Nucleic Acids and DNA Replication
Senior 5 · Biology
Nucleic Acids and DNA Replication
Lesson 1 of 5
25 min
Each of your body cells contains about two metres of DNA. The nucleus that holds it is only about 6 µm across. If the DNA were simply stuffed inside, it would tangle like a net, and the cell could never copy it or read its genes. Instead it is wound, coiled and folded with proteins in a precise order. This unit studies the chemistry of DNA and RNA and how DNA is copied. It starts with the package, the chromosome, and with the units the molecule is built from, the nucleotides.
Worked example 1: how tightly is DNA packed?
A diploid human cell contains about base pairs, and each base pair adds 0.34 nm to the length of the double helix. (a) Calculate the total length of DNA in metres. (b) How many times longer is this than a nucleus 6 µm across?
Definition
Chromosome: a thread-like structure in the nucleus made of one long DNA molecule packed with proteins, carrying many genes.
Chromatin: the complex of DNA and proteins (mainly histones) that makes up chromosomes. Euchromatin is loosely packed and contains active genes; heterochromatin is densely packed and mostly inactive.
Histones: small, positively charged proteins around which DNA is wound. Nucleosome: a length of DNA (about 147 base pairs) wrapped nearly twice around a core of eight histone molecules.
A eukaryotic chromosome is about one-third DNA and two-thirds protein by mass, with a little RNA. Most of the protein is histone. Histones are rich in the amino acids lysine and arginine, whose side chains carry a positive charge, so they bind tightly to the negatively charged phosphate groups of DNA. Other, non-histone proteins form the scaffold of the chromosome and include enzymes that copy and read the DNA.
The packing changes during the cell cycle. Between divisions most chromatin is in the looser forms (levels 2 to 4), so genes can be read. Before division the chromatin condenses into visible chromosomes (level 5), each made of two identical sister chromatids joined at the centromere. The ends of each chromatid are capped by telomeres, which you meet in Lesson 3.
Prokaryotes are different. A bacterium has a single circular DNA molecule lying free in the cytoplasm in a region called the nucleoid, without histones, and often small extra circles of DNA called plasmids.
Worked example 2: counting nucleosomes
On average, one nucleosome plus its linker DNA takes up about 200 base pairs. Estimate (a) the number of nucleosomes in a diploid human cell with base pairs, and (b) the number of histone molecules in their cores.
A cell must make all these histones again every time it copies its DNA, which is why histone genes are very active during the S phase of the cell cycle.
Definition
Nucleotide: the monomer of nucleic acids, made of a pentose (five-carbon) sugar, a phosphate group and a nitrogenous base.
Purines: bases with a double ring, adenine (A) and guanine (G). Pyrimidines: bases with a single ring, cytosine (C), thymine (T) and uracil (U).
Phosphodiester bond: the bond that links the phosphate group of one nucleotide to carbon 3′ of the sugar of the next, formed by a condensation reaction.
The carbon atoms of the sugar are numbered 1′ to 5′ ("one prime" to "five prime"). The base is attached to carbon 1′ and the phosphate to carbon 5′. DNA nucleotides contain the sugar deoxyribose; RNA nucleotides contain ribose. The only difference is at carbon 2′: ribose carries an –OH group there, and deoxyribose ("minus an oxygen") carries only –H.
| Base | Type | Rings | Found in |
|---|---|---|---|
| Adenine (A) | Purine | 2 | DNA and RNA |
| Guanine (G) | Purine | 2 | DNA and RNA |
| Cytosine (C) | Pyrimidine | 1 | DNA and RNA |
| Thymine (T) | Pyrimidine | 1 | DNA only |
| Uracil (U) | Pyrimidine | 1 | RNA only |
Nucleotides join in a condensation reaction: the phosphate on carbon 5′ of one nucleotide bonds to the –OH on carbon 3′ of the sugar of the previous one, releasing a molecule of water. Repeated, this builds a sugar–phosphate backbone with the bases sticking out to one side. Every strand has a direction: one end has a free phosphate on carbon 5′ (the 5′ end) and the other a free –OH on carbon 3′ (the 3′ end).
Nucleotides have other jobs too. ATP, the energy currency of cells, is an adenine nucleotide with three phosphates, and the coenzymes NAD and FAD are built from nucleotides.
DNA Learning Center (Cold Spring Harbor Laboratory): "How DNA is Packaged (Advanced)". An animation built from real molecular structures: watch the DNA wrap around histones, then coil and loop into a chromosome.
Warning
Common mistakes
Tip
Drawing a nucleotide in an exam: draw the pentagon, put the base on the right at 1′ and the phosphate at top left on 5′, and label all three parts. For a strand, join the phosphate of the next nucleotide to the 3′ carbon.
Practice: chromosomes and nucleotides
Key points
Sources and credits
Figures 1 and 2, the tables, the worked examples and the practice questions are written by Ganzaa.
