---
title: "Genomes of Cells and Viruses"
book: "University Biology — Year 1"
subject: biology
language: en
chapter: 17
exercises: 12
source: https://one-course.com/books/biology/3/en/chapter/17-genomes-of-cells-and-viruses
---

# Chapter 17 — Genomes of Cells and Viruses

Two metres of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) are folded into a nucleus six micrometres across, and folded so that any of twenty thousand [genes](#def-b1-genomes-gene) can be found and read within minutes. A bacterium folds a millimetre and a half into a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) a thousand times shorter, and copies it every twenty minutes. A [virus](#def-b1-genomes-virus) carries a few thousand letters in a [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) shell and reads them with a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) it does not own. This chapter describes the *[genome](#def-b1-genomes-genome)* — the whole of an [organism](https://one-course.com/books/biology/3/en/chapter/1-the-organism-a-system-in-interaction-with-its-environment#def-b1-organism-environment-organism)’s [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) — as a physical object: how the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) of bacteria, of [eukaryotic cells](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-prokeuk), of [organelles](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-prokeuk) and of [viruses](#def-b1-genomes-virus) is organised, what it contains besides [genes](#def-b1-genomes-gene), and why the amount of it says so little about the [organism](https://one-course.com/books/biology/3/en/chapter/1-the-organism-a-system-in-interaction-with-its-environment#def-b1-organism-environment-organism) that carries it.

## 17.1 The bacterial genome

**Definition 17.1 (Genome, chromosome, nucleoid).**

The *genome* of a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) is the totality of its [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain): the information for every [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) and [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) it can make, and the sequences that control when they are made. A *chromosome* is one [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) molecule with the [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) that organise it. A bacterium usually has one, circular, of one to ten million [base pairs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) (*E. coli*: $4.6 \times 10^{6}$, $1.5\,\mathrm{mm}$ long), folded into a region of the [cytoplasm](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell), the *nucleoid*, with no membrane around it. Besides the chromosome many bacteria carry *plasmids*: small circles of a few thousand to a few hundred thousand pairs, in one to hundreds of copies, replicating on their own and carrying optional [genes](#def-b1-genomes-gene) — antibiotic resistance, toxins, the machinery for transferring themselves to another [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell).

**Proposition 17.2 (How a bacterium folds its chromosome).**

A circular [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) whose ends cannot rotate can be twisted like a rubber band: *supercoiling*. [Enzymes](https://one-course.com/books/biology/3/en/chapter/13-enzymes-and-biochemical-catalysis#def-b1-enzymes-enzyme) called *topoisomerases* cut, pass and reseal the strands to add or remove turns; *gyrase* uses [ATP](https://one-course.com/books/biology/3/en/chapter/8-water-and-small-biomolecules#def-b1-water-small-molecules-atp) to introduce negative supercoils, which underwind the helix and make it both more compact and easier to open. The [chromosome](#def-b1-genomes-genome) of *E. coli* is organised into some fifty loops, each supercoiled independently and anchored to a [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) core, so that the $1.5\,\mathrm{mm}$ occupies a [nucleoid](#def-b1-genomes-genome) of about a micrometre — a thousandfold compaction — while any loop can be unwound for reading or copying without disturbing the rest. Small basic [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) (histone-like, though unrelated to [histones](#def-b1-genomes-nucleosome)) bend and bridge the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) throughout.

![A circular chromosome relaxed, supercoiled, and organised into loops. Supercoiling compacts the molecule and stores the energy that helps open it; the loops let one region be unwound at a time.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/fig-be1e5c9d4c2c.svg)

*A circular [chromosome](#def-b1-genomes-genome) relaxed, supercoiled, and organised into loops. Supercoiling compacts the molecule and stores the energy that helps open it; the loops let one region be unwound at a time.*

**Example 17.3 (A dense genome).**

Of the *E. coli* [chromosome](#def-b1-genomes-genome)’s $4.6\,\mathrm{Mb}$, $88\,\%$ codes for [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide): some $4300$ [genes](#def-b1-genomes-gene) of about $1000$ pairs each, packed head to tail with a hundred pairs between them, many grouped into *operons* transcribed together ([Chapter 20](https://one-course.com/books/biology/3/en/chapter/20-control-of-gene-expression#ch-b1-expression-control)). A [plasmid](#def-b1-genomes-genome) of $5\,\mathrm{kb}$ may carry three [genes](#def-b1-genomes-gene) and exist in fifty copies; the resistance [gene](#def-b1-genomes-gene) it carries can spread through a hospital ward’s bacteria in weeks, by conjugation, faster than any mutation could arise.

## 17.2 The eukaryotic genome: chromatin

**Definition 17.4 (Nucleosome, chromatin).**

In a eukaryotic nucleus the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) is wound on [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide): $147\,$ [base pairs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) make 1.7 turns around an octamer of eight *histones* (two each of H2A, H2B, H3, H4, small [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) rich in lysine and arginine that neutralise the phosphates), forming a *nucleosome* $11\,\mathrm{nm}$ across; nucleosomes follow one another every $200\,$ pairs or so, like beads on a string, with a fifth histone, H1, sealing each bead. This *chromatin* folds further: into a fibre of $30\,\mathrm{nm}$, into loops of tens of thousands of pairs anchored on a [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) scaffold, and — at division — into the compact rods of the metaphase [chromosome](#def-b1-genomes-genome), ten thousand times shorter than the naked [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain). *Euchromatin* is the looser, gene-rich, transcribed form of interphase; *heterochromatin* the condensed, gene-poor form that stays compact (around [centromeres](#def-b1-genomes-karyotype), at the ends, and on a switched-off X [chromosome](#def-b1-genomes-genome)).

![Levels of packing of eukaryotic DNA, from the helix to the metaphase chromosome. Each level multiplies the compaction; the whole reaches ten thousand.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/fig-b85f104c060c.svg)

*Levels of packing of eukaryotic [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), from the helix to the metaphase [chromosome](#def-b1-genomes-genome). Each level multiplies the compaction; the whole reaches ten thousand.*

![Left: the chromosomes of one human cell, spread from a cell arrested at metaphase. Right: the same chromosomes sorted by size and banding into a karyotype — twenty-two pairs and XY, forty-six in all. Karyotype: National Human Genome Research Institute, public domain.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/img-95acb18066ab.jpg)

![Left: the chromosomes of one human cell, spread from a cell arrested at metaphase. Right: the same chromosomes sorted by size and banding into a karyotype — twenty-two pairs and XY, forty-six in all. Karyotype: National Human Genome Research Institute, public domain.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/img-945edfff198a.jpg)

*Left: the [chromosomes](#def-b1-genomes-genome) of one human [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell), spread from a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) arrested at metaphase. Right: the same [chromosomes](#def-b1-genomes-genome) sorted by size and banding into a [karyotype](#def-b1-genomes-karyotype) — twenty-two pairs and XY, forty-six in all. [Karyotype](#def-b1-genomes-karyotype): National Human [Genome](#def-b1-genomes-genome) Research Institute, public domain.*

**Definition 17.5 (Karyotype, centromere, telomere).**

The *karyotype* is the set of [chromosomes](#def-b1-genomes-genome) of a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell), sorted by size and banding pattern: humans have 23 pairs (22 autosomes and XY or XX), $6.4 \times 10^{9}$ [base pairs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) in all, $2.2\,\mathrm{m}$; the largest [chromosome](#def-b1-genomes-genome) holds $250\,\mathrm{Mb}$, the smallest $50\,$. Each linear [chromosome](#def-b1-genomes-genome) carries a *centromere*, the constricted region where the two copies stay joined after replication and where the spindle attaches ([Chapter 18](https://one-course.com/books/biology/3/en/chapter/18-dna-replication-and-mitosis#ch-b1-replication-mitosis)), and two *telomeres*, repeated sequences at the ends that protect them from being taken for broken [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) and from shortening at each replication.

**Proposition 17.6 (Genome size does not measure complexity).**

| [organism](https://one-course.com/books/biology/3/en/chapter/1-the-organism-a-system-in-interaction-with-its-environment#def-b1-organism-environment-organism) | [genome](#def-b1-genomes-genome) (Mb) | protein-coding [genes](#def-b1-genomes-gene) |
| --- | --- | --- |
| *E. coli* | 4.6 | $4300$ |
| yeast | 12 | $6000$ |
| fruit fly | 140 | $14\,000$ |
| human | 3200 | $20\,000$ |
| maize | 2300 | $40\,000$ |
| lungfish | $130\,000$ | $\approx20\,000$ |
| *Paris japonica* (a lily) | $150\,000$ | $\approx30\,000$ |

[Genome](#def-b1-genomes-genome) size varies a thousandfold among eukaryotes with no relation to the number of [genes](#def-b1-genomes-gene) or the complexity of the [organism](https://one-course.com/books/biology/3/en/chapter/1-the-organism-a-system-in-interaction-with-its-environment#def-b1-organism-environment-organism) (the *C-value paradox*): a lungfish carries forty times the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) of a human and no more [genes](#def-b1-genomes-gene). The difference is not [genes](#def-b1-genomes-gene) but the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) between them.

## 17.3 What a genome contains

**Definition 17.7 (Anatomy of a gene).**

A *gene* is a stretch of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) transcribed into a functional [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) — usually a messenger for one [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide). A eukaryotic protein-coding gene comprises a *promoter*, the sequence upstream where transcription begins and is controlled; *exons*, the parts kept in the mature message; *introns*, the parts transcribed and then cut out ([Chapter 19](https://one-course.com/books/biology/3/en/chapter/19-gene-expression-transcription-and-translation#ch-b1-gene-expression)); the untranslated regions at each end of the message; and a terminator. A human gene averages $27\,\mathrm{kb}$ with eight exons totalling $1.5\,\mathrm{kb}$: nineteen twentieths of a typical gene is intron. Bacterial genes have no introns.

![A eukaryotic gene: a promoter, exons (kept) alternating with introns (removed after transcription). Drawn to a compressed scale — in a real gene the introns would be twenty times longer than the exons.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/fig-bd379668bed2.svg)

*A eukaryotic [gene](#def-b1-genomes-gene): a [promoter](#def-b1-genomes-gene), [exons](#def-b1-genomes-gene) (kept) alternating with [introns](#def-b1-genomes-gene) (removed after transcription). Drawn to a compressed scale — in a real [gene](#def-b1-genomes-gene) the [introns](#def-b1-genomes-gene) would be twenty times longer than the [exons](#def-b1-genomes-gene).*

**Proposition 17.8 (The census of the human genome).**

Of the $3.2\,\mathrm{Gb}$: about $1.5\,\%$ codes for [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide); $25\,\%$ is [intron](#def-b1-genomes-gene); $45\,\%$ is the remains of *transposable elements* — sequences that copy themselves into new places, mostly long dead (the Alu element alone, $300\,\mathrm{bp}$, is present in a million copies, a tenth of the [genome](#def-b1-genomes-genome)); $8\,\%$ is short repeats in tandem (satellite [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), at [centromeres](#def-b1-genomes-karyotype) and [telomeres](#def-b1-genomes-karyotype)); the rest is unique non-coding sequence that includes the [promoters](#def-b1-genomes-gene), enhancers and [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) [genes](#def-b1-genomes-gene) that control expression. Many [genes](#def-b1-genomes-gene) belong to *families* that arose by duplication (the globins, the olfactory receptors — a thousand of them), and the [genome](#def-b1-genomes-genome) holds thousands of *pseudogenes*, dead copies that no longer work. A [genome](#def-b1-genomes-genome) is not a design but a record.

![What the human genome is made of. The exons that code for protein are a sliver; half the genome is the debris of elements that once copied themselves.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/fig-501648ab9fc0.svg)

*What the human [genome](#def-b1-genomes-genome) is made of. The [exons](#def-b1-genomes-gene) that code for [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) are a sliver; half the [genome](#def-b1-genomes-genome) is the debris of elements that once copied themselves.*

**Example 17.9 (Reading a genome’s size).**

A [genome](#def-b1-genomes-genome) of $4.6\,\mathrm{Mb}$ with no [introns](#def-b1-genomes-gene) and few repeats holds $4300$ [genes](#def-b1-genomes-gene); one of $3200\,\mathrm{Mb}$ with long [introns](#def-b1-genomes-gene) and half its length in repeats holds $20\,000$; one of $130\,000\,\mathrm{Mb}$ holds the same twenty thousand. The size measures how much has accumulated in a lineage’s non-coding [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), and how efficiently it has been removed, not how much the [organism](https://one-course.com/books/biology/3/en/chapter/1-the-organism-a-system-in-interaction-with-its-environment#def-b1-organism-environment-organism) does.

## 17.4 Organelle genomes and viruses

**Definition 17.10 (Organelle genomes).**

[Mitochondria](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#def-b1-eukaryotic-cell-mitochondrion) and [chloroplasts](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#def-b1-eukaryotic-cell-plastid) keep a remnant of their bacterial ancestors’ [chromosome](#def-b1-genomes-genome) ([Chapter 6](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#ch-b1-eukaryotic-cell)): a small circle — $16.6\,\mathrm{kb}$ and 37 [genes](#def-b1-genomes-gene) in human [mitochondria](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#def-b1-eukaryotic-cell-mitochondrion), $120\text{ to }160\,\mathrm{kb}$ and about 100 [genes](#def-b1-genomes-gene) in [chloroplasts](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#def-b1-eukaryotic-cell-plastid) — in many copies per [organelle](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-prokeuk), coding for some of their own [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) and for the [RNAs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) of their ribosomes. The rest of their [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) come from nuclear [genes](#def-b1-genomes-gene). In most animals the mitochondrial [genome](#def-b1-genomes-genome) is inherited from the mother only, with the egg’s [cytoplasm](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell).

**Definition 17.11 (Virus).**

A *virus* is a [genome](#def-b1-genomes-genome) in a [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) shell, the *capsid* — sometimes wrapped in a membrane, the *envelope*, taken from a host [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) — that reproduces only inside a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell), using the [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell)’s ribosomes, energy and precursors. Its [genome](#def-b1-genomes-genome) may be [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) or [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), double- or single-stranded, linear or circular, one molecule or several: from $5\,\mathrm{kb}$ (a few [genes](#def-b1-genomes-gene)) to $1.2\,\mathrm{Mb}$ (a thousand, in the giant viruses). Outside a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) a virus does nothing: it is not a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell), does not metabolise, and is alive only in the sense that it carries information and evolves. The *bacteriophages* are the viruses of bacteria.

![Bacteriophages attached to a bacterium: polyhedral heads holding the DNA, tails through which it will be injected. A single cell will release a hundred new phages within half an hour.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/img-f7c5d16f73d2.jpg)

*Bacteriophages attached to a bacterium: polyhedral heads holding the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), tails through which it will be injected. A single [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) will release a hundred new phages within half an hour.*

**Proposition 17.12 (The two cycles of phage λ\lambdaλ).**

Phage $\lambda$ injects its $48.5\,\mathrm{kb}$ of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) ([Chapter 11](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#ch-b1-nucleic-acids)) into *E. coli*, where it circularises. Two [fates](https://one-course.com/books/biology/3/en/chapter/9-lipids#def-b1-lipids-triglyceride) follow. In the *[lytic cycle](#prop-b1-genomes-lambda)* the phage’s [genes](#def-b1-genomes-gene) are transcribed by the host’s polymerase, its [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) is replicated a hundredfold, [capsid](#def-b1-genomes-virus) [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) are made and assembled, the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) is packed into them, and an [enzyme](https://one-course.com/books/biology/3/en/chapter/13-enzymes-and-biochemical-catalysis#def-b1-enzymes-enzyme) dissolves the wall: the [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) bursts, releasing a hundred phages, forty minutes after infection. In the *[lysogenic cycle](#prop-b1-genomes-lambda)* the phage [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) is inserted into the host [chromosome](#def-b1-genomes-genome) and silenced by a repressor of its own making: the *prophage* is copied with the [chromosome](#def-b1-genomes-genome) for generations, invisible, until damage to the host’s [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) lifts the repression and the [lytic cycle](#prop-b1-genomes-lambda) resumes. The choice is a molecular switch, one of the first understood ([Chapter 20](https://one-course.com/books/biology/3/en/chapter/20-control-of-gene-expression#ch-b1-expression-control)).

![Phage : lytic cycle (red) or lysogenic (green), and the induction that turns the second into the first.](https://one-course.com/images/onecourse/chapters/biology-3/b1-genomes/fig-8007a59a7fdc.svg)

*Phage $\lambda$: [lytic cycle](#prop-b1-genomes-lambda) (red) or lysogenic (green), and the induction that turns the second into the first.*

**Example 17.13 (Viruses with RNA genomes).**

Influenza carries eight segments of single-stranded [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) and its own polymerase to copy them, since [cells](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) have no [enzyme](https://one-course.com/books/biology/3/en/chapter/13-enzymes-and-biochemical-catalysis#def-b1-enzymes-enzyme) that copies [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain); its polymerase makes one error per $10\,000$ bases and the [virus](#def-b1-genomes-virus) changes every season. A retrovirus (HIV) carries [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) and a *reverse transcriptase* that copies it into [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), which is inserted into the host [chromosome](#def-b1-genomes-genome) like a prophage — a permanent infection. The mechanisms, and the immune response to them, are the Year 3 volume’s; here they mark the range of what a [genome](#def-b1-genomes-genome) can be.

## 17.5 Exercises

**Exercise 17.1 ★.**

Compare the bacterial and the eukaryotic [genome](#def-b1-genomes-genome): number and shape of the [chromosomes](#def-b1-genomes-genome), location, [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) that organise them, and [gene](#def-b1-genomes-gene) density.

**Solution of Exercise 17.1.**

Bacterium: one circular [chromosome](#def-b1-genomes-genome) (plus [plasmids](#def-b1-genomes-genome)) in a [nucleoid](#def-b1-genomes-genome) without a membrane, compacted by supercoiling and small basic [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide), about $90\,\%$ coding. Eukaryote: several linear [chromosomes](#def-b1-genomes-genome) in a nucleus, wound on [histones](#def-b1-genomes-nucleosome) into [chromatin](#def-b1-genomes-nucleosome), a few percent coding.

**Exercise 17.2 ★.**

Describe a [nucleosome](#def-b1-genomes-nucleosome) and give the compaction factor of each level of [chromatin](#def-b1-genomes-nucleosome) folding.

**Solution of Exercise 17.2.**

147 [base pairs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) wound 1.7 times around an octamer of [histones](#def-b1-genomes-nucleosome) (two each of H2A, H2B, H3, H4), sealed by H1, one every 200 pairs. Beads on a string $\times 6$; $30\,\mathrm{nm}$ fibre $\times 40$; loops $\times 1000$; metaphase [chromosome](#def-b1-genomes-genome) $\times 10\,000$.

**Exercise 17.3 ★.**

From the census figure, what fraction of the human [genome](#def-b1-genomes-genome) codes for [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide), and what is the largest category?

**Solution of Exercise 17.3.**

$1.5\,\%$; transposable elements and their remains, $45\,\%$.

**Exercise 17.4 ★.**

What is a [virus](#def-b1-genomes-virus), and in what sense is it not alive?

**Solution of Exercise 17.4.**

A [genome](#def-b1-genomes-genome) ([DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) or [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain)) in a [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) [capsid](#def-b1-genomes-virus), sometimes enveloped, that reproduces only inside a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) with the [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell)’s machinery. Outside a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) it has no metabolism, no growth, no response — an inert particle; it is “alive” only in carrying heritable information that evolves.

**Exercise 17.5 ★★.**

Compute the length of the *E. coli* [chromosome](#def-b1-genomes-genome) and the number of nucleosome-sized turns it would need if it were eukaryotic; explain how the bacterium compacts it instead.

**Solution of Exercise 17.5.**

$4.6 \times 10^{6}\times 0.34 = 1.56\,\mathrm{mm}$; $4.6 \times 10^{6}/200 = 23\,000$ [nucleosomes](#def-b1-genomes-nucleosome). Instead: negative supercoiling by gyrase and folding into some fifty loops on a [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) core, with small basic [proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) bending the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) — a thousandfold, into a [nucleoid](#def-b1-genomes-genome) of a micrometre.

**Exercise 17.6 ★★.**

A human [gene](#def-b1-genomes-gene) of $27\,\mathrm{kb}$ has $1.5\,\mathrm{kb}$ of [exons](#def-b1-genomes-gene) in eight pieces. Compute the mean [exon](#def-b1-genomes-gene) and [intron](#def-b1-genomes-gene) lengths and the fraction of the primary transcript that is discarded.

**Solution of Exercise 17.6.**

[Exons](#def-b1-genomes-gene) $1500/8 = 190\,\mathrm{bp}$; [introns](#def-b1-genomes-gene) $25\,500/7 = 3640\,\mathrm{bp}$; $25.5/27 = 94\,\%$ of the transcript is discarded.

**Exercise 17.7 ★★.**

Using the table, compute the [genes](#def-b1-genomes-gene) per megabase for *E. coli*, yeast, the fruit fly, the human and the lungfish. Comment on the trend.

**Solution of Exercise 17.7.**

*E. coli* 930 [genes](#def-b1-genomes-gene) per Mb; yeast 500; fly 100; human 6; lungfish 0.15. [Gene](#def-b1-genomes-gene) density falls by four orders of magnitude while [gene](#def-b1-genomes-gene) number rises fivefold: the extra [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) is non-genic.

**Exercise 17.8 ★★.**

The Alu element is $300\,\mathrm{bp}$ and present in a million copies. What fraction of the [genome](#def-b1-genomes-genome) is Alu? If each copy arose by retrotransposition (an [RNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) copied back to [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) and inserted), how many insertions per generation would produce a million copies in $60$ million years at $20$ years a generation?

**Solution of Exercise 17.8.**

$10^6\times 300 = 3 \times 10^{8}\,\mathrm{bp}$: $9\,\%$ of the [genome](#def-b1-genomes-genome). $60\times
10^6/20 = 3 \times 10^{6}$ generations: one new insertion every three generations, on average, somewhere in the lineage.

**Exercise 17.9 ★★.**

Explain why the mitochondrial [genome](#def-b1-genomes-genome) is inherited maternally, and what this implies for tracing ancestry.

**Solution of Exercise 17.9.**

The egg contributes the [cytoplasm](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) and its [mitochondria](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#def-b1-eukaryotic-cell-mitochondrion); the sperm’s few [mitochondria](https://one-course.com/books/biology/3/en/chapter/6-functional-organization-of-the-eukaryotic-cell#def-b1-eukaryotic-cell-mitochondrion) are excluded or destroyed after fertilisation. The mitochondrial [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) therefore passes unmixed from mother to child, and its accumulated mutations trace maternal lineages back through time.

**Exercise 17.10 ★★★.**

Phage $\lambda$ in the lysogenic state is copied once per host generation; in the lytic state it makes a hundred copies in $40\,\mathrm{min}$. In a well-fed culture doubling every $20\,\mathrm{min}$, compare the two strategies over two hours; in a starving culture that does not divide, compare them again. Why does the switch respond to the host’s condition?

**Solution of Exercise 17.10.**

Fed culture, two hours: lysogeny gives $2^6 = 64$ copies (one per host division); lysis gives 100 phages in $40\,\mathrm{min}$, and their progeny $100^3 = 10^6$ in two hours if hosts abound — lysis wins by far. Starving culture: lysogeny gives one copy, safe inside a living [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell); lysis gives 100 phages with no [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) to infect, which decay. The switch reads the host’s state because the best strategy depends on whether new hosts will be available.

**Exercise 17.11 ★★★.**

A lungfish [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) carries $130\,\mathrm{Gb}$: compute the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) length, the number of [nucleosomes](#def-b1-genomes-nucleosome) and the mass of [histones](#def-b1-genomes-nucleosome) per [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell), and the time to replicate it at the human fork speed ($50\,\mathrm{bp}/\mathrm{s}$ per fork) with one origin per $100\,\mathrm{kb}$. What does a large [genome](#def-b1-genomes-genome) cost a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell)?

**Solution of Exercise 17.11.**

$1.3 \times 10^{11}\times 0.34\,\mathrm{nm} = 44\,\mathrm{m}$ (haploid); $6.5 \times 10^{8}$ [nucleosomes](#def-b1-genomes-nucleosome); [histones](#def-b1-genomes-nucleosome) $6.5 \times 10^{8}\times 108\,000\times
1.66\times 10^{-24} = 117\,\mathrm{pg}$. Origins: $1.3 \times 10^{6}$, each replicating $50\,\mathrm{kb}$ on each side at $50\,\mathrm{bp}/\mathrm{s}$: $1000\,\mathrm{s}$ — the time is not the problem, given enough origins; the cost is the [nucleotides](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-nucleotide) ($130\,\mathrm{pg}$ of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) per division), the [histones](#def-b1-genomes-nucleosome), the time to make them, and a nucleus and [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) many times larger, which is why such [cells](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) divide slowly.

**Exercise 17.12 ★★★.**

“The [genome](#def-b1-genomes-genome) is a record, not a design.” Discuss in a paragraph with pseudogenes, transposable elements, [gene](#def-b1-genomes-gene) families and the C-value paradox.

**Solution of Exercise 17.12.**

A design would contain what is needed and no more; a record contains what happened. Pseudogenes are the corpses of duplicated [genes](#def-b1-genomes-gene) that died by mutation; transposable elements are parasites that copied themselves for tens of millions of years and were never removed; [gene](#def-b1-genomes-gene) families show duplication followed by divergence; and the C-value paradox shows that the amount of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) reflects a lineage’s history of accumulation and loss rather than its needs. Selection keeps the [genes](#def-b1-genomes-gene) working and lets the rest drift: what we read in a [genome](#def-b1-genomes-genome) is mostly history.

## 17.6 Problem: Two Metres in Six Micrometres

**Problem 17.1.**

Weekend problem — a human nucleus measured from the helix to the chromosome: lengths, volumes, nucleosomes, histones and the packing ratio at every level, ending on the total compaction of metaphase

A human diploid nucleus is a sphere of $6\,\text{µ}\mathrm{m}$ diameter holding $6.4 \times 10^{9}$ [base pairs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) on 46 [chromosomes](#def-b1-genomes-genome); the largest [chromosome](#def-b1-genomes-genome) carries $250\,\mathrm{Mb}$, the smallest $50\,$. Take $0.34\,\mathrm{nm}$ per pair, $2\,\mathrm{nm}$ for the helix diameter, $650\,\mathrm{Da}$ per pair, $200$ pairs per [nucleosome](#def-b1-genomes-nucleosome), a [histone](#def-b1-genomes-nucleosome) octamer of $108\,\mathrm{kDa}$, and $1.66 \times 10^{-24}\,\mathrm{g}$ per dalton.

**Part I — Lengths and volumes.**

1. Compute the total length of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) in the nucleus.
2. Compute the number of turns of the [double helix](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) it contains.
3. Compute the length of the largest and of the smallest [chromosome](#def-b1-genomes-genome) ’s [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) .
4. Compute the volume of the nucleus.
5. Compute the volume of the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) as a cylinder, and the fraction of the nucleus it occupies.
6. Compute the mass of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) in the nucleus in picograms.
7. The nucleus contains about $25\,\mathrm{pg}$ of [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) . What fraction of the nuclear mass is [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) , if water is $80\,\%$ of the nucleus (density $1.1\,\mathrm{g}/\mathrm{mL}$ )?

**Part II — [Nucleosomes](#def-b1-genomes-nucleosome).**

8. Compute the number of [nucleosomes](#def-b1-genomes-nucleosome) in the nucleus.
9. Compute the mass of [histones](#def-b1-genomes-nucleosome) and compare with the mass of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) .
10. The $200\,$ pairs of one [nucleosome](#def-b1-genomes-nucleosome) span $68\,\mathrm{nm}$ of helix but occupy a bead $11\,\mathrm{nm}$ long. Compute the compaction factor of the “beads on a string”.
11. The $30\,\mathrm{nm}$ fibre holds six [nucleosomes](#def-b1-genomes-nucleosome) per $11\,\mathrm{nm}$ of its length. Compute its compaction factor relative to naked [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) .
12. Compute the length of the $30\,\mathrm{nm}$ fibre for the whole [genome](#def-b1-genomes-genome) , and compare it with the nucleus’s diameter.
13. Each [nucleosome](#def-b1-genomes-nucleosome) must be taken apart and reassembled when the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) is replicated or transcribed. How many [nucleosomes](#def-b1-genomes-nucleosome) are reassembled in S phase ( $8\,\mathrm{h}$ )? Per second?

**Part III — Loops and [chromosomes](#def-b1-genomes-genome).**

14. Loops of $75\,\mathrm{kb}$ of the $30\,\mathrm{nm}$ fibre hang from a scaffold. Compute the length of fibre in one loop and the number of loops in the [genome](#def-b1-genomes-genome) .
15. A metaphase chromatid of the largest [chromosome](#def-b1-genomes-genome) is $10\,\text{µ}\mathrm{m}$ long. Compute the compaction factor from naked [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) to metaphase [chromosome](#def-b1-genomes-genome) .
16. Compute the volume of that chromatid as a cylinder of $0.7\,\text{µ}\mathrm{m}$ diameter, and the fraction of it that is [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) .
17. The 46 [chromosomes](#def-b1-genomes-genome) at metaphase, each a rod of the same density: compute their total volume and compare it with the interphase nucleus.
18. Explain why interphase [chromatin](#def-b1-genomes-nucleosome) cannot be packed as tightly as metaphase [chromatin](#def-b1-genomes-nucleosome) .

**Part IV — Finding a [gene](#def-b1-genomes-gene).**

19. A [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) must find one $20\,\mathrm{bp}$ site in the [genome](#def-b1-genomes-genome) . If it tested one random site per millisecond, how long would the search take? What does this say about how sites are found?
20. The [genome](#def-b1-genomes-genome) ’s $20\,000\,$ [genes](#def-b1-genomes-gene) average $27\,\mathrm{kb}$ . What fraction of the [genome](#def-b1-genomes-genome) is inside [genes](#def-b1-genomes-gene) ? What fraction is coding, at $1.5\,\mathrm{kb}$ of [exons](#def-b1-genomes-gene) per [gene](#def-b1-genomes-gene) ?
21. Each [chromosome](#def-b1-genomes-genome) occupies its own territory of the nucleus. Compute the volume of the territory of the largest [chromosome](#def-b1-genomes-genome) if territories are proportional to [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) content, and the concentration of [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) inside it in [base pairs](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#thm-b1-nucleic-acids-helix) per cubic micrometre.
22. A lungfish nucleus of the same [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) density would have what volume for $260\,\mathrm{Gb}$ (diploid)? What diameter?
23. Compute the number of [histone](#def-b1-genomes-nucleosome) octamers a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) must make in S phase and the [amino acids](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-aminoacid) they contain ( $1000\,$ residues per octamer). Compare with the $3 \times 10^{9}\,$ residues of [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) a [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell) makes in a day.
24. Explain in two sentences why bacteria can do without [nucleosomes](#def-b1-genomes-nucleosome) and eukaryotes cannot.
25. State the result: the total compaction factor from the helix to the metaphase [chromosome](#def-b1-genomes-genome) , and the factors at each level.

**Solution of Problem 17.1.**

**1.** $6.4 \times 10^{9}\times 0.34\,\mathrm{nm} = 2.18\,\mathrm{m}$. **2.** $6.4 \times 10^{9}/10 = 6.4 \times 10^{8}$ turns. **3.** $2.5 \times 10^{8}\times 0.34 = 8.5\,\mathrm{cm}$; $1.7\,\mathrm{cm}$. **4.** $\frac{4}{3}\pi\times 3^3 = 113\,\text{µ}\mathrm{m}^{3}$. **5.** $\pi\times(1\,\mathrm{nm})^2\times 2.18\,\mathrm{m} =
6.8 \times 10^{-18}\,\mathrm{m}^{3} = 6.8\,\text{µ}\mathrm{m}^{3}$: $6\,\%$ of the nucleus. **6.** $6.4 \times 10^{9}\times 650\times 1.66\times 10^{-24} =
6.9 \times 10^{-12}\,\mathrm{g} = 6.9\,\mathrm{pg}$. **7.** Nuclear mass $113\times 10^{-12}\,\mathrm{mL}\times 1.1 =
124\,\mathrm{pg}$; [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) $5.6\,\%$ of it, [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) $20\,\%$. **8.** $6.4 \times 10^{9}/200 = 3.2 \times 10^{7}$. **9.** $3.2 \times 10^{7}\times 108\,000\times 1.66\times 10^{-24} =
5.7\,\mathrm{pg}$: about equal to the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain). **10.** $68/11 = 6.2$. **11.** Six [nucleosomes](#def-b1-genomes-nucleosome), $1200\,\mathrm{bp}$ $= 408\,\mathrm{nm}$ of helix, in $11\,\mathrm{nm}$: factor $37$. **12.** $2.18/37 = 5.9\,\mathrm{cm}$ of fibre — ten thousand times the nuclear diameter, folded within it. **13.** All $3.2 \times 10^{7}$, plus the same number of new ones on the second copy: $6.4 \times 10^{7}$ in $28\,800\,\mathrm{s}$, about $2200$ per second. **14.** $75\,000\times 0.34/37 = 690\,\mathrm{nm}$ of fibre per loop; $6.4 \times 10^{9}/75\,000 = 85\,000$ loops. **15.** $8.5\,\mathrm{cm}/10\,\text{µ}\mathrm{m} = 8500$. **16.** $\pi\times 0.35^2\times 10 = 3.85\,\text{µ}\mathrm{m}^{3}$; [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) $\pi\times 10^{-6}\times 0.085\,\mathrm{m} = 0.27\,\text{µ}\mathrm{m}^{3}$: $7\,\%$ — the rest is [histone](#def-b1-genomes-nucleosome) and scaffold [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) and water. **17.** Total [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) $6.4 \times 10^{9}$ pairs at the same density ($2.5 \times 10^{8}$ pairs in $3.85\,\text{µ}\mathrm{m}^{3}$, per chromatid; two chromatids per [chromosome](#def-b1-genomes-genome)): $2\times 6.4\times 10^9/2.5\times 10^8\times
3.85 = 197\,\text{µ}\mathrm{m}^{3}$, larger than the interphase nucleus because the [chromosomes](#def-b1-genomes-genome) are now rods with space between them. **18.** Interphase [chromatin](#def-b1-genomes-nucleosome) must be read and copied: polymerases and their factors need access to the [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain), so most of it stays as the open $30\,\mathrm{nm}$ fibre and loops; metaphase [chromatin](#def-b1-genomes-nucleosome) is inert and can be packed for transport. **19.** $6.4 \times 10^{9}$ sites at $10^3$ per second: $6.4 \times 10^{6}$ seconds, 74 days. [Proteins](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) do not search at random: they bind [DNA](https://one-course.com/books/biology/3/en/chapter/11-nucleotides-and-nucleic-acids#def-b1-nucleic-acids-chain) non-specifically and slide along it, and many copies search in parallel, so a site is found in seconds. **20.** $20\,000\times 27\,\mathrm{kb} = 540\,\mathrm{Mb}$, $17\,\%$ of $3.2\,\mathrm{Gb}$; coding $20\,000\times 1.5 =
30\,\mathrm{Mb}$, $0.9\,\%$ (about 1.5% with the shorter [genes](#def-b1-genomes-gene) counted more carefully). **21.** $113\times 2\times 250/6400 = 8.8\,\text{µ}\mathrm{m}^{3}$ (two copies); $5 \times 10^{8}/8.8 = 5.7 \times 10^{7}\,\mathrm{bp}/\text{µ}\mathrm{m}^{3}$, the same as the whole nucleus. **22.** $2.6 \times 10^{11}/5.7 \times 10^{7} = 4600\,\text{µ}\mathrm{m}^{3}$: diameter $21\,\text{µ}\mathrm{m}$, forty times the human nucleus in volume. **23.** $3.2 \times 10^{7}$ octamers, $3.2 \times 10^{10}$ residues — a tenth of the [cell](https://one-course.com/books/biology/3/en/chapter/5-the-cell-unit-of-life#def-b1-cell-unit-of-life-cell)’s daily [protein](https://one-course.com/books/biology/3/en/chapter/12-amino-acids-and-proteins#def-b1-proteins-peptide) synthesis, spent on packaging. **24.** A bacterium’s [chromosome](#def-b1-genomes-genome) is a thousand times shorter and supercoiling in loops suffices to fit it into a micrometre; a eukaryote must fold a length ten thousand times its nucleus and needs a hierarchy of packing, of which the [nucleosome](#def-b1-genomes-nucleosome) is the first level. **25.** About $8500$ ($8.5\,\mathrm{cm}$ into $10\,\text{µ}\mathrm{m}$), built as $\times 6$ ([nucleosomes](#def-b1-genomes-nucleosome)), $\times 6$ more ($30\,\mathrm{nm}$ fibre, $\times 37$ in all), $\times 27$ more (loops, $\times 1000$ in all), and $\times 8$ more (metaphase condensation).