Biodegradation and Bioremediation Exam 4 - Final Exam

Question 1

What are the processes that control the fate of pollutants?

Answer 1

-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*

Question 2

Abiotic degradation vs. Microbial degradation

Answer 2

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).

Question 3

What is biodegradation?

Answer 3

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

Question 4

What is transformation?

Answer 4

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.

Question 5

What is mineralization (or ultimate biodegradation)?

Answer 5

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.

Question 6

What is cometabolism?

Answer 6

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

Question 7

What is bioremediation?

Answer 7

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).

Question 8

What does anthropogenic mean?

Answer 8

Produced by humans.

Question 9

What does Xenobiotic mean?

Answer 9

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

Question 10

What is bioaccumulation?

Answer 10

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

Question 11

What does biomagnification mean?

Answer 11

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.

Question 12

What is bioavailability?

Answer 12

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.

Question 13

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?

Answer 13

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.

Question 14

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

Answer 14

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

Question 15

What is the NPL?

Answer 15

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

Question 16

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

Answer 16

The structure of organic compounds.

Question 17

Classification of organic compounds:
What are functional groups?

Answer 17

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

Question 18

What are examples of ring structures?

Answer 18

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.

Question 19

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

Answer 19

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.

Question 20

What are the different classes of organic compounds?

Answer 20

1. Hydrocarbons
2. Organic compounds containing oxygen
3. Organic compounds containing nitrogen
4. Other

Question 21

What are the different types of hydrocarbons?

Answer 21

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.

Question 22

What are the different organic compounds containing oxygen?

Answer 22

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

Question 23

What are the different organic compounds containing nitrogen?

Answer 23

Amines, amides, nitriles (has triple bond)

Question 24

What are the “other” classified organic compounds?

Answer 24

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

Question 25

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

Answer 25

12. Called the "dirty dozen" Ex: DDT, Mirex, Aldrin, Hexachlorobenzene

Question 26

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

Answer 26

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.

Question 27

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

Answer 27

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

Question 28

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

Answer 28

Glycolysis and TCA cycle

Question 29

What are the two intermediate products produced in glycolysis?

Answer 29

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

Question 30

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

Answer 30

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.

Question 31

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

Answer 31

Carbon cycle in the natural ecosystem.

Question 32

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

Answer 32

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

Question 33

Describe glycolysis and what is generated in the pathway.

Answer 33

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.

Question 34

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

Answer 34

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.

Question 35

Central Metabolism: Peripheral pathways.

Answer 35

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.

Question 36

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

Answer 36

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

Question 37

What are examples of hydrocarbons?

Answer 37

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

Question 38

What is the smallest aromatic hydrocarbon?

Answer 38

Benzene (single ring structure) (is unsaturated)

Question 39

How do microbes break down alkanes?

Answer 39

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

Question 40

What are monooxygenases? What are diooxygenases?

Answer 40

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.

Question 41

Are all alkanes degraded at the same rate?

Answer 41

NO!

Question 42

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

Answer 42

n-Alkanes of intermediate chain length (C10-C24) are degraded most rapidly. Short-chain alkanes (500) have low water solubility and are not easily absorbed by microbial cells. More resistant to degradation.

Question 43

Does branching reduce biodegradation rate?

Answer 43

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

Question 44

Cycloalkanes: Cyclohexane degradation.

Answer 44

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.

Question 45

Aromatic hydrocarbons: What are the two examples given?

Answer 45

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

Question 46

Aerobic metabolism: Describe Benzene biodegradation.

Answer 46

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.

Question 47

What are Alkyl-substituted benzenes?

Answer 47

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.

Question 48

What is the smallest PAH molecule?

Answer 48

Naphthalene. It has the fewest benzene rings.

Question 49

What happens in the Naphthalene Degradation pathway?

Answer 49

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

Question 50

General theme of aerobic metabolism and degradation pathways is...?

Answer 50

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

Question 51

What are the different kinds of oxygenases?

Answer 51

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

Question 52

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

Answer 52

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.

Question 53

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

Answer 53

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.

Question 54

What is the general pattern for ease of degradation?

Answer 54

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

Question 55

What are the microorganisms involved in hydrocarbon degradation?

Answer 55

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

Question 56

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

Answer 56

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.

Question 57

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

Answer 57

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.

Question 58

What are the four biodegradation mechanisms of chlorinated compounds?

Answer 58

-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.

Question 59

Metabolism of halogenated aromatics:

Answer 59

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

Question 60

What is a pesticide?

Answer 60

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

Question 61

What are the two most common pesticides used?

Answer 61

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.

Question 62

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

Answer 62

-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.

Question 63

How do we measure persistence of pesticides?

Answer 63

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

Question 64

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

Answer 64

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

Question 65

What are the characteristics of 2,4-D?

Answer 65

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.

Question 66

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

Answer 66

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

Question 67

Describe the biodegradability of 2,4-D.

Answer 67

-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.

Question 68

What is the structure of Atrazine?

Answer 68

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.

Question 69

What are the characteristics of atrazine?

Answer 69

-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

Question 70

What is an endocrine disruptor?

Answer 70

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

Question 71

Describe the biodegradation of atrazine.

Answer 71

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

Question 72

What are the atrazine degrading bacteria?

Answer 72

Pseudomonas strain ADP, Agrobacterium radiobacter, Rhodococcus species

Question 73

What is DDT?

Answer 73

-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

Question 74

What are the characteristics of DDT?

Answer 74

-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

Question 75

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

Answer 75

DDT

Question 76

Which chemicals were introduced shortly after WWII?

Answer 76

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

Question 77

Describe the transformation of DDT/

Answer 77

-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.

Question 78

Trichloroethylene and perochloroethylene. What are they?

Answer 78

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

Question 79

What is the density for TCE? How about PCE?

Answer 79

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

Question 80

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

Answer 80

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

Question 81

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

Answer 81

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

Question 82

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

Answer 82

-PCE is nonbiodegradable -TCE can be cometabolized

Question 83

Cometabolic degradation of TCE under aerobic conditions:

Answer 83

-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.

Question 84

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

Answer 84

-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

Question 85

Anaerobic conditions: PCE and TCE can undergo?

Answer 85

Anaerobic respiration or cometabolic process.

Question 86

Anaerobic degradation pathway for PCE:

Answer 86

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.

Question 87

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

Answer 87

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

Question 88

For Anaerobic degradation, what organisms are involved?

Answer 88

-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)

Question 89

PCBs

Answer 89

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