D1.2 Protein synthesis

Transcription: making RNA from a DNA template

The instructions for making a polypeptide are stored in a gene as a sequence of bases in DNA. In eukaryotes the DNA stays in the nucleus, but polypeptides are made on ribosomes in the cytoplasm. A copy of the gene is therefore made in the form of messenger RNA, which carries the base sequence to the ribosomes. Making this RNA copy is called transcription.

The enzyme that carries out transcription is RNA polymerase. It has three main roles:

• It binds to the DNA at the start of a gene and unwinds the double helix.

• It separates the two strands over a short stretch of about 10–20 base pairs by breaking the hydrogen bonds between bases, so that the bases of one strand are exposed.

• It links RNA nucleotides together to form an RNA strand complementary to the template strand, by forming covalent phosphodiester bonds between the ribose of one nucleotide and the phosphate of the next.

RNA polymerase moves along the gene, building the RNA as it goes. Behind it, the RNA strand separates from the template and the two DNA strands rejoin into a double helix. When RNA polymerase reaches the end of the gene, it releases the completed RNA molecule. Unlike DNA polymerase, RNA polymerase does not need a primer: it can start a new strand on its own.

The steps of transcription in order are:

1. RNA polymerase binds to the DNA at the start of a gene.

2. RNA polymerase unwinds the double helix and separates the strands over a short region, exposing the bases of the template strand.

3. Free RNA nucleotides pair with the exposed DNA bases by complementary base pairing, forming hydrogen bonds.

4. RNA polymerase links the RNA nucleotides with phosphodiester bonds, forming a strand of RNA.

5. The RNA separates from the DNA, and the DNA strands rewind into a double helix.

6. At the end of the gene, the RNA is released. In eukaryotes this RNA then leaves the nucleus through the nuclear pores.

The RNA that carries the base sequence of a gene to the ribosomes is messenger RNA (mRNA). Not all transcription makes mRNA: the genes for transfer RNA (tRNA) and ribosomal RNA (rRNA) are also transcribed, but these RNAs are not translated into polypeptides. Instead they take part in translation themselves.

Complementary base pairing in transcription

Template strand and coding strand

Only one of the two DNA strands of a gene is transcribed. The strand that RNA polymerase reads is the template strand (also called the antisense strand). The mRNA is complementary to it.

The other strand is the coding strand (also called the sense strand). It is not used in transcription, but it has the same base sequence as the mRNA, except that it contains thymine wherever the mRNA contains uracil. Its sequence is therefore the one usually written when a gene sequence is published.

A pairs with U

RNA contains the base uracil (U) instead of thymine. As RNA nucleotides line up along the template strand, each forms hydrogen bonds with the complementary DNA base. The pairing rules are the same as in DNA except where adenine is involved:

Hydrogen bonds are weak individually, so the RNA can separate easily from the template once RNA polymerase has moved on, but together they are strong enough to hold each new nucleotide in place long enough for it to be linked to the chain. The specificity of the pairing is what ensures that the mRNA carries an accurate copy of the gene.

Stability of DNA templates

Transcription separates the two DNA strands only temporarily, and it does not use up or alter the template. RNA polymerase reads the bases of the template strand but does not change them, and the DNA strands rejoin behind it. The same gene can therefore be transcribed over and over again, producing many mRNA molecules from one copy of the gene.

This stability matters most in cells that no longer divide. Neurons in the brain and muscle fibres in the heart can last for the whole life of the organism, many decades in a human. They never replicate their DNA again, so the one copy they have must keep its base sequence unchanged while it is transcribed thousands of times. DNA is well suited to this because its bases are protected inside the double helix and held by many hydrogen bonds, and because it is chemically more stable than RNA. mRNA molecules, by contrast, are broken down within minutes to hours, which allows a cell to change which proteins it makes.

Transcription and gene expression

A human cell contains about 20,000 protein-coding genes, but no cell uses all of them. A red blood cell precursor makes large amounts of haemoglobin, while a cell in the pancreas makes insulin; neither makes the other protein, although both have the genes for both. The process by which the information in a gene is used to make a product is called gene expression.

Transcription is the first stage of gene expression, so it is a key point at which expression can be switched on or off. If a gene is not transcribed, no mRNA is made and the polypeptide cannot be produced. Cells control which genes are transcribed in response to signals from inside and outside the cell, for example hormones. Some genes, such as those for the enzymes of glycolysis, are expressed in almost every cell all the time; others are expressed only in particular cell types or at particular times.

Differences in gene expression explain how cells with identical genomes become specialised. During differentiation, each cell type comes to express its own set of genes. All the cells of the body share the same DNA, but they differ in the genes they transcribe, which is a clear example of unity and diversity at the level of cells.

Translation: making a polypeptide from mRNA

In the second stage of gene expression, the base sequence of the mRNA is used to build a polypeptide with a particular sequence of amino acids. This is called translation, because information in the "language" of bases is converted into the "language" of amino acids.

Translation takes place on ribosomes in the cytoplasm. In eukaryotes, mRNA made in the nucleus leaves through the nuclear pores and binds to a ribosome. Some ribosomes are free in the cytosol and make proteins that stay in the cell; others are attached to the rough endoplasmic reticulum and make proteins that are secreted or sent to membranes. Prokaryotes have no nucleus, so translation can begin while the mRNA is still being transcribed.

The roles of mRNA, ribosomes and tRNA

Three kinds of RNA work together in translation, and each has a distinct job.

mRNA carries the code

mRNA carries the base sequence copied from the gene. The bases are read in groups of three, called codons, from one end of the molecule to the other. Each codon specifies one amino acid, so the sequence of codons fixes the sequence of amino acids in the polypeptide.

Ribosomes are the site of translation

A ribosome is built from rRNA and proteins, arranged in two subunits of different sizes. Prokaryotic ribosomes (70S) are smaller than the ribosomes in the cytoplasm of eukaryotes (80S), but they work in the same way.

• The small subunit has the binding site for mRNA. The mRNA lies in a groove on the small subunit, between the two subunits.

• The large subunit has binding sites for tRNA. Two tRNA molecules can bind at the same time, next to each other, each paired with a neighbouring codon of the mRNA.

• The large subunit also catalyses the formation of peptide bonds between amino acids. The catalytic activity comes from its rRNA, not its proteins, so the ribosome acts as a ribozyme.

tRNA brings the amino acids

Each tRNA molecule is a single strand of about 76–90 nucleotides that folds back on itself, with hydrogen bonds between complementary bases in some regions, into a shape like a clover leaf. Two parts of it matter for translation:

• the anticodon, a sequence of three bases in a loop at one end, which pairs with a codon on the mRNA;

• the amino acid attachment site at the 3′ end of the molecule (which always ends in the bases CCA), where a specific amino acid is carried.

Each tRNA carries only the amino acid that matches its anticodon. The correct amino acid is attached by an enzyme called aminoacyl-tRNA synthetase, using energy from ATP. There are 20 of these enzymes, one for each amino acid, and each recognises both its amino acid and the shape and anticodon of the tRNAs that should carry it. This step is as important for accuracy as base pairing, because a tRNA with the wrong amino acid would insert it into the polypeptide.

Codons and anticodons

Translation depends on complementary base pairing between the mRNA and the tRNAs, in the same way that transcription depends on pairing between DNA and RNA.

The codon is on the mRNA. The matching triplet on the tRNA is the anticodon. When a tRNA arrives at the ribosome, its three anticodon bases form hydrogen bonds with the three bases of the codon: A with U and C with G. Only a tRNA whose anticodon is complementary to the codon can bind stably, so the codon decides which tRNA, and therefore which amino acid, is added next.

The codon and anticodon are antiparallel, like the two strands of DNA. The codon AUG, read 5′ to 3′, pairs with the anticodon UAC, written 3′ to 5′. Both are RNA, so neither contains thymine.

Features of the genetic code

The genetic code is the set of rules that relates codons to amino acids. It has several features that explain how a sequence of only four bases can specify proteins made from 20 different amino acids.

A triplet code

Proteins are built from 20 different amino acids, so the code must have at least 20 different "words". With four bases there are only four single-base words, which is too few. Pairs of bases give 16 combinations, still too few. Triplets of bases give 64 combinations, which is more than enough.

The genetic code is therefore a triplet code: each amino acid is specified by a group of three bases. The code is also non-overlapping and read without gaps: the ribosome reads the mRNA three bases at a time, one codon after another, from a fixed starting point. Where reading starts therefore sets the "reading frame" for the whole message.

Degeneracy

Of the 64 codons, 61 code for amino acids and 3 are stop signals. With 61 codons for 20 amino acids, most amino acids are coded by more than one codon. This feature is called degeneracy. Leucine, serine and arginine each have six codons; most amino acids have two or four. Only methionine (AUG) and tryptophan (UGG) have a single codon each.

Codons for the same amino acid usually differ only in the third base: GCU, GCC, GCA and GCG all code for alanine. Because of this, a change in the third base of a codon often has no effect on the polypeptide. Degeneracy therefore makes the code more tolerant of some mutations, an idea developed in D1.3 Mutations and gene editing.

Universality

With very few exceptions, the same codons code for the same amino acids in all living organisms, from bacteria to plants to humans, and in viruses too. This is called the universality of the genetic code. The few known variations, such as in mitochondria and some single-celled eukaryotes, affect only a handful of codons.

Universality is strong evidence that all life shares a common ancestry: the code was established in the earliest cells and has been inherited by all their descendants, because almost any change to it would have altered every protein at once. Universality also makes genetic engineering possible. In 1982 human insulin made by bacteria (Humulin) became the first drug from recombinant DNA approved in the USA: E. coli given the human insulin gene translates it into the same amino acid sequence as a human cell does.

Start and stop codons

Translation begins at a start codon, AUG, which also codes for methionine. Every polypeptide therefore starts with methionine, although it is often removed later. Translation ends at one of three stop codons, UAA, UAG or UGA. No tRNA has an anticodon for a stop codon. Instead, a protein called a release factor binds, and the completed polypeptide is released from the ribosome.

Case study: cracking the first codon

In 1961 it was known that the sequence of bases in DNA determined the sequence of amino acids in proteins, but not which base combination coded for which amino acid. At the US National Institutes of Health, Marshall Nirenberg and Heinrich Matthaei tested this with a cell-free system: an extract of broken E. coli cells that contained ribosomes, tRNAs, enzymes and amino acids, and could make protein if it was given RNA to translate.

On 27 May 1961, Matthaei added a synthetic RNA made only of uracil nucleotides (poly-U) to the extract. He set up 20 tubes, each containing all 20 amino acids but with a different one labelled with radioactive carbon-14. If poly-U was translated, only the tube with the labelled form of the correct amino acid would produce radioactive protein.

Source: Matthaei’s experiment of 27 May 1961, Marshall Nirenberg papers, NIH National Library of Medicine; published in Nirenberg and Matthaei, PNAS 47:1588, 1961.

Only the tube with labelled phenylalanine made radioactive protein, and adding poly-U increased its radioactivity more than 500-fold. The protein produced was polyphenylalanine, a chain made only of phenylalanine. Since poly-U contains only the codon UUU, UUU must code for phenylalanine. Nirenberg presented the result at the International Congress of Biochemistry in Moscow in August 1961.

The experiment showed how a hypothesis about the code could be tested directly. Over the next five years, Nirenberg, Har Gobind Khorana and others used synthetic RNAs of known sequence to assign all 64 codons, confirming that the code is a triplet code and that it is degenerate. Nirenberg, Khorana and Robert Holley, who determined the structure of a tRNA, shared the 1968 Nobel Prize in Physiology or Medicine.

Using the genetic code table

The genetic code is usually shown as a table of mRNA codons. To find a codon, the first base gives the row block, the second base the column and the third base the row within the block.

The standard genetic code, written as mRNA codons. Amino acids use their three-letter abbreviations.

Deducing an amino acid sequence from a DNA strand takes two steps. First write the mRNA, by pairing with the template strand or by copying the coding strand with U for T. Then divide the mRNA into codons from the start codon and look each one up.

When the starting point is a DNA strand, one extra step comes first. From the template strand, each base is paired with its RNA partner; from the coding strand, the sequence is copied with U in place of T. Keeping the 5′ and 3′ ends labelled avoids reading the codons backwards.

Elongation: building the polypeptide step by step

Once translation has started, the polypeptide is lengthened one amino acid at a time as the ribosome moves along the mRNA. This stage, elongation, repeats the same cycle of three steps for every codon.

1. Codon recognition. A tRNA carrying an amino acid arrives at the ribosome. Its anticodon pairs with the next codon of the mRNA by complementary base pairing, so the tRNA binds next to the tRNA that holds the growing polypeptide. Two tRNAs are now bound to the large subunit side by side.

2. Peptide bond formation. The large subunit catalyses a peptide bond between the amino acid on the new tRNA and the end of the growing chain. The whole polypeptide is transferred to the new tRNA, so the chain is now one amino acid longer and attached to the tRNA on the newest codon. The reaction is a condensation reaction.

3. Translocation. The ribosome moves along the mRNA by exactly one codon (three bases). The tRNA that has given up its chain leaves the ribosome and can collect another amino acid. The tRNA carrying the polypeptide moves into the neighbouring position, and the next codon is exposed for a new tRNA.

These steps repeat until the ribosome reaches a stop codon. The polypeptide is then released, and the ribosome separates into its two subunits. A ribosome adds roughly 15–20 amino acids per second in bacteria, and several ribosomes can translate one mRNA at the same time, one behind another, so many copies of a polypeptide are made quickly from a single mRNA.

Mutations that change protein structure: sickle cell anaemia

The sequence of amino acids in a polypeptide follows directly from the base sequence of its gene, so a change to the base sequence can change the protein. A change to a single base is called a point mutation. Many point mutations have no effect, but some alter one amino acid with serious consequences. Sickle cell anaemia is the best-studied example.

From one base to one amino acid

Adult haemoglobin is made of four polypeptides, two α-globin and two β-globin chains. The β-globin gene, HBB, is on chromosome 11. The normal allele codes for haemoglobin A (HbA). In the sickle cell allele, the sixth codon of the gene has one base changed: the coding strand has GTG instead of GAG. This is a base substitution of thymine for adenine.

Glutamic acid has a charged, hydrophilic R group, while valine has a non-polar, hydrophobic one. This single change makes a hydrophobic patch on the surface of the haemoglobin molecule. When the oxygen concentration is low, for example in capillaries of working muscle, the hydrophobic patches on neighbouring HbS molecules stick together and the haemoglobin polymerises into long, rigid fibres inside the red blood cell.

Consequences for the cell and the person

The fibres distort the red blood cell into a stiff, curved sickle shape. Sickle cells have several harmful effects:

• They are less flexible than normal cells and block narrow capillaries, which reduces the blood supply to tissues and causes episodes of severe pain and damage to organs.

• They are destroyed much faster than normal red blood cells, after about 10–20 days instead of about 120, so the person has anaemia: a shortage of red blood cells, which causes tiredness and shortness of breath.

• Repeated blockages damage the spleen, lungs, kidneys and brain, and increase the risk of infections and stroke.

A person with two copies of the sickle cell allele has sickle cell anaemia. A person with one copy is a carrier with sickle cell trait, and usually has mild or no symptoms. About 300,000 babies are born with sickle cell anaemia each year, most of them in sub-Saharan Africa. The allele is common there because carriers are partly protected against malaria, a link explored in D4.1 Natural selection.

The example shows the chain of cause and effect from molecules to the whole organism: one base change in DNA, one amino acid changed in a polypeptide, a change in the shape and behaviour of the protein, a change in the shape of a cell, and a disease that affects many organs. It illustrates form and function at every level of organisation.

Directionality of transcription and translation (HL only)

Transcription is 5′ to 3′

Like DNA polymerase, RNA polymerase can add nucleotides only to the free 3′ –OH group at the end of the growing strand. Each new RNA nucleotide is joined by its 5′ phosphate to the 3′ carbon of the ribose at the end of the chain. RNA is therefore synthesised in the 5′ to 3′ direction. The template strand is antiparallel to the RNA, so RNA polymerase moves along the template strand in its 3′ to 5′ direction.

The first part of the mRNA to be made is its 5′ end. This end contains the start codon and the beginning of the coding sequence, so the 5′ end of an mRNA corresponds to the start of the polypeptide.

Translation is 5′ to 3′

Ribosomes also read mRNA in the 5′ to 3′ direction, codon by codon from the start codon near the 5′ end to a stop codon nearer the 3′ end. Because transcription and translation run in the same direction, a prokaryotic ribosome can attach to the 5′ end of an mRNA and begin translating it while RNA polymerase is still making the 3′ end. The amino acid coded by the first codon becomes the amino terminus (N-terminus) of the polypeptide, and the last amino acid becomes its carboxyl terminus (C-terminus).

Initiation of transcription at the promoter (HL only)

RNA polymerase does not bind to DNA at random. Transcription of each gene starts at a particular sequence called the promoter, which lies just before (upstream of) the part of the gene that is transcribed.

In eukaryotes, RNA polymerase cannot recognise a promoter on its own. Proteins called transcription factors bind to specific base sequences in the promoter first, and then help RNA polymerase to bind in the correct position and orientation. Only when this initiation complex has formed does RNA polymerase begin to unwind the DNA and transcribe the gene. A terminator sequence at the end of the gene causes RNA polymerase to stop and release the RNA.

Because transcription cannot start without the right transcription factors, they are one of the main ways in which gene expression is controlled. A cell expresses a gene only if it contains the transcription factors that recognise that gene’s promoter. Further sequences called enhancers, which can lie thousands of base pairs away, bind activator proteins that increase transcription; other sequences bind repressor proteins that reduce it. Signals such as hormones often act by switching transcription factors on or off, which is how a single signal can change the expression of many genes at once. These mechanisms are developed further in D2.2 Gene expression.

Non-coding sequences in DNA (HL only)

Only about 1–2% of the human genome codes for the amino acid sequences of polypeptides, in roughly 20,000 protein-coding genes. Most of the rest consists of non-coding sequences. Many of these have no known function, but several kinds are essential.

Genes for tRNA and rRNA show that a gene does not have to code for a polypeptide: their final products are the RNA molecules themselves. Human cells have hundreds of copies of the rRNA genes, arranged in long repeated arrays, because a growing cell needs millions of ribosomes. The telomeres at the chromosome ends consist of the sequence TTAGGG repeated hundreds to thousands of times in humans.

Processing of mRNA in eukaryotes (HL only)

Post-transcriptional modification

In eukaryotes the RNA made by transcription, called pre-mRNA (or the primary transcript), is not yet ready to be translated. It is modified in the nucleus in three ways before it is exported to the cytoplasm as mature mRNA. These changes are called post-transcriptional modification.

1. Removal of introns. Most eukaryotic genes are split into coding sections called exons separated by non-coding sections called introns. Both are transcribed. The introns are then cut out of the pre-mRNA and the exons are joined together. This process, splicing, is carried out by a large complex of RNA and proteins called the spliceosome.

2. Addition of a 5′ cap. A modified guanine nucleotide (7-methylguanosine) is added to the 5′ end of the RNA, linked in an unusual 5′ to 5′ orientation.

3. Addition of a 3′ poly-A tail. A chain of adenine nucleotides, often about 100–250 long, is added to the 3′ end.

The 5′ cap and the poly-A tail stabilise the mRNA. Enzymes in the cytoplasm that break down RNA usually start at the ends of the molecule, and the cap and tail protect the ends from them, so the mRNA lasts long enough to be translated many times. The cap also helps the mRNA leave the nucleus and is the place where the small ribosomal subunit binds at the start of translation. Prokaryotic genes generally have no introns, and prokaryotic mRNA has no cap.

Alternative splicing

Splicing does not always join all the exons of a gene in the same way. In alternative splicing, particular exons are included in the mature mRNA in some cells and left out in others. Different combinations of exons give different mRNAs, which are translated into different polypeptides. One gene can therefore code for several variants of a protein.

Alternative splicing is very common. About 95% of human genes that have more than one exon are alternatively spliced. In an extreme case, the Dscam gene of the fruit fly Drosophila melanogaster, which helps nerve cells recognise one another, has enough alternative exons to produce 38,016 different versions of its protein in principle. This helps to explain how about 20,000 human protein-coding genes can produce a much larger number of different proteins.

Initiation of translation and the A, P and E sites (HL only)

The three tRNA binding sites

The large subunit of a ribosome has three binding sites for tRNA, arranged side by side along the mRNA. During elongation each tRNA passes through them in order:

• the A site (aminoacyl site) binds the incoming tRNA carrying its amino acid;

• the P site (peptidyl site) holds the tRNA carrying the growing polypeptide chain;

• the E site (exit site) holds the tRNA that has given up its chain, just before it leaves the ribosome.

Initiation

Translation begins with the assembly of the ribosome on the mRNA. In eukaryotes the steps are:

1. The small ribosomal subunit attaches to the 5′ end of the mRNA, at the 5′ cap.

2. The small subunit moves along the mRNA in the 5′ to 3′ direction until it reaches the first AUG, the start codon.

3. The initiator tRNA, which carries methionine and has the anticodon UAC, pairs with the start codon.

4. The large subunit attaches, so that the initiator tRNA sits in the P site. This is the only tRNA that enters directly at the P site.

5. A second tRNA, with an anticodon complementary to the second codon, binds at the A site, and elongation begins with the first peptide bond.

The sites during elongation

With the A, P and E sites named, the elongation cycle can be described precisely. A charged tRNA binds at the A site by codon–anticodon pairing. The polypeptide on the tRNA in the P site is transferred to the amino acid on the tRNA in the A site, forming a peptide bond. The ribosome then moves 5′ to 3′ along the mRNA by one codon, so the tRNA in the A site (now holding the chain) moves to the P site, and the empty tRNA moves to the E site and leaves. The A site is empty again, ready for the next tRNA.

Modification of polypeptides into their functional state (HL only)

A polypeptide released from a ribosome is often not yet functional. Many are changed after translation, in a variety of ways called post-translational modification: removing amino acids from the ends, cutting the chain into pieces, adding carbohydrate groups (glycosylation) or phosphate groups, forming disulfide bonds or combining with other polypeptides. Proteins made for secretion are modified in the rough endoplasmic reticulum and the Golgi apparatus.

From pre-proinsulin to insulin

Insulin, the hormone made by β cells in the pancreas, is a clear example. Its gene codes for a single polypeptide of 110 amino acids, called pre-proinsulin, which is converted to insulin in two stages.

1. Removal of the signal peptide. Pre-proinsulin begins with a signal peptide of 24 amino acids, which directs the ribosome to the rough endoplasmic reticulum, so the polypeptide is fed into the ER as it is made. Inside the ER, an enzyme cuts off the signal peptide, leaving proinsulin (86 amino acids). Proinsulin folds, and three disulfide bonds form between cysteine R groups.

2. Removal of the C-peptide. Proinsulin is carried in vesicles to the Golgi apparatus and packed into secretory vesicles. There, enzymes cut out the middle section, the C-peptide (with two pairs of amino acids at its ends). What remains is insulin: an A chain of 21 amino acids and a B chain of 30 amino acids, held together by two disulfide bonds, with a third disulfide bond inside the A chain.

Only the mature, two-chain form binds to the insulin receptor. Making insulin as a single chain first ensures that the A and B chains fold correctly and that the right cysteines are paired, which would be very unlikely if the two chains were made separately. The C-peptide is secreted with the insulin in equal amounts, so doctors measure it in the blood to estimate how much insulin a person’s pancreas is producing.

Recycling of amino acids by proteasomes (HL only)

All the proteins of a cell together form its proteome. A proteome is never fixed. Proteins become damaged or misfolded, some are needed only briefly, and the cell’s needs change. A functional proteome therefore depends on proteins being broken down constantly and replaced by newly made ones. Some regulatory proteins last only minutes, while others last for days.

Most proteins in the cytoplasm and nucleus are broken down by proteasomes. A proteasome is a large, barrel-shaped complex of protease enzymes, with its active sites inside the central channel, where they cannot attack other proteins by accident.

1. A protein to be destroyed is tagged by enzymes that attach a chain of several molecules of ubiquitin, a small protein of 76 amino acids.

2. The ubiquitin chain is recognised by the cap of the proteasome.

3. Using energy from ATP, the proteasome unfolds the protein and feeds it into its central channel, where it is hydrolysed into short peptides. The ubiquitin is released and reused.

4. The peptides are broken down into amino acids by other enzymes in the cytoplasm. The amino acids are then used by ribosomes to make new proteins.

The importance of this recycling is shown by medicine. Myeloma cells, a type of cancerous plasma cell, make huge amounts of antibody and depend heavily on proteasomes to remove faulty proteins. Bortezomib, a drug that inhibits proteasomes, was approved in 2003 to treat multiple myeloma: blocking protein breakdown causes damaged proteins to build up until the cancer cells die.

Exam practice

Protein synthesis appears in every part of the assessment. Paper 1A questions ask you to identify the location of each stage, the role of a type of RNA, or the amino acid coded by a codon. Paper 1B and Paper 2 Section A give a DNA or mRNA sequence and a codon table and ask you to deduce a polypeptide or the effect of a mutation. Paper 2 Section B often asks you to explain transcription or translation in an extended answer, or to compare and contrast the two stages. HL questions add the A, P and E sites, mRNA processing and insulin.

Parts (b) and (c) of the question need the table of mRNA codons for the standard genetic code.

Self-check

• To do:

  I can describe transcription and the roles of RNA polymerase, hydrogen bonds and A–U base pairing.

• To do:

  I can distinguish the template strand from the coding strand.

• To do:

  I can explain why DNA templates are stable and why transcription controls gene expression.

• To do:

  I can describe the roles of mRNA, ribosomes and tRNA, using the terms codon and anticodon correctly.

• To do:

  I can explain why the code is a triplet code, and what degeneracy and universality mean.

• To do:

  I can use the codon table to deduce an amino acid sequence from mRNA or DNA.

• To do:

  I can explain the elongation cycle: codon recognition, peptide bond formation and translocation.

• To do:

  I can explain how the sickle cell mutation changes haemoglobin and red blood cells.

• To do:

  I can explain 5′ to 3′ transcription and translation, and the role of the promoter and transcription factors. (HL)

• To do:

  I can outline the roles of non-coding DNA, splicing, the 5′ cap, the poly-A tail and alternative splicing. (HL)

• To do:

  I can describe the initiation of translation and the roles of the A, P and E sites. (HL)

• To do:

  I can outline the conversion of pre-proinsulin to insulin and the recycling of proteins by proteasomes. (HL)

[7 max]