Biodegradation and Bioremediation Exam 4 - Final Exam Flashcards

You may prefer our related Brainscape-certified flashcards:
1
Q

What are the processes that control the fate of pollutants?

A

-Physiochemical processes
Ex: sorption/desorption, volatilization, leaching & runoff, hydrolysis, photolysis, oxidation-reduction reaction
-Biological processes:
Mostly mediated by microbes (plants can transform some pollutants). Microbes are the most important agent when it comes to biodegradation*

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Abiotic degradation vs. Microbial degradation

A

Abiotic: Typically incomplete degradation of organic contaminants, produces biproducts, and occurs relatively fast.
Microbial (biological): Break down the carbon compound and mineralize these organic pollutants and produce benign product (CO2 and water).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is biodegradation?

A

The biologically catalyzed reactions that reduce the complexity of chemicals. Larger molecules becoming smaller. Molecular weight decreases.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is transformation?

A

The alteration in the structure of the original compound without consideration if what the products are. Products can be smaller or larger than original compound.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is mineralization (or ultimate biodegradation)?

A

The conversion of organic compounds to cell material and inorganic constituents such as CO2, water, chloride, ammonium, nitrate, and phosphate. Most desirable form of biodegradation.* Want to convert toxic compound to carbon and water.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is cometabolism?

A

The transformation of an organic compound by a microorganism that is unable to use the substrate as a source of carbon or energy.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is bioremediation?

A

Is the use of biological agents to detoxify contaminants in the soil and other chemical compounds. This reaction leads to detoxification and happens in the environment (in the field).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What does anthropogenic mean?

A

Produced by humans.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What does Xenobiotic mean?

A

A chemical that is foreign to the biosphere. Derived from the Greek words xeno (stranger) and bios (life).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is bioaccumulation?

A

The accumulation of a pollutant in living tissue. Hydrophobic compounds in fat tissue, for example.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What does biomagnification mean?

A

The increase in concentration of pollutant in organisms as one moves up the food chain. For those hydrophobic compounds that accumulate in living organisms at the lower part of the food chain, then the predators would prey on these organisms containing these toxic compounds and then it builds up and increases in predators.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is bioavailability?

A

The accessibility of a chemical for microbial degradation or assimilation. A lot of times, when chemical compounds are absorbed by soil or sediments, then their degradation is slowed and then less biodegradable.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the most oxidized form of carbon? Most reduced? All other organic compounds have a valence in between. What does that mean in terms of biodegradation?

A

Most oxidized: CO2
Most reduced: Methane
-This means that any carbon compounds with chemical valence in between, can undergo reactions and are unstable to a certain extent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

In terms of biodegradability, there are two key factors. What are they?

A

Thermodynamically: all organic chemicals are unstable to varying degrees.
Kinetically: their degradation can be very slow.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the NPL?

A

National Priorities List.
Is a federal list of the nation’s hazardous waste sites eligible for investigation and cleanup under the Superfund program.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What affects the stability and toxicity of a compound, and whether or not they are biodegradable?

A

The structure of organic compounds.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Classification of organic compounds:
What are functional groups?

A

Individual atoms and small clusters of atoms with a definable set of chemical activities. Ex: Carboxyl group, hydroxyl group, methoxyl group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What are examples of ring structures?

A

Aromatic rings: 6C like benzene
Saturated rings: No double bond
Homocyclic rings: Same atom on all parts of the ring, like benzene
Heterocyclic rings: Different atoms in the ring structure. Ex: benzene ring but change out a carbon for nitrogen.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Classes of organic compounds:
What are hydrocarbons? What’s the difference between a hydrocarbon and carbohydrate?

A

Hydrocarbons have carbon-hydrogen in their structure.
Carbohydrate has carbon, hydrogen, and oxygen in its structure. This is what we eat.
Hydrocarbon is what we feed our cars, for example.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the different classes of organic compounds?

A
  1. Hydrocarbons
  2. Organic compounds containing oxygen
  3. Organic compounds containing nitrogen
  4. Other
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What are the different types of hydrocarbons?

A

Alkanes: C-C
Alkenes: C - - C (double bond)
Alkynes: C - - - C (triple)
Aromatic hydrocarbons: Arenes (like benzene). Alternating double and single bonds between carbon atoms.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What are the different organic compounds containing oxygen?

A

Alcohols, ethers, aldehydes & ketones, carboxylic acids, carboxylic acid derivatives

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are the different organic compounds containing nitrogen?

A

Amines, amides, nitriles (has triple bond)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What are the “other” classified organic compounds?

A

Halides (acyl halide, alkyl halide, aryl halide) (a lot of resistant compounds are halides) and sulfur containing compounds (thiols).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Persistent Organic Pollutants (POPs):
How many are there? What are they called? A few examples?

A
  1. Called the “dirty dozen”
    Ex: DDT, Mirex, Aldrin, Hexachlorobenzene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Persistent Organic Pollutants (POPs):
What do they all have in common?

A

All have saturated and unsaturated ring structures, some are aromatic, some aren’t.
Lot of Cl in structures, the more Cl then the more resistant they are. Br and Cl are trouble for biodegradation.
Saturated rings are fairly stable, too. Benzene is hard to break, but when two are linked together, even harder to break.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is important to note about the EPA’s priority toxic pollutant list?

A

There are more organic than inorganic compounds on the list. Many of the organic compounds on the list are chlorinated solvents.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

In order for microbes to metabolize carbohydrates, they must go through…?

A

Glycolysis and TCA cycle

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What are the two intermediate products produced in glycolysis?

A

Pyruvate and acetyl-coA, and they will enter the TCA cycle.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What happens if microbes encounter a compound that they have never seen before?

A

They will modify it into something that that they are familiar with (by making new enzymes, for ex) and more easily to breakdown. Then, these products are funneled into the central pathways.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

The degradation of organic pollutants is really an extension of the …?

A

Carbon cycle in the natural ecosystem.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What are the central pathways?
Why are the pathways a key for?

A

Glycolysis and Tricarboxylic acid cycle (TCA).
Key for carbon and energy that microbes need for growth.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Describe glycolysis and what is generated in the pathway.

A

8 ATP molecules are generated from one glucose molecule that is metabolized. There are two key intermediate products (The last two): pyruvate and acetyl-coA. Acetyl-CoA will enter the TCA cycle.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Describe the TCA cycle and what is generated in this pathway.

A

Additional 30 ATP molecules produced. CO2 is also a product. All the carbon compounds in the TCA cycle are called metabolites, and are the building blocks for microbes to grow. These carbon compounds are used for microbes to undergo biosynthesis. Also called the Krebs cycle and citric acid cycle.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Central Metabolism:
Peripheral pathways.

A

Microbes develop peripheral pathways in order to metabolize toxic organic compounds. For example, hydrocarbons are attacked by oxygenases and then degraded via peripheral pathways. Then these degraded compounds are funneled into the central pathways.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What is the structure of a hydrocarbon?
What are all the different structure possibilities?

A

CmHn… They have carbon and hydrogen atoms in their structures.
-Can be saturated or unsaturated (double or triple bond)
-Can have straight chain structures or ring structures.
-If it has straight chains, then it is aliphatic
-If it has benzene rings, then it is aromatic
-If it is a saturated ring structure, then it is alicyclic

37
Q

What are examples of hydrocarbons?

A

Straight chain alkane, branched alkane, cycloalkane, and aromatic (these are all saturated)

38
Q

What is the smallest aromatic hydrocarbon?

A

Benzene (single ring structure) (is unsaturated)

39
Q

How do microbes break down alkanes?

A

Step 1: Initial transformation by mono- or diooxygenases (enzyme that adds oxygen)
Step 2: Formation of fatty acids (something that microbes are familiar with)
Step 3: Beta oxidation:
Two carbon atoms are removed in the form of acetyl-CoA and acyl-CoA at the carboxyl terminal. The bond is broken between the second carbon/beta carbon and the third carbon/gamma carbon, hence the name beta oxidation. Acetyl-CoA is transferred to the TCA cycle. For the rest of the chain structure, it will go back and repeat the process until all the carbons in the molecule have been metabolized.
Important product formed: acetyl-CoA

40
Q

What are monooxygenases?
What are diooxygenases?

A

Mono: Catalyze the insertion of one atom of molecular oxygen (O2) into the substrate, while the second atom is reduced to water.
Dio: Incorporate both atoms of O2 into their substrates.
note: both end up with the same product, but the initial step is different.

41
Q

Are all alkanes degraded at the same rate?

A

NO!

42
Q

What type of alkanes are degraded the quickest? What is the second quickest? The slowest?

A

n-Alkanes of intermediate chain length (C10-C24) are degraded most rapidly.
Short-chain alkanes (<C4) are volatile and toxic. They degrade the second quickest.
Long-chain alkanes (mw>500) have low water solubility and are not easily absorbed by microbial cells. More resistant to degradation.

43
Q

Does branching reduce biodegradation rate?

A

YES! Typically microbes have to form new enzymes to figure out how to deal with branching.

44
Q

Cycloalkanes:
Cyclohexane degradation.

A

Cyclohexane has 6 atoms in ring structure.
Monooxygenase inserts oxygen in the initial step of this degradation. An -OH will be added onto the ring structure. Another monooxygenase is used to add another oxygen. Now there are 7 atoms in the structure, and it is unstable. Then, it opens up to a chain structure with a carboxyl group on one end and a hydroxyl group on the other. More oxidation reactions occur and we end up with fatty acid that undergoes beta oxidation.
Just another example of a modification and then the product ending up in the TCA cycle.

45
Q

Aromatic hydrocarbons:
What are the two examples given?

A

BTEX and PAHs.
Have benzene structure.
BTEX: Benzene, toluene, ethylbenzene, xylenes. These molecules typically exist together because when crude oil is processed, it undergoes a distillation process, and these are low boiling point distillation products that come out together.
PAHs: have more than one benzene. Polycyclic aromatic hydrocarbon

46
Q

Aerobic metabolism:
Describe Benzene biodegradation.

A

Difficult to break because of the structure. Only the electrons surrounding the carbon bend together, making the ring structure more stable.
-To degrade benzene, microbes still have the same strategy. Insert oxygen into the ring structure, and we will end up with the formation of Catechol (important intermediate because it is not stable)**. After the formation of this, the benzene ring will open up. Ring cleavage occurs between two hydroxyl groups or adjacent to to one of the hydroxyl groups. If it undergoes ortho cleavage, then we get the formation of short fatty acid chain and then undergoes further reaction producing succinic acid (one of the carbons in the TCA cycle) and acetyl-CoA (goes into the TCA cycle). If it undergoes Meta cleavage, we end up with aldehyde, and then that’s further metabolized. We will get acetaldehyde and pyruvic acid (or pyruvate, the metabolite right before acetyl-CoA). These are simple carbon compounds that can be easily metabolized by microbes.
TAKE HOME: Aromatic hydrocarbons are more resistant to degradation. The degradation of benzene ring involves hydroxylation. The first metabolite is Catechol. Catechol usually means there will be ring cleavage. Meta and Ortho.

47
Q

What are Alkyl-substituted benzenes?

A

One or more alkyl groups attached to the benzene ring. To break down, initial mechanism is similar, just hydroxylation. Once we have hydroxyl in the ring, ring cleavage happens.
Note: Diol is a compound containing two hydroxyl groups.

48
Q

What is the smallest PAH molecule?

A

Naphthalene. It has the fewest benzene rings.

49
Q

What happens in the Naphthalene Degradation pathway?

A

Initial degradation involves oxygenases.
-Uses diooxygenase.
-Ring cleavage pattern is Meta

50
Q

General theme of aerobic metabolism and degradation pathways is…?

A

Doesn’t matter if it is a long chain or aromatic. Will involve oxygenases. With aromatic compounds, ring cleavage occurs.

51
Q

What are the different kinds of oxygenases?

A

Monooxygenases (also called mixed-function oxygenases):
Flavin-containing monooxygenases and iron-containing monooxygenases
Dioxygenases:
Aromatic ring dioxygenases and aromatic ring-cleavage dioxygenases

52
Q

Anaerobic metabolism:
What are the hydrocarbon activation mechanisms? Describe each mechanism
What increases with activation mechanisms?

A

Hydroxylation: Involves insertion of hydroxyl group.
carboxylation: Involves insertion of carboxyl group into substrate.
condensation: Involves the reaction of small hydrocarbon molecule, combining to form one molecule.
-Molecular weight increases, substrate becomes larger before they are degraded into a simpler compound.

53
Q

Anaerobic metabolism:
After the hydrocarbon activation mechanisms, what happens?

A

Further transformation goes on, but we don’t really know much about it. We do know that they all form Benzoyl-CoA (key metabolite in anaerobic conditions). After that we have a reductive ring cleavage. Eventually, formation of acetyl-CoA and then that’s metabolized in central pathway.

54
Q

What is the general pattern for ease of degradation?

A

N-alkanes -> Branched alkanes -> Low molecular weight aromatics (benzene) -> Cyclic alkanes (cyclohexane) -> high molecular weight aromatics (PAHs ex)

55
Q

What are the microorganisms involved in hydrocarbon degradation?

A

Pseudomonas, Corynebacterium, Mycobacterium, Oleispira, Oleiphilus, Thalassolituus, Alcanivorax, and Cycloclasticus

56
Q

Hydrocarbons:
Other substituted aromatics:
What are the substituents that make it easier for the substrate to be degraded?

A

Hydroxyl, amine, methyl, phenyl groups because they render the molecule more reactive for electrophilic reactions. These functional groups donate e- to the ring and higher e- density on the ring structure and the reactions like electrons, so reaction happens easier.

57
Q

Hydrocarbons:
Other substituted aromatics:
What are the substituents that make it harder for the substrate to be degraded?

A

Halogens (Br, Cl, Fl), nitro (NO2), and sulfonate (SO3) groups. The groups tend to deactivate molecule for electrophilic attack. They withdraw e- from aromatic ring.

58
Q

What are the four biodegradation mechanisms of chlorinated compounds?

A

-Nucleophilic displacement (hydrolysis)
-Reductive dechlorination: Happens under anaerobic conditions. removes HCl and then chlorine atom is removed.
-Oxygenation: Add oxygen, leads to hydroxylation and end up with catechol.
-Elimination: Elimination of HCl and formation of double bond. Each step we remove one chlorine atom and add double bond.

59
Q

Metabolism of halogenated aromatics:

A

Halogen atoms can be removed before the ring cleavage or after the ring cleavage. two possibilities

60
Q

What is a pesticide?

A

Any agent used to kill or control undesired insects, weeds, rodents, fungi, bacteria or other organisms.

61
Q

What are the two most common pesticides used?

A

Glyphosate and Atrazine. Both are herbicides. Glyphosate is the top used because it is round up used on crops. Mostly used on corn and soybeans and in the mid-west.

62
Q

What are the factors affecting the persistence of pesticides in soil?

A

-Chemicals: nature of the chemical determines toxicity, stability, and biodegradability. Concentration also matters. the higher the conc, the longer it takes for microbes to degrade.
-Microorganisms: the number of microbes and their activities are important. An example of microbes developing an ability to degrade a chemical that they have never seen before is with Aldicarb (highly toxic nematocide, as microbes figured out how to break it down quickly, called enhanced biodegradation)
-Environmental conditions: affects activity of microbes and rate of degradation. temperature, moisture, organic matter content, and clay content, and pH.

63
Q

How do we measure persistence of pesticides?

A

Using half life. This is the time period in which 50% of pesticides is degraded.

64
Q

For the first-order kinetics, what equation do we use?

A

t1/2 = ln (2/k)
t1/2 is supposed to have 1/2 tiny.

65
Q

What are the characteristics of 2,4-D?

A

It is the most used pesticide in the industrial sector.
-Systemic herbicide
-Selective (control rot leaf weeds)
-Acts as a growth regulator (at low conc, stimulate growth of plants, at high conc, inhibit growth)
-Moderate toxicity (oral LD50 = 300-100 mg/kg)
-Field half life is about 6 days. Doesn’t stay long in the soil. If organic matter is high, may stay in the soil for 8 days.
-Pka of 2.73… not absorbed by soil well.

66
Q

What is LD50?
For a chemical to be considered moderately toxic, what is the LD50 range?

A

A single dose of chemical that is required to kill 50% of test animals. Unit: mg/kg of animal body weight.
Range: 500-5000

67
Q

Describe the biodegradability of 2,4-D.

A

-Readily biodegradable and mineralized
-Catalyzed by monooxygenase
-Ortho ring cleavage
-Ring cleavage occurs BEFORE dichlorination.
-Degraded to succinate and acetyl-CoA, which enter TCA cycle.

68
Q

What is the structure of Atrazine?

A

Ring in structure. 3 Nitrogen atoms and 3 Carbon atoms, so heterocyclic aromatic ring. Only one chlorine atom as substituent. Used on corn in the mid-west.

69
Q

What are the characteristics of atrazine?

A

-Systemic
-Selective (controls rot weed & grass weed)
-Photosynthetic inhibitor
-LD50 = 51 mg/kg (tested on rats)
-Moderate toxicity
-Endocrine disruptor
-Drinking water standard is 3ppb, but at 0.1 ppb atrazine can turn male frogs into female frogs.
-Field half-lives, stays around longer than 2,4-D. Depending on conditions, can stay in soil from 60days -1 year

70
Q

What is an endocrine disruptor?

A

Chemicals that may interfere with the body’s endocrine system and produce adverse developmental, reproductive, neurological, and immune effects in both humans and wildlife.

71
Q

Describe the biodegradation of atrazine.

A

-Moderately biodegradable.
-Catalyzed by hydroxylases.
-Removal of chlorine atom via hydrolysis
-End product: cyanuric acid

72
Q

What are the atrazine degrading bacteria?

A

Pseudomonas strain ADP, Agrobacterium radiobacter, Rhodococcus species

73
Q

What is DDT?

A

-Organochlorine insecticide
-Has two aromatic rings connected to a C atom. This C connected to another C with 3 Cl connected to that C.
-Pretty resistant to biodegradation due to Cl atoms.
-The world health organization strongly endorsed the indoor spraying of DDT to control malaria carrying mosquitos in developing countries

74
Q

What are the characteristics of DDT?

A

-Non-systemic insecticide
-Mode of contact: Targets sodium balance of nerve membranes
-Toxicity: LD50 =217 mg/kg
-Endocrine disruptor
-Biomagnification: DDT is not water soluble (but is fat soluble!!) and is known for its biomagnification effect.
-Half-life = 10 years

75
Q

What is the most resistant to biodegradation out of all three chemicals?

A

DDT

76
Q

Which chemicals were introduced shortly after WWII?

A

2,4-D and DDT. DDT banned in 70s, 2,4-D still being used.

77
Q

Describe the transformation of DDT/

A

-Doesn’t transform easily. In aerobic conditions, it’s stable and stays in form of DDT
-Under anaerobic conditions, DDT can undergo elimination and dichlorination.
-Two minor metabolites: DDD and DDE (double bond in DDE)
-These two accumulate until there are aerobic conditions, then ring cleavage can happen. Ring cleavage does not occur under anaerobic conditions. Cometabolism occurs under aerobic conditions.

78
Q

Trichloroethylene and perochloroethylene. What are they?

A

-Both are chlorinated ethylenes.
-Belong to a group of organic pollutants called Volatile organic chemicals (VOCs) and are chlorinated.
-Perochloroethylene harder to degrade.

79
Q

What is the density for TCE? How about PCE?

A

-TCE: 1.46 g/ml
-PCE: 1.62
Both have higher density than water

80
Q

Why is there such a build up of TCE and PCE?

A

Used in degreasing (80% TCE) and dry cleaning (60% PCE).

81
Q

What is the oral LD50 (rats) for TCE?
What about PCE?

A

LD50 = 4920 mg/kg
LD50 = 2629 mg/kg
-potential human carcinogen
-liver damage

82
Q

Under aerobic conditions, Is PCE biodegradable? How about TCE?

A

-PCE is nonbiodegradable
-TCE can be cometabolized

83
Q

Cometabolic degradation of TCE under aerobic conditions:

A

-MOase used in initial step.
-TCE epoxide intermediate
-Intermediate can bind to MOase and other molecules spontaneously OR can be modified to TCE diol and Dichoroacetic acid.

84
Q

What are the organisms that can carry out cometabolism of TCE?

A

-Methanotrophs (use methane as C source) (use methane monooxygenase)
-Aromatic degraders: use monooxygenase and transform TCE. Ex: Pseudomonas cepacia G4
-Ammonia oxidizers: use ammonia oxygenase

85
Q

Anaerobic conditions:
PCE and TCE can undergo?

A

Anaerobic respiration or cometabolic process.

86
Q

Anaerobic degradation pathway for PCE:

A

PCE transformed to TCE. TCE, under mild reducing conditions, transformed to isomers of DCE. Then, under strong reducing conditions, transformed to vinyl chloride. Under more strong reducing conditions, transformed to ethylene.

87
Q

When is there high redox potential with the mild and strong reducing conditions of the anaerobic degradation pathway for PCE?

A

Higher redox potential for mild reducing conditions.
Lower redox potential under strong reducing conditions

88
Q

For Anaerobic degradation, what organisms are involved?

A

-Mixed cultures of bacteria
-Pure culture: Dehalococcoides ethenogenes…. This organism uses an electron donor: H2 and electron acceptor: PCE
-Cometabolism by methanogens (anaerobes that produce methane)

89
Q

PCBs

A

Most resistant out of all chemicals
half life: 10-80 years
-exists as big mixture and is chemically inert