Biochemistry and Enzymology

Enzymology
• “Every chemical reaction by living things is
catalyzed by enzymes”
• What are Enzymes?
• Enzymes= Apoenzymes+ Coenzymes/cofactors
• Complex structure (primary, secondary, etc
• Efficient/specific
• Reduce the activation energy barrier
 Enzymes
• Enzyme acivity is affected by several factors
• Concentration of enzymes/substrates
• pH, temperature, cations (eg Ca)
• Inhibition (positive/negative)
• Feed back/End product inhibition (positive)
• Denaturation (negative)
 Naming and Classification
• Traditional adding “ase” to the substrate
• Modern numbering (according to the enzyme
convention)
• Grouped into four categories
• Oxidoreductase, hydrolases, isomerases,
Synthases
 Naming and classification
• Oxido-reductases=oxidation reduction
reactions
• Fe2+ Fe3+
• Hydrolases (deploymerization) +water

• C-C-C-C-C C-C Co2

• Synthatase (the opposite)-water
• Polymerization
 Paming and Classification
• Isomerization
• changing one isomer to the other
• Glucose--fructose
• Galactose-fructose,glucose
• Epimerization
• Change the orientation of functional groups
• D-amino acid---to L amino acid
 Important soil enzymes
• Many enzymes
• Cellulase, lignin degrading enzymes
• Phosphatases (Phytate)
• Urease
• These enzymes are also soil fertility indicators
CHAPTER II: Biogeochemical cycles

Carbon cycle and Nitrogen cycle

• Microorganisms are “nature’s garbage disposal”
• They convert organic carbon to CO2
• Complete the biological cycle that was initiated
during photosynthesis
• is the driving force behind nearly all of the nutrient
cycling
 Carbon cycle
• These include the nitrogen, sulfur, and
phosphorus cycles
• Global carbon cycles are closely tied to
biological productivity
• soil organic matter (SOM) turnover
Table: Constituents of Carbon organic residues
No Residues Composition Microorganisms
% DW
1 Cellulose 15-60 Clostridium,
Streptomyces,
Trichoderma,
Chaetomium
Penicillum
2 Hemicellulose 10-30 Fungi
Actinomycetes,
Mycorrhizas
3 Lignin 5-30 Fungi, white rot
fungi
4 Protein 2-15 many
5 Soluble substances 10 many
(sugars amino acids
 Cellulose
• It is a polymer of glucose/cellobiose
• Represents more than half of plant residue
carbon
• Component of algal and fungal cell walls
• A molecular weight of 1 million
• Microbial decomposition is by
depolymerization
• Highly polymerized cellulose (cotton)------
Paper-----------Carboxylmethylcellulose
 Cellulose
• Cellulase has three components
• Endoglucanase, cleave randomly
• Exoglucanase cleave 1 or 2 units from the non
reducing part of the molecule
• Its depolymerization is difficult
• For it is often associated with hemicellulose
and lignin
• Soil Animals involve in the process?
 Pathways of cellulosis
• C-C-C-C-C-C-C...............
• Cellulase system
• Exocellulase, Endocellulase, B-glycosidase
• Exocellulase breaks the ploymer at the outer
part to give oligosaccharides
• C-C-C-C-C, C-C-C-C, C-C-C-C-C-C-
 Cellulolysis
• Endoglucanase breaks them into two carbon
• C-C, C-C C-C, C-C(cellobiose)
• B-glycosidase beaks the Cellobisose into
glucose
• C-C C
• Only fewer organisms contain all of them
• So microorganisms work in a team
 Cellulolysis
• Obligatory celluloytic bacteria
• Bacteroids, Cytophaga
• Others (Pseudomonas, Bacillus)
• Fungi (Fungi imperfecti)
• Penicillum, Trichoderma, Aspergillus,
Chetomium, Helminthosporium, Fusarium
• Many (?) (storage fungi, field fungi etc
 Hemicellulose
• They are polymers of hexoses, pentoses,and
uronic acids
• Constitute up to 1/3rd of plant residue carbon
• Pectin is a polymer of galacto-uronic acid with
MW (400,000)
• Has an important structural role in plants
• Key component of plant cell walls
 Cont…
• The decomposition 3-stage process
• Pectin esterases, depolymerases/oxidases
• The enzyme system is repressed by high sugar
level in fresh residues
• Arthrobacter, Pseudomonas, Bacillus ,
Streptomyces, many soil fungi
• Pectinases are involved in the penetration of
plants (Rhizobium, Mycorrhiza, pathogens)
 Lignin
• The most resistant component of plant
residues
• It is the 3rd most abundant carbohydrate
• MW , 10,00-1,000,000
• A complex non-uniform polymer of aromatic
nuclei
• Building block of phenyl-propane (C6C3)
 cont…
• The random structure and strong linkages
• Make lignin very resistant to microbial/and
other decomposition process
• The decomposition is a three-stage process
• Esterification of the methoxyl group
• Depolymerization process/splitting of phenol
• Oxidation of the linear molecules
• A very limited microrganisms degrade the
entire molecule
 Lignin degradation…
• The degradation is similar to biodegradation
of pesticides/agrochemicals
• Only few groups of bacteria and fungi are
involved
• Pseudomonas, Bacillus, root-rot fungus
(Panorochaete chrysogenum)
• Selected and Genetically modified microbes
are commercialized for waste treatment
 Degeradation of hydrocarbons
• Hydrocarbons are organic compounds
containing carbon, hydrogen
• They are classified as saturated, unsaturated
and aromatic hydrocarbons.
• Alkanes (normal, branched and cyclic
paraffins), aromatics, and polycyclic
hydrocarbons
• They are organic pollutants of groundwater,
soil and air
Hydrocarbon degrdation
 Hydrocarbon....
• Who is who in degradation ?
• All major groups are involved
• Bacteria are the dominant ones.
• Eg. Actinobacter, Alcaligenes spp,
Mycobacterium spp., Arthrobacter spp.,
Bacillus, Corynebacterium spp., Micrococcus
spp., Flavobacter spp., Nocardia spp, and
Pseudomonas
 Biodegradation
• Individual bacteria can metabolize only a
limited range of hydrocarbon substrates
• Bacterial consortium with broad enzymatic
capacities is required to synergistically
degrade complex mixtures of pollutant
• Eg. consortia of Bacillus sp., Pseudomonas sp.
and Micrococcus sp. showed maximum
degradation of diesel and benzene.
Biochemistry of degradation
Biochemistry of degradation
Biodegradation of benzene, toluene,
ethylbenzene, and xylene
 Summary
• Biodegradation of hydrocarbons involve
different commuities of bacteria working
together
• For complete microbial-degradation involve
1) Multiple pathways
2) oxidoreductase enzymes (including
monooxygenases, dioxygenases, peroxidases
and laccases)
3) occur either aerobically or anaerobically