Microbiology Final Exam Study Guide

Distinguish how fermentation and respiration differ.

Fermentation forms organic acids and takes place in the absence of oxygen, while respiration forms water and carbon dioxide in the presence of oxygen.

______ of recently isolated viruses indicates that some viruses contain larger genomes than some bacterial genomes

Genomics analysis

A change in allele frequencies in a set of organisms over time is called __________.

evolution

The Proteobacteria are phylogenetically diverse. Interestingly, closely-related organisms may have very different metabolisms while similar metabolisms are spread throughout the various classes of the phylum. What process most likely contributed to these similarities?

exchanges of genetic material between mature, adult organisms

If ΔG0 is negative, the reaction is

exergonic and energy will be released.

Pathogenic genes

exotoxin genes endotoxin genes

Which of the following events might trigger induction of a temperate bacteriophage?

exposure to UV light

Coliforms in a water sample indicate ________ contamination.

fecal

C. difficile infections are on the rise, both in elderly hospitalized patients receiving antibiotics and in younger populations having no previous contact either with a hospital environment or antibiotics. What is the most effective treatment for chronic C. difficile infections?

fecal transplants from a healthy donor

______ is the first sign of an infection that resulted in the release of endotoxin

fever

Factors that enhance an organism's ability to adhere to host tissues include __________.

fimbriae

In the developed countries of the world, most intestinal infections are transmitted via

food

Severe cases of Staphylococcus aureus food poisoning may require treatment

for dehydration

Transfer RNA (tRNA) molecules

function to transfer the correct amino acids to the ribosome during translation.

What organisms are the most likely pathogens to grow in food that is solute-loaded or has low water activity?

fungi

Some Archaea live in remarkably saline environments. What is the challenge of living in a highly saline environment?

In a highly saline environment, most cells desiccate. Extreme halophiles have specialized adaptations to prevent desiccation.

Staphylococcus aureus is a particularly dangerous organism when in food due to the enterotoxins some species produce. These toxins are dangerous because they are __________.

heat-stable, acid-tolerant superantigen toxins Submit

A drug designed to inhibit reverse transcriptase activity would target

hepadnaviruses and retroviruses

Mice that are injected with only the R strain of Streptococcus pneumoniae

stay healthy, because their immune systems can kill this strain easily.

RNA that has hydrogen bonded to itself forms a

stem loop

Metagenomics

study of genetic material from an environmental sample

The oxic atmosphere created conditions that led to the evolution of various new metabolic pathways, such as

sulfide oxidation, nitrification and iron oxidation

A person who attended a picnic early in the day develops a very high fever and is unresponsive by the evening. This person most likely has been exposed to a(n)

superantigen

What type of transport uses two transport proteins?

symport

Which form of active transport employs diffusion?

symport

Which type of active transport protein moves two molecules into the cell at the same time?

symport

The reduction potential (E0′) of a substance reflects its tendency to donate or accept electrons. The larger the difference (ΔE0′) between the reduction potentials of the electron donor and the electron acceptor, __________.

the greater the change in free energy (ΔG0′), and the greater the energy released

How is the lytic cycle different from the lysogenic cycle with respect to the infected host cell?

the host cell dies during the lytic stage

The collective term for the functional collection of microbes living on or in the human body, as opposed to a general term for organisms in an environmental habitat, is

the human microbiome

The collective term for the organisms living on or in the human body, as opposed to a general term for organisms in an environmental habitat, is

the human microbiome

The very first DNA sequencing technology called the Sanger method relies on

the incorporation of dideoxynucleotides that terminate chain extension during DNA synthesis.

The first genome sequenced was that of a(n)

virus

Housekeeping genes

ribosomal genes peptidoglycan synthesis genes membrane lipid genes

Some antibiotics inhibit protein synthesis by disruption of translation through interactions with the

ribosome

the site of translation is

ribosomes in the cell cytoplasm

which antibiotic inhibits RNA synthesis

rifampin

Polypeptides and proteins must fold properly to be functional. Hydrogen bonds between the oxygen and nitrogen atoms of the peptide bonds are crucial to which level of protein structure?

secondary structure

Evolution is driven by

selection pressure applied to random mutation

The spread of pathogens through the blood and lymph systems that results in a bloodborne systemic infection is called

septicemia

description of an operon

several genes, next to each other in prokaryotic DNA, that are transcribed as a single piece of mRNA

Horizontal gene transfer is one plausible explanation as to why organisms in Archaea, Bacteria, and Eukarya still ....

share so many genes among such distinct domains.

If an oxidation reaction occurs,

simultaneous reduction of a different compound will also occur, because electrons do not generally exist alone in solution.

Cellular integrity and cell wall stabilization of the Halobacterium are aided by

sodium ions

Hot, sulfur-rich environments associated with terrestrial sulfur-rich springs are called

solfataras

What ensures that the single strands of DNA do not come back together?

stabilizing proteins

It is difficult to attain good selective toxicity with antiviral drugs because of the fact that __________.

viruses require host cells to replicate themselves

The most important potential common source of infectious disease is

water

Pickling is a type of food preservation utilizing

weak acids

The vagina of an adult female is

weakly acidic

When would endotoxins be released from a bacterial cell?

when the cell dies

The change in free energy for a particular reaction is most useful in determining

whether there will be a requirement or production of energy.

Why is ATP necessary for active transport?

ATP provides energy to transfer material against its concentration gradient.

________ led to the discovery that pathogenic organisms often lack genes for amino acid biosynthesis.

Genomic analysis

true statement about DNA replication

---The leading strand is built continuously, and the lagging strand is built in pieces. ---The two strands of parental DNA are separated during DNA replication. ---DNA polymerase builds a new strand by adding DNA nucleotides one at a time ---Because the two strands of parental DNA run in opposite directions, the new strands must be made in different ways. ---The lagging strand is made of a series of pieces that must be joined together to make a continuous strand.____

Roles of enzymes

-binding only one specific substrate to the enzyme active site -lowering the activation energy of a reaction -straining chemical bonds in a substrate so that they break easier

true statements about extremophiles

-can be found in environments with high salinity, such as the great salt lake or with low temperatures such as the antarctic -can include members of the bacteria or archaea that live in extreme environments -use specialized enzymes in their metabolic pathways

true statements regarding DNA and RNA synthesis

-overall direction of chain growth is from the 5' to 3' end -DNA is the template for both DNA and RNA synthesis -the template strand is antiparallel to the newly synthesized strand

Steps to the divergence from LUCA

1. biological building blocks appeared (amino acids, nucleosides and sugars) 2. Self replicating and catalytic RNA developed 3. Protein synthesis and protein enzymes appeared 4. DNA genomes developed, along with the processes of the DNA replication and transcription 5. Lipid bilayers surrounded the earliest cells and allowed the formation of cellular compartments 6. Bacteria and Archaea diverged 7. Archaea and Eukarya diverged

steps to complete 16 S rRNA amplification and analysis

1. isolate DNA 2. Amplify 16S gene by PCR 3. run on agarose gel, check for correct size 4. Sequence 5. Align sequences; generate tree

What temperature is most commonly used in autoclaves to sterilize growth media and other devices prior to experimentation?

121 degrees C

What is thought to be the maximum temperature for life to exist?

150 degrees C

What is the net production of ATP in glycolysis

2 ATP

Which step is the step for which glycolysis is named?

4th

In which direction does DNA polymerase synthesize DNA for the lagging strand?

5' to 3'

DNA replication always proceeds in only one direction because the ________ of the incoming nucleotide is attached to the free ________ of the growing DNA strand.

5'-phosphate / 3'-hydroxyl

advantage of a monolayer cell membrane

A monolayer membrane is more stable at high temperatures.

Insertion sequences target which areas on a target DNA sequence?

A sequence of nucleotides identical to the inverted repeat sequence found on the insertion sequence itself

What is the benefit for a bacteriophage to be a temperate (or lysogenic) virus?

A single infection event can produce millions of new viral particles instead of hundreds of viral particles.

TRUE about research on the human microbiome

Advanced nucleic acid sequencing techniques were needed before a good understanding of its microbial abundance and diversity could be developed.

Why would it be highly advantageous to a cell to form a mutualism (and eventually an endosymbiotic association) with a prokaryote capable of aerobic cellular respiration?

Aerobic cellular respiration involves an electron transport chain with oxygen as the terminal electron acceptor. This produces large amounts of ATP as the electron transport chain produces the greatest amount of ATP in cellular respiration.

Homologous recombination has been observed in

All three domains (Archaea, Bacteria, and Eukarya

Where would you expect to find electron transport chains in a prokaryote?

Along the plasma membrane

_______ catalyzes the reaction between the appropriate amino acid and ATP to form an activated amino acid: amino acid + ATP ↔ aminoacyl-AMP + P-P.

Aminoacyl-tRNA synthetase

The term "respiration" is often used more broadly than is strictly accurate. The term "anaerobic respiration" may sound counterintuitive, but many different molecules can serve as electron donors or electron acceptors for prokaryotes. Which of the examples below is the best example of anaerobic respiration?

An organism uses an electron transport chain with sulfur as the terminal electron acceptor

Many Proteobacteria share substantial metabolic similarities, but not all of these are classified together. Why is this the case?

Analysis of 16S rRNA gene sequences indicates that they should be classified in different phylogenetic lineages.

______ can develop in a bacterium as a result of spontaneous mutation.

Antibiotic resistance

Part complete Why are antibiotics often ineffective in treating food poisoning (food intoxication)?

Antibiotics target bacteria; they do not damage toxins.

Many pharmaceutical drugs specifically inhibit transcription in Bacteria but not Archaea or Eukarya. Why would drugs that inhibit transcription only affect Bacteria and not Archaea even though they are both prokaryotes?

Archaea and Eukarya have very similar RNA polymerases that are different than bacterial RNA polymerases.

Inorganic compounds can be reduced by microbes either for biosynthesis (assimilatory reductions) or for energy metabolism (dissimilative reductions) purposes. What is the role of the inorganic compound that is reduced in dissimilative reductions?

As terminal electron acceptors for anaerobic respiration

Penicillin and other β-lactam antibiotics inhibit cell-wall synthesis. What makes them effective at killing bacterial cells?

Bacteria are generally hypertonic relative to their environment, so they burst when their cell wall is weakened by the action of these antibiotics.

How is bacterial translation different from eukaryotic translation?

Bacteria can begin translation before transcription has terminated.

Why is visualization not sufficient to properly identify bacteria?

Bacteria have a limited set of shapes and many unrelated bacteria share the same shape.

Elderly individuals have greater proportions of ________ in their gut microbiota compared with younger individuals.

Bacteroidetes

Actinobacteria are called high GC Gram positive bacteria. What does this tell you about them?

Because guanine bonds to cytosine with 3 hydrogen bonds, compared with only 2 hydrogen bonds for adenine-thymine pairs, the DNA will have a relatively high melting point compared with low GC bacteria.

most common probiotics?

Bifidobacterium species

Which type of transposon would contain a gene for transposase?

Both simple and complex transposons

Bacterial conjugation is often referred to as bacterial sex. Why is this term inaccurate?

Conjugation does not result in the formation of new offspring

How do complex transposons differ from simple transposons?

Complex transposons code for additional genetic elements, such as antibiotic resistance genes; simple transposons only code for the transposase gene essential for the tranposon itself.

_____ breaks down hydrogen bonds during replication

DNA helicase

During DNA replication, Okazaki fragments are linked together by ________, an enzyme that creates phosphodiester bonds between nicked fragments of DNA.

DNA ligase

Which enzyme joins the gaps between synthesized DNA fragments of the lagging strand?

DNA ligase

_____ seals the gaps between the pieces of DNA in the lagging strand

DNA ligase

_____ builds new strands of DNA

DNA polymerases

List the steps of the central dogma of molecular biology in the correct order.

DNA → RNA → protein

In the process of transcription, promoters are specific sequences of ________ that are recognized by ________.

DNA/sigma factors

When an individual has severe diarrhea, as can occur with cholera, rehydration solution with glucose, salt, sodium bicarbonate, and potassium chloride can be administered. Why is it important to use a solution like this rather than simply giving the individual water?

Diarrhea causes the loss of electrolytes, not just fluids. It is important to replace the electrolytes as well as the water.

In most salt lakes, which microbial group is the major oxygenic phototroph?

Dunaliella, a eukaryotic alga

Why will the microbiota in the vagina of a woman of reproductive age differ from that of the same woman before puberty and after menopause?

During the reproductive years, the vagina contains significant amounts of glycogen that is fermented by Lactobacillus acidophilus to produce lactic acid, creating an acidic environment. Glycogen is absent before puberty and after menopause.

tRNA is released from the ribosome at the ________ site.

E

Membrane transport proteins are required for which mode(s) of antibiotic resistance?

Efflux pumps, beta-lactamases, and modification of porins all utilize membrane transport proteins.

Why do all enzymatic reactions need activation energy?

Energy is required to disrupt a substrate's stable electron configuration.

Some viruses, especially animal viruses, have an envelope surrounding their nucleocapsid. This envelope may have viral proteins embedded in it. Why are the viral proteins more readily recognized and targeted by the immune system than the envelope?

Enveloped viruses are often coated with animal cell membrane as they leave the cell. This membrane is a major component of the viral envelope. The viral proteins are more readily recognized by the immune system, as they are more distinct from the materials normally found in and on the cells. However, the envelope can contain several types of viral components as well.

Which U.S. government agency monitors water utility reports?

Environmental Protection Agency

Why are enzymes important to biological systems?

Enzymes decrease the amount of activation energy required for chemical reactions to occur.

Which archaeal phylum contains many extreme halophiles, methanogens, some marine hyperthermophiles, and Thermoplasma?

Euryarchaeota

Food that is heavily salted or candied does not need to be refrigerated. Why not?

Extremely concentrated solutions are very hypertonic and therefore desiccate microorganisms. As a result, there is no need for lower temperatures through refrigeration to slow growth.

Why does FADH2 yield less ATP than NADH?

FADH2 electrons enter the electron transport chain at a lower energy level.

What is the difference between a facultative anaerobe, an aerotolerant anaerobe, and an obligate anaerobe?

Facultative anaerobes can use oxygen, producing more ATP than without it. Aerotolerant anaerobes are unaffected by oxygen, but cannot use it. Obligate anaerobes require an oxygen-free environment to survive.

Microbes capable of fermentation are often used in food. What is the main function of fermentation for the microbes?

Fermentation regenerates NAD+ so that glycolysis can continue.

Part complete A microbiologist wants to study the virus particles from a urine sample, but not any bacteria that might be present. How can the bacteria be eliminated without harming the viruses?

Filter the sample with a 0.2 ïm pore filter.

How is generalized transduction different from specialized transduction?

Generalized transduction is initiated during lytic cycle of a virulent bacteriophage; specialized transduction is initiated during the lysogenic cycle of a temperate bacteriophage.

It is hypothesized that early photosynthesis was anoxygenic. Think about the role of oxygen in photosynthesis as carried out by green plants, green algae, and cyanobacteria (as opposed to modern organisms that use anoxygenic photosynthesis). What would have been different in anoxygenic photosynthesis (or is different in modern organisms that use anoxygenic photosynthesis)?

Green plants, green algae, and cyanobacteria split H2O to replace an excited electron in noncyclic photophosphorylation. Oxygen is released into the atmosphere. In anoxygenic photosynthesis, a different molecule (such as H2S) is split and a different product (such as sulfur) is released.

Halobacteria tend to have fewer hydrophobic amino acids in their proteins than other bacteria. Why?

In a highly saline environment, hydrophobic proteins have an increased likelihood of precipitating out of solution.

Horizontal gene transfer refers to the transfer of genes from one organism to another, as occurs during conjugation between bacteria. How does this differ from vertical gene transfer?

In horizontal gene transfer, genes are transferred from one mature adult organism to another. In vertical gene transfer, genes are transferred from adults to offspring.

How would one increase the concentration of a particular polypeptide in a cell?

Increase the level of transcription

________ are common features of transcription termination sequences in all three domains of life.

Inverted repeats

How does the protozoan Trypanosoma evade detection by the immune system?

It can change the surface antigens frequently, preventing the immune system from tracking it.

Important for adherence of bacteria to host tissues

adhesins slime layer capsule

true statement about fermentation

It is an alternative way to return electron carriers to their oxidized state.

You discover a new type of archaeon. After analyzing its genome in the lab, you realize that it is missing the genes needed for glycolysis. What might you guess about this organism based on that information?

It is an obligate symbiont.

What is the fate of the prophage during the lysogenic stage?

It is copied every time the host DNA replicates.

benefit of studying the human microbiome

It may allow for more finely targeted probiotics.It may allow for the development of personalized medical treatments.It may allow for increased recognition of disease biomarkers.

In which direction does the replication fork move?

It moves ahead of the newly synthesized DNA.

What is the role of pyruvic acid in fermentation?

It takes the electrons from NADH, oxidizing it back into NAD+.

What does the minimum inhibitory concentration (MIC) of a chemical tell you?

It tells you the lowest concentration of the chemical that is needed to inhibit the growth of a specific microorganism.

Iron is considered an essential element for many bacteria. Based on the animation, how would lack of iron affect energy production of a bacterium?

Lack of iron would mean lack of heme, and thus lower amounts of functioning cytochrome proteins. This would mean lower energy yields.

_______ is a bacterial pathogens is found in aquatic environments and is commonly present in air conditioning systems

Legionella pneumophila

Antifungal medications are often used topically. Why is this the case?

Like human cells, fungal cells are eukaryotic. To develop systemic fungal medications requires finding specific characteristics of fungal cells that can be targeted, such as the ergosterol in fungal cell membranes.

Endotoxins are also known as

Lipid a

types of metabolism found in archaea

aerobic respiration chemolithotrophy chemoorganotrophy

Glycolysis produces energy in the form of

NADH and ATP

Compared with an endotoxin, would a bacterial exotoxin generally be more likely to function after it had been significantly heated?

No, because exotoxins are heat-labile and less resistant to heating than endotoxins.

true statement about evolutionary origin of all 3 domains

all domains evolved from a shared ancestor: LUCA

_______ is commonly transmitted by the fecal-oral route.

Norovirus

It is hypothesized that early photosynthesis was anoxygenic. If so, what was the effect of the appearance of organisms using oxygenic photosynthesis?

Organisms using oxygenic photosynthesis release oxygen into the atmosphere, causing an increase in the oxygen in the atmosphere and allowing for the development of aerobes.

During the initiation step of translation, the fMet charged tRNA assembles in which site of the ribosome

P site

Bacteria that are resistant to sulfonamide have enzymes that have a greater affinity for what?

PABA

Why would an efflux pump for penicillin located on a bacterial cell membrane not be effective at providing resistance to the drug?

Penicillin disrupts the cell wall, which is located outside of the cell membrane.

You want to know whether the virulence genes present in Bordetella pertussis are evolutionarily related to genes in the less pathogenic species Bordetella bronchiseptica or if the virulence genes were acquired via horizontal gene transfer. What characteristic(s) would you compare to answer this question?

Percentage of GC content and codon usage

Why does the structure of plant and bacterial cells illustrate the reason for having few enveloped viruses that infect these cells?

Plant and bacterial cells contain cell walls that limit the virus from budding out and obtaining the envelope.

How are plasmids different than chromosomes?

Plasmids contain genes that are NOT essential for cellular growth and replication.

Why must primase be used before DNA polymerase when replicating DNA?

Primase provides an RNA primer with a 3' end on which DNA polymerase can act.

What is meant by substrate-level phosphorylation?

Production of ATP by transferring phosphates directly from metabolic products to ADP

explain the endosymbiont hypothesis

Prokaryotes capable of cellular respiration and prokaryotes capable of photosynthesis took up residence in larger prokaryotes, forming obligate mutualisms. The prokaryotes capable of cellular respiration evolved into mitochondria and the prokaryotes capable of photosynthesis evolved into chloroplasts.

Which phylum harbors the most functional diversity observed and also has the most cultured representatives?

Proteobacteria

How does the proton gradient help ATP synthase to make ATP?

Protons move from outside the membrane to inside the membrane.

The first catalytic and self-replication biological molecule was most likely

RNA

If the hypothesis stating viruses evolved prior to living organisms on Earth is TRUE, the first type of viruses in the world were likely

RNA viruses

Reverse transcriptase is a(n)

RNA-dependent DNA polymerase.

The enzyme replicase is a(n) _________.

RNA-dependent RNA polymerase

What is one piece of evidence that supports the RNA world hypothesis?

RNAs can have catalytic activity.

If you wanted to culture a methanogen, what would be one of the steps you would have to take?

Removing all O2 from the headspace of the culture.

How does replicative transposition differ from cut-and-paste transposition?

Replicative transposition results in the transposon being copied to a new location; in cut-and-paste transposition, the entire transposon moves to the new location.

How might efflux pumps increase antibiotic resistance in bacteria?

Resistant bacteria can have more efflux pumps, and can have less specific efflux pumps.

Some organisms are capable of using aerobic respiration or anaerobic respiration but use aerobic respiration preferentially. Why is aerobic respiration favored?

Respiration with oxygen as a terminal electron acceptor generates more energy than respiration with other terminal electron acceptors.

Chemical reactions involving ________ have been proposed as energy-yielding reactions for the earliest organisms on Earth.

S and H2

Which finding is most surprising from Griffith's experiments?

S strain cells are isolated from the blood of mice infected with heat-killed S strains and live R strain

A retrovirus has a genome that consists of __________.

SSRNA

Considering that they require an oxygen-free environment, how do obligate anaerobes survive in the human body?

They are able to survive in places where aerobic organisms quickly use the available oxygen. They can also survive in areas with impaired blood flow (reducing oxygen availability).

Part complete Salmonellosis is most frequently caused by

Salmonella enterica serovars Typhimurium and Enteritidis.

How is simple diffusion different from other types of passive transport?

Simple diffusion does not require a permease.

What is a specific advantage of using small subunit ribosomal RNA (SSU rRNA) gene sequences for phylogenetic analysis compared with DNA sequences?

Standard primers exist for SSU rRNA gene sequences, including universal primers.

virulence factors would be found in Staphylococcus aureus

Staphylokinase

How are superantigens different from other types of exotoxins?

Superantigens cause an overstimulation of the host immune system.

You experimentally change the DNA sequence directly upstream of a start codon of an operon in E. coli to investigate the function of this region of DNA. Analysis reveals that after the change, the same amount of mRNA is made from the operon, but there are very few proteins made from the operon. What is the most likely function of the DNA sequence that you changed?

The DNA sequence likely functions as a ribosome-binding site.

What most likely explains the recovery of live S strain cells from a mouse injected with heat-killed S strain mixed with live R strain cells?

The R strain picked up the S strain DNA, enabling it to produce a capsule

What is meant when a bacterium is said to become "resistant" to an antibiotic?

The bacterium is neither killed nor inhibited by the antibiotic

How does a capsule help certain bacteria evade detection by the immune system?

The capsule is composed of polysaccharides that are similar to those found in the host; thus, the immune system does not recognize it as foreign.

What will happen to a cell that is placed in a solution containing a high concentration of sugar, a molecule that cannot pass across the cell membrane?

The cell will lose its interior water, causing it to shrivel up and possibly die.

What must occur for bacterial conjugation to take place?

The cells must come into contact with each other.

Why is no energy required in passive transport?

The concentration gradient drives the movement.

Reheating food to a temperature sufficient to kill bacteria is helpful in making food safer. However, is there a way that one can get food poisoning despite food having been reheated?

Toxins may be heat-stable above temperatures that kill bacteria.

Microbial species have a core genome and a pan genome. What is the difference between the two?

The core genome is a set of genes shared by all members of a species, while the pan genome includes the core genes as well as genes that are not shared by all members.

Why is reduction the term used to describe the gain of an electron?

The electron acceptor's net charge decreases.

If the gene that codes for transposase is mutated so that it no longer produces the fully functional enzyme, how will the insertion sequence be affected?

The insertion sequence would lose its ability to effect its own movement.

Plaque assays are often used to estimate the number of virions in a sample of a particular volume (the titer). The count is given as plaque-forming units. Which of the following is NOT generally a concern that must be considered in evaluating the results of plaque assays?

The largest problem is that single viruses may create multiple plaques, resulting in overestimates of the number of viruses present.

How is the pan genome differentiated for a given species?

The pan genome is in addition to the core genome and only found in some members of a given species.

What makes an insertion sequence different from other DNA sequences found in a cell?

They are capable of effecting their own movement from one location to another on DNA.

How do stabilizing proteins work on the DNA?

They bind to the single-stranded DNA.

How do fibrinolysins enhance a pathogen's virulence?

They break down fibrin proteins that are involved in clot formation, allowing the cells to penetrate deep into damaged skin.

explains why promoters for the same sigma subunit do not have identical sequences

The sequences within the promoter region at -10 and -35 are the most important for recognition by the sigma subunit.

Why is the DNA synthesis of the lagging strand considered discontinuous?

The synthesis is moving in the opposite direction from the replication fork

How is anaerobic respiration different from aerobic respiration?

The terminal electron acceptor in anaerobic respiration is not oxygen.

________ is the time needed to kill all the bacteria in a particular culture at a certain temperature.

The thermal death time

How is translation terminated?

When a protein called a release factor enters and binds to the A site

Highly alkaline environments, like those in which haloalkaliphiles are found, are best described by which of the following statements?

These environments contain relatively low concentrations of hydrogen ions.

Why are flowcharts useful for dichotomous keys?

They allow the researcher to visualize relationships between different bacteria

How are immune cells able to detect foreign pathogens?

They are able to detect structures on the surfaces of foreign cells that are not found in the host.

What is the hallmark of dichotomous keys?

They consist of a series of paired statements, in which only one statement of each pair applies to a given organism.

What is the function of the connector proteins?

They link the leading strand DNA polymerase and the lagging strand DNA polymerase together.

Why are ATPases associated with active transport proteins?

They provide transport proteins with the energy needed to pump molecules against their concentration gradients.

What is unique about transduction compared to normal bacteriophage infection?

Transduction transfers DNA from the chromosome of one cell to another.

What is the hallmark of all horizontal gene transfers?

Transfer of DNA between organisms of the same generation

How does the proton motive force lead to production of ATP?

Translocation of three to four protons drives the F0 component of ATPase, which in turn phosphorylates one ADP into ATP.

Which of the following microorganisms actually grows inside the macrophage?

Tuberculosis bacterium

Part complete What is one difference between ubiquinones and cytochromes?

Ubiquinones are not made of protein; cytochromes are

Which transport protein employs transporters that move molecules only in one direction?

Uniport and Symport

How is osmosis different from simple diffusion?

Water movement is driven by the concentration of solutes rather than its own concentration.

Isolating a bacterium of the ________ class would be of high impact due to it only having one cultured representative.

Zetaproteobacteria

a recombinant cell is

a cell that receives DNA from an outside source and incorporates it into its own

An endogenous pyrogen is

a chemical produced by a host's own immune system that causes fever.

Homologous

a gene that is related in different species by being inherited from a common ancestor

Paralogs

a gene that is related in different species by being inherited from a common ancestor and that has a different function (occurs via gene duplication)

archaea are

a group of diverse microorganisms that inhabit almost every environment on Earth, including the colon of humans and other mammals.

Which condition favors a lysogenic life cycle in bacteriophages?

a lack of host bacteria

What kind of bond is formed when two amino acids join together?

a peptide bond

An open reading frame (ORF) encodes for

a polypeptide

Lysogenic viral DNA integrating into the host genome is referred to as

a prophage

A reaction that involves the transfer of electrons from one molecule to another is referred to as

a redox reaction

The mouse model of obesity suggests that __________ is linked to increased body mass.

a reduction in Bacteroidetes

definition of polycistronic mRNA

a single piece of mRNA that contains the transcript for multiple genes.

What is the intermediate product formed by pyruvic acid during alcoholic fermentation?

acetyldehyde

________ dominate the infant gut microbiota.

actinobacteria

The portion of an enzyme to which substrates bind is referred to as the

active site

A gene for a specific trait may have more than one form, allowing the trait to vary. These sequence variants of a gene are called

alleles

Nonspecific permeases

allow a variety of molecules to cross the cytoplasmic membrane.

An operon is a useful genetic element, because it

allows coordinated expression of multiple related genes in prokaryotes

The structure and function of a protein are determined by its ________ sequence.

amino acid

DNA participates in protein synthesis through

an RNA intermediate

The reactions involved in producing larger compounds from smaller compounds is called

anabolism

The sum of all biosynthetic reactions in a cell is known as

anabolism

Which of the following are the hosts for most enveloped viruses?

animals

Linking an ORF with a specific function is an example of gene

annotation

Sodium and potassium ions need to be pumped simultaneously against their concentration gradients. Which one of the transport proteins would be most effective at this?

antiport

Which type of active transport protein uses one protein to pump two different molecules?

antiport and symport

The use of chemical agents directly on exposed body surfaces to destroy or inhibit vegetative pathogens is

antisepsis

The major distinguishing difference between antiseptics and disinfectants is __________.

antiseptics can be used on living tissue

Biochemical tests....

are the main methods used to identify unknown bacteria

Nitrifying Thaumarchaeota can outcompete nitrifying bacteria in acidic environments because Thaumarchaeota

are well-adapted to very low NH3 concentrations.

In which stage does formation of mature viruses occur?

assembly

The disk-diffusion test is used for

assessing antimicrobial activity.

AT-rich DNA will denature/melt

at a lower temperature than GC-rich DNA.

A pathogen must __________ in order for it to cause disease.

attach and multiply

For bacteriophages and animal viruses ________ is the step in the viral life cycle that determines host cell specificity.

attachment

The decrease or loss of virulence of a pathogen is referred to as

attentuation

A chemical that denatures proteins is most likely to be classified as a(n) ________ agent.

bactericidal

For organisms to be considered members of the same species, they must __________.

be genetically and phenotypically cohesive

According to the RNA world hypothesis, which of the following was the correct sequence of developments?

biological building blocks (e.g., amino acids, sugars, and nucleosides), then RNA (including catalytic and self-replicating RNA), then protein synthesis, then DNA, then lipid bilayers surrounding early cellular life

The host DNA is usually degraded during which stage?

biosynthesis

Polycistronic transcription units are common in

both Archaea and Bacteria.

Which of the following could be used to distinguish between Klebsiella and Escherichia?

butanediol fermentation

Competent cells are cells that

can take up DNA from their surrounding environment and integrate it into their own chromosomes by recombination.

What component(s) make up the structure of a virion?

capsid and genome

An outer coat consisting of a dense, well-defined polymer layer surrounding a cell and used in attachment is called a

capsule

A chemoorganotroph and a chemolithotroph in the same environment would NOT compete for

carbon

Whether an organism is classified as a photoheterotroph or a photoautotroph depends on its

carbon source

_______ pathways are essential for microorganisms to obtain energy, because biosynthetic reactions for cellular growth generally require energy input.

catabolic

Where does the energy required for anabolic reactions come from

catabolic reactions

The degree of susceptibility a food has to microbial activity is determined by its

chemical characteristics, physical characteristics, and water content

The process of generating ATP using a proton gradient is referred to as

chemiosmosis.

Autotrophs are always __________.

chemolithotrophs

Some Archaea are --------- and use organic compounds as electron donors for energy metabolism.

chemoorganotrophs

The critical step in making water safe to drink is_____-

chlorination.

The enzyme transposase may be coded for by insertion sequences on a

chromosome, phage or plasmid

Genes that are encoded for polymerases, gyrases, ribosomal proteins, and other proteins essential to replication, transcription, and translation are present on

chromosomes

For a carbon source, chemoorganotrophs generally use compounds such as

citrate, fumerate, and glucose

A triplet of bases on an mRNA molecule is known as a(n)

codon

______ usage varies from one organism to the next.

codon

Gram-negative, rod-shaped bacteria that are facultative anaerobes, are non-spore formers, and ferment lactose to acid and gas are __________.

coliforms

Clostridium perfringens causes gas gangrene, a serious infection of the muscle tissues that can lead to amputation. Clostridium are Gram-positive endospore-formers and obligate anaerobes that are killed when exposed to oxygen. Which of the following virulence factors would be most helpful to this organism in establishing an infection?

collagenase, an enzyme that destroys collagen, which is a major protein of connective tissues

Obligate anaerobes are likely to be found in the __________.

colon

Cellular receptors may be composed of

combinations of proteins, carbohydrates and or lipids

In general, prokaryotic genome size is linked to its metabolism and interaction with the environment. Which type of prokaryote typically has the smallest genome?

endosymbiont

Horizontal gene transfer

complicates the construction of phylogenetic trees and the interpretation of specific traits in relation to evolution.

Plasmids function in bacterial cells to __________.

confer to a cell additional genetic traits that are needed only under certain circumstances

Horizontal gene flow is accomplished in prokaryotes by __________.

conjugation, transduction and transformation

When a transposon is cut from one location in genome and pasted into a new location, it is called __________.

conservative transposition

A transducing phage

contains fragments of the host chromosome instead of the viral genome.

The most common route of transmission of Salmonella enterica typhi worldwide is through

contaminated water

Legionella pneumophila is generally transmitted by

contaminated water in coolers, pools and domestic water systems

What has occurred when organisms share a trait that was NOT inherited from a common ancestor?

convergent evolution

vibrio

curved rods

Eukaryotic Signature genes

cytoskeleton genes membrane remodeling genes

An exotoxin that has the ability to kill or damage host cells is referred to as

cytotoxin

Fecal coliforms appear ______ on EMB agar while non fecal coliforms appear _____

dark blue/black red

What characteristic of DNA allows two connected DNA polymerases to synthesize both the leading and lagging strands?

dna is flexible

Most prokaryotic genomes are ....

double-stranded circular DNA.

Gene duplication is essential to organisms because __________.

duplicate genes can evolve into new genes without losing the functionality of the original gene

Which is one major difference between anaerobic and aerobic respiration?

electron acceptor

The early energy reactions used hydrogen, which is a powerful

electron donor

The earliest photosynthetic microbes, before the cyanobacterial lineage developed, oxidized substances other than water. What was produced by these microbes instead of oxygen?

elemental sulfur

In Bacteria, a chromosome can be distinguished from a plasmid, because a chromosome is a genetic element that

encodes for essential functional genes

____ is the functional unit of genetic information

gene

ortholog

gene that is related in different species by being inherited from a common ancestor and that has a the same function

The size and shape of viral particles is largely governed by the size and packaging of the viral

genome

Knowledge of an organism's ______ yields important clues to how an organism functions and its evolutionary history.

genome sequence

the study of the entire genetic makeup of an organism.

genomics

The Embden-Meyerhof-Parnas pathway is another name for

glycolysis

monophyletic

group of organisms in a phylogeny that have a common ancestor

Staphylococcus aureus is a common causative agent of foodborne disease because it

grows on many foods, is present in some humans that work in food processing, and produces several heat-stable enterotoxins.

Horizontal gene transfer

is common and may sometime occur between unrelated organisms.

Which of the following is an important factor in the development of dental caries?

high sugar diet

The process in which related DNA sequences from two different sources are exchanged is called

homologous recombination

Proteobacteria include many different classes of bacteria with great diversity; however, many share similar metabolic characteristics. What mechanism can best explain this similarity?

horizontal gene transfer

The pan genome of a microbial species is constantly changing because of

horizontal gene transfer

Regarding the viral membrane of an enveloped virus, the lipids are derived from the ________, and the proteins are encoded by ________.

host's cell membrane / viral genes

summarizes why housekeeping genes can be used in multilocus sequence typing (MLST)

housekeeping genes are less likely to be under environmental selection

enzyme that breaks down the "glue" that holds cells together

hyaluronidase

The two strands of the DNA double helix are held together by

hydrogen bonds between nucleotide bases.

Where would one find an uncharged tRNA molecule in a ribosome?

in the P and E sites

viral replication is

independent of the host cell's DNA but dependent on the host cell's enzymes and metabolism

The presence of specific ________ signals that a given water source might be contaminated with pathogens.

indicator organisms

When a virus enters a host cell in which it can replicate, the process is called a(n)

infection

Viral replication occurs

intracellularly

Irradiation of food uses

ionizing radiation

Your laboratory supervisor has given you a plastic petri dish filled with soil to sterilize using radiation. What type of radiation will you use?

ionizing radiation

The use of amino acids to make proteins

is an example of anabolism

Integration of linear transforming DNA into the chromosome

is catalyzed by the RecA gene.

In metabolism, energy that is not used

is given off as heat

Why is a release of endotoxin into the bloodstream potentially deadly?

it can lower the blood pressure and cause the patient to go into shock

Supercoiling is important for DNA structure, because

it condenses the DNA so that it can fit inside the cell.

if a substance is reduced

it gains electrons

What is the fate of the NAD+ newly regenerated by fermentation?

it returns to glycolysis to pick up more electrons

The gut microbiota is relatively stable over long time periods in healthy adults, suggesting ______

its highly evolved role in the human body.

Which strand will require more RNA primers to complete synthesis?

lagging strand

The most heavily colonized human organ by bacteria is the ________, containing 1011-1012 bacterial cells per gram.

large intestine

Which DNA strand is synthesized continuously?

leading strand

________ formed the semipermeable membrane-like surfaces for the earliest life forms.

lipid bilayers

ATP-binding cassette transport systems have high substrate affinity and thus help microorganisms survive in _______

low nutrient environments.

Halobacterium salinarum and certain other extreme halophiles carry out light-driven synthesis of ATP under what condition?

low oxygen concentrations

Some bacteriophage possess an enzyme similar to ________, which makes a small hole in the bacterial cell wall, allowing the viral nucleic acid to enter.

lysozyme

________ in saliva cleaves glycosidic linkages in the peptidoglycan that is present in bacterial cell walls, weakening the wall and potentially causing cell lysis.

lysozyme

A ________ infection results in death of the host cell.

lytic

A virus that kills its host is said to be

lytic or virulent

_____ can be translated into a protein

mRNA

The codon on the ________ matches with the anticodon on the ________ to direct the addition of the correct amino acid to the growing polypeptide chain.

mRNA/tRNA

Genes encoding compounds such as pyruvate, acetyl-CoA, fructose-6-phosphate, oxaloacetate, and other small organic compounds could be part of a(n)

metabolome

: the study of all intermediates and small molecules produced by reactions within an organism.

metabolomics

The total genetic complement of all cells within a microbial community is called a(n

metagenome

the study of all of the genetic material of all organisms in a particular habitat.

metagenomics

methanogens produce_______

methane as a part of their energy metabolism

Food poisoning generally results from the ingestion of food containing ________

microbial toxins.

Viral structural proteins and proteins involved in the release of new viral particles that are synthesized after genomic replication begins would be considered __________.

middle or late proteins

Two eukaryotic organelles that are hypothesized to be the result of endosymbiosis are the ________ and the ________.

mitochondria and chloroplasts

A bacterium that uses CO2 as an electron source, but cannot use it as a carbon source, is considered a _____

mixotroph.

Which of the following can be used as a final electron acceptor for aerobic respiration?

molecular oxygen

Once equilibrium is reached,

molecules move, but there is no net movement in a particular direction.

The topoisomerase called ________ introduces positive supercoils in DNA, which stabilizes DNA and prevents the DNA helix from denaturing at high temperatures.

reverse DNA gyrase

While not all members of ________ are pathogenic, two medically relevant species cause meningitis and gonorrhea in humans.

neisseria

A patient who has been hospitalized with uncontrolled muscle spasms has probably been infected with bacteria that secrete a(n)

neurotoxin

In Bacteria, the most common oxidized form of nitrogen is ________ and of sulfur is ________.

nitrate / sulfate

Flour and sugar are classified as ________ foods.

non-perishable

The most common source of individual foodborne botulism outbreaks are due to consumption of

nonacid, home-canned vegetables

Stop codons are also called ________ codons.

nonsense

Nearly 90% of all foodborne illnesses are associated with __________.

norovirus, Salmonella, Clostridium perfringens, and Campylobacter jejuni

In all cells, genes are composed of

nucleic acids.

When packaged in the virion, the complete complex of nucleic acid and protein is known as the virus

nucleocapsid

eukaryotic transcription occurs in the

nucleus

______ are formed on the lagging strand during DNA synthesis

okazaki fragments

The human microbiome contains all

organisms present in and on the body

Acidophiles

organisms that can be found growing at pH values below 4

Hyperthermophiles

organisms that thrive in environments above 80 degrees C

Thermophiles

organisms that thrive in environments between 50 and 60 degrees C

Halophiles

organisms that thrive in salt concentrations of more than 25%

Genome assembly relies on

overlap of a large number of short sequences

Enteric bacteria are a subgroup of Gammaproteobacteria that can be characterized by which of the following test results?

oxidase-negative and catalase positive

Fermentation occurs when there is no usable external electron acceptor (like O2) available for respiration. Fermentation products are made following glycolysis as a result of reactions that __________.

oxidize NADH so that NAD+ can be reused again in glycolysis

In aerobic respiration, the final electron acceptor is

oxygen

The best term to describe the general process by which microorganisms cause diseases is known as

pathogenesis

In which stage is the viral DNA introduced into the cell?

penetration

Which antibiotic is overcome by beta-lactamases?

penicillin

Clostridium perfringens food poisoning leads to diarrhea, because the

permeability of the intestinal epithelium is altered by the toxin it produces.

A cell that allows the complete replication cycle of a virus to take place is said to be a

permissive host

The process by which white blood cells ingest and kill bacteria is called

phagocytosis

Polyphasic taxonomy uses methods that include

phenotypic, genotypic and phylogenetic methods

The evolutionary history of a group of organisms is called its ________ and it is inferred from ________.

phylogeny / nucleotide sequence data

When a solution composed of bacteria and infectious virions are mixed and spread on an agar plate, ________ form where viruses lyse the host cells.

plaques

result of translation

polypeptide

The order Lactobacillales within Firmicutes are also called the lactic acid bacteria, because these bacteria

produce lactate

Weight gain and obesity may be partly caused by certain gut microbial communities that

produce more volatile fatty acids by fermentation.

Viral proteins are categorized as early, middle, and late. Early proteins typically are necessary for

production of viral mRNA and copying the viral genome

What is the initial target of RNA polymerase?

promoter

Exotoxins are ________, but endotoxins are ________.

proteins / lipopolysaccharide-lipoprotein complexes

Gene function is annotated based on homology between the ORFs of a genome and proteins whose function has been proven experimentally. What "-omic" approach could help us determine the function and structure of proteins encoded by uncharacterized ORFs?

proteomics

the study of all of the proteins produced by an organism.

proteomics

ribosomes contain

rRNA

A key concept in evolution is that all mutations are

random

The principle behind salt or sugar preservation is to

reduce water activity (aw).

Deltaproteobacteria share which of the following characteristics?

reduction of iron, sulfate and sulfur

Psychrotolerant microorganisms can survive and grow at

refrigeration temperatures.

Activation energy is the energy

required for a chemical reaction to begin.

The process of synthesizing proteins involves translating one "language," nucleic acid sequences, into another "language," amino acid sequences. The cellular component that does the actual translating from codons to amino acids is the __________.

tRNA

_______ carry amino acids to the ribosomes

tRNA

The genome of a _____ can replicate along with the host genome during lysogeny.

temperate phage

The rate of contaminant microbial growth during the exponential phase in food depends on

temperature, nutrient value, and water content.

RNA polymerase is guided by the

template strand of DNA

When a transducing phage interacts with a new host cell,

the DNA from the previous host can recombine with the new host chromosome.

How does the ribosome know if the entering charged tRNA is correct?

the anticodon on the tRNA base pairs to the codon on the mRNA

What characteristic of the S strain allows it to evade the immune system of the mice?

the cells have a capsule

The proton motive force (PMF) is driven by __________.

the difference in charge across the plasma membrane with protons outside the membrane

During an oxidation reaction,

the donor molecule loses an electron and becomes oxidized.

Gene duplication is thought to have had a significant influence on the evolution of microbes because __________.

the duplicated gene can be mutated, possibly leading to a useful new gene function or product, while the original copy can still perform its original (and possibly essential) genetic function

LUCA

the last organism prior to the divergence of bacteria and archaea

true statement about methanogenic and extremely halophilic archaea

the methanogens are obligate anaerobes; the extreme halophiles are mostly obligate aerobes

Functional analysis of the genome of a prokaryote shows that 20% of the genome is for metabolism, 1 % for biosynthesis of amino acids, 8% for peptide ABC transporters, and 2% for replication. What can you determine about the environment in which this organism lives?

the organism lives in an environment rich in organic material particularly amino acids and proteins

Microorganisms were probably restricted to the oceans and subsurface environments until

the ozone layer was made.

Microbes that thrive in acidic environments seem to have "cost free" ATP energy available to them due to the pre-existing H+ gradient across the cytoplasmic membrane. However, this is not entirely true because __________.

the protons entering the cell must be consumed to prevent the cytoplasm from becoming too acidic; therefore electrons are required as H+ are combined with O2 to form water

The Baltimore scheme used to classify viruses is based on ________.

the relationship of the viral genome to its mRNA

What would be the fate of a lytic bacteriophage if the host cell died prior to the assembly stage?

the virus would not be able to infect a new host

Despite ether-linked lipids being a hallmark of the Archaea, the thermophilic sulfate-reducing bacteria in ________ also contain ether-linked lipids, which suggests they may be more closely related to Archaea than many other groups in Bacteria.

thermodesulfobacterium

The genes for 16S rRNA are used to determine genetic relatedness amongst microbes because __________.

these highly conserved genes are of adequate length to show deep relationships

true statement regarding redox reactions

they involve an oxidation reaction coupled with a reduction reaction

Most Alphaproteobacteria are oligotrophic, meaning __________.

they preferentially grow in nutrient poor environments

How are viruses different from cells?

they require a host in order to reproduce

the key characteristic of ______ is the ability to sequence long, single molecules of DNA.

third-generation sequencing

A researcher wanted to determine the LD50 (lethal dose that kills 50% of the infected hosts) for a newly isolated bacterial pathogen. Mice were inoculated with diluted cultures containing between 101 and 107 cells. After two days, all of the mice had died EXCEPT for the uninoculated controls. Which of the following is the most likely explanation?

this pathogen is highly virulent in mice

In E. coli, the consensus sequence for the Pribnow box (the -10 sequence) is TATAAT. Therefore, __________.

this will be the strongest -10 promoter sequence

The most abundant genes in prokaryotic genomes are

those involved in metabolism

In complementary base pairing of DNA, adenine pairs with ________ (or ________ in RNA) and cytosine always pairs with ________.

thymine / uracil / guanine

Early and late viral proteins are classified according to their relative

time of synthesis following host infection

The concentration of infectious plaque forming units (pfu) per volume of fluid is known as the viral

titer

What is the function of the structural elements of a virus?

to package and protect the viral genome

the study of all of the RNA produced by an organism.

transcriptomics

Which of the following is an example of horizontal gene transfer in bacteria?

transduction, conjugation and transformation

Increasing genetic variability by the uptake of DNA from the environment is __________.

transformation

The uptake of free DNA from the environment is referred to as ________, while the transfer of DNA with cell-to-cell contact is known as ________.

transformation/conjugation

most mobile DNA consists of

transposable elements

Each adenine-thymine base pair has ________ hydrogen bonds, while each guanine-cytosine base pair has ________ hydrogen bond(s).

two/three

Efflux pumps can be used to pump antibiotics out of a cell once they enter to protect the cell. This will be done against the concentration gradient of the antibiotic. Which of the active transports would most likely be used?

uniport

Chemolithotrophs that obtain electrons from donors, such as sulfide, --------to obtain energy as chemoorganotrophs.

use the same electron transport chains

A higher number of methanogenic Archaea are found in the guts of mice and humans who are obese. It is thought that the methanogens help to foster obesity by__________.

using H2, thus allowing further fermentation of substrates

The growth of viruses in a culture is described as a one-step growth curve, because

virion numbers show no increase during intracellular replication and can only be counted after the virions burst from the host cell

Certain traits that allow pathogens to create infection and cause disease are termed

virulence factor