AP Biology

## Learning Outcomes

- Explain how mRNA codons are translated into an amino acid sequence.
- Describe the roles of mRNA, tRNA, rRNA, ribosomes, amino acids, and enzymes in translation.
- Compare the initiation, elongation, and termination stages of translation.
- Predict how changes in codons, start codons, stop codons, or reading frame affect a protein.
- Use the genetic code to identify amino acids from mRNA codons.
- Connect translation errors or mutations to changes in protein structure and phenotype.

## AP Biology Syllabus

Translation belongs in Unit 6, Gene Expression and Regulation, and connects strongly to Big Idea 3: living systems store, retrieve, transmit, and respond to information. For AP Biology, focus less on memorizing every named protein factor and more on explaining how information in mRNA is converted into a polypeptide and how changes in this process can affect gene expression, protein function, and phenotype.

- DNA stores genetic information; mRNA carries a transcribed copy of that information to the ribosome.
- The ribosome reads mRNA codons in the 5′ to 3′ direction.
- Each codon specifies an amino acid or a stop signal according to the genetic code.
- tRNA molecules use anticodons to match codons and deliver amino acids.
- Translation occurs in three major phases: initiation, elongation, and termination.
- The amino acid chain grows by peptide bond formation and becomes a polypeptide.
- The genetic code is redundant, so some DNA or mRNA changes do not alter the amino acid sequence.
- Mutations that alter start codons, stop codons, or the reading frame can strongly affect protein production.

## Test Your Knowledge

Attempt these questions before reading this article. If you find some difficult or cannot remember the answers, look more closely at that area during your revision.

1. In what direction does a ribosome read mRNA, and in what direction does the polypeptide grow?
2. What is the role of tRNA during translation?
3. Why does a substitution mutation in a codon not always change the final protein?
4. What happens when a ribosome reaches a stop codon?
5. How would an insertion of one nucleotide near the beginning of a coding sequence affect translation?

## Introduction

Translation is the stage of gene expression in which the nucleotide sequence of an mRNA molecule is used to build a polypeptide. Transcription produces RNA from a DNA template; translation then converts the “language” of nucleic acids into the “language” of proteins. This process is central to the link between genotype and phenotype because proteins help determine cell structure, enzyme activity, signaling, transport, and many other traits.

A ribosome does not read mRNA one nucleotide at a time. Instead, it reads groups of three RNA nucleotides called codons. Each codon corresponds to one amino acid or to a signal to stop translation. The order of codons in the mRNA determines the order of amino acids in the polypeptide, which can then fold and be modified to become a functional protein.

> **Key Term: translation**
> The process in which a ribosome uses the codon sequence of an mRNA molecule to synthesize a polypeptide.
>
> **Key Term: codon**
> A three-nucleotide sequence in mRNA that specifies an amino acid or a stop signal during translation.

### Preparing the mRNA, ribosome, and charged tRNAs

Translation requires several molecular components working together: mRNA, tRNA, amino acids, ribosomes, and enzymes. The mRNA provides the codon sequence. Transfer RNA, or tRNA, acts as an adaptor molecule between mRNA codons and amino acids. Each tRNA has an anticodon that can base-pair with a complementary mRNA codon, and each tRNA carries a specific amino acid.

> **Key Term: tRNA**
> Transfer RNA; an RNA molecule that carries a specific amino acid and has an anticodon that pairs with an mRNA codon.
>
> **Key Term: anticodon**
> A three-nucleotide sequence on a tRNA molecule that base-pairs with a complementary codon on mRNA.

Before a tRNA can participate in translation, it must be “charged” with the correct amino acid. This is done by enzymes called aminoacyl-tRNA synthetases. Each synthetase attaches a specific amino acid to the correct tRNA, using ATP as an energy source. This charging step is vital because the ribosome mainly checks codon-anticodon pairing; it does not independently verify whether the amino acid attached to the tRNA is correct.

Ribosomes are made of ribosomal RNA, or rRNA, and proteins. Each ribosome has a small subunit and a large subunit. During translation, the small subunit helps bind mRNA and match codons with anticodons, while the large subunit helps form peptide bonds between amino acids. In many biology courses, the ribosome is described as having three tRNA-binding sites:

- The A site receives the incoming aminoacyl-tRNA.
- The P site holds the tRNA carrying the growing polypeptide chain.
- The E site is where an empty tRNA exits the ribosome.

> **Key Term: ribosome**
> A cellular structure made of rRNA and proteins that reads mRNA and catalyzes polypeptide synthesis.

The genetic code is shared by nearly all living organisms, with only a few exceptions. This shared code is evidence for common ancestry. The code is also redundant, meaning that more than one codon can specify the same amino acid. For example, several different codons may code for leucine, serine, or arginine. This explains why some mutations change a DNA or mRNA sequence without changing the amino acid sequence of the protein.

> **Test Tip:**
> If an AP question gives you a codon table, read mRNA codons from 5′ to 3′. Do not use the DNA template strand directly unless you first convert it into the correct mRNA sequence.

### Initiation sets the reading frame at the start codon

Initiation is the first stage of translation. Its main job is to assemble the ribosome, mRNA, and first tRNA in the correct position. This matters because the ribosome must establish the correct reading frame: the grouping of nucleotides into codons.

> **Key Term: reading frame**
> The way an mRNA sequence is divided into consecutive three-nucleotide codons during translation.

Translation usually begins at the start codon AUG. AUG codes for methionine. In many prokaryotes, the first methionine is chemically modified, but AP Biology questions usually focus on the larger idea: AUG starts translation and sets the reading frame.

> **Key Term: start codon**
> The mRNA codon AUG, which usually signals the beginning of translation and codes for methionine.

During initiation, the small ribosomal subunit binds to the mRNA. The initiator tRNA, carrying methionine, pairs with the AUG start codon. Then the large ribosomal subunit joins, forming a complete ribosome. The initiator tRNA begins in the P site, leaving the A site open for the next tRNA.

The start codon is not just the first amino acid signal; it determines how the rest of the mRNA will be read. Consider this mRNA segment:

```text
5′-AUG GAA UUU CCG UAA-3′
```

The ribosome reads it as:

```text
AUG | GAA | UUU | CCG | UAA
Met | Glu | Phe | Pro | Stop
```

If translation began one nucleotide later, the codons would be grouped differently:

```text
UGG | AAU | UUC | CGU | ...
Trp | Asn | Phe | Arg | ...
```

The amino acid sequence would be very different. This is why insertions or deletions near the beginning of a coding sequence can have large effects if they shift the reading frame.

> **Exam Warning:**
> Do not confuse the start of transcription with the start of translation. Transcription begins at a DNA promoter and produces RNA. Translation begins at a start codon on mRNA and produces a polypeptide.

In eukaryotic cells, translation occurs in the cytoplasm, either on free ribosomes or on ribosomes attached to the rough endoplasmic reticulum. Proteins made on free ribosomes often function in the cytosol, nucleus, mitochondria, or other internal locations. Proteins made on ribosomes bound to the rough ER often enter the endomembrane system, become membrane proteins, or are secreted. In prokaryotes, which lack a nucleus, transcription and translation can occur in the same cellular region, and translation can begin while transcription is still taking place.

### Elongation builds the polypeptide one codon at a time

Elongation is the stage in which amino acids are added to the growing polypeptide chain. The ribosome moves along the mRNA, reading one codon at a time in the 5′ to 3′ direction. The polypeptide grows from its amino end, called the N-terminus, toward its carboxyl end, called the C-terminus.

A typical elongation cycle has three main steps.

First, a charged tRNA enters the A site. Its anticodon base-pairs with the mRNA codon exposed in that site. For example, if the mRNA codon is GAA, a tRNA with the complementary anticodon CUU can bind, carrying the amino acid glutamic acid.

Second, the ribosome forms a peptide bond. The growing polypeptide is transferred from the tRNA in the P site to the amino acid on the tRNA in the A site. The ribosome’s rRNA helps catalyze this reaction, so the ribosome is not just a platform; it also has catalytic activity.

Third, the ribosome translocates, meaning it moves one codon along the mRNA. The tRNA that now carries the growing polypeptide shifts from the A site to the P site. The empty tRNA shifts to the E site and exits. The A site is now open for the next charged tRNA.

> **Key Term: elongation**
> The stage of translation in which the ribosome adds amino acids to the growing polypeptide chain.

This cycle repeats until the ribosome reaches a stop codon. Each round depends on accurate codon-anticodon pairing. However, the genetic code allows some flexibility at the third nucleotide position of many codons. This is often called wobble. Because of wobble and redundancy, different codons can code for the same amino acid. For AP Biology, the key point is that a DNA or mRNA sequence change does not always change the protein sequence.

For example, suppose an mRNA codon changes from GAA to GAG. Both codons specify glutamic acid. This is a silent mutation because the amino acid sequence remains unchanged. In contrast, a change from GAA to GUA would change the amino acid from glutamic acid to valine, which is a missense mutation. A change from an amino-acid codon to a stop codon can shorten the protein; this is a nonsense mutation.

> **Test Tip:**
> When asked whether a mutation affects a protein, check the codon table before assuming the amino acid changes. The code is redundant, so some substitutions have no effect on the amino acid sequence.

Frameshift mutations are often more damaging than single-base substitutions. If one nucleotide is inserted or deleted within the coding sequence, all downstream codons may be regrouped. This can change many amino acids and may create an early stop codon. Insertions or deletions in multiples of three may add or remove amino acids without shifting every codon after the mutation.

Elongation also uses energy. ATP is used earlier to charge tRNAs, and GTP is used during steps such as tRNA entry and ribosome movement. AP Biology usually does not require memorization of every energy molecule used at each substep, but you should know that translation requires energy and molecular building blocks.

### Termination releases the completed polypeptide

Termination begins when a stop codon enters the ribosome’s A site. The three main stop codons are UAA, UAG, and UGA. These codons do not code for amino acids. Instead, they signal that translation should end.

> **Key Term: stop codon**
> An mRNA codon that signals the end of translation; the common stop codons are UAA, UAG, and UGA.

No tRNA carries an amino acid for a stop codon. Instead, a protein called a release factor binds in the A site. The release factor causes the completed polypeptide to detach from the tRNA in the P site. The ribosomal subunits then separate from the mRNA and from each other, and the components can be reused.

> **Key Term: release factor**
> A protein that binds to a stop codon in the ribosome and triggers release of the completed polypeptide.

Termination affects protein length. If a mutation creates an early stop codon, translation ends too soon, often producing a shortened, nonfunctional protein. If a mutation removes a normal stop codon, translation may continue into extra sequence until another stop codon is reached. This can produce an abnormally long protein that may fold incorrectly or be degraded by the cell.

After translation, a polypeptide may need additional processing before it becomes a functional protein. It may fold into a specific three-dimensional shape, join with other polypeptides, have chemical groups added, or be transported to a specific cellular location. Since protein shape affects protein function, changes in amino acid sequence can affect phenotype by altering folding, active sites, binding sites, or stability.

> **Exam Warning:**
> Ribosomes do not proofread in the same way DNA polymerase does during DNA replication. If an exam asks why a DNA sequence change may not change a protein, the best answer is usually redundancy of the genetic code, not ribosome proofreading.

Translation is also a point where gene expression can be regulated. A cell may have mRNA present but control whether it is translated, how long it remains stable, or whether the resulting protein is active. For example, small RNA molecules can bind complementary mRNA molecules and reduce translation by causing mRNA degradation or blocking ribosome access. This connects translation to the wider AP Biology topic of gene regulation: phenotype depends not only on which genes exist, but also on when, where, and how strongly they are expressed.

### Applying translation to exam-style problems

Many AP Biology translation questions ask you to interpret a sequence. The safest method is step-by-step:

1. Identify whether the sequence is DNA or RNA.
2. If needed, transcribe DNA into mRNA using complementary base-pairing.
3. Find the start codon AUG.
4. Split the mRNA into codons from the start codon.
5. Use the codon table to identify amino acids.
6. Stop when you reach UAA, UAG, or UGA.
7. Compare the original and changed amino acid sequences if a mutation is involved.

For example:

> **Question:**
> A coding mRNA sequence begins 5′-AUG UUU GGC UAA-3′. What polypeptide is produced?

Read from the start codon:

```text
AUG | UUU | GGC | UAA
Met | Phe | Gly | Stop
```

The polypeptide is methionine-phenylalanine-glycine. The stop codon is not an amino acid and is not included in the polypeptide.

Now consider a substitution:

```text
Original: 5′-AUG UUU GGC UAA-3′
Mutant:   5′-AUG UUC GGC UAA-3′
```

UUU and UUC both code for phenylalanine, so this substitution does not change the amino acid sequence. It is silent at the protein level.

Now consider an insertion:

```text
Original: 5′-AUG UUU GGC UAA-3′
Mutant:   5′-AUG UAU UGG CUA A...-3′
```

Adding one nucleotide after the start codon shifts the reading frame. The codons after the insertion change, so the amino acid sequence changes. The original stop codon may no longer be in frame, so termination may occur later or earlier depending on the new sequence.

> **Test Tip:**
> On free-response questions, earn points by linking the molecular change to the outcome: “The insertion shifts the reading frame, changing downstream codons, which changes the amino acid sequence and may alter protein shape and function.”

AP questions may also ask you to connect translation to experimental data. For example, if mRNA levels stay the same but protein levels decrease, regulation may be occurring after transcription, possibly through reduced translation or increased protein degradation. If mRNA and protein levels both decrease, regulation may have occurred before or during transcription. If mRNA and protein levels remain the same but enzyme activity changes, the regulation may be post-translational, such as activation or inhibition of the protein.

## Key Point Checklist

This article has covered the following key knowledge points:

- Translation converts the codon sequence of mRNA into the amino acid sequence of a polypeptide.
- Ribosomes read mRNA in the 5′ to 3′ direction.
- Polypeptides grow from the N-terminus to the C-terminus.
- Codons are three-nucleotide mRNA sequences that specify amino acids or stop signals.
- tRNA molecules carry amino acids and use anticodons to pair with mRNA codons.
- Aminoacyl-tRNA synthetases attach the correct amino acids to tRNAs.
- Initiation begins at the start codon AUG, which usually codes for methionine.
- The start codon sets the reading frame for the rest of translation.
- During elongation, tRNAs enter the A site, peptide bonds form, and the ribosome translocates.
- Stop codons do not code for amino acids; release factors bind and trigger termination.
- The genetic code is redundant, so some mutations do not change the amino acid sequence.
- Frameshift and nonsense mutations often have strong effects on protein structure and function.

## Key Terms and Concepts

- translation
- codon
- tRNA
- anticodon
- ribosome
- rRNA
- aminoacyl-tRNA synthetase
- start codon
- reading frame
- elongation
- A site
- P site
- E site
- peptide bond
- polypeptide
- stop codon
- release factor
- genetic code
- silent mutation
- missense mutation
- nonsense mutation
- frameshift mutation
- wobble
- N-terminus
- C-terminus


Translation - Initiation, elongation, termination