, Table of Contents
Chapter 1: Cells, Genomes, and the Diversity of Life
Chapter 2: Cell Chemistry and Bioenergetics
Chapter 3: Proteins
Chapter 4: DNA, Chromosomes, and Genomes
Chapter 5: DNA Replication, Repair, and Recombination
Chapter 6: How Cells Read the Genome: From DNA to Protein
Chapter 7: Control of Gene Expression
Chapter 8: Analyzing Cells, Molecules, and Systems
Chapter 9: Visualizing Cells and Their Molecules
Chapter 10: Membrane Structure
Chapter 11: Small-Molecule Transport and Electrical Properties of Membranes
Chapter 12: Intracellular Organization and Protein Sorting
Chapter 13: Intracellular Membrane Traffic
Chapter 14: Energy Conversion and Metabolic Compartmentation: Mitochondria and Chloroplasts
Chapter 15: Cell Signaling
Chapter 16: The Cytoskeleton
Chapter 17: The Cell Cycle
Chapter 18: Cell Death
Chapter 19: Cell Junctions and the Extracellular Matrix
Chapter 20: Cancer
Chapter 21: Development of Multicellular Organisms
Chapter 22: Stem Cells in Tissue Homeostasis and Regeneration
Chapter 23: Pathogens and Infection
Chapter 24: The Innate and Adaptive Immune Systems
,Chapter 1: Cells, Genomes, and the Diversity of Life
Questions
1. Which molecular feature is universally conserved across all known free-living cellular organisms on Earth?
A. Synthesis of a peptidoglycan cell wall containing alternating N-acetylglucosamine and N-acetylmuramic
acid
B. Assembly of the plasma membrane from ether-linked, branched isoprenoid lipids that span the
membrane as a monolayer
C. Coupling of ATP synthesis to a light-driven proton pump such as bacteriorhodopsin embedded in the
plasma membrane
D. Use of DNA as the hereditary template transcribed into RNA and translated into protein via a shared
genetic code
E. Enclosure of the genomic DNA within a double-membrane nuclear envelope that separates transcription
from translation
2. A newly characterized hydrothermal vent microorganism derives its metabolic energy from oxidizing
hydrogen sulfide (H2S) and assimilates carbon from inorganic carbon dioxide (CO2). How is this organism
classified?
A. Photoheterotroph
B. Photoautotroph
C. Chemoautotroph
D. Chemoheterotroph
E. Mixotroph
,3. Human myoglobin and the human beta-globin subunit are both oxygen-binding heme proteins that arose
from an ancestral globin gene duplication within the vertebrate lineage. How are these two genes related?
A. Orthologs
B. Analogs
C. Xenologs
D. Paralogs
E. Alleles
4. Which structural and genetic features provide direct empirical evidence supporting the endosymbiotic origin
of mitochondria from an alpha-proteobacterial ancestor? Select all that apply.
A. A double-membrane envelope where the inner membrane contains cardiolipin and lacks cholesterol
B. Universal reliance on eukaryotic RNA polymerase II for all organellar messenger RNA transcription
C. Use of bacterial-type ribosomes whose translation is inhibited by chloramphenicol and tetracycline
D. Presence of an independent, circular double-stranded DNA genome lacking extensive histone wrapping
E. Direct continuity and free lipid exchange between the mitochondrial inner membrane and the
endoplasmic reticulum
5. When Carl Woese reconstructed the universal tree of life using small subunit ribosomal RNA (SSU rRNA)
sequence comparisons, which fundamental conclusion reshaped evolutionary biology?
A. All prokaryotes form a single monophyletic kingdom distinctly separate from plants and animals
B. Eukaryotes evolved prior to bacteria through the progressive loss of metabolic pathways
C. Fungi share a closer phylogenetic ancestor with vascular plants than with multicellular metazoans
D. Viruses represent the ancestral baseline from which primitive cellular genomes evolved
E. Cellular life diverges into three distinct primary domains: Bacteria, Archaea, and Eukaryotes
6. Which model organism is uniquely advantageous for genetic screens dissecting programmed cell death
(apoptosis) due to its transparent body, invariant cell lineage of 959 somatic cells, and mapped cell fates?
A. Caenorhabditis elegans
, B. Drosophila melanogaster
C. Saccharomyces cerevisiae
D. Arabidopsis thaliana
E. Danio rerio
7. Two species of bacteria inhabiting an enteric biofilm exchange antibiotic resistance genes encoded on a
conjugative plasmid without vertical cell division. Which evolutionary mechanism does this genetic exchange
exemplify?
A. Gene duplication and divergence
B. Horizontal gene transfer
C. Exon shuffling
D. Retrotransposition
E. Polyploidization
8. Which cellular features represent distinct architectural hallmarks of eukaryotic cells that are absent from
typical bacterial and archaeal cells? Select all that apply.
A. Translation of messenger RNA into polypeptides using ribonucleoprotein ribosomes
B. A dynamic internal protein cytoskeleton composed of actin filaments and tubulin microtubules
C. A semipermeable amphipathic lipid bilayer that regulates passive solute diffusion
D. A membrane-bound nucleus housing the linear chromosomal genome
E. An endomembrane system mediating vesicular trafficking between the endoplasmic reticulum and Golgi
9. Human alpha-tubulin and mouse alpha-tubulin perform identical structural roles in microtubule assembly
and diverged solely due to the speciation event separating primates and rodents. How are these two genes
classified?
A. Paralogs
B. Pseudogenes
C. Orthologs
, D. Neomorphs
E. Homoplasies
10. Which model organism is the primary reference system for dissecting plant-specific molecular genetics,
photomorphogenesis, and flower development due to its small sequenced genome and rapid 6-week life
cycle?
A. Zea mays
B. Oryza sativa
C. Nicotiana tabacum
D. Arabidopsis thaliana
E. Chlamydomonas reinhardtii
11. Phylogenomic analyses of the newly discovered Asgard archaea have illuminated the origin of the
eukaryotic lineage. Which eukaryotic signature features are encoded within Asgard archaeal genomes? Select
all that apply.
A. Genes encoding actin-related cytoskeletal proteins capable of dynamic filament formation
B. Subunits of the ESCRT-III complex involved in membrane remodeling and scission
C. Complete genes for 80S ribosomes sensitive to cycloheximide and alpha-amanitin
D. Homologs of eukaryotic small Ras-superfamily GTPases involved in membrane trafficking
E. Enzymes for synthesizing cellulose cell walls identical to vascular plant walls
12. Why are embryonic development and organogenesis frequently investigated in the zebrafish (Danio rerio)
rather than the laboratory mouse (Mus musculus)?
A. Zebrafish lack an innate immune system, enabling effortless xenograft transplantation of human tissues
B. Zebrafish undergo direct development without undergoing gastrulation or germ layer specification
C. Zebrafish possess a haploid genome that prevents dominant-negative genetic masking during
mutagenesis
D. Zebrafish embryos are transparent, develop externally, and allow live optical tracking of cell migration
, E. Zebrafish share 100% amino acid identity with human metabolic enzymes across all organ systems
13. A researcher isolates an obligate anaerobic microbe from a mammalian colonic mucosal biopsy.
Biochemical profiling shows it gains all ATP from substrate-level phosphorylation during glucose fermentation
and requires dietary organic carbon. How is this organism categorized?
A. Chemoheterotroph
B. Chemoautotroph
C. Photoautotroph
D. Photoheterotroph
E. Lithoheterotroph
14. Which biological advantages make the budding yeast Saccharomyces cerevisiae an indispensable
eukaryotic model organism in biomedical research? Select all that apply.
A. It possesses an invariant cell lineage of exactly 959 cells with mapped embryonic apoptotic events
B. It undergoes rapid cell division with a doubling time of approximately 90 minutes in rich glucose media
C. It can be stably propagated as either a haploid or diploid cell, facilitating recessive mutant isolation
D. Its core cell-cycle machinery and cyclin-dependent kinase cascades are functionally conserved with
human homologs
E. It possesses high-efficiency homologous recombination, allowing precise targeted gene knockouts
15. Comparative genomics reveals that nearly all conserved core genes shared between humans and
Drosophila encode proteins dedicated to which primary cellular process?
A. Biomineralization of the extracellular matrix, including hydroxyapatite deposition during vertebrate bone
formation
B. Neuroendocrine feedback control of renal glomerular filtration rate in response to changes in blood
pressure
C. Basic cell metabolism, DNA replication, transcription, translation, and protein trafficking
D. Diversification of adaptive immune receptors by V(D)J rearrangement and somatic hypermutation of
antibody genes
, E. Myelination of peripheral axons by Schwann cell membranes to accelerate saltatory nerve conduction
16. Which mechanism of genome evolution provides the raw genetic substrate for one gene copy to retain its
original essential function while the second copy mutates to acquire a novel biological activity
(neofunctionalization)?
A. Nonsense-mediated mRNA decay
B. Alternative pre-mRNA splicing
C. Gene duplication followed by divergence
D. DNA methylation and genomic imprinting
E. Conservative site-specific Cre-lox recombination
17. Why is Escherichia coli the premier bacterial model organism for elucidating the universal molecular
mechanisms of DNA replication and the genetic code?
A. It contains linear chromosomes flanked by telomeres that replicate identically to human chromosomes
B. It has membrane-bound organelles, including a nucleus and mitochondria, that mirror eukaryotic
compartmentalization
C. It is an obligate intracellular parasite that must be grown inside cultured eukaryotic host cells for genetic
analysis
D. Its genes contain introns removed by spliceosomes, so its RNA splicing mechanisms are identical to
those of humans
E. It is easily cultured and fast-growing, and its lac operon revealed fundamental mechanisms of
transcriptional repression
18. What is the primary driving thermodynamic force that enables all living cells to maintain their highly
ordered, non-equilibrium internal chemical states?
A. Passive equilibrium distribution of inorganic ions across the plasma membrane, which generates internal
chemical order
B. Conversion of covalent bonds into stronger electrostatic attractions in a reversible cycle that stores
energy at no net cost
, C. Complete cessation of entropy production inside the cell, so that internal disorder never increases over
time
D. Continuous dissipation of free energy derived from the catabolism of nutrients or absorption of solar
photons
E. Direct absorption of ambient heat from the environment to power endergonic biosynthetic reactions
throughout the cell
19. An evolutionary biologist sequences the complete genome of a newly isolated unicellular eukaryote and
compares its gene families to human, yeast (S. cerevisiae), and bacterial homologs. Review the genomic data
below.
Gene Family Total Copies in Sequence Sequence Predicted
Isolate Identity to Identity to Function
Human Bacterial
Homolog Homolog
ATP Synthase 1 68% 52% Mitochondrial
Subunit beta oxidative
phosphorylation
Actin 3 84% 12% Cytoskeletal
filament
dynamics
Small Subunit 1 72% 34% Ribosomal
(18S) rRNA decoding center
DNA 1 61% 18% Nuclear
Polymerase lagging-strand
delta DNA replication
A. The isolate lacks functional mitochondria because its ATP synthase identity to bacteria exceeds 50%
B. The multiple actin copies indicate that the organism lacks cytoskeletal regulation
Chapter 1: Cells, Genomes, and the Diversity of Life
Chapter 2: Cell Chemistry and Bioenergetics
Chapter 3: Proteins
Chapter 4: DNA, Chromosomes, and Genomes
Chapter 5: DNA Replication, Repair, and Recombination
Chapter 6: How Cells Read the Genome: From DNA to Protein
Chapter 7: Control of Gene Expression
Chapter 8: Analyzing Cells, Molecules, and Systems
Chapter 9: Visualizing Cells and Their Molecules
Chapter 10: Membrane Structure
Chapter 11: Small-Molecule Transport and Electrical Properties of Membranes
Chapter 12: Intracellular Organization and Protein Sorting
Chapter 13: Intracellular Membrane Traffic
Chapter 14: Energy Conversion and Metabolic Compartmentation: Mitochondria and Chloroplasts
Chapter 15: Cell Signaling
Chapter 16: The Cytoskeleton
Chapter 17: The Cell Cycle
Chapter 18: Cell Death
Chapter 19: Cell Junctions and the Extracellular Matrix
Chapter 20: Cancer
Chapter 21: Development of Multicellular Organisms
Chapter 22: Stem Cells in Tissue Homeostasis and Regeneration
Chapter 23: Pathogens and Infection
Chapter 24: The Innate and Adaptive Immune Systems
,Chapter 1: Cells, Genomes, and the Diversity of Life
Questions
1. Which molecular feature is universally conserved across all known free-living cellular organisms on Earth?
A. Synthesis of a peptidoglycan cell wall containing alternating N-acetylglucosamine and N-acetylmuramic
acid
B. Assembly of the plasma membrane from ether-linked, branched isoprenoid lipids that span the
membrane as a monolayer
C. Coupling of ATP synthesis to a light-driven proton pump such as bacteriorhodopsin embedded in the
plasma membrane
D. Use of DNA as the hereditary template transcribed into RNA and translated into protein via a shared
genetic code
E. Enclosure of the genomic DNA within a double-membrane nuclear envelope that separates transcription
from translation
2. A newly characterized hydrothermal vent microorganism derives its metabolic energy from oxidizing
hydrogen sulfide (H2S) and assimilates carbon from inorganic carbon dioxide (CO2). How is this organism
classified?
A. Photoheterotroph
B. Photoautotroph
C. Chemoautotroph
D. Chemoheterotroph
E. Mixotroph
,3. Human myoglobin and the human beta-globin subunit are both oxygen-binding heme proteins that arose
from an ancestral globin gene duplication within the vertebrate lineage. How are these two genes related?
A. Orthologs
B. Analogs
C. Xenologs
D. Paralogs
E. Alleles
4. Which structural and genetic features provide direct empirical evidence supporting the endosymbiotic origin
of mitochondria from an alpha-proteobacterial ancestor? Select all that apply.
A. A double-membrane envelope where the inner membrane contains cardiolipin and lacks cholesterol
B. Universal reliance on eukaryotic RNA polymerase II for all organellar messenger RNA transcription
C. Use of bacterial-type ribosomes whose translation is inhibited by chloramphenicol and tetracycline
D. Presence of an independent, circular double-stranded DNA genome lacking extensive histone wrapping
E. Direct continuity and free lipid exchange between the mitochondrial inner membrane and the
endoplasmic reticulum
5. When Carl Woese reconstructed the universal tree of life using small subunit ribosomal RNA (SSU rRNA)
sequence comparisons, which fundamental conclusion reshaped evolutionary biology?
A. All prokaryotes form a single monophyletic kingdom distinctly separate from plants and animals
B. Eukaryotes evolved prior to bacteria through the progressive loss of metabolic pathways
C. Fungi share a closer phylogenetic ancestor with vascular plants than with multicellular metazoans
D. Viruses represent the ancestral baseline from which primitive cellular genomes evolved
E. Cellular life diverges into three distinct primary domains: Bacteria, Archaea, and Eukaryotes
6. Which model organism is uniquely advantageous for genetic screens dissecting programmed cell death
(apoptosis) due to its transparent body, invariant cell lineage of 959 somatic cells, and mapped cell fates?
A. Caenorhabditis elegans
, B. Drosophila melanogaster
C. Saccharomyces cerevisiae
D. Arabidopsis thaliana
E. Danio rerio
7. Two species of bacteria inhabiting an enteric biofilm exchange antibiotic resistance genes encoded on a
conjugative plasmid without vertical cell division. Which evolutionary mechanism does this genetic exchange
exemplify?
A. Gene duplication and divergence
B. Horizontal gene transfer
C. Exon shuffling
D. Retrotransposition
E. Polyploidization
8. Which cellular features represent distinct architectural hallmarks of eukaryotic cells that are absent from
typical bacterial and archaeal cells? Select all that apply.
A. Translation of messenger RNA into polypeptides using ribonucleoprotein ribosomes
B. A dynamic internal protein cytoskeleton composed of actin filaments and tubulin microtubules
C. A semipermeable amphipathic lipid bilayer that regulates passive solute diffusion
D. A membrane-bound nucleus housing the linear chromosomal genome
E. An endomembrane system mediating vesicular trafficking between the endoplasmic reticulum and Golgi
9. Human alpha-tubulin and mouse alpha-tubulin perform identical structural roles in microtubule assembly
and diverged solely due to the speciation event separating primates and rodents. How are these two genes
classified?
A. Paralogs
B. Pseudogenes
C. Orthologs
, D. Neomorphs
E. Homoplasies
10. Which model organism is the primary reference system for dissecting plant-specific molecular genetics,
photomorphogenesis, and flower development due to its small sequenced genome and rapid 6-week life
cycle?
A. Zea mays
B. Oryza sativa
C. Nicotiana tabacum
D. Arabidopsis thaliana
E. Chlamydomonas reinhardtii
11. Phylogenomic analyses of the newly discovered Asgard archaea have illuminated the origin of the
eukaryotic lineage. Which eukaryotic signature features are encoded within Asgard archaeal genomes? Select
all that apply.
A. Genes encoding actin-related cytoskeletal proteins capable of dynamic filament formation
B. Subunits of the ESCRT-III complex involved in membrane remodeling and scission
C. Complete genes for 80S ribosomes sensitive to cycloheximide and alpha-amanitin
D. Homologs of eukaryotic small Ras-superfamily GTPases involved in membrane trafficking
E. Enzymes for synthesizing cellulose cell walls identical to vascular plant walls
12. Why are embryonic development and organogenesis frequently investigated in the zebrafish (Danio rerio)
rather than the laboratory mouse (Mus musculus)?
A. Zebrafish lack an innate immune system, enabling effortless xenograft transplantation of human tissues
B. Zebrafish undergo direct development without undergoing gastrulation or germ layer specification
C. Zebrafish possess a haploid genome that prevents dominant-negative genetic masking during
mutagenesis
D. Zebrafish embryos are transparent, develop externally, and allow live optical tracking of cell migration
, E. Zebrafish share 100% amino acid identity with human metabolic enzymes across all organ systems
13. A researcher isolates an obligate anaerobic microbe from a mammalian colonic mucosal biopsy.
Biochemical profiling shows it gains all ATP from substrate-level phosphorylation during glucose fermentation
and requires dietary organic carbon. How is this organism categorized?
A. Chemoheterotroph
B. Chemoautotroph
C. Photoautotroph
D. Photoheterotroph
E. Lithoheterotroph
14. Which biological advantages make the budding yeast Saccharomyces cerevisiae an indispensable
eukaryotic model organism in biomedical research? Select all that apply.
A. It possesses an invariant cell lineage of exactly 959 cells with mapped embryonic apoptotic events
B. It undergoes rapid cell division with a doubling time of approximately 90 minutes in rich glucose media
C. It can be stably propagated as either a haploid or diploid cell, facilitating recessive mutant isolation
D. Its core cell-cycle machinery and cyclin-dependent kinase cascades are functionally conserved with
human homologs
E. It possesses high-efficiency homologous recombination, allowing precise targeted gene knockouts
15. Comparative genomics reveals that nearly all conserved core genes shared between humans and
Drosophila encode proteins dedicated to which primary cellular process?
A. Biomineralization of the extracellular matrix, including hydroxyapatite deposition during vertebrate bone
formation
B. Neuroendocrine feedback control of renal glomerular filtration rate in response to changes in blood
pressure
C. Basic cell metabolism, DNA replication, transcription, translation, and protein trafficking
D. Diversification of adaptive immune receptors by V(D)J rearrangement and somatic hypermutation of
antibody genes
, E. Myelination of peripheral axons by Schwann cell membranes to accelerate saltatory nerve conduction
16. Which mechanism of genome evolution provides the raw genetic substrate for one gene copy to retain its
original essential function while the second copy mutates to acquire a novel biological activity
(neofunctionalization)?
A. Nonsense-mediated mRNA decay
B. Alternative pre-mRNA splicing
C. Gene duplication followed by divergence
D. DNA methylation and genomic imprinting
E. Conservative site-specific Cre-lox recombination
17. Why is Escherichia coli the premier bacterial model organism for elucidating the universal molecular
mechanisms of DNA replication and the genetic code?
A. It contains linear chromosomes flanked by telomeres that replicate identically to human chromosomes
B. It has membrane-bound organelles, including a nucleus and mitochondria, that mirror eukaryotic
compartmentalization
C. It is an obligate intracellular parasite that must be grown inside cultured eukaryotic host cells for genetic
analysis
D. Its genes contain introns removed by spliceosomes, so its RNA splicing mechanisms are identical to
those of humans
E. It is easily cultured and fast-growing, and its lac operon revealed fundamental mechanisms of
transcriptional repression
18. What is the primary driving thermodynamic force that enables all living cells to maintain their highly
ordered, non-equilibrium internal chemical states?
A. Passive equilibrium distribution of inorganic ions across the plasma membrane, which generates internal
chemical order
B. Conversion of covalent bonds into stronger electrostatic attractions in a reversible cycle that stores
energy at no net cost
, C. Complete cessation of entropy production inside the cell, so that internal disorder never increases over
time
D. Continuous dissipation of free energy derived from the catabolism of nutrients or absorption of solar
photons
E. Direct absorption of ambient heat from the environment to power endergonic biosynthetic reactions
throughout the cell
19. An evolutionary biologist sequences the complete genome of a newly isolated unicellular eukaryote and
compares its gene families to human, yeast (S. cerevisiae), and bacterial homologs. Review the genomic data
below.
Gene Family Total Copies in Sequence Sequence Predicted
Isolate Identity to Identity to Function
Human Bacterial
Homolog Homolog
ATP Synthase 1 68% 52% Mitochondrial
Subunit beta oxidative
phosphorylation
Actin 3 84% 12% Cytoskeletal
filament
dynamics
Small Subunit 1 72% 34% Ribosomal
(18S) rRNA decoding center
DNA 1 61% 18% Nuclear
Polymerase lagging-strand
delta DNA replication
A. The isolate lacks functional mitochondria because its ATP synthase identity to bacteria exceeds 50%
B. The multiple actin copies indicate that the organism lacks cytoskeletal regulation
