Biochemistry: Nucleic Acid Components

• Biochemistry 214, Theme C Nucleic Acids, Lecture 1 Nucleic Acid Components

Key Concepts

• Deoxyribonucleic acids (DNA) are linear polymers of four nucleotides: adenine, guanine, cytosine and thymine.
• Ribonucleic acids (RNA) are linear polymers of four nucleotides: adenine, guanine, cytosine and uracil.
• Nucleotides can also serve as coenzymes, co-substrates and as regulatory molecules.

Outcomes

• Key concepts: ribonucleic acid (RNA), deoxyribonucleic acid (DNA), N-base, purine, pyrimidine, phosphodiester bond, tautomer, nucleoside, nucleotide

Nucleic Acids Introduction

• In 1944, Oswald Avery, Colin MacLeod & Maclyn McCarty found that DNA from pathogenic Pneumococcus strains transferred into non-pathogenic strains making them pathogenic.
• In 1952, Hershey and Chase showed that DNA transferred from a virus to a bacterium contains sufficient information to direct synthesis of new virus.
• DNA was determined to be the genetic substance as a result of this experiment.
• Rosalind Franklin and Maurice Wilkins used X-ray diffraction studies on stretched DNA.
• This showed that DNA could only possess a helical structure.
• The cross structure indicated a helical structure, and strong spots at top and bottom indicated a helical rise of 0.34 nm = 3.4 Å.
• In 1953 Watson and Crick proposed the double-helical model of DNA structure.
• Watson, Crick & Wilkins won the Nobel prize for this Model.
• Meselson and Stahl discovered semiconservative replication in 1958.

Nucleic acids DNA and RNA

• Deoxyribonucleic acid (DNA) is a linear polymer of nucleotides which consists of sugar, nitrogen base, and phosphoric acid.
• Includes the purines adenine and guanine, and the pyrimidines thymine and cytosine.
• Ribonucleic acid (RNA) is a linear polymer of nucleotides which consists of sugar, nitrogen base, and phosphoric acid.
• Includes the purines adenine and guanine, and the pyrimidines uracil and cytosine.
• Sugar unit contains Deoxyribose or ribose.
• RNA contains D-ribose.
• DNA 2-deoxy-D-ribose.
• Nitrogen bases (N-bases) have a pyrimidine-imidazole ring structure.
• Unsaturated and unsubstituted bases seldom occur naturally

Nitrogen Bases

• Purines such as adenine and guanine are present in DNA and RNA
• Pyrimidines Cytosine, present in DNA and RNA
• Pyrimidines Thymine occurs only in DNA
• Pyrimidines Uracil only occurs in RNA
• Nucleoside is made of a sugar and N-base
• B-N-glycosidic bond is formed between C'-1 (ribose or deoxyribose) and N-1 (pyrimidine) or N-9 (purine).
• Adenine + ribose = adenosine
• Adenine + deoxyribose = deoxyadenosine
• Guanine + ribose = guanosine
• Guanine + deoxyribose = deoxyguanosine
• Cytosine + ribose = cytidine
• Cytosine + deoxyribose = deoxycytidine
• Uracil + ribose = uridine(only in RNA)
• Thymine + deoxyribose = deoxythymidine(only in DNA)
• Nucleotide = nucleoside + phosphate.

RNA Monomeric Moieties

• Adenine + adenosine and adenosine 5'-monophosphate form adenine
• Guanine + guanosine and guanosine 5'-monophosphate from guanine
• Cytosine + cytidine and cytidine 5'-monophosphate form cytosine
• Uracil + uridine and uridine 5'-monophosphate form uracil

DNA Monomeric Moieties

• Adenine + deoxyadenosine and deoxyadenosine 5'-monophosphate form adenine
• Guanine + deoxyguanosine and deoxyguanosine 5'-monophosphate form guanine.
• Cytosine + deoxycytidine and deoxycytidine 5'-monophosphate form cytosine
• Thymine + deoxythymidine and deoxythymidine 5'-monophosphate form thymine

Nucleotide Functions

• dNTPs and NTPs: building blocks for DNA and RNA synthesis.
• DNA and RNA are polymers of monomeric dNMP and NMP units.
• Regulatory molecules (messengers) in their cyclic form e.g.
• 3', 5'-cyclic AMP (cAMP forms from ATP).
• 3', 5'- cyclic GMP (cGMP forms from GMP).
• Several nucleotides are coenzymes and co-substrates in metabolism.
• ATP - adenosine triphosphate is the carrier of "chemical energy" in cells (activated phosphate).
• Amino and keto are the most common tautomerization of N-bases
• Imino and enol are less common tautomerization of N-bases
• N-bases and phosphate groups of nucleotides are weak acids and dissociate at pH 7.4
• Nucleotide properties have buffering properties due to their phosphate groups (weak acids) and N-bases (weak bases).
• The properties of nucleotides include weak bases and resonance structures

Resonance Structures

• Double bond character
• Absorb UV light
• Amphipathic with tendency to be more hydrophobic
• Relatively insoluble
• Functional groups form H-bonds
• Nucleotides complex with Mg2+.
• At physiological pH, nucleotides possess negatively charged phosphate groups.
• Nucleotides form complexes with Mg2+
• ATP is mostly complexed with Mg2+
• Nucleotides absorb UV light (also RNA & DNA) – purine and pyrimidine resonance structures.
• Absorption maximum is ~260 nm.
• Conjugated double bonds determine concentration with spectrophotometer
• Formation of phosphodiester linkages requires energy to supply NTPs and dNTPs.
• This involves the Hydrolysis of pyrophosphate (PPi).
• Stability and formation of phosphodiester linkages are kinetically stable but thermodynamically unstable.
• Acid conditions break down DNA and RNA
• Enzymes (nucleases) split phosphodiester bonds.