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6.1 Structure of Nucleic Acids and DNA Replication

Syllabus
9700–2028–2029
Topic
6.1
Level
AS

Learning objectives

6.1.1Nucleotide structure• Nucleotide structure, including phosphorylated nucleotide ATP6.1.2Purines (adenine, guanine)• Purines (adenine, guanine): double ring structure6.1.3Pyrimidines (cytosine, thymine, uracil)• Pyrimidines (cytosine, thymine, uracil): single ring structure6.1.4DNA double helix structure• DNA double helix structure:- Complementary base pairing between antiparallel strands (5′ to 3′ and 3′ to 5′)- Hydrogen bonding differences: C-G vs A-T- Phosphodiester bonds linking nucleotides6.1.5Semi-conservative DNA replication• Semi-conservative DNA replication during S phase:- Roles of DNA polymerase and DNA ligase- Leading strand vs lagging strand replication- DNA polymerase adds nucleotides only in 5′ to 3′ direction6.1.6RNA (mRNA) structure• RNA (mRNA) structure

A nucleotide is a phosphate, pentose sugar and nitrogenous base

A nucleotide is one building block of a nucleic acid. It contains three components: a pentose sugar, a phosphate group and a nitrogenous base. Many nucleotides can join to form a polynucleotide such as DNA or RNA.

  • Pentose sugar: DNA nucleotides contain deoxyribose; RNA nucleotides contain ribose. The sugar identity helps distinguish which nucleic-acid context the nucleotide belongs to.
  • Phosphate group: The phosphate contributes to the sugar–phosphate backbone when nucleotides join in a nucleic-acid strand. It is one component of a nucleotide, not a whole nucleic acid.
  • Nitrogenous base: The base is classified as a purine (adenine or guanine, double-ring) or a pyrimidine (cytosine, thymine or uracil, single-ring). The classification names the base structure; it does not replace the sugar or phosphate components.
  • ATP boundary: ATP is a phosphorylated nucleotide: adenine and ribose are attached to three phosphate groups. Its phosphate groups make it suitable for energy transfer in cell processes, but ATP is not a DNA or RNA strand and is not itself a nucleic acid.

The three-part structure supports two different biological roles: repeated sugar–phosphate connections allow nucleotides to build a nucleic-acid chain, while the attached bases provide the base identities used in sequence and pairing rules. ATP uses a nucleotide-like structure with additional phosphate groups for energy transfer, so “nucleotide” is a component-level description rather than a synonym for DNA, RNA or ATP.

A nitrogenous base alone is not a nucleotide, and a nucleotide is not the same as a nucleic-acid polymer. Purine/pyrimidine describes the base; deoxyribose/ribose describes the sugar. ATP is a phosphorylated nucleotide with an energy-transfer role, not a DNA/RNA building strand.

Purines have two rings; adenine and guanine are purines

A purine is a nitrogenous base with a fused double-ring structure. In the nucleic acids studied here, the two purines are adenine (A) and guanine (G).

  • Where they occur: Adenine and guanine can be the nitrogenous base in nucleotides that contribute to both DNA and RNA. The sugar and phosphate are the other nucleotide components; the base name alone is not a complete nucleotide.
  • How the class is used: In a DNA or RNA sequence, A and G identify purine bases. Their complementary partners are pyrimidines: A pairs with T in DNA or U in RNA, while G pairs with C.
  • Necessary contrast: Pyrimidines have a single-ring structure. The pyrimidines in this course are cytosine (C), thymine (T) and uracil (U). Purine/pyrimidine is a structural classification, not a synonym for a whole nucleotide or a rule that names the partner without checking the actual base.

The double-ring feature lets a learner classify A and G from the base category, while the surrounding sugar/phosphate context determines whether that base is part of a DNA or RNA nucleotide. Complementary pairing then uses the actual base identity, with one purine pairing with one pyrimidine to maintain the regular width of a nucleic-acid strand pair.

Purine does not mean “the whole nucleotide” and does not mean “a base that can be identified only by its partner”. Learn the two purines directly: adenine and guanine. Do not treat thymine as an RNA purine or uracil as a DNA purine.

Pyrimidines have one ring and differ between DNA and RNA

A pyrimidine is a nitrogenous base with a single-ring structure. The pyrimidines in this course are cytosine (C), thymine (T) and uracil (U).

  • Cytosine: C is used in both DNA and RNA nucleotides.
  • Thymine: T is the pyrimidine used in DNA; it pairs with adenine in DNA.
  • Uracil: U replaces T in RNA; it can pair with adenine in an RNA sequence.
  • Pairing boundary: C pairs with the purine G in both DNA and RNA. A purine–pyrimidine pair maintains the regular spacing across a paired nucleic-acid strand. The ring classification describes the base, not the complete nucleotide.

The DNA/RNA context determines which pyrimidine is present: DNA uses T, whereas RNA uses U, while C is shared. Therefore the same base category can support different nucleic-acid sequences, but a sequence must be read with its molecule type known before assigning the complementary partner.

Uracil is not an additional DNA base in this course, and thymine is not the usual RNA pyrimidine. Pyrimidine means a single-ring nitrogenous base; it does not mean a whole nucleotide or automatically identify the sugar and phosphate attached to it.

DNA is an antiparallel double helix held by complementary pairs

DNA is a double helix made from two polynucleotide strands. Each has a deoxyribose-phosphate backbone outside, while bases face inward and pair complementarily.

  • Phosphodiester bonds covalently link adjacent deoxyribose sugars and phosphates along each strand.
  • The strands are antiparallel: one runs 5-prime to 3-prime and the other 3-prime to 5-prime.
  • Adenine pairs with thymine using two hydrogen bonds.
  • Cytosine pairs with guanine using three hydrogen bonds.
  • Each pair contains one purine and one pyrimidine, helping maintain regular spacing between the backbones.

Continuous covalent backbones support each strand, while hydrogen bonds between inward-facing complementary bases hold the strands together. Antiparallel direction and pairing mean one strand's sequence determines the other's complementary sequence.

Hydrogen bonds join bases across strands; phosphodiester bonds join nucleotides within one strand. The strands are antiparallel, not parallel, and A-T has two hydrogen bonds while C-G has three.

Semi-conservative replication keeps one original strand per product

During S phase, semi-conservative DNA replication produces two DNA molecules from one original. Each product contains one original template strand and one newly synthesised complementary strand.

  1. Hydrogen bonds between complementary bases break and the two original antiparallel strands separate; each acts as a template.
  2. Free DNA nucleotides align by complementary pairing: A with T and C with G.
  3. DNA polymerase forms phosphodiester bonds while adding nucleotides only in the 5-prime-to-3-prime direction.
  4. The leading strand is synthesised continuously towards the replication fork. The lagging strand is synthesised as Okazaki fragments because polymerase still works only 5-prime to 3-prime.
  5. DNA ligase joins the lagging-strand fragments into a continuous backbone. The result is two molecules, each with one original and one new strand.

Complementary pairing copies the sequence, while polymerase direction explains continuous leading and discontinuous lagging synthesis. Ligase completes the lagging backbone; retaining each original template creates the semi-conservative outcome.

Semi-conservative means each complete product keeps one whole original strand, not random old fragments in both strands. Hydrogen bonds separate the templates, while phosphodiester bonds form the new backbones; other replication enzymes are not required here.

mRNA carries a copied sequence from DNA to a ribosome

RNA is a nucleic acid made from nucleotides and is typically a single polynucleotide strand. Messenger RNA (mRNA) is an RNA transcript copy of a gene that carries information from DNA to a ribosome.

  • Sugar: DNA nucleotides contain deoxyribose; RNA nucleotides contain ribose.
  • Bases: DNA uses adenine, thymine, cytosine and guanine (A, T, C, G). RNA uses adenine, uracil, cytosine and guanine (A, U, C, G); U replaces T in RNA.
  • Strands: DNA is typically a double-stranded antiparallel helix. RNA molecules are typically single-stranded, so an RNA molecule is not automatically a second DNA-like helix.
  • Stability and role: DNA is relatively stable and suited to retaining genetic information. mRNA is a more temporary, mobile transcript that can be read by a ribosome; this lets information be used without moving the DNA molecule.
  • Shared structure: Both are polynucleotides with sugar–phosphate backbones joined by phosphodiester bonds and nitrogenous bases projecting from the backbone.

The sugar and base differences distinguish the two nucleic acids, while strand arrangement supports their typical roles: DNA provides a stable information store, whereas a single-stranded mRNA copy can carry a selected sequence to a ribosome. “Typically” matters—RNA structure is not being defined as an absolute rule that every RNA molecule must be single-stranded or equally short-lived.

mRNA is not DNA with thymine: it contains ribose and uracil. A DNA coding strand and its mRNA transcript can have a related sequence, but the RNA uses U where DNA uses T. This card establishes RNA structure and mRNA’s transcript role; detailed transcription/translation steps belong to the next protein-synthesis topic.