6.1 Structure of Nucleic Acids and DNA Replication

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.

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.

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 a double helix made from two polynucleotide strands. Each strand has a deoxyribose–phosphate backbone on the outside, while the nitrogenous bases face inward and pair by complementarity.

• Backbone and direction: Covalent phosphodiester bonds link deoxyribose sugars and phosphate groups along each strand. The two strands run antiparallel: one is 5′→3′ while the other is 3′→5′.
• A–T comparison: Adenine (A), a purine, pairs with thymine (T), a pyrimidine, using two hydrogen bonds.
• C–G comparison: Cytosine (C), a pyrimidine, pairs with guanine (G), a purine, using three hydrogen bonds.
• Shared consequence: Each pair combines one purine with one pyrimidine, helping maintain a regular distance between the backbones. Hydrogen bonds hold the strands together but can be separated during replication; phosphodiester bonds keep each individual backbone intact.

The outward-facing sugar–phosphate backbones provide continuous covalent support, while inward-facing complementary bases hold the two strands together through hydrogen bonds. Antiparallel direction and specific pairing mean that the sequence on one strand determines the complementary sequence on the other, giving DNA both stability and a usable template for copying.

Hydrogen bonds join complementary bases across the two strands; phosphodiester bonds join adjacent nucleotides within one backbone. The strands are antiparallel, not parallel. The A–T and C–G comparison is a bond-and-pairing aid, not a complete replication mechanism; replication details belong to card 4574. Staff-only visual brief retained in the Topic Blueprint: show two antiparallel backbones, inward bases, bond types and 2-vs-3 hydrogen-bond contrast; no image is generated here.

Semi-conservative DNA replication produces two DNA molecules from one original molecule. Each product contains one original template strand and one newly synthesised complementary strand.

1. Separate the templates: Hydrogen bonds between complementary bases break, so the double helix opens and the two original antiparallel strands are exposed. Each original strand remains intact and acts as a template.
2. Match free nucleotides: Free DNA nucleotides align with exposed template bases by complementary pairing: A with T and C with G. This selects the sequence of each new strand.
3. Extend new strands: DNA polymerase joins adjacent nucleotides by forming phosphodiester bonds. It can extend a new strand only in the 5′→3′ direction, so the two templates are copied differently.
4. Account for leading and lagging synthesis: The leading strand is made continuously in the direction of the replication fork. The lagging strand is made as short Okazaki fragments because polymerase still works only 5′→3′; DNA ligase joins the fragments into a continuous strand.
5. Check the outcome: The original molecule has become two DNA molecules, each with one old strand and one new complementary strand: each product = 1 original strand + 1 new strand.

Complementary base pairing copies the information, while the fixed 5′→3′ direction of DNA polymerase explains why one new strand is continuous and the other is assembled in fragments. Ligase completes the lagging-strand backbone; the semi-conservative result follows because each original strand is retained as a template in one product.

Semi-conservative means that each complete DNA product keeps one whole original strand; it does not mean random pieces of old DNA are mixed into both strands. Hydrogen bonds open between the templates, whereas phosphodiester bonds form the new backbones. Staff-only visual brief retained in the Topic Blueprint: show one replication fork, antiparallel templates, continuous leading synthesis, Okazaki fragments and ligase joining; no image is generated here.

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.