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MICR 2420 > Pre Midterm Notes > Flashcards

Pre Midterm Notes Flashcards

1
Q

what did Holger Jannasch discover

A
  • unculturable marine bacteria

- decomposition of material in the depths of the ocean takes 100x longer than on land

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2
Q

what will you find where there are rich sources of carbon in not hot undersea oases

A

life!

  • cold seeps
  • whale fall
  • shipwrecks
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3
Q

true or false: most life forms around hydrothermal vents require sunlight for survival

A

true

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4
Q

what is eutrophication

A
  • oxygen dead zone
  • excessive richness of nutrients in a lake or other body of water, frequently due to runoff from the land, which causes a dense growth of plant life and death of animal life from lack of oxygen.
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5
Q

what do all species of bacteria have a need for?

A

nitrogen and phosphorous

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6
Q

anoxic

A

water without oxygen

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7
Q

what is soil?

A
  • complex mixture of decaying organic and mineral material

- life support for vast # of microbes, as well as terrestrial plants

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8
Q

what is in the organic horizon and what decomposes it

A

leaf litter, organic matter, top layer

decomposed by fungi, actibonmyctes, slime molds

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9
Q

what is in the aerated horizon?

A

decomposed organic particles and minerals

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10
Q

what is in the elutriated horizon?

A

insoluble particles

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11
Q

what is in the B horizon?

A

clay and minerals

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12
Q

which agricultural practice would be most harmful to soil microbes?

a) applying drainage to poorly drained soil
b) application of sewage sludge
c) driving over the soil with heavy equipment
d) application of manufactured fertilizer pellets
e) application of raw barnyard manure

A

d) application of manufactured fertilizer pellets

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13
Q

what are the levels of soil?

A
  1. organic horizon
  2. aerated horizon
  3. elutriated horizon
  4. B horizon
  5. water table
  6. water-saturated horizon
  7. bedrock
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14
Q

what do roots from plants secrete in soil?

A

polysaccharides

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15
Q

true of false: a soil particle supports a lot of microbe life

A

true

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16
Q

what is streptomyces?

A
  • a major genus of soil bacteria
  • notable for the antibiotics they make
  • responsible for smell of soil
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17
Q

what are nematodes?

A

microscopic works that reside in the top 15cm of the soil

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18
Q

what do microbes in the rhizosphere do?

A
  • help proest plants from pathogens
  • may fix nitrogen
  • feed off nutrients provided by plant
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19
Q

what are endomycorrhizae?

A
  • fungi that invade the root cell
  • form arbuscules
  • completely dependent on host, can’t sexually reproduce
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20
Q

how do endophytes grow?

A

within plant tissue

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21
Q

what are the 3 domains of life?

A

eukarya
bacteria
archaea

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22
Q

what are the 2 kingdoms of unicellular organisms?

A

bacteria

archaea

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23
Q

what are the 2 kingdoms of multicellular organisms?

A

plants

animals (including fungi)

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24
Q

what is the kingdom made of both unicellular and multicellular organisms?

A

protists (including algae)

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25
Q

what are the 8 functions of life?

A 
respiration
regulation 
reproduction
excretion
growth
nutrition
transport
synthesis
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26
Q

what are carbohydrates building blocks?

A

monosaccarides

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27
Q

what are proteins building blocks?

A

amino acids

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28
Q

what are nucleic acids building blocks?

A

nucleotides

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29
Q

what are lipids building blocks?

A

glycerol

fatty acids

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30
Q

what is life on Earth made from?

A

stardust: remnants of supernovae

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31
Q

what does life require?

A
  • continual imputes of energy

- temperature range the permits liquid water

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32
Q

how did ER and nuclear envelope of eukaryotes evolve?

A

from infoldings of the plasma membrane in a primordial cell

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33
Q

how does mitochondrion produce energy?

A

from chemical components

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34
Q

how does chloroplast produce energy?

A

from chemical components

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35
Q

what did Robert Hooke do?

A
  • built first microscope

- coined term cell

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36
Q

what did Antonie Van Leeuwenhoek do?

A

1st person to observe single celled organism

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37
Q

what did Edward Jenner do?

A

introduced vaccination against small pox

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38
Q

how was small pox vaccination created?

A

developed from cowpox scab

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39
Q

what did Lazzaro Spallanzani do?

A

1st to show that broth sterilized failed to grow microbes

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40
Q

what did Louis Pasteur do?

A
  • discovered fermentative metabolism

- Used swan-necked flasks to demonstrate that microbes are not produced through spontaneous generation

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41
Q

what did Florence Nightingale do?

A
  • founder of medical epidemiology
  • Demonstrated that infection caused more morbidity than any other condition during the Crimean War
  • Persuaded the British Army to adopt more hygienic conditions to counteract infection
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42
Q

what did Robert Koch do?

A
  • 1st to determine specific microbes cause specific diseases

- developed Koch’s postulates

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43
Q

what did Angelina and Walter Hesse do?

A

1st to use slid medium to culture microbes

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44
Q

what did Ignaz Semmelweis do?

A

1st proponent of hand-washing as an important process for physicians in hospitals

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45
Q

what did Joseph Lister do?

A

Pioneered the use of a clean (free-from microbes) operating area for his patient

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46
Q

who was involved in the discovery of viruses?

A

Dmitry Ivanovsky
Martinus Beijerinick
Wendell Stanley

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47
Q

according to the 3 domain model of classification, the ancestors of mitochondria are:

a. cyanobacteria
b. fungi
c. proteobacteria
d. archaea
e. protocista

A

c. proteobacteria

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48
Q

analysis of 165 rRNA gene sequence showed that

a. plants and animals are as distant from bacteria as they are to each other
b. all microbes are only distinctly related to the eukaryotes
c. Achaea are almost as distant from bacteria as they are from eukaryotes
d. viruses are closely related to prokaryotes

A

c. Achaea are almost as distant from bacteria as they are from eukaryotes

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49
Q

a photosynthetic organism that utilizes inorganic iron as an electron source and fixes its own carbon would be called:

a. photolithoautotroph
b. photochemoheterotroph
c. photolithoheterotroph
d. chemolithoheterotroph
e. chemolithoautotroph

A

a. photolithoautotroph

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50
Q

which of the following consists of prokaryotic cells:

a. bacteria and fungi
b. archaea and fungi
c. viruses and bacteria
d. bacteria and archaea
e. archaea and viruses

A

d. bacteria and archaea

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51
Q

which of the following statements is false regarding archaea:

a. some archaea were originally wrongly identified as bacteria
b. archaea does not use fatty acids to build their membrane phospholipids
c. all methanogens are archaea
d. all archaea possess pseudopeptidoglycan
e. S-layers are very common in many archaea species

A

d. all archaea possess pseudopeptidoglycan

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52
Q

which is our closest relative in this group:

a. dinoflagellate
b. choanoflagellate
c. euglenia
d. ameba
e. fungi

A

b. choanoflagellate

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53
Q

what is the primary role of a mushroom’s underground mycelium:

a. absorbing nutrients
b. anchoring
c. sexual reproduction
d. asexual reproduction
e. protection

A

a. absorbing nutrients

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54
Q

which of the following statements is not true:

a. fungi are saprophytic
b. fungi are never photosynthetic
c. mycorrhizae help some plants grow
d. fungi are extracellular digesters
e. all fungi are multicellular

A

e. all fungi are multicellular

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55
Q

what does the contractile vacuole of an amoeba do:

a. controls the shape of the cell
b. controls the water content of the cell
c. help the cell move
d. helps the cell digest food

A

b. controls the water content of the cel

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56
Q

true or false: most viruses have a broad range of hosts

A

false

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57
Q

what are viruses made of:

a. some form of protein coat, and nucleic acid
b. always an envelope, capsid and DNA
c. only nucleic acid
d. always tegument and nucleic acid

A

a. some form of protein coat, and nucleic acid

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58
Q

EBV, the cause of mono, is a large, ds DNA virus surrounded by an envelope. according to the Baltimore scheme, its classified as:

a. group I
b. group II
c. Group III
d. group IV
e. Group V

A

a. group I

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59
Q 
some E. coli divide themselves every min into 2 equal parts that are each he same size as the original organism. the Petri dish is which we started observing this process was full at 12.00.
when was it half full?
a. 6.00
b. 9.00
c. 11.30
d. 11.59
A

d. 11.59

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60
Q

you ingest 200 Salmonella enteric cells. They all make it through your stomach and into the intestine where they start to multiply. the average generation period is 2 hours. you eel sick when there’s > 1.5 million present. how long will this take?

a. about an hour
b. about a day
c. about 3 days
d. about a week
e. about a month

A

b. about a day

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61
Q

bacterial cultures go through a lag because:

a. they gradually begin to die
b. they are synthesizing new enzymes in order to use nutrients in their medium
c. they are being exposed to increasing amounts of their own waste product
d. the DNA and protein synthesis in the culture has not caught up with cell division

A

b. they are synthesizing new enzymes in order to use nutrients in their medium

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62
Q

which of the following is not an example a microbial biofilm:

a. dental plaque
b. cryptogamic crust
c. pond scum
d. boat hull biofouling

A

b. cryptogamic crust

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63
Q

which method would you choose to get an overall picture of the bacterial species present in a given ecosystem?

a. metagenomics
b. proteomics
c. metabonomics
d. phylogenomics
e. metatranscriptomics

A

d. phylogenomics

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64
Q

what kind of organisms can grow within the aphasic zone?

a. phototrophs and lithotrophs
b. lithotrophs only
c. heterotrophs only
d. phototrophs, heterotrophs and lithotrophs
e. heterotrophs and lithotrophs

A

e. heterotrophs and lithotrophs

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65
Q

true or false: some bacteria can be seen with the naked eye

A

true - Thiomargarita namibiensis

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66
Q

what percent of known microbes can be cultured using traditional methods?

A

0.1%

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67
Q

what did Sergei Winogradsky do?

A
  • among 1st to study bacteria in natural habitat
  • discovered lithotrophs
  • developed enrichment cultures
  • built Winogradsky column
  • showed importance of bacteria in geochemical cycling
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68
Q

what are endosymbionts?

A

organisms that live symbiotically inside other organisms

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69
Q

what did Lynn Margulis do?

A

Proposed that eukaryotic organelles, such as mitochondria and chloroplasts, evolved by endosymbiosis from prokaryotic cells engulfed by proto-eukaryotes

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70
Q

what did carl Woese discover?

A

prokaryotes in hot springs:

Archaea

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71
Q

what are some stresses prokaryotes face

A

predation
nutrition limitation
osmotic stress
temperature/pH fluctuation

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72
Q

what traits do all prokaryotes share?

A
  • thick, complex outer envelope
  • compact genome
  • tightly coordinated cell functions
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73
Q

what comes in a Mollicutes?

A

DNA
Ribosomes
Cytoplasm
Plasma membrane

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74
Q

pros of mollicutes

A
  • doesn’t require a lot of energy to survive

- Small -compact and can squeeze through small space

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75
Q

cons of mollicutes

A
  • Difficult to maintain –usually needs a eukaryotic host cell to keep it safe
  • Complicated diet required (cannot synthesize many of its required nutrients)
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76
Q

how many genes required for life have an unknown function?

A

149/473

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77
Q

what are cell walls made up of?

A
  • Peptidoglycan
  • Polymer of sugars and amino acids
  • Sugars are N-acetyl glucosamine and N-acetyl muramic acid
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78
Q

what is a gram positive bacteria composed of?

A 
DNA  
Ribosomes
Cytoplasm 
Plasma membrane 
Thick cell wall (20-80nm)
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79
Q

pros of the gram positive model

A
  • Strong –teichoic acid threads through the peptidoglycan layers, adding strength
  • Resistant to osmotic lysis
  • several pleasing shapes to choose from (coccoid, rod, spiral)
  • Available in Gram stained purple!
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80
Q

cons of the gram positive model

A
  • Must be kept away from lysozyme at all costs!

- Sensitive to antibiotics that target the cell wall (e.g. penicillin)

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81
Q

what is a gram negative bacteria composed of?

A
  • DNA
    Ribosomes
    Cytoplasm
    Plasma membrane
    Thin cell wall (just 1 or 2 sheets of peptidoglycan)
    Outer membrane (contains lipopolysaccharide)
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82
Q

pros of gram negative model

A
  • Able to defend itself against a wide range of toxic molecules
  • Has a built-in storage compartment –the periplasmic space
  • Resistant to osmotic lysis
  • A wide range of pleasing shapes to choose from
  • Available in Gram stained red
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83
Q

cons of gram negative model

A
  • toxic if not handled correctly
  • Requires a bigger genome to make the more complex cell wall
    – can be expensive to maintain
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84
Q

examples of gram negative

A

E. coli

h pylori

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85
Q

what is the waxy model?

A

mycobacterial cell envelope

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86
Q

describe the mycobacterial cell envelope

A
  • Most complex of all bacterial cell envelopes
  • Include unusual membrane lipids (mycolicacids)
  • Form thick, waxy surface that is exceptionally hydrophobic and resistant to chemicals (and phagocytosis)
  • Acid fast bacilli
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87
Q

what are mycobacteria resistant to?

A 
Osmotic lysis
Detergents
Dryness
Many disinfectants
Most antibiotics
Oxidative bursts
Phagocytosis
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88
Q

what’s the downside to mycobacteria?

A

often very slow growing

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89
Q

describe the S-layer

A
  • S = ‘Surface’ (5-25nm thick)
  • An additional protective layer (bacterial chainmail!)
  • Crystalline layer of thick subunits
  • Highly ordered
  • Can flex to allow movement of molecules
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90
Q

what is the S-layer composed of?

A

Protein or glycoprotein

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91
Q

what is the capsule also known as?

A

the slime layer

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92
Q

why does the capsule appear as clear halos around the cell?

A

hard to stain

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93
Q

why is the capsule also known as the slime layer?

A

Consists of a slippery coat of loosely bound polysaccharides

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94
Q

what is the role of the capsule?

A

important role in pathogens

for preventing phagocytosis/activation of the innate immune system

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95
Q

true or false: you can have a thylakoid in a gram positive option

A

false: only gram negative

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96
Q

what is the thylakoid made of?

A
  • Specialist systems of extensively folded lamellae (sheets) of membranes
  • packed with photosynthetic proteins and electron carriers
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97
Q

what does the thylakoid do?

A

Maximize photosynthetic capability of the cell

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98
Q

what organism is responsible for ~50% of atmospheric O2?

A

Prochlorococcus marinus

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99
Q

true. or false: carboxysomes are only available for gram negative?

A

true

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100
Q

describe carboxysomes

A

Contain enzymes used to fix CO2

  • Found in all cyanobacteria as well as some chemotrophs that fix CO2
  • Have a characteristic polyhedral shape
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101
Q

where are gas vesicles able to be present?

A

aquatic, photosynthetic variants

some heterotrophs

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102
Q

describe gas vesicles

A

Thin ‘balloons’ made of extremely hydrophobic protein

- Allow a microbe to maintain a set buoyancy optimal to its preferred conditions in the water column

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103
Q

what do storage granules do?

A
  • store excess energy to be used when nutrients are low
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104
Q

how is energy stored in storage granules?

A

Usually stored in the form of glycogen, polyhydroxybutyrate (PHB) (biodegradable plastic) or poly-3-hydroxyalkanoate (PHA)

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105
Q

where can magnetosomes be present?

A

gram negative, aquatic species

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106
Q

what are magnetosomes and what do they do?

A
  • Membrane-bound crystals of magnetite (Fe3O4)

- Allow a motile bacterium to orient itself with the Earth’s magnetic field

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107
Q

what are advantages of magnetosomes?

A

narrow size distribution (25–55nm)

  • uniform morphology
  • high purity
  • presence of a membrane (lipids and proteins)
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108
Q

pili can be:

A
  • long or short
  • flexible or brittle
  • curly or straight
  • singular or twisted together in rope-like bundle
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109
Q

what do pili do?

A
  • important organelles for bacterial adhesion
  • Some types are used in bacterial sex (conjugation)
  • Some types are used in a specialist type of bacterial motility –‘twitching motility’
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110
Q

what do pathogens use pili for?

A

attach to host cells and initiate disease

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111
Q

what are stalks?

A
  • Membrane-embedded extension of the cytoplasm of some aquatic bacteria
  • Gram Negative option only
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112
Q

what do stalks do?

A
  • Tip of stalk secretes factors –“Holdfasts”
  • Act as an antenna to seek out nutrients (particularly phosphates)
  • Allow bacterium to remain in a favourable location
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113
Q

what are rotary flagella?

A
  • Organelles of motility
  • Available for both G+ and G-models
  • Rigid, long, helical, protein structures
  • Anchored in the cell membrane (G+) or outer membrane (G-)
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114
Q

true or false: rotary flagella are anchored in the cell membrane for G-

A

false: that’s from gram positive

gram negative in the outer membrane

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115
Q

what do rotary flagella do?

A

work together with chemoreceptors to propel bacterium in optimal directions using ‘runs’ and ‘tumbles

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116
Q

how fast do flagellum turn?

A

1000 - 30,000rpm

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117
Q

what do nanotubes do?

A
  • Especially important for biofilm-forming microbes
  • Allow transmission of material between cells
  • Can occur cross-species
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118
Q

what are nanotubes?

A
  • Extensions of the cell envelope that connect the cytoplasm (or periplasmin G-bacteria) between 2 different cells
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119
Q

what is a thermophile?

A

archaea that likes the heat

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120
Q

describe Pyrococcus furiosus

A

a thermophile as well as a barophile

  • Can only survive at temps >70C (prefers 100C!)
  • An anaerobe that metabolizes sulfur to H2S
  • Lives in deep-sea hydrothermal vent
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121
Q

what are psychrophiles?

A

Largely uncultured archaea: anaerobic heterotrophs, sulfate reducers or nitrite-reducing methanotrophs Live in deep, permanently cold water

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122
Q

what are halophiles and give an example

A

example: Haloquadratum walsbyi
- Likes hypersaline pools and in some extreme salt pools may be the only life form present
- Phototroph that forms fragile sheets that float near the surface of the water
- Uses gas-filled vesicles to float

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123
Q

what are acidophilus and give an example

A

example: Ferroplasma acidiphilum
- Oxidizes sulfur from FeS2 to form H2SO4
- Generates pH of 0 (or less!)
- Has no cell wall
- Can be found in acid mine tailings

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124
Q

what do methanogens do?

A
  • able to generate methane from CO2and H2, formate, acetate and other small molecules
  • Rely on bacterial species to provide them with essential nutrients
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125
Q

what is the basic reaction for methanogens

A

CO2+ 4H2–> CH4+ 2H2O

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126
Q

archaea cell membrane vs. bacterial

A
  • Archaea use L-glycerol linked to side chains using ether links
  • Bacteria use D-glycerol linked to side chains suing ester links
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127
Q

what do archaea have instead of fatty acid?

A

side chains composed of repeating units of isoprene

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128
Q

describe phototrophic archaea

A
  • do not use chlorophyll and are not photosynthetic
    •Instead use a retinal-based ion pump called ‘bacteriorhodopsin’
    •Ion pump is coupled to ATP synthesis for the cell
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129
Q

what is more complex in eukaryotes than prokaryotes?

A

structure and form

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130
Q

what is more complex in prokaryotes than eukaryotes

A

metabolism

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131
Q

what did all eukaryotes descend from?

A

an ancestral cell that engulfed a bacterial endosymbiont–which became a mitochondrion

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132
Q

what did all phototrophs eukaryotes descend from?

A

an ancestral cell that additionallyengulfed the bacterial ancestor of chloroplast

133
Q

how much of eukaryote DNA sequence is noncoding?

A

50-90%

134
Q

what clade do animals and fungi fit into?

A

opisthokonts

135
Q

what did the first choanoflagellate sequence reveal?

A
  • Five immunoglobulin genes
    •Yet choanoflagellates have no immune system
    •Collagen, cadherin and integrin domains
    •Yet choanoflagellates have no skeleton nor any matrix binding cells together
    •Tyrosine kinase genes
    •Yet choanoflagellates are not known to communicate/signal with each other
136
Q

characteristics of fungi

A 
- eukaryotes
•Reproduce using spores
•Unicellular forms
•Heterotrophic
•Absorptive nutrition
•Cell walls made of chitin
•Cell membranes contain ergosterol
•Nature’s recycler
137
Q

describe yeast

A 
- unicellular fungi
•Do not use hyphae to obtain nutrients
•Some yeasts are dimorphic
•Either unicellular or have mycelia, depending on the environmental conditions
•Important in food manufacture
138
Q

life cycle of yeast

A

alternates between haploid (1n) and diploid (2n) forms

139
Q

explain yeast haploid form

A

develops gametes for fertilization, producing a 2n zygote

140
Q

explain yeast diploid form

A

undergoes meiosis, restoring the haploid form

141
Q

how do fungi grow hyphae?

A

with cell walls of chitin

142
Q

what is chitin

A
  • Chitin consists of beta-linked polymers of N-acetyl glucosamine
    •Has immense tensile strength (greater than that of steel!)
    •Enables it to penetrate even tough food source
143
Q

what is the mycelium?

A

A branched mass of extending hypha

144
Q

describe characteristics of truffles

A
  • Fruiting body of a subterranean mushroom
  • Grow symbiotically with trees such as hazel and oak
    •Weight for weight, more valuable than gold
    •Requires a good truffle pig or dog to locate them
145
Q

what are ophiocordyceps?

A
  • Fungal spores enter ant’s body through enzymic action

- Somehow interfere with brain activity, and make ant behave very strangely

146
Q

what is fly agaric also known as

A

santa’s little helper

147
Q

describe fly agaric

A
  • A ‘true mushroom’
    •In the same family as some of the most toxic mushrooms known
  • less toxic but has hallucinogenic properties.
148
Q

what are microsporidia?

A

fungi that have lost much of their genomes and have non-functional mitochondria

149
Q

true or false: water molds have fungus like filaments that infect plants and a

A

true

150
Q

describe Amebas

A
  • Look like microscopic, amorphous lumps of jelly
    •Have ‘ectoplasm’ and ‘endoplasm’
    •Able to move through the production of pseudopods(false feet)
    •Undertake highly controlled, complex motion
    •Free-living predators in soil or water
151
Q

how do amebas engulf their prey?

A

using phagocytosis

152
Q

what is the brain eating amoeba?

A

Naegleria fowlerii

153
Q

describe slime molds

A
  • Used to be thought of as fungi (hence mold)
    •have cellulose, not chitin, in their cell walls
    •Single celled communities of ameba
154
Q

what are radiolarians?

A

Amoebas with shells (tests) made of silica

155
Q

what is algae?

A
  • Primary producers in most ecosystems

* Can be primary and secondary symbionts

156
Q

describe primary endosymbiotic algae

A
  • share their lineage with plants
    •Useful models of plant physiology
    •2 major clades
157
Q

what are the 2 major clades of primary endosymbiotic algae

A

chlorophyta (green algae)

rhodophyta (red algae)

158
Q

what are the 2 secondary endosymbiotic algae?

A

diatoms

kelps

159
Q

describe diatoms

A

-Unicellular algae with a unique, protective bipartate shell made of silica (glass)
•Frustules
•Dead diatoms sink to the sediment and form ‘diatomaceous earth

160
Q

describe kelp

A
  • brown algae’
    •Store lipids such as leucocin for energy needs
    •Unrooted, they form floating forests that support diverse ecosystems
161
Q

what are alveolate?

A
  • Named for the flattened vacuoles (alveoli) within their outer cortex
    •Most have cilia or flagella
    •Highly structured)
    •Are generally predators
    •Complex genetic system, sexual reproduction
162
Q

what are dinoflagellates

A

phototrophic alveolates

possess 2 flagella

163
Q

what is the James Bond protist and why is it called this?1

A

Euplotidium

its called this because it causes bacteria to extrude their cell contents

164
Q

what do apicomplexans use to gain entry to host cells?

A

an apical complex

165
Q

definition of virus

A

a non-cellular particle that must infecta hostcell, where it reproduces

166
Q

true or false: viruses can infect everything except other viruses

A

false: they can infect viruses too

167
Q

what is host range?

A

each species of virus infects a particular group of host species

168
Q

what are the different types of virus structures?

A 
icosahedral
filamentous
multiple helical packages
complex viruses
asymmetrical viruses
169
Q

characteristics of icosahedral virus structure

A
  • 20 triangular faces –the largest number possible

- Natural selection has favoured the packaging of the most material within the smallest number of repeating sub units

170
Q

characteristics of filamentous virus structure

A
  • Genome (in this case RNA) is coiled into the helical capsidstructure
  • Can vary in size to accommodate varying lengths of genomic material
171
Q

characteristics of multiple helical packages virus structure

A
  • enables influenza virus to package different numbers of RNA segments into different virions
  • Process enables rapid evolution of new strains
172
Q

characteristic of complex viruses structure

A

Icosahedral head coat plus a helical ‘neck’ that acts as an elaborate delivery device

173
Q

characteristics of asymmetrical viruses structure

A
  • No symmetrical capsid: the double-stranded DNA genome is stabilized by covalent connection of its 2 strands at each end
  • Instead of a capsid, the DNA is enclosed by a core envelope surrounded by an outer membrane
  • Contain a large number of accessory proteins
  • Appear to have evolved from degenerate cell
174
Q

describe viral genomes

A

Usually very simple, and genes are efficiently packaged

175
Q

what are viroids?

A
  • extremely simple viruses: there is no protective capsid
    •Usually RNA molecules that infect plants
    •Some have catalytic activity
176
Q

what do prions consist of

A

protein only

177
Q

how do prions work?

A
  • interaction with the normal form of the protein results in transformation to the prion form
  • Multiple prion proteins aggregate and cause cell death, creating sponge-like holes in brain tissue
178
Q

how are viruses classified?

A

•Genome composition
•Capsid symmetry
•Envelope (presence or absence, and structure, if present)
•Size of virus particle (range from 30-400nm across;
•Host range (not always very useful
- promotes

179
Q

what is the most important criterion in classifying viruses?

A

genome composition

180
Q

7 ways mRNA is produces by a virus

Baltimore classification

A 
Group I: dsDNA viruses
Group II: ssDNA viruses
Group III: dsRNA viruses
Group IV: (+)sense ssRNA viruses
Group V: (-) sense ssRNA viruses
Group VI: retroviruses
Group VII: pararetroviruses
181
Q

what is Group I: dsDNA viruses

A
  • make their own DNA polymerase (or use the host’s)

•Transcribe their genes using a standard RNA polymerase (or use the host’s

182
Q

what does Group I: dsDNA viruses consist of?

A

bacteriophageT4, Giruses, baculovirus, pox viruses, and most known archaeal viruses

183
Q

what is Group II: ssDNA viruses

A
  • require host DNA polymerase to generate the complementary strand
    •(resulting dsDNA can then be transcribed by the host RNA polymerase)
184
Q

what does Group II: ssDNA viruses consist of?

A

bacteriophageM13, parvovirus, geminivirus

185
Q

what is Group III: dsRNA viruses

A
  • require a viral RNA-dependent RNA polymerase to generate mRNA
    •Because this RNA polymerase is required immediately after infection, it’s usually made and packaged in the virion
186
Q

what does Group III: dsRNA viruses consist of?

A

reovirusessuch as rotavirus and phytoreovirus

187
Q

what is Group IV: (+)sense ssRNA viruses

A

(+) strand is the coding strand
•Serves directly as mRNA
• needs synthesis of the (-) strand to make a ds intermediate for replication purposes

188
Q

what does Group IV: (+)sense ssRNA viruses consist of?

A

poliovirus, rhinovirus, rubella virus, coronaviruses(e.g. SARS), flaviviruses(e.g. West Nile virus)

189
Q

what is Group V: (-) sense ssRNA viruses

A
  • Genomes consist of template RNA
    •Require a viral RNA-dependent RNA polymerase for transcription of (-)RNA to (+)mRNA
    •May be segmented viruses (and thus can recombine and evolve quickly
190
Q

what does Group V: (-) sense ssRNA viruses consist of?

A

s influenza virus, hantavirus, ebolavirus, rabies virus, measles virus

191
Q

what is Group VI: retroviruses

A

(+) strand RNA genomes, RNA reverse transcribing viruses
•Instead of RNA polymerase they package their own reverse transcriptase
•Transcribes the RNA into dsDNA
•dsDNA gets incorporated into the host genome and directs the expression of the viral gene

192
Q

what does Group VI: retroviruses consist of?

A

HIV, SIV, FL

193
Q

what is Group VII: pararetroviruses

A

DNA reverse transcribing viruses
•require reverse transcriptase (viral or host
)•Copy genomes into RNA
•Then reverse transcribe this to DNA

194
Q

what does Group VII: pararetroviruses consist of?

A

hepatitis B virus, cauliflower mosaic virus

195
Q

what is HERV?

A

•Human Endogenous Retroviruses
•Make up 8% of the human genome
- remains of ancient viruses that once infected the germline and incorporated themselves into our genome
•Over the millennia, they have become degraded and non-functional

196
Q

Edward Jenner vaccinated against smallpox using:

a) Killed smallpox virus
b) A recombinant protein derived from smallpox
c) Live cowpox virus
d) Killed cowpox virus
e) A toxoid

A

c) Live cowpox virus

197
Q

lithotrophs are:

a) Organisms that use light to obtain energy
b) Organisms that prefer to live under high pressure
c) Organisms that use minerals for biosynthesis
d) Usually protists
e) Always able to survive at high temperature

A

c) Organisms that use minerals for biosynthesis

198
Q

Treating cows with antibiotics against cellulolytic bacteria:

a) Would prevent shedding of pathogens such as Escherichia coli 0157:H7 by the cows
b) Would permit the cows to obtain sufficient nutrition from plant materials
c) Would have an overall beneficial effect on the microbiota
d) Would inhibit the ability of the cow to obtain sufficient nutrition from foods such as hay
e) Would improve the health of the animal

A

d) Would inhibit the ability of the cow to obtain sufficient nutrition from foods such as hay

199
Q

Carl Woese pioneered:

a) The use of mitochondria in endosymbiotic theory
b) A method to sequence DNA
c) The use of Gram staining in identifying bacteria
d) The study of molecular biology
e) The use of rRNA to build phylogenetic tree

A

e) The use of rRNA to build phylogenetic tree

200
Q

Bacteriorhodopsin is:

a) A retinal-containing transmembrane protein
b) A retinal-containing cytoplasmic protein
c) A chlorophyll-containing cytoplasmic protein
d) A chlorophyll-containing transmembrane protein
e) Only found in bacteria

A

a) A retinal-containing transmembrane protein

201
Q

Fungi:

a) Benefit animals and plants
b) Mainly harm plants and benefit animals
c) Mainly harm animals and benefit plants
d) Neither benefit nor harm animals or plants
e) Can both benefit and harm animals and plants

A

e) Can both benefit and harm animals and plants

202
Q

The Protozoa are _________________________ and usually ________________:

a) Prokaryotes / Unicellular
b) Eukaryotes / Unicellular
c) Eukaryotes / Amitochondriate
d) Eukaryotes / Multicellular
e) Parasitic / Saprophytes

A

b) Eukaryotes / Unicellular

203
Q

. Organisms A, B and C are all found in one community. Organism A utilizes glucose andgenerates lactate. Organism B converts lactate to CO2 + Hydrogen, and organism C generatesmethane from the hydrogen and CO. This relationship between organisms A, B and C is called:

a) Metabolism
b) Commensalism
c) Syntropism
d) Competition
e) Ecosystem

A

c) Syntropism

204
Q

Viroids are:

a) Small stretches of RNA encased in a primitive capsid
b) Small stretches of DNA encased in a primitive capsid
c) Infectious particles that usually infect archaea
d) ‘Naked’ infectious RNA molecules
e) ‘Naked’ infectious DNA molecules

A

d) ‘Naked’ infectious RNA molecules

205
Q

Prokaryotes called ___________ do not have a cell wall, and the ___________ do not have peptidoglycan.

a) Archaea / Mycobacteria
b) Mycoplasma / Archaea
c) Mycobacteria / Gram-negative bacteria
d) Streptococcus / Pseudomonas aeruginosa
e) Plasmodium / slime molds

A

b) Mycoplasma / Archaea

206
Q

in a lichen, the ____________ provides protection, and the Cyanobacterium provides ___________:

a) algae / vitamins
b) fungus / sunlight
c) Rhizobium / nitrogen compound
d) fungus / organic molecules
e) algae / organic molecules

A

d) fungus / organic molecules

207
Q

Acid fast bacteria can be stained in the Ziehl-Neelsen procedure using:

a) carbolfuschin
b) saffranin
c) India ink
d) phenol red
e) crystal violet

A

a) carbolfuschin

208
Q

if you had a cell with the structures listed below, what would be the outermost layer of this hypothetical cell?

a) Outer membrane
b) Capsule
c) Surface (S)-layer
d) LPS
e) Arabinogalactan

A

b) Capsule

209
Q

which terms describe a prokaryote that grows best at 100°C at pH 2 and has specific requirement for light and carbon dioxide?

a) Photoautotrophic, acidophilic, hyperthermophile
b) Photoautotrophic, acidophilic, thermophile
c) Hyperthermophilic, barophilic, chemolithotroph
d) Thermophilic, alkaliphilic, autotroph
e) Hyperthemophilic, alkaliphilic, phototroph

A

a) Photoautotrophic, acidophilic

210
Q

Which terms describe a prokaryote that grows best at 25°C at pH 10 and has a specific requirement for organic carbon for growth?

a) Psychrophilic, heterotrophic, alkaliphilic
b) Mesophilic, chemolithotrophic, alkaliphilic
c) Photosynthetic, psychrophilic, heterotrophic
d) Mesophilic, heterotrophic, alkaliphilic
e) Thermophilic, autotrophic, alkaliphilic

A

d) Mesophilic, heterotrophic, alkaliphilic

211
Q

Thylakoids are:

a) Sites of photosynthesis in chloroplasts and cyanobacteria
b) Storage granules specifically found inside photoautotrophs
c) Membranes of mitochondria
d) Often associated with the nucleoids of bacteria
e) Ancient precursors of chloroplasts

A

a) Sites of photosynthesis in chloroplasts and cyanobacteria

212
Q

Teichoic acids are:

a) Found in Gram negative cells only
b) Found in Gram positive cells only
c) Are a form of bacterial lipid
d) A cytoplasmic molecule
e) A stabilization factor for the bacterial nucleoid

A

b) Found in Gram positive cells only

213
Q

.A bacterial cell with a tuft of flagella emerging from one pole only is said to be:

a) Monotrichous’
b) Piliated
c) Peritrichous
d) Non-motile
e) Lophotrichous

A

e) Lophotrichous

214
Q

Bacterial flagella are usually:

a) Long, helical, flexible
b) Powered by ATP
c) Short, helical, inflexible
d) Powered by a proton motive force
e) Made of microtubule

A

d) Powered by a proton motive force

215
Q

Nitrogen fixing bacteria:

a) Are always associated with legumes encased in their root nodules
b) Convert nitrate to nitrogen gas
c) Contribute to atmospheric pollution
d) Convert nitrogen gas to ammonia
e) Are always anaerobic

A

d) Convert nitrogen gas to ammonia

216
Q

Animals are most closely related to:

a) Choanoflagellates
b) Amoeba
c) Green algae
d) Fungi
e) Diatoms

A

a) Choanoflagellates

217
Q

Protists are:

a) Always unicellular
b) A paraphyletic group of organisms
c) Usually photosynthetic
d) A group that excludes protozoa
e) Only able to reproduce asexual

A

b) A paraphyletic group of organisms

218
Q

The node of a phylogenetic tree:

a) Demonstrates early divergence from an ancestral cell
b) Demonstrates recent divergence from an ancestral cell
c) Is always drawn as a vertical line
d) Is the root, indicating the most distantly related species
e) Represents the last common ancestor of the associated branches, which no longer exist

A

e) Represents the last common ancestor of the associated branches, which no longer exist

219
Q

A girus is a giant virus that:

a) Has a peptidoglycan cell wall
b) Is able to replicate outside of a host cell
c) Has an unusually large genome
d) Is known to infect metazoans
e) All of the above

A

c) Has an unusually large genome

220
Q

The bacterial slime layer, or capsule, is:

a) A slippery outer layer of loosely bound polysaccharides
b) Also known as S-layer
c) Made of murein
d) Easily stained with crystal violet
e) Used by the bacterium to prevent dessication

A

a) A slippery outer layer of loosely bound polysaccharides

221
Q

The part of a bacterial cell that is being investigated for use as a biodegradable plastic is:

a) Plasma membrane
b) Storage granule
c) Magnetosome
d) Carboxysome
e) Teichoic acid

A

b) Storage granule

222
Q

Group IV viruses in the Baltimore classification system are viruses that are:

a) Single stranded, positive sense RNA viruses
b) Retroviruses
c) Double stranded DNA viruses
d) Single stranded, negative sense RNA viruses
e) Single stranded DNA viruses

A

a) Single stranded, positive sense RNA viruses

223
Q

Which of the following is not a DNA virus?

a) parvovirus
b) bacteriophage M13
c) rhinovirus
d) Smallpox virus
e) bacteriophage T4

A

c) rhinovirus

224
Q

Burst size is:

a) The number of bacterial cells lysed by a virulent phage
b) The number of viral particles released by a phage during the lytic phase
c) The capacity of a bacterial cell cytoplasm for hosting assembled bacteriophage
d) The number of bacterial cells required in order to visualize a plaque
e) Always higher for archaea than bacteria

A

b) The number of viral particles released by a phage during the lytic phase

225
Q

Which of the following statements is false about mycorrhizae?

a) Mycorrhizae are essential to all plant life
b) Mycorrhizae help plants to assimilate extra nutrients from the soil
c) In return for mycorrhizae activity, plants reward the associated fungus with nutrients such as sugars
d) The mycorrhizae from a single fungus can stretch underground for several kilometers
e) Mycorrhizae aid in nutrient assimilation from soil because they offer a much larger surface area for absorption than plant roots.

A

a) Mycorrhizae are essential to all plant life

226
Q

how do humans protect against microbial invaders?

A
  • Non-specific defences

•Adaptive and non-adaptive immune defences

227
Q

what percentage of your weight is compromises microbes on/in your body?

a. 0.05-0.09
b. 0.1-0.9
c. 1-3
d. 4-5
e. 6-10

A

c. 1-3

228
Q

what are pathobiots?

A

life in/on us but don’t do use any harm until we get sick, then they take advantage of us

229
Q

what are commensal

organisms?

A

Bacteria normally found at various non-sterile body site

230
Q

what is the Microbiota?

A
  • The consortium of colonizing microbes

- indicates the cell consortium

231
Q

what is the microbiome

A
  • The consortium of colonizing microbes

- indicates the genetic potential of the consortium

232
Q

what do ruminants rely on microbes for?

A

digestion of cellulose

233
Q

why do some insects require microbes

A

allow digestion of their dietary substrates

234
Q

true or false: microbes can cause a disease if they reach an abnormal location

A

true

235
Q

how many bacterial species are there per individual?

A

~200

236
Q

true or false: there’s more human genes than microbial genes associated with us

A

false: at least 100x more microbial genes associated with us than our human gene

237
Q

what microbes lives on our face

A

demodex mites

238
Q

ratio of bacteria to human in humans

A

1.3 bacteria to 1 human

239
Q

which these diseases is thought to emerge as a result of an imbalanced microbiota

a) autism
b) colorectal cancer
c) type 1 diabetes
d) chronic depression
e) Parkinson’s disease

A

all of them!

240
Q

why is the skin difficult for microbes to colonize

A

Dry, salty, acidic, protective oils

241
Q

where are most microbes on the skin and how many are there?

A

moist areas:
Scalp, ears, armpits, genital and anal area
10^12

242
Q

what kind of bacteria colonize the skin?

A

gram positive

243
Q

what is body odour the result of?

A

microbes breaking down certain things causing the bad smell

244
Q

what is a human infants mouth colonized by?

A

Non-pathogenic Neisseriaspp. (Gram negative cocci)

•Streptococcus, Lactobacillus spp. (Gram positive rods

245
Q

as teeth emerge, what other bacteria begin growing in the mouth

A

Prevotella and Fusobacteriumspp.: between gums and teeth •Streptococcus mutans: tooth enamel

246
Q

what is the most common site of infection in humans?

A

oral and respiratory tract

247
Q

what are nostrils and nasopharynx dominated by?

A

Firmicutes and Actinomycetes

248
Q

what is nasopharynx populated by?

A

Staphylococcus aureus and S. epidermidis

249
Q

what is oropharynx composition similar to?

A

microbes to saliva

250
Q

what kind of microbes mainly live in the lungs

A

anaerobes

251
Q

where in the body are usually sterile or near sterile?

A

kidney and urinary bladder

252
Q

what are virulent bacteriophages?

A

Bacteriophages which predominantly carry out the lytic pathway

253
Q

what are temperate bacteriophages?

A

Bacteriophages which predominantly carry out the lysogenic pathway

254
Q

what is a prophage?

A

the bacteriophage DNA as part of the host genome

255
Q

what kind of immune system do bacteria and archaea have?

A

an adaptive immune system

256
Q

how do prokaryotes multiple?

A

through binary fission

257
Q

what is most prokaryote genomes made of?

A

DNA that is formed into a loop

258
Q

describe bacterial DNA replication

A
  • semi-conservative

- bidirectional

259
Q

what is vertical transmission

A

binary fission

260
Q

define binary fission

A

identical genome copies produced

261
Q

what is horizontal transmission?

A
  • transformation
  • transduction
  • conjugation
262
Q

what is bacterial transformation?

A
  • uptake of naked DNA by a bacterium to use in its own genome
  • uptake of plasmid DNA by a bacterium for continued autonomous replication of the plasmid in a new host
263
Q

what is a plasmid

A

extra chromosomal DNA, usually much smaller than the chromosome itself
•Usually encode accessory function

264
Q

how do plasmids replicate?

A

Replication is autonomous

•i.e. not tied to the replication of the chromosome

265
Q

what does conjugation require?

A
  • cell-cell contact that is mediated by a structure called the ‘sex pilus
  • presence of F+
266
Q

true of false: packaging viral DNA into capsids is a sloppy process

A

true

267
Q

what is the bacterial species with the fastest generation time?

A

Clostridium perfringens

10 mins

268
Q

what is the bacterial species with the lowest know generation time?

A

Mycobacterium leprae

14 days

269
Q

what are the 4 phases of bacterial growth?

A

lag phase
exponential phase
stationary phase
death phase

270
Q

describe early exponential phase of bacterial growth

A

cells growing at the maximum rate possible based on conditions available

271
Q

explain late exponential phase of bacterial growth

A

slowing of growth rate due to cell density

272
Q

why do cell numbers stop rising in the stationary phase of bacterial growth?

A
  • Lack of a key nutrient

•Build up of waste product

273
Q

what do cells do to survive during the stationary phase of bacterial growth?

A
  • Become smaller
    •Produce stress response proteins
    •Some may sporulate
274
Q

what do chemostats do?

A

allow growth phase to be controlled

275
Q

what is bacterial cell sporulation?

A
  • Certain G+ genera are able to place themselves into suspended animation when the going gets tough
    •Endospore formation
    •An alternative pathway in the growth cycle
276
Q

true or false: endospores tend to be very weak

A

false: very strong

277
Q

what happens to cells that can’t sporulate?

A 
- Cells get smaller
•Cell walls get thicker
•Glycogen stores are laid down
•Nutrient transporters are expressed
•Stress response proteins are expressed
278
Q

what are fimbrial jackets?

A

elaborate coats that some bacterial species knit themselves made out of cellulose and fimbrial proteins

279
Q

how can biofilms be bad?

A

can damage equipment,
can contaminate abiotic surfaces introduced in the body,
can cause tooth decay

280
Q

how can biofilms be good?

A

allow microbes to work together to effectively metabolize

281
Q

what are biofilms?

A

a thin, slimy film of bacteria that adheres to a surface

282
Q

true or false: biofilms are composed of only one bacterial specie

A

false: Biofilms may be composed of a single bacterial species or of several collaborating species

283
Q

what binds biofilms together?

A

Exopolysaccharides

284
Q

what are oligotrophs?

A

bacteria in most soil and water ecosystem

285
Q

describe oligotrophs

A
  • Have a high rate of growth at low nutrient concentrations•
    Will die if given rich media sources
    •Many aquatic bacteria once considered to be ‘unculturable’ can actually be easily cultured in low nutrient concentration
286
Q

what is an ecosystem?

A

collection of populations of species + their habitat

287
Q

what is a population?

A

a group of species living in a common location

288
Q

what is a community?

A

The sum of all the populations of different species

289
Q

what is a niche?

A

a set of conditions enabling an organism to grow and reproduce

290
Q

true or false: every molecule in nature can be used as a source of carbon or energy by a microorganism somewhere

A

true

291
Q

true or false: Microbes are found in every environment on Earth

A

true

292
Q

describe phylogenomics

A

Profiling ecosystem composition based on taxonomic reference genes such as the 16S rRNA gene

293
Q

describe metagenomics

A

•Sequencing and assembling entire genomes from ecosystem

294
Q

describe Metatranscriptomics (meta-RNAseq)

A

•Sequencing entire collections of mRNA from an ecosystem and mapping the reads back to genomes to identify them

295
Q

describe proteomics

A

Obtaining amino acid sequences and identifying the collection of signatures from a given ecosystem

296
Q

describe lipidomics

A

Using advanced chromatography and spectroscopy techniques to identify lipid signatures in a given ecosystem

297
Q

describe metabolomics

A

Using various analytical chemistry methods to detect and identify molecules from an ecosystem

298
Q

how do microbes contribute to an ecosystem?

A

Utilize their collectively diverse metabolisms to acquire energy and assimilate elements into biomass
•Detoxify wastes
•Protect symbiotic partners from predation and/or hostile environments
• modulate a host’s development and behaviour

299
Q

what is assimilation?

A

processes by which organisms acquire an element to build into cells

300
Q

what are primary producers?

A

Organisms that produce biomass from inorganic carbon

301
Q

true or false: if the organic compound is not in the environment, microbes can assimilate it from mineral (inorganic) sources

A

true

302
Q

what is dissimilation?

A

The process of breaking down organic nutrients into inorganic minerals (usually through oxidation)

303
Q

what are the most common assimilatory and dissimilatory cycles known to biology?

A

carbon and nitrogen cycles

304
Q

what does the food web rely on primary producers for?

A
  • Absorbing energy from outside of the ecosystem

•Assimilating minerals into biomass

305
Q

what factors most influence the ecosystem?

A 
availability to water
temperature
pH
salinity
availability to oxygen (or other electron acceptors)
306
Q

what is symbiosis?

A

organisms adapting to the presence of other organisms

307
Q

what is mutualism?

A

interactions between organisms of two different species, in which each organism benefits from the interaction in some way

308
Q

what is synergism?

A

The interaction of things resulting in the overall effect that is greater than the sum of individual effects of any of them

309
Q

what is commensalism?

A

members of one species gain benefits while those of the other species neither benefit nor are harmed

310
Q

what is amensalism?

A

any relationship between organisms of different species in which one organism is inhibited or destroyed while the other organism remains unaffected

311
Q

what is parasitism?

A

benefits at the expense of another organism usually of different species

312
Q

what are the primary producers in the ocean?

A

bacteria and algae

313
Q

what are 4 types of plankton?

A

1) Microplankton(20-200μm)
2) Nanoplankton(2-20μm)
3) Picoplankton(0.3-2μm)
4) Femtoplankton(<0.3μm)

314
Q

where are radiolarians concentrated?

A

on top of contours of Chlorophyll A in the water

315
Q

true or false: plankton tend to be found concentrated in thin layers

A

true

316
Q

true or false: the stomach has a very low pH

A

true:

fes microbes survive

317
Q

which microbe survives in the stomach?

A

helicobacter pylori

318
Q

what is decreased stomach acidity known as?

A

hypochlorydia

319
Q

where is the most important microbial ecosystem in the human body?

A

the colon

320
Q

what do you have in a gut microbial with a high diversity of species?

A
  • healthy ecosystem
  • balance
  • functional redundancy
  • resistance to damage
321
Q

what do you have in a gut microbial with a low diversity of species?

A
  • sick ecosystem
  • imbalance
  • functional disability
  • susceptibility to damage
322
Q

what are microbes called that break barriers when the host is compromised?

A

opportunistic pathogens or pathobionts

323
Q

how is the microbiota protective?

A

competitive exclusion
environmental modification
host stimulation

324
Q

what is a gnotobiotic animal?

A

An animal where the associated microbiota is knownand defined

325
Q

what abnormal physiology do gnotobiotic animals have?

A
  • poorly developed immune systems
  • lower cardiac output
  • require more calories
  • thin, poorly developed intestinal walls
  • abnormal ceca
  • odd behaviour
  • misshapen mitochondria
326
Q

who is David Vetter?

A
  • born with very impaired immune system

- lived for 12 years in a completely sterile environment

327
Q

where is the home of endoliths?

A

extreme cold: polar regions

328
Q

wha makes archaea viruses different than bacteriophage ?

A

capsule is spindle-shaped with strange turrets

MICR 2420 (2 decks)

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