Hereditary information needs a stable store

Genetic material is a molecular store of hereditary information that can be copied and passed from a cell to daughter cells, or from parents to offspring. In every living organism, that genetic material is DNA, a nucleic acid that stores information in the sequence of its nucleotide bases.

Nucleic acid is a biological polymer made from nucleotide subunits that stores or transfers genetic information. The two examples you need here are DNA, deoxyribonucleic acid, and RNA, ribonucleic acid. Their names come from their sugars: deoxyribose in DNA and ribose in RNA.

The virus exception that is not really an exception

Some viruses use RNA as their genetic material. That is worth knowing, but it does not overturn the statement that living organisms use DNA. A virus is an acellular infectious particle that can replicate only by using the machinery of a host cell. Because viruses are not self-sustaining cells and cannot reproduce independently, they are not considered living organisms in this syllabus.

The neat point is this: RNA viruses are real, but they sit outside the claim about living organisms. So, for IB wording, all living organisms use DNA as their genetic material; some non-living viruses use RNA.

The three-part subunit

Nucleotide is a monomer of nucleic acids made from a pentose sugar, a phosphate group and a nitrogenous base. A pentose sugar is a five-carbon monosaccharide that forms the central attachment point in a nucleotide. A phosphate group is a negatively charged phosphorus-containing group that contributes to the acidic character of nucleic acids. A nitrogenous base is a nitrogen-containing ring molecule that forms the variable, information-carrying part of a nucleotide.

In a nucleotide, the base and phosphate are attached to the sugar. In the standard symbolic diagram used in this course, draw the phosphate as a circle, the pentose sugar as a pentagon and the base as a rectangle. The exact chemistry is more detailed than the symbol, but the relative positions matter: phosphate—sugar—base, with the sugar in the middle.

Reading and drawing nucleotide diagrams

When you are asked to draw a nucleotide, keep it simple and conventional. The circle, pentagon and rectangle are enough unless the question asks for chemical detail. If carbon numbering is shown, the base is attached to carbon 1 of the sugar and the phosphate to carbon 5. That numbering becomes useful later when we talk about 5′ and 3′ directionality.

A strong covalent chain

A covalent bond is a chemical bond in which atoms share pairs of electrons. In DNA and RNA, covalent bonds join the phosphate of one nucleotide to the pentose sugar of the next nucleotide. Repeating this linkage produces an alternating sugar–phosphate chain.

The sugar–phosphate backbone is the continuous covalently bonded chain of alternating sugars and phosphates in a nucleic acid strand. This backbone is strong and regular, which is exactly what you want for a molecule that must preserve the order of bases. The bases project from the backbone; the backbone holds the sequence together.

Notice the division of labour. The sugar–phosphate backbone gives each strand structural strength. The bases carry the code. If the backbone were weak and easily broken, hereditary information would be much less reliably stored.

Four bases, many possible messages

DNA and RNA each use four nitrogenous bases. In DNA the bases are adenine, thymine, guanine and cytosine, written A, T, G and C. In RNA the bases are adenine, uracil, guanine and cytosine, written A, U, G and C. So the swap to remember is simple: DNA has thymine; RNA has uracil.

Nitrogenous bases in DNA and RNA, showing shared and unique bases.

Each nucleotide contains one base, so a nucleic acid strand can be read as a sequence of bases. Because the sugar and phosphate parts allow nucleotides to link in the same general way regardless of which base is present, many different base sequences are possible.

That is the start of the code idea. A code is a system in which symbols are given meanings. In nucleic acids, the symbols are base sequences. The chemical alphabet is small, but the possible messages become enormous as the molecule gets longer.

RNA is a nucleotide polymer

Monomer is a small molecular subunit that can be covalently joined to similar subunits to build a larger molecule. Polymer is a large molecule made from many repeating monomer units. RNA is a single, unbranched polymer of nucleotide monomers.

Students often lose marks here by drawing a row of bases and forgetting the backbone. An RNA polymer diagram should show repeated phosphate–sugar units with bases attached to the sugars. In the simple IB style, use a chain of circles and pentagons with rectangles attached to the pentagons.

Condensation builds the chain

Condensation reaction is a chemical reaction in which two molecules are covalently joined and a water molecule is released. When RNA nucleotides join, a bond forms between the phosphate of one nucleotide and the sugar of the next. Water is eliminated during the reaction.

Polymerization gives RNA properties that single nucleotides do not have. A single nucleotide can be a subunit; a chain of nucleotides can carry a sequence, fold into shapes and, in some cases, act in catalysis. That is an example of an emergent property: the polymer can do things that its separate monomers cannot do on their own.

Two strands, paired bases

A DNA molecule consists of two nucleotide strands. Each strand has a sugar–phosphate backbone, and the bases project inward where they pair with bases on the other strand.

A hydrogen bond is a weak intermolecular attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom. In DNA, hydrogen bonds form between specific pairs of bases. A pairs with T, and G pairs with C. A complementary base pair is a pair of bases that can hydrogen bond together in a nucleic acid: A with T in DNA, and G with C.

Antiparallel arrangement

Antiparallel strands are two polymer strands aligned side by side but running in opposite chemical directions. In DNA diagrams, you should show the two strands antiparallel. You do not have to draw the helical twist unless a question specifically asks for it.

A double helix is a two-stranded coiled molecular structure in which the strands wind around the same axis. The helix is the real three-dimensional form of DNA, but for most syllabus diagrams the important features are the two backbones, the antiparallel orientation, and A–T and G–C base pairing.

Do not spend time memorizing the number of hydrogen bonds or the relative lengths of the bases for this statement. The required pairing rules are A with T and G with C, based on hydrogen bonding.

The three required differences

DNA and RNA are both nucleic acids, but you need three clear contrasts: number of strands, bases and sugar.

Key differences between DNA and RNA.

DNA is usually double-stranded; RNA is usually single-stranded. DNA contains A, T, G and C; RNA contains A, U, G and C. DNA contains deoxyribose; RNA contains ribose.

Ribose and deoxyribose

Ribose and deoxyribose are both pentose sugars. The difference is at carbon 2 of the sugar: ribose has an OH group there, while deoxyribose has H instead. In words, deoxyribose has one fewer oxygen atom than ribose. For a sketch, draw the pentose ring and make the carbon 2 difference obvious: OH for ribose, H for deoxyribose.

Examples and the RNA-first linking idea

DNA and RNA are examples of nucleic acids. DNA is the genetic material of living organisms. RNA has several cellular roles, including carrying copied genetic information and helping with protein synthesis.

This also links to the question of why RNA is often suggested as a possible first genetic material. Compared with DNA, RNA is single-stranded and can fold into shapes more readily; in later topics you meet RNA molecules that act as catalysts. That combination — storing sequence information and sometimes helping reactions occur — makes RNA a plausible early molecule before the DNA–protein system became established.

Complementarity makes copying possible

Replication is the process in which DNA is copied to produce two DNA molecules with the same base sequence. Complementary base pairing is what makes replication accurate. When the two DNA strands separate, each original strand acts as a template. Free nucleotides are added according to the pairing rules: A with T, and G with C.

The result is semi-conservative replication, a type of DNA replication in which each new DNA molecule contains one original strand and one newly synthesized strand. The old strand is conserved as half of each new molecule.

Complementarity in gene expression

Gene expression is the use of information in a gene to produce a functional product in a cell. A gene is a section of DNA with a base sequence that contributes to a functional product. The first stage of gene expression is often transcription.

Transcription is the synthesis of an RNA copy from a DNA template strand. Complementary base pairing is again the key, but RNA uses uracil: A on the DNA template pairs with U in RNA, while T pairs with A, G with C and C with G.

Translation is the synthesis of a polypeptide using the base sequence of an RNA molecule. Complementary base pairing is involved here too, as RNA sequences are matched during protein synthesis. The detail belongs in Topic D1.2, but the principle belongs here: hydrogen-bond-based complementarity allows genetic information to be copied and expressed.

Sequence diversity

DNA stores information in the order of bases along a strand. At each position there are four possible bases: A, T, G or C. For a sequence of length $n$, where $n$ is the number of base positions in the sequence, the number of possible sequences is $4^n$. That number grows very quickly as $n$ increases.

A DNA molecule can also be any length, so the diversity is not just “four bases”. It is any length of molecule with any possible base sequence. That is why DNA has such a vast capacity for information storage.

Great economy of storage

DNA stores huge amounts of information in a very small volume. Its narrow molecule can be packed into chromosomes, nuclei, cells, gametes and viruses with remarkable economy. A long base sequence does not require many different chemical subunits; it uses a repeated backbone and four bases arranged in different orders.

This is a lovely example of simple chemistry producing a powerful biological property. The molecule is repetitive enough to be stable and easy to copy, but variable enough in base sequence to store effectively limitless information.

One code across life

A codon is a sequence of three bases in DNA or RNA that corresponds to a meaning in protein synthesis. A genetic code is the set of rules by which codons are translated into amino acids or start and stop signals during protein synthesis.

There are 64 possible codons because each of the three positions can contain one of four bases. Most codons specify amino acids, one codon acts as a start signal, and three act as stop signals. You do not need to memorize specific codons here.

Evidence for common ancestry

The striking fact is that almost all organisms use the same genetic code. There are minor exceptions, but the code is overwhelmingly conserved across life.

Universal common ancestry is the hypothesis that all living organisms descend from a shared ancestral population. Conservation of the genetic code supports this because it is unlikely that many unrelated origins of life would independently settle on essentially the same codon meanings. A shared code makes most sense if life inherited it from a common ancestor and then diversified.

This is the unity-and-diversity theme in one sentence: base sequences vary enormously, but the coding system used to interpret them is nearly universal.

5′ and 3′ ends

Directionality is the chemical polarity of a nucleic acid strand caused by different groups being exposed at its two ends. A nucleotide strand has a 5′ end and a 3′ end because the sugar carbons are numbered.

The 5′ terminal is the end of a DNA or RNA strand with a free phosphate attached to carbon 5 of the sugar. The 3′ terminal is the end with carbon 3 of the sugar available for linkage to another nucleotide. In the sugar–phosphate backbone, nucleotides are linked in a 5′ to 3′ arrangement.

Why direction matters

Enzymes and ribozymes are shape-specific. An enzyme is a biological catalyst made mostly of protein that speeds up a chemical reaction without being used up. A ribozyme is an RNA molecule that catalyses a chemical reaction. Because active sites are three-dimensional, nucleotides and strands must face the correct way to fit and react.

In replication and transcription, new nucleotides are added to the 3′ end of the growing strand. The 5′ phosphate of the incoming nucleotide is joined to the sugar at the 3′ end, so the new strand is synthesized 5′ to 3′.

In translation, the ribosome reads along the RNA molecule in the 5′ to 3′ direction. So directionality is not a decorative label on diagrams; it controls how replication, transcription and translation proceed.

Equal-width base pairs

Purine is a nitrogenous base with a two-ring molecular structure. Adenine and guanine are purines. Pyrimidine is a nitrogenous base with a one-ring molecular structure. Cytosine and thymine are pyrimidines.

In DNA, each base pair contains one purine and one pyrimidine: $A$–$T$ and $C$–$G$. This matters because the two correct base pairs have equal length, keeping the distance between the two sugar–phosphate backbones constant.

If purine paired with purine, the pair would be too wide. If pyrimidine paired with pyrimidine, the pair would be too narrow. Purine-to-pyrimidine bonding helps the DNA helix keep the same three-dimensional structure regardless of the base sequence. That stability is one reason DNA can store any sequence without the whole molecule changing shape each time the order of bases changes.

DNA wrapped around histones

Nucleosome is a DNA-packaging unit in eukaryotes in which DNA is wrapped around a core of histone proteins. Histone is a positively charged DNA-associated protein that helps package eukaryotic DNA.

A nucleosome contains a core of eight histone proteins. The DNA molecule wraps around this histone octamer. A further histone protein holds the structure together by attaching to the linker DNA, which is the short stretch of DNA between adjacent nucleosomes.

This is the level of detail required: DNA wrapped around eight histones, plus an additional histone attached to linker DNA. Do not drift into chromosome supercoiling beyond this unless another topic asks for it.

Using molecular visualization software

Molecular visualization software lets you rotate a nucleosome model and inspect how DNA associates with the histone proteins. In practice, you should be able to identify the DNA wrapped around the protein core, distinguish the histone core from linker DNA, and notice that the association is helped by attraction between negatively charged DNA phosphate groups and positively charged regions of histone proteins.

The skill is not just “look at a pretty model”. Use the software to study spatial relationships: DNA on the outside, histone proteins forming the core, and the wrapping that compacts DNA while still allowing access to genetic information.

The problem Hershey and Chase tested

By the mid-twentieth century, scientists knew chromosomes contained DNA and protein, but many expected protein to be the genetic material because proteins are built from 20 amino acid types. DNA, with only four nucleotide types, seemed too simple to some biologists. Hershey and Chase tested which molecule actually entered bacteria and directed viral production.

A bacteriophage is a virus that infects bacteria. They used T2 bacteriophages, which have DNA inside a protein coat. If the phage transforms a bacterium into a virus-producing cell, the genetic material must be the part that enters the bacterium.

Radioactive labelling made the experiment possible

A radioisotope is an unstable isotope that emits detectable radiation as its nucleus changes to a more stable form. DNA contains phosphorus but not sulfur; protein contains sulfur but not phosphorus. Hershey and Chase used radioactive phosphorus to label DNA and radioactive sulfur to label protein.

This is a Nature of Science point: new technology can open up experiments that were previously impossible. Once radioisotopes became available as research tools, scientists could trace particular molecules through biological systems rather than merely infer where they might have gone.

Blender, centrifuge, pellet, supernatant

After labelled phages infected bacteria, the mixture was agitated to remove phage coats from the outside of the bacterial cells. It was then centrifuged. A pellet is the dense material collected at the bottom of a centrifuge tube after spinning. A supernatant is the liquid above the pellet after centrifugation.

The bacterial cells formed the pellet. Detached viral protein coats remained mainly in the supernatant. Radioactive phosphorus was found mostly in the pellet, while radioactive sulfur was found mostly in the supernatant.

These results support the conclusion that DNA, not protein, entered the bacteria and carried the instructions for producing new viruses. The experiment therefore provided strong evidence that DNA is the genetic material.

Testing the tetranucleotide hypothesis

The tetranucleotide hypothesis was the proposal that DNA consisted of a repeating sequence containing equal amounts of the four bases. If true, DNA would have had very little sequence diversity, making it a poor candidate for genetic material.

Chargaff and others measured the relative amounts of bases in DNA from many life forms. The data showed that the four bases are not present in equal amounts. Different species have different base compositions, so DNA is not just a monotonous repeat.

Chargaff-style base composition data showing that double-stranded DNA has A≈T and G≈C, while base proportions vary between genomes.

The base patterns that mattered

Chargaff’s data showed an important pattern in double-stranded DNA: the amount of adenine is approximately equal to thymine, and the amount of guanine is approximately equal to cytosine. That fits the structure of DNA, because A pairs with T and G pairs with C.

Across diverse organisms, the proportions of A plus T compared with G plus C can vary. That variation is further evidence that DNA sequences are not fixed repeats. In RNA viruses, the pattern may differ because the genetic material is RNA rather than double-stranded DNA.

Induction, falsification and certainty

Inductive reasoning is reasoning in which general conclusions are drawn from observed patterns. The problem of induction is that no number of observations can prove that all unobserved cases will follow the same pattern.

Falsifiability is the feature of a scientific claim that it can, in principle, be shown false by evidence. Falsification is the rejection of a claim when evidence contradicts it. Chargaff’s data falsified the tetranucleotide hypothesis because the bases were not always present in equal amounts. This gives science a kind of certainty about what is not the case, even when broad positive claims remain open to further testing.

Together with Hershey and Chase, Chargaff’s work helped move biology away from protein as the assumed genetic material and toward DNA as a molecule with both stability and vast sequence diversity.