microbiology final

The region of DNA where RNA polymerase binds to transcribe one or more genes is called?

Promoter

Which reaction would have the most negative dG?

ATP -> AMP

A methanogenic archaea living within a landfill produces methane gas that can be used for energy. Which pathway below is correct for energy production by this bacterium?

CO2 + H2 -> ETS -> CH4 + ATP

A methanogenic archaea living within a landfill produces methane gas that can be used for energy. Which pathway below is correct for carbon assimilation (biosynthesis pathway) by this bacterium?

CO2 -> Calvin cycle -> G3P -> glucose

______________ is the breakdown of complex molecules into smaller ones, while ____________ include reactions that build cell material.

Catabolism, anabolism

Which structure acts as both a barrier and a facilitator for the uptake of nutrients and other substances in the environment?

Cell membrane

The oxidation of inorganic nutrients and fixation of inorganic carbon defines a

Chemolithoautotroph

A soil bacterium oxidizes sugars and other organic compounds in the soil for energy and to build cell material. This type of microbe is a:

Chemoorganotroph

Directed movements toward or away from a chemical or physical signal are known as

Chemotaxis

Which of the following is a process that involves cell-to-cell contact to move a plasmid from a donor cell to a recipient cell?

Conjugation

The chloroplast of plants and algae are derived from what type of ancestral cell?

Cyanobacteria

In the figure below, which models DNA semiconservative replication, the numeral I points to ________, II points to ________, and III points to _______. (image)

New daughter strands; origin; replication fork

How does the reductive (reverse) TCA cycle participate in carbon fixation?

Some of the TCA reactions occur in reverse, assimilating small amounts of CO2

You are measuring growth in a bacterial culture. The number of viable cells remains constant, and when you check the medium, you find that the carbon source has been used up. In which phase of growth is the culture?

Stationary phase

In the blood brain barrier paper, the researchers added Evans blue tracer (looks red under fluorescent light) and DAPI stain which stains DNA (looks blue under fluorescent light) into the blood of the two groups of mice in the experiment. They then looked at sections of the brains of those mice. Some of the sections are shown in the images below. If there was no impact of the gut microbiome on the permeability of the BBB, what would you expect to see? (image)

The Evans blue dye would be limited in how much it permeated the BBB in both groups of mice

Hydrogen-generating reactions in Syntrophus and Syntrophomonas have delta G°' greater than but near 0. Can these organisms obtain energy from the formation of hydrogen (can those reactions go forward)?

Yes—but only if there is sufficient utilization of H2 to drive the process forward by the ratio of concentration of products to reactants

You are a microbiologist working on an infectious disease called Miceattack, which kills laboratory mice within 2-3 days. You suspect that the culprit is a bacterium called Bacillus killmicus; however, your colleagues are skeptical. You have already shown that the blood from the diseased mice have rod-shaped bacteria associated with it whereas blood from healthy mice do not. Following Koch's postulates, you have also isolated the bacterium in pure culture and shown that it is the same rod-shaped bacterium you see in the sick animals. What would you do next to convince your colleagues? (You must follow Koch's postulates)

You would reinject the isolated bacteria into healthy mice. If the previously healthy mice get sick, you would reisolate the bacterium in pure culture. If this is identical to the original bacterium, this is definitive proof that Bacillus killmicus causes Miceattack.

All of the following are used by prokaryotic cells for attaching to solid surfaces EXCEPT

endospore

The lipopolysaccharide of the outer membrane is of medical importance because it acts as a(n)

endotoxin

EF-G-GTP

enters the ribosome A site and with hydrolysis of GTP allows the 30S and 50S subunits to rotate

release factor 3

enters the ribosome A site to release the last tRNA and a release factor

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

entropy

DNA from a bacterium could not be added to the DNA of a eukaryote because they are different types of DNA molecules.

false

The first microscope ever built (by Robert Hooke) had a magnification power of 30X. This was high enough to be able to see most bacteria.

false

Malonyl-ACP is a key intermediate in which biosynthetic pathway:

fatty acid

Which of these techniques can be used to localize the DNA sequence at the origin of replication in a bacterial cell?

fluorescence microscopy

The ability of cohesive ends of DNA from different organisms to ________ constitutes the basis of recombinant DNA technology.

form complementary base pairs

Thinking about how a E. coli uses glucose and lactose, when both glucose and lactose are added to the growth medium, E. coli will likely have a growth curve that:

grows, levels off, and then grows again.

initiation factor 2

guides initiator tRNA to the P site of the ribosome

EE-Tu-GTP

guides tRNAs to the A site of the ribosome

You are a scientist at the university agricultural extension, and you get a call from Mr. Rawley from our story in the "Farmer's Dilemma." Mr. Rawley has questions and concerns about the construction of genetically modified organisms and says: "I just can't understand how a piece of bacterial DNA can become a permanent part of a corn cell. The DNA replication machinery of a plant cell won't replicate bacterial DNA... it is foreign! It is from another kingdom of life for gosh sakes! And another thing, there is no way that the transcription and translation machinery of a corn cell are going to generate a protein product by following instructions provided by a bacterial gene! I can smell a boondoggle from a mile away, and I'm telling you that this whole idea has major problems. It just can't work!! Sounds like a big waste of money to me." Question: Is Mr. Rawley correct that bacterial DNA cannot become a permanent part of a corn cell? Why or why not?

No, he is not correct because DNA sequences are universal, therefore bacterial DNA can be integrated into the corn DNA and "read" by corn cell DNA and RNA proteins

Which of the following is NOT an end product of fermentation?

pyruvate

During biofilm formation, as more and more cells bind to the surface, they begin sending signals to each other in a process called

quorum sensing

which of the following are required for the termination of translation

release factors

initiation factor 3

bind to the E site of the ribisome to prevent association of 30S and 50S subunits

During replication, the lagging strand is synthesized ________, while the leading strand can be synthesized ________.

discontinuously; continuously

resolution is the smallest distance by which two objects can be ________ and still be ________

separated, distinguished

A feature common to all cellular control mechanisms is

the ability to sense that something inside or around the cell has changed

The primary precursor molecule for lipid production is acetyl-CoA

true

tRNAs usually have a longer half life than mRNAs

true

Chemoorganotrophy is a term describing microorganisms that

use preformed organic compounds as a source of electrons and obtain energy through fermentations or organic respiration.

The sigma-70 factor of E. coli (RpoD) recognizes promoters for

"housekeeping" genes

As a researcher and medical doctor, you make several observations about the appearance of ulcers in patients that you see: 1. Bacteria are always associated with ulcers. 2. Ulcers are cured by antibiotics. 3. Cured only when bacteria are eradicated, otherwise chronic. Which of the following would be the correct application of Koch's postulates: Select one:

1) Certain bacteria are always associated with an ulcer and these are not found in individual without ulcers. 2) These bacteria have been isolated from patients with an ulcer and grown in pure culture. 3) When these bacteria are introduced to a new host an ulcer occurs. 4) The same bacteria are recovered from the individual with the ulcer.

In the figure below, which of the four fatty acids adds fluidity to a membrane?

C; cis bonds = more fluid

You are monitoring growth of a bacterial culture in your lab. If the final cell density (Nt) was 109 cells/ml and the starting cell density was (N0) 104 cells/ml, what is the number of generations (n) that occurred? Use the formula: n = 3.3 (log Nt - log N0)

16.5

Amino acids arise from multiple places from central carbon metabolism. The amino acids important in nitrogen metabolism arise from which key intermediate?

2-oxoglutarate

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 ________.

3; make carbon backbones of many lengths

Many restriction enzymes recognize palindromic sequences on double-stranded DNA. Among the following, which is a palindromic sequence?

5'-GGATCC-3'3'-CCTAGG-5'

In the figure below, which label represents the promoter? (image)

A

As a researcher and medical doctor, you make several observations about the appearance of ulcers in patients that you see: 1. Bacteria are always associated with ulcers. 2. Ulcers are cured by antibiotics. 3. Cured only when bacteria are eradicated, otherwise chronic. You decide to sequence the 16S rRNA gene from three bacterial isolates from patients with and without ulcers. The sequences are below. Which two are most closely related? A.TGCCTTCGGC B.TGCCGTGGGC C.TCGCATACTT

A and B

The significance of the Shine-Dalgarno sequence is that it is the site where

A ribosome binds to mRNA so that it can initiate translation

Which of the following types of molecules may passively diffuse across a membrane?

A small charge neutral molecule such as water

The DtxR protein is expressed under low levels of iron and is responsible for upregulating toxin genes in Cornyebacterium diphtheriae. The DtxR protein is considered a _____________ and must bind to the DNA by_______________.

Activator; recognizing the promoter for the toxin genes and fitting into the major groove of the DNA helix

In the blood brain barrier paper, the researchers were able to demonstrate the link between specific bacteria and metabolites from those bacteria on the permeability of the blood brain barrier by doing what?

Adding specific bacteria and separately adding specific metabolites to the experimental mice

Attenuation is a common strategy for gene regulation for what kind of genes?

Amino acid biosynthesis genes

The two main functional regions of a tRNA molecule are:

Anticodon region and 3' acceptor end

You have isolated a bacterium from a host spring that must transport potassium (K+) into the cell, but you do not find any channel proteins specific to potassium and when you add an inhibitor of the use of ATP you find that the organism can still transport potassium. However, you also find that sodium (Na+) is also moved out of the cell at this time and there is usually a high concentration of sodium in the cell. What is the mechanism of potassium transport in this bacterium?

Antiport

The first person to see bacteria under the microscope:

Antoni van Leeuwenhoek

A bacterium that you are characterizing has lipid structures like the one in the image below. What type of bacterium do you most likely have:

Archaea

All of the following are true statements about bacterial S-layers EXCEPT that they

Are found in all bacteria

Which of the following are synthesized via a branched pathway involving chorismate?

Aromatic amino acids

In the figure below what letter represents the Shine-Dalgarno sequence? (image)

B

Which energy carrier(s) also carry electrons by reducing one or more aromatic rings?

Both FAD+ and NAD+

The sliding clamp is used in DNA replication to ________ and is loaded by ________.

Bring and tether DNA polymerase to the chromosome; a clamp-loader complex

The only transport pathway that can move pre-folded proteins is called:

Twin arginase translocase

In order for septation to occur, which process must finish first?

DNA replication

You have isolated a new bacterium and you want to characterize its metabolism and so you want to know exactly what compounds it uses for growth. This would be best examined by growing the organism in a:

Defined medium

In an environment with no oxygen and high organic matter content with high nitrogen content. Which dissimilatory pathway would likely be favored?

Denitrification

All of these are methods used by bacteria to resist antibiotics Except:

Develop a new cell wall

In the figure below, which depicts the activation step in bacterial DNA replication, the letter Q points to ________, and the letters R and S point to ________, respectively. (image)

DnaA protein; 9-mer repeats within oriC and 13-mer repeats

During conjugation when a 'fertility plasmid' becomes integrated into the genome of the new cell, this new cell with the integrated F genes is referred to as what?

Hfr

While testing the chemiosmotic theory, researchers prepared "inside-out" vesicles. In an inside-out vesicle, the F1 subunit of the proton-ATPase faces outward. Using the figure below, which statement is true about the key results of these experiments. (image)

Either a high concentration of protons inside the cell or a highly positive charge inside the cell can drive ATP synthesis by moving protons down a concentration or charge gradient

Some bacteria in the human gut microbiota primarily feed on glucose derivatives from mucus secretions, in essence they "farm" the mucus. The mucus contains many sugar-acids which tend to be catabolized by which pathway?

Entner-Doudoroff pathway

Large genomes with a high portion of non-coding DNA are characteristic of

Eukaryotes

Prokaryotes and Eukaryotes differ by:

Eukaryotes contain a nucleus and membrane bound organelles, while prokaryotes do not

When the population doubles during each given unit of time, the growth is:

Exponential

Purines and pyrimidines are generated from the intermediate ribulose 1,5-bisphosphate

False

The TCA cycle functions in energy production by producing reducing agents and in anabolic function.

False

A sulfate reducing bacterium (an autotroph) living in seawater on the iron surface of bridge support may be detrimental to the integrity of that bridge material. Which pathway below is correct for electron flow and energy production by this bacterium and shows the product that can facilitate corrosion of the iron support? (sulfate = SO42-)

Fe -> ETS -> SO42- + ATP

The metabolites that appeared to drive the decrease in permeability in the blood brain barrier in mice are derived from what source?

Fermentation by gut microbe

Which of the following is NOT true of initiation of transcription?

GTP hydrolysis catalyzes bubble formation in DNA so that DNA polymerase can replicate a DNA strand

What is the correct pathway with major processes and intermediates given below for energy production by E. coli anaerobic respiration using nitrate (NO3-)?

Glucose -> glycolysis -> pyruvate -> acetyl-CoA -> TCA cycle -> ETS + NO3 -> ATP + NO2

What is the correct pathway with major processes and intermediates given below for energy production by E. coli during aerobic respiration?

Glucose -> glycolysis -> pyruvate -> acetyl-CoA -> TCA cycle -> ETS + O2-> ATP + water

Which two amino acids are important for nitrogen sensing and regulation in most bacteria?

Glutamate and glutamine

Sigma factors are used for:

Guiding the RNA polymerase to the promoter for transcription

What types of bacteria would NOT perform the Calvin cycle, to fix CO2?

Heterotrophs

A microbe has the capacity to do both fermentation and respiration. Under what conditions will the products of glycolysis be used for fermentation rather than respiration?

In the absence of oxygen or other strong terminal electron acceptor

All of the following are reasons to oxidize glucose in a series of steps EXCEPT to

Increase the deltaG of the reaction

In anaplerotic reactions,

Intermediates in a pathway are regenerated

The term secondary metabolite means a compound that:

Is not used in central carbon metabolism

How does the AraC regulatory protein turn on transcription in the presence of arabinose?

It becomes more flexible, so that the dimer can bind to the araI components of DNA and interact with RNA polymerase to permit transcription.

Which of the following statements about the prokaryotic flagella is INCORRECT?

It moves with a whiplike motion.

Which of the following is FALSE regarding the polarity and aging of Caulobacter crescentus?

It results in two cell types, each with a monotrichous flagellum

You are part of a research team discovering and characterizing new antibiotics. One promising molecule is very similar in structure to that of N-formylmethionine. What is the likely mechanism by which it attacks bacteria and would it be likely to harm human cells?

It would likely displace N-formylmethionine in translation leading to dysfunctional proteins. It would not be harmful to humans because eukaryotes use methionine to start translation.

All of these are ways to coordinately activate genes and/or operons to respond to a given stimulus, except:

Leader sequence

You have isolated a novel compound from a marine bacterium and are hopeful that it will be a useful antibiotic. In characterizing the structure of the compound, you find it is a relatively large molecule (~2000 Daltons) and has many amine groups. This compound will likely affect which cell structure and which type of microorganism?

Lipopolysaccharide because the amine groups give it a positive charge which disrupts the electrostatic interactions of LPS in the membrane; Gram negative bacteria which have LPS

Cells are dividing more than dying and nutrients are plentiful with few waste products

Log phase

Using the genetic sequence below the table, first find the start codon then translate the peptide starting at the start codon. Which of the following peptides might the message below the table code for? 5'-GAGUUAUGCACGGGUUCUAUGUGUAG-3' (image)

MET-HIS-GLY-PHE-TYR-VAL

What does it mean to say that the genetic code is redundant?

More than one codon can specify the same amino acid

What is shown in the figure below?

Multidrug resistance efflux pump

Based on this "electron tower" of standard reduction potentials, which of the following reactions could yield energy for an organism? (image)

NO3- + 2H+ --> NO2- + H2O

When you look at a cross section of a bacterial cell, you find regions with lots of ribosomes and a large region in which ribosomes are absent. The region in which ribosomes are absent is called the:

Nucleoid

The term ________ describes a polycistronic messenger RNA whose expression is under control of a promoter

Operon

At some hydrothermal vents, giant tube worms have been found that have no gut, but they host high densities of bacteria. The nearby vent water is rich in minerals, dissolved gases like CO2, and hydrogen sulfide, but low in organic matter content. Which dissimilatory pathway would yield the most energy for the bacteria in this environment?

Oxidation of hydrogen sulfide to sulfur or sulfate

Which of the following is NOT a terminal electron acceptor in anaerobic respirations?

Oxygen

In the blood brain barrier paper, the researchers used what kind of mice for their experiment?

Pathogen free mice and germ free mice

Which of the following pathways is NOT a route for CO2 assimilation?

Pentose phosphate pathway

All of these are examples of how microbes have shaped human history EXCEPT:

Photoautotrophic metabolism that produces carbon dioxide

You have enriched for bacterium from the human mouth and have colonies with different colors and morphology on a plate. If you want to characterize any one of these bacteria, what do you need to do next?

Pick one colony to streak onto a new plate and check for purity before continuing with biochemical test

The holoenzyme for transcription consists of:

RNA polymerase and the sigma factor

Which of the following is NOT part of initiation of transcription?

RNA polymerase pauses and the Rho protein binds to the mRNA

In gene regulation, ________ prevent transcription, whereas ________ stimulate transcription.

Repressors; activators

In the blood brain barrier paper, what where the metabolites that appeared to directly drive the decrease in permeability in the blood brain barrier in mice?

Short chain fatty acids

When the intracellular iron concentration is low, iron-scavenging molecules called ________ are produced.

Siderophore

At some hydrothermal vents, giant tube worms have been found (over 6 t tall!) that have no gut, but they host high densities of bacteria. The nearby vent water is rich in minerals, dissolved gases like CO2, and hydrogen sulfide, but low in organic matter content. Given this information which of these is a reasonable hypothesis for how these tube worms can grow so large?

The associated bacteria make energy by chemolithotrophic pathways and biomass from fixing carbon, and transfer this carbon and nutrients to the worms. The worms then use these transferred nutrients in assimilatory metabolism to grow.

G-C rich regions of DNA require more energy to melt. This is because:

The bases guanine and cytosine share three hydrogen bonds rather than the two hydrogen bonds between adenine and thymine

What is the most likely explanation for a Gram-positive bacterium appearing pink after performing a Gram stain?

The decolorizer was left on for too long

The figure below shows the production of antibiotic from bacterial cells over time using two cultures at different starting cell densities. Which statement below is true based on this figure:

The denser culture produced more antibiotic earlier in the growth cycle and just after the period of growth arrest, while the less dense culture produced a higher yield of antibiotic later.

You are a scientist working on characterizing marine microbes that have a major role in the global nitrogen cycle. You finally culture the bacteria you are interested in and find it can grow at twice the rate that you expected, and you suspect it can make proteins more quickly than other bacteria. You want to better characterize genes involved in translation, particularly the enzymatic component of the ribosome. To do that, you must sequence which gene(s) involved in translation?

The gene(s) encoding for the rRNA in the large subunit of the ribosome

The importance of the stop codon UAG is that it

The importance of the stop codon UAG is that it

In the blood brain barrier paper, the researchers added Evans blue tracer (looks red under fluorescent light) and DAPI stain which stains DNA (looks blue under fluorescent light) into the blood of the two groups of mice in the experiment. They then looked at sections of the brains of those mice. Some of the sections are shown in the images below. What does this show? (image)

The mice with no gut microbiome have increased permeability of the BBB as seen by the release of Evans blue dye into the brain tissue

What is the connection between catabolic pathways like respiration and biosynthesis?

The production of reducing power, energy, and building blocks from catabolism for biosynthesis

Protons have different sources and different fates in bacterial ETS. Which of the following processes does NOT generate protons?

The production of water from the use of oxygen as a terminal electron acceptor

Reduction potential is defined as

The tendency of a compound to accept electrons.

Which of the following is true of Fts proteins?

They form a ring in the area where cell division will occur.

Environments with high prevalence of antibiotics can facilitate rapid adaptive evolution, why?

This is a highly selective environment

Enzymes that modify the supercoiling of a DNA molecule are called

Topoisomerases

Transcription and translation occurs in all organisms. What is unique about these processes in prokaryotes?

Transcription and translation occur simultaneously in prokaryotes

The ability to synthesize tryptophan is not universal among the Chlamydiaceae, but some strains within Chlamydiaceae have a predicted tryptophan biosynthetic pathway and encode an ortholog of TrpR. In a Chlamydia infection, the bacterial cells sense low levels of tryptophan in host cells and likely respond by what mechanism?

TrpR holorepressor is not bound to operator and allows for tryptophan biosynthesis

In photosynthesis, electrons from water or hydrogen sulfide are moved into the membrane bound electron transport system and to NADP+ as a final electron acceptor. This generates a proton potential and reducing potential.

True

The ATP synthase enzyme uses a chemical gradient in ADP/ATP to move ADP and generate ATP.

True

A crucial part of the process to create GMO corn is the construction of the right plasmid. The plasmid used in this process is originally from Agrobacterium which can naturally infect plant cells. The plasmid is grown in E. coli so that we can make many copies of the plasmid quickly and then the plasmid is isolated and grown in Agrobacterium which can then infect corn cells and integrate DNA from the plasmid into the corn genome. Knowing this information, what components should the plasmid include?

an ori for E. coli, ori for Agrobacterium, a selectable marker such as antibiotic resistance, the gene of interest along with a eukaryotic promoter

The image below shows what two processes for the lac operon? (image)

cAMP and CRP bind DNA and increase rate of transcription; allolactose binds the repressor protein allowing lac gene operon transcription

Most biosynthetic pathways use the products of

catabolism

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.

cell wall; peptide

Topoisomerase II

changes DNA conformation by adding supercoils

Topoisomerase I

changes DNA conformation by relaxing negative supercoils

When double-stranded DNA replicates, the newly made strand is related to its template strand because the two strands have

complementary sequences and are antiparallel to each other.

Cells are dying more than dividing and nutrients are completely depleted

death phase

Cells are synthesizing enzymes and other molecules needed for growth, no net change in cell density

lag phase

All of the following are components of peptidoglycan EXCEPT

lipopolyaccharide

helicase

melts the DNA helix during DNA replication

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 ________.

methanogenesis; chemolithotroph

Shape-determining proteins in bacteria include FtsZ, MreB, and CreS proteins. In growing a lab strain of E. coli, you find that suddenly you see a population of the bacterium that are cocci rather than rods. You suspect there is a mutation in which gene?

mreB gene

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 a type of

mycobacteria

Extreme thermophilic Archaea have ________ chains in their membrane in order to maintain membrane stability.

terpenoid

Which name refers to having flagella attached all around the cell?

peritrichous

In a two-component signal transduction system, a ________ is transferred from a sensor kinase to a ________ in response to an environmental signal

phosphate; response regulator

Besides the nucleoid, two other kinds of DNA molecules that may be present in the cytoplasm of a bacterial cell are ________ and the genomes of ________.

plasmids; bacteriophages

As a cell divides and divides again, a new cell wall is formed in one area of the cell. Over generations this process results in cells that look identical but differ in physiology, including susceptibility to antibiotics. This process is known as

polar aging

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?

production of carbohydrates with three to seven carbon atoms, which can be utilized in biosynthesis

The figure below represents what type of differentiation?

sporulation

Cells are dividing and some cells are dying, nutrients are depleted and waste materials accumulate, no net change in cell density

stationary phase

The first steps in bacterial DNA replication are represented in the figure below, in which the letters T and U point to ________, respectively (image)

strand separation at the 13-mer repeats and binding of DnaA proteins at the 9-mer repeats

Which of the following substrates is an electron donor in organotrophy?

succinate

DNA polymerase III

synthesizes DNA in DNA replication

DNA primase

synthesizes RNA primers for DNA replication

What type of microscopy is used to view the internal structures of a specimen?

transmission electron

Specific membrane components, particularly ________, determine which substances are transported across the membrane.

transport proteins