GATE Biotechnology Bioprocess Engineering and Process Biotechnology Syllabus

Name the phases of microbial growth in a batch culture in order.

Lag phase, exponential (log) phase, deceleration phase, stationary phase, and death (decline) phase.

Define the biomass yield coefficient $Y_{X/S}$ and product yield $Y_{P/S}$.

$Y_{X/S} = -\dfrac{dX}{dS} = \dfrac{\text{mass of cells produced}}{\text{mass of substrate consumed}}$; $Y_{P/S} = -\dfrac{dP}{dS} = \dfrac{\text{mass of product formed}}{\text{mass of substrate consumed}}$.

Write the substrate-utilization equation including growth and maintenance terms.

$$-\frac{dS}{dt} = \frac{1}{Y_{X/S}}\frac{dX}{dt} + \frac{1}{Y_{P/S}}\frac{dP}{dt} + m X$$ where $m$ is the maintenance coefficient (substrate used for cell upkeep, not growth).

State the Luedeking–Piret model for product formation and define its constants.

$$\frac{1}{X}\frac{dP}{dt} = q_P = \alpha\mu + \beta$$ $\alpha$ = growth-associated coefficient, $\beta$ = non-growth-associated coefficient. Growth-associated ($\beta=0$), mixed, or non-growth-associated ($\alpha=0$).

Classify ethanol, lactic acid, penicillin, and primary vs secondary metabolites by growth association.

Growth-associated (primary metabolites, e.g., ethanol, lactic acid) form during exponential growth. Non-growth-associated (secondary metabolites, e.g., penicillin, many antibiotics) form mainly during the stationary phase.

Distinguish structured and unstructured kinetic models of cell growth.

Unstructured models treat biomass as a single homogeneous component (one variable, e.g., Monod). Structured models divide the cell into multiple components/compartments (RNA, protein, etc.), accounting for internal composition and physiological state.

Distinguish segregated and non-segregated (distributed) cell models.

Segregated models treat the population as a collection of discrete, heterogeneous individual cells. Non-segregated (distributed) models treat cells as an average uniform population (lumped). Combined with structured/unstructured this gives four model classes.

Compare batch, fed-batch, and continuous bioprocesses by feed/withdrawal.

Batch: all nutrients added at start, no feed/withdrawal during run. Fed-batch: substrate fed during run, no withdrawal (volume increases). Continuous: substrate fed and broth withdrawn continuously at steady state (constant volume).

State the main advantage of fed-batch operation over batch.

Controlled substrate feeding avoids substrate inhibition and catabolite (e.g., glucose/Crabtree) repression, allowing high cell densities and prolonged production of secondary metabolites while keeping substrate low.

For a steady-state chemostat (CSTR, sterile feed, no death), relate specific growth rate to dilution rate.

At steady state $\mu = D$. The growth rate self-adjusts to match the dilution rate; the cell mass balance $\dfrac{dX}{dt}=(\mu-D)X=0$ gives $\mu=D$.

Give the steady-state chemostat expressions for residual substrate $\bar S$ and biomass $\bar X$.

$$\bar S = \frac{K_S D}{\mu_{max}-D}, \qquad \bar X = Y_{X/S}\,(S_0 - \bar S)$$ valid for $D < \mu_{max}$.

Define washout in a chemostat and give the critical dilution rate.

Washout is loss of all cells when $D$ exceeds the maximum achievable growth rate. Critical dilution rate: $$D_{crit} = \mu_{max}\frac{S_0}{K_S + S_0} \approx \mu_{max}\ (S_0 \gg K_S)$$

Write the expression for biomass productivity in a chemostat and note its optimum.

Productivity $= D\bar X = D\,Y_{X/S}(S_0-\bar S)$. It passes through a maximum at an optimum dilution rate $$D_{opt} = \mu_{max}\left(1 - \sqrt{\frac{K_S}{K_S + S_0}}\right)$$

What is a turbidostat and how does it differ from a chemostat?

A turbidostat is a continuous culture that holds cell density (turbidity) constant by adjusting the feed/dilution rate in response to optical density. A chemostat instead holds the dilution rate (and hence a limiting nutrient) constant.

Distinguish microbial reactors from enzyme reactors.

Microbial (cell/fermenter) reactors grow living cells that self-replicate and carry out reactions with growth kinetics (Monod). Enzyme reactors use isolated (often immobilized) enzymes — no growth — following Michaelis–Menten kinetics.

Write the Michaelis–Menten equation used in enzyme reactor design.

$$v = \frac{V_{max}[S]}{K_M + [S]}$$ where $v$ is reaction rate, $V_{max}$ the maximum rate, $K_M$ the Michaelis constant ($[S]$ at $v = V_{max}/2$).

Name three common configurations of immobilized-enzyme reactors.

Packed-bed (fixed-bed) reactor, continuous stirred-tank (CSTR) reactor, and fluidized-bed reactor (also membrane reactors).

What is the goal of bioprocess scale-up and name common scale-up criteria.

Goal: reproduce lab/pilot performance at production scale. Common criteria kept constant: volumetric power input $P/V$, $k_La$ (oxygen transfer), impeller tip speed, and mixing time. Usually only one can be held constant at a time.

Why can't geometric similarity plus constant impeller speed maintain all parameters during scale-up?

Quantities like $P/V$, tip speed ($\pi N D$), Reynolds number, and mixing time scale differently with vessel size $D$. Holding one constant forces the others to change, so a compromise criterion (commonly constant $P/V$ or $k_La$) is chosen.

Define the volumetric oxygen transfer rate (OTR) equation.

$$\text{OTR} = k_L a\,(C^* - C_L)$$ where $k_L a$ is the volumetric mass-transfer coefficient, $C^*$ the saturation dissolved-oxygen concentration, and $C_L$ the bulk DO. At steady state OTR equals the oxygen uptake rate (OUR).

What is the purpose of media formulation, and what are the major nutrient categories required?

To supply all nutrients for growth and product formation economically. Categories: carbon source, nitrogen source, minerals/trace elements, growth factors/vitamins, plus oxygen (aerobic) and a buffer; defined (synthetic) vs complex media.

Distinguish defined (synthetic) and complex media.

Defined media have all chemical components in known concentrations (reproducible, costly, lower yields). Complex media use ingredients of unknown exact composition (e.g., yeast extract, peptone, corn-steep liquor) — cheaper and richer but variable and harder to analyze.

Name two statistical/experimental approaches used for media optimization.

Plackett–Burman design (screening of significant factors) and Response Surface Methodology (RSM) such as central composite or Box–Behnken designs for optimizing levels; also one-factor-at-a-time (OFAT) as a basic method.

Why is sterilization of media and air essential in fermentation, and what does asepsis prevent?

To eliminate contaminating microorganisms that compete for nutrients, degrade product, or produce toxins, ensuring a pure (axenic) culture. Asepsis maintains the desired organism alone and prevents spoilage and process failure.

Compare batch and continuous sterilization of media.

Batch sterilization heats the whole vessel (e.g., $121\,^{\circ}\text{C}$) then cools — simpler but slow, with more nutrient damage. Continuous sterilization passes media through a high-temperature short-time heat exchanger — less nutrient damage, energy efficient, suited to large scale.

State the thermal death (Del) factor used to design heat sterilization.

$$\nabla = \ln\frac{N_0}{N} = \int_0^t k_d\,dt$$ where $N_0,N$ are initial/final spore numbers and $k_d$ the death-rate constant; sterilization follows first-order (logarithmic) death kinetics.

Give the Arrhenius dependence of the thermal death-rate constant and its design implication.

$$k_d = A\,e^{-E_d/RT}$$ Because spore death has a high activation energy $E_d$ relative to nutrient degradation, high-temperature short-time (HTST) treatment kills spores while minimizing nutrient loss.

How is process air sterilized for aerobic fermentation, and by what mechanism does the filter work?

By passing through depth or membrane (HEPA) fiber filters. Mechanisms: inertial impaction, interception, diffusion (Brownian), and electrostatic attraction capture microbes — not simple sieving — so submicron particles are removed.

Distinguish absolute (membrane) filters from depth filters for air/media sterilization.

Absolute/membrane filters have defined pore size (e.g., $0.22\,\mu\text{m}$) removing all larger particles by sieving. Depth filters use a thick fibrous bed capturing particles throughout the depth by impaction/diffusion; rated nominally, not absolutely.

In dead-end vs cross-flow (tangential) filtration, how does the feed move relative to the membrane?

Dead-end: feed flows perpendicular to the membrane, all solids accumulate as a cake (good for low solids). Cross-flow: feed flows tangentially across the membrane, sweeping the surface to limit cake buildup — used for cell harvesting/microfiltration of broths.