Nucleotides and Nucleic Acids

What is the Principle of Macromolecular Organisation?
All macromolecules are constructed by polymerization of low molecular weight units, all of similar structure and all joined by covalent bonds.

Concept 1: biopolymers are formed from monomeric units.

• proteins = amino acids
  
• nucleic acids = nucleotides

Concept 2: macromolecules have different orders of structure.

• primary = sequence of monomers
• secondary = local folding of primary structure
• tertiary = 3D-folding of the macromolecule

What are the functions of nucleotides?

• genetic material, information transfer
• hormone action, information transfer
• structural components of ribosomes
• catalysts = ribozymes
• metabolism
  energy transfer
  coenzymes and vitamins

• Nucleotide = base -- sugar -- phosphate, all three covalently linked to each other
  
• Nucleoside = base -- sugar, covalently linked by a glycosidic bond

• bases = purines and pyrimidines (see Chemistry lecture)

• purines = adenine (A) and guanine (G)
• pyrimidines = cytosine (C), uracil (U), thymine (T)

Which are found in DNA and which in RNA?

• DNA contains A, G, C and T
• RNA contains A, G, C and U

• caffeine -- coffee,
• theophylline -- tea

• ribose and deoxyribose

• RNA = ribonucleic acid
• DNA = deoxyribonucleic acid

• nucleoside = base - sugar
• nucleotide = base - sugar - phosphate

• beta-N-glycosidic bond
• covalent bonds involving carbohydrates are glycosidic bonds or glycosidic links
• the base - sugar covalent bond in a nucleoside or nucleotide is an N-glycosidic link because it involves the N of the purine or pyrimidine ring
• it is a beta-glycosidic link because it projects above the plane of the carbohydrate ring (see Chemistry lecture)

Other nucleosides:

• cordycepin, an adenosine analog, an antibiotic, inhibits RNA synthesis
• cytosine arabinoside, a cytidine analog, an anti-cancer drug, inhibits DNA synthesis

How many phosphate groups are commonly found in nucleotides?

• either 1, 2, or 3
• base-sugar-phosphate, nucleoside monophosphate, eg AMP, adenosine monophosphate
• base-sugar-phosphate-phosphate, nucleoside diphosphate, eg ADP, adenosine diphosphate
• base-sugar-phosphate-phosphate-phosphate, nucleoside triphosphate, eg ATP, adenosine triphosphate

• this is the bond between an alcohol on the ribose ring and an acid, phosphate, which is an ester bond.

• this is the bond between two phosphoric acids, which is an anhydride bond.

• components of vitamins and coenzymes such as thiamine (vitamin B1), riboflavin (vitamin B2).
• high chemical bond energy in the anhydride is used to drive metabolism (principally ATP).
• monomeric building blocks of nucleic acids.
• signal transduction: 3'-5' cyclic AMP is an intracellular hormone that is produced in response to extracellular hormones such as glucagon or epinephrine (adrenalin).

What is the evidence that DNA is the genetic material?

• 1869: nucleic acid isolated from bacteria and yeast by Hoppe-Seyler's lab. Rich in 5 of the 6 abundant elements of the biosphere, CHONP, but no S.
• 1944: Avery, MacLeod and McCarty showed nucleic acid (DNA) = genetic material. DNA extracted from pathogenic Diplococcus pneumoniae transformed a non-pathogenic strain into a virulent one.
• 1952: Hershey and Chase showed that DNA is the genetic material in bacterial viruses or bacteriophages. They grew 'phage in radioactive S35 to label proteins (there is no S in DNA!) and in radioactive P32 to label DNA. Upon infection of the bacterium E.coli the S35 remained outside while the 32P was found inside the bacterium. Removal of the S35-labelled proteins from the culture did not prevent the production of new 'phage.

What is the structure of DNA?
How are the nucleotides linked together in nucleic acids?
What is the basic structure of DNA?

• by 1950: DNA structure is a linear polymer of deoxy-nucleotides linked by phosphodiester covalent bonds between the 5 and 3 C of adjacent deoxyribose rings. It has a density consistent with more than one chain.
• by 1950: Chargaff: purines (A+G) = pyrimidines (C+T) and A=T, G=C.
• 1953: Franklin and Wilkins: first good X-ray diffraction studies of DNA fibers indicated a helical structure.

• Watson, Crick and Wilkins

insights:
bases are H-bond donars and acceptors.
two complementary strands produces a feature required of genetic code: each strand may serve as a template for synthesis of the other, a requirement for semi-conservative replication.

• bases are H-bond donars and acceptors, purine to pyrimidine. This was based on Chargaff's rules and model building to figure out the rules meant hydrogen bonded base pairs.
• X-ray diffraction pattern that of a helix, density indicates two strands.

From their article published in the journal Nature:

"We wish to suggest a structure for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest.

"The novel feature of the structure is the manner in which the two chains are held together by the purine and pyrimidine bases.....a single base from one chain being hydrogen-bonded to a single base from the other chain.......one of the pair must be a purine and the other a pyrimidine........only specific pairs of bases can bond together.

"These pairs are adenine (purine) with thymine (pyrimidine), and guanine (purine) with cytosine (pyrimidine).

"In other words, if an adenine forms one member of a pair, on either chain, then on these assumptions the other member must be thymine; similarly for guanine and cytosine.

"......it follows that if the sequence of bases on one chain is given, then the sequence of bases on the other chain is automatically determined.

"It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material."

J. D. Watson and F. H. C. Crick
Nature 171, 737-738, 1953

What are the key features of the Watson-Crick model?

1. two anti-parallel chains in a double helix (polarity 5-->3 in one and 3-->5 in the other)
2. complementary strands (base sequence read 5-->3 in one strand complements base sequence read 3-->5 in the other strand)
3. complementarity due to specific H-bonds (A with T has 2 bonds, G with C has 3 bonds)
4. held together by non-covalent bonds (H-bonding A=T and G=C between anti-parallel chains and by base stacking interactions)
5. bases inside = more hydrophobic environment
6. sugar phosphates outside = hydrophillic environment

What is the Principle of Macromolecular Structure applied to DNA?

• Nucleic acids are constructed by polymerization of five different monomers
  • Concept 1:
    biopolymers are formed from monomeric units covalently linked together: for nucleic acids these are nucleotides
  • Concept 2:
    macromolecules have different orders of structure.
    primary structure = sequence of nucleotides
    secondary structure = double helix

• Tertiary structure is supercoiled DNA. It is stabilized by nuclear proteins such as histones, which allow DNA to pack into a tightly coiled and dense chromosome.

• Hint: What is the charge on the phosphodiester backbone of DNA?
  Negative.
• Therefore histones will have a net positive charge to neutralize the negative charge on the phosphodiester backbone of the DNA.

Remember: Principle of Macromolecular Organization

• Primary structure= sequence of monomeric units (nucleotides)
• Secondary structure = double helix
• Tertiary structure = supercoiled

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Bich 107 lecture notes on Nucleic Acids were last updated 09/19/05

Comments to Martyn Gunn