How Does a Gene Make a Protein?: Going Further 9–12

Proteins do the work

You know from Grade 10 that a gene is a stretch of DNA that carries the code for a character, and that the cell uses it to make a protein Grade 10: DNA. Why a protein? Because proteins do almost all the work in a living thing.

Protein	Where	What it does
amylase	saliva, and juice from the pancreas	cuts starch into sugar
hemoglobin	red blood cells	picks up oxygen in the lungs and lets it go in the body
keratin	hair, nails, the outer skin	tough fibers
collagen	skin, bone, tendons	strong ropes that hold the body together; about a quarter to a third of all your protein
actin and myosin	muscle cells	slide past each other to make a muscle pull
insulin	made in the pancreas, carried in the blood	a hormone: tells cells to take in sugar
antibodies	made by white blood cells	grab germs so that they can be destroyed

A protein that speeds up a chemical reaction, like amylase, is called an enzyme. Thousands of different enzymes run the chemistry in every cell.

The proteins a cell makes decide what kind of cell it is. A red blood cell is a bag of about 270 million hemoglobin molecules Grade 10: Red blood cells. A muscle cell is packed with actin and myosin. The cells at the root of a hair pump out keratin, about a centimeter of hair a month. Yet almost every cell in your body has the same DNA, the same genes. What makes a cell a muscle cell is which of its genes it uses. Cells of one kind work together as a tissue, and tissues as organs and systems Grade 8: Cell, tissue and organ: your body works because its specialized cells make the right proteins.

A chain that folds

A protein is a long chain of small molecules called amino acids, joined end to end like the beads of a mala. Living things use 20 kinds of amino acid. A protein chain is usually a few hundred long: one of hemoglobin’s chains has 146; the longest human protein, titin, in muscle, has over 34,000.

What makes one protein different from another is the order of its amino acids. Some amino acids are attracted to water and some avoid it; some carry an electric charge, positive or negative. So as soon as a chain is made, it folds up by itself into a particular shape: the parts that avoid water tuck inside, the charged parts stay outside, and opposite charges pull together. The same order always folds into the same shape. And the shape decides the job: amylase has a groove that a starch chain fits into, hemoglobin has pockets that hold oxygen, collagen chains twist together into ropes. You met the same idea with spider silk, whose repeating order of amino acids makes it strong (Inside a spider’s thread).

A computer drawing of a hemoglobin molecule on a black background: four tangled ribbons, two red and two blue, coiled into many spirals and packed into a rounded shape, with four small green ring-shaped groups held among them — **Figure 17.1** One molecule of hemoglobin, worked out from X-ray measurements. Each ribbon is a chain of about 140 amino acids, folded mostly into spirals: two chains of one kind (red) and two of another (blue). The green groups are the heme, each holding an iron atom that grabs oxygen. The whole molecule is about 5.5 nm across: about 10,000 of them side by side would just cross the width of a fine human hair. Photo: Richard Wheeler (Zephyris), CC BY-SA 3.0

Two proteins are made of exactly the same number of each kind of amino acid. Will they have the same shape?

Pick an answer to see why.

Four letters, twenty amino acids: the code

So a gene must hold an order of amino acids. But DNA has only four different bases, A, T, G and C Grade 10: DNA, and there are twenty amino acids to choose from. How can four letters name twenty things?

Not one letter per amino acid: that names only 4. Two letters per amino acid gives 4 × 4 = 16 pairs (AA, AT, AG, AC, TA…), still not enough. Three letters give 4 × 4 × 4 = 64, more than enough. And that is how the cell does it: the gene is read in groups of three bases, and each group, called a codon, stands for one amino acid. The rule that says which codon means which amino acid is the genetic code.

The code is read not on the DNA itself but on an RNA copy of it, so it is usually written with U (uracil) in place of T, as RNA has it Grade 10: RNA. Here it is: all 64 codons, with each amino acid’s three-letter short name (Ala for alanine, Gly for glycine…; the full names are listed below the table).

First letter	Second letter U	Second letter C	Second letter A	Second letter G
U	UUU Phe	UCU Ser	UAU Tyr	UGU Cys
	UUC Phe	UCC Ser	UAC Tyr	UGC Cys
	UUA Leu	UCA Ser	UAA Stop	UGA Stop
	UUG Leu	UCG Ser	UAG Stop	UGG Trp
C	CUU Leu	CCU Pro	CAU His	CGU Arg
	CUC Leu	CCC Pro	CAC His	CGC Arg
	CUA Leu	CCA Pro	CAA Gln	CGA Arg
	CUG Leu	CCG Pro	CAG Gln	CGG Arg
A	AUU Ile	ACU Thr	AAU Asn	AGU Ser
	AUC Ile	ACC Thr	AAC Asn	AGC Ser
	AUA Ile	ACA Thr	AAA Lys	AGA Arg
	AUG Met, Start	ACG Thr	AAG Lys	AGG Arg
G	GUU Val	GCU Ala	GAU Asp	GGU Gly
	GUC Val	GCC Ala	GAC Asp	GGC Gly
	GUA Val	GCA Ala	GAA Glu	GGA Gly
	GUG Val	GCG Ala	GAG Glu	GGG Gly

The amino acids: Ala alanine, Arg arginine, Asn asparagine, Asp aspartic acid, Cys cysteine, Gln glutamine, Glu glutamic acid, Gly glycine, His histidine, Ile isoleucine, Leu leucine, Lys lysine, Met methionine, Phe phenylalanine, Pro proline, Ser serine, Thr threonine, Trp tryptophan, Tyr tyrosine, Val valine.

Look at the table and you will notice three things.

61 codons name amino acids, and 3 mean “stop”: UAA, UAG and UGA end the protein.
AUG means “start here”. Every protein begins with methionine (Met); many have it cut off later.
Most amino acids have more than one codon, often differing only in the third letter: GUU, GUC, GUA and GUG all mean valine. Only methionine and tryptophan have one each. So some changes in the third letter make no difference at all.

A story from science

Cracking the code

In 1961 the American biochemist Marshall Nirenberg and the German Heinrich Matthaei mashed up bacteria to get a liquid that could still build proteins, and fed it an artificial RNA made of nothing but U: UUUUUU… Out came a chain made of only one amino acid, phenylalanine. The first word of the code was read: UUU means Phe.

The next step needed RNA with known patterns of letters, and the chemist who could make them was Har Gobind Khorana. He was born in 1922 in Raipur, a village of about a hundred people in Punjab (now in Pakistan), where, he later wrote, his family was practically the only one that could read. His father, a village tax clerk, made sure the children were educated; Khorana studied chemistry in Lahore and in England, and by 1960 had his own laboratory in the USA. There his team built RNAs with repeating patterns. UCUCUC… for example, read in threes, is UCU CUC UCU CUC…, and it made a chain of serine and leucine, turn and turn about. Pattern by pattern, by 1966 all 64 codons had been worked out. In 1968 Khorana and Nirenberg shared the Nobel Prize with Robert Holley, who had read the whole order of letters of the molecule that carries amino acids to the ribosome. Khorana went on to make the first artificial gene.

A black-and-white portrait photograph of a man with dark hair and round glasses, in a jacket and tie — **Figure 17.2** Har Gobind Khorana (1922–2011). Photo: Unknown author, Public domain

Why can’t the genetic code use two-letter codons?

Pick an answer to see why.

Step 1: copying the gene

Your DNA stays in the nucleus, like a precious book that never leaves the library. But proteins are built outside it, in the cytoplasm, by ribosomes Grade 8: Ribosomes. So the cell sends out a copy of the one gene it needs, as messenger RNA (mRNA). Making that copy is transcription.

An enzyme, RNA polymerase, sits on the DNA at the start of the gene and unzips a short stretch of the double helix, breaking the weak hydrogen bonds between the base pairs.
One of the two strands, the template strand, is used as the pattern. RNA nucleotides floating in the nucleus pair with its bases, one by one, by the pairing rule: A with U, T with A, G with C, C with G.
The enzyme joins them into a chain and moves along the gene. Behind it the new mRNA peels away, and the DNA zips up again.
At the end of the gene the finished mRNA is let go. It leaves the nucleus through a nuclear pore Grade 8: Nucleus and goes to the ribosomes.

Because the mRNA pairs with the template strand, it ends up with the same letters as the other strand of the DNA, the coding strand, except that it has U wherever the coding strand has T.

Figure 17.3 The first seven codons of the human gene for β-globin, one of the chains of hemoglobin. Each letter of the mRNA pairs with a letter of the template strand, so the mRNA reads the same as the coding strand, with U in place of T. Only the letters are shown; in a cell the mRNA peels off the DNA as it is made.

Step 2: reading the message

At a ribosome the mRNA is read, three letters at a time, and turned into a chain of amino acids. This is translation: from the language of bases into the language of amino acids.

The amino acids are brought by transfer RNA (tRNA) Grade 10: RNA. A tRNA is a short RNA, folded into an L shape. At one end it carries one particular amino acid; at the other it has three bases, its anticodon, which pair with a codon. So the tRNA carrying valine has an anticodon that pairs with a valine codon, and nothing else. (Many tRNAs pair loosely at the third letter, so one tRNA can read two or three codons for the same amino acid.) The tRNA is the dictionary: it is what links each codon to its amino acid.

The small part of a ribosome attaches near the start of the mRNA and slides along it to the first AUG. A tRNA carrying methionine pairs with it, and the large part of the ribosome joins on, clamping the mRNA between the two.
The next codon sits in the ribosome. The tRNA whose anticodon fits it arrives with its amino acid.
The ribosome joins the new amino acid to the chain. The chain now hangs from the newest tRNA, and the ribosome moves along the mRNA by three letters. The empty tRNA leaves, to pick up another amino acid.
This repeats, codon after codon, until a stop codon comes into the ribosome. No tRNA fits a stop codon. The finished chain is let go, and folds into its shape.

In a human cell a ribosome adds roughly 5 to 10 amino acids a second; in bacteria, up to about 20. Many ribosomes read one mRNA at the same time, one behind the other, so a single message makes many copies of its protein.

The real mRNA for β-globin passes through a ribosome. Press Next codon to add each amino acid, then skip to the end to see the stop codon. (Not to scale: a real ribosome covers about ten codons.)

Codon being read: GUG
Its tRNA brings: Val (valine)
Chain so far: 1 amino acid

The ribosome has found the start codon, AUG, and a tRNA has brought methionine. The next tRNA has arrived: its letters pair with the next codon. Press Next codon to join its amino acid to the chain.

Worked example

How long is the message, and how long does it take?

The β-globin chain in hemoglobin has 146 amino acids. It is made with a methionine at the front, which is cut off afterwards.

a.How many letters of mRNA, from the start codon to the end of the stop codon, does it take to code for it?
b.If a ribosome adds 6 amino acids a second, about how long does it take to make one chain?

Answer

a.Codons: 146 amino acids + 1 methionine + 1 stop codon = 148 codons. Letters: 148 × 3 = 444 letters. That is exactly the length of the coding part of the real gene.
b.The ribosome adds 147 amino acids (146 + the methionine), so the time is:

$t = \frac{147\ \text{amino acids}}{6\ \text{amino acids/s}} = 24.5\ \text{s}$
About 25 seconds: less than half a minute for one chain.

A codon on the mRNA reads GCA. Which amino acid will the ribosome add, and what carries it there?

Pick an answer to see why.

Where in a cell does each step happen?

Pick an answer to see why.

Figure 17.4 The whole journey, from a gene to a working protein, in one of your cells. Each mRNA is finished, and has left the nucleus, before ribosomes read it. Not to scale: a nucleus is about 6 µm across, a ribosome about 25 nm, a thousand times smaller than drawn here beside it.

One wrong letter

In Grade 9 you met mutations: sudden changes in the genes that can be passed on, like the change that causes sickle-cell anemia Grade 9: Mutation. Now you can see exactly what one does.

Look again at the start of the β-globin gene. The amino acid at position 6 (counting from the valine after the methionine, which is cut off) is glutamic acid, coded by GAG. In the gene for sickle hemoglobin, the A in the middle of that codon is a T: GAG has become GTG, and in the mRNA, GUG. GUG codes for valine. One letter of the gene’s 444, one amino acid of the protein’s 146.

But they are very different amino acids. Glutamic acid carries a negative charge and likes water. Valine has no charge and avoids water: it leaves a small greasy patch on the outside of the hemoglobin molecule. While the hemoglobin holds oxygen, it does little harm. When the hemoglobin has given up its oxygen, in the small blood vessels of the body, the greasy patch of one molecule sticks into a pocket on the next. The molecules join into long, stiff fibers, which stretch the red blood cell out of its soft disc shape into a stiff, curved sickle.

Figure 17.5 From one letter to a whole cell. On the left, the usual hemoglobin; on the right, sickle hemoglobin. The molecules and cells are drawn at different scales: a hemoglobin molecule is about 5.5 nm across, a red blood cell about 7.5 µm, more than a thousand times bigger. The real fibers are thicker bundles of 14 strands of molecules, simplified here.

Stiff sickle cells can’t squeeze through the narrowest blood vessels the way soft discs do Grade 10: Red blood cells. They jam, block the flow, and cause bouts of terrible pain and damage to organs. They also break up after 10 to 20 days instead of 120, so the body runs short of red cells: anemia. That is the whole chain of cause and effect: a change in the DNA changes a protein’s structure, the structure changes what it does, and that changes the cell and the body.

A microscope view of a blood smear: many round, pale purple red blood cells, and among them several long, thin, curved cells shaped like a crescent; an arrow points to one. A larger white blood cell with a dark, lumpy nucleus sits in the middle. — **Figure 17.6** Blood from a person with sickle-cell anemia, seen through a microscope. Among the round red cells are long, curved sickle cells (the arrow points to one). The large cell with the purple nucleus is a white blood cell. Photo: Paulo Henrique Orlandi Mourao, CC BY-SA 4.0

Everyone has two copies of the β-globin gene, one from each parent Grade 10: Mendel’s laws. A person with two sickle copies has sickle-cell disease. A person with one sickle copy and one usual copy, a carrier, makes both kinds of hemoglobin, and is almost always healthy. Carriers have an advantage, too: they are much less likely to die of severe malaria, because the malaria parasite lives inside red blood cells and does badly in those that contain sickle hemoglobin. So where malaria killed many people for many generations, the sickle gene became common: in Africa, in India, and in parts of Nepal’s Terai, whose forests were full of malaria until it was brought under control in the 1950s and 60s. Surveys in western Nepal since 2017 have found carriers in roughly one person in ten to one in seven in some villages. Nepal’s National Public Health Laboratory and its partners tested 6,000 people in Bardiya in 2017–18, and Lumbini Province has offered free screening since 2022.

A story from science

How the wrong letter was found

In 1949 the American chemist Linus Pauling and his team put hemoglobin from healthy people and from people with sickle-cell anemia in an electric field. The sickle hemoglobin moved differently: its molecules carried a different electric charge. They called sickle-cell anemia “a molecular disease”, the first disease traced to a fault in one kind of molecule. In 1956 and 1957 Vernon Ingram in Cambridge cut both hemoglobins into small pieces and compared them. Out of the whole chain, exactly one amino acid was different: valine in place of glutamic acid. That explained the charge: glutamic acid is charged, valine is not. When the genetic code was cracked in the 1960s, it predicted the DNA change, and when genes could at last be read, there it was: T in place of A, in codon 6.

A carrier of the sickle-cell gene has one usual and one sickle copy of the β-globin gene. What is in their red blood cells?

Pick an answer to see why.

Kinds of change

Not every change in a gene does harm, and not every change does it the same way. Try some real changes in the β-globin gene, all known from real people.

The start of the β-globin gene (its coding strand), split into codons, with the amino acid each one codes for. Pick a change and compare the protein with the usual one. Changed letters and amino acids are in red.

Protein length: 146 of 146 amino acids
Amino acids changed: 0

The start of the usual gene. Its 444 letters code for 146 amino acids, after the first methionine (which is cut off), then a stop. Pick a change.

The changes fall into a few kinds:

A silent change: a letter changes, but the new codon means the same amino acid (CAT and CAC both mean histidine). The protein is exactly the same. Many people carry one or other of these two versions, with no difference.
A change of meaning: the new codon means a different amino acid, as in sickle hemoglobin (valine) and hemoglobin C (lysine) at the same spot. How much it matters depends on where the change is and how different the new amino acid is: many such changes do little; some, like sickle hemoglobin, change the protein’s behavior completely.
A new stop: the new codon is a stop codon. The chain ends too soon and the protein is useless. A stop at codon 17 of β-globin is one cause of β-thalassemia, a disease in which the body can’t make enough hemoglobin.
A letter added or lost: the cell reads in threes from the start, so every codon after the change is read wrongly. This is a frameshift. The chain becomes nonsense until, by chance, a stop codon turns up. An extra G between codons 8 and 9 is one of the commonest causes of β-thalassemia in northern India.

Most changes in DNA are copying mistakes, or damage by ultraviolet light, X-rays and some chemicals Grade 9: Mutation. The cell repairs nearly all of them. Of the few that last, most are harmless, some are harmful, and a very few turn out useful. They are the raw material of evolution.

Gene to trait: the whole chain

Put the pieces together and you have an explanation, step by step, of how DNA decides what a living thing is like:

The order of bases in a gene is copied into mRNA (transcription).
The ribosome reads the mRNA three bases at a time and builds a chain with the matching order of amino acids (translation), using the genetic code.
The order of amino acids decides how the chain folds, and so the protein’s shape.
The shape decides the protein’s job: carrying oxygen, cutting starch, pulling a muscle.
Specialized cells make the proteins their job needs, and work together in tissues, organs and systems.
So a change in the order of bases can change a protein, a cell and the whole body: a trait.

The evidence for each link comes from experiments you have read about: Sanger showed that each protein has an exact order; Nirenberg and Khorana read the code; Ingram found that one changed amino acid makes sickle hemoglobin; and bacteria given a human gene make the human protein.

Activity

Investigate: an enzyme in your mouth

You need: a little plain boiled rice (or a piece of plain roti or bread with no sugar), a glass of water, and a clock.

Rinse your mouth with water.
Put a spoonful of rice in your mouth. Chew it steadily, without swallowing, and notice the taste at the start.
Keep chewing. Every 30 seconds, note whether it tastes any sweeter. Stop at 3 minutes.
Rinse, and try again with a small piece of cucumber or a boiled egg white, which have almost no starch. Does it get sweeter this time?
If you can, compare: does the rice get sweet faster if you chew it more thoroughly?

What you should see

The rice and the roti start to taste sweet after a minute or two: the enzyme amylase in your saliva is cutting the starch into a sugar (maltose). The cucumber or egg white does not get sweeter, because it has little starch for the enzyme to cut. Chewing well mixes in more saliva and gives the enzyme more surface to work on, so the sweetness comes sooner. The amylase in your mouth was built by your salivary-gland cells, following a gene on chromosome 1.

In short

Proteins do most of the work of living things: enzymes such as amylase, hemoglobin, keratin, collagen, insulin, antibodies. Specialized cells are specialized because of the proteins they make.
A protein is a chain of amino acids (20 kinds). Their order decides how it folds, its shape, and so its job.
The genetic code turns DNA’s order of bases into an order of amino acids: each codon of three bases means one amino acid, or stop. 4³ = 64 codons; AUG means start; UAA, UAG and UGA mean stop. The same code is used by almost all life.
Transcription, in the nucleus: the gene is copied into mRNA, pairing with the template strand.
Translation, at a ribosome: tRNAs with matching anticodons bring the amino acids, which are joined in the order of the codons until a stop codon.
A change in one base can change one amino acid (sickle hemoglobin), nothing (a silent change) or end the chain early; a base added or lost shifts every codon after it.

Questions

A gene has 900 bases that code for its protein, from the start codon to the end of the stop codon. About how many amino acids does the protein have?

Pick an answer to see why.

Which of these changes in the coding letters of a gene is most likely to leave the protein unchanged?

Pick an answer to see why.

a.

Explain why a cell needs mRNA at all. Why doesn’t the ribosome read the DNA directly?

Answer

The DNA stays inside the nucleus, safely packed in the chromosomes, while proteins are made at ribosomes in the cytoplasm. Sending out mRNA copies of a gene, through the nuclear pores, keeps the precious master copy safe and unchanged, while many short-lived copies of just the gene that is needed go out to the ribosomes. Many copies of the mRNA, each read by many ribosomes at once, also let the cell make a lot of one protein quickly; and when the cell needs less, it stops copying the gene and the old mRNAs are broken down.

b.

Part of the template strand of a gene reads TAC AAA CCG TTA ACT.

i.Write the mRNA.
ii.Write the order of amino acids.
iii.What would happen if the fourth codon’s template letters TTA changed to ATT?

Answer

i.mRNA: AUG UUU GGC AAU UGA.
ii.Met–Phe–Gly–Asn, then UGA is a stop codon, so the chain ends.
iii.ATT on the template gives UAA in the mRNA, which is also a stop codon. So the chain would end one codon earlier: Met–Phe–Gly, without the asparagine. (A made-up stretch, for practice.)

c.

Hemoglobin C is caused by a change in the same codon as sickle hemoglobin: GAG becomes AAG.

i.Which amino acid replaces glutamic acid?
ii.Glutamic acid has a negative charge; lysine has a positive charge. Pauling’s method separated molecules by their electric charge. Would it tell hemoglobin C apart from usual hemoglobin? Explain.

Answer

i.AAG codes for lysine (Lys).
ii.Yes. Usual hemoglobin has a negatively charged glutamic acid at that spot, and hemoglobin C has a positively charged lysine there, so the whole molecule of hemoglobin C carries a different charge (more positive), and in an electric field it moves differently. (It does: hemoglobin C moves even less than sickle hemoglobin towards the positive side, because valine, in sickle hemoglobin, has no charge at all.)

d.

A student says: “A muscle cell and a red blood cell must have different DNA, because they make different proteins.” Use what you know to say whether the student is right.

Answer

The student is wrong. Almost every cell in the body came from the same fertilized egg by mitosis, so they have the same DNA, with the same genes (mature red blood cells actually lose their nucleus, but the cells they grew from had the full set). What differs is which genes each cell uses: a developing red blood cell transcribes the globin genes over and over and makes huge amounts of hemoglobin; a muscle cell transcribes the genes for actin and myosin. The different proteins make the cells different in shape and job.

e.

Use the evidence about sickle-cell anemia to construct an explanation of how the structure of DNA determines the structure and function of a protein, and so the working of a whole body. Your answer should go from the DNA to the person.

Answer

DNA: in the gene for β-globin, the codon for the sixth amino acid is GAG; in the sickle gene, one base is different, GTG.
mRNA: transcription copies the difference: GAG becomes GUG.
Amino acid order: by the genetic code, GAG means glutamic acid and GUG means valine, so the ribosome puts valine in place of glutamic acid; Ingram found exactly this, and nothing else, different in sickle hemoglobin.
Protein structure: glutamic acid is charged and attracted to water; valine is uncharged and avoids water, so sickle hemoglobin has a greasy patch on its surface (Pauling found its charge was different). When it has given up its oxygen, the patch sticks to the next molecule and the molecules join into long stiff fibers.
Cell: the fibers stretch the red blood cell into a stiff sickle shape.
Body: sickle cells block small blood vessels, causing pain and organ damage, and they break down early, causing anemia. A person with two sickle copies has the disease; with one copy, enough usual hemoglobin is made to stay healthy.

So the order of bases in DNA sets the order of amino acids, which sets the protein’s shape and how it behaves, and that decides how the cells and the body work.

f.

Human insulin is now made by bacteria that have been given the human insulin gene. What does this tell us about the genetic code? Why is it useful?

Answer

The bacteria read the human gene and build exactly the same chain of amino acids as a human cell does, so they must read each codon as the same amino acid: the genetic code is the same in bacteria and in humans (it is almost universal across all life). It is useful because bacteria can be grown in huge tanks to make large amounts of insulin with exactly the human sequence, cheaply and reliably, instead of extracting it from the pancreas of pigs and cows, whose insulins differ from ours by one or three amino acids.

Where to go next

How Does One Cell Become a Whole Person? Every cell has the same genes. How cells become skin, muscle or brain by using different ones.
Why Aren’t You Exactly Like Your Brother or Sister? Where the variety in genes comes from: the shuffling of chromosomes, and mutations like the ones in this topic.
How Does DNA Show That All Life Is Related? One genetic code for bacteria, rice and you, and what the small differences between our proteins tell us about our relatives.