What are effects of non-coding region mutations?

Promoter mutations. Alter transcription factor binding, increasing or decreasing transcription. A weaker promoter for a tumour suppressor reduces its expression and increases cancer risk.

What are promoter mutations?

Alter transcription factor binding, increasing or decreasing transcription. A weaker promoter for a tumour suppressor reduces its expression and increases cancer risk.

What are splice-site mutations?

Disrupt the GT...AG signals at intron boundaries, causing exon skipping or intron retention. Many beta-thalassaemia and Marfan syndrome alleles are splice-site mutations.

What are enhancer and silencer mutations?

Change tissue-specific or developmental-stage expression.

What are mutations in non-coding RNA genes?

A mutation in a microRNA gene can dysregulate dozens of target mRNAs.

Beta-globin gene, codon 6, sense strand changes from GAG to GTG (a single A to T substitution).

Codon 6 changes from GAG to GUG.

Glutamic acid (charged, hydrophilic) is replaced by valine (uncharged, hydrophobic). This is a non-conservative missense mutation at a surface residue.

The hydrophobic valine creates a sticky patch on the beta-globin surface. Under low oxygen, the deoxygenated haemoglobin (HbS) polymerises into long fibres, deforming red blood cells into rigid sickled shapes.

What is organism level?

Sickled cells block capillaries (vaso-occlusive pain crises), are destroyed by the spleen (chronic haemolytic anaemia) and have a shortened lifespan. Heterozygotes are carriers with partial resistance to malaria, which explains the high allele frequency in malarial regions.

§-Syllabus dot point

NSWBiologySyllabus dot point

Inquiry Question 1: How does mutation introduce new alleles into a population?

Assess the significance of 'coding' and 'non-coding' DNA segments in the process of mutation and investigate the effects of different mutations on a protein's amino acid sequence

A focused answer to the HSC Biology Module 6 dot point on how mutations alter protein products. Coding versus non-coding regions, silent missense and nonsense substitutions, frameshift consequences, splice-site mutations, and a worked sickle cell example.

Generated by Claude Opus 4.89 min answerUpdated 2026-06-21

Reviewed by: AI editorial process; not yet individually human-reviewed

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What this dot point is asking
The answer
Examples in context

What this dot point is asking

NESA wants you to trace the consequence of a mutation through the DNA, mRNA and protein levels, and explain why mutations in non-coding regions can also affect phenotype. The standard worked example is sickle cell anaemia.

The answer

A mutation's effect on protein depends on where it lands (coding vs non-coding region) and what kind of change it is (silent, missense, nonsense or frameshift).

Coding vs non-coding DNA

Coding DNA (exons). Translated into amino acids. A mutation here directly changes the protein sequence (or stops translation).

Non-coding DNA. Includes promoters, enhancers, introns, splice sites, untranslated regions (UTRs) and non-coding RNA genes. Not translated, but mutations here can still change the amount, timing or splicing of the protein.

In humans, less than 2% of the genome codes directly for protein. Most regulatory sequence is non-coding, so non-coding mutations are common and important.

The figure below shows a gene laid out along the DNA and where each kind of mutation lands. A coding (exon) mutation rewrites the protein's amino acids directly; a non-coding mutation leaves the amino acid sequence intact but changes how much, when or how correctly the protein is made.

Effects on amino acid sequence (coding region mutations)

Silent mutation. A substitution that does not change the amino acid because the genetic code is degenerate (e.g. GGA and GGC both code for glycine). No effect on protein sequence.

Missense mutation. A substitution that changes one amino acid for another. Effect depends on:

Which amino acid changes. A conservative change (one hydrophobic for another) often preserves function. A non-conservative change (charged to non-polar, as in sickle cell) is more likely to disrupt folding or activity.
Where in the protein. Changes at the active site of an enzyme or at a protein-protein interface are usually catastrophic; changes in loops or surface residues may be tolerated.

Nonsense mutation. A substitution that creates a premature stop codon (UAA, UAG, UGA). The protein is truncated and usually non-functional. Many Duchenne muscular dystrophy alleles are nonsense mutations in the dystrophin gene.

Frameshift mutation. An insertion or deletion of a number of bases not divisible by three shifts the reading frame from the mutation onward. The amino acid sequence past the mutation is essentially random, and a premature stop codon usually appears within a few codons, producing a truncated, non-functional protein.

The diagram below works through all three single-base outcomes on one real codon. The wild-type mRNA codon GAG codes for glutamic acid (Glu). Changing just one base sends it down a different path: a silent, a missense or a nonsense result. Every codon and amino acid shown is the genuine genetic-code outcome.

Effects of non-coding region mutations

Promoter mutations: Alter transcription factor binding, increasing or decreasing transcription. A weaker promoter for a tumour suppressor reduces its expression and increases cancer risk.
Splice-site mutations: Disrupt the GT...AG signals at intron boundaries, causing exon skipping or intron retention. Many beta-thalassaemia and Marfan syndrome alleles are splice-site mutations.
Enhancer and silencer mutations: Change tissue-specific or developmental-stage expression.
Mutations in non-coding RNA genes: A mutation in a microRNA gene can dysregulate dozens of target mRNAs.

Worked example: sickle cell anaemia

DNA: Beta-globin gene, codon 6, sense strand changes from GAG to GTG (a single A to T substitution).
mRNA: Codon 6 changes from GAG to GUG.
Protein: Glutamic acid (charged, hydrophilic) is replaced by valine (uncharged, hydrophobic). This is a non-conservative missense mutation at a surface residue.
Cell level: The hydrophobic valine creates a sticky patch on the beta-globin surface. Under low oxygen, the deoxygenated haemoglobin (HbS) polymerises into long fibres, deforming red blood cells into rigid sickled shapes.
Organism level: Sickled cells block capillaries (vaso-occlusive pain crises), are destroyed by the spleen (chronic haemolytic anaemia) and have a shortened lifespan. Heterozygotes are carriers with partial resistance to malaria, which explains the high allele frequency in malarial regions.

Summary table

Mutation type	Region	Effect on protein
Silent	Coding	None
Missense	Coding	One amino acid changed (effect depends on chemistry and location)
Nonsense	Coding	Premature stop; truncated, non-functional
Frameshift	Coding	Reading frame shifted; mostly non-functional
Promoter	Non-coding	Altered amount of protein
Splice site	Non-coding	Faulty mRNA; usually non-functional protein

Worked exam answers

Worked example 1 - one base, three outcomes (3 marks)

Question. The mRNA codon GAG codes for glutamic acid. Give one single-base change that produces (a) a silent, (b) a missense and (c) a nonsense mutation, naming the outcome each time. (GAA = Glu, GUG = Val, UAG = stop.)

Model answer. (a) Silent: GAG to GAA - the third base changes but it still codes glutamic acid, because the genetic code is degenerate, so the amino acid sequence is unchanged. (b) Missense: GAG to GUG - glutamic acid is replaced by valine, a different amino acid (this is the sickle-cell change). (c) Nonsense: GAG to UAG - the codon becomes a premature stop codon, so translation ends early and the protein is truncated.

Marker's note: 1 mark each for a correct, clearly named change. The silent answer must keep the amino acid the same; the nonsense answer must land on UAA, UAG or UGA. Giving a codon that does not match the stated outcome earns nothing for that part.

Worked example 2 - read the new frame (4 marks)

Question. The mRNA 5'-AUG GAG UUU AAA-3' (Met-Glu-Phe-Lys) gains a single base so it reads 5'-AUG CGA GUU UAA A-3'. Give the new amino acid sequence and name the mutation. (CGA = Arg, GUU = Val, UAA = stop.)

Model answer. Reading from the start codon in threes: AUG - CGA - GUU - UAA, which translates to Met - Arg - Val - stop. Inserting one base (not a multiple of three) has shifted the reading frame, so this is a frameshift mutation: every codon after the insertion is re-read, the original Phe-Lys is lost, and a premature stop truncates the chain, giving a non-functional protein.

Marker's note: 1 mark for grouping the codons correctly from AUG, 1 mark for the correct translation, 1 mark for naming the frameshift, 1 mark for explaining the downstream/truncation effect. A wrongly grouped frame loses the first two marks even if "frameshift" is named.

Worked example 3 - nonsense in beta-globin (2 marks)

Question. A mutation in the beta-globin gene at codon 39 changes CAG to TAG. Classify it and state its effect.

Model answer. This is a substitution (point mutation). CAG codes for glutamine, whereas TAG is a stop codon, so it is a nonsense mutation producing a truncated beta-globin chain. The phenotype is beta-thalassaemia, with severe anaemia because functional beta-globin is not made.

Marker's note: 1 mark for identifying the nonsense substitution (sense codon to stop), 1 mark for the truncated-protein / non-functional consequence. Just writing "mutation" without "nonsense / premature stop" caps at 1 mark.

Worked example 4 - the non-coding case (3 marks)

Question. Explain how a mutation that does not change any amino acid can still alter the phenotype. Use a named example.

Model answer. A mutation in non-coding DNA is not translated, but it can still change the protein product. For example, the lactase-persistence allele is a single C to T substitution at position -13910, in a regulatory region upstream of the LCT gene. It strengthens a transcription-factor binding site, keeping LCT transcription active in adulthood, so much more lactase is produced. The lactase protein itself is unchanged in sequence, but its amount is higher, changing the phenotype (adults can digest lactose).

Marker's note: 1 mark for stating non-coding DNA is regulatory/not translated, 1 mark for a valid named example, 1 mark for linking it to a change in amount/timing/splicing rather than sequence. A silent (coding) mutation is also accepted as an example of "no amino-acid change".

Exam technique

Always check the codon table before claiming an amino acid change: Many substitutions are silent because the code is degenerate - state the codon before and after and name the amino acid each time.
Name the type precisely: Silent, missense, nonsense, frameshift (coding); promoter, splice-site, enhancer (non-coding). The exact term lifts a Band 4 answer to Band 6.
Justify "how bad" with chemistry and location: Markers reward "charged glutamic acid to hydrophobic valine" and "at the active site / a surface loop" - not just "the protein changes".
Read the frame from the start codon (AUG) in threes: For an indel question, regroup the whole sequence; remember a deletion or insertion of a multiple of three is in-frame, not a frameshift.
Don't forget non-coding DNA: If asked to "assess the significance" of coding vs non-coding, give a regulatory example (promoter or splice site) and the "less than 2% is coding" fact.

Note

Think of a gene as a recipe written in three-letter words, where each word tells the cell which ingredient (amino acid) to add next. A mutation is a typo. Some typos don't matter: the misspelled word still means the same ingredient (a silent change), like writing "colour" instead of "color". Some swap one ingredient for another (missense) - usually fine, unless it's a key ingredient, like salt for sugar; that single swap is exactly what causes sickle cell anaemia. Some typos turn a word into "THE END" too early (nonsense), so the dish is half-made and useless. And if you add or drop a letter, every word after it gets misread (frameshift) - the rest of the recipe turns to gibberish. Not all of the cookbook is recipe steps, though: a lot of it is notes in the margin saying how much to make and when. Mistakes in those margins (non-coding DNA) never change a single ingredient, but they can still ruin the meal - which is why those "non-coding" parts matter just as much.

Examples in context

Example 1. Cystic fibrosis and the F508del mutation. Around 1 in 2500 babies in Australia is born with cystic fibrosis, and the most common cause is the F508del mutation in the CFTR gene. The mutation is an in-frame deletion of three nucleotides (CTT) in exon 11, which removes the codon for phenylalanine at position 508 of the CFTR chloride channel protein. Because exactly three bases are removed, the reading frame is preserved (this is not a frameshift), but the missing amino acid causes the protein to misfold and be degraded by the cell's quality control machinery before reaching the cell membrane. The lung epithelium cannot then move chloride ions, mucus thickens, and recurrent infection follows.

Example 2. A non-coding mutation in lactase persistence. Most adult mammals lose the ability to digest lactose, but roughly 35 percent of Australian adults of European ancestry can. The mutation is not in the coding region of the lactase gene (LCT) itself but in a regulatory region 14 kilobases upstream, within an intron of an adjacent gene. A single C to T substitution at position -13910 creates a stronger binding site for a transcription factor, keeping LCT transcription active in adulthood. Although the lactase protein itself is unchanged, the amount made is much higher. This is a textbook example of why non-coding DNA matters and why focussing only on coding regions misses important phenotypic variation.

Exam-style practice questions

Practice questions written in the style of NESA exam questions on this dot point, with worked answer explainers. The year tag is the paper they imitate, not the source.

2024 HSC4 marksThe faulty CFTR allele is often caused by the deletion of three nucleotides. Explain how the deletion of nucleotides in the CFTR gene removes only one amino acid. Include reference to the nucleotides that code for the isoleucine and phenylalanine amino acids. (Use the codon chart provided.)

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Recognise that three deleted nucleotides span two codons, then use the redundancy of the genetic code. Sample answer: A triplet of mRNA nucleotides codes for one amino acid, but the three deleted nucleotides span across two codons - the codon for isoleucine and the codon for phenylalanine - so you would expect both to be affected. However, isoleucine can be coded by several different triplets. The correct coding is AUC, but after the deletion the remaining code is AUU, which also codes for isoleucine. Thus only the phenylalanine is removed. Marks: 4 = thorough explanation referring to isoleucine, phenylalanine and the final sequence; 3 = sound explanation referring to appropriate amino acids/deletion effects; 2 = some understanding of how mRNA codes for amino acids; 1 = some relevant information. Common error: not grasping that the deletion spanned two codons / that multiple codons code the same amino acid.

Source: NESA 2024 HSC Biology examination and marking guidelines.

2022 HSC4 marksThe EGFR protein includes a receptor and an enzyme component, and its function is to help regulate cell division. EGFR mutations are present in about 32% of Non-Small Cell Lung Cancer cases. Explain how a mutation in the EGFR gene could result in changes in protein structure and function to increase the risk of lung cancer.

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Link mutation to amino-acid change to altered structure/function, then to uncontrolled cell division. Sample answer: A mutation of the EGFR gene is a change in its DNA base sequence/codons. If this change is in a coding region it can change the amino acid sequence of the polypeptide, altering the folding and properties of the protein and so its function. For example, a change in the enzyme region could alter the active site and therefore enzyme activity, changing the rate of DNA replication and cell division. Since EGFR helps control cell division, the mutation can lead to uncontrolled cell division, and lung cancer is the result of uncontrolled cell division. Marks: 4 = explains the link between mutation, EGFR structure and regulation of cell division AND links cancer to uncontrolled division; 3 = describes the link to protein structure and links cancer to uncontrolled division; 2 = outlines an effect of mutation on EGFR; 1 = relevant information. Use the stimulus and link the changed structure to loss of cell-division control.

Source: NESA 2022 HSC Biology examination and marking guidelines.

2023 HSC4 marks5-Bromouracil (bU) bonds with adenine in place of thymine, then binds with guanine during replication, making a guanine-cytosine pair instead of an adenine-thymine pair. Describe the possible effects on a protein if this mutation occurred within a gene.

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Trace the base change through polypeptide synthesis to several possible protein outcomes. Sample answer: During polypeptide synthesis an mRNA strand is made from the DNA template, and the sequence of bases codes for specific amino acids. After the bU substitution, the mutated strand contains guanine and continues to reproduce the mutated gene. Possible effects: (1) if the new (mutated) codon still codes for the same amino acid, there is no change to the protein (silent); (2) if it codes for a different amino acid, a different polypeptide forms, which could fold differently and produce a non-functioning protein; (3) if the mutation creates a STOP codon, the chain terminates early, and if it disrupts the AUG START, translation will not begin. Marks: 4 = comprehensive understanding of how the mutation could alter the amino acid sequence AND relates a changed sequence to protein structure/function; 3 = sound understanding of one pathway and a structure/function link; 2 = identifies a possible way it alters the DNA/amino acid sequence; 1 = relevant information.

Source: NESA 2023 HSC Biology examination and marking guidelines.

2023 HSC2 marksThe normal Huntingtin protein has 10-26 repeats of CAG; in Huntington's disease there are 37-80 repeats, altering protein structure. Using the graph (age of onset vs number of CAG repeats), explain the relationship between the number of CAG repeats and the age of onset of Huntington's disease.

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State the inverse relationship and support it with a data point and a structural reason. Sample answer: As the number of CAG repeats increases, the age of onset of Huntington's disease decreases - e.g. with about 60 CAG repeats the age of onset is around 20 years. The increased CAG repeats lead to the alteration of the protein responsible for the disease at an earlier age (change in protein structure occurs at an earlier stage). Marks: 2 = explains the relationship AND makes relevant reference to the graph data OR the effect of increased repeats on protein structure; 1 = makes the relationship evident OR makes some reference to the data. Common error: not identifying the independent/dependent variables or not using data to explain the relationship.

Source: NESA 2023 HSC Biology examination and marking guidelines.

Practice questions

Original practice questions graded from foundation to exam level, each with a full worked solution. Try them before revealing the solution.

foundation2 marksDefine the terms 'coding DNA' and 'non-coding DNA', and state one example of a non-coding region.

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1 mark - coding DNA. Coding DNA (the exons) is the sequence that is transcribed and then translated into the amino acid sequence of a protein. A mutation here can directly change the protein product.

1 mark - non-coding DNA + example. Non-coding DNA is not translated into protein, but it can still affect the protein's amount, timing or splicing. Acceptable examples: a promoter, an enhancer, an intron, a splice site, a UTR, or a non-coding RNA gene (name any one).

The discriminator is "translated into amino acids" (coding) versus "not translated but still regulatory" (non-coding). Naming a non-coding region without saying it is not translated caps at 1 mark.

foundation3 marksDistinguish between a silent, a missense and a nonsense mutation in terms of their effect on the amino acid sequence.

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1 mark - silent: A substitution that does not change the amino acid, because the genetic code is degenerate (e.g. GAG and GAA both code for glutamic acid). The protein sequence is unchanged.
1 mark - missense: A substitution that changes the codon so that one amino acid is replaced by a different amino acid (e.g. GAG to GUG: glutamic acid to valine).
1 mark - nonsense: A substitution that changes a codon into a premature stop codon (UAA, UAG or UGA), so translation ends early and a truncated protein is produced.

Each row must tie the codon change to its specific effect on the amino acid sequence (no change / one swapped / early stop). Listing the three names without their effects does not earn full marks.

foundation3 marksAn mRNA codon reads GAG, coding for glutamic acid. A single substitution changes it to GUG. Using the property of the amino acids, explain why this change can disrupt the protein. (GUG = valine.)

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1 mark - identify the change: GAG codes for glutamic acid and GUG codes for valine, so this is a missense substitution - one amino acid is swapped for another.
1 mark - the chemistry: Glutamic acid is charged and hydrophilic, whereas valine is uncharged and hydrophobic, so this is a non-conservative change in the chemical property of the residue.
1 mark - the consequence: Changing a surface residue from hydrophilic to hydrophobic creates a "sticky" hydrophobic patch, which can alter folding or interactions of the protein (in haemoglobin this drives HbS polymerisation and sickling).

Full marks need the named amino acids, the property change (charged to hydrophobic), and a folding/function consequence. A bald "the protein changes" caps at 1 mark.

core4 marksThe mRNA sequence 5'-AUG GAG UUU AAA-3' codes for Met-Glu-Phe-Lys. A single base is inserted so the sequence becomes 5'-AUG CGA GUU UAA A-3'. Determine the new amino acid sequence and name the type of mutation, explaining its effect on the protein. (CGA = Arg, GUU = Val, UAA = stop.)

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1 mark - read the new frame: Splitting the mutated mRNA into codons from the start gives AUG - CGA - GUU - UAA.
1 mark - translate: AUG = Met, CGA = Arg, GUU = Val, UAA = stop: the new peptide is Met-Arg-Val then translation stops.
1 mark - name the mutation: Inserting one base (not a multiple of three) shifts the reading frame, so this is a frameshift mutation.
1 mark - effect: Every codon after the insertion is changed, the original Phe-Lys is lost, and a premature stop truncates the chain, so the protein is almost certainly non-functional.

Award the read-the-frame and translation marks only if the codons are grouped correctly from AUG; the frameshift name needs the "not divisible by three" reason for full credit.

core4 marksExplain why a mutation in a non-coding region of DNA can still change an organism's phenotype, using two different non-coding examples.

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1 mark - principle: Non-coding DNA is not translated, but much of it regulates when, where and how much a protein is made, or how the pre-mRNA is processed - so a change here can alter the protein product indirectly.
1 mark + 1 mark - two worked examples (1 each): Promoter mutation: weakens or strengthens transcription-factor binding, lowering or raising the amount of protein made (e.g. a weaker promoter for a tumour-suppressor gene reduces its expression and raises cancer risk). Splice-site mutation: disrupts the GU...AG intron signals, causing exon skipping or intron retention, so a faulty mRNA and usually a non-functional protein result (e.g. many beta-thalassaemia alleles).
1 mark - significance: Because less than 2% of the human genome is protein-coding, most regulatory sequence is non-coding, so non-coding mutations are common and important - focusing only on coding regions misses much phenotypic variation.

Two genuinely different non-coding mechanisms are required; giving two promoter examples earns only one of the two example marks.

core5 marksUsing sickle cell anaemia as an example, describe how a single base substitution in coding DNA leads to a changed phenotype. Trace your answer from DNA through to the organism.

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1 mark - DNA: In the beta-globin gene at codon 6, a single A to T substitution changes the sense-strand triplet from GAG to GTG.
1 mark - mRNA and amino acid: The mRNA codon changes from GAG to GUG, so glutamic acid is replaced by valine - a non-conservative missense mutation (charged/hydrophilic to uncharged/hydrophobic).
1 mark - protein: The hydrophobic valine creates a sticky patch on the beta-globin surface; under low oxygen, deoxygenated haemoglobin (HbS) polymerises into fibres.
1 mark - cell: The fibres deform red blood cells into rigid sickle shapes.
1 mark - organism: Sickled cells block capillaries (vaso-occlusive pain crises) and are destroyed by the spleen (haemolytic anaemia); heterozygotes gain partial malaria resistance, explaining the high allele frequency in malarial regions.

A Band 6 response is a continuous DNA -> mRNA -> protein -> cell -> organism chain with the property change (charged to hydrophobic) named as the cause.

exam7 marks'A mutation only matters if it changes a protein's amino acid sequence.' Assess this statement, referring to coding and non-coding DNA and to the different types of point mutation.

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"Assess" requires a judgement on the statement, supported by evidence on both sides. The expected verdict is that the statement is too narrow - it is largely false.

Where the statement holds (1-2 marks): Many serious mutations DO change the amino acid sequence: missense swaps one amino acid (sickle cell: Glu to Val), nonsense inserts a premature stop (truncated, non-functional protein, e.g. some Duchenne alleles), and frameshift indels scramble every downstream codon. These directly support the statement.
Where the statement fails - coding (1-2 marks): A silent substitution changes a base but, because the code is degenerate, leaves the amino acid unchanged - a mutation that does NOT alter the sequence, contradicting the claim that only sequence-changing mutations matter (and silent changes can still affect splicing or translation speed).
Where the statement fails - non-coding (2 marks): Less than 2% of the genome codes for protein. Promoter/enhancer mutations change the amount or timing of an unchanged protein; splice-site mutations cause exon skipping and faulty mRNA; a microRNA-gene mutation can dysregulate many target mRNAs. None of these change a coding amino acid sequence, yet all can change phenotype (e.g. lactase persistence from a regulatory -13910 C to T change).
Judgement (1 mark): The statement is largely false: while sequence-changing coding mutations are important, mutations can matter through non-coding regulation and splicing without altering any amino acid, and some sequence-changing mutations (silent) do not. A response that only lists mutation types without an explicit, supported verdict caps below full marks.

exam6 marksA point mutation in the second codon of an mRNA could be silent, missense or nonsense. For the codon GAG (glutamic acid), give one single-base change producing each outcome, and explain how the same kind of event (a single substitution) can have such different consequences. (GAA = Glu, GUG = Val, UAG = stop.)

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Target a response that supplies three accurate codon changes and then explains the variation using the structure of the genetic code.

The three changes (3 marks, 1 each). Silent: GAG to GAA - still glutamic acid, because the third "wobble" base often does not change the amino acid (degeneracy). Missense: GAG to GUG - glutamic acid becomes valine, a different amino acid. Nonsense: GAG to UAG - a premature stop codon, ending translation early.

Why one type of event differs so much (2-3 marks). The genetic code is degenerate/redundant, so many third-position (and some first-position) changes are silent. A change that lands on a base that does alter the triplet's meaning gives a missense result, and whether that matters depends on the chemistry and location of the swapped amino acid. A change that converts a sense codon into one of the three stop codons (UAA/UAG/UGA) is nonsense and truncates the protein. So the position within the codon and which base is substituted decide the outcome, even though the physical event - one base swapped - is identical.

Full marks need three correct, clearly labelled codon changes AND an explanation grounded in degeneracy / codon position rather than chance alone.