Nucleotides

· Nucleotides are the monomers of nucleic acids: DNA and RNA.
· Each nucleotide contains a pentose sugar, a phosphate group and a nitrogenous base.
· In DNA, the sugar is deoxyribose.
· In RNA, the sugar is ribose.
· ATP is a phosphorylated nucleotide: adenine + ribose + three phosphate groups.
· Structural formulae are not expected, but you must know the components and how they relate to nucleic acid structure.

ATP is a phosphorylated nucleotide made from adenine, ribose and three phosphate groups. It is structurally related to nucleotides used to build nucleic acids. Source

Purines and pyrimidines

· DNA and RNA bases are divided into purines and pyrimidines.
· Purines have a double-ring structure: adenine (A) and guanine (G).
· Pyrimidines have a single-ring structure: cytosine (C), thymine (T) and uracil (U).
· Thymine occurs in DNA; uracil occurs in RNA.
· Structural formulae for bases are not expected, but ring type and base names are exam-relevant.

DNA structure

· DNA is a double helix made of two polynucleotide strands.
· Each strand has a sugar-phosphate backbone with bases projecting inwards.
· Nucleotides in one strand are linked by phosphodiester bonds.
· The two strands are antiparallel: one runs 5′ to 3′, the other runs 3′ to 5′.
· Bases pair by complementary base pairing: A pairs with T, C pairs with G.
· A–T base pairs form 2 hydrogen bonds.
· C–G base pairs form 3 hydrogen bonds, making them slightly more stable.
· Complementary base pairing allows DNA to be replicated accurately.

This diagram shows the double helix, the sugar-phosphate backbone and complementary base pairing. Use it to link A–T and C–G pairing with hydrogen bonding and antiparallel strand arrangement. Source

DNA replication: semi-conservative replication

· DNA replication occurs during the S phase of the cell cycle.
· Replication is semi-conservative: each new DNA molecule contains one original parental strand and one newly synthesised strand.
· The two parental strands separate and act as templates for new complementary strands.
· Free nucleotides align by complementary base pairing.
· DNA polymerase joins new nucleotides together by forming phosphodiester bonds.
· DNA polymerase can only add nucleotides in the 5′ to 3′ direction.
· This directional limitation causes different replication patterns on the two strands.

Leading and lagging strands

· The leading strand is synthesised continuously in the 5′ to 3′ direction.
· The lagging strand is synthesised discontinuously in short sections because DNA polymerase still works only 5′ to 3′.
· Short sections on the lagging strand are joined together by DNA ligase.
· DNA ligase forms phosphodiester bonds between DNA fragments.
· Exam focus: explain the difference between leading and lagging strand replication as a consequence of antiparallel DNA and 5′ to 3′ DNA polymerase activity.
· Knowledge of other replication enzymes or different types of DNA polymerase is not expected.

This diagram shows why leading strand synthesis is continuous while lagging strand synthesis occurs in fragments. It helps explain why DNA polymerase adding nucleotides only 5′ to 3′ creates different replication patterns. Source

RNA structure using mRNA as an example

· RNA is usually single-stranded.
· mRNA is a type of RNA involved in carrying genetic information for protein synthesis.
· RNA nucleotides contain ribose sugar, phosphate and one nitrogenous base.
· RNA contains uracil (U) instead of thymine (T).
· RNA bases include adenine (A), guanine (G), cytosine (C) and uracil (U).
· In exam answers, compare RNA with DNA using: single-stranded vs double-stranded, ribose vs deoxyribose, and uracil vs thymine.

This diagram shows mRNA as a single-stranded RNA molecule. For CIE 6.1, use it mainly to remember that RNA contains ribose, phosphate and bases including uracil. Source

Common exam wording to use

· Complementary base pairing means A pairs with T and C pairs with G in DNA.
· DNA strands are antiparallel, so one strand runs 5′ to 3′ and the other runs 3′ to 5′.
· Phosphodiester bonds join nucleotides within a strand.
· Hydrogen bonds join complementary bases between strands.
· Semi-conservative replication produces two DNA molecules, each with one parental strand and one newly synthesised strand.
· DNA polymerase synthesises new DNA only in the 5′ to 3′ direction.
· DNA ligase joins fragments of DNA on the lagging strand.