA molecule?

  11. What would the sequence of complementary nucleotides be, to the DNA strand having the following nitrogen base sequence: A G C T T G ?

  12. What physical object does the DNA molecule resemble?

  13. What two scientists discovered the true structure of DNA?

  14. How many nucleotides are present in a DNA molecule that is 20 nucleotides long?

  15. How many different molecules are bonded together in a single nucleotide?

  16. For numbers 1-11 on the diagram below, identify the molecule.

Quiz

Answers