Directional Structure of Nucleic Acids
Directional Structure of Nucleic Acids
- DNA molecules are made up of two polynucleotide strands lying side by side, running in opposite directions; the strands are said to be antiparallel
- Each DNA polynucleotide strand..
- is made up of alternating deoxyribose sugars and phosphate groups bonded together to form the sugar-phosphate backbone
- is said to have a 3’ (3 prime) end and a 5’ (5 prime) end
- These numbers relate to which carbon atom on the pentose sugar could be bonded with another nucleotide
- Because the strands are antiparallel, one is known as the 5’ to 3’ strand and the other is known as the 3’ to 5’ strand
- The nitrogenous bases of each nucleotide project out from the backbone toward the interior of the double-stranded DNA molecule
- This gives the strand of DNA its directionality:
- The nitrogenous base is always attached to carbon number 1
- Carbon number 3 has a hydroxyl group (-OH) that can form bonds to adjacent nucleotides
- The phosphate group always attached to carbon number 5
Diagram of nucleotides joined together in a strand
A single DNA polynucleotide strand showing 3 nucleotides in a sequence
How Nucleotide Structure Affects DNA Synthesis
- During DNA and RNA synthesis, the 3' and 5' ends of each nucleotide determine the direction in which new nucleotides are added to the growing strand
- The enzyme that catalyzes DNA replication
- DNA polymerase can build the new strand in only one direction (5’ to 3’ direction)
- This is due to enzyme specificity and the way that the substrate and enzyme fit together
- So one strand is synthesized continuously
- But the other strand has to be synthesized in short sections and joined together
- This is a direct consequence of the directionality of nucleotides and their polymers DNA and RNA
- Replication is dealt with in detail in Topic 6.2
Complementary Base Pairing
- The 2 antiparallel DNA polynucleotide strands that make up the DNA molecule are held together by hydrogen bonds between the nitrogenous bases
- These hydrogen bonds always occur between the same pairs of bases:
- The purine adenine (A) always pairs with the pyrimidine thymine (T) – 2 hydrogen bonds are formed between these bases
- The purine guanine (G) always pairs with the pyrimidine cytosine (C) – 3 hydrogen bonds are formed between these bases
- This is known as complementary base pairing
Base Pairing in DNA Diagram
Base pairing in DNA; A—T linked by 2 hydrogen bonds; C—G linked by 3 hydrogen bonds
The Double Helix
- DNA is not two-dimensional as shown in the diagram above
- DNA is described as a double helix
- This refers to the three-dimensional shape that DNA molecules form
DNA Base Pairing and the Double Helix Diagram
The classical double helix shape of a DNA molecule
Exam Tip
Make sure you can name the different components of a DNA molecule (sugar-phosphate backbone, nucleotide, complementary base pairs, hydrogen bonds), and make sure you are able to locate these on a diagram.
Remember that covalent bonds join the nucleotides in the sugar-phosphate backbone, and hydrogen bonds join the bases of the 2 complementary strands together.
Remember that the bases are complementary, so the number of A = T and C = G. You could be asked to determine how many bases are present in a DNA molecule if given the number of just one of the bases.