3.3.1 Outline DNA nucleotide structure in
terms of sugar (deoxyribose), base
Outline means to give a brief account or summary. .
Sugar is deoxyribose which differs from ribose in having one less oxygen on carbon 2.
Phosphate is the PO4-3 group.
Bases are nitrogen based ring structures of which there are 4 different kinds.
3.3.2 State the names of the four bases in
State means to give a specific name, value or other brief answer without explanation or calculation.
Nucleosides are the combination of sugar and base only and are not required for the syllabus. You will however see the terms used in the literature.
These are the four bases which are universally found in living things.
In 1950 Edwin Chargaff determined that within an organism there was same approx the same amount of A as T and the same amount of G=C.
Chargaff surveyed a wide variety of organsims and found in the ratio of A:T, G:C consistently across the range of his specimens
These ratios became known as Chargaff's ratio's and would later prove to be a significant clue to the structure of DNA.
NB: As of July 2011 there are now be more than four bases. The new addtions to the list tend to be modifications of the bases above (e.g. adding methyl groups to cytosine) and are invloved in processes that modify transription/ translation or silnce genes. The details are not examined on this course.
3.3.3 Outline how DNA nucleotides are
linked together by covalent bonds
into a single strand (2).
Outline means to give a brief summary.
DNA is composed of two polynucleotides chains.
Nucleotides are covalently bonded between the phosphate of one nucleotide to the C3 of the second nucleotide.
The phosphate group creates a bridge connecting C5 on one pentose with the C3 on the next pentose.
The bond is a phosphodiester bond which indicates that there are two covalent bonds formed between the -OH and the acidic phosphate group.
The image is of one polynucleotide chain.
The sugar phosphate backbone which provides the stable backbone of one of the helices.
Covalent bonds that link the nucleotides along the backbone of the molecule.
The bases projecting into the centre.
At one end there is pentose with 5' (said "five prime" ) carbon which is free from bonding.
At the other end there is a 3' carbon free from bonding to other nucleotides.
Additional nucleotides are joined to the 3' end of the existing polynucleotide chain.
3.3.4 Explain how a DNA double helix is
formed using complementary base pairing and hydrogen bonds (3).
complementary means matching, is different from complimentary, which means being nice. You may recall that in 1950 Edwin Chargaff working in Columbia University USA had determined that the mass of the bases(in a DNA speciment) formed ratios of A:T and G:C. This held true when taking samples from individuals within a population or when comparing species across large classification divides. In the cell of any organism the mass of Adenine seems to be about the same as the mass of Thymine. The mass of Cytosine seems to be about the same as the mass of Guanine.
Three years later the significance of Chargaff's Rule was realize by Watson and Crick at the Cavendish Laboratory in Cambridge, England. Watson an American geneticist and Crick an English physicist began model building DNA based on a collection of results from other researchers, including Chargaff. The model building technique uses the principles of chemistry such as molecular structure and bond angles as then developed by Linus Pauling. Together with the data from X-ray crystallography studies (the combined work of Wilkins and Franklin ) they began to build DNA and part of that process involved the pairing of the bases in the centre of the helix.
Explain means to give a detailed account of causes, reasons or mechanisms.
The molecular distance from Adenine combined with Thymine is the same as the molecular distance between Guanine combined with cytosine. This gave a uniform distance that could fill the centre of the helix.
The complementary bases are formed (A-T, G-C) when hydrogen bonded occur between the two bases in a pair.
Refer to the diagram and notes in the next section..
3.3.5 Draw and label a simple diagram of
the molecular structure of DNA(1) .
Draw means to be able to represent by means of pencil lines.
This image of DNA shows the arrangement of the two polynucleotide chains but not the helical shape which can be seen in the space filled model below.
This is image shows:
a)The number followed by the prime (') determined the carbon in deoxyribose free from bonding to another nucleotide.
b) Note that the two chains are in opposite directions 3' to 5' is parallel to 5' to 3' chain.
The anti-parallel chains have a uniform distance (2nm) between the outside of the two sugar phosphate backbones
Complementary base pairs: Inside the double helix bases form one strand hydrogen bond to bases on the opposite strand but always in the following way:
a) Adenine hydrogen binds to Thymine
b) Cytosine hydrogen bonds to Guanine
The three-dimensional structure of DNA was discovered in 1953 by Watson and Crick in Cambridge, using the experimental data of Wilkins and Franklin in London, for which work they won a Nobel prize. Ms Franklin however died before the award and the Nobel Prize is never awarded posthumously.
The main features of the structure are:
The strands are antiparallel, i.e. they run in opposite directions thus 5' to 3' is parallel to 3' to 5'.
The two strands are wound round each other to form a double helix (not a spiral, despite what some textbooks say).
DNA is a right handed double stranded helix of uniform diameter. The two strands of polynucleotide are anti-parallel.
3.3.1 Outline of nucleotide structure
3.3.2 Names of the bases
3.3.4 Base pairing
3.3.5 DNA molecular structure
Recommended reading: Watson, J. D. (1999) Double Helix. London: Penguin Books. Has edition has an introduction by Steve Jones.