Hereditary information needs a stable store

Genetic material is a molecular store of hereditary information. Cells copy it and pass it to daughter cells, and parents 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. The 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. Know this, but don’t let it undo the rule for living organisms: living organisms use DNA. A virus is an acellular infectious particle that can replicate only by using the machinery of a host cell. Since viruses are not self-sustaining cells and cannot reproduce independently, this syllabus does not consider them living organisms.

Here’s the tidy version for IB wording: RNA viruses exist, but they fall outside the claim about living organisms. 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; it gives nucleic acids part of their acidic character. A nitrogenous base is a nitrogen-containing ring molecule, which makes up the variable, information-carrying part of a nucleotide.

In a nucleotide, the base and phosphate both attach to the sugar. For 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 real chemistry has more detail than this symbol shows, but the relative positions still matter: 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 conventional. Use the circle, pentagon and rectangle unless the question asks for chemical detail. Where carbon numbering is shown, the base attaches to carbon 1 of the sugar and the phosphate to carbon 5. That numbering is useful 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, covalent bonds link the phosphate of one nucleotide to the pentose sugar of the next nucleotide. Repeating this linkage forms 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.

There’s a clear division of labour here. 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, they are adenine, uracil, guanine and cytosine, written A, U, G and C. The swap is easy to remember: DNA has thymine; RNA has uracil.

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

Each nucleotide contains 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, whatever base is present, which allows many different base sequences to form.

This is where the code idea begins. A code is a system in which symbols are given meanings. In nucleic acids, base sequences act as the symbols. 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 make a larger molecule. A Polymer is a large molecule built from many repeating monomer units. RNA is one single, unbranched polymer made of nucleotide monomers.

A common mark-loser is drawing just a row of bases and leaving out the backbone. In an RNA polymer diagram, show the repeating phosphate–sugar units, with 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 lack. One nucleotide can act as a subunit; a nucleotide chain can carry a sequence, fold into shapes and, in some cases, act in catalysis. This is an emergent property: the polymer can do things that the separate monomers cannot do on their own.

Two strands, paired bases

A DNA molecule is made from 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 form between particular 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 lined up side by side but running in opposite chemical directions. In DNA diagrams, show the two strands 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: 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. Look at carbon 2 of the sugar: ribose has an OH group there, while deoxyribose has H instead. Put simply, deoxyribose has one fewer oxygen atom than ribose. In a sketch, draw the pentose ring and show the carbon 2 difference clearly: 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 links 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. Because RNA can store sequence information and sometimes help reactions occur, it is 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 copy accurate. Once the two DNA strands separate, each original strand serves as a template. Free nucleotides then join according to the pairing rules: A with T, and G with C.

The outcome is semi-conservative replication, a type of DNA replication where each new DNA molecule has one original strand and one newly synthesized strand. Half of each new molecule conserves the old strand.

Complementarity in gene expression

Gene expression uses the information in a gene to make a functional product in a cell. A gene is a section of DNA with a base sequence that contributes to a functional product. Often, the first stage of gene expression is transcription.

Transcription synthesizes an RNA copy from a DNA template strand. Complementary base pairing does the work again, 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 synthesizes a polypeptide using the base sequence of an RNA molecule. Complementary base pairing matters here as well, because 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 through the order of bases along a strand. At any one position, four bases are possible: 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 $n$ gets larger, that number rises very fast.

A DNA molecule can be any length as well, so its diversity is not just a matter of “four bases”. It comes from any length of molecule with any possible base sequence. That gives DNA its vast capacity for information storage.

Great economy of storage

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

Simple chemistry produces a powerful biological property here. The molecule is repetitive enough to be stable and easy to copy, while its base sequence is variable enough 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 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 arrive independently at 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 means 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 where carbon 3 of the sugar is available for linkage to another nucleotide. In the sugar–phosphate backbone, nucleotides link in a 5′ to 3′ arrangement.

Why direction matters

Enzymes and ribozymes depend on shape. 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 reads along the RNA molecule in the 5′ to 3′ direction. Directionality, then, 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, every 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 paired with another purine would make the pair too wide. Two pyrimidines together would be too narrow. Purine-to-pyrimidine bonding lets the DNA helix keep the same three-dimensional structure, whatever 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

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 wraps around this histone octamer. Another histone protein helps hold the structure in place by attaching to the linker DNA, the short stretch of DNA between adjacent nucleosomes.

Keep the detail at this level: DNA wrapped around eight histones, plus an additional histone attached to linker DNA. Don’t 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 spot the DNA wrapped around the protein core, tell the histone core apart 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 isn’t 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. Even so, many expected protein to be the genetic material, since proteins are built from 20 amino acid types. DNA, with only four nucleotide types, seemed too simple to some biologists. Hershey and Chase set out to test which molecule actually entered bacteria and directed viral production.

A bacteriophage is a virus that infects bacteria. Hershey and Chase used T2 bacteriophages, which have DNA inside a protein coat. If the phage turns 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 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 were previously out of reach. Once scientists had radioisotopes as research tools, they could trace particular molecules through biological systems instead of only inferring where those molecules 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. The mixture 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 therefore gave strong evidence that DNA is the genetic material.