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Exam 3 Microbio Flashcards

Microbiology

1
Q

Define catabolism

A

Breakdown of complex molecules into smaller ones

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2
Q

Define anabolism

A

Process by which chemical energy is used to build complex molecules from simpler components

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3
Q

Define and distinguish among chemoorganotrophy, lithotrophy, and phototrophy

A
  1. Chemoorganotrophy: use of complex carbon containing compounds to extract energy for cell growth
  2. Lithotrophy: use of inorganic compounds to extract energy for cell growth
  3. Phototrophy: the process by which light energy is harvested to make chemical energy and reducing power
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4
Q

Identify cellular energy intermediates

A
  1. Proton motive force
  2. NADH
  3. ATP
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5
Q

Describe how energy intermediates can help drive unfavorable reactions in cells

A

Energy intermediates have favorable reactions, so the cell couples them with the unfavorable to get the reaction to occur

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6
Q

Identify three carbon sources for catabolism

A
  1. Polysaccharides
  2. Lipids and amino acids
  3. Aromatic compounds
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7
Q

Define fermentation and respiration and identify the important similarities and differences between them

A
  1. Fermentation: incomplete breakdown (oxidation) of organic molecules using the breakdown products themselves as electron acceptors
  2. Respiration: complete breakdown (oxidation) of organic molecules with electron transfer to a terminal electron acceptor
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8
Q

Define oxidation and reduction

A
  1. Oxidation: loss of electrons
  2. Reduction: gain of electrons
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9
Q

Identify which has more stored energy, an oxidized molecule or a reduced one

A

Reduced molecules

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10
Q

Explain why the triphosphate group of ATP (or other nucelotides) contains high energy bonds

A

The phosphates have negative charges that repel each other and it’s very favorable to break said bond
–this breakage can be paired with unfavorable reactions in the cell to make them go

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11
Q

Identify 3 cellular electron carriers

A
  1. ATP
  2. NADH
  3. FADH
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12
Q

Describe glucose in terms of what kind of molecule it is and how many carbons it contains. Is the carbon in glucose reduced or oxidized?

A

Glucose is a 6 carbon sugar that gets oxidized

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13
Q

Distinguish the EMP (glycolysis), ED, and PPP pathways with respect to their primary objective (getting energy or molecular building blocks)

A
  1. EMP: most common form of glycolysis
    –solely for energy generation
  2. PPP pathway: building molecules (biosynthesis)
  3. ED: splits the difference between PPP and EMP (used by E.coli)
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14
Q

List the inputs and outputs of glycolysis (EMP pathway)–which molecules and how many of each?

A

Input: glucose + 2 ATP
Output: 2 pyruvate, 4ATP, 2NADH

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15
Q

Describe the net energy yield of glycolysis in terms of ATP and reduced NADH

A

2 ATP and 2 NADH

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16
Q

Describe what kind of bacteria often use the ED pathway

A

E.Coli

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17
Q

Distinguish between NAD+/NADH and NADP+/NADPH in terms of what these energy
intermediates are primarily used for in cells (energy vs. biosynthesis)

A

NADP+ uses biosynthesis, other is for energy generation

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18
Q

Describe how NADH can be oxidized to regenerate NAD+ in the absence of oxygen

A

Fermentation

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19
Q

Describe the process of fermentation and typical fermentation products

A

Catabolism with the electrons being transferred back on to the products of glycolysis (namely pyruvate)
–Typical products might include: lactic acid, ethanol, carbon dioxide, NAD+, beer, wine

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20
Q

Define and distinguish among homolactic, heterolactic, ethanolic, and mixed-acid fermentation

A
  1. Homolactic: products-2 lactic acid, 2 NAD+
  2. Heterlactic: lactic acid, ethanol, CO2, NAD+
  3. Ethanolic: 2 ethanol, 2 CO2, 2 NAD+
  4. Mixed-acid: Redox is balanced by making acetate, formate, lactate, succinate, ethanol, H2, CO2
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21
Q

Describe the TCA cycle in terms of its molecular inputs and outputs (identity and number) and what the TCA cycle does to carbon compounds

A

Takes input of Acetyl-CoA to fully oxidize carbon dioxide
Outputs: 2 CO2, 3 NADH, ATP/GTP

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22
Q

Define and distinguish substrate-level phosphorlaytion and oxidative phosphorylation

A
  1. Substrate-level phosphorylation: produces ATP in glycolysis or TCA cycle
  2. Oxidative phosphorylation: overall process of electron transport and ATP generation
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23
Q

Define an electron transport system in terms of its 3 essential components, their order in the chain, and the overall function of an ETS within cells

A
  1. NADH: quinone oxidoreductase
  2. Mobile electron carrier (quinones)
  3. Terminal oxidase (cytochromes)
    Function: pumping protons
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24
Q

Name and describe the features of each component of an ETS with respect to receiving, carrying, and donating electrons and pumping protons

A
  1. NADH: quinone oxidoreductase takes electrons from donor and passes to mobile
  2. Mobile electron carrier (quinones)
    also passes protons
  3. Terminal oxidase (cytochromes)
    also pumps protons
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25
Q

Describe how quinones transfer protons from the cytoplasm to outside the membrane

A

Oxidation of NADH and reduction of Q is coupled to pumping 4 H+ across the membrane

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26
Q

Describe a redox tower and what it indicates

A

Electrons flow step wise from one carrier to another, losing energy as they go until they reach terminal electro acceptor.

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27
Q

Describe the proton motive force in terms of it being an electrochemical gradient

A

Charges line up at high concentration (very localized) and wants to flow back into cell because of their gradient/charge
–cells harness PMF to generate ATP

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28
Q

Describe the function of the F1F0ATPase: its power source and its cellular function

A

Consumes the proton motive force to make ATP – uses proton gradient as power source to spin

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29
Q

Identify 3 cellular functions or apparatuses that are powered by the proton motive force

A
  1. Flagellar rotation
  2. Antiporters
  3. ATP generation
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30
Q

Compare the energy yield of fermentation and respiration using glucose as the starting compound

A
  1. Fermentation –> 2 ATP/glucose
  2. Respiration –> 38 ATP/glucose
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31
Q

Describe how the potential of electrons changes as they are passed down an ETS

A

Lose energy (pumps H+) as they go down

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32
Q

Explain how an ETS can connect oxidation of carbon compound to ATP generation

A

Take electrons from glucose, puts on NAD+ to make NADH, passed from NADH to ETS, pumps protons and establishes PMF which is then harnessed by F1FO to make ATP

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33
Q

Identify common terminal electron acceptors and compare them in terms of their reduction potentials (how good they are at taking electrons)

A
  1. Nitrate – pretty decent electron acceptor
  2. Sulfate – not good electron acceptor
  3. Extracellular metals (Fe3+) – pretty good electron acceptor
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34
Q

Identify alternative, inorganic electron donors (food) that microbes can use

A

H2, sulfur, ammonium

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35
Q

Define anammox in terms of its electron donor and the conditions under which it takes place

A

Anammox is anaerobic ammonium oxidation – ammonium is the electron donor and it can only happen in oxygen free conditions

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36
Q

Describe how sulfur oxidation can be both helpful and harmful to human activity

A
  1. Helpful: biomining
  2. Can cause acidification –> erode structures
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37
Q

Define hydrogenotrophy and methylotrophy

A
  1. Hydrogenotrophy : using H2
  2. Methylotrophy: using one carbon compound
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38
Q

Define photosynthesis

A

Conversion of light energy into chemical energy

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39
Q

Identify the important outputs of photosynthesis

A

ATP and NADPH

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40
Q

Define photoexcitation and photolysis and describe how they relate to an electron transport system

A
  1. Photoexcitation: uses energy embedded in light
  2. This leads to photolysis – light driven separation of an electron from a donor molecule (its then transferred to ETS)
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41
Q

Describe the steps in photosynthesis

A

Chlorophyll aborbs light, electron separated from light, electron goes to ETS, ETS pumps H+ to make PMF go and drive ATP synthesis

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42
Q

Describe the function of the antenna complex and the name the light absorbing pigment contained therein

A

Antenna complex holds chlorophyll molecules to maximize light absorption – like a satellite

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43
Q

Explain why the antenna complex is arranged in a circle around the reaction center (and define the reaction center)

A

Circular to maximize light absorption.
Reaction center: a protein complex where electron transfer to ETS occurs

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44
Q

Describe the oxygenic Z pathway in terms of its inputs, electron source, and outputs and in what organisms it is found

A
  1. Takes electrons from water
  2. Electrons used to pump H+ and make NADPH
  3. Used by cyanobacteria and plants
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45
Q

Describe anaerobic photosystem I in terms of its input, electron source, output

A

Takes electrons from H2 or H2S, makes NADPH, doesn’t pump protons but makes proton graident

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46
Q

Describe anaerobic photosystem II in terms of its inputs, electron source, and outputs

A
  1. Takes electrons from chlorophyll itself
  2. Too weak to make NADPH
  3. Pumps a few H+ to make ATP and returns the electron
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47
Q

Define cyclic photophosphorylation

A

When the energy of the electron is too low to make NADPH – it pumps a few protons to make ATP

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48
Q

Describe the function of bacteriorhodopsin and identify the light absorbing pigment therein

A

They are light-powered proton pumps and use retinal as their pigment

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49
Q

Describe the function of the Calvin cycle and the type of organism that performs the Calvin cycle

A

Convert carbon dioxide into sugar. Autotrophs perform that

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50
Q

Define the inputs and outputs of the Calvin cycle

A

Inputs: carbon dioxide, ATP, NADPH
Outputs: glucose, ADP, and NADPH+

51
Q

Define the function of the Rubisco enzyme

A

The enzyme that fixes carbon dioxide in the Calvin cycle

52
Q

Define the function of the carboxysome

A

Place where carbon fixation takes places

53
Q

Explain why microbes use “less-expensive” amino acids in proteins that are secreted or are on the cell exterior

A

Because proteins secreted outside of the cell can’t be recycled

54
Q

Construct a timeline of life on earth with respect to the appearance of bacteria and eukaryotic cells

A

Earth (4.5 B), Microbial life (~3 B), atmospheric oxygen appears (~2 B), eukaryotic life (~1.9 B)

55
Q

Identify and describe the basic requirements for life on Earth

A
  1. Availability of essential elements (CHONPS)
  2. Continual source of energy (sun)
  3. Temperature range permitting liquid water
56
Q

Briefly describe the history of Earth with respect to its approximate age and when oxygen appeared and reached its present level

A

Oxygen appeared around 2.4 byr and reached its present level about 0.6 byr ago

57
Q

Identify geological evidence for early life

A
  1. Stromatolites
  2. Microfossils
  3. Biosignatures
58
Q

Describe a stromatolite

A

bulbous masses of layered limestone accreted by microbial mats (fossils of microbial mats)

59
Q

Describe microfossils

A

Fossils preserving the microscopic cellular structure of prehistoric microbes

60
Q

Describe biosignatures such as isotope ratios and banded iron formations

A

Biosignature: chemical indicators of early life
1. Isotope ratio: given element can be altered by biological activity
2.Banded iron: oxidized minerals that suggest period of alternative oxygen-rich and anoxic (oxygen free) conditions

61
Q

Describe how early life may have conducted metabolism before the appearance of O2 in the atmosphere

A
  1. Anaerobic oxidation reduction reactions
  2. Light driven ion pumps
  3. Methanogenesis
62
Q

Briefly describe models for early life: the prebiotic soup model and the RNA world hypothesis

A
  1. Prebiotic soup: which chemical reactions gave rise to organic compounds and then cells (organic molecules arose abiotically from simple chemicals through electric discharge)
  2. RNA hypothesis: RNA was used as the early info storage molecule and for catalysis
63
Q

Briefly describe outstanding questions about early life and define panspermia

A
  1. How did non-life become life?
  2. How did so many species evolve so quickly?
    Panspermia: life originated elsewhere and then “seeded” life one arth
64
Q

Describe how DNA sequences can be used as a molecular clock

A

It’s assumed mutations occur at a constant rate so when DNA changes significantly, it gives a rough estimate of there being a lineage splitting event

65
Q

Define phylogeny

A

The evolutionary history of a group of organisms

66
Q

Explain why 16S rDNA is most widely used as a molecular clock

A

Found in all domains of life, functionally constant, conserved (changes slowly), sufficient length, no horizontal gene transfer

67
Q

Describe phylogenetic tree and its purpose

A

Allows you to compare aligned sequences and calculate genetic distance among sequences

68
Q

Distinguish between a rooted tree and an unrooted tree based on their definitions and what they look like

A
  1. Rooted: shows position of common ancestor (rectangular)
  2. Unrooted: shows only the relationships of species to one another, no ancestor (circular)
69
Q

Identify the 3 domains of life and identify the domain that was first identify using 16s rDNA

A
  1. Bacteria, Archaea, Eukarya
  2. Carl Woese used 16s to discover Archaea
70
Q

Describe adaptive and experimental evolution and give examples of each

A
  1. Experimental evolution – thinks that happen in the lab (i.e Woese)
  2. Adaptive (industrial revolution – butterflies)
71
Q

Explain how a new species is defined

A

Look at phylogeny (with 16s to establish relatedness) and ecological niche (does it live in the same place/have similar traits to its relatives)

72
Q

Define endosymbiosis

A

Form of mutualism in which one species grows within the other

73
Q

Identify eukaryotic cellular organelles that likely began as endosymbiotic bacteria

A

Mitochondria and chloroplasts

74
Q

Correctly identify and order the the taxonomic hierarchy, from domain to species

A

King Philip Came Over For Good Soup

75
Q

Describe how many bacterial phyla are known

76
Q

Identify the 4 well studied bacterial phyla discussed in class

A

Proteobacteria
Actinobacteria
Firmicutes
Cyanabacteria

77
Q

Identify which of the phyla we discussed are gram positive or gram negative

A

Actinobacteria and Firmicutes are postive
Proteobacteria are negative
Cyanobacteria is kind of like both?

78
Q

List the 6 classes of protobacteria

A

Alpha
Beta
Gamma
Epilson
Zeta

79
Q

What genus does Rhizobium, Rickettsia, and Caulobacter belong to?

A

Alpha proteobacteria

80
Q

What genus does Neisseria belong to

A

Beta proteobacteria

81
Q

What genus does Escherichia coli and Pseudomonas aeruginosa belong to?

A

Gamma proteobacteria

82
Q

Describe what would happen in a bacterial culture containing iron and an iron lithotroph – what would happen to the iron and to the color of the medium?

A

Iron would be oxidized, medium would turn red (rust)

83
Q

What genus does Bdellovibrio belong to?

A

Delta proteobacteria

84
Q

Describe the unusual bacteriovorous lifestyle of Bdellovibrio

A

Gets into bacterial cell and eats them from inside out (parasite of other gram negative species)

85
Q

What genus does Helicobacter pylori belong to?

A

epsilson proteobacteria

86
Q

Describe the key features of the phylum Cyanobacteria

A

Oxygenic photoautotrophs

87
Q

Describe the function of cyanobacterial heterocysts, akinetes, and carboxysomes

A
  1. Heterocysts: Fix nitrogen
  2. Akinetes: dormant state of a cell (not spores) that withstand extreme conditions
  3. Carboxysomes: place where carbon fixation occurs
88
Q

Explain why gas vesicles that maintain buoyancy are important for Cyanobacteria

A

They need light hence why they float

89
Q

Define cyanobacterial hormogonia

A

Pieces of a cell filament that detach and then grow into new filaments by cell division

90
Q

Distinguish between Firmicutes and Actinobacteria with respect to the GC content of their DNA

A

Firmicutes have low GC
Actinobacteria have high GC

91
Q

Identify 2 genera in Firmicutes

A
  1. Bacillus
  2. Clostridium
92
Q

What can be associate with its delta endotoxin that is used as a biological insecticide

A

Bacillus thuringiensis

93
Q

What can be associated with production of botulism toxin, “botox”

A

Clostridium botulinum

94
Q

What can be associated with hospital-acquired diarrhea

A

Clostridium difficile (C. diff)

95
Q

Identify several types of Firmicutes

A
  1. lactic acid bacteria
  2. Listeria
  3. Staphylococcus
  4. Streptococcus
96
Q

Describe what MRSA means

A

Methicillin resistent staphylococcus aureus

97
Q

Describe how lactic acid bacteria are used in the food industry

A

used in yogurt, cheese, etc

98
Q

Identify a genus in the Mollicutes

A

Mycoplasma

99
Q

Describe the unusual cell envelope of the Mollicutes

A

no cell wall, just membrane

100
Q

Explain how Mollicutes have cell shape in the absence of a wall

A

internal protein based cytoskeleton

101
Q

Identify a genus of Actinobacteria

A

Streptomyces

102
Q

Describe the cellular structure (mycelium) of Streptomyces species

A

Tree root looking fungus

103
Q

What species is associated with the production of clinically useful antibiotics

A

Streptomyces

104
Q

Identify members of Actinobacteria

A

Mycobacterium

105
Q

Name two disease caused by Mycobacteria species

A

Turboculosis
Leprosy

106
Q

Briefly describe the unusual cell wall structure of Mycobacteria. What two components do they have that other bacteria do not?

A

Mycolic acids and phenolic glycolipids
–don’t have typical outer membrane

107
Q

Describe the domain Archaea in terms of some archaeal habitats and the occurrence of pathogens

A

No pathogens
Live in extreme and normal environments

108
Q

Name four key features of archaea that make them distinct from bacteria

A

Different lipids
Different cell wall structures
Different genomic features
Different metabolic features

109
Q

Describe how archaeal lipids differ from bacterial lipids

A

Have ether links
Branched fatty acid
Extensive branches

110
Q

Describe how archaeal cell walls differ from bacterial cell walls

A

Don’t have normal peptidoglycan – might have pseudo peptidoglycan
Some don’t even have a wall

111
Q

Describe how archaeal genes have similarities and differences from bacteria and eukaryotes

A

Bacteria: circular chromosomes, similar density/gene size, presence of operons

Eukaryotes: presence of Introns and machinery similar to eukaryotes

112
Q

Identify the two major phyla of archaea discussed in class

A
  1. Crenarchaeota (cren = spring)
  2. Euryarchaeota (eury = diverse)
113
Q

Describe the common habitats for thermophiles in the phylum Crenarchaeota

A

Hot springs and geysers

114
Q

Describe features of hot springs and geysers that are important for thermophiles

A

Reduced minerals, low O2 contenct, steep temperature gradients, acidity

115
Q

Describe how Sulfolobales species can respire in volcanic habitats

A

Oxidize H2S to generate energy

116
Q

Describe the extreme habitat and metabolism of Pyrodictium species

A

Live in black smoker (barophiles and hyperthermophiles)

117
Q

Associate euryarchaeota with?

A

Methanogens

118
Q

Describe the principal features that define methanogens

A

Make methane

119
Q

Identify four common habitats of methanogens

A

Underneath pond
Underneath ocean floor
Sewage treatment plants
Landfills

120
Q

Describe the habitat of members of the class Haloarchaea

A

Super salty places – Salterns

121
Q

Describe the function of bacterioruberin

A

Red pigment that protects Archaea from intense sunlight

122
Q

Identify the NaCl concentration typically required by halophilic archaea

123
Q

Describe how most haloarchaea use light energy to increase the proton motive force

A

Use bacterhodopsin as a light pump

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