Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

40 Chapter 1: Cells and Genomes
1–5 You have begun to characterize a sample obtained
from the depths of the oceans on Europa, one of Jupiter’s
moons. Much to your surprise, the sample contains
a life-form that grows well in a rich broth. Your preliminary
analysis shows that it is cellular and contains DNA,
RNA, and protein. When you show your results to a colleague,
she suggests that your sample was contaminated
with an organism from Earth. What approaches might
you try to distinguish between contamination and a
novel cellular life-form based on DNA, RNA, and protein?
1–6 It is not so difficult to imagine what it means to feed
on the organic molecules that living things produce. That
is, after all, what we do. But what does it mean to “feed” on
sunlight, as phototrophs do? Or, even stranger, to “feed” on
rocks, as lithotrophs do? Where is the “food,” for example,
in the mixture of chemicals (H 2 S, H 2 , CO, Mn + , Fe 2+ , Ni 2+ ,
CH 4 , and NH 4 + ) that spews from a hydrothermal vent?
1–7 How many possible different trees (branching patterns)
can in theory be drawn to display the evolution of
bacteria, archaea, and eukaryotes, assuming that they all
arose from a common ancestor?
1–8 The genes for ribosomal RNA are highly conserved
(relatively few sequence changes) in all organisms on
Earth; thus, they have evolved very slowly over time. Were
ribosomal RNA genes “born” perfect?
1–9 Genes participating in informational processes
such as replication, transcription, and translation are
transferred between species much less often than are
genes involved in metabolism. The basis for this inequality
is unclear at present, but one suggestion is that it relates
to the underlying complexity of the two types of processes.
Informational processes tend to involve large aggregates
of different gene products, whereas metabolic reactions
are usually catalyzed by enzymes composed of a single
protein. Why would the complexity of the underlying process—informational
or metabolic—have any effect on the
rate of horizontal gene transfer?
1–10 Animal cells have neither cell walls nor chloroplasts,
whereas plant cells have both. Fungal cells are
somewhere in between; they have cell walls but lack chloroplasts.
Are fungal cells more likely to be animal cells that
gained the ability to make cell walls, or plant cells that lost
their chloroplasts? This question represented a difficult
issue for early investigators who sought to assign evolutionary
relationships based solely on cell characteristics
and morphology. How do you suppose that this question
was eventually decided?
Earthworm
Insect
Salamander
Goldfish
Clam
Frog
INVERTEBRATES
VERTEBRATES
Rabbit Whale
Chicken Cat
Cobra
Human
Cow
Nematode
Chlamydomonas
Paramecium
PLANTS
PROTOZOA
Barley
Figure Q1–2 Phylogenetic tree for hemoglobin genes from a variety
of species (Problem 1–11). The legumes are highlighted in green. The
lengths of lines that connect the present-day species represent the
evolutionary distances that separate them.
Lotus
Alfalfa
Bean
1–11 When plant hemoglobin Q1.3 genes were first discovered
in legumes, it was so surprising to find a gene typical
of animal blood that it was hypothesized that the plant
gene arose by horizontal transfer from an animal. Many
more hemoglobin genes have now been sequenced, and
a phylogenetic tree based on some of these sequences is
shown in Figure Q1–2.
A. Does Figure this tree 01-03 support Problem or refute 01-50 the hypothesis that
the plant hemoglobins arose by horizontal gene transfer?
B. Supposing Phylogenetic that the tree plant hemoglobin for hemoglobin genes were genes from
originally a derived variety from of a parasitic species. nematode, The legumes for example, are shown
what would
in
you
green.
expect the phylogenetic tree to look like?
1–12 Rates of evolution appear to vary in different lineages.
For example, the rate of evolution in the rat lineage
is significantly higher than in the human lineage. These
rate differences are apparent whether one looks at changes
in nucleotide sequences that encode proteins and are subject
to selective pressure or at changes in noncoding nucleotide
sequences, which are not under obvious selection
pressure. Can you offer one or more possible explanations
for the slower rate of evolutionary change in the human
lineage versus the rat lineage?