Test Bank Microbiology An Evolving Science 4th Edition by John W. Foster

$25.00
Test Bank Microbiology An Evolving Science 4th Edition by John W. Foster

Test Bank Microbiology An Evolving Science 4th Edition by John W. Foster

$25.00
Test Bank Microbiology An Evolving Science 4th Edition by John W. Foster
MICROBIOLOGY AN EVOLVING SCIENCE 4TH EDITION BY JOHN W. FOSTER TEST BANK

CHAPTER 1: Microbial Life: Origin and Discovery

MULTIPLE CHOICE

  1. Viruses are
a.infectious agents that infect exclusively multicellular organisms.
b.noncellular particles that take over the metabolism of a cell to generate more virus particles.
c.pathogens that replicate in complex growth media.
d.cellular particles that belong to the archaea domain.
e.microbes that consist of lipid membrane–enclosed genomes.

ANS: B DIF: Easy REF: 1.1

OBJ: 1.1a Recall the definition of a microbe | 1.1b List examples of microbes

MSC: Remembering

  1. Analysis of DNA sequences reveals
a.the ancient convergence of two cell types (i.e., prokaryotes and eukaryotes).
b.that prokaryotes and eukaryotes evolved from a common ancestral cell.
c.that bacteria share a common ancestor with archaea but not with eukarya.
d.that prokaryotes are cells with a nucleus.
e.that the genome of Haemophilus influenzae has about 2 billion base pairs.

ANS: B DIF: Easy REF: 1.1

OBJ: 1.1d Explain the implications of microbial genome sequencing

MSC: Understanding

  1. Which of these groups are considered to be microbes but NOT considered to be cells?
a.virusesd.protists
b.bacteriae.filamentous fungi
c.archaea

ANS: A DIF: Easy REF: 1.1

OBJ: 1.1a Recall the definition of a microbe | 1.1c Describe some problems with the definition of a microbe MSC: Understanding

  1. A microbe is commonly defined as a ________ that requires a microscope to be seen.
a.virusd.multicellular eukaryote
b.bacteriume.living organism
c.single-cellular prokaryote

ANS: E DIF: Easy REF: 1.1

OBJ: 1.1a Recall the definition of a microbe MSC: Remembering

  1. Which one of the following statements regarding microbial cells is FALSE?
a.Microbial cells acquire food, gain energy to build themselves, and respond to environmental change.
b.Most single-celled organisms require a microscope to render them visible, but some bacterial cells are large enough to be seen with naked eyes.
c.Microbes function as individual entities.
d.Many microbes form complex multicellular assemblages.
e.Viruses are not considered microbial cells.

ANS: C DIF: Easy REF: 1.1

OBJ: 1.1a Recall the definition of a microbe MSC: Understanding

  1. Which of the following statements is FALSE?
a.A genome is the total genetic information contained in an organism’s chromosomal DNA.
b.If a microbe’s genome includes genes for nitrogenase, that microbe probably can fix nitrogen.
c.By comparing DNA sequences of different organisms, we can figure out how closely related they are.
d.Fred Sanger developed the first applicable DNA sequencing method.
e.Fred Sanger completed the sequences of Haemophilus influenzae.

ANS: E DIF: Easy REF: 1.1

OBJ: 1.1d Explain the implications of microbial genome sequencing

MSC: Remembering

  1. The first cellular genomes to be sequenced were those of
a.humans.d.prions.
b.bacteria.e.fungi.
c.viruses.

ANS: B DIF: Easy REF: 1.1

OBJ: 1.1d Explain the implications of microbial genome sequencing

MSC: Remembering

  1. The environment of early Earth may have contained all of the following EXCEPT
a.ferrous iron.d.oxygen.
b.methane.e.hydrogen gas.
c.ammonia.

ANS: D DIF: Medium REF: Special Topic 1.1

OBJ: 1.1a Recall the definition of a microbe MSC: Remembering

  1. The development of the theory of the “RNA world” resulted from the discovery of
a.archaea.d.ribozymes.
b.prions.e.endosymbionts.
c.bacteria.

ANS: D DIF: Medium REF: 1.6

OBJ: 1.6b Explain how studies on microbes fostered our knowledge of DNA function and enhanced DNA technology MSC: Remembering

  1. What is the evidence that living cells existed on Earth up to 3.8 billion years ago?
a.microfossilsd.Martian folded rock formations
b.16S ribosomal RNAe.diatom shells
c.Miller and Urey’s experiments

ANS: A DIF: Medium REF: Special Topic 1.1

OBJ: 1.5a Explain why microbes can be challenging to classify taxonomically | 1.5b Outline how microbial classification has changed over time MSC: Remembering

  1. What did van Leeuwenhoek discover using microscopic observations before and after drinking hot beverages?
a.Heat did not kill microbes.
b.Heat killed microbes.
c.Heat did not kill algae.
d.Caffeine in coffee killed microbes.
e.The existence of spiral-shaped microbes.

ANS: B DIF: Medium REF: 1.2

OBJ: 1.2b Explain why the microscope is an important tool in the field of microbiology | 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Analyzing

  1. Tyndall’s spontaneous generation experiments occasionally failed due to
a.nutrient chirality.d.lack of oxygen.
b.dust.e.endospores.
c.fermentation.

ANS: E DIF: Easy REF: 1.2

OBJ: 1.2d Compare and contrast Spallanzani’s, Pasteur’s, and Tyndall’s experiments that tested spontaneous generation MSC: Analyzing

  1. The discovery of microbes occurred in the ________ century?
a.seventeenthd.twentieth
b.eighteenthe.twenty-first
c.nineteenth

ANS: C DIF: Easy REF: 1.2

OBJ: 1.2b Explain why the microscope is an important tool in the field of microbiology

MSC: Remembering

  1. Robert Koch won the Nobel Prize for his contribution to medical bacteriology regarding
a.Escherichia coli.d.rabies.
b.Bacillus subtilis.e.smallpox.
c.Mycobacterium tuberculosis.

ANS: C DIF: Medium REF: 1.3 OBJ: 1.3b List Koch’s postulates

MSC: Remembering

  1. How did European invaders to North America kill much of the native population?
a.tuberculosisd.HIV
b.leprosye.bubonic plague
c.smallpox

ANS: C DIF: Medium REF: 1.2

OBJ: 1.2a List both positive and negative impacts that microbes have had on human history

MSC: Understanding

  1. Florence Nightingale
a.is best known as the founder of professional nursing.
b.was the first to use disinfectant to demonstrate the significance of aseptic technique.
c.developed the pie chart of mortality data during the Crimean War.
d.performed the first controlled experiment on the chemical conversion of matter, known today as chemotherapy.
e.argued that the environment of early Earth contained mainly reduced compounds.

ANS: A DIF: Easy REF: 1.2

OBJ: 1.2a List both positive and negative impacts that microbes have had on human history | 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Remembering

  1. Who developed the concept of medical statistics?
a.Francis Crickd.Louis Pasteur
b.Florence Nightingalee.Alexander Fleming
c.Edward Jenner

ANS: B DIF: Easy REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Remembering

  1. The first person to visualize individual microbial cells was
a.Antonie van Leeuwenhoek.d.Lady Montagu.
b.Robert Hooke.e.Edward Jenner.
c.Louis Pasteur.

ANS: A DIF: Easy REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Remembering

  1. Semmelweis and Lister noted that many of their patients’ deaths were due to
a.fungi.d.pathogen transmission by doctors.
b.Escherichia coli.e.Staphylococcus.
c.chlorine.

ANS: D DIF: Medium REF: 1.3

OBJ: 1.3a Describe what constitutes a pure culture and how to obtain one

MSC: Understanding

  1. What is the standard sterilization method for the controlled study of microbes?
a.boilingd.autoclaving
b.pasteurizatione.irradiation
c.filter sterilization

ANS: D DIF: Medium REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Remembering

  1. How does the Winogradsky column differ from Koch’s plate media?
a.Koch’s media creates a gradient from oxygen-rich conditions at the surface to highly reduced conditions below.
b.The Winogradsky column is used for culturing viruses.
c.The Winogradsky column is used for growing extremophiles.
d.The Winogradsky column uses the kinds of nutrients that feed humans.
e.The bacteria that Winogradsky isolated can grow only on inorganic minerals.

ANS: E DIF: Easy REF: 1.4

OBJ: 1.4a List Winogradsky’s contributions to microbial culture technique | 1.4b Define what distinguishes lithotrophs from other organisms MSC: Understanding

  1. Suppose Pasteur’s swan-necked flasks containing boiled broth became cloudy twenty-four hours after boiling. Which choice could best explain the turbidity or cloudiness in the broth without supporting spontaneous generation?
a.Endospores in the broth survived boiling and grew after the broth cooled.
b.Contaminating organisms in the broth killed by boiling became alive again after the broth cooled.
c.Chemicals in the broth came together to form living organisms.
d.The broth allowed light to pass through it with less interference after boiling.
e.Solid material in the broth dissolved during boiling.

ANS: A DIF: Difficult REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall | 1.2d Compare and contrast Spallanzani’s, Pasteur’s, and Tyndall’s experiments that tested spontaneous generation MSC: Applying

  1. Which of the following is NOT considered to be an extremophilic condition for bacteria?
a.high alkalinityd.high nutrients
b.high salinitye.high temperature
c.high acidity

ANS: D DIF: Medium REF: 1.4

OBJ: 1.4c Explain the role of microbes in geochemical cycling, especially that of nitrogen

MSC: Remembering

  1. The use of agar as a more robust gelling agent in solid media was suggested by
a.Robert Koch.d.Louis Pasteur.
b.Ignaz Semmelweis.e.Richard Petri.
c.Angelina Hesse.

ANS: C DIF: Easy REF: 1.3

OBJ: 1.3a Describe what constitutes a pure culture and how to obtain one | 1.3c Assess some of the practical obstacles in applying Koch’s postulates MSC: Remembering

  1. It took the advent of the polymerase chain reaction to detect the presence of the causative agent for which disease?
a.anthraxd.rabies
b.tuberculosise.smallpox
c.AIDS

ANS: C DIF: Difficult REF: 1.3

OBJ: 1.3c Assess some of the practical obstacles in applying Koch’s postulates | 1.3f Describe how viruses were discovered MSC: Understanding

  1. The word “vaccination” is derived from the Latin word vacca, which means
a.inject.d.cow.
b.smallpox.e.pustule.
c.immunize.

ANS: D DIF: Easy REF: 1.3

OBJ: 1.3d Recall the contributions of various individuals to the discovery and implementation of vaccination | 1.3e Compare the roles of immunization, antiseptics, and antibiotics in human disease treatment and prevention MSC: Remembering

  1. What was the basis for the original smallpox vaccine?
a.chickenpox virusd.smallpox virus
b.cowpox viruse.anthrax
c.rabies virus

ANS: B DIF: Medium REF: 1.3

OBJ: 1.3d Recall the contributions of various individuals to the discovery and implementation of vaccination MSC: Remembering

  1. Penicillin was first used to save the lives of many people during which war?
a.the U.S. Civil Ward.World War I
b.the Korean Ware.World War II
c.the Vietnam War

ANS: E DIF: Easy REF: 1.3

OBJ: 1.3e Compare the roles of immunization, antiseptics, and antibiotics in human disease treatment and prevention MSC: Remembering

  1. How do many animal endosymbionts grow?
a.on the surface of the hostd.on inorganic minerals
b.on low nutrientse.in biofilms
c.by reducing iron oxide

ANS: E DIF: Medium REF: 1.4

OBJ: 1.4d Compare the roles of animal endosymbionts and plant endosymbionts

MSC: Remembering

  1. All of the following are true about penicillin EXCEPT that it
a.was discovered by Alexander Fleming.
b.was an accidental discovery.
c.is produced by a bacterium.
d.was the first antibiotic used by humans.
e.was purified by Florey and Chain.

ANS: C DIF: Difficult REF: 1.3

OBJ: 1.3e Compare the roles of immunization, antiseptics, and antibiotics in human disease treatment and prevention MSC: Remembering

  1. Which of the following statements regarding viruses is FALSE?
a.Most are too small to be seen by a light microscope.
b.They are “filterable agents” that can pass through porcelain filters that have a pore size that blocks microbes.
c.Their genomes could be composed of DNA or RNA.
d.They are smaller than plasmids and prions.
e.Viral particles, when pure enough, can be crystallized.

ANS: D DIF: Medium REF: 1.3

OBJ: 1.3f Describe how viruses were discovered MSC: Analyzing

  1. You have isolated a bacterium that you believe to be the causative agent of a new disease in frogs. How would you test the third of Koch’s postulates?
a.Determine the shape of the bacterial cells.
b.Inject the bacteria into a healthy frog.
c.Isolate the bacterium from a sick frog.
d.Show that the bacterium is not present in healthy frogs.
e.Grow a pure culture of the bacterium outside the frog.

ANS: B DIF: Difficult REF: 1.3 OBJ: 1.3b List Koch’s postulates

MSC: Applying

  1. How did Sergei Winogradsky grow lithotrophs?
a.enrichment cultured.endosymbiosis
b.organic mediae.chain of infection
c.pure culture

ANS: A DIF: Easy REF: 1.4

OBJ: 1.4a List Winogradsky’s contributions to microbial culture technique | 1.4b Define what distinguishes lithotrophs from other organisms MSC: Understanding

  1. Organisms that live symbiotically inside a larger organism are known as
a.organelles.d.endosymbionts.
b.cyanobacteria.e.chloroplasts.
c.mitochondria.

ANS: D DIF: Easy REF: 1.4

OBJ: 1.4d Compare the roles of animal endosymbionts and plant endosymbionts

MSC: Remembering

  1. Animal microbiomes are NOT significant in
a.digesting plant fibers.d.converting ammonia to nitrate.
b.bioluminescence.e.providing nutrients to the host.
c.protection from pathogens.

ANS: D DIF: Easy REF: 1.4

OBJ: 1.4d Compare the roles of animal endosymbionts and plant endosymbionts

MSC: Applying

  1. Carl Woese’s discovery replaced the classification scheme of five kingdoms with a scheme of three
a.phyla.d.orders.
b.domains.e.genera.
c.classes.

ANS: B DIF: Easy REF: 1.5

OBJ: 1.5b Outline how microbial classification has changed over time | 1.5d Describe the importance of DNA sequencing in classification MSC: Remembering

  1. The gene expression machinery of archaea is MOST similar to
a.monera.d.eukaryotes.
b.prokaryotes.e.mitochondria.
c.bacteria.

ANS: D DIF: Medium REF: 1.5

OBJ: 1.5e Compare and contrast archaea, bacteria, and eukaryotes

MSC: Understanding

  1. In the three-domain model, the bacterial ancestor of mitochondria derives from ancient
a.fungi.d.archaea.
b.cyanobacteria.e.protists.
c.respiring bacteria.

ANS: C DIF: Medium REF: 1.5

OBJ: 1.5c Appraise endosymbiosis as an explanation for mitochondria and chloroplasts

MSC: Remembering

  1. Which of the following organelles are thought to be of prokaryotic origin?
a.chloroplastd.chloroplast and mitochondria
b.mitochondriae.chloroplast and nucleus
c.nucleus

ANS: D DIF: Medium REF: 1.5

OBJ: 1.5c Appraise endosymbiosis as an explanation for mitochondria and chloroplasts

MSC: Understanding

  1. In the three-domain model, the bacterial ancestor of chloroplasts derives from ancient
a.fungi.d.archaea.
b.cyanobacteria.e.protists.
c.proteobacteria.

ANS: B DIF: Medium REF: 1.5

OBJ: 1.5c Appraise endosymbiosis as an explanation for mitochondria and chloroplasts

MSC: Remembering

  1. Which commonly used microbial classification advancement led to the tree by Carl Woese in 1977?
a.comparative genomicsd.protein sequencing
b.microscopye.16S rRNA sequencing
c.X-ray diffraction

ANS: E DIF: Medium REF: 1.5

OBJ: 1.5b Outline how microbial classification has changed over time | 1.5d Describe the importance of DNA sequencing in classification MSC: Understanding

  1. Electron microscopes use what to focus the beam of electrons?
a.electromagnetsd.X-ray diffraction
b.a condenser lense.glass
c.light rays

ANS: A DIF: Easy REF: 1.6

OBJ: 1.6a Describe the roles of the electron microscope and the ultracentrifuge in advancing our knowledge of cell structure and function MSC: Remembering

  1. Peter Mitchell and Jennifer Moyle discovered the ________ theory in the 1960s.
a.germplasmd.DNA synthesis
b.evolutione.polymerase chain reaction
c.chemiosmotic

ANS: C DIF: Easy REF: 1.6

OBJ: 1.6a Describe the roles of the electron microscope and the ultracentrifuge in advancing our knowledge of cell structure and function MSC: Remembering

  1. The X-ray diffraction studies by which of the following scientists concluded that DNA was a double helix?
a.James Watsond.Maurice Wilkins
b.Rosalind Frankline.Kary Mullis
c.Francis Crick

ANS: B DIF: Easy REF: 1.6

OBJ: 1.6a Describe the roles of the electron microscope and the ultracentrifuge in advancing our knowledge of cell structure and function MSC: Remembering

  1. What feature of bacteria facilitated the DNA revolution in the 1970s?
a.They are very small.d.All of their genes were known.
b.They readily recombine DNA.e.They do not cause disease.
c.They have very large genomes.

ANS: B DIF: Medium REF: 1.6

OBJ: 1.6b Explain how studies on microbes fostered our knowledge of DNA function and enhanced DNA technology MSC: Understanding

  1. This scientist first discovered the process of transformation.
a.Francis Crickd.Louis Pasteur
b.Robert Koche.Frederick Griffith
c.Edward Jenner

ANS: E DIF: Difficult REF: 1.6

OBJ: 1.6b Explain how studies on microbes fostered our knowledge of DNA function and enhanced DNA technology MSC: Remembering

  1. Taq polymerase forms the basis of a technique for
a.comparative genomics.d.DNA amplification.
b.recombinant DNA.e.protein synthesis.
c.X-ray diffraction.

ANS: D DIF: Easy REF: 1.6

OBJ: 1.6c State some uses of microbes in medicine and industry

MSC: Understanding

  1. In 1975, scientists held a conference at Asilomar to regulate and restrict the field of
a.recombinant DNA.d.DNA amplification.
b.comparative genomics.e.forensic microbiology.
c.DNA sequencing.

ANS: A DIF: Medium REF: 1.6

OBJ: 1.6c State some uses of microbes in medicine and industry

MSC: Understanding

  1. The study of and cause of disease in humans, animals, and plants is called
a.microbiology.d.epidemiology.
b.phylogeny.e.forensics.
c.genomics.

ANS: D DIF: Medium REF: 1.6

OBJ: 1.6c State some uses of microbes in medicine and industry

MSC: Remembering

  1. The ultracentrifuge is a high-speed centrifuge ideally suited for separating individual
a.cellular proteins and nucleotides.d.secondary metabolites.
b.microbial cells.e.base pairs.
c.mold spores.

ANS: A DIF: Medium REF: 1.6

OBJ: 1.6a Describe the roles of the electron microscope and the ultracentrifuge in advancing our knowledge of cell structure and function MSC: Understanding

SHORT ANSWER

  1. What is the MOST recent evidence suggesting that all life on Earth shares a common ancestry?

ANS:

Many genomes have now been sequenced, and those sequences are available in databases for comparison. This field is referred to as comparative genomics. Comparisons have revealed that there is a set of core genes shared by all organisms.

DIF: Difficult REF: 1.1 | 1.5

OBJ: 1.1d Explain the implications of microbial genome sequencing | 1.5b Outline how microbial classification has changed over time MSC: Analyzing

  1. How are prokaryotes and eukaryotes different?

ANS:

A prokaryote lacks a nucleus and membrane-bounded organelles, whereas a eukaryote has a nucleus and membrane-bounded organelles.

DIF: Easy REF: 1.1 | 1.5 OBJ: 1.1a Recall the definition of a microbe

MSC: Remembering

  1. How do microbes help in the extraction of minerals?

ANS:

Several lithotrophic bacteria help in the rapid oxidation of minerals, which generates strong acids that expedite the breakdown of mineral ore. Currently, approximately 20% of the world’s copper, as well as some uranium and zinc, is produced by bacterial leaching.

DIF: Medium REF: 1.2

OBJ: 1.2a List both positive and negative impacts that microbes have had on human history

MSC: Applying

  1. Antonie van Leeuwenhoek worked as a cloth draper, inspecting the quality of cloth. How did this lead to his interest in microscopy?

ANS:

His work introduced him to magnifying lenses. He began the hobby of grinding lenses, ultimately making a microscope that enabled him to observe single-celled microbes.

DIF: Medium REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Understanding

  1. What was the major complaint about Lazzaro Spallanzani’s experiment to disprove spontaneous generation, and how did Louis Pasteur’s swan-neck flasks overcome this?

ANS:

Spallanzani’s flasks were plugged so as not to let organisms accidentally enter the boiled medium. Opponents argued that no growth was observed simply due to the lack of oxygen. Pasteur’s swan-neck flasks did not allow organisms to enter the flask but did allow oxygen to enter. Growth was still not observed.

DIF: Medium REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Evaluating

  1. Describe the discoveries of Louis Pasteur while working with the French beer and wine manufacturers in assessing alcohol versus vinegar production during fermentation.

ANS:

Previously, it was believed that the conversion of grapes and grain to wine and beer was a spontaneous chemical process. Pasteur discovered that this fermentation was caused by living yeast, which did not require oxygen for growth. He also discovered that when the grapes or grain are contaminated with bacteria instead of yeast, acetic acid is produced instead of alcohol.

DIF: Medium REF: 1.2

OBJ: 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Understanding

  1. Describe the effects of three microbial diseases that have significantly affected human populations throughout history.

ANS:

Answers may vary. Some examples include bubonic plague, which killed one-third of Europe’s population in the fourteenth century; tuberculosis, which was common in the nineteenth century; AIDS, which affects many people today; and smallpox, which killed a large number of native North Americans.

DIF: Medium REF: 1.2

OBJ: 1.2a List both positive and negative impacts that microbes have had on human history | 1.2c Identify the contributions of the following individuals: Nightingale, Hooke, van Leeuwenhoek, Pasteur, and Tyndall MSC: Applying

  1. Why did it take so long for humans to determine that microbes cause infectious diseases?

ANS:

Microbes are too small to be seen with the naked eye, so until powerful-enough microscopes were invented, humans did not know that microbes existed. Even after humans were aware of the presence of microbes, they did not suspect them of causing disease until people such as Joseph Lister and Ignaz Semmelweis performed experiments that showed antiseptics decrease the incidence of infection.

DIF: Difficult REF: 1.2 | 1.3

OBJ: 1.2b Explain why the microscope is an important tool in the field of microbiology

MSC: Understanding

  1. Robert Koch’s postulates have not been used to prove HIV as the causative agent of AIDS. Why not?

ANS:

Answers may vary, but a major reason is that humans cannot be injected with HIV to see if they develop AIDS, and a suitable animal host doesn’t exist for testing.

DIF: Medium REF: 1.3

OBJ: 1.3c Assess some of the practical obstacles in applying Koch’s postulates

MSC: Understanding

  1. Define “attenuation” and describe some mechanisms used to attenuate pathogens.

ANS:

Attenuation results in a weakened organism that will not produce full-blown disease but will generate immunity. Answers for mechanisms may vary, but heat treatment or aging for various periods or natural attenuation in the host are mentioned in the chapter.

DIF: Medium REF: 1.3

OBJ: 1.3d Recall the contributions of various individuals to the discovery and implementation of vaccination | 1.3e Compare the roles of immunization, antiseptics, and antibiotics in human disease treatment and prevention MSC: Applying

  1. What is the significance of the work of Ignaz Semmelweis and Joseph Lister?

ANS:

They showed that use of antiseptics on doctors’ hands and medical instruments drastically reduced the mortality rate of hospital patients. They made these observations before Robert Koch’s germ theory of disease.

DIF: Medium REF: 1.3

OBJ: 1.3e Compare the roles of immunization, antiseptics, and antibiotics in human disease treatment and prevention MSC: Understanding

  1. How would you use Robert Koch’s postulates to prove that a specific organism causes a new disease in mice?

ANS:

See Figure 1.17 in the textbook:

(1) The suspected organism is found in all diseased mice, but is absent from healthy mice.

(2) The suspected organism is isolated from the diseased mice and grown in pure culture.

(3) When the suspected organism is introduced into a healthy mouse, the same disease occurs.

(4) The same strain of microbe is obtained from the newly diseased mouse.

DIF: Difficult REF: 1.3 OBJ: 1.3b List Koch’s postulates

MSC: Applying

  1. Explain why the organisms that were studied by Sergei Winogradsky could not be grown on Robert Koch’s plate media containing agar or gelatin.

ANS:

The organisms studied by Winogradsky were lithotrophs, which feed solely on inorganic substances. Koch’s plate media contained organic nutrient sources, which may even be toxic to the organisms he was attempting to grow.

DIF: Medium REF: 1.4

OBJ: 1.4a List Winogradsky’s contributions to microbial culture technique

MSC: Analyzing

  1. Is it true that only culturable bacteria contribute to ecology? Explain your answer.

ANS:

No, this is not a true statement. It is estimated that barely 0.1% of microbial species can be cultured. The work of Winogradsky and later microbial ecologists showed that bacteria are necessary for geochemical cycling. Many of these organisms can’t be grown in pure culture on laboratory media but can be grown in enrichment culture such as a Winogradsky column.

DIF: Difficult REF: 1.4

OBJ: 1.4c Explain the role of microbes in geochemical cycling, especially that of nitrogen

MSC: Analyzing

  1. Define the term “endosymbiont” and give an example of an endosymbiotic relationship found in nature.

ANS:

An endosymbiont is an organism living symbiotically inside a larger organism. Examples may vary, but include the following: Rhizobium in a leguminous plant, bioluminescent bacteria in the light organs of fish and squid, and photosynthetic algae and coral.

DIF: Medium REF: 1.4

OBJ: 1.4d Compare the roles of animal endosymbionts and plant endosymbionts

MSC: Applying

  1. Give two reasons why microbes have been difficult to classify.

ANS:

First, even with the use of light microscopes, only the basic shape of microbes can be determined, and many microbes have similar shapes even though they are very different in other ways. Second, microbes do not fit the classic definition of a species, which is a group of organisms that interbreed. Microbes typically reproduce asexually. When they do exchange genes, they may do so with distantly related species.

DIF: Medium REF: 1.5

OBJ: 1.5a Explain why microbes can be challenging to classify taxonomically

MSC: Analyzing

  1. Briefly explain the endosymbiosis theory and the evidence that supports it.

ANS:

The endosymbiosis theory proposes that mitochondria and chloroplasts evolved from bacteria that were engulfed by pre-eukaryotic cells, and that over time these endosymbiotic prokaryotic cells lost the ability to survive outside of the host cell but were maintained as organelles. Evidence supporting the endosymbiosis theory includes the fact that mitochondria and chloroplasts possess circular DNA with similarity to modern bacteria.

DIF: Medium REF: 1.5

OBJ: 1.5c Appraise endosymbiosis as an explanation for mitochondria and chloroplasts

MSC: Understanding

  1. What were Rosalind Franklin’s contributions toward discovering the structure of DNA, and why wasn’t she one of the recipients of the Nobel Prize for this discovery?

ANS:

She was an X-ray crystallographer who studied the structure of DNA. Her X-ray micrographs showed for the first time that DNA was a double helix. A colleague showed her micrographs to James Watson, who was also studying the structure of DNA. Watson and Francis Crick published their model of the structure of DNA in the journal Nature and denied that they had used Franklin’s micrographs. Franklin also died before the awarding of the prize.

DIF: Medium REF: 1.6

OBJ: 1.6a Describe the roles of the electron microscope and the ultracentrifuge in advancing our knowledge of cell structure and function MSC: Understanding

  1. Briefly describe how the ultracentrifuge is used to determine the sizes of cellular macromolecules.

ANS:

The ultracentrifuge uses centrifugal forces to separate cell components. Theodor Svedberg calculated that the particle sizes could be determined based on the rate of sedimentation of the particles in an ultracentrifuge.

DIF: Medium REF: 1.6

OBJ: 1.6a Describe the roles of the electron microscope and the ultracentrifuge in advancing our knowledge of cell structure and function MSC: Understanding

  1. If you want to produce DNA polymerases like those used in polymerase chain reaction (PCR) for amplification of DNA, from which natural environment would you try to isolate the producers?

ANS:

Since DNA polymerase in PCR must survive many rounds of cycling to near-boiling temperatures, the most conducive environment for finding DNA polymerase, such as the enzymes used in PCR reactions, would be searching for microbes in an environment where the temperature is extremely high.

DIF: Difficult REF: 1.6

OBJ: 1.6c State some uses of microbes in medicine and industry

MSC: Applying

CHAPTER 3: Cell Structure and Function

MULTIPLE CHOICE

  1. E. coli and Sinorhizobium cell-surface proteins enable colonization of ________ and ________, respectively.
a.the human intestinal epithelium; animal skin
b.legume plants; the human intestinal epithelium
c.the human intestinal epithelium; legume plants
d.legume plants; animal skin
e.cantaloupe; spinach

ANS: C DIF: Medium REF: 3.1

OBJ: 3.1a Describe the components of the bacterial cell envelope

MSC: Remembering

  1. The capsule polysaccharides form a slippery mucous layer that inhibits
a.diffusion.d.lysis.
b.phagocytosis.e.osmosis.
c.attachment.

ANS: B DIF: Easy REF: 3.3

OBJ: 3.3a Describe the structure and functions of the bacterial cell wall

MSC: Remembering

  1. We cannot see the molecules within a cell, but ________ and ________ analysis generate a remarkably detailed view.
a.structural; geneticd.microscopy; subcellular
b.microscopy; genetice.chemical; genetic
c.chemical; subcellular

ANS: D DIF: Medium REF: 3.1

OBJ: 3.1a Describe the components of the bacterial cell envelope

MSC: Remembering

  1. The z-ring is
a.made up of an actin-like polymer.
b.involved in segregation of two to four nucleoids.
c.controlled by a nutrient-dependent regulator.
d.involved in replication but not cytokinesis.
e.involved in preventing transcription of noncoding regions of DNA.

ANS: C DIF: Difficult REF: 3.1

OBJ: 3.1a Describe the components of the bacterial cell envelope

MSC: Analyzing

  1. Polyamines are ________ charged when the pH is near neutral.
a.notd.super
b.negativelye.randomly
c.positively

ANS: C DIF: Medium REF: 3.1

OBJ: 3.1b Name the chemical components within a bacterial cell

MSC: Remembering

  1. The proteins embedded in a membrane require that region to be
a.crystalline.d.negatively charged.
b.hydrophobic.e.positively charged.
c.flexible.

ANS: B DIF: Medium REF: 3.1

OBJ: 3.1b Name the chemical components within a bacterial cell

MSC: Remembering

  1. Mary Jane Osborn discovered that inner and outer membranes are different in density by using
a.genetic analysis.d.protein synthesis.
b.X-ray crystallography.e.fluorescent.
c.ultracentrifugation.

ANS: C DIF: Easy REF: 3.1

OBJ: 3.1c Explain how lysis and ultracentrifugation contribute to cell fractionation

MSC: Remembering

  1. Cells must be broken open in order to then fractionate the components. Each of the following can be used in bacterial cell breakage EXCEPT
a.French press.d.ultracentrifugation.
b.lysozyme .e.ultrasonic vibration.
c.mild detergent.

ANS: D DIF: Medium REF: 3.1

OBJ: 3.1c Explain how lysis and ultracentrifugation contribute to cell fractionation

MSC: Understanding

  1. Some bacterial cells are inedible for humans because of the
a.high ion content in the cytoplasm.
b.high proportion of nucleic acids that humans degrade to the waste product uric acid.
c.peptide-linked sugars in the cell wall cannot be digested.
d.high uric acid content of the cytoplasm.
e.high polyamine content, which is toxic.

ANS: B DIF: Difficult REF: 3.1

OBJ: 3.1b Name the chemical components within a bacterial cell

MSC: Understanding

  1. Which of these experiments would NOT be a reason to fractionate bacterial cells?
a.to obtain membrane fractions to study transport proteins
b.to purify ribosome subunits to study translation
c.to obtain periplasmic proteins to study chaperons from that space
d.to obtain cytoplasmic proteins such as FtsZ
e.to study the growth rate of E. coli in the presence of lactose

ANS: D DIF: Medium REF: 3.1

OBJ: 3.1d List some uses of cell fractionation MSC: Applying

  1. All of the statements about genetic analysis of cells complementing cell fractionation are true EXCEPT that it
a.is used to identify which genes and proteins are involved in a process.
b.can be used by identifying phenotypes under a microscope.
c.can be used to identify the exact change in protein sequences giving a particular phenotype.
d.has never been used to study FtsZ.
e.can be used to study cell division.

ANS: D DIF: Difficult REF: 3.1

OBJ: 3.1e Compare cell fractionation to genetic analysis MSC: Evaluating

  1. The molecule shown below is ________ and may play a role in ________.
a.phosphatidylethanolamine; heat response
b.cardiolipin; heat response
c.phosphatidylglycerol; heat response
d.cardiolipin; starvation
e.phosphatidylglycerol; heat response

ANS: D DIF: Medium REF: 3.2

OBJ: 3.2a Describe cell membrane structure MSC: Understanding

  1. Specific membrane components, particularly ________, determine which substances are transported across the membrane.
a.phospholipidsd.polysaccharides
b.proteinse.leaflets
c.ions

ANS: B DIF: Easy REF: 3.2

OBJ: 3.2b List the functions of membrane proteins MSC: Remembering

  1. In the figure below, which of the four fatty acids adds fluidity to a membrane, and what type of bond allows this to happen?
a.A; saturated bondd.C; cis
b.B; transe.D; double
c.B; cis

ANS: D DIF: Medium REF: 3.2

OBJ: 3.2a Describe cell membrane structure MSC: Applying

  1. A medically important example of active transport is that of drug ________ proteins powered by the hydrogen ion gradient.
a.effluxd.diffusion
b.porine.lysis
c.membrane-permeant

ANS: A DIF: Medium REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Remembering

  1. Extreme thermophiles have ________ chains in their membrane in order to maintain membrane stability.
a.lipoproteind.terpenoid
b.hopanoide.cardiolipin
c.cholesterol

ANS: D DIF: Medium REF: 3.2

OBJ: 3.2a Describe cell membrane structure MSC: Remembering

  1. Which of the following types of molecules may passively diffuse across a membrane?
a.an amino acid in a low pH environment
b.a weak acid in a high pH environment
c.a large polar molecule such as a sugar
d.a small uncharged molecule such as water
e.No molecules can diffuse across a membrane.

ANS: D DIF: Easy REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Applying

  1. You are studying life-forms in extreme environments, and you have discovered a microorganism with cardiolipin, hopanoids, and ester linkages in the membrane. It also has teichoic acids, galactans, and phenolic glycolipids in the cell wall. In addition, it is a porin similar to OmpA. This microorganism is most likely related to
a.eukaryotic cells.d.Gram-positive bacteria.
b.archaea.e.Gram-negative bacteria.
c.mycobacteria.

ANS: C DIF: Difficult REF: 3.2 | 3.3

OBJ: 3.2a Describe cell membrane structure | 3.3a Describe the structure and functions of the bacterial cell wall MSC: Analyzing

  1. Which of the following reinforces and stiffens membranes in bacteria?
a.hopanoidsd.peptidoglycans
b.polyaminese.lipids
c.sterols

ANS: A DIF: Easy REF: 3.2

OBJ: 3.2a Describe cell membrane structure MSC: Understanding

  1. You study a bacterium that grows in very low-nutrient aqueous environments. Which type of transport mechanism is required to deliver nutrients from these environments where they are at a lower concentration than inside the cell?
a.aquaporinsd.passive diffusion
b.active transporte.Such bacteria cannot exist.
c.facilitated diffusion

ANS: B DIF: Difficult REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Analyzing

  1. How can weak acids and weak bases cause pH stress to cells?
a.Only weak acids can cause stress by diffusing across a membrane at low pH.
b.Weak acids and weak bases do not cause stress.
c.If a cell has transporters that are not well regulated, weak acids or weak bases can accumulate inside the cells and cause stress.
d.At certain pHs, both weak acids or weak bases will be uncharged and thus are small uncharged molecules that can diffuse across a membrane and cause pH stress inside the cell.
e.Weak bases will only cause pH stress at low pH.

ANS: D DIF: Difficult REF: 3.2

OBJ: 3.2d Explain how membrane-permeant weak acids and bases cause pH stress

MSC: Applying

  1. Water can move across a membrane via passive diffusion but that movement is aided by
a.aquaporins.d.ethanol2.
b.ion transporters.e.weak acids and bases.
c.active transport.

ANS: A DIF: Medium REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Remembering

  1. Efflux pumps send antibiotics, such as the protein synthesis–inhibitor tetracycline, out of the bacterial cells, enabling them to grow in the presence of antibiotics. Which of the following therapeutic approaches will be LEAST effective?
a.Switch to an antibiotic that is not a substrate of the efflux pump.
b.Augment the treatment with an efflux inhibitor.
c.Increase the concentration of tetracycline.
d.Augment the treatment with an ATP synthase inhibitor.
e.Add a second antibiotic to the therapy.

ANS: C DIF: Difficult REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Evaluating

  1. Cell wall growth patterns of a variety of bacteria have been studied using fluorescently labeled D-amino acids. This approach has worked because
a.fluorescent amino acids block further cell wall synthesis and thus provide a snapshot of the cell wall at a particular time.
b.ribosomes cannot incorporate any fluorescence and thus cannot use fluorescent amino acids; it all goes to cell wall.
c.vancomycin can block the incorporation of D-alanine into protein and thus force it into the cell wall.
d.the labeled amino acids are D-amino acids, not L-amino acids.; thus, they only were incorporated into cell wall.
e.This approach has not worked.

ANS: D DIF: Difficult REF: 3.2

OBJ: 3.3a Describe the structure and functions of the bacterial cell wall

MSC: Evaluating

  1. The bacterial cell wall of mycobacteria is highly hydrophobic due to presence of
a.lipoproteins.d.polysaccharides.
b.phenolic glycolipids.e.glycoproteins.
c.phospholipids.

ANS: B DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Remembering

  1. The lipopolysaccharide of the outer membrane is of medical importance because it acts as a(n)
a.endotoxin.d.enterotoxin.
b.exotoxin.e.antibiotic.
c.toxoid.

ANS: A DIF: Easy REF: 3.3

OBJ: 3.3a Describe the structure and functions of the bacterial cell wall

MSC: Remembering

  1. The ________ is the region between the cytoplasmic membrane and the outer membrane in Gram-negative cells.
a.periplasmd.lipopolysaccharide
b.cytoplasme.S-layer
c.lysozyme

ANS: A DIF: Easy REF: 3.3

OBJ: 3.3a Describe the structure and functions of the bacterial cell wall

MSC: Remembering

  1. The structure shown below is found in the ________ of some bacteria and the larger molecules are connected by the ________ cross-link shown at the arrow.
a.cell wall; sugard.cell wall; peptide
b.cell membrane; peptidee.nucleoid membrane; peptide
c.cell membrane; sugar

ANS: D DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. All of the following are components of peptidoglycan EXCEPT
a.N-acetylglucosamine.d.amino acids.
b.N-acetylmuramic acid.e.peptide cross-links.
c.lipopolysaccharide.

ANS: C DIF: Easy REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. Which is NOT a component of a Gram-negative bacterium’s wall?
a.peptidoglycand.diaminopimelic acid
b.teichoic acide.MurNac
c.N-acetylmuramic acid

ANS: B DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. All of the following are true statements about bacterial S-layers EXCEPT that they
a.are commonly found in Gram-positive cells as well as in archaea.
b.are a crystalline layer consisting of protein or glycoprotein.
c.present a formidable physical barrier to predators or parasites.
d.are found in bacteria freshly isolated from natural sources.
e.are found in bacteria isolated from laboratory cultures.

ANS: E DIF: Difficult REF: 3.3

OBJ: 3.3a Describe the structure and functions of the bacterial cell wall

MSC: Understanding

  1. One similarity between a Gram-negative cell envelope and that of mycobacteria is that mycobacteria have
a.lipid A.d.S-layers.
b.teichoic acids.e.ampicillin.
c.a porin.

ANS: C DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. Lipopolysaccharides are found in
a.all bacteria.d.archaea.
b.Gram-positive bacteria.e.eukaryotes.
c.Gram-negative bacteria.

ANS: C DIF: Easy REF: 3.3

OBJ: 3.3a Describe the structure and functions of the bacterial cell wall

MSC: Understanding

  1. All of the following are true about prokaryotic outer membranes EXCEPT that they
a.are lipid bilayers composed of identical phospholipids.
b.are found only in Gram-negative bacteria.
c.contain endotoxin.
d.contain proteins involved in transport.
e.contain lipopolysaccharide.

ANS: A DIF: Difficult REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. Bacterial shape is determined by
a.tubulin and actin.d.S-layers.
b.cell membrane.e.a protein called crescentin.
c.cytoskeleton.

ANS: C DIF: Medium REF: 3.3

OBJ: 3.3c State the names and functions of the bacterial cytoskeleton proteins

MSC: Understanding

  1. All of the following are true for DNA-binding proteins EXCEPT that they
a.can form protective crystalline structures around organized DNA.
b.condense prokaryotic DNA.
c.can act as regulators of gene expression.
d.determine the shape of the cell.
e.help to keep cells viable for a longer duration of time.

ANS: D DIF: Medium REF: 3.4

OBJ: 3.4a Recall the structure of the bacterial nucleoid MSC: Understanding

  1. All of the following are true of supercoiling in chromosomal DNA EXCEPT that it
a.doubles back and twists upon itself.
b.facilitates RNA transcription.
c.results in compaction.
d.is generated by gyrase.
e.is maintained by DNA-binding proteins.

ANS: B DIF: Difficult REF: 3.4

OBJ: 3.4a Recall the structure of the bacterial nucleoid MSC: Understanding

  1. A ________ is a term used to designate a single messenger RNA molecule being translated by multiple ribosomes.
a.coupled.thylakoid
b.periplasme.polysome
c.carboxysome

ANS: E DIF: Easy REF: 3.4

OBJ: 3.4b Compare and contrast prokaryotes and eukaryotes with respect to DNA replication, transcription, and translation MSC: Understanding

  1. Which of the following is true of Fts proteins?
a.They form a ring in the area where cell division will occur.
b.They aid in DNA replication.
c.They are involved in peptidoglycan synthesis.
d.They are involved in making proteins.
e.They are important in transcription.

ANS: A DIF: Easy REF: 3.3

OBJ: 3.4c Describe bacterial cell division; include the replisome, cell expansion, and septation

MSC: Understanding

  1. The partition that results from the inward growth of the cell envelope from opposite directions is known as the
a.divisome.d.colony.
b.septum.e.Z-ring.
c.wall.

ANS: B DIF: Easy REF: 3.4

OBJ: 3.4c Describe bacterial cell division; include the replisome, cell expansion, and septation

MSC: Understanding

  1. In order for septation to occur, which process must finish first?
a.transcription and translationd.cell wall synthesis
b.membrane synthesise.synthesis of mreB
c.DNA replication

ANS: C DIF: Medium REF: 3.4

OBJ: 3.4c Describe bacterial cell division; include the replisome, cell expansion, and septation

MSC: Understanding

  1. Which of the following is FALSE regarding the polarity and aging of Caulobacter crescentus?
a.The protein TipN is involved.
b.The two poles of the cell are different.
c.It contributes to a life cycle.
d.It results in two cell types (i.e., stalked cell and swarmer).
e.It results in two cell types, each with a monotrichous flagellum.

ANS: E DIF: Medium REF: 3.5

OBJ: 3.5a Describe the cell cycle and cell structure of the asymmetric Caulobacter crescentus

MSC: Understanding

  1. Which of the following is described as an attachment organelle that is a membrane-bound extension of the cytoplasm?
a.pilid.stalks
b.fimbriaee.flagella
c.sex pili

ANS: D DIF: Medium REF: 3.6

OBJ: 3.6a List some specialized structures that are only found in certain species

MSC: Remembering

  1. Which name refers to having flagella attached at one or both ends of the cell?
a.peritrichousd.bitrichous
b.lophotrichouse.flagellated
c.monotrichous

ANS: B DIF: Easy REF: 3.6

OBJ: 3.6b Recall the structures and functions of thylakoids, carboxysomes, storage granules, pili, stalks, nanotubes, and flagella MSC: Remembering

  1. Directed movements toward or away from a chemical or physical signal are known as
a.gliding.d.locomotion.
b.flagellation.e.slime layer.
c.chemotaxis.

ANS: C DIF: Easy REF: 3.6

OBJ: 3.6c Explain how chemoreceptors and magnetosomes direct flagellar motility

MSC: Remembering

  1. Light is harvested by protein complexes called
a.thylakoids.d.storage granules.
b.carboxysomes.e.magnetosomes.
c.gas vesicles.

ANS: A DIF: Easy REF: 3.6

OBJ: 3.6b Recall the structures and functions of thylakoids, carboxysomes, storage granules, pili, stalks, nanotubes, and flagella MSC: Understanding

  1. Which of the following materials is found in aquatic bacteria and used for positioning in the water column?
a.gas vesicled.glycogen
b.sulfure.magnetosome
c.polyphosphate

ANS: A DIF: Easy REF: 3.6

OBJ: 3.6b Recall the structures and functions of thylakoids, carboxysomes, storage granules, pili, stalks, nanotubes, and flagella MSC: Understanding

  1. All of the following are used by prokaryotic cells for attaching to solid surfaces EXCEPT
a.endospore.d.fimbriae.
b.capsule.e.pili.
c.stalks.

ANS: A DIF: Easy REF: 3.6

OBJ: 3.6b Recall the structures and functions of thylakoids, carboxysomes, storage granules, pili, stalks, nanotubes, and flagella MSC: Understanding

  1. Which of the following statements about the prokaryotic flagella is INCORRECT?
a.It is driven by the cell’s transmembrane proton current.
b.It is embedded in the layers of the cell envelope.
c.It is observed by electron microscopy.
d.It moves with a whiplike motion.
e.It is used for chemotaxis.

ANS: D DIF: Easy REF: 3.6

OBJ: 3.6b Recall the structures and functions of thylakoids, carboxysomes, storage granules, pili, stalks, nanotubes, and flagella MSC: Understanding

  1. The bacterial flagellum is a helical protein filament whose ________ motor moves the cell in search of a more favorable environment.
a.shakingd.whiplike
b.vibratinge.propeller-like
c.wavelike

ANS: E DIF: Easy REF: 3.7

OBJ: 3.6c Explain how chemoreceptors and magnetosomes direct flagellar motility

MSC: Understanding

  1. With respect to the proteins involved in the polarity of Caulobacter, which of the following statements is FALSE?
a.DivJ is a marker for stalk and is produced at an old pole where PodJ had previously been located.
b.The stalk develops at a pole where PodJ is found.
c.After cell division, TipN localizes at the new cell pole opposite the stalk.
d.PodJ is a marker for flagella and interacts with TipN at the new pole.
e.After elongation and prior to division, TipN localizes to the septum.

ANS: B DIF: Difficult REF: 3.5

OBJ: 3.5a Describe the cell cycle and cell structure of the asymmetric Caulobacter crescentus

MSC: Analyzing

  1. Polar aging of symmetrical bacteria such as E. coli plays a role in stress responses in which of the following ways?
a.Antibiotics only affect older poles of stressed cells.
b.Alternators and accelerators are better at responding to stress.
c.Proteins damaged by stresses accumulate at old poles, thereby allowing new poles to continue growing.
d.Newer poles are more resistant to acidity and heat.
e.Newer poles produce flagella and can swim away from stress.

ANS: C DIF: Difficult REF: 3.5

OBJ: 3.5b Explain the causes and consequences of polar aging in apparently symmetrical bacteria

MSC: Analyzing

SHORT ANSWER

  1. List and briefly describe four components of a typical bacterial cell.

ANS:

Possible answers include the following: cytoplasm-gel-like network of proteins and macromolecules; cell membrane surrounds cytoplasm, made of phospholipids and hydrophobic proteins; cell wall surrounds cell membrane, rigid structure of polysaccharides and peptides; lipopolysaccharide membrane surrounds cell wall of Gram-negative cells, made of lipids and polysaccharides; capsule surrounds envelope of some organisms, made of polysaccharides, prevents phagocytosis; flagellum used for cell motility; nucleoid coiled chromosome not surrounded by membrane.

DIF: Medium REF: 3.1

OBJ: 3.1a Describe the components of the bacterial cell envelope | 3.1b Name the chemical components within a bacterial cell MSC: Remembering

  1. Describe four ways cells can be broken open in order to isolate the cellular components.

ANS:

Mild detergent lysis disrupts the cell membrane without denaturing cellular components. Sonication is the use of high-frequency sound waves to disrupt cell membranes. Enzymes are proteins that can be used to break open cells. Mechanical disruption uses methods such as a French press to lyse cells.

DIF: Difficult REF: 3.1

OBJ: 3.1c Explain how lysis and ultracentrifugation contribute to cell fractionation

MSC: Remembering

  1. As proteins are found in various subcellular fractions, how could they be further analyzed?

ANS:

A proteomic approach to knowing about these proteins would involve running gel electrophoresis on a particular fraction followed by digestion with trypsin and then mass spectroscopy. Identities of the proteins or fragments are determined based on comparison to databases.

DIF: Medium REF: 3.1 OBJ: 3.1d List some uses of cell fractionation

MSC: Remembering

  1. Explain how a genetic approach can be used to understand cell division. Give an example.

ANS:

First, genetic mutants are obtained that have various phenotypic variations in the cell division process, such as a loss of function. Then the defective protein can be determined. Once determined, further work can identify the exact mutation involved. For example, various mutations in ftsZ have been found that either fail to divide or form abnormal blebs. The exact amino acids changes are now known.

DIF: Difficult REF: 3.1 OBJ: 3.1e Compare cell fractionation to genetic analysis

MSC: Applying

  1. The periplasm in Gram-negative bacteria is filled with proteins. Describe the importance of these proteins.

ANS:

The periplasm contains proteins involved in sugar transport into the cell. It also contains chaperones that may be involved in stress responses. In addition, the periplasm contains enzymes involved in making cell wall. Many of these are called penicillin-binding proteins (pbps) and are targets of antibiotics such as penicillin.

DIF: Difficult REF: 3.2 | 3.3

OBJ: 3.2b List the functions of membrane proteins | 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria MSC: Understanding

  1. Explain what happens when a cell comes into contact with water or ethanol. Why is 70% ethanol commonly used to treat wounds and surfaces?

ANS:

Water can cross cell membranes by osmosis, but ethanol can dissolve both polar and nonpolar substances, thus harming the integrity of the membrane. In the presence of water, ethanol can denature proteins. The 70% ethanol disrupts the membrane sufficiently that the cells lyse.

DIF: Difficult REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Understanding

  1. The permeability of weak acids and bases across a membrane has implications for pharmaceutical treatment of disease. Assuming equal effectiveness in the lab, what type of molecule would be best to treat a bacterium growing in stomach acid, and why?

ANS:

An effective medicine that is a weak acid would be best because most of it would be uncharged in the stomach acid and thus more of it would be able to diffuse into the cell.

DIF: Medium REF: 3.2

OBJ: 3.2d Explain how membrane-permeant weak acids and bases cause pH stress

MSC: Applying

  1. Describe any two roles for membrane proteins.

ANS:

Answers can include any of the following: membrane proteins are involved in transport of ions and nutrients across the membrane. They provide structural support for the cell by connecting different layers of the cell envelope or anchoring structures that extend from the cell, such as flagella. They also sense external signals such as presence of nutrients or toxins. They are involved in secretion of toxins, proteins, and molecules for communication.

DIF: Easy REF: 3.2 OBJ: 3.2b List the functions of membrane proteins

MSC: Understanding

  1. Describe the types of molecules that can move through a membrane via passive diffusion.

ANS:

Small uncharged molecules such as water, oxygen, and carbon dioxide can move through a membrane via passive diffusion.

DIF: Easy REF: 3.2

OBJ: 3.2c Differentiate among passive diffusion, passive transport, and active transport

MSC: Understanding

  1. What unusual lipids are found in mycobacteria, and of what benefit are they to these bacteria?

ANS:

Mycobacteria contain mycolic acids and phenolic glycolipids in their cell envelope. The mycolic acids are responsible for the acid-fastness of the bacteria, an important tool in identification. The bilayer formed by the mycolic acids, interleaved with the phenol derivatives, affords the organism a waxiness. This prevents phagocytosis by macrophages and also excludes many antibiotics.

DIF: Difficult REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. Describe the Gram-negative cell envelope. Why are porins necessary in the outer membrane of Gram-negative cells?

ANS:

Covering the cytoplasmic membrane is a thin layer of peptidoglycan. Over the peptidoglycan cell wall is an outer membrane that is a bilayer of phospholipids and lipopolysaccharide. There are proteins in the outer membrane called porins that are necessary for transporting substances such as nutrients across the membrane. Without the porins, very few substances could cross the outer membrane. The periplasm is between the outer and inner membranes and contains many enzymes.

DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. From your knowledge of Gram-positive and Gram-negative cell envelopes, why would penicillin be more effective in killing Gram-positive organisms than Gram-negative organisms?

ANS:

Penicillin prevents cross-linking of peptidoglycan. Since Gram-positive organisms have many more layers of peptidoglycan than Gram-negative organisms, the penicillin can have a much larger effect. Also, Gram-negative organisms have an extra outer membrane that Gram-positive organisms do not have, and this membrane can prevent penicillin from entering the cell as easily.

DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Applying

  1. Describe two mechanisms that archaea may use to enhance the heat stability of the membrane.

ANS:

First of all, the archaea have ether linkages between the glycerol and fatty acids, rather than ester linkages. Secondly, terpenoid chains are found in many extreme thermophiles. These may cyclize and stiffen the membrane, making it more tolerant of heat.

DIF: Medium REF: 3.2 OBJ: 3.2a Describe cell membrane structure

MSC: Applying

  1. Describe how vancomycin affects the cell wall of Gram-positive bacteria. How have some cells developed resistance?

ANS:

Gram-positive bacteria have a D-ala- D-ala dipeptide involved in cross-linking strands. Vancomycin prevents the cross bridge from forming. Some cells have developed resistance by using lactic acid in the cross bridge, and thus, vancomycin no longer has an effect.

DIF: Medium REF: 3.3

OBJ: 3.3b Compare the cell envelopes of firmicutes, proteobacteria, and mycobacteria

MSC: Understanding

  1. Explain how bacteria can produce proteins more quickly than eukaryotes do.

ANS:

Bacteria have no membrane around the nucleoid. This transcription and translation can be coupled with no need to transport the mRNA out of a nucleus.

DIF: Easy REF: 3.4

OBJ: 3.4b Compare and contrast prokaryotes and eukaryotes with respect to DNA replication, transcription, and translation MSC: Applying

  1. Compare and contrast FtsZ and tubulin. Why do the similarities support evolution of prokaryotes and eukaryotes from a common ancestor?

ANS:

FtsZ is a protein that forms a Z ring around the equator of a prokaryotic cell, where septation and division will take place. It is a homolog of tubulin, which is involved in mitosis in eukaryotes. They are similar in that they are both involved in cell division. The major difference is that FtsZ is present in prokaryotes and tubulin is found in eukaryotes. Since they are homologs, they likely evolved from a common ancestral cell.

DIF: Difficult REF: 3.3

OBJ: 3.3c State the names and functions of the bacterial cytoskeleton proteins

MSC: Understanding

  1. Which age class of M. tuberculosis (age 1 or age 3) do you think would be more resistant to quinolones, which block gyrase that supercoils DNA?

ANS:

The polar-aging phenomenon of M. tuberculosis results in daughter cells that differ in growth rate. Since gyrase plays an important role in DNA replication, the faster-growing accelerator cells (age 2 and age 3) will be more susceptible to quinolone-class antibiotics, which inhibit gyrase activity.

DIF: Medium REF: 3.5

OBJ: 3.5c Recall how some bacteria, such as actinomycetes, can reverse polar aging

MSC: Evaluating

  1. Explain how any two specialized structures are involved in bacterial photosynthesis.

ANS:

Thylakoids are structures of extensively folded membrane containing the photosynthetic pigments that maximize the collection of light energy. Carboxysomes contain enzyme Rubisco used in carbon fixation. Gas vesicles will aid aquatic bacteria, including a variety of phototrophs, to position themselves at the optimal point in the water column to collect light.

DIF: Medium REF: 3.6

OBJ: 3.6b Recall the structures and functions of thylakoids, carboxysomes, storage granules, pili, stalks, nanotubes, and flagella MSC: Understanding

  1. Explain the movement of a bacterium possessing flagella away from a toxic chemical.

ANS:

Counterclockwise spinning of the flagella causes the cell to swim a long distance in one direction. Clockwise spinning causes the cell to tumble randomly. These motions are used together to result in a biased random walk that moves the cell in the overall direction away from the toxic chemical.

DIF: Medium REF: 3.6

OBJ: 3.6c Explain how chemoreceptors and magnetosomes direct flagellar motility

MSC: Understanding

  1. Penicillin-binding proteins (pbps) are proteins located in the periplasmic space in Gram-negative bacteria and are involved in synthesizing the cell wall. Thus, they are a target for antibiotics and are of interest to drug developers. Describe how one could obtain these pbps for further study.

ANS:

After harvesting and washing cells, one would add sucrose to the cell suspension. This provides osmotic support. One would then add lysozyme to degrade the cell wall and obtain spheroplasts. Once the spheroplasts are obtained, they are transferred to distilled water to osmotically shock the cells and thus release the contents, including pbps, into the extracellular medium. Other compartments such as the cytoplasm and membranes are removed by ultracentrifugation.

DIF: Difficult REF: 3.1 OBJ: 3.1d List some uses of cell fractionation

MSC: Applying

CHAPTER 13: Energetics and Catabolism

MULTIPLE CHOICE

  1. Which of the following statements is NOT true regarding the electron donors in prokaryotic metabolism?
a.The use of organic compounds as electron donors is known as organotrophy.
b.Chemolithotrophy refers to the use of inorganic molecules as electron sources.
c.Photolysis of water provides electrons to phototrophic organisms such as cyanobacteria.
d.Electrons can be obtained from inorganic chemicals such as H2S.
e.Oxygen can serve as an electron donor.

ANS: E DIF: Easy REF: 13.1

OBJ: 13.1b Categorize microbes based on how they acquire energy

MSC: Remembering

  1. Chemoorganotrophy is a term describing microorganisms that
a.use preformed organic compounds as a source of electrons and obtain energy through fermentations or organic respiration.
b.obtain electrons and H+ via photolysis of H2O or H2S, producing O2 or S2, respectively.
c.perform photolysis of small organic molecules.
d.use carbon dioxide as the carbon source.
e.pull electrons off minerals to donate to electron transport systems.

ANS: A DIF: Difficult REF: 13.1

OBJ: 13.1b Categorize microbes based on how they acquire energy

MSC: Understanding

  1. A bacterium capable of producing methane and water from carbon dioxide and hydrogen performs a type of metabolism called ________ and, given its sources of electrons, it is a ________.
a.methanogenesis; chemolithotroph
b.respiration; heterotroph
c.fermentation; chemoorganotroph
d.carbon fixation; phototroph
e.sulfur bacterium; chemolithotroph

ANS: A DIF: Medium REF: 13.1

OBJ: 13.1b Categorize microbes based on how they acquire energy

MSC: Understanding

  1. The laws of thermodynamics indicate that systems tend to become less ordered and that ________, a measure of disorder or randomness of the universe, always increases.
a.entropyd.molecular stability
b.enthalpye.activation energy
c.Gibbs free energy

ANS: A DIF: Easy REF: 13.1

OBJ: 13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy MSC: Remembering

  1. The Gibbs equation describes the relationship between the components of free energy change and can be generally expressed as
a.DG = DG° + RT ln Keq.
b.DG = DH – TDS.
c.ADP + Pi D ATP + H2O.
d.K = T°C + 273.
e.DG = -2.303 RT log [C] [D] / [A] [B].

ANS: B DIF: Easy REF: 13.1

OBJ: 13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy MSC: Remembering

  1. Which of the following statements is FALSE with respect to heterotrophic organisms?
a.They use preformed organic compounds for biosynthesis.
b.Most organotrophs are also heterotrophs.
c.Along with decomposers, they are ecologically defined as consumers.
d.Some can generate methane as an end product.
e.They utilize glycolysis and other pathways to generate energy.

ANS: D DIF: Medium REF: 13.1

OBJ: 13.1b Categorize microbes based on how they acquire energy

MSC: Understanding

  1. Hydrogen-generating reactions in Syntrophus and Syntrophomonas have DG°’ > 0. Can these organisms obtain energy from hydrogen formation?
a.No, they cannot.
b.No—they produce energy by breaking down molecules such as benzoate or butyrate.
c.Yes—hydrogen-producing microorganisms coexist in syntrophy with H2-consuming bacteria. Utilization of H2 (DG°’ < 0) drives the process forward.
d.Yes, but only when oxygen is present.
e.Yes—this happens in sewage but never in a laboratory setting.

ANS: C DIF: Difficult REF: 13.1

OBJ: 13.1a Define catabolism, energy, enthalpy, entropy, and syntrophy

MSC: Analyzing

  1. Using the table below, what is the best method for obtaining energy from catabolizing ethanol, and why?
a.the catabolism of ethanol without an oxidant, because the DG is almost positive
b.the oxidation of ethanol with as the oxidant is because of the large yield of energy released
c.the oxidation of ethanol with oxygen, because the DG is the largest negative number indicating the large yield of energy released.
d.The oxidation of ethanol yields too little biomass to be catabolized.
e.None—ethanol can only be catabolized syntrophically.

ANS: D DIF: Difficult REF: 13.1

OBJ: 13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy MSC: Evaluating

  1. In amphibolic pathways, enzymes do NOT
a.function only in the biosynthetic direction.
b.function only in the catabolic direction.
c.function in both directions.
d.carry out reactions that are otherwise thermodynamically impossible.
e.have activity dependent on concentrations of reactants and products.

ANS: D DIF: Medium REF: 13.1 | 13.5

OBJ: 13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy | 13.5g Define amphibolic reactions and describe their regulation

MSC: Understanding

  1. A metabolic process allowing for anaerobic degradation of benzoate to acetate is diagrammed below. This metabolism can happen because
a.benzoate contains a great deal of energy and ATP can be made.
b.the catabolism of benzoate by the cell on the left produces hydrogen that is then used by the cell on the right to reduce sulfate.
c.the catabolism of benzoate by the cell on the left produces hydrogen that is then used by a methanogen.
d.the catabolism of benzoate to acetate releases so much energy that it overcomes the positive DG of H2 production.
e.the cell on the left swims away from the H2 that it produces in order to balance the thermodynamics.

ANS: B DIF: Difficult REF: 13.2

OBJ: 13.2c Express the relationship between DeltaG° and DeltaG; include the effect of changing concentrations of reactants and products MSC: Analyzing

  1. In most environments, the nutrient concentrations outside the cell are lower than inside the cell. If the concentration gradient is NOT favorable, a microbial cell obtains nutrients through
a.active, energy-dependent transport.d.forming biofilms.
b.facilitated diffusion.e.simple diffusion.
c.swim and tumble.

ANS: A DIF: Easy REF: 13.2

OBJ: 13.2d Describe the relationship between energy and concentration gradients

MSC: Remembering

  1. When studying an enzymatic reaction, should one consider DG, DG0, or DG0‘ when considering the thermodynamics of the reaction, and why?
a.DG0, because it considers standard conditions as well as biochemically relevant conditions such as the concentrations of substrates and products
b.DG0, because it considers standard conditions
c.DG, because it considers defined conditions such as pH
d.DG, because it considers concentrations of reactants as products.
e.DG0, because it considers entropy and enthalpy.

ANS: A DIF: Medium REF: 13.2

OBJ: 13.2a Recall the conditions required for the standard Gibbs free energy change, DeltaG°, and the biochemical Gibbs free energy change, DeltaG°’ MSC: Understanding

  1. What technique can be used to determine entropy and enthalpy changes associated with biochemical reactions?
a.nuclear magnetic resonanced.mass spectroscopy
b.calorimetrye.measurement of light levels
c.electron microscopy

ANS: B DIF: Easy REF: 13.1

OBJ: 13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy MSC: Understanding

  1. Which of the following phenomena is sufficient to transport nutrients to cells that lack chemotactic motility?
a.active, ATP-dependent transportd.quorum sensing
b.diffusione.biofilm formation
c.turbulent flow

ANS: B DIF: Easy REF: 13.2

OBJ: 13.2d Describe the relationship between energy and concentration gradients

MSC: Understanding

  1. Glycolytic reactions with a near-zero DG°’ can participate in the overall pathway of gluconeogenesis because they
a.are irreversible.
b.are reversible.
c.contradict the laws of thermodynamics.
d.have low energy of activation values.
e.do not depend on concentrations of reactants and products.

ANS: B DIF: Medium REF: 13.2

OBJ: 13.2c Express the relationship between DeltaG° and DeltaG; include the effect of changing concentrations of reactants and products MSC: Understanding

  1. The DG for a reaction can be calculated by using DG0 and adding in
a.entropy, enthalpy, and the log of the ratio of reactants to products.
b.entropy, enthalpy, pH, and the log of the ratio of the reactants to products.
c.the gas constant, absolute temperature, and the log of the ratio of the reactants to products.
d.the log of the ratio of the reactants to products.
e.the gas constant, absolute temperature, pH, and the log of the ratio of the reactants to products.

ANS: C DIF: Medium REF: 13.2

OBJ: 13.2c Express the relationship between DeltaG° and DeltaG; include the effect of changing concentrations of reactants and products MSC: Analyzing

  1. In their work with soil bacteria, McInerney and colleagues have found microorganisms that display metabolic pathways with net DG values as small as -20 kJ/mol. This is an example of
a.the capacity of microorganisms to conquer a wide variety of environments.
b.microorganisms contradicting the laws of thermodynamics.
c.growth near thermodynamic equilibrium.
d.growth that depends on the concentration of reactants but not products.
e.enthalpic growth.

ANS: C DIF: Medium REF: 13.2

OBJ: 13.2b Calculate the DeltaG°’ of a coupled reaction MSC: Evaluating

  1. The molecule shown below carries energy in the cell but it needs to be stabilized. It is a ________ molecule and is stabilized when it ________.
a.NADPH; forms a cyclic molecule
b.NADPH; complexes with Mg2+
c.ATP; donates its electrons to a cytochrome
d.ATP; complexes with Mg2+
e.ATP; forms a cyclic molecule

ANS: D DIF: Difficult REF: 13.3

OBJ: 13.3c Compare and contrast ATP and NADH MSC: Analyzing

  1. In many bacteria, the electron carrier ________ is used for biosynthesis, whereas ________ feeds the electron transport system.
a.NADPH; NADHd.chlorophyll; NADPH
b.FADH2; NADPHe.pyruvate; acetyl-S-CoA
c.NADH; acetyl-S-CoA

ANS: A DIF: Easy REF: 13.3

OBJ: 13.3b Define energy carriers and provide examples MSC: Remembering

  1. All of the following are reasons to oxidize glucose in a series of steps EXCEPT to
a.generate smaller amounts of energy in a controlled fashion and when needed.
b.control the usage of energy in a cell by using more steps.
c.minimize the release of heat with more small steps.
d.control the catabolism versus biosynthetic aspects of oxidizing glucose via concentrations of reactants and end products.
e.increase the DG of the reaction.

ANS: E DIF: Medium REF: 13.1

OBJ: 13.3a Explain why glucose is oxidized in a series of steps instead of a single step

MSC: Understanding

  1. Which of the following is FALSE with respect to enzymes that use the reducing equivalents NADH and NADPH?
a.Some enzymes only use NADH.
b.Some enzymes only use NADPH.
c.Some enzymes may use either NADPH or NADH.
d.FADH2 can be used as a substitute.
e.NADPH is more often used in biosynthesis.

ANS: D DIF: Easy REF: 13.3

OBJ: 13.3d Recall why metabolic reactions require enzymes MSC: Remembering

  1. The graph shown below diagrams the energy involved in the
a.difference in activation energy of a reaction with and without an inhibitor at an allosteric site.
b.difference in the activation energy of a reaction with and without an enzyme.
c.activation energy needed to initiate the Embden-Meyerhof pathway.
d.difference in synthrophic reactions with and without a hydrogen utilizing partner.
e.difference in activation energy with NADH versus NADPH.

ANS: B DIF: Difficult REF: 13.3

OBJ: 13.3d Recall why metabolic reactions require enzymes MSC: Evaluating

  1. The base adenine forms from ________ in experiments simulating the origin of life on Earth.
a.carbon dioxide and nitrated.adenosine and PO4
b.ethanol and ureae.ribose and RNA
c.methane and ammonia

ANS: C DIF: Medium REF: 13.3

OBJ: 13.3b Define energy carriers and provide examples MSC: Remembering

  1. Hydrolysis of ATP with the release of pyrophosphate is the driving force of which of the following reactions?
a.DNA and RNA synthesis
b.peptide bond formation
c.fatty acid synthesis
d.transport across a membrane
e.production of glucose-6-phosphate from glucose

ANS: A DIF: Medium REF: 13.3

OBJ: 13.3b Define energy carriers and provide examples MSC: Remembering

  1. Not all enzymes are proteins; in some enzymes, the catalytic properties depend on
a.DNA.d.lipids.
b.RNA.e.terpenoids.
c.polysaccharides.

ANS: B DIF: Medium REF: 13.3

OBJ: 13.3d Recall why metabolic reactions require enzymes MSC: Remembering

  1. Although ATP is the main energy carrier in living organisms, other molecules may also serve as energy carriers in metabolic reactions. Which of the following molecules does NOT carry energy?
a.nucleotides such as GTPd.glucose
b.phosphoenolpyruvatee.nucleotides such as CTP and UDP
c.creatine phosphate

ANS: D DIF: Medium REF: 13.3

OBJ: 13.3b Define energy carriers and provide examples MSC: Understanding

  1. The activity of the enzyme below is controlled in various ways using several of the binding sites shown. The two sites are the ________ site and the ________ site.
a.active; inhibitord.substrate; allosteric
b.catalytic; inhibitore.catalytic; allosteric
c.substrate; inhibitor

ANS: E DIF: Medium REF: 13.3

OBJ: 13.3d Recall why metabolic reactions require enzymes MSC: Analyzing

  1. Which of the following is NOT correct with respect to the redox pair NAD+/NADH?
a.The nicotinamide ring is a relatively stable aromatic structure.
b.The nicotinamide ring is a heteroaromatic because it has a noncarbon atom in position 4.
c.The nicotinamide ring may accept two electrons at carbon 1, becoming a nonaromatic ring.
d.The reduced, nonaromatic ring of NADH is at a higher energy than the aromatic ring of NAD+.
e.NADH can accept electrons from an electron transport system.

ANS: E DIF: Difficult REF: 13.3

OBJ: 13.3b Define energy carriers and provide examples MSC: Analyzing

  1. The enzyme pyruvate kinase catalyzes the conversion of phosphoenolpyruvate to pyruvate; the phosphate group is transferred to ADP to form ATP. This reaction is an example of
a.ATP synthesis by substrate-level phosphorylation.
b.the use of a proton concentration gradient by [H+]-ATPases to synthesize ATP.
c.ATP coupled to FADH2 oxidation.
d.a P-Type ATPase activity.
e.oxidative phosphorylation.

ANS: A DIF: Easy REF: 13.3 | 13.5

OBJ: 13.3c Compare and contrast ATP and NADH MSC: Understanding

  1. Which of the following pairs is mismatched?
a.Embden-Meyerhof-Parnas pathway—2 ATP, 2 NADH
b.Entner-Doudoroff pathway—1 ATP, 1 NADH, and 1 NADPH
c.pentose phosphate pathway—1 ATP, 2 NADPH
d.glyoxylate bypass—2 NADH, 1 FADH2
e.bacterial tricarboxylic acid cycle—3 NADH, 1 FADH2, 1 ATP

ANS: D DIF: Medium REF: 13.5

OBJ: 13.5a Compare and contrast fermentation and respiration; include substrates, products, mode of ATP production, and ATP yield MSC: Understanding

  1. The process of prioritized consumption of substrates is known as catabolite
a.induction.d.repression.
b.poisoning.e.attenutation.
c.competition.

ANS: D DIF: Medium REF: 13.4

OBJ: 13.4a Compare and contrast carbohydrates, lipids, peptides, and aromatic molecules as substrates for microbial metabolism MSC: Understanding

  1. Disparate animal groups, such as ruminants and humans, can digest a variety of plant fibers because they harbor cellulase-producing bacteria such as
a.Staphylococcus aureus and Bacillus subtilis.
b.Salmonella and Shigella.
c.Escherichia coli and Enterococcus faecalis.
d.Bacteroides and Ruminococcus.
e.Escherichia chrysanthemi and Erwinia uredovora.

ANS: D DIF: Medium REF: 13.4

OBJ: 13.4a Compare and contrast carbohydrates, lipids, peptides, and aromatic molecules as substrates for microbial metabolism MSC: Analyzing

  1. Fatty acids enter the TCA cycle after being degraded to what molecule?
a.acetyl-phosphated.citrate
b.malonyl-S-CoAe.pyruvate
c.acetyl-S-CoA

ANS: C DIF: Easy REF: 13.4

OBJ: 13.4b Recall the major forms of catabolism. MSC: Remembering

  1. The figure shown below diagrams three pathways for the metabolism of glucose. Pathway ________ is most likely to be used for biosynthesis because it can be used to ________.
a.1; generate glucose
b.2; make carbon backbones of many lengths
c.3; make carbon backbones of many lengths
d.1; make carbon backbones of many lengths
e.3; generate glucose

ANS: E DIF: Easy REF: 13.5

OBJ: 13.5b Name the three main catabolic routes from glucose to pyruvate

MSC: Understanding

  1. Glucose is activated by ________ phosphorylation(s) by ATP during the first stage of the Embden-Meyerhof-Parnas pathway.
a.oned.four
b.twoe.Glucose is not phosphorylated.
c.three

ANS: B DIF: Easy REF: 13.5

OBJ: 13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC: Remembering

  1. In glycolysis, dihydroxyacetone phosphate is isomerized to ________, which reenters the pathway.
a.glucose 6-phosphated.fructose 6-phosphate
b.glyceraldehyde 3-phosphatee.pyruvate
c.phosphoenolpyruvate

ANS: B DIF: Easy REF: 13.5

OBJ: 13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC: Remembering

  1. Some intestinal bacteria, such as Escherichia coli, feed on ________ from mucus secretions using the Entner-Doudoroff pathway.
a.gluconated.2-oxoglutarate
b.glucosee.oxaloacetate
c.pyruvate

ANS: A DIF: Difficult REF: 13.5

OBJ: 13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway MSC: Remembering

  1. Bacteria synthesize ribose for nucleotides using which pathway?
a.Embden-Meyerhof-Parnasd.tricarboxylic acid cycle
b.Entner-Doudoroffe.electron transport system
c.pentose phosphate shunt

ANS: C DIF: Easy REF: 13.5

OBJ: 13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway MSC: Remembering

  1. Which of the following molecules is responsible for the distinctive flavor of Swiss cheese?
a.lactated.propionate
b.glucosee.acetate
c.galactose

ANS: D DIF: Easy REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Remembering

  1. Which of the following is NOT an end product of fermentation?
a.carbon dioxided.butanol
b.acetonee.propionate
c.pyruvate

ANS: C DIF: Medium REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Understanding

  1. The dye ________ turns ________ in the presence of acid products and is included in fermentation broth for some diagnostic tests.
a.phenol red; yellowd.malachite green; blue
b.aniline blue; greene.MacConkey; white
c.ethidium bromide; pink

ANS: A DIF: Easy REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Understanding

  1. The energy yield from fermentation is lower than from respiration because
a.fermentation uses NAD+, not NADP+.
b.respiration completely oxidizes glucose to CO2, resulting in greater generation of NADH and thus ATP.
c.respiration uses the TCA cycle, which has many steps that directly produce ATP or GTP.
d.fermentation shunts much of the carbon from glucose to biosynthesis.
e.fermentation relies on the glyoxylate bypass, which bypasses ATP production.

ANS: B DIF: Medium REF: 13.5

OBJ: 13.5a Compare and contrast fermentation and respiration; include substrates, products, mode of ATP production, and ATP yield MSC: Analyzing

  1. In the pentose phosphate shunt, glucose 6-phosphate is oxidized to 6-phosphogluconate, which is then decarboxylated to ribulose 5-phosphate. What is the main metabolic role of this pathway?
a.production of ATP and NADH + H+
b.regeneration of NADP+
c.production of carbohydrates with three to seven carbon atoms, which can be utilized in biosynthesis
d.production of pyruvate to feed the Krebs cycle
e.oxidation of glucose to carbon dioxide

ANS: C DIF: Medium REF: 13.5

OBJ: 13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway MSC: Applying

  1. Clostridium acetobutylicum has been used to produce which solvents?
a.acetate and butyrated.formate and ethanol
b.acetone and butanole.propanol and mixed acids
c.methanol and ethanol

ANS: B DIF: Medium REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Applying

  1. Which of the following is evidence that the Entner-Doudoroff (ED) route might have evolved earlier than the Embden-Meyerhof-Parnas pathway (EMP)?
a.ED involves a larger number of reactions and produces more energy and reducing equivalents with respect to EMP.
b.6-phosphogluconate is dehydrated to form pyruvate and glyceraldehyde 3-phosphate, which may then reenter the EMP pathway.
c.ED involves fewer substrate-level phosphorylations and yields less energy and fewer reductants than EMP.
d.They are both used to catabolize glucose.
e.They both use ATP to phosphorylate glucose.

ANS: C DIF: Difficult REF: 13.5

OBJ: 13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway MSC: Analyzing

  1. Some bacteria in the human gut microbiota primarily feed on glucose derivatives from mucus secretions. Which of the following is NOT correct with respect to “mucus farming” by bacteria?
a.Bacteroides thetaiotaomicron and other bacteria induce the colon to produce mucus.
b.Mucus-derived sugar acids are metabolized via the Entner-Doudoroff pathway.
c.Sugar acids must be converted to 6-phosphogluconate in order to enter the Entner-Doudoroff pathway.
d.The glucose derivatives are converted to glucose and degraded via the Embden-Meyerhof-Parnas pathway.
e.This metabolism has been studied via genomics and genetic studies.

ANS: D DIF: Medium REF: 13.5

OBJ: 13.5d Hypothesize under what conditions cells will favor the EMP, the ED, or the pentose phosphate pathway MSC: Analyzing

  1. Ethanolic fermentation is used in making beverages such as beer, wine, and pulque. It is carried out by yeast and
a.lactobacillus.d.zymomonas.
b.leuconostoc.e.clostridium.
c.propionibacterium.

ANS: D DIF: Easy REF: 13.5

OBJ: 13.5e Distinguish among various types of fermentation (e.g., lactic acid, ethanolic, and mixed acid) MSC: Remembering

  1. Which of the diagrammed molecules is a global signal of nutritional status?
a.pyruvated.acetyl-CoA
b.2-oxoglutaratee.acetyl-P
c.oxaloacetate

ANS: E DIF: Easy REF: 13.6

OBJ: 13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC: Understanding

  1. Amino acids can be synthesized using which one of the molecules from the diagram below?
a.isocitrated.2-oxoglutarate
b.succinyl-CoAe.fumarate
c.oxaloacetate

ANS: D DIF: Easy REF: 13.6

OBJ: 13.6b Recall the roles that the TCA cycle and the glyoxylate bypass play in cell metabolism

MSC: Remembering

  1. Pyruvate dehydrogenase complex connects glycolysis to respiration. Which is a correct mechanism for how the activity of this enzyme complex is regulated?
a.There is no need to regulate this enzyme complex.
b.The activity is inhibited by CoA and NAD+.
c.Gene expression is repressed by carbon starvation and low oxygen levels.
d.The activity is inhibited by citrate.
e.The activity is enhanced by the presence of acetyl-CoA and NADH.

ANS: C DIF: Difficult REF: 13.6

OBJ: 13.6c Describe the function and regulation of the pyruvate dehydrogenase complex

MSC: Applying

  1. ________ enters the tricarboxylic acid cycle by condensing with oxaloacetate to form ________.
a.Succinoyl-S-CoA; fumarated.Citrate; isocitrate
b.Acetyl-S-CoA; citratee.Acetyl phosphate; citrate
c.Pyruvate; citrate

ANS: B DIF: Easy REF: 13.6

OBJ: 13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC: Remembering

  1. The greatest amount of reduced coenzyme NADH + H+ is produced during which stage of aerobic respiration?
a.glycolysisd.glyoxylate bypass
b.pyruvate conversion to acetyl-S-CoAe.oxidative phosphorylation
c.tricarboxylic acid cycle

ANS: C DIF: Easy REF: 13.6

OBJ: 13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC: Remembering

  1. Pathways involving both anabolic and catabolic reactions are referred to as
a.amphibolic.d.ambidextrous.
b.amphipathic.e.syntrophibolic.
c.ambivalent.

ANS: A DIF: Medium REF: 13.5

OBJ: 13.5g Define amphibolic reactions and describe their regulation

MSC: Analyzing

  1. Oxidative catabolism of benzoate and other aromatic compounds is catalyzed by
a.2-oxoglutarate:NADPH oxidoreductase.
b.benzoyl-S-CoA reductase.
c.specific dioxygenases.
d.NADPH:ferredoxin oxidoreductase.
e.catechol 2,3, monooxygenase.

ANS: C DIF: Medium REF: 13.7

OBJ: 13.6e Compare and contrast aerobic and anaerobic benzoate catabolism

MSC: Understanding

  1. All oxidative catabolism of toluene and other benzene derivatives proceeds through
a.benzoyl-S-CoA.d.cis, cis-muconate.
b.aniline.e.D-gluconate.
c.catechols.

ANS: C DIF: Medium REF: 13.6

OBJ: 13.6e Compare and contrast aerobic and anaerobic benzoate catabolism

MSC: Understanding

  1. Species of Pseudomonas and Rhodococcus can degrade benzoate and other aromatic molecules, either aerobically or anaerobically. Which of the following is NOT correct regarding anaerobic degradation of aromatic molecules?
a.It takes longer than aerobic degradation.
b.It is critical because bacterial anaerobic habitats are more abundant than aerobic ones.
c.Benzoate is activated to benzoyl-CoA prior to its degradation.
d.It proceeds via production of catechols.
e.The high initial investment of energy comes from either anaerobic phototrophy or anaerobic respiration.

ANS: D DIF: Easy REF: 13.6

OBJ: 13.6e Compare and contrast aerobic and anaerobic benzoate catabolism

MSC: Analyzing

  1. Each of the following was used to elucidate the TCA cycle EXCEPT
a.using radiolabeled acetate to determine which carbons were oxidized to CO2 .
b.the use of crude enzyme preparations from a variety of sources such as cucumber seeds and beef liver.
c.adding a variety of short-chain fatty acids commonly found in cells to detect activity.
d.the use of C14-labeled carbon compounds as a source of carbon under anoxic conditions.
e.using C13 to determine which intermediates are enriched under various growth conditions.

ANS: D DIF: Medium REF: 13.6

OBJ: 13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples MSC: Applying

SHORT ANSWER

  1. Define “organotroph” and “heterotroph.” Are these terms equivalent?

ANS:

They are not equivalent, but similar. An organotroph uses preformed organic compounds to yield energy. A heterotroph uses preformed organic compounds for biosynthesis. Most organotrophs are also heterotrophs.

DIF: Easy REF: 13.Intro

OBJ: 13.1a Define catabolism, energy, enthalpy, entropy, and syntrophy

MSC: Analyzing

  1. How can a technique such as calorimetry be used to measure DG?

ANS:

The amount of heat released by a reaction or a set of reactions, either in vitro or in a living system, can be measured by a calorimeter. If the reactions are maintained at constant temperature, the release of heat gives a measure of DH. If measurements are made at different temperatures, the entropic term—TDS—can be estimated from heat-release dependence on temperature. From the Gibbs-Helmholtz equation, DG = DH -TDS.

DIF: Difficult REF: 13.1

OBJ: 13.1c Use the Gibbs free energy change to determine if a given metabolic reaction can supply a cell with energy MSC: Applying

  1. What are the differences among DG, DG°, and DG°’?

ANS:

DG is the change in Gibbs free energy for a reaction under defined conditions. DG° is the change in Gibbs free energy for a reaction at standard conditions of temperature (298 K) and pressure (1 atm), with all reactants and products at a concentration of 1M. DG°’ is similar to DG°, with one other condition: that the reaction occurs at pH 7; this is commonly used in biochemistry.

DIF: Easy REF: 13.2

OBJ: 13.2a Recall the conditions required for the standard Gibbs free energy change, DeltaG°, and the biochemical Gibbs free energy change, DeltaG°’ MSC: Understanding

  1. Why is magnesium an essential nutrient for all living cells?

ANS:

Mg2+ partly neutralizes the negative changes of the phosphates in ATP, thereby stabilizing the structure in solution. Generally, any enzyme that requires ATP actually requires Mg2+-ATP. As such, it is an essential nutrient.

DIF: Easy REF: 13.3 OBJ: 13.3b Define energy carriers and provide examples

MSC: Understanding

  1. All nucleotide triphosphates carry energy. Provide examples of reactions that are driven by the release of energy from GTP, CTP, and TTP.

ANS:

GTP is specifically used in the initiation and elongation processes of protein synthesis. All nucleotide triphosphates, ATP, GTP, CTP, and TTP, as well as their corresponding deoxynucleotide triphosphates, provide the energy for their own incorporation into RNA and DNA, respectively.

DIF: Medium REF: 13.3 OBJ: 13.3b Define energy carriers and provide examples

MSC: Understanding

  1. What is the phosphotransferase system (PTS) and why is the advantage for a microbial cell to have a PTS?

ANS:

The PTS consists of several enzymes that couple the phosphorylation of sugar molecules, such as glucose or mannose, to their transport across the cell membrane. Enzymes involved in the PTS are important in determining which nutrients from the environment (or medium) certain microorganisms can import and catabolize.

DIF: Medium REF: 13.3

OBJ: 13.3d Recall why metabolic reactions require enzymes MSC: Analyzing

  1. What is substrate-level phosphorylation? Provide two examples from bacterial metabolism.

ANS:

Phosphorylation of ADP at the substrate-level consists of the transfer of a phosphoryl group from a metabolic intermediate to form ATP. In glycolysis, substrate-level phosphorylation takes place when pyruvate kinase converts phosphoenolpyruvate and ADP to pyruvate and ATP. In the TCA cycle, ATP is formed when ADP is phosphorylated by succinyl-S-CoA synthetase during the conversion of succinyl-S-CoA to succinate and coenzyme A.

DIF: Medium REF: 13.3 | 13.5

OBJ: 13.3b Define energy carriers and provide examples | 13.5a Compare and contrast fermentation and respiration; include substrates, products, mode of ATP production, and ATP yield

MSC: Understanding

  1. The catabolism of glucose is central to the overall hydrolysis of polysaccharides in an environment. Compare and contrast the analogous catabolism of polyaromatic compounds found in nature.

ANS:

Polyaromatic compounds found in nature include lignin found in plants and polycyclic aromatic hydrocarbons found in petroleum. As these compounds are hydrolyzed, benzene is produced just as glucose is the product from polysaccharides. Benzene will be converted to benzoate and vanillin that are converted to acetyl-CoA and hydrolyzed further via the TCA cycle. Similarly, glucose is degraded to pyruvate, then to acetyl-CoA, and further hydrolyzed via the TCA cycle.

DIF: Medium REF: 13.4

OBJ: 13.4a Compare and contrast carbohydrates, lipids, peptides, and aromatic molecules as substrates for microbial metabolism MSC: Analyzing

  1. Define the human metagenome. Describe an example to demonstrate the importance of the metagenome.

ANS:

The human metagenome is composed of the human genome and the genomes of all the organisms in human gut microbiota. This is important because there are organisms present in our microbiota that we depend on to carry out reactions we cannot perform. Humans obtain some amino acids and vitamins from gut microorganisms. As such, to get a more complete picture of all the metabolic activities present in a human, the metagenome must be considered. Also, genes could be found in gut microbes that code for proteins that utilize the N-acetyl glucosamine, sialic acid and fucose found in breast milk (and not metabolized by humans). Studies with Bacteroides and Ruminococcus sp. serve as examples. Examples may vary but can include studies examining the genes involved in digesting a variety of xyloglucan from sources such as tomatoes versus lettuce.

DIF: Difficult REF: 13.4

OBJ: 13.4c Explain how genomic studies have contributed to our understanding of microbial catabolism MSC: Applying

  1. Describe the Entner-Doudoroff (ED) pathway. What are the advantages to microorganisms that display the ED pathway?

ANS:

Glucose is oxidized to the sugar acid 6-phosphogluconate, a central metabolite in the Entner-Doudoroff pathway. 6-Phosphogluconate may arise from other sources, such as the bacterial catabolism of intestinal mucus, and is further oxidized to 2-oxo-3-deoxy-6-phosphogluconate, which breaks down to the glycolysis intermediates glyceraldehyde and pyruvate. Microorganisms using ED produce only one ATP, half of that produced in glycolysis, but the electrons transferred are equivalent: one NADH + H+ and one NADPH + H+are generated in ED.

DIF: Medium REF: 13.5

OBJ: 13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC: Understanding

  1. The flavor and other properties of cheeses derive from the type of fermenting microorganisms used. How do the “eyes” and the characteristic flavor of Swiss cheese originate?

ANS:

Fermentation of milk sugars by Propionibacterium freudenreichii produces lactate, which is further oxidized to propionate and acetate. Fermentation also produces CO2, which makes the “eyes” (holes). Other flavors come from succinate, which is formed by the reaction between lactate and two molecules of aspartate. This reaction releases CO2, which further increases the size and number of “eyes.”

DIF: Difficult REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Understanding

  1. What is mixed-acid fermentation? Provide examples of industrial uses of its products.

ANS:

Some enteric bacteria produce a series of mono- and dicarboxylic acids from pyruvate. Depending on the pH, the mixture may include succinate, lactate, acetate, or formate, plus ethanol, CO2, and H2. Regeneration of NAD+ and free coenzyme A also take place in the process. Some bacteria, such as Clostridium spp., possess the metabolic capability to synthesize isopropanol and butanol, which are valuable solvents. Lactic acid is part of the biochemical makeup of yogurt and cheeses. Ethanol can be used as a solvent and is found in alcoholic beverages.

DIF: Difficult REF: 13.5

OBJ: 13.5e Distinguish among various types of fermentation (e.g., lactic acid, ethanolic, and mixed acid) MSC: Applying

  1. Describe the diagnostic use of sorbitol MacConkey agar to test for the presence of E. coli O157:H7.

ANS:

The sugar source in this medium is sorbitol. Also present in the medium is an indicator dye that turns red in the presence of acids. An organism that ferments sorbitol produces acids, and the colony will appear red. These plates are used to screen for E. coli O157:H7 because this strain, unlike most E. coli, is incapable of fermenting sorbitol. When grown on these plates, the colonies appear pale rather than red. The appearance of pale colonies indicates a high probability of E. coli O157:H7.

DIF: Medium REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Applying

  1. Escherichia coli degrades human waste in the colon using mixed-acid fermentation. Why is this a factor of concern in some medical procedures, such as colonoscopy?

ANS:

Molecular hydrogen (H2) and CO2 are among the products of mixed-acid fermentation of the carbohydrate solution used to flush the colon. These gases can be used as energy sources for intestinal methanogenic microbes through the production of methane. However, excess H2 and CH4 may ignite during polyp removal by electrocauterization, thus causing the so-called colonic explosion.

DIF: Difficult REF: 13.5

OBJ: 13.5f Identify some food and industrial applications of microbial fermentation

MSC: Applying

  1. In the pentose phosphate shunt (PPS), sugars exchange short carbohydrate moieties to form carbohydrates with varying chain lengths. What metabolic mechanisms allow these exchanges to occur? What are the metabolic advantages of the PPS pathway?

ANS:

Pairs of sugars exchange portions of their molecules through specific enzymatic reactions, rendering new molecules without any loss of carbon. For example, the pentose ribose 5-phosphate and xylulose 5-phosphate react to form the C3 glyceraldehyde 3-phosphate and the C7 carbohydrate sedoheptulose 7-phosphate. In turn, these sugars may be converted to the C4 erythrose 4-phosphate and the C6 fructose 6-phosphate. Some PPS intermediates are anabolic precursors. For example, ribose 5-phosphate is used for nucleotide biosynthesis, and erythrose 4-phosphate is used for aromatic amino acids. The reducing equivalent NADPH is produced by several PPS reactions and used in biosynthesis. If pathway intermediates are not used in biosynthesis, they may be converted to fructose 6-phosphate and reenter glycolysis.

DIF: Difficult REF: 13.5

OBJ: 13.5c Compare and contrast glycolysis (EMP pathway), the Entner-Doudoroff (ED) pathway, and the pentose phosphate pathway; include key intermediates and net products

MSC: Analyzing

  1. Treponema pallidum, the causative agent of syphilis, was shown to be lacking a TCA cycle. Explain the significance of this finding.

ANS:

  1. pallidum’s genome encodes key enzymes for glycolysis and fermentation, but not for the TCA cycle or electron transport. Although the genome also codes for transport proteins for sugars and amino acids, there are no genes that code for any enzymes involved in either the biosynthesis or breakdown of amino acids. T. pallidum, and other obligate pathogens, therefore must depend on its host’s metabolism to supply many fundamental and essential nutrients and transport them with the transport proteins.

DIF: Difficult REF: 13.6

OBJ: 13.6b Recall the roles that the TCA cycle and the glyoxylate bypass play in cell metabolism

MSC: Remembering

  1. Hans Krebs’s strategy to determine the biochemical intermediates involved in aerobic respiration was to use substrate molecules of varying lengths. What led Krebs to take this approach?

ANS:

Many short-chain molecules with variable numbers of carboxyl groups were known to exist in the cells of aerobic organisms. Krebs tested carboxylic acids for their capacity to induce or stimulate respiration in different animal and plant tissues and analyzed their chemical structure relationships. Feeding bacteria with 14C-radiolabeled acetate helped to determine what was the fate of carbons entering the TCA cycle and to confirm the reactions in the pathway.

DIF: Difficult REF: 13.6

OBJ: 13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples MSC: Remembering

  1. How does the efficiency of energy capture by ATP formation in bacterial tricarboxylic acid cycle compare with that of mitochondria?

ANS:

Whereas mitochondria are enclosed in an intracellular environment that is relatively constant, bacteria must spend energy in adapting to ever-changing environments. Although less efficient in ATP production, bacteria spend energy to achieve flexibility through keeping stable ionic potentials during extreme changes in external pH and redox conditions.

DIF: Medium REF: 13.6

OBJ: 13.6a Summarize the Krebs TCA cycle; include substrates, products, and key intermediates

MSC: Analyzing

  1. Soils and waters become contaminated with industrial aromatic compounds and efforts are made to use bacteria to clean up these areas. Describe the experiment and finding from phenanthrene metabolism in the Antarctic.

ANS:

Soils from the Antarctic were incubated at a variety of temperatures. C14-labeled phenanthrene was added to the soils and a respirometer was used to collect C14-carbon dioxide. Metabolism was demonstrated in this fashion, and in fact, warmer temperatures yielded faster metabolism than lower temperatures that would be found in the Antarctic. These findings suggest that the organisms involved were psychrotrophs that could tolerate cold, not psychrophiles that thrived only in the cold.

DIF: Medium REF: 13.6

OBJ: 13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples MSC: Understanding

  1. What metabolic pathway does Mycobacterium tuberculosis use that allows it to grow slowly inside macrophages? What led to this discovery, and what practical application can further analysis of this pathway have?

ANS:

Using 13C metabolic precursors to label infected cells, it was found that M. tuberculosis uses the glyoxylate bypass to catabolize lipids. The pathogen uses much of the carbon to produce sugars and amino acids for its own biosynthetic pathways. Enzymes of the glyoxylate pathway can be used as targets in the design of new antibiotics to treat tuberculosis.

DIF: Difficult REF: 13.6

OBJ: 13.6f Explain how isotopes are used in studies of metabolic pathways; provide specific examples MSC: Evaluating

CHAPTER 21: Microbial Ecology

MULTIPLE CHOICE

  1. The instrument shown in step 5 of the figure below is used for what metagenomics step?
a.DNA isolationd.cell lysis
b.DNA sequencinge.sequence assembly
c.sample filtering

ANS: B DIF: Medium REF: 21.1

OBJ: 21.1c Outline the steps required to obtain metagenomic data

MSC: Remembering

  1. The Dutch microbiologist van Niel first demonstrated anoxygenic photosynthesis in soil and water bacteria. He generalized his work by hypothesizing that
a.every molecule in nature can be used as a source of nitrogen by some microorganism.
b.photosynthesis results in oxygen production.
c.microbes are found in every environment on Earth.
d.microbes cannot live deep within Earth.
e.photosynthesis occurs deep within Earth.

ANS: C DIF: Easy REF: 21.2

OBJ: 21.2c Restate van Niel’s two hypotheses of microbial ecology

MSC: Remembering

  1. What does the following rarefaction curve NOT suggest about the samples?
a.More soil sequences were collected.
b.Indoor air samples appear to be sequenced at enough depth.
c.Water samples were not sequenced at enough depth.
d.More sequencing should be done for these samples.
e.Soil samples were not sequenced at enough depth.

ANS: A DIF: Difficult REF: 21.1

OBJ: 21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC: Analyzing

  1. Synechococcus, a cyanobacterium, is a free-living marine organism that fixes CO2 into biomass while producing molecular oxygen utilized by swarms of heterotrophic bacteria. Which of the following is the most likely habitat of this bacterium?
a.euphotic zone of the pelagic environment
b.the benthos
c.the littoral zone
d.lake sediments
e.aphotic zone

ANS: A DIF: Medium REF: 21.5

OBJ: 21.5a Compare the properties of the distinct regions of the marine habitat | 21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC: Evaluating

  1. The following image illustrates a syntrophic relationship between an archaeon and a bacterium. The technique used to generate this image was
a.light microscopy.d.fluorescence in situ hybridization.
b.transmission electron microscopy.e.atomic force microscopy.
c.metagenomics.

ANS: D DIF: Medium REF: 21.1

OBJ: 21.1f Describe techniques that circumvent the limitations of metagenomic analysis

MSC: Understanding

  1. The term “metagenome” was coined by Jo Handelsman and colleagues in 1998 to refer to
a.shotgun cloning.
b.screening of libraries for expression of genes.
c.the DNA sequence obtained directly from a mixture of genomes.
d.the DNA sequence taken directly from a colony.
e.all uncultured organisms from a community.

ANS: C DIF: Easy REF: 21.1

OBJ: 21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC: Remembering

  1. A rarefaction curve is the
a.number of sequences generated from a metagenome.
b.number of SSU rRNA sequences found in a metagenome.
c.number of OTUs found as a function of increasing sample size.
d.total number of OTUs from all combined genes in a metagenome.
e.number of organisms in an environment.

ANS: C DIF: Difficult REF: 21.1

OBJ: 21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC: Understanding

  1. What does functional annotation in metagenomic analysis involve?
a.determining the number of species in the sample
b.calculating the %G+C in the metagenome
c.finding homologs or recurring peptide motifs that infer the function of the sequence
d.making contigs and scaffolds and assembling the sequence
e.analyzing the RNA sequences to see what was transcribed

ANS: C DIF: Medium REF: 21.1

OBJ: 21.1e Compare the approaches used for functional annotation

MSC: Remembering

  1. Which of the following is NOT true regarding food webs in ecosystems?
a.Primary producers assimilate minerals into biomass.
b.Primary producers absorb energy from outside the ecosystem.
c.Grazers convert 10% of carbon back to carbon dioxide.
d.Consumers convert 90% of biomass carbon to atmospheric CO2.
e.All energy gained by an ecosystem is eventually lost as heat.

ANS: C DIF: Difficult REF: 21.2

OBJ: 21.2b Explain why all ecosystems require microbes | 21.2e Evaluate the roles of primary producers, consumers, and decomposers in food webs | 21.2f Distinguish different levels of consumers

MSC: Understanding

  1. The availability of oxygen and other electron acceptors is the most important determinant of the types of metabolism in a habitat. Which of the following is NOT true about anaerobic environments?
a.They have slower rates of assimilation compared to aerobic habitats.
b.Their rates of dissimilation are slower compared to aerobic environments.
c.Microbes sometimes use minerals such as NO2– to oxidize organic compounds.
d.Anaerobic microbial biomass far exceeds that of the oxygenated biosphere.
e.Respiration of organic compounds is highly dissimilatory, reducing them to CO2.

ANS: E DIF: Difficult REF: 21.2

OBJ: 21.2h Describe the contributions of oxygen levels, pH, salinity, and temperature to metabolic processes MSC: Analyzing

  1. Culturing methods often detect organisms that may be rare in the environment but prevail when nutrients appear. What are these typically called?
a.weed organismsd.OTUs
b.protistse.microbial dark matter
c.rhizobia

ANS: A DIF: Medium REF: 21.1

OBJ: 21.1b Propose questions that can only be answered with a metagenomics approach

MSC: Remembering

  1. Which of the following are the main consumers of biomass in the ocean?
a.multicellular organismsd.heterotrophic bacteria
b.fish and tube wormse.fungi
c.protists and viruses

ANS: C DIF: Difficult REF: 21.2

OBJ: 21.2e Evaluate the roles of primary producers, consumers, and decomposers in food webs | 21.2g Compare the importance of microbial producers and consumers to that of multicellular producers and consumers in both marine and terrestrial ecosystems

MSC: Remembering

  1. The algal and fungal interaction within a lichen would best be described as
a.mutualism.d.amensalism.
b.synergism.e.parasitism.
c.commensalism.

ANS: A DIF: Easy REF: 21.3

OBJ: 21.3a Decide whether a particular symbiotic relationship is an example of mutualism, synergism, commensalism, amensalism, or parasitism | 21.3b Distinguish among mutualism, synergism, commensalism, amensalism, and parasitism MSC: Remembering

  1. Lichens consist of an intimate mutualistic symbiosis between a fungus, an alga, and/or cyanobacteria. What is one primary role of the cyanobacteria in this association?
a.protection of the symbiontsd.recycling of waste products
b.nitrogen fixatione.degradation of lignin
c.decomposition of toxic compounds

ANS: B DIF: Medium REF: 21.3

OBJ: 21.3c Identify the partners present in lichens MSC: Understanding

  1. Which step is NOT common for metagenomic processing and analysis?
a.FISHd.contig assembly
b.binninge.scaffold assembly
c.functional annotation

ANS: A DIF: Medium REF: 21.1

OBJ: 21.1c Outline the steps required to obtain metagenomic data | 21.1e Compare the approaches used for functional annotation MSC: Understanding

  1. The relationship among endosymbiotic microbes in the termite gut that results in complex metabolic fluxes with a negative DG, which would NOT happen for individual members, is called
a.mutualism.d.predation.
b.parasitism.e.syntrophy.
c.exothermic association.

ANS: E DIF: Medium REF: 21.4

OBJ: 21.4a Define holobiont and syntrophy | 21.4b Describe the organisms in and functions of the termite hindgut microbiome MSC: Understanding

  1. Metatranscriptomics is the study of ________ obtained from an environmental community.
a.lipidsd.DNA
b.proteinse.RNA
c.organisms

ANS: E DIF: Easy REF: 21.1

OBJ: 21.1f Describe techniques that circumvent the limitations of metagenomic analysis

MSC: Remembering

  1. The ________ is a set of conditions, including its habitat, resources, and relations with other species of the ecosystem, that enable an organism to grow and reproduce.
a.benthosd.metagenome
b.environmente.resource requirement
c.niche

ANS: C DIF: Easy REF: 21.2

OBJ: 21.2a Define niche, biomass, and trophic levels MSC: Remembering

  1. In wetlands, Beggiatoa oxidize H2S for energy. Removal of H2S enables growth of other microbes for which H2S is toxic. However, Beggiatoa derives no benefit from these microbes. This interaction is an example of
a.syntrophy.d.amensalism.
b.mutualism.e.synergism.
c.commensalism.

ANS: C DIF: Medium REF: 21.3

OBJ: 21.3a Decide whether a particular symbiotic relationship is an example of mutualism, synergism, commensalism, amensalism, or parasitism | 21.3b Distinguish among mutualism, synergism, commensalism, amensalism, and parasitism MSC: Understanding

  1. The reactions on the right side of the following table occur only
a.under thermophilic conditions.d.under aerobic conditions.
b.under anaerobic conditions.e.in the euphotic zone.
c.deep within Earth’s crust.

ANS: B DIF: Easy REF: 21.2

OBJ: 21.2h Describe the contributions of oxygen levels, pH, salinity, and temperature to metabolic processes MSC: Remembering

  1. Nonphotosynthetic ________ provide minerals and protection for lichen symbiotic partners.
a.planktond.fungi
b.proteobacteriae.cyanobacteria
c.algae

ANS: D DIF: Easy REF: 21.3

OBJ: 21.3c Identify the partners present in lichens MSC: Remembering

  1. Thousands of species of microbes in the cow ________ ferment and break down plant material to small particles.
a.rumend.reticulum
b.stomache.intestine
c.omasum

ANS: A DIF: Easy REF: 21.4

OBJ: 21.4c Recall the names and functions of the four chambers of the rumen gut

MSC: Remembering

  1. Which region of marine habitat refers to the microscopic interface between water and air?
a.pelagic zoned.aphotic zone
b.neustone.benthic zone
c.euphotic zone

ANS: B DIF: Easy REF: 21.5

OBJ: 21.5a Compare the properties of the distinct regions of the marine habitat

MSC: Remembering

  1. The depth of the photic zone at the coastal shelf of marine habitats is
a.100–200 m.d.about 0.1 m.
b.10–20 m.e.about 2 m.
c.about 1 m.

ANS: C DIF: Medium REF: 21.5

OBJ: 21.5a Compare the properties of the distinct regions of the marine habitat

MSC: Understanding

  1. Animal intestinal microbiota typically yields ________, which the host animal can absorb and digest to completion through aerobic respiration.
a.cellulosesd.polysaccharides
b.CO2e.short-chain fatty acids
c.oligosaccharides

ANS: E DIF: Difficult REF: 21.4

OBJ: 21.4d Compare and contrast the termite, cow, and human gut microbiomes

MSC: Understanding

  1. Much of the microbial fermentation in humans occurs in the
a.stomach.d.small intestine.
b.colon.e.esophagus.
c.rumen.

ANS: B DIF: Medium REF: 21.4

OBJ: 21.4e State some contributions of the commensal gut microbiome to human health

MSC: Remembering

  1. A holobiont is defined as an
a.organism that benefits while providing no benefit or a hidden benefit to its host.
b.interaction that harms one partner nonspecifically without an intimate symbiosis.
c.organism that forms an intimate relationship with another, where both benefit.
d.entity composed of multiple types of organisms, including microbes.
e.intimate relationship in which one member benefits while harming a host.

ANS: D DIF: Difficult REF: 21.4

OBJ: 21.4a Define holobiont and syntrophy MSC: Understanding

  1. Which of the following plays an important role in keeping the water column clear enough for the penetration of light?
a.algaed.invertebrates
b.bacteriae.viruses
c.fish

ANS: E DIF: Difficult REF: 21.5

OBJ: 21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC: Remembering

  1. All of the following are likely to be found among the benthic microbes EXCEPT
a.barophiles.d.phototrophs.
b.psychrophiles.e.methanogens.
c.thermophiles.

ANS: D DIF: Medium REF: 21.5

OBJ: 21.5a Compare the properties of the distinct regions of the marine habitat

MSC: Analyzing

  1. The flame-like vertical forms and breakaway pieces of mat in ice-covered Antarctic lakes are caused by
a.limited light penetration in the lake.d.oxygen production.
b.denitrification.e.freeze-thaw cycles.
c.sulfur-reducing bacteria.

ANS: D DIF: Medium REF: Special Topic 21.1

OBJ: 21.5g Recall the properties of the different regions of freshwater habitats

MSC: Understanding

  1. The ________ region of an oligotrophic lake extends to about 10 meters below the surface.
a.neustond.hypolimnion
b.benthice.euphotic
c.epilimnion

ANS: C DIF: Medium REF: 21.5

OBJ: 21.5g Recall the properties of the different regions of freshwater habitats

MSC: Understanding

  1. Which of the following refers to the zone of a lake with higher relative oxygen concentrations?
a.neustond.hypolimnion
b.epilimnione.benthos
c.thermocline

ANS: B DIF: Easy REF: 21.5

OBJ: 21.5g Recall the properties of the different regions of freshwater habitats

MSC: Understanding

  1. Lakes that have dilute concentrations of nutrients are termed
a.eutrophic.d.oligotrophic.
b.syntrophic.e.atrophic.
c.aphotic.

ANS: D DIF: Easy REF: 21.5

OBJ: 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes MSC: Remembering

  1. Eutrophic lakes typically support ten times the microbial concentrations of an oligotrophic lake. Which of the following statements is NOT true of eutrophic lakes?
a.Biochemical oxygen demand is high.
b.Population of aquatic animals is high.
c.Nitrogen and phosphorous levels are usually high.
d.Photosynthetic activities are altered.
e.Algal blooms are common.

ANS: B DIF: Medium REF: 21.5

OBJ: 21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC: Understanding

  1. The high biological oxygen demand that accompanies algal bloom in eutrophic lakes increases the span of the ________ zone.
a.oxygenic epilimniond.anoxic benthic
b.anoxic hypolimnione.oxygenic neuston
c.coastal shelf

ANS: B DIF: Medium REF: 21.5

OBJ: 21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC: Understanding

  1. Compared to eutrophic lakes, the biochemical oxygen demand, or BOD, of oligotrophic lakes is
a.low.d.unpredictable.
b.similar.e.extremely high.
c.high.

ANS: A DIF: Medium REF: 21.5

OBJ: 21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC: Remembering

  1. A graduate student filtered a liter of seawater using a Millipore filter membrane of 2 mm pore size. Her filtrate
a.is sterile.d.contains nanoplankton.
b.contains microplankton.e.contains all plankton.
c.contains picoplankton.

ANS: C DIF: Difficult REF: 21.5

OBJ: 21.5e Contrast the different ways of measuring planktonic community population size

MSC: Understanding

  1. Bacteria found growing in between crystals of solid bedrock as deep as 3 km below Earth’s surface are called
a.endophytes.d.decomposers.
b.symbionts.e.saprophytes.
c.endoliths.

ANS: C DIF: Medium REF: 21.6

OBJ: 21.6b State the properties of the different soil horizons; include microbes typically found in each layer MSC: Remembering

  1. Which of the following is responsible for the characteristic odor of soil?
a.Vibrio sp.d.Staphylococcus sp.
b.Bacillus sp.e.Pseudomonas sp.
c.Streptomyces sp.

ANS: C DIF: Easy REF: 21.6

OBJ: 21.6a Justify the importance of understanding the soil and plant microbial communities

MSC: Remembering

  1. Which term represents the region of soil influenced by plant roots?
a.steled.rhizoplane
b.cortexe.rhizosphere
c.root cap

ANS: E DIF: Easy REF: 21.6

OBJ: 21.6c Outline the relationships in the soil food web MSC: Remembering

  1. Fungi play a much larger and more significant role in the decomposition of terrestrial biomass than they do in marine ecosystems. This is because fungi
a.do not thrive in a marine environment.
b.outcompete bacteria in terrestrial habitats.
c.can degrade the abundant lignin in terrestrial habitats.
d.decompose leghemoglobin rapidly.
e.degrade human waste faster than bacteria.

ANS: C DIF: Difficult REF: 21.6

OBJ: 21.6c Outline the relationships in the soil food web | 21.6h Categorize different types of fungus–plant interactions MSC: Understanding

  1. Lignin decomposition forms
a.arbuscules.d.humus.
b.detritus.e.rhizopus.
c.fruiting bodies.

ANS: D DIF: Easy REF: 21.6

OBJ: 21.6c Outline the relationships in the soil food web MSC: Remembering

  1. Most forest trees require mycorrhizae for growth because
a.forest soils are rich in phosphorous.
b.mycorrhizae limit toxic metal uptake.
c.the mycorrhizal form an ammensalic association.
d.mycorrhizae significantly increase the uptake of nutrients.
e.forest trees do not have deep roots.

ANS: D DIF: Medium REF: 21.6

OBJ: 21.6h Categorize different types of fungus–plant interactions

MSC: Understanding

  1. Rhizosphere bacteria benefit their host plant by
a.degrading plant lignin.
b.attracting symbiotic nematodes.
c.improving water uptake.
d.producing large amounts of photosynthate.
e.discouraging growth of plant pathogens.

ANS: E DIF: Medium REF: 21.6

OBJ: 21.6h Categorize different types of fungus–plant interactions

MSC: Understanding

  1. Vascular abuscular mycorrhizae (VAM) are an example of which of the following?
a.ectomycorrhizaed.lignin decomposer
b.endomycorrhizaee.nitrogen fixer
c.free-living fungus

ANS: B DIF: Difficult REF: 21.6

OBJ: 21.6d Compare and contrast ectomycorrhizae and endomycorrhizae

MSC: Remembering

  1. One of the most important ecological roles of the Florida Everglades is that
a.it is home to beautiful birds.
b.it filters much of the water supply for Florida communities.
c.many bacteria reside in it.
d.nutrients can easily be leached to the lakes.
e.tourists come to see it in large numbers.

ANS: B DIF: Medium REF: 21.6

OBJ: 21.6g Explain why wetlands are among the most productive ecosystems

MSC: Understanding

  1. Which of the following organisms forms a specific mutualistic association with legumes?
a.rhizobiad.morels
b.agrobacteriae.Vibrio sp.
c.E. coli

ANS: A DIF: Easy REF: 21.6

OBJ: 21.6e Recall the benefits endophytes provide to plants and how endophytes impact humans | 21.6f Summarize the colonization of legumes by rhizobia MSC: Remembering

  1. In the legume-rhizobium symbiosis, nitrogen fixation is carried out in nodules by
a.bacteroids that lack a cell wall.
b.intact rhizobia in the plant cortex.
c.plant cells in the presence of symbiotic bacteria.
d.bacteroids in oxygen-rich nodules.
e.photosynthetic bacteroids in plants.

ANS: A DIF: Medium REF: 21.6

OBJ: 21.6e Recall the benefits endophytes provide to plants and how endophytes impact humans | 21.6f Summarize the colonization of legumes by rhizobia MSC: Remembering

  1. Bacteroids remain sequestered within a sac of plant-derived membrane known as the
a.flavonoid.d.nucleosome.
b.infection thread.e.symbiosome.
c.Nod factor.

ANS: E DIF: Easy REF: 21.6

OBJ: 21.6f Summarize the colonization of legumes by rhizobia

MSC: Remembering

  1. Which of the following require endosymbiotic protists and bacteria to digest plant material such as lignin and cellulose?
a.termitesd.humans
b.cattlee.microplankton
c.gorillas

ANS: A DIF: Medium REF: 21.4

OBJ: 21.4b Describe the organisms in and functions of the termite hindgut microbiome

MSC: Remembering

SHORT ANSWER

  1. Explain at least three ways in which metagenomes may overlook organisms in the environment.

ANS:

Possible answers include the following: the sample was not sequenced enough to catch all the microbes in the environment and may miss the “rare biosphere.” The sample was not properly filtered or DNA extracted from all organisms in the sample. The PCR primers may not be general enough and may miss microbes with very divergent sequences.

DIF: Medium REF: 21.1

OBJ: 21.1a Define metagenome, microbiome, operational taxonomic unit, and rarefaction curve

MSC: Remembering

  1. What are the benefits and limitations of different environmental sequencing methods? Explain why ribosomal gene sequencing can be used as an initial screen.

ANS:

SSU rRNA gene sequence libraries generated with primers may miss microbes with 16S rRNA sequences very different than known microbes. An advantage of 16S rRNA amplicon sequencing is that we may quickly identify many taxa present in a community, including relatively rare members that do not yield full genomes when large-scale sequencing is performed. SSU rRNA gene similarity is used to define OTUs. Direct metagenome sequencing can identify those organisms not amplified with traditional SSU rRNA gene primers, but also sequences other genes than SSU rRNA. Metagenomes require large amounts of computational analysis and are typically much more expensive than targeted sequencing technologies.

DIF: Difficult REF: 21.1

OBJ: 21.1d Identify limitations of SSU rRNA sequencing and metagenomic analysis

MSC: Understanding

  1. Describe the steps in sequencing a metagenome.

ANS:

You first sample the microbial target community and either separate it from its surroundings (in the case of terrestrial samples) or filter the sample (in the case of water samples) to only include the organisms of interest. You lyse the cells to extract the DNA and then clone the DNA fragments or amplify them by PCR. The DNA is then sequenced typically via next-generation sequencing such as Illumina. The sequences are then assembled and contigs can be analyzed by computational pipelines.

DIF: Medium REF: 21.1

OBJ: 21.1c Outline the steps required to obtain metagenomic data

MSC: Understanding

  1. Explain the difference between assimilation and dissimilation.

ANS:

Assimilation refers to processes by which organisms acquire an element, such as carbon from CO2, to build into cells. Common kinds of assimilation include carbon dioxide fixation and nitrogen fixation. Dissimilation is the process of breaking down organic nutrients to inorganic minerals such as CO2 and NO2–, usually through oxidation. Microbial dissimilation releases minerals for uptake by plants and other microbes, but microbial dissimilation can decrease habitat quality by removing organic nitrogen.

DIF: Easy REF: 21.2 OBJ: 21.2d Contrast assimilation and dissimilation

MSC: Remembering

  1. Name two factors that differentiate aquatic and terrestrial ecosystems and explain how they affect food cycles in these systems.

ANS:

A major difference appears between marine and terrestrial ecosystems. In the oceans, the smallest inhabitants, phototrophic bacteria, perform most of the CO2 fixation and biomass production. The main consumers are protists and viruses. Viruses are the most numerous replicating forms in the ocean—and they lyse most marine cells before any multicellular predators get a chance to consume them. In terrestrial ecosystems, by contrast, the major primary producers and fixers of CO2 are multicellular plants. Plants generate detritus, discarded biomass such as leaves and stems, that requires decomposition by fungi and bacteria. While viruses are important, multicellular consumers such as worms and insects play a greater role in decomposition.

DIF: Difficult REF: 21.2

OBJ: 21.2e Evaluate the roles of primary producers, consumers, and decomposers in food webs | 21.2f Distinguish different levels of consumers | 21.2g Compare the importance of microbial producers and consumers to that of multicellular producers and consumers in both marine and terrestrial ecosystems MSC: Analyzing

  1. How do microbes live if their metabolic process to generate energy has a positive DG?

ANS:

They live in association with another organism in a relationship known as syntrophy, or “feeding together.” This typically happens when a product from the positive DG is removed fast enough by another organism, resulting in a favorable reaction or a community-balanced negative DG.

DIF: Difficult REF: 21.4 OBJ: 21.4a Define holobiont and syntrophy

MSC: Evaluating

  1. Describe the interaction of Vibrio cholerae with copepods. How did sari cloth help decrease the incidence of cholera in Bangladesh?

ANS:

Vibrio cholerae is a mutualist on the surfaces of the small, invertebrate copepods. The copepods have come to rely on the bacteria to eat through the chitin of their egg cases to release their young. Anwar Huq found that if the Bangladesh people filtered their water through several layers of sari cloth, the incidence of cholera decreased.

DIF: Medium REF: 21.3

OBJ: 21.3a Decide whether a particular symbiotic relationship is an example of mutualism, synergism, commensalism, amensalism, or parasitism MSC: Understanding

  1. How do metatranscriptomics and metaproteomics address functional limitations of metagenomics?

ANS:

Metatranscriptomics, the study of the RNA transcripts (or RNAseq) obtained from an environmental community, and metaproteomics, the study of proteins synthesized by environmental samples, both identify genes that are actually expressed by the target community. These techniques address a major limitation in metagenomics regarding the actual function of microbes in the environment.

DIF: Medium REF: 21.1

OBJ: 21.1d Identify limitations of SSU rRNA sequencing and metagenomic analysis | 21.1e Compare the approaches used for functional annotation MSC: Analyzing

  1. Propose a method to measure biomass production in terms of DNA synthesis. What are the limitations?

ANS:

The rate of DNA synthesis is determined by the uptake of 14C radiolabeled thymidine. A limitation is that addition of the radiolabeled substrate may raise a nutrient concentration to artificially high levels that distort the naturally occurring rates of activity. Another limitation is that not all growing cells incorporate exogenous thymidine into their DNA.

DIF: Medium REF: 21.5

OBJ: 21.5e Contrast the different ways of measuring planktonic community population size

MSC: Evaluating

  1. Compare and contrast the photic zones of freshwater lake and pelagic ecosystems.

ANS:

The photic zone in the marine habitat is called the euphotic zone and is up to 200 meters deep except near the coastal shelf. In lakes, the epilimnion reaches only about 10 meters in depth, making it much shallower than the marine euphotic zone. Both regions are oligotrophic and contain a wide diversity of phototroph primary producers.

DIF: Medium REF: 21.5

OBJ: 21.5a Compare the properties of the distinct regions of the marine habitat | 21.5g Recall the properties of the different regions of freshwater habitats MSC: Understanding

  1. Explain how metagenomics and metatranscriptomics have been used to assess ocean diversity.

ANS:

A 2015 study led by Shinichi Sunagawa showed that the abundant Prochlorococcus and Synechococcus constitute only a small fraction of the microbes present. Abundant heterotrophs included Proteobacteria, many of which have proteorhodopsins for photoheterotrophy. Also abundant were the Thaumarchaeota, which oxidize ammonia released by fish and other organisms.

Metatranscriptomes were compared to those amplified from metagenomic DNA of the same microbial community. The most highly expressed genes included those encoding functional elements of photosynthesis, such as light-harvesting proteins and Rubisco. Genes for DNA repair were also highly expressed, presumably to correct UV damage in the open ocean. But the most highly expressed genes were some of the rarest in the metagenomes, and 40% of all expressed genes had no counterpart in the metagenome.

DIF: Difficult REF: 21.5

OBJ: 21.5d Evaluate the role of metagenomic approaches to understanding the marine microbial community MSC: Understanding

  1. The net biomass of a population does not indicate productivity within an ecosystem. Explain.

ANS:

At each trophic level above the producers, about 90% of biomass is consumed for energy generation. Biomass is a small fraction of productivity because it misses the amount of carbon cycled through respiration.

DIF: Difficult REF: 21.5

OBJ: 21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC: Understanding

  1. Explain how viruses select for increased diversity of microbial plankton in the oceans.

ANS:

Recent studies indicate that cell lysis by viruses breaks down about half of microbial biomass. Virus particles represent a significant sink for carbon and nitrogen. They accelerate the return of minerals to producers and necessitate a larger base of producers to sustain the ecosystem. Some marine viruses are highly host specific, infecting only certain species of dinoflagellates or cyanobacteria. Their presence selects for diverse communities containing numerous scattered species. Other viruses attack many hosts—and they transfer genes from one host to another, such as the genes encoding photosystems. Thus, marine viruses are a dominant force determining community species distribution and genome content.

DIF: Difficult REF: 21.5

OBJ: 21.5f Outline the relationships present in a marine food web; include the role of viruses

MSC: Understanding

  1. Define BOD, and explain why it can be used to measure the pollution level of lakes. Describe how effluents carrying high levels of nutrients can cause eutrophication.

ANS:

BOD is an abbreviation for biochemical oxygen demand, which is the amount of oxygen removed from water by aerobic respiration. A eutrophic lake is one in which the upper layers have become depleted of oxygen as a consequence of an overgrowth of microbial producers. Problems arise when effluents entering a lake carry high concentrations of nutrients, relieving nitrogen limitation and causing an overgrowth of phototrophs. The cell mass of the phototrophs sinks to the bottom, where an overgrowth of heterotrophs then depletes oxygen.

DIF: Medium REF: 21.5

OBJ: 21.5b Identify factors that control the biochemical oxygen demand (BOD) | 21.5h Identify factors that lead to eutrophic conditions and compare eutrophic lakes to oligotrophic lakes

MSC: Applying

  1. Explain how endoliths derive energy inside bedrock, where there is no sunlight.

ANS:

Endoliths are chemilithotrophs. It is believed that radioactive decay of uranium may be the energy source for these bacteria. Uranium-238 decay generates hydrogen radicals that combine to form hydrogen gas. The hydrogen gas combines with CO2 from carbonate rock, providing an electron donor and a carbon source for methanogens and other endolithic lithotrophs.

DIF: Medium REF: 21.6

OBJ: 21.6b State the properties of the different soil horizons; include microbes typically found in each layer MSC: Understanding

  1. Describe the initiation process for legume-rhizobium symbiosis.

ANS:

The legume exudes signaling molecules called flavonoids into its rhizosphere. The flavonoids are detected by rhizobial bacteria, which respond by chemotaxis, swimming toward the root surface. Flavonoids then induce bacterial expression of Nod factors. The bacterial Nod factor induces the root hair to curl around it and ultimately surround the bacterium with plant cell envelope. The bacterium then induces growth of a tube poking into the plant cell. As the tube grows, bacteria proliferate, forming a column of cells that projects down the tube.

DIF: Medium REF: 21.6

OBJ: 21.6f Summarize the colonization of legumes by rhizobia

MSC: Remembering

  1. In any environment, pathogens are always outnumbered by a vast community of neutral or helpful microbes. Describe some beneficial as well as devastating incidences of plant pathogens.

ANS:

Answers may vary. A plant virus is associated with the production of striped tulips, which are much admired by tulip fanciers. Agrobacterium tumefaciens causes crown gall tumors on plants. It is applied widely for commercial plant engineering as a natural genetic transformation system. Ophiostoma novo-ulmi, a fungus carried by bark beetles, which bore into the xylem of elm trees, damaging the tree’s transport vessels and allow access for fungal spores.

DIF: Difficult REF: 21.6

OBJ: 21.6h Categorize different types of fungus–plant interactions

MSC: Analyzing

  1. Describe the process of haustorial parasitism.

ANS:

Some fungal pathogens generate specialized structures to acquire nutrients from plants. A hypha grows across the plant’s epidermis, penetrating the cell wall and generating an ingrowth of a bulbous extension called a haustorium. The haustorium never penetrates the plant cell membrane, instead it causes the membrane to invaginate, while expanding into the volume of the plant cell. The haustorium takes up nutrients such as sucrose, generated by adjacent chloroplasts. Depending on the species of fungus, haustorial parasitism can lead to mild growth retardation, or it can rapidly kill the plant.

DIF: Difficult REF: 21.6

OBJ: 21.6h Categorize different types of fungus–plant interactions

MSC: Understanding

  1. Describe the technique pioneered by Robert Hungate of the University of California at Davis to study anaerobic microbiology of the rumen. What types of questions can be answered with this technique?

ANS:

Robert Hungate pioneered the use of the fistulated, or cannulated, cow to study anaerobic microbes of the rumen. A fistulated cow is a cow in which an artificial connection is surgically made between the rumen and the animal’s exterior. Samples may be taken from the rumen to determine what types of microbes are present, and different foods can be put into the rumen to determine what changes occur.

DIF: Easy REF: 21.4

OBJ: 21.4c Recall the names and functions of the four chambers of the rumen gut

MSC: Understanding

  1. What is coral bleaching? What is its possible cause?

ANS:

Coral bleaching occurs when coral zooxanthellae symbionts die or are expelled from the coral. The zooxanthellae are photosynthetic protists that are sensitive to climate change and pollution. Upon losing the endosymbionts, the coral turns white and soon dies, unless its symbionts return.

DIF: Medium REF: 21.3

OBJ: 21.3d Describe the relationship between corals and zooxanthellae

MSC: Applying

+
-
Only 0 units of this product remain

You might also be interested in