Genome and proteome

A cell contains genetic material that provides instructions for producing functional products, including proteins. Its genome is its complete set of genetic material. It includes all its genes as well as DNA that does not code for proteins.

A gene is a sequence of DNA that can contribute to the production of a functional product. That product may be a protein or a functional RNA molecule. Genes are therefore part of the genome, but they do not account for all of its DNA.

The proteome is the full range of proteins a cell is able to produce. Unlike the genome, which consists of genetic material, the proteome consists of proteins.

Why cells with the same genome can have different proteomes

Cells do not necessarily use all their genes in the same way. When a gene is expressed, its information is used to produce a functional product. Different cells express different genes, so they can produce different sets of proteins even when they have the same genome.

Messenger RNA structure

Messenger RNA (mRNA) is a single-stranded nucleic acid made of a chain of repeating units called nucleotides. Each nucleotide contains a ribose sugar, a phosphate group and one of four bases: adenine, uracil, cytosine or guanine.

The nucleotides are joined through their sugars and phosphate groups, forming a sugar–phosphate backbone. The bases extend from this backbone. Although each nucleotide has the same type of sugar and phosphate group, its base can vary, giving an mRNA molecule a particular base sequence.

Base sequence and codons

The base sequence carries information in groups of three bases called codons. During translation, the codons are read in order. Most codons specify an amino acid, so their sequence determines the order in which amino acids are joined to form a polypeptide. A stop codon marks the end of the sequence to be translated rather than specifying an amino acid.

Transfer RNA structure

Transfer RNA (tRNA) is a short, single-stranded RNA molecule. Parts of the strand fold back on themselves, and complementary bases in different parts of the same strand pair. This holds the molecule in a folded shape.

The folded tRNA has two regions that allow it to link a sequence of bases to an amino acid:

• An anticodon is a sequence of three bases that can pair with a complementary three-base sequence, called a codon, on messenger RNA (mRNA).
• An amino acid attachment site holds a specific amino acid.

When a tRNA anticodon pairs with a complementary mRNA codon, the tRNA positions its amino acid so that it can be added to a growing polypeptide. The tRNA therefore links the codon’s base sequence to the amino acid added.

Transcription

Transcription produces an RNA copy of a DNA sequence. The two DNA strands separate in the region being copied, exposing their bases. One DNA strand acts as the template for the new RNA strand.

Free RNA nucleotides pair with the exposed bases on the template strand by complementary base pairing. RNA uses uracil instead of thymine: adenine on the DNA template pairs with uracil in RNA, while thymine pairs with adenine. Cytosine pairs with guanine, and guanine pairs with cytosine.

The enzyme RNA polymerase joins the RNA nucleotides together to form an RNA strand. The order of bases in the template therefore determines the order of bases in the RNA copy.

Transcription and mRNA formation

When a protein-coding DNA sequence is transcribed in a prokaryote, the RNA produced is messenger RNA (mRNA) directly.

In a eukaryote, transcription of a protein-coding sequence first produces pre-mRNA. This RNA is then spliced: sections called introns are removed, and the remaining sections, called exons, are joined together. The result is mRNA.

Translation

Translation is the production of a polypeptide using the sequence of codons in messenger RNA (mRNA). A polypeptide is a chain of amino acids joined by peptide bonds. Each codon is a sequence of three bases in the mRNA; the order of the codons determines the order of amino acids in the chain.

A ribosome binds to the mRNA and moves along it, bringing successive codons into position. Transfer RNA (tRNA) molecules carry specific amino acids to the ribosome. Each tRNA has an anticodon: a sequence of three bases that pairs with a complementary mRNA codon. This pairing places the corresponding amino acid in the correct position in the growing chain.

The ribosome brings the amino acids together so that peptide bonds form between them. As the ribosome moves along the mRNA, the polypeptide grows in the order specified by the codon sequence. Translation ends when the ribosome reaches a stop codon, and the completed polypeptide is released.

ATP supplies energy for processes in translation, including the attachment of each amino acid to its corresponding tRNA before that tRNA delivers it to the ribosome.

Applying the genetic code

The genetic code relates the sequence of bases in a nucleic acid to the sequence of amino acids in a polypeptide. The sequence used to read the code is messenger RNA (mRNA).

An mRNA sequence is read in consecutive, non-overlapping groups of three bases. Each triplet is a codon: it specifies an amino acid or a stop signal. A stop codon marks the end of the polypeptide sequence; it does not add an amino acid.

More than one codon can specify the same amino acid. For example, both CUU and CUC specify leucine.

Finding the mRNA sequence

Before using a genetic-code table, identify whether the supplied sequence is mRNA or one of the two DNA strands:

• mRNA: use the sequence directly, reading it from the $$5'$$ end to the $$3'$$ end.
• DNA template strand: write the complementary mRNA sequence. DNA A pairs with RNA U, DNA T with RNA A, DNA C with RNA G, and DNA G with RNA C. The strands run in opposite directions, so a template written $$3'$$ to $$5'$$ gives mRNA written $$5'$$ to $$3'$$.
• DNA coding strand: the mRNA has the same base sequence in the same direction, except that RNA has uracil (U) wherever the coding strand has thymine (T).

Reading mRNA codons

Use the specified starting point or reading frame to divide the mRNA into triplets. The reading frame matters because starting at a different base changes the groups of three and can therefore change the amino acid sequence.

Read each codon in order from $$5'$$ to $$3'$$, using the supplied genetic-code information to find its amino acid. Write the amino acids in that order, stopping at a stop codon if one is present.

For example, suppose the DNA template is $$3'\text{-TAC GAA ACT-}5'$$. Its complementary mRNA is $$5'\text{-AUG CUU UGA-}3'$$. In the indicated reading frame, the codons are AUG, CUU and UGA:

• AUG specifies methionine.
• CUU specifies leucine.
• UGA is a stop codon.

The resulting polypeptide sequence is therefore methionine–leucine. The stop codon adds no amino acid. The corresponding DNA coding strand is $$5'\text{-ATG CTT TGA-}3'$$: it matches the mRNA sequence apart from T in place of U.

Interpreting nucleic acid experimental data

Experimental data can test a claim about what a nucleic acid does. The aim is to decide whether changing the nucleic acid, or comparing samples that differ in it, produces the result predicted by the claim.

What was compared and measured?

First identify what was changed or compared. For example, an experiment might compare a sample in which DNA has been broken down with an otherwise similar sample in which DNA remains intact. Then identify what was measured: this is the result used to judge whether the proposed role still occurs.

A control provides a reference for the comparison. If the control is treated in the same way as the test sample except for the change being investigated, a difference between their results is more readily linked to that change. Other differences between samples could offer alternative explanations.

Relating results to a claim

Compare the measured results with the control and with the prediction made by the claim. Consider whether a difference is clear enough to distinguish it from variation or limits in the measurements.

• Results support a claim when the observed pattern matches its prediction. Support does not necessarily prove the claim or rule out every alternative explanation.
• Results contradict a claim when they show a pattern inconsistent with what the claim predicts under the tested conditions.
• Results do not resolve a claim when they cannot distinguish it from alternatives. For example, a measurement may be too uncertain to show whether a meaningful difference exists.

Example: testing a role in trait transfer

Suppose a claim states that DNA in a bacterial sample is needed to transfer a trait to recipient bacteria. Samples are prepared in the same way except that DNA is broken down in one, RNA is broken down in another, and neither nucleic acid is broken down in a control. Each sample is then tested for its ability to transfer the trait.

If trait transfer occurs with the control and the RNA-treated sample, but not with the DNA-treated sample, the pattern supports the claim that intact DNA is needed for transfer in this experiment. The control shows that transfer occurs when the nucleic acids are left intact; the RNA-treated sample provides a comparison with a different nucleic acid being broken down.

The conclusion depends on the treatments specifically breaking down the intended nucleic acids without otherwise preventing transfer. The results do not, by themselves, establish every possible role of DNA or RNA in other conditions.