Chapter 1: Cells and Genomes
Imagine two spherical cells, one of which is 5000 times larger in volume than the other. The smaller is a prokaryote, and the larger cell is a eukaryote with 20% of its volume confined in a spherical nucleus. If the diameter of the prokaryotic cell is 0.7 micrometers, what is the diameter of the nucleus in the eukaryotic cell in micrometers? Write down your answer as a number only.
Answer: 7 Difficulty: 3 Section: Genetic Information in Eukaryotes Feedback: The volume of the nucleus is 1000 times that of the prokaryotic cell in this example (that is, 20% × 5000), which means its diameter should be 10 times larger.
Didinium nasutum is a single-celled eukaryote that can hunt and feed on other living cells. It has an elaborate anatomy with beating cilia, a "mouth opening," an "anal aperture," and a set of contractile bundles; it can also shoot "darts" to paralyze its prey. What group of living cells does D. nasutum represent? A. Protozoa B. Yeasts C. Algae D. Animals E. It can belong to any of the above
Answer: A Difficulty: 1 Section: Genetic Information in Eukaryotes Feedback: Protozoa are generally quite complicated in their structure and behavior despite being single-celled, as exemplified by D. nasutum.
Judged by the average number of nucleotide-pair differences per 1000 nucleotide pairs, which of the following pairs show the highest difference? A. The genomes of S. cerevisiae and M. musculus B. The genomes of two different E. coli strains C. The ribosomal RNA genes from human and E. coli D. The transfer RNA genes in a human and M. musculus E. The genomes of two humans
Answer: A Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: Mostly due to horizontal gene transfers, different strains of bacteria can vary wildly in their genomic sequences; however, the difference between the whole genomes of two species as distantly related as the budding yeast and the mouse is by far greater. In comparison, two human individuals differ in a few nucleotide pairs per 1000 nucleotide pairs of their genome. Genes such as ribosomal RNA genes are highly conserved and show a significant identity even between H. sapiens and E. coli.
Based on the variation of genome size and gene number in the organisms presented in the following graph, which organism has the highest number of genes per unit length of their genome? (Note the logarithmic scale.) A. H. sapiens B. M. musculus C. A. thaliana D. C. elegans E. E. coli
Answer: E Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: E. coli has the highest ratio of gene number to genome size among the organisms shown in the graph. The lowest ratio belongs to H. sapiens. The ratio for each organism corresponds to the linear difference in the length of the red and blue bars for that organism. If the graph was not drawn in logarithmic scale, this comparison might not have been as straightforward.
In the following paragraph, fill in the blanks (indicated by numbers) with either Archaea (A), Bacteria (B), or Eukaryotes (E). Your answer would be a three-letter string composed of letters A, B, and E only, e.g. ABE. "Methanococcus jannaschii is an anaerobic thermophilic microbe that belongs to the domain ... (1) and is found in extreme environments such as hydrothermal vents. It lives at temperatures near the boiling point of water and at pressures over 200 times higher than at sea level. Its genome sequence, identified in 1996, revealed that most of its metabolic processes are similar to those in ... (2), while its genetic machinery is more similar to that of ... (3)."
Answer: ABE Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: Archaea usually live in extreme environments, and resemble eukaryotes more in their genetic machinery, and bacteria more in their metabolic machinery.
Imagine a segment of DNA (within a gene) encoding a certain amount of information in its nucleotide sequence. When this segment is fully transcribed into mRNA and then translated into protein, in general, ... A. the protein sequence would carry more information compared to the DNA and mRNA sequences, because its alphabet has 20 letters. B. the protein sequence would carry less information compared to the DNA and mRNA sequences, because several codons can correspond to one amino acid. C. the amount of information in the mRNA sequence is lower, because the mRNA has been transcribed using only one of the DNA strands as the template. D. the amount of information in the mRNA sequence is higher, because several mRNA molecules can be transcribed from one DNA molecule.
Answer: B Difficulty: 3 Section: The Universal Features of Cells on Earth Feedback: There are 64 (that is, 4^3) nucleotide triplets or codons using four types of nucleotide monomers, whereas each codon encodes one out of only 20 amino acids. Therefore, some sequence information is lost when translating from mRNA to protein sequences, such that it is not usually possible to deduce the original mRNA sequence given a translated polypeptide sequence.
Comparing the genomes of present-day mitochondria or chloroplasts with the genomes of their corresponding bacteria reveals that these organelles do not have many of the genes that are essential for their function. For instance, they lack the many genes that are required for DNA replication. What has happened to these genes? A. They have been lost during evolution, since the organelles no longer rely on DNA replication. B. The required genes are kept in the nucleus, but many have evolved by gene transfer from the organelle. C. These genes have undergone mutations and have changed beyond recognition, but are still present in the organelle. D. The organelles do not replicate their DNA; they import new DNA from the nucleus. E. The required genes are on plasmids that are separate from the organelle's genome.
Answer: B Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: During the evolution of mitochondria and chloroplasts, many essential organelle genes are thought to have been transferred to the nuclear genome.
It is a model organism used to study various cell processes such as regulation of the eukaryotic cell cycle. Mutants are available for every gene in its exceptionally small genome. It can live indefinitely in either a haploid or a diploid state. Which of the following describes this organism? A. It can reproduce only asexually. B. It is a fungus. C. It lacks a cell wall. D. Its cell cycle is typically much slower than that of human cells. E. All of the above
Answer: B Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: It is the yeast Saccharomyces cerevisiae.
Which of the following would you NOT expect to find in a bacterial cell? A. Swimming using flagella B. Having a cell wall around the plasma membrane C. ATP production in mitochondria D. Protein production on the ribosome E. Sexual exchange of DNA with other bacteria
Answer: C Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: Bacterial cells do not have membrane-enclosed organelles such as mitochondria.
Scientists discover more than ten thousand new species of living organisms every year. What is shared between all of these organisms? A. They are made of cells, whose nuclei enclose their DNA. B. They obtain their energy from sunlight. C. They produce and use adenosine triphosphate (ATP). D. Their genome contains at least 1000 genes. E. All of the above.
Answer: C Difficulty: 2 Section: The Universal Features of Cells on Earth Feedback: All living organisms are made of cells. However, only a minority of them are eukaryotes with defined cell nuclei. Not all cells obtain their energy directly from sunlight. However, regardless of the energy source, the main energy currency used by all known living cells is ATP. Some prokaryotic genomes contain only a few hundred genes.
Which of the following processes that happens inside a cell DOES NOT normally require consumption of free energy by the cell? A. Replication of the genetic material B. Import of nutrients from the environment C. Diffusion of small molecules within the cell D. Regulation of gene expression E. Synthesis of enzymes that catalyze cellular reactions
Answer: C Difficulty: 2 Section: The Universal Features of Cells on Earth Feedback: Diffusion is a spontaneous process driven by the thermal energy of randomly moving molecules, and normally does not require energy expenditure by the cell. For the other mentioned processes, free energy is required. If a cell "dies," these processes would stop or get out of control, but small molecules would still diffuse.
Out of nearly 5000 protein-coding gene families, there is a set of nearly 300 conserved gene families that are found in species from all domains of life. When one looks at the general functions assigned to these gene families, it is found that ... A. the majority of them function in cell-to-cell signaling. B. the majority of them are poorly characterized. C. more than one-third of them are involved in translation or amino acid transport and metabolism. D. more than one-half of the shared families are involved in DNA replication and transcription. E. Nearly all of them are involved in energy production and carbohydrate metabolism.
Answer: C Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: A significant fraction of the ubiquitous gene families across the three domains of life is involved in translation and amino acid metabolism and transport. Other metabolic processes such as carbohydrate and coenzyme metabolism and transport also constitute a large subset. This is only a rough sketch of the core ancestral gene set, but is nevertheless informative. Please refer to Table 1-1 for details.
Gene duplication can give rise to homologous genes that are part of gene families. For example, there are six actin genes in the genome of most mammalian species. In humans, the ACTB gene, which encodes a cytoskeletal actin, is expressed ubiquitously, while ACTC1 is expressed mainly in cardiac cells. Although bacteria lack the eukaryotic cytoskeletal organization, the bacterial MreB gene bears recognizable sequence similarity to mammalian actin genes and codes for a protein that is similar to actin in structure and function. Which of the following statements is true about these genes? A. ACTB is homologous to ACTC1 but not to MreB. B. ACTB is orthologous to ACTC1 but not to MreB. C. ACTB is paralogous to ACTC1 but not to MreB. D. MreB is orthologous to ACTB but not to ACTC1. E. ACTB is paralogous to both ACTC1 and MreB.
Answer: C Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: Gene duplication within a single genome results in paralogous genes (such as human ACTB and ACTC1 genes), whereas other homologous genes that share direct ancestry are called orthologs (in this case, some ancestor of MreB is presumably a distant actin ortholog). These genes all belong to the actin family.
Which of the following is true regarding Escherichia coli? A. Most of our understanding about mitosis comes from studies on this model organism. B. It is a rod-shaped bacterium that can only grow in the gut of humans and other vertebrates. C. Two strains of E. coli can differ by up to 0.1% in their genomes. D. E. coli strain K-12 encodes about 4300 proteins. E. The E. coli (strain K-12) genome is about 430 million nucleotide pairs long.
Answer: D Difficulty: 1 Section: The Diversity of Genomes and the Tree of Life Feedback: E. coli is a prokaryotic model organism; although the discovery of many fundamental molecular mechanisms were aided by studies using E. coli, the eukaryotic process of mitosis is best studied in simple eukaryotic cells. E. coli can be easily cultured in the lab in nutrient media. Its genome of 4.6 million nucleotide pairs codes for about 4300 different proteins. But this number is reported for the K-12 strain. Other strains can be different in up to 50% of their genes, a significant diversity which has been explained by the process of horizontal gene transfer.
Which of the following is NOT true regarding the tree of life? A. Most bacteria and archaea have 1000 to 6000 genes in their genomes. B. Eukaryotes are more similar to archaea than to bacteria with respect to the proteins that act on their DNA. C. Most bacteria and archaea have genome sizes between one and ten million nucleotide pairs, whereas eukaryotic genomes can be millions of times larger. D. Archaeal species were thought to belong to the eukaryotic world before sequence analysis placed them in a separate domain of life. E. Photosynthetic bacteria are thought to be the ancestors of the eukaryotic chloroplasts.
Answer: D Difficulty: 1 Section: The Diversity of Genomes and the Tree of Life Feedback: Most prokaryotes have small genomes (106 to 107 nucleotide pairs) and code for between 1000 and 6000 genes. Archaea are more similar to bacteria in their metabolism, but more similar to eukaryotes with respect to their DNA replication, DNA repair, and DNA packaging proteins (archaeal histones). Before the comparison of DNA sequences of highly conserved genes placed them in a separate domain, archaeal organisms were classified as bacteria.
A virus ... A. is a type of cell. B. has genetic material made of proteins. C. can only infect a single host species. D. can act as a vector for gene transfer. E. cannot persist in its host for more than one cell generation.
Answer: D Difficulty: 1 Section: The Diversity of Genomes and the Tree of Life Feedback: Viruses are not living cells, but use the cellular machinery of their hosts to replicate their genetic material, which is made of DNA or RNA. They can act as vectors for horizontal gene transfer between cells of the same or different species. Infection is followed by either lysis (killing of the host cell) or the persistence of the viral genome in the host cell (which can last for many cell generations).
Which of the following does NOT typically involve horizontal gene transfer? A. Sexual reproduction in humans B. Bacteriophage infection of bacteria C. The evolutionary history of the eukaryotic cell D. The accidental duplication of a small region of a bacterial chromosome followed by cell division E. Introduction of plasmids into bacteria in a laboratory
Answer: D Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: Introduction of genes into bacteria or eukaryotes by viral infection or artificially in the laboratory are examples of horizontal gene transfer, as is sexual reproduction between members of the same eukaryotic species. A great deal of horizontal gene transfer has occurred during the evolution of eukaryotic cells, such as in the process that led to the development of mitochondria (see Figure 12-3).
In terms of cellular lifestyle, different kingdoms of life can be likened to hunters, farmers, and scavengers. Which of the following is true in this scheme? A. The ancestral eukaryotic cell was a farmer, but it turned into a hunter once it acquired mitochondria. B. Plant cells are considered scavengers, because their cell wall does not allow them to move. C. Most protozoa are hunters, whereas animal cells are farmers. D. The ancestral eukaryotic cell was a hunter, but upon acquiring chloroplasts it made the transition into farming. E. Fungi are scavengers without mitochondria.
Answer: D Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: In this lifestyle analogy, acquiring a symbiont chloroplast allowed cells to transition from hunting to farming. Other cells such as fungi evolved into scavengers instead, while protozoa and animal cells maintained their hunting habits. Fungi contain mitochondria.
Which of the following groups of living organisms has the highest variation in haploid genome size? A. Mammals B. Fish C. Fungi D. Protozoa E. Prokaryotes
Answer: D Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: The smallest and largest genomes in eukaryotes are found in protozoans. Please refer to Figure 1-32.
To trace family relationships between distantly related organisms such as humans, algae, bacteria, and archaea, one should compare their genomes in regions ... A. that evolve rapidly. B. that have a higher mutation rate. C. that code for proteins. D. where mutations are hardly tolerated. E. where most mutations are selectively neutral.
Answer: D Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: Highly conserved genes that code for optimized, essential, protein or RNA molecules should be studied to trace family relationships across distant taxa. Mutations in these regions (such as the genes that code for ribosomal RNAs) are usually eliminated, making the sequence recognizable even after billions of years of evolutionary history.
A mutation in the cdc28 gene in the budding yeast Saccharomyces cerevisiae causes cell-cycle arrest, giving rise to unbudded cells that look like "dumbbells." Treatment of wild-type cells with nocodazole, a drug that destabilizes some cytoskeletal polymers, leads to a similar phenotype. Based only on these observations, which statement is true regarding cdc28? A. cdc28 codes for a master regulatory kinase that phosphorylates other proteins. B. Nocodazole binds to the protein coded by the cdc28 gene. C. The product of the cdc28 gene is responsible for resistance to nocodazole. D. The product of the cdc28 gene is involved in cell cycle regulation. E. The product of cdc28 destabilizes the same cytoskeletal polymers that nocodazole also destabilizes.
Answer: D Difficulty: 3 Section: The Diversity of Genomes and the Tree of Life Feedback: Genetic analysis of mutations can give clues about gene functions. For example, if a mutation causes cell-cycle arrest, the affected gene is interpreted to have a role in cell-cycle progression. However, this does not necessarily mean that its product physically interacts with (binds to) another cellular component that is also involved in this process.
What is the order of the following evolutionary landmarks (A to D), from the oldest to the most recent? Your answer would be a four-letter string composed of letters A to D, with the oldest event on the left. A. Divergence of human and bird lineages B. Divergence of human and chimpanzee lineages C. Divergence of A. thaliana lineage from the conifers lineage D. Divergence of fish and insect lineages
Answer: DACB Difficulty: 3 Section: Genetic Information in Eukaryotes Feedback: The vertebrates and insects separated about 700 million years ago. Humans and birds separated about 300 million years ago. All flowering plants share a common ancestor that lived about 150 million years ago. Humans and chimpanzees are separated by only a few million years.
Indicate if each of the following descriptions matches RNA (R) or DNA (D). Your answer would be a five-letter string composed of letters R and D only, e.g. RDDRR. ( ) It is mainly found as a long, double-stranded molecule. ( ) It contains the sugar ribose. ( ) It normally contains the bases thymine, cytosine, adenine, and guanine. ( ) It can normally adopt distinctive folded shapes. ( ) It can be used as the template for protein synthesis.
Answer: DRDRR Difficulty: 1 Section: The Universal Features of Cells on Earth Feedback: Unlike DNA, cellular RNA is mainly polymerized as single-stranded molecules, allowing for folding into distinctive structures. Messenger RNAs (mRNAs) carry the information for protein synthesis. RNA contains the sugar ribose. Thymine is found in DNA.
All cells ... A. have membrane transport proteins. B. synthesize proteins on the ribosome. C. replicate their genome by DNA polymerization. D. transcribe their genetic information by RNA polymerization. E. All of the above.
Answer: E Difficulty: 1 Section: The Universal Features of Cells on Earth Feedback: All living cells replicate their DNA by the same overall mechanism of templated polymerization. They also transcribe the genetic information into RNA form using the same mechanism. Translation of this information into protein form is mediated by the ribosome in all cells. Additionally, all cellular membranes have membrane transport proteins that control the flow of material through the membranes.
Laboratory strains of the model organism Escherichia coli that are resistant to antibiotics are very often used in research laboratories as well as in the biotechnology industry. If cultures of such bacteria were allowed to contaminate the environment uncontrollably, it is possible that at some point, pathogenic bacteria such as Neisseria meningitidis (which causes meningitis and can cause death, especially in children) could acquire the same antibiotic-resistance gene, causing a meningitis outbreak that is difficult to treat. In this scenario, which of the following mechanisms is a more likely source of the antibiotic-resistance gene in N. meningitidis? A. Random new gene generation B. Intragenic mutation C. Gene duplication D. DNA segment shuffling E. Horizontal gene transfer
Answer: E Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: Horizontal gene transfer is common in bacteria and can result in the acquisition of new antibiotic-resistance genes by pathogenic bacteria.
Mitochondria and chloroplasts are thought to have evolved from free-living aerobic bacteria that were engulfed by an ancestral anaerobic cell and established a mutually beneficial (symbiotic) relationship with it. Which of the following statements is NOT true about these organelles? A. They are similar in size to small bacteria. B. They have their own circular genomic DNA. C. They have their own ribosomes. D. They have their own transfer RNAs. E. They are found in all eukaryotes.
Answer: E Difficulty: 1 Section: Genetic Information in Eukaryotes Feedback: Many eukaryotes lack chloroplasts, and some have lost their mitochondria.
All cells in a multicellular organism have normally developed from a single cell and share the same genome, but can nevertheless be wildly different in their shape and function. What in the eukaryotic genome is responsible for this cell-type diversity? A. The genes that encode transcription regulatory proteins B. The regulatory sequences that control the expression of genes C. The genes that code for molecules involved in receiving cellular signals D. The genes that code for molecules involved in sending cellular signals to other cells E. All of the above
Answer: E Difficulty: 1 Section: Genetic Information in Eukaryotes Feedback: The eukaryotic genome codes for not only various proteins and RNA molecules, but also regulatory molecules that control the expression of other genes. Noncoding regulatory sequences are used to tune the expression level of the cellular genes. The cell actively exchanges signals with other cells in the organism, which help it decide which genes to express.
It is a model organism used to study various cell and developmental processes such as the growth of developing body parts in the right place and with the correct shape. It develops from a fertilized egg to an adult in a little over a week, and has been a favorite of geneticists for almost a century. Some of its cells have giant chromosomes whose banding patterns have been extremely helpful in classical genetic studies. Which of the following describes this organism? A. It is a vertebrate. B. Its genome is only 10 million nucleotide pairs long. C. There are many more duplicate genes in this organism compared to humans. D. Although useful for genetic studies, the molecular mechanisms governing its development are irrelevant to human development. E. It normally only reproduces sexually.
Answer: E Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: It is the fruit fly Drosophila melanogaster.
It is a model organism used to study various eukaryotic cell and developmental processes such as cell division and cell death. Its hermaphrodite adult is composed of exactly 959 somatic (non-germ) cells, the lineage of each of which has been worked out with great precision. It is approximately 1 mm long. Which of the following describes this organism? A. It is a vertebrate. B. It is a plant pathogen that destroys many crops. C. Its genome codes for a few thousand genes. D. It can fly. E. It can be frozen indefinitely in a state of suspended animation.
Answer: E Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: It is the nematode worm Caenorhabditis elegans.
This model organism is particularly well suited for studying developmental processes in higher animals. It develops from a fertilized egg to an adult in only two to three months, and its body is transparent for the first two weeks, making it easy to observe cell behavior during development. Which of the following describes this organism? A. It is a vertebrate. B. It is well suited for genetic analysis. C. Its early stages of development occur outside of the mother's body. D. Its genome size is almost half that of humans. E. All of the above.
Answer: E Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: It is the zebrafish Danio rerio.
Which of the following structures is exclusively found in eukaryotic cells? A. Plasma membrane B. Cell wall C. Chromosome D. Ribosome E. Lysosome
Answer: E Difficulty: 2 Section: Genetic Information in Eukaryotes Feedback: Membrane-bound organelles such as lysosomes are normally not found in prokaryotes. Please note that using the same names for some structures in both prokaryotes and eukaryotes (e.g., cell wall) does not necessarily mean that these structures share the same molecular structure.
Indicate if each of the following descriptions matches messenger RNAs (M), ribosomal RNAs (R), or transfer RNAs (T). Your answer would be a four-letter string composed of letters M, R, and T only, e.g. RRRT. ( ) They contain codons. ( ) They contain anticodons. ( ) They are (covalently) attached to amino acids. ( ) They are at the core of a complex that carries out protein synthesis.
Answer: MTTR Difficulty: 1 Section: The Universal Features of Cells on Earth Feedback: Ribosomal RNA forms the core of the ribosome, an RNA-protein complex. Each transfer RNA is covalently attached to a specific amino acid at one end, and displays at its other end the anticodon sequence that can pair with a codon in a messenger RNA.
Indicate if each of the following descriptions matches lithotrophic (L), organotrophic (O), or phototrophic (P) organisms. Your answer would be a four-letter string composed of letters L, O, and P only, e.g. LLPP. ( ) They feed on other living organisms or their organic products. ( ) They are responsible for the current oxygen-rich atmosphere of the Earth. ( ) They are all known to be prokaryotic. ( ) They are the primary energy converters in hydrothermal vents in the ocean floor.
Answer: OPLL Difficulty: 1 Section: The Diversity of Genomes and the Tree of Life Feedback: While organotrophs (such as animals) feed on organic material produced by other organisms, the primary energy converters obtain their energy from the nonliving world. Phototrophs (such as plants) use the energy of sunlight. Molecular oxygen, a by-product of phototrophs, has changed the Earth's atmosphere and the entire biosphere. In hydrothermal vents, anaerobic lithotrophic microbes live in conditions similar to those in the early days of life on Earth.
Indicate if each of the following statements is true (T) or false (F). Your answer would be a five-letter string composed of letters T and F only, e.g. FFTFF. ( ) Animals ultimately depend on bacteria for fixation of the atmospheric nitrogen. ( ) If one finds animals in an isolated ecosystem, there should be photosynthetic organisms in that ecosystem as well. ( ) Carbon fixation can be carried out by bacteria only. ( ) All eukaryotes are organotrophs. ( ) Compared to eukaryotic cells, prokaryotes show greater biochemical diversity.
Answer: TFFFT Difficulty: 2 Section: The Diversity of Genomes and the Tree of Life Feedback: We rely on plants as our source of organic carbon and nitrogen. Plants in turn rely on bacteria for organic nitrogen, but can fix carbon by themselves. Hydrothermal vents provide an example of a secluded ecosystem that lacks photosynthetic organisms.