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Microbiology > Unit 3 > Flashcards

Unit 3 Flashcards

1
Q

What is transformation

A

uptake of free DNA from the environment

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2
Q

What is competence

A

When bacteria have the ability to take up foreign DNA

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3
Q

During transformation what type of DNA is taken up and why

A

Only ssDNA to prevent bringing in a virus/mutation

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4
Q

What are the two strategies for transformation

A

looking for a specific DNA sequence: 11bp sequence that tells bacteria the DNA is from their population or waiting for quorum so that only DNA from its population is taken up

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5
Q

what is transduction

A

Incorporation of foreign bacterial DNA mediated by viruses

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6
Q

What is the lytic cycle and what are bacteria called when they use this cycle

A

When bacteriophage infect a cell, replicate via rolling circle replication, then lyse the cell; baceriophage are virulent

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7
Q

What is the lysogenic cycle and what are the bacteria called when they use this cycle

A

Cell is infected, genome circularizes, then bacteriophage goes dormant due to lack of resources. Cell then gains resources or becomes stressed to virus ressurects itself, replicates, then lyses cell; temperate phage

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8
Q

What is generalized transduction

A

Random incorporation of any bacterial chromosomal fragments within an infectious phage

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9
Q

What is the process of generalized transduction

A

Viral DNA is injected into host, breaking up host chromosome. Packaging occurs when DNA is put into viral shells but some of the host DNA can be put in these shells. When cell is lysed bacteriophage leave to infect other cells. When shell goes to infect cells some receive host DNA that can be incorporated into new cell if advantageous

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10
Q

What is specialized transduction

A

Only happens in lysogenic cycle. When bacteriophage ressurects itself, it takes only certain parts of the genome (the parts directly next to it) thus, packaged viruses will be defective and host DNA can be incorporated into new cell when “infection” occurs

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11
Q

What organisms are intercellular mobile genetic elements and what does that mean

A

Plasmids and bacteriphages; means they can direct their own movement between bacterial genomes

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12
Q

What organisms are intracellular mobile genetic elements and what does it mean

A

Insertion Sequences and transposons; they can direct their own movement within bacterial genomes

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13
Q

What is methanogenesis in archaea

A

using anaerobic respiration to produce E; not much E is made so methanogens are just barely living

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14
Q

How is methanogensis in sediment environments an example of syntrophy between archaea and bacteria

A

Lack of O so bacteria must go through fermentation but products are toxin when in high concentration. Archaea use products to produce methane so no toxins for bacteria and archaea get food

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15
Q

How do bacteria and archaea work together in rumeneints

A

Volatile fatty acids (VFAs) along with H2 and CO2 are products of bacterial fermentation but are toxin when in high concentrations so archaea use those products for methanogenesis

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16
Q

Why do rabbits have two types of poop

A

They have regular poop to get rid of waste but also poop known as cecal pellets. These are pellets that have partially digested food in them that are then reingested to get more nutrients

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17
Q

How do microbes work in the human intestine

A

Microbes go through fermentation to break down material that we can’t. This creates short chain fatty acids that are a source of E for colonocyntes as they go into the mitochondria, through beta oxidation, into the TCA cycle to make reducing power to generate electrons for ATP synthesis

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18
Q

What are halophiles

A

Archaea that grow in very high salt concentrations and at lower O levels, produce pigments

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19
Q

How do halophiles produce pigment

A

via a bacteriorhodopsin that uses a light driven proton pump to generate PMF for ATP synthesis. They have retinal hydrocarbons that have two forms (cis or trans) that are switched between depending on light

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20
Q

How does halorhodopsin work

A

With chloride ions that enhance PMF creating more of a potential difference

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21
Q

How do sensory rhodopsin work

A

There are two; one that senses red/infared light and one that sense damaging/blue light. Archaea want to move towards the light but not too close. As such they move towards the red light via phosphorylation but also move away from blue via phosphorylation when too close.

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22
Q

How do bacteria adapt to living in hypersaline environments

A

They maintain homeostatsis via compatible solutes which don’t interfere with biochemical reactions and help maintain concentration intra and extracellularly

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23
Q

How do bacteria make it to a plant for crown gall disease

A

Rhizobacteriaceae move towards a wonded plant when they release metabolites and chemotaxis towards it and enter it

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24
Q

What causes the tumor to grow on plants for crown gall disease

A

The TI plasmid in the bacteria that causes a change in gene expression via conjugation

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25
Q

How do cyanobacteria fix N

A

They have specialized cells, heterocysts, that can fix nitrogen. They have specialized membranes that exclude oxygen from entering them so that they can fix N while the other cells can go through photosynthesis

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26
Q

How does symbiotic N fixation work between bacteria and plants

A

bacteria are attracted to plants via flavanoids. As bacteria move towards the plant, Nod factors are released which change gene expression in the plant as well as rhicadhesion which allow the bacteria to adhere to the root hair. Once bacteria infect the plant they proliferate to make a nodule. In the nodule nitrogenase enzymes are made that fix N. Nitrogenase breaks triple bonds in N to produce ammonia which is made into amino acids for bacteria

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27
Q

Where does does nitrogenase get the E to convert N to ammonia

A

Bacteroids convert sugar in organic acids which is put into the CAC then the ETC to make a PMF for ATP synthesis

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28
Q

What happens to bacteria once they make it into the plant for N fixation

A

A shepherd’s hook forms that wraps around the bacteria to hold it. An infection thread is made only in the presence of Rhizobium that moves thrughout the cell so that a symbiosome is formed, keeping the bacteria in one place. The bacteria then become bacteroids that contribute to ATP synthesis

29
Q

What do bacteria do in nitrosification, whay do they use for it, and what else is needed for it

A

Converting NH4 to NO2 via ammonia monooxygenase (AMMO). Requires a lot of thylakoid membranes to increase SA for more AMO

30
Q

what do methnotrophic bacteria use to convert CH4 to CO2 and what else is needed for it

A

methan monooxygenase (MMO) also requires a lot of thylakoid membranes to maximize MMOs

31
Q

How are AMO and MMO similar

A

They have different functions but both will oxidize ammonia if given the opportunity

32
Q

Explain the realtionship between sphagnum, archaea, and methanotrophic bacteria

A

Bacteria ferment the organic matter that is on the floor of the ocean, archaea eat the products of fermentation prodcuing methane, methanotrophic bacteria convert the methane into CO2 for the plant

33
Q

What are microbial mats

A

microbes that lived in multispecie communites comprised mainly of primary producers

34
Q

What are biofilms

A

Microbial mats but typically thinner and are not really made of primary producers

35
Q

How are biofilms helpful for bacteria

A

They allow the bacteria to be able to secrete molecules that won’t freely diffuse so that a quorum can be sensed as well as molecules broken down for E

36
Q

What is the life cycle of biofilms

A

Individual motile bacteria make their way onto a new surface, if good resources on surface, bacteria will diffrentiate and lose flagella so E can be used for replication. Bacteria move closer together to form a colony and make a capsule (Biofilm) that grows and remodels. Eventually the biofilm becomes overpopulated so diffrentiation happens again and motile bacteria leave tos start again

37
Q

What is a virus

A

Genetic element capable of replication indepdent of host cell chromosomes but not of cells

38
Q

What does it mean for viruses to be obligate intracellular parasites

A

They can’t survive without host cell

39
Q

What type of genetic material do viruses use

A

RNA or DNA, ds or ss but never both, they will only use one

40
Q

What type of viruses are more common among animal viruses

A

enveloped viruses as they have viral glycoproteins involved in adhesion to target cells and viral enzymes that free virus should it stick to cell bc of proteins

41
Q

What is the eclipse period of bacteriophages

A

When infection has happened but there are no viruses since they are disassembled

42
Q

What is the latent period of bacteriophages

A

When there are no extracellular viruses but there can be intracellular viruses

43
Q

What is the rise period of bacteriophages

A

When the number of extracellular viruses begin to rise; lysis begins

44
Q

What is burst size

A

number of viruses released from a single infected bacterium; varies from virus to virus

45
Q

What is key part of the myoviridae bacteria

A

They have a contractile tail that twists so that noncontractile tube is driven into bacterial membrane so that DNA is released

46
Q

Explain the infection process of T4 bacteriophage

A

Attach to cell via tail fibers (legs) attachment to OmpC, needed to ensure that virus infects correct host. Tail pins (teeth of “stomach”) unfold and are driven into cell. Contractile tail twists so tube is driven into cell causing infection. Lysozyme is driven into cell to degrade peptidoglycan of cell

47
Q

Explain how restricion endonuclease works to defend bacteria

A

Enzymes, EcoR1, cuts DNA at palindromes so that H bonds are the only ones left. DNA is now restricted meaning its basically inactive. However to prevent restriction of cell genome a methyl group is added so identical sequences on genome to prevent restriction

48
Q

Explain how the toxin antitoxin works to defend bacteria

A

Genes are built into chromosome so that bacteria doesn’t become food for virus to infect its brethren. LsoA is toxin while LsoB is antitoxin. Although viruses try to stop cell function, the enzymes are alreadly made so that the toxin will cause death. However Dmd protein is used by virus to bind to LsoA and act like LsoB so phage can replicate

49
Q

Explain how CRISP works to defend bacteria

A

Immunity from previous bacteria are passed on during replication in genome. Spacer regions of genome hold DNA sequences that are similar to viral genomes. When bacteria is infected, spacer become trascribed and cleaved into small chunks that will bind to Cas protein as well as viral mRNA to cleave it

50
Q

What is expressed in cells to supress the lytic cycle

A

Viral repressor gene represses lytic cycle through positive control. Which is controlled via the C1 protein through positive control. The C1 protein is broken down when lexA is broken down from the SOS regulon causing the viruse to resurrect itself

51
Q

How does having a bacteriophage in the lytic cycle help bacteria?

A

The repressor protein that prevents virus resurrection also prevents new infection but only from identical viruses

52
Q

When will a bacteriophage go into lysogeny

A

When there are a lack of resources meaning less viruses would be able to be made and when there is a high multiplicity of infection (MOI) meaning that should the virus lyse the cell, there would be no host for those viruses to infect

53
Q

What type of virus is polio virus

A

a + ssRNA virus

54
Q

How do babies receive passive immunity

A

They receive IgG from their mothers through the placenta or milk. Lasts only a few weeks and allows babies to develop own immunity

55
Q

What was the benefit of Salk’s vaccine

A

Prevented viremia (infection getting into blood) via IgG but required boosting

56
Q

What was the benefit of Sabin’s vaccine

A

oral vaccine, easy for kids, and made it so that polio couldn’t spread via mucosal layer (had IgA antibodies)

57
Q

How does polio bind to a host

A

The viral proteins of the virus bind to necl-5 receptor. VP 2 and 3 specifically bind to the receptor causuing a conformational change of proteins so that the viral RNA genome is injected into the host

58
Q

How does polio replicate

A

Instead of capping a 5’ methyl cap, polio uses ires sites to trick ribosomes into binding to it to start translation. This creates a giant protein that goes through autoproteolytic activity to create protiens. One of which is RNAP then makes a new RNA copy resulting in - ssRNA which serves as a template to make more + ssRNA.

59
Q

What is site specific recombination

A

Moving of DNA that does not depend on recA or DNA similarity but specific sequences of DNA

60
Q

How are insertion sequences different to transposons

A

ISs only have one gene that encodes tranposase and IRs on each end for movement while transposons (Tns) contain IS elements as well as multiple genes

61
Q

What are composite transposons

A

when two ISs flank tranposase and other genes

62
Q

What are noncomposite transposons

A

When IRs flank transposase and other genes, usually antibiotic resisitance

63
Q

What is conservative transposition, what it another name for it, and how does it affect the copy number

A

transposon is cut out and moved to a new site AKA cut and paste. Same copy number

64
Q

What is replicative transposition and how does it affect the copy number

A

transposon is replicated and copy is placed somewhere else. Adds to the copy number

65
Q

How does replicative transposition work

A

Plasmid or chromosome is nicked at target sites then join together forming cointegrate. Replication occurs so there are two circles making an 8. Resolvase enzyme recombines internal resoultion sites (IRS) so that circles are broken apart.

66
Q

What are integrons

A

Mobile pieces of DNA with the ability to acquire novel genes

67
Q

How do integrons work to take in new DNA

A

instead of IRs, integrase takes new DNA. int brings DNA between aatC and aatI via integrase site. recombination allows the gene to be replicated intot the genome directly after aatI site, pushing all “novel” genes back

68
Q

What is the difference between Salk’s vaccine and Sabin’s vaccine for Polio

A

Salk’s vaccine uses IgG serum so it provided antibodies in the bloodstream. People were protected from the diesase but not from being infectious. Sabin’s vaccine used both IgG and IgA serums so it protected agaisnt infection and the disease, however it could cause paralytic poliomyleitis

69
Q

What is the poliovirus life cycle

A
  1. Attaches to cell via necl-5 receptors and tail fibers
  2. +ssRNA enters the cell with its VPg protein
  3. Genome is translated into a giant protein
  4. Protein goes through autoproteolytic activity
  5. A bunch of new proteins are made in waves
  6. +ssRNA is made from -ssRNA

Microbiology (5 decks)

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