1. Topic 2 Molecular biology
2.6 Structure of DNA and RNA
IB Biology SFP - Mark Polko

2. IB Biology SFP - Mark Polko
Nature of science
Experimental design—accurate, quantitative measurements in enzyme experiments require replicates to ensure reliability. (3.2)
Understandings:
The nucleic acids DNA and RNA are polymers of nucleotides.
DNA differs from RNA in the number of strands present, the base composition and the type of pentose.
DNA is a double helix made of two antiparallel strands of nucleotides linked by hydrogen bonding between complementary base pairs.
IB Biology SFP - Mark Polko

3. IB Biology SFP - Mark Polko
Applications and skills
Application: Crick and Watson’s elucidation of the structure of DNA using model making.
Skill: Drawing simple diagrams of the structure of single nucleotides of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.
ToK
The story of the elucidation of the structure of DNA illustrates that cooperation and collaboration among scientists exists alongside competition between research groups. To what extent is research in secret ‘anti-scientific’? What is the relationship between shared and personal knowledge in the natural sciences?
Essential idea: The structure of DNA allows efficient storage of genetic information.
IB Biology SFP - Mark Polko

4. IB Biology SFP - Mark Polko
Some important notes
In diagrams of DNA structure, the helical shape does not need to be shown, but the two strands should be shown antiparallel. Adenine should be shown paired with thymine and guanine with cytosine, but the relative lengths of the purine and pyrimidine bases do not need to be recalled, nor the numbers of hydrogen bonds between the base pairs
IB Biology SFP - Mark Polko

5. Nucleis acids and nucleotides
The nucleic acids RNA and DNA are polymeres of nucleotides
Nucleic acids were first discovered when extracted from the nuclei of cells. There are tow types, RNA and DNA. Nucleic acids are very large polymers constructed form linking together nucleotides. These nucleotides consist out of three parts:
A sugar, which has five carbons so is a pentose.
A phosphate group, which is the acidic negatively charged part of the nucleic acids.
A base, that contains nitrogen and has one or two rings of atoms as its structure.
IB Biology SFP - Mark Polko

6. Nucleis acids and nucleotides
The nucleic acids RNA and DNA are polymeres of nucleotides
Complementary base pairing
Adenine, Thymine and Uracil are capable of forming two Hydrogen bonds while Cytosine and Guanine can form three. So Adenine (A) can form a base pair with Thymine (T) (or uracil (U) in RNA) and Cytosine (C) can form a base pair with Guanine (G).
All organic bases have a complicated molecular structure involving ring compounds. Adenine and Guanine are purines, ‘big’ 2-ring structures; Cytosine, Thymine and Uracil are pyrimidines, ‘small’ 1-ring structures.
IB Biology SFP - Mark Polko

7. IB Biology SFP - Mark Polko

8. Nucleis acids and nucleotides
The nucleic acids RNA and DNA are polymeres of nucleotides
LINK
Since the reactions involved are (again) condensation reactions, the equation becomes:
phosphate + sugar + organic base → nucleotide + 2 water
The nucleotides can be linked together to form a single chain by a condensation reaction between the phosphate of one nucleotide and the sugar of another. The sugar and phosphate form the ‘backbone’ of the nucleic acid with the organic bases sticking out.
Covalent bonds are formed between the phosphate and sugar and a single strand is made with a ‘backbone’ of phosphate and (deoxy)ribose and an organic base attached to every ribose.
IB Biology SFP - Mark Polko

9. Nucleis acids and nucleotides
The nucleic acids RNA and DNA are polymeres of nucleotides
Knowing that the structure of DNA is a ‘double helix’ (a twisted ladder) we need to fit two DNA molecules together. Since some of the organic bases can form bonds with certain others, we can combine the DNA strands this way. The sugar and phosphate ‘backbones’ run antiparallel forming the sides of the ladder with the organic base pairs as rungs in between.
IB Biology SFP - Mark Polko

10. Differences between RNA and DNA
DNA differs from RNA in the number of strands normally present, the base composition and the type of pentose
There are three important differences between the two types of nucleic acids.
The sugar of DNA is deoxyribose and the sugar of RNA is ribose.
There are usually two polymers of nucleotides in DNA and one in RNA.
Three of the four bases are the same but where DNA has thymine, RNA has uracil.
IB Biology SFP - Mark Polko

11. Drawing DNA and RNA molecules
Only the simplified structure on the right is needed to draw. Make sure they are linked properly.
One strand fro RNA and two strands for DNA. Make sure that you don’t get confused with base pairing and thymine vs uracil.
IB Biology SFP - Mark Polko

12. Crick and Watson modelling of DNA structure
Crick and Watson’s modelling of the DNA structure of DNA using modelling
Crick and Watson’s success in discovering the model of DNA was based on using the evidence to develop possible structures for DNA and testing them by model building. Their first model consisted of a triple helix, with bases on the outside and magnesium holding the two strands together with ionic bonds to the phosphate groups on each strand.
The helix shape and the spacing between the subunits of DNA fitted the x-ray diffraction pattern obtained by Rosalind Franklin
IB Biology SFP - Mark Polko

13. Crick and Watson modelling of DNA structure
Crick and Watson’s modelling of the DNA structure of DNA using modelling
While making the model they discovered that there could not have been enough magnesium available to form the crosslinks between the strands. Another mistake was that this first model did not take into account that the amount of adenine should have been the same as the amount of thymine and cytosine of guanine.
So they paired the bases together, made it double stranded and found that the two strand should run in antiparallel direction to each other to make it fit. This lead to their second model, which had all the bond sizes and angles correct. This model convinced every expert in the field because it looked just right. This started a great biological revolution.
IB Biology SFP - Mark Polko

14. Topic 2 Molecular biology
2.6 Structure of DNA and RNA
IB Biology SFP - Mark Polko