Hereditary information needs a stable store

Genetic material is a molecular store of hereditary information. Cells can copy it and pass it to daughter cells, and parents can pass it to offspring. In every living organism, that genetic material is DNA, a nucleic acid that stores information in the sequence of its nucleotide bases.

A nucleic acid is a biological polymer made from nucleotide subunits, used to store or transfer genetic information. The two examples needed here are DNA, deoxyribonucleic acid, and RNA, ribonucleic acid. Their names come from the sugars they contain: deoxyribose in DNA and ribose in RNA.

The virus exception that is not really an exception

Some viruses use RNA as their genetic material. You need to know that, but it doesn't change the rule for living organisms: they use DNA. A virus is an acellular infectious particle that can replicate only by using the machinery of a host cell. Viruses are not self-sustaining cells and cannot reproduce independently, so they are not considered living organisms in this syllabus.

Here's the tidy IB distinction: RNA viruses are real, but they fall outside the claim about living organisms. For IB wording, all living organisms use DNA as their genetic material; some non-living viruses use RNA.

The three-part subunit

A nucleotide is a monomer of nucleic acids made from a pentose sugar, a phosphate group and a nitrogenous base. The pentose sugar is a five-carbon monosaccharide, and it acts as the central attachment point in a nucleotide. A phosphate group is a negatively charged phosphorus-containing group that gives nucleic acids their acidic character. The nitrogenous base is a nitrogen-containing ring molecule; it is the variable, information-carrying part of the nucleotide.

In a nucleotide, both the base and the phosphate attach to the sugar. For the standard symbolic diagram in this course, draw the phosphate as a circle, the pentose sugar as a pentagon and the base as a rectangle. The real chemistry has more detail, of course, but the positions are the part to remember: phosphate—sugar—base, with the sugar in the middle.

Reading and drawing nucleotide diagrams

If you’re asked to draw a nucleotide, keep it simple and use the usual convention. A circle, pentagon and rectangle are enough unless the question specifically asks for chemical detail. When carbon numbering is shown, the base attaches to carbon 1 of the sugar and the phosphate to carbon 5. That numbering matters later for 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, these bonds link the phosphate of one nucleotide to the pentose sugar of the next. Repeating the same linkage builds 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. It is strong and regular, which suits a molecule that has to preserve the order of bases. The bases project from the backbone; the backbone keeps the sequence held together.

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

Four bases, many possible messages

DNA and RNA each use four nitrogenous bases. DNA uses adenine, thymine, guanine and cytosine, written A, T, G and C. RNA uses adenine, uracil, guanine and cytosine, written A, U, G and C. The swap is the easy bit to remember: DNA has thymine; RNA has uracil.

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

Each nucleotide carries one base, so you can read a nucleic acid strand as a sequence of bases. The sugar and phosphate parts let nucleotides link in the same general way, whichever base is present, so many different base sequences can be made.

This is where the code idea begins. A code is a system in which symbols are given meanings. In nucleic acids, those symbols are base sequences. The chemical alphabet is small, but as the molecule gets longer, the number of possible messages becomes enormous.

RNA is a nucleotide polymer

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

Students often lose marks here because they draw only a row of bases and leave out the backbone. An RNA polymer diagram needs repeated phosphate–sugar units, with the bases attached to the sugars. For the simple IB style, draw a chain of circles and pentagons, with rectangles attached to the pentagons.

Condensation builds the chain

A Condensation reaction is a chemical reaction in which two molecules are covalently joined and a water molecule is released. As RNA nucleotides join, a bond forms between the phosphate of one nucleotide and the sugar of the next. The reaction eliminates water.

Polymerization gives RNA properties that single nucleotides don’t have. One nucleotide can act as a subunit; a chain of nucleotides can carry a sequence, fold into shapes and, in some cases, act in catalysis. This 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 has two nucleotide strands. Each strand has a sugar–phosphate backbone, with the bases pointing inward so they can pair with bases on the opposite 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 join specific base pairs. 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, show the two strands as antiparallel. You don't need to draw the helical twist unless the 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. For most syllabus diagrams, though, the key features are the two backbones, the antiparallel orientation, and A–T and G–C base pairing.

Don't 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 for IB you need three clean contrasts: strand number, 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. Look at carbon 2 of the sugar: ribose has an OH group there, while deoxyribose has H instead. Put another way, deoxyribose has one fewer oxygen atom than ribose. In a sketch, draw the pentose ring and make the carbon 2 difference clear: 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 connects to 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 copies DNA, producing two DNA molecules with the same base sequence. Complementary base pairing keeps the process accurate. Once the two DNA strands separate, each original strand works as a template. Free nucleotides then join according to the pairing rules: A with T, and G with C.

This produces 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 kept as half of each new molecule.

Complementarity in gene expression

Gene expression uses the 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. Often, gene expression begins with transcription.

Transcription is the synthesis of an RNA copy from a DNA template strand. Complementary base pairing matters here as well, although 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 plays a role here too, as RNA sequences are matched during protein synthesis. The detail belongs in Topic D1.2, but the principle fits 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. Each position can hold one of four 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. As n increases, that number rises very quickly.

DNA molecules can also vary in 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 doesn’t need many different chemical subunits; it uses a repeated backbone and four bases arranged in different orders.

Simple chemistry gives DNA 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 with a meaning in protein synthesis. A genetic code is the set of rules used to translate codons into amino acids or into 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 don’t need to memorize specific codons here.

Evidence for common ancestry

Almost all organisms use the same genetic code. There are minor exceptions, but across life the code is overwhelmingly conserved.

Universal common ancestry is the hypothesis that all living organisms descend from a shared ancestral population. Conservation of the genetic code supports this idea because many unrelated origins of life would be unlikely to settle independently on essentially the same codon meanings. A shared code fits best with life inheriting it from a common ancestor and then diversifying.

Here’s 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 the different groups 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 where carbon 3 of the sugar is available to link to another nucleotide. Along the sugar–phosphate backbone, nucleotides are joined 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. Since active sites are three-dimensional, nucleotides and strands have to face the right way to fit and react.

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

In translation, the ribosome moves along the RNA molecule in the 5′ to 3′ direction. Directionality isn’t just a label on a diagram; it controls how replication, transcription and translation proceed.

Equal-width base pairs

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

In DNA, each base pair has one purine and one pyrimidine: A–T and C–G. The two correct base pairs are the same length, so the distance between the two sugar–phosphate backbones stays constant.

A purine–purine pair would be too wide. A pyrimidine–pyrimidine pair would be too narrow. By bonding purine to pyrimidine, the DNA helix keeps the same three-dimensional structure no matter what the base sequence is. 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

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

Each nucleosome has a core made from eight histone proteins. The DNA molecule coils around this histone octamer. One more histone protein helps hold the structure in place by attaching to the linker DNA, the short stretch of DNA between adjacent nucleosomes.

This is the level of detail you need: DNA wrapped around eight histones, plus an additional histone attached to linker DNA. Don’t move into chromosome supercoiling unless another topic asks for it.

Using molecular visualization software

Molecular visualization software lets you rotate a nucleosome model and see how DNA sits against the histone proteins. In practice, you should be able to identify the DNA wrapped around the protein core, tell the histone core apart from linker DNA, and recognise 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, with 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. Many still expected protein to be the genetic material, since proteins are built from 20 amino acid types. DNA had only four nucleotide types, so some biologists thought it looked too simple. 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 turns a bacterium into a virus-producing cell, then 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 labelled DNA with radioactive phosphorus and protein with radioactive sulfur.

This is a Nature of Science point: new technology can make experiments possible when they couldn’t be done before. Once radioisotopes were available as research tools, scientists could trace particular molecules through biological systems instead of only inferring 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 stayed 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 gave strong evidence that DNA is the genetic material.