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BIO 286 - Microbiology > Exam 2: Microbial Metabolism; Fermentation and Respiration; Bacterial Growth; Microbial Ecosystems; Nutrient Cycles; Antibiotics and Chemotherapy; (Bio 286 - Microbiology) > Flashcards

Exam 2: Microbial Metabolism; Fermentation and Respiration; Bacterial Growth; Microbial Ecosystems; Nutrient Cycles; Antibiotics and Chemotherapy; (Bio 286 - Microbiology) Flashcards

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Biology 101 flashcards
1
Q

all life requires

A

electron flow (to drive all life processes), energy (to move electrons), materials (to make cell parts)

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2
Q

electron flow

A

drives all life processes; drives ions into and out of cells; used to create ATP

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3
Q

materials to make cell parts

A

nutrients, which must be supplied from environment

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4
Q

macronutrients

A

major elements in cell macromolecules; INCLUDES C, O, H, N, P, S and Mg2+. Ca2+, Fe2+, and K+ (ions necessary for protein function)

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5
Q

micronutrients

A

trace elements necessary for enzyme function; INCLUDES Ni, Co, and other trace metals

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6
Q

complex media

A

ensures growth of a newly discovered bacterium with unknown nutritional requirements

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7
Q

heterotroph

A

microbes using organic carbon (contains at least 1 carbon-hydrogen bond)

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8
Q

autotroph

A

microbes using carbon dioxide (CO2) or inorganic carbon (contains no carbon-hydrogen bond)

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9
Q

typical bacterial cell is ____% carbon (by dry weight)

A

50

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10
Q

phototroph

A

light energy excites electrons; excited molecules are electron donors

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11
Q

chemotroph

A

chemicals are electron donors; chemical is oxidized

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12
Q

oxidation

A

donation of electrons; loss of electrons; loss of H

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13
Q

reduction

A

acceptance of electrons; gain of electrons; gain of H

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14
Q

lithotroph

A

inorganic molecules are electron donors

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15
Q

organotroph

A

organic molecules are electron donors

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16
Q

ultimate electron acceptor - inorganic molecules

A

respiration

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17
Q

ultimate electron acceptor - organic molecules

A

fermentation

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18
Q

different additional nutrients required by different microbes

A

amino acids; N from air (N2) or soil or other organisms; electron acceptors in aerobic vs anaerobic organisms; light vs organic energy source

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19
Q

passive diffusion

A

some gases freely pass through membranes (O2, CO2); follows gradient of material; does not require a protein carrier

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20
Q

facilitated diffusion

A

transporters pass material into and out of cell; follows gradient of material

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21
Q

passive diffusion - require energy

A

NO

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22
Q

passive diffusion - require carrier

A

NO

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23
Q

passive diffusion - accumulate inside

A

NO

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24
Q

facilitated diffusion - require energy

A

NO

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25
Q

facilitated diffusion - require carrier

A

YES

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26
Q

facilitated diffusion - accumulate inside

A

NO

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27
Q

(active transport) ABC transport - require energy

A

YES - ATP

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28
Q

(active transport) ABC transport - require carrier

A

YES

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29
Q

(active transport) ABC transport - accumulate inside

A

YES

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30
Q

(active transport) gradient (symport or antiport) - require energy

A

YES - Ions

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31
Q

(active transport) gradient (symport or antiport) - require carrier

A

YES

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32
Q

(active transport) gradient (symport or antiport) - accumulate inside

A

YES

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33
Q

(active transport) group translocation - require energy

A

YES - PEP

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34
Q

(active transport) group translocation - require carrier

A

YES

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35
Q

(active transport) group translocation - accumulate inside

A

NO

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36
Q

active transport

A

ABC transporters, Symport/Antiport, group translocation

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37
Q

ABC transporters

A

use ATP energy to pass material into cell; transport material against gradient

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38
Q

symport

A

gradient of molecules in same direction

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39
Q

antiport

A

gradient of molecules in opposite directions

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40
Q

symport and antiport

A

gradient of one molecule transports another– electron transport creates Proton-Motive Force, which transports the other molecule; transports material against its gradient

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41
Q

phosphotransferase system (PTS)

A

(group translocation) uses high energy phosphate to pass material into cell – modifies material as it enters cell, allowing gradient to be maintained and continue pushing material into cell (ex: glucose enters to be phosphorylated into glucose-6P)

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42
Q

catabolism

A

breaking down molecules for energy

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43
Q

anabolism

A

(biosynthesis) using energy to build cell components; reduces entropy to increase/create order

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44
Q

metabolism

A

balance between catabolism and anabolism; central biochemical pathways used for both TCA cycle, glycolysis, and pentose phosphate shunt

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45
Q

catabolism - substrates

A

BIG

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46
Q

catabolism - products

A

SMALL

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47
Q

catabolism - bonds

A

BROKEN

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48
Q

catabolism - redox

A

OXIDIZATION

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49
Q

catabolism - energy

A

RELEASE (exergonic, favorable)

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50
Q

anabolism - substrates

A

SMALL

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51
Q

anabolism - products

A

BIG

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52
Q

anabolism - bonds

A

FORMED

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53
Q

anabolism - redox

A

REDUCTION

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54
Q

anabolism - energy

A

USE (endergonic, unfavorable)

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55
Q

enzymes

A

biological catalysts critical for life; nearly always PROTEINS; have an ACTIVE SITE that interacts with substrates; COFACTORS: metals and vitamins

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56
Q

enzyme rate of activity

A

can be changed after enzyme production

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57
Q

ribozyme

A

catalytic RNA enzymes; include ribosomes

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58
Q

classification of enzymes

A

oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases

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59
Q

oxidoreductases

A

enzymes involved in oxidation and reduction

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60
Q

transferases

A

enzymes that attach atoms/groups

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61
Q

hydrolases

A

enzymes that split with addition of water to break down polymers

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62
Q

lyases

A

enzymes that split without addition of water to break down polymers

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63
Q

isomerases

A

enzymes that invert molecular configuration (change handedness, from D to L or L to D)

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64
Q

ligases

A

enzymes that join molecules using nucleoside triphosphate (ie ATP)

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65
Q

Gibbs Free Energy

A

ΔG = ΔH - TΔS (ΔH is change in ENTHALPY and ΔS is change in ENTROPY); ΔG must be negative for reaction to occur spontaneously; ΔG depends on concentrations, where having a low product concentration can drive reactions; useful for determining whether there will be a requirement or production of energy

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66
Q

activation energy

A

energy that is needed to get a reaction started

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67
Q

exergonic reaction

A

-ΔG; products have less energy than reactants

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68
Q

endergonic reaction

A

+ΔG; products have more energy than reactants

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69
Q

biochemical reaction energy

A

entropy is stronger at higher temperatures where breakdown of a large molecule into small ones (such as release of a gas) is favored to occur; diffusion spreads molecules out, which requires energy to contain them

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70
Q

gradient

A

stored energy; represent potential energy

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71
Q

enzymes reduce

A

activation energy

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72
Q

electron transfer

A

major source of cell energy; passage of electrons releases energy; requires electron donor and electron acceptor; electron transport found in all cells

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73
Q

during electron transport

A

-OH accumulates on the inside of a cell membrane and H+ accumulates on the outside of membrane

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74
Q

electron energy can be stored by/in

A

reduced chemicals, concentration gradient, and phosphorylation of chemicals

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75
Q

NAD(H)

A

NICOTINAMIDE ADENINE DINUCLEOTIDE; temporary acceptor/temporary electron holder – 2 electrons and 1 proton; limited amount in cell; NADP is used for anabolism and NAD is used for catabolism

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76
Q

non-protein electron carriers

A

FMNH2, quinones, FADH2

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77
Q

phosphorylation energy

A

LESS ENERGY THAN OXIDOREDUCTION; useful energy level for most cell reactions; no electron donor or acceptor needed; phosphate added via dehydration and released via hydrolysis; ATP IS MOST COMMON

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78
Q

ATP

A

ADENOSINE TRIPHOSPHATE; components: base (adenine), sugar (ribose), and phosphate (3); HIGH ENERGY PHOSPHATE BONDS

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79
Q

substrate level phosphorylation

A

ATP can by hydrolyzed to do work in cell, whereas some molecules can be used to form ATP directly

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80
Q

phosphoenolpyruvate (PEP)

A

able to be used for substrate level phosphorylation

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81
Q

lithotrophy

A

electron donors are inorganic molecules

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82
Q

organotrophy

A

electron donors are organic molecules

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83
Q

phototrophy

A

use light energy to reduce compounds then use those as electron donors

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84
Q

respiration

A

electron acceptors are inorganic molecules

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85
Q

fermentation

A

electron acceptors are organic molecules

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86
Q

three pathways of glucose metabolism

A

glycolysis, entner-doudoroff, and pentose phosphate shunt

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87
Q

glycogen

A

common energy storage polymer in microorganisms

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88
Q

key intermediates of glycolysis

A

glucose 6-phosphate, fructose 6-phosphate, triose phosphate, 3-phosphoglycerate, phosphenolpyruvate, pyruvate

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89
Q

key intermediates of krebs cycle (citric acid cycle)

A

acetyl CoA, α-ketoglutyrate, succinyl CoA, and oxaloacetate

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90
Q

key intermediates of pentose phosphate shunt

A

ribose 5-phosphate, erythrose 4-phosphate, sedheptulose 7-phosphate

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91
Q

glycolysis stage 1

A

“energy is spent in front end to get more later”:: Glucose + 1 ATP -> Glucose 6-phosphate -> fructose 6-phosphate + 1 ATP -> fructose 1,6-biphosphate… uses 2 ATP

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92
Q

glycolysis stage 2

A

“splitting into two molecules double the reactants”:: fructose 1,6-biphosphate -> PGAL + DHAP + 2 NAD -> 2 1,3-biphosphoglycerate

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93
Q

glycolysis stage 3

A

“break even point using substrate level phosphorylation”:: 2 1,3-biphosphoglycerate -> 3 PGA -> 2 PGA… yields 2 ATP

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94
Q

glycolysis stage 4

A

“pay off- net yield of 2 ATP by substrate level phosphorylation”:: 2 PGA -> phosphoenolpyruvate -> pyruvate… yields 2 ATP

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95
Q

entner-doudoroff stage 1

A

“energy is spent in front end to get more later”:: glucose + 1 ATP -> glucose 6-phosphate + NADP+ -> 6-phospho-gluconate -> 2-keto-3-deoxy-6-phosphogluconate… uses 1 ATP

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96
Q

entner-doudoroff stage 2

A

“splitting into two molecules gives one reactant”:: 2-keto-3-deoxy-6-phosphogluconate -> PGAL and Pyruvate + NAD+ -> 1,3 biphosphoglycerate

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97
Q

entner-doudoroff stage 3

A

“break even point using substrate level phosphorylation”:: 1,3 biphosphoglycerate -> 3 PGA -> 2 PGA… yields 1 ATP

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98
Q

entner-doudoroff stage 4

A

“payoff - net yield of ATP by substrate level phosphorylation”:: 2 PGA -> phosphoenolpyruvate -> pyruvate… yields 1 ATP

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99
Q

glycolysis

A

use glucose; 2 ATP used -> 4 ATP made -> 2 ATP NET; 2 NADH made, 2 pyruvates formed, 6 intermediates formed

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100
Q

entner duodoroff

A

use glucose; 1 ATP used -> 2 ATP made -> 1 ATP NET; 1 NADH and 1 NADPH made, 2 pyruvates formed, and 5 intermediates formed (DOES NOT MAKE FRUCTOSE 6-PHOSPHATE)

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101
Q

net gain of ATP per molecule fermented

A

2 ATP

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102
Q

pentose phosphate shunt

A

generates key intermediates; like entner-doudoroff pathway, it forms 6-phosphogluconate which is then converted to key intermediate RIBULOSE-5-PHOSPHATE which in turn produces a series of sugars (each containing 3-7 carbons); this pathway produces 1 ATP and no NADH, but 2 NADPHs for biosynthesis

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103
Q

pyruvate dehydrogenases

A

pyruvates + NAD+ + CoA -> acetyl-CoA + CO2 + NADH + H+ ; END PRODUCTS: acetyl-CoA + CO2 + NADH; multiprotein complex; 3 COFACTORS: TPP (oxidative decarboxylation - enzyme 1), LIPOAMIDE (acyl transformation - enzyme 2), FAD (flavin protein); CoA and NAD

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104
Q

TCA - Citric Acid - Krebs Cycle

A

produces 1 ATP, 3 NADH + H+, and 1 FADH2; can occur counterclockwise, clockwise, or in distinct parts depending on the bacteria; intermediate compounds used in biosynthetic pathways and carbon catabolism: α-ketoglutarate, oxaloacetate, succinyl-CoA

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105
Q

total oxidation of pyruvate

A

for each pyruvate oxidized: 3 CO2 are produced by decarboxylation, 4 NADH and 1 FADH2 are produced by redox reactions, and 1 ATP is produced by substrate level phosphorylation; OXIDATIVE PHOSPHORYLATION

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106
Q

aromatic catabolism

A

bacteria can degrade many compounds; aromatic compounds converted to pyruvate allows growth in wide range of environments and is used for BIOREMDIATION (cleaning up oil spills, industrial site and degrading toxic compounds)

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107
Q

regenerating NAD+

A

glycolysis = 2 NADH; Entner-Doudoroff = 1 NADH and 1 NADPH; Krebs cycle = 4 NADH and 1 FADH2; pentose phosphate also generate reduced NAD(P)H molecules… there is limited amount of NAD in cell, so it must be regenerated for reuse later

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108
Q

fermentation

A

organic molecules; performed by anaerobic microorganisms; PRIMARY PURPOSE: REGENERATE NAD FOR REUSE (electron acceptor is an organic molecule) and SECONDARY PURPOSE: GENERATE ADDITIONAL ENERGY (energy yields are very small) ; as a consequence, growth rates are slower

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109
Q

lactic acid fermentation

A

performed by lactobacteria; muscles/yogurt/sourdough bread use this

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110
Q

mixed acid fermentation

A

performed by E. coli; METABOLIC FLEXIBILITY; dumping electrons vs ATP generation

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111
Q

importance of fermentation for cell

A

electrons from metabolism are dumped; potential source of ATP for cell

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112
Q

importance of fermentation for humans

A

means of classifying bacteria; important source of solvents

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113
Q

reduction potential

A

electrons pass from good donors to good acceptors (ΔG < 0)… NADH + H+ is an excellent electron donor while 1/2 O2 is the strongest electron acceptor… E°’ = 1140 mV corresponding to ΔG°’ = -110 kJ, equivalent to as much energy as 3.6 ATPs… ATP + H2O -> ADP + PO4 (ΔG°’ = -30.5 kJ)… the concentration of the donor or acceptor affects actual ΔE (good acceptor - more electronegative, so oxygen is best acceptor)

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114
Q

redox potential energy

A

molecules differ in their affinity for electrons; moving down the redox energy list is favorable and releases energy

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115
Q

electron transport systems (ETS)

A

electron transport occurs on membranes – inner membrane of bacteria and archaea; inner membrane of mitochondria and chloroplasts… electron acceptor usually present outside cell; needed in large quantities for respiration; electron passage energy must be captured by cell cytoplasm

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116
Q

respiratory ETS

A

electrons form NADH -> O2 release energy (too much energy to capture in one step; requires intermediates; multiple steps)… common features in many ETS pathways (NADH OXIDASE, QUINONES, CYTOCHROMES)

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117
Q

glucose

A

best electron donor

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118
Q

oxygen

A

best electron acceptor

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119
Q

flavoproteins

A

common proteins; flavin cofactor; FAD or FMN; carry two proteins and carry two electrons

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120
Q

quinones

A

isoprenoid lipids dissolved in membrane (the same lipids in archaea membranes); variant structures are known; UQ, MQ, PG; carry protons and electrons

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121
Q

iron sulfur protein

A

cellular proteins; contain non-heme iron; acid labile; iron coordinated by Cys; electron carrier only – only accept electrons (not protons)

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122
Q

cytochromes

A

have heme groups; ELECTRON CARRIERS ONLY (only accept electrons); Heme A, Heme B, Heme C, Heme D (in oxidase), Heme O (in oxidase)

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123
Q

mitochondrial respiratory ETS

A

use favorable movement of electrons in creating a proton gradient; has 4 complexes

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124
Q

4 complexes of mitochondrial respiratory ETS

A

I. electrons from NADH to coenzyme Q … II. electrons from FADH2 to coenzyme Q… III. coenzyme Q to cytochrome C… IV. cytochrome C to O2

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125
Q

Complex II of Mitochondrial respiratory ETS

A

not needed to move electrons from NADH to oxygen in mitochondria

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126
Q

E. Coli respiratory ETS

A

branched electron pathway; different ETS for different concentrations of oxygen; different NADH dehydrogenases (NDH1 -> pumps 4H+/2e- and NDH2 -> pumps 0) and different terminal oxidases (cytochrome bo -> pumps 1H+/e- and cytochrome bd -> 0)… E. Coli can alter its pumping by choosing which branch it uses, so anywhere between 2 to 8 protons can be pumped out from oxidation of one NADH

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127
Q

maximum pumped H+ in E. Coli Respiratory ETS

A

NDH1 + cytochrome bo

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128
Q

minimal pumped H+ in E. Coli Respiratory ETS

A

NDH2 + cytochrome bd

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129
Q

proton motive force (PMF)

A

electrochemical gradient; driven by differences in charge (of ions) and in pH; PMF = Δψ - 60ΔpH [electrical (Δψ) plus chemical (ΔpH) gradient]

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130
Q

NADH ->

A

10 H+ -> 3 ATP

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131
Q

FADH2 ->

A

6 H+ -> 2 ATP

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132
Q

PMF is used directly for cell activities

A

CREATES ATP (ATP synthase at cell membrane); DRIVES FLAGELLAR ROTATION (motors at base of flagella); PUSHES IONS INTO AND OUT OF CELL USING SYMPORT/ANTIPORT

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133
Q

symport

A

same direction as proton movement

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134
Q

antiport

A

opposite direction of proton movement

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135
Q

proton potential creates ATP

A

the F1F0ATP synthase makes ATP: protons enter F0 subunit and cause it to rotate -> F0 ROTATION DRIVES THE F1 SUBUNIT SHAFT WHICH SYNTHESIZES ATP FROM ADP + Pi

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136
Q

3 H+ ->

A

1 ATP

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137
Q

3 protons (H+) move through ATPase

A

to produce 1 ATP

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138
Q

anaerobic respiration

A

occurs in environments lacking oxygen such as gut, deep soil, and deep ocean; other terminal electrons acceptors are used such as nitrogen, sulfur, and metals

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139
Q

nitrate

A

NO3-; most oxidized form of nitrogen

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140
Q

anaerobic respiration begins with the most oxidized reactant

A

so reduction can occur

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141
Q

lithotrophy

A

many materials donate electrons (get oxidized) if a better electron acceptor is present

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142
Q

methanogenesis

A

PERFORMED BY EURYARCHAEOTA; hydrogen donates electrons and CO2 accepts electrons; high CO2 concentrations drive reaction; CO2 + 4H2 -> CH4 + 2H2O; important anaerobic reaction

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143
Q

phototrophy - bacteriorhodopsin

A

absorbs light (membrane protein, purple color); absorbs light -> excites electrons -> electron returns to ground state -> releases energy -> generates proton gradient

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144
Q

phototrophy - chlorophyll

A

absorbs light (different chlorophylls absorb wavelengths – determines where organism can grow: purple bacteria, green bacteria, cyanobacteria, chloroplasts of plants); complexes collect light energy– carotenoids in purple bacteria and antenna complex LH-11 in cyanobacteria and plants

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145
Q

purple bacteria reactions

A

ADP + Pi -> ATP in presence of light; free source of Δp; able to make tons of ATP; still need to generate NADH; bacteriochlorophyll is not good enough donor to accomplish this so the bacteria must use reverse electron transport

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146
Q

purple bacteria light harvesting

A

found in cell membrane; bacteriochlorophyll-protein-carotenoid complex; antennae complex closely associated with reaction center; cell membrane highly invaginated to increase surface area; reverse electron transport makes NADH

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147
Q

green sulfur electron transport

A

reduce Fe/S centers instead of quinones; do anoxygenic photosynthesis like PSI in plants

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148
Q

green sulfur reactions

A

no reverse electron transport; use inorganic sulfur; generate ATP and NADH; H2S + NAD + QADP + Pi -> S + NADH + H + ATP

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149
Q

green (sulfur) bacteria light harvesting

A

bacteriochlorophyll; protein and carotenoid; localized in CHLOROSOMES which perform photosynthesis; better donors and only accept electrons; can make NADH and more power (does not need to use reverse electron transport); uses sulfur instead of oxygen

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150
Q

oxygenic photosynthesis

A

plant-like photosynthetic apparatus or plants are bacteria like; performed by cyanobacteria (formerly blue green algae, thousands of species, lots of variety); extremely important to life on earth

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151
Q

cyanobacteria

A

perform oxygenic photosynthesis; stole “ideas” from green and purple bacteria; have thylakoids; uses H2O instead of sulfur

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152
Q

cyanobacteria and algae

A

found in chloroplast or bacterial membrane; two photosystems (purple and green); non-cyclic electron flow; water is oxidized to O2

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153
Q

generation time

A

time interval required for formation of two cells from one

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154
Q

microbial contamination

A

prevented by use of aseptic technique

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155
Q

microscopy

A

(method to enumerate cells) requires specialized staining to observe non-pigmented bacteria

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156
Q

water activity

A

ratio of vapor pressure of air in equilibrium with a substance to vapor pressure of pure water

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157
Q

binary fission

A

process bacteria use to grow/divide; asexual reproduction

158
Q

binary fission process

A

elongation -> DNA replication -> FtsZ ring forms -> cytokinesis -> cell wall synthesis

159
Q

prior to DNA replication

A

both strands of chromosome are methylated on A residue of sequence GATC

160
Q

FtsZ ring

A

most active in divisome complexes

161
Q

Petroff Hauser chamber

A

counts cells directly; gives an accurate number – but cannot tell if cells are alive or dead (so a stain must be used to distinguish living cells)

162
Q

viable counts

A

counts only cells able to reproduce (form colonies); requires time to form the colonies

163
Q

spectrophotometer

A

measure optical density – but cannot tell if cells are alive or dead; solution must be between 10^7 - 10^10 cells/mL

164
Q

growth cycle

A

lag phase -> log phase -> stationary phase -> death phase

165
Q

lag phase

A

“flat” period of adjustment, enlargement; little growth in bacterial population

166
Q

log phase

A

The period of exponential growth of bacterial population.

167
Q

stationary phase

A

period of equilibrium; microbial deaths balance production of new cells

168
Q

death phase

A

population is decreasing at a logarithmic rate but never reaches zero… optical density and viable cell concentration are least proportional to each other

169
Q

growth kinetics

A

X = 2^Y x X0

170
Q

generation time

A

time for one doubling to take place; doubling time; g = t/Y or Y = t/g

171
Q

continuous culture

A

CHEMOSTAT; Dilution rate F/V; bacteria at steady rate while flow controls growth rate and nutrient conditions control culture density

172
Q

chemostat

A

cell density is controlled by concentration of limiting nutrient; keeps bacteria in late log phase/state

173
Q

biofilms

A

cells secrete material to hold to a surface; cells act together in a mixed community of bacteria stuck to the surface; cells signal to each other using quorum sensing; protects against dispersion and prevents antibiotics from infiltrating

174
Q

endospores

A

protect against bad conditions, disseminates cells, forms inside (“ENDO”) mother cell

175
Q

cells obtain energy from cannibalizing slow responding cells

A

to ensure spore formation in harsh nutrient poor environment

176
Q

endospore structure

A

exosporum (most outer part); coat; CORTEX (for strength, consists of peptidoglycan); core (most inner part, consists of dipicolnic acid)

177
Q

endospore formation

A

Stage 0/1: vegetative cell cycle… polar division… Stage 2: asymmetric cell division… Stage 3: engulfment of prespore… Stage 4: cortex… Stage 5: spore coat… Stage 6/7: maturation/cell lysis… germination of spore back to stage 0/1

178
Q

first stage of committed endospore formation

A

stage II

179
Q

bacterial live birth

A

related to endospore formation, except it is a live birth of the engulfed offspring

180
Q

heterocysts

A

specialized cells that undergo nitrogen fixation; oxygenic photosynthesis in nitrogen cycle

181
Q

myxospores

A

form inside fruiting body; multicellular structure

182
Q

actinomycetes

A

food runs out -> produce aerial hyphae, which protect against bad conditions -> disseminates (spreads) cells

183
Q

Caulobacter life cycle

A

SWARMER CELL - motile, but no division; STALKED CELL - non-motile, but able to undergo cell division (reproduce)

184
Q

optimal growth temperature of bacteria

A

is most related to optimal temperature for enzyme function

185
Q

psychrophile

A

bacteria that prefer cold, thriving at temperatures between 0 C and 25 C.

186
Q

mesophile

A

bacteria that prefers moderate temperature and develops best at temperatures between 25 C and 40 C

187
Q

thermophile

A

bacteria that thrive best at high temperatures, between 40 C and 70 C

188
Q

hyperthermophile

A

bacteria that grow at very high temperatures between 70°C and 110°C

189
Q

effect of temperature on growth

A

increased temperature increases bacterial growth rate and decreased temperature decreases bacterial growth rate… but too hot will cause enzymes to denature and too cold will cause decreases in membrane fluidity and enzymatic activity

190
Q

acidophiles

A

bacteria that grow in acidic pH < 7

191
Q

neutrophiles

A

bacteria that grow at or near neutral pH = 7

192
Q

alkaliphiles

A

bacteria that grow at alkaline pH > 7

193
Q

adapting to pH variations

A

in strongly acidic environment, amino acid decarboxylases drain protons form cell… in slightly acidic conditions, cells use K+/H+ antiport system to remove internal protons… under alkaline stress, Na+/H+ antiport systems scavenge protons from environment

194
Q

cytoplasm pH

A

is always 7

195
Q

isotonic

A

water concentration is equal inside and outside of the cell

196
Q

hypotonic

A

net diffusion of water into cell

197
Q

hypertonic

A

net diffusion of water out of the cell

198
Q

high osmotic pressure

A

will kill bacteria

199
Q

aerobes

A

Bacteria that require oxygen to grow

200
Q

microaerophiles

A

require oxygen concentration lower than air

201
Q

anaerobes

A

Bacteria that grow in the absence of oxygen and are destroyed by oxygen

202
Q

facultative anaerobes

A

can live with or without oxygen, but prefers oxygen

203
Q

aerotolerant

A

do not utilize oxygen but can survive and grow in its presence

204
Q

barophiles

A

organisms that live under extreme pressure

205
Q

xerophiles

A

organisms able to grow in very dry environments (low humidity)

206
Q

nonhalophile

A

A microorganism that cannot grow in the presence of added sodium chloride

207
Q

halotolerant

A

can survive at higher salt concentrations but grow best at low or zero concentrations

208
Q

halophile

A

an organism that can grow in, or favors environments that have very high salt concentrations; needs added salt in order to survive

209
Q

extreme halophile

A

Organism adapted to life in a highly salty environment

210
Q

sterilization

A

kills all vegetative cells and spores

211
Q

disinfection

A

reduces number of pathogens on inanimate surface

212
Q

decontamination

A

makes contaminated surfaces safe to handle by reducing number of microbes present (sanitation)

213
Q

antisepsis

A

killing microbes on living tissue/surface

214
Q

antibiotic

A

antimicrobial compound made by one living organism that affects other organisms

215
Q

bacteriostatic

A

inhibits bacterial growth but does not kill cells

216
Q

bactericidal

A

kills cells (but retains cell “bodies”)

217
Q

bacteriolytic

A

kills cells and lyses cell bodies

218
Q

microbial death rate

A

decimal reduction time – D-VALUE: time required to kill 90% of cells… affected by temperature, type of microorganism, physiological state, and other substances

219
Q

thermal death point

A

lowest possible temperature that will achieve complete killing within ten minutes

220
Q

thermal death time

A

minimum time to achieve complete killing in a liquid solution at a given temperature

221
Q

physical - dry heat

A

INCINERATION (flaming loops) and baking (at 160 degrees C for 2 hours or 171 degrees C for 1 hour)… advantages: cheap and easy / disadvantage: materials must withstand high temperatures and be dry (not aqueous)

222
Q

physical - moist heat

A

boiling (but will not kill endospores), tyndallization (discontinuous boiling), PASTUERIZATION (high heat for a short time), AUTOCLAVING (very high heat)… advantages: cheap and easy / disadvantages: materials must withstand high temperatures

223
Q

pastuerization

A

first devised by Louis Pasteur; commonly used with juice/beer/milk/dairy products; BATCH - 63 C for 30 minutes, HTST - 72 C for 15-20 seconds, or UHT - 121 C for <3 seconds

224
Q

autoclaving

A

commonly used in laboratory; temperatures higher than boiling, using steam pressure at 121 C for 20 minutes; kills all endospores

225
Q

physical - cold

A

FREEZING (ki1lls some cells due to ice crystals formations, but does not kill most bacteria); refrigeration (preservation)… advantages: many products tolerate cold better / disadvantages: very little killing and is expensive

226
Q

physical - filtration

A

pass liquid or gas through a FILTER with sufficiently small pore size (smaller than 1 micrometer); HEPA - filter out >0.3 micrometer particles… advantages: no thermal damage / disadvantages: viruses not eliminated and must be either liquid or gas

227
Q

physical - radiation

A

ULTRAVIOLET (damages DNA with poor pentration), GAMMA RAYS (very good penetration), XRAYS (less penetration)… advantages: very effective with little product damage / disadvantages: dangerous materials need shielding and lack of public trust

228
Q

chemical treatments

A

chemotherapeutics for disease treatment or disinfectants for cleaning surfaces; choice is based upon nature of object, kinds of microbes targeted, and desired effect

229
Q

chemical - phenolics

A

denature proteins and disrupt membranes; used by Joseph Lister; examples: PHENOL (carbolic acid), lysol, CHLOROHEXIDINE; effective on surfaces but may be too toxic to apply to tissue

230
Q

chemicals - alcohols

A

denature proteins and disrupt membranes; examples: ETHANOL, ISOPROPANOL; most effective at 50-70%; increased plasmolysis after damage; commonly used for antisepsis!

231
Q

chemical - oxidants

A

damage proteins and lipids; halogens: CHLORINE (disinfectant), IODINE (antiseptic); HYDROGEN PEROXIDE (H2O2): 3% is a weak antiseptic, with the body and many bacteria breaking this down enzymatically

232
Q

oligodynamic effect

A

inhibition by heavy metals: silver, copper, mercury, gold; produce zone of inhibition

233
Q

chemical - surfactants

A

amphiphilic compounds; disrupt membranes; quaternary ammonium compounds with charged nitrogen and four hydrophobic groups; examples: CEPACOL, ROCCAL

234
Q

chemical - alkylators

A

damage proteins or DNA by adding carbon adducts; examples: FORMALIN, glutaraldehyde, ETHYLENE OXIDE (used to sterilize products via gas); highly noxious

235
Q

fluorescence microscopy

A

allows visualization of cytoskeletal proteins and nuclear proteins

236
Q

opportunistic pathogen

A

causes disease only in the absence of normal host resistance; example: Pseudomonas aeruginosa

237
Q

DnaA functions in Caulobacter

A

initiation of DNA replication, transcriptional regulation

238
Q

ecosystem

A

sum of the total of all organisms and abiotic factors in a particular environment

239
Q

habitat

A

portion of an ecosystem where a community could reside

240
Q

species richness

A

total number of different species present

241
Q

species abundance

A

proportion of each species in an ecosystem

242
Q

guilds

A

metabolically related microbial populations

243
Q

niche

A

habitat shared by a guild; supplies nutrients as well as conditions for growth

244
Q

communities

A

sets of guilds that interact with macroorganisms and abiotic factors in ecosystem

245
Q

allochtonous

A

chemical that comes from outside the ecosystem

246
Q

population

A

all individuals of one species in the same area

247
Q

community 1

A

photic zone: oxygenic phototrophs

248
Q

community 2

A

oxic zone: aerobes and facultative aerobes

249
Q

community 3

A

anoxic sediments: GUILD 1 (denitrifying bacteria and ferric iron-reducing bacteria), GUILD 2 (sulfate reducing bacteria and sulfur reducing bacteria), GUILD 3 (fermentative bacteria), and GUILD 4 (methanogens and acetogens)

250
Q

bigeochemistry

A

study of biologically mediated chemical transformations; defines transformations of a key element by biological or chemical agents (which typically proceed by OXIDATION-REDUCTION reactions)

251
Q

environments and microenvironments

A

physiochemical conditions in a microenvironment are subject to RAPID CHANGE (spatially and temporally)… resources in natural environments are highly variable and many microbes in nature face a FEAST OR FAMINE existence… growth rates of microbes in nature are lower than the maximums defined in laboratory… COMPETITION and COOPERATION occur between microbes in natural systems (syntropy - metabolic cooperation)

252
Q

biofilm

A

mixed community of microbes living on a surface… assemblages of bacterial cells adhered to a surface and enclosed in an ADHESIVE MATRIX excreted by cells and is made of a mixture of polysaccharides… these trap nutrients for microbial growth and help prevent detachment of cells in flowing systems

253
Q

quorum sensing

A

intracellular communication that is critical in development and maintenance of a biofilm; the major intracellular signaling molecules are ACYLATED HOMOSERINE LACTONES… both INTRASPECIES SIGNALING and INTERSPECIES SIGNALING used in biofilms… used by pseudomonas aeroginosa

254
Q

reasons for biofilm formation

A

SELF DEFENSE (resist physical forces that sweep away unattached cells, phagocytosis by immune cells, and penetration of toxins); allow cells to remain in a FAVORABLE NICHE; allows cells to live in CLOSE ASSOCIATION with one another

255
Q

soils

A

loose outer material of earth’s surface; consists of four layers: O, A, B, C horizons

256
Q

O horizon

A

at the surface, with undecomposed plant material

257
Q

A horizon

A

with most microbial growth, rich in organic material and nutrients

258
Q

B horizon

A

subsoil where organic material leached from A horizon gathers, little microbial activity

259
Q

C horizon

A

base that is directly above bedrock and forms from bedrock

260
Q

soils are composed of

A

INORGANIC MINERAL MATTER (~40% of soil volume); ORGANIC MATTER (~5%); AIR AND WATER (~50%); and LIVING ORGANISMS (~5%)

261
Q

soils are formed by interdependent physical, chemical, and biological processes

A

carbon dioxide is formed by respiring organisms that form CARBONIC ACID that breaks down rock…. physical processes such as FREEZING and THAWING break apart rocks, allowing plant roots to penetrate and form an expanded RHIZOSPHERE

262
Q

rhizosphere

A

area around plant roots where plants secrete sugars and other compounds, is rich in organic matter and microbial life

263
Q

terrestrial subsurface

A

deep soil subsurface can extend for SEVERAL HUNDRED METERS below soil surface… archaea and bacteria are believed to exist in deep subsurface in variable concentrations depending on nutrient availability… subsurface microbial life grows in an extremely nutrient-limited environment so small cells are common… deep subsurface is home to a group of organisms that may be the archaea that are most closely related to eukaryotes: LOKIARCHEOTA

264
Q

freshwater

A

highly variable in resources and conditions available for microbial growth; balance between photosynthesis and respiration controls the OXYGEN and CARBON cycles

265
Q

phytoplankton

A

oxygenic phototrophs suspended freely in water, including algae and cyanobacteria

266
Q

benthic species

A

attached to bottom or sides of a lake or stream

267
Q

stratified lakes

A

epilimnion, thermocline, hypolimnion… these layers vary greatly in temperature, oxygen availability, and chemical composition

268
Q

epilimnion

A

warmer, less dense surface water

269
Q

hypolimnion

A

cooler, denser water at bottom of lake or pond

270
Q

thermocline

A

separates the epilimnion and hypolimnion

271
Q

rivers

A

may be well mixed because of rapid water flow; can still suffer from oxygen deficiencies because of high inputs of organic matter from sewage and agricultural/industrial pollution

272
Q

biochemical oxygen demand (BOD)

A

microbial oxygen-consuming capacity of a body of water; increases with influx of organic material (ex: from sewage) then decreases over time

273
Q

marine environment

A

open ocean environment is SALINE, LOW IN NUTRIENTS (especially with respect to nitrogen, iron, and phosphorous), and COOLER… microbial activities taking place in them are major factors in earth’s carbon balance due to the size of oceans

274
Q

oxygen minimum zones (OMZs)

A

regions of oxygen depleted waters at intermediate depths; high oxygen demand, nutrient rich areas – high levels of denitrification and anammox

275
Q

Prochlorococcus (major marine phototroph)

A

accounts for >40% of BIOMASS of marine phototrophs, ~50% of NET PRIMARY PRODUCTION

276
Q

open ocean

A

has a pelagic zone

277
Q

pelagibacter

A

most abundant marine heterotroph; contain PROTEORHODOPSIN (form of rhodopsin that allows cells to use light energy to drive ATP synthesis)

278
Q

oligotroph

A

an organism that grows best at very low nutrient concentrations

279
Q

must abundant microorganisms in oceans

A

viruses

280
Q

> 75% of all ocean water is

A

deep sea

281
Q

organisms that inhabit the deep sea must deal with

A

LOW TEMPERATURE, HIGH PRESSURE, LOW NUTRIENT LEVELS

282
Q

deep sea microbes are

A

PIEZOPHILIC (pressure loving) or piezotolerant; often PSYCHROPHILIC or psychrotolerant (but can also be thermophilic or thermotolerant)

283
Q

piezotolerant

A

tolerate elevated pressure but grow best at low atm

284
Q

piezophile

A

lives optimally at high pressure

285
Q

extreme piezophile

A

an organism requiring extremely high pressure for growth

286
Q

hydrothermal vents

A

CHEMOLITHOTROPHIC bacteria predominate at the vent because they can utilize the inorganic materials; THERMOPHILES and HYPERTHERMOPHILES are also present

287
Q

carbon

A

cycled through all of Earth’s major carbon reservoirs, including atmosphere, land, oceans, sediments, rocks, and biomass…. life on earth is carbon based

288
Q

all nutrient cycles are linked to the

A

CARBON CYCLE

289
Q

largest carbon reservoir

A

SEDIMENTS (and rocks) in Earth’s crust – about 99.5% of carbon, but not biologically available

290
Q

most rapidly transferred carbon reservoir

A

CO2 in atmosphere

291
Q

CO2 transfers

A

removed from atmosphere by PHOTOSYNTHETIC land plants and marine microbes (so a large amount of carbon is found there)… found in HUMUS (DEAD ORGANAIC MATERIAL) than is found in living organisms… CO2 is returned to atmosphere by RESPIRATION and DECOMPOSITION (and by human-related activities)

292
Q

photosynthesis

A

reduces inorganic carbon dioxide to organic carbohydrates; CO2 + H2O -> (CH2O) + O2

293
Q

respiration

A

oxidizes organic carbohydrates to inorganic carbon dioxide; (CH2O) + O2 -> CO2 + H2O

294
Q

two major end products of decomposition

A

methane (CH4) and carbon dioxide (CO2)

295
Q

methane hydrates

A

form when high levels of methane are under high pressure and low temperature; fuel deep-sea ecosystems called COLD SEEPS

296
Q

methanogenesis

A

central to carbon cycling in anoxic environments: most methanogens use CO2 as a terminal electron acceptor, reducing CO2 to CH4 with H2 as an electron donor while some can reduce other substrates to form CH4

297
Q

syntrophy

A

where different microbial taxa (ex: methanogens and other partners) work in cooperation to degrade a compound that neither can perform entirely on their own

298
Q

nitrogen cycle

A

four major nitrogen transformations: NITRIFICATION, DENITRIFICATION, ANAMMOX, and NITROGEN FIXATION

299
Q

nitrogen

A

key constituent of cells; exists in a NUMBER OF OXIDATION STATES (has the largest number of potential oxidation states of the major biological elements)

300
Q

N2

A

most stable form of nitrogen and is a major reservoir (about 70% of earth’s air)… used by prokaryotes that can convert inorganic N2 to organic nitrogen through nitrogen fixation… produced biologically by denitrification (reduction of nitrate to gaseous N2)

301
Q

nitrogen fixation (or ammonification)

A

N2 -> NH3… only performed by bacteria

302
Q

anammox

A

anaerobic respiration of ammonia to N2 gas

303
Q

denitrification and anammox

A

result in losses of organic nitrogen from biosphere

304
Q

nitrogen fixation

A

synthesis of amino groups; fully reduced nitrogen is yielded (necessary for amino acid synthesis because fixed nitrogen is often a limiting factor for cell growth)

305
Q

Haber process

A

makes an industrially fixed nitrogen (ammonia) fertilizer, but is dependent on natural gas… but the oxidized fertilizer runoff contaminates waterways

306
Q

nitrogenase

A

required enzyme used to make atmospheric nitrogen bioavailable through the process of nitrogen fixation [but must stay ANAEROBIC – O2 acts as a competitive inhibitor to be reduced to H2O]

307
Q

four rounds of reduction per N2

A
  1. electron donor (NADH) donates electrons… 2. ATP energy used to bind substrate (in the first round– H+ is bound)… 3. electrons reduce substrate… 4. repeats steps 1-3 three more times for a total of four rounds (4 ATPS, 4 NADH equivalents used)
308
Q

nitrogen fixation limitations

A

energy intensive process (40 ATPS CONSUMED for each N2 fixed to make NH3 – very costly for the cell)… enzyme production strictly regulated (only made when O2 and NH4+ levels are low)… aerobic organisms make special cells to fix N2 (aerobic cells make glucose, anaerobic HETEROCYSTS make NH3)

309
Q

nitrogen

A

limiting factor in environment

310
Q

rhizobium

A

A symbiotic bacterium that lives in the nodules on roots of specific legumes and that incorporates nitrogen gas from the air into a form of nitrogen the plant requires (NH3)

311
Q

nitrogen assimilation

A

incorporation of NH4+ into amino acids: α-ketoglutarate + NH4+ -> glutamine [with α-ketoglutarate being a TCA intermediate]

312
Q

transamination

A

glutamine donates NH3 to make other amino acids:

pyruvate + glutamine -> alanine + α-ketoglutarate…

oxalacetate + glutamine -> aspartate + α-ketoglutarate

313
Q

nitrification

A

NH4+ -> NO2- -> NO3-; oxidation of NH4+ provides electrons/energy

314
Q

nitrosomas

A

species oxidizes NH4+ to NO2-

315
Q

nitrobacter

A

species oxidizes NO2- to NO3-

316
Q

eutrophication

A

pollution of water through excess nitrogen (nitrate), often from excessive fertilizer use causing nitrate runoff

317
Q

denitrification

A

NO3 - -> NO2- -> NO -> N2O -> N2; DISSIMILATORY NITRATE REDUCTION (nitrate is anaerobic electron acceptor)… NO3- is reduced

318
Q

sulfur

A

the bulk occurs in sediments and rocks as SULFATE or SULFIDE minerals (gypsum, pyrite), with OCEANS representing the most significant reservoir of sulfur (as sulfate) ion biosphere

319
Q

hydrogen sulfide

A

major volatile sulfur gas that is produced by bacteria via sulfate reduction or emitted from geochemical sources

320
Q

sulfide

A

toxic to many plants and animals and reacts with numerous metals

321
Q

sulfur dioxide

A

produced by burning of fossil fuels

322
Q

dimethyl sulfide (DMS)

A

MOST ABUNDANT ORGANIC SULFUR COMPOUND IN NATURE; produced primarily in marine environments as a degradation product of dimethylsufoniopropionate (an algal osmolyte; can be transformed via a number of microbial processes

323
Q

iron and manganese cycle

A

iron and manganese cycle between oxidized and reduced states with each other in aquatic ecosystems… FERROUS (Fe2+) and Mn2+ are the more soluble and more accessible forms, while FERRIC (Fe3+) and Mn4+ is less soluble and precipitates

324
Q

phosphorous cycle

A

organic and inorganic phosphates (PO4 2-); PHOSPHOROUS IS A TYPICAL LIMITING NUTRIENT that limits the growth of aquatic photosynthetic autotrophs; alternate forms such as phosphite and hypophosphate rapidly cycle through aquatic ecosystems

325
Q

calcium cycle

A

RESERVOIRS ARE ROCKS AND OCEANS; marine phototrophic microorganisms such as foraminifera use Ca2+ to form exoskeleton

326
Q

silica cycles

A

marine silica cycle is controlled by unicellular eukaryotes (DIATOMS, SILICOFLAGELLATES, RADIOLARIANS) that build cell skeletons (shells) called FRUSTULES

327
Q

phosphorous cycle, calcium cycle, and silica cycle vary from the other nutrient cycles

A

because there is no gaseous phases

328
Q

bacteriostatic

A

inhibit cell growth

329
Q

bactericidal

A

kill viable cells

330
Q

minimum inhibitory concentration (MIC)

A

the smallest concentration (highest dilution) of drug that VISIBLY inhibits growth

331
Q

minimum bactericidal concentration (MBC)

A

The lowest concentration of an antibiotic that truly kills all cells

332
Q

disk diffusion assays

A

kirby-bauer; standardized conditions…. zones of inhibition, where a larger zone indicates more susceptible and a smaller zone indicates more resistant

333
Q

E-test strips

A

drug gradient used and can determine the MIC

334
Q

tube dilution assay

A

the drug is diluted in a series, then inoculated and incubated– where growth stops is the MIC… transfer some of the media after and including the point at which visible growth is stopped to new drug-free media tubes – where growth is no longer visible is the MBC

335
Q

membrane-active drugs

A

detergents; bind to phospholipid and lipid A to disrupt membranes… include POLYMYXIN and GIAMICIDIN

336
Q

DNA replication

A

few clinical drugs affect polymerization; conserved mechanisms can lead to toxicity; DNA gyrase inhibitous… ex: NALADIXIC ACID, NOVOBIOCIN, and FLUOROQUINOLONES

337
Q

naladixic acid

A

A subunit – blocks nicking of DNA strands

338
Q

novobiocin

A

B subunit – blocks ATP hydrolysis

339
Q

transcription of DNA

A

actinomycin D - intercalating agent with no specificity (toxic) and is used a lab reagent … RIFAMPIN – binds to RNA polymerase, specific for bacteria, prevents elongation of transcript after initiation, and is a useful drug against Mycobacterium tuberculosis

340
Q

aminoglycosides

A

BINDS 30S and distorts the ribosome, causing translation errors; examples: STREPTOMYCIN, NEOMYCIN, OXAZOLIDIHONES (prevent formation of 70S ribosome initiation complex)

341
Q

tetracycline

A

BLOCKS A SITE; prevents tRNA entry, but is a reversible reaction… bacteriostatic

342
Q

chloramphenicol

A

BINDS 50S to prevent peptidyl transfer reaction

343
Q

erythromycin

A

BINDS 50S SUBUNIT NEAR P SITE to prevent translocation; Macrolides… Lincosumides

344
Q

translation of DNA

A

aminoglycosides; tetracycline; chloramphenicol; erythromycin

345
Q

metabolic - Sulfa drugs

A

block THFA formation; TETRAHYDROFOLATE is an important carbon and hydrogen carrier; SULFANILAMIDE; TRIMETHOPRIM

346
Q

other metabolic inhibitors

A

ISONIAZID (mycolic acid formation inhibited – main anti-tuberculosis drug); FOSPHOMYCIN (PEP Analog)

347
Q

peptidoglycan inhibitors

A

compound found only in bacteria so it serves as a good target for drugs; steps that are blocked: FOSFOMYCIN, CYCLOSERINE, VANCOMYCIN, BACITRACIN, PENICILLIN (blocks cross linking)

348
Q

D-cycloserine

A

D-ALANINE ANALOG; blocks pentapeptide formation and blocks cell wall formation; cannot assemble peptidoglycan monomer so cells become fragile and lyse – bacteriolytic antibiotic

349
Q

lipid carrier inhibitors

A

VANCOMYCIN (prevents release from lipid carrier) and BACITRACIN (blocks regeneration of carrier after release) – both are very toxic to humans and are not commonly used internally as a result

350
Q

Beta-Lactam Antibiotics - prevent crossing linking

A

“cillin” ending drugs: PENICILLIN (PENAM); CEPHEM; OXACEPHEM; CARBAPENAM; CLAVAM; MONOBACTAM… all have a “beta-lactam” characteristic ring

351
Q

peptidoglycan biosynthesis

A

structural analog to D-Ala; BLOCKS CROSS LINKING, CELLS POP – influenced by penicillin

352
Q

anti-fungal drugs

A

having selective toxicity: NYSTATIN, IMIDAZOLES, AMPHOTERICIN B; other: FLUCYTOSINE, GRISEOFULVON

353
Q

nystatin

A

targets fungal membrane

354
Q

imidazoles

A

inhibit sterol synthesis (of ergosterol of fungi)

355
Q

amphotericin B

A

disrupts cell membrane of fungi

356
Q

flucytosine

A

synthetic pyrimidine analog

357
Q

griseofulvon

A

effective against ringworms/fungi by preventing cell division

358
Q

anti viral drugs

A

AMANTADINE (influenza A virus); ACYCLOVIR (herpes viruses – nucleoside analog); RIBAVIRIN (blocks RNA synthesis)

359
Q

few antivirals

A

due to toxicity problems – viruses use host cell components so they are difficult to target without also targeting host cells

360
Q

anti HIV agents

A

reverse transcriptase inhibitors – AZT (blocks reverse transcriptase), delavirdine, nevirapine… protease inhibitor – INDINAVIR (prevents proper protein development within viral life cycle), nelfinavir, ritonavir

361
Q

preventing drug resistance

A

LIMIT DRUG USE (to decrease selective pressure); PROPER DRUG USE (to ensure elimination of pathogens upon taking complete dose); MULTIPLE DRUG TREATMENTS SO DRUGS CAN WORK SYNGERGISTICALLY (antibiotics can work together more effectively)

362
Q

selective toxicity of antibiotics

A

antibiotics must affect target organism but not the host (humans), so they should have minimal toxic side effects to host and target the microbial pathway that which is not present in the host– target peptidoglycan (bacterial cell wall component), 70S ribosomes (bacterial ribosomes vs 80S of eukaryotes), and biochemical pathways missing in humans

363
Q

broad spectrum

A

antibiotic is effective against many species

364
Q

narrow spectrum

A

antibiotic is effective against few or a single species

365
Q

source of antibiotics

A

most discovered as natural products then modified by artificial means to increase efficacy and decrease toxicity to humans

366
Q

microbial antibiotic biosynthesis

A

antibiotics are SECONDARY METABOLITES… bacteria SECRETE ANTIBIOTICS but also MAKE ENZYMES TO DISABLE ANTIBIOTICS so that the drugs cannot kill the cells that make them

367
Q

antibiotic resistance

A

antibiotics are overused (overprescribed and used in farm animal feed), leading to exerted selective pressure for drug resistant strains

368
Q

HIV Drug Resistance

A

reverse transcriptase has a high error rate, and infrequently one of those errors produces a drug-resistant variant that is selected for by drug regimen

369
Q

antibiotic resistance mechanisms

A
  1. MODIFY TARGET SO THAT IT NO LONGER BINDS ANTIBIOTIC (mutations in ribosomal proteins confer resistance to streptomycin)… 2. DESTROY ANTIBIOTIC BEFORE IT GETS TO CELL (beta-lactamase enzyme specifically destroys penicillins)… 3. ADD MODIFYING GROUPS THAT INACTIVATE ANTIBIOTIC (three classes of enzymes are used to modify/inactivate aminoglycoside antibiotics)… 4. PUMP ANTIBIOTIC OUT OF CELL (specific and nonspecific transport proteins)
370
Q

how drug resistance develops

A

de novo antibiotic resistance develops through gene duplication and/or mutations… can also be acquired via HORIZONTAL GENE TRANSFER (conjugation, transduction, transformation)… recently, has also been attributed to presence of integrons

371
Q

future of drug discovery

A

EVOLUTIONARY PRESSURE IS CONSTANT (so there is a required constant search for new antibiotics)… modern drug discovery: use genomics to identify new targets, design compounds to inhibit targets, alter compound structure to optimize MIC, determine spectrum of compound, and determine pharmaceutical properties

372
Q

eutrophication implications

A

increased input of nutrients –> increased concentration of microbes –> decreased levels of oxygen

373
Q

proteobacteria are the most predominant in

A

aquatic environments

374
Q

Pyrite

A

compounds made with iron and sulfur (FeS2)

375
Q

microbial leaching

A

removal of valuable metals (such as copper) from sulfide ores by microbial activities ((first reaction: oxidation of reduced sulfides to sulfate and release of reduced iron))… but can lead to environmental damage due to acidic conditions of nearby areas like rivers

376
Q

Leptospirillum ferroxidans

A

used in oxidation ponds for leaching copper in mines

377
Q

U6+

A

water soluble uranium

378
Q

U4+

A

not water soluble uranium

379
Q

xenobiotic

A

synthetic chemicals that are not naturally occurring, manmade compounds not found in nature; can be broken down by COMETABOLISM (microbes will break this down alongside other organic molecules – which serve as their primary source of energy)

380
Q

reductive dechlorination

A

breaks down manmade chemicals (xenobiotics) in absence of oxygen; important process because anoxic conditions develop quickly in polluted environments

381
Q

biodegradable polymer

A

polyhydroxybuterate (PHB) – made by bacteria

382
Q

wastewater

A

DOMESTIC SEWAGE OR LIQUID INDUSTRIAL WASTE… “grey water” is water resulting from washing/bathing/cooking and sewage is water contaminated with fecal material

383
Q

(treated wastewater) effluent water is suitable for

A

release into surface waters, release to drinking water purification facilities

384
Q

wastewater treatment

A

primary, secondary, tertiary

385
Q

primary wastewater treatment

A

REMOVAL OF SOLIDS– uses physical separation methods to separate solid and particulate organic and inorganic materials from wastewater

386
Q

secondary wastewater treatment

A

REDUCING BIOLOGICAL OXYGEN DEMAND – uses digestive reactions carried out by microbes under aerobic conditions to treat wastewater with low levels of organic materials to remove organic material… ACTIVATED SLUDE and TRICKLING FILTER (ELIMINATES EXCESS ORGANIC MATERIAL) are most common decomposition processes

387
Q

tertiary wastewater treatment

A

REDUCING NUMBER OF PATHOGENS – any physiochemical or biological treatment added for further processing of secondary treatment effluent… additional removal of organic matter and suspended solids… reduces levels of inorganic nutrients (phosphate, nitrate, nitrite)… phosphorous removal through FeCl3 – PRECIPITATES EXCESS PHOSPHATE

388
Q

new contaminants of wastewater that are biologically active pollutants

A

pharmaceuticals, personal care products, household products, sunscreens

389
Q

purification of drinking water involves

A

SEDIMENTATION to remove particles -> COAGULATION and FLOCCULATION form additional aggregates which settle out -> FILTRATION -> DISINFECTION using CHLORINE GAS or UV radiation

390
Q

biodeterioriation

A

loss of structural integrity of stone or concrete caused by microorganisms (Bacteria, Archaea, Fungi, Algae, Cyanobacteria)… causes corrosion of sewer lines (causing sewer lines to fail!)

BIO 286 - Microbiology (21 decks)

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