GATE Environmental Engineering Environmental Microbiology Syllabus

What are the main phases and microbial groups in anaerobic digestion?

Hydrolysis (breaks polymers to monomers), acidogenesis (to VFAs), acetogenesis (to acetate, $\ce{H2}$, $\ce{CO2}$), and methanogenesis (to $\ce{CH4}$). Methanogens are archaea; the final step yields biogas: $\ce{CH4 + CO2}$.

What is bioremediation and what are its two broad categories?

Bioremediation is the use of microorganisms (or plants) to degrade, transform, or immobilize environmental contaminants. Categories: in situ (treated in place, e.g., bioventing, biosparging) and ex situ (excavated/pumped and treated, e.g., landfarming, bioreactors).

Distinguish biostimulation from bioaugmentation in bioremediation.

Biostimulation adds nutrients (N, P), electron acceptors, or oxygen to enhance the activity of indigenous microbes. Bioaugmentation introduces specialized exogenous microbial strains capable of degrading the target contaminant.

What is phytoremediation and name three of its mechanisms.

Phytoremediation uses plants (with associated microbes) to clean contaminated soil/water. Mechanisms include phytoextraction (uptake/accumulation of metals in shoots), phytodegradation (breakdown in tissues), rhizodegradation (microbial breakdown in the rhizosphere), and phytostabilization.

What is cometabolism in the context of pollutant degradation?

Cometabolism is the transformation of a non-growth substrate (the pollutant) by an enzyme produced for metabolizing a different primary growth substrate. The microbe gains no carbon or energy benefit from degrading the pollutant (e.g., TCE degradation via methane monooxygenase).

List the main reservoirs and microbial transformations of the nitrogen cycle.

Nitrogen fixation ($\ce{N2 -> NH3}$), assimilation, ammonification (organic $\ce{N -> NH4^+}$), nitrification ($\ce{NH4^+ -> NO2^- -> NO3^-}$), denitrification ($\ce{NO3^- -> N2}$), and anammox ($\ce{NH4^+ + NO2^- -> N2}$).

Describe the key microbial transformations in the sulfur cycle.

Sulfate reduction ($\ce{SO4^{2-} -> H2S}$) by sulfate-reducing bacteria under anoxic conditions; sulfur oxidation ($\ce{H2S -> S^0 -> SO4^{2-}}$) by chemolithotrophs like $\textit{Thiobacillus}$; and assimilatory uptake of sulfate into amino acids (cysteine, methionine).

What is the anammox process and why is it significant for wastewater nitrogen removal?

Anammox (anaerobic ammonium oxidation) is the anoxic conversion of ammonium and nitrite directly to $\ce{N2}$: $\ce{NH4^+ + NO2^- -> N2 + 2H2O}$. It removes nitrogen without organic carbon or oxygen for the final step, saving aeration energy compared to conventional nitrification-denitrification.

What are the four levels of protein structure?

Primary (linear amino acid sequence, peptide bonds), secondary (local folding: $\alpha$-helices and $\beta$-sheets via hydrogen bonds), tertiary (overall 3D fold of one polypeptide), and quaternary (assembly of multiple polypeptide subunits).

What bond links amino acids in a protein, and how does it form?

The peptide bond, an amide linkage formed by a condensation (dehydration) reaction between the $\alpha$-carboxyl group of one amino acid and the $\alpha$-amino group of the next, releasing one water molecule: $\ce{-COOH + H2N- -> -CO-NH- + H2O}$.

What stabilizes the secondary structures of proteins?

Hydrogen bonds between the backbone carbonyl oxygen ($\ce{C=O}$) and the amide hydrogen ($\ce{N-H}$) of nearby residues. In the $\alpha$-helix the H-bond is between residues $i$ and $i+4$; in $\beta$-sheets H-bonds form between adjacent strands.

State the base-pairing rules and the bonding in DNA's double helix.

Adenine pairs with thymine via 2 hydrogen bonds; guanine pairs with cytosine via 3 hydrogen bonds. The two antiparallel strands are held by these H-bonds and stabilized by base stacking; the sugar-phosphate backbone is linked by phosphodiester bonds.

What are the key structural differences between DNA and RNA?

DNA: deoxyribose sugar, thymine, usually double-stranded, stable. RNA: ribose sugar (extra $2'$-OH), uracil instead of thymine, usually single-stranded, less stable. Both have a phosphodiester backbone and read $5' \to 3'$.

Name the three main components of a nucleotide.

A nucleotide consists of (1) a pentose sugar (ribose or deoxyribose), (2) a phosphate group, and (3) a nitrogenous base (purine: adenine/guanine; or pyrimidine: cytosine/thymine/uracil).

What is the general structure of a triglyceride (fat)?

A triglyceride is a glycerol molecule esterified with three fatty acid chains. It forms via three condensation (ester-bond) reactions, releasing three water molecules. It is the main energy-storage lipid.

What is the difference between saturated and unsaturated fatty acids?

Saturated fatty acids have no carbon-carbon double bonds (straight chains, solid at room temperature). Unsaturated fatty acids have one ($cis$/$trans$) or more $\ce{C=C}$ double bonds, introducing kinks that lower the melting point (often liquid oils).

What structural feature makes phospholipids amphipathic and suited to membranes?

A phospholipid has a hydrophilic phosphate-containing head and two hydrophobic fatty-acid tails. This amphipathic nature drives self-assembly into bilayers in water, with heads facing outward and tails inward, forming the basis of cell membranes.

Distinguish storage polysaccharides from structural polysaccharides with examples.

Storage: starch (amylose + amylopectin, $\alpha$-glucose) in plants and glycogen in animals/microbes. Structural: cellulose ($\beta$-1,4 glucose) in plant walls and chitin (N-acetylglucosamine) in fungal walls. The glycosidic linkage type ($\alpha$ vs $\beta$) determines digestibility and rigidity.

What bond joins monosaccharides, and how do $\alpha$- and $\beta$-1,4 linkages differ functionally?

The glycosidic bond, formed by condensation between two sugar hydroxyl groups. $\alpha$-1,4 linkages (starch, glycogen) coil and are easily hydrolyzed; $\beta$-1,4 linkages (cellulose) form straight, rigid chains that most organisms cannot digest without cellulase.

List the four major types of bonds/interactions found in biomolecules and rank their relative strength.

From strongest to weakest: covalent bonds (peptide, phosphodiester, glycosidic, ester) $\gg$ ionic bonds > hydrogen bonds > van der Waals forces. Hydrophobic interactions also contribute to folding. Weak non-covalent forces collectively determine 3D structure.

Why are weak non-covalent interactions critical to biomolecular function?

Though individually weak ($\sim 1$–$30\,\text{kJ/mol}$), their large number provides specificity and stability while remaining reversible. This reversibility enables enzyme-substrate binding, DNA strand separation, and protein folding/unfolding under physiological conditions.

What is a chiral center and why is stereoisomerism important in biomolecules?

A chiral (asymmetric) carbon has four different substituents, producing non-superimposable mirror images (enantiomers). Biological systems are stereospecific: enzymes recognize only one configuration, so chirality controls activity (e.g., L-amino acids, D-sugars).

Which stereoisomeric forms of amino acids and sugars predominate in living systems?

Proteins are built almost exclusively from L-amino acids, while naturally occurring sugars are predominantly in the D-configuration (e.g., D-glucose). This biological homochirality is essential for consistent macromolecular structure and enzyme recognition.

Differentiate enantiomers, diastereomers, and epimers.

Enantiomers are non-superimposable mirror images (all chiral centers inverted). Diastereomers are stereoisomers that are not mirror images (some but not all centers differ). Epimers are diastereomers differing in configuration at exactly one chiral center (e.g., glucose vs galactose).

List the essential structural components common to a bacterial cell.

Cell wall, cytoplasmic (plasma) membrane, cytoplasm, nucleoid (DNA), 70S ribosomes, and inclusions. Variable/non-essential structures include capsule, flagella, pili/fimbriae, plasmids, and endospores.

Describe the structure and core function of the cytoplasmic (plasma) membrane.

It is a phospholipid bilayer with embedded proteins (fluid mosaic model), about $7$–$8\,\text{nm}$ thick. It is selectively permeable, controlling transport in/out of the cell, and in bacteria also hosts the electron transport chain for energy (ATP) generation.

How do Gram-positive and Gram-negative cell walls differ structurally?

Gram-positive: thick peptidoglycan layer ($20$–$80\,\text{nm}$) with teichoic acids, no outer membrane; retains crystal violet (stains purple). Gram-negative: thin peptidoglycan plus an outer membrane containing lipopolysaccharide; loses crystal violet, counterstains pink with safranin.

What is peptidoglycan and what is its function in the bacterial cell wall?

Peptidoglycan (murein) is a polymer of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by short peptide bridges. It forms a rigid mesh that provides mechanical strength and resists osmotic lysis. It is the target of penicillin and lysozyme.

What is the structure of the Gram-negative outer membrane, and what is the role of LPS?

The outer membrane is an asymmetric bilayer: phospholipids on the inner leaflet and lipopolysaccharide (LPS) on the outer leaflet, with porin channels for solute passage. LPS (lipid A = endotoxin, core, O-antigen) acts as a permeability barrier and triggers immune/endotoxic responses.