DNA and protein synthesis

In a nutshell

Protein synthesis is how the base sequence of a gene is turned into the amino acid sequence of a polypeptide. It happens in two stages: transcription (a copy of the gene is made as mRNA) and translation (the mRNA is read to build the polypeptide).

This subtopic covers what mRNA and tRNA look like, how each stage works (and how it differs in prokaryotes and eukaryotes), and how you read a base sequence off against the genetic code to get the amino acids.

Assumed knowledge: DNA and RNA structure, DNA, genes and chromosomes (triplets, exons and introns, the code being degenerate).

Core content

The genome and the proteome

• The genome is the complete set of genes in a cell.
• The proteome is the full range of proteins that a cell is able to produce.

The word different matters: the proteome is the range of different proteins the genome can code for, not a count of protein molecules. "Number of proteins" on its own is not credited.

The proteome is larger and more changeable than you might expect, because one genome can produce many proteins (for example, splicing the same gene in different ways), and which proteins a cell actually makes changes with its conditions.

The structure of mRNA and tRNA

Both are single-stranded RNA polynucleotides, but their shapes suit different jobs.

Messenger RNA (mRNA) is a single-stranded, straight (linear) chain that is a copy of a gene. It is read in codons, each codon being a sequence of three bases that codes for one amino acid. mRNA has no base pairing and no hydrogen bonds within it.

Transfer RNA (tRNA) is a single strand folded into a clover-leaf shape, held in that shape by hydrogen bonds between paired bases in the folded regions. It has two functional ends:

• an anticodon: three bases at one end that are complementary to a codon on mRNA;
• an amino acid binding site at the other end, which carries one specific amino acid.

Transcription: making mRNA from DNA

Transcription is the production of mRNA from DNA. In eukaryotes it happens in the nucleus.

1. The hydrogen bonds between the two DNA strands break, so the strands separate and unwind. This exposes the bases of the template strand (only one strand is used as the template).
2. Free RNA nucleotides line up alongside the exposed template bases by complementary base pairing, so A pairs with U, T pairs with A, C pairs with G and G pairs with C. (RNA has uracil (U) in place of thymine.)
3. RNA polymerase joins the RNA nucleotides together by forming phosphodiester bonds, building the new strand.

The key point examiners want: RNA polymerase joins the nucleotides together; it does not cause the base pairing. The nucleotides base-pair with the template first, and RNA polymerase bonds those already-paired nucleotides into a strand.

Still don't get it? · what RNA polymerase actually does

Imagine building a wall against a row of pre-marked studs. The studs (the template strand) tell each brick exactly where it belongs, and the bricks settle into place against them on their own. All the bricklayer does is walk along and cement each brick to the one before it.

Now the exam version. The "studs" are the exposed bases on the DNA template strand. Each free RNA nucleotide finds its place by complementary base pairing against the template (A to U, and so on) all by itself. RNA polymerase is the bricklayer: it travels along and joins the nucleotides together with phosphodiester bonds to make the new strand.

So the mark-scheme sentence is "RNA polymerase joins the RNA nucleotides together", never "RNA polymerase makes the bases pair". Saying it causes the base pairing is the single most common way students lose this mark.

Prokaryotes vs eukaryotes. What happens next depends on the organism:

• In prokaryotes, transcription produces mRNA directly from the DNA.
• In eukaryotes, transcription first produces pre-mRNA. This is then spliced to form the mature mRNA.

Splicing (eukaryotes only)

A eukaryotic gene contains coding sequences (exons) separated by non-coding sequences (introns), so the pre-mRNA transcribed from it contains both.

• Splicing removes the introns from the pre-mRNA.
• The remaining exons are joined together to form the mature mRNA.

Only the mature mRNA leaves the nucleus (through a nuclear pore) to be translated. Prokaryotes have no introns in their genes, so their mRNA needs no splicing.

Translation: making a polypeptide from mRNA

Translation is the production of a polypeptide from the sequence of codons carried by the mRNA. It takes place at a ribosome in the cytoplasm and needs tRNA and ATP.

1. The mRNA associates with a ribosome. The ribosome holds two codons at a time.
2. A tRNA carrying a specific amino acid binds, so that its anticodon pairs with the complementary codon on the mRNA by complementary base pairing.
3. A second tRNA binds at the next codon. The two amino acids they carry are joined by a peptide bond, using energy from ATP.
4. The first tRNA leaves (to collect another copy of its amino acid), the ribosome moves along to the next codon, and the process repeats.
5. The polypeptide is built up amino acid by amino acid until the ribosome reaches a stop codon, when the finished polypeptide is released.

Because the order of codons on the mRNA sets the order the tRNAs line up, the base sequence of the mRNA determines the sequence of amino acids in the polypeptide.

Still don't get it? · codon, anticodon and the amino acid

Think of a parcel delivery. Each tRNA is a delivery van. Painted on the front of the van is an address code (the anticodon). Sitting in the back of the van is a parcel (the amino acid). The van can only stop at the slot on the road (the mRNA codon) whose address matches the code on its front.

Step by step: the mRNA is a row of numbered slots (codons). A tRNA van pulls in only where its front code (anticodon) is complementary to the slot (codon), so A pairs with U, and so on. The parcel it happens to be carrying is decided in advance: each tRNA is specific to one amino acid. Match the vans along the row in codon order, take the parcels out in that order, and you have the amino acids in the right sequence.

The exam wording: the anticodon (on tRNA) is complementary to the codon (on mRNA); the amino acid is carried at the other end and each tRNA is specific to one amino acid. Never write that the anticodon attaches to the amino acid, or that the codon is on the tRNA.

Reading the genetic code (data skill)

You are not asked to recall which codon codes for which amino acid, but you may be given a table of the code and asked to relate a base sequence to the amino acid sequence. Work in threes and keep track of which molecule you are on: DNA triplet, mRNA codon and tRNA anticodon are all complementary to each other (with U replacing T in the RNA). The worked example below shows the routine.

Worked examples

Reading a base sequence into amino acids.

You are given the template DNA strand TAC AAA GGT and this extract of the code (codons are read on the mRNA):

Work through it one step at a time:

1. Transcribe the template DNA to mRNA by complementary base pairing (A to U, T to A, G to C, C to G):
   • TAC → AUG
   • AAA → UUU
   • GGT → CCA
2. Read the mRNA codons against the table: AUG = Met, UUU = Phe, CCA = Pro.
3. Amino acid sequence: Met-Phe-Pro.

If you were instead asked for the tRNA anticodons, they are complementary to the mRNA codons: UAC, AAA, GGU (note these are the same base sequence as the original template DNA, but with U in place of T).

Model 5-mark answer: "Describe how a polypeptide is made during translation." (mRNA has already been made.)

1. The mRNA associates with a ribosome.
2. A tRNA with an anticodon complementary to the mRNA codon binds by complementary base pairing.
3. The tRNA brings a specific amino acid.
4. Amino acids on adjacent tRNAs join by a peptide bond, using ATP.
5. The ribosome moves along the mRNA to the next codon and the process repeats until a stop codon is reached.

Common exam mistakes

• Writing that RNA polymerase causes the base pairing. It does not: the nucleotides base-pair with the template on their own, and RNA polymerase joins them together (phosphodiester bonds). This is the most common lost mark in the whole topic.
• Confusing transcription with DNA replication. In replication both strands are templates and DNA polymerase is used; in transcription only one strand is the template and RNA polymerase is used to make mRNA (not a second DNA strand).
• Saying mRNA leaves the cell. Mature mRNA leaves the nucleus through a nuclear pore and stays in the cell, going to a ribosome in the cytoplasm.
• Saying mRNA (or a codon) "makes" or "produces" amino acids. The base sequence codes for the sequence of amino acids; the amino acids are brought in ready-made by tRNA.
• Describing the anticodon as attaching to the amino acid, or putting the codon on the tRNA. The anticodon is complementary to the codon on the mRNA; the amino acid is carried at the other end of the tRNA.
• Saying tRNA is three nucleotides long or double-stranded. Only the anticodon is three bases; the whole tRNA is a longer single strand folded into a clover-leaf with some paired bases.
• Vague splicing answers such as "mRNA is spliced" or "mRNA contains exons". State it fully: introns are removed from the pre-mRNA and the exons are joined to form mature mRNA.
• Saying the introns removed are made of DNA, or that prokaryotic/plant DNA "does not contain introns" as if that were the splicing answer. Splicing acts on pre-mRNA; introns removed from it are RNA.
• Forgetting to name the base pairing rule with uracil (A pairs with U, not T) when RNA is being made.

Key definitions

• Genome: the complete set of genes in a cell.
• Proteome: the full range of (different) proteins that a cell is able to produce.
• Transcription: the production of mRNA from DNA, in which RNA polymerase joins RNA nucleotides together using one DNA strand as a template.
• Translation: the production of a polypeptide from the sequence of codons carried by mRNA, at a ribosome.
• Codon: a sequence of three bases on mRNA that codes for a specific amino acid.
• Anticodon: a sequence of three bases on tRNA that is complementary to a codon on mRNA.
• Splicing: the removal of introns from pre-mRNA and the joining of the exons to form mature mRNA.

Specification

• I can state that the genome is the complete set of genes in a cell and that the proteome is the full range of proteins a cell is able to produce.
• I can describe the structure of mRNA and of tRNA, and contrast them.
• I can describe transcription as the production of mRNA from DNA, including the role of RNA polymerase in joining mRNA nucleotides.
• I can state that in prokaryotes transcription produces mRNA directly, whereas in eukaryotes it produces pre-mRNA that is then spliced to form mRNA.
• I can describe translation as the production of polypeptides from the codons on mRNA, and state the roles of ribosomes, tRNA and ATP.
• I can relate the base sequence of nucleic acids to the amino acid sequence of a polypeptide when given data about the genetic code.
• I can interpret data from experimental work investigating the role of nucleic acids.

Related notes

• DNA and RNA structure (nucleic acids)
• DNA, genes and chromosomes
• Proteins
• Genetic diversity can arise