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Biology 2051 > Exam One > Flashcards

Exam One Flashcards

1
Q

How do microbes help in agriculture?

A

Bacteria can help plants get Nitrogen

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2
Q

How do microbes help in energy?

A

Can take sugars from plants (cellulose and cornstarch) to make ethanol - biofuels

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3
Q

How do microbes help in food production?

A

Preservatives keep pH low and environment unfriendly for microbes

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4
Q

How many cells are there on earth?

A

25E29cells

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5
Q

Where are the majority of microbes?

A

On marine surfaces (66%)

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6
Q

How old is planet Earth?

A

around 4.5 billion years old

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7
Q

When was the origin of cellular life?

A

around 3.5-3.8 billion years ago

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8
Q

What was early earth like?

A

Anoxic (mostly CO2), much hotter than the present earth.

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9
Q

How were the first biological molecules likely made?

A

They were likely made in mounds of montmorillonite clay associated with hydrothermal springs that have the ability to precipitate so molecules can grow

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10
Q

What is the evidence for RNA as the first genome?

A

RNA can bind small molecules (ATP, nucleotides, amino acids), and catalytic RNA has enzymatic activity

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11
Q

What was the primitive metabolism of early life?

A

Anaerobic, autotrophic, and chemolithotrophic

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12
Q

When was the first evidence for microbial life found? Where?

A

around 3.5 billion years ago in stromatolites

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13
Q

When did oxygenic phototrophic cyanobacteria appear?

A

around 2.8 billion years ago

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14
Q

How did earth shift from an anoxic to an oxic environment?

A

oxygenic phototrophic bacteria appeared, iron was oxidized, oxygen accumulated, an ozone layer formed

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15
Q

What do all prokaryotic cells contain?

A

Cell wall, cytoplasmic membrane, nucleic, cytoplasm, plasmid (in some bacteria), and ribosome

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16
Q

What do all eukaryotic cells contain?

A

Cytoplasmic membrane, ER, ribosomes, nucleus, nucleolus, nuclear membrane, Golgi, cytoplasm

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17
Q

Theory of endosymbiosis

A

Mitochondria and chloroplasts came from chemoorganotroph and cyanobacterium

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18
Q

Supportive evidence for the theory of endosymbiosis

A

Mito and Chloroplasts: have their own genomes, contain their own ribosomes (70S), antibiotics are effective, rRNA sequences are similar to prokaryotic rRNA

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19
Q

How long have prokaryotic cells been on earth

A

about 4.3 billion years

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20
Q

How does the Hydrogen hypothesis explain how the first eukaryotic cell was formed?

A

Archaea cell engulfed a bacterial cell that produced hydrogen. Kept it alive to make hydrogen for the archaea cell because hydrogen is an electron donor

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21
Q

When did the early photosynthetic eukaryotic cell come?

A

1.5 billion years ago

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22
Q

What gene is sequenced in bacteria and archaea to measure phylogeny?

A

16S

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23
Q

What gene is sequenced in eukarya to help phylogeny

A

18S

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24
Q

What are the steps in SSU RNA sequencing?

A

Isolate DNA
Amplify gene by PCR
Run on agarose gel
sequence

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25
Q

Why use SSU RNA instead of another gene?

A

Universally distributed, functionally constant, slow changing, adequate length

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26
Q

If 16S rRNA sequence differed by more than 3%

A

different species

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27
Q

If 16S rRNA sequence differed by more than 5%

A

difference genus

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28
Q

Why is kingdom not included in our taxonomic hierarchy?

A

Kingdom was in place before archaea were discovered. No agreement on wether or not kingdoms should be in the taxonomic hierarchy

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29
Q

How many species are there

A

As of August 2013, there are 10,599 species

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30
Q

How would one identify an organism?

A

Asses its phenotypic properties from general to specific

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31
Q

What are some examples of phenotypic analyses?

A

Morphology, motility, metabolism, physiology, cell lipid chemistry, cell wall chemistry, etc.

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32
Q

tests ability of denatured DNA in a single strand formed from 2 organisms to bond to one another

A

DNA hybridization

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33
Q

In DNA hybridization, if 70-100% of the DNA will anneal

A

same species

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34
Q

In DNA hybridization, if at least 25% of the DNA will anneal

A

same genus

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35
Q

Sequence comparison of several housekeeping genes. Useful for determining different strains of the same species

A

Multilocus Sequence Typing

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36
Q

Steps in multi locus sequence typing

A

Isolate DNA, amplify 6-7 target genes, sequence, analyze alleles, compare with other strains and generate tree

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37
Q

Steps in Fatty Acid Methyl Ester (FAME) Analysis

A

Bacterial culture, extract fatty acids, derivative to form methyl esters, gas chromatography, graph with peaks, compare pattern of peaks, identify

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38
Q

regulates naming of prokaryotes

A

The International Code of Nomenclature of Bacteria

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39
Q

Major taxonomic compilations of Bacteria and Archaea

A

“Bergey’s Manual of Systematic Bacteriology” and “The Prokaryotes”

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40
Q

Formal recognition of a new prokaryotic species requires:

A

Deposition of a sample in 2 international culture collections, and official publication in IJESM

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41
Q

first person to describe microorganisms

A

Robert Hooke (1665)

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42
Q

first person to describe bacteria

A

Antoni van Leeuwenhoek (1676)

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43
Q

Simplest type of microscopy, illuminates specimen and specimen is stained

A

Bright Field

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44
Q

microscopy with a black bacground

A

Dark Field

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45
Q

microscopy that casts a shadow over the cell, a little 3D

A

Phase Contrast

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46
Q

What are the benefits of phase contrast and dark-field microscopy?

A

Visualize live samples and don’t require staining

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47
Q

visualization of auto-fluorescent molecules or fluorescent stians

A

fluorescent microscopy

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48
Q

Limit of resolution of a compound light microscope

A

0.2 micrometers

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49
Q

limit of resolution of an electron microscope

A

0.2-0.4 micrometers

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50
Q

for observing internal cell structures

A

Transmission Electron Microscope

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51
Q

for 3D imaging and viewing surfaces

A

Scanning Electron Microscope

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52
Q

bacteria that is 0.2 micrometer and have no cell wall

A

Mycoplasma sp.

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53
Q

What is the effect of a high surface area to volume ratio

A

aids in nutrient and waste exchange with the environment

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54
Q

What is the size of a eukaryote?

A

around 1 micrometer

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55
Q

What are the four basic components of all microbial cells

A

cytoplasm, cytoplasmic membrane, ribosomes, DNA

56
Q

What is a cytoplasmic membrane made up of?

A

lipid and proteins forming a lipid bilayer

57
Q

What is an archaea lipid bilayer made up of that helps it survive in extreme environments?

A

Phylantyl instead of fatty acids and ether linkages that form strong covalent bonds

58
Q

What connects the lipids in bacteria and eukarya

A

ester linkages

59
Q

What other lipid in the cytoplasmic membrane helps to strengthen eukarya

A

sterols

60
Q

What other lipid in the cytoplasmic membrane helps to strengthen bacteria

A

hopanoids

61
Q

How does the cytoplasmic membrane act as a permeability barrier?

A

Prevents leakage and functions as a gateway for nutrients and wastes

62
Q

What is simple transport driven by?

A

proton motive force

63
Q

What is group translocation driven by

A

phosphoenolpyruvate

64
Q

What is ABC transporter driven by

A

ATP

65
Q

How does the cytoplasmic membrane work in terms of energy conservation?

A

Bacteria and Archaea make ATP in the membrane

66
Q

How does the cytoplasmic membrane act as a protein anchor?

A

site of many proteins that participate in transport, bioenergetics, and chemotaxis

67
Q

What makes up the eukaryotic cytoskeleton?

A

Microfilaments and microtubules

68
Q

polymers of actin; define, maintain, change cell shape; cell motley - cytoplasmic streaming

A

microfilaments

69
Q

polymers of tubulin; maintain cell shape; cell motility - from flagella and cilia; movement of organelles and chromosomes

A

microtubules

70
Q

What makes up the prokaryotic cytoskeleton?

A

FtsZ, FtsA, and MreB

71
Q

protein structure similar to tubing that determines where cell division will occur

A

FtsZ

72
Q

Protein structures similar to actin; (1) helps hold FtsZ proteins; (2) determine where new cell wall will be inserted in an expanding/dividing cell

A
  1. FtsA

2. MreB

73
Q

Eukaryotic cell organelle that is continuous with nuclear outer membrane; contains ribosomes - site of protein synthesis; makes glycoproteins and new membrane material

A

rough ER

74
Q

Eukaryotic cell organelle that is continuous with the rough ER; site of lipid synthesis and carbohydrate metabolism

A

smooth ER

75
Q

chemicals modifies carbohydrates on ER glycoproteins and sorts molecules from the ER

A

Golgi complex

76
Q

produced by budding of the golgi complex, pH 5, contains digestive enzymes (lipase, nuclease, protease), recycle macromolecules, kills foreign bacteria, apoptosis

A

lysosome

77
Q

organelle site of oxidation; contains catalase, superoxide dismutase to degrade H2O2 and O2 respectively

A

peroxisome

78
Q

What are the inner and outer membranes of the mitochondrion are? What about the matrix?

A

Inner: cristae, less permeable and rigid, sites of ETC and ATP
Outer: rigid, somewhat permeable
Matrix: contains enzymes of the citric acid cycle

79
Q

Replaces mito in anaerobic eukaryotes, site of ATP production and citric acid cycle

A

hydrogenosome

80
Q

Aqueous part of the chloroplast, site of the Calvin-Benson Cycle

A

Stroma

81
Q

stacks of flattened membrane disks, contain light harvesting pigments, site of ETC and ATP

A

grant of thylakoids

82
Q

fixes CO2 into organic compounds

A

RuBisCO

83
Q

What is the structure of a cell wall

A

proteins, glycoproteins, and polysaccharides

84
Q

What are the main functions of the cell wall

A

protection, cell shape, preventing osmotic lysis, interact with the environment

85
Q

Cell walls of algae

A

cellulose - polymer of glucose

86
Q

Cell walls of fungi

A

chitin - polymer of N-acetylglucosamine

87
Q

2 bacteria that lack cell wall

A

Mycoplasma & Chlamydia sp.

88
Q

has protein cell wall

A

Planctomycetes sp.

89
Q

What are bacterial cell walls mostly made of

A

peptidoglycan

90
Q

Where is the location of peptidoglycan in gram-negative bacteria?

A

in the periplasm

91
Q

What is the surface of gram-negative bacteria

A

wavy/irregular

92
Q

Attached to the outer membrane of gram-negative bacteria

A

liao-polysaccharides:

O-Specific and Core Polysaccharides

93
Q

What is the surface of the gram-positive bacteria

A

smooth

94
Q

negatively charged polymers on gram positive cells containing glycerophosphate or ribitol residues

A

Teichoic Acids

95
Q

teichoic acids covalently linked to membrane lipids

A

lipoteichoic acids

96
Q

2 sugars attached to N-acetylglucosamine and N-acetylmuramic acid. Linked by Beta(1,4) - lysozyme sensitive

A

peptidoglycan

97
Q

has a pseudomurein cell wall

A

Methanobacterium

98
Q

N-acetylglucosamine attached to N-acetylalosaminuronic acid by lysozyme insensitive Beta(1,3)

A

pseudomurein

99
Q

has polysaccharide cell wall

A

Halococcus

100
Q

Massive collection of sugars that bind sulfate which has utilities as an electron accepter

A

polysaccharide cell walls

101
Q

destroys peptidoglycan by cleaving Beta(1,4) glycosidic bonds; found in animal secretions; major line of defense as infection by Bacteria

A

Lysozyme

102
Q

Short protein filaments on the prokaryotic cell surface. Sticky because the proteins need it to stick to surfaces

A

Fimbriae

103
Q

longer protein filaments on the prokaryotic cell surface; used in conjugation (exchanging genetic info); can help cells move or attach

A

Pili

104
Q

glides via slime secretion

A

Cytophaga

105
Q

glides by a twitching motility (extension/retraction of type IV pili)

A

Myxococcus

106
Q

glides by the ratchet-protein mechanism and is helped by a proton force

A

Flavobacterium

107
Q

Move back and forth by dyein motor proteins (like sperm), and is made of microtubules

A

Eukaryotic flagella and cilia

108
Q

What are the parts of a bacterial flagellum

A

filament, hook, motor

109
Q

embedded in the cytoplasmic membrane

A

motor

110
Q

How fast can a flagellum move a bacterial cell

A

60 cell lengths/ second

111
Q

multiple proteins make up filament; small diameter flagellum - less torque, slower speed; powered by ATP

A

archaea flagella

112
Q

Flagella are attached at one or both ends of the cell; movement more rapid; Ex. Spirrilum

A

Polar

113
Q

Flagella are all around

A

Peritrichous

114
Q

Flagella are multiple on one end

A

Lophotrichous

115
Q

CCW rotation gives movement opposite of CW rotation

A

Reversible Flagella

116
Q

CW rotation moves one way, cell stops and reorients before continuing

A

Unidirectional

117
Q

Run (bundled flagella in CCW rotation) & Tumble (flagella pushed apart in CW rotation)

A

Movement with peritrichous flagella

118
Q

phototrophic bacterium that aggregates at light wavelengths at which its pigments absorb

A

Thiospirillum jenense

119
Q

Small gas-filled structures made of protein that confer buoyancy on cells

A

gas vesicles

120
Q

aquatic microorganism that uses gas vesicles to move up and down

A

Cyanobacteria

121
Q

aquatic microbes that have magnetosomes - Intracellular particles of magnetite that orient cells in a particular direction

A

Magnetospirrilum

122
Q

a prokaryote that has carboxysome - contains ~250molecules of rubisco used for CO2 fixation

A

Halothiobacillus neopolitamus

123
Q

In the Carbon storage deposit

A

Glycogen, poly-beta-hydroxyalkanoate, poly-beta-hydroxybutyrate

124
Q

In the Phosphate storage deposit

A

polyphosphate granules; RNA, DNA, and ATP all need a lot of phosphate

125
Q

In the Sulfur storage deposit

A

sulfur granules stored in periplasm by gram-negative bacteria like the purple sulfur bacteria

126
Q

Described the life cycle of Bacillus subtitles from vegetative cell

A

1876 Ferdinand Cohn

127
Q

survival mechanism by some gram-positive bacteria like bacillus and clostridium

A

endospore

128
Q

cell is not sporulating but is happy, healthy and content

A

vegetative cell

129
Q

has an endospore at a terminal

A

Clostridium botulinum

130
Q

has an endospore at a subterminal space

A

Bacillus subtilis

131
Q

has an endospore at a central space

A

Bacillus anthrax

132
Q

What essential macromolecules are in an endospore

A

nucleic acids, proteins, carbohydrates, lipids, some water

133
Q

What are the layers of an endospore

A

DNA to Cortex to Core Wall to Spore coat to Exospore

134
Q

What is the cortex of an endospore made of

A

lipids

135
Q

released from vegetative cell; can survive indefinite periods of time; resistant to heat, chemicals, radiation, desiccation

A

spore

136
Q

Spore transforms into a vegetative cell that made the spore when conditions become favorable

A

germination

Biology 2051 (7 decks)

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