DNA, Genes and Protein Synthesis

Deoxyribonucleic acid (DNA) carries the genetic instructions for the development, functioning, and reproduction of all known living organisms. Understanding how DNA encodes information, how it replicates, and how that information is expressed as proteins — as well as how gene expression is regulated — is central to A-Level Biology.

Key Definition: A gene is a sequence of DNA nucleotides that codes for a functional polypeptide (or functional RNA molecule such as tRNA or rRNA).

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DNA Structure

The Double Helix

• DNA is a polymer of nucleotides. Each nucleotide consists of: a deoxyribose sugar, a phosphate group, and a nitrogenous base.
• The four bases are: adenine (A), thymine (T), cytosine (C), and guanine (G). Adenine and guanine are purines (double-ring structures); cytosine and thymine are pyrimidines (single-ring structures).
• Two polynucleotide strands run antiparallel (one 5'→3', the other 3'→5') and are held together by hydrogen bonds between complementary base pairs: A=T (two H-bonds) and C≡G (three H-bonds).
• The sugar-phosphate backbone provides structural stability via phosphodiester bonds between the 3' carbon of one sugar and the 5' carbon of the next.
• The double helix is approximately 2 nm in diameter, with one full turn every 10 base pairs (3.4 nm).

Key Definition: Complementary base pairing is the specific pairing of bases in DNA (A with T, C with G) or between DNA and RNA (A with U, C with G), held together by hydrogen bonds.

A diagram of DNA structure would show two parallel strands twisting around each other in a right-handed helix. The outer "rails" represent the sugar-phosphate backbone, with alternating deoxyribose sugars and phosphate groups. The "rungs" of the ladder are the base pairs — shorter rungs represent pyrimidine-purine pairs. The strands run in opposite directions (antiparallel), with 5' and 3' labels at each end.

DNA vs RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose (has an extra –OH on C2)
Bases	A, T, C, G	A, U, C, G
Structure	Double-stranded helix	Usually single-stranded (can fold into secondary structures)
Location	Nucleus (+ mitochondria, chloroplasts)	Nucleus and cytoplasm
Function	Stores genetic information permanently	mRNA (carries code), tRNA (carries amino acids), rRNA (forms ribosomes)
Stability	Very stable (deoxyribose + double strand)	Less stable (ribose more reactive; single strand more susceptible to hydrolysis)

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DNA Replication

DNA replication is semi-conservative — each new molecule consists of one original (parental) strand and one newly synthesised strand. This was demonstrated by the Meselson–Stahl experiment (1958) using heavy nitrogen (¹⁵N) and density gradient centrifugation.

Steps of Replication

1. Helicase unwinds the double helix and breaks hydrogen bonds between base pairs, creating a replication fork. The separated strands are stabilised by single-strand binding proteins.
2. Each exposed strand acts as a template for the synthesis of a new complementary strand.
3. Primase synthesises a short RNA primer complementary to the template strand. This primer provides a free 3'–OH group for DNA polymerase to begin adding nucleotides (DNA polymerase cannot initiate synthesis de novo — it can only extend an existing strand).
4. DNA polymerase III adds complementary free DNA nucleotides to each template strand in the 5'→3' direction only.
5. The leading strand (running 3'→5' as a template) is synthesised continuously in the same direction as the replication fork.
6. The lagging strand (running 5'→3' as a template) is synthesised discontinuously in short sections called Okazaki fragments (each requires its own RNA primer).
7. DNA polymerase I removes the RNA primers and replaces them with DNA nucleotides.
8. DNA ligase joins the Okazaki fragments together by forming phosphodiester bonds between adjacent nucleotides, creating a continuous strand.
9. Two identical DNA molecules result, each consisting of one parental strand and one new strand.

flowchart TD
    A["Helicase unwinds double helix
& breaks H-bonds → replication fork"] --> B["Primase adds RNA primers
to template strands"]
    B --> C["DNA Polymerase III
adds nucleotides 5’→3’"]
    C --> D["Leading strand:
synthesised continuously"]
    C --> E["Lagging strand:
synthesised as Okazaki fragments"]
    D --> F["DNA Polymerase I
removes RNA primers,
replaces with DNA"]
    E --> F
    F --> G["DNA Ligase joins
Okazaki fragments"]
    G --> H["Two identical DNA molecules
(each = 1 parental + 1 new strand)"]

Exam Tip: A common exam question asks why DNA replication is described as "semi-conservative". The answer must include: each new DNA molecule contains one original (conserved) strand and one newly synthesised strand. Reference to the Meselson–Stahl experiment will gain additional marks if requested.

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Genes and the Genetic Code

• A gene is a sequence of DNA nucleotides that codes for a functional polypeptide (or functional RNA).
• The genetic code is read in triplets (codons) — each codon of three bases specifies one amino acid.

Properties of the Genetic Code

Property	Meaning
Degenerate (redundant)	Most amino acids are coded for by more than one codon (e.g., leucine has 6 codons). This provides some protection against the effects of point mutations.
Non-overlapping	Each base is part of only one codon; the code is read in a fixed reading frame
Universal	The same codons code for the same amino acids in almost all organisms (evidence for a common ancestor)
Start codon	AUG (methionine) — signals the beginning of translation
Stop codons	UAA, UAG, UGA — signal the end of translation; they do not code for amino acids

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Transcription

Key Definition: Transcription is the process by which a complementary mRNA copy is synthesised from a DNA template strand, catalysed by RNA polymerase.

Transcription occurs in the nucleus and produces a messenger RNA (mRNA) copy of a gene.

1. RNA polymerase binds to the promoter region upstream of the gene. Transcription factors must first bind to the promoter to enable RNA polymerase to attach (see Gene Expression Regulation below).
2. The enzyme unwinds a short section of DNA, separating the two strands. It reads the template strand (also called the antisense strand) in the 3'→5' direction.
3. Free RNA nucleotides are added complementary to the template strand (A→U, T→A, C→G, G→C), building the mRNA in the 5'→3' direction.
4. In eukaryotes, the initial transcript (pre-mRNA) undergoes post-transcriptional modification (processing):
   • Splicing — removal of introns (non-coding sequences) and joining of exons (coding sequences) by spliceosomes.
   • Addition of a 5' cap (a modified guanine nucleotide) — protects the mRNA from degradation by exonucleases, and is recognised by the ribosome to initiate translation.
   • Addition of a 3' poly-A tail (a chain of 100–200 adenine nucleotides) — protects the mRNA from degradation, aids export from the nucleus through nuclear pores, and assists ribosome attachment.
   • Alternative splicing — different combinations of exons can be joined together, allowing a single gene to code for multiple different polypeptides. This increases the proteome diversity beyond the number of genes.
5. Mature mRNA exits the nucleus through nuclear pores and travels to a ribosome in the cytoplasm.

flowchart TD
    A["DNA in nucleus
(template strand)"] -->|"Transcription
RNA polymerase reads 3’→5’"| B["Pre-mRNA
(primary transcript)"]
    B -->|"Post-transcriptional modification"| C["Splicing: introns removed,
exons joined"]
    C --> D["5’ cap + 3’ poly-A tail added"]
    D --> E["Mature mRNA"]
    E -->|"Exits nucleus
through nuclear pores"| F["mRNA at ribosome
in cytoplasm"]
    F -->|"Translation"| G["tRNA brings amino acids
Anticodon pairs with codon"]
    G --> H["Peptide bonds form
between amino acids"]
    H --> I["Polypeptide released
at stop codon"]
    I --> J["Protein folds into
functional 3D shape"]