Nucleic acids DNA and RNA Done By Majed

Nucleic acids: DNA and RNA Done By Majed Felemban 1

DNA • Double helix – 2 chains • Building blocks – Nucleotides • DNA directs – Is own replication – Directs RNA synthesis → protein synthesis Campbell and Reece, P 86 2

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

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. 4

Replication Transcription Translation 5

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, P 86, 87 6

Roles of Nucleic Acids • RNA – – – Information transmission (m. RNA) Processing and transport (t. RNA, r. RNA, sn. RNA) Catalytic (ribozymes) Regulation and feedback (si. RNA) Unit of inheritance (retroviruses) Other…? Campbell and Reece, P 86, 87 7

NUCLEIC ACID STRUCTURES • Nucleic Acid chemistry is the same for all life on earth. • DNA & RNA are polymers of monomers - nucleotides. • Each nucleotide has three components X (Deoxy)ribonucleic Acid X 1. PHOSPHORIC ACID = STRUCTURAL 2. (DEOXY)RIBOSE SUGAR = STRUCTURAL 3. NITROGENOUS BASES = INFORMATIONAL Campbell and Reece, 86 8

Campbell and Reece, P 87 9

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

Phosphoric Acid & Related Compounds As found in DNA & RNA at p. H 7 • Phosphoric acid is Triprotic. • Reacts with alcohols to form esters. 11

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

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

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

When Phosphate is Bound to a Nucleoside it is Called a Nucleotide • ATP, GTP, CTP, UTP (NTPs) are substrates for RNA synthesis • d. ATP, d. GTP, d. CTP, d. TTP (d. NTPs) are substrates for DNA synthesis 15

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

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

Properties of DNA and RNA • They may be informational eg genomic DNA, m. RNA. • They may be structural eg r. RNA & t. RNA. • Retain 5’& 3’ molecular orientation due to nucleotide asymmetry. • They are often single stranded (typically RNA). • They may be extremely long. 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: 10. 1039/b 803753 a 18

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

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). 20

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. 21

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 = 2 nm. 22

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. 23

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. 24

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