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8.3.2The Control of Gene Expression (A Level only)

Determining Protein Sequences — AQA A Level Biology 7402 Revision Notes & Topical Questions

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📚 AQA A Level Biology 7402 Hub / Topical Revision
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8.3.2 Determining Protein Sequences — AQA A Level Biology 7402 notes: Explain how the base sequence of a gene allows the amino acid sequence of a protein to be predicted, and the limitations of doing so.Genes contain the code for the primary structure (amino acid sequence) of pol…

  • transcribed
  • translated
  • Alternative splicing
  • Post-translational modification
  • Non-coding regions
  • Environment and regulation

Section 1 of 9From DNA to protein

Genes contain the code for the primary structure (amino acid sequence) of polypeptides.

Transcribed
In protein synthesis, the DNA sequence of a gene is transcribed into mRNA, and the mRNA is translated at a ribosome, where each triplet of bases (codon) specifies an amino acid brought by a tRNA.
The relationship is determined by the genetic code, which is almost universal.
If the sequence of a gene is known, the amino acid sequence of its protein can therefore be predicted using a table of the genetic code, and the predicted protein can be compared with databases.

Section 2 of 9Predicting the amino acid sequence

1
Find the gene in the sequenced genome. Computer programs look for start codons (ATG, coding for methionine), stop codons (TAA, TAG, TGA) and the typical signal sequences, such as promoters.
2Exons
Identify the exons (coding sequences) and introns (non-coding regions removed from pre-mRNA by splicing) in eukaryotic genes. Only the exons are translated.
3
Write the mRNA sequence from the template strand (using complementary base pairing, with uracil for thymine).
4
Divide it into codons from the start codon, and use the genetic code table to find the amino acids.

Worked example

  • the template strand 3' TAC GGT CTT ACT 5' gives mRNA AUG CCA GAA UGA - methionine, proline, glutamic acid, then stop.
  • The coding strand has the same sequence as the mRNA except T replaces U.

Section 3 of 9Why the prediction may be incomplete

Why the prediction may be incomplete
Alternative splicing
Alternative splicing different combinations of exons can be joined to give different mRNAs from the same gene, so one gene can code for several proteins. The proteome is therefore larger than the number of genes.
Post-translational modification
Post-translational modification proteins are often altered after synthesis: sugar groups added (glycoproteins), polypeptides cut or joined (e.g. insulin, haemoglobin), phosphates added, and folded into a quaternary structure.
Non-coding regions
Non-coding regions it is hard to be certain which sequences are genes; introns must be removed.
Environment and regulation
Environment and regulation the sequence does not show when and where the protein is made.
Tertiary structure
The three-dimensional tertiary structure is predicted from the amino acid sequence only with software, not with certainty, and protein function may need experimental confirmation.

Section 4 of 9Direct methods and applications

Proteins can also be analysed directly, for example by mass spectrometry, to find the amino acid sequence of peptides and detect modifications, and by X-ray crystallography to determine structure. The proteome of a cell varies with tissue and conditions, so proteomics data complement genomics.

Applications of predicting proteins from genomes include: finding the antigens of pathogens for vaccines; understanding how mutations change proteins (8.1.2) and cause disease; designing drugs that fit the active site of an enzyme; producing recombinant proteins by inserting the gene into bacteria (for example insulin); and comparing the sequences of proteins among species, which shows evolutionary relationships. A cytochrome c with few differences in amino acid sequence suggests a recent common ancestor.

LevelInformation given
GenomeAll the DNA, including all possible genes
TranscriptomemRNA molecules present in a cell at a time
ProteomeThe proteins actually present

Section 5 of 9Exam technique

When asked to find the amino acid sequence, check which strand is given (template or coding), write the mRNA carefully with U, split into triplets from the start codon and use the table provided.

Exam technique
When asked why a gene may code for several proteins, mention alternative splicing and modification after translation.
A mutation question (8.1.2) may ask what happens to the predicted sequence if a base is deleted: all codons after the deletion change (frameshift).
Link with genome sequencing (8.3.1) and non-coding DNA (8.3.3).

Section 6 of 9Using protein sequences to compare species

The sequence of a protein such as cytochrome c or haemoglobin can be compared between species, either directly or by predicting it from DNA.

1
Changes in the DNA accumulate by mutation over time, so the number of amino acid differences between two species increases with the time since they diverged from a common ancestor.
2
A table showing that humans and chimpanzees have identical cytochrome c, whereas humans and yeast differ in many positions, suggests that humans and chimpanzees share a much more recent common ancestor.
3
Differences in DNA are often greater than those in protein sequence because of the degeneracy of the code: many base changes are silent.
4
This is why comparing DNA gives more detail, particularly between closely related species.

Section 7 of 9Exam-style questions

  1. The coding strand of part of a gene reads ATG GAT TTC. Give the sequence of the mRNA and state what the first amino acid is. [2]2 marks

  2. Explain why it may not be possible to predict the exact structure of a protein from the sequence of the gene alone. [3]3 marks

  3. A section of a gene contains an intron. Explain why the intron does not affect the amino acid sequence of the protein. [2]2 marks

Section 8 of 9Key terms

TermMeaning
Primary structureThe sequence of amino acids in a polypeptide.
CodonA triplet of mRNA bases that codes for an amino acid or a stop signal.
ExonA coding sequence in a gene that is found in mature mRNA.
IntronA non-coding sequence in a gene removed from pre-mRNA.
Alternative splicingJoining of exons in different combinations to form different mRNAs.
Post-translational modificationChemical changes to a protein after translation.
TranscriptomeAll the mRNA molecules in a cell at a given time.

Section 9 of 9Exam technique

1
Translating the DNA template strand directly without converting to mRNA.
2
Using T in mRNA instead of U.
3
Starting translation at the wrong place instead of at the start codon.
4
Assuming that the whole gene is translated, including the introns.
5
Forgetting that modifications after translation alter the protein.

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