Nucleic acid structure

Nucleic acids are polymers

• All polymers can be described as a set of simple monomers linked by  certain kind of bond
  • In nucleic acids the monomer is the nucleotide
  • The bond that holds them together is the phosphodiester bond

Nucleotides

- when chemists broke up nucleic acids found

                                                            DNA                                                   RNA

- nitrogenous bases                                    A, G, C, T                                           A, G, C, U

- a sugar                                            deoxyribose                                      ribose

-phosphoric acid                              PO₄^3-                                                   PO₄^3-

- A and G are purines (based on a molecule called purine)

- C, T, and U are pyrimidines (based on a molecule called pyrimidine)

- base and sugar together are a nucleoside

            - look at numbering of atoms in molecules

                        - base atoms are numbered 1-6 (pyrimidines) or 1-9 (purines)

- sugar carbons are numbered 1-5’ (prime)

- when you add the phosphate group onto the nucleoside it is a nucleotide

ester

phosphoester

phosphodiester

Linking nucleotides together

• when nucleotides are joined together, it is with a phosphodiester bond
  • between 3’ carbon of one nucleotide and 5’ carbon of the next
  • so a single strand of nucleic acid has a polarity
    • 5’ end
    • 3’ end
  • because of these and the fact that it is synthesized from 5’ to 3’, nucleic acid sequence is usually written 5’ to 3’ and often these ends are not noted

Structure of double stranded DNA

·         Watson and Crick work

o       Franklin and Wilkins obtained Xray crystallography diffraction patterns

o       Chargaff rules (Table 6.1)

§         From any source of dsDNA, amount of A=T, amount of G=C

·         Model building showed 3D structure of DNA

            - two strands

            - sequence is complementary

            - bases make hydrogen bonds with each other

                        - A-T has 2 H-bonds

                        - G-C has 3 H-bonds

            - sugar-phosphate backbone outside

            - strands twisted around each other        

                        - double helix           

- each base pair offset with respect to previous one so that every 10.5 bp there is a complete turn

                        - two strands are antiparallel

- with their model, if you know the sequence of one strand, you know the other

            - easy replication, just separate strands and fill in the missing sequence

- major groove and minor groove

A,B,Z DNA

B form

Watson and Crick structure is B form DNA

- B form is normal form of DNA in the cell

A form

- double stranded DNA can be in this form under some circumstances

- plane of base pair is not horizontal, but tilted about 20 degrees

- 11 bp/turn rather than 10

- importance is that RNA-DNA hybrids form this, as does double stranded RNA

Z form

- Alex Rich discovered

- helix is left handed, if you follow the major groove if you follow from top or bottom

            - B and A are right handed

- presence and significance are uncertain

Genomes of different organisms

·         Double stranded DNA

o       Most have this

·         Single stranded DNA

o       Some viruses have this, eg. M13 and fX174

·         RNA genomes

o       RNA uses different sugar (ribose)

§         2’ has –OH

o       Also has U base instead of T

o       Viruses are known with both double stranded and single stranded genomes