DNA structure and protein synthesis (HT)

Higher-tier students need a much more detailed picture of DNA — down to the level of nucleotides, base pairing and how proteins are actually built from a gene.

Nucleotides — the building blocks

DNA is a polymer of repeating units called nucleotides. Each nucleotide has three parts:

1. A deoxyribose sugar.
2. A phosphate group.
3. One of four bases — adenine A, thymine (T), cytosine C or guanine (G).

The sugar of one nucleotide bonds to the phosphate of the next, forming a long sugar–phosphate backbone with bases sticking off it.

Two strands and complementary base pairing

DNA is double-stranded. The two strands run anti-parallel and are held together by hydrogen bonds between the bases.

The pairing is complementary:

• A pairs with T
• C pairs with G

So if one strand reads 5'-ATCGGT-3', the other reads 3'-TAGCCA-5'. This is the rule that lets DNA be copied accurately during replication and lets RNA be made from a DNA template.

The genetic code

Each amino acid is coded for by a triplet of bases (a codon) — a sequence of three bases. With 4 bases, there are 4³ = 64 possible codons, more than enough for the 20 amino acids. Some amino acids have several codons (the code is degenerate), and three codons act as stop signals to end the protein.

Protein synthesis — the two stages

A gene is in the nucleus, but protein synthesis happens at ribosomes in the cytoplasm. So the cell uses an intermediate molecule, mRNA (messenger RNA).

Stage 1 — Transcription (in the nucleus)

1. The DNA double helix unwinds at the gene to be expressed.
2. Free RNA nucleotides pair up with the exposed bases on the template strand. (RNA uses uracil (U) instead of T, so an A on DNA pairs with U on RNA.)
3. The mRNA strand is built — a complementary copy of the gene.
4. The mRNA leaves the nucleus through a nuclear pore.

Stage 2 — Translation (at the ribosome)

1. The mRNA attaches to a ribosome.
2. The ribosome reads the mRNA in codons (3 bases at a time).
3. Each codon is matched by a tRNA (transfer RNA) carrying the correct amino acid.
4. Amino acids are joined in order to form the protein chain.
5. When a stop codon is reached, the ribosome releases the finished protein.

The protein then folds into its specific 3D shape, determined by the order of amino acids — and that shape is what gives the protein its function (e.g. enzyme active site).

Mutations and their effects

A mutation is a change in the base sequence of DNA. There are three classes:

1. Insertion — a base is added.
2. Deletion — a base is lost.
3. Substitution — one base is replaced by another.

Frame-shift mutations. Insertions and deletions shift the reading frame — every codon downstream changes, so the resulting protein is usually non-functional.

Substitutions can be:

• Silent — the new codon codes for the same amino acid (degenerate code).
• Missense — different amino acid; the protein may still work, partly work, or fail.
• Nonsense — creates a stop codon early; the protein is truncated and usually non-functional.

The more vital the protein and the bigger the structural change, the more serious the effect.

Non-coding DNA

Most DNA is non-coding — but it's not "junk". Non-coding regions can switch genes on and off (regulation), affect how DNA is packaged, and play roles in evolution.

Links

Built on B6.2 (introduction to DNA, genes and the genome). Connects to B6.5 (variation from mutation) and B6.7 (how genetic engineering inserts new genes that are then transcribed and translated).