1 Nucleic acids: DNA and RNA Done By Majed Felemban

2 DNA Double helix –2 chains Building blocks –Nucleotides DNA directs –Is own replication –Directs RNA synthesis → protein synthesis Campbell and Reece, P86

3 In Eukaryotes (animals, plants, fungi) Complete human genome

4 In Prokaryotes (bacteria, archaea) Main chromosome is one large, continuous loop –Hundreds to thousands of genes May have smaller loops, with a few genes each –May be swapped between bacteria –Antibiotic resistance, etc.

5 Replication Transcription Translation

6 Roles of Nucleic Acids DNA –Responsible for inheritance –Codes for proteins and functional RNAs Genes –Regulatory sequences Control which genes are transcribed, and when –Other unknown functions 80-90% of the human genome has no known function Campbell and Reece, P86, 87

7 Roles of Nucleic Acids RNA –Information transmission (mRNA) –Processing and transport (tRNA, rRNA, snRNA) –Catalytic (ribozymes) –Regulation and feedback (siRNA) –Unit of inheritance (retroviruses) –Other…? Campbell and Reece, P86, 87

8 Nucleic Acid chemistry is the same for all life on earth. DNA & RNA are polymers of monomers - nucleotides. Each nucleotide has three components (Deoxy)ribonucleic Acid NUCLEIC ACID STRUCTURES Campbell and Reece, (DEOXY)RIBOSE SUGAR = STRUCTURAL 3. NITROGENOUS BASES = INFORMATIONAL X X 1. PHOSPHORIC ACID = STRUCTURAL

9 Campbell and Reece, P87

10 Phosphoric Acid & Related Compounds Phosphoric acid is Triprotic. Reacts with CHO’s or alcohols to form esters. D

11 Phosphoric Acid & Related Compounds Phosphoric acid is Triprotic. Reacts with alcohols to form esters. As found in DNA & RNA at pH7 -

12 The sugar may be Ribose (in RNA) or Deoxyribose (in DNA) H RiboseDeoxyribose Phosphate can covalently bond to C 3 and C 5 Bases (A,C,G,T or U) can covalently bond to C 1

13 Bases in DNA and RNA (RNA)(DNA)

14 A Base Joined To A Ribose Sugar Is Called A Nucleoside Pyrimidines bond at N-1 to C-1’ Purines bond N-9 to 1’ Carbon of sugar The carbons in the ribose are now designated as C prime (or C’) to distinguish them from those in the base. or H

15 When Phosphate is Bound to a Nucleoside it is Called a Nucleotide ATP, GTP, CTP, UTP (NTPs) are substrates for RNA synthesis dATP, dGTP, dCTP, dTTP (dNTPs) are substrates for DNA synthesis

16 Mononucleotides as they Occur in DNA & RNA DNA RNA A,C,G or T (DNA) or A,C,G or U (RNA) All nucleotides are asymmetrical

17 5’C = Four Nucleotides With 5’ to 3’ Phosphodiester Linkages 3’C = DNA & RNA are Polymers of Nucleotides All DNA and RNA polymers are asymmetrical with 5’ to 3’ direction.

18 Properties of DNA and RNA They may be informational eg genomic DNA, mRNA. They may be structural eg rRNA & tRNA. Retain 5’& 3’ molecular orientation due to nucleotide asymmetry. They are often single stranded (typically RNA). They may be extremely long. Movie*Movie* Two polymers (or strands) may become double stranded when certain conditions are met ie they are antiparallel & complementary in nucleotide sequence (typically nuclear DNA). * Terao et al., 2008: Lab on a chip DOI: /b803753a

19 Duplex DNA is Antiparallel Duplex DNA is NEVER Parallel! 5’Phosphate 3’OH 5’Phosphate or 5’ 3’ 5’ or

20 Duplex DNA has Complementarity because of Hydrogen Bonds H bonds are weak (~1/20 th of a covalent bond): –Often allows transient contact between molecules (biological signalling systems). –May allow stable contact that can be disrupted and reformed (eg DNA).

21 Hydrogen Bonds Form between O &/or N with H between them eg O-H … O, N … H-N or O-H … N. Are due to electrostatic forces. H is slightly +ve. O &/or N are slightly -ve. Are very weak compared to covalent bonds May be broken & reform under various chemical or physical conditions.

22 Two representations of duplex DNA showing: H bonds between bases and, Covalently bonded Sugar Phosphate backbones. ~10 basepairs per turn of the helix. Duplex DNA width = 2nm.

23 Double Stranded (or Duplex) DNA Is characteristic of genomic DNA. Consists of two separate nucleic acid polymers (“strands”). The two strands are Antiparallel wrt 5’& 3’ ends. They are held together by Hydrogen Bonds between the bases. H-Bond energies are weak BUT there are many of them which makes the duplex DNA very stable. Bases are Complementary such that: – A always pairs with T (2 H Bonds). – C always pairs with G (3 H Bonds). Two strands of complementary antiparallel DNA form a Double Helix eg as found in a chromosome.

24 History of The Double Helix of DNA The structure of the double helix was found by Rosalind Franklin using X-ray crystallography and correctly interpreted by Watson & Crick in 1953 who also used Chargaff’s rule. The bases are Hydrophobic and are in the Centre of the helix where complementary bases pair via H-bonding. The Ribose Sugar and Phosphate groups are on the Outside of the helix where they can H bond to polar solvents like water.

25 Xray diffraction pattern of DNA similar to Franklin’s data (above, 1953). Watson & Crick’s structure for DNA Key data that Watson & Crick worked with Chargaff’s Rule: there is a 1:1 ratio of purines to pyrimidines (because A=T, G  C always).