Exam 3 Flashcards
1
Q
Macronutrients/Macroelements are required in fairly large amounts. What are some examples?
A
Carbon, Oxygen, Nitrogen, Hydrogen, Phosphorus, Sulfur, Selenium
Potassium, Magnesium, Calcium, Sodium
2
Q
Needed to make organic compounds such as amino acids, fatty acids, sugars, and nitrogenase bases
A
Carbon
3
Q
How to Autotrophs and Heterotrophs get carbon?
A
Autotrophs: Use CO2
Heterotrophs: Use organic Compounds
4
Q
How to autotrophs make carbon molecules?
A
CO2 fixation: Calvin-Benson Cycle Reverse Citric Acid pathway Hydroxypropionate pathway Acetyl-CoA pathway
5
Q
How do heterotrophs make carbon molecules
A
They use part of the same pathways to make carbon molecules as autotrophs but with different entry into pathways
6
Q
Biosynthesis pathway that required lots of ATP, CO2, and NADPH to produce sugars
A
Calvin-Benson Cycle
7
Q
Where does the Calvin Benson Cycle occur
A
Phototrophic Eukaryotes: in the chloroplast stroma
Autotrophic Prokaryotes: in the carboxysomes
8
Q
What is the main binding enzyme in the Calvin-Benson cycle and how does it work?
A
Rubisco
It binds Ribulose 1,5-Biphosphate (30 Carbons) to 6CO2. Carboxylated into 12 3-Phosphoglycerate (36 Carbons)
9
Q
An example of a microbe that uses the Calvin-Benson cycle to generate carbon molecules (sugars)
A
Halothiobacillus neopolitans
10
Q
How many times must a cell go through the Calvin Benson cycle to make a single molecule of sugar
A
6 times
11
Q
Use the Acetyl-CoA pathway (acetogenesis) for autotrophic growth
A
Clostridium acetic - this is the only way this microbe can make ATP
12
Q
What is created in Acetyl-CoA
A
Creates ATP and acetone. ATP created is equal to the ATP used.
13
Q
Acetogens are chemo_____
A
Chemoorganotrophs
14
Q
chemoorganotrophs that use CO2 for methanogenesis
A
Methanogens (Archaea)
15
Q
How is methanogenesis coupled with autotrophy
A
Methyl created can go into the Acetyl-CoA pathway
16
Q
A model Archaea organism for the study of methanogensis
A
Methanocaldoccus jannaschii
17
Q
Obligate Aerobes
A
Require 20% oxygen for aerobic respiration
18
Q
MIcroaerophilic Aerobes
A
Require oxygen but at levels lower than atmospheric (5-10%) for aerobic respiration
19
Q
Facultative Aerobes
A
Oxygen is not required, but they grow better with oxygen. Can to Aerobic respiration, Anaerobic respiration, and fermentation
20
Q
What is the first choice in metabolism and the last choice (in regards to oxygen)
A
Aerobic is the first choice, and Fermentation is the last choice
21
Q
Aerotolerant Anaerobes
A
Oxygen is not required and grow no better when oxygen is present; fermentation
22
Q
Obligate Anaerobes
A
oxygen is harmful or lethal; fermentation or anaerobic respiration
23
Q
Reacts with oxygen to form water. Used to remove oxygen from broth
A
Reducing Agent
24
Q
A reducing agent that converts oxygen present in air to water
A
Thyioglycolate broth
25
What is used to test an organism's requirement for oxygen
thyioglycolate broth
26
Using Aerobes in lab
Need culture medium to be oxygenated (allow exposure to air, vigorous shaking, bubbling sterile air into the medium)
27
Using Anaerobes in lab
Need oxygen to be excluded form medium (bottles/tubes completely filled with media and sealed, use a reducing agent, anoxic jars and glove boxes)
28
An example of a toxic form of oxygen
singlet O2 produced by peroxides and others produces as byproducts during respirations
29
detoxifies hydrogen peroxide to release water and oxygen
catalase
30
uses NADH to detoxify hydrogen peroxide into water and NAD+
Peroxidase
31
detoxifies superoxide to produce hydrogen peroxide and oxygen
superoxide dismutase
32
Detoxification of superoxide that will create water and oxygen
superoxide dismutase and catalase in combination
33
detoxifies superoxide with cat c to produce peroxide
superoxide reductase
34
needed to make amino acids and nitrogenous bases
Nitrogen
35
Where do nitrogen fixing microbes get their nitrogen
atmospheric nitrogen (N2)
36
Where do non nitrogen fixing microbes get their nitrogen
use inorganic compounds such as ammonia (NH3) and nitrate (NO3)
37
Needed to make nucleic acids and phospholipids. Obtained form phosphate minerals and free peptides
Phosphorus
38
Needed to make amino acids cysteine and methionine and other vitamins, iron-sulfur proteins. Obtained from sulfates or sulfides
sulfur
39
Needed for some enzymes. Used to maintain solute concentrations. Obtained from free _ or _salts
potassium
40
stabilizes ribosomes, membranes, and nucleic acids and is required by many enzymes. Obtained from salts in various metals
magnesium
41
Stabilizes cell walls
calcium
42
calcium-dipicolinic acid complex
endospores
43
stabilizes cell walls in marine microorganisms; can power ATP synthase
sodium
44
elements needed in very small amounts (i.e. Iron needed for ETC proteins)
micronutrients (trace metals)
45
molecules that bind iron and transport it into the cell
siderophores
46
Sequester the limited iron supply in animal tissues to initiate infection (ex. E coli and Salmonella typhrium)
Enterobactins
47
Sequester the limited iron supply in animal tissues to initiate infection (ex. Marine bacteria)
Aquachelin
48
Organic compounds needed in very small amounts
Growth factors
49
Ex. of growth factors
Folic Acid, B vitamins, Nicotnic Acid (Niacin)
50
reduces spinabifida chance in babies; many bacteria have a biosynthetic pathway to make this
Folic Acid
51
precursor of NAD+
Niacin
52
sum of all catabolic and anabolic reactions
metabolism
53
energy producing reactions
catabolic
54
energy using (biosynthetic) reaction
anabolic
55
freely diffusible coenzymes that act as electron carriers
NAD+/ NADH
56
NAD+ Reduction
Enzyme 1 reacts with electron donor and oxidized form of coenzyme NAD+
Reaction is a part of the citric acid cycle
57
How is NAD+ reduced in the citric acid cycle
Isocitrate is an electron donor. A dehydrogenase oxidizes a substrate by transferring one of more protons and a pair of electrons to an acceptor (NAD/NADP, FAD, or FMN)
58
NADH oxidation
Enzyme II reacts with electron acceptor and reduced form of coenzyme NADH
Reaction is part of the biosynthesis of the amino acid glutamate
59
3 Classes of enzymes
Dehydrogenase, Kinase, Synthase
60
class of enzyme: oxidoreductase, sometimes coupled with phosphorylation
dehydrogenase
61
class of enzyme: phosphorylates
kinase
62
class of enzyme: joins together two molecules
synthase
63
What happens to energy in a redox reaction?
Energy is released and stored in molecules and transported where needed
64
Short term energy storage compounds
ATP (primary energy carrier in the cell that has high energy phosphate bonds)
Derivatives of Coenzyme A - thioester bonds
65
Long term energy storage compounds
Glycogen, Poly-beta-hydroxybutyrate, elemental sulfur
66
Source and process of energy production in chemoorganotrophs
Source: organic compound
Process: fermentation, aerobic respiration, or anaerobic respiration
67
Source and process of energy production in chemolithotrophs
Source: inorganic Compound
Process: primarily aerobic respiration but some are capable of anaerobic respiration
68
A phosphate group is removed form a substrate and added to ADP to make ATP
substrate level phosphorylation
69
inorganic phosphate is added onto ADP to make ATP by ATP synthase
oxidative phosphorylation
70
light-mediated oxidative phosphorylation
photophosphorylaiton
71
Glycolysis
Major pathway of glucose metabolism.
| 2 net ATP (2 in, 4 out) and 2 pyruvate generated per 1 glucose
72
Where does glycolysis occur?
In the cytoplasm of cells capable of using glucose
73
first enzyme used in glycolysis that requires ATP
hexokinase
74
in glycolysis: transfers a phosphate from phosphoenolpyruvate to ADP to make ATP (substrate level phosphorylation)
pyruvate kinase
75
If there is an electron acceptor present will respiration or fermentation occur
respiration
76
If there is no exogenous electron acceptor, will respiration or fermentation occur?
fermentation
77
anaerobic means of generating ATP; organic compounds serve as electron acceptors and donors; substrate level phosphorylation; redox cycling
fermentation
78
creation of waste products regenerates NADH that is used in fermentation
redox cycling
79
cooperative relationship in which the microbes work together to degrade a compound
synthropy
80
can ferment butyrate to acetate for energy if a methanogen is present to use the H2 generated; is not good at regenerating ETC but the methanogen makes ATP from the hydrogen
Synthrophomonas
81
Alcoholic Fermentation in Yeast
Starts with Glycolysis; 2 Ethanol, 2 CO2 are waste products; purpose is to make more NAD+
82
Homolactic fermentation (ex. Streptococcus and Lactococcus)
Converts pyruvate into lactate by lactate dehydrogenase to regenerate NAD+
83
Heterolactic fermentation (ex. Leuconostoc)
No glycolysis at all.
| Glucose goes in and the products are ethanol, lactate, and 1 net ATP (1 in, 2 out)
84
some anaerobic eukaryotes (flagellated protozoan Trichomonas) have _____ that oxidize 1 pyruvate to generate 1 ATP by substrate level phosphorylation
hydrogenosomes
85
What is generated in the oxidation of glucose to 2 pyruvate by glycolysis?
2 pyruvate, 2 NADH, 8 ATP
86
What is generated in the oxidation of each pyruvate to CO2 by the citric acid cycle
1 GTP -> 1 ATP, 4NADH, 1 FADH, 30 ATP
87
Why are NADH and FADH important to the ETC
They each donate protons and electrons creating the proton motive force used by ATP synthase to make ATP by oxidative phosphorylation
88
Also known as the TCA cycle, Tricaroboxylic acid cycle, Kreb's cycle
Citric Acid cycle
89
Products of the Citric acid cycle
CO2 released
NADH and FADH generated for ETC
Organic intermediates used for biosynthesis
A small amount of GTP is made (1 per pyruvate)
90
How can ATP be made from GTP
transferring a phosphate to ADP (substrate level phosphorylation)
91
Terminal electron acceptor for an toxic and an anoxic environment
Oxic: O2
Anoxic: non-oxygen molecule
92
commonly 1st enzyme of ETC; binds NADH, accepting 2 electrons and 2 protons: Releases NAD+, donates 2 electrons and 2 protons to next carrier
NADH dehydrogenases
93
Receives 2 electrons and 2 protons; only donates 2 electrons to the next carrier (still releases the 2 protons)
Flavoproteins (FMN;FAD - flavin adenine dinucleotide)
94
Receives and donates electrons; the amount of electrons transferred depends on the number of iron atoms
Iron-sulfur proteins
95
Have a single iron atom that accepts/donates electrons
Cytochromes
96
Non-protein electron carriers; receive 2 electrons and 2 protons; donates 2 electrons (still releases 2 protons)
Quinones
97
best primary electron donor
NADH
98
best terminal electron acceptor
O2
99
Gram-negative proteobacteria that can oxidize hydrogen
Paracoccus denitrificans
100
includes many quinones that move the electrons using protons in the ETC
Q-Cycle reactions
101
Eukaryotic mitochondrial matrix or prokaryotic cytoplasm ETC
alkaline and electrically negative
102
Environment outside the cell of mitochondrial inter membrane space
acidic and electrically positive
103
ETC in E. coli - aerobic respiration
NADH donates to a flavoprotein, then a couple of quinones, then a pair of cytochromes
104
ETC in E. coli - anaerobic respiration
Final electron acceptor is nitrate reductase
105
Use of a proton motive force to generate ATP (ex. of oxidative phosphorylation)
Chemiosmosis
106
Environment of chemiosmosis
Gram Neg - periplasm
| Gram Pos - space between cytoplasmic membrane and cell wall
107
Ex of Chemoorganotrophs
E. coli & Paracoccus denitrificans
108
Ex. of Chemolithotrophs
Hydrogen oxidation by Ralston eutropha
Sulfur chemolithotroph like beggiatoa
Iron-Oxidizing chemolithorophic Acidithiobacillus ferrooxidans
109
Functions of a pigment in photosynthesis
absorb light energy; transfer light energy to photosynthetic reaction center
110
Location of photosynthetic pigments
Eukaryotes - chloroplasts (thylakoid membrane)
| Prokaryotes - chlorosomes, cytoplasmic membrane, thylakoid membranes
111
What are the thylakoid membranes in a photosynthetic cyanobacterial cell like Cyanothece
the white lines
112
Structure containing antenna bacteriochlorophyll; used by some photosynthetic gram-neg bacteria like the green sulfur Chlorobaculum tepidum and green non-sulfur Chloroflexus; embedded on the membrane
Chlorosome
113
Central pigments of photosynthesis embedded in photosynthetic membranes
Chlorophylls/ Bacteriochlorophylls
114
Chlorophyll is used in ___ phototrophs like Chlamydomonas
oxygenic
115
Bacteriochlorophyll is used in ____ phototrophs like Rhodopseudomonas
anoxygenic
116
Absorbs light energy and transfers it to the reaction center
Antenna
117
Accumulate energy here to initiate photosynthetic electron transport
Reaction Center
118
Antenna pigments; widespread; absorb blue light; give wide array of colors
carotenoids
119
PHotoprotective role of carotenoids
quench toxic oxygen species
120
Cyanobacteria thylakoid membranes and red algal chloroplasts; Absorb yellow or red light (they look blue/green); act as antenna pigments
phycobilins
121
Phycobilins are found in groups attached to _____
photosynthetic membranes
122
ETC in anoxygenic photosynthesis is _____
cyclic
Light energy converts weak donor into strong donor. Cyclic electron flow generates a proton motive force which excites a poor electron donor and makes it a strong one.
123
a green sulfur bacterium also capable of using hydrogen sulfide as an electron donor
Chlorobium
124
How is a proton motive force created in anoxygenic photosynthesis
the quinones are pushing protons out as the pass electrons and the ATPsynthase pushes the protons back in
125
How is ATP made in anoxygenic photosynthesis
Oxidative Phosphorylation, but because it is light driven we call is photo-phosphorylation
126
Purple sulfur proteobacterium used for studying anoxygenic photosynthesis
Rhodobacter capsulatus
127
ETC in oxygenic photosynthesis is ____
```
Not cyclic (Z scheme)
PSII:A poor electron donor (but excellent electron acceptor) becomes an extremely good electron donor when noncyclic electron flow generates a proton motive force.
PSI: cyclic electron flow generates proton motive force
```
128
Example of a microbe that has the ability to do anoxygenic photosynthesis using PSI
Oscillatoria
129
Microbes used to study oxygenic photosynthesis
Prokaryotic cyanobacterium Synechocystis & eukaryotic green alga Chlorella
130
Substrates to Products. Makes ATP by a proton motive force
Catabolism: energy generation
131
Monomers to macromolecules and other cellular constituents by biosynthesis. Uses ATP.
Anabolism: energy consumption
132
Glucose and its derivatives. Obtained from the growth medium or made by gluconeogenesis
Hexoses
133
Ribose and deoxyribose. Made by removing CO2 from hexose.
Pentoses
134
Glycogen, Starch, Peptidoglycan subunits, lipopolysaccharide. Made from activated glucose - UDPG or ADPG
Polysaccharides
135
How are polysaccharides made
From activated Glucose (UDPG or ADPG)
When the UDP on UDPG is cleaved off, the energy released allows of the attachment of the glucose molecule in the cell to create the growing chain of glucose that is glycogen
136
Carbon skeletons from intermediates in glycolysis or citric acid cycle. Derived from inorganic nitrogen source
Amino Acids
137
Gets:
| Carbon from several sources; nitrogen from amino acids
Nucleotides
138
Precursor for purines (A, G)
Inosinic Acid
139
Precursor for pyrimidines (C, T, U)
uridylate
140
Synthesized 2 carbons (acetyl unit) at a time.
biosynthesis of fatty acids
141
holds growing fatty acids as it is synthesized
acyl carrier protein
142
Glycerol, phosphate, and various sugars are added
biosynthesis of lipids
143
Source of electrons for phototrophs
Anoxygenic - inorganic compounds
| Oxygenic - water
144
describes the total number of difference species in a community
species richness
145
the proportion of each species in a community
species abundance
146
Microbial communities consist of ___ of metabolically related organisms
guilds
147
Microbial communities and their natural environment make up an ____
ecosystem
148
The place where the microbe actually lives
microenvironment
149
Suboptimal Growth is due to
Suboptimal resources or growth conditions; distribution of nutrients not uniform in habitat; microbes growing in mixed populations where competition exists
150
Most terrestrial microbial growth occurs on
the surface of soil particles around plant roots in the rhizosphere
151
Hydrogen sulfide is ____ proportional to oxygen levels
inversely
152
levels of organic carbon and oxygen are ____ related in a river
inversely
153
Most abundant photosynthetic microbe
Prochlorococcus
154
require high pressure
extreme piezophile
155
Example of an extreme piezophile
Moritella (700-800 atm)
156
Grow best under high pressure
Piezophile
157
Tolerate elevated pressure but grow best at low pressure
Piezotolerant
158
Chemolithotrophs in hydrothermal vents get there CO2 from this enzyme that helps with the conversion of bicarbonate to CO2 or backwards
Carbonicane Hydrase
159
Example of a Mutualistic relationship in marine invertebrate/bacteria
Rift giant tube worm and sulfide-reducing bacteria.
| Bacteria use sulfide as an electron donor and CO2 on floor to create organic compounds that the worm uses
160
Bacterial assemblages that form on surfaces (can be other microbes besides bacteria)
Also includes waste
biofilms
161
Why do solid surfaces serve as microbial habitats
Nutrients adhere to surface; Surface itself is nutritious
162
Why do biofilms form?
Defense in numbers; allow cells to stay in favorable niche; cells live in close association (metabolic cooperation between species)
163
How do Biofilms form?
Attachment, Colonization (lawn of cells),Development, Active Dispersal (hipster cells leave)
164
intercellular communication, growth, and polysaccharide formation
colonization
165
triggered by environmental factors such as nutrient availibility
active dispersal
166
biofilm mushroom; adhesive matrix holds the biofilm together
Pseudomonas aeruginosa
167
How do biofilms affect cystic fibrosis
don't have a way to clear microbes because of the mucus
168
How do biofilms affect periodontal disease
Microbes on teeth; primarily Streptococcus that form lactic acid
169
How doe biofilms affect infections associated with implants
Breast: Staphylococcus epidermis comes in because it is part of the normal flora on skin and breast glands.
Artificial Joints: Propionibacterium acnes and Staphylococcus species
170
What mechanical issues have biofilms been implicated in?
Pipeline (oil, water) congestion and corrosion; Degradation submerged objects
171
How does Squid-Allivibrio symbiosis work
Allivibrio fischeri bioluminesce in the light organ of the Hawaiian bobtail squid and helps the squid not make a shadow
172
When enough cells assemble in a biofilm (quorum), the concentration of AHL increases which then changes the activity of many genes allowing the cells in the biofilm to
Recruit; Bioluminesce; Make Antibiotics; regulate virulence factors (release toxins)
173
Recognize AHL that activate an activator protein to locate brother and sister cells
Quorum sensing
174
extremely thick biofilms; layers are made of species from different guilds; most commonly found in hyper saline or geothermal habitats with little grazing by animals and competition
microbial mats
175
During the DAY part of a diel cycle in a microbial mat
oxygenic phototrophs are producing oxygen and creating a surface environment in the surface layers; in the lower layers, sulfate reduction occurs
176
During the NIGHT part of a diet cycle in a microbial mat
photosynthesis stops and the mat quickly become anoxic throughout hydrogen sulfide accumulates
