Exam 3 Microbio Flashcards
Microbiology
1
Q
Define catabolism
A
Breakdown of complex molecules into smaller ones
2
Q
Define anabolism
A
Process by which chemical energy is used to build complex molecules from simpler components
3
Q
Define and distinguish among chemoorganotrophy, lithotrophy, and phototrophy
A
- Chemoorganotrophy: use of complex carbon containing compounds to extract energy for cell growth
- Lithotrophy: use of inorganic compounds to extract energy for cell growth
- Phototrophy: the process by which light energy is harvested to make chemical energy and reducing power
4
Q
Identify cellular energy intermediates
A
- Proton motive force
- NADH
- ATP
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
6
Q
Identify three carbon sources for catabolism
A
- Polysaccharides
- Lipids and amino acids
- Aromatic compounds
7
Q
Define fermentation and respiration and identify the important similarities and differences between them
A
- Fermentation: incomplete breakdown (oxidation) of organic molecules using the breakdown products themselves as electron acceptors
- Respiration: complete breakdown (oxidation) of organic molecules with electron transfer to a terminal electron acceptor
8
Q
Define oxidation and reduction
A
- Oxidation: loss of electrons
- Reduction: gain of electrons
9
Q
Identify which has more stored energy, an oxidized molecule or a reduced one
A
Reduced molecules
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
11
Q
Identify 3 cellular electron carriers
A
- ATP
- NADH
- FADH
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
13
Q
Distinguish the EMP (glycolysis), ED, and PPP pathways with respect to their primary objective (getting energy or molecular building blocks)
A
- EMP: most common form of glycolysis
–solely for energy generation - PPP pathway: building molecules (biosynthesis)
- ED: splits the difference between PPP and EMP (used by E.coli)
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
15
Q
Describe the net energy yield of glycolysis in terms of ATP and reduced NADH
A
2 ATP and 2 NADH
16
Q
Describe what kind of bacteria often use the ED pathway
A
E.Coli
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
18
Q
Describe how NADH can be oxidized to regenerate NAD+ in the absence of oxygen
A
Fermentation
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
20
Q
Define and distinguish among homolactic, heterolactic, ethanolic, and mixed-acid fermentation
A
- Homolactic: products-2 lactic acid, 2 NAD+
- Heterlactic: lactic acid, ethanol, CO2, NAD+
- Ethanolic: 2 ethanol, 2 CO2, 2 NAD+
- Mixed-acid: Redox is balanced by making acetate, formate, lactate, succinate, ethanol, H2, CO2
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
22
Q
Define and distinguish substrate-level phosphorlaytion and oxidative phosphorylation
A
- Substrate-level phosphorylation: produces ATP in glycolysis or TCA cycle
- Oxidative phosphorylation: overall process of electron transport and ATP generation
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
- NADH: quinone oxidoreductase
- Mobile electron carrier (quinones)
- Terminal oxidase (cytochromes)
Function: pumping protons
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
- NADH: quinone oxidoreductase takes electrons from donor and passes to mobile
- Mobile electron carrier (quinones)
also passes protons - Terminal oxidase (cytochromes)
also pumps protons
25
Describe how quinones transfer protons from the cytoplasm to outside the membrane
Oxidation of NADH and reduction of Q is coupled to pumping 4 H+ across the membrane
26
Describe a redox tower and what it indicates
Electrons flow step wise from one carrier to another, losing energy as they go until they reach terminal electro acceptor.
27
Describe the proton motive force in terms of it being an electrochemical gradient
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
28
Describe the function of the F1F0ATPase: its power source and its cellular function
Consumes the proton motive force to make ATP -- uses proton gradient as power source to spin
29
Identify 3 cellular functions or apparatuses that are powered by the proton motive force
1. Flagellar rotation
2. Antiporters
3. ATP generation
30
Compare the energy yield of fermentation and respiration using glucose as the starting compound
1. Fermentation --> 2 ATP/glucose
2. Respiration --> 38 ATP/glucose
31
Describe how the potential of electrons changes as they are passed down an ETS
Lose energy (pumps H+) as they go down
32
Explain how an ETS can connect oxidation of carbon compound to ATP generation
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
33
Identify common terminal electron acceptors and compare them in terms of their reduction potentials (how good they are at taking electrons)
1. Nitrate -- pretty decent electron acceptor
2. Sulfate -- not good electron acceptor
3. Extracellular metals (Fe3+) -- pretty good electron acceptor
34
Identify alternative, inorganic electron donors (food) that microbes can use
H2, sulfur, ammonium
35
Define anammox in terms of its electron donor and the conditions under which it takes place
Anammox is anaerobic ammonium oxidation -- ammonium is the electron donor and it can only happen in oxygen free conditions
36
Describe how sulfur oxidation can be both helpful and harmful to human activity
1. Helpful: biomining
2. Can cause acidification --> erode structures
37
Define hydrogenotrophy and methylotrophy
1. Hydrogenotrophy : using H2
2. Methylotrophy: using one carbon compound
38
Define photosynthesis
Conversion of light energy into chemical energy
39
Identify the important outputs of photosynthesis
ATP and NADPH
40
Define photoexcitation and photolysis and describe how they relate to an electron transport system
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)
41
Describe the steps in photosynthesis
Chlorophyll aborbs light, electron separated from light, electron goes to ETS, ETS pumps H+ to make PMF go and drive ATP synthesis
42
Describe the function of the antenna complex and the name the light absorbing pigment contained therein
Antenna complex holds chlorophyll molecules to maximize light absorption -- like a satellite
43
Explain why the antenna complex is arranged in a circle around the reaction center (and define the reaction center)
Circular to maximize light absorption.
Reaction center: a protein complex where electron transfer to ETS occurs
44
Describe the oxygenic Z pathway in terms of its inputs, electron source, and outputs and in what organisms it is found
1. Takes electrons from water
2. Electrons used to pump H+ and make NADPH
3. Used by cyanobacteria and plants
45
Describe anaerobic photosystem I in terms of its input, electron source, output
Takes electrons from H2 or H2S, makes NADPH, doesn't pump protons but makes proton graident
46
Describe anaerobic photosystem II in terms of its inputs, electron source, and outputs
1. Takes electrons from chlorophyll itself
2. Too weak to make NADPH
3. Pumps a few H+ to make ATP and returns the electron
47
Define cyclic photophosphorylation
When the energy of the electron is too low to make NADPH -- it pumps a few protons to make ATP
48
Describe the function of bacteriorhodopsin and identify the light absorbing pigment therein
They are light-powered proton pumps and use retinal as their pigment
49
Describe the function of the Calvin cycle and the type of organism that performs the Calvin cycle
Convert carbon dioxide into sugar. Autotrophs perform that
50
Define the inputs and outputs of the Calvin cycle
Inputs: carbon dioxide, ATP, NADPH
Outputs: glucose, ADP, and NADPH+
51
Define the function of the Rubisco enzyme
The enzyme that fixes carbon dioxide in the Calvin cycle
52
Define the function of the carboxysome
Place where carbon fixation takes places
53
Explain why microbes use "less-expensive" amino acids in proteins that are secreted or are on the cell exterior
Because proteins secreted outside of the cell can't be recycled
54
Construct a timeline of life on earth with respect to the appearance of bacteria and eukaryotic cells
Earth (4.5 B), Microbial life (~3 B), atmospheric oxygen appears (~2 B), eukaryotic life (~1.9 B)
55
Identify and describe the basic requirements for life on Earth
1. Availability of essential elements (CHONPS)
2. Continual source of energy (sun)
3. Temperature range permitting liquid water
56
Briefly describe the history of Earth with respect to its approximate age and when oxygen appeared and reached its present level
Oxygen appeared around 2.4 byr and reached its present level about 0.6 byr ago
57
Identify geological evidence for early life
1. Stromatolites
2. Microfossils
3. Biosignatures
58
Describe a stromatolite
bulbous masses of layered limestone accreted by microbial mats (fossils of microbial mats)
59
Describe microfossils
Fossils preserving the microscopic cellular structure of prehistoric microbes
60
Describe biosignatures such as isotope ratios and banded iron formations
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
Describe how early life may have conducted metabolism before the appearance of O2 in the atmosphere
1. Anaerobic oxidation reduction reactions
2. Light driven ion pumps
3. Methanogenesis
62
Briefly describe models for early life: the prebiotic soup model and the RNA world hypothesis
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
Briefly describe outstanding questions about early life and define panspermia
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
Describe how DNA sequences can be used as a molecular clock
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
Define phylogeny
The evolutionary history of a group of organisms
66
Explain why 16S rDNA is most widely used as a molecular clock
Found in all domains of life, functionally constant, conserved (changes slowly), sufficient length, no horizontal gene transfer
67
Describe phylogenetic tree and its purpose
Allows you to compare aligned sequences and calculate genetic distance among sequences
68
Distinguish between a rooted tree and an unrooted tree based on their definitions and what they look like
1. Rooted: shows position of common ancestor (rectangular)
2. Unrooted: shows only the relationships of species to one another, no ancestor (circular)
69
Identify the 3 domains of life and identify the domain that was first identify using 16s rDNA
1. Bacteria, Archaea, Eukarya
2. Carl Woese used 16s to discover Archaea
70
Describe adaptive and experimental evolution and give examples of each
1. Experimental evolution -- thinks that happen in the lab (i.e Woese)
2. Adaptive (industrial revolution -- butterflies)
71
Explain how a new species is defined
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
Define endosymbiosis
Form of mutualism in which one species grows within the other
73
Identify eukaryotic cellular organelles that likely began as endosymbiotic bacteria
Mitochondria and chloroplasts
74
Correctly identify and order the the taxonomic hierarchy, from domain to species
King Philip Came Over For Good Soup
75
Describe how many bacterial phyla are known
~100
76
Identify the 4 well studied bacterial phyla discussed in class
Proteobacteria
Actinobacteria
Firmicutes
Cyanabacteria
77
Identify which of the phyla we discussed are gram positive or gram negative
Actinobacteria and Firmicutes are postive
Proteobacteria are negative
Cyanobacteria is kind of like both?
78
List the 6 classes of protobacteria
Alpha
Beta
Gamma
Epilson
Zeta
79
What genus does Rhizobium, Rickettsia, and Caulobacter belong to?
Alpha proteobacteria
80
What genus does Neisseria belong to
Beta proteobacteria
81
What genus does Escherichia coli and Pseudomonas aeruginosa belong to?
Gamma proteobacteria
82
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?
Iron would be oxidized, medium would turn red (rust)
83
What genus does Bdellovibrio belong to?
Delta proteobacteria
84
Describe the unusual bacteriovorous lifestyle of Bdellovibrio
Gets into bacterial cell and eats them from inside out (parasite of other gram negative species)
85
What genus does Helicobacter pylori belong to?
epsilson proteobacteria
86
Describe the key features of the phylum Cyanobacteria
Oxygenic photoautotrophs
87
Describe the function of cyanobacterial heterocysts, akinetes, and carboxysomes
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
Explain why gas vesicles that maintain buoyancy are important for Cyanobacteria
They need light hence why they float
89
Define cyanobacterial hormogonia
Pieces of a cell filament that detach and then grow into new filaments by cell division
90
Distinguish between Firmicutes and Actinobacteria with respect to the GC content of their DNA
Firmicutes have low GC
Actinobacteria have high GC
91
Identify 2 genera in Firmicutes
1. Bacillus
2. Clostridium
92
What can be associate with its delta endotoxin that is used as a biological insecticide
Bacillus thuringiensis
93
What can be associated with production of botulism toxin, "botox"
Clostridium botulinum
94
What can be associated with hospital-acquired diarrhea
Clostridium difficile (C. diff)
95
Identify several types of Firmicutes
1. lactic acid bacteria
2. Listeria
3. Staphylococcus
4. Streptococcus
96
Describe what MRSA means
Methicillin resistent staphylococcus aureus
97
Describe how lactic acid bacteria are used in the food industry
used in yogurt, cheese, etc
98
Identify a genus in the Mollicutes
Mycoplasma
99
Describe the unusual cell envelope of the Mollicutes
no cell wall, just membrane
100
Explain how Mollicutes have cell shape in the absence of a wall
internal protein based cytoskeleton
101
Identify a genus of Actinobacteria
Streptomyces
102
Describe the cellular structure (mycelium) of Streptomyces species
Tree root looking fungus
103
What species is associated with the production of clinically useful antibiotics
Streptomyces
104
Identify members of Actinobacteria
Mycobacterium
105
Name two disease caused by Mycobacteria species
Turboculosis
Leprosy
106
Briefly describe the unusual cell wall structure of Mycobacteria. What two components do they have that other bacteria do not?
Mycolic acids and phenolic glycolipids
--don't have typical outer membrane
107
Describe the domain Archaea in terms of some archaeal habitats and the occurrence of pathogens
No pathogens
Live in extreme and normal environments
108
Name four key features of archaea that make them distinct from bacteria
Different lipids
Different cell wall structures
Different genomic features
Different metabolic features
109
Describe how archaeal lipids differ from bacterial lipids
Have ether links
Branched fatty acid
Extensive branches
110
Describe how archaeal cell walls differ from bacterial cell walls
Don't have normal peptidoglycan -- might have pseudo peptidoglycan
Some don't even have a wall
111
Describe how archaeal genes have similarities and differences from bacteria and eukaryotes
Bacteria: circular chromosomes, similar density/gene size, presence of operons
Eukaryotes: presence of Introns and machinery similar to eukaryotes
112
Identify the two major phyla of archaea discussed in class
1. Crenarchaeota (cren = spring)
2. Euryarchaeota (eury = diverse)
113
Describe the common habitats for thermophiles in the phylum Crenarchaeota
Hot springs and geysers
114
Describe features of hot springs and geysers that are important for thermophiles
Reduced minerals, low O2 contenct, steep temperature gradients, acidity
115
Describe how Sulfolobales species can respire in volcanic habitats
Oxidize H2S to generate energy
116
Describe the extreme habitat and metabolism of Pyrodictium species
Live in black smoker (barophiles and hyperthermophiles)
117
Associate euryarchaeota with?
Methanogens
118
Describe the principal features that define methanogens
Make methane
119
Identify four common habitats of methanogens
Underneath pond
Underneath ocean floor
Sewage treatment plants
Landfills
120
Describe the habitat of members of the class Haloarchaea
Super salty places -- Salterns
121
Describe the function of bacterioruberin
Red pigment that protects Archaea from intense sunlight
122
Identify the NaCl concentration typically required by halophilic archaea
1.5 M
123
Describe how most haloarchaea use light energy to increase the proton motive force
Use bacterhodopsin as a light pump
