Nucleotides And Nucleic Acids¶

Part of Module 2: Foundations in biology.

This topic explains how biological information is stored, copied, and expressed. The logic runs in a tight sequence: nucleotides are assembled into nucleic acids, DNA stores genetic information in a form that can be replicated accurately, and transcription plus translation decode that information into proteins. ATP sits alongside this as a related but functionally distinct nucleotide derivative — the immediate energy currency of the cell.

Learning Objectives¶

Nucleotide Structure¶

Nucleotides are the monomer units of nucleic acids. Every nucleotide has three components:

1. A pentose sugar (a five-carbon sugar)
2. A nitrogenous base (containing carbon and nitrogen)
3. A phosphate group

Two pentose sugars appear in biology: - Deoxyribose — found in DNA nucleotides (missing an oxygen on carbon 2, hence "deoxy") - Ribose — found in RNA nucleotides and in ATP

Nucleotides join by condensation reactions: the phosphate group of one nucleotide forms a covalent bond with the sugar of the next, releasing water. This bond is called a phosphodiester bond, and the result is a chain of alternating sugars and phosphates — the sugar-phosphate backbone — with bases projecting inward. Phosphodiester bonds can be broken by hydrolysis, releasing the nucleotide monomers.

DNA Structure¶

Bases and Complementary Pairing¶

DNA nucleotides carry one of four nitrogenous bases: adenine (A), guanine (G), thymine (T), and cytosine (C).

Bases are grouped into two structural categories: - Purines (two fused carbon rings): adenine and guanine - Pyrimidines (one carbon ring): thymine and cytosine

In the double helix, a purine always pairs with a pyrimidine. This maintains a constant width between the two sugar-phosphate backbones. The specific pairings are: - A–T: linked by 2 hydrogen bonds - G–C: linked by 3 hydrogen bonds

This specificity — each base pairing with only one other — is called complementary base pairing, and it is fundamental to both replication and transcription.

The Double Helix¶

Watson and Crick, building on X-ray diffraction data from Rosalind Franklin and others, determined in 1953 that DNA consists of two polynucleotide strands wound around each other in a double helix. The two strands run antiparallel — one runs 5' to 3' in one direction, and the complementary strand runs 3' to 5' in the opposite direction.

Structural features of DNA and their functional significance:

DNA in Chromosomes¶

DNA molecules are extremely long and must be tightly packaged. In eukaryotic cells, DNA wraps around proteins called histones to form DNA-histone complexes. These coil further to form chromatin, which is condensed into chromosomes during cell division. Each chromosome contains a single continuous molecule of DNA. A gene is a short section of DNA at a specific location (its locus) on a chromosome, coding for a polypeptide. The complete set of genes in an organism is the genome; the full range of proteins a cell can produce is the proteome.

RNA Structure¶

RNA (ribonucleic acid) differs from DNA in several ways:

Uracil (U) pairs with adenine in the same way thymine does — this is important for both transcription and translation.

Three Types of RNA¶

mRNA (messenger RNA): - Single-stranded, linear molecule - Contains a base sequence complementary to one strand of DNA - Carries the genetic code from the nucleus to the ribosome - Contains codons (sets of three consecutive bases, each coding for an amino acid or a stop signal) - Small enough to exit the nucleus through nuclear pores

tRNA (transfer RNA): - Single-stranded but folded into a characteristic clover-leaf shape, held by hydrogen bonds between complementary base pairs within the molecule - Contains an anticodon — a specific triplet of bases at one end that recognises and base-pairs with a codon on mRNA - Has an amino acid binding site at the opposite end (the 3' CCA tail), to which the specific amino acid is attached - There are at least 20 types of tRNA, one for each amino acid

rRNA (ribosomal RNA): - Structural and catalytic component of ribosomes - Combines with ribosomal proteins to form the large and small ribosomal subunits - Forms part of the ribosome's active site for peptide bond formation

DNA Replication¶

Semi-Conservative Replication¶

DNA is copied by semi-conservative replication: each new DNA molecule consists of one original (parental) strand and one newly synthesised strand. This means the sequence is perfectly conserved in both daughter molecules.

Step-by-step process:

1. The enzyme DNA helicase travels along the DNA and breaks the hydrogen bonds between complementary base pairs. This unwinds and separates the two strands, creating a replication fork.
2. Each separated strand acts as a template for a new complementary strand.
3. Free DNA nucleotides align opposite the template bases by complementary base pairing (A with T, G with C).
4. The enzyme DNA polymerase catalyses the formation of phosphodiester bonds between adjacent nucleotides, building the new strand in the 5' to 3' direction.
5. Two identical DNA double helices are produced, each with one original strand and one new strand.

The Meselson-Stahl Experiment¶

Before semi-conservative replication was accepted, two models were proposed: conservative replication (original molecule stays intact; completely new copy built) and semi-conservative replication (strands separate; each acts as template).

Meselson and Stahl (1958) resolved this using nitrogen isotopes: - Bacteria were grown on ¹⁵N (heavy nitrogen) medium until all DNA contained only heavy nitrogen. - The bacteria were transferred to ¹⁴N (light nitrogen) medium for one round of replication. - DNA was extracted and centrifuged in a density gradient.

After one replication: all DNA appeared at an intermediate density — one heavy strand (¹⁵N) and one light strand (¹⁴N) in every molecule. This ruled out conservative replication, which would have produced one heavy band and one light band.

After two replications: half the DNA was intermediate density (one ¹⁵N strand + one ¹⁴N strand) and half was light (both strands ¹⁴N). This confirmed semi-conservative replication.

The Genetic Code¶

Features of the Genetic Code¶

The genetic code translates base sequences into amino acid sequences. Its features are:

• Triplet: each amino acid is encoded by a sequence of three consecutive DNA bases (a triplet), read as a codon on mRNA. With four bases, three at a time gives 64 possible combinations — more than enough to code for 20 amino acids.
• Non-overlapping: each base is read only once. In the sequence CGTATC, it is read as CGT then ATC, not as CGT, GTA, TAT, and ATC.
• Degenerate: most amino acids are coded for by more than one codon (e.g. both ACA and ACG code for threonine). This redundancy provides some protection against mutation.
• Universal: with minor exceptions, the same codons specify the same amino acids in virtually all organisms, from bacteria to humans. This is evidence for the common ancestry of life.

Start and Stop Codons¶

Start codon: AUG (methionine) — marks where translation begins on the mRNA. All polypeptides begin with methionine (which is often later removed).

Stop codons: UAA, UAG, UGA — do not code for any amino acid; they signal the ribosome to terminate translation and release the polypeptide.

Reading Codon Tables¶

The genetic code is usually presented as a table of mRNA codons (using U in place of T). For example, phenylalanine is coded by UUU and UUC; leucine by UUA, UUG, CUU, CUC, CUA, and CUG. The degeneracy of the code means the third base position often varies without changing the amino acid specified.

mRNA and tRNA in Detail¶

mRNA Structure¶

mRNA is synthesised during transcription and carries the genetic code from the DNA in the nucleus to the ribosomes in the cytoplasm. Key structural features: - Linear, single-stranded polynucleotide - Contains codons: triplets of bases read by the ribosome during translation - Has a 5' end (where the ribosome first binds) and a 3' end - The start codon AUG is near the 5' end; stop codons mark the 3' end of the coding sequence

tRNA Structure¶

Each tRNA molecule is specific for one amino acid. Its clover-leaf secondary structure arises from intramolecular hydrogen bonding. The key functional features are: - Anticodon loop: contains the three-base anticodon, which base-pairs with the complementary mRNA codon at the ribosome - Amino acid attachment site: the 3' end carries the specific amino acid, attached by an aminoacyl-tRNA synthetase enzyme

Transcription¶

Transcription is the first step in gene expression. It occurs in the nucleus of eukaryotic cells.

Key events:

1. RNA polymerase binds to the DNA at the start of the gene.
2. Hydrogen bonds between the DNA base pairs break, and the double helix unwinds and separates at that region.
3. The antisense strand (also called the template strand) acts as the template. Free RNA nucleotides align opposite it by complementary base pairing.
4. In RNA: uracil (U) pairs with adenine (A) on the template; all other pairings are identical to DNA.
5. RNA polymerase catalyses the formation of phosphodiester bonds between adjacent RNA nucleotides, building the mRNA in the 5' to 3' direction.
6. The mRNA strand produced has the same base sequence as the sense strand (coding strand) of the DNA, except T is replaced by U.
7. Transcription ends when RNA polymerase reaches a stop codon sequence. The RNA polymerase detaches, the mRNA strand is released, and the DNA rewinds into its double helix.
8. The mRNA molecule exits the nucleus through nuclear pores and moves to the cytoplasm for translation.

Translation¶

Translation occurs in the cytoplasm on ribosomes, in both eukaryotic and prokaryotic cells.

Key events:

1. The ribosome attaches to the mRNA strand at the start codon (AUG).
2. A tRNA molecule with the anticodon UAC (complementary to AUG) arrives, carrying methionine. This tRNA occupies the ribosome's P site.
3. A second tRNA molecule, whose anticodon is complementary to the second mRNA codon, arrives carrying its specific amino acid. It occupies the A site.
4. A peptide bond forms between the two amino acids, catalysed by rRNA in the ribosome (using ATP). The first tRNA detaches from its amino acid and leaves the ribosome to collect another amino acid.
5. The ribosome moves along the mRNA by one codon in the 5' to 3' direction (translocation). The second tRNA moves to the P site; the A site is now free for the next tRNA.
6. Steps 3–5 repeat, progressively elongating the polypeptide chain. At any given moment, two tRNA molecules occupy the ribosome simultaneously.
7. Translation terminates when the ribosome reaches a stop codon (UAA, UAG, or UGA). No tRNA recognises stop codons. The completed polypeptide chain is released and folds into its functional three-dimensional shape.

ATP: The Energy Currency of the Cell¶

Structure¶

ATP (adenosine triphosphate) is a nucleotide derivative — it has a similar structure to the monomers of DNA and RNA. It consists of: - Adenine (nitrogenous base) - Ribose (5-carbon pentose sugar) - Three phosphate groups linked in series

The bonds between the phosphate groups are relatively unstable and have a low activation energy, making them easy to break and reform rapidly.

ATP Hydrolysis and Re-synthesis¶

Hydrolysis (releasing energy):

ATP + H₂O → ADP + Pᵢ + energy

Catalysed by ATP hydrolase. The terminal phosphate group is cleaved from ATP, producing adenosine diphosphate (ADP) and inorganic phosphate (Pᵢ). This reaction releases energy that can drive cellular processes.

Re-synthesis (storing energy):

ADP + Pᵢ + energy → ATP + H₂O

Catalysed by ATP synthase. This condensation reaction uses energy from respiration (in mitochondria) or photosynthesis (in chloroplasts) to regenerate ATP. ATP therefore works as a cycle: it is constantly broken down and reformed, not consumed once.

Why ATP Is an Effective Energy Currency¶

ATP is well suited for immediate energy transfer rather than long-term storage. Its key properties:

• Small, manageable energy release: hydrolysis releases a small, controlled amount of energy — less energy is wasted as heat compared with oxidising glucose in a single step.
• Single-step reaction: energy is released in one step, rapidly.
• Rapidly re-synthesised: ATP is constantly regenerated, so it is always immediately available.
• Phosphorylation of other molecules: the released phosphate group can be transferred to other molecules (enzymes, substrates), making them more reactive — a process called phosphorylation.
• Soluble: ATP dissolves in the cytoplasm and can be easily transported to sites of energy need within the cell.
• Universal: ATP is used by virtually all organisms, making it a common cross-topic currency.

Uses of ATP in Cells¶

• Movement: muscle contraction; flagella and cilia beating; movement of chromosomes on the spindle
• Active transport: moving ions and molecules against concentration gradients across membranes
• Biosynthesis: building large molecules including DNA, RNA, polysaccharides, and proteins
• Secretion: packaging and releasing substances from cells (e.g. hormones from glands)
• Signalling: phosphorylation of enzymes and signal molecules to activate them

Protein Synthesis: The Complete Picture¶

Transcription and translation are the two steps of gene expression — the process of decoding a DNA sequence into a functional protein. They connect directly to 2.1.1 Cell structure: transcription occurs in the nucleus; mRNA moves through nuclear pores into the cytoplasm; translation occurs on ribosomes (free or on rough ER); and proteins destined for secretion pass through the Golgi pathway.

The final amino acid sequence produced by translation is the primary structure of the protein. This then folds into secondary, tertiary, and quaternary structures (covered in 2.1.2 Biological molecules) to produce a functional molecule.

Common Confusions¶

• DNA replication is not transcription. Replication copies the entire DNA double helix using DNA polymerase and produces two identical DNA molecules. Transcription copies one gene into a single-stranded mRNA using RNA polymerase. They share the need to separate the strands, but they produce completely different products for completely different purposes.
• tRNA anticodons pair with mRNA codons, not with DNA. During translation, tRNA interacts only with mRNA. The anticodon–codon interaction is between two RNA molecules on the ribosome.
• ATP is not a long-term energy store. Glucose (and later fats) provide long-term storage. ATP provides an immediate, small-scale, recyclable source of energy. Its value lies in being continuously regenerated, not in storing large amounts of energy.
• The degenerate code means redundancy, not ambiguity. One codon always codes for the same amino acid. Multiple codons can code for the same amino acid, but a single codon never codes for more than one amino acid.
• mRNA codons are not the same as DNA triplets. The mRNA codon sequence corresponds to the sense (coding) strand of DNA, with U replacing T. The template (antisense) strand is complementary and antiparallel to the mRNA.
• All polypeptides begin with methionine (because AUG is the start codon), even if the final protein does not have methionine at its N-terminus (it may be cleaved post-translationally).

Practical Skills¶

• DNA precipitation: DNA can be purified and precipitated by adding cold ethanol to a cell lysate. The white precipitate visible is DNA.
• This topic connects tightly to 2.1.1 Cell structure because the nucleus, ribosomes, rough ER, Golgi apparatus, and vesicles are all components of the information-to-protein system.
• Understanding the Meselson-Stahl experiment trains skills in experimental design and interpretation: recognising what a control is, how density-gradient centrifugation works conceptually, and what the intermediate band demonstrates.

Key Terms¶

• Nucleotide: a molecule made from a pentose sugar, a phosphate group, and a nitrogenous base; the monomer of nucleic acids.
• Deoxyribose: the five-carbon sugar in DNA nucleotides, lacking the oxygen on carbon 2.
• Ribose: the five-carbon sugar in RNA nucleotides and ATP.
• Phosphodiester bond: the covalent bond linking the phosphate of one nucleotide to the sugar of the next in a polynucleotide chain.
• Sugar-phosphate backbone: the alternating chain of sugars and phosphates that forms the structural framework of a polynucleotide.
• Purine: a nitrogenous base with two fused carbon rings; adenine and guanine.
• Pyrimidine: a nitrogenous base with one carbon ring; thymine, cytosine, and uracil.
• Complementary base pairing: the specific pairing of bases (A–T or A–U; G–C) via hydrogen bonds in nucleic acids.
• Double helix: the two antiparallel, complementary polynucleotide strands of DNA wound around each other.
• Antiparallel: the two DNA strands run in opposite directions (one 5'→3', the other 3'→5').
• Histone: a protein around which DNA is wound in eukaryotic cells.
• Gene: a section of DNA at a specific locus on a chromosome, coding for one polypeptide.
• Genome: the complete set of genes in an organism.
• Semi-conservative replication: DNA replication in which each new molecule contains one original strand and one newly synthesised strand.
• DNA helicase: the enzyme that unwinds and separates the DNA strands by breaking hydrogen bonds during replication.
• DNA polymerase: the enzyme that builds new DNA strands by joining nucleotides via phosphodiester bonds, working 5' to 3'.
• Triplet: a sequence of three consecutive DNA bases coding for one amino acid.
• Codon: a triplet of bases on mRNA that specifies a particular amino acid or stop signal.
• Anticodon: the triplet of bases on tRNA that base-pairs with a complementary codon on mRNA.
• Start codon: AUG — the codon where translation begins; codes for methionine.
• Stop codon: UAA, UAG, or UGA — signals the ribosome to terminate translation.
• RNA polymerase: the enzyme that synthesises mRNA from the DNA template during transcription.
• Antisense strand: the DNA template strand read by RNA polymerase during transcription (complementary to the mRNA).
• Sense strand: the DNA strand with the same sequence as the mRNA (except T in place of U).
• Transcription: synthesis of a single-stranded mRNA molecule from a DNA template, occurring in the nucleus.
• Translation: synthesis of a polypeptide chain by decoding the codon sequence on mRNA at the ribosome.
• ATP (adenosine triphosphate): a phosphorylated nucleotide derivative; the immediate energy currency of cells.
• ADP (adenosine diphosphate): the product of ATP hydrolysis; combines with inorganic phosphate to regenerate ATP.
• ATP hydrolase: the enzyme that catalyses the hydrolysis of ATP to ADP and inorganic phosphate.
• ATP synthase: the enzyme that catalyses the re-synthesis of ATP from ADP and inorganic phosphate.
• Phosphorylation: the transfer of a phosphate group (from ATP hydrolysis) to another molecule, often making it more reactive.

Connected Pages¶

• 2.1.1 Cell structure
• 2.1.2 Biological molecules
• 2.1.4 Enzymes