AP Biology

## Learning Outcomes

- Explain how codons in mRNA specify the amino acid sequence of a polypeptide.
- Interpret a codon chart to identify amino acids, start signals, and stop signals.
- Distinguish between mRNA codons, tRNA anticodons, and DNA nucleotide sequences.
- Describe why the genetic code is redundant and how this can produce silent mutations.
- Explain how start and stop codons help determine the reading frame during translation.
- Connect the near-universality of the genetic code to evidence for common ancestry.

## AP Biology Syllabus

For AP Biology Unit 6, you should understand how genetic information flows from DNA to RNA to protein and how translation uses mRNA to build a polypeptide. For this subtopic, the focus is not memorizing every codon, but being able to use codon charts, reason from nucleotide sequences, and predict how changes in DNA or mRNA may affect protein structure and phenotype.

- mRNA is read in three-nucleotide units called codons.
- Each codon specifies one amino acid or a stop signal.
- AUG is the usual start codon and codes for methionine.
- 61 of the 64 possible codons code for amino acids; 3 are stop codons.
- More than one codon can code for the same amino acid, making the code redundant.
- tRNA anticodons pair with mRNA codons and bring the correct amino acids to the ribosome.
- The genetic code is nearly shared by all organisms, supporting common ancestry.
- AP questions may provide a codon chart and ask you to apply it to mutations, translation, or evolutionary claims.

## 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. Why are codons read in groups of three nucleotides rather than one or two?
2. If an mRNA codon is UCA, what type of molecule contains the complementary anticodon?
3. How can a mutation in DNA fail to change the amino acid sequence of a protein?
4. Why does a frameshift mutation often have a larger effect than a single base substitution?
5. How does the near-universality of the genetic code support the idea of common ancestry?

## Introduction

Translation is the process by which the information in mRNA is used to assemble a polypeptide, one amino acid at a time. A ribosome reads the mRNA sequence in groups of three nucleotides, and each three-nucleotide unit gives an instruction: add a particular amino acid or stop translation. These instructions are called codons.

Codons are central to the link between genotype and phenotype. A DNA sequence affects the mRNA sequence made during transcription, and the mRNA sequence affects the amino acid sequence made during translation. Since amino acid sequence helps determine protein shape and function, changes in codons can affect traits.

> **Key Term: codon**
> A three-nucleotide sequence in mRNA that specifies an amino acid or a stop signal during translation.

### Codons: the three-base language of mRNA

A codon is made of three RNA nucleotides. Because RNA uses the bases adenine, uracil, cytosine, and guanine, the possible bases in codons are A, U, C, and G. Since each codon has three positions, the total number of possible codons is:

$$4^3 = 64$$

This number matters because cells use 20 common amino acids in proteins. If codons were only one base long, there would be only 4 possible instructions. If codons were two bases long, there would be:

$$4^2 = 16$$

That would not be enough to code for 20 amino acids. A three-base code gives 64 possible codons, which is more than enough to specify 20 amino acids plus stop signals.

> **Key Term: genetic code**
> The set of rules that matches mRNA codons with amino acids or translation stop signals.

A codon chart shows which amino acid corresponds to each mRNA codon. On the AP Biology exam, you are not expected to memorize the full genetic code. If a question requires exact codon-to-amino-acid information, a chart will be provided or the needed information will be included in the question.

> **Test Tip:**
> Codon charts are usually based on mRNA codons, not DNA triplets. If a question gives DNA, first determine whether it is the coding strand or template strand, then convert to the mRNA codon before using the chart.

For example, the mRNA codons UCA, UCC, UCG, and UCU all code for the amino acid serine. These codons differ in their third nucleotide but still give the same amino acid instruction. This feature is a major reason that some mutations do not change the final protein sequence.

When interpreting codons, always pay attention to direction. mRNA is read from the 5′ end toward the 3′ end. A codon chart is also read using the codon in the 5′ to 3′ direction. Reading a sequence backward can give a different codon and therefore a different amino acid.

### Start, stop, and reading frames

Translation begins at a start codon. The most common start codon is AUG. AUG codes for methionine, so newly made polypeptides usually begin with methionine, although this amino acid may later be removed or modified in some proteins.

> **Key Term: start codon**
> A codon, usually AUG, that signals the beginning of translation and establishes the reading frame.

The start codon is more than just the first amino acid instruction. It sets the reading frame, which is the way the mRNA sequence is divided into consecutive three-base codons. Once the ribosome begins at the start codon, it reads the mRNA three nucleotides at a time.

> **Key Term: reading frame**
> The grouping of an mRNA sequence into non-overlapping three-base codons during translation.

Consider this short mRNA sequence:

```text
AUG UCA GGU UAA
```

Read in the correct frame, it contains four codons: AUG, UCA, GGU, and UAA. These correspond to methionine, serine, glycine, and stop. If the ribosome started one nucleotide later, the grouping would change:

```text
UGU CAG GUU ...
```

That new grouping gives different codons and would produce a different amino acid sequence. This is why insertions or deletions that shift the reading frame can be so damaging.

Translation ends when the ribosome reaches a stop codon. Stop codons do not code for amino acids. Instead, release factors bind at the ribosome and cause the completed polypeptide to be released. There are three stop codons: UAA, UAG, and UGA.

> **Key Term: stop codon**
> A codon that does not specify an amino acid and instead signals termination of translation.

Only 61 of the 64 possible codons code for amino acids. The remaining 3 are stop codons. In exam questions, stop codons may also be called nonsense codons because they do not add an amino acid to the polypeptide chain.

> **Exam Warning:**
> Do not say that a stop codon codes for a “stop amino acid.” Stop codons do not code for amino acids. They signal termination by recruiting release factors.

Start and stop codons help define the protein-coding region of an mRNA. Nucleotides before the start codon or after the stop codon may still be part of the mRNA molecule, but they are not translated into the amino acid chain.

### tRNA anticodons connect codons to amino acids

Codons in mRNA do not directly attach to amino acids by themselves. The cell uses transfer RNA, or tRNA, as an adaptor molecule. Each tRNA has an anticodon that can base-pair with a complementary mRNA codon. The tRNA also carries a specific amino acid.

> **Key Term: anticodon**
> A three-nucleotide sequence on a tRNA molecule that base-pairs with a complementary mRNA codon.

For example, if the mRNA codon is AUG, the complementary tRNA anticodon is UAC. The tRNA carrying that anticodon brings methionine to the ribosome. This pairing allows the ribosome to place the correct amino acid in the growing polypeptide.

The base-pairing rules for RNA are:

- A pairs with U
- U pairs with A
- C pairs with G
- G pairs with C

A common AP-style task is to move between DNA, mRNA, tRNA, and amino acid sequence. The safest approach is to identify what type of sequence you are given before doing any conversion.

If the DNA coding strand is given, it has the same base sequence as the mRNA except that DNA has T where RNA has U. For example:

```text
DNA coding strand: 5′-ATG TCA GGT-3′
mRNA codons:       5′-AUG UCA GGU-3′
```

If the DNA template strand is given, the mRNA is complementary to it. For example:

```text
DNA template strand: 3′-TAC AGT CCA-5′
mRNA codons:        5′-AUG UCA GGU-3′
```

Notice that the mRNA sequence is the same in both examples, but the starting DNA strand was different. AP questions may test whether you can tell the difference.

> **Test Tip:**
> Before using a codon chart, write “mRNA” above the sequence you plan to translate. If you have not converted the sequence into mRNA codons, do not use the chart yet.

During translation, the ribosome has binding sites that position mRNA and tRNA molecules so amino acids can be joined. The ribosome catalyzes peptide bond formation between amino acids. After each codon is read, the ribosome moves along the mRNA to the next codon. This stepwise movement is called translocation. Translation continues until a stop codon enters the ribosome.

In prokaryotes, transcription and translation can occur at the same time because there is no nucleus separating DNA from ribosomes. Multiple ribosomes may translate the same mRNA at once, forming a polyribosome, also called a polysome. Eukaryotic cells separate transcription in the nucleus from translation in the cytoplasm or on ribosomes associated with the rough endoplasmic reticulum, but the codon rules are the same.

### Redundancy, mutations, and common ancestry

The genetic code is redundant, meaning that more than one codon can specify the same amino acid. This is also called degeneracy of the genetic code. Redundancy does not mean that one codon specifies multiple amino acids. For AP Biology, keep the direction clear: one codon specifies one amino acid or a stop signal, but one amino acid may be specified by multiple codons.

> **Key Term: redundancy**
> A feature of the genetic code in which multiple codons can code for the same amino acid.

This redundancy helps explain silent mutations. A silent mutation changes a DNA or mRNA sequence but does not change the amino acid sequence of the protein. For instance, if a mutation changes an mRNA codon from UCA to UCC, the amino acid is still serine. The polypeptide sequence is unchanged at that position.

> **Key Term: silent mutation**
> A nucleotide change that does not alter the amino acid sequence of the polypeptide.

Silent mutations are often associated with changes in the third base of a codon, although not every third-base change is silent. You must use the codon chart or information in the question rather than assume.

Not all mutations are silent. A missense mutation changes a codon so that a different amino acid is added. This may or may not affect protein function, depending on the role of that amino acid in protein folding, active sites, binding sites, or stability. A nonsense mutation changes an amino acid codon into a stop codon. This usually shortens the protein and can strongly affect function.

Insertions and deletions can be especially harmful if they are not in multiples of three nucleotides. Adding or removing one or two bases shifts the reading frame, changing every codon after the mutation. This is called a frameshift mutation.

> **Key Term: frameshift mutation**
> An insertion or deletion that changes the reading frame of codons, altering downstream amino acid instructions.

For example, compare these mRNA sequences:

```text
Original: AUG UCA GGU UAC UAA
Mutant:   AUG UAG GUU ACU AA...
```

If one nucleotide is deleted or inserted near the beginning, the ribosome may read completely different codons after that point. The result may be a very different amino acid sequence and an early stop codon.

> **Exam Warning:**
> A substitution changes one nucleotide and usually affects at most one codon. A frameshift mutation can change many codons downstream. Do not treat all mutations as having equal effects.

The genetic code is nearly the same across organisms. Bacteria, plants, fungi, and animals generally use the same codons for the same amino acids. This shared code is strong evidence that modern organisms descended from common ancestors. If organisms had separate origins, there would be no clear reason to expect the same codon system, ribosome function, and nucleic acid-based information flow across so many forms of life.

AP Biology may connect this idea to evolution. Shared molecular features, such as DNA, RNA, ribosomes, and the genetic code, support common ancestry. Differences among organisms still exist, but the basic system of codon-based translation is widely conserved.

A useful way to think about the genetic code is that it links two biological languages. Nucleic acids store information in nucleotide sequences. Proteins carry out many cell functions through amino acid sequences and three-dimensional structures. Translation converts the nucleotide language of mRNA into the amino acid language of proteins.

This connection also helps explain how genotype can affect phenotype. A change in DNA may change mRNA codons. A codon change may change an amino acid sequence. A changed amino acid sequence may change protein structure or function. A changed protein may alter a trait. However, each “may” matters: due to redundancy, regulation, protein folding, and environmental effects, not every DNA change produces a visible phenotype.

## Key Point Checklist

This article has covered the following key knowledge points:

- Codons are three-nucleotide sequences in mRNA.
- The genetic code matches codons with amino acids or stop signals.
- A three-base code gives 64 possible codons.
- 61 codons code for amino acids, while 3 are stop codons.
- AUG is the usual start codon and codes for methionine.
- Stop codons do not code for amino acids; they trigger termination.
- tRNA anticodons pair with mRNA codons and bring amino acids to the ribosome.
- Codon charts on AP questions are usually read using mRNA codons in the 5′ to 3′ direction.
- The genetic code is redundant because multiple codons can code for the same amino acid.
- Redundancy can allow silent mutations that do not change the amino acid sequence.
- Frameshift mutations can alter many downstream codons.
- The near-universality of the genetic code supports common ancestry.

## Key Terms and Concepts

- codon
- genetic code
- start codon
- reading frame
- stop codon
- anticodon
- redundancy
- silent mutation
- frameshift mutation


Translation - Codons and the genetic code