The modern eukaryotic cell probably arose from an ancestral prokaryotic archaean in several steps, including the origin of a flexible cell surface and the enclosure of the genetic material in a nucleus. Later, endosymbioses of proteobacteria and cyanobacteria led to the origins of mitochondria and chloroplasts.

Question 1

Loss of the stiff prokaryotic cell wall allowed infolding of the cell membrane, greatly increasing the surface area of the cell without increasing its volume. These infoldings also allowed for greater structure within the cell and eventually led to the evolution of the endoplasmic reticulum.

Question 2

When atmospheric oxygen concentrations were low early in Earth’s history, organisms could use only anaerobic respiration. Increased availability of atmospheric oxygen allowed the evolution of aerobic respiration, which proceeds more rapidly and harvests energy more efficiently than anaerobic respiration does. But as cells increased in size, they would decrease in surface area-to-volume ratio unless the cell membrane had infoldings. Increased levels of atmospheric oxygen also led to the endosymbiosis of an aerobic bacterium (the ancestor of the eukaryotic mitochondrion), which facilitated the evolution of aerobic eukaryotes.

Background for Questions 3–4: Ribosomal RNA (rRNA) genes are present in the nuclear genome of eukaryotes. There are also rRNA genes in the genomes of mitochondria and chloroplasts. Therefore photosynthetic eukaryotes have three different sets of rRNA genes, which encode the structural RNA of three separate sets of ribosomes. The gene tree below shows the evolutionary relationships among rRNA gene sequences isolated from the nuclear genomes of humans, yeast, and corn; from a prokaryotic archaean (Halobacterium), a proteobacterium (E. coli), and a cyanobacterium (Chlorobium); and from the mitochondrial and chloroplast genomes of corn.

Question 3

The three rRNA genes of corn are not one another’s closest relatives because the nuclear, mitochondrial, and chloroplast genomes have different origins, and the relationships shown in the tree reconstruct the endosymbiotic events that gave rise to mitochondria and chloroplasts.

Question 4

The mitochondrial genome of corn is more closely related to the genome of E. coli than it is to the nuclear genome of corn because the mitochondria were derived from an endosymbiosis with a proteobacterium. Likewise, the chloroplast genome of corn is more closely related to the genome of Chlorobium than it is to the nuclear genome of corn because the chloroplasts were derived from an endosymbiosis with a cyanobacterium.

Question 5

The term “protists” is used, for convenience, to refer to a diverse group of distantly related, polyphyletic microbial eukaryotes. Some protists are more closely related to each of the major groups of multicellular eukaryotes (including plants, fungi, and animals) than they are to one another.