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Biochemistry > microbiology exam 3 > Flashcards

microbiology exam 3 Flashcards

1
Q

what is the most common starting pathway for the breakdown of sugar

A

the most common pathway is glucose

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2
Q

What three general products of the central metabolic pathways does a cell require to carry out biosynthesis

A

ATP
NADPH
precursor metabolites

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3
Q

What is the purpose of the transition step

A

the transition step links glycosis to the TCA cycle

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4
Q

how do enzymes speed up their reactions

A

By lowering the activation energy

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5
Q

what are anabolic reactions

A

Anabolic reactions are biosynthetic reactions that require energy for the conversion of molecular subunits to larger molecules

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6
Q

what is the purpose of the proton motive force

A

the proton force is used to syntesize ATP

Form of energy generated as an electron transport chain moves protons across a membrane to create a chemiosmotic gradient.

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7
Q

why would fermentation lead to a slow movement of food spoilage

A

Fermentation will lead to production of acidic by-products, dropping the pH of the food below a level that bacteria can tolerate.

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8
Q

why would a cell ferment than respire

A

There is no oxygen present and it cannot use anaerobic respiration OR it lacks the ability to respire (i.e., no electron transport chain).

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9
Q

How can glycosis occur

A

Glycosis may occur under aneorobic or aerobic conditions

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10
Q

which of the following processes generates the greatest amount of energy ?

A

Anaerobic respiration generates 34 ATP

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11
Q

Where does oxygen generate from in the photorophic production of energy

A

oxygen generates from water

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12
Q

the term precuror metabolites refers to molecules

A

they are used in biosynthesis

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13
Q

the electron transport system referred to

A

requires a membrane AND generates a concentration gradient of protons

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14
Q

what is the sum of all chemical reactions

A

metabolism

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15
Q

what is the difference between anabolism and catabolism

A

annabolism or biosynthesis is the set of chemical reactions that helps cells syntesize and assemble the subunits of macromocules using ATP

catabolism is the set of chemical reactions that degrade compounds releasing their energy

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16
Q

how do chemoorganotrophs obtain energy

A

chemoorganotrophs obtain energy by degrading organic compounds or oxidizing organic compounds

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17
Q

tell me the difference between endergonic and exergonic

A

endergonic requires a net input of energy and the products have more free energy than the starting compounds

on the other hand exergonic releases energy because the starting compounds have more energy than the products

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18
Q

define enzyme
subtrate
and activation energy

A

enzyme is a protein that functions as a biological catalyst speeding up the conversion of one substance

the substrate is the substance on which the enzyme acts on

activation energy is the initial energy required to break a bond

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19
Q

explain ATP

A

ATP is the main energy currency of cells made up of ribosomes, adenine, and 3 phosphate groups

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20
Q

how is ADP made

A

ADP isa Molecule that accepts an inorganic phosphate (Pi ) generating ATP

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21
Q

what two processes do chemoorganotrophs use

A

substrate-level phosphorylation
Synthesis of ATP using the energy released in an exergonic chemical reaction during the breakdown of the energy source.

oxidative phosphorylation
Synthesis of ATP using the energy of a proton motive force created by harvesting chemical energy; the synthesis is catalyzed by ATP synthase

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22
Q

what is photophosphorylation

A

photophosphorylation
Synthesis of ATP using the energy of a proton motive force created by harvesting radiant energy.

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23
Q

what is the purpose of glycolysis

A

the purpose of glycoses is to split glucose with 6 carbons into two pyruvate molecules with 3 carbons each

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24
Q

what is the purpose of the pentose phosphate pathway

A

the primary role of the pentose phosphate pathway is for the production of precursor metabolites NADPH

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25
Q

What is the role of the TCA cycle

A

the role of the TCA cycle is to generate reducing power, precursor metabolites, ATP

And with the transition step it oxidizes the pyruvate releasing CO2.

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26
Q

what is the role of cellular respiration

A

Cellular respiration transfers electrons from glucose to the electron transport chain to the terminal electron acceptor

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27
Q

why does fermentation recycle electrons

A

fermentation recycles electron carriers in a cell that cannot respire so that it can continue to make ATP

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28
Q

explain the process of metabolic processes

A

aerobic respiration uses the electron transport chain and oxygen as the terminal electron acceptor. the atp generated by the substrate level phosphorylation is 2 in glycosis and 2 in the tca cycle and oxidative phosphorylation is 34 giving off 38 maximum.

anerobic respiration uses an electron transport chain and the terminal electron acceptor for molecules other than oxygen such as nitrite and sulfate

fermentation doesn’t use the electron transport chain. organic molecule or pyruvate derative is the terminal electron acceptor .2 glycosis total from subtrate level and 0 from oxidative phosphorylation and in total 2 atp

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29
Q

describe the characteristics of enzyme inhibitors.

A

competitive inhibition is when the inhibitor binds to the active site on the enzyme blocks the substrate and example is a sulfa drug

Unnoncompetitive inhibition is when the inhibitor changes the shape of the enzyme so that subunits cant bind to the active site

noncompetitive inhibition is when the enzyme shape is changed making the enzyme no longer functional.

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30
Q

what do central metabolic pathways generate

A

they generate ATP
precursor metabolites
reducing power nadh, fadh2, and nadph

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31
Q

describe the products of glycolysis

A

Converts 1 glucose to 2 pyruvate molecules; net yield = 2 ATP, 2 NADH
Investment phase:
2 ATP consumed
2 phosphate groups added
Glucose split to two 3-carbon molecules
Pay-off phase:
3-carbon molecules converted to pyruvate
Generates 4 ATP, 2 NADH

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32
Q

products of the pentose phosphate pathway

A

Breaks down glucose
Important in biosynthesis for precursor metabolites
Ribose 5-phosphate, erythrose 4-phosphate
Also generates variable amount of NADPH
Product glyceraldehyde-3-phosphate can enter glycolysis

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33
Q

describes what happens in the transition step

A

CO2 is removed from pyriuvate and the electron transfer reduces nad plus to nadh plus

2 acetylcoa
links previous pathway to tca cycle

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34
Q

describe the tca cycle

A

Completes oxidation of glucose
Produces
2 CO2
2 ATP
6 NADH
2 FADH2
Precursor metabolites

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35
Q

describe the importance of the electron transport chain

A

Accepts electrons from NADH, FADH2
Energy released as electrons are passed from one carrier to the next
Energy pumps protons across membrane
Prokaryotes: cytoplasmic membrane
Eukaryotes: inner mitochondrial membrane
Creates electrochemical
gradient called proton motive force

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36
Q

describe the components of the electron transport chain

A

Quinones
Lipid-soluble; move freely in membrane
Can transfer electrons between complexes

Cytochromes
Contain heme, molecule with iron atom at center
used to distinguish bacteria

Flavoproteins
Proteins to which a flavin is attached
FAD, other flavins synthesized from riboflavi

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37
Q

describe the electron transport chain of mitochondria

A

Complex I (NADH dehydrogenase complex)
Accepts electrons from NADH, transfers to ubiquinone
Pumps 4 protons

Complex II (succinate dehydrogenase complex)
Accepts electrons FADH2, “downstream” of those carried by NADH
Transfers electrons to ubiquinone

Complex III (cytochrome bc1 complex)
Accepts electrons from ubiquinone from Complex I or II
4 protons pumped; electrons transferred to cytochrome c

Complex IV (cytochrome c oxidase complex)
Accepts electrons from cytochrome c, pumps 2 protons
Transfers electrons to terminal electron acceptor (O2

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38
Q

how does atp sunthase use the proton motive force

A

Energy required to establish gradient; energy is released when gradient is removed or reduced
ATP synthase allows protons to flow down gradient in controlled manner
Uses energy to add phosphate group to ADP
1 ATP formed from

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39
Q

describe nucleotide synthesis

A

DNA, RNA initially synthesized as ribonucleotides which can be converted to deoxyribonucleotides
Purines: atoms added to ribose 5-phosphate to form ring
Pyrimidines: ring made, then attached to ribose 5-phosphate

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40
Q

describe aromatic amino acids

A

Amino acids are feedback inhibitors of enzymes that directs branch to its own synthesis
Amino acids also inhibit formation of original 7-carbon compound
Result is that cell does not make amino acids that are already present

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41
Q

what is the role of glutamate in amino acid synthesis

A

Glutamate provides bacteria a mechanism for incorporation of nitrogen into organic material

Glutamate is synthesized in a single-step reaction that adds ammonia to α-ketoglutarate
Transamination can then generate other amino acids

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42
Q

describe lipid synthesis

A

Requires fatty acids and glycerol
Fatty acids: 2-carbon units added to acetyl group from acetyl-CoA
Usually 14, 16, or 18 carbon atoms
Glycerol: synthesized from dihydroxyacetone phosphate generated during glycolysis

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43
Q

describe the calvin cycle

A

Three essential stages of Calvin cycle
Incorporation of CO2 into organic compounds
Reduction of resulting molecule
Regeneration of starting compound
Six “turns” of cycle incorporate 6 CO2 molecules into one molecule of fructose-6-phosphate
Consumes 18 ATP, 12 NADPH per fructose molecule

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44
Q

describe carbon fixation

A

Incorporation of CO2 into organic compounds by chemolithoautotrophs and photoautotrophs

Consumes a great deal of ATP, reducing power

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45
Q

cyclic versus noncyclic phosphorylation

A

Cyclic photophosphorylation – used to synthesize ATP, but not reducing power
Photosystem I produces ATP
Reaction-center chlorophyll emit high-energy electrons
Transferred to electron transport chain (ETC) to pump protons across membrane
returned to same reaction-center chlorophylls

Non-cyclic photophosphorylation – produce both ATP and reducing power
Electrons from photosystem II establish proton motive force and are then donated to photosystem I
Photosystem II replenishes electrons by reducing NADP+ to NADPH and generates oxygen (process is oxygenic)
Electrons from photosystem I reduce

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46
Q

subtrate level phosphorylation versus oxidative phosphorylation

A

Substrate-level phosphorylation:
2 ATP (from glycolysis; net gain)
2 ATP (from the TCA cycle)
4 ATP (total)

Oxidative phosphorylation:
6 ATP (from reducing power gained in glycolysis)
6 ATP (from reducing power gained in transition step)
22 ATP (from reducing power gained in TCA cycle)
34 (total)
Total ATP gain (theoretical maximum) = 38

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47
Q

groups of chemolithotrophs

A

Chemolithotrophs fall into four general groups:
Hydrogen bacteria oxidize hydrogen gas.
Sulfur bacteria oxidize hydrogen sulfide.
Iron bacteria oxidize reduced forms of iron.
Nitrifying bacteria include two groups:
one oxidizes ammonia forming nitrite
another oxidizes nitrite producing nitrate

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48
Q

describe the role of photosystems

A

Reaction-center pigments donate excited electrons to electron transport chain
T
he energy of the electrons is used to pump protons across the membrane to generate a proton motive force

An ATPase uses that energy to synthesize ATP
The process called photophosphorylation to reflect its dependence on radiant energy.

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49
Q

describe the first stage of photosynthesis

A

Photosynthetic processes are considered in two stages.
The first stage, the light-dependent reactions, captures radiant energy and uses it to generate the following compounds needed to synthesize organic compounds from CO2:
ATP
Reducing power (NADPH or NADH)

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50
Q

chapter 11

what are the characteristics regarding anoxygenic phototrophs

A

may be motile
contian bacteriachlorophyll
harvest energy from sunlight
contain chlorosomes
may use inorganic or organoc compounds to generate reducing power like hydrogen sulfide
C6H12O6 +12S +6H2O

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51
Q

name the genera that can form a resting stage that allows them to survive the dry periods that occur in many soil.

A

Endospores—Bacillus and Clostridium

Conidia—Streptomyces-
Microcysts —myxobacteria

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52
Q

give the description of each aneorobic chemotrophs
Propionibacterium species

Lactic acid bacteria

Methanogens

Sulfur and sulfate-reducing bacteria

Clostridium species

A

Archaea, live in anaerobic environments with H2 and CO2. methanogens

Found in mud with organic material and oxidized sulfur compounds is sulfur and sulfate reducing bacteria

Generally in endospore form in soil, but will germinate to vegetative form when anaerobic conditions arise. Gram-positive rods. clostridium species

Gram-positive, catalase-negative, grow in aerobic environments but only ferment, producing acidic conditions. lactic acid bacteria

Gram-positive pleomorphic (irregular shaped) rods, fermenters, often used in Swiss cheese production.

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53
Q

review all the differences between archaea and bacteria

A

archaea are prokaryotic organisms and belong to their own domain.

the ribosomal and protein sequences of archaea are related to eukarya than bacteria.

the domain archaea are closely related to the domain eukarya.

Characteristics that define archaea include unique membrane lipids, cell wall construction and composition, and metabolic pathways.

Adaptations to metabolic pathways allow archaea to live in extreme environments, such as areas with high levels of salt (halophiles) or high temperatures (thermophiles)

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54
Q

why are nitrogen fixing bacteria important

A

can go into an organic matieral by incoroporating N2

help limit CO2 build up in the atmosphere

incoroporate CO2 into organic matieral

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55
Q

what can oxygenic photrophs do

A

include the cyanonbacteria
generate o2
are primary producers
play a role in nitrogen fixation

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56
Q

what is a method that cyanobacteria do not use

A

cyanobacteria do not use this method of isolating nitrogenase into endospores only germinate at night to protect their nitrogenase from oxygen

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57
Q

what are the characteristics of nitrifying bacteria, sulfur oxidizing bacteria, and hydrogen oxidizing bacteria

A

nitrifying bacteria is gram negative oxidizes inorganic matieral like ammonia

hydrogen oxidizing bacteria use H2 as an energy with O2 as tea and negative obligate chemolitirophs

sulfur oxidizing bacteria negative rods/spirals may filaments, oxidizes hydrogen sulfide with o2 as tea

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58
Q

describe mycobacterium thermus deinococcus micrococcus pseudomonas species

A

micrococcus species gram positive cocci found in soil dust particles and obligate aerobes pigment colonies slaty conditions
mycobacterium plemorphic rods bad stain. human diseases.resist destaining
Acid fast

pseudomonas species negative polar flagella
pigments harmless but can be pathogens of humans

thermus speices negagtive stain unusual cell wall and survive well in high heat

deinococcus species gram positive odd multicelluar cell wall resist gamma radiation

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59
Q

what are the characteristics of coliforms

A

facultative anaerobes
gram positive and negative
facultative anaerobes
indicators at fecal pollution
ferment lactose
entobacteriaceacea

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60
Q

Entobacterria are what

A

Gram-negative rods
Facultative aneorobes
Coliforms that ferment lactose
Names from intenstinal tracks of human animals
Form microbiota

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61
Q

Match members of chemoorganotrophs with the disease they cause

A

Mycovacterium liprae Leprosy Hanson disease
Yersinia pestis bubonic and pneumonic plague

Vibrio vulfinificus systemic illness, especially with liver disease
Pseudomonas aerguinosa opportuniistic disease in hospitalized patients
Vibrio parahemolyticus gastrointestinal disease

62
Q

Describe conidia cysts microcysts and endospores

A

Endpospores formed by gram positive bacillus and clostridium species highly heat resistant

Cysts can resist drying and if radiation and negative azotoboctar species

Mocrocysts gram negative myoxybacterial fruiting bodies and moderately resistant to heat /radiation

Conidia positive streptomyces and resistant to drying and tips of hyphae

63
Q

Describe argobacterium and rhizobiu

A

Obtain nutrients from plants
Are terrestrial microbes
Grab negative bacilli

Rhizobia: Gram-negative rods that often fix nitrogen and form relationships with legumes
Live as endosymbionts in nodules on roots of legumes

Agrobacterium: Gram-negative rods
Can genetically alter plants for their own benefit

Ti plasmid of A. tumefaciens is transferred through wounded plant tissue

ability to synthesize plant growth hormone; results in plant tumor

Agrobacterium use opine as nutrient

64
Q

Description for each method of nutrient retention for aquatic bacteria

A

Unusual movement magneto using a special type of flagellum housed with periplasm to move through thick mud

Formation of store granules accumulated sulfur nitrate phosphate with cytoplasm of cell

Prosthecate bacteria extension of cell wall increase cell surface area. distinct method of bacteria
-Caulobacter is model for cellular differentiation

Predator of organisms bacteria prey upon other cells directly

Sheathed bacteria self form, change and taste within a tube. The rule allows cells to talk to solid object. chains of cells
Include Gram-negative rods Sphaerotilus, Leptothrix
Motile swarmer cells exit open end of sheath, move to new surface, attach

65
Q

Match obtaining nutrients from legionella species
Bdellovibrio species
Epulopiscum species
Photobsacterium species and vibrio

A

Bdelllovibrio species gram-negative curved rod that prey on e.coli highly motile
Parasite attaches secretes digestive enzymes; forms hole in cell wall of prey

Parasite divides while attached; daughter cells released when host cell lyses

Legionella species reside in protozoa. negative obligate aerobes utilize immuno acids

Photo bacterium/ vibrio species Forman Endo symbiotic relationship relationship with certain types of fish and squid and bioluminescence

Epulopiscum species gram positive cigar shaped bacteria reside in the intensity Al tract of surgeonfish

66
Q

What is true about mycoplasma

A

Lack a peptiodglycan cell wall
Difficult to filter growth media
Penicillins no affect

67
Q

Describe the thermophe nanoarchae
Sulfur oxidizers
Thermophillic extreme acidophiles
Sulfur reducing hyperthermophiles
Methane generating hyperthermophiles

A

nanoarchae grow as 400 mm attached to the surface Ignononcoccus

Sulfur oxidizers obligate Aerobes that use oxygen as a terminal electron acceptor ph 1 and 6 oxidize sulfurcompounds

Thermophillic extreme acidophiles Members grow optimally below ph 2. Original isolated from a coal waste pile

Sulfur reducing hyperthermophiles use sulfur was tea generating H2s obligate anaerobes hot sulgur environments /hydrothermal vents

Methane generating hyperthermophiles oxidize H2 using CO2 as tea to yield gas. 97 C growth methanothermus

methanoyprus grows 122 C

68
Q

describic thermophilic extreme acidophiles

A

Thermoplasma, Picrophilus growing in extremely acidic, hot environments

Thermoplasma grow optimally at pH 2, lyses at neutral pH

Picrophilus tolerate even more acidic conditions, grow optimally at pH below 1

69
Q

describe extreme halophiles

A

Most can grow in saturated salt solutions

Aerobic or facultatively anaerobic chemoheterotrophs

Phylum eucharyarchetoa

Variety of shapes: rods, cocci, discs, triangles
Includes Halobacterium, Halorubrum, Natrono-bacterium, Natronococcus

70
Q

describe methanongens

A

Methanogens are group of methane-producing archaea

Oxidize H2 gas to generate ATP

Alternatives energy sources include formate, methanol, acetate

CO2 as terminal electron acceptor

71
Q

Anaerobic Chemoorganotrophs Anaerobic Respiration

A

Chemoorganotrophs oxidize organic compounds (for example glucose) to obtain energy
Anaerobes often use sulfur, sulfate as electron acceptor
Sulfur and Sulfate Reducing Bacteria
Produce hydrogen sulfide

co2 plus H2s

72
Q

fermentation

A

glucose plus pyruvate is lactic acid

The genera Clostridium and Clostridioides are common fermenters

73
Q

clostridia

A

Gram-positive rods that can form endospores
Common soil inhabitants that live in the anaerobic microenvironments

Endospores tolerate O2, heat, drying, chemicals, and irradiation

Germinate and multiply when conditions become favorable

74
Q

lactic acid bacteria

A

Gram-positive bacteria that produce lactic acid as a product of fermentation

Most can grow in aerobic environments; lack catalase so they only ferment

Streptococcus inhabit oral cavity; normal microbiota

Lactococcus species used to make cheese
Enterococcus inhabit human, animal intestinal tract
Lactobacillus rod-shaped, common in mouth, vagina

75
Q

purple bacteria

A

Gram-negative; appear red, orange, or purple
Photosynthetic apparatus in cytoplasmic membrane

76
Q

purple sulfur bactera

A

Large cells; some motile
May have gas vesicles to control depth
Most store sulfur in intracellular granules
use H2S to generate reducing power

77
Q

wolbachia

A

Wolbachia: W. pipientis is only known species
Infects arthropods and parasitic worms

Parasite kills male embryos or embryos resulting from mating
resides in filarial worms causing river blindness and elephantiasis; debilitating inflammation results from immune response to Wolbachia

78
Q

Obligate Intracellular Parasites Chlamydia, Chlamydophila

A

infectious elementary bodies
Released when cell ruptures
Chlamydia trachomatis causes eye

infections and STI similar to gonorrhea

Chlamydophila species cause types of pneumonia

79
Q

obligate intracellular parasites

A

Coxiella: C. burnetii is only characterized species

Obligate intracellular bacterium; can survive outside host cell as spore-like structures called small-cell variants (SCVs) formed during intracellular growth

C. burnetii causes Q fever

80
Q

Obligate Intracellular Parasites Rickettsia, Orientia, Ehrlichia

A

arthropod-transmitted human diseases
R. rickettsii (Rocky Mountain spotted fever)
R. prowazekii (epidemic typhus)
O. tsutsugamushi (scrub typhus)
E. chaffeensis (human ehrlichiosis)

81
Q

obligate intracellular parasites

A

Obligate Intracellular Parasites cannot reproduce outside a host cell: host cells supply compounds need to synthesize

82
Q

Bacteria That Inhabit Mucous Membranes Treponema and Borrelia

A

Treponema and Borrelia: Gram-negative spirochetes

Treponema are obligate anaerobes or microaerophiles; often inhabit mouth, genital tract

T. pallidum causes syphilis,

Borrelia includes three pathogens, transmitted by arthropods such as ticks and lice
B. recurrentis and B. hermsii cause relapsing fever
B. burgdorferi causes Lyme disease
Borrelia genome is linear chromosome

83
Q

Bacteria That Inhabit Mucous Membranes Neisseria

A

: Gram-negative,kidney bean-shaped cocci found in pairs

; grow on mucous membranes
Typically strict aerobes; some grow anaerobically
N. gonorrhoeae (gonorrhea), N. meningitidis (meningitis)
Nutritionally fastidious

84
Q

Bacteria That Inhabit Mucous Membranes Mycoplasma

A

Mycoplasma: lack cell wall
Most have sterols for added strength and rigidity

Colony growth produces characteristic “fried egg” appearance

M. pneumoniae causes walking pneumonia;” antibiotics target peptidoglycan synthesis not effective

85
Q

Bacteria That Inhabit Mucous Membranes Haemophilus

A

Gram-negative coccobacilli
“Blood-loving”: require hematin and/or NAD,
common microbiota of respiratory tract
H. influenzae causes ear infections, respiratory infections, meningitis
H. ducreyi causes the STI chancroid

86
Q

Bacteria That Inhabit Mucous Membranes Campylobacter and Helicobacter

A

Campylobacter and Helicobacter: microaerophilic Gram-negative curved rods

C. jejuni typically lives in intestinal tract of poultry
Causes diarrhea in humans
H. pylori causes ulcers
Produces urease, which breaks down urea to ammonia

87
Q

Bacteria That Inhabit Mucous Membranes Bordetella

A

Gram-negative coccobacilli
Aerobic

Nutritionally fastidious
B. pertussis causes whooping cough in humans

B. bronchiseptica causes “kennel cough” in dogs

88
Q

Bacteria That Inhabit Mucous Membranes Bifidobacterium

A

Gram-positive irregular rods
Anaerobes; reside primarily in intestinal tract of humans and other animals

89
Q

Bacteria That Inhabit Mucous Membranes Bacteroides

A

Gram-negative rods and coccobacilli
Small; strict anaerobes that inhabit mouth, intestinal tract, genital tract of humans and other animals
Important in digestion

90
Q

Animals as Habitats Bacteria That Inhabit Mucous Membranes

A

Respiratory system
Streptococcus, Corynebacterium
Genitourinary system
Lactobacillus (vagina)
Intestinal tract
Clostridium, Enterobacteriaceae

91
Q

Animals as Habitats Bacteria That Inhabit the Skin

A

Staphylococcus species inhabit the skin
Skin typically dry, salty; inhospitable
Staphylococcus are Gram-positive cocci
Facultative anaerobes; catalase-positive

S. epidermidis

S. aureus (skin and wound infections; food poisoning)
S. saprophyticus (urinary tract infections)

92
Q

The Genera Thioplaca and Thiomargarita

A

Sulfur (energy source) and nitrate (terminal electronacceptor
Thioploca species form long sheaths; cells shuttle betweensulfur-rich sediments and nitrate-rich water
Thiomargarita namibiensis cells can reach 0.75 millimeter

Cells have a nitrate storage vacuolesurrounded by cytoplasm containing globules of s

93
Q

genus spirullum

A

Gram-negative spiral-shaped microaerophilic bacteria
S. volutans stores phosphate as volutin granules
Metachromatic granules

94
Q

bacteria that store compounds

A

Some bacteria form nutrient storage granules
Anoxygenic phototrophs often store sulfur granules as electron source
Some bacteria store phosphate
Some store compounds that can be used to generate ATP

95
Q

Magnetotactic Bacteria

A

Magnetotactic bacteria contain a string of magnetic crystals that align cells with Earth’s magnetism

Allows movement up or down in water or sediments

Magnetospirillum are Gram-negative; spiral-shaped

96
Q

spirochetes

A

Gram-negatives with spiral shape and flexible cell wall

Endoflagella or axial filament contained within periplasm at each end of the cell allow corkscrew-like motion

Spirochaeta live in muds, anaerobic waters
Leptospira are aerobes; some free-living, others inhabit animals
L. interrogans causes leptospirosis

97
Q

bioluminescent bacteria

A

Symbiotic relationships with certain fish, squid
Help with camouflage,
Luminescence catalyzed by enzyme luciferase
Luciferase controlled by quorum sensing

Gram-negative straight or curved rods, facultative anaerobes, marine environments

98
Q

Thriving in Terrestrial Environments Myxobacteria -

Streptomyces

A

Aerobic Gram-negative rods with unique developmental stage and resting form
Favorable conditions: secrete slime layer, form swarm
Nutrients depleted: cells congregate into fruiting body
mycoxy bacteria the thing from spongebob red flower

Streptomycrs of aerobic Gram- positive bacteria
Growth resembles fungi: form mass of branching hyphae called mycelium
Chains of spores (conidia)
Conidia resistant to drying; easily spread by air currents
Produce extracellular enzymes, geosmins

99
Q

genus azobacter

A

Gram-negative pleomorphic rods

Form resting cell called a cyst

Withstand drying and UV radiation
Fix nitrogen in aerobic conditions

High respiratory rate maintains low O2 in a cell

Protein binds nitrogenase, protects from O2 damage

100
Q

endospore formeers

A

Gram-positive rods
Clostridium species are obligate anaerobes
Bacillus include obligate and facultative anaerobes

Both can cause disease:
C. tetani causes tetanus
B. anthracis causes anthrax

101
Q

epcophysiology diversity

A

Ecophysiology: Study of the adaptations of physiological mechanisms that prokaryotes use to live in terrestrial and aquatic environments

102
Q

descroibe the family entobacteriaccdes and the genus vibrio

A

Found in marine environments, require some Na+ for growth
Gram-negative straight or slightly curved rods
Pathogens include V. cholerae, which causes cholera
Some are bioluminescent

Gram-negative rods found in intestinal tract of humans, other animals; some thrive in soil

103
Q

Faculatatuve aneorobes

A

Use aneorobic respiration but can ferment if o2 is not available

Cyanobacteria gram positive phlemorpjic rods
Wide spread
Coryneforms or diphtheroids
C diphtheria causes diphtheria

104
Q

Aerobic chemoorganotrophs

A

Oxidized organic compounds for energy
Use oxygen as tea
Organic compounds plus o2 (tea) co2+h2o

105
Q
A

Aquifex have maximum growth at 95 degrees , Hydrogenobactera among few hydrogen-oxidizing bacteria that are obligate chemolithotrophs

Thermophilic; typically live in hot springs

O2 requirements low; possibly available in certain niches due to photochemical processes that split water

h2 energy source + 1/2 O2 terminal electron acceptor = h2O

106
Q

nitrifieers

A

Nitrifiers are a diverse group of Gram-negatives

Oxidize inorganic nitrogen compounds for energy

Can deplete water of O2 if wastes high in ammonium

Ammonium oxidizers: Nitrosomonas, Nitrosococcus
nh4+ 1/2 o2 terminal electron acceptor — no2- +H2O+ 2h+

Nitrite oxidizers: Nitrobacter, Nitrococcus

NO2- (energy source)+1/2 O2 terminal electron accpetor —-> NO3-

107
Q

filamentous sulfur oxidizers

A

Beggiatoa, Thiothrix: sulfur springs

Store sulfur as intracellular granules

Beggiatoa filaments move by gliding motility

Thiothrix filaments immobile; progeny cells detach, move via gliding motility

108
Q

unicelluat sulfur oxidizers

A

Acidithiobacillus: terrestrial and aquatic habitats
Unicellular sulfur oxidizers

Oxidize metal sulfides; oxidation of gold sulfide produces sulfuric acid; lower pH converts metal to soluble form

Can oxidize sulfur in fuels to sulfate

109
Q

aerobic chemolithotrophs

A

gain energy by oxidizing reduced inorganic chemicals

Sulfur-oxidizing bacteria:
Gram-negative rods, spirals

oxygen is terminal electron acceptor; generates sulfuric acid

sulfur (energy source)=1/2 o2 as tea —. h2o-h2so4

110
Q

purple non sulfur bacteria

A

use organic molecules instead of H_2 S as source of electrons
Lack gas vesicles

May store sulfur; granules form outside cell

Most can grow aerobically in absence of light using chemotrophic metabolism

Representatives include Rhodobacter, Rhodopseudomonas

111
Q

green bacteria

A

Gram-negative;

Use H2S; form sulfur granules outside of cell

lack flagella

Strict anaerobes

Representatives include Chlorobium, Pelodictyon

112
Q

Filamentous Anoxygenic Phototrophic Bacteria

A

Form multicellular arrangements
Exhibit gliding motility
Many have chlorosomes

Metabolically diverse

Some preferentially use organic compounds to generate reducing power, can grow in dark aerobically using chemotrophic metabolism

Chloroflexus best studied, especially thermophilic strains found in hot springs

113
Q

oxygenic photrophs

A

Cyanobacteria
Earliest oxygenic phototrophs

Use water as source of electrons for reducing power

harvest sunlight to convert CO2 into organic compounds

Diverse group of Gram-negative bacteria

6CO2 carbon source + 6H2O electron bacteria —> C6H12O6+ 6O2

114
Q

cyanobacteria

A

Morphologically diverse
Unicellular: cocci, rods, spirals

Multicellular: filamentous associations: trichomes

motile trichomodes

Also have phycobiliproteins

115
Q

what are primary producers

consumer

decomposers

A

primary producers Autotrophs that convert CO2 into organic materials; serve as a food source for other ecosystem members

consumer- Heterotrophs that eat other organisms; several together can create a food chain, while multiple chains create a food web.

decomposers Heterotrophs that digest the remains of the other two groups in ecosystems; specialize in digesting complex molecules such as cellulosse

116
Q

define ammonification
Denitrification
Nitrogen fixation
Nitrification

A

Deamination of organic compounds yielding NH4 is ammomnification

dentrification Reduces nitrate through a series of steps to nitrogen gas

nitrogen fixation Removes N2 from the air with the primary product of NH4+

nitrification The oxidation of NH4+ to NO2− and NO3−

117
Q

Which of the following factors can influence the ability of an organism to compete successfully for a habitat?

A

The rate at which the organism multiplies.

The ability of the organism to withstand adverse environmental conditions.

e ability of the organism to inhibit other microbes by producing antimicrobial compounds

118
Q

Place the layers that would exist in a microbial mat in the correct order from top to bottom layer

A

A green layer filled with photosynthetic cyanobacteria.

A reddish-pink layer consisting of purple sulfur bacteria.

A black layer filled with sulfate-reducing obligate anaerobes.

119
Q

define metagenomics

dna microarrays

flouorescent in situ hybridization

A

metagenomics
Using microbial DNA sequence information to observe commonly conserved genes for particular traits.

flourecent in situ Using fluorescent probes to look for specific microbes in an area/community.

Comparing microbial populations by studying gene expression.
dna microarrays

120
Q

the effect of environmental pH on population composition.

A

Lactococcus lactis right behind 4.0

Lactobacillus species most acidic 3.0

Yeasts and molds ph 5.5

Putrefying bacteria is ph 6.8

121
Q

idenntify the steps that can lead to “dead zone” formation in bodies of water such as Lake Erie and the Gulf of Mexico.

A

Algae/cyanobacteria grow, using photosynthesis to produce organic compounds

organic compounds

Aerobic decomposition of organic compounds by heterotrophs depletes oxygen

Animals flee hypoxic environment or die

122
Q

define
Microenvironment Population
Community
Biosphere
Ecosystem
Ecology
Ecological niche

A

Study of the interaction of organisms with each other and their environment, Ecology

Organisms of the same type in a given environment, Population

All of the different organisms in a location is a Community

Community of organisms and the non-living environment with which they interact , Ecosystem

All of the ecosystems on Earth Biosphere

Role of an organism in a particular ecosystem , Ecological nichet

Environment immediately surrounding an individual microbe. microenvironment

123
Q

Select the factors that play a role in microbial competition

A

Ability to produce antimicrobial compounds.

Ability to multiply faster than other microbes in the environment.

Ability to withstand adverse environmental conditions.

124
Q

ways in which microbes are identified and classified in the laboratory.

A

16S rRNA sequencing
18S rRNA sequencing
Deducing amino acid sequences in ribosomal proteins

125
Q

what researchers can learn about a microbial community using metagenomics.

A

They can identify the genes that are present in a microbial community.

Knowing what genes are present in a community may facilitate identification of microbes.

They may learn what role a particular microbe has in the environment.

126
Q

Steps involved in creating an aquatic dead zone into the correct sequence.

A

River water carrying nutrients acquired from urban, agricultural and industrial areas flows into the sea

Algae and cyanobacteria (primary producers) use excess phosphates and nitrates for growth, multiplying rapidly.

heterotrophic microbes metabolize the organic compounds made by primary producers, and consume dissolved O2.

Depletion of dissolved O2 results in large hypoxic zone, causing animals to flee or die.

127
Q

TRUE statements regarding microbes in soil.

A

Dry soils favor the formation of bacterial endospores.

Acidic soil suppresses bacterial growth, allowing fungi to flourish.

Algae and protozoa tend to grow near the soil surface rather than at deeper levels.

128
Q

Soil organisms with their characteristics.

Bacillus species

Azospirillum species

Streptomyces specie

A

Produce antibiotics Streptomyces species

Form endospores Bacillus species

Fix nitrogen azospirillum species

129
Q

Sulfur oxidation
Nitrification
Methanogenesis Ammonification Denitrification
Anammox
Carbon fixation
Nitrogen fixation

A

Process in which NH4+ is oxidized to NO3−2 Nitrification

Process that reduces NO3−, converting it to gaseous forms such as N2O and N2 Denitrification

Process that converts CO2 to an organic form by living organisms Carbon fixation

Anaerobic oxidation of NH4+ as an energy source Anammox

Oxidation of H2S and SO as energy sources sulfur oxidation

Oxidation of hydrogen gas, using CO2 as a terminal electron acceptor, and generating CH43, Methanogenesis

Reduction of N2 to form NH3 for incorporation into cellular material8Nitrogen fixation

Decomposition process that converts organic nitrogen into NH3 ammonification

130
Q

list the types of symbiotic relationships

A

Living organisms interact with each other in symbiotic relationships
Mutualistic: both organisms benefit from relationship

Commensalistic: one benefits; other unaffected

Parasitic: one benefits; other is harmed

131
Q

microbial competition

A

Ability to compete related to rate of multiplication, also

ability to withstand adverse environmental conditions

132
Q

describe microbial communities

A

Microbial communities
Often grow as biofilms attached to solid substrates or at air-water interfaces

Microbial mat is a specific type: thick, dense, highly organized structure composed of distinct layers

Photosynthetic cyanobacteria (green)
Anoxygenic phototrophic purple sulfur bacteria (pink)
Obligate anaerobic sulfate-reducers (black)

133
Q

what is metagenomics

A

Metagenomics is cultivation-independent study of communities or their members by analyzing genetic material taken from an environment

134
Q

descripe the aquatic habitats

A

Oligotrophic (nutrient poor) waters limit growth of autotrophs due to lack of inorganic nutrients

Eutrophic (nutrient rich) waters encourage growth of autotrophs, which produce organic compounds that foster growth of heterotrophs in lower layers

135
Q

what are the characteristics of soil

A

Soil forms as rock weathers
Water, temperature changes cause rock to crack, break

Bacteria, fungi use as carbon sources, produce acids, other chemicals that gradually decompose the rocks

As soil slowly forms, plants begin to grow
When these die and decay, accumulated organic materials form humus

Soil environment can change abruptly

Clay soils more likely to be anaerobic; sandy soils more likely to be aerobic

136
Q

describe the microorganism rhizobacteria in soil

A

Rhizosphere: zone of soil adhering to plant roots
Root cells secrete organic molecules used by microbes
Higher concentrations of Gram-negatives

137
Q

microorganisms in soil

A

Most are aerobes, grow in top 10 centimeters of soil, degrade complex

Some are free-living, others live symbiotically

Mycorrhizas are fungi growing in symbiotic relationship with plant roots
Assist individual plants AND create hyphal networks that link various plants

Algae, protozoa also found in most soils
Algae depend on sunlight for energy, so mostly live on or near soil surface

138
Q

biogchemical cycling

A

Biogeochemical cycles are paths elements take as they flow through biotic and abiotic components of ecosystems
Important in recycling limited amounts of elements
Carbon, nitrogen cycles particularly important
Involve stable gaseous forms with global impact

Elements continually cycle, but energy does not
Must be continually added to ecosystem to fuel life
human activites have major impact

Conversion of N2 into ammonia-containing fertilizers has increased food production,
Increased amount of fixed nitrogen available leads to pollution of lakes,

Burning fossil fuels releases CO2 along with other carbon containing gases which raise global temperature the greenhouse effect

139
Q

three puposes in metabolism

A

Elements have three purposes in metabolism

Biosynthesis (biomass
production)
Required for all organisms; many different pathways

Energy source
Reduced carbon compounds such as sugars, lipids, amino acids used by chemoorganotrophs

Terminal electron acceptor
In aerobic conditions, O2 is used
In anaerobic conditions, prokaryotes may use nitrate, nitrite, sulfate, or carbon dioxide

140
Q

methane oxidation and methagonesis

A

anaerobic environments, CO2 used by methanogens
These archaea obtain energy by oxidating hydrogen gas, using CO2 as terminal electron acceptor
Generate methane CH4

Methane enters atmosphere, is oxidized by ultraviolet light and chemical ions, forms carbon monoxide (CO) and CO2

141
Q

nitrogen fixation cycle

A

N2 is reduced to ammonia

Can be incorporated into cellular material
Enzyme complex nitrogenase catalyzes
Requires tremendous energy since N2 has very stable triple bond

142
Q

azobacter diatrophs form relationships with higher order organisms

A

Heterotrophic, aerobic, Gram-negative rods; may be main suppliers of fixed nitrogen in ecosystems that lack plants with nitrogen-fixing symbionts (for example, grasslands)

Dominant free-living anaerobic soil diazotrophs are members of genus Clostridium

143
Q

sulfur cycle

A

microbes assimilate as sulfatereducing and the incorporating into biomass

Decomposition of sulfur-containing amino acids releases hydrogen sulfide gas

144
Q

phosphorous and other cycles

A

Phosphorus is component of nucleic acids, phospholipids, ATP
Most plants, microbes take up as orthophosphate

145
Q

relatiobnship between microrganisms and eukaryotes

A

Microorganisms and herbivores
Microbes inhabit specialized compartment, digest cellulose and hemicellulose of plant material

146
Q

nitrogen fixers and planters

A

Plant-bacterial communication - Plant root secretions attract appropriate rhizobial species that colonize roots

Root hairs curl - Bacteria produce Nod factors (NFs) that induce root hair to curl, trapping the bacterial cells
Bacteria pass through infection thread - Rhizobia travel through infection threads into plant cells where they become a specialized nitrogen-fixing cell called a bacteroid

Nitrogen-fixing nodule forms - Relationship not obligate, but offers competitive advantage to both partners

147
Q

what is a type of symbiotic nitrogen fixer and planter

A

Rhizobia include members of diverse group of genera
Most agriculturally important symbiotic nitrogen-fixing bacteria
Grow within nodules on roots of legumes, including alfalfa, clover, peas, beans, peanuts

148
Q

mutualistic relationshipas between microorganisms and eukaryotes

A

Mycorrhizas are fungi in symbiotic relationships with plant roots
Fungi help plants take up phosphorus, other nutrients; they gain nutrients from root secretions

Endomycorrhizas: fungi penetrate root cells, grow within them

Ectomycorrhizas: fungi grow around plant cells, form sheath around root; associate with certain trees

149
Q

whar are energy sources for ecosystems

A

bacteria archea oxidize H2S use energy to fix CO2

hydrothermal vents release h2s
Chemotrophs harvest energy trapped in chemical bonds

150
Q
A

Biochemistry (7 decks)

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