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Biochemistry and Microbial Biotechnology

B.Sc. 2nd Year | MB 201 | Complete Theory Notes

Course: Biochemistry and Microbial Biotechnology

Course No.: MB 201 (Major)

Full Marks: 100

Pass Marks: 35

Nature: Theory

Total Lecture Hours: 150

Note: These notes focus on theory. Practical MB 202 is not included.

Contents

1. Living Cell and Biochemical Functions 2. Macromolecules and Biomolecules 3. Enzymes and Enzyme Kinetics 4. Microbial Metabolism 5. Microbial Genetics 6. Concept of Biotechnology 7. Fermentation Process 8. Agricultural Microbial Biotechnology 9. Biotechnology in Dairy Industry 10. Methods in Genetic Engineering 11. Enzyme Technology 12. Exam Revision and Important Questions

1. Living Cell and Understanding of Its Biochemical Functions

1.1 Biochemistry

Biochemistry is the branch of science concerned with the chemical substances, chemical reactions and molecular processes occurring within living organisms.

Relationship of Biochemistry with Other Sciences

Elements of Life

The major elements of living organisms are carbon, hydrogen, oxygen, nitrogen, phosphorus and sulfur.

Important mineral elements include sodium, potassium, calcium, magnesium, iron and chlorine, together with various trace elements.

Organic Compounds of Living Cells

Water: The Solvent of Life

Cell Biomembrane

Biomembranes consist mainly of phospholipids and proteins arranged according to the fluid mosaic model.

Cell membrane ↓ Phospholipid bilayer ↓ Membrane proteins ↓ Carbohydrates + Cholesterol ↓ Selective permeability ↓ Transport + Recognition + Communication ↓ Cellular homeostasis

Functions of Biomembrane

Important questions: Explain the fluid mosaic model. Discuss the functions of biomembrane. Explain the importance of water in living organisms.
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2. Macromolecules and Biomolecules

2.1 Carbohydrates

Carbohydrates are polyhydroxy aldehydes or ketones, or substances that yield these compounds upon hydrolysis.

Classification

Class Examples
Monosaccharides Glucose, fructose, ribose
Disaccharides Sucrose, lactose, maltose
Polysaccharides Starch, glycogen, cellulose

Functions

2.2 Amino Acids

Amino acids are the basic structural units of proteins.

General structure: H | H2N - C - COOH | R

2.3 Proteins

Proteins are polymers of amino acids joined by peptide bonds.

Levels of Protein Structure

  1. Primary structure
  2. Secondary structure
  3. Tertiary structure
  4. Quaternary structure

2.4 Lipids

Lipids are relatively water-insoluble organic compounds that are generally soluble in non-polar solvents.

2.5 Nucleic Acids

DNA and RNA are nucleic acids responsible for storage, transmission and expression of genetic information.

DNA RNA
Deoxyribose Ribose
Thymine Uracil
Usually double stranded Usually single stranded
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3. Enzymes and Enzyme Kinetics

Enzymes are biological catalysts that increase the rate of biochemical reactions without being consumed.

3.1 Classification of Enzymes

  1. Oxidoreductases
  2. Transferases
  3. Hydrolases
  4. Lyases
  5. Isomerases
  6. Ligases

3.2 Cofactor and Coenzyme

3.3 Isoenzymes

Isoenzymes are different molecular forms of an enzyme that catalyze the same reaction.

3.4 Enzyme-Substrate Reaction

E + S ↓ ES complex ↓ E + P

3.5 Michaelis-Menten Equation

v = Vmax[S] / (Km + [S])

Km is the substrate concentration at which the reaction velocity reaches half of Vmax.

3.6 Factors Affecting Enzyme Activity

3.7 Enzyme Inhibition

Type Km Vmax
Competitive Increases Unchanged
Non-competitive Unchanged in ideal case Decreases
Uncompetitive Decreases Decreases
Memory trick: Competitive inhibition → "Km changes, Vmax stays."
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4. Microbial Metabolism

Metabolism is the complete set of chemical reactions occurring inside a living cell.

4.1 Catabolism and Anabolism

Catabolism Anabolism
Breakdown of complex molecules Synthesis of complex molecules
Usually releases energy Usually requires energy
Produces ATP and reducing equivalents Uses ATP and reducing equivalents

4.2 Exergonic and Endergonic Reactions

4.3 ATP as Energy Currency

Nutrients ↓ Catabolism ↓ NADH + FADH2 ↓ Electron transport ↓ Proton gradient ↓ ATP synthase ↓ ATP ↓ Cellular work + Biosynthesis

4.4 Glycolysis / EMP Pathway

Glycolysis is a ten-step pathway in which one glucose molecule is converted into two molecules of pyruvate. It occurs in the cytosol and does not directly require oxygen. :contentReference[oaicite:1]{index=1}

Complete Glycolytic Pathway

1. Glucose ↓ [Hexokinase / Glucokinase] ATP → ADP ↓ 2. Glucose-6-phosphate ↓ [Phosphoglucose isomerase] ↓ 3. Fructose-6-phosphate ↓ [Phosphofructokinase-1] ATP → ADP ↓ 4. Fructose-1,6-bisphosphate ↓ [Aldolase] ↓ 5. DHAP + Glyceraldehyde-3-phosphate ↓ [Triose phosphate isomerase] ↓ 6. 2 Glyceraldehyde-3-phosphate ↓ [Glyceraldehyde-3-phosphate dehydrogenase] 2 NAD+ + 2 Pi → 2 NADH + 2 H+ ↓ 7. 2 × 1,3-Bisphosphoglycerate ↓ [Phosphoglycerate kinase] 2 ADP → 2 ATP ↓ 8. 2 × 3-Phosphoglycerate ↓ [Phosphoglycerate mutase] ↓ 9. 2 × 2-Phosphoglycerate ↓ [Enolase] 2 H2O released ↓ 10. 2 × Phosphoenolpyruvate ↓ [Pyruvate kinase] 2 ADP → 2 ATP ↓ 2 × Pyruvate

Energy Accounting of Glycolysis

Event Per glucose
ATP consumed 2 ATP
ATP produced 4 ATP
Net ATP 2 ATP
NADH produced 2 NADH
Pyruvate 2 molecules
Water 2 H2O

Glycolysis has an ATP-investment phase followed by an ATP-payoff phase. The two NADH are generated during the glyceraldehyde-3-phosphate dehydrogenase step. :contentReference[oaicite:2]{index=2}

Irreversible / Regulatory Steps

  1. Hexokinase/glucokinase
  2. Phosphofructokinase-1
  3. Pyruvate kinase
Exam trick: Remember glycolysis as:

2 ATP used → 4 ATP made → Net 2 ATP + 2 NADH.

4.5 Oxidative Decarboxylation of Pyruvate

Pyruvate is converted into acetyl-CoA by the pyruvate dehydrogenase complex.

Pyruvate ↓ [Pyruvate dehydrogenase complex] ↓ Acetyl-CoA + CO2 + NADH
Per pyruvate: Pyruvate + CoA + NAD+ → Acetyl-CoA + CO2 + NADH + H+ Per glucose: 2 Pyruvate → 2 Acetyl-CoA + 2 CO2 + 2 NADH

Components of Pyruvate Dehydrogenase Complex

Important cofactors include TPP, lipoamide, CoA, FAD and NAD+.

4.6 TCA Cycle / Citric Acid Cycle

The TCA cycle oxidizes acetyl-CoA and generates NADH, FADH2 and GTP/ATP for subsequent energy production.

Acetyl-CoA + Oxaloacetate ↓ Citrate ↓ [Aconitase] ↓ Isocitrate ↓ [Isocitrate dehydrogenase] NAD+ → NADH CO2 released ↓ α-Ketoglutarate ↓ [α-Ketoglutarate dehydrogenase] NAD+ → NADH CO2 released ↓ Succinyl-CoA ↓ [Succinyl-CoA synthetase] GDP + Pi → GTP ↓ Succinate ↓ [Succinate dehydrogenase] FAD → FADH2 ↓ Fumarate ↓ [Fumarase] H2O added ↓ Malate ↓ [Malate dehydrogenase] NAD+ → NADH ↓ Oxaloacetate →

Yield per Acetyl-CoA

Product Amount
NADH 3
FADH2 1
GTP/ATP 1
CO2 2

Yield per Glucose

2 Acetyl-CoA enter TCA NADH = 6 FADH2 = 2 GTP/ATP = 2 CO2 = 4

Regulatory Enzymes

4.7 Electron Transport Chain and Oxidative Phosphorylation

The electron transport chain transfers electrons from NADH and FADH2 through membrane-associated electron carriers and establishes a proton gradient used for ATP synthesis.

NADH ↓ Complex I ↓ Coenzyme Q ↓ Complex III ↓ Cytochrome c ↓ Complex IV ↓ O2 ↓ H2O FADH2 ↓ Complex II ↓ Coenzyme Q ↓ Complex III ↓ Cytochrome c ↓ Complex IV ↓ O2 ↓ H2O Electron transport ↓ Proton pumping ↓ Proton motive force ↓ ATP synthase ↓ ATP

Important Complexes

Complex Major function
Complex I NADH dehydrogenase; transfers electrons from NADH
Complex II Succinate dehydrogenase; transfers electrons from FADH2 pathway
Complex III Transfers electrons to cytochrome c
Complex IV Transfers electrons to O2 and forms H2O
ATP synthase Uses proton motive force to synthesize ATP
Important ATP note: Do not write a fixed ATP number for every microorganism without qualification. Respiratory chains differ among microorganisms. Modern biochemical estimates commonly use approximately 2.5 ATP/NADH and 1.5 ATP/FADH2 in mitochondrial oxidative phosphorylation, while bacterial yields can vary depending on the respiratory chain and organism.

4.8 Glycogenesis

Glycogenesis is the synthesis of glycogen from glucose.

Glucose ↓ Glucose-6-phosphate [Hexokinase / Glucokinase] ↓ Glucose-1-phosphate [Phosphoglucomutase] ↓ UDP-glucose [UDP-glucose pyrophosphorylase] ↓ Glycogen primer ↓ [Glycogen synthase] ↓ Glycogen ↓ [Branching enzyme] ↓ Branched glycogen

Energy Requirement

ATP is required for formation of glucose-6-phosphate and UTP is used in activation of glucose as UDP-glucose.

4.9 Glycogenolysis

Glycogenolysis is the breakdown of glycogen to glucose-1-phosphate and subsequently glucose-6-phosphate.

Glycogen ↓ [Glycogen phosphorylase] ↓ Glucose-1-phosphate ↓ [Phosphoglucomutase] ↓ Glucose-6-phosphate ↓ Glycolysis / Other pathways

Key Enzyme

Glycogen phosphorylase cleaves α-1,4 glycosidic bonds using inorganic phosphate.

4.10 Pentose Phosphate Pathway

The pentose phosphate pathway provides NADPH and pentose phosphates such as ribose-5-phosphate.

Glucose-6-phosphate ↓ [Glucose-6-phosphate dehydrogenase] NADP+ → NADPH ↓ 6-Phosphogluconolactone ↓ [6-Phosphogluconolactonase] ↓ 6-Phosphogluconate ↓ [6-Phosphogluconate dehydrogenase] NADP+ → NADPH CO2 released ↓ Ribulose-5-phosphate ↓ Ribose-5-phosphate + Xylulose-5-phosphate ↓ Transketolase / Transaldolase reactions ↓ Fructose-6-phosphate + Glyceraldehyde-3-phosphate

Products

Exam trick: PPP = NADPH + Pentose. Do not write NADH as the major reducing product of this pathway.

4.11 Entner-Doudoroff Pathway

The Entner-Doudoroff pathway is an alternative pathway of glucose catabolism found in many bacteria.

Glucose ↓ Glucose-6-phosphate ↓ 6-Phosphogluconate ↓ KDPG ↓ Pyruvate + Glyceraldehyde-3-phosphate ↓ Pyruvate + ATP + NADH

Characteristic Yield

The pathway generally produces one ATP directly per glucose, together with NADH and NADPH, although the exact accounting depends on the organism and pathway variant.

4.12 Phosphoketolase Pathway

The phosphoketolase pathway is characteristic of certain heterofermentative microorganisms and uses phosphoketolase enzymes to cleave sugar phosphate intermediates.

Pentose phosphate / Sugar phosphate ↓ Phosphoketolase ↓ Acetyl-phosphate + Glyceraldehyde-3-phosphate ↓ Acetyl-CoA / Acetate + Pyruvate ↓ Lactate / Ethanol / Acetate

4.13 Fermentative Metabolism

Fermentation allows regeneration of NAD+ when an external terminal electron acceptor is not used.

Lactic Acid Fermentation

Glucose ↓ Glycolysis ↓ Pyruvate ↓ [Lactate dehydrogenase] NADH → NAD+ ↓ Lactate
Glucose → 2 Lactate + Net 2 ATP

Alcoholic Fermentation

Glucose ↓ Glycolysis ↓ Pyruvate ↓ [Pyruvate decarboxylase] CO2 released ↓ Acetaldehyde ↓ [Alcohol dehydrogenase] NADH → NAD+ ↓ Ethanol
Glucose → 2 Ethanol + 2 CO2 + Net 2 ATP

4.14 Lipid Metabolism

Triglycerides ↓ Lipases ↓ Glycerol + Fatty acids Glycerol ↓ Glycerol-3-phosphate ↓ DHAP ↓ Glycolysis Fatty acids ↓ Activation ↓ Fatty acyl-CoA ↓ β-oxidation ↓ Acetyl-CoA ↓ TCA ↓ ETC ↓ ATP

4.15 β-Oxidation of Fatty Acids

β-oxidation is the repeated oxidation of fatty acyl-CoA producing acetyl-CoA, NADH and FADH2.

Fatty acid ↓ [Acyl-CoA synthetase] ↓ Fatty acyl-CoA ↓ 1. Oxidation [Acyl-CoA dehydrogenase] FAD → FADH2 ↓ 2. Hydration [Enoyl-CoA hydratase] H2O added ↓ 3. Oxidation [β-Hydroxyacyl-CoA dehydrogenase] NAD+ → NADH ↓ 4. Thiolysis [β-Ketothiolase] ↓ Acetyl-CoA + shortened fatty acyl-CoA ↓ Cycle repeats

Energy from β-Oxidation

Each cycle produces one NADH and one FADH2 and releases one acetyl-CoA, except for the final cleavage which produces two acetyl-CoA units.

Memory trick: β-oxidation steps: Oxidation → Hydration → Oxidation → Thiolysis.

4.16 Protein Metabolism

Proteins ↓ Proteases ↓ Peptides ↓ Peptidases ↓ Amino acids ↓ Transamination / Deamination ↓ Carbon skeleton ↓ Pyruvate / Acetyl-CoA / TCA intermediates ↓ Energy / Biosynthesis

4.17 Transamination

Transamination is the transfer of an amino group from an amino acid to an α-keto acid.

Amino acid + α-ketoglutarate ↔ α-keto acid + glutamate Enzyme: Aminotransferase Coenzyme: Pyridoxal phosphate (PLP)

4.18 Oxidative Deamination

Glutamate + NAD(P)+ + H2O ↔ α-ketoglutarate + NH4+ + NAD(P)H

The reaction is catalyzed by glutamate dehydrogenase.

4.19 Interrelationship of Carbohydrate, Lipid and Protein Metabolism

CARBOHYDRATES ↓ Glucose ↓ Glycolysis ↓ Pyruvate ↓ Acetyl-CoA ↓ TCA Cycle ↓ NADH + FADH2 ↓ ETC ↓ ATP LIPIDS ↓ Fatty acids ↓ β-oxidation ↓ Acetyl-CoA ---------------→ TCA PROTEINS ↓ Amino acids ↓ Transamination / Deamination ↓ Pyruvate / Acetyl-CoA / TCA intermediates

4.20 ATP Accounting: Important Examination Point

ATP values from oxidative phosphorylation depend on the organism, respiratory chain and coupling efficiency. Therefore, distinguish between direct substrate-level phosphorylation and ATP generated through electron transport.

Pathway Important energy products
Glycolysis Net 2 ATP + 2 NADH
Pyruvate oxidation 2 NADH per glucose
TCA 6 NADH + 2 FADH2 + 2 GTP per glucose
PPP NADPH + pentose sugars
β-oxidation NADH + FADH2 + acetyl-CoA per cycle
Most important correction: NADH and NADPH are NOT interchangeable.

NADH → mainly associated with catabolic energy generation and electron transport.
NADPH → mainly provides reducing power for biosynthetic and reductive reactions.
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5. Microbial Genetics

5.1 DNA

5.2 RNA

5.3 DNA Replication

Parent DNA ↓ Helicase unwinds DNA ↓ Primer synthesis ↓ DNA polymerase extends new strand ↓ Leading strand + Lagging strand ↓ Okazaki fragments ↓ Primer removal ↓ DNA ligase ↓ Two daughter DNA molecules

Important Enzymes

Enzyme Function
Helicase Unwinds DNA
Primase Synthesizes RNA primer
DNA polymerase Synthesizes DNA
DNA ligase Joins DNA fragments
Topoisomerase Relieves supercoiling

5.4 Transcription

DNA ↓ Promoter recognition ↓ Initiation ↓ Elongation ↓ Termination ↓ RNA

5.5 Translation

mRNA ↓ Ribosome ↓ Initiation ↓ tRNA brings amino acids ↓ Peptide bond formation ↓ Elongation ↓ Stop codon ↓ Termination ↓ Protein

5.6 Central Dogma

DNA ↓ transcription RNA ↓ translation PROTEIN

5.7 Genetic Code

5.8 Lac Operon

Regulatory gene ↓ Repressor protein ↓ Operator ↓ Structural genes ↓ β-galactosidase Permease Transacetylase

Lactose Absent

Lactose absent ↓ Active repressor ↓ Operator blocked ↓ Transcription OFF

Lactose Present

Lactose ↓ Allolactose ↓ Repressor inactivated ↓ Operator available ↓ Transcription ON
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6. Concept of Biotechnology

Biotechnology is the application of organisms, cells, enzymes and biological processes to produce useful products or services.

Major Areas

Applications

Risks and Hazards

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7. Fermentation Process

7.1 Fermentation

Industrial fermentation is the controlled cultivation of microorganisms or cells for production of useful metabolites, enzymes, biomass or other products.

7.2 Solid-State Fermentation

Microorganisms grow on moist solid substrates with little or no free-flowing water.

7.3 Submerged Fermentation

Microorganisms grow in a liquid nutrient medium under controlled conditions.

Solid-state Submerged
Low free water Liquid medium
Often suitable for fungi Widely used industrially

7.4 General Fermentation Process

Microorganism selection ↓ Strain improvement ↓ Inoculum preparation ↓ Medium preparation ↓ Sterilization ↓ Inoculation ↓ Fermentation ↓ Monitoring ↓ Harvest ↓ Downstream processing ↓ Final product

7.5 Fermentor Components

7.6 Ethanol Production

Sugar / Molasses ↓ Medium preparation ↓ Sterilization ↓ Yeast inoculation ↓ Fermentation ↓ Ethanol + CO2 ↓ Distillation ↓ Ethanol
C6H12O6 → 2 C2H5OH + 2 CO2 + energy

7.7 Beer Production

Barley ↓ Malting ↓ Mashing ↓ Wort ↓ Boiling + Hops ↓ Cooling ↓ Yeast inoculation ↓ Fermentation ↓ Maturation ↓ Filtration / Packaging ↓ Beer

7.8 Acetic Acid Production

Ethanol ↓ Acetic acid bacteria ↓ Acetaldehyde ↓ Acetic acid
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8. Agricultural Microbial Biotechnology

8.1 Biofertilizers

Biofertilizers contain beneficial living microorganisms that improve nutrient availability or plant growth.

Examples

8.2 Biological Nitrogen Fixation

Atmospheric N2 ↓ Nitrogen-fixing microorganisms ↓ Nitrogenase ↓ NH3 / NH4+ ↓ Assimilation ↓ Organic nitrogen compounds

Nitrogenase is highly oxygen-sensitive in many nitrogen-fixing systems and requires substantial energy in the form of ATP.

8.3 Composting

Organic waste ↓ Microbial decomposition ↓ Heat generation ↓ Further degradation ↓ Stabilization ↓ Mature compost

8.4 Plant Tissue Culture

Explant ↓ Surface sterilization ↓ Culture initiation ↓ Shoot multiplication ↓ Root formation ↓ Hardening ↓ Transfer to soil ↓ New plant

8.5 Cell Fusion

Plant cells ↓ Protoplast isolation ↓ Protoplast fusion ↓ Hybrid cell ↓ Selection ↓ Regeneration ↓ Hybrid plant
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9. Biotechnology in Dairy Industry

9.1 Pasteurization

Pasteurization is controlled heat treatment used to destroy pathogenic microorganisms and reduce microbial load while retaining acceptable product quality.

Method Typical condition
LTLT 63°C for 30 minutes
HTST 72°C for 15 seconds

9.2 Yoghurt Production

Milk ↓ Standardization ↓ Heat treatment ↓ Cooling ↓ Starter culture ↓ Incubation ↓ Lactic acid production ↓ Coagulation ↓ Cooling ↓ Yoghurt

9.3 Cheese Production

Milk ↓ Pasteurization ↓ Starter culture ↓ Acidification ↓ Coagulation ↓ Curd ↓ Cutting ↓ Whey removal ↓ Pressing ↓ Salting ↓ Ripening ↓ Cheese

9.4 Ice Cream Production

Milk / Cream ↓ Mixing ↓ Pasteurization ↓ Homogenization ↓ Cooling ↓ Aging ↓ Freezing ↓ Whipping ↓ Hardening ↓ Ice cream
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10. Methods in Genetic Engineering

10.1 Recombinant DNA Technology

Recombinant DNA technology involves joining DNA fragments from different sources and introducing the recombinant molecule into a suitable host.

10.2 Gene Cloning

Target gene identification ↓ DNA isolation / amplification ↓ Vector selection ↓ Restriction digestion ↓ Ligation ↓ Recombinant DNA ↓ Transformation ↓ Selection ↓ Screening ↓ Expression ↓ Desired product

10.3 Restriction Enzymes

Restriction endonucleases recognize specific DNA sequences and cleave DNA.

10.4 DNA Ligase

DNA ligase joins DNA fragments by forming phosphodiester bonds.

10.5 Vectors

Features of a Good Vector

10.6 Transformation

Transformation is the introduction of foreign DNA into a recipient cell.

10.7 Applications

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11. Enzyme Technology

11.1 Microbial Enzymes

Microorganisms are important industrial sources of enzymes because they grow rapidly, can be cultivated at large scale and can produce extracellular enzymes.

11.2 Enzyme Production

Microorganism selection ↓ Screening ↓ Strain improvement ↓ Inoculum ↓ Fermentation ↓ Enzyme production ↓ Recovery ↓ Purification ↓ Concentration ↓ Formulation ↓ Enzyme product

11.3 Amylase

Starch ↓ Amylase ↓ Dextrins ↓ Maltose / smaller sugars

11.4 Protease

Protein ↓ Protease ↓ Peptides ↓ Amino acids

11.5 Chitinase

Chitinases hydrolyze chitin and have applications in agriculture, biotechnology and waste utilization.

11.6 Pectinase

Pectinases degrade pectin and are important in fruit juice processing and other plant-material industries.

11.7 Downstream Processing

Fermentation broth ↓ Cell separation ↓ Enzyme recovery ↓ Concentration ↓ Purification ↓ Formulation ↓ Final enzyme
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12. Exam Revision and Important Questions

12.1 Most Important Metabolism Flowchart

GLUCOSE ↓ GLYCOLYSIS ↓ PYRUVATE ↓ ACETYL-CoA ↓ TCA CYCLE ↓ NADH + FADH2 ↓ ETC ↓ ATP GLUCOSE ↓ PPP ↓ NADPH + Ribose-5-P FATTY ACIDS ↓ β-OXIDATION ↓ Acetyl-CoA ↓ TCA PROTEINS ↓ Amino acids ↓ Transamination / Deamination ↓ Metabolic intermediates ↓ Energy / Biosynthesis

12.2 High-Value 10-Mark Questions

  1. Explain glycolysis with all enzymatic steps and energy yield.
  2. Describe TCA cycle with enzymes, energy yield and significance.
  3. Explain electron transport chain and oxidative phosphorylation.
  4. Describe pentose phosphate pathway and explain the significance of NADPH.
  5. Explain β-oxidation of fatty acids with energy production.
  6. Describe microbial metabolism and interrelationship of major metabolic pathways.
  7. Explain fermentation pathways with suitable examples.
  8. Describe DNA replication with enzymes involved.
  9. Explain transcription and translation.
  10. Explain lac operon and regulation of gene expression.
  11. Describe industrial fermentation and fermentor design.
  12. Explain recombinant DNA technology and gene cloning.
  13. Describe microbial enzyme production and downstream processing.

12.3 Important 5-Mark Questions

12.4 Metabolism Answer Trick

For a 10-mark metabolism question, use this order:

1. Definition
2. Site/location
3. Starting substrate
4. Complete pathway
5. Enzyme at every important step
6. ATP consumption
7. ATP production
8. NADH / FADH2 / NADPH production
9. CO2 / H2O production
10. Regulation
11. Biological significance
12. Overall reaction / net yield

12.5 Fast Memory Tricks

GLYCOLYSIS: 2 ATP used ↓ 4 ATP produced ↓ Net 2 ATP + 2 NADH + 2 Pyruvate TCA: 3 NADH + 1 FADH2 + 1 GTP + 2 CO2 per acetyl-CoA β-OXIDATION: Oxidation ↓ Hydration ↓ Oxidation ↓ Thiolysis PPP: NADPH + Pentose CENTRAL DOGMA: DNA ↓ RNA ↓ Protein GENE CLONING: Gene ↓ Restriction ↓ Ligation ↓ Vector ↓ Host ↓ Selection ↓ Screening ↓ Expression FERMENTATION: Inoculum ↓ Medium ↓ Sterilization ↓ Fermentation ↓ Harvest ↓ Downstream processing
Very important for exam preparation:

When drawing a metabolic pathway, do not write only the arrows. Write the enzyme name underneath or beside each reaction and mark energy changes such as ATP → ADP, NAD+ → NADH, NADP+ → NADPH, FAD → FADH2, CO2 released and H2O used/formed.

This makes the pathway much more complete and suitable for a B.Sc. long-answer question.
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