3.3 DNA Structure 12/12/10 8:02 PM

Topic 3: Chemistry of Life3.3 DNA Structure

Orange book: pg. 54-59Green book: pg. 35

3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate (pg. 54).

3.3.2 State the names of the four bases in DNA (pg. 57)

3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand (pg. 57).

3.3.4 Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonding (pg. 57).

3.3.5 Draw and label a simple diagram of the molecular structure of DNA.

3.3.1 Nucleotides 12/12/10 8:02 PM

3.3.1 Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.

Orange book: pg. 54-59Green book: pg. 35

To do:Visit the following website http://www.pbs.org/wgbh/nova/genome/dna.html#Journey into DNA Animation - This is a simple introduction which takes you from the cell right down to the structural level of DNA.Draw the basic structure of a nucleotide in your green exercise book.

DNA and its close relative RNA are perhaps the most important molecules in biology. They contain the instructions that make every single living organism on the planet, and yet it is only in the past 50 years that we have begun to understand them. DNA stands for deoxyribonucleic acid and RNA for ribonucleic acid, and they are called nucleic acids because they are weak acids, first found in the nuclei of cells. They are polymers, composed of monomers called nucleotides.

NucleotidesNucleotides have three parts to them:a phosphate group (PO42- ), which is negatively charged, and gives nucleic acids their acidic properties.

a pentose sugar, which has 5 carbon atoms in it. By convention the carbon atoms are numbered as shown (1', 2', etc, read as "one prime", "two prime", etc), to distinguish them from the carbon atoms in the base. If carbon 2' has a hydroxyl group attached (as shown), then the sugar is ribose, found in RNA. If the carbon 2' just has a hydrogen atom attached instead, then the sugar is deoxyribose, found in DNA.

a nitrogenous base. There are five different bases (and you don't need to know their structures), but they all contain the elements carbon, hydrogen, oxygen and nitrogen.

3.3.2 Bases 12/12/10 8:02 PM

3.3.2 State the names of the four bases in DNA

Orange book: pg. 57Green book: pg. 35

To do:List the names of the four bases found in DNA in your green books.

Since there are five bases, there are five different nucleotides:

Base: Adenine (A)Cytosine (C)Guanine (G) Thymine (T) Uracil (U)

The bases are usually represented by the first letter in their name. The base thymine is found in DNA only and the base uracil is found in RNA only, so there are four different bases present at a time in one nucleic acid molecule.

Pyrimidines: Thymine and cytosine are pyrimidines. Note that all three words contain a 'y' (note that uracil does not fit this pattern). Purines: Adenine and guanine are purines (notice the word 'nine' in both adenine and guanine!).

3.3.3 Polymerisation 12/12/10 8:02 PM

3.3.3 Outline how DNA nucleotides are linked together by covalent bonds into a single strand.

Orange book: pg. 57Green book: pg. 35

To do:View the animation “Journey into DNA”This is a simple introduction which takes you from the cell right down to the structural level of DNA.http://www.pbs.org/wgbh/nova/genome/dna.html#View the animation “Summary of DNA”A complete overview of the structure of DNA.http://207.207.4.198/pub/flash/24/menu.swfDraw and label a single strand of DNA to show how a nucleotide is attached to the 3’ end of the growing strand.

Nucleotide PolymerisationNucleotides polymerise by forming phosphodiester (covalent) bonds between carbon 3' of the sugar and an oxygen atom of the phosphate.

This is a condensation polymerisation reaction.

The bases do not take part in the polymerisation, so there is a sugar-phosphate backbone with the bases extending off it. This means that the nucleotides can join together in any order along the chain. Two nucleotides form a dinucleotide, three form a trinucleotide, a few form an oligonucleotide, and many form a polynucleotide.

A polynucleotide has a free phosphate group at one end, called the 5' end because the phosphate is attached to carbon 5' of the sugar, and a free OH group at the other end, called the 3' end because it's on carbon 3' of the sugar. The terms 3' and 5' are often used to denote the different ends of a DNA molecule.

3.3.4 DNA Structure 12/12/10 8:02 PM

3.3.4 Explain how a DNA double helix is formed using complementary base pairing and

hydrogen bonding.

Orange book: pg. 57Green book: pg. 35

To do:Draw a double stranded diagram of DNA to show complementary base pairing with the correct number of hydrogen bonds.Annotate the diagram using the points below.

Structure of DNAThe three-dimensional structure of DNA was discovered in 1953 by Watson and Crick inCambridge, using experimental data of Wilkins and Franklin in London, for which work they won a Nobel prize. The main features of the structure are:

DNA is double-stranded, so there are two polynucleotide stands alongside each other. The strands are antiparallel, i.e. they run in opposite directions.

The two strands are wound round each other to form a double helix.

The two strands are joined together by hydrogen bonds between the bases. The bases therefore form base pairs, which are like rungs of a ladder.

The base pairs are specific. A only binds to T (remember ‘At’), and C only binds to G (and G with C). These are called complementary base pairs. This means that whatever the sequence of bases along one strand, the sequence of bases on the other stand must be complementary to it.

3.3.5 Drawing DNA 12/12/10 8:02 PM

3.3.5 Draw and label a simple diagram of the molecular structure of DNA.

Orange book: pg. 57Green book: pg. 35

To doYou have already done this in previous objectives so by now you should be able to draw and label the structure of DNA to show: complementary base pairing hydrogen bonding double strand (anti-parallel) covalent bonds nucleotides phosphate sugar bases phosphate-sugar backbone

* ExtraYour syllabus does not ask you to distinguish between RNA and DNA, however the following table will help you as we go onto the HL section related to this topic.

Comparison of DNA and RNA

Characteristic DNA RNA

sugar present Deoxyribose Ribose

Structure Double helix Single Strand

Adenine (A) present ✔ ✔

Thymine (T) present ✔ X

Uracil (U) present X ✔

Cytosine (C) present ✔ ✔

Guanine (G) present ✔ ✔

HW3: DNA Questions (26 Marks) 12/12/10 8:02 PM

1. Complete the table to show three differences between the structure of DNA and RNA. (3)

Structure of DNA Structure of RNA1. 1.2. 2.3. 3.

2. Read through the following account of the structure of deoxyribonucleic acid (DNA), then write on the dotted lines the most appropriate word or words to complete the account. (5)

DNA is a molecule consisting of a long chain of nucleotides, which are joined together by ................................... reactions. Each nucleotide in DNA consists of a nitrogenous base, a phosphate group and ................................... .The nitrogenous base may be adenine, guanine, cytosine or .................................... . A molecule of DNA is made up of two polynucleotide chains coiled into a ................................... . The two chains are held together by ................................... bonds between the nitrogenous bases

3. The diagram shows part of a molecule of DNA

(a) Complete the diagram with the first letters of the appropriate complementary base. (1)

(b) What is represented by:(i) the part of the molecule in box B; (1)(ii) the dotted lines between the complementary base pairs? (1)

4. The table shows the percentage of different bases in DNA from different organisms.

Source ofDNA

Adenine %

Guanine %

Thymine %

Cytosine %

Human 30 20 30 20Rat 28 22 28 22Yeast 31 19 31 19Turtle 28 22 28 22E.coli 24Salmon 29 21 29 21Sea urchin

33 17 33 17

(a) What information about the ratios of different bases in DNA can you work out from the table? (2)

(b) Give the results that you would expect for DNA from the E.coli bacterium. Explain how you arrived at your answer. (3)

(c) Turtles have the same percentages of the four different bases as rats. Explain why they can still be very different animals. (1)

5. The table below shows the percentage of different bases in the DNA from a virus.Adenine %

Guanine %

Thymine %

Cytosine %

25 24 33 18

(a) Describe how the ratios of the different bases in this virus differ from those in the first table. (1)

(b) The structure of the DNA in this virus is not the same as DNA in other organisms. Suggest what this difference in DNA structure might be. (1)

(c) The diagram shows the structure of a DNA nucleotide.

Name the parts of the nucleotide labelled A and Y. (2)

6. The table shows the percentage composition of bases in the DNA of cattle and octopus.

Organism Adenine Cytosine Guanine ThymineCattle 29 21Octopus 33 33

(a) Use your knowledge of the structure of DNA to calculate the missing values and complete the table above. (1)

(b) Explain your answer. (2)

(c) Describe two differences between the structure of DNA and RNA. (2)