From DNA to Protein

In one gene for hemoglobin, the protein that carries oxygen in red blood cells, a single DNA letter can be different: GTG where most people have GAG on the coding strand. That one change can let red blood cells bend into stiff, curved sickle shapes. A red blood cell is usually a soft, round disc that squeezes through tiny blood vessels. How can one letter, out of hundreds in the gene, change the shape of a whole cell?

Explore: transcribe, translate and mutate a gene

The simulation shows a short DNA template strand as lettered blocks. You build the messenger RNA that pairs with it, then use a codon chart to turn every three letters into an amino acid. A mutate button swaps, adds or removes one letter and rebuilds the chain.

DNA template

Or type your own template strand, written 3′ to 5′ (A, T, C, G; 3 to 15 letters) Use it

Steps

1. Build the mRNA 2. Translate

Mutate the DNA

Swap one letter Add one letter Remove one letter

Spot

letter 4 of 15

New letter ATCG

Mutate Undo mutation Reset

Codon chart (partial, from this lesson): AUG = Met, start GAG, GAA = Glu GUG = Val UUU, UUC = Phe GGC = Gly AAA = Lys UAA, UAG, UGA = stop Met methionine, Glu glutamic acid, Val valine, Phe phenylalanine, Gly glycine, Lys lysine.

In this sketch: DNA A pairs with RNA U, T with A, C with G, G with C. Reading begins at the first AUG (the usual start codon) and ends at a stop codon. Only the codons in the chart are named; any other shows a ?.

Rule to keep: ribosomes read mRNA three bases at a time, so one added or removed letter shifts every codon after it, while a swapped letter changes at most one codon, unless it removes or creates the AUG where reading begins.

Try this.

1. Predict the mRNA letters for the first three DNA blocks, then build the mRNA and check.
2. Find the codon where the chain starts and the codon where it stops. Predict what the stop codon adds to the chain, then translate and see.
3. Predict whether swapping one letter will change zero, one or many amino acids. Try three different spots.
4. Predict what adding one letter near the start does to the chain. Compare it with removing one.

Explain: copying a gene into messenger RNA

Protein synthesis is the making of a protein from the instructions in a gene, and it happens in two stages. In plant and animal cells the chromosomes stay in the nucleus, but proteins are built outside it. So the cell first makes a portable copy.

RNA is a nucleic acid, a chain of nucleotides like DNA, with three differences:

Feature	DNA	RNA
Strands	two, twisted into a double helix	usually one
Sugar	deoxyribose	ribose
Bases	A, T, C, G	A, U, C, G (uracil, U, in place of T)

Transcription is the first stage: an enzyme copies the base order of one gene into a strand of RNA. The enzyme unwinds a short piece of DNA and reads one strand, the template strand, pairing a new RNA base with each DNA base: DNA A with RNA U, T with A, C with G, G with C. The copy is messenger RNA (mRNA), the RNA that carries a gene’s instructions to the protein-building machinery.

Like DNA, RNA has direction: its two ends differ (biologists call them 5′ and 3′), and it is built and read one way only.

In cells with a nucleus, the mRNA leaves through pores in the nuclear membrane. Bacteria have no nucleus, so both stages happen in their cytoplasm.

Explain: reading the message three letters at a time

Translation is the second stage: the cell reads the mRNA and builds a chain of amino acids. An amino acid is one of the small building blocks of proteins; living things use about twenty common kinds. A ribosome is the structure that reads mRNA and joins amino acids together.

The ribosome reads the mRNA in groups of three bases. Each group of three is a codon, and each codon stands for one amino acid or for “stop.” With four bases there are 4 × 4 × 4 = 64 possible codons. In the standard code, 61 of them stand for amino acids and three, UAA, UAG and UGA, are stop codons. The codon AUG stands for methionine and is the usual start codon, where reading begins.

Transfer RNA (tRNA) is a small RNA that carries one amino acid and has a stretch of three bases, its anticodon, that pairs with a matching codon. As each tRNA pairs with its codon, the ribosome links its amino acid to the chain. At a stop codon no amino acid is added, and the chain is released. It folds into a shape that lets the protein do its job.

Here is part of the codon chart.

mRNA codon	Meaning
AUG	methionine (Met), start
GAG, GAA	glutamic acid (Glu)
GUG	valine (Val)
UUU, UUC	phenylalanine (Phe)
GGC	glycine (Gly)
AAA	lysine (Lys)
UAA, UAG, UGA	stop

Work one example. A DNA template strand, written from its 3′ end on the left to its 5′ end on the right, reads TAC CTC CTT AAA ACT.

1. Pair each base: the mRNA is AUG GAG GAA UUU UGA.
2. Translate: Met, Glu, Glu, Phe, then UGA means stop.
3. The chain is Met–Glu–Glu–Phe. The stop codon adds nothing.

Specialized cells make different proteins from the same genes: young red blood cells fill with hemoglobin, while some pancreas cells make insulin.

The genetic code, the set of codon meanings, is almost the same in every living thing, with a few exceptions, such as in some bacteria and in mitochondria. So a bacterium can read a suitably prepared gene for a human protein. In 1979 a team put man-made genes for the two chains of human insulin into E. coli; the bacteria made the chains, and once joined outside the cells, tests recognized them as insulin.

Explain: when one letter changes

A mutation is a change in the base order of DNA, from a rare copying error or from damage. Three kinds:

• A substitution swaps one base for another.
• An insertion adds one or more bases.
• A deletion removes one or more bases.

A substitution can be a silent mutation, one that leaves the amino acid the same because more than one codon stands for it (GAG and GAA both mean Glu). It can change one amino acid. Or it can turn a codon into a stop, cutting the chain short.

An insertion or deletion of one base causes a frameshift, a shift in how the bases are grouped into codons. Take THE CAT ATE THE RAT, delete the first T, and read in threes: HEC ATA TET HER AT. The analogy breaks because mRNA has no spaces; the ribosome groups letters from where it started.

Now the opening puzzle. In the usual numbering of beta-globin, a hemoglobin chain, the sixth amino acid is glutamic acid, coded by GAG. (Some databases count the starting methionine and call it the seventh.) The coding strand is the DNA strand that matches the mRNA letter for letter, with T where the mRNA has U. In the sickle allele this strand reads GTG, so the mRNA codon is GUG and valine replaces glutamic acid. Glutamic acid carries an electric charge and valine does not. Hemoglobin with valine there can stick together into stiff rods, mostly when it is low on oxygen, and the rods bend the cell into a sickle.

A person has two copies of this gene. With one sickle allele and one usual allele, a person has sickle cell trait and usually has no symptoms. Sickle cell disease happens when a person has a disease-causing change on both copies, and at least one of them is the sickle change.

Elaborate: is a mutation good or bad?

If the sickle allele can cause disease, why is it common in some places? Look at two kinds of real data.

Measure	Group or place	Year	Value	Units
Sickle cell trait positive screens	44 US states combined	2010	15.5	per 1,000 newborns screened
Sickle cell trait positive screens	Montana	2010	0.8	per 1,000 newborns screened
Sickle cell trait positive screens	Mississippi	2010	34.1	per 1,000 newborns screened
Sickle cell trait positive screens	Black or African American newborns, 13 states reporting race	2010	73.1	per 1,000 newborns screened
Sickle cell trait positive screens	White newborns, same 13 states	2010	3.0	per 1,000 newborns screened
Protection by sickle cell trait against mild malaria	children in two groups, coast of Kenya	published 2005	50	percent
Protection by sickle cell trait against hospital admission for malaria	same Kenyan children	published 2005	75	percent

Sources: rows 1 to 5, a CDC report (Ojodu and colleagues, MMWR, 2014) on newborns screened in 2010 in 44 states; screens were not confirmed diagnoses. Rows 6 and 7, Williams and colleagues (Journal of Infectious Diseases, 2005). Race groups are record labels; the allele follows family ancestry.

1. How many times higher is the Mississippi rate than the Montana rate?
2. In the Kenyan children, which outcome did the trait protect against more strongly?
3. Can the newborn rows alone tell you why the trait is more common in some groups?

Design problem

Use the simulation as a model to test this question: which kind of mutation most often changes the amino acid chain, a substitution, an insertion or a deletion? Plan a fair test.

One way to do it

• Hypothesis: If ribosomes read in threes, then one-base insertions and deletions will change the chain more often than substitutions.
• Independent variable: the kind of mutation (substitution, insertion or deletion of one base).
• Dependent variable: whether the chain changed, and how many amino acids changed.
• Constants: the same starting DNA, one mutation per trial, the same codon chart.
• Control: translate the starting DNA with no mutation, so you know the normal chain.
• Trials: 20 of each kind at randomly chosen spots; report the percent that changed the chain.

If insertions and deletions change the chain in almost every trial while some substitutions change nothing, the hypothesis is supported. The limit: a model of one short gene shows the chain, not whether a real folded protein still works.

Evaluate: check your thinking

A red blood cell changes shape because DNA letters are read in order: the gene is copied into mRNA, and ribosomes read it three letters at a time. Change GAG to GTG and one codon means valine, not glutamic acid. That one amino acid lets hemoglobin form rods that bend the cell, while many other changes would do nothing.

Science practices you used: predicting and testing with a model, translating a code with a chart, reading a data table and comparing rates, making a claim from evidence with reasoning, and planning a fair test with a control and repeated trials.