AP Syllabus focus:
‘The phenotype of a cell or organism depends on which genes are expressed and the levels of their gene products.’
Cells with the same genome can look and behave very differently. This page explains how gene expression patterns and the amount of gene products produced determine cellular and organismal phenotype.
Core idea: phenotype reflects expressed genes and product levels
A cell’s observable traits arise from the specific set of molecules it contains and uses, especially proteins (and functional RNAs). The DNA sequence provides potential; expression determines what is actually made.
This diagram summarizes the two major fates of an expressed gene: transcription to mRNA followed by translation into protein, or transcription into a functional noncoding RNA. It reinforces that gene expression is not synonymous with “making protein,” because some expressed genes produce RNAs that act directly in the cell. Source
Phenotype: The observable characteristics of a cell or organism produced by gene products and their interactions with the environment.
What “which genes are expressed” means
Within a genome, only some genes are actively used in a particular cell at a particular time.
Expressed gene: a gene whose information is used to produce a functional product (often a protein).
Genes not expressed do not contribute directly to the cell’s current structure/function, even though they are present in DNA.
Why “levels of gene products” matter
Phenotype depends not just on presence/absence, but on how much product is made and maintained.
High vs low protein abundance can shift cell behaviour (e.g., enzyme capacity, receptor number, structural protein content).
Protein activity depends on concentration, localisation, and interaction partners; changing product levels can rewire pathway output.
How gene products create phenotype
Gene products influence phenotype by controlling cellular structures and biochemical reactions.
This labeled schematic shows translation: a ribosome reads mRNA codons, tRNAs deliver amino acids, and a polypeptide chain is assembled. It helps connect gene expression to phenotype by making clear how cellular machinery controls the production rate of protein gene products. Source
Proteins as direct determinants of traits
Enzymes set metabolic rates and which substrates are converted to which products.
Structural proteins (e.g., cytoskeletal components) affect cell shape, motility, and mechanical strength.
Transport proteins (channels/carriers) determine what enters/leaves the cell, influencing ion balance and nutrient uptake.
Signalling proteins (receptors, kinases) determine how a cell responds to external cues, shaping behaviour such as division or secretion.
RNAs as functional gene products
Even when no protein is made, some genes affect phenotype through RNA function.
Noncoding RNAs can bind targets and alter cellular outcomes by modulating which products persist or are used.
Gene expression patterns produce different cellular phenotypes
Different cell types (and the same cell under different conditions) show distinct expression profiles.
Cell identity reflects a stable expression program: the “on/off” status and typical levels of key gene products.
Cell state reflects flexible, short-term shifts in expression and product levels in response to nutrients, stress, or signals.
Thresholds and dose effects
Phenotypic changes often occur when product levels cross functional thresholds.
Too little of a product can limit a pathway (rate-limiting step).
Excess product can saturate binding sites, increase pathway flux, or cause imbalances (e.g., overactive signalling).
Measuring expression to connect genotype to phenotype
AP Biology commonly links phenotype to measurable differences in gene products.
mRNA abundance is often used as a proxy for gene expression, but it does not always predict protein levels.
Protein abundance/activity more directly predicts phenotype because proteins carry out most cellular functions.
This figure highlights the essential components required to translate an mRNA into a protein: ribosomal subunits, mRNA, and tRNA. It supports the idea that phenotype tracks protein abundance because translation is a key control point determining how much protein a cell actually produces from a transcript. Source
Phenotype may change without DNA sequence change if expression levels shift.
Important caveats when interpreting gene expression
mRNA can be produced but not efficiently used; protein levels depend on production and loss rates.
Proteins can persist after mRNA decreases, delaying phenotypic changes.
Small changes in a regulatory protein’s level can cause large downstream phenotypic effects because it influences many targets.
FAQ
By altering the abundance or activity of existing gene products.
Examples include changing protein degradation rates, altering localisation within the cell, or shifting binding partner availability, which changes pathway output without switching new genes on.
Because phenotype tracks protein amount and activity more closely than mRNA.
Differences in translation efficiency, protein folding, or protein stability can lead to different protein concentrations and therefore different cellular behaviours.
A dose effect occurs when trait strength changes with product concentration.
Small increases in a transcriptional regulator or receptor can cause disproportionately large shifts in downstream pathway activity, producing graded phenotypic changes.
They look for concordant changes at the product/function level.
Typical checks include measuring protein abundance/activity and assessing whether the altered pathway output plausibly drives the observed trait change.
Yes; environment can shift product levels and therefore phenotype.
Nutrient availability, toxins, temperature, and signalling molecules can alter production or turnover of key proteins, producing reversible phenotypic shifts without altering DNA.
Practice Questions
State two ways in which gene expression can influence a cell’s phenotype. (2 marks)
Any two valid statements (1 mark each), e.g.:
Determines which proteins (or functional RNAs) are produced in the cell.
Changes the levels/amounts of gene products, altering pathway rates or cell behaviour.
Explain how two cells with identical DNA can have different phenotypes, referring to both which genes are expressed and the levels of gene products. (5 marks)
Identical genomes can show different phenotypes due to different patterns of gene expression (1).
Different sets of genes are switched on/off in each cell, producing different gene products (1).
Differences in the amounts of a given gene product can change cellular activity/traits (1).
Proteins act as enzymes/structural/signalling molecules, so altered product levels change metabolism/structure/responses (1).
mRNA level may not equal protein level due to differences in translation efficiency and/or protein stability, affecting phenotype (1).
