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Microbiology > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

What is the genome-wide study of the structure, function, and regulation of an organism’s proteins called?

A

proteomics

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2
Q

The field of study that can reveal how genes function, reveal how organisms interact with the environment, and show evolutionary relationships is

A

comparative genomics

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3
Q

What do scientists call the entire complement of RNA produced under a given set of conditions?

A

transcriptome

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4
Q

What is the analysis of pooled environmental DNA or RNA called?

A

metagenomics

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5
Q

Sequencing an organism’s genome often leads to identification of hypothetical proteins; which are characterized as

A

proteins that likely exist through their function is unknown

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6
Q

An organism’s entire complement of genetic information, including noncoding DNA is known as the

A

genome

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7
Q

Which genetic material is most closely related to the nuclear-encoded mitochondrial genes that are required for translation and energy generation?

A

bacterial genes

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8
Q

Which of the following is NOT included in the genome?

A

proteins

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9
Q

Which of the following is NOT a mechanism of horizontal gene transfer?

A

vertical inheritance

IS: transformation, transduction, conjugation

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10
Q

Which of these organisms is likely to have the largest genome?

A

a yeast cell

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11
Q

What are the short DNA fragments called that are used to initiate DNA synthesis in Sanger dideoxy sequencing method?

A

primers

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12
Q

Agarose gel electrophoresis is used to

A

separate DNA fragments by size

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13
Q

In bacteria, DNA modification enzymes modify

A

host DNA to protect it from host restriction enzymes

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14
Q

Southern blotting is a method of hybridization used to identify a target

A

DNA fragment

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15
Q

The in vitro alteration of genetic material is known as

A

genetic engineering

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16
Q

Which technique would you use to change the amino acid serine to the amino acid arginine?

A

site-directed mutagenesis

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17
Q

Subunit vaccines

A

contain only a specific protein or two from a pathogen that the immune system can recognize

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18
Q

What method of mutagenesis would be best to determine if a gene is essential for a prokaryote

A

cassette mutagenesis

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19
Q

DNA can be synthesized from RNA samples by using

A

reverse transcriptase

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20
Q

DNA molecules that have short, single-stranded overhangs are said to have

A

sticky ends

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21
Q

A shuttle vector that can be used in both bacteria and yeast should be able to

A

replicate both bacterial and yeast cells

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22
Q

When a DNA gel is run, a standard sample with fragments of known size is often run in one well. Why is it important to use a standard sample?

A

When an electrophoresis gel is run, small differences in the environment can influence how far the fragments travel. Having a standard sample allows one to compare the test fragments with fragments of known size that have been run under the same conditions

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23
Q

Why was metagenomics so useful in identifying previously unknown Archaea?

A

Metagenomics makes it easier to find and identify species that are difficult to culture

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24
Q

Why was metagenomics so useful in identifying previously unknown Archaea?

A

Metagenomics makes it easier to find and identify species that are difficult to culture.

Does not require full genomes

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25
Q

An important clue that a sequence is a functional ORF is that

A

It has a similar sequence to a sequence known to encode a functional protein domain in another species, it has a start and stop codon, it has a ribosome binding site

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26
Q

If a researcher finds a sequence of DNA that has an unusual codon bias compared with the rest of the DNA for the organism, this probably means that

A

The DNA does not contain functional genes or the DNA contains functional genes that were obtained through horizontal gene transfer

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27
Q

Which of these is true about genome size?

A

Bacterial and archaeal, but not eukaryl, genome sizes generally correlate with ORF content

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28
Q

What can you predict if you find an organism that has an exceptionally tiny genome?

A

It is probably a symbiont that is dependent on its host.

Because it does not need to produce as many proteins itself and can use the host’s proteins.

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29
Q

An example of heterologous expression would be

A

Inserting an unknown gene from one bacterium into another unrelated bacterium to see what was produced.

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30
Q

If you did a metagenomic analysis of a natural pond environment, you would probably find that

A

virus genes were the most abundant genes present

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31
Q

A researcher planning to determine the genomes of all the species present in a diverse wetland environment using metagenomics would encounter the problem that

A

it is difficult to assemble complete genomes when many species are present

32
Q

The proteome and the translatome

A

differ because the translatome includes only proteins produced under specific conditions and the term proteome can be broader

Whether an organism has a mutation does not affect whether its proteome and translatome are the same.

33
Q

If you compare a bacterium and a eukaryote of the same genome size

A

the bacterium likely has more genes.

34
Q

What question could best be answered using comparative genomics?

A

What is the minimum number of genes necessary for life?

35
Q

In phylogeny, which of the following is NOT a domain

A

Plantae

36
Q

Energy-generating metabolism in primitive cells may have relied on what substance?

A

pyrite

37
Q

Which of the following choices is NOT a reason to utilize small subunit rRNA genes in phylogenetic analysis?

A

They have no enzymatic function

Reasons to utilize small subunit rRNA genes: they are large enough to provide an evolutionary history, they are functionally constant, they are universally distributed

38
Q

Homologous sequences descended from the same ancestral sequence found in different species are known as

A

orthologs

39
Q

Which of the following processes permits novel functions to develop through continues mutation?

A

gene duplication

40
Q

To what domain would an organism that has ether-linked membrane lipids and no peptidoglycan belong to?

A

Archaea

41
Q

One of the hypotheses about eukaryotic cell formation proposes that a nucleus-bearing cell acquired a mitochondrial-precursor cel by endosymbiosis. Which of the following statements reflects a major problem with this hypothesis?

A

Bacteria and Eukarya have similar membrane lipids.

42
Q

Which of the following events took place after the endosymbiotic events leading to the formation of mitochondria

A

the development of multicellular eukaryotes

43
Q

What is the recommended DNA-DNA hybridization value to say that two organisms are members of the same species?

A

70%

44
Q

Which technique is frequently used in phylogenetic analysis to obtain sufficient copies of a gene for sequencing?

A

PCR

45
Q

What is the name of the hypothesis that mitochondria and chloroplasts originated from prokaryotic organisms?

A

endosymbiotic hypothesis

46
Q

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

A

RNAs can have catalytic activity

47
Q

Which statements describe the evidence that supports the endosymbiotic theory?

A

Chloroplasts and mitochondria have a double-stranded, circular piece of DNA in their cytoplasm

48
Q

When determining taxonomic relationships via multilocus sequence typing (MLST) why are “housekeeping” genes generally used?

A

housekeeping genes encode essential functions in cells and are always located on the chromosome

49
Q

There has been considerable concern that chemicals released into the atmosphere are damaging the ozone shield, leading to regulations affecting the use of these chemicals. What would be the effect if the ozone shield were severely damaged or lost?

A

Large amounts of UV radiation would reach Earth’s surface and kill many living organisms

50
Q

You discover a parasitic bacterium with a tiny genome. Most likely, this tiny genome developed through

A

deletion, redundant functions can be removed in this way.

51
Q

The polymerase chain reaction has revolutionized molecular genetics. Despite all of the advantages of PCR, it does have limitations. Which of the following is NOT a limitation of PCR

A

It requires very pure and high-quality DNA

Limitations include: it is more error prone than most DNa replication, PCR is so sensitive that it contamination can easily occur, and it is necessary to know something about the sequence of the DNA sample prior to amplifying a specific region

52
Q

Electrophoresis can be used to separate molecules by size, shape, and charge. When DNA samples are run in an electrophoresis gel, the different bands produced generally represent fragments of different sizes. Why is the size of the fragment the most critical factor in determining how far it migrates on a gel when DNA fragments are compared?

A

DNA moves toward a positive charge due to the negative charge on its phosphate groups. The charge is consistent because all DNA nucleotides have a single phosphate group rather than having more diverse patterns of charges. Because the charge is relatively consistent, size is the most important factor determining how far fragments move.

53
Q

What might be a reason that a researcher would decide to use Northern blotting instead of Southern blotting?

A

To determine the extent to which a gene is being transcribed in a particular tissue

54
Q

If a restriction enzyme that recognizes GGCAT and cuts between the two guanine residues is mixed with DNA that has the sequence CCGATTATAATCCCGCGGCATATTAGGGCGG, how many pieces would be in the resulting product?

A

two

55
Q

Sarah has cloned a gene that codes for the protein EN. EN breaks down cellulose. She wants to collect a large concentration of this protein for research. Which vector should she choose

A

expression vector

56
Q

Which of the following is NOT an obstacle for expressing cloned eukaryotic genes in bacteria?

A

ALL are obstacles: the host may not be able to perform post-translational modifications, sequences may need editing due to codon usage, introns must be removed.

57
Q

When using a reporter gene to investigate expression of a target protein, the promoter of the _____ is ligated to the coding sequence of the _____

A

target gene/reporter gene

58
Q

An example of heterologous expression is

A

a bacterium expressing a human insulin gene

59
Q

DNA synthesis during PCR differs from natural DNA synthesis in that

A

thermostable DNA polymerase is used, DNA primers are used.

60
Q

If you were trying to determine whether mice have a similar gene to a particular human gene that you wanted to study, then you could run the mouse DNA on a gel and use a probe with a sequence form the

A

human gene with conditions for less stringent hybridization.

61
Q

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

A

RNAs can have catalytic activity

62
Q

Which of the following populations would be most likely to demonstrate genetic drift?

A

A researcher transfers bacteria into fresh medium but accidentally collects only a very small quantity of bacteria in the process.

63
Q

In the Escherichia coli LTEE, one strain rapidly increased its population size by evolving the ability to use citrate as a carbon source. If citrate had not been present, then __________.

A

there would have been no selective advantage to having the mutation that allowed bacteria to use citrate

64
Q

What traits did the last universal common ancestor (LUCA) probably have?

A

Used hydrogen (H2) as an energy source, anaerobic

65
Q

What findings would support the RNA world hypothesis for viral origins over the selfish DNA hypothesis?

A

Evidence that viruses existed long before gene transfer agents, and evidence that the earliest viruses had RNA genomes.

66
Q

What would happen if you skipped sequence alignment while trying to construct a phylogeny?

A

it would be difficult or impossible to determine positional homology.

67
Q

If you used an enrichment culture that was selective for the species that you wanted to grow but not counterselective for other species, then

A

the desired species could grow, but many other species could successfully grow in the same conditions and possible even out-compete it

68
Q

a good selective medium for a nitrogen-fixing bacterium such as Azobacter would be

A

a medium containing atmospheric air without fixed nitrogen

69
Q

You collect a water sample knowing that it contains a high density of a microbe of interest. However, a culture produced from this sample has much higher densities of other species and only a low density of the microbe of interest. The most likely explanation is __________.

A

enrichment bias

70
Q

The quickest and easiest way to obtain a pure culture of an aerobic microbe that grows well on agar is to use __________.

A

a series of streak plates, selecting a well-isolated colony from each to produce the nest streak plate.

71
Q

a pure culture is also called

A

axenic

72
Q

Having high nutrient concentrations in a culture __________.

A

can inhibit the growth of microbes that require the nutrient but that do not normally encounter it in high concentrations.

73
Q

A limitation of staining cells is that

A

staining does not generally provide insights into phylogeny

74
Q

Denaturing gradient gel electrophoresis (DGGE) can be used to resolve phylotypes because __________.

A

even very similar orthologs have different melting profiles

75
Q

If you used viability staining to distinguish living and dead cells but found that some living cells appeared red, then the most likely explanation would be that __________.

A

the red cells were still alive but had damaged cytoplasmic membranes

In viability staining, the green stain enters all of the cells, but the red stain generally only enters dead cells because it cannot pass through an intact cell membrane. If a cell had a badly damaged cell membrane, then that could allow the red stain to pass through.

76
Q

If you placed a cell with the gfp gene into an anoxic habitat, then __________.

A

the cell would not appear fluorescent green, so a different gene would need to be used

The gfp gene codes for green fluorescent protein (GFP), which is only fluorescent under oxic conditions. However, there is no reason that the gene would be mutated simply because conditions were anoxic.

Microbiology (3 decks)

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