Grade by Grade
D. Molecular Genetics · Molecular Genetics

The Genetic Code: Codons, Reading Frames and Decoding DNA

D2.2 D2.1 D3.3 D3.7 A1.12About 70 minutes
Learning goals
  • I can explain why the genetic code uses three-base codons and describe how it was cracked.
  • I can use a codon table to translate mRNA into an amino-acid sequence, starting at AUG and ending at a stop codon.
  • I can describe the features of the code: triplet, redundant, unambiguous, non-overlapping, with start and stop signals, and nearly universal.
  • I can analyse a simulated DNA strand to find the protein it codes for and to recognize an anomaly compared with a reference.
  • I can work backwards from a protein to possible DNA sequences.

Words to know

codon
A sequence of three mRNA nucleotides that codes for one amino acid or a stop signal.
anticodon
The three tRNA nucleotides that pair with a codon on mRNA.
start codon
AUG; it codes for methionine and sets where translation begins.
stop codon
UAA, UAG or UGA; codons with no amino acid that signal the end of translation.
reading frame
The way a sequence is divided into consecutive triplets, set by the start codon.
redundancy (degeneracy)
The property that most amino acids are coded by more than one codon.
open reading frame (ORF)
A stretch of DNA or RNA that starts with a start codon and runs a long way without a stop codon; it may be a gene.

A four-letter alphabet, a twenty-word dictionary

DNA and mRNA are written with 4 bases. Proteins are built from 20 amino acids. How can a 4-letter alphabet specify 20 different "words"? The answer, worked out in the early 1960s, is one of the most important discoveries in biology: the genetic code. In this lesson you will learn to read it like a scientist, and use it to analyse simulated DNA sequences (expectation D2.2).

Why triplets?

If one base coded for one amino acid, there would be only 4 possible codes. Pairs of bases give 4 × 4 = 16, still fewer than 20. Triplets give 4 × 4 × 4 = 64 possible codons, which is enough. In 1961, Francis Crick, Sydney Brenner and colleagues confirmed experimentally that the code is read in groups of three: adding or deleting one or two bases in a viral gene destroyed it, but adding or deleting three often restored its function.

1 base per code word4¹ = 4 words2 bases per word4² = 16 words3 bases per word4³ = 64 words20 amino acids needed
Why the code must use triplets. With 4 bases, pairs give only 16 combinations, too few for 20 amino acids. Triplets give 64, more than enough, so several codons can share one amino acid. (Bar lengths are to scale.)

Cracking the code

Also in 1961, Marshall Nirenberg and Heinrich Matthaei made an artificial mRNA containing only uracil, poly-U (UUUUUU...), and added it to a mixture of everything needed for protein synthesis from broken-open E. coli cells. The mixture made a protein containing only phenylalanine. So UUU codes for phenylalanine: the first codon was decoded. Within a few years, Nirenberg's group and Har Gobind Khorana's group (who made RNAs with repeating patterns such as UCUCUC...) had worked out all 64 codons. Nirenberg, Khorana and Robert Holley (who determined the first tRNA structure) shared the 1968 Nobel Prize in Physiology or Medicine.

Features of the genetic code

  1. Triplet: each codon is three nucleotides.
  2. Start signal: AUG both codes for methionine (Met) and marks where translation begins, which sets the reading frame.
  3. Stop signals: UAA, UAG and UGA code for no amino acid; they end translation.
  4. Redundant (degenerate): 61 codons code for only 20 amino acids, so most amino acids have several codons. Usually these differ only in the third base (for example, GGU, GGC, GGA and GGG all code for glycine). This protects against some mutations.
  5. Unambiguous: each codon codes for only one amino acid.
  6. Non-overlapping, no gaps: codons are read one after another, with no bases shared or skipped.
  7. Nearly universal: the same code is used by bacteria, plants, animals and fungi. There are a few small exceptions (for example, in human mitochondria UGA codes for tryptophan instead of stop). The universal code is why a human gene can be read correctly by a bacterium, which makes much of biotechnology possible.

Codons are always written as mRNA, 5′→3′.

First two basesthird = Uthird = Cthird = Athird = G
UU…UUU PheUUC PheUUA LeuUUG Leu
UC…UCU SerUCC SerUCA SerUCG Ser
UA…UAU TyrUAC TyrUAA StopUAG Stop
UG…UGU CysUGC CysUGA StopUGG Trp
CU…CUU LeuCUC LeuCUA LeuCUG Leu
CC…CCU ProCCC ProCCA ProCCG Pro
CA…CAU HisCAC HisCAA GlnCAG Gln
CG…CGU ArgCGC ArgCGA ArgCGG Arg
AU…AUU IleAUC IleAUA IleAUG Met
AC…ACU ThrACC ThrACA ThrACG Thr
AA…AAU AsnAAC AsnAAA LysAAG Lys
AG…AGU SerAGC SerAGA ArgAGG Arg
GU…GUU ValGUC ValGUA ValGUG Val
GC…GCU AlaGCC AlaGCA AlaGCG Ala
GA…GAU AspGAC AspGAA GluGAG Glu
GG…GGU GlyGGC GlyGGA GlyGGG Gly
The standard genetic code (mRNA codons, read 5′→3′). AUG (Met) is also the start codon. UAA, UAG and UGA are stop codons.
DNA template 3′→5′TACAAACCGGTAATTmRNA 5′→3′AUGUUUGGCCAUUAAamino acidMetPheGlyHisStoptranscriptiontranslation (use the codon table)
Decoding a gene. The template strand is transcribed into mRNA, and each mRNA codon is looked up in the codon table. Translation starts at AUG and ends at the stop codon.
Worked example

Example 1: From template DNA to protein

The template strand of a gene reads 3′-TACAAACCGGTAATT-5′. Find the mRNA and the amino-acid sequence.

  1. Transcribe (pair with the template, U for T): 5′-AUG UUU GGC CAU UAA-3′.
  2. Look up each codon: AUG = Met (start), UUU = Phe, GGC = Gly, CAU = His, UAA = stop.
  3. The protein is Met-Phe-Gly-His. The stop codon adds no amino acid.

mRNA 5′-AUGUUUGGCCAUUAA-3′; protein Met-Phe-Gly-His.

Worked example

Example 2: Find the start codon first

Translate this mRNA: 5′-CCAUGGAGUAUGACUGAGC-3′.

  1. Translation does not start at the first base. Scan from the 5′ end for the first AUG: C C AUG ... (starting at the 3rd base).
  2. Read in triplets from there: AUG GAG UAU GAC UGA.
  3. AUG = Met, GAG = Glu, UAU = Tyr, GAC = Asp, UGA = stop.
  4. The bases before the AUG (CC) and after the stop codon (GC) are untranslated.

Met-Glu-Tyr-Asp.

Reading frames

Any sequence can be divided into triplets in three ways, depending on where you start. These are the three reading frames. Double-stranded DNA has three frames on each strand, so six in all. The start codon tells the ribosome which frame to use. A shift of one or two bases (for example, by inserting a base) puts the ribosome in a different frame and changes every amino acid downstream: a frameshift.

When scientists search a newly sequenced genome for genes, one clue is an open reading frame (ORF): a stretch beginning with ATG and running for a long way (hundreds of codons) without a stop codon. In random sequence, a stop codon turns up on average every 64 ÷ 3 ≈ 21 codons, so a long ORF is unlikely to happen by chance.

AUGGCCAUGGCGCCCAGAframe 1MetAlaMetAlaProArgframe 2TrpProTrpArgProframe 3GlyHisGlyAlaGln5′3′
The same RNA read in three reading frames gives three different amino-acid sequences. The ribosome uses the frame set by the start codon (AUG), here frame 1.
Worked example

Example 3: Analysing a simulated strand for an anomaly

A reference gene's coding strand is 5′-ATG GAG CCT GTT AAA TGA-3′. Three patients have these versions. For each, find the protein and describe the anomaly.

(a) 5′-ATG GAG CCT GTA AAA TGA-3′ (b) 5′-ATG GAG CCT GAT AAA TGA-3′ (c) 5′-ATG TAG CCT GTT AAA TGA-3′

  1. Reference mRNA: AUG GAG CCU GUU AAA UGA → Met-Glu-Pro-Val-Lys.
  2. (a) Codon 4 is GUA instead of GUU. GUA also codes for Val: protein Met-Glu-Pro-Val-Lys, unchanged (a silent change).
  3. (b) Codon 4 is GAU (T→A in the second position). GAU codes for Asp: Met-Glu-Pro-Asp-Lys (one amino acid changed, a missense change).
  4. (c) Codon 2 is UAG, a stop codon: the protein is only Met (a nonsense change; the protein is cut short).

(a) no change in protein; (b) Val → Asp; (c) protein stops after Met. (You will classify these mutations formally in Mutations and Mutagens.)

Worked example

Example 4: From protein back to DNA

A short peptide is Met-Trp-Lys. (a) How many different mRNA sequences (with a stop codon UAA) could code for it? (b) Write one possible coding strand.

  1. Met has 1 codon (AUG). Trp has 1 codon (UGG). Lys has 2 codons (AAA, AAG).
  2. Number of mRNAs = 1 × 1 × 2 = 2 (with the stop codon fixed as UAA).
  3. One possibility: mRNA 5′-AUG UGG AAA UAA-3′, so the coding strand is 5′-ATG TGG AAA TAA-3′.

(a) 2; (b) for example 5′-ATGTGGAAATAA-3′.

Just for fun

In 2010, scientists at the J. Craig Venter Institute built a bacterial genome from scratch and hid coded "watermarks" in its DNA, including the names of the scientists and a quotation from the writer James Joyce. Your genome has no hidden messages, as far as anyone knows.

Hands-on activity

Write a secret message in codons

You need: paper, a pencil, the codon table above, and a family member.

Scientists use a one-letter code for amino acids:

A Ala, C Cys, D Asp, E Glu, F Phe, G Gly, H His, I Ile, K Lys, L Leu, M Met, N Asn, P Pro, Q Gln, R Arg, S Ser, T Thr, V Val, W Trp, Y Tyr.

(The letters B, J, O, U, X and Z are not used.)

  1. Choose a short word that uses only these letters, such as HELP, CANADA or MAPLE.
  2. Write an mRNA that codes for it, starting with AUG (M) and ending with a stop codon. For HELP: AUG CAU GAA CUU CCU UAA.
  3. Give your family member only the template DNA strand (3′→5′) for your mRNA (for HELP: 3′-TAC GTA CTT GAA GGA ATT-5′).
  4. They must transcribe it, translate it with the table, and convert to one-letter codes, ignoring the first M.
  5. Swap roles. For a challenge, hide your start codon after a few extra bases, so the decoder must find the AUG first.

What to look for: the decoder should get MHELP (the M is the start methionine). Because the code is redundant, you and your partner may write different mRNAs for the same word: both are correct.

Your turn

1

Translate the mRNA 5′-AUGCAUGAACUUCCUUAA-3′.

2

Find the protein coded by the coding strand 5′-ATGAAACGCATTAGCTGA-3′.

3

How many codons code for amino acids, and how many are stop codons?

4

What did Nirenberg and Matthaei's poly-U experiment show?

5

Explain why a mutation in the third base of a codon often has no effect on the protein.

6

A simulated gene's coding strand is 5′-ATGGAGCCGTTAAATGA-3′, compared with the reference 5′-ATGGAGCCTGTTAAATGA-3′. Describe the anomaly and its effect.

More practice: warm-up

1

What is the start codon, and which amino acid does it code for?

2

Name the three stop codons.

3

What does UGG code for?

4

How many bases are in a codon?

5

How many reading frames does a double-stranded DNA molecule have?

More practice: on your own

1

The template strand of a gene is 3′-TACGTACTTGAAGGAATT-5′. Write the mRNA and the protein.

2

How many different mRNA sequences could code for the dipeptide Met-Gly (not counting the stop codon)? Explain.

3

Explain why a bacterium can make human insulin from the human coding sequence.

4

A section of mRNA reads 5′-GGAUGACUGAUAGC-3′. Find the start codon and translate.

5

Why is the third position of a codon sometimes called the "wobble" position?

Challenge

1

Read the mRNA 5′-AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA-3′ in all three frames on this strand. Which frame is most likely to be the real gene? Explain.

2

The probability that a random codon is a stop codon is 3/64. What is the probability that 100 random codons in a row contain no stop codon? What does this tell you about long ORFs?

3

Human mitochondria read UGA as tryptophan. A mitochondrial gene containing UGA in the middle is inserted into a bacterium. Predict the result and explain why genetic engineers must check for such cases.

Check your understanding

Quiz

1.

Why must codons be at least three nucleotides long?

2.

What is the amino-acid sequence coded by the mRNA 5′-GCAUGUGGAAGUAGC-3′?

3.

Which statement about the genetic code is FALSE?

4.

A reference codon GAA (Glu) changes to GAG in a patient. What happens to the protein?

5.

Which experiment first matched a codon to an amino acid?

6.

How many different mRNA codon sequences could code for Met-Phe (stop codon not counted)?

For parents and teachers

Big idea (D2.2, D3.3, D3.7): the genetic code is a dictionary of 64 three-letter mRNA codons: 61 for amino acids and 3 stop signals. Your teen should be able to go DNA → mRNA → protein confidently, and spot how a change in a DNA sequence changes (or doesn't change) the protein.

How to help: Play the "secret message" game from the activity. It is good practice for tests. Check that your teen starts reading at AUG, not at the first letter.

Common difficulties:

  • Translating the DNA coding strand directly instead of the mRNA (it works only if T is read as U), or translating the template strand by mistake.
  • Starting at the first base instead of the start codon.
  • Counting the stop codon as an amino acid.
  • Reading codons from the 3′ end.