MIC102

Cells of the immune system detect the presence of an invader by recognizing key features of different groups of microbes, their microbe-associated molecular patterns (MAMPs).

Which of the MAMPs shown below is present in bacterial cells?

Select all options that apply.

Chitin

Flagellin

Ergosterol

Lipopolysaccharide

Double-stranded RNA

Pilin

Murein

Flagellin

Lipopolysaccharide

Pilin

Murein

Bacteria have structures made of distinctive MAMPs including flagellin (flagella), pilin (pili, fimbriae), murein (cell wall), and lipopolysaccharide (outer membrane of gram-negative bacteria).

dsRNA is produced during RNA virus infections.

Chitin is a component of fungal cell wall

Ergosterol is a component of fungal membrane

The defining feature of "microorganisms" is their:

A. Lack of a nucleus

B. Small number

C. Small size

D. Small impact on the planet

E. Limited number of habitats

Small size

Which type of living cell is most abundant in and on the human body?

A. Human cells

B. Yeast cells

C. Archaeal cells

D. Bacterial cells

E. Viral particles

Bacterial cells

Which is not a potential energy source for microbes:

A. Carbon dioxide gas (CO2)

B. Cellulose [(C6H10O5)n]

C. Methane (CH4)

D. Infrared radiation

E. Uranium

Carbon dioxide gas (CO2) bc it's inorganic and some organisms are carbon "fixing" and expend energy turning CO2 into usable carbohydrates.

Does the traditional concept of species apply to prokaryotes?

A. Yes, because individuals from the same species can breed to produce fertile offspring.

B. Yes, because visible characteristics provide clear distinctions between species.

C. No, because bacteria acquire mutations in their DNA.

D. No, because bacteria and archaea are asexual and have high levels of horizontal gene transfer.

E. I do not know.

No, because bacteria and archaea are asexual and have high levels of horizontal gene transfer. The "traditional" concept of species is that organisms are considered the same species if they breed (or have the potential to breed) and produce fertile offspring. While prokaryotes frequently take up fragments of DNA, and may incorporate DNA into their chromosome or maintain it stably on a plasmid, they do not perform sexual reproduction. That is to say, they do not merge their genomes to recombine genes.

S-layer and capsule

s-layer (which most bacteria have) just outside the cell wall and a capsule layer (which many bacteria can have) as the outer-most layer.

Which 3 solutes move most efficiently across a phospholipid bilayer by simple diffusion?

Water bc it's not charged, Carbon dioxide bc it's non-polar, Ethanol (C2H5OH) bc it's small and amphiphilic.

(1) What would happen if a beaker containing a solution of dissolved solutes (B) was connected to a beaker of pure water (A)?

(2) What would happen if a selective barrier (e.g., CM) was installed?

(1) Osmosis: there would be a net movement of water into beaker B due to diffusion from an area of higher water concentration to an area of lower water concentration. (2) The osmotic pressure would increase and there would be a net movement of water into the beaker with solute.

β-lactam antibiotics, such as penicillin, inhibit transpeptidase activity during cell wall synthesis. What would happen to a gram-positive bacterium if it was growing in the presence of penicillin in a hypotonic solution?

What if the bacterium is gram-negative? What if the bacterium is not growing (in a resting state)? What if the solution is hypertonic? What if lysozyme is added instead of penicillin?

Lysis

Bacteria, archaea, and eukaryotes enclose their genome in a membrane-bound compartment called the nucleus.

False (only eukaryotes have a nucleus)

Which group is the most highly-evolved product of evolution?

All living species are equally evolved and share a common ancestor (LUCA)

Which statement describes evidence in support of the endosymbiosis theory of organellogenesis for mitochondria and chloroplasts?

Select all options that apply.

Chloroplasts use 80S ribosomes to synthesize protein, just as bacteria do

Mitochondria use similar division machinery as bacteria

Mitochondria have linear genomes, just as most bacteria do

Chloroplasts have a double membrane, while mitochondria do not

Mitochondria use similar division machinery as bacteria

Which structure is found in the cell envelope of a typical gram-positive bacterium?

Select all options that apply.

Peptidoglycan cell wall (murein)

Teichoic acid

Outer membrane

Phospholipid

Lipopolysaccharide

Peptidoglycan cell wall (murein)

Teichoic acid

Phospholipid

Which structure is found in the cell envelope of a typical gram-negative bacterium?

Select all options that apply.

Phospholipid

Teichoic acid

Peptidoglycan cell wall (murein)

Outer membrane

Lipopolysaccharide

Phospholipid

Peptidoglycan cell wall (murein)

Outer membrane

Lipopolysaccharide

s-layer

Proteins that attach to the cell wall of a bacteria and then the capsule encapsulates everything. In Archaea there is ONLY an s-layer and no cell wall/peptidoglycan

capsule

polysaccharide and/or polymer of amino acids

Lipopolysaccharide (LPS)

fatty acid, phosphorylated disaccharide, and repeating units of sugars

Phospholipids

fatty acid tails connected to glycerophosphate heads via ester bonds

peptidoglycan (murein)

glycan chains composed of N-acetylglucosamine alternating with an N-acetylmuramic acid subunits and cross linked with peptide bonds.

Species that are isolated from the environment and then passaged (cultured) many times in the laboratory sometimes lose the ability to make structures that are unnecessary for growth in artificial culture. (Why waste the energy making something you don't need?)

For example, some Streptococcus species lose their ability to make a thick, slime layer after extended periods of lab culturing.

How might the loss of its slime layer impact the ability of Streptococcus mutans, a causative agent of dental cavities, to colonize and persist in its host (us)?

Select all options that apply.

Decreased biofilm formation

Increased risk of phagocytosis (clearance by host immune defenses)

Increased resistance to desiccation (water loss)

Decreased attachment to surfaces

Decreased biofilm formation

Increased risk of phagocytosis (clearance by host immune defenses)

Decreased attachment to surfaces

slime layer

Slime layers help cells retain water, slow the diffusion of nutrients away from the cell, attach to surfaces, avoid being cleared (engulfed) by phagocytic immune cells or bound by immune molecules, evade viral infections (by blocking access to the bacterial structures they bind to), and more.

Which factor needs to be considered when culturing an acidophile?

Select all options that apply.

pH of the media

Gas mixture of the atmosphere

Incubation temperature

Natural habitat of the organism

Elemental composition of the media

pH of the media

Gas mixture of the atmosphere

Incubation temperature

Natural habitat of the organism

Elemental composition of the media

True or False: The cell membrane is an important site of energy production.

True (The phospholipid bilayer of the cell membrane is impervious to ions, such as H+ or Na+, which allows the cells to build a transmembrane ion gradient, with the charged ions trapped outside the cell membrane. The resultant electrochemical gradient (e.g., proton motive force) is a form of stored energy the cells can use to make ATP, rotate flagella, transport molecules across the membrane, and more.

Note: Because it is critical to cell function, every cell MUST have an ion motive force of some kind to survive, even if it doesn't have an electron transport chain (e.g., is strictly fermentative).

Consider this chemical reaction: ATP + H2O --> ADP + Pi.

Identify the FALSE statement regarding this reaction.

It is coupled to less energetically-favorable reactions during biosynthesis

It is exergonic (releases energy)

It is irreversible

It involves the cleavage of a high-energy phosphate bond

It is irreversible

Which form of the electron carrier NAD+/NADH contains the least amount of energy and electrons?

Select the best option of those available.

NAD+ (oxidized form)

NADH and NAD+ have the same amount of energy and electrons (rearranged)

NADH (reduced form)

NAD+ (oxidized form) --> NAD+ has 1 less hydrogen (H) atom and, therefore, 2 fewer electrons than NADH. The molecule with fewer electrons is the more oxidized form.

Tip: use the mnemonic OIL RIG: oxidation is loss (of electrons), reduction is gain (of electrons).

Photosynthetic cyanobacteria (carbon source: atmosphere)

photoautotroph aka photosynthesis

animal pathogen

chemoheterotroph (if the source of energy and reducing power. is a chemical sources microbes are said to be chemotrophs and microbes that obtain their carbon from organic compounds are called heterotrophs)

A species growing under the surface of the rock in a desert (carbon source: atmosphere; electron source: minerals in the rock)

chemoautotroph (if the source of energy and reducing power. is a chemical sources microbes are said to be chemotrophs and if they are using inorganic sources of carbon (such as carbon dioxide) are named autotrophs)

Photosynthetic purple non-sulfur bacterium (carbon and electron source: organic acids)

photoheterotroph (light + get their energy from other organisms)

Ideal molecular clock features

Gene has to be present in all orgs, its good to see the same RNA in eveything

Needs to be conserved over billions of years of evolution so they tend to have central functions and they're not changing so drastically so quickly which would not be conserved

But we also consider divergent regions that when they do change they have evolutionary benefits

osmosis

net movemnet of water from an area of [higher] water concentration to an area of [lower]

osmotic pressure

the pressure that must be applied to the solution side to stop fluid movemnt across a semi-permeable membrane

True or False: Bacteria can perform DNA replication, RNA transcription, and protein translation on the same gene simultaneously (at the same time).

True: In eukaryotes, DNA replication and transcription can only happen inside the nucleus, while translation takes place in the cytoplasm or endoplasmic reticulum. Bacteria and archaea DO NOT have a membrane enclosing their DNA, DNA replisomes, RNA polymerase, and ribosomes can access the DNA/RNA in the same place in the cell and at ~the same time.

Nitrogen is assimilated during which stage of cell growth metabolism?

Biosynthesis: Reduced nitrogen (ammonia) is linked to 2-oxoglutarate, an acid produced during the TCA cycle, to form amino acids that can transfer amino or amido groups to other molecules.

Identify the true statement about building blocks, precursor metabolites, and macromolecules:

Building blocks are more oxidized than precursor metabolites

Building blocks are polymerized to produce macromolecules

Energy is consumed during building block synthesis

Building blocks are polymerized to produce macromolecules

Energy is consumed during building block synthesis

Identify the binding site for RNA polymerase during transcription:

Ribosome binding site (aka Shine-Dalgarno)

Sense codon

Promoter

DnaA box

Promoter

Termination of transcription requires...

Separation of the DNA template and newly synthesized RNA

Degradation of the RNA

Recruitment of a sigma factor

A collision between RNA polymerase and a ribosome

Formation of a hairpin structure by the double-stranded DNA template

Termination sequences have inverted repeats of GC-rich sequences. After being synthesized, the single-strand of RNA will base pair with itself to for a "hair pin" structure. The formation of this structure in a growing RNA molecule will slow RNA polymerase down long enough for RNAP to dissociate or recruit a terminator protein that will separate the newly-synthesized RNA from its template DNA.

True or False: Each 3-base codon specifies a unique amino acid in the "genetic code". In other words, there are the same number of codons as amino acids.

False: Because there are only ~20 amino acids, there is redundancy in the code, with highly-abundance amino acids being encoded by more codons

Which activity is specifically and directly involved in the elongation stage of transcription?

Select all options that apply.

Breaking of hydrogen bonds between DNA bases

Linkage of the 3' OH of one ribonucleotide (nt) to a 5' phosphate of the nt being added

The formation of hairpin loops in the newly-synthesized transcript

You Answered Synthesis of an RNA primer

Association of a sigma factor with core RNA polymerase to form a holoenzyme

Recruitment of Rho factor

The two strands of DNA in the DNA helix must be separated to allow RNAP access to the DNA template.

RNA synthesis involves the formation of a phosphodiester bond between the 3' OH group of the ribonucleotide at the end of the growing strand and the alpha phosphate (closest to the ribose) of the incoming nucleoside triphosphate (rNTP).

A sigma factor is recruited to initiate transcription but dissociates from RNAP during the transition from the initiation stage to the elongation stage of transcription.

Hairpin structures and the Rho factor play a role in transcription termination. As the textbook notes, RNAP sometimes moves past potential termination sites (hairpin structures) during elongation with the help of protein factor Nus.

Unlike DNAP, RNAP can synthesize a complementary strand without a primer to extend from.

Which activity occurs during the synthesis of DNA, RNA, and protein?

Formation of peptide bonds:

Formation of peptide bonds

Linkage of polymers to form monomers

Production of ATP equivalents

Mismatch repair

Assembly of a protein-nucleic acid complex during initiatio

Assembly of a protein-nucleic acid complex during initiation: Each of these processes has 3 stages: (1) formation of an initiation complex made of proteins and nucleic acids; (2) elongation of a polymer through the linkage of monomers (e.g., amino acids linked by a peptide bond); and (3) termination.

Macromolecular synthesis is very expensive to perform, with energy expended to synthesize the building blocks, link the monomers, separate strands of nucleic acid, recruit and incorporate the correct components (e.g., aminoacylated tRNA, complementary base pair), translocate mRNA, degrade proteins, repair DNA (e.g., mismatch repair), and more.

Bacterial cells can replicate much faster than eukaryotic cells.

Which bacterial feature facilitates rapid growth?

Select all options that apply.

A larger, more complex ribosome

The transcription of multiple genes from a single promoter

Distinct compartments for transcription and translation in the cell

Concatenation of newly-replicated chromosomes

Polycistronic messenger RNA

The transcription of multiple genes from a single promoter

Polycistronic messenger RNA

Being able to transcribe and translate simultaneously saves time and energy, and co-transcriptional translation is only possible for organisms that do not have their genome sequestered inside a membrane-bound compartment (nucleus).

The polycistronic organization of many prokaryote genes into operons is also more efficient. This arrangement allows sets of genes to be expressed after the initiation of transcription from just one promoter, rather than having to recruit RNAP to multiple promoters and regulate these promoters independently. The mRNA that is produced from the operon is polycistronic, just as the encoding DNA is.

The 70S bacterial ribosome is smaller and contains fewer ribosomal proteins than the 80S eukaryotic ribosome.

Listed below are some key steps in murein synthesis:

1 - Release of NAG-NAM-peptide from a lipid carrier

2 - Transpeptidase activity

3 - Linkage between NAM-pentapeptide and NAG

4 - Linkage of NAM to a pentapeptide

5 - Transglycosidase activity

6 - Translocation of NAG-NAM-pentapeptide across the cell membrane

Identify the correct sequence of steps that occurs during cell wall synthesis, starting with the monosaccharide subunits.

4,3,6,1,5,2

Linkage of NAM to a pentapeptide

Linkage between NAM-pentapeptide and NAG

Translocation of NAG-NAM-pentapeptide across the cell membrane

Release of NAG-NAM-peptide from a lipid carrier

Transglycosidase activity

Transpeptidase activity

The human microbiota includes thousands of species of bacteria, archaea, fungi, and protozoa. Collectively this microbial community has many different functions and activities.

Which of the following functions and/or activities is performed by the human microbiota?

Select all options that apply.

Influencing our mental health

Influencing the development of our immune system

Producing vitamins

Influencing the level of inflammation

Producing short-chain fatty acids through fermentation

Influencing our mental health

Influencing the development of our immune system

Producing vitamins

Influencing the level of inflammation

Producing short-chain fatty acids through fermentation

True or False: Germ-free (no microbiota) mice are healthier than mice colonized with gut microbes from conventionally-raise mice (i.e., that are not germ-free).

False

How does the presence of flagella impact the ability of Vibrio cholerae to infect mice?

Increase

Decrease

No change

Increase

How does the presence of flagella impact the ability of Vibrio cholerae to attach to host cells?

Increase

Decrease

No change

Increase

Predict which structure(s) a virus or immune cell could access from outside intact gram-negative bacterial cells.

Select all that apply.

A. Capsule (CA)

B. Cell membrane (CM)

C. Lipopolysaccharide (LPS)

D. Peptidoglycan (PG)

E. S-layer (S)

Capsule

Lipopolysaccharide

S-layer

A. CA: If present, the capsule is the outer-most layer of the cell and accessible to factors in the environment. Note that a tightly-associated capsule could shield more internal layers, but not all bacteria make capsule, and their synthesis can be dependent upon growth conditions and other factors.

C. LPS: The lipopolysaccharide makes up the outer leaf of the outer membrane and may be exposed to the outside environment. The outer membrane shields the peptidoglycan and cell membrane from the external environment, such that these structures would never be accessible to a bacteriophage or immune cell(e.g., macrophage) on an intact gram-negative cell.

E. S layer: In organisms with an s-layer, this crystalline monolayer of protein around the cell is outside the outer membrane, and therefore can be accessible to the outside environment...provided the cell doesn't have a capsule to shield it

Why do bacteria store excess nutrients (e.g., carbon, phosphate, and sulfur) in insoluble granules, rather than in a soluble form in their cytoplasm?

A. Removing potential solutes from the cytosol effectively decreases the concentration of available water in the cytosol.

B. The enzymes that will act on the nutrients are found inside the inclusions.

C. To allow the cell to take up more of the nutrient overall.

D. These solutes spontaneously aggregate inside of the cell.

To allow the cell to take up more of the nutrient overall.

By forming aggregates of potential solutes, their effective concentration is decreased in the cytosol, which will enhance the transport of additional nutrients into the cell. Consider the transport of soluble nutrients as a chemical reaction: nutrients outside à nutrients inside. If the soluble nutrient concentration is kept low in the cytoplasm (because the reaction product is removed by binding it into insoluble granules), this favors there action going forward (more transported nutrient).

Predicting bacterial growth (exponential increase): Your classmate fixes herself anegg salad sandwich but before eating it, realizes it is 10 AM and she'll be late for MIC102. She sets the sandwich on the counter and does not return until 1 PM, then eats it. Initially the sandwich had 1000 cells of Salmonella enterica serovar Purge, which has aggeneration time of 30 minutes under these conditions.

Calculation: If the infectious dose (ID 50 ) for S. Purge is 1x104 cells, is it likely she'll get infected?

First calculate the number of generations that have passed: 3 hours / [0.5 hours /generation] = 6 generations (doublings)

Then double the initial number of cells 6 times: 1000 --> 2000 --> 4000--> 8000 --> 16,000 --> 32K --> 64K = 6.4x10^4 cells

Then compare the final number of cells with the ID50 , the number of cells (dose)which lead to infection in 50% of individuals: 6.4x104 >> 1x10^4 ; yes, she ingested more than the ID50 and therefore is likely to get infected

Which molecule is the more reduced form in each pair?

H 2 O/O2 , CO 2 /[CH 2 O], N 2 /NH 3 , Fe 2+ /Fe 3+

H 2 O

CH 2 O

NH 3

Fe 2+

How would it impact ATP synthesis if this organism was exposed to amphipathic detergent that permeabilized membranes?

Increase ATP

Decrease ATP

No change

Decrease ATP

The accumulation of protons (H+ ) on one side of the cellmembrane generates an electrochemical gradient, also called the proton motiveforce (PMF). The potential energy of the PMF is converted to chemical energy inthe form of ATP by the passage of protons through the ATP synthase. If the cellmembrane becomes permeable, protons will leak (diffuse) back into thecytoplasm without passing through the ATP synthase. ATP synthesis would soonhalt and other essential functions of the PMF would be lost; the cell would soonperish.

Each step is required for the initiation of DNA replication.

Organize them into the proper sequence (1-6).

i. At high [DnaA-ATP], DnaA-ATP binds to DnaA boxes at oriC and melts the H-bondsat this locus

iii. Single-strand binding (SSB) proteins keep strands apart

v. Helicase breaks H-bonds, separate strands

iv. The full Replisome assembles onto replication bubble

ii. Primase (DNA-dependent RNA polymerase) makes a short RNA prime

Escherichia coli replisomes can synthesize DNA at a rate of ~1000base pairs (bp) per second, with this rate reflecting the semi-conservative replication of both strands at each replication fork. How long will it take for E. coli to replicate its chromosome of 4.6 x 106 bp (in minutes)?

Solution:4.6 x 106 bp / 1000 bp/sec = 4.6 x 103 sec / 60 sec/min = 76.7 min

This calculation is for one replisome...but there are two!

76.7 min per replisome / 2 replisomes = 38.3 min

If a deleterious mutation occurred in the mutS gene, would the overall mutation rate:

A. Increase

B. Decrease

C. Not change

Increase

MutS is an essential component of mismatch repair. Went it it is lost, the final error rate goes up ~100-fold, which means that there is a much higher likelihood of mutations accumulating. Fun fact: scientists use ΔmutS (deletion) "mutator" strains to generate random mutations within a DNA fragment. They insert the DNA fragment into a plasmid and allow the mutator strain to grow and replicate the plasmid. They then purify the plasmids and study impact of the mutations that have accumulated during plasmid replication in the absence of mismatch repair.

Does co-transcriptional translation occur inside the eukaryotic cell?(Hint: they have organelles.)

Yes

No

Yes; he nuclear genes of eukaryotes are transcribed in the nucleus. ThemRNA is then processed to remove intervening introns and add a 5' cap and poly-A tail.It is then exported to either the cytoplasm or rough endoplasmic reticulum, where theribosomes are located, for translation. Thus, the transcription and translation of nucleargenes are separated both in time and space in eukaryotes.

Wild type sentence (DNA sequence):

Her kat ate a rat.

Her cat ate a hat.

Her bca tat e ara t....

Her cat.

Silent

Missense

Frameshift

Nonsense

Deleterious errors will be most costly to a cell and its progeny if they occur during...

DNA replication

Translation

Transcription

DNA replication

Which mutation will (most likely) have the least impact on the phenotype of a cell:

A. Insertion of a single nucleotide in the middle of the coding region of a gene

B. Accumulation of thymine dimers induced by ultraviolet light

C. Transposon insertion between the -35 and -10 promoter region of a gene

D. Deletion of several sense codons near the 3' end of a gene

E. Translocation of an entire, intact operon

Deletion of several sense codons near the 3' end of a gene

Can DNA be passed from a dead donor to a live recipient by conjugation?

Yes or No

No; It requires a living donor that can synthesize and retract the pilus, nick the Factor at the nic site in the origin of transfer (oriT), transport the single-stranded plasmid DNA through the pore and into the recipient, etc. It also requires a living recipient that can, for example, synthesize a complementary strand and circularize the newly-synthesized DNA into a plasmid.

Can DNA be passed between very distantly related species?

Yes or No

Yes; It depends on the conjugation system. In some cases, DNA can even be transferred from bacteria to yeast or to plants. For example, the bacterium Agrobacterium tumefaciens injects the T1 plasmid into plant cells to force them to make its preferred carbon source and multiply, producing the crown gall (shown on the cover slide).

Would [Griffith's transformation] experiment have worked if Streptococcus pneumoniae was not naturally competent?

Yes or No

No;

Griffith's experiment would NOT have worked if the cells had not actively taken up DNA on their own. Notice that he did not induce transient competence in the rough strain cells (R, recipient) through an artificial transformation protocol (e.g., electroporation or chemical treatment with heat shock). In the scenario, he simply injected the heat-killed smooth (S, donor) and R cells together. The R cells took up DNA released by the heat-killed S cells, some of which encoded the genes for capsule biosynthesis that was expressed to produce capsule and evade clearance by the mouse immune system.

Which is an example of a spontaneous mutation?

UV light triggers the formation of pyrimidine dimers

A single strand of DNA is brought into the cell and recombined onto the chromosome

DNA polymerase inserts a nucleotide that is non-complementary to the template strand

A base analog is incorporated into a strand of DNA during replication

DNA polymerase inserts a nucleotide that is non-complementary to the template strand

Which form of DNA transfer can take place even if the donor is no longer alive?

Select all options that apply.

Transformation

Transduction

Conjugation

Transformation does not require a living donor; in fact, cells can be transformed with pure DNA in the laboratory.

Conjugation requires a living donor cell that will transfer DNA to a living recipient cell.

Transduction requires only bacteriophage that carry the target DNA (from a bacterial donor that is now dead) and a permissive host cell (which that specific virus can replicate in), but not a living donor.

Note: because a living bacterial cell is the original host of the virus that packaged the bacterial DNA to form the "transducing particle", this option was also accepted.

Which of the following can be transferred horizontally through DNA exchange?

Select all options that apply.

The ability to perform conjugation

Antibiotic resistance genes

Capsule biosynthesis genes

Segments of the bacterial chromosome

The ability to perform conjugation

Antibiotic resistance genes

Capsule biosynthesis genes

Segments of the bacterial chromosome

True or false: Bacteria acquire mutations that make them resistant to antibiotics only after being exposed to antibiotics.

False; Mutations arise before they are acted on by natural selection. In other words, antibiotic resistance is not induced by exposure to the selective treatment

Which of the following protects bacteria from viral infection?

Restriction endonuclease

Methylase

Transduction

Transposase

Restriction endonuclease;

Restriction endonucleases (REs) protect bacteria from bacteriophage infection by recognizing a particular DNA sequence and cutting the DNA. If the genome of an invading DNA virus contains the recognition sequence, its genome will be cut by the RE and protect the bacterial cell from viral replication. The bacterium's DNA is protected by a partner methylase that methylates the recognition sequence of its partner RE and thereby prevents it from cutting the DNA.

True or false: Only bacterial genes can be cloned into and expressed (transcribed and translated) by bacterial cells.

False;

Many eukaryotic and archaeal proteins can be cloned and expressed inside of bacteria, although these proteins may not go through the same post-translational modifications as if they had been synthesized in their native host. Because bacteria don't have splicing machinery, the introns must be removed before the gene is inserted into bacteria. This is usually done by reverse transcribing the fully spliced, mature mRNA into double-strand DNA (using the retroviral enzyme reverse transcripase) that can serves as template during PCR or inserted into a vector.

An exonuclease is an enzyme that removes nucleotides (breaks the phosphodiester bond between them) from the end of a nucleic acid strand.

An endonuclease is an enzyme that cuts (breaks the phosphodiester bond) within a nucleic acid strand.

Identify the enzyme that is an endonuclease:

Methylase of a restriction-modification system

DNA ligase

DNA polymerase with proofreading activity

Restriction enzyme

Restriction enzyme;

Restriction enzymes bind to their specific recognition sequence and cut within the DNA molecule.

DNA polymerases with proofreading activity perform a 3' to 5' exonuclease activity during proofreading

Compare in vitro DNA replication (in vitro = in a test tube; PCR) with in vivo DNA replication (occurs in living cells).

Which PCR element serves the same function as the enzyme helicase?

72oC temperature step

DNA oligonucleotides (primers)

A DNA template

Heat-stable DNA polymerase (Taq)

dNTPs

95oC temperature step

~60oC temperature step

95oC temperature step

Compare in vitro DNA replication (in vitro = in a test tube; PCR) with in vivo DNA replication (occurs in living cells).

Which PCR element serves the same function as the enzyme primase?

95oC temperature step

~60oC temperature step

72oC temperature step

Heat-stable DNA polymerase (Taq)

DNA oligonucleotides (primers)

dNTPs

A DNA template

DNA oligonucleotides (primers)

During in vitro DNA replication (PCR), DNA oligonucleotides (primers) are used that have been chemically-synthesized and are complementary to the 5' and 3' end of the sequence to be amplified. The primers anneal to the denatured strands in a sequence-dependent fashion and provide a free 3'OH for DNAP to extend from. The primers remain as an integral part of the amplified double-stranded DNA molecule (amplicon).

During in vivo DNA replication, primase, a DNA-dependent RNA polymerase, synthesizes a short RNA primer for DNAP to extend from. RNA primers are subsequently removed and the gap filled in by another DNAP.

Compare in vitro DNA replication (in vitro = in a test tube; PCR) with in vivo DNA replication (occurs in living cells).

Which aspect of PCR is also present during the in vivo DNA replication of Thermus aquaticus, the bacterium that was the original source of Taq DNA polymerase?

Select all options that apply.

DNA oligonucleotides (primers)

Heat-stable DNA polymerase (Taq)

A DNA template

72oC temperature step

95oC temperature step

dNTPs

~60oC temperature step

Heat-stable DNA polymerase (Taq)

A DNA template

72oC temperature step

dNTPs

72oC temperature step - yes; T. aquaticus is a thermophile that grows best at ~70oC and its DNA polymerase activity is optimal at this temp

Heat-stable DNA polymerase (Taq) - yes; Note: You can buy Taq enzyme in from a biological supply company. The DNAP gene from T. aquaticus was engineered into E. coli and put under the control of an inducible promoter that can be activated for high levels of gene transcription and protein production. The Taq is then separated from all other cell components and packaged for sale.

DNA oligonucleotide primers - no; RNA primers are synthesized by RNA primase in the cell

Pool of dNTPs - yes; a mixture of ATP, TTP, CTP, and GTP provides the monomers for DNA synthesis

Template - yes; DNA serves as the template for the synthesis of complementary strands of DNA

Which statement about two-component stress response system is true?

The response regulator is de-phosphorylated by the sensory histidine kinase

Once a two-component response system is activated, it continues responding indefinitely

The sensory histidine kinase transfers a phosphate reside to the response regulator to activate it

The periplasmic domain of a response regulator is bound by the stressor

The sensory histidine kinase binds the DNA to activate or repress transcription

The sensory histidine kinase transfers a phosphate reside to the response regulator to activate it

Which statement about quorum sensing is true?

Select all options that apply.

It measures the size of individual cells in a population

It is a mechanism used by bacteria to coordinate group behaviors

It is used by all quorum-sensing species to activate light production

It is dependent upon the concentration of signaling molecules

It is a mechanism used by bacteria to coordinate group behaviors.

It is dependent upon the concentration of signaling molecules.

Bacteria use quorum sensing to detect the size of the cell population (not the size of individual cells) and regulate gene expression to perform activities as a group, such as the light production, biofilm formation, virulence factor release, and more. The sensing of the quorum (bacterial density) is dependent upon the concentration of autoinducer molecules that are produced by individual cells and accumulate with increase cell density.

Sporulation is a process by which

Endospore-formers can reproduce and increase their population size

Phosphorylation of regulatory proteins leads to cell type-specific gene expression

An inert endospore is revived under favorable environmental conditions

All gram-positive species survive harsh environmental conditions

Phosphorylation of regulatory proteins leads to cell type-specific gene expression

How does the fungus Coccidioides get inside a human host?

Through the inhalation of contaminated dust

Through contact with a contaminated surface

Through its injection by an insect vector

Through the inhalation of respiratory droplets expelled from infected people

Through ingestion of contaminated food

Through the inhalation of contaminated dust

Which statement about fungi is false?

They have ergosterol in their membranes

Some species can grow either as a yeast form or filamentous form

Fungi are highly motile

Some species form symbiotic relationships with plants

They have a cell wall that is resistant to antibiotics

Fungi are highly motile

Identify the TRUE statement about a typical viral replication cycle.

Select all options that apply.

During viral replication, the viral genome is always integrated into the host genome

Viral genes are transcribed during replication

Viruses take advantage of (hijack) normal host cell processes to achieve replication

Virus only infect bacteria and eukaryotes, not archaea

Viruses are more abundant than cellular organisms

All viral proteins are synthesized at the same time immediately after the genome enters the host cell

Viral genes are transcribed during replication

Viruses take advantage of (hijack) normal host cell processes to achieve replication.

Viruses are more abundant than cellular organisms.

Identify components that are present in the virions of ALL types of viruses (i.e., the components that every virus would have).

Select all options that apply.

Capsomeres

Ribosomes

Surface ligand

Nucleic acid

RNA-dependent RNA Polymerase

Phospholipid bilayer

Double-stranded DNA

Capsomeres

Surface ligand

Nucleic acid

All viruses must have a surface ligand of some kind to bind the host cell receptor. They also must have a capsid of assembled capsomeres to enclose the genome, which is made of nucleic acids (either RNA or DNA, ss or ds, + or - sense strands). For naked (non-enveloped) viruses, capsid proteins will serve as the surface ligand that binds the host receptor.

True or False: All viruses kill their host cell in the process of being released.

False; Viruses that "bud" (a.k.a. "exocytose") from the membrane of the host cell do not trigger host cell lysis, although viral replication may eventually exhaust the cell and interfere with its normal function.

Which type of virus MUST have the gene for RNA-dependent RNA polymerase encoded on its genome?

Select all options that apply.

Double-strand DNA virus

Positive (+) sense RNA virus

Negative (-) sense RNA virus

Positive (+) sense RNA retrovirus

Double-strand RNA virus

Positive (+) sense RNA virus

Negative (-) sense RNA virus

Double-strand RNA virus

All RNA viruses must encode RNA-dependent polymerases on their genome, and/or enclose the enzyme inside their capsid, to facilitate the replication of their genome. This is because the cellular hosts do not have enzymes that can replicate an RNA genome (i.e., synthesize RNA using an RNA template).

B lymphocyte (B cell)

Make antibodies

Cytotoxic T lymphocyte (T cell)

Kill infected host cells

Helper T lymphocyte (T cell)

Activate other immune cells with cytokines

Neutrophil

Phagocytose and kill bacterial pathogens

Monocyte/Macrophage

Clean up cellular debris

Many factors influence whether a microbe will be successful at colonizing a host and establishing an infection.

Which factor influences the likelihood of infection?

Select all options that apply.

The host's history of prior infection with that microbe

The immune competence of the host

The virulence of the pathogen

The number of microbes

The host's history of prior infection with that microbe

The immune competence of the host

The virulence of the pathogen

The number of microbes

(Based on video of the MEGA plate experiment; source: Baym et al, 2016): Which was the most likely mechanism by which the bacteria on the MEGA plate became resistant to the antibiotic trimethoprim on the plate?

A. It entered stationary phase

B. The trimethoprim target (dihydrofolate reductase) mutated

C. Acquisition of an efflux pump through horizontal transfer

D. Expression of an enzyme that inactivates the drug

E. A mutator strain arose with an DNA polymerase that does not proof read during DNA replication

The trimethoprim target (dihydrofolate reductase) mutated

Yes! The most common type of mutation that was associated with antibioticresistance were single nucleotide polymorphisms (SNPs, base substitutions) inthe gene encoding the enzyme inhibited by trimethoprim, dihydrofolatereductase

Would administering anti-H. pylori therapy to the entire population of Tibet with be good for public health overall? What are the pros (arguments in favor) of such an approach? What are the cons to this approach?

Pro: H. pylori causes disease and death. Some strains circulating in Tibet cause significant disease, especially in hosts with high-risk genetic backgrounds and diet.

Cons: (reasons NOT to treat everyone in the country with abx)• Abx can disrupt the microbiota, which has functions important for human health. E.g., feed gut cells (SCFA fermentation products), provide vitamins, promote immune system development, reduce colonization by pathogens, influence mental health, regulate glucose metabolism, and more.

H. pylori can protect against active tuberculosis and allergic diseases for some hosts. (Note: Tuberculosis is a more prevalent in Tibet.).

Antibiotic resistance is more likely to arise.

Antibiotics can have side effects and even trigger anaphylaxis.• Antibiotics are expensive!

Best approach: Screen for individuals at high risk of disease from H. pylori infection &eradicate it with narrow spectrum antibiotics that specifically targets H. pylori (and as few other species as possible)