DNA and protein synthesis — AQA A-Level Biology
Test yourself on DNA and protein synthesis with AQA A-Level practice questions.
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DNA and protein synthesis explained
The genome is the complete set of genes in a cell.
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It belongs to a specific cell or organism, not a species or population. Note that the genome is not simply 'all the DNA', as eukaryotic DNA includes significant non-coding regions outside of genes, such as multiple repeats. The proteome is the full range of proteins that a cell is able to produce. The two are linked but distinct. Every body cell of an organism carries the same genome, yet a liver cell and a muscle cell contain different proteins because different genes are expressed. In eukaryotes, the proteome is larger than the gene count because pre-mRNA from one gene can be alternatively spliced, and proteins can be modified after translation.
The structure of molecules of messenger RNA (mRNA) and of transfer RNA (tRNA).
Both are single-stranded polynucleotides built from RNA nucleotides: ribose, a phosphate group and one of adenine, uracil, cytosine or guanine, joined by phosphodiester bonds. mRNA is a long, linear molecule transcribed from one gene, so its length varies with the gene. It has no hydrogen bonding along its length, so its bases are exposed and can be read in threes as codons. It is short-lived, broken down after translation so that a protein is not made indefinitely. tRNA is far shorter, around eighty nucleotides, and folds back on itself. Hydrogen bonds between complementary bases within the same strand pull it into a clover-leaf shape, with one loop carrying three exposed bases called the anticodon and the opposite end carrying an amino acid binding site.
Transcription as the production of mRNA from DNA. The role of RNA polymerase in joining mRNA nucleotides.
Transcription produces mRNA from DNA. The DNA double helix unwinds and hydrogen bonds between complementary bases break. Only the template strand is copied. Free RNA nucleotides align opposite exposed bases: RNA uracil pairs with DNA adenine, adenine with thymine, cytosine with guanine, and guanine with cytosine. RNA polymerase catalyses phosphodiester bond formation between adjacent RNA nucleotides, building a single-stranded RNA molecule. In eukaryotes, this occurs in the nucleoplasm producing pre-mRNA, which is spliced. In prokaryotes, it occurs in the cytoplasm directly producing mRNA. The enzyme separates the strands as it moves, and DNA strands rejoin behind it. At a stop signal, RNA polymerase detaches and the RNA is released.
In prokaryotes, transcription results directly in the production of mRNA from DNA.
Prokaryotic genes are continuous because their DNA contains no introns. Therefore, transcription in a bacterium directly produces functional mRNA. There is no pre-mRNA stage and no splicing is required. Because prokaryotes lack a nuclear envelope, ribosomes can begin translating the mRNA while it is still being transcribed. The bacterial DNA is a circular molecule lying free in the cytoplasm, unassociated with histones. Bacteria are used in recombinant DNA technology to produce human proteins because the genetic code is universal, meaning the same codons specify the same amino acids across organisms. However, bacteria cannot splice pre-mRNA, so they fail to produce functional proteins if given unmodified eukaryotic genes containing introns.
In eukaryotes, transcription results in the production of pre- mRNA; this is then spliced to form mRNA.
A eukaryotic gene is split: coding sequences called exons are interrupted by non-coding sequences called introns. Transcription copies the whole gene, introns and exons alike, producing pre-mRNA. Before it can be translated, spliceosomes cut the pre-mRNA at the intron-exon boundaries, remove the introns and join the exons together, forming mature mRNA. This then leaves the nucleus through a nuclear pore and attaches to a ribosome. Splicing matters for two reasons. First, if the introns remained, the ribosome would read them in triplets and build a completely wrong polypeptide. Second, the exons from one pre-mRNA can be joined in different combinations, so a single gene can yield several different mRNAs and therefore several different polypeptides, which is part of the reason the proteome is larger than the genome.
Translation as the production of polypeptides from the sequence of codons carried by mRNA. The roles of ribosomes, tRNA and ATP.
Translation builds a polypeptide from the codons on mRNA. The mRNA binds to a ribosome, which holds two codons at a time. A tRNA whose anticodon is complementary to the first codon binds by hydrogen bonds, carrying one specific amino acid; a second tRNA binds at the adjacent codon. A peptide bond forms between the two amino acids, catalysed by the ribosome. The first tRNA detaches and is reused, and the ribosome moves along exactly three bases to the next codon. The cycle repeats until a stop codon is reached, when the completed polypeptide is released and folds into its tertiary structure. ATP is required to attach each amino acid to its tRNA (amino acid activation) and provides energy for the process; peptide bond formation is catalysed by the ribosome.
Students should be able to: relate the base sequence of nucleic acids to the amino acid sequence of polypeptides, when provided with suitable data about the genetic code interpret data from experimental work investigating the role of nucleic acids.
Questions require translating between DNA, mRNA, tRNA, and amino acid sequences using a provided table. Apply base pairing rules carefully: mRNA is complementary to the DNA template strand, but uses uracil (U) instead of thymine (T). For example, a DNA template triplet 'TAC' transcribes to an mRNA codon 'AUG'. The tRNA anticodon is complementary to the mRNA codon (e.g., 'UAC'). Always verify if the table lists mRNA codons or DNA triplets. Group bases into triplets from the correct reading frame; a frameshift alters the downstream polypeptide. When interpreting experimental data, like radioactive labelling of nucleic acids, identify the independent variable, cite specific data points, and link trends to protein synthesis mechanisms.
Your focus
- Define genome and proteome, naming the cell or organism as the unit in both.
- Explain why two cells from the same organism share a genome but have different proteomes.
- Explain why a eukaryotic cell can produce more different proteins than it has genes, using splicing of pre-mRNA.
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- Draw and label a tRNA molecule, marking the anticodon and the amino acid binding site.
- Give three differences between a DNA molecule and a tRNA molecule, writing both sides of each difference.
- Explain how the structure of tRNA allows a specific amino acid to be delivered to a specific mRNA codon.
- Describe transcription as an ordered sequence of steps.
- Write the mRNA base sequence produced from a given DNA template strand.
- Explain the role of RNA polymerase in joining mRNA nucleotides.
- Explain why a bacterium produces functional mRNA directly, referring to the absence of introns.
- Suggest why a bacterium given an unmodified human gene may fail to produce a functional protein.
- Distinguish 'the genetic code is universal' from 'the genetic code is degenerate' and state which explains bacterial expression of human genes.
- Recognise that while the genetic code is universal, the mechanisms of transcription and translation differ between prokaryotes and eukaryotes.
- Describe how pre-mRNA is converted into mature mRNA, naming introns, exons and splicing.
- Explain why a polypeptide translated from unspliced pre-mRNA would have the wrong amino acid sequence.
- Explain how alternative combinations of exons allow one gene to code for more than one polypeptide.
- Describe translation in sequence from mRNA binding to release of the completed polypeptide.
- Explain the specific role of the ribosome, of tRNA and of ATP in forming a polypeptide.
- Explain how a change to a tRNA anticodon alters the protein produced and its function.
- Convert a given DNA template sequence into mRNA codons and then into an amino acid sequence using a supplied table.
- Deduce the tRNA anticodons required to translate a given mRNA sequence.
- Interpret data from a labelling or cell-free experiment to state which nucleic acid carries out a stated role.
DNA and protein synthesis exam tips
Marking Points
- The genome is defined as the complete set of genes in a cell or organism.
- The proteome is defined as the full range of proteins that a cell is able to produce.
- The genome codes for the proteins of the proteome.
- Different cells in the same organism have different proteomes due to differential gene expression.
- one mark for both being single-stranded polynucleotides containing ribose and uracil, with phosphodiester bonds between nucleotides
- one mark for mRNA being linear with exposed bases read as triplets called codons, one mRNA carrying the code for one polypeptide
- one mark for tRNA being folded into a clover-leaf shape held by hydrogen bonds between complementary bases in the same strand
- one mark for tRNA having an anticodon of three exposed bases and a binding site that attaches a specific amino acid
- one mark for a stated comparison such as tRNA containing few nucleotides while mRNA contains many
- Hydrogen bonds between complementary DNA bases break, separating the strands and exposing the template.
- Only one DNA strand, the template strand, is transcribed; the other is the coding strand.
- Free RNA nucleotides align opposite exposed complementary bases: RNA uracil pairs with DNA adenine, RNA adenine with DNA thymine, RNA cytosine with DNA guanine, and RNA guanine with DNA cytosine.
- RNA polymerase catalyses the formation of phosphodiester bonds between adjacent RNA nucleotides, joining them into a single-stranded RNA molecule.
- The RNA molecule is released and the DNA strands rejoin behind the enzyme; in eukaryotes the product is pre-mRNA, which is spliced.
- Stating that prokaryotic DNA does not contain introns, meaning there is no pre-mRNA stage.
- Explaining that functional mRNA is produced directly from transcription without the need for splicing.
- Explaining that transcription and translation can occur simultaneously in the cytoplasm because there is no nuclear envelope.
- Explaining that a bacterium cannot splice pre-mRNA, so it cannot remove introns from an unmodified eukaryotic gene.
- Stating that the genetic code is universal, meaning the same codons code for the same amino acids in all organisms.
- Transcription produces pre-mRNA containing both introns and exons.
- Splicing removes the introns and joins the exons together.
- The mature mRNA leaves the nucleus through a nuclear pore and attaches to a ribosome.
- Bacteria have no spliceosomes, so they cannot splice pre-mRNA or remove introns.
- Different combinations of exons produce different mRNAs, and so different polypeptides, from one gene.
- mRNA binds to a ribosome and the bases are read in triplets as codons
- tRNA anticodons bind to complementary mRNA codons by hydrogen bonds, each tRNA carrying a specific amino acid
- peptide bonds form between adjacent amino acids, catalysed by the ribosome
- the ribosome moves along the mRNA to the next codon, with tRNA released and reused
- the process continues to a stop codon, after which the polypeptide folds into its tertiary structure
- ATP is used to attach each amino acid to its tRNA and provides energy for translation; peptide bond formation is catalysed by the ribosome
- Convert a DNA base sequence into the correct complementary mRNA sequence by substituting uracil in place of thymine.
- Group the bases into triplets from the correct starting point to establish the proper reading frame.
- Read the supplied table accurately, ensuring you distinguish between mRNA codons and tRNA anticodons, to list the amino acids in the correct order.
- Derive tRNA anticodons by applying complementary base pairing rules to the mRNA codons.
- Describe trends shown by experimental data using specific values before explaining them in terms of nucleic acid function.
- Identify the independent variable in an experiment and use the results to deduce the specific role of a nucleic acid.
Examiner Tips
- 💡Anchor both definitions to 'a cell' or 'an organism' to ensure accuracy.
- 💡If asked why the proteome is larger than the number of genes, explain the alternative splicing of pre-mRNA.
- 💡In a comparison table write both sides of every difference, such as 'DNA is double-stranded whereas tRNA is single-stranded'; a one-sided statement scores nothing.
- 💡AQA applies the list rule here, so give exactly the number of differences asked for and no more.
- 💡Bank three secure differences you can always reach for: the sugar and base, the number of strands, and the overall shape.
- 💡Name the specific bonds: hydrogen bonds between complementary bases, and phosphodiester bonds between adjacent nucleotides.
- 💡Remember the difference in products: in eukaryotes the immediate product is pre-mRNA which requires splicing, whereas prokaryotes produce mRNA directly.
- 💡In recombinant DNA questions, specify that the 'genetic code' is universal, meaning the same codons code for the same amino acids.
- 💡When asked why a bacterium cannot make a functional human protein from an unmodified gene, state that it cannot splice pre-mRNA, so introns remain.
- 💡Remember the workaround for expressing eukaryotic genes in bacteria: cDNA made by reverse transcriptase from mature mRNA already has its introns removed.
- 💡Remember exons EXit the nucleus to be expressed; introns stay IN.
- 💡In eukaryotic transcription answers, include a splicing line to show the full process.
- 💡In genetic engineering questions, explain that cDNA produced from mature mRNA by reverse transcriptase contains no introns.
- 💡Name the bond at every stage: hydrogen bonds for codon-anticodon, peptide bonds between amino acids.
- 💡To link a tRNA mutation to a disease, use the chain: wrong amino acid, altered tertiary structure, protein cannot carry out its function.
- 💡Write the mRNA sequence directly underneath the DNA sequence and bracket it into triplets before using the data table.
- 💡Always check the table heading first to confirm whether it provides mRNA codons, tRNA anticodons, or DNA triplets.
- 💡When instructed to use a figure or table, explicitly quote actual values with their units to support your explanation.
Common Mistakes
- Equating the genome to 'all the DNA in a cell'; correction: eukaryotic DNA includes non-coding regions outside of genes.
- Defining the genome as all the genes in a species; correction: the genome refers to a cell or organism.
- Giving the proteome as 'the number of proteins'; correction: it is the full range of proteins a cell can produce.
- Claiming liver and muscle cells differ because they have different genomes; correction: they differ in their proteomes due to gene expression.
- writing deoxyribose or thymine into an RNA answer instead of ribose and uracil
- calling tRNA double-stranded because it contains hydrogen bonds, when it is one strand folded back on itself
- saying the anticodon is identical to the codon rather than complementary to it
- stating that tRNA carries 'an amino acid' without saying a specific amino acid determined by its anticodon
- placing the amino acid binding site on the anticodon loop
- Naming DNA polymerase as the enzyme that joins RNA nucleotides; correction: it is RNA polymerase that catalyses phosphodiester bond formation between RNA nucleotides.
- Stating that both DNA strands are transcribed; correction: only the template strand is transcribed, and the other is the coding strand.
- Putting thymine into the mRNA sequence; correction: RNA contains uracil instead of thymine, so RNA uracil pairs with DNA adenine on the template.
- Assuming transcription always occurs in the nucleus; correction: eukaryotic transcription occurs in the nucleoplasm, but prokaryotic transcription occurs in the cytoplasm.
- Claiming prokaryotes make pre-mRNA and splice it quickly; they do not produce pre-mRNA at all because their genes lack introns.
- Assuming that all transcribed bases in prokaryotes code for amino acids; prokaryotic mRNA still contains untranslated regions (UTRs) and ribosome-binding sites.
- Writing that 'DNA is universal'; this is imprecise. The correct biological principle is that the genetic code is universal.
- Offering 'the genetic code is degenerate' as the reason a bacterium can express a human gene; degeneracy refers to multiple codons coding for one amino acid, whereas universality allows cross-species expression.
- Stating that the mechanisms of transcription and translation are universal; while the genetic code is universal, the enzymes (like RNA polymerase) and ribosomes (70S vs 80S) differ between prokaryotes and eukaryotes.
- Saying exons are removed and introns are joined; this is the wrong way round.
- Claiming introns are cut out of the DNA rather than out of the pre-mRNA.
- Placing splicing in the cytoplasm; it happens in the nucleus before the mRNA leaves.
- Writing that pre-mRNA is translated and the product trimmed afterwards.
- Dismissing introns as useless; some contain sequences that regulate transcription.
- saying the tRNA anticodon is complementary to the DNA rather than to the mRNA codon
- describing the ribosome as 'reading' the mRNA with no mention of tRNA or anticodons
- stating that ATP directly drives peptide bond formation or ribosome movement; correction: ATP charges each amino acid onto its tRNA and provides energy for translation, while peptide bonds are catalysed by the ribosome
- writing that hydrogen bonds join the amino acids, when peptide bonds join amino acids and hydrogen bonds hold codon to anticodon
- saying a changed anticodon stops the protein being made, when it inserts a different amino acid and alters the tertiary structure
- Pairing adenine with thymine when writing an mRNA sequence; ensure you pair adenine with uracil instead.
- Looking up a DNA triplet in a table that lists mRNA codons; always convert the DNA sequence to mRNA first if the table requires it.
- Starting the triplets from the wrong base, causing a frameshift; carefully identify the start codon or the specified starting base to maintain the correct reading frame.
- Drawing a conclusion the data do not support, such as calling a difference significant; only state significance if a statistical test is provided.